diff --git a/bench/FERMI/README b/bench/FERMI/README
index f8772483d138959b34b004698547ddf9e4418f4b..db3f527bdc10550eb1bea4008637ff1fbb2ea395 100644
--- a/bench/FERMI/README
+++ b/bench/FERMI/README
@@ -14,7 +14,7 @@ lmp_linux_mixed
lmp_linux_double
The precision (single, mixed, double) refers to the GPU and USER-CUDA
-pacakge precision. See the README files in the lib/gpu and lib/cuda
+package precision. See the README files in the lib/gpu and lib/cuda
directories for instructions on how to build the packages with
different precisions. The GPU and USER-CUDA sub-sections of the
doc/Section_accelerate.html file also describes this process.
diff --git a/doc/.gitignore b/doc/.gitignore
index bcd8f6db717a6e3871380308172b0733b68951eb..7d309492372d297fac364eae71dcfd75f80b8010 100644
--- a/doc/.gitignore
+++ b/doc/.gitignore
@@ -1,4 +1,5 @@
/html
+/spelling
/LAMMPS.epub
/LAMMPS.mobi
/Manual.pdf
diff --git a/doc/Makefile b/doc/Makefile
index e05715522bfdac192984c96ca8156fd4166e60cc..79558674d75ccf99ba7ccfb29ebe4966b0356c7c 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -22,7 +22,7 @@ endif
SOURCES=$(wildcard src/*.txt)
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
-.PHONY: help clean-all clean epub html pdf old venv
+.PHONY: help clean-all clean epub html pdf old venv spelling
# ------------------------------------------
@@ -44,6 +44,10 @@ clean-all:
clean:
rm -rf $(RSTDIR) html
+ rm -rf spelling
+
+clean-spelling:
+ rm -rf spelling
html: $(OBJECTS)
@(\
@@ -64,6 +68,17 @@ html: $(OBJECTS)
@rm -rf html/USER/*/*.[sg]*
@echo "Build finished. The HTML pages are in doc/html."
+spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+ @(\
+ . $(VENV)/bin/activate ;\
+ pip install sphinxcontrib-spelling ;\
+ cp -r src/* $(RSTDIR)/ ;\
+ cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
+ sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
+ deactivate ;\
+ )
+ @echo "Spell check finished."
+
epub: $(OBJECTS)
@mkdir -p epub
@rm -f LAMMPS.epub
diff --git a/doc/src/2001/input_commands.html b/doc/src/2001/input_commands.html
index 6f7266f2ca4824c737b0990e486230da8a947df9..797d6bec4e92b81c71ee6d76f6107dcdf1105be7 100644
--- a/doc/src/2001/input_commands.html
+++ b/doc/src/2001/input_commands.html
@@ -464,7 +464,7 @@ the angletype option can only be assigned to a "fix style" of "shake",
entirely rigid (e.g. water)
the angletype option enables an additional check when SHAKE constraints
are computed: if a cluster is of size 3 and both bonds in
- the cluster are of a bondtype specified by the 2nd paramter of
+ the cluster are of a bondtype specified by the 2nd parameter of
angletype, then the cluster is SHAKEn with an additional angle
constraint that makes it rigid, using the equilibrium angle appropriate
to the specified angletype
@@ -476,7 +476,7 @@ IMPORTANT NOTE: the angletype option has one additional affect, namely
since they will not be SHAKEn but neither will the angle force by computed
for style region, a coeff of INF means + or - infinity (all the way
to the boundary)
-an atom can be assigned to multiple constraints, the contraints will be
+an atom can be assigned to multiple constraints, the constraints will be
applied in the reverse order they are assigned to that atom
(e.g. each timestep, the last fix assigned to an atom will be applied
to it first, then the next-to-last applied second, etc)
@@ -689,7 +689,7 @@ coeffs: types
remainder
no other parameters required
-used with "create temp" commmand to initialize velocities of atoms
+used with "create temp" command to initialize velocities of atoms
by default, the "create temp" command initializes the velocities of all atoms,
this command limits the initialization to a group of atoms
this command is only in force for the next "create temp" command, any
@@ -1263,7 +1263,7 @@ when using constraints with the minimizer, fixes are
applied when atoms move except for the following
fixes associated with temperature control are not allowed
(rescale, hoover/drag, langevin)
-the minimizer does not invoke the "fix style shake" contraints on
+the minimizer does not invoke the "fix style shake" constraints on
bond lengths
the minimizer does not invoke pressure control or volume control settings
for good convergence, should specify use of smooth nonbond force fields
@@ -1566,7 +1566,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any sizes
can be used that are supported by native machine libraries
this command is optional - if not used, a default
mesh size will be chosen to satisfy accuracy criterion - if used, the
- specifed mesh size will override the default
+ specified mesh size will override the default
</PRE>
<HR>
<H3>
@@ -1788,7 +1788,7 @@ if the style is 2, restart information will be written alternately to files
when the minimizer is invoked this command means create a restart file
at the end of the minimization with the filename filename.timestep.min
a restart file stores atom and force-field information in binary form
-allows program to restart from where it left off (see "read restart" commmand)
+allows program to restart from where it left off (see "read restart" command)
Default = 0
</PRE>
diff --git a/doc/src/99/basics.html b/doc/src/99/basics.html
index a9a9cb4a8ddc021827d84d4e66ccdcf4dc58ec83..b6236f4bf9f68c78a77e0da4e2b40f48e470f336 100644
--- a/doc/src/99/basics.html
+++ b/doc/src/99/basics.html
@@ -167,7 +167,7 @@ tool on the small-system data file.</P>
<P>
(6) flow</P>
<P>
-2-d flow of Lennard-Jones atoms in a channel using various contraint
+2-d flow of Lennard-Jones atoms in a channel using various constraint
options.</P>
<P>
(7) polymer</P>
@@ -201,7 +201,7 @@ The tools directory also has a F77 program called setup_chain.f
(compile and link with print.c) which can be used to generate random
initial polymer configurations for bead-spring models like those used
in examples/polymer. It uses an input polymer definition file (see
-examples/polymer for two sample def files) that specfies how many
+examples/polymer for two sample def files) that specifies how many
chains of what length, a random number seed, etc.</P>
</BODY>
</HTML>
diff --git a/doc/src/99/crib.html b/doc/src/99/crib.html
index 0944980b17a081693c9e1b73a97137b6e6c154c2..80d64d370314ed1ddc1c5d4d47c09317480c6bb3 100755
--- a/doc/src/99/crib.html
+++ b/doc/src/99/crib.html
@@ -40,7 +40,7 @@ Note: this file is somewhat out-of-date for LAMMPS 99.</P>
<LI>
maxtype = max # of atom types
<LI>
- maxbond = max # of bonds to compute on one procesor
+ maxbond = max # of bonds to compute on one processor
<LI>
maxangle = max # of angles to compute on one processor
<LI>
diff --git a/doc/src/99/input_commands.html b/doc/src/99/input_commands.html
index b90402715376a1e83f0af349496f6b7badb048f6..baea02b5c2cebe620f9ec2083ae5540e214a2ef0 100644
--- a/doc/src/99/input_commands.html
+++ b/doc/src/99/input_commands.html
@@ -294,7 +294,7 @@ assign a group of atoms to a particular constraint
use appropriate number of coeffs for a particular style
the constraint itself is defined by the "fix style" command
multiple groups of atoms can be assigned to the same constraint
-an atom can be assigned to multiple constraints, the contraints will be
+an atom can be assigned to multiple constraints, the constraints will be
applied in the reverse order they are assigned to that atom
(e.g. each timestep, the last fix assigned to an atom will be applied
to it first, then the next-to-last applied second, etc)
@@ -477,7 +477,7 @@ coeffs: types
remainder
no other parameters required
-used with "create temp" commmand to initialize velocities of atoms
+used with "create temp" command to initialize velocities of atoms
by default, the "create temp" command initializes the velocities of all atoms,
this command limits the initialization to a group of atoms
this command is only in force for the next "create temp" command, any
@@ -1124,7 +1124,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any size
can be used that are supported by native machine libraries
this command is optional - if not used, a default
mesh size will be chosen to satisfy accuracy criterion - if used, the
- specifed mesh size will override the default
+ specified mesh size will override the default
Default = none
</PRE>
@@ -1343,7 +1343,7 @@ value of 0 means never create one
program will toggle between 2 filenames as the run progresses
so always have at least one good file even if the program dies in mid-write
restart file stores atom positions and velocities in binary form
-allows program to restart from where it left off (see "read restart" commmand)
+allows program to restart from where it left off (see "read restart" command)
Default = 0
</PRE>
diff --git a/doc/src/Eqs/pair_kolmogorov_crespi_z.jpg b/doc/src/Eqs/pair_kolmogorov_crespi_z.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..3d37ff25be9752bf72a84ce9001d9cacd09a4f51
Binary files /dev/null and b/doc/src/Eqs/pair_kolmogorov_crespi_z.jpg differ
diff --git a/doc/src/Eqs/pair_kolmogorov_crespi_z.tex b/doc/src/Eqs/pair_kolmogorov_crespi_z.tex
new file mode 100644
index 0000000000000000000000000000000000000000..fb7ebf8dc4c3d38ab23ad25017983e6bdbb71687
--- /dev/null
+++ b/doc/src/Eqs/pair_kolmogorov_crespi_z.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+\thispagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
+ V_{ij} & = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\
+ \rho_{ij}^2 = \rho_{ji}^2 & = & x_{ij}^2 + y_{ij}^2 ~\hspace{2cm} (\mathbf{n_i}\equiv\hat \mathbf{z})\\
+ f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right) ^{2n}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 1da854c483dc9184cc77f33aa07e31c4073572ec..bb7a1452bc2e97349512f8015adb142cabb08f01 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="21 Feb 2017 version">
+<META NAME="docnumber" CONTENT="10 Mar 2017 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
-21 Feb 2017 version :c,h4
+10 Mar 2017 version :c,h4
Version info: :h4
diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf
index 5b776defca36759dadaaabebcc6df409000d52cd..37201275fe4b4efa0da77afbb72e6c55a127c042 100644
Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index c36c961de3706f9cff0ad9d7ecd4c262425aeac3..6e526dcb51e9dee30e79017ebb2056f934f933fd 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -281,12 +281,12 @@ the "minimize"_minimize.html command. A parallel tempering
3.4 Commands listed by category :link(cmd_4),h4
-This section lists all LAMMPS commands, grouped by category. The
-"next section"_#cmd_5 lists the same commands alphabetically. The
+This section lists core LAMMPS commands, grouped by category.
+The "next section"_#cmd_5 lists all commands alphabetically. The
next section also includes (long) lists of style options for entries
that appear in the following categories as a single command (fix,
compute, pair, etc). Commands that are added by user packages are not
-included in these categories, but they are in the next section.
+included in the categories here, but they are in the next section.
Initialization:
@@ -361,7 +361,7 @@ Settings:
"timer"_timer.html,
"timestep"_timestep.html
-Operations within timestepping (fixes) and diagnositics (computes):
+Operations within timestepping (fixes) and diagnostics (computes):
"compute"_compute.html,
"compute_modify"_compute_modify.html,
@@ -1016,6 +1016,7 @@ package"_Section_start.html#start_3.
"eff/cut"_pair_eff.html,
"exp6/rx"_pair_exp6_rx.html,
"gauss/cut"_pair_gauss.html,
+"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"lennard/mdf"_pair_mdf.html,
"list"_pair_list.html,
"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
@@ -1091,7 +1092,7 @@ package"_Section_start.html#start_3.
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
+"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c)
:line
diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt
index f2ef9863940ad49c369a8d8783b4c26abf652606..832c5718ab6bc738c82959da47c856f598a296ed 100644
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@@ -574,11 +574,11 @@ group of atoms correctly. :dd
{Bad quadratic solve for particle/line collision} :dt
-This is an internal error. It should nornally not occur. :dd
+This is an internal error. It should normally not occur. :dd
{Bad quadratic solve for particle/tri collision} :dt
-This is an internal error. It should nornally not occur. :dd
+This is an internal error. It should normally not occur. :dd
{Bad real space Coulomb cutoff in fix tune/kspace} :dt
@@ -912,7 +912,7 @@ Atoms can not be added afterwards to this fix option. :dd
{Cannot append atoms to a triclinic box} :dt
-The simulation box must be defined with edges alligned with the
+The simulation box must be defined with edges aligned with the
Cartesian axes. :dd
{Cannot balance in z dimension for 2d simulation} :dt
@@ -992,7 +992,7 @@ file. :dd
LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6
factor that partitions the computation between real space and k-space
-for Disptersion interactions. :dd
+for Dispersion interactions. :dd
{Cannot create an atom map unless atoms have IDs} :dt
@@ -1327,7 +1327,7 @@ Self-explanatory. :dd
This file is created when you use some LAMMPS features, to indicate
what paper you should cite on behalf of those who implemented
-the feature. Check that you have write priveleges into the directory
+the feature. Check that you have write privileges into the directory
you are running in. :dd
{Cannot open log.lammps for writing} :dt
@@ -2005,7 +2005,7 @@ Self-explanatory. :dd
{Cannot use fix reax/bonds without pair_style reax} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Cannot use fix rigid npt/nph and fix deform on same component of stress tensor} :dt
@@ -2088,7 +2088,7 @@ Self-explanatory. :dd
{Cannot use lines with fix srd unless overlap is set} :dt
-This is because line segements are connected to each other. :dd
+This is because line segments are connected to each other. :dd
{Cannot use multiple fix wall commands with pair brownian} :dt
@@ -2131,7 +2131,7 @@ Self-explanatory. :dd
{Cannot use newton pair with born/gpu pair style} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Cannot use newton pair with buck/coul/cut/gpu pair style} :dt
@@ -2291,7 +2291,7 @@ Self-explanatory. :dd
{Cannot use newton pair with zbl/gpu pair style} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Cannot use non-zero forces in an energy minimization} :dt
@@ -2641,11 +2641,11 @@ uses a pairwise neighbor list. :dd
{Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt
-Radius cannot be bigger than 1/2 of a non-axis periodic dimention. :dd
+Radius cannot be bigger than 1/2 of a non-axis periodic dimension. :dd
{Compute chunk/atom bin/sphere radius is too large for periodic box} :dt
-Radius cannot be bigger than 1/2 of any periodic dimention. :dd
+Radius cannot be bigger than 1/2 of any periodic dimension. :dd
{Compute chunk/atom compute array is accessed out-of-range} :dt
@@ -2706,15 +2706,15 @@ It will only store IDs if its compress option is enabled. :dd
{Compute chunk/atom stores no coord1 for compute property/chunk} :dt
-Only certain binning options for comptue chunk/atom store coordinates. :dd
+Only certain binning options for compute chunk/atom store coordinates. :dd
{Compute chunk/atom stores no coord2 for compute property/chunk} :dt
-Only certain binning options for comptue chunk/atom store coordinates. :dd
+Only certain binning options for compute chunk/atom store coordinates. :dd
{Compute chunk/atom stores no coord3 for compute property/chunk} :dt
-Only certain binning options for comptue chunk/atom store coordinates. :dd
+Only certain binning options for compute chunk/atom store coordinates. :dd
{Compute chunk/atom variable is not atom-style variable} :dt
@@ -2735,11 +2735,11 @@ is used to find clusters. :dd
{Compute cna/atom cutoff is longer than pairwise cutoff} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Compute cna/atom requires a pair style be defined} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Compute com/chunk does not use chunk/atom compute} :dt
@@ -2747,7 +2747,7 @@ The style of the specified compute is not chunk/atom. :dd
{Compute contact/atom requires a pair style be defined} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Compute contact/atom requires atom style sphere} :dt
@@ -2760,7 +2760,7 @@ since those atoms are not in the neighbor list. :dd
{Compute coord/atom requires a pair style be defined} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Compute damage/atom requires peridynamic potential} :dt
@@ -2790,7 +2790,7 @@ Self-explanatory. :dd
{Compute erotate/asphere requires extended particles} :dt
-This compute cannot be used with point paritlces. :dd
+This compute cannot be used with point particles. :dd
{Compute erotate/rigid with non-rigid fix-ID} :dt
@@ -2835,7 +2835,7 @@ Cannot compute order parameter beyond cutoff. :dd
{Compute hexorder/atom requires a pair style be defined} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Compute improper/local used when impropers are not allowed} :dt
@@ -2881,11 +2881,11 @@ Cannot compute order parameter beyond cutoff. :dd
{Compute orientorder/atom requires a pair style be defined} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Compute pair must use group all} :dt
-Pair styles accumlate energy on all atoms. :dd
+Pair styles accumulate energy on all atoms. :dd
{Compute pe must use group all} :dt
@@ -2935,7 +2935,7 @@ The style of the specified compute is not chunk/atom. :dd
{Compute property/local cannot use these inputs together} :dt
Only inputs that generate the same number of datums can be used
-togther. E.g. bond and angle quantities cannot be mixed. :dd
+together. E.g. bond and angle quantities cannot be mixed. :dd
{Compute property/local does not (yet) work with atom_style template} :dt
@@ -3079,7 +3079,7 @@ Self-explanatory. :dd
{Compute temp/asphere requires extended particles} :dt
-This compute cannot be used with point paritlces. :dd
+This compute cannot be used with point particles. :dd
{Compute temp/body requires atom style body} :dt
@@ -3524,12 +3524,12 @@ path and name are correct. :dd
{Could not process Python file} :dt
-The Python code in the specified file was not run sucessfully by
+The Python code in the specified file was not run successfully by
Python, probably due to errors in the Python code. :dd
{Could not process Python string} :dt
-The Python code in the here string was not run sucessfully by Python,
+The Python code in the here string was not run successfully by Python,
probably due to errors in the Python code. :dd
{Coulomb PPPMDisp order has been reduced below minorder} :dt
@@ -3638,7 +3638,7 @@ Self-explanatory. :dd
{Cutoffs missing in pair_style buck/long/coul/long} :dt
-Self-exlanatory. :dd
+Self-explanatory. :dd
{Cutoffs missing in pair_style lj/long/coul/long} :dt
@@ -4385,7 +4385,7 @@ Self-explanatory. :dd
{Fix ave/chunk does not use chunk/atom compute} :dt
-The specified conpute is not for a compute chunk/atom command. :dd
+The specified compute is not for a compute chunk/atom command. :dd
{Fix ave/chunk fix does not calculate a per-atom array} :dt
@@ -4617,11 +4617,11 @@ An index for the array is out of bounds. :dd
{Fix ave/time compute does not calculate a scalar} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Fix ave/time compute does not calculate a vector} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Fix ave/time compute does not calculate an array} :dt
@@ -4970,7 +4970,7 @@ Self-explanatory. :dd
{Fix langevin angmom requires extended particles} :dt
-This fix option cannot be used with point paritlces. :dd
+This fix option cannot be used with point particles. :dd
{Fix langevin omega is not yet implemented with kokkos} :dt
@@ -6171,7 +6171,7 @@ map command will force an atom map to be created. :dd
{Initial temperatures not all set in fix ttm} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Input line quote not followed by whitespace} :dt
@@ -6199,7 +6199,7 @@ Eigensolve for rigid body was not sufficiently accurate. :dd
{Insufficient Jacobi rotations for triangle} :dt
-The calculation of the intertia tensor of the triangle failed. This
+The calculation of the inertia tensor of the triangle failed. This
should not happen if it is a reasonably shaped triangle. :dd
{Insufficient memory on accelerator} :dt
@@ -6463,15 +6463,15 @@ Self-explanatory. :dd
{Invalid attribute in dump custom command} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Invalid attribute in dump local command} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Invalid attribute in dump modify command} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Invalid basis setting in create_atoms command} :dt
@@ -6737,7 +6737,7 @@ or cause multiple files to be written. :dd
Filenames used with the dump xyz style cannot be binary or cause files
to be written by each processor. :dd
-{Invalid dump_modify threshhold operator} :dt
+{Invalid dump_modify threshold operator} :dt
Operator keyword used for threshold specification in not recognized. :dd
@@ -6751,7 +6751,7 @@ The fix is not recognized. :dd
{Invalid fix ave/time off column} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Invalid fix box/relax command for a 2d simulation} :dt
@@ -7313,7 +7313,7 @@ Self-explanatory. Check the input script or data file. :dd
{LJ6 off not supported in pair_style buck/long/coul/long} :dt
-Self-exlanatory. :dd
+Self-explanatory. :dd
{Label wasn't found in input script} :dt
@@ -7361,7 +7361,7 @@ This should not occur. Report the problem to the developers. :dd
Lost atoms are checked for each time thermo output is done. See the
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved futher than one processor's sub-domain away before
+box, or moved further than one processor's sub-domain away before
reneighboring. :dd
{MEAM library error %d} :dt
@@ -7526,7 +7526,7 @@ Self-explanatory. :dd
{Molecule template ID for create_atoms does not exist} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Molecule template ID for fix deposit does not exist} :dt
@@ -7552,7 +7552,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Molecule toplogy/atom exceeds system topology/atom} :dt
+{Molecule topology/atom exceeds system topology/atom} :dt
The number of bonds, angles, etc per-atom in the molecule exceeds the
system setting. See the create_box command for how to specify these
@@ -7792,7 +7792,7 @@ Self-explanatory. :dd
{Must use variable energy with fix addforce} :dt
-Must define an energy vartiable when applyting a dynamic
+Must define an energy variable when applying a dynamic
force during minimization. :dd
{Must use variable energy with fix efield} :dt
@@ -8042,7 +8042,7 @@ Self-explanatory. :dd
{Non digit character between brackets in variable} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Non integer # of swaps in temper command} :dt
@@ -8663,7 +8663,7 @@ not be invoked by bond_style quartic. :dd
{Pair style does not support compute group/group} :dt
The pair_style does not have a single() function, so it cannot be
-invokded by the compute group/group command. :dd
+invoked by the compute group/group command. :dd
{Pair style does not support compute pair/local} :dt
@@ -8948,11 +8948,11 @@ Self-explanatory. :dd
{Pair yukawa/colloid requires atom style sphere} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Pair yukawa/colloid requires atoms with same type have same radius} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Pair yukawa/colloid/gpu requires atom style sphere} :dt
@@ -9166,7 +9166,7 @@ Self-explanatory. :dd
{Python function evaluation failed} :dt
-The Python function did not run succesfully and/or did not return a
+The Python function did not run successfully and/or did not return a
value (if it is supposed to return a value). This is probably due to
some error condition in the function. :dd
@@ -10025,7 +10025,7 @@ make sense in between runs. :dd
{Threshhold for an atom property that isn't allocated} :dt
-A dump threshhold has been requested on a quantity that is
+A dump threshold has been requested on a quantity that is
not defined by the atom style used in this simulation. :dd
{Timestep must be >= 0} :dt
@@ -10087,7 +10087,7 @@ to a large size. :dd
{Too many atom triplets for pair bop} :dt
The number of three atom groups for angle determinations exceeds the
-expected number. Check your atomic structrure to ensure that it is
+expected number. Check your atomic structure to ensure that it is
realistic. :dd
{Too many atoms for dump dcd} :dt
@@ -10155,7 +10155,7 @@ to a large size. :dd
{Too many timesteps} :dt
-The cummulative timesteps must fit in a 64-bit integer. :dd
+The cumulative timesteps must fit in a 64-bit integer. :dd
{Too many timesteps for NEB} :dt
@@ -10654,7 +10654,7 @@ Only atom-style variables can be used. :dd
{Variable for region cylinder is invalid style} :dt
-Only equal-style varaibles are allowed. :dd
+Only equal-style variables are allowed. :dd
{Variable for region is invalid style} :dt
@@ -10666,7 +10666,7 @@ Self-explanatory. :dd
{Variable for region sphere is invalid style} :dt
-Only equal-style varaibles are allowed. :dd
+Only equal-style variables are allowed. :dd
{Variable for restart is invalid style} :dt
@@ -10707,7 +10707,7 @@ Self-explanatory. :dd
{Variable has circular dependency} :dt
A circular dependency is when variable "a" in used by variable "b" and
-variable "b" is also used by varaible "a". Circular dependencies with
+variable "b" is also used by variable "a". Circular dependencies with
longer chains of dependence are also not allowed. :dd
{Variable name between brackets must be alphanumeric or underscore characters} :dt
@@ -10796,7 +10796,7 @@ Self-explanatory. :dd
{Variable name for fix deform does not exist} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Variable name for fix efield does not exist} :dt
@@ -11083,7 +11083,7 @@ for a dihedral) and adding a small amount of stretch. :dd
{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
-Self-explantory. :dd
+Self-explanatory. :dd
{Calling write_dump before a full system init.} :dt
@@ -11414,7 +11414,7 @@ The command options you have used caused atoms to be lost. :dd
Lost atoms are checked for each time thermo output is done. See the
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved futher than one processor's sub-domain away before
+box, or moved further than one processor's sub-domain away before
reneighboring. :dd
{MSM mesh too small, increasing to 2 points in each direction} :dt
@@ -11452,7 +11452,7 @@ i.e. the first molecule in the template. :dd
{Molecule template for fix shake has multiple molecules} :dt
-The fix shake command will only recoginze molecules of a single
+The fix shake command will only recognize molecules of a single
type, i.e. the first molecule in the template. :dd
{More than one compute centro/atom} :dt
@@ -11537,7 +11537,7 @@ neigh_modify exclude command. :dd
If a thermo_style command is used after a thermo_modify command, the
settings changed by the thermo_modify command will be reset to their
-default values. This is because the thermo_modify commmand acts on
+default values. This is because the thermo_modify command acts on
the currently defined thermo style, and a thermo_style command creates
a new style. :dd
@@ -11589,7 +11589,7 @@ This may not be what you intended. :dd
{One or more dynamic groups may not be updated at correct point in timestep} :dt
-If there are other fixes that act immediately after the intitial stage
+If there are other fixes that act immediately after the initial stage
of time integration within a timestep (i.e. after atoms move), then
the command that sets up the dynamic group should appear after those
fixes. This will insure that dynamic group assignments are made
@@ -11886,7 +11886,7 @@ Self-explanatory. :dd
{Using largest cutoff for buck/long/coul/long} :dt
-Self-exlanatory. :dd
+Self-explanatory. :dd
{Using largest cutoff for lj/long/coul/long} :dt
diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt
index 438284c9da4173b6edbb14e415d362714bd72f86..93e994750683bc4d5682fbd38c19f35478b3ca14 100644
--- a/doc/src/Section_history.txt
+++ b/doc/src/Section_history.txt
@@ -37,7 +37,7 @@ pitfalls or alternatives.
Please see some of the closed issues for examples of how to
suggest code enhancements, submit proposed changes, or report
-possible bugs and how they are resoved.
+possible bugs and how they are resolved.
As an alternative to using GitHub, you may e-mail the
"core developers"_http://lammps.sandia.gov/authors.html or send
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index b69d69614ab5813294e2a8485c1d9e45a637dd5d..8cfbe1c46c9418458f691f19a73101ec1b4aac5e 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -573,7 +573,7 @@ LJ epsilon of O-O = 0.16275
LJ sigma of O-O = 3.16435
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
-Note that the when using the TIP4P pair style, the neighobr list
+Note that the when using the TIP4P pair style, the neighbor list
cutoff for Coulomb interactions is effectively extended by a distance
2 * (OM distance), to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
@@ -618,7 +618,7 @@ any of the parameters above, though it becomes a different model in
that mode of usage.
The SPC/E (extended) water model is the same, except
-the partial charge assignemnts change:
+the partial charge assignments change:
O charge = -0.8476
H charge = 0.4238 :all(b),p
@@ -863,7 +863,7 @@ boundary conditions in specific dimensions. See the command doc pages
for details.
The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
-time the simluation box is created. This happens in one of 3 ways.
+time the simulation box is created. This happens in one of 3 ways.
If the "create_box"_create_box.html command is used with a region of
style {prism}, then a triclinic box is setup. See the
"region"_region.html command for details. If the
@@ -982,10 +982,10 @@ used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
"create_atoms"_create_atoms.html command.
-A second use is to run Parinello-Rahman dyanamics via the "fix
+A second use is to run Parinello-Rahman dynamics via the "fix
npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
-tensor. The analalog for an "energy minimization"_minimize.html is
+tensor. The analog for an "energy minimization"_minimize.html is
the "fix box/relax"_fix_box_relax.html command.
A third use is to shear a bulk solid to study the response of the
@@ -1392,7 +1392,7 @@ custom"_dump.html command.
There is also a "dump local"_dump.html format where the user specifies
what local values to output. A pre-defined index keyword can be
-specified to enumuerate the local values. Two additional kinds of
+specified to enumerate the local values. Two additional kinds of
keywords can also be specified (c_ID, f_ID), where a
"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
provides the values to be output. In each case, the compute or fix
@@ -1525,7 +1525,7 @@ Variables that generate values to output :h5,link(variable)
"Variables"_variable.html defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or
atomfile-style variables generate a global scalar value, global vector
-or values, or a per-atom vector, resepctively, when accessed. The
+or values, or a per-atom vector, respectively, when accessed. The
formulas used to define these variables can contain references to the
thermodynamic keywords and to global and per-atom data generated by
computes, fixes, and other variables. The values generated by
@@ -1585,7 +1585,7 @@ Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
-aggregate motiion of particles) and its thermal velocity. The sum of
+aggregate motion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
@@ -1640,14 +1640,14 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
-DPD thermostatting alters pairwise interactions in a manner analagous
+DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of "fix
langevin"_fix_langevin.html.
Any of the thermostatting fixes can use temperature computes that
remove bias which has two effects. First, the current calculated
temperature, which is compared to the requested target temperature, is
-caluclated with the velocity bias removed. Second, the thermostat
+calculated with the velocity bias removed. Second, the thermostat
adjusts only the thermal temperature component of the particle's
velocities, which are the velocities with the bias removed. The
removed bias is then added back to the adjusted velocities. See the
@@ -1888,7 +1888,7 @@ instances of LAMMPS to perform different calculations.
The lammps_open_no_mpi() function is similar except that no MPI
communicator is passed from the caller. Instead, MPI_COMM_WORLD is
-used to instantiate LAMMPS, and MPI is initialzed if necessary.
+used to instantiate LAMMPS, and MPI is initialized if necessary.
The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.
@@ -1976,7 +1976,7 @@ The lammps_get_natoms() function returns the total number of atoms in
the system and can be used by the caller to allocate space for the
lammps_gather_atoms() and lammps_scatter_atoms() functions. The
gather function collects atom info of the requested type (atom coords,
-types, forces, etc) from all procsesors, orders them by atom ID, and
+types, forces, etc) from all processors, orders them by atom ID, and
returns a full list to each calling processor. The scatter function
does the inverse. It distributes the same kinds of values,
passed by the caller, to each atom owned by individual processors.
@@ -2013,7 +2013,7 @@ a simple Lennard-Jones fluid model. Also, see "this
section"_Section_howto.html#howto_21 of the manual for an analogous
discussion for viscosity.
-The thermal conducitivity tensor kappa is a measure of the propensity
+The thermal conductivity tensor kappa is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given
by Fourier's law
@@ -2099,7 +2099,7 @@ and grad(Vstream) is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time.
-The first method is to perform a non-equlibrium MD (NEMD) simulation
+The first method is to perform a non-equilibrium MD (NEMD) simulation
by shearing the simulation box via the "fix deform"_fix_deform.html
command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
thermostat the fluid via the SLLOD equations of motion.
@@ -2125,7 +2125,7 @@ the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
swapped between atoms in two different layers of the simulation box in
a different dimension. This induces a velocity gradient which can be
monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
-The fix tallies the cummulative momentum transfer that it performs.
+The fix tallies the cumulative momentum transfer that it performs.
See the "fix viscosity"_fix_viscosity.html command for details.
The fourth method is based on the Green-Kubo (GK) formula which
@@ -2268,7 +2268,7 @@ atoms with same local defect structure | chunk ID = output of "compute centro/at
Note that chunk IDs are integer values, so for atom properties or
computes that produce a floating point value, they will be truncated
to an integer. You could also use the compute in a variable that
-scales the floating point value to spread it across multiple intergers.
+scales the floating point value to spread it across multiple integers.
Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
pencils, 3d bins = boxes, spherical bins, cylindrical bins.
@@ -2353,7 +2353,7 @@ largest cluster or fastest diffusing molecule. :l
Example calculations with chunks :h5
-Here are eaxmples using chunk commands to calculate various
+Here are examples using chunk commands to calculate various
properties:
(1) Average velocity in each of 1000 2d spatial bins:
@@ -2424,7 +2424,7 @@ which both have their up- and downsides.
The first approach is to set desired real-space an kspace accuracies
via the {kspace_modify force/disp/real} and {kspace_modify
force/disp/kspace} commands. Note that the accuracies have to be
-specified in force units and are thus dependend on the chosen unit
+specified in force units and are thus dependent on the chosen unit
settings. For real units, 0.0001 and 0.002 seem to provide reasonable
accurate and efficient computations for the real-space and kspace
accuracies. 0.002 and 0.05 work well for most systems using lj
@@ -2444,7 +2444,7 @@ performance. This approach provides a fast initialization of the
simulation. However, it is sensitive to errors: A combination of
parameters that will perform well for one system might result in
far-from-optimal conditions for other simulations. For example,
-parametes that provide accurate and fast computations for
+parameters that provide accurate and fast computations for
all-atomistic force fields can provide insufficient accuracy or
united-atomistic force fields (which is related to that the latter
typically have larger dispersion coefficients).
@@ -2478,7 +2478,7 @@ arithmetic mixing rule substantially increases the computational cost.
The computational overhead can be reduced using the {kspace_modify
mix/disp geom} and {kspace_modify splittol} commands. The first
command simply enforces geometric mixing of the dispersion
-coeffiecients in kspace computations. This introduces some error in
+coefficients in kspace computations. This introduces some error in
the computations but will also significantly speed-up the
simulations. The second keyword sets the accuracy with which the
dispersion coefficients are approximated using a matrix factorization
@@ -2497,7 +2497,7 @@ to specify this command explicitly.
6.25 Polarizable models :link(howto_25),h4
In polarizable force fields the charge distributions in molecules and
-materials respond to their electrostatic environements. Polarizable
+materials respond to their electrostatic environments. Polarizable
systems can be simulated in LAMMPS using three methods:
the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
@@ -2551,7 +2551,7 @@ this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
charge-on-spring models by the methods outlined in the next two
sections. The assignment of masses to the additional degrees of
freedom can lead to unphysical trajectories if care is not exerted in
-choosing the parameters of the poarizable models and the simulation
+choosing the parameters of the polarizable models and the simulation
conditions.
In the core-shell model the vibration of the shells is kept faster
@@ -2727,18 +2727,18 @@ If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
relative motion of the core and the shell should in theory be
stable. However numerical fluctuation can introduce a small
momentum to the system, which is noticable over long trajectories.
-Therefore it is recomendable to use the "fix
+Therefore it is recommendable to use the "fix
momentum"_fix_momentum.html command in combination with "compute
temp/cs"_compute_temp_cs.html when equilibrating the system to
prevent any drift.
-When intializing the velocities of a system with core/shell pairs, it
+When initializing the velocities of a system with core/shell pairs, it
is also desirable to not introduce energy into the relative motion of
the core/shell particles, but only assign a center-of-mass velocity to
the pairs. This can be done by using the {bias} keyword of the
"velocity create"_velocity.html command and assigning the "compute
temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
-"velocity"_velocity.html commmand, e.g.
+"velocity"_velocity.html command, e.g.
velocity all create 1427 134 bias yes temp CSequ
velocity all scale 1427 temp CSequ :pre
@@ -2808,7 +2808,7 @@ CS-Info # header of additional section :pre
6.27 Drude induced dipoles :link(howto_27),h4
The thermalized Drude model, similarly to the "core-shell"_#howto_26
-model, representes induced dipoles by a pair of charges (the core atom
+model, represents induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
("Lamoureux and Roux"_#howto-Lamoureux):
diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt
index 228c7199fd30e58c549f7dbe671aac2cca73d132..7d1fe03d0171e10990b711915bfb837abb1e4197 100644
--- a/doc/src/Section_modify.txt
+++ b/doc/src/Section_modify.txt
@@ -159,17 +159,17 @@ pack_comm_vel: add velocity info to communication buffer (required)
pack_comm_hybrid: store extra info unique to this atom style (optional)
unpack_comm: retrieve an atom's info from the buffer (required)
unpack_comm_vel: also retrieve velocity info (required)
-unpack_comm_hybrid: retreive extra info unique to this atom style (optional)
+unpack_comm_hybrid: retrieve extra info unique to this atom style (optional)
pack_reverse: store an atom's info in a buffer communicating partial forces (required)
pack_reverse_hybrid: store extra info unique to this atom style (optional)
unpack_reverse: retrieve an atom's info from the buffer (required)
-unpack_reverse_hybrid: retreive extra info unique to this atom style (optional)
+unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional)
pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
pack_border_vel: add velocity info to buffer (required)
pack_border_hybrid: store extra info unique to this atom style (optional)
unpack_border: retrieve an atom's info from the buffer (required)
unpack_border_vel: also retrieve velocity info (required)
-unpack_border_hybrid: retreive extra info unique to this atom style (optional)
+unpack_border_hybrid: retrieve extra info unique to this atom style (optional)
pack_exchange: store all an atom's info to migrate to another processor (required)
unpack_exchange: retrieve an atom's info from the buffer (required)
size_restart: number of restart quantities associated with proc's atoms (required)
@@ -369,7 +369,7 @@ pre_force_respa: same as pre_force, but for rRESPA (optional)
post_force_respa: same as post_force, but for rRESPA (optional)
final_integrate_respa: same as final_integrate, but for rRESPA (optional)
min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
-min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional)
+min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional)
min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
min_pushstore: push the minimization LIFO stack one element down (optional)
min_popstore: pop the minimization LIFO stack one element up (optional)
@@ -517,7 +517,7 @@ class. See region.h for details.
inside: determine whether a point is in the region
surface_interior: determine if a point is within a cutoff distance inside of surc
surface_exterior: determine if a point is within a cutoff distance outside of surf
-shape_update : change region shape if set by time-depedent variable :tb(s=:)
+shape_update : change region shape if set by time-dependent variable :tb(s=:)
:line
@@ -601,16 +601,16 @@ Adding keywords for the "thermo_style custom"_thermo_style.html command
"here"_Section_modify.html#mod_13 on this page.
Adding a new math function of one or two arguments can be done by
-editing one section of the Variable::evaulate() method. Search for
+editing one section of the Variable::evaluate() method. Search for
the word "customize" to find the appropriate location.
Adding a new group function can be done by editing one section of the
-Variable::evaulate() method. Search for the word "customize" to find
+Variable::evaluate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
Accessing a new atom-based vector can be done by editing one section
-of the Variable::evaulate() method. Search for the word "customize"
+of the Variable::evaluate() method. Search for the word "customize"
to find the appropriate location.
Adding new "compute styles"_compute.html (whose calculated values can
@@ -740,7 +740,7 @@ entry to add to the USER-MISC/README file in that dir, along with the
contribute several individual features. :l
If you want your contribution to be added as a user-contribution and
-it is several related featues, it is probably best to make it a user
+it is several related features, it is probably best to make it a user
package directory with a name like USER-FOO. In addition to your new
files, the directory should contain a README text file. The README
should contain your name and contact information and a brief
@@ -785,10 +785,10 @@ file for how to format the cite itself. The "Restrictions" section of
the doc page should indicate that your command is only available if
LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
See other user package doc files for examples of how to do this. The
-prerequiste for building the HTML format files are Python 3.x and
+prerequisite for building the HTML format files are Python 3.x and
virtualenv, the requirement for generating the PDF format manual
is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least
-"make html" and carefully inspect and proofread the resuling HTML format
+"make html" and carefully inspect and proofread the resulting HTML format
doc page before submitting your code. :l
For a new package (or even a single command) you should include one or
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index b9b96d66ade7a9a7f4396a2453d6d41af3eb187b..e6a0132e2cd9d30aa957f9b867a34e766b4e4a45 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -94,7 +94,7 @@ Package, Description, Author(s), Doc page, Example, Library
:tb(ea=c)
The "Authors" column lists a name(s) if a specific person is
-responible for creating and maintaining the package.
+responsible for creating and maintaining the package.
(1) The COLLOID package includes Fast Lubrication Dynamics pair styles
which were created by Amit Kumar and Michael Bybee from Jonathan
@@ -462,7 +462,7 @@ options you are optimizing for: CPU acceleration via OpenMP, GPU
acceleration, or Intel Xeon Phi. (You can build multiple times to
create LAMMPS executables for different hardware.) It also requires a
C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is
-used, and an appopriate KOKKOS_ARCH setting should be made in your
+used, and an appropriate KOKKOS_ARCH setting should be made in your
Makefile.machine for your GPU hardware and NVIDIA software.
The simplest way to do this is to use Makefile.kokkos_cuda or
@@ -955,8 +955,8 @@ multi-replica simulations in LAMMPS. Multi-replica methods included
in the package are nudged elastic band (NEB), parallel replica
dynamics (PRD), temperature accelerated dynamics (TAD), parallel
tempering, and a verlet/split algorithm for performing long-range
-Coulombics on one set of processors, and the remainded of the force
-field calcalation on another set.
+Coulombics on one set of processors, and the remainder of the force
+field calculation on another set.
To install via make or Make.py:
@@ -1176,7 +1176,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
The "Authors" column lists a name(s) if a specific person is
-responible for creating and maintaining the package.
+responsible for creating and maintaining the package.
(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
@@ -1295,13 +1295,13 @@ integrators with improved stability.
See these doc pages to get started:
-"bond_style oxdna_fene"_bond_oxdna_fene.html
-"pair_style oxdna_excv"_pair_oxdna_excv.html
+"bond_style oxdna/fene"_bond_oxdna.html
+"pair_style oxdna/..."_pair_oxdna.html
"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
Supporting info: /src/USER-CGDNA/README, "bond_style
-oxdna_fene"_bond_oxdna_fene.html, "pair_style
-oxdna_excv"_pair_oxdna_excv.html, "fix
+oxdna/fene"_bond_oxdna.html, "pair_style
+oxdna/..."_pair_oxdna.html, "fix
nve/dotc/langevin"_fix_nve_dotc_langevin.html
Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
@@ -1778,7 +1778,7 @@ particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
-For technical details about this implemention of ReaxFF, see
+For technical details about this implementation of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
@@ -1848,7 +1848,7 @@ See this doc page to get started:
The persons who created the USER-SMTBQ package are Nicolas Salles,
Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
-these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
+these email addresses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
them directly if you have any questions.
Examples: examples/USER/smtbq
diff --git a/doc/src/Section_perf.txt b/doc/src/Section_perf.txt
index 39fe734cce72e6c7b9922a31d647f29e4479c702..0cc79b094333da98aed76917e26cb759e908225e 100644
--- a/doc/src/Section_perf.txt
+++ b/doc/src/Section_perf.txt
@@ -69,7 +69,7 @@ bench/in.lj input script.
For all the benchmarks, a useful metric is the CPU cost per atom per
timestep. Since performance scales roughly linearly with problem size
-and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained
+and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained
potentials), the run time of any problem using the same model (atom
style, force field, cutoff, etc) can then be estimated.
diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt
index bd4dfcf538217e7fa6c12ee0e8a6311957f58fa9..50807e2d95011143b05a17d331e004d84ea5264e 100644
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@@ -97,7 +97,7 @@ current LAMMPS library interface and how to call them from Python.
Section 11.8 gives some examples of coupling LAMMPS to other tools via
Python. For example, LAMMPS can easily be coupled to a GUI or other
visualization tools that display graphs or animations in real time as
-LAMMPS runs. Examples of such scripts are inlcluded in the python
+LAMMPS runs. Examples of such scripts are included in the python
directory.
Two advantages of using Python to run LAMMPS are how concise the
@@ -177,7 +177,7 @@ of Python and your machine to successfully build LAMMPS. See the
lib/python/README file for more info.
If you want to write Python code with callbacks to LAMMPS, then you
-must also follow the steps overviewed in the preceeding section (11.1)
+must also follow the steps overviewed in the preceding section (11.1)
for running LAMMPS from Python. I.e. you must build LAMMPS as a
shared library and insure that Python can find the python/lammps.py
file and the shared library.
@@ -325,7 +325,7 @@ sudo python setup.py install :pre
Again, the "sudo" is only needed if required to copy PyPar files into
your Python distribution's site-packages directory.
-If you have successully installed PyPar, you should be able to run
+If you have successfully installed PyPar, you should be able to run
Python and type
import pypar :pre
@@ -369,7 +369,7 @@ user privilege into the user local directory type
python setup.py install --user :pre
-If you have successully installed mpi4py, you should be able to run
+If you have successfully installed mpi4py, you should be able to run
Python and type
from mpi4py import MPI :pre
@@ -610,7 +610,7 @@ lmp = lammps() :pre
create an instance of LAMMPS, wrapped in a Python class by the lammps
Python module, and return an instance of the Python class as lmp. It
-is used to make all subequent calls to the LAMMPS library.
+is used to make all subsequent calls to the LAMMPS library.
Additional arguments to lammps() can be used to tell Python the name
of the shared library to load or to pass arguments to the LAMMPS
@@ -662,7 +662,7 @@ or integers (int **) is returned. You need to specify the appropriate
data type via the type argument.
For extract_compute() and extract_fix(), the global, per-atom, or
-local data calulated by the compute or fix can be accessed. What is
+local data calculated by the compute or fix can be accessed. What is
returned depends on whether the compute or fix calculates a scalar or
vector or array. For a scalar, a single double value is returned. If
the compute or fix calculates a vector or array, a pointer to the
@@ -774,7 +774,7 @@ demo.py, invoke various LAMMPS library interface routines,
simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
split.py, same as simple.py but running in parallel on a subset of procs,
gui.py, GUI go/stop/temperature-slider to control LAMMPS,
-plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
+plot.py, real-time temperature plot with GnuPlot via Pizza.py,
viz_tool.py, real-time viz via some viz package,
vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 2146830753cf26d9ceb80acf3cbc18431eb71d7d..47643569e66f38409c9e7534f7dffe37da9de570 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -80,7 +80,7 @@ This section has the following sub-sections:
Read this first :h5,link(start_2_1)
-If you want to avoid building LAMMPS yourself, read the preceeding
+If you want to avoid building LAMMPS yourself, read the preceding
section about options available for downloading and installing
executables. Details are discussed on the "download"_download page.
@@ -251,7 +251,7 @@ re-compile, after typing "make clean" (which will describe different
clean options).
The LMP_INC variable is used to include options that turn on ifdefs
-within the LAMMPS code. The options that are currently recogized are:
+within the LAMMPS code. The options that are currently recognized are:
-DLAMMPS_GZIP
-DLAMMPS_JPEG
@@ -362,7 +362,7 @@ installed on your platform. If MPI is installed on your system in the
usual place (under /usr/local), you also may not need to specify these
3 variables, assuming /usr/local is in your path. On some large
parallel machines which use "modules" for their compile/link
-environements, you may simply need to include the correct module in
+environments, you may simply need to include the correct module in
your build environment, before building LAMMPS. Or the parallel
machine may have a vendor-provided MPI which the compiler has no
trouble finding.
@@ -430,7 +430,7 @@ use the KISS library described above.
You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules"
-for their compile/link environements, you may simply need to include
+for their compile/link environments, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding.
@@ -450,7 +450,7 @@ you must also manually specify the correct library, namely -lsfftw or
The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
-calulations, particularly in parallel or on GPUs. Fourier transform
+calculations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
@@ -682,7 +682,7 @@ various make commands that can be used to manipulate packages.
If you use a command in a LAMMPS input script that is part of a
package, you must have built LAMMPS with that package, else you will
get an error that the style is invalid or the command is unknown.
-Every command's doc page specfies if it is part of a package. You can
+Every command's doc page specifies if it is part of a package. You can
also type
lmp_machine -h :pre
@@ -1008,7 +1008,7 @@ Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
rename if desired. Likewise it creates an executable named
src/lmp_auto, which you can rename using the -o switch if desired.
-The most recently executed Make.py commmand is saved in
+The most recently executed Make.py command is saved in
src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
the last command, or you can save a sequence of one or more Make.py
commands to a file and invoke the file of commands using "-r". You
@@ -1064,7 +1064,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the
-fPIC flag which is required for inclusion in a shared library. The
build will create the file liblammps_foo.so which another application
-can link to dyamically. It will also create a soft link liblammps.so,
+can link to dynamically. It will also create a soft link liblammps.so,
which will point to the most recently built shared library. This is
the file the Python wrapper loads by default.
@@ -1416,8 +1416,8 @@ LAMMPS is compiled with CUDA=yes.
numa Nm :pre
This option is only relevant when using pthreads with hwloc support.
-In this case Nm defines the number of NUMA regions (typicaly sockets)
-on a node which will be utilizied by a single MPI rank. By default Nm
+In this case Nm defines the number of NUMA regions (typically sockets)
+on a node which will be utilized by a single MPI rank. By default Nm
= 1. If this option is used the total number of worker-threads per
MPI rank is threads*numa. Currently it is always almost better to
assign at least one MPI rank per NUMA region, and leave numa set to
@@ -1481,7 +1481,7 @@ replica runs on on one or a few processors. Note that with MPI
installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
-To run multiple independent simulatoins from one input script, using
+To run multiple independent simulations from one input script, using
multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
of the manual. World- and universe-style "variables"_variable.html
are useful in this context.
@@ -1760,7 +1760,7 @@ The first section provides a global loop timing summary. The {loop time}
is the total wall time for the section. The {Performance} line is
provided for convenience to help predicting the number of loop
continuations required and for comparing performance with other,
-similar MD codes. The {CPU use} line provides the CPU utilzation per
+similar MD codes. The {CPU use} line provides the CPU utilization per
MPI task; it should be close to 100% times the number of OpenMP
threads (or 1 of no OpenMP). Lower numbers correspond to delays due
to file I/O or insufficient thread utilization.
diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt
index f469390cedad8c225c86dae7725cb4cbad79de11..83fb7a6bcec30936c8f8ad6e09b2998c90a02408 100644
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@@ -471,7 +471,7 @@ These tools were written by Aidan Thompson at Sandia.
restart2data tool :h4,link(restart)
NOTE: This tool is now obsolete and is not included in the current
-LAMMPS distribution. This is becaues there is now a
+LAMMPS distribution. This is because there is now a
"write_data"_write_data.html command, which can create a data file
from within an input script. Running LAMMPS with the "-r"
"command-line switch"_Section_start.html#start_7 as follows:
diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html
index 2f3bf4a6cf8a7d9d0f65a3aa3805b6109af12959..f4c33f5076bda70c594aa432904728fdf7b16eae 100644
--- a/doc/src/USER/atc/man_consistent_fe_initialization.html
+++ b/doc/src/USER/atc/man_consistent_fe_initialization.html
@@ -27,7 +27,7 @@
syntax</a></h2>
<p>fix_modify AtC consistent_fe_initialization <on | off></p>
<ul>
-<li><on|off> = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field </li>
+<li><on|off> = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt
index 088e6db11357f997ee014cec2f719b4cf4cb9391..f7f655a639bf677575b1e03f19b5e9326b2cb2c0 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@@ -20,7 +20,7 @@ coprocessors via offloading neighbor list and non-bonded force
calculations to the Phi. The same C++ code is used in both cases.
When offloading to a coprocessor from a CPU, the same routine is run
twice, once on the CPU and once with an offload flag. This allows
-LAMMPS to run on the CPU cores and coprocessor cores simulataneously.
+LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
[Currently Available USER-INTEL Styles:]
@@ -115,7 +115,7 @@ coprocessor and an Intel compiler are required. For this, the
recommended version of the Intel compiler is 14.0.1.106 or
versions 15.0.2.044 and higher.
-Although any compiler can be used with the USER-INTEL pacakge,
+Although any compiler can be used with the USER-INTEL package,
currently, vectorization directives are disabled by default when
not using Intel compilers due to lack of standard support and
observations of decreased performance. The OpenMP standard now
@@ -428,7 +428,7 @@ to the card. This allows for overlap of MPI communication of forces
with computation on the coprocessor when the "newton"_newton.html
setting is "on". The default is dependent on the style being used,
however, better performance may be achieved by setting this option
-explictly.
+explicitly.
When using offload with CPU Hyper-Threading disabled, it may help
performance to use fewer MPI tasks and OpenMP threads than available
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt
index 3d31344c247a73f6dc2405545e1014e63b628d16..3bfd4bf37902e1429398676532d2ec06fd5f0017 100644
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@@ -217,7 +217,7 @@ best performance its CCFLAGS setting should use -O3 and have a
KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note
the minimal required compute capability is 2.0, but this will give
-signicantly reduced performance compared to Kepler generation GPUs
+significantly reduced performance compared to Kepler generation GPUs
with compute capability 3.x. For the LINK setting, "nvcc" should not
be used; instead use g++ or another compiler suitable for linking C++
applications. Often you will want to use your MPI compiler wrapper
@@ -234,7 +234,7 @@ provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in "Section 5.3"_Section_accelerate.html#acc_3.
-KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
+KOKKOS_ARCH=KNC enables compiler switches needed when compiling for an
Intel Phi processor.
KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
@@ -272,7 +272,7 @@ coprocessor support you need to insure there are one or more MPI tasks
per coprocessor, and choose the number of coprocessor threads to use
per MPI task (via the "-k" command-line switch discussed below). The
product of MPI tasks * coprocessor threads/task should not exceed the
-maximum number of threads the coproprocessor is designed to run,
+maximum number of threads the coprocessor is designed to run,
otherwise performance will suffer. This value is 240 for current
generation Xeon Phi(TM) chips, which is 60 physical cores * 4
threads/core. Note that with the KOKKOS package you do not need to
@@ -333,7 +333,7 @@ device=CUDA are the same.
You must still use the "-k on" "command-line
switch"_Section_start.html#start_7 to enable the KOKKOS package, and
-specify its additional arguments for hardware options appopriate to
+specify its additional arguments for hardware options appropriate to
your system, as documented above.
Use the "suffix kk"_suffix.html command, or you can explicitly add a
diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt
index 8c90e1fd3a53f0ab5d05ced017f7122fecbf75d8..bdd3707ccb80130284817d86a3eec53a698c2a2a 100644
--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@@ -81,7 +81,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a "binary restart
-files"_restart.html. Thus when retarting a simulation from a restart
+files"_restart.html. Thus when restarting a simulation from a restart
file, you need to re-specify angle_coeff commands.
[Related commands:]
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index 89572c0c726b321e2aa70f77921dc2db9a8d130c..d5c82f16ac951ebd86c3194658bfcc0826c1cb9f 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -103,7 +103,7 @@ turns off the {first} option.
It is OK to use the {first} keyword with a group that has not yet been
defined, e.g. to use the atom_modify first command at the beginning of
-your input script. LAMMPS does not use the group until a simullation
+your input script. LAMMPS does not use the group until a simulation
is run.
The {sort} keyword turns on a spatial sorting or reordering of atoms
@@ -116,7 +116,7 @@ various other factors. As a general rule, sorting is typically more
effective at speeding up simulations of liquids as opposed to solids.
In tests we have done, the speed-up can range from zero to 3-4x.
-Reordering is peformed every {Nfreq} timesteps during a dynamics run
+Reordering is performed every {Nfreq} timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering
occurs at the first reneighboring that occurs after the target
timestep. The reordering is performed locally by each processor,
@@ -130,7 +130,7 @@ the processor's 1d list of atoms.
The goal of this procedure is for atoms to put atoms close to each
other in the processor's one-dimensional list of atoms that are also
near to each other spatially. This can improve cache performance when
-pairwise intereractions and neighbor lists are computed. Note that if
+pairwise interactions and neighbor lists are computed. Note that if
bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.
@@ -138,7 +138,7 @@ cache locality will be undermined.
NOTE: Running a simulation with sorting on versus off should not
change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
-to diverging trajectories over time when comparing two simluations.
+to diverging trajectories over time when comparing two simulations.
Various commands, particularly those which use random numbers
(e.g. "velocity create"_velocity.html, and "fix
langevin"_fix_langevin.html), may generate (statistically identical)
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index 9ba817a663b477987c86be89a61be95a23e97984..3d5c0a4f3dab4f955580e3307d24c71170bbe983 100644
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@@ -115,7 +115,7 @@ particle.
For the {ellipsoid} style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
-vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
+vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
For the {dipole} style, a point dipole is defined for each point
@@ -149,7 +149,7 @@ Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
-individual physical bodies from penetretating each other.
+individual physical bodies from penetrating each other.
The {wavepacket} style is similar to {electron}, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
@@ -165,7 +165,7 @@ For the {tri} style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
-The {template} style allows molecular topolgy (bonds,angles,etc) to be
+The {template} style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the "molecule"_molecule.html
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms
@@ -195,7 +195,7 @@ the {bstyle} argument. Body particles can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc.
-The "body"_body.html doc page descibes the body styles LAMMPS
+The "body"_body.html doc page describes the body styles LAMMPS
currently supports, and provides more details as to the kind of body
particles they represent. For all styles, each body particle stores
moments of inertia and a quaternion 4-vector, so that its orientation
@@ -280,7 +280,7 @@ The {dpd} style is part of the USER-DPD package for dissipative
particle dynamics (DPD).
The {meso} style is part of the USER-SPH package for smoothed particle
-hydrodyanmics (SPH). See "this PDF
+hydrodynamics (SPH). See "this PDF
guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
The {wavepacket} style is part of the USER-AWPMD package for the
diff --git a/doc/src/balance.txt b/doc/src/balance.txt
index b9d36452a66b51abc3487536c8ea93ecdff7f47d..79728d6569b392606bdf0206949c2b10a692e606 100644
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@@ -12,7 +12,7 @@ balance command :h3
balance thresh style args ... keyword args ... :pre
-thresh = imbalance threshhold that must be exceeded to perform a re-balance :ulb,l
+thresh = imbalance threshold that must be exceeded to perform a re-balance :ulb,l
one style/arg pair can be used (or multiple for {x},{y},{z}) :l
style = {x} or {y} or {z} or {shift} or {rcb} :l
{x} args = {uniform} or Px-1 numbers between 0 and 1
@@ -30,7 +30,7 @@ style = {x} or {y} or {z} or {shift} or {rcb} :l
{shift} args = dimstr Niter stopthresh
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
- stopthresh = stop balancing when this imbalance threshhold is reached
+ stopthresh = stop balancing when this imbalance threshold is reached
{rcb} args = none :pre
zero or more keyword/arg pairs may be appended :l
keyword = {weight} or {out} :l
@@ -76,13 +76,13 @@ sub-domain sizes and shapes on-the-fly during a "run"_run.html.
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or when
-the computational cost varies signficantly between different
+the computational cost varies significantly between different
particles. E.g. a model of a vapor/liquid interface, or a solid with
an irregular-shaped geometry containing void regions, or "hybrid pair
style simulations"_pair_hybrid.html which combine pair styles with
different computational cost. In these cases, the LAMMPS default of
dividing the simulation box volume into a regular-spaced grid of 3d
-bricks, with one equal-volume sub-domain per procesor, may assign
+bricks, with one equal-volume sub-domain per processor, may assign
numbers of particles per processor in a way that the computational
effort varies significantly. This can lead to poor performance when
the simulation is run in parallel.
@@ -91,7 +91,7 @@ The balancing can be performed with or without per-particle weighting.
With no weighting, the balancing attempts to assign an equal number of
particles to each processor. With weighting, the balancing attempts
to assign an equal aggregate computational weight to each processor,
-which typically inducces a diffrent number of atoms assigned to each
+which typically induces a different number of atoms assigned to each
processor. Details on the various weighting options and examples for
how they can be used are "given below"_#weighted_balance.
@@ -222,7 +222,7 @@ listed in ascending order. They represent the fractional position of
the cutting place. The left (or lower) edge of the box is 0.0, and
the right (or upper) edge is 1.0. Neither of these values is
specified. Only the interior Ps-1 positions are specified. Thus is
-there are 2 procesors in the x dimension, you specify a single value
+there are 2 processors in the x dimension, you specify a single value
such as 0.75, which would make the left processor's sub-domain 3x
larger than the right processor's sub-domain.
@@ -266,7 +266,7 @@ assigned, particles are migrated to their new owning processor, and
the balance procedure ends.
NOTE: At each rebalance operation, the bisectioning for each cutting
-plane (line in 2d) typcially starts with low and high bounds separated
+plane (line in 2d) typically starts with low and high bounds separated
by the extent of a processor's sub-domain in one dimension. The size
of this bracketing region shrinks by 1/2 every iteration. Thus if
{Niter} is specified as 10, the cutting plane will typically be
@@ -286,24 +286,32 @@ above. It performs a recursive coordinate bisectioning (RCB) of the
simulation domain. The basic idea is as follows.
The simulation domain is cut into 2 boxes by an axis-aligned cut in
-the longest dimension, leaving one new box on either side of the cut.
-All the processors are also partitioned into 2 groups, half assigned
-to the box on the lower side of the cut, and half to the box on the
-upper side. (If the processor count is odd, one side gets an extra
-processor.) The cut is positioned so that the number of particles in
-the lower box is exactly the number that the processors assigned to
-that box should own for load balance to be perfect. This also makes
-load balance for the upper box perfect. The positioning is done
-iteratively, by a bisectioning method. Note that counting particles
-on either side of the cut requires communication between all
-processors at each iteration.
+one of the dimensions, leaving one new sub-box on either side of the
+cut. Which dimension is chosen for the cut depends on the particle
+(weight) distribution within the parent box. Normally the longest
+dimension of the box is cut, but if all (or most) of the particles are
+at one end of the box, a cut may be performed in another dimension to
+induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in
+shape.
+
+After the cut is made, all the processors are also partitioned into 2
+groups, half assigned to the box on the lower side of the cut, and
+half to the box on the upper side. (If the processor count is odd,
+one side gets an extra processor.) The cut is positioned so that the
+number of (weighted) particles in the lower box is exactly the number
+that the processors assigned to that box should own for load balance
+to be perfect. This also makes load balance for the upper box
+perfect. The positioning of the cut is done iteratively, by a
+bisectioning method (median search). Note that counting particles on
+either side of the cut requires communication between all processors
+at each iteration.
That is the procedure for the first cut. Subsequent cuts are made
recursively, in exactly the same manner. The subset of processors
-assigned to each box make a new cut in the longest dimension of that
-box, splitting the box, the subset of processsors, and the particles
-in the box in two. The recursion continues until every processor is
-assigned a sub-box of the entire simulation domain, and owns the
+assigned to each box make a new cut in one dimension of that box,
+splitting the box, the subset of processors, and the particles in the
+box in two. The recursion continues until every processor is assigned
+a sub-box of the entire simulation domain, and owns the (weighted)
particles in that sub-box.
:line
@@ -368,7 +376,7 @@ of about 0.8 often results in the best performance, since the number
of neighbors is likely to overestimate the ideal weight.
This weight style is useful for systems where there are different
-cutoffs used for different pairs of interations, or the density
+cutoffs used for different pairs of interactions, or the density
fluctuates, or a large number of particles are in the vicinity of a
wall, or a combination of these effects. If a simulation uses
multiple neighbor lists, this weight style will use the first suitable
@@ -402,7 +410,7 @@ decrease the weights so that the ratio of max weight to min weight
decreases by {factor}. In both cases the intermediate weight values
increase/decrease proportionally as well. A value = 1.0 has no effect
on the {time} weights. As a rule of thumb, effective values to use
-are typicall between 0.5 and 1.2. Note that the timer quantities
+are typically between 0.5 and 1.2. Note that the timer quantities
mentioned above can be affected by communication which occurs in the
middle of the operations, e.g. pair styles with intermediate exchange
of data witin the force computation, and likewise for KSpace solves.
diff --git a/doc/src/body.txt b/doc/src/body.txt
index 0ea975539d226de950ce3fa1597859c7946b5c67..d44f82d4cc6703ed41c23dd08b2f1d294d45ceca 100644
--- a/doc/src/body.txt
+++ b/doc/src/body.txt
@@ -82,7 +82,7 @@ internal stress that induces fragmentation :ul
then the interaction between pairs of particles is likely to be more
complex than the summation of simple sub-particle interactions. An
example is contact or frictional forces between particles with planar
-sufaces that inter-penetrate.
+surfaces that inter-penetrate.
These are additional LAMMPS commands that can be used with body
particles of different styles
@@ -105,7 +105,7 @@ in the sections below.
The {nparticle} body style represents body particles as a rigid body
with a variable number N of sub-particles. It is provided as a
-vanillia, prototypical example of a body particle, although as
+vanilla, prototypical example of a body particle, although as
mentioned above, the "fix rigid"_fix_rigid.html command already
duplicates its functionality.
@@ -140,7 +140,7 @@ for more details.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
-simulation box XYZ axes, not with respect to the prinicpal axes of the
+simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each sub-particle are specified as its x,y,z
displacement from the center-of-mass of the body particle. The
@@ -218,7 +218,7 @@ wish; see the "read_data"_read_data.html command for more details.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
-simulation box XYZ axes, not with respect to the prinicpal axes of the
+simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each vertex are specified as its x,y,z displacement
from the center-of-mass of the body particle. The center-of-mass
diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt
index 0b5731dcb41d007f07f37a2b4801a28bedf6b5de..400c3e0be4c9e1b7fb1fd98936208ad19f384896 100644
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart
-files"_restart.html. Thus when retarting a simulation from a restart
+files"_restart.html. Thus when restarting a simulation from a restart
file, you need to re-specify bond_coeff commands.
[Related commands:]
diff --git a/doc/src/bond_oxdna_fene.txt b/doc/src/bond_oxdna.txt
similarity index 69%
rename from doc/src/bond_oxdna_fene.txt
rename to doc/src/bond_oxdna.txt
index 23018c2ab7096eb847559b019a1d302da2d47951..3a10058812e7eeefbc2f7ba16bfb2decce429b45 100644
--- a/doc/src/bond_oxdna_fene.txt
+++ b/doc/src/bond_oxdna.txt
@@ -6,20 +6,20 @@
:line
-bond_style oxdna_fene command :h3
+bond_style oxdna/fene command :h3
[Syntax:]
-bond_style oxdna_fene :pre
+bond_style oxdna/fene :pre
[Examples:]
-bond_style oxdna_fene
+bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525 :pre
[Description:]
-The {oxdna_fene} bond style uses the potential
+The {oxdna/fene} bond style uses the potential
:c,image(Eqs/bond_oxdna_fene.jpg)
@@ -37,14 +37,14 @@ Delta (distance)
r0 (distance) :ul
NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
-for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
-and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of
-"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients
+for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
+and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
+"pair_style oxdna/excv"_pair_oxdna.html). The coefficients
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
+Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/.
A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
+DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
A technical report with more information on the model, the structure of the input file,
the setup tool and the performance of the LAMMPS-implementation of oxDNA
can be found "here"_PDF/USER-CGDNA-overview.pdf.
@@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
-"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
+"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
[Default:] none
diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt
index ee35672aa1194b001640d9a95a7ec59c53d47c34..169d56ecbe4e7c75fce57abd58078dff9404a0cb 100644
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@@ -15,7 +15,7 @@ Bond Styles :h1
bond_morse
bond_none
bond_nonlinear
- bond_oxdna_fene
+ bond_oxdna
bond_quartic
bond_table
bond_zero
diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt
index c6556e0fc91d1a4ab8d5a9a3c5e1d0dc726dafe2..2c7a890d4cfb406abf018fb4787917f797fcc963 100644
--- a/doc/src/change_box.txt
+++ b/doc/src/change_box.txt
@@ -101,11 +101,11 @@ Instead you could do something like this, assuming the simulation box
is non-periodic and atoms extend from 0 to 20 in all dimensions:
change_box all x final -10 20
-create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre
+create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre
change_box all x final -10 20 boundary f s s
create_atoms 1 single -5 5 5
-change_box boundary s s s # this will work :pre
+change_box all boundary s s s # this will work :pre
NOTE: Unlike the earlier "displace_box" version of this command, atom
remapping is NOT performed by default. This command allows remapping
@@ -258,8 +258,8 @@ command.
:line
The {ortho} and {triclinic} keywords convert the simulation box to be
-orthogonal or triclinic (non-orthongonal). See "this
-section"_Section_howto#howto_13 for a discussion of how non-orthongal
+orthogonal or triclinic (non-orthogonal). See "this
+section"_Section_howto#howto_13 for a discussion of how non-orthogonal
boxes are represented in LAMMPS.
The simulation box is defined as either orthogonal or triclinic when
@@ -289,7 +289,7 @@ the create_box command is encountered in the input script.
The {remap} keyword remaps atom coordinates from the last saved box
size/shape to the current box state. For example, if you stretch the
box in the x dimension or tilt it in the xy plane via the {x} and {xy}
-keywords, then the {remap} commmand will dilate or tilt the atoms to
+keywords, then the {remap} command will dilate or tilt the atoms to
conform to the new box size/shape, as if the atoms moved with the box
as it deformed.
diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt
index 667938768b4da009f9313b01c317b9a58237a2ef..8248d654d32265924b3e25734fb19d40d2c3b0f5 100644
--- a/doc/src/comm_style.txt
+++ b/doc/src/comm_style.txt
@@ -39,7 +39,7 @@ sizes and shapes. Again there is one tile per processor. To acquire
information for nearby atoms, communication must now be done with a
more complex pattern of neighboring processors.
-Note that this command does not actually define a partitoining of the
+Note that this command does not actually define a partitioning of the
simulation box (a domain decomposition), rather it determines what
kinds of decompositions are allowed and the pattern of communication
used to enable the decomposition. A decomposition is created when the
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index 8ecfd81af1d042ba906e026ca0d269eb5ee2754e..eed190aeb25df73b632acd00ffd76d39509b284e 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -235,7 +235,7 @@ section of "this page"_Section_commands.html#cmd_5.
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
-"ti"_compute_ti.html - thermodyanmic integration free energy values
+"ti"_compute_ti.html - thermodynamic integration free energy values
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
"vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt
index 439ff5192cac1742f104406cdce81bcaceda56ba..813da15eeadeed76c43a5f933f52e272d9653cbc 100644
--- a/doc/src/compute_angmom_chunk.txt
+++ b/doc/src/compute_angmom_chunk.txt
@@ -22,7 +22,7 @@ compute 1 fluid angmom/chunk molchunk :pre
[Description:]
-Define a computation that calculates the angular momemtum of multiple
+Define a computation that calculates the angular momentum of multiple
chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a "compute
diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt
index 0a48ccb5be3080fdd201cc0834371f6f3843f553..4e4b03d16762c97eb44fb010f131d63ab0d1fd4f 100644
--- a/doc/src/compute_centro_atom.txt
+++ b/doc/src/compute_centro_atom.txt
@@ -18,8 +18,8 @@ lattice = {fcc} or {bcc} or N = # of neighbors per atom to include :l
zero or more keyword/value pairs may be appended :l
keyword = {axes} :l
{axes} value = {no} or {yes}
- {no} = do not calulate 3 symmetry axes
- {yes} = calulate 3 symmetry axes :pre
+ {no} = do not calculate 3 symmetry axes
+ {yes} = calculate 3 symmetry axes :pre
:ule
[Examples:]
@@ -108,7 +108,7 @@ symmetry axis, followed by the second, and third symmetry axes in
columns 5-7 and 8-10.
The centrosymmetry values are unitless values >= 0.0. Their magnitude
-depends on the lattice style due to the number of contibuting neighbor
+depends on the lattice style due to the number of contributing neighbor
pairs in the summation in the formula above. And it depends on the
local defects surrounding the central atom, as described above. For
the {axes yes} case, the vector components are also unitless, since
diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt
index e6083ad615014ba3d403b7d338adc1bb2d5cff0b..b3b09ffa71efb1150d3f19abc4808c37133b3556 100644
--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@@ -386,7 +386,7 @@ If {compress yes} is set, and the {compress} keyword comes before the
{limit} keyword, the compression operation is performed first, as
described below, which resets {Nchunk}. The {limit} keyword is then
applied to the new {Nchunk} value, exactly as described in the
-preceeding paragraph. Note that in this case, all atoms will end up
+preceding paragraph. Note that in this case, all atoms will end up
with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or
compute/fix/variable value) may have been > {Nc}, because of the
compression operation.
@@ -459,7 +459,7 @@ The original chunk IDs (before renumbering) can be accessed by the
which outputs the original IDs as one of the columns in its global
output array. For example, using the "compute cluster/atom" command
discussed above, the original 5 unique chunk IDs might be atom IDs
-(27,4982,58374,857838,1000000). After compresion, these will be
+(27,4982,58374,857838,1000000). After compression, these will be
renumbered to (1,2,3,4,5). The original values (27,...,1000000) can
be output to a file by the "fix ave/chunk"_fix_ave_chunk.html command,
or by using the "fix ave/time"_fix_ave_time.html command in
@@ -538,7 +538,7 @@ is set to {yes}, an out-of-domain atom will have its chunk ID set to
to the first or last bin in both the radial and axis dimensions. If
{discard} is set to {mixed}, which is the default, the radial
dimension is treated the same as for {discard} = no. But for the axis
-dimensinon, it will only have its chunk ID set to the first or last
+dimension, it will only have its chunk ID set to the first or last
bin if bins extend to the simulation box boundary in the axis
dimension. This is the case if the {bound} keyword settings are
{lower} and {upper}, which is the default. If the {bound} keyword
diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt
index 9867d86efb0e99652d35b6fe95127022220914a7..74240b515d2199c28d9b7e7be66cff64746123a1 100644
--- a/doc/src/compute_cna_atom.txt
+++ b/doc/src/compute_cna_atom.txt
@@ -42,7 +42,7 @@ performed on mono-component systems.
The CNA calculation can be sensitive to the specified cutoff value.
You should insure the appropriate nearest neighbors of an atom are
-found within the cutoff distance for the presumed crystal strucure.
+found within the cutoff distance for the presumed crystal structure.
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
neighbors for perfect BCC crystals. These formulas can be used to
obtain a good cutoff distance:
diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt
index a5fdb224bc6c66658deed73dc87bab7d406fa21a..b0e0c14e424ae0de3d043c2686bbc19be9e938f0 100644
--- a/doc/src/compute_com.txt
+++ b/doc/src/compute_com.txt
@@ -25,7 +25,7 @@ Define a computation that calculates the center-of-mass of the group
of atoms, including all effects due to atoms passing thru periodic
boundaries.
-A vector of three quantites is calculated by this compute, which
+A vector of three quantities is calculated by this compute, which
are the x,y,z coordinates of the center of mass.
NOTE: The coordinates of an atom contribute to the center-of-mass in
diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt
index 0367b2fe95b8b0d634308ba18ee7c7214e7a3eb2..854a5778ec0cd3ec81b3b778aedbf3474ed42197 100644
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@@ -70,7 +70,7 @@ The ID of the previously specified "compute
orientorder/atom"_compute_orientorder/atom command is specified as
{orientorderID}. The compute must invoke its {components} option to
calculate components of the {Ybar_lm} vector for each atoms, as
-described in its documenation. Note that orientorder/atom compute
+described in its documentation. Note that orientorder/atom compute
defines its own criteria for identifying neighboring atoms. If the
scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
orientorder/atom compute is larger than the specified {threshold},
diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt
index 94f49492d12e150b1a23b29b297a13039bdec5d4..918fbf65eff0c4172e92a8d551ce74e1a9f59cd1 100644
--- a/doc/src/compute_damage_atom.txt
+++ b/doc/src/compute_damage_atom.txt
@@ -47,7 +47,7 @@ any command that uses per-atom values from a compute as input. See
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
-The per-atom vector values are unitlesss numbers (damage) >= 0.0.
+The per-atom vector values are unitless numbers (damage) >= 0.0.
[Restrictions:]
diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt
index 04409f7e45266b3b8a3dff49780a27f255eb8bd5..ce00f7f12a5b9daae8a2b9ce9ae07a03188c41b4 100644
--- a/doc/src/compute_dilatation_atom.txt
+++ b/doc/src/compute_dilatation_atom.txt
@@ -50,7 +50,7 @@ This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
Section_howto 15 for an overview of LAMMPS output options.
-The per-atom vector values are unitlesss numbers (theta) >= 0.0.
+The per-atom vector values are unitless numbers (theta) >= 0.0.
[Restrictions:]
diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt
index 566dcfc0a0ea03e960087da19927a1325a1b2a26..decf0bc8b905ed4ac7160ea268b8b7ff4914c60c 100644
--- a/doc/src/compute_displace_atom.txt
+++ b/doc/src/compute_displace_atom.txt
@@ -25,7 +25,7 @@ Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects
due to atoms passing thru periodic boundaries.
-A vector of four quantites per atom is calculated by this compute.
+A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz).
diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt
index d1ebd72ae5cf66360c6cd63133cd6690a693e632..5e3a0c8599d533af3313cbe711c5d64ab77c680d 100644
--- a/doc/src/compute_event_displace.txt
+++ b/doc/src/compute_event_displace.txt
@@ -14,7 +14,7 @@ compute ID group-ID event/displace threshold :pre
ID, group-ID are documented in "compute"_compute.html command
event/displace = style name of this compute command
-threshold = minimum distance anyparticle must move to trigger an event (distance units) :ul
+threshold = minimum distance any particle must move to trigger an event (distance units) :ul
[Examples:]
@@ -37,7 +37,7 @@ further than the threshold distance.
NOTE: If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum,
then this compute will not be able to distinguish that motion from
-local atom displacements and may generate "false postives."
+local atom displacements and may generate "false positives."
[Output info:]
diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt
index f62efcff2ebc54b01920f98126b144c574c5b940..3136b1fd18f849bcf6c69b328983b8aa135d5c50 100644
--- a/doc/src/compute_global_atom.txt
+++ b/doc/src/compute_global_atom.txt
@@ -55,7 +55,7 @@ M is the actual length of the input vector, then an output value of
0.0 is assigned to the atom.
An example of how this command is useful, is in the context of
-"chunks" which are static or dyanmic subsets of atoms. The "compute
+"chunks" which are static or dynamic subsets of atoms. The "compute
chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs
to each atom. It's output can be used as the {index} parameter for
this command. Various other computes with "chunk" in their style
@@ -192,7 +192,7 @@ reference thermodynamic keywords and various other attributes of
atoms, or invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of generating a vector of
global quantities which the {index} parameter will reference for
-assignement of global values to atoms.
+assignment of global values to atoms.
:line
@@ -207,7 +207,7 @@ See "Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector or array values will be in whatever units the
-corresponsing input values are in.
+corresponding input values are in.
[Restrictions:] none
diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt
index 720d26ce761db261b51c9defdc21237309f685ab..e8adac3deb5e71a5cd3ed3c15088868b3b8768f5 100644
--- a/doc/src/compute_heat_flux.txt
+++ b/doc/src/compute_heat_flux.txt
@@ -38,7 +38,7 @@ subtracted to a group of atoms.
The compute takes three arguments which are IDs of other
"computes"_compute.html. One calculates per-atom kinetic energy
({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
-third calcualtes per-atom stress ({stress-ID}).
+third calculates per-atom stress ({stress-ID}).
NOTE: These other computes should provide values for all the atoms in
the group this compute specifies. That means the other computes could
@@ -83,7 +83,7 @@ The heat flux can be output every so many timesteps (e.g. via the
post-processing operation, an autocorrelation can be performed, its
integral estimated, and the Green-Kubo formula above evaluated.
-The "fix ave/correlate"_fix_ave_correlate.html command can calclate
+The "fix ave/correlate"_fix_ave_correlate.html command can calculate
the autocorrelation. The trap() function in the
"variable"_variable.html command can calculate the integral.
diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt
index 59a459b0d78b677814943c71f98e2f8ace0514ff..b0dbb12aea8d5e7e1e5d982f0d4d656b9d0c2ffb 100644
--- a/doc/src/compute_inertia_chunk.txt
+++ b/doc/src/compute_inertia_chunk.txt
@@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section
defined and examples of how they can be used to measure properties of
a system.
-This compute calculates the 6 components of the symmetric intertia
+This compute calculates the 6 components of the symmetric inertia
tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The
calculation includes all effects due to atoms passing thru periodic
boundaries.
diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt
index 42dbca255d9c389a4efc65a9f7f61c2e43e0b34e..f806c5e29266752bae1859a33bcf8eb1101eb99c 100644
--- a/doc/src/compute_msd.txt
+++ b/doc/src/compute_msd.txt
@@ -33,7 +33,7 @@ passing thru periodic boundaries. For computation of the non-Gaussian
parameter of mean-squared displacement, see the "compute
msd/nongauss"_compute_msd_nongauss.html command.
-A vector of four quantites is calculated by this compute. The first 3
+A vector of four quantities is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group. The 4th element is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt
index 7382ca87dea37aeb3a4705c258664d186cd15979..7f31b61ed0bda808a94a5a45e3c4d165f4e3c1cf 100644
--- a/doc/src/compute_msd_chunk.txt
+++ b/doc/src/compute_msd_chunk.txt
@@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section
defined and examples of how they can be used to measure properties of
a system.
-Four quantites are calculated by this compute for each chunk. The
+Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
center-of-mass. The 4th component is the total squared displacement,
i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt
index b92ceaacdef7328b10e58e60d79706a62ba225dc..198da999e0a3c36af28e45f173dc9683aca3aa50 100644
--- a/doc/src/compute_msd_nongauss.txt
+++ b/doc/src/compute_msd_nongauss.txt
@@ -30,12 +30,12 @@ Define a computation that calculates the mean-squared displacement
(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
including all effects due to atoms passing thru periodic boundaries.
-A vector of three quantites is calculated by this compute. The first
+A vector of three quantities is calculated by this compute. The first
element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx*dx + dy*dy +
dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
-group. The 3rd component is the nonGaussian diffusion paramter NGP =
+group. The 3rd component is the nonGaussian diffusion parameter NGP =
3*drfourth/(5*drsquared*drsquared), i.e.
:c,image(Eqs/compute_msd_nongauss.jpg)
@@ -48,7 +48,7 @@ others.
If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
-displacment of each atom is calcluated.
+displacment of each atom is calculated.
See the "compute msd"_compute_msd.html doc page for further important
NOTEs, which also apply to this compute.
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index d2b34ed110406247caf1802827ba638e042d7a5a..0602dab81bd5902838a01d52432a881db684f710 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -43,7 +43,7 @@ style van der Waals interaction or not) is tallied in {evdwl}. If
as a global scalar by this compute. This is useful when using
"pair_style hybrid"_pair_hybrid.html if you want to know the portion
of the total energy contributed by one sub-style. If {evalue} is
-specfied as {evdwl} or {ecoul}, then just that portion of the energy
+specified as {evdwl} or {ecoul}, then just that portion of the energy
is stored as a global scalar.
NOTE: The energy returned by the {evdwl} keyword does not include tail
@@ -52,7 +52,7 @@ corrections, even if they are enabled via the
Some pair styles tally additional quantities, e.g. a breakdown of
potential energy into a dozen or so components is tallied by the
-"pair_style reax"_pair_reax.html commmand. These values (1 or more)
+"pair_style reax"_pair_reax.html command. These values (1 or more)
are stored as a global vector by this compute. See the doc page for
"individual pair styles"_pair_style.html for info on these values.
diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt
index 0d420b22025813f2917a20924a4eb3d7976f3d8a..012121099454b45d3ea43fa025aba16de6257f22 100644
--- a/doc/src/compute_pair_local.txt
+++ b/doc/src/compute_pair_local.txt
@@ -47,7 +47,7 @@ force cutoff distance for that interaction, as defined by the
"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html
commands.
-The value {dist} is the distance bewteen the pair of atoms.
+The value {dist} is the distance between the pair of atoms.
The value {eng} is the interaction energy for the pair of atoms.
diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt
index 8e2fd17f2444492aee885a5a9d8d742c1eaa293d..6de3a79e5b1d1e6ecbac41bbe0c45d1b890d86b3 100644
--- a/doc/src/compute_pe_atom.txt
+++ b/doc/src/compute_pe_atom.txt
@@ -51,7 +51,7 @@ these terms is included in the pair energy, not the dihedral energy.
The KSpace contribution is calculated using the method in
"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
as specified by the "kspace_style pppm"_kspace_style.html command.
-For PPPM, the calcluation requires 1 extra FFT each timestep that
+For PPPM, the calculation requires 1 extra FFT each timestep that
per-atom energy is calculated. This "document"_PDF/kspace.pdf
describes how the long-range per-atom energy calculation is performed.
diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt
index 75491cfb146b7be07cdb187c0a782a929ee0da16..788213fc65985cb86bee7a08b3e78f50adf423cc 100644
--- a/doc/src/compute_plasticity_atom.txt
+++ b/doc/src/compute_plasticity_atom.txt
@@ -44,7 +44,7 @@ This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
Section_howto 15 for an overview of LAMMPS output options.
-The per-atom vector values are unitlesss numbers (lambda) >= 0.0.
+The per-atom vector values are unitless numbers (lambda) >= 0.0.
[Restrictions:]
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index 9e8c2a3b4644a1700ea24dccf948e7c06344a32c..ae62859b17420b87c7dc0d95eadc776b285285ee 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -89,7 +89,7 @@ commands"_compute.html to determine which ones include a bias.
Also note that the N in the first formula above is really
degrees-of-freedom divided by d = dimensionality, where the DOF value
-is calcluated by the temperature compute. See the various "compute
+is calculated by the temperature compute. See the various "compute
temperature"_compute.html styles for details.
A compute of this style with the ID of "thermo_press" is created when
diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt
index 3bed9c06779c4f46ae10011c4b848ee90e23ca5a..b9d4944b30740cfcb28313811a6885296c65acf4 100644
--- a/doc/src/compute_property_chunk.txt
+++ b/doc/src/compute_property_chunk.txt
@@ -64,7 +64,7 @@ can only be used if the {compress} keyword was set to {yes} for the
"compute chunk/atom"_compute_chunk_atom.html command referenced by
chunkID. This means that the original chunk IDs (e.g. molecule IDs)
will have been compressed to remove chunk IDs with no atoms assigned
-to them. Thus a compresed chunk ID of 3 may correspond to an original
+to them. Thus a compressed chunk ID of 3 may correspond to an original
chunk ID (molecule ID in this case) of 415. The {id} attribute will
then be 415 for the 3rd chunk.
diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt
index 1c9de277bc7af5af0e0b8c6eb509ed01c9787ee6..acbc0e4f0cc30d478d407a52b7e5effce8370938 100644
--- a/doc/src/compute_rdf.txt
+++ b/doc/src/compute_rdf.txt
@@ -73,7 +73,7 @@ post-process a dump file to calculate it. This is because using the
which may slow down your simulation. If you specify a {Rcut} <= force
cutoff, you will force an additional neighbor list to be built at
every timestep this command is invoked (or every reneighboring
-timestep, whichever is less frequent), which is inefficent. LAMMPS
+timestep, whichever is less frequent), which is inefficient. LAMMPS
will warn you if this is the case. If you specify a {Rcut} > force
cutoff, you must insure ghost atom information out to {Rcut} + {skin}
is communicated, via the "comm_modify cutoff"_comm_modify.html
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index 5cdd58fbc253a8bb58a9ccd9dcb987059f2d272c..077ad57d81b6bb1acd7d328e4e3f819867e71510 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -123,7 +123,7 @@ The {vx}, {vy}, {vz}, {fx}, {fy}, {fz} attributes are components of
the COM velocity and force on the COM of the body.
The {omegax}, {omegay}, and {omegaz} attributes are the angular
-velocity componennts of the body around its COM.
+velocity components of the body around its COM.
The {angmomx}, {angmomy}, and {angmomz} attributes are the angular
momentum components of the body around its COM.
diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt
index 658f41cdca212878ef8743e569dbf44f899efa08..aadda495331b7048493f7c04b0db35ff4c2c8fea 100644
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@@ -93,7 +93,7 @@ parameters will denote the z1=h, z2=k, and z3=l (in a global since)
zone axis of an intersecting Ewald sphere. Diffraction intensities
will only be computed at the intersection of the reciprocal lattice
mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the
-example 3D intestiety data and the intersection of a \[010\] zone axis
+example 3D intensity data and the intersection of a \[010\] zone axis
in the below image.
:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)
diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt
index 95af1b216364d18eff679bf51219a5e2bc511558..adece9334361d154d3f7d7a62de19b0eaac01a93 100644
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@@ -35,7 +35,7 @@ any command that uses per-particle values from a compute as input.
See "Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
-The per-particle values will be given dimentionless, see "units"_units.html.
+The per-particle values will be given dimensionless, see "units"_units.html.
[Restrictions:]
diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt
index 3dc642da3296b654bc4e19c25b8366d24fe1ca59..d09c8069cc99bf73ac0af134f240b42d3e7f9be8 100644
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@@ -92,7 +92,7 @@ The KSpace contribution is calculated using the method in
"(Heyes)"_#Heyes for the Ewald method and by the methodology described
in "(Sirk)"_#Sirk for PPPM. The choice of KSpace solver is specified
by the "kspace_style pppm"_kspace_style.html command. Note that for
-PPPM, the calcluation requires 6 extra FFTs each timestep that
+PPPM, the calculation requires 6 extra FFTs each timestep that
per-atom stress is calculated. Thus it can significantly increase the
cost of the PPPM calculation if it is needed on a large fraction of
the simulation timesteps.
diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt
index 43e1588fa073dbfea226919b55eba4299329fffb..495366b34501b65e785bff5ec6e442ff02e89b96 100644
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
@@ -138,7 +138,7 @@ This compute is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This compute requires that atoms store angular momementum and a
+This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt
index 04b707bcce2d770aa10c52a042c829fcbfbecdae..f72b886cc47afa0b0f7badd75b39ef943375002d 100644
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
@@ -120,7 +120,7 @@ This compute is part of the BODY package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This compute requires that atoms store angular momementum and a
+This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
command.
diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt
index d565c951346b6bc2420e601d5954b075c7cf88bb..f877f6ece84b9a2429d64949eea298e20d98ef74 100644
--- a/doc/src/compute_temp_chunk.txt
+++ b/doc/src/compute_temp_chunk.txt
@@ -44,7 +44,7 @@ compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 :pre
Define a computation that calculates the temperature of a group of
atoms that are also in chunks, after optionally subtracting out the
center-of-mass velocity of each chunk. By specifying optional values,
-it can also calulate the per-chunk temperature or energies of the
+it can also calculate the per-chunk temperature or energies of the
multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a "compute
@@ -122,7 +122,7 @@ concept is somewhat ill-defined. In some cases, you can use the
{adof} and {cdof} keywords to adjust the calculated degress of freedom
appropriately, as explained below.
-Note that the per-chunk temperature calulated by this compute and the
+Note that the per-chunk temperature calculated by this compute and the
"fix ave/chunk temp"_fix_ave_chunk.html command can be different.
This compute calculates the temperature for each chunk for a single
snapshot. Fix ave/chunk can do that but can also time average those
@@ -208,7 +208,7 @@ This compute also optionally calculates a global array, if one or more
of the optional values are specified. The number of rows in the array
= the number of chunks {Nchunk} as calculated by the specified
"compute chunk/atom"_compute_chunk_atom.html command. The number of
-columns is the number of specifed values (1 or more). These values
+columns is the number of specified values (1 or more). These values
can be accessed by any command that uses global array values from a
compute as input. Again, see "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt
index 54eebd6d8fd3c96fcb6ad5b3e61a801d5b5141c6..3b6f774d33b923bd2249b0d284cdb89bd3418d17 100644
--- a/doc/src/compute_temp_profile.txt
+++ b/doc/src/compute_temp_profile.txt
@@ -118,7 +118,7 @@ needed, the subtracted degrees-of-freedom can be altered using the
NOTE: When using the {out} keyword with a value of {bin}, the
calculated temperature for each bin does not include the
-degrees-of-freedom adjustment described in the preceeding paragraph,
+degrees-of-freedom adjustment described in the preceding paragraph,
for fixes that constrain molecular motion. It does include the
adjustment due to the {extra} option, which is applied to each bin.
diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt
index 29ada25c9cf333fc03854392702a10582805d48c..a0d9a3c5f702ea42c77d8a18f433743f73500f77 100644
--- a/doc/src/compute_vacf.txt
+++ b/doc/src/compute_vacf.txt
@@ -27,7 +27,7 @@ function (VACF), averaged over a group of atoms. Each atom's
contribution to the VACF is its current velocity vector dotted into
its initial velocity vector at the time the compute was specified.
-A vector of four quantites is calculated by this compute. The first 3
+A vector of four quantities is calculated by this compute. The first 3
elements of the vector are vx * vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt
index ea573a135679df497f442bd623ffbef12c7a3634..d084fcee66e7edbe1c794fb88e537b7621c1a0b5 100644
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@@ -217,6 +217,10 @@ This compute is part of the VORONOI package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
+It also requiers you have a copy of the Voro++ library built and
+installed on your system. See instructions on obtaining and
+installing the Voro++ software in the src/VORONOI/README file.
+
[Related commands:]
"dump custom"_dump.html, "dump local"_dump.html
diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt
index ec7a6f4d8a50b872ee229c0b7f50b88d27c85f70..98c3c24a0b9635d5d9dd17f7ec84e85a60a3829d 100644
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@@ -101,7 +101,7 @@ positions.
For the {random} style, N particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the
-speficied random number {seed}, resulting in the same set of particles
+specified random number {seed}, resulting in the same set of particles
coordinates, independent of how many processors are being used in the
simulation. If the {region-ID} argument is specified as NULL, then
the created particles will be anywhere in the simulation box. If a
@@ -134,6 +134,17 @@ not overlap existing atoms inappropriately, especially if molecules
are being added. The "delete_atoms"_delete_atoms.html command can be
used to remove overlapping atoms or molecules.
+NOTE: You cannot use any of the styles explained above to create atoms
+that are outside the simulation box; they will just be ignored by
+LAMMPS. This is true even if you are using shrink-wrapped box
+boundaries, as specified by the "boundary"_boundary.html command.
+However, you can first use the "change_box"_change_box.html command to
+temporarily expand the box, then add atoms via create_atoms, then
+finally use change_box command again if needed to re-shrink-wrap the
+new atoms. See the "change_box"_change_box.html doc page for an
+example of how to do this, using the create_atoms {single} style to
+insert a new atom outside the current simulation box.
+
:line
Individual atoms are inserted by this command, unless the {mol}
diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt
index bddc0c0ec8ab56aaf2af6a4cb32cdcce28a16634..8cb40eff44a66189d2ff37aadbd0c25ccd5a00c3 100644
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@@ -82,7 +82,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a "binary
-restart files"_restart.html. Thus when retarting a simulation from a
+restart files"_restart.html. Thus when restarting a simulation from a
restart file, you need to re-specify dihedral_coeff commands.
[Related commands:]
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index 5f8ee1ee88e2330049e50301addbb8a3c51cbcfc..1c65b1cdbf5833d0f80f97142b9ee1db84ad6fbd 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -225,7 +225,7 @@ This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
-of xlo, etc, since they repesent a bounding box. See "this
+of xlo, etc, since they represent a bounding box. See "this
section"_Section_howto.html#howto_12 of the doc pages for a geometric
description of triclinic boxes, as defined by LAMMPS, simple formulas
for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
@@ -545,7 +545,7 @@ that the coordinate values may be far outside the box bounds printed
with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using
{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
the box size. Atoms that have passed through a periodic boundary will
-have the corresponding cooordinate increased or decreased by 1.0.
+have the corresponding coordinate increased or decreased by 1.0.
The image flags can be printed directly using the {ix}, {iy}, {iz}
attributes. For periodic dimensions, they specify which image of the
diff --git a/doc/src/dump_custom_vtk.txt b/doc/src/dump_custom_vtk.txt
index b84817327b076e077b220794f7a78c9714138dd0..f15d20f849692cd49176d0ce39d0619dc1f28900 100644
--- a/doc/src/dump_custom_vtk.txt
+++ b/doc/src/dump_custom_vtk.txt
@@ -211,7 +211,7 @@ charge.
There are several options for outputting atom coordinates. The {x},
{y}, {z} attributes are used to write atom coordinates "unscaled", in
the appropriate distance "units"_units.html (Angstroms, sigma, etc).
-Additionaly, you can use {xs}, {ys}, {zs} if you want to also save the
+Additionally, you can use {xs}, {ys}, {zs} if you want to also save the
coordinates "scaled" to the box size, so that each value is 0.0 to
1.0. If the simulation box is triclinic (tilted), then all atom
coords will still be between 0.0 and 1.0. Use {xu}, {yu}, {zu} if you
@@ -224,7 +224,7 @@ values may be far outside the box bounds printed with the snapshot.
Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except
that the unwrapped coordinates are scaled by the box size. Atoms that
have passed through a periodic boundary will have the corresponding
-cooordinate increased or decreased by 1.0.
+coordinate increased or decreased by 1.0.
The image flags can be printed directly using the {ix}, {iy}, {iz}
attributes. For periodic dimensions, they specify which image of the
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index f5085846df1fc2d988af8379479fd6822c04e11d..3fa267d2b099a252bce78e49d24c69609dffac2a 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -99,7 +99,7 @@ included in the image or movie and how it appears. A series of such
images can easily be manually converted into an animated movie of your
simulation or the process can be automated without writing the
intermediate files using the dump movie style; see further details
-below. Other dump styles store snapshots of numerical data asociated
+below. Other dump styles store snapshots of numerical data associated
with atoms in various formats, as discussed on the "dump"_dump.html
doc page.
@@ -237,7 +237,7 @@ diameter, which can be used as the {diameter} setting.
:line
-The various kewords listed above control how the image is rendered.
+The various keywords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The "dump modify"_dump_modify.html
also has options specific to the dump image style, particularly for
@@ -261,7 +261,7 @@ the input script defines, e.g. Angstroms.
The {bond} keyword allows to you to alter how bonds are drawn. A bond
is only drawn if both atoms in the bond are being drawn due to being
in the specified group and due to other selection criteria
-(e.g. region, threshhold settings of the
+(e.g. region, threshold settings of the
"dump_modify"_dump_modify.html command). By default, bonds are drawn
if they are defined in the input data file as read by the
"read_data"_read_data.html command. Using {none} for both the bond
@@ -356,7 +356,7 @@ is used to define body particles with internal state
body style. If this keyword is not used, such particles will be drawn
as spheres, the same as if they were regular atoms.
-The "body"_body.html doc page descibes the body styles LAMMPS
+The "body"_body.html doc page describes the body styles LAMMPS
currently supports, and provides more details as to the kind of body
particles they represent and how they are drawn by this dump image
command. For all the body styles, individual atoms can be either a
@@ -442,7 +442,7 @@ degrees.
The {center} keyword determines the point in simulation space that
will be at the center of the image. {Cx}, {Cy}, and {Cz} are
-speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
+specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose strange
@@ -476,8 +476,8 @@ smaller. {Zfactor} must be a value > 0.0.
The {persp} keyword determines how much depth perspective is present
in the image. Depth perspective makes lines that are parallel in
simulation space appear non-parallel in the image. A {pfactor} value
-of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
-which is an orthographic rendering with no persepctive. A {pfactor}
+of 0.0 means that parallel lines will meet at infinity (1.0/pfactor),
+which is an orthographic rendering with no perspective. A {pfactor}
value between 0.0 and 1.0 will introduce more perspective. A {pfactor}
value > 1 will create a highly skewed image with a large amount of
perspective.
@@ -638,7 +638,7 @@ pipe:: Input/output error :pre
which can be safely ignored. Other warnings
and errors have to be addressed according to the FFmpeg documentation.
One known issue is that certain movie file formats (e.g. MPEG level 1
-and 2 format streams) have video bandwith limits that can be crossed
+and 2 format streams) have video bandwidth limits that can be crossed
when rendering too large of image sizes. Typical warnings look like
this:
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 0cf30e3c920ab92754aeef9a9a69cb13fdad97f4..b5daa6416e91912ab30eef406dec4d4078deb419 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -426,7 +426,7 @@ regions.
The {scale} keyword applies only to the dump {atom} style. A scale
value of {yes} means atom coords are written in normalized units from
-0.0 to 1.0 in each box dimension. If the simluation box is triclinic
+0.0 to 1.0 in each box dimension. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. A
value of {no} means they are written in absolute distance units
(e.g. Angstroms or sigma).
@@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold.
If an atom-style variable is used as the attribute, then it can
produce continuous numeric values or effective Boolean 0/1 values
-which may be useful for the comparision operator. Boolean values can
+which may be useful for the comparison operator. Boolean values can
be generated by variable formulas that use comparison or Boolean math
operators or special functions like gmask() and rmask() and grmask().
See the "variable"_variable.html command doc page for details.
diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt
index 0238d9b4f266a2f0a5e8892a54fbcb489a1125f3..8943192176ab874ffda17224309096f1e2152655 100644
--- a/doc/src/fix_ave_chunk.txt
+++ b/doc/src/fix_ave_chunk.txt
@@ -67,7 +67,7 @@ fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre
[NOTE:]
-If you are trying to replace a deprectated fix ave/spatial command
+If you are trying to replace a deprecated fix ave/spatial command
with the newer, more flexible fix ave/chunk and "compute
chunk/atom"_compute_chunk_atom.html commands, you simply need to split
the fix ave/spatial arguments across the two new commands. For
@@ -189,7 +189,7 @@ chunk/atom"_compute_chunk_atom.html command must remain constant. If
the {ave} keyword is set to {running} or {window} then {Nchunk} must
remain constant for the duration of the simulation. This fix forces
the chunk/atom compute specified by chunkID to hold {Nchunk} constant
-for the appropriate time windows, by not allowing it to re-calcualte
+for the appropriate time windows, by not allowing it to re-calculate
{Nchunk}, which can also affect how it assigns chunk IDs to atoms.
More details are given on the "compute
chunk/atom"_compute_chunk_atom.html doc page.
@@ -301,7 +301,7 @@ sample values" divided by {Nrepeat}. In other words it is an average
of an average.
If the {norm} setting is {none}, a similar computation as for the
-{sample} seting is done, except the individual "average sample values"
+{sample} setting is done, except the individual "average sample values"
are "summed sample values". A summed sample value is simply the chunk
value summed over atoms in the sample, without dividing by the number
of atoms in the sample. The output value for the chunk on the
@@ -410,7 +410,7 @@ chunk/atom"_compute_chunk_atom.html command supports them. The OrigID
column is only used if the {compress} keyword was set to {yes} for the
"compute chunk/atom"_compute_chunk_atom.html command. This means that
the original chunk IDs (e.g. molecule IDs) will have been compressed
-to remove chunk IDs with no atoms assigned to them. Thus a compresed
+to remove chunk IDs with no atoms assigned to them. Thus a compressed
chunk ID of 3 may correspond to an original chunk ID or molecule ID of
415. The OrigID column will list 415 for the 3rd chunk.
diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt
index bd097f291acab389c4d5c44fd9e7a3c1815b3663..371f2f66a88f5394bac76c74e18a811939eb6961 100644
--- a/doc/src/fix_ave_correlate.txt
+++ b/doc/src/fix_ave_correlate.txt
@@ -64,7 +64,7 @@ fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\]
[Description:]
Use one or more global scalar values as inputs every few timesteps,
-calculate time correlations bewteen them at varying time intervals,
+calculate time correlations between them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
"variables"_variable.html or used by other "output
@@ -219,7 +219,7 @@ to {upper} then each input value is correlated with every succeeding
value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l
If {type} is set
-to {lower} then each input value is correlated with every preceeding
+to {lower} then each input value is correlated with every preceding
value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l
If {type} is set to {auto/upper} then each input value is correlated
diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt
index 569cdc96cf6c3d53a090f94ce3b036c46d515316..266e3f0e38488694dfce0b442a607a6851483377 100644
--- a/doc/src/fix_ave_time.txt
+++ b/doc/src/fix_ave_time.txt
@@ -33,7 +33,7 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title
vector = all input values are global vectors or global arrays
{ave} args = {one} or {running} or {window M}
one = output a new average value every Nfreq steps
- running = output cummulative average of all previous Nfreq steps
+ running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
{start} args = Nstart
Nstart = start averaging on this timestep
@@ -223,7 +223,7 @@ output as-is without further averaging.
If the {ave} setting is {running}, then the values produced on
timesteps that are multiples of {Nfreq} are summed and averaged in a
-cummulative sense before being output. Each output value is thus the
+cumulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceding
values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the "unfix"_unfix.html
@@ -320,7 +320,7 @@ input values are averaged and {mode} = vector. The global array has #
of rows = length of the input vectors and # of columns = number of
inputs.
-If the fix prouduces a scalar or vector, then the scalar and each
+If the fix produces a scalar or vector, then the scalar and each
element of the vector can be either "intensive" or "extensive",
depending on whether the values contributing to the scalar or vector
element are "intensive" or "extensive". If the fix produces an array,
diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt
index 8473fa8152a4f7b386b8c4443d24c18c99665ea9..f148e6f99663fe6028e83a246f334b5160ddb470 100644
--- a/doc/src/fix_balance.txt
+++ b/doc/src/fix_balance.txt
@@ -15,12 +15,12 @@ fix ID group-ID balance Nfreq thresh style args keyword args ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
balance = style name of this fix command :l
Nfreq = perform dynamic load balancing every this many steps :l
-thresh = imbalance threshhold that must be exceeded to perform a re-balance :l
+thresh = imbalance threshold that must be exceeded to perform a re-balance :l
style = {shift} or {rcb} :l
shift args = dimstr Niter stopthresh
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
- stopthresh = stop balancing when this imbalance threshhold is reached
+ stopthresh = stop balancing when this imbalance threshold is reached
{rcb} args = none :pre
zero or more keyword/arg pairs may be appended :l
keyword = {weight} or {out} :l
@@ -63,14 +63,14 @@ perform "static" balancing, before or between runs, see the
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or
-where the computational cost varies signficantly between different
+where the computational cost varies significantly between different
atoms. E.g. a model of a vapor/liquid interface, or a solid with
an irregular-shaped geometry containing void regions, or
"hybrid pair style simulations"_pair_hybrid.html which combine
pair styles with different computational cost. In these cases, the
LAMMPS default of dividing the simulation box volume into a
regular-spaced grid of 3d bricks, with one equal-volume sub-domain
-per procesor, may assign numbers of particles per processor in a
+per processor, may assign numbers of particles per processor in a
way that the computational effort varies significantly. This can
lead to poor performance when the simulation is run in parallel.
@@ -78,7 +78,7 @@ The balancing can be performed with or without per-particle weighting.
With no weighting, the balancing attempts to assign an equal number of
particles to each processor. With weighting, the balancing attempts
to assign an equal aggregate computational weight to each processor,
-which typically inducces a diffrent number of atoms assigned to each
+which typically induces a different number of atoms assigned to each
processor.
NOTE: The weighting options listed above are documented with the
@@ -216,7 +216,7 @@ for a single value, except that the bounds used for each bisectioning
take advantage of information from neighboring cuts if possible, as
well as counts of particles at the bounds on either side of each cuts,
which themselves were cuts in previous iterations. The latter is used
-to infer a density of pariticles near each of the current cuts. At
+to infer a density of particles near each of the current cuts. At
each iteration, the count of particles on either side of each plane is
tallied. If the counts do not match the target value for the plane,
the position of the cut is adjusted based on the local density. The
@@ -239,7 +239,7 @@ assigned, particles migrate to their new owning processor as part of
the normal reneighboring procedure.
NOTE: At each rebalance operation, the bisectioning for each cutting
-plane (line in 2d) typcially starts with low and high bounds separated
+plane (line in 2d) typically starts with low and high bounds separated
by the extent of a processor's sub-domain in one dimension. The size
of this bracketing region shrinks based on the local density, as
described above, which should typically be 1/2 or more every
@@ -249,7 +249,7 @@ typically be positioned to better than 1 part in 1000 accuracy
be accurate to better than 1 part in a million. Thus there is no need
to set {Niter} to a large value. This is especially true if you are
rebalancing often enough that each time you expect only an incremental
-adjustement in the cutting planes is necessary. LAMMPS will check if
+adjustment in the cutting planes is necessary. LAMMPS will check if
the threshold accuracy is reached (in a dimension) is less iterations
than {Niter} and exit early.
@@ -275,7 +275,7 @@ at each iteration.
That is the procedure for the first cut. Subsequent cuts are made
recursively, in exactly the same manner. The subset of processors
assigned to each box make a new cut in the longest dimension of that
-box, splitting the box, the subset of processsors, and the atoms in
+box, splitting the box, the subset of processors, and the atoms in
the box in two. The recursion continues until every processor is
assigned a sub-box of the entire simulation domain, and owns the atoms
in that sub-box.
diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt
index 98ba472327cc254d636a49d2cbd4bc4e48f55ab9..83364b9efbbb0b6b9135707c15cae7353ca5b0da 100644
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
@@ -79,8 +79,8 @@ part of bonds, angles, etc.
NOTE: One data structure that is not updated when a bond breaks are
the molecule IDs stored by each atom. Even though one molecule
-becomes two moleclues due to the broken bond, all atoms in both new
-moleclues retain their original molecule IDs.
+becomes two molecules due to the broken bond, all atoms in both new
+molecules retain their original molecule IDs.
Computationally, each timestep this fix operates, it loops over all
the bonds in the system and computes distances between pairs of bonded
@@ -122,7 +122,7 @@ by this fix are "intensive".
These are the 2 quantities:
(1) # of bonds broken on the most recent breakage timestep
-(2) cummulative # of bonds broken :ul
+(2) cumulative # of bonds broken :ul
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
index 3d00b60844d82471f69ccb19bcfb145e92543521..a44c3103ddd10489fe639b85e42168d5749c57c3 100644
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@@ -118,8 +118,8 @@ of new bonds, angles, etc.
NOTE: One data structure that is not updated when a bond breaks are
the molecule IDs stored by each atom. Even though two molecules
-become one moleclue due to the created bond, all atoms in the new
-moleclue retain their original molecule IDs.
+become one molecule due to the created bond, all atoms in the new
+molecule retain their original molecule IDs.
If the {atype} keyword is used and if an angle potential is defined
via the "angle_style"_angle_style.html command, then any new 3-body
@@ -218,7 +218,7 @@ by this fix are "intensive".
These are the 2 quantities:
(1) # of bonds created on the most recent creation timestep
-(2) cummulative # of bonds created :ul
+(2) cumulative # of bonds created :ul
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt
index 38c5e17c60165c6a4bc1b674031598a4e72d33de..ca7069e2478de279e063b5e43f1a82d29fe1f9b1 100644
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
@@ -81,7 +81,7 @@ by this processor on this timestep.
The criterion for matching molecule IDs is how bond swaps performed by
this fix conserve chain length. To use this features you must setup
the molecule IDs for your polymer chains in a certain way, typically
-in the data file, read by the "read_data"_read_data.html comand.
+in the data file, read by the "read_data"_read_data.html command.
Consider a system of 6-mer chains. You have 2 choices. If the
molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
swaps will conserve chain length. For a particular momoner there will
@@ -124,7 +124,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
-during thermodyanmic output via the "thermo_style
+during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
@@ -151,8 +151,8 @@ the Boltzmann criterion.
This fix computes two statistical quantities as a global 2-vector of
output, which can be accessed by various "output
commands"_Section_howto.html#howto_15. The first component of the
-vector is the cummulative number of swaps performed by all processors.
-The second component of the vector is the cummulative number of swaps
+vector is the cumulative number of swaps performed by all processors.
+The second component of the vector is the cumulative number of swaps
attempted (whether accepted or rejected). Note that a swap "attempt"
only occurs when swap partners meeting the criteria described above
are found on a particular timestep. The vector values calculated by
@@ -168,7 +168,7 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-The setings of the "special_bond" command must be 0,1,1 in order to
+The settings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of bead-spring chains with FENE or
harmonic bonds. This means that pairwise interactions between bonded
atoms are turned off, but are turned on between atoms two or three
diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt
index 96701b170ea47735e692a3ab2232885e07fd852d..83e5a826521767bd487d5f545ba0eac0cc4903c4 100644
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@@ -54,7 +54,7 @@ The external pressure tensor is specified using one or more of the
keywords. These keywords give you the ability to specify all 6
components of an external stress tensor, and to couple various of
these components together so that the dimensions they represent are
-varied together during the mimimization.
+varied together during the minimization.
Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
@@ -103,7 +103,7 @@ far. In all cases, the particle positions at each iteration are
unaffected by the chosen value, except that all particles are
displaced by the same amount, different on each iteration.
-NOTE: Appling an external pressure to tilt dimensions {xy}, {xz}, {yz}
+NOTE: Applying an external pressure to tilt dimensions {xy}, {xz}, {yz}
can sometimes result in arbitrarily large values of the tilt factors,
i.e. a dramatically deformed simulation box. This typically indicates
that there is something badly wrong with how the simulation was
@@ -122,7 +122,7 @@ well-defined minimization problem. This is because the objective
function being minimized changes if the box size/shape changes. In
practice this means the minimizer can get "stuck" before you have
reached the desired tolerance. The solution to this is to restart the
-minmizer from the new adjusted box size/shape, since that creates a
+minimizer from the new adjusted box size/shape, since that creates a
new objective function valid for the new box size/shape. Repeat as
necessary until the box size/shape has reached its new equilibrium.
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
index 9edd660b046860df36fbc82369cfa4ced6eafb1f..c943cde4897d65f9af50f2a765272144843bd0e3 100644
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@@ -44,7 +44,7 @@ lammps/potentials directory: charmm22.cmap and charmm36.cmap.
The data file read by the "read_data" must contain the topology of all
the CMAP interactions, similar to the topology data for bonds, angles,
-dihedrals, etc. Specically it should have a line like this
+dihedrals, etc. Specially it should have a line like this
in its header section:
N crossterms :pre
diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt
index e2be03f46b31fc9aa35459b11575aa41ab4f66c2..e48dedacd9e17c54b7f4a28d588d173a821ad289 100644
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@@ -59,7 +59,7 @@ always apply to the entire system and there can only be one instance
of the colvars fix at a time. The colvars fix will only communicate
the minimum information necessary and the colvars library supports
multiple, completely independent collective variables, so there is
-no restriction to functionaliry by limiting the number of colvars fixes.
+no restriction to functionality by limiting the number of colvars fixes.
The {input} keyword allows to specify a state file that would contain
the restart information required in order to continue a calculation from
@@ -100,7 +100,7 @@ output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative energy change due to this fix. The scalar value
+cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt
index a19f42c77c2a2aa678e71f0de78f732cadd7bb42..cd4d6adfdf03dc2e8332ffb3eec9e338de1b2240 100644
--- a/doc/src/fix_controller.txt
+++ b/doc/src/fix_controller.txt
@@ -107,7 +107,7 @@ When choosing the values of the four constants, it is best to first
pick a value and sign for {alpha} that is consistent with the
magnitudes and signs of {pvar} and {cvar}. The magnitude of {Kp}
should then be tested over a large positive range keeping {Ki}={Kd}=0.
-A good value for {Kp} will produce a fast reponse in {pvar}, without
+A good value for {Kp} will produce a fast response in {pvar}, without
overshooting the {setpoint}. For many applications, proportional
feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where
there is a substantial lag time in the response of {pvar} to a change
@@ -175,7 +175,7 @@ equal-style versus internal-style variable interchangeably.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currenlty, no information about this fix is written to "binary restart
+Currently, no information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index 1478d47df1fcce46676b521707e43466b1aa3436..8c3a9fa49976103e38300676ab35113b944a4fe8 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -580,10 +580,10 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
You cannot apply x, y, or z deformations to a dimension that is
-shrink-wrapped via the "boundary"_boundary.html comamnd.
+shrink-wrapped via the "boundary"_boundary.html command.
You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
-xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd.
+xy) that is shrink-wrapped via the "boundary"_boundary.html command.
[Related commands:]
diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index ea9c5643ddde69a1e23ef55f5e013b0199200463..a1dd5f6434d147ed6d1b2c2d855bd100dfb98534 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -15,7 +15,7 @@ fix ID group-ID deposit N type M seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
deposit = style name of this fix command :l
N = # of atoms or molecules to insert :l
-type = atom type to assign to inserted atoms (offset for moleclue insertion) :l
+type = atom type to assign to inserted atoms (offset for molecule insertion) :l
M = insert a single atom or molecule every M steps :l
seed = random # seed (positive integer) :l
one or more keyword/value pairs may be appended to args :l
@@ -140,7 +140,7 @@ the molecule.
If the molecule template contains more than one molecule, the relative
probability of depositing each molecule can be specified by the
-{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are
+{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are
specified, where N is the number of molecules in the template. Each
time a molecule is deposited, a random number is used to sample from
the list of relative probabilities. The N values must sum to 1.0.
@@ -192,7 +192,7 @@ LAMMPS prints a warning message.
NOTE: If you are inserting finite size particles or a molecule or
rigid body consisting of finite-size particles, then you should
typically set R larger than the distance at which any inserted
-particle may overlap with either a previouly inserted particle or an
+particle may overlap with either a previously inserted particle or an
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.
diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt
index 8fc72bbdadada2bb0faf6b9f4d2d55b3f647ad58..42778d79781c80ced6c90855f7fefe78f62d7207 100644
--- a/doc/src/fix_eos_table.txt
+++ b/doc/src/fix_eos_table.txt
@@ -17,7 +17,7 @@ eos/table = style name of this fix command
style = {linear} = method of interpolation
file = filename containing the tabulated equation of state
N = use N values in {linear} tables
-keyword = name of table keyword correponding to table file :ul
+keyword = name of table keyword corresponding to table file :ul
[Examples:]
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index 749642f57c203c753bc51fc425be0b56fed5b6a7..e8d515e1f32f76f09d966d3d4910997c68108af1 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -17,7 +17,7 @@ eos/table/rx = style name of this fix command
style = {linear} = method of interpolation
file1 = filename containing the tabulated equation of state
N = use N values in {linear} tables
-keyword = name of table keyword correponding to table file
+keyword = name of table keyword corresponding to table file
file2 = filename containing the heats of formation of each species (optional)
deltaHf = heat of formation for a single species in energy units (optional)
energyCorr = energy correction in energy units (optional)
diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt
index 0243cbe977894c580cbd79925d3c7d4a63d4ff05..ed6c6d03775d5fe11195b3c3d6ccfc7eb365c909 100644
--- a/doc/src/fix_evaporate.txt
+++ b/doc/src/fix_evaporate.txt
@@ -31,9 +31,9 @@ fix 1 solvent evaporate 1000 10 surface 38277 molecule yes :pre
[Description:]
Remove M atoms from the simulation every N steps. This can be used,
-for example, to model evaporation of solvent particles or moleclues
+for example, to model evaporation of solvent particles or molecules
(i.e. drying) of a system. Every N steps, the number of atoms in the
-fix group and within the specifed region are counted. M of these are
+fix group and within the specified region are counted. M of these are
chosen at random and deleted. If there are less than M eligible
particles, then all of them are deleted.
@@ -74,7 +74,7 @@ are relevant to this fix.
This fix computes a global scalar, which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative number of deleted atoms. The scalar value calculated by
+cumulative number of deleted atoms. The scalar value calculated by
this fix is "intensive".
No parameter of this fix can be used with the {start/stop} keywords of
diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt
index 79b5abe5b05d9fea86792a6b074b7037a84362d3..ca7625e2d0aa97882d9880d6b2ed1ed82dd238d0 100644
--- a/doc/src/fix_gle.txt
+++ b/doc/src/fix_gle.txt
@@ -62,7 +62,7 @@ as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
optimal for a given application and the system of choice can be
obtained from "(GLE4MD)"_#GLE4MD.
-Equilibrium sampling a temperature T is obtained by specifiying the
+Equilibrium sampling a temperature T is obtained by specifying the
target value as the {Tstart} and {Tstop} arguments, so that the diffusion
matrix that gives canonical sampling for a given A is computed automatically.
However, the GLE framework also allow for non-equilibrium sampling, that
@@ -116,7 +116,7 @@ output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative energy change due to this fix. The scalar value
+cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index 04b0fd091e5bdf8b66e23af01fa2caa0358e8ec8..2cf1665c30ee07f93ca955bfa47176819e8e63a1 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -76,7 +76,7 @@ specified as an equal-style "variable"_variable.html. If the value is
a variable, it should be specified as v_name, where name is the
variable name. In this case, the variable will be evaluated each
timestep, and its value used to determine the quantity. You should
-insure that the variable calculates a result in the approriate units,
+insure that the variable calculates a result in the appropriate units,
e.g. force/mass or degrees.
Equal-style variables can specify formulas with various mathematical
diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt
index c9295eca693887a25669a6c6dad8f650b2cf6ebb..3f7650466f268b6b685e0a69c85c4366b5161244 100644
--- a/doc/src/fix_halt.txt
+++ b/doc/src/fix_halt.txt
@@ -15,15 +15,16 @@ fix ID group-ID halt N attribute operator avalue keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
halt = style name of this fix command :l
N = check halt condition every N steps :l
-attribute = hstyle or v_name :l
- hstyle = {bondmax}
+attribute = {bondmax} or {tlimit} or v_name :l
+ bondmax = length of longest bond in the system
+ tlimit = elapsed CPU time
v_name = name of "equal-style variable"_variable.html :pre
operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
avalue = numeric value to compare attribute to :l
-string = text string to print with optional variable names :l
zero or more keyword/value pairs may be appended :l
-keyword = {error} :l
- {error} value = {hard} or {soft} or {continue} :pre
+keyword = {error} or {message} :l
+ {error} value = {hard} or {soft} or {continue}
+ {message} value = {yes} or {no} :pre
:ule
[Examples:]
@@ -40,14 +41,33 @@ specified by the "run"_run.html or "minimize"_minimize.html command.
The specified group-ID is ignored by this fix.
-The specified {attribute} can be one of the {hstyle} options listed
-above, or an "equal-style variable"_variable.html referenced as
-{v_name}, where "name" is the name of a variable that has been defined
-previously in the input script.
-
-The only {hstyle} option currently implemented is {bondmax}. This
-will loop over all bonds in the system, compute their current
-lengths, and set {attribute} to the longest bond distance.
+The specified {attribute} can be one of the options listed above,
+namely {bondmax} or {tlimit}, or an "equal-style
+variable"_variable.html referenced as {v_name}, where "name" is the
+name of a variable that has been defined previously in the input
+script.
+
+The {bondmax} attribute will loop over all bonds in the system,
+compute their current lengths, and set {attribute} to the longest bond
+distance.
+
+The {tlimit} attribute queries the elapsed CPU time (in seconds) since
+the current run began, and sets {attribute} to that value. This is an
+alternative way to limit the length of a simulation run, similar to
+the "timer"_timer.html timeout command. There are two differences in
+using this method versus the timer command option. The first is that
+the clock starts at the beginning of the current run (not when the
+timer or fix command is specified), so that any setup time for the run
+is not included in the elapsed time. The second is that the timer
+invocation and syncing across all processors (via MPI_Allreduce) is
+not performed once every {N} steps by this command. Instead it is
+performed (typically) only a small number of times and the elapsed
+times are used to predict when the end-of-the-run will be. Both of
+these attributes can be useful when performing benchmark calculations
+for a desired length of time with minmimal overhead. For example, if
+a run is performing 1000s of timesteps/sec, the overhead for syncing
+the timer frequently across a large number of processors may be
+non-negligble.
Equal-style variables evaluate to a numeric value. See the
"variable"_variable.html command for a description. They calculate
@@ -100,6 +120,14 @@ Note that you may wish use the "unfix"_unfix.html command on the fix
halt ID, so that the same condition is not immediately triggered in a
subsequent run.
+The optional {message} keyword determines whether a message is printed
+to the screen and logfile when the half condition is triggered. If
+{message} is set to yes, a one line message with the values that
+triggered the halt is printed. If {message} is set to no, no message
+is printed; the run simply exits. The latter may be desirable for
+post-processing tools that extract thermodyanmic information from log
+files.
+
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
@@ -118,4 +146,4 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Default:]
-The option defaults are error = hard.
+The option defaults are error = hard and message = yes.
diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt
index be13925897934518b488f50386eb1c33b2b146b4..c9a791ae4ece3069805ac86172ffae4805361076 100644
--- a/doc/src/fix_indent.txt
+++ b/doc/src/fix_indent.txt
@@ -107,7 +107,7 @@ fashion. For the latter, see the {start} and {stop} keywords of the
"run"_run.html command and the {elaplong} keyword of "thermo_style
custom"_thermo_style.html for details.
-For example, if a spherical indenter's x-position is specfied as v_x,
+For example, if a spherical indenter's x-position is specified as v_x,
then this variable definition will keep it's center at a relative
position in the simulation box, 1/4 of the way from the left edge to
the right edge, even if the box size changes:
@@ -121,7 +121,7 @@ variable x equal "2.5 + 5*elaplong*dt"
variable x equal vdisplace(2.5,5) :pre
If a spherical indenter's radius is specified as v_r, then these
-variable definitions will grow the size of the indenter at a specfied
+variable definitions will grow the size of the indenter at a specified
rate.
variable r0 equal 0.0
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index b387117d8340958ae80c8d1a762af31b3161cb43..a3d0fb7eaab8b1832ebbb2e0a29e8e55a7a9e09b 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -307,7 +307,7 @@ setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative energy change due to this fix. The scalar value
+cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive". Note that calculation of this
quantity requires setting the {tally} keyword to {yes}.
diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt
index 4b09d695b9d25d45fdb1910723695508cb2b18ca..d3112d529d26d62ec8940340c23738023bf69ae9 100644
--- a/doc/src/fix_langevin_eff.txt
+++ b/doc/src/fix_langevin_eff.txt
@@ -80,7 +80,7 @@ setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative energy change due to this fix. The scalar value
+cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive". Note that calculation of this
quantity requires setting the {tally} keyword to {yes}.
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index 62265a3bc17f0568e8e72cd0ea3e4292fd2ed28d..fc6203b0f2c1967613e81b694977c9dd26accfcf 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -328,7 +328,7 @@ fix must be used in conjunction with the
"lb/viscous"_fix_lb_viscous.html fix if the force coupling constant is
set by default, or either the "lb/viscous"_fix_lb_viscous.html fix or
one of the "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html or
-"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specifiy
+"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specify
their own value for the force coupling constant.
[Related commands:]
diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt
index afdfa9e892cbd280b5d7e3f15834f5b51a08d9f6..9c95cdc452e498ae3a3f2c51ce04ea97375f66b2 100644
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@@ -53,7 +53,7 @@ default method for computing P.
For fixes that calculate a contribution to the potential energy of the
system, the {energy} keyword will include that contribution in
thermodynamic output of potential energy. This is because the {energy
-yes} setting must be specfied to include the fix's global or per-atom
+yes} setting must be specified to include the fix's global or per-atom
energy in the calculation performed by the "compute
pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html
commands. See the "thermo_style"_thermo_style.html command for info
diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt
index 9bbe252c1fc9290994b341880ed20ed1bc80a8b3..7cb40ad1320e365153d3d3165df06a8a1f064750 100644
--- a/doc/src/fix_move.txt
+++ b/doc/src/fix_move.txt
@@ -58,7 +58,7 @@ nve"_fix_nve.html command). It is up to you to decide whether
periodic boundaries are appropriate with the kind of atom motion you
are prescribing with this fix.
-NOTE: As dicsussed below, atoms are moved relative to their initial
+NOTE: As discussed below, atoms are moved relative to their initial
position at the time the fix is specified. These initial coordinates
are stored by the fix in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command
@@ -131,7 +131,7 @@ This style also sets the velocity of each atom to (omega cross Rperp)
where omega is its angular velocity around the rotation axis and Rperp
is a perpendicular vector from the rotation axis to the atom. If the
defined "atom_style"_atom_style.html assigns an angular velocity or
-angular moementum or orientation to each atom ("atom
+angular momentum or orientation to each atom ("atom
styles"_atom_style.html sphere, ellipsoid, line, tri, body), then
those properties are also updated appropriately to correspond to the
atom's motion and rotation over time.
diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt
index c613a598feef2224013fead93b25c46964e2a2a6..0e09f8a9c56f1ef73b34ae6bf6f82bbce6912978 100644
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@@ -83,7 +83,7 @@ produces additional output files. The range finder functionality
(step 4) outputs files defining pair and bonded interaction ranges.
The force matching functionality (step 5) outputs tabulated force
files for every interaction in the system. Other diagnostic files can
-also be output depending on the paramters in the MS-CG library input
+also be output depending on the parameters in the MS-CG library input
script. Again, see the documentation provided with the MS-CG library
for more info.
@@ -108,7 +108,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
The MS-CG library uses C++11, which may not be supported by older
compilers. The MS-CG library also has some additional numeric library
-dependencies, which are describd in its documentation.
+dependencies, which are described in its documentation.
Currently, the MS-CG library is not setup to run in parallel with MPI,
so this fix can only be used in a serial LAMMPS build and run
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index 059498a84349cfa69ff6e6c067947e6157bcfabd..3d151a724b10e915e147d64c02e5bd238853a4ac 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -136,7 +136,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index ad5ffd8026acd987a3aa5f15cb91dd1cbde9fcd6..3a273be595321ebe793f7eb7896cb4aeffe0d2b5 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -135,7 +135,7 @@ This fix is part of the BODY package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
command.
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index 40cc7ed2b2cef84dcb088bb0e7edb44350414e59..8fe98f1818a7c2b513bbca698407c65417f668fc 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -161,7 +161,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index c098ae216b39a4f25db27ad5481f73bde78ab0bc..772920df61cc32cfdc1a0aa9c2f788507881323d 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -160,7 +160,7 @@ This fix is part of the BODY package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
command.
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index 817e6985c5e6c8639ce1d13bf66f07ac99d702db..03846a2558196d1d4cafad7b77d563fc026ff053 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -71,7 +71,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt
index 8cc2ceb396a1ae21d181b18f7f53340745e1a052..5f1b2715464c01468494f8fb0da33bd46c1c5ec4 100644
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
@@ -25,7 +25,7 @@ Perform updates of position and orientation, but not velocity or
angular momentum for atoms in the group each timestep. In other
words, the force and torque on the atoms is ignored and their velocity
and angular momentum are not updated. The atom velocities and
-angularm momenta are used to update their positions and orientation.
+angular momenta are used to update their positions and orientation.
This is useful as an implicit time integrator for Fast Lubrication
Dynamics, since the velocity and angular momentum are updated by the
@@ -49,7 +49,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt
index 7709805abf8d21fbcae0ea97ae7320ba014e6f1d..604b5391cd180e064207ca3cd5a02d2335470ac7 100644
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
@@ -47,7 +47,7 @@ This fix is part of the BODY package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
command.
diff --git a/doc/src/fix_nve_limit.txt b/doc/src/fix_nve_limit.txt
index 6a83d715d24106d137cb2b1105c910cd6ec44b03..2ecec83e9ce8bf5886a1d66dc4c50046a7f74882 100644
--- a/doc/src/fix_nve_limit.txt
+++ b/doc/src/fix_nve_limit.txt
@@ -48,8 +48,8 @@ unaltered, pressures computed by thermodynamic output will still be
very large for overlapped configurations.
NOTE: You should not use "fix shake"_fix_shake.html in conjunction
-with this fix. That is because fix shake applies contraint forces
-based on the predicted postitions of atoms after the next timestep.
+with this fix. That is because fix shake applies constraint forces
+based on the predicted positions of atoms after the next timestep.
It has no way of knowing the timestep may change due to this fix,
which will cause the constraint forces to be invalid. A better
strategy is to turn off fix shake when performing initial dynamics
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 625662772475fb3a2105906e457ae10f190182a6..77de1dea40af798aa0935aa84c7c9670316c848a 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -137,7 +137,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index d12903acfdaf8758271ed00a52cef5e7f555954c..1f04b85c8b749bbc0babd8bbbc0707cb88c3b0a0 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -136,7 +136,7 @@ This fix is part of the BODY package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
command.
diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt
index 2d772ba6be35107b211b58d5fd33e10d5713605d..e92d1640cd6d643d3574680555f1f286518755a8 100644
--- a/doc/src/fix_nvt_sllod_eff.txt
+++ b/doc/src/fix_nvt_sllod_eff.txt
@@ -35,7 +35,7 @@ radial velocity of electrons are also updated and thermostatted.
Likewise the temperature calculated by the fix, using the compute it
creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html doc
page), is performed with a "compute
-temp/deform/eff"_compute_temp_deform_eff.html commmand that includes
+temp/deform/eff"_compute_temp_deform_eff.html command that includes
the eFF contribution to the temperature from the electron radial
velocity.
diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt
index 8573d99508a3d01715ecb91e21001cd92899ac2a..20ff94866ea3ad0c92fde75042cad455494bcc92 100644
--- a/doc/src/fix_orient.txt
+++ b/doc/src/fix_orient.txt
@@ -31,7 +31,7 @@ The fix applies an orientation-dependent force to atoms near a planar
grain boundary which can be used to induce grain boundary migration
(in the direction perpendicular to the grain boundary plane). The
motivation and explanation of this force and its application are
-described in "(Janssens)"_#Janssens. The adaptiation to bcc crystals
+described in "(Janssens)"_#Janssens. The adaptation to bcc crystals
is described in "(Wicaksono1)"_#Wicaksono1. The computed force is only
applied to atoms in the fix group.
diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt
index 10a0c95c80191ed8fd5b75097d68ac68aff20e6a..aad6c2bfaa401bcb0af6e76851f849cb67c1af0c 100644
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@@ -43,7 +43,7 @@ fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 :pre
Calculate the dynamical matrix from molecular dynamics simulations
based on fluctuation-dissipation theory for a group of atoms.
-Consider a crystal with \(N\) unit cells in three dimensions labelled
+Consider a crystal with \(N\) unit cells in three dimensions labeled
\(l = (l_1, l_2, l_3)\) where \(l_i\) are integers. Each unit cell is
defined by three linearly independent vectors \(\mathbf\{a\}_1\),
\(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelipiped,
@@ -183,7 +183,7 @@ This fix requires LAMMPS be built with an FFT library. See the
[Default:]
-The option defaults are sysdim = the same dimemsion as specified by
+The option defaults are sysdim = the same dimension as specified by
the "dimension"_dimension.html command, and nasr = 20.
:line
diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt
index 90ed84a8bfd265761bfb8e5e1faff26305798595..f2c10184ddb4f997a80d765e45d2a6ee1620fde3 100644
--- a/doc/src/fix_pour.txt
+++ b/doc/src/fix_pour.txt
@@ -107,7 +107,7 @@ atoms in the molecule.
If the molecule template contains more than one molecule, the relative
probability of depositing each molecule can be specified by the
-{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are
+{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are
specified, where N is the number of molecules in the template. Each
time a molecule is inserted, a random number is used to sample from
the list of relative probabilities. The N values must sum to 1.0.
@@ -144,7 +144,7 @@ command for the temperature compute you are using.
All other keywords are optional with defaults as shown below.
-The {diam} option is only used when inserting atoms and specifes the
+The {diam} option is only used when inserting atoms and specifies the
diameters of inserted particles. There are 3 styles: {one}, {range},
or {poly}. For {one}, all particles will have diameter {D}. For
{range}, the diameter of each particle will be chosen randomly and
@@ -175,7 +175,7 @@ some other way.
The {vol} option specifies what volume fraction of the insertion
volume will be filled with particles. For particles with a size
specified by the {diam range} keyword, they are assumed to all be of
-maximum diamter {Dhi} for purposes of computing their contribution to
+maximum diameter {Dhi} for purposes of computing their contribution to
the volume fraction.
The higher the volume fraction value, the more particles are inserted
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 8c9164c25d91d533739d412ab4f0dad1bdc5fc72..aef534ad25fcc1ea9e8d3aaddef04c9bd48a35e5 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -121,7 +121,7 @@ as described below.
Per-atom properties that are defined by the "atom
style"_atom_style.html are initialized when atoms are created, e.g. by
the "read_data"_read_data.html or "create_atoms"_create_atoms.html
-commands. The per-atom properaties defined by this fix are not. So
+commands. The per-atom properties defined by this fix are not. So
you need to initialize them explicitly. This can be done by the
"read_data"_read_data.html command, using its {fix} keyword and
passing it the fix-ID of this fix.
diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt
index e9769ed33bec87c0c21f873d10c85b20fb3b0082..b1a1dd5c428488f6162f02f50f87ef038676b4ac 100644
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@@ -71,7 +71,7 @@ or AMBER, can have a strong effect on energies and forces, and
produces a different model than the published versions.
NOTE: The "fix qeq/comb"_fix_qeq_comb.html command must still be used
-to perform charge equliibration with the "COMB
+to perform charge equilibration with the "COMB
potential"_pair_comb.html. The "fix qeq/reax"_fix_qeq_reax.html
command can be used to perform charge equilibration with the "ReaxFF
force field"_pair_reax_c.html, although fix qeq/shielded yields the
@@ -81,7 +81,7 @@ are the same. Eventually the fix qeq/reax command will be deprecated.
The QEq method minimizes the electrostatic energy of the system (or
equalizes the derivative of energy with respect to charge of all the
atoms) by adjusting the partial charge on individual atoms based on
-interactions with their neighbors within {cutoff}. It reqires a few
+interactions with their neighbors within {cutoff}. It requires a few
parameters, in {metal} units, for each atom type which provided in a
file specified by {qfile}. The file has the following format
@@ -91,7 +91,7 @@ file specified by {qfile}. The file has the following format
Ntype chi eta gamma zeta qcore :pre
There is one line per atom type with the following parameters.
-Only a subset of the parameters is used by each QEq style as descibed
+Only a subset of the parameters is used by each QEq style as described
below, thus the others can be set to 0.0 if desired.
{chi} = electronegativity in energy units
@@ -167,7 +167,7 @@ zero net charge.
NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is
non-trivial. Charges on atoms are not guaranteed to equilibrate with
arbitrary choices of these parameters. We do not develop these QEq
-paramters. See the examples/qeq directory for some examples.
+parameters. See the examples/qeq directory for some examples.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 58a541cc9dd6d27a147272bad47c55cf4abb6f22..30c5003e7288d70d38bdb8f34e3a81c6e5083e2e 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -42,12 +42,12 @@ Only charges on the atoms in the specified group are equilibrated.
The fix relies on the pair style (COMB in this case) to calculate the
per-atom electronegativity (effective force on the charges). An
electronegativity equalization calculation (or QEq) is performed in an
-interative fashion, which in parallel requires communication at each
+iterative fashion, which in parallel requires communication at each
iteration for processors to exchange charge information about nearby
atoms with each other. See "Rappe_and_Goddard"_#Rappe_and_Goddard and
"Rick_and_Stuart"_#Rick_and_Stuart for details.
-During a run, charge equilibration is peformed every {Nevery} time
+During a run, charge equilibration is performed every {Nevery} time
steps. Charge equilibration is also always enforced on the first step
of each run. The {precision} argument controls the tolerance for the
difference in electronegativity for all atoms during charge
@@ -55,7 +55,7 @@ equilibration. {Precision} is a trade-off between the cost of
performing charge equilibration (more iterations) and accuracy.
If the {file} keyword is used, then information about each
-equilibration calculation is written to the specifed file.
+equilibration calculation is written to the specified file.
:line
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index d0266480a8fe6ea270d5228df863d477b2de47fc..a26934dfb496f2aac3e088879e5117a822badc99 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -33,14 +33,14 @@ typically used in conjunction with the ReaxFF force field model as
implemented in the "pair_style reax/c"_pair_reax_c.html command, but
it can be used with any potential in LAMMPS, so long as it defines and
uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html
-command should be used to perform charge equliibration with the "COMB
+command should be used to perform charge equilibration with the "COMB
potential"_pair_comb.html. For more technical details about the
charge equilibration performed by fix qeq/reax, see the
"(Aktulga)"_#Aktulga paper.
The QEq method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions
-with their neighbors. It reqires some parameters for each atom type.
+with their neighbors. It requires some parameters for each atom type.
If the {params} setting above is the word "reax/c", then these are
extracted from the "pair_style reax/c"_pair_reax_c.html command and
the ReaxFF force field file it reads in. If a file name is specified
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index a85e140b62c42fa9936c1f4e1882757da02fe7c5..1fd1b3ca5a18f2db3d1f6054f771ba52f8bdaf3a 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -34,7 +34,7 @@ written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0. For time-averaged chemical species analysis,
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
-The format of the output file should be self-explantory.
+The format of the output file should be self-explanatory.
:line
diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt
index 596ca54b6710da6314d6f4c2d59cabee43e9ba30..c8ec20daaa4ae3953b2660a2770607b15610533e 100644
--- a/doc/src/fix_restrain.txt
+++ b/doc/src/fix_restrain.txt
@@ -88,7 +88,7 @@ conformation. You may need to experiment to determine what value of K
works best for a given application.
For the case of finding a minimum energy structure for a single
-molecule with particular restratins (e.g. for fitting forcefield
+molecule with particular restraints (e.g. for fitting forcefield
parameters or constructing a potential energy surface), commands such
as the following may be useful:
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index a38948e560048aca0915b4b0f532f37ba876b63f..e086656f5dba48eeb667204e33bc7d62548a0f94 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -129,7 +129,7 @@ number of small rigid bodies. Each body is assigned to the atom
closest to the geometrical center of the body. The fix operates using
local lists of rigid bodies owned by each processor and information is
exchanged and summed via local communication between neighboring
-processors when ghost atom info is accumlated.
+processors when ghost atom info is accumulated.
NOTE: To use the {rigid/small} styles the ghost atom cutoff must be
large enough to span the distance between the atom that owns the body
@@ -262,7 +262,7 @@ and bond interactions within each rigid body, as they no longer
contribute to the motion. The "neigh_modify
exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
commands are used to do this. If the rigid bodies have strongly
-overalapping atoms, you may need to turn off these interactions to
+overlapping atoms, you may need to turn off these interactions to
avoid numerical problems due to large equal/opposite intra-body forces
swamping the contribution of small inter-body forces.
@@ -325,7 +325,7 @@ simulation. The effects of these keywords are similar to those
defined in "fix npt/nph"_fix_nh.html
NOTE: Currently the {rigid/npt}, {rigid/nph}, {rigid/npt/small}, and
-{rigid/nph/small} styles do not support triclinic (non-orthongonal)
+{rigid/nph/small} styles do not support triclinic (non-orthogonal)
boxes.
The target pressures for each of the 6 components of the stress tensor
@@ -530,7 +530,7 @@ back into the box.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
-simulation box XYZ axes, not with respect to the prinicpal axes of the
+simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
@@ -580,7 +580,7 @@ also accounted for by this fix.
:line
-If your simlulation is a hybrid model with a mixture of rigid bodies
+If your simulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with "fix nve"_fix_nve.html, "fix
nvt"_fix_nh.html, "fix npt"_fix_nh.html, and "fix nph"_fix_nh.html.
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index c0deedfa6305a22449e73efc9c88b0c742ebc09d..6a800f386535294714de33964bac7e2f3ee6e383 100644
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@@ -21,7 +21,7 @@ solver = {lammps_rk4,rkf45} = rk4 is an explicit 4th order Runge-Kutta method; r
minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45)
maxSteps = maximum number of steps for the rkf45 solver (rkf45 only)
relTol = relative tolerance for the rkf45 solver (rkf45 only)
-absTol = absolute tolernace for the rkf45 solver (rkf45 only)
+absTol = absolute tolerance for the rkf45 solver (rkf45 only)
diag = Diagnostics frequency for the rkf45 solver (optional, rkf45 only) :ul
[Examples:]
@@ -63,7 +63,7 @@ control on the error. For error control, use the rkf45 ODE solver.
The rkf45 method adjusts the step-size so that the local truncation error is held
within the specified absolute and relative tolerances. The initial step-size {h0}
-can be specified by the user or estimated internally. It is recommeded that the user
+can be specified by the user or estimated internally. It is recommended that the user
specify {h0} since this will generally reduced the number of ODE integration steps
required. {h0} is defined as {dt / min_steps} if min_steps >= 1. If min_steps == 0,
{h0} is estimated such that an explicit Euler method would likely produce
diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt
index e21736b3656750968a3e2f1849e5743907b1a1ad..3523233cee6172a830708cebca035a34497ff044 100644
--- a/doc/src/fix_saed_vtk.txt
+++ b/doc/src/fix_saed_vtk.txt
@@ -52,7 +52,7 @@ intensities at a single snapshot.
To produce output in the image data vtk format ghost data is added
outside the {Kmax} range assigned in the compute saed. The ghost data is
assigned a value of -1 and can be removed setting a minimum isovolume
-of 0 within the vizualiziton software. SAED images can be created by
+of 0 within the visualization software. SAED images can be created by
visualizing a spherical slice of the data that is centered at
R_Ewald*\[h k l\]/norm(\[h k l\]), where R_Ewald=1/lambda.
@@ -88,7 +88,7 @@ averaging is done; values are simply generated on timesteps
:line
-The output for fix ave/time/saed is a file writen with the 3rd generation
+The output for fix ave/time/saed is a file written with the 3rd generation
vtk image data formatting. The filename assigned by the {file} keyword is
appended with _N.vtk where N is an index (0,1,2...) to account for multiple
diffraction intensity outputs.
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 4f63556c527ca26404212d589da829f1ad8ee481..a860aad1282369d990c2e98b84f2c26f143dada6 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -47,7 +47,7 @@ enables a longer timestep.
[SHAKE vs RATTLE:]
The SHAKE algorithm was invented for schemes such as standard Verlet
-timesteppnig, where only the coordinates are integrated and the
+timestepping, where only the coordinates are integrated and the
velocities are approximated as finite differences to the trajectories
("Ryckaert et al. (1977)"_#Ryckaert). If the velocities are
integrated explicitly, as with velocity Verlet which is what LAMMPS
@@ -119,7 +119,7 @@ contribution to the pressure of the system (virial) is also accounted
for.
NOTE: This command works by using the current forces on atoms to
-caculate an additional constraint force which when added will leave
+calculate an additional constraint force which when added will leave
the atoms in positions that satisfy the SHAKE constraints (e.g. bond
length) after the next time integration step. If you define fixes
(e.g. "fix efield"_fix_efield.html) that add additional force to the
@@ -133,7 +133,7 @@ forces (to atoms that fix shake operates on).
The {mol} keyword should be used when other commands, such as "fix
deposit"_fix_deposit.html or "fix pour"_fix_pour.html, add molecules
-on-the-fly during a simulation, and you wish to contrain the new
+on-the-fly during a simulation, and you wish to constrain the new
molecules via SHAKE. You specify a {template-ID} previously defined
using the "molecule"_molecule.html command, which reads a file that
defines the molecule. You must use the same {template-ID} that the
@@ -210,7 +210,7 @@ which can lead to poor energy conservation. You can test for this in
your system by running a constant NVE simulation with a particular set
of SHAKE parameters and monitoring the energy versus time.
-SHAKE or RATTLE should not be used to contrain an angle at 180 degrees
+SHAKE or RATTLE should not be used to constrain an angle at 180 degrees
(e.g. linear CO2 molecule). This causes numeric difficulties.
[Related commands:] none
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index 4ea592be1b835271efe72a30d30fb88f8454e387..feb65b2312823ece1b261e5349750500018b6ed7 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -27,7 +27,7 @@ fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre
[Description:]
-This fix creates reads a traingulated surface from a file in .STL format.
+This fix creates reads a triangulated surface from a file in .STL format.
For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions.
The radius of the new particle is that of the minimum circle which encompasses the triangle vertices.
diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt
index 3f3940cd11e78e79b72dbdfe33e0ce4629e9fb1c..68961a1512d1ba80ddd72da8024333cc51180103 100644
--- a/doc/src/fix_spring_self.txt
+++ b/doc/src/fix_spring_self.txt
@@ -30,7 +30,7 @@ location at the time the fix command was issued. At each timestep,
the magnitude of the force on each atom is -Kr, where r is the
displacement of the atom from its current position to its initial
position. The distance r correctly takes into account any crossings
-of periodic boundary by the atom since it was in its intitial
+of periodic boundary by the atom since it was in its initial
position.
With the (optional) dir flag, one can select in which direction the
diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt
index 13519ecfad94728a00fe5aa3b5b130d3436ab4dc..31660fe77a0edaed0084a5027ce84e0ec8d73cdd 100644
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@@ -54,18 +54,18 @@ fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5 :pre
[Description:]
-Treat a group of partilces as stochastic rotation dynamics (SRD)
+Treat a group of particles as stochastic rotation dynamics (SRD)
particles that serve as a background solvent when interacting with big
(colloidal) particles in groupbig-ID. The SRD formalism is described
in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a
cheap coarse-grained solvent is that SRD particles do not interact
with each other, but only with the solute particles, which in LAMMPS
can be spheroids, ellipsoids, or line segments, or triangles, or rigid
-bodies containing multiple spherioids or ellipsoids or line segments
+bodies containing multiple spheriods or ellipsoids or line segments
or triangles. The collision and rotation properties of the model
imbue the SRD particles with fluid-like properties, including an
effective viscosity. Thus simulations with large solute particles can
-be run more quickly, to measure solute propoerties like diffusivity
+be run more quickly, to measure solute properties like diffusivity
and viscosity in a background fluid. The usual LAMMPS fixes for such
simulations, such as "fix deform"_fix_deform.html, "fix
viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html,
@@ -182,7 +182,7 @@ can be used to scale down their effective collision radius by an
amount {rfactor}, so that SRD particle will only collide with one big
particle at a time. For example, in a Lennard-Jones system at a
temperature of 1.0 (in reduced LJ units), the minimum separation
-bewteen two big particles is as small as about 0.88 sigma. Thus an
+between two big particles is as small as about 0.88 sigma. Thus an
{rfactor} value of 0.85 should prevent dual collisions.
The {bounce} keyword can be used to limit the maximum number of
@@ -230,7 +230,7 @@ error or warning is generated. Similarly, if the ratio of any bin
dimension with {hgrid} exceeds (1 +/- tolerance), then an error or
warning is generated.
-NOTE: The fix srd command can be used with simluations the size and/or
+NOTE: The fix srd command can be used with simulations the size and/or
shape of the simulation box changes. This can be due to non-periodic
boundary conditions or the use of fixes such as the "fix
deform"_fix_deform.html or "fix wall/srd"_fix_wall_srd.html commands
@@ -241,7 +241,7 @@ box shape changes. This re-binning is always done so as to fit an
integer number of bins in the current box dimension, whether it be a
fixed, shrink-wrapped, or periodic boundary, as set by the
"boundary"_boundary.html command. If the box size or shape changes,
-then the size of the search bins must be recalculated avery
+then the size of the search bins must be recalculated every
reneighboring. Note that changing the SRD bin size may alter the
properties of the SRD fluid, such as its viscosity.
@@ -345,15 +345,15 @@ commands"_Section_howto.html#howto_15. The vector values calculated
by this fix are "intensive", meaning they do not scale with the size
of the simulation. Technically, the first 8 do scale with the size of
the simulation, but treating them as intensive means they are not
-scaled when printed as part of thermodyanmic output.
+scaled when printed as part of thermodynamic output.
These are the 12 quantities. All are values for the current timestep,
except for quantity 5 and the last three, each of which are
-cummulative quantities since the beginning of the run.
+cumulative quantities since the beginning of the run.
(1) # of SRD/big collision checks performed
(2) # of SRDs which had a collision
-(3) # of SRD/big colllisions (including multiple bounces)
+(3) # of SRD/big collisions (including multiple bounces)
(4) # of SRD particles inside a big particle
(5) # of SRD particles whose velocity was rescaled to be < Vmax
(6) # of bins for collision searching
diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt
index 177591d8e7478a09d4d60351c34d9144e319eba1..9c1dd538da0f70177cc9bb725702a80b2da018cc 100644
--- a/doc/src/fix_temp_berendsen.txt
+++ b/doc/src/fix_temp_berendsen.txt
@@ -127,7 +127,7 @@ output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative energy change due to this fix. The scalar value
+cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt
index 7e53926516ce1c8dc7db474404a3b8ecb194d824..4129ad73c8fdbe514592b1a33d38e509c74f6f93 100644
--- a/doc/src/fix_temp_csvr.txt
+++ b/doc/src/fix_temp_csvr.txt
@@ -39,7 +39,7 @@ scaling factor from a suitably chosen (gaussian) distribution rather
than having it determined from the time constant directly. In the case
of {temp/csld} the velocities are updated to a linear combination of
the current velocities with a gaussian distribution of velocities at
-the desired temperature. Both termostats are applied every timestep.
+the desired temperature. Both thermostats are applied every timestep.
The thermostat is applied to only the translational degrees of freedom
for the particles, which is an important consideration for finite-size
@@ -136,7 +136,7 @@ These fixes are not invoked during "energy minimization"_minimize.html.
These fixes compute a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative energy change due to the fix. The scalar value
+cumulative energy change due to the fix. The scalar value
calculated by this fix is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt
index f38d20d0d784efda909b41a7954b5b15ffa3ced9..eff25297c1e295f6bcb775d65147dfac932ea956 100644
--- a/doc/src/fix_temp_rescale.txt
+++ b/doc/src/fix_temp_rescale.txt
@@ -44,7 +44,7 @@ ramped value between the {Tstart} and {Tstop} temperatures at the
beginning and end of the run.
NOTE: This thermostat will generate an error if the current
-temperature is zero at the end of a timestep it is inovoked on. It
+temperature is zero at the end of a timestep it is invoked on. It
cannot rescale a zero temperature.
{Tstart} can be specified as an equal-style "variable"_variable.html.
@@ -134,7 +134,7 @@ output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative energy change due to this fix. The scalar value
+cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt
index c39651e05ca0e49d3e5c3dc2f3b464cafba9c9a9..f87c1a219249438c0864dba1f2880b0f1bfae9d8 100644
--- a/doc/src/fix_temp_rescale_eff.txt
+++ b/doc/src/fix_temp_rescale_eff.txt
@@ -52,7 +52,7 @@ output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative energy change due to this fix. The scalar value
+cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt
index beb9f689334bc596954fa52d85a833d23825239b..3c81d62ee0aa7c136765e59267b0a9d85f1a8333 100644
--- a/doc/src/fix_tfmc.txt
+++ b/doc/src/fix_tfmc.txt
@@ -41,7 +41,7 @@ can be used to extend the time scale of atomistic simulations, in
particular when long time scale relaxation effects must be considered;
some interesting examples are given in the review by "(Neyts)"_#Neyts.
An example of a typical use case would be the modelling of chemical
-vapour deposition (CVD) processes on a surface, in which impacts by
+vapor deposition (CVD) processes on a surface, in which impacts by
gas-phase species can be performed using MD, but subsequent relaxation
of the surface is too slow to be done using MD only. Using tfMC can
allow for a much faster relaxation of the surface, so that higher
diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt
index 9038a12709982bf1df7082bd4dee04067fe48f11..a807feaec72a95d11976f4188e8308bd97978e58 100644
--- a/doc/src/fix_thermal_conductivity.txt
+++ b/doc/src/fix_thermal_conductivity.txt
@@ -109,10 +109,10 @@ are relevant to this fix.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative kinetic energy transferred between the bottom and middle
+cumulative kinetic energy transferred between the bottom and middle
of the simulation box (in the {edim} direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
-and accumlates thereafter, once every N steps. The units of the
+and accumulates thereafter, once every N steps. The units of the
quantity are energy; see the "units"_units.html command for details.
The scalar value calculated by this fix is "intensive".
@@ -141,7 +141,7 @@ of this idea.
When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange kinetic energy
-bewteen solvent particles.
+between solvent particles.
[Related commands:]
diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt
index 2e7318da146fcf91f682d3d1410a48f71a1dc41f..48dfd254a00de377ddb027c8d8e1c77d54e209a3 100644
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@@ -106,7 +106,7 @@ electron stopping coupling parameter. C_e, rho_e, and kappa_e are
specified as parameters to the fix. The other quantities are derived.
The form of the heat diffusion equation used here is almost the same
as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the
-electronic density is explicitly reprensented, rather than being part
+electronic density is explicitly represented, rather than being part
of the specific heat parameter.
Currently, fix ttm assumes that none of the user-supplied parameters
@@ -151,7 +151,7 @@ output timestep. The timestep itself is given in the first column.
The next Nx*Ny*Nz columns contain the temperatures for the atomic
subsystem, and the final Nx*Ny*Nz columns contain the temperatures for
the electronic subsystem. The ordering of the Nx*Ny*Nz columns is
-with the z index varing fastest, y the next fastest, and x the
+with the z index varying fastest, y the next fastest, and x the
slowest.
These fixes do not change the coordinates of their atoms; they only
@@ -300,7 +300,7 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more
info.
These fixes can only be used for 3d simulations and orthogonal
-simlulation boxes. You must also use periodic
+simulation boxes. You must also use periodic
"boundary"_boundary.html conditions.
[Related commands:]
diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt
index 5bae961ada085e7d1ff1f6c54de9d287a277c097..47b3cfc67a2dbe667ce2af1799368b50dc741f50 100644
--- a/doc/src/fix_vector.txt
+++ b/doc/src/fix_vector.txt
@@ -136,7 +136,7 @@ An array is produced if multiple input values are specified.
The length of the vector or the number of rows in the array grows
by 1 every {Nevery} timesteps.
-If the fix prouduces a vector, then the entire vector will be either
+If the fix produces a vector, then the entire vector will be either
"intensive" or "extensive", depending on whether the values stored in
the vector are "intensive" or "extensive". If the fix produces an
array, then all elements in the array must be the same, either
diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt
index 8b9c0d3cb68a4326b35b847839f738015f7165af..5fbbc67ca52838ff290fd3d666d0b5f7cb68f17a 100644
--- a/doc/src/fix_viscosity.txt
+++ b/doc/src/fix_viscosity.txt
@@ -102,7 +102,7 @@ parameter.
An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in "Section
6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations
-deform the simmulation box via the "fix deform"_fix_deform.html
+deform the simulation box via the "fix deform"_fix_deform.html
command. Thus they cannot be run on a charged system using a "PPPM
solver"_kspace_style.html since PPPM does not currently support
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
@@ -116,10 +116,10 @@ are relevant to this fix.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
-cummulative momentum transferred between the bottom and middle of the
+cumulative momentum transferred between the bottom and middle of the
simulation box (in the {pdim} direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
-and accumlates thereafter, once every N steps. The units of the
+and accumulates thereafter, once every N steps. The units of the
quantity are momentum = mass*velocity. The scalar value calculated by
this fix is "intensive".
@@ -147,7 +147,7 @@ See the "Maginn paper"_#Maginn for an example of using this algorithm
in a computation of alcohol molecule properties.
When running a simulation with large, massive particles or molecules
-in a background solvent, you may want to only exchange momenta bewteen
+in a background solvent, you may want to only exchange momenta between
solvent particles.
[Related commands:]
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index 024719f057d3fe288d328fa1b6835ce385f81c68..6d76956620c4334314e3b3311972f1fb3196a111 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -136,7 +136,7 @@ of 1/volume.
The {wall/colloid} interaction is derived by integrating over
constituent LJ particles of size {sigma} within the colloid particle
and a 3d half-lattice of Lennard-Jones 12/6 particles of size {sigma}
-in the wall. As mentioned in the preceeding paragraph, the density of
+in the wall. As mentioned in the preceding paragraph, the density of
particles in the wall and colloid can be different, as specified by
the {epsilon} pre-factor.
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 40cd5c8c746bb3dd89f1232f90692e3ec3f32420..5f1679604e365ae0c3c2b59db43331c4b4925b02 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -85,7 +85,7 @@ versions used Kn and Kt from the pairwise interaction and hardwired
dampflag to 1, rather than letting them be specified directly. This
means you can set the values of the wall/particle coefficients
appropriately in the current code to reproduce the results of a
-prevoius Hertzian monodisperse calculation. For example, for the
+previous Hertzian monodisperse calculation. For example, for the
common case of a monodisperse system with particles of diameter 1, Kn,
Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were
previously.
diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt
index cfee0d99775089907c6c5e81c80451f515a7ea87..92fb042194db78bbf7d38794a4c49ee65dcbfa09 100644
--- a/doc/src/fix_wall_gran_region.txt
+++ b/doc/src/fix_wall_gran_region.txt
@@ -153,7 +153,7 @@ material.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Similiar to "fix wall/gran"_fix_wall_gran.html command, this fix
+Similar to "fix wall/gran"_fix_wall_gran.html command, this fix
writes the shear friction state of atoms interacting with the wall to
"binary restart files"_restart.html, so that a simulation can continue
correctly if granular potentials with shear "history" effects are
@@ -169,7 +169,7 @@ So you must re-define your region and if it is a moving region, define
its motion attributes in a way that is consistent with the simulation
that wrote the restart file. In particular, if you want to change the
region motion attributes (e.g. its velocity), then you should ensure
-the postition/orientation of the region at the initial restart
+the position/orientation of the region at the initial restart
timestep is the same as it was on the timestep the restart file was
written. If this is not possible, you may need to ignore info in the
restart file by defining a new fix wall/gran/region command in your
diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt
index 594e3db06d0958f5ad9b41588059aa6118a316d3..4d7756c237d708840fc085a27b0540bdbe35c45d 100644
--- a/doc/src/fix_wall_piston.txt
+++ b/doc/src/fix_wall_piston.txt
@@ -24,7 +24,7 @@ keyword = {pos} or {vel} or {ramp} or {units} :l
{ramp} = use a linear velocity ramp from 0 to vz
{temp} args = target damp seed extent
target = target velocity for region immediately ahead of the piston
- damp = damping paramter (time units)
+ damp = damping parameter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
{units} value = {lattice} or {box}
diff --git a/doc/src/group.txt b/doc/src/group.txt
index ab975af75632a36b39db8a9e62e0d7d672dfc1bc..afa218c5a34880aa0ef71935be0d1f825fd79c08 100644
--- a/doc/src/group.txt
+++ b/doc/src/group.txt
@@ -144,7 +144,7 @@ or exclude from a group.
For example, these lines define a variable "eatom" that calculates the
potential energy of each atom and includes it in the group if its
-potential energy is above the threshhold value -3.0.
+potential energy is above the threshold value -3.0.
compute 1 all pe/atom
compute 2 all reduce sum c_1
@@ -165,7 +165,7 @@ group command invokes it. Because the eatom variable computes the
per-atom energy via the pe/atom compute, it will only be current if a
run has been performed which evaluated pairwise energies, and the
pe/atom compute was actually invoked during the run. Printing the
-thermodyanmic info for compute 2 insures that this is the case, since
+thermodynamic info for compute 2 insures that this is the case, since
it sums the pe/atom compute values (in the reduce compute) to output
them to the screen. See the "Variable Accuracy" section of the
"variable"_variable.html doc page for more details on insuring that
diff --git a/doc/src/if.txt b/doc/src/if.txt
index aa93c73790472a78893c4dab0a9e4c0b6b4e6bc0..52fad5aea756031760c56e6e7ec4183266f9212c 100644
--- a/doc/src/if.txt
+++ b/doc/src/if.txt
@@ -37,7 +37,7 @@ if "$\{eng\} > $\{eng_previous\}" then "jump file1" else "jump file2" :pre
[Description:]
This command provides an if-then-else capability within an input
-script. A Boolean expression is evaluted and the result is TRUE or
+script. A Boolean expression is evaluated and the result is TRUE or
FALSE. Note that as in the examples above, the expression can contain
variables, as defined by the "variable"_variable.html command, which
will be evaluated as part of the expression. Thus a user-defined
@@ -93,7 +93,7 @@ system temperature has reached a certain value, and if so, breaks out
of the loop to finish the run. Note that any variable could be
checked, so long as it is current on the timestep when the run
completes. As explained on the "variable"_variable.html doc page,
-this can be insured by includig the variable in thermodynamic output.
+this can be insured by including the variable in thermodynamic output.
variable myTemp equal temp
label loop
diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt
index a3bd9a973a45291bc6e995acd02aebf9019a5bc7..0c2beaef18c07dc3cfcc8ad136a8940486bdeef8 100644
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other improper styles, the hybrid improper style does not store
improper coefficient info for individual sub-styles in a "binary
-restart files"_restart.html. Thus when retarting a simulation from a
+restart files"_restart.html. Thus when restarting a simulation from a
restart file, you need to re-specify improper_coeff commands.
[Related commands:]
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index d1eca6d5d9e602245fc54ea718d28c0aff13f2ba..705b1cf742a77c749cc97dd8f93c87adc489471f 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -36,7 +36,7 @@ j,k, and l.
The "ring" improper style implements the improper potential introduced
by Destree et al., in Equation (9) of "(Destree)"_#Destree. This
potential does not affect small amplitude vibrations but is used in an
-ad-hoc way to prevent the onset of accidentially large amplitude
+ad-hoc way to prevent the onset of accidentally large amplitude
fluctuations leading to the occurrence of a planar conformation of the
three bonds i-j, j-k and j-l, an intermediate conformation toward the
chiral inversion of a methine carbon. In the "Impropers" section of
diff --git a/doc/src/info.txt b/doc/src/info.txt
index 605dafa851f224598f608827bb8b9c372e963ceb..0b761ccc15fd0b0e8afa48859726c15d1a04bfeb 100644
--- a/doc/src/info.txt
+++ b/doc/src/info.txt
@@ -94,7 +94,7 @@ The {time} category prints the accumulated CPU and wall time for the
process that writes output (usually MPI rank 0).
The {configuration} command prints some information about the LAMMPS
-version and architection and OS it is run on. Where supported, also
+version and architecture and OS it is run on. Where supported, also
information about the memory consumption provided by the OS is
reported.
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index e746ea782a83968c5684a9bf426e843b50cc2a53..1b1a209511309d3538d6125a78f0dcc642434348 100644
--- a/doc/src/jump.txt
+++ b/doc/src/jump.txt
@@ -87,7 +87,7 @@ system temperature has reached a certain value, and if so, breaks out
of the loop to finish the run. Note that any variable could be
checked, so long as it is current on the timestep when the run
completes. As explained on the "variable"_variable.html doc page,
-this can be insured by includig the variable in thermodynamic output.
+this can be insured by including the variable in thermodynamic output.
variable myTemp equal temp
label loop
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 013e61965f4da520f10bba42359096931adb9bd4..cb57863ad0cdcc846cd6761626ec5dfa3d06b31d 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -98,7 +98,7 @@ Coulombics.
The {overlap} keyword can be used in conjunction with the {minorder}
keyword with the PPPM styles to adjust the amount of communication
-that occurs when values on the FFT grid are exchangeed between
+that occurs when values on the FFT grid are exchanged between
processors. This communication is distinct from the communication
inherent in the parallel FFTs themselves, and is required because
processors interpolate charge and field values using grid point values
@@ -122,7 +122,7 @@ neighbor processors. The {minorder} keyword limits how small the
{order} setting can become. The minimum allowed value for PPPM is 2,
which is the default. If {minorder} is set to the same value as
{order} then no reduction is allowed, and LAMMPS will generate an
-error if the grid communcation is non-nearest-neighbor and {overlap}
+error if the grid communication is non-nearest-neighbor and {overlap}
is set to {no}. The {minorder} keyword is not currently supported in
MSM.
@@ -284,7 +284,7 @@ of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder, optimal
performance and accuracy in the results is obtained when these values
are different.
-The {disp/auto} option controlls whether the pppm/disp is allowed to
+The {disp/auto} option controls whether the pppm/disp is allowed to
generate PPPM parameters automatically. If set to {no}, parameters have
to be specified using the {gewald/disp}, {mesh/disp},
{force/disp/real} or {force/disp/kspace} keywords, or
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 492d1d88e7436eb21f6fc0cc5142ca677cd77733..e5c47e82302c39a84928da730d1810942ed3a018 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -131,7 +131,7 @@ reduce force aliasing errors and increase the accuracy of the method
for a given mesh size. Or a coarser mesh can be used for the same
target accuracy, which saves CPU time. However, there is a trade-off
since FFTs on two meshes are now performed which increases the
-compuation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov,
+computation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov,
and "(Hockney)"_#Hockney for details of the method.
For high relative accuracy, using staggered PPPM allows the mesh size
@@ -174,7 +174,7 @@ using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
-can speed-up long-range calulations, particularly in parallel or on
+can speed-up long-range calculations, particularly in parallel or on
GPUs. The use of the -DFFT_SINGLE flag is discussed in "this
section"_Section_start.html#start_2_4 of the manual. MSM does not
currently support the -DFFT_SINGLE compiler switch.
@@ -233,7 +233,7 @@ simulation cell. One way to handle this issue if you have a long
simulation where the box size changes dramatically, is to break it
into shorter simulations (multiple "run"_run.html commands). This
works because the grid size is re-computed at the beginning of each
-run. Another way to ensure the descired accuracy requirement is met
+run. Another way to ensure the described accuracy requirement is met
is to run a short simulation at the maximum expected tilt or length,
note the required grid size, and then use the
"kspace_modify"_kspace_modify.html {mesh} command to manually set the
@@ -255,7 +255,7 @@ are estimated using equations 33 and 46 of "(Wang)"_#Wang.
See the "kspace_modify"_kspace_modify.html command for additional
options of the K-space solvers that can be set, including a {force}
-option for setting an absoulte RMS error in forces, as opposed to a
+option for setting an absolute RMS error in forces, as opposed to a
relative RMS error.
:line
@@ -341,7 +341,7 @@ kspace_style none :pre
Adam Hilger, NY (1989).
:link(Kolafa)
-[(Kolafa)] Kolafa and Perram, Molecular Simualtion, 9, 351 (1992).
+[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
:link(Petersen)
[(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995).
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 0e4f3a8db8e9d19c79006f737da1df0a00607a18..3186865fb6a23e8800cc619c418f1ab626056b77 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -194,6 +194,7 @@ fix_meso.html
fix_meso_stationary.html
fix_momentum.html
fix_move.html
+fix_mscg.html
fix_msst.html
fix_neb.html
fix_nh.html
@@ -218,6 +219,7 @@ fix_nve_manifold_rattle.html
fix_nve_noforce.html
fix_nve_sphere.html
fix_nve_tri.html
+fix_nvk.html
fix_nvt_asphere.html
fix_nvt_body.html
fix_nvt_manifold_rattle.html
@@ -432,6 +434,7 @@ pair_gromacs.html
pair_hbond_dreiding.html
pair_hybrid.html
pair_kim.html
+pair_kolmogorov_crespi_z.html
pair_lcbop.html
pair_line_lj.html
pair_list.html
@@ -458,7 +461,7 @@ pair_multi_lucy_rx.html
pair_nb3b_harmonic.html
pair_nm.html
pair_none.html
-pair_oxdna_excv.html
+pair_oxdna.html
pair_peri.html
pair_polymorphic.html
pair_quip.html
@@ -497,7 +500,7 @@ pair_zero.html
bond_class2.html
bond_fene.html
bond_fene_expand.html
-bond_oxdna_fene.html
+bond_oxdna.html
bond_harmonic.html
bond_harmonic_shift.html
bond_harmonic_shift_cut.html
diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt
index 2de23310b87ce4e321c7e9b55cc46b7dfd8d3858..a3f2c5d0bf5aaa430740076b09ea39fad0b35baa 100644
--- a/doc/src/minimize.txt
+++ b/doc/src/minimize.txt
@@ -48,7 +48,7 @@ soft"_pair_soft.html potential can be used to un-overlap atoms while
running dynamics.
Note that you can minimize some atoms in the system while holding the
-coordiates of other atoms fixed by applying "fix
+coordinates of other atoms fixed by applying "fix
setforce"_fix_setforce.html to the other atoms. See a fuller
discussion of using fixes while minimizing below.
@@ -58,7 +58,7 @@ which atom coordinates are changed. An inner iteration is then
performed using a line search algorithm. The line search typically
evaluates forces and energies several times to set new coordinates.
Currently, a backtracking algorithm is used which may not be optimal
-in terms of the number of force evaulations performed, but appears to
+in terms of the number of force evaluations performed, but appears to
be more robust than previous line searches we've tried. The
backtracking method is described in Nocedal and Wright's Numerical
Optimization (Procedure 3.1 on p 41).
@@ -201,7 +201,7 @@ minimum to the specified energy or force tolerance.
Note that a cutoff Lennard-Jones potential (and others) can be shifted
so that its energy is 0.0 at the cutoff via the
"pair_modify"_pair_modify.html command. See the doc pages for
-inidividual "pair styles"_pair_style.html for details. Note that
+individual "pair styles"_pair_style.html for details. Note that
Coulombic potentials always have a cutoff, unless versions with a
long-range component are used (e.g. "pair_style
lj/cut/coul/long"_pair_lj.html). The CHARMM potentials go to 0.0 at
diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt
index 9e738cee50b8ee53d8d03a900b26c40fda83eb1f..ecec62256a82a3b2e67f9fe64a2af6f796f0c66e 100644
--- a/doc/src/molecule.txt
+++ b/doc/src/molecule.txt
@@ -155,7 +155,7 @@ The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
should be the values consistent with the current orientation of the
rigid body around its center of mass. The values are with respect to
-the simulation box XYZ axes, not with respect to the prinicpal axes of
+the simulation box XYZ axes, not with respect to the principal axes of
the rigid body itself. LAMMPS performs the latter calculation
internally.
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index 649e521eee87d1948b1f5dbef8dd6dd002b5e9d6..a5fa03552cbdd75dcb4ce93f399064c22b7d8daa 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -58,7 +58,7 @@ would see with one or more physical processors per replica. See
discussion.
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
-minimization across all the replicas. The mimimizer uses whatever
+minimization across all the replicas. The minimizer uses whatever
timestep you have defined in your input script, via the
"timestep"_timestep.html command. Often NEB will converge more
quickly if you use a timestep about 10x larger than you would normally
@@ -81,7 +81,7 @@ inter-replica springs and the forces they feel and their motion is
computed in the usual way due only to other atoms within their
replica. Conceptually, the non-NEB atoms provide a background force
field for the NEB atoms. They can be allowed to move during the NEB
-minimiation procedure (which will typically induce different
+minimization procedure (which will typically induce different
coordinates for non-NEB atoms in different replicas), or held fixed
using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
Note that the "partition"_partition.html command can be used to invoke
@@ -97,7 +97,7 @@ Conceptually, the initial configuration for the first replica should
be a state with all the atoms (NEB and non-NEB) having coordinates on
one side of the energy barrier. A perfect energy minimum is not
required, since atoms in the first replica experience no spring forces
-from the 2nd replica. Thus the damped dynamics minimizaiton will
+from the 2nd replica. Thus the damped dynamics minimization will
drive the first replica to an energy minimum if it is not already
there. However, you will typically get better convergence if the
initial state is already at a minimum. For example, for a system with
@@ -366,7 +366,7 @@ parameters.
There are 2 Python scripts provided in the tools/python directory,
neb_combine.py and neb_final.py, which are useful in analyzing output
from a NEB calculation. Assume a NEB simulation with M replicas, and
-the NEB atoms labelled with a specific atom type.
+the NEB atoms labeled with a specific atom type.
The neb_combine.py script extracts atom coords for the NEB atoms from
all M dump files and creates a single dump file where each snapshot
diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt
index c16b667f7d48d9751253aa3d58873045b2db1efc..5c149d892ddbbc2d35be8af744d1beab3f812e27 100644
--- a/doc/src/neigh_modify.txt
+++ b/doc/src/neigh_modify.txt
@@ -34,8 +34,10 @@ keyword = {delay} or {every} or {check} or {once} or {cluster} or {include} or {
M,N = exclude if one atom in pair is type M, other is type N
group group1-ID group2-ID
group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd
- molecule group-ID
- groupname = exclude if both atoms are in the same molecule and in the same group
+ molecule/intra group-ID
+ group-ID = exclude if both atoms are in the same molecule and in group
+ molecule/inter group-ID
+ group-ID = exclude if both atoms are in different molecules and in group
none
delete all exclude settings
{page} value = N
@@ -52,7 +54,7 @@ neigh_modify every 2 delay 10 check yes page 100000
neigh_modify exclude type 2 3
neigh_modify exclude group frozen frozen check no
neigh_modify exclude group residue1 chain3
-neigh_modify exclude molecule rigid :pre
+neigh_modify exclude molecule/intra rigid :pre
[Description:]
@@ -130,9 +132,11 @@ The {exclude type} option turns off the pairwise interaction if one
atom is of type M and the other of type N. M can equal N. The
{exclude group} option turns off the interaction if one atom is in the
first group and the other is the second. Group1-ID can equal
-group2-ID. The {exclude molecule} option turns off the interaction if
-both atoms are in the specified group and in the same molecule, as
-determined by their molecule ID.
+group2-ID. The {exclude molecule/intra} option turns off the
+interaction if both atoms are in the specified group and in the same
+molecule, as determined by their molecule ID. The {exclude
+molecule/inter} turns off the interaction between pairs of atoms that
+have different molecule IDs and are both in the specified group.
Each of the exclude options can be specified multiple times. The
{exclude type} option is the most efficient option to use; it requires
@@ -195,8 +199,8 @@ binsize of 1/2 the cutoff.
If the "delay" setting is non-zero, then it must be a multiple of the
"every" setting.
-The exclude molecule option can only be used with atom styles that
-define molecule IDs.
+The molecule/intra and molecule/inter exclude options can only be used
+with atom styles that define molecule IDs.
The value of the {page} setting must be at least 10x larger than the
{one} setting. This insures neighbor pages are not mostly empty
diff --git a/doc/src/package.txt b/doc/src/package.txt
index de7e0f5c22adf9a3d78e857fd91e47f050d551e4..02afb8d6200ed159de48fb7003c5e25e5291e87e 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -110,7 +110,7 @@ USER-OMP.
If this command is specified in an input script, it must be near the
top of the script, before the simulation box has been defined. This
is because it specifies settings that the accelerator packages use in
-their intialization, before a simultion is defined.
+their initialization, before a simulation is defined.
This command can also be specified from the command-line when
launching LAMMPS, using the "-pk" "command-line
@@ -166,7 +166,7 @@ neighbor list building is performed on the CPU. GPU neighbor list
building currently cannot be used with a triclinic box. GPU neighbor
list calculation currently cannot be used with
"hybrid"_pair_hybrid.html pair styles. GPU neighbor lists are not
-compatible with comannds that are not GPU-enabled. When a non-GPU
+compatible with commands that are not GPU-enabled. When a non-GPU
enabled command requires a neighbor list, it will also be built on the
CPU. In these cases, it will typically be more efficient to only use
CPU neighbor list builds.
@@ -199,7 +199,7 @@ the default.
The {split} keyword can be used for load balancing force calculations
between CPU and GPU cores in GPU-enabled pair styles. If 0 < {split} <
1.0, a fixed fraction of particles is offloaded to the GPU while force
-calculation for the other particles occurs simulataneously on the CPU.
+calculation for the other particles occurs simultaneously on the CPU.
If {split} < 0.0, the optimal fraction (based on CPU and GPU timings)
is calculated every 25 timesteps, i.e. dynamic load-balancing across
the CPU and GPU is performed. If {split} = 1.0, all force
@@ -295,7 +295,7 @@ For more details, including examples of how to set the OMP_NUM_THREADS
environment variable, see the discussion of the {Nthreads} setting on
this doc page for the "package omp" command. Nthreads is a required
argument for the USER-OMP package. Its meaning is exactly the same
-for the USER-INTEL pacakge.
+for the USER-INTEL package.
NOTE: If you build LAMMPS with both the USER-INTEL and USER-OMP
packages, be aware that both packages allow setting of the {Nthreads}
@@ -347,7 +347,7 @@ automatically throughout the run. This typically give performance
within 5 to 10 percent of the optimal fixed fraction.
The {ghost} keyword determines whether or not ghost atoms, i.e. atoms
-at the boundaries of proessor sub-domains, are offloaded for neighbor
+at the boundaries of processor sub-domains, are offloaded for neighbor
and force calculations. When the value = "no", ghost atoms are not
offloaded. This option can reduce the amount of data transfer with
the coprocessor and can also overlap MPI communication of forces with
@@ -516,7 +516,7 @@ for OpenMPI. Check your MPI documentation for additional details.
What combination of threads and MPI tasks gives the best performance
is difficult to predict and can depend on many components of your
input. Not all features of LAMMPS support OpenMP threading via the
-USER-OMP packaage and the parallel efficiency can be very different,
+USER-OMP package and the parallel efficiency can be very different,
too.
Optional keyword/value pairs can also be specified. Each has a
@@ -527,7 +527,7 @@ multi-threaded in addition to force calculations. If {neigh} is set
to {no} then neighbor list calculation is performed only by MPI tasks
with no OpenMP threading. If {mode} is {yes} (the default), a
multi-threaded neighbor list build is used. Using {neigh} = {yes} is
-almost always faster and should produce idential neighbor lists at the
+almost always faster and should produce identical neighbor lists at the
expense of using more memory. Specifically, neighbor list pages are
allocated for all threads at the same time and each thread works
within its own pages.
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index c9dd31d57bede8a0714b2568ad3c01cd8d600a5a..457a797d95d32342519ff9954aef3aff1fa0b3ec 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -68,7 +68,7 @@ See the "pair_coeff"_pair_coeff.html doc page for alternate ways to
specify the path for the potential file.
As an example, the potentials/AlCu.adp file, included in the
-potentials directory of the LAMMPS distrbution, is an extended {setfl}
+potentials directory of the LAMMPS distribution, is an extended {setfl}
file which has tabulated ADP values for w elements and their alloy
interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types
and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 08490c601a4554b05f96267ab18ab66f39d85138..27fb6c10fe09c622b9599146a93aae7ca3c6ade2 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -34,7 +34,7 @@ non-linear regression model.
The method implements the recently proposed machine learning access to
atomic forces as discussed extensively in the following publications -
"(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise
-of the method is to map the atomic enviornment numerically into a
+of the method is to map the atomic environment numerically into a
fingerprint, and use machine learning methods to create a mapping to the
vectorial atomic forces.
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index 6d0b1b00884cc72825bbb54ba8f9ad8460e04465..2e3083c34b6bdbcde60963903624b1bde15e4efb 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -53,7 +53,7 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO)
Potential of "(Brenner)"_#Brenner. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
-intial AIREBO; it is just a subset of the potential energy terms.
+initial AIREBO; it is just a subset of the potential energy terms.
The AIREBO potential consists of three terms:
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index 49c6c8db622ffd9e7759cc11c44a4083f0c05ff2..4e792754b832d408c16042193060a319a91431da 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -73,7 +73,7 @@ more instructions on how to use the accelerated styles effectively.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-For atom type pairs I,J and I != J, coeffiecients must be specified.
+For atom type pairs I,J and I != J, coefficients must be specified.
No default mixing rules are used.
This pair style does not support the "pair_modify"_pair_modify.html shift
diff --git a/doc/src/pair_body.txt b/doc/src/pair_body.txt
index 622cc88f882449e42d1c1a7d0f5013e2f76639a1..7899da832bdbf722bb1c5403dd547890bae5cdb1 100644
--- a/doc/src/pair_body.txt
+++ b/doc/src/pair_body.txt
@@ -59,7 +59,7 @@ computed and summed. If the distance is not within the cutoff, no
interactions between the body and point particle are computed.
The interaction between two sub-particles, or a sub-particle and point
-particle, or betwee two point particles is computed as a Lennard-Jones
+particle, or between two point particles is computed as a Lennard-Jones
interaction, using the standard formula
:c,image(Eqs/pair_lj.jpg)
diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt
index 0dbd1fc5dd9a4ecf3d8a7f38092237919fab1f97..9251fc4e703c683673b671e4498246bde252402e 100644
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@@ -36,11 +36,11 @@ developed by Pettifor ("Pettifor_1"_#Pettifor_1,
"Pettifor_2"_#Pettifor_2, "Pettifor_3"_#Pettifor_3) and later updated
by Murdick, Zhou, and Ward ("Murdick"_#Murdick, "Ward"_#Ward).
Currently, BOP potential files for these systems are provided with
-LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with
+LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A system with
only a subset of these elements, including a single element (e.g. C or
Cu or Al or Ga or Zn or CdZn), can also be modeled by using the
appropriate alloy file and assigning all atom types to the
-singleelement or subset of elements via the pair_coeff command, as
+single element or subset of elements via the pair_coeff command, as
discussed below.
The BOP potential consists of three terms:
@@ -49,7 +49,7 @@ The BOP potential consists of three terms:
where phi_ij(r_ij) is a short-range two-body function representing the
repulsion between a pair of ion cores, beta_(sigma,ij)(r_ij) and
-beta_(sigma,ij)(r_ij) are respectively sigma and pi bond ingtegrals,
+beta_(sigma,ij)(r_ij) are respectively sigma and pi bond integrals,
THETA_(sigma,ij) and THETA_(pi,ij) are sigma and pi bond-orders, and
U_prom is the promotion energy for sp-valent systems.
@@ -78,8 +78,8 @@ levels of the recursive representations for both the sigma and the pi
bond-orders. Bond-order terms can be understood in terms of molecular
orbital hopping paths based upon the Cyrot-Lackmann theorem
("Pettifor_1"_#Pettifor_1). The sigma bond-order with a half-full
-valence shell is used to interpolate the bond-order expressiont that
-incorporated explicite valance band filling. This pi bond-order
+valence shell is used to interpolate the bond-order expression that
+incorporated explicit valance band filling. This pi bond-order
expression also contains also contains a three-member ring term that
allows implementation of an asymmetric density of states, which helps
to either stabilize or destabilize close-packed structures. The pi
@@ -299,7 +299,7 @@ of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The
function can contain up to 10 term thus 10 constants. The first line
can contain up to five constants. If the spline has more than five
terms the second line will contain the remaining constants The
-following lines will then contain the constants for the remainaing g0,
+following lines will then contain the constants for the remaining g0,
g1, g2... (for e_1-e_1-e_2) and the other three body
interactions :l
:ule
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index c060856d60c22d6db732747bf92acea5c6441938..92e74bbba310768cd9bcfabd16870ce8a63834ca 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -86,7 +86,7 @@ For style {comb}, the provided potential file {ffield.comb} contains
all currently-available 2nd generation COMB parameterizations: for Si,
Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
{comb3}, the potential file {ffield.comb3} contains all
-currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
+currently-available 3rd generation COMB parameterizations: O, Cu, N, C,
H, Ti, Zn and Zr. The status of the optimization of the compounds, for
example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
following table:
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index b3d5fdef27c66de8b8d32a03980d628708c28775..43bd13127aa207fa7e55a08474ebe215ff3063ff 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -127,15 +127,15 @@ summation method, described in "Wolf"_#Wolf, given by:
:c,image(Eqs/pair_coul_wolf.jpg)
where {alpha} is the damping parameter, and erc() and erfc() are
-error-fuction and complementary error-function terms. This potential
+error-function and complementary error-function terms. This potential
is essentially a short-range, spherically-truncated,
charge-neutralized, shifted, pairwise {1/r} summation. With a
-manipulation of adding and substracting a self term (for i = j) to the
+manipulation of adding and subtracting a self term (for i = j) to the
first and second term on the right-hand-side, respectively, and a
small enough {alpha} damping parameter, the second term shrinks and
the potential becomes a rapidly-converging real-space summation. With
a long enough cutoff and small enough alpha parameter, the energy and
-forces calcluated by the Wolf summation method approach those of the
+forces calculated by the Wolf summation method approach those of the
Ewald sum. So it is a means of getting effective long-range
interactions with a short-range potential.
@@ -188,7 +188,7 @@ but there is no conceptual problem with extending it to nitrides and
carbides (such as SiC, TiN). Pair coul/strietz used by itself or with
any other pair style such as EAM, MEAM, Tersoff, or LJ in
hybrid/overlay mode. To do this, you would need to provide a
-Streitz-Mintmire parameterizaion for the material being modeled.
+Streitz-Mintmire parameterization for the material being modeled.
:line
@@ -222,7 +222,7 @@ molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the "howto section"_Section_howto.html#howto_8 for more
information on how to use the TIP4P pair styles and lists of
-parameters to set. Note that the neighobr list cutoff for Coulomb
+parameters to set. Note that the neighbor list cutoff for Coulomb
interactions is effectively extended by a distance 2*qdist when using
the TIP4P pair style, to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt
index 498e1873df0d57d7c6c87c6cf8880cf4f3596b9e..fc2042a90178dbb64f6d58823828df78b6902bc3 100644
--- a/doc/src/pair_coul_diel.txt
+++ b/doc/src/pair_coul_diel.txt
@@ -23,11 +23,11 @@ pair_coeff 1 4 78. 1.375 0.112 :pre
[Description:]
-Style {coul/diel} computes a Coulomb correction for implict solvent
-ion interactions in which the dielectric perimittivity is distance dependent.
+Style {coul/diel} computes a Coulomb correction for implicit solvent
+ion interactions in which the dielectric permittivity is distance dependent.
The dielectric permittivity epsilon_D(r) connects to limiting regimes:
One limit is defined by a small dielectric permittivity (close to vacuum)
-at or close to contact seperation between the ions. At larger separations
+at or close to contact separation between the ions. At larger separations
the dielectric permittivity reaches a bulk value used in the regular Coulomb
interaction coul/long or coul/cut.
The transition is modeled by a hyperbolic function which is incorporated
@@ -48,7 +48,7 @@ Examples of the use of this type of Coulomb interaction include implicit
solvent simulations of salt ions
"(Lenart)"_#Lenart and of ionic surfactants "(Jusufi)"_#Jusufi.
Note that this potential is only reasonable for implicit solvent simulations
-and in combiantion with coul/cut or coul/long. It is also usually combined
+and in combination with coul/cut or coul/long. It is also usually combined
with gauss/cut, see "(Lenart)"_#Lenart or "(Jusufi)"_#Jusufi.
The following coefficients must be defined for each pair of atom
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index 7072b1702dd9bff1d3661a10eeee7f6bdf123b2d..62a5faffedd9d7096d82e7a1e8618df313d5d147 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -88,7 +88,7 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
where T is the temperature set by the "pair_style"_pair_style.html
command so it does not need to be specified.
-For style {dpd/tstat}, the coefficiencts defined for each pair of
+For style {dpd/tstat}, the coefficients defined for each pair of
atoms types via the "pair_coeff"_pair_coeff.html command is the same,
except that A is not included.
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index ed09ce4d991cb8200dcc7d1a94672019c83883f4..4d3c2b2deae20ae1b31141d3fe9a44cfbca3a7b0 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -273,7 +273,7 @@ style. However the DYNAMO {setfl} file must has two
lines added to it, at the end of the file:
line 1: Comment line (ignored)
-line 2: N Coefficient0 Coefficient1 ... CoeffincientN :ul
+line 2: N Coefficient0 Coefficient1 ... CoefficientN :ul
The last line begins with the degree {N} of the polynomial function
{h(x)} that modifies the cross interaction between A and B elements.
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index 6881b53434ade79ae66be068398a823d349f02cf..cdfc2657524ae590ed97b6f8d299418ec7e55bb5 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -95,7 +95,7 @@ entries would be required, etc.
At the moment, only a single element parametrization is
implemented. However, the author is not aware of other
-multi-element EDIP parametrizations. If you know any and
+multi-element EDIP parameterization. If you know any and
you are interest in that, please contact the author of
the EDIP package.
diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt
index 6be8cdc785d6801702ff1392b4604321e28ef92e..ee7dc9993296b92e353961284670052624ce11b6 100644
--- a/doc/src/pair_eff.txt
+++ b/doc/src/pair_eff.txt
@@ -149,7 +149,7 @@ command.
:line
-The {limit/eradius} and {pressure/evirials} keywrods are optional.
+The {limit/eradius} and {pressure/evirials} keywords are optional.
Neither or both must be specified. If not specified they are unset.
The {limit/eradius} keyword is used to restrain electron size from
@@ -197,7 +197,7 @@ partitioning changes, the total energy remains similar).
:line
-NOTE: This implemention of eFF gives a reasonably accurate description
+NOTE: This implementation of eFF gives a reasonably accurate description
for systems containing nuclei from Z = 1-6 in "all electron"
representations. For systems with increasingly non-spherical
electrons, Users should use the ECP representations. ECPs are now
@@ -284,7 +284,7 @@ that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
These pair styles require that particles store electron attributes
-such as radius, radial velocity, and radital force, as defined by the
+such as radius, radial velocity, and radial force, as defined by the
"atom_style"_atom_style.html. The {electron} atom style does all of
this.
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 47078f9a8fe924103e31e8d5372f8da1098f7514..e74bb364d47822fcacf9bb9f55a7e56e476352ee 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -97,7 +97,7 @@ pair_coeff * * Na Cl ffield.eim Na Na Na Cl :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The filename is the EIM potential file. The Na and Cl arguments
(before the file name) are the two elements for which info will be
-extracted from the potentail file. The first three trailing Na
+extracted from the potential file. The first three trailing Na
arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The
final Cl argument maps LAMMPS atom type 4 to the EIM Cl element.
@@ -107,7 +107,7 @@ This can be used when an {eim} potential is used as part of the
that will be used with other potentials.
The ffield.eim file in the {potentials} directory of the LAMMPS
-distribution is formated as follows:
+distribution is formatted as follows:
Lines starting with # are comments and are ignored by LAMMPS. Lines
starting with "global:" include three global values. The first value
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index dafba2c44c09f34e92b66f0edcba6db7889a8f21..47045a5933cef253d1d5c47b1af097d5c0b92139 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -63,7 +63,7 @@ reaction kinetics solver is applied, where the difference is defined
to be the internal chemical energy (uChem).
The fourth argument specifies the type of scaling that will be used
-to scale the EXP-6 paramters as reactions occur. Currently, there
+to scale the EXP-6 parameters as reactions occur. Currently, there
are three scaling options: {exponent}, {polynomial} and {none}.
Exponent scaling requires two additional arguments for scaling
@@ -72,7 +72,7 @@ is computed by phi^exponent, where phi is the number of molecules
represented by the coarse-grain particle and exponent is specified
as a pair coefficient argument for {Rm} and {epsilon}, respectively.
The {Rm} and {epsilon} parameters are multiplied by the scaling
-factor to give the scaled interaction paramters for the CG particle.
+factor to give the scaled interaction parameters for the CG particle.
Polynomial scaling requires a filename to be specified as a pair
coeff argument. The file contains the coefficients to a fifth order
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index d4530d37dd1ae4e904867780095c21085cf5cabc..373a82fa809d762c336f0b23539a9310dd5dfc7a 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -224,7 +224,7 @@ normal direction (along the line joining the 2 sphere centers). The
last 3 (8-10) the components of the relative velocity in the
tangential direction.
-These extra quantites can be accessed by the "compute
+These extra quantities can be accessed by the "compute
pair/local"_compute_pair_local.html command, as {p1}, {p2}, ...,
{p10}.
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index b3c9b5b5d50d6fc4cbdb01e45b6a9c332b4e9289..9641e294fad4781f4a73719cf06a12adfcb36db5 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -101,13 +101,13 @@ pair_coeff settings for all possible I,J type pairs. Only I,J type
pairs for atoms which act as joint donors/acceptors need to be
specified; all other type pairs are assumed to be inactive.
-NOTE: A "pair_coeff"_pair_coeff.html command can be speficied multiple
+NOTE: A "pair_coeff"_pair_coeff.html command can be specified multiple
times for the same donor/acceptor type pair. This enables multiple
hydrogen types to be assigned to the same donor/acceptor type pair.
For other pair_styles, if the pair_coeff command is re-used for the
same I.J type pair, the settings for that type pair are overwritten.
For the hydrogen bond potentials this is not the case; the settings
-are cummulative. This means the only way to turn off a previous
+are cumulative. This means the only way to turn off a previous
setting, is to re-use the pair_style command and start over.
For the {hbond/dreiding/lj} style the list of coefficients is as
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 47451cf14a8a5a5709ce73a8461a5e0d20e7dbe7..7ef54e7f07fbb40222b450a1275884fffb1bbdd3 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -63,7 +63,7 @@ Note that an individual pair style can be used multiple times as a
sub-style. For efficiency this should only be done if your model
requires it. E.g. if you have different regions of Si and C atoms and
wish to use a Tersoff potential for pure Si for one set of atoms, and
-a Tersoff potetnial for pure C for the other set (presumably with some
+a Tersoff potential for pure C for the other set (presumably with some
3rd potential for Si-C interactions), then the sub-style {tersoff}
could be listed twice. But if you just want to use a Lennard-Jones or
other pairwise potential for several different atom type pairs in your
@@ -189,7 +189,7 @@ potentials.
Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying weightings that change the strength of pairwise
-interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
+interactions between pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the
"special_bonds"_special_bonds.html command. Different weights can be
assigned to different pair hybrid sub-styles via the "pair_modify
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index 04d8d23dba431b1e3fbb19389772710ed10bb091..5a623e5ece39d4b482b9fa11a40921639df4b938 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -46,7 +46,7 @@ model. You should get an error or warning message from either LAMMPS
or KIM if there is an incompatibility.
The argument {printflag} is optional. If it is set to a non-zero
-value then a KIM dsecriptor file is printed when KIM is invoked. This
+value then a KIM descriptor file is printed when KIM is invoked. This
can be useful for debugging. The default is to not print this file.
Only a single pair_coeff command is used with the {kim} style which
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7bd917caaa5935bb602cbebaf7115d5f03d9137
--- /dev/null
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -0,0 +1,72 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style kolmogorov/crespi/z command :h3
+
+[Syntax:]
+
+pair_style hybrid/overlay kolmogorov/crespi/z cutoff :pre
+
+[Examples:]
+
+pair_style hybrid/overlay kolmogorov/crespi/z 20.0
+pair_coeff * * none
+pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
+
+pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
+pair_coeff * * rebo CH.airebo C C
+pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
+
+[Description:]
+
+The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
+potential as described in "(KC05)"_#KC05. An important simplification is made,
+which is to take all normals along the z-axis.
+
+:c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
+
+It is important to have a suffiently large cutoff to ensure smooth forces.
+Energies are shifted so that they go continously to zero at the cutoff assuming
+that the exponential part of {Vij} (first term) decays sufficiently fast.
+This shift is achieved by the last term in the equation for {Vij} above.
+
+This potential is intended for interactions between two layers of graphene.
+Therefore, to avoid interaction between layers in multi-layered materials,
+each layer should have a separate atom type and interactions should only
+be computed between atom types of neighbouring layers.
+
+The parameter file (e.g. CC.KC), is intended for use with metal
+"units"_units.html, with energies in meV. An additional parameter, {S},
+is available to facilitate scaling of energies in accordance with
+"(vanWijk)"_#vanWijk.
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair_style {none}.
+
+[Restrictions:]
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+"pair_none"_pair_none.html
+"pair_style hybrid/overlay"_pair_hybrid.html
+
+[Default:] none
+
+:line
+
+:link(KC05)
+[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+
+:link(vanWijk)
+[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino,
+Physical Review Letters, 113, 135504 (2014)
diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt
index bb1146b64e16c5cf220481a032265b6ac2a6895f..44cfeb48e96ca4043c8e811d2950ae1243dc126a 100644
--- a/doc/src/pair_line_lj.txt
+++ b/doc/src/pair_line_lj.txt
@@ -39,7 +39,7 @@ function of the line segment length and the specified sub-particle
size for that particle type. If a line segment has a length L and is
of type I, then the number of spheres N that represent the segment is
calculated as N = L/sizeI, rounded up to an integer value. Thus if L
-is not evenly divisibly by sizeI, N is incremented to include one
+is not evenly divisible by sizeI, N is incremented to include one
extra sphere. The centers of the spheres are spaced equally along the
line segment. Imagine N+1 equally-space points, which include the 2
end points of the segment. The sphere centers are halfway between
@@ -48,7 +48,7 @@ each pair of points.
The LJ interaction between 2 spheres on different line segments (or a
sphere on a line segment and a point particles) is computed with
sub-particle epsilon, sigma, and cutoff values that are set by the
-pair_coeff command, as described below. If the distance bewteen the 2
+pair_coeff command, as described below. If the distance between the 2
spheres is greater than the sub-particle cutoff, there is no
interaction. This means that some pairs of sub-particles on 2 line
segments may interact, but others may not.
@@ -90,7 +90,7 @@ The {sizeI} and {sizeJ} coefficients are the sub-particle sizes for
line particles of type I and type J. They are used to define the N
sub-particles per segment as described above. These coefficients are
actually stored on a per-type basis. Thus if there are multiple
-pair_coeff commmands that involve type I, as either the first or
+pair_coeff commands that involve type I, as either the first or
second atom type, you should use consistent values for sizeI or sizeJ
in all of them. If you do not do this, the last value specified for
sizeI will apply to all segments of type I. If typeI or typeJ refers
@@ -112,7 +112,7 @@ cutoff is used.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-For atom type pairs I,J and I != J, coeffiecients must be specified.
+For atom type pairs I,J and I != J, coefficients must be specified.
No default mixing rules are used.
This pair style does not support the "pair_modify"_pair_modify.html
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index e2af7eaeeb8c3838645729f62bc8a4aa486cade4..fdc0b133dd15a3fc4e45beda408479c77c44cdf9 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -197,7 +197,7 @@ molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the "howto section"_Section_howto.html#howto_8 for more
information on how to use the TIP4P pair styles and lists of
-parameters to set. Note that the neighobr list cutoff for Coulomb
+parameters to set. Note that the neighbor list cutoff for Coulomb
interactions is effectively extended by a distance 2*qdist when using
the TIP4P pair style, to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index a4fb3f0274aed9658859df4faf6c02f00982dbda..517bb3d20b0095d33a0506e86c3d876f7d7af83b 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -91,7 +91,7 @@ molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the "howto section"_Section_howto.html#howto_8 for more
information on how to use the TIP4P pair style. Note that the
-neighobr list cutoff for Coulomb interactions is effectively extended
+neighbor list cutoff for Coulomb interactions is effectively extended
by a distance 2*qdist when using the TIP4P pair style, to account for
the offset distance of the fictitious charges on O atoms in water
molecules. Thus it is typically best in an efficiency sense to use a
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index 0cb0a998fe69edf0b6e6408933b0574d1e7579f2..133773abd086c0db43f4f49ef942fca4af1a7449 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -51,7 +51,7 @@ commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
-innner (distance units)
+inner (distance units)
outer (distance units) :ul
The last 2 coefficients are optional inner and outer cutoffs. If not
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index 784f1f7f520d4e54e1c22338613152537d8a55a5..e372092cf0630944ff6397b3e16a0214ce368a62 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -106,7 +106,7 @@ pair_coeff 1 1 1.0 9.5 :pre
The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones
and Coulomb potential modified by a soft core, in order to avoid
singularities during free energy calculations when sites are created
-or anihilated "(Beutler)"_#Beutler,
+or annihilated "(Beutler)"_#Beutler,
:c,image(Eqs/pair_lj_soft.jpg)
@@ -120,14 +120,14 @@ are the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the "dielectric"_dielectric.html command.
The coefficient lambda is an activation parameter. When lambda = 1 the
-pair potentiel is identical to a Lennard-Jones term or a Coulomb term
+pair potential is identical to a Lennard-Jones term or a Coulomb term
or a combination of both. When lambda = 0 the interactions are
deactivated. The transition between these two extrema is smoothed by a
soft repulsive core in order to avoid singularities in potential
-energy and forces when sites are created or anihilated and can overlap
+energy and forces when sites are created or annihilated and can overlap
"(Beutler)"_#Beutler.
-The paratemers n, alpha_LJ and alpha_C are set in the
+The parameters n, alpha_LJ and alpha_C are set in the
"pair_style"_pair_style.html command, before the cutoffs. Usual
choices for the exponent are n = 2 or n = 1. For the remaining
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
@@ -164,7 +164,7 @@ Style {lj/cut/tip4p/long/soft} implements a soft-core version of the
TIP4P water model. The usage of this pair style is documented in the
"pair_lj"_pair_lj.html styles. The soft-core version introduces the
lambda parameter to the list of arguments, after epsilon and sigma in
-the "pair_coeff"_pair_coeff.html command. The paratemers n, alpha_LJ
+the "pair_coeff"_pair_coeff.html command. The parameters n, alpha_LJ
and alpha_C are set in the "pair_style"_pair_style.html command,
before the cutoffs.
@@ -175,7 +175,7 @@ an inner and outer cutoff. The usage of this pair style is documented
in the "pair_charmm"_pair_charmm.html styles. The soft-core version
introduces the lambda parameter to the list of arguments, after
epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and
-before the optional eps14 and sigma14). The paratemers n,
+before the optional eps14 and sigma14). The parameters n,
alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html
command, before the cutoffs.
@@ -192,7 +192,7 @@ in several water models).
NOTES: When using the core-softed Coulomb potentials with long-range
solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free
energy calculation in which sites holding electrostatic charges are
-being created or anihilated (using "fix adapt/fep"_fix_adapt_fep.html
+being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html
and "compute fep"_compute_fep.html) it is important to adapt both the
lambda activation parameter (from 0 to 1, or the reverse) and the
value of the charge (from 0 to its final value, or the reverse). This
diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt
index 5dbd7f4b80b0d482da2d9a53e67e3cf0e2dbe0df..daa2e37b688c36314d6c571aa0b0ae93acf0be56 100644
--- a/doc/src/pair_lubricate.txt
+++ b/doc/src/pair_lubricate.txt
@@ -94,7 +94,7 @@ Style {lubricate} requires monodisperse spherical particles; style
{lubricate/poly} allows for polydisperse spherical particles.
The viscosity {mu} can be varied in a time-dependent manner over the
-course of a simluation, in which case in which case the pair_style
+course of a simulation, in which case in which case the pair_style
setting for {mu} will be overridden. See the "fix adapt"_fix_adapt.html
command for details.
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index ba46a135a25602983f38fa439b3e1d899d392f5a..08e53cb38cdf079aa141b474571a486339eca68e 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -140,5 +140,5 @@ for more info.
:link(Lenosky)
[(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter,
-Kress, Modelling Simulation Materials Science Enginerring, 8, 825
+Kress, Modelling Simulation Materials Science Engineering, 8, 825
(2000).
diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt
index 53ae53df23c4391da55796ea3a9b9817c428d10c..f8b0c9f0713c99856cbce64bb199ee55068bebbf 100644
--- a/doc/src/pair_mgpt.txt
+++ b/doc/src/pair_mgpt.txt
@@ -75,7 +75,7 @@ proceeds. After each time step, the atomic volume should be updated
by the code as Omega = V/N. In addition, the volume term E_vol and
the potentials v_2, v_3 and v_4 have to be removed at the end of the
time step, and then respecified at the new value of Omega. In all
-smulations, Omega must remain within the defined volume range for
+simulations, Omega must remain within the defined volume range for
E_vol and the potentials for the given material.
The default option volpress yes in the "pair_coeff"_pair_coeff.html
diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt
index fec00ed44c32bf856d8769d4eba75a22598920f3..ad602db9f1e02cb1792acb2d1711ad0e189eacdc 100644
--- a/doc/src/pair_mie.txt
+++ b/doc/src/pair_mie.txt
@@ -57,7 +57,7 @@ cutoff specified in the pair_style command is used.
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the mie/cut pair styles can be mixed.
-If not explicity defined, both the repulsive and attractive gamma
+If not explicitly defined, both the repulsive and attractive gamma
exponents for different atoms will be calculated following the same
mixing rule defined for distances. The default mix value is
{geometric}. See the "pair_modify" command for details.
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 73bc1a314f52863825cd275827e456f9f62744fa..c5e3a3c3995ef17e54174975d28cebc5c410980c 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -80,7 +80,7 @@ the {morse} and {morse/smooth/linear} styles.
The {morse/soft} variant is similar to the {lj/cut/soft} pair style
in that it modifies the potential at short range to have a soft core.
This helps to avoid singularities during free energy calculation in
-which sites are created or anihilated. The formula differs from that
+which sites are created or annihilated. The formula differs from that
of {lj/cut/soft}, and is instead given by:
:c,image(Eqs/pair_morse_soft.jpg)
diff --git a/doc/src/pair_oxdna_excv.txt b/doc/src/pair_oxdna.txt
similarity index 64%
rename from doc/src/pair_oxdna_excv.txt
rename to doc/src/pair_oxdna.txt
index 23a727b3b99c52e7b36af473166d0f1c5af58bd3..ba2a3e4b013125cb63a1712461fe1f92b9d5ab32 100644
--- a/doc/src/pair_oxdna_excv.txt
+++ b/doc/src/pair_oxdna.txt
@@ -6,36 +6,36 @@
:line
-pair_style oxdna_excv command :h3
-pair_style oxdna_stk command :h3
-pair_style oxdna_hbond command :h3
-pair_style oxdna_xstk command :h3
-pair_style oxdna_coaxstk command :h3
+pair_style oxdna/excv command :h3
+pair_style oxdna/stk command :h3
+pair_style oxdna/hbond command :h3
+pair_style oxdna/xstk command :h3
+pair_style oxdna/coaxstk command :h3
[Syntax:]
pair_style style :pre
-style = {hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk} :ul
+style = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
[Examples:]
-pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
-pair_coeff * * oxdna_excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna_stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna_hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna_xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
[Description:]
The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
-excluded volume interaction {oxdna_excv}, the stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
-and coaxial stacking interaction {oxdna_coaxstk} as well
-as the hydrogen-bonding interaction {oxdna_hbond} between complementary pairs of nucleotides on
+excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
+and coaxial stacking interaction {oxdna/coaxstk} as well
+as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
opposite strands.
The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
@@ -46,13 +46,13 @@ We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge
for a detailed description of the oxDNA force field.
NOTE: These pair styles have to be used together with the related oxDNA bond style
-{oxdna_fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna_fene"_bond_oxdna_fene.html). The coefficients
+{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
+"bond_style oxdna/fene"_bond_oxdna.html). The coefficients
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/Â and /duplex2/.
+Example input and data files can be found in examples/USER/cgdna/examples/duplex1/Â and /duplex2/.
A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
+DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
A technical report with more information on the model, the structure of the input file,
the setup tool and the performance of the LAMMPS-implementation of oxDNA
can be found "here"_PDF/USER-CGDNA-overview.pdf.
@@ -67,7 +67,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
-"bond_style oxdna_fene"_bond_oxdna_fene.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html
+"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html
[Default:] none
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index 240d9f3bda79b29f9fadb226fe1b09223c7108d2..6ffd8122aa49f794dac275409c3fb75cc6258893 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -116,7 +116,7 @@ cutoff distance for truncating interactions, and s00 and alpha are
used as a bond breaking criteria. m_lambdai and m_taubi are the
viscoelastic relaxation parameter and time constant,
respectively. m_lambdai varies within zero to one. For very small
-values of m_lambdai the viscoelsatic model responds very similar to a
+values of m_lambdai the viscoelastic model responds very similar to a
linear elastic model. For details please see the description in
"(Mtchell2011)".
diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt
index a90f65931b4340dc2a5df5fb6670b6f95ef785ae..12dcd244e254eabb66569b5e5be2d59166b38912 100644
--- a/doc/src/pair_quip.txt
+++ b/doc/src/pair_quip.txt
@@ -45,12 +45,12 @@ See the "pair_coeff"_pair_coeff.html doc page for alternate ways
to specify the path for the potential file.
A QUIP potential is fully specified by the filename which contains the
-parameters of the potential in XML format, the initialisation string,
+parameters of the potential in XML format, the initialization string,
and the map of atomic numbers.
GAP potentials can be obtained from the Data repository section of
"http://www.libatoms.org"_http://www.libatoms.org, where the
-appropriate initialisation strings are also advised. The list of
+appropriate initialization strings are also advised. The list of
atomic numbers must be matched to the LAMMPS atom types specified in
the LAMMPS data file or elsewhere.
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index f404fa41817b04abb1dc9ca96e70be54b30d94a7..0242bab18559778a489049b546e453005399c6b7 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -58,17 +58,17 @@ cutoff (distance units) :ul
The parameters used depend on the type of the interacting particles,
i.e. ellipsoids or LJ spheres. The type of a particle is determined
-by the diameters specified for its 3 shape paramters. If all 3 shape
+by the diameters specified for its 3 shape parameters. If all 3 shape
parameters = 0.0, then the particle is treated as an LJ sphere. The
epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If
-the 3 shape paraemters are > 0.0, then the particle is treated as an
+the 3 shape parameters are > 0.0, then the particle is treated as an
ellipsoid (even if the 3 parameters are equal to each other).
A12 specifies the energy prefactor which depends on the types of the
two interacting particles.
For ellipsoid/ellipsoid interactions, the interaction is computed by
-the formulas in the supplementary docuement referenced above. A12 is
+the formulas in the supplementary document referenced above. A12 is
the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ
units:
@@ -79,8 +79,8 @@ composing the ellipsoids and epsilon_LJ determines the interaction
strength of the spherical particles.
For ellipsoid/LJ sphere interactions, the interaction is also computed
-by the formulas in the supplementary docuement referenced above. A12
-has a modifed form (see "here"_PDF/pair_resquared_extra.pdf for
+by the formulas in the supplementary document referenced above. A12
+has a modified form (see "here"_PDF/pair_resquared_extra.pdf for
details):
:c,image(Eqs/pair_resquared2.jpg)
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt
index b9efeb8fc3f589cc133775a3937996cbc0d7a23a..393bbc066525c90db749a8d80acdfedca93ad4a9 100644
--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@@ -31,7 +31,7 @@ pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is
defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions
-between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to preceed a cross interaction.
+between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction.
In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a
number of floats and integers, the {ulsph} {pair coeff} definition is organised using
keywords. These keywords mark the beginning of different sets of parameters for particle properties,
diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt
index c70af68b306a2f5eda1bbace68a6df71cae0eda4..714188de32979cdd88789d4ef88629f4083b7dfb 100644
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
@@ -36,7 +36,7 @@ atoms. This interactions depend on interatomic distance
The parameters appearing in the upper expressions are set in the
ffield.SMTBQ.Syst file where Syst corresponds to the selected system
-(e.g. field.SMTBQ.Al2O3). Exemples for TiO<sub>2</sub>,
+(e.g. field.SMTBQ.Al2O3). Examples for TiO<sub>2</sub>,
Al<sub>2</sub>O<sub>3</sub> are provided. A single pair_coeff command
is used with the SMTBQ styles which provides the path to the potential
file with parameters for needed elements. These are mapped to LAMMPS
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index f240779050bf47823053e7dcab4ab860f63dfb30..ec1c06729a9cf18cf5ffeccecb30359de0124b20 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -60,7 +60,7 @@ them. This functionality is now available in a more general form
through the "fix adapt"_fix_adapt.html command, as explained below.
Note that if you use an old input script and specify Astart and Astop
without a cutoff, then LAMMPS will interpret that as A and a cutoff,
-which is probabably not what you want.
+which is probably not what you want.
The "fix adapt"_fix_adapt.html command can be used to vary A for one
or more pair types over the course of a simulation, in which case
diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt
index d25debe91b5ec090c66b96eda7bc8bce9e7a3ba0..2387056a1b7b4b06235c3d8d88ad5edec4bccbdf 100644
--- a/doc/src/pair_sph_heatconduction.txt
+++ b/doc/src/pair_sph_heatconduction.txt
@@ -20,7 +20,7 @@ pair_coeff * * 1.0 2.4 :pre
[Description:]
The sph/heatconduction style computes heat transport between SPH particles.
-The transport model is the diffusion euqation for the internal energy.
+The transport model is the diffusion equation for the internal energy.
See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
LAMMPS.
diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt
index 21ca049272f24922fafb074ee2d5c68a1bb1af96..957f901425993d91b248c9a7172a45b0753abd44 100644
--- a/doc/src/pair_sph_idealgas.txt
+++ b/doc/src/pair_sph_idealgas.txt
@@ -27,7 +27,7 @@ according to the ideal gas equation of state:
where gamma = 1.4 is the heat capacity ratio, rho is the local
density, and e is the internal energy per unit mass. This pair style
also computes Monaghan's artificial viscosity to prevent particles
-from interpentrating "(Monaghan)"_#ideal-Monoghan.
+from interpenetrating "(Monaghan)"_#ideal-Monoghan.
See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
LAMMPS.
diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt
index 8498841131b8a506f8d4adc0b342273ac3bbfb36..ef89c4ad3eaf351d07dad07e953b6dc4ea3eb139 100644
--- a/doc/src/pair_sph_lj.txt
+++ b/doc/src/pair_sph_lj.txt
@@ -24,7 +24,7 @@ to the Lennard-Jones equation of state, which is computed according to
Ree's 1980 polynomial fit "(Ree)"_#Ree. The Lennard-Jones parameters
epsilon and sigma are set to unity. This pair style also computes
Monaghan's artificial viscosity to prevent particles from
-interpentrating "(Monaghan)"_#Monoghan.
+interpenetrating "(Monaghan)"_#Monoghan.
See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
LAMMPS.
diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt
index 2b0b6d119cb7c3263ed4a443cf2fe5a3e42227cc..9177ca80b868e417e3bf8a23d30f267fd882f3ff 100644
--- a/doc/src/pair_sph_taitwater.txt
+++ b/doc/src/pair_sph_taitwater.txt
@@ -28,7 +28,7 @@ where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
reference density and c_0 the reference speed of sound.
This pair style also computes Monaghan's artificial viscosity to
-prevent particles from interpentrating "(Monaghan)"_#Monaghan.
+prevent particles from interpenetrating "(Monaghan)"_#Monaghan.
See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
LAMMPS.
diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt
index a951cccbc33d86ef40a06790aad4fad1714eaf6a..c1eff12cbf65ccf4f7fffcbfed4a5e37bc9759da 100644
--- a/doc/src/pair_srp.txt
+++ b/doc/src/pair_srp.txt
@@ -86,7 +86,7 @@ the beginning of a run. This means you must specify the number of
types in your system accordingly; usually to be one larger than what
would normally be the case, e.g. via the "create_box"_create_box.html
or by changing the header in your "data file"_read_data.html. The
-ficitious "bond particles" are inserted at the beginning of the run,
+fictitious "bond particles" are inserted at the beginning of the run,
and serve as placeholders that define the position of the bonds. This
allows neighbor lists to be constructed and pairwise interactions to
be computed in almost the same way as is done for actual particles.
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index 6504edb2a57aeed64904d6ad49d4debd13c976cd..ba79aee40d6ec044ce9e63e2ea8cafad5f76c598 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -33,7 +33,7 @@ pair_coeff * 3 morse.table ENTRY1 7.0 :pre
Style {table} creates interpolation tables from potential energy and
force values listed in a file(s) as a function of distance. When
-performing dynamics or minimation, the interpolation tables are used
+performing dynamics or minimization, the interpolation tables are used
to evaluate energy and forces for pairwise interactions between
particles, similar to how analytic formulas are used for other pair
styles.
@@ -180,7 +180,7 @@ NOTE: If you use "R" or "RSQ", the tabulated distance values in the
file are effectively ignored, and replaced by new values as described
in the previous paragraph. If the distance value in the table is not
very close to the new value (i.e. round-off difference), then you will
-be assingning energy/force values to a different distance, which is
+be assigning energy/force values to a different distance, which is
probably not what you want. LAMMPS will warn if this is occurring.
If used, the parameter "BITMAP" is also followed by 2 values {rlo} and
diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt
index e4eed927f51eab4c4deb016662dc0600f7887e30..42a5bbdfe2285c61c67ad980eecca779666f553b 100644
--- a/doc/src/pair_tri_lj.txt
+++ b/doc/src/pair_tri_lj.txt
@@ -42,7 +42,7 @@ triangle, for purposes of this pair style, are generated in the
following manner. Assume the triangle is of type I, and sigma_II has
been specified. We want a set of spheres with centers in the plane of
the triangle, none of them larger in diameter than sigma_II, which
-completely cover the triangle's area, but with minimial overlap and a
+completely cover the triangle's area, but with minimal overlap and a
minimal total number of spheres. This is done in a recursive manner.
Place a sphere at the centroid of the original triangle. Calculate
what diameter it must have to just cover all 3 corner points of the
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 7c18623d11054bbeb982a7c54b151e963a61f80d..8928ca451b71313a1e20501f631b6d48e9bc2320 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -39,6 +39,7 @@ Pair Styles :h1
pair_hbond_dreiding
pair_hybrid
pair_kim
+ pair_kolmogorov_crespi_z
pair_lcbop
pair_line_lj
pair_list
@@ -65,7 +66,7 @@ Pair Styles :h1
pair_nb3b_harmonic
pair_nm
pair_none
- pair_oxdna_excv
+ pair_oxdna
pair_peri
pair_polymorphic
pair_quip
diff --git a/doc/src/partition.txt b/doc/src/partition.txt
index ccef3590505dd0a6fc52dab603f45200bb8a6da0..9c1d560c83069077dbb99d3ea572b8d794dcd158 100644
--- a/doc/src/partition.txt
+++ b/doc/src/partition.txt
@@ -39,7 +39,7 @@ such a variable is used in a "jump"_jump.html command.
The "partition" command is another mechanism for having as input
script operate differently on different partitions. It is basically a
-prefix on any LAMMPS command. The commmand will only be invoked on
+prefix on any LAMMPS command. The command will only be invoked on
the partition(s) specified by the {style} and {N} arguments.
If the {style} is {yes}, the command will be invoked on any partition
diff --git a/doc/src/prd.txt b/doc/src/prd.txt
index 1ad66ee441e99a6f3006c08b8c97cc81da0e500a..607c367afdbdc47718d1d87fd060babafffe7d09 100644
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@@ -133,7 +133,7 @@ event.
The event check is performed by a compute with the specified
{compute-ID}. Currently there is only one compute that works with the
-PRD commmand, which is the "compute
+PRD command, which is the "compute
event/displace"_compute_event_displace.html command. Other
event-checking computes may be added. "Compute
event/displace"_compute_event_displace.html checks whether any atom in
@@ -230,7 +230,7 @@ files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For
the PRD command, these contain the thermodynamic output for each
replica. You will see short runs and minimizations corresponding to
the dynamics and quench operations of the loop listed above. The
-timestep will be reset aprpopriately depending on whether the
+timestep will be reset appropriately depending on whether the
operation advances time or not.
After the PRD command completes, timing statistics for the PRD run are
diff --git a/doc/src/processors.txt b/doc/src/processors.txt
index adf2a0920f2bdcfe28366a1529ba8074358f5794..781049af9cce84d928dc5385e577f7d27dc38a49 100644
--- a/doc/src/processors.txt
+++ b/doc/src/processors.txt
@@ -27,7 +27,7 @@ keyword = {grid} or {map} or {part} or {file} :l
{map} arg = {cart} or {cart/reorder} or {xyz} or {xzy} or {yxz} or {yzx} or {zxy} or {zyx}
cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
- xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering
+ xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering
{numa} arg = none
{part} args = Psend Precv cstyle
Psend = partition # (1 to Np) which will send its processor layout
@@ -104,7 +104,7 @@ regular grid is initially created, regardless of which
If load-balancing is never invoked via the "balance"_balance.html or
"fix balance"_fix_balance.html commands, then the initial regular grid
will persist for all simulations. If balancing is performed, some of
-the methods invoked by those commands retain the logical toplogy of
+the methods invoked by those commands retain the logical topology of
the initial 3d grid, and the mapping of processors to the grid
specified by the processors command. However the grid spacings in
different dimensions may change, so that processors own sub-domains of
@@ -179,7 +179,7 @@ The first non-blank, non-comment line should have
Px Py Py :pre
These must be compatible with the total number of processors
-and the Px, Py, Pz settings of the processors commmand.
+and the Px, Py, Pz settings of the processors command.
This line should be immediately followed by
P = Px*Py*Pz lines of the form:
@@ -244,7 +244,7 @@ The {part} keyword affects the factorization of P into Px,Py,Pz.
It can be useful when running in multi-partition mode, e.g. with the
"run_style verlet/split"_run_style.html command. It specifies a
-dependency bewteen a sending partition {Psend} and a receiving
+dependency between a sending partition {Psend} and a receiving
partition {Precv} which is enforced when each is setting up their own
mapping of their processors to the simulation box. Each of {Psend}
and {Precv} must be integers from 1 to Np, where Np is the number of
@@ -271,7 +271,7 @@ processors, it could create a 4x2x10 grid, but it will not create a
4.
NOTE: If you use the "partition"_partition.html command to invoke
-different "processsors" commands on different partitions, and you also
+different "processors" commands on different partitions, and you also
use the {part} keyword, then you must insure that both the sending and
receiving partitions invoke the "processors" command that connects the
2 partitions via the {part} keyword. LAMMPS cannot easily check for
diff --git a/doc/src/python.txt b/doc/src/python.txt
index 7da69a0319ca82cafcff9c84122648b9c2bdab64..be6d1b215f3512295eb571918564838add33ca0f 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -143,7 +143,7 @@ numeric or string value, as specified by the {format} keyword.
As explained on the "variable"_variable.html doc page, the definition
of a python-style variable associates a Python function name with the
variable. This must match the {func} setting for this command. For
-exampe these two commands would be self-consistent:
+example these two commands would be self-consistent:
variable foo python myMultiply
python myMultiply return v_foo format f file funcs.py :pre
@@ -174,7 +174,7 @@ a longer string, the {length} keyword can be specified with its {Nlen}
value set to a larger number (the code allocates space for Nlen+1 to
include the string terminator). If the Python function generates a
string longer than the default 63 or the specified {Nlen}, it will be
-trunctated.
+truncated.
:line
@@ -356,7 +356,7 @@ python loop invoke :pre
This has the effect of looping over a series of 10 short runs (10
timesteps each) where the pair style cutoff is increased from a value
of 1.0 in distance units, in increments of 0.1. The looping stops
-when the per-atom potential energy falls below a threshhold of -4.0 in
+when the per-atom potential energy falls below a threshold of -4.0 in
energy units. More generally, Python can be used to implement a loop
with complex logic, much more so than can be created using the LAMMPS
"jump"_jump.html and "if"_if.html commands.
@@ -372,7 +372,7 @@ LAMMPS, more than the single value that can be passed back via a
return statement. This cutoff value in the "cut" variable is then
substituted (by LAMMPS) in the pair_style command that is executed
next. Alternatively, the "LAMMPS command option" line could be used
-in place of the 2 preceeding lines, to have Python insert the value
+in place of the 2 preceding lines, to have Python insert the value
into the LAMMPS command string.
NOTE: When using the callback mechanism just described, recognize that
@@ -384,7 +384,7 @@ file() functions, so long as the command would work if it were
executed in the LAMMPS input script directly at the same point.
However, a Python function can also be invoked during a run, whenever
-an associated LAMMPS variable it is assigned to is evaluted. If the
+an associated LAMMPS variable it is assigned to is evaluated. If the
variable is an input argument to another LAMMPS command (e.g. "fix
setforce"_fix_setforce.html), then the Python function will be invoked
inside the class for that command, in one of its methods that is
diff --git a/doc/src/quit.txt b/doc/src/quit.txt
index 809fb2e38ba1a7e63db9638a40eab5423c2737aa..843d3de7f3545dfd330f7e7624fe21a3c3c6e430 100644
--- a/doc/src/quit.txt
+++ b/doc/src/quit.txt
@@ -17,7 +17,7 @@ status = numerical exit status (optional)
[Examples:]
quit
-if "$n > 10000" then "quit 1":pre
+if "$n > 10000" then "quit 1" :pre
[Description:]
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index 9ddc9d89218bb79d9496fce812f8eb306c8a3800..86c123527bfb633b1bd6070a0567d2d708a30fa2 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -180,7 +180,7 @@ used appropriately when each data file is read, the values in those
sections will be stored correctly in the larger data structures
allocated by the use of the {extra} keywords. E.g. the substrate file
can list mass and pair coefficients for type 1 silicon atoms. The
-water file can list mass and pair coeffcients for type 1 and type 2
+water file can list mass and pair coefficients for type 1 and type 2
hydrogen and oxygen atoms. Use of the {extra} and {offset} keywords
will store those mass and pair coefficient values appropriately in
data structures that allow for 3 atom types (Si, H, O). Of course,
@@ -574,7 +574,7 @@ spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e.
template-atom = which atom within a template molecule the atom is
template-index = which molecule within the molecule template the atom is part of
theta = internal temperature of a DPD particle
-triangleflag = 1 for triangular particles, 0 for point or sperhical particles
+triangleflag = 1 for triangular particles, 0 for point or spherical particles
volume = volume of Peridynamic particle (distance^3 units)
x,y,z = coordinates of atom (distance units) :ul
diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt
index e454c180abd45bc0522d52ec61bdadc9bf1cd7f2..381e29f6e0df6ea808e3be2a7f5920228bed5f49 100644
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@@ -58,7 +58,7 @@ read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/
Read atom information from a dump file to overwrite the current atom
coordinates, and optionally the atom velocities and image flags and
-the simluation box dimensions. This is useful for restarting a run
+the simulation box dimensions. This is useful for restarting a run
from a particular snapshot in a dump file. See the
"read_restart"_read_restart.html and "read_data"_read_data.html
commands for alternative methods to do this. Also see the
@@ -214,7 +214,7 @@ you wish to change this after the dump snapshot is read.
If the {box} keyword is specified with a {yes} value, then the current
simulation box dimensions are replaced by the dump snapshot box
dimensions. If the {box} keyword is specified with a {no} value, the
-current simulatoin box is unchanged.
+current simulation box is unchanged.
If the {purge} keyword is specified with a {yes} value, then all
current atoms in the system are deleted before any of the operations
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index d59b5313fdf785d5816400f66f424255d5897dbc..d0f4b16175c7863a306475dcb950196d8af438c1 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -31,7 +31,7 @@ information is stored (and not stored) in a restart file is given
below. Basically this operation will re-create the simulation box
with all its atoms and their attributes as well as some related global
settings, at the point in time it was written to the restart file by a
-previous simluation. The simulation box will be partitioned into a
+previous simulation. The simulation box will be partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors in the current simulation and the settings of the
"processors"_processors.html command. The partitioning can later be
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 4ce230da7b55c6493e7c2d22ffd21c10b4bcbd40..885e5e45f8c647031742c372bc6df9797d84b5cc 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -212,7 +212,7 @@ both of the spheres.
The {units} keyword determines the meaning of the distance units used
to define the region for any argument above listed as having distance
-units. It also affects the scaling of the velocity vector specfied
+units. It also affects the scaling of the velocity vector specified
with the {vel} keyword, the amplitude vector specified with the
{wiggle} keyword, and the rotation point specified with the {rotate}
keyword, since they each involve a distance metric.
@@ -283,9 +283,9 @@ velocity:
variable dx equal ramp(0,10)
region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL :pre
-Note that the initial displacemet is 0.0, though that is not required.
+Note that the initial displacement is 0.0, though that is not required.
-Either of these varaibles would "wiggle" the region back and forth in
+Either of these variables would "wiggle" the region back and forth in
the y direction:
variable dy equal swiggle(0,5,100)
@@ -352,7 +352,7 @@ high-coordinate flat end cap, and index 3 is the curved cone surface.
In the last example above, a {cone} region is defined along the z-axis
that is open at the zlo value (e.g. for use as a funnel).
-For all other styles, the {open} keyword is ignored. As inidcated
+For all other styles, the {open} keyword is ignored. As indicated
above, this includes the {intersect} and {union} regions, though their
sub-regions can be defined with the {open} keyword.
diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt
index 2e7153e38c312438b9e6869112eaf9b7f8fedbec..291558e0e527d41a6c0ae7a53b854cfd12eb476a 100644
--- a/doc/src/replicate.txt
+++ b/doc/src/replicate.txt
@@ -53,7 +53,7 @@ top of each other.
NOTE: You cannot use the replicate command on a system which has a
molecule that spans the box and is bonded to itself across a periodic
-boundary, so that the molecule is efffectively a loop. A simple
+boundary, so that the molecule is effectively a loop. A simple
example would be a linear polymer chain that spans the simulation box
and bonds back to itself across the periodic boundary. More realistic
examples would be a CNT (meant to be an infinitely long CNT) or a
diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt
index da8c8d6895b117935ffb0bdfe06621dbce742c22..860ee68033b2180ce7cd2291be3995a4cf5460ba 100644
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@@ -40,7 +40,7 @@ rerun ../run7/dump.file.gz skip 2 dump x y z box yes :pre
[Description:]
-Perform a psuedo simulation run where atom information is read one
+Perform a pseudo simulation run where atom information is read one
snapshot at a time from a dump file(s), and energies and forces are
computed on the shapshot to produce thermodynamic or other output.
@@ -121,7 +121,7 @@ with the {start/stop} keywords. Note that if you define neither of
the {start}/{stop} or {first}/{last} keywords, then LAMMPS treats the
pseudo run as going from 0 to a huge value (effectively infinity).
This means that any quantity that a fix scales as a fraction of
-elapsed time in the run, will essentially remain at its intiial value.
+elapsed time in the run, will essentially remain at its initial value.
Also note that an error will occur if you read a snapshot from the
dump file with a timestep value larger than the {stop} setting you
have specified.
@@ -178,7 +178,7 @@ a timestep it expects to be, LAMMPS will flag an error.
The various forms of LAMMPS output, as defined by the
"thermo_style"_thermo_style.html, "thermo"_thermo.html,
"dump"_dump.html, and "restart"_restart.html commands occur on
-specific timesteps. If successvive dump snapshots skip those
+specific timesteps. If successive dump snapshots skip those
timesteps, then no output will be produced. E.g. if you request
thermodynamic output every 100 steps, but the dump file snapshots are
every 1000 steps, then you will only see thermodynamic output every
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 3154465f68fb5805e9650d581a4b58333cfc3282..5e0c2a9ea54e4d4d7b1837ac55575d9a847f21f2 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -97,7 +97,7 @@ timestep of a run unless it is a multiple of N. A restart file is
written on the last timestep of a minimization if N > 0 and the
minimization converges.
-Instead of a numeric value, N can be specifed as an "equal-style
+Instead of a numeric value, N can be specified as an "equal-style
variable"_variable.html, which should be specified as v_name, where
name is the variable name. In this case, the variable is evaluated at
the beginning of a run to determine the next timestep at which a
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 2dafabebb594ce687d10c7608d82a0918c090775..b30a17686d8c235e4c7f7d8a7267928b03d58f72 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -76,7 +76,7 @@ Specifically, this style performs all computation except the
"kspace_style"_kspace_style.html portion of the force field on the 1st
partition. This include the "pair style"_pair_style.html, "bond
style"_bond_style.html, "neighbor list building"_neighbor.html,
-"fixes"_fix.html including time intergration, and output. The
+"fixes"_fix.html including time integration, and output. The
"kspace_style"_kspace_style.html portion of the calculation is
performed on the 2nd partition.
@@ -105,23 +105,23 @@ to control this, e.g.
procssors * * * part 1 2 multiple :pre
You can also use the "partition"_partition.html command to explicitly
-specity the processor layout on each partition. E.g. for 2 partitions
+specify the processor layout on each partition. E.g. for 2 partitions
of 60 and 15 processors each:
partition yes 1 processors 3 4 5
partition yes 2 processors 3 1 5 :pre
When you run in 2-partition mode with the {verlet/split} style, the
-thermodyanmic data for the entire simulation will be output to the log
+thermodynamic data for the entire simulation will be output to the log
and screen file of the 1st partition, which are log.lammps.0 and
screen.0 by default; see the "-plog and -pscreen command-line
switches"_Section_start.html#start_7 to change this. The log and
screen file for the 2nd partition will not contain thermodynamic
-output beyone the 1st timestep of the run.
+output beyond the 1st timestep of the run.
See "Section 5"_Section_accelerate.html of the manual for
performance details of the speed-up offered by the {verlet/split}
-style. One important performance consideration is the assignemnt of
+style. One important performance consideration is the assignment of
logical processors in the 2 partitions to the physical cores of a
parallel machine. The "processors"_processors.html command has
options to support this, and strategies are discussed in
@@ -182,7 +182,7 @@ for hybrid coarse-grained/all-atom models. The {hybrid} keyword
requires as many level assignments as there are hybrid substyles,
which assigns each sub-style to a rRESPA level, following their order
of definition in the pair_style command. Since the {hybrid} keyword
-operates on pair style computations, it is mututally exclusive with
+operates on pair style computations, it is mutually exclusive with
either the {pair} or the {inner}/{middle}/{outer} keywords.
When using rRESPA (or for any MD simulation) care must be taken to
diff --git a/doc/src/set.txt b/doc/src/set.txt
index 42ede23b8545ca6b70ea2f2f1a0b3ee3e5445896..659eecd30d313737758cdfd792b7c52caf015f60 100644
--- a/doc/src/set.txt
+++ b/doc/src/set.txt
@@ -374,7 +374,7 @@ header of the data file read by the "read_data"_read_data.html
command. These keywords do not allow use of an atom-style variable.
Keywords {meso/e}, {meso/cv}, and {meso/rho} set the energy, heat
-capacity, and density of smmothed particle hydrodynamics (SPH)
+capacity, and density of smoothed particle hydrodynamics (SPH)
particles. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to
using SPH in LAMMPS.
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index 70c6a3031b6a26984d0f8026ee9062bb51ca0af5..127719cdb5f678eef1bb30d62ea2caa15f488b7c 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -91,7 +91,7 @@ a disabled suffix is turned back on. The use of these 2 commands lets
your input script use a standard LAMMPS style (i.e. a non-accelerated
variant), which can be useful for testing or benchmarking purposes.
Of course this is also possible by not using any suffix commands, and
-explictly appending or not appending the suffix to the relevant
+explicitly appending or not appending the suffix to the relevant
commands in your input script.
NOTE: The default "run_style"_run_style.html verlet is invoked prior to
diff --git a/doc/src/tad.txt b/doc/src/tad.txt
index 5b0f5a006ce02d9eab48e55a90ef9567a4aaa2d8..04c7d708f691c6d01007e276213f64fd19e8a58f 100644
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@@ -130,7 +130,7 @@ transition event.
The event check is performed by a compute with the specified
{compute-ID}. Currently there is only one compute that works with the
-TAD commmand, which is the "compute
+TAD command, which is the "compute
event/displace"_compute_event_displace.html command. Other
event-checking computes may be added. "Compute
event/displace"_compute_event_displace.html checks whether any atom in
@@ -144,7 +144,7 @@ NEB is determined by the {neb_style} keyword and must be a damped
dynamics minimizer. The tolerances and limits for each NEB
calculation can be set by the {neb} keyword. As discussed on the
"neb"_neb.html, it is often advantageous to use a larger timestep for
-NEB than for normal dyanmics. Since the size of the timestep set by
+NEB than for normal dynamics. Since the size of the timestep set by
the "timestep"_timestep.html command is used by TAD for performing
dynamics, there is a {neb_step} keyword which can be used to set a
larger timestep for each NEB calculation if desired.
@@ -258,7 +258,7 @@ number of replicas or processors.
Note that within a single state, the dynamics will typically
temporarily continue beyond the event that is ultimately chosen, until
-the stopping criterionis satisfied. When the event is eventually
+the stopping criterion is satisfied. When the event is eventually
executed, the timestep counter is reset to the value when the event
was detected. Similarly, after each quench and NEB minimization, the
timestep counter is reset to the value at the start of the
diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt
index 6faea206f49e4eda6e3b8d5670717c33e0c34c20..1d5d34995cd3cc979f3537b529950032be2ea4ba 100644
--- a/doc/src/thermo.txt
+++ b/doc/src/thermo.txt
@@ -30,7 +30,7 @@ The content and format of what is printed is controlled by the
"thermo_style"_thermo_style.html and
"thermo_modify"_thermo_modify.html commands.
-Instead of a numeric value, N can be specifed as an "equal-style
+Instead of a numeric value, N can be specified as an "equal-style
variable"_variable.html, which should be specified as v_name, where
name is the variable name. In this case, the variable is evaluated at
the beginning of a run to determine the next timestep at which
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index 6cdb8a3cc87871b88c0583bf8766ba910e12ee21..36ec7bf12e06586b3fdd284f399dc3250628a2f4 100644
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@@ -36,7 +36,7 @@ args = list of arguments for a particular style :l
elaplong = timesteps since start of initial run in a series of runs
dt = timestep size
time = simulation time
- cpu = elapsed CPU time in seconds
+ cpu = elapsed CPU time in seconds since start of this run
tpcpu = time per CPU second
spcpu = timesteps per CPU second
cpuremain = estimated CPU time remaining in run
@@ -226,7 +226,7 @@ simulation time, also in time "units"_units.html, which is simply
not been reset. If the timestep has changed (e.g. via "fix
dt/reset"_fix_dt_reset.html) or the timestep has been reset (e.g. via
the "reset_timestep" command), then the simulation time is effectively
-a cummulative value up to the current point.
+a cumulative value up to the current point.
The {cpu} keyword is elapsed CPU seconds since the beginning of this
run. The {tpcpu} and {spcpu} keywords are measures of how fast your
@@ -236,7 +236,7 @@ time per CPU second, where simulation time is in time
picoseconds per CPU second. The {spcpu} keyword is the number of
timesteps per CPU second. Both quantities are on-the-fly metrics,
measured relative to the last time they were invoked. Thus if you are
-printing out thermodyamic output every 100 timesteps, the two keywords
+printing out thermodynamic output every 100 timesteps, the two keywords
will continually output the time and timestep rate for the last 100
steps. The {tpcpu} keyword does not attempt to track any changes in
timestep size, e.g. due to using the "fix dt/reset"_fix_dt_reset.html
@@ -289,7 +289,7 @@ The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta},
{cellgamma}, correspond to the usual crystallographic quantities that
define the periodic unit cell of a crystal. See "this
section"_Section_howto.html#howto_12 of the doc pages for a geometric
-description of triclinic periodic cells, including a precise defintion
+description of triclinic periodic cells, including a precise definition
of these quantities in terms of the internal LAMMPS cell dimensions
{lx}, {ly}, {lz}, {yz}, {xz}, {xy}.
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index 358ec75a53ecc6d29c90e0e58075690e5ba76141..39a6c542b77a17229b286ac2adf3c725d880a440 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -16,7 +16,7 @@ timer args :pre
{off} = do not collect or print any timing information
{loop} = collect only the total time for the simulation loop
{normal} = collect timer information broken down by sections (default)
- {full} = like {normal} but also include CPU and thread utilzation
+ {full} = like {normal} but also include CPU and thread utilization
{sync} = explicitly synchronize MPI tasks between sections
{nosync} = do not synchronize MPI tasks between sections (default)
{timeout} elapse = set walltime limit to {elapse}
@@ -48,11 +48,11 @@ detailed per section information. With the {normal} setting, timing
information for portions of the timestep (pairwise calculations,
neighbor list construction, output, etc) are collected as well as
information about load imbalances for those sections across
-procsessors. The {full} setting adds information about CPU
+processors. The {full} setting adds information about CPU
utilization and thread utilization, when multi-threading is enabled.
With the {sync} setting, all MPI tasks are synchronized at each timer
-call which measures load imbalance for each section more accuractly,
+call which measures load imbalance for each section more accurately,
though it can also slow down the simulation by prohibiting overlapping
independent computations on different MPI ranks Using the {nosync}
setting (which is the default) turns this synchronization off.
diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt
index c2f4a16207e395b7c5c8406862f006fa1a5a29bf..518b90854b543bb9c611972f76906b2e9a308d84 100644
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/tutorial_drude.txt
@@ -72,17 +72,17 @@ In both these force fields hydrogen atoms are treated as non-polarizable. :l
The motion of of the Drude particles can be calculated by minimizing
-the energy of the induced dipoles at each timestep, by an interative,
+the energy of the induced dipoles at each timestep, by an iterative,
self-consistent procedure. The Drude particles can be massless and
therefore do not contribute to the kinetic energy. However, the
-relaxed method is computationall slow. An extended-lagrangian method
+relaxed method is computational slow. An extended-lagrangian method
can be used to calculate the positions of the Drude particles, but
this requires them to have mass. It is important in this case to
decouple the degrees of freedom associated with the Drude oscillators
from those of the normal atoms. Thermalizing the Drude dipoles at
temperatures comparable to the rest of the simulation leads to several
problems (kinetic energy transfer, very short timestep, etc.), which
-can be remediated by the "cold Drude" technique ("Lamoureux and
+can be remediate by the "cold Drude" technique ("Lamoureux and
Roux"_#Lamoureux).
Two closely related models are used to represent polarization through
@@ -270,7 +270,7 @@ be stable, for example if the atomic polarizability is too high for
instance, a DP can escape from its DC and be captured by another DC,
which makes the force and energy diverge and the simulation
crash. Even without reaching this extreme case, the correlation
-between nearby dipoles on the same molecule may be exagerated. Often,
+between nearby dipoles on the same molecule may be exaggerated. Often,
special bond relations prevent bonded neighboring atoms to see the
charge of each other's DP, so that the problem does not always appear.
It is possible to use screened dipole dipole interactions by using the
diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt
index 6966bb90b9cf9e62a485945d6f16d204dade623d..5d3491782e98b891f025b76d037525e54f293b74 100644
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/tutorial_pylammps.txt
@@ -328,7 +328,7 @@ IPyLammps Examples :h2
Examples of IPython notebooks can be found in the python/examples/pylammps
subdirectory. To open these notebooks launch {jupyter notebook} inside this
directory and navigate to one of them. If you compiled and installed
-a LAMMPS shared library with execeptions, PNG, JPEG and FFMPEG support
+a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.
Validating a dihedral potential :h3
diff --git a/doc/src/units.txt b/doc/src/units.txt
index 87436b6307196f1d20f72411b34ca67c0fc04b55..0b856dcc68b67a9f7df9f159e779f8fb5a097379 100644
--- a/doc/src/units.txt
+++ b/doc/src/units.txt
@@ -73,7 +73,7 @@ dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)
electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon
density = mass/volume, where rho* = rho sigma^dim :ul
-Note that for LJ units, the default mode of thermodyamic output via
+Note that for LJ units, the default mode of thermodynamic output via
the "thermo_style"_thermo_style.html command is to normalize all
extensive quantities by the number of atoms. E.g. potential energy is
extensive because it is summed over atoms, so it is output as
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index 29d50a2b8e6fbd962162732fc6a72d1ce4a1cfa8..e32e82ef4d38bed75e0dd67f9b619109c01174b3 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -501,7 +501,7 @@ the group.
:line
-Numers, constants, and thermo keywords :h4
+Numbers, constants, and thermo keywords :h4
Numbers can contain digits, scientific notation
(3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs.
@@ -576,7 +576,7 @@ returns 0.0.
These relational and logical operators can be used as a masking or
selection operation in a formula. For example, the number of atoms
-whose properties satifsy one or more criteria could be calculated by
+whose properties satisfy one or more criteria could be calculated by
taking the returned per-atom vector of ones and zeroes and passing it
to the "compute reduce"_compute_reduce.html command.
@@ -623,7 +623,7 @@ Floor() if the largest integer not greater than its argument. Round()
is the nearest integer to its argument.
The ramp(x,y) function uses the current timestep to generate a value
-linearly intepolated between the specified x,y values over the course
+linearly interpolated between the specified x,y values over the course
of a run, according to this formula:
value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) :pre
@@ -669,7 +669,7 @@ sequence of output timesteps:
The stride(x,y,z) function uses the current timestep to generate a new
timestep. X,y >= 0 and z > 0 and x <= y are required. The generated
timesteps increase in increments of z, from x to y, i.e. it generates
-the sequece x,x+z,x+2z,...,y. If y-x is not a multiple of z, then
+the sequence x,x+z,x+2z,...,y. If y-x is not a multiple of z, then
similar to the way a for loop operates, the last value will be one
that does not exceed y. For any current timestep, the next timestep
in the sequence is returned. Thus if stride(1000,2000,100) is used
@@ -781,7 +781,7 @@ is for a vector-style variable where "name" is replaced by the name of
the variable.
These functions operate on a global vector of inputs and reduce it to
-a single scalar value. This is analagous to the operation of the
+a single scalar value. This is analogous to the operation of the
"compute reduce"_compute_reduce.html command, which performs similar
operations on per-atom and local vectors.
@@ -1068,7 +1068,7 @@ in the reference should be replaced by the name of a variable defined
elsewhere in the input script.
As discussed on this doc page, equal-style variables generate a single
-global numeric value, vector-style variables gerarate a vector of
+global numeric value, vector-style variables generate a vector of
global numeric values, and atom-style and atomfile-style variables
generate a per-atom vector of numeric values. All other variables
store one or more strings.
@@ -1169,7 +1169,7 @@ would print out both the current and initial volume periodically
during the run.
Note that it is a mistake to enclose a variable formula in double
-quotes if it contains variables preceeded by $ signs. For example,
+quotes if it contains variables preceded by $ signs. For example,
variable vratio equal "$\{vfinal\}/$\{v0\}" :pre
@@ -1214,7 +1214,7 @@ three kinds of behavior:
(1) The variable may be evaluated accurately. If it contains
references to a compute or fix, and these values were calculated on
-the last timestep of a preceeding run, then they will be accessed and
+the last timestep of a preceding run, then they will be accessed and
used by the variable and the result will be accurate.
(2) LAMMPS may not be able to evaluate the variable and will generate
diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt
index ae32a94e840d32d0c25bd384bcca70a4fc51e596..840716085feff0aaf6b7790befc98b902be87ea3 100644
--- a/doc/src/write_dump.txt
+++ b/doc/src/write_dump.txt
@@ -53,7 +53,7 @@ support optional arguments and thus LAMMPS needs to be able to cleanly
separate the two sets of args.
Note that if the specified filename uses wildcard characters "*" or
-"%", as supported by the "dump"_dump.html commmand, they will operate
+"%", as supported by the "dump"_dump.html command, they will operate
in the same fashion to create the new filename(s). Normally, "dump
image"_dump_image.html files require a filename with a "*" character
for the timestep. That is not the case for the write_dump command; no
@@ -78,7 +78,7 @@ else LAMMPS will generate an error message.
For example, it is not possible to dump per-atom energy with this
command before a run has been performed, since no energies and forces
have yet been calculated. See the "variable"_variable.html doc page
-sectinn on Variable Accuracy for more information on this topic.
+section on Variable Accuracy for more information on this topic.
[Related commands:]
diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py
index 2b4950519a44d41d10501e5a0683242442cec09b..9cca50b3bf2089e6195d32b16f816317a3ca03ef 100644
--- a/doc/utils/sphinx-config/conf.py
+++ b/doc/utils/sphinx-config/conf.py
@@ -299,4 +299,11 @@ more information about the code and its uses.
epub_author = 'The LAMMPS Developers'
-
+# configure spelling extension if present
+import importlib.util
+spelling_spec = importlib.util.find_spec("sphinxcontrib.spelling")
+if spelling_spec:
+ extensions.append('sphinxcontrib.spelling')
+
+ spelling_lang='en_US'
+ spelling_word_list_filename='false_positives.txt'
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb08e4e97e5b19ad0713819f173a78555d0ff42d
--- /dev/null
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -0,0 +1,2667 @@
+aa
+aat
+abc
+abf
+absTol
+Acc
+Accelrys
+acceptor
+Acceptor
+acceptors
+accomodate
+accuracies
+ach
+achived
+achives
+ackland
+Ackland
+acolor
+acos
+Acta
+actinide
+adaptation
+addforce
+addtorque
+Adhikari
+adiam
+Adjiman
+adof
+adp
+Adri
+adusting
+advect
+advection
+advects
+afer
+affine
+Afshar
+agilio
+Agilio
+agni
+Ai
+Aidan
+aij
+airebo
+Aj
+ajaramil
+akohlmey
+Aktulga
+al
+alain
+Alain
+alat
+Albe
+alchemical
+AlCu
+Alderton
+Alejandre
+alessandro
+Alessandro
+aliceblue
+allocaters
+allosws
+AlO
+alond
+Alonso
+amap
+Amatrix
+Amit
+amu
+Amzallag
+Andzelm
+Ang
+angmom
+angmomx
+angmomy
+angmomz
+Angs
+anharmonic
+anharmonicity
+aniso
+anisotropic
+ansi
+antiquewhite
+Antisymmetrized
+antisymmetry
+Antonelli
+aperiodic
+api
+Appl
+Apu
+arccos
+arcsin
+arg
+args
+artefacts
+Arun
+asin
+Askari
+askoose
+asphere
+ASPHERE
+aspherical
+Asq
+assinged
+associdate
+Asta
+Astart
+Astop
+asub
+asubrama
+Asumming
+atan
+atc
+AtC
+ATC
+athomps
+atobody
+atomeye
+atomfile
+atomID
+atomistic
+atomt
+attogram
+attograms
+attrac
+Atw
+Atwater
+atwt
+augt
+AuO
+autocorrelation
+automagically
+Avalos
+avalue
+aveforce
+Avendano
+avi
+AVX
+awpmd
+AWPMD
+Axel
+Ay
+Ayton
+Az
+azimuthal
+ba
+Babadi
+backcolor
+backend
+Baczewski
+Bal
+balancer
+Balasubramanian
+Ballenegger
+Bammann
+Barashev
+barostat
+barostated
+barostating
+barostatted
+barostatting
+Barostatting
+barosttating
+Barrat
+Bartels
+barycenter
+barye
+Bashford
+Baskes
+Batra
+Bayly
+bb
+bcc
+bcolor
+bdiam
+Beckman
+behaviour
+Belak
+Bellott
+benchmarking
+Bennet
+Berardi
+Beraun
+berendsen
+Berendsen
+berger
+Berkowitz
+berlin
+Berne
+Beutler
+bgq
+Bh
+biaxial
+Biersack
+bigint
+bilayer
+bilayers
+binsize
+binstyle
+biomolecular
+biomolecule
+Biomolecules
+Biophys
+Biosym
+bisectioning
+bispectrum
+Bispectrum
+bitmapped
+bitrate
+bitrates
+Bitzek
+Blaise
+blanchedalmond
+blocksize
+blueviolet
+bn
+bni
+bodyflag
+bodystyle
+Bogaerts
+Bogusz
+Bohrs
+bondchk
+bondings
+bondmax
+bondtype
+Bonet
+boolean
+Boresch
+Botero
+Botu
+Bouguet
+bount
+boxcolor
+bpclermont
+br
+Branicio
+brennan
+Brilliantov
+Broadwell
+brownian
+brownw
+Bryantsev
+btype
+buckPlusAttr
+bugfixes
+Bulatov
+burlywood
+Bussi
+Buyl
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diff --git a/doc/utils/txt2html/README.html b/doc/utils/txt2html/README.html
index 90ddaa1c49940c16cd64f7a37b649b9ba627c111..b92214425e8abd971f5c62e76094dd9e942e1c96 100644
--- a/doc/utils/txt2html/README.html
+++ b/doc/utils/txt2html/README.html
@@ -205,7 +205,7 @@ which are converted into HTML.
<LI> "}" (right bracket) --> turn-off italics by
inserting a </I> </UL>
-<P>If a backspace '\' preceeds any of the bold/italic mark-up characters,
+<P>If a backspace '\' precedes any of the bold/italic mark-up characters,
then mark-up is not performed; the mark-up character is simply left in
the text.
</P>
diff --git a/doc/utils/txt2html/txt2html.cpp b/doc/utils/txt2html/txt2html.cpp
index d7f411be9b219ceb661697b1f6979f1fb96cd02d..ff71c262c8d556d1ca47caa1890ebeec7723ec6a 100644
--- a/doc/utils/txt2html/txt2html.cpp
+++ b/doc/utils/txt2html/txt2html.cpp
@@ -561,7 +561,7 @@ void substitute(string &s)
string punctuation = ".,?!;:()";
// substitute for bold & italic markers
- // if preceeded by \ char, then leave markers in text
+ // if preceded by \ char, then leave markers in text
n = s.find_first_of("[]{}");
while (n != string::npos) {
diff --git a/examples/KAPPA/README b/examples/KAPPA/README
index ee70766d94c7d0cc1e4c3410a1a7c830e163fc83..d025797bfa9d1699e86b55e2f5306a56beacfa0d 100644
--- a/examples/KAPPA/README
+++ b/examples/KAPPA/README
@@ -85,7 +85,7 @@ Kappa = 3.45
(4) in.mp
dQ = 15087 / 100 / 18.82^2 / 2
- 15087 = cummulative delta energy, tallied by fix thermal/conductivity
+ 15087 = cumulative delta energy, tallied by fix thermal/conductivity
100 = 20,000 steps at 0.005 tau timestep = run time in tau
xy box area = 18.82^2
divide by 2 since energy flux goes in 2 directions due to periodic z
diff --git a/examples/README b/examples/README
index 87f14779ac5fb13b070001fd93bfb35fa2fcd92e..5880bb78d76762a56f261505f21683533afa07b5 100644
--- a/examples/README
+++ b/examples/README
@@ -93,7 +93,7 @@ peri: Peridynamic model of cylinder impacted by indenter
pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script
-qeq: use of QEQ pacakge for charge equilibration
+qeq: use of QEQ package for charge equilibration
reax: RDX and TATB models using the ReaxFF
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void
diff --git a/examples/USER/atc/README b/examples/USER/atc/README
index f3a852dfe32409b128ccce046d42d56526d3e50d..aa874f330027dcea5d7d24d63c9badf8264aea2f 100644
--- a/examples/USER/atc/README
+++ b/examples/USER/atc/README
@@ -65,7 +65,7 @@ elastic:
in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms
in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation
in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field
- in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field
+ in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field
in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
@@ -146,7 +146,7 @@ elastic:
in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms
in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation
in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field
- in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field
+ in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field
in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
diff --git a/examples/USER/atc/fluids/in.bar1d_fluids b/examples/USER/atc/fluids/in.bar1d_fluids
index 63ef0e2744bb190b6912f8823d37fa4722d657a5..af152bfbab998005421b95ebfcccefa8fb4d09fe 100644
--- a/examples/USER/atc/fluids/in.bar1d_fluids
+++ b/examples/USER/atc/fluids/in.bar1d_fluids
@@ -1,6 +1,6 @@
#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at
+# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
diff --git a/examples/USER/atc/thermal/in.bar1d b/examples/USER/atc/thermal/in.bar1d
index e8b61c412aba33d1d44d30897b0ba97f50f9dd19..5591f7177d3513dcefd772e68d9ccdbbcd9b246d 100644
--- a/examples/USER/atc/thermal/in.bar1d
+++ b/examples/USER/atc/thermal/in.bar1d
@@ -1,6 +1,6 @@
#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at 40.
+# temperature is initially 20 everywhere and the left boundary BC is fixed at 40.
# The result should show heat diffusing through the FEM to the MD and back out
# to the FEM on the right. Insufficient time is captured to reach the linear
# steady state, but heat crossing both boundaries should be observed.
diff --git a/examples/USER/atc/thermal/in.bar1d_all_atoms b/examples/USER/atc/thermal/in.bar1d_all_atoms
index 6b855f37b164160fc16abdb131b40d1b9d03e391..2c8851137f0da42a6dc3801dec63f48861404665 100644
--- a/examples/USER/atc/thermal/in.bar1d_all_atoms
+++ b/examples/USER/atc/thermal/in.bar1d_all_atoms
@@ -1,6 +1,6 @@
#AtC Thermal Coupling
# This benchmark tests thermostats applied in all atom simulations. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at
+# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
diff --git a/examples/USER/atc/thermal/in.bar1d_combined b/examples/USER/atc/thermal/in.bar1d_combined
index 1f960dbab788859167efb26e2fdb49fe859595e8..767544d2d439dd27ec87f3693a71b4fdcbfdb419 100644
--- a/examples/USER/atc/thermal/in.bar1d_combined
+++ b/examples/USER/atc/thermal/in.bar1d_combined
@@ -1,6 +1,6 @@
#AtC Thermal Coupling
# This benchmark tests heat conducting into an MD region at a fixed temperature at one end. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at
+# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing the boundaries should be observed,
diff --git a/examples/USER/atc/thermal/in.bar1d_flux b/examples/USER/atc/thermal/in.bar1d_flux
index 0103f00b5b822fd0073505e3115fc055f2d94d6f..eae32ec5b2b4d7c58cad512ca1bc73b889f1261b 100644
--- a/examples/USER/atc/thermal/in.bar1d_flux
+++ b/examples/USER/atc/thermal/in.bar1d_flux
@@ -1,6 +1,6 @@
#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at
+# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
diff --git a/examples/USER/atc/thermal/in.bar1d_frac_step b/examples/USER/atc/thermal/in.bar1d_frac_step
index ca722e79aa76dad587723981b1940945b9f33919..eddec44b521ae0c97a1c16502c01e462d841101a 100644
--- a/examples/USER/atc/thermal/in.bar1d_frac_step
+++ b/examples/USER/atc/thermal/in.bar1d_frac_step
@@ -1,6 +1,6 @@
#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at
+# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
diff --git a/examples/USER/atc/thermal/in.bar1d_hoover b/examples/USER/atc/thermal/in.bar1d_hoover
index 50e8f02166d92c91dddc3628d97021fa892d244e..2f0518d0d28518484aa802dd65d665a8d1c57ab5 100644
--- a/examples/USER/atc/thermal/in.bar1d_hoover
+++ b/examples/USER/atc/thermal/in.bar1d_hoover
@@ -1,6 +1,6 @@
# AtC Thermal Coupling
# This benchmark tests thermostats applied in all atom simulations. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at
+# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
diff --git a/examples/USER/atc/thermal/in.bar1d_interpolate b/examples/USER/atc/thermal/in.bar1d_interpolate
index e7db0d3856c9f56df36b7e6e28ba80b36960005d..0333bf117d043ad3e094e814c92221a6d1dbf75d 100644
--- a/examples/USER/atc/thermal/in.bar1d_interpolate
+++ b/examples/USER/atc/thermal/in.bar1d_interpolate
@@ -1,6 +1,6 @@
#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at
+# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
diff --git a/examples/USER/atc/thermal/in.bar1d_lumped b/examples/USER/atc/thermal/in.bar1d_lumped
index eb305a6252444b9ad25f47d58b0ee9a164c0a362..153f7b632d8e52a682e36dd988079b86a928ba88 100644
--- a/examples/USER/atc/thermal/in.bar1d_lumped
+++ b/examples/USER/atc/thermal/in.bar1d_lumped
@@ -1,6 +1,6 @@
#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region. The
-# temperature is intially 20 everywhere and the left boundary BC is fixed at
+# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
diff --git a/examples/USER/lb/confined_colloid/in.confined_colloids b/examples/USER/lb/confined_colloid/in.confined_colloids
index 37cd52e621f8b91aded0cc63cdacf1e8f0275627..b7b8958e9af43d9e60b44dacdf6629dbb3c5851f 100755
--- a/examples/USER/lb/confined_colloid/in.confined_colloids
+++ b/examples/USER/lb/confined_colloid/in.confined_colloids
@@ -67,7 +67,7 @@ timestep 0.0006
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
-# (however, this fix does not explicity apply a force back on to these
+# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix).
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003.
diff --git a/examples/USER/lb/microrheology/in.microrheology_default_gamma b/examples/USER/lb/microrheology/in.microrheology_default_gamma
index 4937a2cb20e6eaf7d43152ab435b30a61e328a60..8c3b684ff798f50fb5a38873ef3a177cea39224e 100755
--- a/examples/USER/lb/microrheology/in.microrheology_default_gamma
+++ b/examples/USER/lb/microrheology/in.microrheology_default_gamma
@@ -61,7 +61,7 @@ group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
-# (however, this fix does not explicity apply a force back on to these
+# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix).
# Use the standard LB integration scheme, a fluid viscosity = 1.0, fluid
# density= 0.0009982071, lattice spacing dx=1.2, and mass unit, dm=0.003.
diff --git a/examples/USER/lb/microrheology/in.microrheology_set_gamma b/examples/USER/lb/microrheology/in.microrheology_set_gamma
index 7b84bdaf63f0b7977e2754fc70443f346a582861..1f744220f092a3fc16dd282a38a17017472c13f4 100755
--- a/examples/USER/lb/microrheology/in.microrheology_set_gamma
+++ b/examples/USER/lb/microrheology/in.microrheology_set_gamma
@@ -61,7 +61,7 @@ group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
-# (however, this fix does not explicity apply a force back on to these
+# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
diff --git a/examples/USER/lb/planewall/in.planewall_default_gamma b/examples/USER/lb/planewall/in.planewall_default_gamma
index bf0cfcb3c73e148c05de0bf389cf1e7665bab0a4..83f42ebddd30247bd1141dd5b39c545ccea04f50 100755
--- a/examples/USER/lb/planewall/in.planewall_default_gamma
+++ b/examples/USER/lb/planewall/in.planewall_default_gamma
@@ -54,7 +54,7 @@ velocity all set 0.0 0.0 0.0 units box
#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
-# (however, this fix does not explicity apply a force back on to these
+# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
diff --git a/examples/USER/lb/planewall/in.planewall_set_gamma b/examples/USER/lb/planewall/in.planewall_set_gamma
index a048411b01cc447f3259db71ad4bcc545960f6b9..47d8266a1c182d49884cd1046095813d975f4b54 100755
--- a/examples/USER/lb/planewall/in.planewall_set_gamma
+++ b/examples/USER/lb/planewall/in.planewall_set_gamma
@@ -54,7 +54,7 @@ velocity all set 0.0 0.0 0.0 units box
#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
-# (however, this fix does not explicity apply a force back on to these
+# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
diff --git a/examples/USER/lb/polymer/data.polymer b/examples/USER/lb/polymer/data.polymer
index d3c39ad39b1cc53be1a6a86583ac67d24f2629b2..da974446cb4f6a6243ed5f9afa6aaacbc598a397 100755
--- a/examples/USER/lb/polymer/data.polymer
+++ b/examples/USER/lb/polymer/data.polymer
@@ -1,1040 +1,1040 @@
-Position data for a 32-bead polymer consisting of 31-vertex extended spheres
-
-992 atoms
-31 bonds
-
-2 atom types
-1 bond types
-
-0 40 xlo xhi
-0 40 ylo yhi
-0 40 zlo zhi
-
-Atoms
-
-1 1 21.0439 24.2646 23.1337 1
-2 2 20.3839 24.2646 23.3669 1
-3 2 20.8557 23.6306 23.3629 1
-4 2 21.5866 23.883 23.3569 1
-5 2 21.5866 24.6463 23.3569 1
-6 2 20.8558 24.8987 23.3629 1
-7 2 20.3839 24.2646 22.9005 1
-8 2 20.8558 23.6306 22.9045 1
-9 2 21.5866 23.883 22.9105 1
-10 2 21.5866 24.6463 22.9105 1
-11 2 20.8557 24.8987 22.9045 1
-12 2 21.6158 24.2646 23.5374 1
-13 2 21.2339 24.8002 23.5425 1
-14 2 20.595 24.6026 23.5511 1
-15 2 20.595 23.9267 23.5511 1
-16 2 21.2339 23.7291 23.5425 1
-17 2 21.6158 24.2646 22.73 1
-18 2 21.2339 24.8002 22.7249 1
-19 2 20.595 24.6026 22.7163 1
-20 2 20.595 23.9267 22.7163 1
-21 2 21.2339 23.7291 22.7249 1
-22 2 21.3444 24.2646 23.7659 1
-23 2 21.1464 24.5394 23.7693 1
-24 2 20.8215 24.436 23.7749 1
-25 2 20.8215 24.0933 23.7749 1
-26 2 21.1464 23.9899 23.7693 1
-27 2 21.3444 24.2646 22.5015 1
-28 2 21.1464 24.5394 22.4981 1
-29 2 20.8214 24.436 22.4925 1
-30 2 20.8214 24.0933 22.4925 1
-31 2 21.1464 23.9899 22.4981 1
-32 1 21.5789 25.5745 23.3738 2
-33 2 20.9189 25.5745 23.6069 2
-34 2 21.3907 24.9404 23.603 2
-35 2 22.1216 25.1929 23.597 2
-36 2 22.1216 25.9562 23.597 2
-37 2 21.3907 26.2086 23.603 2
-38 2 20.9189 25.5745 23.1406 2
-39 2 21.3907 24.9404 23.1446 2
-40 2 22.1216 25.1929 23.1505 2
-41 2 22.1216 25.9562 23.1505 2
-42 2 21.3907 26.2086 23.1446 2
-43 2 22.1507 25.5745 23.7775 2
-44 2 21.7688 26.1101 23.7826 2
-45 2 21.13 25.9125 23.7912 2
-46 2 21.13 25.2365 23.7912 2
-47 2 21.7688 25.039 23.7826 2
-48 2 22.1507 25.5745 22.97 2
-49 2 21.7688 26.1101 22.965 2
-50 2 21.13 25.9125 22.9563 2
-51 2 21.13 25.2365 22.9563 2
-52 2 21.7688 25.039 22.965 2
-53 2 21.8794 25.5745 24.006 2
-54 2 21.6814 25.8493 24.0094 2
-55 2 21.3564 25.7458 24.015 2
-56 2 21.3564 25.4032 24.015 2
-57 2 21.6814 25.2997 24.0094 2
-58 2 21.8794 25.5745 22.7416 2
-59 2 21.6814 25.8493 22.7382 2
-60 2 21.3564 25.7458 22.7326 2
-61 2 21.3564 25.4032 22.7326 2
-62 2 21.6814 25.2997 22.7382 2
-63 1 22.5101 25.4302 22.2914 3
-64 2 21.8501 25.4302 22.5246 3
-65 2 22.322 24.7961 22.5206 3
-66 2 23.0528 25.0485 22.5146 3
-67 2 23.0528 25.8118 22.5146 3
-68 2 22.322 26.0643 22.5206 3
-69 2 21.8501 25.4302 22.0582 3
-70 2 22.322 24.7961 22.0622 3
-71 2 23.0528 25.0485 22.0682 3
-72 2 23.0528 25.8118 22.0682 3
-73 2 22.322 26.0643 22.0622 3
-74 2 23.082 25.4302 22.6951 3
-75 2 22.7001 25.9657 22.7002 3
-76 2 22.0612 25.7682 22.7088 3
-77 2 22.0612 25.0922 22.7088 3
-78 2 22.7001 24.8947 22.7002 3
-79 2 23.082 25.4302 21.8877 3
-80 2 22.7001 25.9657 21.8826 3
-81 2 22.0612 25.7682 21.874 3
-82 2 22.0612 25.0922 21.874 3
-83 2 22.7001 24.8947 21.8826 3
-84 2 22.8107 25.4302 22.9236 3
-85 2 22.6126 25.705 22.927 3
-86 2 22.2877 25.6015 22.9326 3
-87 2 22.2877 25.2589 22.9326 3
-88 2 22.6126 25.1554 22.927 3
-89 2 22.8107 25.4302 21.6592 3
-90 2 22.6126 25.705 21.6558 3
-91 2 22.2877 25.6015 21.6502 3
-92 2 22.2877 25.2589 21.6502 3
-93 2 22.6126 25.1554 21.6558 3
-94 1 23.895 25.0537 22.2951 4
-95 2 23.235 25.0537 22.5282 4
-96 2 23.7068 24.4196 22.5243 4
-97 2 24.4377 24.672 22.5183 4
-98 2 24.4377 25.4353 22.5183 4
-99 2 23.7068 25.6877 22.5243 4
-100 2 23.235 25.0537 22.0619 4
-101 2 23.7068 24.4196 22.0659 4
-102 2 24.4377 24.672 22.0718 4
-103 2 24.4377 25.4353 22.0718 4
-104 2 23.7068 25.6877 22.0659 4
-105 2 24.4668 25.0537 22.6988 4
-106 2 24.0849 25.5892 22.7039 4
-107 2 23.4461 25.3916 22.7125 4
-108 2 23.4461 24.7157 22.7125 4
-109 2 24.0849 24.5181 22.7039 4
-110 2 24.4668 25.0537 21.8913 4
-111 2 24.0849 25.5892 21.8863 4
-112 2 23.4461 25.3916 21.8776 4
-113 2 23.4461 24.7157 21.8776 4
-114 2 24.0849 24.5181 21.8863 4
-115 2 24.1955 25.0537 22.9273 4
-116 2 23.9975 25.3284 22.9307 4
-117 2 23.6725 25.225 22.9363 4
-118 2 23.6725 24.8823 22.9363 4
-119 2 23.9975 24.7789 22.9307 4
-120 2 24.1955 25.0537 21.6629 4
-121 2 23.9975 25.3284 21.6595 4
-122 2 23.6725 25.225 21.6538 4
-123 2 23.6725 24.8823 21.6538 4
-124 2 23.9975 24.7789 21.6595 4
-125 1 24.6582 26.0898 21.6598 5
-126 2 23.9982 26.0898 21.893 5
-127 2 24.4701 25.4557 21.889 5
-128 2 25.2009 25.7081 21.883 5
-129 2 25.2009 26.4714 21.883 5
-130 2 24.4701 26.7238 21.889 5
-131 2 23.9982 26.0898 21.4266 5
-132 2 24.4701 25.4557 21.4306 5
-133 2 25.2009 25.7081 21.4366 5
-134 2 25.2009 26.4714 21.4366 5
-135 2 24.4701 26.7238 21.4306 5
-136 2 25.2301 26.0898 22.0635 5
-137 2 24.8482 26.6253 22.0686 5
-138 2 24.2093 26.4277 22.0772 5
-139 2 24.2093 25.7518 22.0772 5
-140 2 24.8482 25.5542 22.0686 5
-141 2 25.2301 26.0898 21.2561 5
-142 2 24.8482 26.6253 21.251 5
-143 2 24.2093 26.4277 21.2424 5
-144 2 24.2093 25.7518 21.2424 5
-145 2 24.8482 25.5542 21.251 5
-146 2 24.9587 26.0898 22.292 5
-147 2 24.7607 26.3645 22.2954 5
-148 2 24.4358 26.2611 22.301 5
-149 2 24.4358 25.9185 22.301 5
-150 2 24.7607 25.815 22.2954 5
-151 2 24.9587 26.0898 21.0276 5
-152 2 24.7607 26.3645 21.0242 5
-153 2 24.4358 26.2611 21.0186 5
-154 2 24.4358 25.9184 21.0186 5
-155 2 24.7607 25.815 21.0242 5
-156 1 25.7401 26.9511 22.0433 6
-157 2 25.0801 26.9511 22.2765 6
-158 2 25.552 26.3171 22.2725 6
-159 2 26.2828 26.5695 22.2666 6
-160 2 26.2828 27.3328 22.2666 6
-161 2 25.552 27.5852 22.2725 6
-162 2 25.0801 26.9511 21.8102 6
-163 2 25.552 26.3171 21.8141 6
-164 2 26.2828 26.5695 21.8201 6
-165 2 26.2828 27.3328 21.8201 6
-166 2 25.552 27.5852 21.8141 6
-167 2 26.312 26.9511 22.4471 6
-168 2 25.9301 27.4867 22.4521 6
-169 2 25.2912 27.2891 22.4608 6
-170 2 25.2912 26.6132 22.4608 6
-171 2 25.9301 26.4156 22.4521 6
-172 2 26.312 26.9511 21.6396 6
-173 2 25.9301 27.4867 21.6345 6
-174 2 25.2912 27.2891 21.6259 6
-175 2 25.2912 26.6132 21.6259 6
-176 2 25.9301 26.4156 21.6345 6
-177 2 26.0406 26.9511 22.6755 6
-178 2 25.8426 27.2259 22.6789 6
-179 2 25.5177 27.1225 22.6845 6
-180 2 25.5177 26.7798 22.6845 6
-181 2 25.8426 26.6764 22.6789 6
-182 2 26.0406 26.9511 21.4111 6
-183 2 25.8426 27.2259 21.4077 6
-184 2 25.5177 27.1225 21.4021 6
-185 2 25.5177 26.7798 21.4021 6
-186 2 25.8426 26.6764 21.4077 6
-187 1 26.6309 26.6387 20.9623 7
-188 2 25.9709 26.6387 21.1955 7
-189 2 26.4427 26.0047 21.1916 7
-190 2 27.1736 26.2571 21.1856 7
-191 2 27.1736 27.0204 21.1856 7
-192 2 26.4427 27.2728 21.1916 7
-193 2 25.9709 26.6387 20.7292 7
-194 2 26.4427 26.0047 20.7331 7
-195 2 27.1736 26.2571 20.7391 7
-196 2 27.1736 27.0204 20.7391 7
-197 2 26.4427 27.2728 20.7331 7
-198 2 27.2028 26.6387 21.3661 7
-199 2 26.8208 27.1743 21.3712 7
-200 2 26.182 26.9767 21.3798 7
-201 2 26.182 26.3008 21.3798 7
-202 2 26.8208 26.1032 21.3712 7
-203 2 27.2027 26.6387 20.5586 7
-204 2 26.8209 27.1743 20.5535 7
-205 2 26.182 26.9767 20.5449 7
-206 2 26.182 26.3008 20.5449 7
-207 2 26.8208 26.1032 20.5535 7
-208 2 26.9314 26.6387 21.5946 7
-209 2 26.7334 26.9135 21.598 7
-210 2 26.4084 26.81 21.6036 7
-211 2 26.4084 26.4674 21.6036 7
-212 2 26.7334 26.364 21.598 7
-213 2 26.9314 26.6387 20.3301 7
-214 2 26.7334 26.9135 20.3267 7
-215 2 26.4084 26.8101 20.3211 7
-216 2 26.4084 26.4674 20.3211 7
-217 2 26.7334 26.364 20.3267 7
-218 1 27.7333 27.3399 21.5562 8
-219 2 27.0733 27.3399 21.7894 8
-220 2 27.5451 26.7058 21.7855 8
-221 2 28.276 26.9582 21.7795 8
-222 2 28.276 27.7215 21.7795 8
-223 2 27.5451 27.974 21.7855 8
-224 2 27.0733 27.3399 21.3231 8
-225 2 27.5451 26.7058 21.327 8
-226 2 28.276 26.9582 21.333 8
-227 2 28.276 27.7215 21.333 8
-228 2 27.5451 27.974 21.327 8
-229 2 28.3051 27.3399 21.96 8
-230 2 27.9232 27.8754 21.9651 8
-231 2 27.2844 27.6779 21.9737 8
-232 2 27.2844 27.0019 21.9737 8
-233 2 27.9232 26.8043 21.9651 8
-234 2 28.3051 27.3399 21.1525 8
-235 2 27.9232 27.8754 21.1474 8
-236 2 27.2844 27.6779 21.1388 8
-237 2 27.2844 27.0019 21.1388 8
-238 2 27.9232 26.8044 21.1474 8
-239 2 28.0338 27.3399 22.1885 8
-240 2 27.8358 27.6147 22.1919 8
-241 2 27.5108 27.5112 22.1975 8
-242 2 27.5108 27.1686 22.1975 8
-243 2 27.8358 27.0651 22.1919 8
-244 2 28.0338 27.3399 20.924 8
-245 2 27.8358 27.6147 20.9206 8
-246 2 27.5108 27.5112 20.915 8
-247 2 27.5108 27.1686 20.915 8
-248 2 27.8358 27.0651 20.9206 8
-249 1 28.2741 26.7179 22.7311 9
-250 2 27.6141 26.7179 22.9642 9
-251 2 28.086 26.0838 22.9603 9
-252 2 28.8168 26.3362 22.9543 9
-253 2 28.8168 27.0995 22.9543 9
-254 2 28.086 27.352 22.9603 9
-255 2 27.6141 26.7179 22.4979 9
-256 2 28.086 26.0838 22.5019 9
-257 2 28.8168 26.3362 22.5078 9
-258 2 28.8168 27.0995 22.5078 9
-259 2 28.086 27.352 22.5019 9
-260 2 28.846 26.7179 23.1348 9
-261 2 28.4641 27.2534 23.1399 9
-262 2 27.8252 27.0559 23.1485 9
-263 2 27.8252 26.3799 23.1485 9
-264 2 28.4641 26.1823 23.1399 9
-265 2 28.846 26.7179 22.3273 9
-266 2 28.4641 27.2534 22.3223 9
-267 2 27.8252 27.0559 22.3136 9
-268 2 27.8252 26.3799 22.3136 9
-269 2 28.4641 26.1823 22.3223 9
-270 2 28.5746 26.7179 23.3633 9
-271 2 28.3766 26.9927 23.3667 9
-272 2 28.0517 26.8892 23.3723 9
-273 2 28.0517 26.5466 23.3723 9
-274 2 28.3766 26.4431 23.3667 9
-275 2 28.5746 26.7179 22.0989 9
-276 2 28.3766 26.9927 22.0955 9
-277 2 28.0517 26.8892 22.0899 9
-278 2 28.0517 26.5466 22.0899 9
-279 2 28.3766 26.4431 22.0955 9
-280 1 26.9358 26.2738 22.9979 10
-281 2 26.2757 26.2738 23.2311 10
-282 2 26.7476 25.6397 23.2271 10
-283 2 27.4785 25.8921 23.2211 10
-284 2 27.4785 26.6554 23.2211 10
-285 2 26.7476 26.9079 23.2271 10
-286 2 26.2757 26.2738 22.7647 10
-287 2 26.7476 25.6397 22.7687 10
-288 2 27.4785 25.8921 22.7747 10
-289 2 27.4785 26.6554 22.7747 10
-290 2 26.7476 26.9079 22.7687 10
-291 2 27.5076 26.2738 23.4016 10
-292 2 27.1257 26.8093 23.4067 10
-293 2 26.4869 26.6118 23.4154 10
-294 2 26.4869 25.9358 23.4154 10
-295 2 27.1257 25.7382 23.4067 10
-296 2 27.5076 26.2738 22.5942 10
-297 2 27.1257 26.8093 22.5891 10
-298 2 26.4869 26.6118 22.5805 10
-299 2 26.4869 25.9358 22.5805 10
-300 2 27.1257 25.7382 22.5891 10
-301 2 27.2363 26.2738 23.6301 10
-302 2 27.0383 26.5486 23.6335 10
-303 2 26.7133 26.4451 23.6391 10
-304 2 26.7133 26.1025 23.6391 10
-305 2 27.0383 25.999 23.6335 10
-306 2 27.2363 26.2738 22.3657 10
-307 2 27.0383 26.5486 22.3623 10
-308 2 26.7133 26.4451 22.3567 10
-309 2 26.7133 26.1025 22.3567 10
-310 2 27.0383 25.999 22.3623 10
-311 1 27.733 25.5139 23.9181 11
-312 2 27.0729 25.5139 24.1512 11
-313 2 27.5448 24.8798 24.1473 11
-314 2 28.2756 25.1323 24.1413 11
-315 2 28.2756 25.8956 24.1413 11
-316 2 27.5448 26.148 24.1473 11
-317 2 27.0729 25.5139 23.6849 11
-318 2 27.5448 24.8798 23.6889 11
-319 2 28.2756 25.1323 23.6948 11
-320 2 28.2756 25.8956 23.6948 11
-321 2 27.5448 26.148 23.6889 11
-322 2 28.3048 25.5139 24.3218 11
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-782 2 31.9696 27.0741 31.4857 26
-783 2 32.4414 26.4401 31.4897 26
-784 2 33.1723 26.6925 31.4956 26
-785 2 33.1723 27.4558 31.4956 26
-786 2 32.4414 27.7082 31.4897 26
-787 2 33.2014 27.0741 32.1226 26
-788 2 32.8195 27.6097 32.1277 26
-789 2 32.1807 27.4121 32.1363 26
-790 2 32.1807 26.7362 32.1363 26
-791 2 32.8195 26.5386 32.1277 26
-792 2 33.2014 27.0741 31.3151 26
-793 2 32.8195 27.6097 31.3101 26
-794 2 32.1807 27.4121 31.3014 26
-795 2 32.1807 26.7362 31.3014 26
-796 2 32.8195 26.5386 31.3101 26
-797 2 32.9301 27.0741 32.3511 26
-798 2 32.7321 27.3489 32.3545 26
-799 2 32.4071 27.2454 32.3601 26
-800 2 32.4071 26.9028 32.3601 26
-801 2 32.7321 26.7994 32.3545 26
-802 2 32.9301 27.0741 31.0867 26
-803 2 32.7321 27.3489 31.0833 26
-804 2 32.4071 27.2454 31.0777 26
-805 2 32.4071 26.9028 31.0777 26
-806 2 32.7321 26.7994 31.0833 26
-807 1 31.7049 27.9673 32.3567 27
-808 2 31.0449 27.9673 32.5899 27
-809 2 31.5167 27.3332 32.5859 27
-810 2 32.2476 27.5856 32.5799 27
-811 2 32.2476 28.3489 32.5799 27
-812 2 31.5167 28.6014 32.5859 27
-813 2 31.0449 27.9673 32.1235 27
-814 2 31.5167 27.3332 32.1275 27
-815 2 32.2476 27.5856 32.1335 27
-816 2 32.2476 28.3489 32.1335 27
-817 2 31.5167 28.6014 32.1275 27
-818 2 32.2767 27.9673 32.7604 27
-819 2 31.8948 28.5028 32.7655 27
-820 2 31.256 28.3053 32.7742 27
-821 2 31.256 27.6293 32.7742 27
-822 2 31.8948 27.4317 32.7655 27
-823 2 32.2767 27.9673 31.953 27
-824 2 31.8948 28.5028 31.9479 27
-825 2 31.256 28.3053 31.9393 27
-826 2 31.256 27.6293 31.9393 27
-827 2 31.8948 27.4317 31.9479 27
-828 2 32.0054 27.9673 32.9889 27
-829 2 31.8074 28.2421 32.9923 27
-830 2 31.4824 28.1386 32.9979 27
-831 2 31.4824 27.796 32.9979 27
-832 2 31.8074 27.6925 32.9923 27
-833 2 32.0054 27.9673 31.7245 27
-834 2 31.8074 28.2421 31.7211 27
-835 2 31.4824 28.1386 31.7155 27
-836 2 31.4824 27.796 31.7155 27
-837 2 31.8074 27.6925 31.7211 27
-838 1 30.3399 27.7351 32.7342 28
-839 2 29.6799 27.7351 32.9674 28
-840 2 30.1517 27.101 32.9634 28
-841 2 30.8826 27.3535 32.9574 28
-842 2 30.8826 28.1168 32.9574 28
-843 2 30.1517 28.3692 32.9634 28
-844 2 29.6799 27.7351 32.5011 28
-845 2 30.1517 27.101 32.505 28
-846 2 30.8826 27.3535 32.511 28
-847 2 30.8826 28.1168 32.511 28
-848 2 30.1517 28.3692 32.505 28
-849 2 30.9117 27.7351 33.138 28
-850 2 30.5298 28.2706 33.143 28
-851 2 29.891 28.0731 33.1517 28
-852 2 29.891 27.3971 33.1517 28
-853 2 30.5298 27.1996 33.143 28
-854 2 30.9117 27.7351 32.3305 28
-855 2 30.5298 28.2706 32.3254 28
-856 2 29.891 28.0731 32.3168 28
-857 2 29.891 27.3971 32.3168 28
-858 2 30.5298 27.1996 32.3254 28
-859 2 30.6404 27.7351 33.3664 28
-860 2 30.4424 28.0099 33.3698 28
-861 2 30.1174 27.9064 33.3754 28
-862 2 30.1174 27.5638 33.3754 28
-863 2 30.4424 27.4603 33.3698 28
-864 2 30.6404 27.7351 32.102 28
-865 2 30.4424 28.0099 32.0986 28
-866 2 30.1174 27.9064 32.093 28
-867 2 30.1174 27.5638 32.093 28
-868 2 30.4424 27.4603 32.0986 28
-869 1 29.8305 28.063 34.0352 29
-870 2 29.1705 28.063 34.2684 29
-871 2 29.6424 27.429 34.2644 29
-872 2 30.3732 27.6814 34.2584 29
-873 2 30.3732 28.4447 34.2584 29
-874 2 29.6424 28.6971 34.2644 29
-875 2 29.1705 28.063 33.8021 29
-876 2 29.6424 27.429 33.806 29
-877 2 30.3732 27.6814 33.812 29
-878 2 30.3732 28.4447 33.812 29
-879 2 29.6424 28.6971 33.806 29
-880 2 30.4024 28.063 34.439 29
-881 2 30.0205 28.5986 34.444 29
-882 2 29.3816 28.401 34.4527 29
-883 2 29.3816 27.7251 34.4527 29
-884 2 30.0205 27.5275 34.444 29
-885 2 30.4024 28.063 33.6315 29
-886 2 30.0205 28.5986 33.6264 29
-887 2 29.3816 28.401 33.6178 29
-888 2 29.3816 27.7251 33.6178 29
-889 2 30.0205 27.5275 33.6264 29
-890 2 30.1311 28.063 34.6674 29
-891 2 29.933 28.3378 34.6708 29
-892 2 29.6081 28.2344 34.6764 29
-893 2 29.6081 27.8917 34.6764 29
-894 2 29.933 27.7883 34.6708 29
-895 2 30.1311 28.063 33.403 29
-896 2 29.933 28.3378 33.3996 29
-897 2 29.6081 28.2344 33.394 29
-898 2 29.6081 27.8917 33.394 29
-899 2 29.933 27.7883 33.3996 29
-900 1 30.2349 27.8319 35.3927 30
-901 2 29.5749 27.8319 35.6258 30
-902 2 30.0468 27.1978 35.6219 30
-903 2 30.7776 27.4503 35.6159 30
-904 2 30.7776 28.2136 35.6159 30
-905 2 30.0468 28.466 35.6219 30
-906 2 29.5749 27.8319 35.1595 30
-907 2 30.0468 27.1978 35.1634 30
-908 2 30.7776 27.4503 35.1694 30
-909 2 30.7776 28.2136 35.1694 30
-910 2 30.0468 28.466 35.1634 30
-911 2 30.8068 27.8319 35.7964 30
-912 2 30.4249 28.3675 35.8015 30
-913 2 29.786 28.1699 35.8101 30
-914 2 29.786 27.4939 35.8101 30
-915 2 30.4249 27.2964 35.8015 30
-916 2 30.8068 27.8319 34.9889 30
-917 2 30.4249 28.3675 34.9839 30
-918 2 29.786 28.1699 34.9752 30
-919 2 29.786 27.4939 34.9752 30
-920 2 30.4249 27.2964 34.9839 30
-921 2 30.5354 27.8319 36.0249 30
-922 2 30.3374 28.1067 36.0283 30
-923 2 30.0125 28.0032 36.0339 30
-924 2 30.0125 27.6606 36.0339 30
-925 2 30.3374 27.5571 36.0283 30
-926 2 30.5354 27.8319 34.7604 30
-927 2 30.3374 28.1067 34.7571 30
-928 2 30.0125 28.0032 34.7514 30
-929 2 30.0125 27.6606 34.7514 30
-930 2 30.3374 27.5571 34.7571 30
-931 1 30.9967 26.7242 34.8903 31
-932 2 30.3366 26.7242 35.1234 31
-933 2 30.8085 26.0901 35.1195 31
-934 2 31.5393 26.3426 35.1135 31
-935 2 31.5393 27.1059 35.1135 31
-936 2 30.8085 27.3583 35.1195 31
-937 2 30.3366 26.7242 34.6571 31
-938 2 30.8085 26.0901 34.6611 31
-939 2 31.5393 26.3426 34.6671 31
-940 2 31.5393 27.1059 34.6671 31
-941 2 30.8085 27.3583 34.6611 31
-942 2 31.5685 26.7242 35.294 31
-943 2 31.1866 27.2598 35.2991 31
-944 2 30.5478 27.0622 35.3077 31
-945 2 30.5478 26.3862 35.3077 31
-946 2 31.1866 26.1887 35.2991 31
-947 2 31.5685 26.7242 34.4866 31
-948 2 31.1866 27.2598 34.4815 31
-949 2 30.5478 27.0622 34.4728 31
-950 2 30.5478 26.3862 34.4728 31
-951 2 31.1866 26.1887 34.4815 31
-952 2 31.2972 26.7242 35.5225 31
-953 2 31.0991 26.999 35.5259 31
-954 2 30.7742 26.8955 35.5315 31
-955 2 30.7742 26.5529 35.5315 31
-956 2 31.0991 26.4494 35.5259 31
-957 2 31.2972 26.7242 34.2581 31
-958 2 31.0991 26.999 34.2547 31
-959 2 30.7742 26.8955 34.2491 31
-960 2 30.7742 26.5529 34.2491 31
-961 2 31.0991 26.4494 34.2547 31
-962 1 29.9072 26.1623 34.144 32
-963 2 29.2472 26.1623 34.3772 32
-964 2 29.719 25.5283 34.3732 32
-965 2 30.4499 25.7807 34.3672 32
-966 2 30.4499 26.544 34.3672 32
-967 2 29.719 26.7964 34.3732 32
-968 2 29.2472 26.1623 33.9109 32
-969 2 29.719 25.5282 33.9148 32
-970 2 30.4499 25.7807 33.9208 32
-971 2 30.4499 26.544 33.9208 32
-972 2 29.719 26.7964 33.9148 32
-973 2 30.479 26.1623 34.5478 32
-974 2 30.0971 26.6979 34.5528 32
-975 2 29.4583 26.5003 34.5615 32
-976 2 29.4583 25.8244 34.5615 32
-977 2 30.0971 25.6268 34.5528 32
-978 2 30.479 26.1623 33.7403 32
-979 2 30.0971 26.6979 33.7352 32
-980 2 29.4583 26.5003 33.7266 32
-981 2 29.4583 25.8244 33.7266 32
-982 2 30.0971 25.6268 33.7352 32
-983 2 30.2077 26.1623 34.7762 32
-984 2 30.0097 26.4371 34.7796 32
-985 2 29.6847 26.3336 34.7852 32
-986 2 29.6847 25.991 34.7852 32
-987 2 30.0097 25.8876 34.7796 32
-988 2 30.2077 26.1623 33.5118 32
-989 2 30.0097 26.4371 33.5084 32
-990 2 29.6847 26.3336 33.5028 32
-991 2 29.6847 25.991 33.5028 32
-992 2 30.0097 25.8875 33.5084 32
-
-Bonds
-
-1 1 1 32
-2 1 32 63
-3 1 63 94
-4 1 94 125
-5 1 125 156
-6 1 156 187
-7 1 187 218
-8 1 218 249
-9 1 249 280
-10 1 280 311
-11 1 311 342
-12 1 342 373
-13 1 373 404
-14 1 404 435
-15 1 435 466
-16 1 466 497
-17 1 497 528
-18 1 528 559
-19 1 559 590
-20 1 590 621
-21 1 621 652
-22 1 652 683
-23 1 683 714
-24 1 714 745
-25 1 745 776
-26 1 776 807
-27 1 807 838
-28 1 838 869
-29 1 869 900
-30 1 900 931
-31 1 931 962
+Position data for a 32-bead polymer consisting of 31-vertex extended spheres
+
+992 atoms
+31 bonds
+
+2 atom types
+1 bond types
+
+0 40 xlo xhi
+0 40 ylo yhi
+0 40 zlo zhi
+
+Atoms
+
+1 1 21.0439 24.2646 23.1337 1
+2 2 20.3839 24.2646 23.3669 1
+3 2 20.8557 23.6306 23.3629 1
+4 2 21.5866 23.883 23.3569 1
+5 2 21.5866 24.6463 23.3569 1
+6 2 20.8558 24.8987 23.3629 1
+7 2 20.3839 24.2646 22.9005 1
+8 2 20.8558 23.6306 22.9045 1
+9 2 21.5866 23.883 22.9105 1
+10 2 21.5866 24.6463 22.9105 1
+11 2 20.8557 24.8987 22.9045 1
+12 2 21.6158 24.2646 23.5374 1
+13 2 21.2339 24.8002 23.5425 1
+14 2 20.595 24.6026 23.5511 1
+15 2 20.595 23.9267 23.5511 1
+16 2 21.2339 23.7291 23.5425 1
+17 2 21.6158 24.2646 22.73 1
+18 2 21.2339 24.8002 22.7249 1
+19 2 20.595 24.6026 22.7163 1
+20 2 20.595 23.9267 22.7163 1
+21 2 21.2339 23.7291 22.7249 1
+22 2 21.3444 24.2646 23.7659 1
+23 2 21.1464 24.5394 23.7693 1
+24 2 20.8215 24.436 23.7749 1
+25 2 20.8215 24.0933 23.7749 1
+26 2 21.1464 23.9899 23.7693 1
+27 2 21.3444 24.2646 22.5015 1
+28 2 21.1464 24.5394 22.4981 1
+29 2 20.8214 24.436 22.4925 1
+30 2 20.8214 24.0933 22.4925 1
+31 2 21.1464 23.9899 22.4981 1
+32 1 21.5789 25.5745 23.3738 2
+33 2 20.9189 25.5745 23.6069 2
+34 2 21.3907 24.9404 23.603 2
+35 2 22.1216 25.1929 23.597 2
+36 2 22.1216 25.9562 23.597 2
+37 2 21.3907 26.2086 23.603 2
+38 2 20.9189 25.5745 23.1406 2
+39 2 21.3907 24.9404 23.1446 2
+40 2 22.1216 25.1929 23.1505 2
+41 2 22.1216 25.9562 23.1505 2
+42 2 21.3907 26.2086 23.1446 2
+43 2 22.1507 25.5745 23.7775 2
+44 2 21.7688 26.1101 23.7826 2
+45 2 21.13 25.9125 23.7912 2
+46 2 21.13 25.2365 23.7912 2
+47 2 21.7688 25.039 23.7826 2
+48 2 22.1507 25.5745 22.97 2
+49 2 21.7688 26.1101 22.965 2
+50 2 21.13 25.9125 22.9563 2
+51 2 21.13 25.2365 22.9563 2
+52 2 21.7688 25.039 22.965 2
+53 2 21.8794 25.5745 24.006 2
+54 2 21.6814 25.8493 24.0094 2
+55 2 21.3564 25.7458 24.015 2
+56 2 21.3564 25.4032 24.015 2
+57 2 21.6814 25.2997 24.0094 2
+58 2 21.8794 25.5745 22.7416 2
+59 2 21.6814 25.8493 22.7382 2
+60 2 21.3564 25.7458 22.7326 2
+61 2 21.3564 25.4032 22.7326 2
+62 2 21.6814 25.2997 22.7382 2
+63 1 22.5101 25.4302 22.2914 3
+64 2 21.8501 25.4302 22.5246 3
+65 2 22.322 24.7961 22.5206 3
+66 2 23.0528 25.0485 22.5146 3
+67 2 23.0528 25.8118 22.5146 3
+68 2 22.322 26.0643 22.5206 3
+69 2 21.8501 25.4302 22.0582 3
+70 2 22.322 24.7961 22.0622 3
+71 2 23.0528 25.0485 22.0682 3
+72 2 23.0528 25.8118 22.0682 3
+73 2 22.322 26.0643 22.0622 3
+74 2 23.082 25.4302 22.6951 3
+75 2 22.7001 25.9657 22.7002 3
+76 2 22.0612 25.7682 22.7088 3
+77 2 22.0612 25.0922 22.7088 3
+78 2 22.7001 24.8947 22.7002 3
+79 2 23.082 25.4302 21.8877 3
+80 2 22.7001 25.9657 21.8826 3
+81 2 22.0612 25.7682 21.874 3
+82 2 22.0612 25.0922 21.874 3
+83 2 22.7001 24.8947 21.8826 3
+84 2 22.8107 25.4302 22.9236 3
+85 2 22.6126 25.705 22.927 3
+86 2 22.2877 25.6015 22.9326 3
+87 2 22.2877 25.2589 22.9326 3
+88 2 22.6126 25.1554 22.927 3
+89 2 22.8107 25.4302 21.6592 3
+90 2 22.6126 25.705 21.6558 3
+91 2 22.2877 25.6015 21.6502 3
+92 2 22.2877 25.2589 21.6502 3
+93 2 22.6126 25.1554 21.6558 3
+94 1 23.895 25.0537 22.2951 4
+95 2 23.235 25.0537 22.5282 4
+96 2 23.7068 24.4196 22.5243 4
+97 2 24.4377 24.672 22.5183 4
+98 2 24.4377 25.4353 22.5183 4
+99 2 23.7068 25.6877 22.5243 4
+100 2 23.235 25.0537 22.0619 4
+101 2 23.7068 24.4196 22.0659 4
+102 2 24.4377 24.672 22.0718 4
+103 2 24.4377 25.4353 22.0718 4
+104 2 23.7068 25.6877 22.0659 4
+105 2 24.4668 25.0537 22.6988 4
+106 2 24.0849 25.5892 22.7039 4
+107 2 23.4461 25.3916 22.7125 4
+108 2 23.4461 24.7157 22.7125 4
+109 2 24.0849 24.5181 22.7039 4
+110 2 24.4668 25.0537 21.8913 4
+111 2 24.0849 25.5892 21.8863 4
+112 2 23.4461 25.3916 21.8776 4
+113 2 23.4461 24.7157 21.8776 4
+114 2 24.0849 24.5181 21.8863 4
+115 2 24.1955 25.0537 22.9273 4
+116 2 23.9975 25.3284 22.9307 4
+117 2 23.6725 25.225 22.9363 4
+118 2 23.6725 24.8823 22.9363 4
+119 2 23.9975 24.7789 22.9307 4
+120 2 24.1955 25.0537 21.6629 4
+121 2 23.9975 25.3284 21.6595 4
+122 2 23.6725 25.225 21.6538 4
+123 2 23.6725 24.8823 21.6538 4
+124 2 23.9975 24.7789 21.6595 4
+125 1 24.6582 26.0898 21.6598 5
+126 2 23.9982 26.0898 21.893 5
+127 2 24.4701 25.4557 21.889 5
+128 2 25.2009 25.7081 21.883 5
+129 2 25.2009 26.4714 21.883 5
+130 2 24.4701 26.7238 21.889 5
+131 2 23.9982 26.0898 21.4266 5
+132 2 24.4701 25.4557 21.4306 5
+133 2 25.2009 25.7081 21.4366 5
+134 2 25.2009 26.4714 21.4366 5
+135 2 24.4701 26.7238 21.4306 5
+136 2 25.2301 26.0898 22.0635 5
+137 2 24.8482 26.6253 22.0686 5
+138 2 24.2093 26.4277 22.0772 5
+139 2 24.2093 25.7518 22.0772 5
+140 2 24.8482 25.5542 22.0686 5
+141 2 25.2301 26.0898 21.2561 5
+142 2 24.8482 26.6253 21.251 5
+143 2 24.2093 26.4277 21.2424 5
+144 2 24.2093 25.7518 21.2424 5
+145 2 24.8482 25.5542 21.251 5
+146 2 24.9587 26.0898 22.292 5
+147 2 24.7607 26.3645 22.2954 5
+148 2 24.4358 26.2611 22.301 5
+149 2 24.4358 25.9185 22.301 5
+150 2 24.7607 25.815 22.2954 5
+151 2 24.9587 26.0898 21.0276 5
+152 2 24.7607 26.3645 21.0242 5
+153 2 24.4358 26.2611 21.0186 5
+154 2 24.4358 25.9184 21.0186 5
+155 2 24.7607 25.815 21.0242 5
+156 1 25.7401 26.9511 22.0433 6
+157 2 25.0801 26.9511 22.2765 6
+158 2 25.552 26.3171 22.2725 6
+159 2 26.2828 26.5695 22.2666 6
+160 2 26.2828 27.3328 22.2666 6
+161 2 25.552 27.5852 22.2725 6
+162 2 25.0801 26.9511 21.8102 6
+163 2 25.552 26.3171 21.8141 6
+164 2 26.2828 26.5695 21.8201 6
+165 2 26.2828 27.3328 21.8201 6
+166 2 25.552 27.5852 21.8141 6
+167 2 26.312 26.9511 22.4471 6
+168 2 25.9301 27.4867 22.4521 6
+169 2 25.2912 27.2891 22.4608 6
+170 2 25.2912 26.6132 22.4608 6
+171 2 25.9301 26.4156 22.4521 6
+172 2 26.312 26.9511 21.6396 6
+173 2 25.9301 27.4867 21.6345 6
+174 2 25.2912 27.2891 21.6259 6
+175 2 25.2912 26.6132 21.6259 6
+176 2 25.9301 26.4156 21.6345 6
+177 2 26.0406 26.9511 22.6755 6
+178 2 25.8426 27.2259 22.6789 6
+179 2 25.5177 27.1225 22.6845 6
+180 2 25.5177 26.7798 22.6845 6
+181 2 25.8426 26.6764 22.6789 6
+182 2 26.0406 26.9511 21.4111 6
+183 2 25.8426 27.2259 21.4077 6
+184 2 25.5177 27.1225 21.4021 6
+185 2 25.5177 26.7798 21.4021 6
+186 2 25.8426 26.6764 21.4077 6
+187 1 26.6309 26.6387 20.9623 7
+188 2 25.9709 26.6387 21.1955 7
+189 2 26.4427 26.0047 21.1916 7
+190 2 27.1736 26.2571 21.1856 7
+191 2 27.1736 27.0204 21.1856 7
+192 2 26.4427 27.2728 21.1916 7
+193 2 25.9709 26.6387 20.7292 7
+194 2 26.4427 26.0047 20.7331 7
+195 2 27.1736 26.2571 20.7391 7
+196 2 27.1736 27.0204 20.7391 7
+197 2 26.4427 27.2728 20.7331 7
+198 2 27.2028 26.6387 21.3661 7
+199 2 26.8208 27.1743 21.3712 7
+200 2 26.182 26.9767 21.3798 7
+201 2 26.182 26.3008 21.3798 7
+202 2 26.8208 26.1032 21.3712 7
+203 2 27.2027 26.6387 20.5586 7
+204 2 26.8209 27.1743 20.5535 7
+205 2 26.182 26.9767 20.5449 7
+206 2 26.182 26.3008 20.5449 7
+207 2 26.8208 26.1032 20.5535 7
+208 2 26.9314 26.6387 21.5946 7
+209 2 26.7334 26.9135 21.598 7
+210 2 26.4084 26.81 21.6036 7
+211 2 26.4084 26.4674 21.6036 7
+212 2 26.7334 26.364 21.598 7
+213 2 26.9314 26.6387 20.3301 7
+214 2 26.7334 26.9135 20.3267 7
+215 2 26.4084 26.8101 20.3211 7
+216 2 26.4084 26.4674 20.3211 7
+217 2 26.7334 26.364 20.3267 7
+218 1 27.7333 27.3399 21.5562 8
+219 2 27.0733 27.3399 21.7894 8
+220 2 27.5451 26.7058 21.7855 8
+221 2 28.276 26.9582 21.7795 8
+222 2 28.276 27.7215 21.7795 8
+223 2 27.5451 27.974 21.7855 8
+224 2 27.0733 27.3399 21.3231 8
+225 2 27.5451 26.7058 21.327 8
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+990 2 29.6847 26.3336 33.5028 32
+991 2 29.6847 25.991 33.5028 32
+992 2 30.0097 25.8875 33.5084 32
+
+Bonds
+
+1 1 1 32
+2 1 32 63
+3 1 63 94
+4 1 94 125
+5 1 125 156
+6 1 156 187
+7 1 187 218
+8 1 218 249
+9 1 249 280
+10 1 280 311
+11 1 311 342
+12 1 342 373
+13 1 373 404
+14 1 404 435
+15 1 435 466
+16 1 466 497
+17 1 497 528
+18 1 528 559
+19 1 559 590
+20 1 590 621
+21 1 621 652
+22 1 652 683
+23 1 683 714
+24 1 714 745
+25 1 745 776
+26 1 776 807
+27 1 807 838
+28 1 838 869
+29 1 869 900
+30 1 900 931
+31 1 931 962
diff --git a/examples/USER/lb/polymer/in.polymer_default_gamma b/examples/USER/lb/polymer/in.polymer_default_gamma
index 4344dc0ef8a905127c5f2810a3f9abd831abfd46..954e5a69235cf54103ba5d29ab5b9b83cf12ac3d 100755
--- a/examples/USER/lb/polymer/in.polymer_default_gamma
+++ b/examples/USER/lb/polymer/in.polymer_default_gamma
@@ -1,107 +1,107 @@
-#===========================================================================#
-# polymer test #
-# #
-# Run consists of a lone 32-bead coarse-grained polymer #
-# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
-# #
-# Here, gamma (used in the calculation of the monomer-fluid interaction #
-# force) is set by the user (gamma = 0.03 for this simulation...this #
-# value has been calibrated a priori through simulations of the drag #
-# force acting on a single particle of the same radius). #
-# Sample output from this run can be found in the file: #
-# 'dump.polymer.lammpstrj' #
-# and viewed using, e.g., the VMD software. #
-# #
-#===========================================================================#
-
-units nano
-dimension 3
-boundary p p p
-atom_style hybrid molecular
-special_bonds fene
-read_data data.polymer
-
-#----------------------------------------------------------------------------
-# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
-# to ensure that the particles belonging to a given processor remain inside
-# that processors lattice-Boltzmann grid.
-#----------------------------------------------------------------------------
-neighbor 0.5 bin
-neigh_modify delay 0 every 1 check yes
-neigh_modify exclude type 2 2
-neigh_modify exclude type 2 1
-
-#----------------------------------------------------------------------------
-# Implement a hard-sphere interaction between the particles at the center of
-# each monomer (use a truncated and shifted Lennard-Jones potential).
-#----------------------------------------------------------------------------
-bond_style fene
-bond_coeff 1 60.0 2.25 4.14195 1.5
-pair_style lj/cut 1.68369
-pair_coeff 1 1 4.14195 1.5 1.68369
-pair_coeff 1 2 4.14195 1.5 1.68369
-pair_coeff 2 2 0 1.0
-
-mass * 0.000000771064
-timestep 0.00003
-
-#----------------------------------------------------------------------------
-# ForceAtoms are the particles at the center of each monomer which
-# do not interact with the fluid, but are used to implement the hard-sphere
-# interactions.
-# FluidAtoms are the particles representing the surface of the monomer
-# which do interact with the fluid. Monomer surface is shell of radius 0.7
-#----------------------------------------------------------------------------
-group ForceAtoms type 1
-group FluidAtoms type 2
-
-#---------------------------------------------------------------------------
-# Create a lattice-Boltzmann fluid covering the simulation domain.
-# This fluid feels a force due to the particles specified through FluidAtoms
-# (however, this fix does not explicity apply a force back on to these
-# particles. This is accomplished through the use of the lb/viscous
-# fix).
-# Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
-# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
-# dm=0.0000166368.
-# Use the default method to calculate the interaction force between the
-# particles and the fluid. This calculation requires the surface area
-# of the composite object represented by each particle node. By default
-# this area is assumed equal to dx*dx; however, since this is not the case
-# here, it is input through the setArea keyword (i.e. particles of type 2
-# correspond to a surface area of 0.2025=4 Pi R^2/N ).
-# Use the trilinear interpolation stencil to distribute the force from
-# a given particle onto the fluid mesh (results in a smaller hydrodynamic
-# radius than if the Peskin stencil is used).
-# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
-# seed=15003). This enables the particles to undergo Brownian motion in
-# the fluid.
-#----------------------------------------------------------------------------
-fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
-
-#----------------------------------------------------------------------------
-# Apply the force from the fluid to the particles, and integrate their
-# motion, constraining them to move and rotate together as a single rigid
-# spherical object.
-# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
-# shell) should move and rotate together, this fix is applied to all of
-# the atoms in the system. However, since the central atoms should not
-# feel a force due to the fluid, they are excluded from the fluid force
-# calculation.
-#----------------------------------------------------------------------------
-fix 2 FluidAtoms lb/viscous
-fix 3 all rigid molecule
-
-#----------------------------------------------------------------------------
-# To ensure that numerical errors do not lead to a buildup of momentum in the
-# system, the momentum_lb fix is used every 10000 timesteps to zero out the
-# total (particle plus fluid) momentum in the system.
-#----------------------------------------------------------------------------
-fix 4 all lb/momentum 10000 linear 1 1 1
-
-#----------------------------------------------------------------------------
-# Write position and velocity coordinates into a file every 2000 time steps.
-#----------------------------------------------------------------------------
-
-dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
-run 2000001
+#===========================================================================#
+# polymer test #
+# #
+# Run consists of a lone 32-bead coarse-grained polymer #
+# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
+# #
+# Here, gamma (used in the calculation of the monomer-fluid interaction #
+# force) is set by the user (gamma = 0.03 for this simulation...this #
+# value has been calibrated a priori through simulations of the drag #
+# force acting on a single particle of the same radius). #
+# Sample output from this run can be found in the file: #
+# 'dump.polymer.lammpstrj' #
+# and viewed using, e.g., the VMD software. #
+# #
+#===========================================================================#
+
+units nano
+dimension 3
+boundary p p p
+atom_style hybrid molecular
+special_bonds fene
+read_data data.polymer
+
+#----------------------------------------------------------------------------
+# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
+# to ensure that the particles belonging to a given processor remain inside
+# that processors lattice-Boltzmann grid.
+#----------------------------------------------------------------------------
+neighbor 0.5 bin
+neigh_modify delay 0 every 1 check yes
+neigh_modify exclude type 2 2
+neigh_modify exclude type 2 1
+
+#----------------------------------------------------------------------------
+# Implement a hard-sphere interaction between the particles at the center of
+# each monomer (use a truncated and shifted Lennard-Jones potential).
+#----------------------------------------------------------------------------
+bond_style fene
+bond_coeff 1 60.0 2.25 4.14195 1.5
+pair_style lj/cut 1.68369
+pair_coeff 1 1 4.14195 1.5 1.68369
+pair_coeff 1 2 4.14195 1.5 1.68369
+pair_coeff 2 2 0 1.0
+
+mass * 0.000000771064
+timestep 0.00003
+
+#----------------------------------------------------------------------------
+# ForceAtoms are the particles at the center of each monomer which
+# do not interact with the fluid, but are used to implement the hard-sphere
+# interactions.
+# FluidAtoms are the particles representing the surface of the monomer
+# which do interact with the fluid. Monomer surface is shell of radius 0.7
+#----------------------------------------------------------------------------
+group ForceAtoms type 1
+group FluidAtoms type 2
+
+#---------------------------------------------------------------------------
+# Create a lattice-Boltzmann fluid covering the simulation domain.
+# This fluid feels a force due to the particles specified through FluidAtoms
+# (however, this fix does not explicitly apply a force back on to these
+# particles. This is accomplished through the use of the lb/viscous
+# fix).
+# Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
+# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
+# dm=0.0000166368.
+# Use the default method to calculate the interaction force between the
+# particles and the fluid. This calculation requires the surface area
+# of the composite object represented by each particle node. By default
+# this area is assumed equal to dx*dx; however, since this is not the case
+# here, it is input through the setArea keyword (i.e. particles of type 2
+# correspond to a surface area of 0.2025=4 Pi R^2/N ).
+# Use the trilinear interpolation stencil to distribute the force from
+# a given particle onto the fluid mesh (results in a smaller hydrodynamic
+# radius than if the Peskin stencil is used).
+# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
+# seed=15003). This enables the particles to undergo Brownian motion in
+# the fluid.
+#----------------------------------------------------------------------------
+fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
+
+#----------------------------------------------------------------------------
+# Apply the force from the fluid to the particles, and integrate their
+# motion, constraining them to move and rotate together as a single rigid
+# spherical object.
+# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
+# shell) should move and rotate together, this fix is applied to all of
+# the atoms in the system. However, since the central atoms should not
+# feel a force due to the fluid, they are excluded from the fluid force
+# calculation.
+#----------------------------------------------------------------------------
+fix 2 FluidAtoms lb/viscous
+fix 3 all rigid molecule
+
+#----------------------------------------------------------------------------
+# To ensure that numerical errors do not lead to a buildup of momentum in the
+# system, the momentum_lb fix is used every 10000 timesteps to zero out the
+# total (particle plus fluid) momentum in the system.
+#----------------------------------------------------------------------------
+fix 4 all lb/momentum 10000 linear 1 1 1
+
+#----------------------------------------------------------------------------
+# Write position and velocity coordinates into a file every 2000 time steps.
+#----------------------------------------------------------------------------
+
+dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
+run 2000001
diff --git a/examples/USER/lb/polymer/in.polymer_setgamma b/examples/USER/lb/polymer/in.polymer_setgamma
index b5108a60fa2a9eca201d256746e4ffdbe5b2385a..75b8d67ada2c64d00e9af6003914ca02d090e9e5 100755
--- a/examples/USER/lb/polymer/in.polymer_setgamma
+++ b/examples/USER/lb/polymer/in.polymer_setgamma
@@ -1,105 +1,105 @@
-#===========================================================================#
-# polymer test #
-# #
-# Run consists of a lone 32-bead coarse-grained polymer #
-# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
-# #
-# Here, gamma (used in the calculation of the monomer-fluid interaction #
-# force) is set by the user (gamma = 0.03 for this simulation...this #
-# value has been calibrated a priori through simulations of the drag #
-# force acting on a single particle of the same radius). #
-# Sample output from this run can be found in the file: #
-# 'dump.polymer.lammpstrj' #
-# and viewed using, e.g., the VMD software. #
-# #
-# Santtu Ollila #
-# santtu.ollila@aalto.fi #
-# Aalto University #
-# August 14, 2013 #
-#===========================================================================#
-
-units nano
-dimension 3
-boundary p p p
-atom_style hybrid molecular
-special_bonds fene
-read_data data.polymer
-
-#----------------------------------------------------------------------------
-# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
-# to ensure that the particles belonging to a given processor remain inside
-# that processors lattice-Boltzmann grid.
-#----------------------------------------------------------------------------
-neighbor 0.5 bin
-neigh_modify delay 0 every 1 check yes
-neigh_modify exclude type 2 2
-neigh_modify exclude type 2 1
-
-#----------------------------------------------------------------------------
-# Implement a hard-sphere interaction between the particles at the center of
-# each monomer (use a truncated and shifted Lennard-Jones potential).
-#----------------------------------------------------------------------------
-bond_style fene
-bond_coeff 1 60.0 2.25 4.14195 1.5
-pair_style lj/cut 1.68369
-pair_coeff 1 1 4.14195 1.5 1.68369
-pair_coeff 1 2 4.14195 1.5 1.68369
-pair_coeff 2 2 0 1.0
-
-mass * 0.000000771064
-timestep 0.00003
-
-#----------------------------------------------------------------------------
-# ForceAtoms are the particles at the center of each monomer which
-# do not interact with the fluid, but are used to implement the hard-sphere
-# interactions.
-# FluidAtoms are the particles representing the surface of the monomer
-# which do interact with the fluid.
-#----------------------------------------------------------------------------
-group ForceAtoms type 1
-group FluidAtoms type 2
-
-#---------------------------------------------------------------------------
-# Create a lattice-Boltzmann fluid covering the simulation domain.
-# This fluid feels a force due to the particles specified through FluidAtoms
-# (however, this fix does not explicity apply a force back on to these
-# particles. This is accomplished through the use of the rigid_pc_sphere
-# fix).
-# Use the LB integration scheme of Ollila et. al. (for stability reasons,
-# this integration scheme should be used when a large user set value for
-# gamma is specified), a fluid viscosity = 0.023333333,
-# fluid density= 0.0000166368,
-# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
-# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
-# seed=15003). This enables the particles to undergo Brownian motion in
-# the fluid.
-#----------------------------------------------------------------------------
-fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
-
-#----------------------------------------------------------------------------
-# Apply the force from the fluid to the particles, and integrate their
-# motion, constraining them to move and rotate together as a single rigid
-# spherical object.
-# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
-# shell) should move and rotate together, this fix is applied to all of
-# the atoms in the system. However, since the central atoms should not
-# feel a force due to the fluid, they are excluded from the force
-# calculation through the use of the 'innerNodes' keyword.
-# NOTE: This fix should only be used when the user specifies a value for
-# gamma (through the setGamma keyword) in the lb_fluid fix.
-#----------------------------------------------------------------------------
-fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
-
-#----------------------------------------------------------------------------
-# To ensure that numerical errors do not lead to a buildup of momentum in the
-# system, the momentum_lb fix is used every 10000 timesteps to zero out the
-# total (particle plus fluid) momentum in the system.
-#----------------------------------------------------------------------------
-fix 3 all lb/momentum 10000 linear 1 1 1
-
-#----------------------------------------------------------------------------
-# Write position and velocity coordinates into a file every 2000 time steps.
-#----------------------------------------------------------------------------
-
-dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
-run 2000001
+#===========================================================================#
+# polymer test #
+# #
+# Run consists of a lone 32-bead coarse-grained polymer #
+# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
+# #
+# Here, gamma (used in the calculation of the monomer-fluid interaction #
+# force) is set by the user (gamma = 0.03 for this simulation...this #
+# value has been calibrated a priori through simulations of the drag #
+# force acting on a single particle of the same radius). #
+# Sample output from this run can be found in the file: #
+# 'dump.polymer.lammpstrj' #
+# and viewed using, e.g., the VMD software. #
+# #
+# Santtu Ollila #
+# santtu.ollila@aalto.fi #
+# Aalto University #
+# August 14, 2013 #
+#===========================================================================#
+
+units nano
+dimension 3
+boundary p p p
+atom_style hybrid molecular
+special_bonds fene
+read_data data.polymer
+
+#----------------------------------------------------------------------------
+# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
+# to ensure that the particles belonging to a given processor remain inside
+# that processors lattice-Boltzmann grid.
+#----------------------------------------------------------------------------
+neighbor 0.5 bin
+neigh_modify delay 0 every 1 check yes
+neigh_modify exclude type 2 2
+neigh_modify exclude type 2 1
+
+#----------------------------------------------------------------------------
+# Implement a hard-sphere interaction between the particles at the center of
+# each monomer (use a truncated and shifted Lennard-Jones potential).
+#----------------------------------------------------------------------------
+bond_style fene
+bond_coeff 1 60.0 2.25 4.14195 1.5
+pair_style lj/cut 1.68369
+pair_coeff 1 1 4.14195 1.5 1.68369
+pair_coeff 1 2 4.14195 1.5 1.68369
+pair_coeff 2 2 0 1.0
+
+mass * 0.000000771064
+timestep 0.00003
+
+#----------------------------------------------------------------------------
+# ForceAtoms are the particles at the center of each monomer which
+# do not interact with the fluid, but are used to implement the hard-sphere
+# interactions.
+# FluidAtoms are the particles representing the surface of the monomer
+# which do interact with the fluid.
+#----------------------------------------------------------------------------
+group ForceAtoms type 1
+group FluidAtoms type 2
+
+#---------------------------------------------------------------------------
+# Create a lattice-Boltzmann fluid covering the simulation domain.
+# This fluid feels a force due to the particles specified through FluidAtoms
+# (however, this fix does not explicitly apply a force back on to these
+# particles. This is accomplished through the use of the rigid_pc_sphere
+# fix).
+# Use the LB integration scheme of Ollila et. al. (for stability reasons,
+# this integration scheme should be used when a large user set value for
+# gamma is specified), a fluid viscosity = 0.023333333,
+# fluid density= 0.0000166368,
+# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
+# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
+# seed=15003). This enables the particles to undergo Brownian motion in
+# the fluid.
+#----------------------------------------------------------------------------
+fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
+
+#----------------------------------------------------------------------------
+# Apply the force from the fluid to the particles, and integrate their
+# motion, constraining them to move and rotate together as a single rigid
+# spherical object.
+# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
+# shell) should move and rotate together, this fix is applied to all of
+# the atoms in the system. However, since the central atoms should not
+# feel a force due to the fluid, they are excluded from the force
+# calculation through the use of the 'innerNodes' keyword.
+# NOTE: This fix should only be used when the user specifies a value for
+# gamma (through the setGamma keyword) in the lb_fluid fix.
+#----------------------------------------------------------------------------
+fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
+
+#----------------------------------------------------------------------------
+# To ensure that numerical errors do not lead to a buildup of momentum in the
+# system, the momentum_lb fix is used every 10000 timesteps to zero out the
+# total (particle plus fluid) momentum in the system.
+#----------------------------------------------------------------------------
+fix 3 all lb/momentum 10000 linear 1 1 1
+
+#----------------------------------------------------------------------------
+# Write position and velocity coordinates into a file every 2000 time steps.
+#----------------------------------------------------------------------------
+
+dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
+run 2000001
diff --git a/examples/USER/misc/agni/Al_jpc.agni b/examples/USER/misc/agni/Al_jpc.agni
new file mode 100644
index 0000000000000000000000000000000000000000..0a82a3c8f42549407f8a6d955c93d8842f7378fb
--- /dev/null
+++ b/examples/USER/misc/agni/Al_jpc.agni
@@ -0,0 +1,3020 @@
+# DATE: 2017-02-24 CONTRIBUTOR: Venkatesh Botu <botuvenkatesh@gmail.com> CITATION: Botu, V., Batra, R., Chapman, J., and Ramprasad, R., J. Phys. Chem. C, 121 (1), 511 (2017).
+# This potential is an updated version of Al_prb.agni, which is now deprecated.
+# This potential file is parameterized for metal units
+
+generation 1
+n_elements 1
+
+element Al
+
+interaction Al
+Rc 8.0
+Rs 0.0
+neighbors 500
+eta 0.0036 0.0357 0.0715 0.1251 0.2144 0.3573 0.7147 1.4294
+sigma 13.8949549437
+lambda 1e-08
+b 102.870264493
+n_train 3000
+endVar
+
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diff --git a/examples/USER/misc/agni/Al_prb.agni b/examples/USER/misc/agni/Al_prb.agni
deleted file mode 100644
index a191b222206b876546114b9bf88358eb50a14219..0000000000000000000000000000000000000000
--- a/examples/USER/misc/agni/Al_prb.agni
+++ /dev/null
@@ -1,1019 +0,0 @@
-# DATE: 2016-11-11 CONTRIBUTOR: Venkatesh Botu <botuvenkatesh@gmail.com> CITATION: Botu, V. and Ramprasad, R., Phys. Rev. B, 92, 094306 (2015)
-# This potential file is parameterized for metal units
-
-generation 1
-n_elements 1
-
-element Al
-
-interaction Al
-Rc 8.0
-Rs 0.0
-neighbors 500
-eta 0.0036 0.0357 0.0715 0.1251 0.2144 0.3573 0.7147 1.4294
-sigma 7.54312006335
-lambda 1e-08
-b -116.143708049
-n_train 1000
-endVar
-
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diff --git a/examples/USER/misc/agni/in.adatom b/examples/USER/misc/agni/in.adatom
index b39b104deb98632f0ad5baab27727abcdf274e93..45653e61043503536bd53c4908a1b35135dd6a03 100644
--- a/examples/USER/misc/agni/in.adatom
+++ b/examples/USER/misc/agni/in.adatom
@@ -5,7 +5,7 @@ boundary p p f
read_data adatom.data
pair_style agni
-pair_coeff * * Al_prb.agni Al
+pair_coeff * * Al_jpc.agni Al
neighbor 0.3 bin
neigh_modify delay 2 check yes
diff --git a/examples/USER/misc/agni/in.vacancy b/examples/USER/misc/agni/in.vacancy
index 94226b0e9a1c00c669b6773737872e0b417f8aba..4f6dd0fc8c8400aa28d9ca6bd0bbc5d94df44aa4 100644
--- a/examples/USER/misc/agni/in.vacancy
+++ b/examples/USER/misc/agni/in.vacancy
@@ -4,7 +4,7 @@ boundary p p p
read_data vacancy.data
pair_style agni
-pair_coeff * * Al_prb.agni Al
+pair_coeff * * Al_jpc.agni Al
neighbor 0.3 bin
neigh_modify delay 2 check yes
diff --git a/examples/USER/misc/agni/log.21Feb17.adatom.g++.1 b/examples/USER/misc/agni/log.21Feb17.adatom.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..5243b83ec9af953233c7ad50b17a1c98f1be4754
--- /dev/null
+++ b/examples/USER/misc/agni/log.21Feb17.adatom.g++.1
@@ -0,0 +1,87 @@
+LAMMPS (21 Feb 2017)
+ using 1 OpenMP thread(s) per MPI task
+
+processors * * 1
+units metal
+boundary p p f
+read_data adatom.data
+ orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 181 atoms
+
+pair_style agni
+pair_coeff * * Al_jpc.agni Al
+Reading potential file Al_jpc.agni with DATE: 2017-02-24
+
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+timestep 0.0005
+velocity all create 500 12345
+fix 1 all nvt temp 250 250 0.2
+fix 5 all momentum 1 linear 1 1 1
+
+thermo 100
+thermo_style custom step ke temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+ update every 1 steps, delay 2 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 8.3
+ ghost atom cutoff = 8.3
+ binsize = 4.15, bins = 5 4 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair agni, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Memory usage per processor = 2.69795 Mbytes
+Step KinEng Temp
+ 0 11.633413 500
+ 100 4.6059939 197.964
+ 200 7.3700149 316.76065
+ 300 6.0443913 259.78581
+ 400 6.1631189 264.88868
+ 500 6.2647272 269.25577
+ 600 5.2732539 226.6426
+ 700 5.6514471 242.89721
+ 800 6.5572407 281.8279
+ 900 6.0576738 260.35669
+ 1000 6.5622233 282.04205
+Loop time of 51.9308 on 1 procs for 1000 steps with 181 atoms
+
+Performance: 0.832 ns/day, 28.850 hours/ns, 19.256 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 51.89 | 51.89 | 51.89 | 0.0 | 99.92
+Neigh | 0.023158 | 0.023158 | 0.023158 | 0.0 | 0.04
+Comm | 0.0049036 | 0.0049036 | 0.0049036 | 0.0 | 0.01
+Output | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.00
+Modify | 0.010244 | 0.010244 | 0.010244 | 0.0 | 0.02
+Other | | 0.002483 | | | 0.00
+
+Nlocal: 181 ave 181 max 181 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 563 ave 563 max 563 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 19484 ave 19484 max 19484 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19484
+Ave neighs/atom = 107.646
+Neighbor list builds = 33
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:52
diff --git a/examples/USER/misc/agni/log.21Feb17.adatom.g++.4 b/examples/USER/misc/agni/log.21Feb17.adatom.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..9419888e989b659f5e3aa042a03f2f7801e381df
--- /dev/null
+++ b/examples/USER/misc/agni/log.21Feb17.adatom.g++.4
@@ -0,0 +1,87 @@
+LAMMPS (21 Feb 2017)
+ using 1 OpenMP thread(s) per MPI task
+
+processors * * 1
+units metal
+boundary p p f
+read_data adatom.data
+ orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
+ 2 by 2 by 1 MPI processor grid
+ reading atoms ...
+ 181 atoms
+
+pair_style agni
+pair_coeff * * Al_jpc.agni Al
+Reading potential file Al_jpc.agni with DATE: 2017-02-24
+
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+timestep 0.0005
+velocity all create 500 12345
+fix 1 all nvt temp 250 250 0.2
+fix 5 all momentum 1 linear 1 1 1
+
+thermo 100
+thermo_style custom step ke temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+ update every 1 steps, delay 2 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 8.3
+ ghost atom cutoff = 8.3
+ binsize = 4.15, bins = 5 4 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair agni, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Memory usage per processor = 3.06041 Mbytes
+Step KinEng Temp
+ 0 11.633413 500
+ 100 4.6059941 197.96401
+ 200 7.3700154 316.76067
+ 300 6.0443913 259.78581
+ 400 6.1631193 264.8887
+ 500 6.2647281 269.25581
+ 600 5.2732537 226.64259
+ 700 5.651448 242.89725
+ 800 6.5572405 281.82789
+ 900 6.0576741 260.3567
+ 1000 6.562224 282.04208
+Loop time of 14.5263 on 4 procs for 1000 steps with 181 atoms
+
+Performance: 2.974 ns/day, 8.070 hours/ns, 68.841 timesteps/s
+99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 12.858 | 13.227 | 13.574 | 8.0 | 91.06
+Neigh | 0.0056965 | 0.0058173 | 0.0060787 | 0.2 | 0.04
+Comm | 0.92934 | 1.276 | 1.6455 | 25.7 | 8.78
+Output | 0.00013971 | 0.00017625 | 0.00025463 | 0.0 | 0.00
+Modify | 0.012693 | 0.012756 | 0.012911 | 0.1 | 0.09
+Other | | 0.004066 | | | 0.03
+
+Nlocal: 45.25 ave 52 max 40 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Nghost: 376.5 ave 382 max 366 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 4871 ave 5578 max 4374 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 19484
+Ave neighs/atom = 107.646
+Neighbor list builds = 33
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:14
diff --git a/examples/USER/misc/agni/log.21Feb17.vacancy.g++.1 b/examples/USER/misc/agni/log.21Feb17.vacancy.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..9194d7841980134e9d16d9f7af8c7100a8d974c1
--- /dev/null
+++ b/examples/USER/misc/agni/log.21Feb17.vacancy.g++.1
@@ -0,0 +1,87 @@
+LAMMPS (21 Feb 2017)
+ using 1 OpenMP thread(s) per MPI task
+
+units metal
+boundary p p p
+read_data vacancy.data
+ orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 31 atoms
+
+pair_style agni
+pair_coeff * * Al_jpc.agni Al
+Reading potential file Al_jpc.agni with DATE: 2017-02-24
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+
+timestep 0.0005
+velocity all create 1000 12345
+fix 1 all nvt temp 900 900 200
+fix 5 all momentum 1 linear 1 1 1
+
+
+thermo 100
+thermo_style custom step ke etotal temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+ update every 1 steps, delay 2 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 8.3
+ ghost atom cutoff = 8.3
+ binsize = 4.15, bins = 2 2 2
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair agni, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Memory usage per processor = 2.73416 Mbytes
+Step KinEng TotEng Temp
+ 0 3.8778043 3.8778043 1000
+ 100 2.9986261 2.9986261 773.27937
+ 200 3.6860314 3.6860314 950.54599
+ 300 3.813315 3.813315 983.36961
+ 400 3.7330285 3.7330285 962.6655
+ 500 3.5875467 3.5875467 925.14896
+ 600 3.5331529 3.5331529 911.12202
+ 700 2.6509449 2.6509449 683.62008
+ 800 3.3763492 3.3763492 870.68582
+ 900 3.903673 3.903673 1006.6709
+ 1000 3.0884824 3.0884824 796.45133
+Loop time of 9.02712 on 1 procs for 1000 steps with 31 atoms
+
+Performance: 4.786 ns/day, 5.015 hours/ns, 110.777 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 9.0039 | 9.0039 | 9.0039 | 0.0 | 99.74
+Neigh | 0.011892 | 0.011892 | 0.011892 | 0.0 | 0.13
+Comm | 0.0061693 | 0.0061693 | 0.0061693 | 0.0 | 0.07
+Output | 0.00014615 | 0.00014615 | 0.00014615 | 0.0 | 0.00
+Modify | 0.0035009 | 0.0035009 | 0.0035009 | 0.0 | 0.04
+Other | | 0.001521 | | | 0.02
+
+Nlocal: 31 ave 31 max 31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 869 ave 869 max 869 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 4360 ave 4360 max 4360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4360
+Ave neighs/atom = 140.645
+Neighbor list builds = 53
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:09
diff --git a/examples/USER/misc/agni/log.21Feb17.vacancy.g++.4 b/examples/USER/misc/agni/log.21Feb17.vacancy.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..d5d8e3a4814229bdb02af5dc6a9a597e9fb4292f
--- /dev/null
+++ b/examples/USER/misc/agni/log.21Feb17.vacancy.g++.4
@@ -0,0 +1,87 @@
+LAMMPS (21 Feb 2017)
+ using 1 OpenMP thread(s) per MPI task
+
+units metal
+boundary p p p
+read_data vacancy.data
+ orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 31 atoms
+
+pair_style agni
+pair_coeff * * Al_jpc.agni Al
+Reading potential file Al_jpc.agni with DATE: 2017-02-24
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+
+timestep 0.0005
+velocity all create 1000 12345
+fix 1 all nvt temp 900 900 200
+fix 5 all momentum 1 linear 1 1 1
+
+
+thermo 100
+thermo_style custom step ke etotal temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+ update every 1 steps, delay 2 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 8.3
+ ghost atom cutoff = 8.3
+ binsize = 4.15, bins = 2 2 2
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair agni, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Memory usage per processor = 2.72175 Mbytes
+Step KinEng TotEng Temp
+ 0 3.8778044 3.8778044 1000
+ 100 2.9986263 2.9986263 773.27942
+ 200 3.6860315 3.6860315 950.54602
+ 300 3.8133145 3.8133145 983.3695
+ 400 3.7330282 3.7330282 962.66543
+ 500 3.5875466 3.5875466 925.14895
+ 600 3.5331523 3.5331523 911.12186
+ 700 2.6509448 2.6509448 683.62005
+ 800 3.3763493 3.3763493 870.68584
+ 900 3.9036733 3.9036733 1006.671
+ 1000 3.0884818 3.0884818 796.45116
+Loop time of 2.46785 on 4 procs for 1000 steps with 31 atoms
+
+Performance: 17.505 ns/day, 1.371 hours/ns, 405.212 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.0737 | 2.299 | 2.3902 | 8.7 | 93.16
+Neigh | 0.0025222 | 0.0027327 | 0.0028174 | 0.2 | 0.11
+Comm | 0.059817 | 0.15141 | 0.37684 | 33.8 | 6.14
+Output | 0.0001502 | 0.00016767 | 0.00021219 | 0.0 | 0.01
+Modify | 0.0098755 | 0.010248 | 0.010664 | 0.3 | 0.42
+Other | | 0.004321 | | | 0.18
+
+Nlocal: 7.75 ave 8 max 7 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost: 617.25 ave 621 max 612 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 1090 ave 1131 max 993 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+
+Total # of neighbors = 4360
+Ave neighs/atom = 140.645
+Neighbor list builds = 53
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/USER/misc/agni/log.9Nov16.adatom.g++.1 b/examples/USER/misc/agni/log.9Nov16.adatom.g++.1
deleted file mode 100644
index 1b39652b41e556a3ead8152d419e95fd195375a1..0000000000000000000000000000000000000000
--- a/examples/USER/misc/agni/log.9Nov16.adatom.g++.1
+++ /dev/null
@@ -1,82 +0,0 @@
-LAMMPS (9 Nov 2016)
- using 1 OpenMP thread(s) per MPI task
-
-processors * * 1
-units metal
-boundary p p f
-read_data adatom.data
- orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 181 atoms
-
-pair_style agni
-pair_coeff * * Al_prb.agni Al
-Reading potential file Al_prb.agni with DATE: 2016-11-11
-
-neighbor 0.3 bin
-neigh_modify delay 2 check yes
-
-timestep 0.0005
-velocity all create 500 12345
-fix 1 all nvt temp 250 250 0.2
-fix 5 all momentum 1 linear 1 1 1
-
-thermo 100
-thermo_style custom step ke temp
-
-# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
-
-run 1000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 2 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 8.3
- ghost atom cutoff = 8.3
- binsize = 4.15 -> bins = 5 4 10
-Memory usage per processor = 2.37049 Mbytes
-Step KinEng Temp
- 0 11.633413 500
- 100 4.049974 174.06646
- 200 5.8983472 253.50889
- 300 5.3667309 230.66021
- 400 4.9343935 212.0785
- 500 5.4054496 232.32432
- 600 6.1779127 265.52452
- 700 6.3749266 273.9921
- 800 6.0701481 260.89283
- 900 6.4582394 277.57286
- 1000 6.4047444 275.27366
-Loop time of 20.8273 on 1 procs for 1000 steps with 181 atoms
-
-Performance: 2.074 ns/day, 11.571 hours/ns, 48.014 timesteps/s
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 20.79 | 20.79 | 20.79 | 0.0 | 99.82
-Neigh | 0.022742 | 0.022742 | 0.022742 | 0.0 | 0.11
-Comm | 0.0040836 | 0.0040836 | 0.0040836 | 0.0 | 0.02
-Output | 0.00011086 | 0.00011086 | 0.00011086 | 0.0 | 0.00
-Modify | 0.0089345 | 0.0089345 | 0.0089345 | 0.0 | 0.04
-Other | | 0.001819 | | | 0.01
-
-Nlocal: 181 ave 181 max 181 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 562 ave 562 max 562 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 18810 ave 18810 max 18810 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 18810
-Ave neighs/atom = 103.923
-Neighbor list builds = 33
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:20
diff --git a/examples/USER/misc/agni/log.9Nov16.adatom.g++.4 b/examples/USER/misc/agni/log.9Nov16.adatom.g++.4
deleted file mode 100644
index 132e6468e2f6b44bd5720c64724fe09767f9d75c..0000000000000000000000000000000000000000
--- a/examples/USER/misc/agni/log.9Nov16.adatom.g++.4
+++ /dev/null
@@ -1,82 +0,0 @@
-LAMMPS (9 Nov 2016)
- using 1 OpenMP thread(s) per MPI task
-
-processors * * 1
-units metal
-boundary p p f
-read_data adatom.data
- orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
- 2 by 2 by 1 MPI processor grid
- reading atoms ...
- 181 atoms
-
-pair_style agni
-pair_coeff * * Al_prb.agni Al
-Reading potential file Al_prb.agni with DATE: 2016-11-11
-
-neighbor 0.3 bin
-neigh_modify delay 2 check yes
-
-timestep 0.0005
-velocity all create 500 12345
-fix 1 all nvt temp 250 250 0.2
-fix 5 all momentum 1 linear 1 1 1
-
-thermo 100
-thermo_style custom step ke temp
-
-# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
-
-run 1000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 2 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 8.3
- ghost atom cutoff = 8.3
- binsize = 4.15 -> bins = 5 4 10
-Memory usage per processor = 2.48695 Mbytes
-Step KinEng Temp
- 0 11.633413 500
- 100 4.049974 174.06646
- 200 5.8983472 253.50889
- 300 5.3667309 230.66021
- 400 4.9343935 212.0785
- 500 5.4054496 232.32432
- 600 6.1779127 265.52451
- 700 6.3749266 273.9921
- 800 6.0701481 260.89283
- 900 6.4582394 277.57286
- 1000 6.4047444 275.27366
-Loop time of 5.96868 on 4 procs for 1000 steps with 181 atoms
-
-Performance: 7.238 ns/day, 3.316 hours/ns, 167.541 timesteps/s
-99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 5.4176 | 5.4602 | 5.5505 | 2.3 | 91.48
-Neigh | 0.0056074 | 0.0060464 | 0.0062635 | 0.3 | 0.10
-Comm | 0.39544 | 0.48696 | 0.53111 | 7.9 | 8.16
-Output | 0.0001545 | 0.00015736 | 0.0001595 | 0.0 | 0.00
-Modify | 0.010492 | 0.011565 | 0.012588 | 0.9 | 0.19
-Other | | 0.003794 | | | 0.06
-
-Nlocal: 45.25 ave 47 max 42 min
-Histogram: 1 0 0 0 0 0 0 0 2 1
-Nghost: 374.75 ave 380 max 373 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs: 4702.5 ave 4868 max 4389 min
-Histogram: 1 0 0 0 0 0 0 1 1 1
-
-Total # of neighbors = 18810
-Ave neighs/atom = 103.923
-Neighbor list builds = 33
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:05
diff --git a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1 b/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
deleted file mode 100644
index 07912609ba860421f75ffd24d74e22cf4a39ab44..0000000000000000000000000000000000000000
--- a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
+++ /dev/null
@@ -1,82 +0,0 @@
-LAMMPS (9 Nov 2016)
- using 1 OpenMP thread(s) per MPI task
-
-units metal
-boundary p p p
-read_data vac.data
- orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 31 atoms
-
-pair_style agni
-pair_coeff * * Al_prb.agni Al
-Reading potential file Al_prb.agni with DATE: 2016-11-11
-neighbor 0.3 bin
-neigh_modify delay 2 check yes
-
-
-timestep 0.0005
-velocity all create 1000 12345
-fix 1 all nvt temp 900 900 200
-fix 5 all momentum 1 linear 1 1 1
-
-
-thermo 100
-thermo_style custom step ke etotal temp
-
-# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
-
-run 1000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 2 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 8.3
- ghost atom cutoff = 8.3
- binsize = 4.15 -> bins = 2 2 2
-Memory usage per processor = 2.40842 Mbytes
-Step KinEng TotEng Temp
- 0 3.8778043 3.8778043 1000
- 100 2.8126642 2.8126642 725.32391
- 200 3.7110413 3.7110413 956.9955
- 300 3.2361084 3.2361084 834.52081
- 400 3.4625769 3.4625769 892.92201
- 500 3.4563307 3.4563307 891.31126
- 600 2.8486344 2.8486344 734.59982
- 700 3.1183057 3.1183057 804.14208
- 800 2.9164818 2.9164818 752.09618
- 900 3.464416 3.464416 893.39629
- 1000 3.5954546 3.5954546 927.18825
-Loop time of 3.86777 on 1 procs for 1000 steps with 31 atoms
-
-Performance: 11.169 ns/day, 2.149 hours/ns, 258.547 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 3.8463 | 3.8463 | 3.8463 | 0.0 | 99.44
-Neigh | 0.011294 | 0.011294 | 0.011294 | 0.0 | 0.29
-Comm | 0.0057271 | 0.0057271 | 0.0057271 | 0.0 | 0.15
-Output | 0.00014257 | 0.00014257 | 0.00014257 | 0.0 | 0.00
-Modify | 0.0029459 | 0.0029459 | 0.0029459 | 0.0 | 0.08
-Other | | 0.001395 | | | 0.04
-
-Nlocal: 31 ave 31 max 31 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 878 ave 878 max 878 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 4334 ave 4334 max 4334 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 4334
-Ave neighs/atom = 139.806
-Neighbor list builds = 51
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4 b/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
deleted file mode 100644
index 82bd4467bc738aa1586b7e577056856847711e5d..0000000000000000000000000000000000000000
--- a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
+++ /dev/null
@@ -1,82 +0,0 @@
-LAMMPS (9 Nov 2016)
- using 1 OpenMP thread(s) per MPI task
-
-units metal
-boundary p p p
-read_data vac.data
- orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 31 atoms
-
-pair_style agni
-pair_coeff * * Al_prb.agni Al
-Reading potential file Al_prb.agni with DATE: 2016-11-11
-neighbor 0.3 bin
-neigh_modify delay 2 check yes
-
-
-timestep 0.0005
-velocity all create 1000 12345
-fix 1 all nvt temp 900 900 200
-fix 5 all momentum 1 linear 1 1 1
-
-
-thermo 100
-thermo_style custom step ke etotal temp
-
-# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
-
-run 1000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 2 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 8.3
- ghost atom cutoff = 8.3
- binsize = 4.15 -> bins = 2 2 2
-Memory usage per processor = 2.3974 Mbytes
-Step KinEng TotEng Temp
- 0 3.8778044 3.8778044 1000
- 100 2.8126642 2.8126642 725.32391
- 200 3.7110413 3.7110413 956.99549
- 300 3.2361084 3.2361084 834.52081
- 400 3.4625769 3.4625769 892.92201
- 500 3.4563307 3.4563307 891.31126
- 600 2.8486343 2.8486343 734.59981
- 700 3.1183057 3.1183057 804.14208
- 800 2.9164819 2.9164819 752.09618
- 900 3.4644161 3.4644161 893.39631
- 1000 3.5954546 3.5954546 927.18824
-Loop time of 1.11007 on 4 procs for 1000 steps with 31 atoms
-
-Performance: 38.916 ns/day, 0.617 hours/ns, 900.843 timesteps/s
-99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.906 | 0.99469 | 1.0291 | 5.1 | 89.61
-Neigh | 0.0026186 | 0.0027665 | 0.0028622 | 0.2 | 0.25
-Comm | 0.066125 | 0.10079 | 0.1896 | 16.2 | 9.08
-Output | 0.00012875 | 0.00014615 | 0.00018787 | 0.2 | 0.01
-Modify | 0.0080338 | 0.0083079 | 0.00861 | 0.2 | 0.75
-Other | | 0.003372 | | | 0.30
-
-Nlocal: 7.75 ave 8 max 7 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Nghost: 623.5 ave 630 max 616 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs: 1083.5 ave 1131 max 988 min
-Histogram: 1 0 0 0 0 0 0 1 1 1
-
-Total # of neighbors = 4334
-Ave neighs/atom = 139.806
-Neighbor list builds = 51
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01
diff --git a/examples/USER/misc/gauss-diel/in.gauss-diel b/examples/USER/misc/gauss-diel/in.gauss-diel
index 3e2be5b4d62b2a797eda2bfdbe38a122ab2d8eb0..5aa7ae71574dad8413de9e54e771afa791284e82 100644
--- a/examples/USER/misc/gauss-diel/in.gauss-diel
+++ b/examples/USER/misc/gauss-diel/in.gauss-diel
@@ -81,7 +81,7 @@ group sds subtract all cions
velocity all create 1. 87287 dist gaussian
neighbor 1.5 multi
-neigh_modify exclude molecule sds
+neigh_modify exclude molecule/intra sds
neigh_modify every 5 delay 0 check yes
fix 1 all nve/limit 0.2
diff --git a/examples/USER/misc/gauss-diel/in.gauss-diel-cg b/examples/USER/misc/gauss-diel/in.gauss-diel-cg
index ed2101622084e39915b8d50ec81567048a3cfc4f..51032c3d3226b7fa755593e159eedca8e610b259 100644
--- a/examples/USER/misc/gauss-diel/in.gauss-diel-cg
+++ b/examples/USER/misc/gauss-diel/in.gauss-diel-cg
@@ -81,7 +81,7 @@ group sds subtract all cions
velocity all create 1. 87287 dist gaussian
neighbor 1.5 multi
-neigh_modify exclude molecule sds
+neigh_modify exclude molecule/intra sds
neigh_modify every 5 delay 0 check yes
fix 1 all nve/limit 0.2
diff --git a/examples/USER/misc/gauss-diel/in.gauss-diel-split b/examples/USER/misc/gauss-diel/in.gauss-diel-split
index f13859863b8d6c59e445ab1cf20e526b16f6718d..b6a17371d1fe9e74ac8cdb2ff61cdeb7feeeb8c8 100644
--- a/examples/USER/misc/gauss-diel/in.gauss-diel-split
+++ b/examples/USER/misc/gauss-diel/in.gauss-diel-split
@@ -84,7 +84,7 @@ group sds subtract all cions
velocity all create 1. 87287 dist gaussian
neighbor 1.5 multi
-neigh_modify exclude molecule sds
+neigh_modify exclude molecule/intra sds
neigh_modify every 5 delay 0 check yes
fix 1 all nve/limit 0.2
diff --git a/examples/USER/misc/kolmogorov-crespi/data.bilayer-graphene b/examples/USER/misc/kolmogorov-crespi/data.bilayer-graphene
new file mode 100644
index 0000000000000000000000000000000000000000..6c6ad3cb7cfe92179dd8ca009b95545816351f79
--- /dev/null
+++ b/examples/USER/misc/kolmogorov-crespi/data.bilayer-graphene
@@ -0,0 +1,266 @@
+info: xyz2data 18:31, Mon 27-02-2017
+256 atoms
+2 atom types
+
+ 0.00000000 17.04000000 xlo xhi
+ 0.00000000 19.67609717 ylo yhi
+ -20.00000000 40.00000000 zlo zhi
+
+Atoms
+
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diff --git a/examples/USER/misc/kolmogorov-crespi/data.graphene-adsorbant b/examples/USER/misc/kolmogorov-crespi/data.graphene-adsorbant
new file mode 100644
index 0000000000000000000000000000000000000000..35cd7c91f354335e4f0813606a36571b52e0d230
--- /dev/null
+++ b/examples/USER/misc/kolmogorov-crespi/data.graphene-adsorbant
@@ -0,0 +1,139 @@
+info: xyz2data 11:52, Tue 28-02-2017
+129 atoms
+2 atom types
+
+ 0.00000000 17.04000000 xlo xhi
+ 0.00000000 19.67609717 ylo yhi
+ -10.00000000 40.00000000 zlo zhi
+
+Atoms
+
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+ 25 1 0.00000000 14.75707288 0.00000000
+ 26 1 1.42000000 14.75707288 0.00000000
+ 27 1 2.13000000 15.98682895 0.00000000
+ 28 1 3.55000000 15.98682895 0.00000000
+ 29 1 0.00000000 17.21658503 0.00000000
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+ 31 1 2.13000000 18.44634110 0.00000000
+ 32 1 3.55000000 18.44634110 0.00000000
+ 33 1 4.26000000 0.00000000 0.00000000
+ 34 1 5.68000000 0.00000000 0.00000000
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+ 36 1 7.81000000 1.22975607 0.00000000
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+ 38 1 5.68000000 2.45951215 0.00000000
+ 39 1 6.39000000 3.68926822 0.00000000
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+ 42 1 5.68000000 4.91902429 0.00000000
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+ 46 1 5.68000000 7.37853644 0.00000000
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+ 48 1 7.81000000 8.60829251 0.00000000
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+ 51 1 6.39000000 11.06780466 0.00000000
+ 52 1 7.81000000 11.06780466 0.00000000
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+ 57 1 4.26000000 14.75707288 0.00000000
+ 58 1 5.68000000 14.75707288 0.00000000
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+ 60 1 7.81000000 15.98682895 0.00000000
+ 61 1 4.26000000 17.21658503 0.00000000
+ 62 1 5.68000000 17.21658503 0.00000000
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+ 64 1 7.81000000 18.44634110 0.00000000
+ 65 1 8.52000000 0.00000000 0.00000000
+ 66 1 9.94000000 0.00000000 0.00000000
+ 67 1 10.65000000 1.22975607 0.00000000
+ 68 1 12.07000000 1.22975607 0.00000000
+ 69 1 8.52000000 2.45951215 0.00000000
+ 70 1 9.94000000 2.45951215 0.00000000
+ 71 1 10.65000000 3.68926822 0.00000000
+ 72 1 12.07000000 3.68926822 0.00000000
+ 73 1 8.52000000 4.91902429 0.00000000
+ 74 1 9.94000000 4.91902429 0.00000000
+ 75 1 10.65000000 6.14878037 0.00000000
+ 76 1 12.07000000 6.14878037 0.00000000
+ 77 1 8.52000000 7.37853644 0.00000000
+ 78 1 9.94000000 7.37853644 0.00000000
+ 79 1 10.65000000 8.60829251 0.00000000
+ 80 1 12.07000000 8.60829251 0.00000000
+ 81 1 8.52000000 9.83804859 0.00000000
+ 82 1 9.94000000 9.83804859 0.00000000
+ 83 1 10.65000000 11.06780466 0.00000000
+ 84 1 12.07000000 11.06780466 0.00000000
+ 85 1 8.52000000 12.29756073 0.00000000
+ 86 1 9.94000000 12.29756073 0.00000000
+ 87 1 10.65000000 13.52731681 0.00000000
+ 88 1 12.07000000 13.52731681 0.00000000
+ 89 1 8.52000000 14.75707288 0.00000000
+ 90 1 9.94000000 14.75707288 0.00000000
+ 91 1 10.65000000 15.98682895 0.00000000
+ 92 1 12.07000000 15.98682895 0.00000000
+ 93 1 8.52000000 17.21658503 0.00000000
+ 94 1 9.94000000 17.21658503 0.00000000
+ 95 1 10.65000000 18.44634110 0.00000000
+ 96 1 12.07000000 18.44634110 0.00000000
+ 97 1 12.78000000 0.00000000 0.00000000
+ 98 1 14.20000000 0.00000000 0.00000000
+ 99 1 14.91000000 1.22975607 0.00000000
+100 1 16.33000000 1.22975607 0.00000000
+101 1 12.78000000 2.45951215 0.00000000
+102 1 14.20000000 2.45951215 0.00000000
+103 1 14.91000000 3.68926822 0.00000000
+104 1 16.33000000 3.68926822 0.00000000
+105 1 12.78000000 4.91902429 0.00000000
+106 1 14.20000000 4.91902429 0.00000000
+107 1 14.91000000 6.14878037 0.00000000
+108 1 16.33000000 6.14878037 0.00000000
+109 1 12.78000000 7.37853644 0.00000000
+110 1 14.20000000 7.37853644 0.00000000
+111 1 14.91000000 8.60829251 0.00000000
+112 1 16.33000000 8.60829251 0.00000000
+113 1 12.78000000 9.83804859 0.00000000
+114 1 14.20000000 9.83804859 0.00000000
+115 1 14.91000000 11.06780466 0.00000000
+116 1 16.33000000 11.06780466 0.00000000
+117 1 12.78000000 12.29756073 0.00000000
+118 1 14.20000000 12.29756073 0.00000000
+119 1 14.91000000 13.52731681 0.00000000
+120 1 16.33000000 13.52731681 0.00000000
+121 1 12.78000000 14.75707288 0.00000000
+122 1 14.20000000 14.75707288 0.00000000
+123 1 14.91000000 15.98682895 0.00000000
+124 1 16.33000000 15.98682895 0.00000000
+125 1 12.78000000 17.21658503 0.00000000
+126 1 14.20000000 17.21658503 0.00000000
+127 1 14.91000000 18.44634110 0.00000000
+128 1 16.33000000 18.44634110 0.00000000
+129 2 10.00000000 10.00000000 3.30000000
diff --git a/examples/USER/misc/kolmogorov-crespi/in.atom-diffusion b/examples/USER/misc/kolmogorov-crespi/in.atom-diffusion
new file mode 100644
index 0000000000000000000000000000000000000000..5e3135a8b418c18ee0ec37a61f58d39f436659e0
--- /dev/null
+++ b/examples/USER/misc/kolmogorov-crespi/in.atom-diffusion
@@ -0,0 +1,45 @@
+# Initialization
+units metal
+boundary p p p
+atom_style atomic
+processors * * 1 # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data data.graphene-adsorbant # read lammps data file
+mass 1 12.0107 # carbon mass (g/mole) | membrane
+mass 2 12.0107 # carbon mass (g/mole) | adsorbate
+# Neighbor update settings
+neighbor 2.0 bin
+neigh_modify every 1
+neigh_modify delay 0
+neigh_modify check yes
+# Separate atom groups
+group membrane type 1
+group adsorbant type 2
+
+######################## Potential defition ########################
+pair_style hybrid/overlay kolmogorov/crespi/z 14.0
+####################################################################
+pair_coeff * * none
+pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
+####################################################################
+
+#### Simulation settings ####
+timestep 0.0001
+fix thermostat adsorbant nve
+fix rigid_membrane membrane setforce 0 0 0
+compute COM1 membrane com
+compute COM2 adsorbant com
+############################
+
+# Output
+#dump 1 all xyz 100 trajec.xyz
+#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
+thermo 100
+thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
+thermo_modify line one format float %14.8f
+
+###### Run molecular dynamics ######
+run 10000
diff --git a/examples/USER/misc/kolmogorov-crespi/in.bilayer-graphene b/examples/USER/misc/kolmogorov-crespi/in.bilayer-graphene
new file mode 100644
index 0000000000000000000000000000000000000000..3d63fc09ed0683976fdf9391d68c51ef1e136488
--- /dev/null
+++ b/examples/USER/misc/kolmogorov-crespi/in.bilayer-graphene
@@ -0,0 +1,45 @@
+# Initialization
+units metal
+boundary p p p
+atom_style atomic
+processors * * 1 # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data data.bilayer-graphene # read lammps data file
+mass 1 12.0107 # carbon mass (g/mole) | membrane
+mass 2 12.0107 # carbon mass (g/mole) | adsorbate
+# Neighbor update settings
+neighbor 2.0 bin
+neigh_modify every 1
+neigh_modify delay 0
+neigh_modify check yes
+# Separate atom groups
+group membrane type 1
+group adsorbant type 2
+
+######################## Potential defition ########################
+pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
+####################################################################
+pair_coeff * * rebo CH.airebo C C # chemical
+pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
+####################################################################
+
+#### Simulation settings ####
+timestep 0.0001
+velocity all create 300.0 12345
+fix thermostat all nve
+compute COM1 membrane com
+compute COM2 adsorbant com
+############################
+
+# Output
+#dump 1 all xyz 100 trajec.xyz
+#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
+thermo 10
+thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
+thermo_modify line one format float %14.8f
+
+###### Run molecular dynamics ######
+run 1000
diff --git a/examples/USER/misc/kolmogorov-crespi/log.atom-diffusion b/examples/USER/misc/kolmogorov-crespi/log.atom-diffusion
new file mode 100644
index 0000000000000000000000000000000000000000..5ed654221788e3dd5927a325df0e874f19f8fa47
--- /dev/null
+++ b/examples/USER/misc/kolmogorov-crespi/log.atom-diffusion
@@ -0,0 +1,189 @@
+LAMMPS (17 Nov 2016)
+# Initialization
+units metal
+boundary p p p
+atom_style atomic
+processors * * 1 # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data data.graphene-adsorbant # read lammps data file
+ orthogonal box = (0 0 -10) to (17.04 19.6761 40)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 129 atoms
+mass 1 12.0107 # carbon mass (g/mole) | membrane
+mass 2 12.0107 # carbon mass (g/mole) | adsorbate
+# Neighbor update settings
+neighbor 2.0 bin
+neigh_modify every 1
+neigh_modify delay 0
+neigh_modify check yes
+# Separate atom groups
+group membrane type 1
+128 atoms in group membrane
+group adsorbant type 2
+1 atoms in group adsorbant
+
+######################## Potential defition ########################
+pair_style hybrid/overlay kolmogorov/crespi/z 14.0
+####################################################################
+pair_coeff * * none
+pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
+####################################################################
+
+#### Simulation settings ####
+timestep 0.0001
+fix thermostat adsorbant nve
+fix rigid_membrane membrane setforce 0 0 0
+compute COM1 membrane com
+compute COM2 adsorbant com
+############################
+
+# Output
+#dump 1 all xyz 100 trajec.xyz
+#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
+thermo 100
+thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
+thermo_modify line one format float %14.8f
+
+###### Run molecular dynamics ######
+run 10000
+Neighbor list info ...
+ 2 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 16
+ ghost atom cutoff = 16
+ binsize = 8 -> bins = 3 3 7
+Memory usage per processor = 2.48399 Mbytes
+Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
+ 0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
+ 100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
+ 200 0.02000000 -0.02562011 -0.02650010 0.05318658 0.00000000 3.31198892
+ 300 0.03000000 -0.02562011 -0.02748822 0.11290898 0.00000000 3.32658305
+ 400 0.04000000 -0.02562011 -0.02868854 0.18545625 0.00000000 3.34632324
+ 500 0.05000000 -0.02562011 -0.02996656 0.26269978 0.00000000 3.37059992
+ 600 0.06000000 -0.02562011 -0.03120006 0.33725276 0.00000000 3.39872815
+ 700 0.07000000 -0.02562011 -0.03229421 0.40338328 0.00000000 3.42999603
+ 800 0.08000000 -0.02562011 -0.03318758 0.45737874 0.00000000 3.46370507
+ 900 0.09000000 -0.02562011 -0.03385069 0.49745690 0.00000000 3.49919977
+ 1000 0.10000000 -0.02562011 -0.03428002 0.52340564 0.00000000 3.53588638
+ 1100 0.11000000 -0.02562011 -0.03449041 0.53612164 0.00000000 3.57324216
+ 1200 0.12000000 -0.02562011 -0.03450775 0.53717016 0.00000000 3.61081749
+ 1300 0.13000000 -0.02562011 -0.03436312 0.52842859 0.00000000 3.64823296
+ 1400 0.14000000 -0.02562011 -0.03408851 0.51183115 0.00000000 3.68517357
+ 1500 0.15000000 -0.02562011 -0.03371417 0.48920613 0.00000000 3.72138134
+ 1600 0.16000000 -0.02562011 -0.03326714 0.46218758 0.00000000 3.75664759
+ 1700 0.17000000 -0.02562011 -0.03277063 0.43217815 0.00000000 3.79080541
+ 1800 0.18000000 -0.02562011 -0.03224395 0.40034589 0.00000000 3.82372274
+ 1900 0.19000000 -0.02562011 -0.03170282 0.36763982 0.00000000 3.85529629
+ 2000 0.20000000 -0.02562011 -0.03115972 0.33481494 0.00000000 3.88544626
+ 2100 0.21000000 -0.02562011 -0.03062440 0.30246010 0.00000000 3.91411185
+ 2200 0.22000000 -0.02562011 -0.03010433 0.27102702 0.00000000 3.94124749
+ 2300 0.23000000 -0.02562011 -0.02960514 0.24085558 0.00000000 3.96681976
+ 2400 0.24000000 -0.02562011 -0.02913096 0.21219623 0.00000000 3.99080483
+ 2500 0.25000000 -0.02562011 -0.02868478 0.18522907 0.00000000 4.01318637
+ 2600 0.26000000 -0.02562011 -0.02826867 0.16007955 0.00000000 4.03395384
+ 2700 0.27000000 -0.02562011 -0.02788403 0.13683143 0.00000000 4.05310113
+ 2800 0.28000000 -0.02562011 -0.02753171 0.11553708 0.00000000 4.07062542
+ 2900 0.29000000 -0.02562011 -0.02721220 0.09622581 0.00000000 4.08652629
+ 3000 0.30000000 -0.02562011 -0.02692571 0.07891041 0.00000000 4.10080498
+ 3100 0.31000000 -0.02562011 -0.02667226 0.06359229 0.00000000 4.11346382
+ 3200 0.32000000 -0.02562011 -0.02645177 0.05026555 0.00000000 4.12450573
+ 3300 0.33000000 -0.02562011 -0.02626406 0.03892009 0.00000000 4.13393390
+ 3400 0.34000000 -0.02562011 -0.02610893 0.02954399 0.00000000 4.14175142
+ 3500 0.35000000 -0.02562011 -0.02598618 0.02212545 0.00000000 4.14796110
+ 3600 0.36000000 -0.02562011 -0.02589566 0.01665409 0.00000000 4.15256529
+ 3700 0.37000000 -0.02562011 -0.02583722 0.01312208 0.00000000 4.15556569
+ 3800 0.38000000 -0.02562011 -0.02581079 0.01152492 0.00000000 4.15696329
+ 3900 0.39000000 -0.02562011 -0.02581636 0.01186148 0.00000000 4.15675830
+ 4000 0.40000000 -0.02562011 -0.02585398 0.01413478 0.00000000 4.15495012
+ 4100 0.41000000 -0.02562011 -0.02592375 0.01835185 0.00000000 4.15153731
+ 4200 0.42000000 -0.02562011 -0.02602587 0.02452390 0.00000000 4.14651764
+ 4300 0.43000000 -0.02562011 -0.02616057 0.03266513 0.00000000 4.13988811
+ 4400 0.44000000 -0.02562011 -0.02632813 0.04279292 0.00000000 4.13164506
+ 4500 0.45000000 -0.02562011 -0.02652889 0.05492664 0.00000000 4.12178432
+ 4600 0.46000000 -0.02562011 -0.02676317 0.06908643 0.00000000 4.11030130
+ 4700 0.47000000 -0.02562011 -0.02703129 0.08529164 0.00000000 4.09719124
+ 4800 0.48000000 -0.02562011 -0.02733352 0.10355859 0.00000000 4.08244950
+ 4900 0.49000000 -0.02562011 -0.02767004 0.12389788 0.00000000 4.06607186
+ 5000 0.50000000 -0.02562011 -0.02804086 0.14631034 0.00000000 4.04805502
+ 5100 0.51000000 -0.02562011 -0.02844575 0.17078211 0.00000000 4.02839708
+ 5200 0.52000000 -0.02562011 -0.02888415 0.19727899 0.00000000 4.00709829
+ 5300 0.53000000 -0.02562011 -0.02935502 0.22573844 0.00000000 3.98416189
+ 5400 0.54000000 -0.02562011 -0.02985670 0.25605986 0.00000000 3.95959511
+ 5500 0.55000000 -0.02562011 -0.03038669 0.28809268 0.00000000 3.93341053
+ 5600 0.56000000 -0.02562011 -0.03094143 0.32162137 0.00000000 3.90562766
+ 5700 0.57000000 -0.02562011 -0.03151597 0.35634628 0.00000000 3.87627492
+ 5800 0.58000000 -0.02562011 -0.03210361 0.39186361 0.00000000 3.84539210
+ 5900 0.59000000 -0.02562011 -0.03269556 0.42764084 0.00000000 3.81303330
+ 6000 0.60000000 -0.02562011 -0.03328042 0.46299030 0.00000000 3.77927044
+ 6100 0.61000000 -0.02562011 -0.03384380 0.49704060 0.00000000 3.74419758
+ 6200 0.62000000 -0.02562011 -0.03436783 0.52871353 0.00000000 3.70793588
+ 6300 0.63000000 -0.02562011 -0.03483104 0.55670974 0.00000000 3.67063945
+ 6400 0.64000000 -0.02562011 -0.03520832 0.57951248 0.00000000 3.63250187
+ 6500 0.65000000 -0.02562011 -0.03547159 0.59542438 0.00000000 3.59376331
+ 6600 0.66000000 -0.02562011 -0.03559125 0.60265655 0.00000000 3.55471782
+ 6700 0.67000000 -0.02562011 -0.03553879 0.59948637 0.00000000 3.51572023
+ 6800 0.68000000 -0.02562011 -0.03529110 0.58451568 0.00000000 3.47719153
+ 6900 0.69000000 -0.02562011 -0.03483635 0.55703035 0.00000000 3.43962129
+ 7000 0.70000000 -0.02562011 -0.03418150 0.51745146 0.00000000 3.40356509
+ 7100 0.71000000 -0.02562011 -0.03336032 0.46781889 0.00000000 3.36963482
+ 7200 0.72000000 -0.02562011 -0.03243997 0.41219328 0.00000000 3.33847933
+ 7300 0.73000000 -0.02562011 -0.03152342 0.35679665 0.00000000 3.31075400
+ 7400 0.74000000 -0.02562011 -0.03074422 0.30970201 0.00000000 3.28707906
+ 7500 0.75000000 -0.02562011 -0.03025182 0.27994115 0.00000000 3.26798907
+ 7600 0.76000000 -0.02562011 -0.03018799 0.27608346 0.00000000 3.25387900
+ 7700 0.77000000 -0.02562011 -0.03065928 0.30456818 0.00000000 3.24495492
+ 7800 0.78000000 -0.02562011 -0.03171321 0.36826788 0.00000000 3.24119821
+ 7900 0.79000000 -0.02562011 -0.03332635 0.46576624 0.00000000 3.24235091
+ 8000 0.80000000 -0.02562011 -0.03540847 0.59160963 0.00000000 3.24792582
+ 8100 0.81000000 -0.02562011 -0.03782107 0.73742737 0.00000000 3.25723999
+ 8200 0.82000000 -0.02562011 -0.04040358 0.89351498 0.00000000 3.26946524
+ 8300 0.83000000 -0.02562011 -0.04299943 1.05040805 0.00000000 3.28368734
+ 8400 0.84000000 -0.02562011 -0.04547588 1.20008497 0.00000000 3.29896495
+ 8500 0.85000000 -0.02562011 -0.04773539 1.33664998 0.00000000 3.31438148
+ 8600 0.86000000 -0.02562011 -0.04971913 1.45654768 0.00000000 3.32908572
+ 8700 0.87000000 -0.02562011 -0.05140498 1.55844058 0.00000000 3.34231951
+ 8800 0.88000000 -0.02562011 -0.05280154 1.64284923 0.00000000 3.35343297
+ 8900 0.89000000 -0.02562011 -0.05394019 1.71166905 0.00000000 3.36188901
+ 9000 0.90000000 -0.02562011 -0.05486563 1.76760281 0.00000000 3.36725955
+ 9100 0.91000000 -0.02562011 -0.05562624 1.81357448 0.00000000 3.36921674
+ 9200 0.92000000 -0.02562011 -0.05626439 1.85214388 0.00000000 3.36752214
+ 9300 0.93000000 -0.02562011 -0.05680723 1.88495335 0.00000000 3.36201704
+ 9400 0.94000000 -0.02562011 -0.05725852 1.91222952 0.00000000 3.35261669
+ 9500 0.95000000 -0.02562011 -0.05759110 1.93233038 0.00000000 3.33931122
+ 9600 0.96000000 -0.02562011 -0.05774152 1.94142215 0.00000000 3.32217490
+ 9700 0.97000000 -0.02562011 -0.05760814 1.93336063 0.00000000 3.30138553
+ 9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
+ 9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
+ 10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
+Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
+
+Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
+131.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
+Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
+Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
+Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
+Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
+Other | | 0.01361 | | | 3.56
+
+Nlocal: 129 ave 129 max 129 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1867 ave 1867 max 1867 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 290 ave 290 max 290 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 290
+Ave neighs/atom = 2.24806
+Neighbor list builds = 1
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/misc/kolmogorov-crespi/log.bilayer-graphene b/examples/USER/misc/kolmogorov-crespi/log.bilayer-graphene
new file mode 100644
index 0000000000000000000000000000000000000000..3a5f1236339fb8be9978dd3391d57df776cb9e2b
--- /dev/null
+++ b/examples/USER/misc/kolmogorov-crespi/log.bilayer-graphene
@@ -0,0 +1,192 @@
+LAMMPS (17 Nov 2016)
+# Initialization
+units metal
+boundary p p p
+atom_style atomic
+processors * * 1 # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data data.bilayer-graphene # read lammps data file
+ orthogonal box = (0 0 -20) to (17.04 19.6761 40)
+ 2 by 2 by 1 MPI processor grid
+ reading atoms ...
+ 256 atoms
+mass 1 12.0107 # carbon mass (g/mole) | membrane
+mass 2 12.0107 # carbon mass (g/mole) | adsorbate
+# Neighbor update settings
+neighbor 2.0 bin
+neigh_modify every 1
+neigh_modify delay 0
+neigh_modify check yes
+# Separate atom groups
+group membrane type 1
+128 atoms in group membrane
+group adsorbant type 2
+128 atoms in group adsorbant
+
+######################## Potential defition ########################
+pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
+####################################################################
+pair_coeff * * rebo CH.airebo C C # chemical
+Reading potential file CH.airebo with DATE: 2011-10-25
+pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
+####################################################################
+
+#### Simulation settings ####
+timestep 0.0001
+velocity all create 300.0 12345
+fix thermostat all nve
+compute COM1 membrane com
+compute COM2 adsorbant com
+############################
+
+# Output
+#dump 1 all xyz 100 trajec.xyz
+#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
+thermo 10
+thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
+thermo_modify line one format float %14.8f
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+ 3 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 16
+ ghost atom cutoff = 16
+ binsize = 8 -> bins = 3 3 8
+Memory usage per processor = 3.22197 Mbytes
+Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
+ 0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
+ 10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
+ 20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357
+ 30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673
+ 40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055
+ 50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486
+ 60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952
+ 70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441
+ 80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946
+ 90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458
+ 100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973
+ 110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489
+ 120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004
+ 130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519
+ 140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038
+ 150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562
+ 160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099
+ 170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654
+ 180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235
+ 190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851
+ 200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512
+ 210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230
+ 220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016
+ 230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883
+ 240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845
+ 250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913
+ 260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097
+ 270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408
+ 280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849
+ 290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424
+ 300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129
+ 310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957
+ 320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898
+ 330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935
+ 340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046
+ 350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207
+ 360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390
+ 370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561
+ 380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688
+ 390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734
+ 400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664
+ 410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442
+ 420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033
+ 430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405
+ 440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527
+ 450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373
+ 460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918
+ 470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143
+ 480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030
+ 490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565
+ 500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740
+ 510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547
+ 520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981
+ 530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040
+ 540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724
+ 550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032
+ 560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963
+ 570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517
+ 580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691
+ 590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478
+ 600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871
+ 610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856
+ 620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416
+ 630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531
+ 640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176
+ 650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323
+ 660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937
+ 670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986
+ 680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430
+ 690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229
+ 700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343
+ 710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729
+ 720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344
+ 730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148
+ 740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098
+ 750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156
+ 760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282
+ 770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441
+ 780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599
+ 790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726
+ 800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792
+ 810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773
+ 820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647
+ 830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393
+ 840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995
+ 850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439
+ 860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713
+ 870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805
+ 880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706
+ 890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408
+ 900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904
+ 910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186
+ 920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247
+ 930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078
+ 940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670
+ 950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015
+ 960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101
+ 970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915
+ 980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
+ 990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
+ 1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
+Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
+
+Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
+120.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
+Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
+Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
+Other | | 0.008904 | | | 0.40
+
+Nlocal: 64 ave 64 max 64 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1265 ave 1265 max 1265 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 11824 ave 11824 max 11824 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 23648 ave 23648 max 23648 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 94592
+Ave neighs/atom = 369.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/USER/misc/srp/in.srp b/examples/USER/misc/srp/in.srp
index 234026e9cbab393b814ade4740f86b43d8d8252d..018d916292b112f44816913add50ca1c99faffd4 100644
--- a/examples/USER/misc/srp/in.srp
+++ b/examples/USER/misc/srp/in.srp
@@ -24,7 +24,7 @@ pair_coeff 1 1 dpd 60.0 4.5 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0
-# auto normalization of thermo quantites is turned off by pair srp
+# auto normalization of thermo quantities is turned off by pair srp
# just divide by natoms
variable natoms equal count(all)
variable nPotEng equal c_thermo_pe/v_natoms
diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/README b/examples/USER/phonon/3-3D-FCC-Cu-EAM/README
index 57e7be53948bfae5ebc0df24c6d411783887ddb6..235c66e256ffc42cdb29fc80368cac0ea9cee51b 100644
--- a/examples/USER/phonon/3-3D-FCC-Cu-EAM/README
+++ b/examples/USER/phonon/3-3D-FCC-Cu-EAM/README
@@ -1,5 +1,5 @@
This directory illustrates the usage of fix-phonon to calculate the dynamical
-matrix as well as phonon dispersion curve for FCC Cu based on EAM potentail.
+matrix as well as phonon dispersion curve for FCC Cu based on EAM potential.
The files under this directory:
diff --git a/examples/USER/phonon/4-Graphene/README b/examples/USER/phonon/4-Graphene/README
index 1e16f0af690aabce589912e6a47642f0f3e9ba1f..3791bc679cf5cd5d208fb1528f34403e3837ae74 100644
--- a/examples/USER/phonon/4-Graphene/README
+++ b/examples/USER/phonon/4-Graphene/README
@@ -1,5 +1,5 @@
This directory illustrates the usage of fix-phonon to calculate the dynamical
-matrix as well as phonon dispersion curve for Graphene based on a Tersoff potentail.
+matrix as well as phonon dispersion curve for Graphene based on a Tersoff potential.
The files under this directory:
diff --git a/examples/USER/tally/README b/examples/USER/tally/README
index 4c2e40e76e45cc49cbbd0b49cf1cfef0eaf46bad..fcc58e6e0df1819c667dc7bddaa5381b0bdf300d 100644
--- a/examples/USER/tally/README
+++ b/examples/USER/tally/README
@@ -3,4 +3,4 @@ Examples and tests for USER-TALLY compute styles.
The examples in this directory show where and how compute tally styles
are equivalent to other facilities in LAMMPS and thus they can also be
used to validate their correct function. Various columns should have
-equivalent or idential output as indicated in the input.
+equivalent or identical output as indicated in the input.
diff --git a/examples/VISCOSITY/README b/examples/VISCOSITY/README
index 88b874cd6541bd530001436f6260b1b3ce948938..38bee0c58d438178f79218f662ef581da3f6d07f 100644
--- a/examples/VISCOSITY/README
+++ b/examples/VISCOSITY/README
@@ -24,7 +24,7 @@ times; the G-K and Einstein systems need to run longer to generate good statisti
The scripts were all run on a single processor. They all run in a
minute or so and produce the accompanying log files and profile files
-(for velocity or momemtum flux).
+(for velocity or momentum flux).
See the Movies page of the LAMMPS web site
(http://lammps.sandia.gov/movies.html), for animations of the NEMD
@@ -74,7 +74,7 @@ eta = 0.997 = running average output as last log file column
eta is computed directly within the script, by performing a time
integration of the formula discussed in Section 6.21 of the manual,
-analagous to the formula for thermal conductivity given on the compute
+analogous to the formula for thermal conductivity given on the compute
heat/flux doc page - the resulting value prints at the end of the run
and is in the log file
@@ -84,7 +84,7 @@ eta = 1.07
eta is computed directly within the script, by performing a time
integration of the formula discussed in Section 6.21 of the manual,
-analagous to the formula for thermal conductivity given on the compute
+analogous to the formula for thermal conductivity given on the compute
heat/flux doc page - the resulting value prints at the end of the run
and is in the log file
diff --git a/examples/accelerate/README b/examples/accelerate/README
index 2a494a1680364d79f4adc712b78e37f42d48be97..1fab296a53c830ccc4e688c3c95db8358b96d23d 100644
--- a/examples/accelerate/README
+++ b/examples/accelerate/README
@@ -130,7 +130,7 @@ lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half < in.lj
mpirun -np 2 lmp_kokkos_omp -k on t 4 -sf kk < in.lj # 2 MPI, 4 thread/MPI
Note that when running with just 1 thread/MPI, "-pk kokkos neigh half"
-was speficied to use half neighbor lists which are faster when running
+was specified to use half neighbor lists which are faster when running
on just 1 thread.
** KOKKOS package for CUDA
diff --git a/examples/rigid/in.rigid.tnr b/examples/rigid/in.rigid.tnr
index 6be5ba529c7211b090d9d3cfd1d40b7a840f5352..7d8d74b3cbb59211249f667d62d4b9cec3240e55 100644
--- a/examples/rigid/in.rigid.tnr
+++ b/examples/rigid/in.rigid.tnr
@@ -20,7 +20,7 @@ velocity all create 1.4 109345
group rods type 2
group tethers subtract all rods
-neigh_modify exclude molecule rods delay 0 every 1
+neigh_modify exclude molecule/intra rods delay 0 every 1
# Specify the pair potentials
diff --git a/potentials/Ta06A_pot.snap b/examples/snap/Ta06A.snap
similarity index 100%
rename from potentials/Ta06A_pot.snap
rename to examples/snap/Ta06A.snap
diff --git a/potentials/W_2940_2017_2.pot.snap b/examples/snap/W_2940_2017_2.snap
similarity index 77%
rename from potentials/W_2940_2017_2.pot.snap
rename to examples/snap/W_2940_2017_2.snap
index ea98d65c9e5b07f83a6da98df4bb3e2461d79fd8..51eee41a0a00be9c1f34ec77c5b8e25be4c70924 100644
--- a/potentials/W_2940_2017_2.pot.snap
+++ b/examples/snap/W_2940_2017_2.snap
@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
diff --git a/examples/snap/W_2940_2017_2.snapcoeff b/examples/snap/W_2940_2017_2.snapcoeff
index 98a5c5063500cbb249f0755dd59b00589d8b38cc..dcfea3feafd3ef8f305c3504476473fa5cf8df2a 100644
--- a/examples/snap/W_2940_2017_2.snapcoeff
+++ b/examples/snap/W_2940_2017_2.snapcoeff
@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# LAMMPS SNAP coefficients for W
diff --git a/examples/snap/W_2940_2017_2.snapparam b/examples/snap/W_2940_2017_2.snapparam
index 7ff57c905d146dabab2bc52b37fd7f2f5095801e..e0b20005e6a50d4a264b91995cbb1ffe96d2fcd7 100644
--- a/examples/snap/W_2940_2017_2.snapparam
+++ b/examples/snap/W_2940_2017_2.snapparam
@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# required
rcutfac 4.73442
diff --git a/examples/snap/W.SNAP_HePair.pot b/examples/snap/W_2940_2017_2_He_JW2013.snap
similarity index 82%
rename from examples/snap/W.SNAP_HePair.pot
rename to examples/snap/W_2940_2017_2_He_JW2013.snap
index eb5ee4dfbe3cc970eb825788998494c908ae5748..45a31955b3a1c21138bcb6a62dbd877804909fdc 100644
--- a/examples/snap/W.SNAP_HePair.pot
+++ b/examples/snap/W_2940_2017_2_He_JW2013.snap
@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
diff --git a/examples/snap/in.snap.Ta06A b/examples/snap/in.snap.Ta06A
index fc0b122948d005ef66adafd4752144104a4b4be1..38a24b8c0644cc404dd285e739da8ba14e29ab5f 100644
--- a/examples/snap/in.snap.Ta06A
+++ b/examples/snap/in.snap.Ta06A
@@ -24,7 +24,7 @@ mass 1 180.88
# choose potential
-include Ta06A_pot.snap
+include Ta06A.snap
# Setup output
diff --git a/examples/snap/in.snap.W.2940 b/examples/snap/in.snap.W.2940
index 7d81b4c78e63c084264f72d6124e9c65c082a747..e1abf861e6f0b4a981de55f510acb33a5caca07b 100644
--- a/examples/snap/in.snap.W.2940
+++ b/examples/snap/in.snap.W.2940
@@ -24,7 +24,7 @@ mass 1 183.84
# choose potential
-include W_2940_2017_2.pot.snap
+include W_2940_2017_2.snap
# Setup output
diff --git a/examples/snap/in.snap.hybrid.WSNAP.HePair b/examples/snap/in.snap.hybrid.WSNAP.HePair
index d2710bca772ef203bd2ad3fb13733411151f7780..1f16fa64a28902f97b32b25d9500b9c78fca1cd0 100644
--- a/examples/snap/in.snap.hybrid.WSNAP.HePair
+++ b/examples/snap/in.snap.hybrid.WSNAP.HePair
@@ -27,7 +27,7 @@ group tungsten type 1
group helium type 2
# choose potential
-include W.SNAP_HePair.pot
+include W_2940_2017_2_He_JW2013.snap
# Setup output
diff --git a/lib/atc/LinearSolver.cpp b/lib/atc/LinearSolver.cpp
index ea31a64a747cae33a652e6209ba8ba6d7b176ea4..655d6130c4530b1ba818c141be64fed5b568f8d5 100644
--- a/lib/atc/LinearSolver.cpp
+++ b/lib/atc/LinearSolver.cpp
@@ -65,7 +65,7 @@ LinearSolver::LinearSolver(
matrixModified_(false),
allowReinitialization_(false),
homogeneousBCs_(false),
- bcs_(NULL), // null implies no contraints will be added later
+ bcs_(NULL), // null implies no constraints will be added later
rhs_(NULL),
rhsDense_(), b_(NULL),
matrix_(A),
diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index d60a9e90f774179fb1fa2bcf6d8b61452786048f..e8c7e88324a9e88299c4c7c1834ce4c7b21e8e90 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -1,5 +1,5 @@
-// -*- c++ -*-
+// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
@@ -7,6 +7,7 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
+
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
@@ -23,20 +24,31 @@ bool compare(colvar::cvc *i, colvar::cvc *j) {
}
-colvar::colvar(std::string const &conf)
- : colvarparse(conf)
+colvar::colvar()
+{
+ // Initialize static array once and for all
+ init_cv_requires();
+}
+
+
+int colvar::init(std::string const &conf)
{
cvm::log("Initializing a new collective variable.\n");
+ colvarparse::init(conf);
+
int error_code = COLVARS_OK;
+ colvarmodule *cv = cvm::main();
+
get_keyval(conf, "name", this->name,
- (std::string("colvar")+cvm::to_str(cvm::colvars.size()+1)));
+ (std::string("colvar")+cvm::to_str(cv->variables()->size()+1)));
- if (cvm::colvar_by_name(this->name) != NULL) {
+ if ((cvm::colvar_by_name(this->name) != NULL) &&
+ (cvm::colvar_by_name(this->name) != this)) {
cvm::error("Error: this colvar cannot have the same name, \""+this->name+
"\", as another colvar.\n",
INPUT_ERROR);
- return;
+ return INPUT_ERROR;
}
// Initialize dependency members
@@ -44,14 +56,13 @@ colvar::colvar(std::string const &conf)
this->description = "colvar " + this->name;
- // Initialize static array once and for all
- init_cv_requires();
-
kinetic_energy = 0.0;
potential_energy = 0.0;
error_code |= init_components(conf);
- if (error_code != COLVARS_OK) return;
+ if (error_code != COLVARS_OK) {
+ return cvm::get_error();
+ }
size_t i;
@@ -59,8 +70,6 @@ colvar::colvar(std::string const &conf)
if (get_keyval(conf, "scriptedFunction", scripted_function,
"", colvarparse::parse_silent)) {
- // Make feature available only on user request
- provide(f_cv_scripted);
enable(f_cv_scripted);
cvm::log("This colvar uses scripted function \"" + scripted_function + "\".");
@@ -76,8 +85,8 @@ colvar::colvar(std::string const &conf)
}
}
if (x.type() == colvarvalue::type_notset) {
- cvm::error("Could not parse scripted colvar type.");
- return;
+ cvm::error("Could not parse scripted colvar type.", INPUT_ERROR);
+ return INPUT_ERROR;
}
cvm::log(std::string("Expecting colvar value of type ")
@@ -86,8 +95,9 @@ colvar::colvar(std::string const &conf)
if (x.type() == colvarvalue::type_vector) {
int size;
if (!get_keyval(conf, "scriptedFunctionVectorSize", size)) {
- cvm::error("Error: no size specified for vector scripted function.");
- return;
+ cvm::error("Error: no size specified for vector scripted function.",
+ INPUT_ERROR);
+ return INPUT_ERROR;
}
x.vector1d_value.resize(size);
}
@@ -154,7 +164,7 @@ colvar::colvar(std::string const &conf)
}
}
}
- feature_states[f_cv_linear]->enabled = lin;
+ set_enabled(f_cv_linear, lin);
}
// Colvar is homogeneous if:
@@ -168,7 +178,7 @@ colvar::colvar(std::string const &conf)
homogeneous = false;
}
}
- feature_states[f_cv_homogeneous]->enabled = homogeneous;
+ set_enabled(f_cv_homogeneous, homogeneous);
}
// Colvar is deemed periodic if:
@@ -188,7 +198,7 @@ colvar::colvar(std::string const &conf)
"Make sure that you know what you are doing!");
}
}
- feature_states[f_cv_periodic]->enabled = b_periodic;
+ set_enabled(f_cv_periodic, b_periodic);
}
// check that cvcs are compatible
@@ -202,7 +212,7 @@ colvar::colvar(std::string const &conf)
"by using components of different types. "
"You must use the same type in order to "
"sum them together.\n", INPUT_ERROR);
- return;
+ return INPUT_ERROR;
}
}
@@ -215,44 +225,110 @@ colvar::colvar(std::string const &conf)
f.type(value());
f_accumulated.type(value());
+ x_old.type(value());
+ v_fdiff.type(value());
+ v_reported.type(value());
+ fj.type(value());
+ ft.type(value());
+ ft_reported.type(value());
+ f_old.type(value());
+ f_old.reset();
+
+ x_restart.type(value());
+ after_restart = false;
+
reset_bias_force();
+ // TODO use here information from the CVCs' own natural boundaries
+ error_code |= init_grid_parameters(conf);
+
+ get_keyval(conf, "timeStepFactor", time_step_factor, 1);
+
+ error_code |= init_extended_Lagrangian(conf);
+ error_code |= init_output_flags(conf);
+
+ // Start in active state by default
+ enable(f_cv_active);
+ // Make sure dependency side-effects are correct
+ refresh_deps();
+
+ if (cvm::b_analysis)
+ parse_analysis(conf);
+
+ if (cvm::debug())
+ cvm::log("Done initializing collective variable \""+this->name+"\".\n");
+
+ return error_code;
+}
+
+
+int colvar::init_grid_parameters(std::string const &conf)
+{
+ colvarmodule *cv = cvm::main();
+
get_keyval(conf, "width", width, 1.0);
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
- return;
+ return INPUT_ERROR;
}
lower_boundary.type(value());
- lower_wall.type(value());
upper_boundary.type(value());
upper_wall.type(value());
- feature_states[f_cv_scalar]->enabled = (value().type() == colvarvalue::type_scalar);
+ set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar));
if (is_enabled(f_cv_scalar)) {
if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) {
- provide(f_cv_lower_boundary);
enable(f_cv_lower_boundary);
}
+ std::string lw_conf, uw_conf;
- get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0);
- if (lower_wall_k > 0.0) {
+ if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0, parse_silent)) {
+ cvm::log("Warning: lowerWallConstant and lowerWall are deprecated, "
+ "please define a harmonicWalls bias instead.\n");
+ lower_wall.type(value());
get_keyval(conf, "lowerWall", lower_wall, lower_boundary);
- enable(f_cv_lower_wall);
+ lw_conf = std::string("\n\
+ lowerWallConstant "+cvm::to_str(lower_wall_k*width*width)+"\n\
+ lowerWalls "+cvm::to_str(lower_wall)+"\n");
}
if (get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary)) {
- provide(f_cv_upper_boundary);
enable(f_cv_upper_boundary);
}
- get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0);
- if (upper_wall_k > 0.0) {
+ if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0, parse_silent)) {
+ cvm::log("Warning: upperWallConstant and upperWall are deprecated, "
+ "please define a harmonicWalls bias instead.\n");
+ upper_wall.type(value());
get_keyval(conf, "upperWall", upper_wall, upper_boundary);
- enable(f_cv_upper_wall);
+ uw_conf = std::string("\n\
+ upperWallConstant "+cvm::to_str(upper_wall_k*width*width)+"\n\
+ upperWalls "+cvm::to_str(upper_wall)+"\n");
+ }
+
+ if (lw_conf.size() && uw_conf.size()) {
+ if (lower_wall >= upper_wall) {
+ cvm::error("Error: the upper wall, "+
+ cvm::to_str(upper_wall)+
+ ", is not higher than the lower wall, "+
+ cvm::to_str(lower_wall)+".\n",
+ INPUT_ERROR);
+ return INPUT_ERROR;
+ }
+ }
+
+ if (lw_conf.size() || uw_conf.size()) {
+ cvm::log("Generating a new harmonicWalls bias for compatibility purposes.\n");
+ std::string const walls_conf("\n\
+harmonicWalls {\n\
+ name "+this->name+"w\n\
+ colvars "+this->name+"\n"+lw_conf+uw_conf+
+ "}\n");
+ cv->append_new_config(walls_conf);
}
}
@@ -271,16 +347,7 @@ colvar::colvar(std::string const &conf)
", is not higher than the lower boundary, "+
cvm::to_str(lower_boundary)+".\n",
INPUT_ERROR);
- }
- }
-
- if (is_enabled(f_cv_lower_wall) && is_enabled(f_cv_upper_wall)) {
- if (lower_wall >= upper_wall) {
- cvm::error("Error: the upper wall, "+
- cvm::to_str(upper_wall)+
- ", is not higher than the lower wall, "+
- cvm::to_str(lower_wall)+".\n",
- INPUT_ERROR);
+ return INPUT_ERROR;
}
}
@@ -289,83 +356,90 @@ colvar::colvar(std::string const &conf)
cvm::error("Error: trying to expand boundaries that already "
"cover a whole period of a periodic colvar.\n",
INPUT_ERROR);
+ return INPUT_ERROR;
}
if (expand_boundaries && hard_lower_boundary && hard_upper_boundary) {
cvm::error("Error: inconsistent configuration "
"(trying to expand boundaries with both "
"hardLowerBoundary and hardUpperBoundary enabled).\n",
INPUT_ERROR);
+ return INPUT_ERROR;
}
- get_keyval(conf, "timeStepFactor", time_step_factor, 1);
+ return COLVARS_OK;
+}
- {
- bool b_extended_Lagrangian;
- get_keyval(conf, "extendedLagrangian", b_extended_Lagrangian, false);
- if (b_extended_Lagrangian) {
- cvm::real temp, tolerance, period;
+int colvar::init_extended_Lagrangian(std::string const &conf)
+{
+ bool b_extended_Lagrangian;
+ get_keyval(conf, "extendedLagrangian", b_extended_Lagrangian, false);
- cvm::log("Enabling the extended Lagrangian term for colvar \""+
- this->name+"\".\n");
+ if (b_extended_Lagrangian) {
+ cvm::real temp, tolerance, period;
- // Make feature available only on user request
- provide(f_cv_extended_Lagrangian);
- enable(f_cv_extended_Lagrangian);
- provide(f_cv_Langevin);
-
- // The extended mass will apply forces
- enable(f_cv_gradient);
-
- xr.type(value());
- vr.type(value());
- fr.type(value());
-
- const bool found = get_keyval(conf, "extendedTemp", temp, cvm::temperature());
- if (temp <= 0.0) {
- if (found)
- cvm::error("Error: \"extendedTemp\" must be positive.\n", INPUT_ERROR);
- else
- cvm::error("Error: a positive temperature must be provided, either "
- "by enabling a thermostat, or through \"extendedTemp\".\n",
- INPUT_ERROR);
- }
+ cvm::log("Enabling the extended Lagrangian term for colvar \""+
+ this->name+"\".\n");
- get_keyval(conf, "extendedFluctuation", tolerance);
- if (tolerance <= 0.0) {
- cvm::error("Error: \"extendedFluctuation\" must be positive.\n", INPUT_ERROR);
- }
- ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
- cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " kcal/mol/U^2");
+ enable(f_cv_extended_Lagrangian);
- get_keyval(conf, "extendedTimeConstant", period, 200.0);
- if (period <= 0.0) {
- cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", INPUT_ERROR);
- }
- ext_mass = (cvm::boltzmann() * temp * period * period)
- / (4.0 * PI * PI * tolerance * tolerance);
- cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " kcal/mol/(U/fs)^2 (U: colvar unit)");
-
- {
- bool b_output_energy;
- get_keyval(conf, "outputEnergy", b_output_energy, false);
- if (b_output_energy) {
- enable(f_cv_output_energy);
- }
- }
+ xr.type(value());
+ vr.type(value());
+ fr.type(value());
- get_keyval(conf, "extendedLangevinDamping", ext_gamma, 1.0);
- if (ext_gamma < 0.0) {
- cvm::error("Error: \"extendedLangevinDamping\" may not be negative.\n", INPUT_ERROR);
- }
- if (ext_gamma != 0.0) {
- enable(f_cv_Langevin);
- ext_gamma *= 1.0e-3; // convert from ps-1 to fs-1
- ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / cvm::dt());
+ const bool found = get_keyval(conf, "extendedTemp", temp, cvm::temperature());
+ if (temp <= 0.0) {
+ if (found)
+ cvm::error("Error: \"extendedTemp\" must be positive.\n", INPUT_ERROR);
+ else
+ cvm::error("Error: a positive temperature must be provided, either "
+ "by enabling a thermostat, or through \"extendedTemp\".\n",
+ INPUT_ERROR);
+ return INPUT_ERROR;
+ }
+
+ get_keyval(conf, "extendedFluctuation", tolerance);
+ if (tolerance <= 0.0) {
+ cvm::error("Error: \"extendedFluctuation\" must be positive.\n", INPUT_ERROR);
+ return INPUT_ERROR;
+ }
+ ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
+ cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " kcal/mol/U^2");
+
+ get_keyval(conf, "extendedTimeConstant", period, 200.0);
+ if (period <= 0.0) {
+ cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", INPUT_ERROR);
+ }
+ ext_mass = (cvm::boltzmann() * temp * period * period)
+ / (4.0 * PI * PI * tolerance * tolerance);
+ cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " kcal/mol/(U/fs)^2 (U: colvar unit)");
+
+ {
+ bool b_output_energy;
+ get_keyval(conf, "outputEnergy", b_output_energy, false);
+ if (b_output_energy) {
+ enable(f_cv_output_energy);
}
}
+
+ get_keyval(conf, "extendedLangevinDamping", ext_gamma, 1.0);
+ if (ext_gamma < 0.0) {
+ cvm::error("Error: \"extendedLangevinDamping\" may not be negative.\n", INPUT_ERROR);
+ return INPUT_ERROR;
+ }
+ if (ext_gamma != 0.0) {
+ enable(f_cv_Langevin);
+ ext_gamma *= 1.0e-3; // convert from ps-1 to fs-1
+ ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / cvm::dt());
+ }
}
+ return COLVARS_OK;
+}
+
+
+int colvar::init_output_flags(std::string const &conf)
+{
{
bool b_output_value;
get_keyval(conf, "outputValue", b_output_value, true);
@@ -387,7 +461,7 @@ colvar::colvar(std::string const &conf)
if (get_keyval(conf, "outputSystemForce", temp, false, colvarparse::parse_silent)) {
cvm::error("Option outputSystemForce is deprecated: only outputTotalForce is supported instead.\n"
"The two are NOT identical: see http://colvars.github.io/totalforce.html.\n", INPUT_ERROR);
- return;
+ return INPUT_ERROR;
}
}
@@ -395,28 +469,7 @@ colvar::colvar(std::string const &conf)
get_keyval_feature(this, conf, "outputAppliedForce", f_cv_output_applied_force, false);
get_keyval_feature(this, conf, "subtractAppliedForce", f_cv_subtract_applied_force, false);
- // Start in active state by default
- enable(f_cv_active);
- // Make sure dependency side-effects are correct
- refresh_deps();
-
- x_old.type(value());
- v_fdiff.type(value());
- v_reported.type(value());
- fj.type(value());
- ft.type(value());
- ft_reported.type(value());
- f_old.type(value());
- f_old.reset();
-
- x_restart.type(value());
- after_restart = false;
-
- if (cvm::b_analysis)
- parse_analysis(conf);
-
- if (cvm::debug())
- cvm::log("Done initializing collective variable \""+this->name+"\".\n");
+ return COLVARS_OK;
}
@@ -637,7 +690,7 @@ int colvar::parse_analysis(std::string const &conf)
std::string runave_outfile;
get_keyval(conf, "runAveOutputFile", runave_outfile,
- std::string(cvm::output_prefix+"."+
+ std::string(cvm::output_prefix()+"."+
this->name+".runave.traj"));
size_t const this_cv_width = x.output_width(cvm::cv_width);
@@ -693,7 +746,7 @@ int colvar::parse_analysis(std::string const &conf)
get_keyval(conf, "corrFuncNormalize", acf_normalize, true);
get_keyval(conf, "corrFuncOutputFile", acf_outfile,
- std::string(cvm::output_prefix+"."+this->name+
+ std::string(cvm::output_prefix()+"."+this->name+
".corrfunc.dat"));
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@@ -730,11 +783,12 @@ colvar::~colvar()
}
// remove reference to this colvar from the CVM
- for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin();
- cvi != cvm::colvars.end();
+ colvarmodule *cv = cvm::main();
+ for (std::vector<colvar *>::iterator cvi = cv->variables()->begin();
+ cvi != cv->variables()->end();
++cvi) {
if ( *cvi == this) {
- cvm::colvars.erase(cvi);
+ cv->variables()->erase(cvi);
break;
}
}
@@ -892,7 +946,6 @@ int colvar::collect_cvc_values()
cvm::to_str(x, cvm::cv_width, cvm::cv_prec)+".\n");
if (after_restart) {
- after_restart = false;
if (cvm::proxy->simulation_running()) {
cvm::real const jump2 = dist2(x, x_restart) / (width*width);
if (jump2 > 0.25) {
@@ -1122,8 +1175,7 @@ int colvar::calc_colvar_properties()
// initialize the restraint center in the first step to the value
// just calculated from the cvcs
- // TODO: put it in the restart information
- if (cvm::step_relative() == 0) {
+ if (cvm::step_relative() == 0 && !after_restart) {
xr = x;
vr.reset(); // (already 0; added for clarity)
}
@@ -1148,6 +1200,8 @@ int colvar::calc_colvar_properties()
ft_reported = ft;
}
+ // At the end of the first update after a restart, we can reset the flag
+ after_restart = false;
return COLVARS_OK;
}
@@ -1173,51 +1227,17 @@ cvm::real colvar::update_forces_energy()
f -= fj;
}
- // Wall force
- colvarvalue fw(x);
- fw.reset();
-
- if (is_enabled(f_cv_lower_wall) || is_enabled(f_cv_upper_wall)) {
-
- if (cvm::debug())
- cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n");
-
- // For a periodic colvar, both walls may be applicable at the same time
- // in which case we pick the closer one
- if ( (!is_enabled(f_cv_upper_wall)) ||
- (this->dist2(x, lower_wall) < this->dist2(x, upper_wall)) ) {
-
- cvm::real const grad = this->dist2_lgrad(x, lower_wall);
- if (grad < 0.0) {
- fw = -0.5 * lower_wall_k * grad;
- if (cvm::debug())
- cvm::log("Applying a lower wall force("+
- cvm::to_str(fw)+") to \""+this->name+"\".\n");
- }
-
- } else {
-
- cvm::real const grad = this->dist2_lgrad(x, upper_wall);
- if (grad > 0.0) {
- fw = -0.5 * upper_wall_k * grad;
- if (cvm::debug())
- cvm::log("Applying an upper wall force("+
- cvm::to_str(fw)+") to \""+this->name+"\".\n");
- }
- }
- }
-
// At this point f is the force f from external biases that will be applied to the
// extended variable if there is one
if (is_enabled(f_cv_extended_Lagrangian)) {
if (cvm::debug()) {
- cvm::log("Updating extended-Lagrangian degrees of freedom.\n");
+ cvm::log("Updating extended-Lagrangian degree of freedom.\n");
}
cvm::real dt = cvm::dt();
- colvarvalue f_ext(fr.type());
+ colvarvalue f_ext(fr.type()); // force acting on the extended variable
f_ext.reset();
// the total force is applied to the fictitious mass, while the
@@ -1226,7 +1246,7 @@ cvm::real colvar::update_forces_energy()
// f_ext: total force on extended variable (including harmonic spring)
// f: - initially, external biasing force
// - after this code block, colvar force to be applied to atomic coordinates
- // ie. spring force + wall force
+ // ie. spring force (fb_actual will be added just below)
fr = f;
f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
@@ -1259,8 +1279,6 @@ cvm::real colvar::update_forces_energy()
if (this->is_enabled(f_cv_periodic)) this->wrap(xr);
}
- // TODO remove the wall force
- f += fw;
// Now adding the force on the actual colvar (for those biases who
// bypass the extended Lagrangian mass)
f += fb_actual;
@@ -1286,8 +1304,10 @@ cvm::real colvar::update_forces_energy()
void colvar::communicate_forces()
{
size_t i;
- if (cvm::debug())
+ if (cvm::debug()) {
cvm::log("Communicating forces from colvar \""+this->name+"\".\n");
+ cvm::log("Force to be applied: " + cvm::to_str(f_accumulated) + "\n");
+ }
if (is_enabled(f_cv_scripted)) {
std::vector<cvm::matrix2d<cvm::real> > func_grads;
@@ -1364,7 +1384,7 @@ int colvar::update_cvc_flags()
active_cvc_square_norm = 0.;
for (size_t i = 0; i < cvcs.size(); i++) {
- cvcs[i]->feature_states[f_cvc_active]->enabled = cvc_flags[i];
+ cvcs[i]->set_enabled(f_cvc_active, cvc_flags[i]);
if (cvcs[i]->is_enabled()) {
n_active_cvcs++;
active_cvc_square_norm += cvcs[i]->sup_coeff * cvcs[i]->sup_coeff;
diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h
index 2cf3d2dac512b7492452940393067e8d6f7088ef..0cbda450b8af878ba611f1689cc8d85628e8e0e5 100644
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@@ -227,11 +227,23 @@ public:
/// Constructor
- colvar(std::string const &conf);
+ colvar();
+
+ /// Main init function
+ int init(std::string const &conf);
/// Parse the CVC configuration and allocate their data
int init_components(std::string const &conf);
+ /// Init defaults for grid options
+ int init_grid_parameters(std::string const &conf);
+
+ /// Init extended Lagrangian parameters
+ int init_extended_Lagrangian(std::string const &conf);
+
+ /// Init output flags
+ int init_output_flags(std::string const &conf);
+
private:
/// Parse the CVC configuration for all components of a certain type
template<typename def_class_name> int init_components_type(std::string const &conf,
diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp
index 48c16e887af95c9e623aa3b8b525b54594e10ca2..32cfadf3b6c84aae0af422fb63f6bcad0d870158 100644
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@@ -98,7 +98,7 @@ cvm::atom_group::atom_group()
cvm::atom_group::~atom_group()
{
- if (is_enabled(f_ag_scalable)) {
+ if (is_enabled(f_ag_scalable) && !b_dummy) {
(cvm::proxy)->clear_atom_group(index);
index = -1;
}
@@ -418,7 +418,7 @@ int cvm::atom_group::parse(std::string const &conf)
// We need to know the fitting options to decide whether the group is scalable
parse_error |= parse_fitting_options(group_conf);
- if (is_available(f_ag_scalable_com) && !b_rotate) {
+ if (is_available(f_ag_scalable_com) && !b_rotate && !b_center) {
enable(f_ag_scalable_com);
enable(f_ag_scalable);
}
@@ -500,14 +500,16 @@ int cvm::atom_group::add_atom_numbers(std::string const &numbers_conf)
int cvm::atom_group::add_index_group(std::string const &index_group_name)
{
- std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
- std::list<std::vector<int> >::iterator index_groups_i = cvm::index_groups.begin();
- for ( ; names_i != cvm::index_group_names.end() ; ++names_i, ++index_groups_i) {
+ colvarmodule *cv = cvm::main();
+
+ std::list<std::string>::iterator names_i = cv->index_group_names.begin();
+ std::list<std::vector<int> >::iterator index_groups_i = cv->index_groups.begin();
+ for ( ; names_i != cv->index_group_names.end() ; ++names_i, ++index_groups_i) {
if (*names_i == index_group_name)
break;
}
- if (names_i == cvm::index_group_names.end()) {
+ if (names_i == cv->index_group_names.end()) {
cvm::error("Error: could not find index group "+
index_group_name+" among those provided by the index file.\n",
INPUT_ERROR);
diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp
index fdd2b6254ca12dd8b450244f72c75f8b570f8a2f..3779c82aa300b86814a8f3ab23eaf1b161c34946 100644
--- a/lib/colvars/colvarbias.cpp
+++ b/lib/colvars/colvarbias.cpp
@@ -19,20 +19,6 @@ colvarbias::colvarbias(char const *key)
rank = 1;
- if (bias_type == std::string("abf")) {
- rank = cvm::n_abf_biases+1;
- }
- if (bias_type == std::string("harmonic") ||
- bias_type == std::string("linear")) {
- rank = cvm::n_rest_biases+1;
- }
- if (bias_type == std::string("histogram")) {
- rank = cvm::n_histo_biases+1;
- }
- if (bias_type == std::string("metadynamics")) {
- rank = cvm::n_meta_biases+1;
- }
-
has_data = false;
b_output_energy = false;
reset();
@@ -48,7 +34,11 @@ int colvarbias::init(std::string const &conf)
colvarparse::init(conf);
if (name.size() == 0) {
+
+ // first initialization
+
cvm::log("Initializing a new \""+bias_type+"\" instance.\n");
+ rank = cvm::num_biases_type(bias_type);
get_keyval(conf, "name", name, bias_type+cvm::to_str(rank));
{
@@ -69,7 +59,7 @@ int colvarbias::init(std::string const &conf)
// lookup the associated colvars
std::vector<std::string> colvar_names;
if (get_keyval(conf, "colvars", colvar_names)) {
- if (colvars.size()) {
+ if (num_variables()) {
cvm::error("Error: cannot redefine the colvars that a bias was already defined on.\n",
INPUT_ERROR);
return INPUT_ERROR;
@@ -80,7 +70,7 @@ int colvarbias::init(std::string const &conf)
}
}
- if (!colvars.size()) {
+ if (!num_variables()) {
cvm::error("Error: no collective variables specified.\n", INPUT_ERROR);
return INPUT_ERROR;
}
@@ -89,6 +79,8 @@ int colvarbias::init(std::string const &conf)
cvm::log("Reinitializing bias \""+name+"\".\n");
}
+ output_prefix = cvm::output_prefix();
+
get_keyval(conf, "outputEnergy", b_output_energy, b_output_energy);
return COLVARS_OK;
@@ -98,7 +90,7 @@ int colvarbias::init(std::string const &conf)
int colvarbias::reset()
{
bias_energy = 0.0;
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
colvar_forces[i].reset();
}
return COLVARS_OK;
@@ -132,12 +124,13 @@ int colvarbias::clear()
}
}
+ colvarmodule *cv = cvm::main();
// ...and from the colvars module
- for (std::vector<colvarbias *>::iterator bi = cvm::biases.begin();
- bi != cvm::biases.end();
+ for (std::vector<colvarbias *>::iterator bi = cv->biases.begin();
+ bi != cv->biases.end();
++bi) {
if ( *bi == this) {
- cvm::biases.erase(bi);
+ cv->biases.erase(bi);
break;
}
}
@@ -185,21 +178,29 @@ int colvarbias::add_colvar(std::string const &cv_name)
int colvarbias::update()
{
- // Note: if anything is added here, it should be added also in the SMP block of calc_biases()
- // TODO move here debug msg of bias update
+ if (cvm::debug()) {
+ cvm::log("Updating the "+bias_type+" bias \""+this->name+"\".\n");
+ }
+
has_data = true;
+
+ bias_energy = 0.0;
+ for (size_t ir = 0; ir < num_variables(); ir++) {
+ colvar_forces[ir].reset();
+ }
+
return COLVARS_OK;
}
void colvarbias::communicate_forces()
{
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
if (cvm::debug()) {
cvm::log("Communicating a force to colvar \""+
- colvars[i]->name+"\".\n");
+ variables(i)->name+"\".\n");
}
- colvars[i]->add_bias_force(colvar_forces[i]);
+ variables(i)->add_bias_force(colvar_forces[i]);
}
}
diff --git a/lib/colvars/colvarbias.h b/lib/colvars/colvarbias.h
index 12397dcb8fa0ba8aa2356fd776d1a8ccb16b4546..6d5776d3db87047c78ff15c637d6703ceeb77300 100644
--- a/lib/colvars/colvarbias.h
+++ b/lib/colvars/colvarbias.h
@@ -32,17 +32,39 @@ public:
/// Add a new collective variable to this bias
int add_colvar(std::string const &cv_name);
- /// Add a new collective variable to this bias
- size_t number_of_colvars() const
+ /// How many variables are defined for this bias
+ inline size_t num_variables() const
{
return colvars.size();
}
+ /// Access the variables vector
+ inline std::vector<colvar *> *variables()
+ {
+ return &colvars;
+ }
+
+ /// Access the i-th variable
+ inline colvar * variables(int i) const
+ {
+ return colvars[i];
+ }
+
/// Retrieve colvar values and calculate their biasing forces
/// Return bias energy
virtual int update();
- // TODO: move update_bias here (share with metadynamics)
+ /// \brief Compute the energy of the bias with alternative values of the
+ /// collective variables (suitable for bias exchange)
+ virtual int calc_energy(std::vector<colvarvalue> const &values =
+ std::vector<colvarvalue>(0))
+ {
+ cvm::error("Error: calc_energy() not implemented.\n", COLVARS_NOT_IMPLEMENTED);
+ return COLVARS_NOT_IMPLEMENTED;
+ }
+
+ /// Send forces to the collective variables
+ virtual void communicate_forces();
/// Load new configuration - force constant and/or centers only
virtual int change_configuration(std::string const &conf);
@@ -51,10 +73,13 @@ public:
virtual cvm::real energy_difference(std::string const &conf);
/// Give the total number of bins for a given bias.
+ // FIXME this is currently 1D only
virtual int bin_num();
/// Calculate the bin index for a given bias.
+ // FIXME this is currently 1D only
virtual int current_bin();
//// Give the count at a given bin index.
+ // FIXME this is currently 1D only
virtual int bin_count(int bin_index);
//// Share information between replicas, whatever it may be.
virtual int replica_share();
@@ -62,9 +87,6 @@ public:
/// Perform analysis tasks
virtual void analyze() {}
- /// Send forces to the collective variables
- virtual void communicate_forces();
-
/// \brief Constructor
colvarbias(char const *key);
@@ -135,6 +157,9 @@ public:
return COLVARS_OK;
}
+ /// Use this prefix for all output files
+ std::string output_prefix;
+
/// If this bias is communicating with other replicas through files, send it to them
virtual int write_state_to_replicas()
{
@@ -162,7 +187,7 @@ protected:
/// through each colvar object
std::vector<colvar *> colvars;
- /// \brief Current forces from this bias to the colvars
+ /// \brief Current forces from this bias to the variables
std::vector<colvarvalue> colvar_forces;
/// \brief Current energy of this bias (colvar_forces should be obtained by deriving this)
diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp
index ccfa401697693bb97a2d403c6cc06da3f2f32d9e..d039004f09d47f3b216c62a3e5d5304e9cb89678 100644
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@@ -30,9 +30,8 @@ int colvarbias_abf::init(std::string const &conf)
{
colvarbias::init(conf);
- provide(f_cvb_scalar_variables);
enable(f_cvb_scalar_variables);
- provide(f_cvb_history_dependent);
+ enable(f_cvb_calc_pmf);
// TODO relax this in case of VMD plugin
if (cvm::temperature() == 0.0)
@@ -221,9 +220,6 @@ colvarbias_abf::~colvarbias_abf()
delete [] system_force;
system_force = NULL;
}
-
- if (cvm::n_abf_biases > 0)
- cvm::n_abf_biases -= 1;
}
@@ -319,11 +315,11 @@ int colvarbias_abf::update()
}
// update the output prefix; TODO: move later to setup_output() function
- if ( cvm::n_abf_biases == 1 && cvm::n_meta_biases == 0 ) {
- // This is the only ABF bias
- output_prefix = cvm::output_prefix;
+ if (cvm::num_biases_feature(colvardeps::f_cvb_calc_pmf) == 1) {
+ // This is the only bias computing PMFs
+ output_prefix = cvm::output_prefix();
} else {
- output_prefix = cvm::output_prefix + "." + this->name;
+ output_prefix = cvm::output_prefix() + "." + this->name;
}
if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
diff --git a/lib/colvars/colvarbias_alb.cpp b/lib/colvars/colvarbias_alb.cpp
index 9e414d4db49637087dc954ff8239a5465287664e..d096ac3daf15a508e076b38e2dc1e18368f321b7 100644
--- a/lib/colvars/colvarbias_alb.cpp
+++ b/lib/colvars/colvarbias_alb.cpp
@@ -40,11 +40,8 @@ int colvarbias_alb::init(std::string const &conf)
{
colvarbias::init(conf);
- provide(f_cvb_scalar_variables);
enable(f_cvb_scalar_variables);
- provide(f_cvb_history_dependent);
-
size_t i;
// get the initial restraint centers
@@ -138,8 +135,6 @@ int colvarbias_alb::init(std::string const &conf)
colvarbias_alb::~colvarbias_alb()
{
- if (cvm::n_rest_biases > 0)
- cvm::n_rest_biases -= 1;
}
diff --git a/lib/colvars/colvarbias_histogram.cpp b/lib/colvars/colvarbias_histogram.cpp
index 900ad213d51d6d0301063d6edba45561e285a0e7..502a7455b1ed4ab99ec9c6d553e621ec4a4ff7d7 100644
--- a/lib/colvars/colvarbias_histogram.cpp
+++ b/lib/colvars/colvarbias_histogram.cpp
@@ -24,10 +24,7 @@ int colvarbias_histogram::init(std::string const &conf)
{
colvarbias::init(conf);
- provide(f_cvb_scalar_variables);
enable(f_cvb_scalar_variables);
-
- provide(f_cvb_history_dependent);
enable(f_cvb_history_dependent);
size_t i;
@@ -104,9 +101,6 @@ colvarbias_histogram::~colvarbias_histogram()
delete grid;
grid = NULL;
}
-
- if (cvm::n_histo_biases > 0)
- cvm::n_histo_biases -= 1;
}
@@ -127,14 +121,14 @@ int colvarbias_histogram::update()
// At the first timestep, we need to assign out_name since
// output_prefix is unset during the constructor
if (cvm::step_relative() == 0) {
- out_name = cvm::output_prefix + "." + this->name + ".dat";
+ out_name = cvm::output_prefix() + "." + this->name + ".dat";
cvm::log("Histogram " + this->name + " will be written to file \"" + out_name + "\"");
}
}
if (out_name_dx.size() == 0) {
if (cvm::step_relative() == 0) {
- out_name_dx = cvm::output_prefix + "." + this->name + ".dx";
+ out_name_dx = cvm::output_prefix() + "." + this->name + ".dx";
cvm::log("Histogram " + this->name + " will be written to file \"" + out_name_dx + "\"");
}
}
diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp
index 01a04d1a016dbb116f707296cfd54bb99ad86f83..b0acfe974a188a179de18da36d1c537e70f77995 100644
--- a/lib/colvars/colvarbias_meta.cpp
+++ b/lib/colvars/colvarbias_meta.cpp
@@ -43,7 +43,7 @@ int colvarbias_meta::init(std::string const &conf)
{
colvarbias::init(conf);
- provide(f_cvb_history_dependent);
+ enable(f_cvb_calc_pmf);
get_keyval(conf, "hillWeight", hill_weight, 0.0);
if (hill_weight > 0.0) {
@@ -59,9 +59,9 @@ int colvarbias_meta::init(std::string const &conf)
get_keyval(conf, "hillWidth", hill_width, std::sqrt(2.0 * PI) / 2.0);
cvm::log("Half-widths of the Gaussian hills (sigma's):\n");
- for (size_t i = 0; i < colvars.size(); i++) {
- cvm::log(colvars[i]->name+std::string(": ")+
- cvm::to_str(0.5 * colvars[i]->width * hill_width));
+ for (size_t i = 0; i < num_variables(); i++) {
+ cvm::log(variables(i)->name+std::string(": ")+
+ cvm::to_str(0.5 * variables(i)->width * hill_width));
}
{
@@ -73,8 +73,10 @@ int colvarbias_meta::init(std::string const &conf)
comm = single_replica;
}
- // This implies gradients for all colvars
- enable(f_cvb_apply_force);
+ // in all cases, the first replica is this bias itself
+ if (replicas.size() == 0) {
+ replicas.push_back(this);
+ }
get_keyval(conf, "useGrids", use_grids, true);
@@ -84,14 +86,14 @@ int colvarbias_meta::init(std::string const &conf)
expand_grids = false;
size_t i;
- for (i = 0; i < colvars.size(); i++) {
- colvars[i]->enable(f_cv_grid);
- if (colvars[i]->expand_boundaries) {
+ for (i = 0; i < num_variables(); i++) {
+ variables(i)->enable(f_cv_grid);
+ if (variables(i)->expand_boundaries) {
expand_grids = true;
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": Will expand grids when the colvar \""+
- colvars[i]->name+"\" approaches its boundaries.\n");
+ variables(i)->name+"\" approaches its boundaries.\n");
}
}
@@ -100,7 +102,7 @@ int colvarbias_meta::init(std::string const &conf)
get_keyval(conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent);
if (get_keyval(conf, "saveFreeEnergyFile", dump_fes_save, false, colvarparse::parse_silent)) {
cvm::log("Option \"saveFreeEnergyFile\" is deprecated, "
- "please use \"keepFreeEnergyFiles\" instead.");
+ "please use \"keepFreeEnergyFile\" instead.");
}
get_keyval(conf, "keepFreeEnergyFiles", dump_fes_save, dump_fes_save);
@@ -154,6 +156,20 @@ int colvarbias_meta::init(std::string const &conf)
get_keyval(conf, "writeHillsTrajectory", b_hills_traj, false);
+ init_well_tempered_params(conf);
+ init_ebmeta_params(conf);
+
+ if (cvm::debug())
+ cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+
+ ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
+
+ save_delimiters = false;
+ return COLVARS_OK;
+}
+
+
+int colvarbias_meta::init_well_tempered_params(std::string const &conf)
+{
// for well-tempered metadynamics
get_keyval(conf, "wellTempered", well_tempered, false);
get_keyval(conf, "biasTemperature", bias_temperature, -1.0);
@@ -164,8 +180,12 @@ int colvarbias_meta::init(std::string const &conf)
cvm::log("Well-tempered metadynamics is used.\n");
cvm::log("The bias temperature is "+cvm::to_str(bias_temperature)+".\n");
}
+ return COLVARS_OK;
+}
+int colvarbias_meta::init_ebmeta_params(std::string const &conf)
+{
// for ebmeta
target_dist = NULL;
get_keyval(conf, "ebMeta", ebmeta, false);
@@ -203,11 +223,6 @@ int colvarbias_meta::init(std::string const &conf)
get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, 0);
}
- if (cvm::debug())
- cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+
- ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
-
- save_delimiters = false;
return COLVARS_OK;
}
@@ -234,9 +249,6 @@ colvarbias_meta::~colvarbias_meta()
delete target_dist;
target_dist = NULL;
}
-
- if (cvm::n_meta_biases > 0)
- cvm::n_meta_biases -= 1;
}
@@ -314,23 +326,45 @@ colvarbias_meta::delete_hill(hill_iter &h)
int colvarbias_meta::update()
{
- if (cvm::debug())
- cvm::log("Updating the metadynamics bias \""+this->name+"\""+
- ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
+ int error_code = COLVARS_OK;
+
+ // update base class
+ error_code |= colvarbias::update();
+
+ // update grid definition, if needed
+ error_code |= update_grid_params();
+ // add new biasing energy/forces
+ error_code |= update_bias();
+ // update grid content to reflect new bias
+ error_code |= update_grid_data();
+
+ if (comm != single_replica &&
+ (cvm::step_absolute() % replica_update_freq) == 0) {
+ // sync with the other replicas (if needed)
+ error_code |= replica_share();
+ }
+
+ error_code |= calc_energy();
+ error_code |= calc_forces();
+ return error_code;
+}
+
+
+int colvarbias_meta::update_grid_params()
+{
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
+ if (cvm::debug()) {
+ cvm::log("Metadynamics bias \""+this->name+"\""+
+ ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
+ ": current coordinates on the grid: "+
+ cvm::to_str(curr_bin)+".\n");
+ }
if (expand_grids) {
-
// first of all, expand the grids, if specified
- if (cvm::debug())
- cvm::log("Metadynamics bias \""+this->name+"\""+
- ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
- ": current coordinates on the grid: "+
- cvm::to_str(curr_bin)+".\n");
-
bool changed_grids = false;
int const min_buffer =
(3 * (size_t) std::floor(hill_width)) + 1;
@@ -339,9 +373,9 @@ int colvarbias_meta::update()
std::vector<colvarvalue> new_lower_boundaries(hills_energy->lower_boundaries);
std::vector<colvarvalue> new_upper_boundaries(hills_energy->upper_boundaries);
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
- if (! colvars[i]->expand_boundaries)
+ if (! variables(i)->expand_boundaries)
continue;
cvm::real &new_lb = new_lower_boundaries[i].real_value;
@@ -349,10 +383,10 @@ int colvarbias_meta::update()
int &new_size = new_sizes[i];
bool changed_lb = false, changed_ub = false;
- if (!colvars[i]->hard_lower_boundary)
+ if (!variables(i)->hard_lower_boundary)
if (curr_bin[i] < min_buffer) {
int const extra_points = (min_buffer - curr_bin[i]);
- new_lb -= extra_points * colvars[i]->width;
+ new_lb -= extra_points * variables(i)->width;
new_size += extra_points;
// changed offset in this direction => the pointer needs to
// be changed, too
@@ -362,21 +396,21 @@ int colvarbias_meta::update()
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": new lower boundary for colvar \""+
- colvars[i]->name+"\", at "+
+ variables(i)->name+"\", at "+
cvm::to_str(new_lower_boundaries[i])+".\n");
}
- if (!colvars[i]->hard_upper_boundary)
+ if (!variables(i)->hard_upper_boundary)
if (curr_bin[i] > new_size - min_buffer - 1) {
int const extra_points = (curr_bin[i] - (new_size - 1) + min_buffer);
- new_ub += extra_points * colvars[i]->width;
+ new_ub += extra_points * variables(i)->width;
new_size += extra_points;
changed_ub = true;
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": new upper boundary for colvar \""+
- colvars[i]->name+"\", at "+
+ variables(i)->name+"\", at "+
cvm::to_str(new_upper_boundaries[i])+".\n");
}
@@ -401,7 +435,7 @@ int colvarbias_meta::update()
new_hills_energy_gradients->lower_boundaries = new_lower_boundaries;
new_hills_energy_gradients->upper_boundaries = new_upper_boundaries;
- new_hills_energy_gradients->setup(new_sizes, 0.0, colvars.size());
+ new_hills_energy_gradients->setup(new_sizes, 0.0, num_variables());
new_hills_energy->map_grid(*hills_energy);
new_hills_energy_gradients->map_grid(*hills_energy_gradients);
@@ -418,25 +452,32 @@ int colvarbias_meta::update()
}
}
}
+ return COLVARS_OK;
+}
+
+int colvarbias_meta::update_bias()
+{
// add a new hill if the required time interval has passed
- if ((cvm::step_absolute() % new_hill_freq) == 0) {
+ if ((cvm::step_absolute() % new_hill_freq) == 0 &&
+ is_enabled(f_cvb_history_dependent)) {
- if (cvm::debug())
+ if (cvm::debug()) {
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": adding a new hill at step "+cvm::to_str(cvm::step_absolute())+".\n");
+ }
cvm::real hills_scale=1.0;
if (ebmeta) {
- hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index());
- if(cvm::step_absolute() <= long(ebmeta_equil_steps)) {
- cvm::real const hills_lambda =
- (cvm::real(long(ebmeta_equil_steps) - cvm::step_absolute())) /
- (cvm::real(ebmeta_equil_steps));
- hills_scale = hills_lambda + (1-hills_lambda)*hills_scale;
- }
+ hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index());
+ if(cvm::step_absolute() <= long(ebmeta_equil_steps)) {
+ cvm::real const hills_lambda =
+ (cvm::real(long(ebmeta_equil_steps) - cvm::step_absolute())) /
+ (cvm::real(ebmeta_equil_steps));
+ hills_scale = hills_lambda + (1-hills_lambda)*hills_scale;
+ }
}
if (well_tempered) {
@@ -471,160 +512,165 @@ int colvarbias_meta::update()
}
}
- // sync with the other replicas (if needed)
- if (comm != single_replica) {
+ return COLVARS_OK;
+}
- // reread the replicas registry
- if ((cvm::step_absolute() % replica_update_freq) == 0) {
- update_replicas_registry();
- // empty the output buffer
- if (replica_hills_os.is_open())
- replica_hills_os.flush();
- read_replica_files();
+int colvarbias_meta::update_grid_data()
+{
+ if ((cvm::step_absolute() % grids_freq) == 0) {
+ // map the most recent gaussians to the grids
+ project_hills(new_hills_begin, hills.end(),
+ hills_energy, hills_energy_gradients);
+ new_hills_begin = hills.end();
+
+ // TODO: we may want to condense all into one replicas array,
+ // including "this" as the first element
+ if (comm == multiple_replicas) {
+ for (size_t ir = 0; ir < replicas.size(); ir++) {
+ replicas[ir]->project_hills(replicas[ir]->new_hills_begin,
+ replicas[ir]->hills.end(),
+ replicas[ir]->hills_energy,
+ replicas[ir]->hills_energy_gradients);
+ replicas[ir]->new_hills_begin = replicas[ir]->hills.end();
+ }
}
}
- // calculate the biasing energy and forces
- bias_energy = 0.0;
- for (size_t ir = 0; ir < colvars.size(); ir++) {
- colvar_forces[ir].reset();
+ return COLVARS_OK;
+}
+
+
+int colvarbias_meta::calc_energy(std::vector<colvarvalue> const &values)
+{
+ size_t ir = 0;
+
+ for (ir = 0; ir < replicas.size(); ir++) {
+ replicas[ir]->bias_energy = 0.0;
}
- if (comm == multiple_replicas)
- for (size_t ir = 0; ir < replicas.size(); ir++) {
- replicas[ir]->bias_energy = 0.0;
- for (size_t ic = 0; ic < colvars.size(); ic++) {
- replicas[ir]->colvar_forces[ic].reset();
- }
- }
- if (use_grids) {
+ std::vector<int> const curr_bin = values.size() ?
+ hills_energy->get_colvars_index(values) :
+ hills_energy->get_colvars_index();
- // get the forces from the grid
-
- if ((cvm::step_absolute() % grids_freq) == 0) {
- // map the most recent gaussians to the grids
- project_hills(new_hills_begin, hills.end(),
- hills_energy, hills_energy_gradients);
- new_hills_begin = hills.end();
-
- // TODO: we may want to condense all into one replicas array,
- // including "this" as the first element
- if (comm == multiple_replicas) {
- for (size_t ir = 0; ir < replicas.size(); ir++) {
- replicas[ir]->project_hills(replicas[ir]->new_hills_begin,
- replicas[ir]->hills.end(),
- replicas[ir]->hills_energy,
- replicas[ir]->hills_energy_gradients);
- replicas[ir]->new_hills_begin = replicas[ir]->hills.end();
- }
+ if (hills_energy->index_ok(curr_bin)) {
+ // index is within the grid: get the energy from there
+ for (ir = 0; ir < replicas.size(); ir++) {
+
+ bias_energy += replicas[ir]->hills_energy->value(curr_bin);
+ if (cvm::debug()) {
+ cvm::log("Metadynamics bias \""+this->name+"\""+
+ ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
+ ": current coordinates on the grid: "+
+ cvm::to_str(curr_bin)+".\n");
+ cvm::log("Grid energy = "+cvm::to_str(bias_energy)+".\n");
}
}
+ } else {
+ // off the grid: compute analytically only the hills at the grid's edges
+ for (ir = 0; ir < replicas.size(); ir++) {
+ calc_hills(replicas[ir]->hills_off_grid.begin(),
+ replicas[ir]->hills_off_grid.end(),
+ bias_energy,
+ values);
+ }
+ }
- std::vector<int> curr_bin = hills_energy->get_colvars_index();
- if (cvm::debug())
- cvm::log("Metadynamics bias \""+this->name+"\""+
- ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
- ": current coordinates on the grid: "+
- cvm::to_str(curr_bin)+".\n");
+ // now include the hills that have not been binned yet (starting
+ // from new_hills_begin)
- if (hills_energy->index_ok(curr_bin)) {
+ for (ir = 0; ir < replicas.size(); ir++) {
+ calc_hills(replicas[ir]->new_hills_begin,
+ replicas[ir]->hills.end(),
+ bias_energy);
+ if (cvm::debug()) {
+ cvm::log("Hills energy = "+cvm::to_str(bias_energy)+".\n");
+ }
+ }
- // within the grid: add the energy and the forces from there
+ return COLVARS_OK;
+}
- bias_energy += hills_energy->value(curr_bin);
- for (size_t ic = 0; ic < colvars.size(); ic++) {
- cvm::real const *f = &(hills_energy_gradients->value(curr_bin));
- colvar_forces[ic].real_value += -1.0 * f[ic];
- // the gradients are stored, not the forces
- }
- if (comm == multiple_replicas)
- for (size_t ir = 0; ir < replicas.size(); ir++) {
- bias_energy += replicas[ir]->hills_energy->value(curr_bin);
- cvm::real const *f = &(replicas[ir]->hills_energy_gradients->value(curr_bin));
- for (size_t ic = 0; ic < colvars.size(); ic++) {
- colvar_forces[ic].real_value += -1.0 * f[ic];
- }
- }
- } else {
+int colvarbias_meta::calc_forces(std::vector<colvarvalue> const &values)
+{
+ size_t ir = 0, ic = 0;
+ for (ir = 0; ir < replicas.size(); ir++) {
+ for (ic = 0; ic < num_variables(); ic++) {
+ replicas[ir]->colvar_forces[ic].reset();
+ }
+ }
- // off the grid: compute analytically only the hills at the grid's edges
+ std::vector<int> const curr_bin = values.size() ?
+ hills_energy->get_colvars_index(values) :
+ hills_energy->get_colvars_index();
- calc_hills(hills_off_grid.begin(), hills_off_grid.end(), bias_energy);
- for (size_t ic = 0; ic < colvars.size(); ic++) {
- calc_hills_force(ic, hills_off_grid.begin(), hills_off_grid.end(), colvar_forces);
+ if (hills_energy->index_ok(curr_bin)) {
+ for (ir = 0; ir < replicas.size(); ir++) {
+ cvm::real const *f = &(replicas[ir]->hills_energy_gradients->value(curr_bin));
+ for (ic = 0; ic < num_variables(); ic++) {
+ // the gradients are stored, not the forces
+ colvar_forces[ic].real_value += -1.0 * f[ic];
+ }
+ }
+ } else {
+ // off the grid: compute analytically only the hills at the grid's edges
+ for (ir = 0; ir < replicas.size(); ir++) {
+ for (ic = 0; ic < num_variables(); ic++) {
+ calc_hills_force(ic,
+ replicas[ir]->hills_off_grid.begin(),
+ replicas[ir]->hills_off_grid.end(),
+ colvar_forces,
+ values);
}
-
- if (comm == multiple_replicas)
- for (size_t ir = 0; ir < replicas.size(); ir++) {
- calc_hills(replicas[ir]->hills_off_grid.begin(),
- replicas[ir]->hills_off_grid.end(),
- bias_energy);
- for (size_t ic = 0; ic < colvars.size(); ic++) {
- calc_hills_force(ic,
- replicas[ir]->hills_off_grid.begin(),
- replicas[ir]->hills_off_grid.end(),
- colvar_forces);
- }
- }
}
}
// now include the hills that have not been binned yet (starting
// from new_hills_begin)
- calc_hills(new_hills_begin, hills.end(), bias_energy);
- for (size_t ic = 0; ic < colvars.size(); ic++) {
- calc_hills_force(ic, new_hills_begin, hills.end(), colvar_forces);
- }
-
- if (cvm::debug())
- cvm::log("Hills energy = "+cvm::to_str(bias_energy)+
- ", hills forces = "+cvm::to_str(colvar_forces)+".\n");
-
- if (cvm::debug())
+ if (cvm::debug()) {
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": adding the forces from the other replicas.\n");
+ }
- if (comm == multiple_replicas)
- for (size_t ir = 0; ir < replicas.size(); ir++) {
- calc_hills(replicas[ir]->new_hills_begin,
- replicas[ir]->hills.end(),
- bias_energy);
- for (size_t ic = 0; ic < colvars.size(); ic++) {
- calc_hills_force(ic,
- replicas[ir]->new_hills_begin,
- replicas[ir]->hills.end(),
- colvar_forces);
+ for (ir = 0; ir < replicas.size(); ir++) {
+ for (ic = 0; ic < num_variables(); ic++) {
+ calc_hills_force(ic,
+ replicas[ir]->new_hills_begin,
+ replicas[ir]->hills.end(),
+ colvar_forces,
+ values);
+ if (cvm::debug()) {
+ cvm::log("Hills forces = "+cvm::to_str(colvar_forces)+".\n");
}
- if (cvm::debug())
- cvm::log("Hills energy = "+cvm::to_str(bias_energy)+
- ", hills forces = "+cvm::to_str(colvar_forces)+".\n");
}
+ }
return COLVARS_OK;
}
+
void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter h_first,
colvarbias_meta::hill_iter h_last,
cvm::real &energy,
std::vector<colvarvalue> const &colvar_values)
{
- std::vector<colvarvalue> curr_values(colvars.size());
- for (size_t i = 0; i < colvars.size(); i++) {
- curr_values[i].type(colvars[i]->value());
+ size_t i = 0;
+ std::vector<colvarvalue> curr_values(num_variables());
+ for (i = 0; i < num_variables(); i++) {
+ curr_values[i].type(variables(i)->value());
}
if (colvar_values.size()) {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
curr_values[i] = colvar_values[i];
}
} else {
- for (size_t i = 0; i < colvars.size(); i++) {
- curr_values[i] = colvars[i]->value();
+ for (i = 0; i < num_variables(); i++) {
+ curr_values[i] = variables(i)->value();
}
}
@@ -632,11 +678,11 @@ void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter h_first,
// compute the gaussian exponent
cvm::real cv_sqdev = 0.0;
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
colvarvalue const &x = curr_values[i];
colvarvalue const ¢er = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
- cv_sqdev += (colvars[i]->dist2(x, center)) / (half_width*half_width);
+ cv_sqdev += (variables(i)->dist2(x, center)) / (half_width*half_width);
}
// compute the gaussian
@@ -658,14 +704,14 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
std::vector<colvarvalue> const &values)
{
// Retrieve the value of the colvar
- colvarvalue const x(values.size() ? values[i] : colvars[i]->value());
+ colvarvalue const x(values.size() ? values[i] : variables(i)->value());
// do the type check only once (all colvarvalues in the hills series
// were already saved with their types matching those in the
// colvars)
hill_iter h;
- switch (colvars[i]->value().type()) {
+ switch (variables(i)->value().type()) {
case colvarvalue::type_scalar:
for (h = h_first; h != h_last; h++) {
@@ -674,7 +720,7 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].real_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
- (colvars[i]->dist2_lgrad(x, center)).real_value );
+ (variables(i)->dist2_lgrad(x, center)).real_value );
}
break;
@@ -687,7 +733,7 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].rvector_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
- (colvars[i]->dist2_lgrad(x, center)).rvector_value );
+ (variables(i)->dist2_lgrad(x, center)).rvector_value );
}
break;
@@ -699,7 +745,7 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].quaternion_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
- (colvars[i]->dist2_lgrad(x, center)).quaternion_value );
+ (variables(i)->dist2_lgrad(x, center)).quaternion_value );
}
break;
@@ -710,7 +756,7 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].vector1d_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
- (colvars[i]->dist2_lgrad(x, center)).vector1d_value );
+ (variables(i)->dist2_lgrad(x, center)).vector1d_value );
}
break;
@@ -739,13 +785,13 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
// TODO: improve it by looping over a small subgrid instead of the whole grid
- std::vector<colvarvalue> colvar_values(colvars.size());
- std::vector<cvm::real> colvar_forces_scalar(colvars.size());
+ std::vector<colvarvalue> colvar_values(num_variables());
+ std::vector<cvm::real> colvar_forces_scalar(num_variables());
std::vector<int> he_ix = he->new_index();
std::vector<int> hg_ix = (hg != NULL) ? hg->new_index() : std::vector<int> (0);
cvm::real hills_energy_here = 0.0;
- std::vector<colvarvalue> hills_forces_here(colvars.size(), 0.0);
+ std::vector<colvarvalue> hills_forces_here(num_variables(), 0.0);
size_t count = 0;
size_t const print_frequency = ((hills.size() >= 1000000) ? 1 : (1000000/(hills.size()+1)));
@@ -757,7 +803,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
(he->index_ok(he_ix)) && (hg->index_ok(hg_ix));
count++) {
size_t i;
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i);
}
@@ -766,7 +812,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
calc_hills(h_first, h_last, hills_energy_here, colvar_values);
he->acc_value(he_ix, hills_energy_here);
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
hills_forces_here[i].reset();
calc_hills_force(i, h_first, h_last, hills_forces_here, colvar_values);
colvar_forces_scalar[i] = hills_forces_here[i].real_value;
@@ -795,7 +841,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
for ( ; (he->index_ok(he_ix)); ) {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i);
}
@@ -851,6 +897,21 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first
// **********************************************************************
+int colvarbias_meta::replica_share()
+{
+ // sync with the other replicas (if needed)
+ if (comm == multiple_replicas) {
+ // reread the replicas registry
+ update_replicas_registry();
+ // empty the output buffer
+ if (replica_hills_os.is_open())
+ replica_hills_os.flush();
+ read_replica_files();
+ }
+ return COLVARS_OK;
+}
+
+
void colvarbias_meta::update_replicas_registry()
{
if (cvm::debug())
@@ -975,7 +1036,6 @@ void colvarbias_meta::update_replicas_registry()
}
}
-
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\": the list of replicas contains "+
cvm::to_str(replicas.size())+" elements.\n");
@@ -984,7 +1044,8 @@ void colvarbias_meta::update_replicas_registry()
void colvarbias_meta::read_replica_files()
{
- for (size_t ir = 0; ir < replicas.size(); ir++) {
+ // Note: we start from the 2nd replica.
+ for (size_t ir = 1; ir < replicas.size(); ir++) {
if (! (replicas[ir])->replica_state_file_in_sync) {
// if a new state file is being read, the hills file is also new
@@ -1352,9 +1413,9 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
cvm::real h_weight;
get_keyval(data, "weight", h_weight, hill_weight, parse_silent);
- std::vector<colvarvalue> h_centers(colvars.size());
- for (size_t i = 0; i < colvars.size(); i++) {
- h_centers[i].type(colvars[i]->value());
+ std::vector<colvarvalue> h_centers(num_variables());
+ for (size_t i = 0; i < num_variables(); i++) {
+ h_centers[i].type(variables(i)->value());
}
{
// it is safer to read colvarvalue objects one at a time;
@@ -1362,14 +1423,14 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
std::string centers_input;
key_lookup(data, "centers", centers_input);
std::istringstream centers_is(centers_input);
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
centers_is >> h_centers[i];
}
}
- std::vector<cvm::real> h_widths(colvars.size());
+ std::vector<cvm::real> h_widths(num_variables());
get_keyval(data, "widths", h_widths,
- std::vector<cvm::real> (colvars.size(), (std::sqrt(2.0 * PI) / 2.0)),
+ std::vector<cvm::real>(num_variables(), (std::sqrt(2.0 * PI) / 2.0)),
parse_silent);
std::string h_replica = "";
@@ -1406,6 +1467,13 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
int colvarbias_meta::setup_output()
{
+ output_prefix = cvm::output_prefix();
+ if (cvm::num_biases_feature(colvardeps::f_cvb_calc_pmf) > 1) {
+ // if this is not the only free energy integrator, append
+ // this bias's name, to distinguish it from the output of the other
+ // biases producing a .pmf file
+ output_prefix += ("."+this->name);
+ }
if (comm == multiple_replicas) {
@@ -1421,10 +1489,10 @@ int colvarbias_meta::setup_output()
// those by another replica
replica_hills_file =
(std::string(pwd)+std::string(PATHSEP)+
- cvm::output_prefix+".colvars."+this->name+"."+replica_id+".hills");
+ cvm::output_prefix()+".colvars."+this->name+"."+replica_id+".hills");
replica_state_file =
(std::string(pwd)+std::string(PATHSEP)+
- cvm::output_prefix+".colvars."+this->name+"."+replica_id+".state");
+ cvm::output_prefix()+".colvars."+this->name+"."+replica_id+".state");
delete[] pwd;
// now register this replica
@@ -1492,13 +1560,14 @@ int colvarbias_meta::setup_output()
}
if (b_hills_traj) {
- std::string const traj_file_name(cvm::output_prefix+
+ std::string const traj_file_name(cvm::output_prefix()+
".colvars."+this->name+
( (comm != single_replica) ?
("."+replica_id) :
("") )+
".hills.traj");
if (!hills_traj_os.is_open()) {
+ cvm::backup_file(traj_file_name.c_str());
hills_traj_os.open(traj_file_name.c_str());
}
if (!hills_traj_os.is_open())
@@ -1585,16 +1654,6 @@ void colvarbias_meta::write_pmf()
colvar_grid_scalar *pmf = new colvar_grid_scalar(*hills_energy);
pmf->setup();
- std::string fes_file_name_prefix(cvm::output_prefix);
-
- if ((cvm::n_meta_biases > 1) || (cvm::n_abf_biases > 0)) {
- // if this is not the only free energy integrator, append
- // this bias's name, to distinguish it from the output of the other
- // biases producing a .pmf file
- // TODO: fix for ABF with updateBias == no
- fes_file_name_prefix += ("."+this->name);
- }
-
if ((comm == single_replica) || (dump_replica_fes)) {
// output the PMF from this instance or replica
pmf->reset();
@@ -1607,7 +1666,7 @@ void colvarbias_meta::write_pmf()
pmf->multiply_constant(well_temper_scale);
}
{
- std::string const fes_file_name(fes_file_name_prefix +
+ std::string const fes_file_name(this->output_prefix +
((comm != single_replica) ? ".partial" : "") +
(dump_fes_save ?
"."+cvm::to_str(cvm::step_absolute()) : "") +
@@ -1632,7 +1691,7 @@ void colvarbias_meta::write_pmf()
cvm::real const well_temper_scale = (bias_temperature + cvm::temperature()) / bias_temperature;
pmf->multiply_constant(well_temper_scale);
}
- std::string const fes_file_name(fes_file_name_prefix +
+ std::string const fes_file_name(this->output_prefix +
(dump_fes_save ?
"."+cvm::to_str(cvm::step_absolute()) : "") +
".pmf");
diff --git a/lib/colvars/colvarbias_meta.h b/lib/colvars/colvarbias_meta.h
index a88a34ba00a7749895390cd81e5179687ebb5599..01921eaf640855f40fabcd8147b4815e7579cd89 100644
--- a/lib/colvars/colvarbias_meta.h
+++ b/lib/colvars/colvarbias_meta.h
@@ -36,8 +36,20 @@ public:
colvarbias_meta(char const *key);
virtual int init(std::string const &conf);
+ virtual int init_well_tempered_params(std::string const &conf);
+ virtual int init_ebmeta_params(std::string const &conf);
virtual ~colvarbias_meta();
+
virtual int update();
+ virtual int update_grid_params();
+ virtual int update_bias();
+ virtual int update_grid_data();
+ virtual int replica_share();
+
+ virtual int calc_energy(std::vector<colvarvalue> const &values =
+ std::vector<colvarvalue>(0));
+ virtual int calc_forces(std::vector<colvarvalue> const &values =
+ std::vector<colvarvalue>(0));
virtual std::string const get_state_params() const;
virtual int set_state_params(std::string const &state_conf);
@@ -102,18 +114,18 @@ protected:
/// \brief Calculate the values of the hills, incrementing
/// bias_energy
virtual void calc_hills(hill_iter h_first,
- hill_iter h_last,
- cvm::real &energy,
- std::vector<colvarvalue> const &values = std::vector<colvarvalue> (0));
+ hill_iter h_last,
+ cvm::real &energy,
+ std::vector<colvarvalue> const &values = std::vector<colvarvalue>(0));
/// \brief Calculate the forces acting on the i-th colvar,
/// incrementing colvar_forces[i]; must be called after calc_hills
/// each time the values of the colvars are changed
virtual void calc_hills_force(size_t const &i,
- hill_iter h_first,
- hill_iter h_last,
- std::vector<colvarvalue> &forces,
- std::vector<colvarvalue> const &values = std::vector<colvarvalue> (0));
+ hill_iter h_first,
+ hill_iter h_last,
+ std::vector<colvarvalue> &forces,
+ std::vector<colvarvalue> const &values = std::vector<colvarvalue>(0));
/// Height of new hills
diff --git a/lib/colvars/colvarbias_restraint.cpp b/lib/colvars/colvarbias_restraint.cpp
index 84630984e5085fb9b07e96ca9ad8da9480608b62..159d9eae6451bbfc9a307d8507d64888188c5bc7 100644
--- a/lib/colvars/colvarbias_restraint.cpp
+++ b/lib/colvars/colvarbias_restraint.cpp
@@ -33,17 +33,15 @@ int colvarbias_restraint::init(std::string const &conf)
int colvarbias_restraint::update()
{
- bias_energy = 0.0;
-
- if (cvm::debug())
- cvm::log("Updating the restraint bias \""+this->name+"\".\n");
+ // Update base class (bias_energy and colvar_forces are zeroed there)
+ colvarbias::update();
// Force and energy calculation
- for (size_t i = 0; i < colvars.size(); i++) {
- colvar_forces[i].type(colvars[i]->value());
+ for (size_t i = 0; i < num_variables(); i++) {
+ bias_energy += restraint_potential(i);
+ colvar_forces[i].type(variables(i)->value());
colvar_forces[i].is_derivative();
colvar_forces[i] = restraint_force(i);
- bias_energy += restraint_potential(i);
}
if (cvm::debug())
@@ -59,8 +57,6 @@ int colvarbias_restraint::update()
colvarbias_restraint::~colvarbias_restraint()
{
- if (cvm::n_rest_biases > 0)
- cvm::n_rest_biases -= 1;
}
@@ -102,18 +98,18 @@ int colvarbias_restraint_centers::init(std::string const &conf)
bool null_centers = (colvar_centers.size() == 0);
if (null_centers) {
// try to initialize the restraint centers for the first time
- colvar_centers.resize(colvars.size());
- colvar_centers_raw.resize(colvars.size());
- for (i = 0; i < colvars.size(); i++) {
- colvar_centers[i].type(colvars[i]->value());
+ colvar_centers.resize(num_variables());
+ colvar_centers_raw.resize(num_variables());
+ for (i = 0; i < num_variables(); i++) {
+ colvar_centers[i].type(variables(i)->value());
colvar_centers[i].reset();
- colvar_centers_raw[i].type(colvars[i]->value());
+ colvar_centers_raw[i].type(variables(i)->value());
colvar_centers_raw[i].reset();
}
}
if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) {
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
if (cvm::debug()) {
cvm::log("colvarbias_restraint: parsing initial centers, i = "+cvm::to_str(i)+".\n");
}
@@ -129,7 +125,7 @@ int colvarbias_restraint_centers::init(std::string const &conf)
return INPUT_ERROR;
}
- if (colvar_centers.size() != colvars.size()) {
+ if (colvar_centers.size() != num_variables()) {
cvm::error("Error: number of centers does not match "
"that of collective variables.\n", INPUT_ERROR);
return INPUT_ERROR;
@@ -142,10 +138,10 @@ int colvarbias_restraint_centers::init(std::string const &conf)
int colvarbias_restraint_centers::change_configuration(std::string const &conf)
{
if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) {
- for (size_t i = 0; i < colvars.size(); i++) {
- colvar_centers[i].type(colvars[i]->value());
+ for (size_t i = 0; i < num_variables(); i++) {
+ colvar_centers[i].type(variables(i)->value());
colvar_centers[i].apply_constraints();
- colvar_centers_raw[i].type(colvars[i]->value());
+ colvar_centers_raw[i].type(variables(i)->value());
colvar_centers_raw[i] = colvar_centers[i];
}
}
@@ -269,7 +265,7 @@ int colvarbias_restraint_centers_moving::init(std::string const &conf)
size_t i;
if (get_keyval(conf, "targetCenters", target_centers, colvar_centers)) {
- if (colvar_centers.size() != colvars.size()) {
+ if (colvar_centers.size() != num_variables()) {
cvm::error("Error: number of target centers does not match "
"that of collective variables.\n");
}
@@ -308,9 +304,9 @@ int colvarbias_restraint_centers_moving::update()
// at each simulation step (or stage, if applicable)
// (take current stage into account: it can be non-zero
// if we are restarting a staged calculation)
- centers_incr.resize(colvars.size());
- for (size_t i = 0; i < colvars.size(); i++) {
- centers_incr[i].type(colvars[i]->value());
+ centers_incr.resize(num_variables());
+ for (size_t i = 0; i < num_variables(); i++) {
+ centers_incr[i].type(variables(i)->value());
centers_incr[i] = (target_centers[i] - colvar_centers_raw[i]) /
cvm::real( target_nstages ? (target_nstages - stage) :
(target_nsteps - cvm::step_absolute()));
@@ -326,10 +322,10 @@ int colvarbias_restraint_centers_moving::update()
&& (cvm::step_absolute() % target_nsteps) == 0
&& stage < target_nstages) {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
colvar_centers_raw[i] += centers_incr[i];
colvar_centers[i] = colvar_centers_raw[i];
- colvars[i]->wrap(colvar_centers[i]);
+ variables(i)->wrap(colvar_centers[i]);
colvar_centers[i].apply_constraints();
}
stage++;
@@ -341,10 +337,10 @@ int colvarbias_restraint_centers_moving::update()
} else if ((cvm::step_relative() > 0) && (cvm::step_absolute() <= target_nsteps)) {
// move the restraint centers in the direction of the targets
// (slow growth)
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
colvar_centers_raw[i] += centers_incr[i];
colvar_centers[i] = colvar_centers_raw[i];
- colvars[i]->wrap(colvar_centers[i]);
+ variables(i)->wrap(colvar_centers[i]);
colvar_centers[i].apply_constraints();
}
}
@@ -363,7 +359,7 @@ int colvarbias_restraint_centers_moving::update_acc_work()
{
if (b_output_acc_work) {
if ((cvm::step_relative() > 0) || (cvm::step_absolute() == 0)) {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
// project forces on the calculated increments at this step
acc_work += colvar_forces[i] * centers_incr[i];
}
@@ -381,14 +377,14 @@ std::string const colvarbias_restraint_centers_moving::get_state_params() const
if (b_chg_centers) {
size_t i;
os << "centers ";
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< colvar_centers[i];
}
os << "\n";
os << "centers_raw ";
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< colvar_centers_raw[i];
@@ -429,10 +425,10 @@ int colvarbias_restraint_centers_moving::set_state_params(std::string const &con
std::ostream & colvarbias_restraint_centers_moving::write_traj_label(std::ostream &os)
{
if (b_output_centers) {
- for (size_t i = 0; i < colvars.size(); i++) {
- size_t const this_cv_width = (colvars[i]->value()).output_width(cvm::cv_width);
+ for (size_t i = 0; i < num_variables(); i++) {
+ size_t const this_cv_width = (variables(i)->value()).output_width(cvm::cv_width);
os << " x0_"
- << cvm::wrap_string(colvars[i]->name, this_cv_width-3);
+ << cvm::wrap_string(variables(i)->name, this_cv_width-3);
}
}
@@ -448,7 +444,7 @@ std::ostream & colvarbias_restraint_centers_moving::write_traj_label(std::ostrea
std::ostream & colvarbias_restraint_centers_moving::write_traj(std::ostream &os)
{
if (b_output_centers) {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< colvar_centers[i];
@@ -539,9 +535,9 @@ int colvarbias_restraint_k_moving::update()
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow(lambda, force_k_exp);
- cvm::log("Restraint " + this->name + ", stage " +
- cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda));
- cvm::log("Setting force constant to " + cvm::to_str(force_k));
+ cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage)
+ + " : lambda = " + cvm::to_str(lambda)
+ + ", k = " + cvm::to_str(force_k));
}
// TI calculation: estimate free energy derivative
@@ -557,7 +553,7 @@ int colvarbias_restraint_k_moving::update()
// Square distance normalized by square colvar width
cvm::real dist_sq = 0.0;
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
dist_sq += d_restraint_potential_dk(i);
}
@@ -569,7 +565,8 @@ int colvarbias_restraint_k_moving::update()
if (cvm::step_absolute() % target_nsteps == 0 &&
cvm::step_absolute() > 0) {
- cvm::log("Lambda= " + cvm::to_str(lambda) + " dA/dLambda= "
+ cvm::log("Restraint " + this->name + " Lambda= "
+ + cvm::to_str(lambda) + " dA/dLambda= "
+ cvm::to_str(restraint_FE / cvm::real(target_nsteps - target_equil_steps)));
// ...and move on to the next one
@@ -584,9 +581,9 @@ int colvarbias_restraint_k_moving::update()
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow(lambda, force_k_exp);
- cvm::log("Restraint " + this->name + ", stage " +
- cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda));
- cvm::log("Setting force constant to " + cvm::to_str(force_k));
+ cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage)
+ + " : lambda = " + cvm::to_str(lambda)
+ + ", k = " + cvm::to_str(force_k));
}
}
@@ -721,11 +718,11 @@ int colvarbias_restraint_harmonic::init(std::string const &conf)
colvarbias_restraint_centers_moving::init(conf);
colvarbias_restraint_k_moving::init(conf);
- for (size_t i = 0; i < colvars.size(); i++) {
- if (colvars[i]->width != 1.0)
- cvm::log("The force constant for colvar \""+colvars[i]->name+
+ for (size_t i = 0; i < num_variables(); i++) {
+ if (variables(i)->width != 1.0)
+ cvm::log("The force constant for colvar \""+variables(i)->name+
"\" will be rescaled to "+
- cvm::to_str(force_k / (colvars[i]->width * colvars[i]->width))+
+ cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+
" according to the specified width.\n");
}
@@ -751,22 +748,22 @@ int colvarbias_restraint_harmonic::update()
cvm::real colvarbias_restraint_harmonic::restraint_potential(size_t i) const
{
- return 0.5 * force_k / (colvars[i]->width * colvars[i]->width) *
- colvars[i]->dist2(colvars[i]->value(), colvar_centers[i]);
+ return 0.5 * force_k / (variables(i)->width * variables(i)->width) *
+ variables(i)->dist2(variables(i)->value(), colvar_centers[i]);
}
colvarvalue const colvarbias_restraint_harmonic::restraint_force(size_t i) const
{
- return -0.5 * force_k / (colvars[i]->width * colvars[i]->width) *
- colvars[i]->dist2_lgrad(colvars[i]->value(), colvar_centers[i]);
+ return -0.5 * force_k / (variables(i)->width * variables(i)->width) *
+ variables(i)->dist2_lgrad(variables(i)->value(), colvar_centers[i]);
}
cvm::real colvarbias_restraint_harmonic::d_restraint_potential_dk(size_t i) const
{
- return 0.5 / (colvars[i]->width * colvars[i]->width) *
- colvars[i]->dist2(colvars[i]->value(), colvar_centers[i]);
+ return 0.5 / (variables(i)->width * variables(i)->width) *
+ variables(i)->dist2(variables(i)->value(), colvar_centers[i]);
}
@@ -840,6 +837,8 @@ colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls(char co
colvarbias_restraint_moving(key),
colvarbias_restraint_k_moving(key)
{
+ lower_wall_k = 0.0;
+ upper_wall_k = 0.0;
}
@@ -849,7 +848,11 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
colvarbias_restraint_moving::init(conf);
colvarbias_restraint_k_moving::init(conf);
- provide(f_cvb_scalar_variables);
+ get_keyval(conf, "lowerWallConstant", lower_wall_k,
+ (lower_wall_k > 0.0) ? lower_wall_k : force_k);
+ get_keyval(conf, "upperWallConstant", upper_wall_k,
+ (upper_wall_k > 0.0) ? upper_wall_k : force_k);
+
enable(f_cvb_scalar_variables);
size_t i;
@@ -857,9 +860,9 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
bool b_null_lower_walls = false;
if (lower_walls.size() == 0) {
b_null_lower_walls = true;
- lower_walls.resize(number_of_colvars());
- for (i = 0; i < colvars.size(); i++) {
- lower_walls[i].type(colvars[i]->value());
+ lower_walls.resize(num_variables());
+ for (i = 0; i < num_variables(); i++) {
+ lower_walls[i].type(variables(i)->value());
lower_walls[i].reset();
}
}
@@ -872,9 +875,9 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
bool b_null_upper_walls = false;
if (upper_walls.size() == 0) {
b_null_upper_walls = true;
- upper_walls.resize(number_of_colvars());
- for (i = 0; i < colvars.size(); i++) {
- upper_walls[i].type(colvars[i]->value());
+ upper_walls.resize(num_variables());
+ for (i = 0; i < num_variables(); i++) {
+ upper_walls[i].type(variables(i)->value());
upper_walls[i].reset();
}
}
@@ -890,17 +893,17 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
}
if ((lower_walls.size() == 0) || (upper_walls.size() == 0)) {
- for (i = 0; i < colvars.size(); i++) {
- if (colvars[i]->is_enabled(f_cv_periodic)) {
+ for (i = 0; i < num_variables(); i++) {
+ if (variables(i)->is_enabled(f_cv_periodic)) {
cvm::error("Error: at least one variable is periodic, "
- "both walls must be provided .\n", INPUT_ERROR);
+ "both walls must be provided.\n", INPUT_ERROR);
return INPUT_ERROR;
}
}
}
if ((lower_walls.size() > 0) && (upper_walls.size() > 0)) {
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
if (lower_walls[i] >= upper_walls[i]) {
cvm::error("Error: one upper wall, "+
cvm::to_str(upper_walls[i])+
@@ -909,13 +912,24 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
INPUT_ERROR);
}
}
+ if (lower_wall_k * upper_wall_k == 0.0) {
+ cvm::error("Error: lowerWallConstant and upperWallConstant, "
+ "when defined, must both be positive.\n",
+ INPUT_ERROR);
+ return INPUT_ERROR;
+ }
+ force_k = lower_wall_k * upper_wall_k;
+ // transform the two constants to relative values
+ // (allow changing both via force_k)
+ lower_wall_k /= force_k;
+ upper_wall_k /= force_k;
}
- for (i = 0; i < colvars.size(); i++) {
- if (colvars[i]->width != 1.0)
- cvm::log("The force constant for colvar \""+colvars[i]->name+
+ for (i = 0; i < num_variables(); i++) {
+ if (variables(i)->width != 1.0)
+ cvm::log("The force constant for colvar \""+variables(i)->name+
"\" will be rescaled to "+
- cvm::to_str(force_k / (colvars[i]->width * colvars[i]->width))+
+ cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+
" according to the specified width.\n");
}
@@ -935,20 +949,20 @@ int colvarbias_restraint_harmonic_walls::update()
void colvarbias_restraint_harmonic_walls::communicate_forces()
{
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
if (cvm::debug()) {
cvm::log("Communicating a force to colvar \""+
- colvars[i]->name+"\".\n");
+ variables(i)->name+"\".\n");
}
- colvars[i]->add_bias_force_actual_value(colvar_forces[i]);
+ variables(i)->add_bias_force_actual_value(colvar_forces[i]);
}
}
cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const
{
- colvar *cv = colvars[i];
- colvarvalue const &cvv = colvars[i]->actual_value();
+ colvar *cv = variables(i);
+ colvarvalue const &cvv = variables(i)->actual_value();
// For a periodic colvar, both walls may be applicable at the same time
// in which case we pick the closer one
@@ -958,21 +972,21 @@ cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const
cvm::real const upper_wall_dist2 = cv->dist2(cvv, upper_walls[i]);
if (lower_wall_dist2 < upper_wall_dist2) {
cvm::real const grad = cv->dist2_lgrad(cvv, lower_walls[i]);
- if (grad < 0.0) { return grad; }
+ if (grad < 0.0) { return 0.5 * grad; }
} else {
cvm::real const grad = cv->dist2_lgrad(cvv, upper_walls[i]);
- if (grad > 0.0) { return grad; }
+ if (grad > 0.0) { return 0.5 * grad; }
}
return 0.0;
}
if (lower_walls.size() > 0) {
cvm::real const grad = cv->dist2_lgrad(cvv, lower_walls[i]);
- if (grad < 0.0) { return grad; }
+ if (grad < 0.0) { return 0.5 * grad; }
}
if (upper_walls.size() > 0) {
cvm::real const grad = cv->dist2_lgrad(cvv, upper_walls[i]);
- if (grad > 0.0) { return grad; }
+ if (grad > 0.0) { return 0.5 * grad; }
}
return 0.0;
}
@@ -981,7 +995,8 @@ cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const
cvm::real colvarbias_restraint_harmonic_walls::restraint_potential(size_t i) const
{
cvm::real const dist = colvar_distance(i);
- return 0.5 * force_k / (colvars[i]->width * colvars[i]->width) *
+ cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k;
+ return 0.5 * force_k * scale / (variables(i)->width * variables(i)->width) *
dist * dist;
}
@@ -989,15 +1004,16 @@ cvm::real colvarbias_restraint_harmonic_walls::restraint_potential(size_t i) con
colvarvalue const colvarbias_restraint_harmonic_walls::restraint_force(size_t i) const
{
cvm::real const dist = colvar_distance(i);
- return -0.5 * force_k / (colvars[i]->width * colvars[i]->width) *
- dist;
+ cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k;
+ return - force_k * scale / (variables(i)->width * variables(i)->width) * dist;
}
cvm::real colvarbias_restraint_harmonic_walls::d_restraint_potential_dk(size_t i) const
{
cvm::real const dist = colvar_distance(i);
- return 0.5 / (colvars[i]->width * colvars[i]->width) *
+ cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k;
+ return 0.5 * scale / (variables(i)->width * variables(i)->width) *
dist * dist;
}
@@ -1054,16 +1070,16 @@ int colvarbias_restraint_linear::init(std::string const &conf)
colvarbias_restraint_centers_moving::init(conf);
colvarbias_restraint_k_moving::init(conf);
- for (size_t i = 0; i < colvars.size(); i++) {
- if (colvars[i]->is_enabled(f_cv_periodic)) {
+ for (size_t i = 0; i < num_variables(); i++) {
+ if (variables(i)->is_enabled(f_cv_periodic)) {
cvm::error("Error: linear biases cannot be applied to periodic variables.\n",
INPUT_ERROR);
return INPUT_ERROR;
}
- if (colvars[i]->width != 1.0)
- cvm::log("The force constant for colvar \""+colvars[i]->name+
+ if (variables(i)->width != 1.0)
+ cvm::log("The force constant for colvar \""+variables(i)->name+
"\" will be rescaled to "+
- cvm::to_str(force_k / colvars[i]->width)+
+ cvm::to_str(force_k / variables(i)->width)+
" according to the specified width.\n");
}
@@ -1113,19 +1129,19 @@ cvm::real colvarbias_restraint_linear::energy_difference(std::string const &conf
cvm::real colvarbias_restraint_linear::restraint_potential(size_t i) const
{
- return force_k / colvars[i]->width * (colvars[i]->value() - colvar_centers[i]);
+ return force_k / variables(i)->width * (variables(i)->value() - colvar_centers[i]);
}
colvarvalue const colvarbias_restraint_linear::restraint_force(size_t i) const
{
- return -1.0 * force_k / colvars[i]->width;
+ return -1.0 * force_k / variables(i)->width;
}
cvm::real colvarbias_restraint_linear::d_restraint_potential_dk(size_t i) const
{
- return 1.0 / colvars[i]->width * (colvars[i]->value() - colvar_centers[i]);
+ return 1.0 / variables(i)->width * (variables(i)->value() - colvar_centers[i]);
}
@@ -1279,16 +1295,16 @@ int colvarbias_restraint_histogram::update()
size_t vector_size = 0;
size_t icv;
- for (icv = 0; icv < colvars.size(); icv++) {
- vector_size += colvars[icv]->value().size();
+ for (icv = 0; icv < num_variables(); icv++) {
+ vector_size += variables(icv)->value().size();
}
cvm::real const norm = 1.0/(std::sqrt(2.0*PI)*gaussian_width*vector_size);
// calculate the histogram
p.reset();
- for (icv = 0; icv < colvars.size(); icv++) {
- colvarvalue const &cv = colvars[icv]->value();
+ for (icv = 0; icv < num_variables(); icv++) {
+ colvarvalue const &cv = variables(icv)->value();
if (cv.type() == colvarvalue::type_scalar) {
cvm::real const cv_value = cv.real_value;
size_t igrid;
@@ -1309,7 +1325,9 @@ int colvarbias_restraint_histogram::update()
}
}
} else {
- // TODO
+ cvm::error("Error: unsupported type for variable "+variables(icv)->name+".\n",
+ COLVARS_NOT_IMPLEMENTED);
+ return COLVARS_NOT_IMPLEMENTED;
}
}
@@ -1320,8 +1338,8 @@ int colvarbias_restraint_histogram::update()
bias_energy = 0.5 * force_k_cv * p_diff * p_diff;
// calculate the forces
- for (icv = 0; icv < colvars.size(); icv++) {
- colvarvalue const &cv = colvars[icv]->value();
+ for (icv = 0; icv < num_variables(); icv++) {
+ colvarvalue const &cv = variables(icv)->value();
colvarvalue &cv_force = colvar_forces[icv];
cv_force.type(cv);
cv_force.reset();
@@ -1363,10 +1381,10 @@ int colvarbias_restraint_histogram::update()
std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os)
{
if (b_write_histogram) {
- std::string file_name(cvm::output_prefix+"."+this->name+".hist.dat");
+ std::string file_name(cvm::output_prefix()+"."+this->name+".hist.dat");
std::ofstream os(file_name.c_str());
- os << "# " << cvm::wrap_string(colvars[0]->name, cvm::cv_width)
- << " " << "p(" << cvm::wrap_string(colvars[0]->name, cvm::cv_width-3)
+ os << "# " << cvm::wrap_string(variables(0)->name, cvm::cv_width)
+ << " " << "p(" << cvm::wrap_string(variables(0)->name, cvm::cv_width-3)
<< ")\n";
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
diff --git a/lib/colvars/colvarbias_restraint.h b/lib/colvars/colvarbias_restraint.h
index cbdd9c44d163a3c4684eafafaeb07cfa0a9b0495..98b967abdb1ba6a50754e2f26c3d9600e742557a 100644
--- a/lib/colvars/colvarbias_restraint.h
+++ b/lib/colvars/colvarbias_restraint.h
@@ -260,6 +260,12 @@ protected:
/// \brief Location of the upper walls
std::vector<colvarvalue> upper_walls;
+ /// \brief If both walls are defined, use this k for the lower
+ cvm::real lower_wall_k;
+
+ /// \brief If both walls are defined, use this k for the upper
+ cvm::real upper_wall_k;
+
virtual cvm::real colvar_distance(size_t i) const;
virtual cvm::real restraint_potential(size_t i) const;
virtual colvarvalue const restraint_force(size_t i) const;
diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp
index d99da56386f05970d4d90f30d1cee27811390aa0..786bc032d2ab11e5eb466c1ef3b43dda01809560 100644
--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@@ -48,8 +48,6 @@ colvar::cvc::cvc(std::string const &conf)
get_keyval(conf, "period", period, 0.0);
get_keyval(conf, "wrapAround", wrap_center, 0.0);
- // All cvcs implement this
- provide(f_cvc_debug_gradient);
get_keyval_feature((colvarparse *)this, conf, "debugGradients",
f_cvc_debug_gradient, false, parse_silent);
@@ -63,6 +61,8 @@ colvar::cvc::cvc(std::string const &conf)
int colvar::cvc::init_total_force_params(std::string const &conf)
{
+ if (cvm::get_error()) return COLVARS_ERROR;
+
if (get_keyval_feature(this, conf, "oneSiteSystemForce",
f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) {
cvm::log("Warning: keyword \"oneSiteSystemForce\" is deprecated: "
@@ -72,6 +72,19 @@ int colvar::cvc::init_total_force_params(std::string const &conf)
f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) {
cvm::log("Computing total force on group 1 only");
}
+
+ if (! is_enabled(f_cvc_one_site_total_force)) {
+ // check whether any of the other atom groups is dummy
+ std::vector<cvm::atom_group *>::iterator agi = atom_groups.begin();
+ agi++;
+ for ( ; agi != atom_groups.end(); agi++) {
+ if ((*agi)->b_dummy) {
+ provide(f_cvc_inv_gradient, false);
+ provide(f_cvc_Jacobian, false);
+ }
+ }
+ }
+
return COLVARS_OK;
}
@@ -87,8 +100,7 @@ cvm::atom_group *colvar::cvc::parse_group(std::string const &conf,
group->key = group_key;
if (b_try_scalable) {
- // TODO rewrite this logic in terms of dependencies
- if (is_available(f_cvc_scalable_com) && is_available(f_cvc_com_based)) {
+ if (is_available(f_cvc_scalable_com) && is_enabled(f_cvc_com_based)) {
enable(f_cvc_scalable_com);
enable(f_cvc_scalable);
// The CVC makes the feature available;
diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h
index a230cae8a9a04bf9b42e4b769f8e693062b8926d..ec215cbad107485d84f534d6c0eeeaff7b552e96 100644
--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@@ -343,6 +343,15 @@ public:
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
+ /// Redefined to override the distance ones
+ virtual cvm::real dist2(colvarvalue const &x1,
+ colvarvalue const &x2) const;
+ /// Redefined to override the distance ones
+ virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
+ colvarvalue const &x2) const;
+ /// Redefined to override the distance ones
+ virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
+ colvarvalue const &x2) const;
};
diff --git a/lib/colvars/colvarcomp_angles.cpp b/lib/colvars/colvarcomp_angles.cpp
index 4c3390a8bd1de9bf0fb37288d114d6cb8177daca..0204f3b4b1b50d83c58fe4d27be05c015cae1f10 100644
--- a/lib/colvars/colvarcomp_angles.cpp
+++ b/lib/colvars/colvarcomp_angles.cpp
@@ -21,7 +21,7 @@ colvar::angle::angle(std::string const &conf)
function_type = "angle";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
@@ -40,7 +40,7 @@ colvar::angle::angle(cvm::atom const &a1,
function_type = "angle";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
@@ -259,7 +259,7 @@ colvar::dihedral::dihedral(std::string const &conf)
b_periodic = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
@@ -285,7 +285,7 @@ colvar::dihedral::dihedral(cvm::atom const &a1,
b_periodic = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
b_1site_force = false;
diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp
index 7481dd360ba170e327a31977d21c33d47f4507a1..f46270246f5abbfd304568c3d7a0dca6317efbd3 100644
--- a/lib/colvars/colvarcomp_distances.cpp
+++ b/lib/colvars/colvarcomp_distances.cpp
@@ -23,7 +23,7 @@ colvar::distance::distance(std::string const &conf)
function_type = "distance";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
@@ -44,7 +44,7 @@ colvar::distance::distance()
function_type = "distance";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
b_no_PBC = false;
x.type(colvarvalue::type_scalar);
}
@@ -106,7 +106,7 @@ colvar::distance_vec::distance_vec(std::string const &conf)
: distance(conf)
{
function_type = "distance_vec";
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
x.type(colvarvalue::type_3vector);
}
@@ -115,7 +115,7 @@ colvar::distance_vec::distance_vec()
: distance()
{
function_type = "distance_vec";
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
x.type(colvarvalue::type_3vector);
}
@@ -176,7 +176,7 @@ colvar::distance_z::distance_z(std::string const &conf)
function_type = "distance_z";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
x.type(colvarvalue::type_scalar);
// TODO detect PBC from MD engine (in simple cases)
@@ -228,7 +228,7 @@ colvar::distance_z::distance_z()
function_type = "distance_z";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
x.type(colvarvalue::type_scalar);
}
@@ -372,7 +372,7 @@ colvar::distance_xy::distance_xy(std::string const &conf)
function_type = "distance_xy";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
x.type(colvarvalue::type_scalar);
}
@@ -383,7 +383,7 @@ colvar::distance_xy::distance_xy()
function_type = "distance_xy";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
x.type(colvarvalue::type_scalar);
}
@@ -479,7 +479,7 @@ colvar::distance_dir::distance_dir(std::string const &conf)
: distance(conf)
{
function_type = "distance_dir";
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
x.type(colvarvalue::type_unit3vector);
}
@@ -488,7 +488,7 @@ colvar::distance_dir::distance_dir()
: distance()
{
function_type = "distance_dir";
- provide(f_cvc_com_based);
+ enable(f_cvc_com_based);
x.type(colvarvalue::type_unit3vector);
}
@@ -529,6 +529,27 @@ void colvar::distance_dir::apply_force(colvarvalue const &force)
}
+cvm::real colvar::distance_dir::dist2(colvarvalue const &x1,
+ colvarvalue const &x2) const
+{
+ return (x1.rvector_value - x2.rvector_value).norm2();
+}
+
+
+colvarvalue colvar::distance_dir::dist2_lgrad(colvarvalue const &x1,
+ colvarvalue const &x2) const
+{
+ return colvarvalue((x1.rvector_value - x2.rvector_value), colvarvalue::type_unit3vector);
+}
+
+
+colvarvalue colvar::distance_dir::dist2_rgrad(colvarvalue const &x1,
+ colvarvalue const &x2) const
+{
+ return colvarvalue((x2.rvector_value - x1.rvector_value), colvarvalue::type_unit3vector);
+}
+
+
colvar::distance_inv::distance_inv(std::string const &conf)
: distance(conf)
diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp
index e3ccd4ecf5815fcabc0bf7b337a06bf32340c1e7..8252f77e6270d309fdf0db3bad08644ab1c1745b 100644
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@@ -14,9 +14,6 @@
colvardeps::~colvardeps() {
size_t i;
- for (i=0; i<feature_states.size(); i++) {
- if (feature_states[i] != NULL) delete feature_states[i];
- }
// Do not delete features if it's static
// for (i=0; i<features.size(); i++) {
// if (features[i] != NULL) delete features[i];
@@ -34,16 +31,34 @@ colvardeps::~colvardeps() {
}
-void colvardeps::provide(int feature_id) {
- feature_states[feature_id]->available = true;
+void colvardeps::provide(int feature_id, bool truefalse) {
+ feature_states[feature_id].available = truefalse;
+}
+
+
+void colvardeps::set_enabled(int feature_id, bool truefalse) {
+// if (!is_static(feature_id)) {
+// cvm::error("Cannot set feature " + features()[feature_id]->description + " statically in " + description + ".\n");
+// return;
+// }
+ if (truefalse) {
+ // Resolve dependencies too
+ enable(feature_id);
+ } else {
+ feature_states[feature_id].enabled = false;
+ }
}
bool colvardeps::get_keyval_feature(colvarparse *cvp,
- std::string const &conf, char const *key,
- int feature_id, bool const &def_value,
- colvarparse::Parse_Mode const parse_mode)
+ std::string const &conf, char const *key,
+ int feature_id, bool const &def_value,
+ colvarparse::Parse_Mode const parse_mode)
{
+ if (!is_user(feature_id)) {
+ cvm::error("Cannot set feature " + features()[feature_id]->description + " from user input in " + description + ".\n");
+ return false;
+ }
bool value;
bool const found = cvp->get_keyval(conf, key, value, def_value, parse_mode);
if (value) enable(feature_id);
@@ -52,19 +67,19 @@ bool colvardeps::get_keyval_feature(colvarparse *cvp,
int colvardeps::enable(int feature_id,
- bool dry_run /* default: false */,
- // dry_run: fail silently, do not enable if available
- // flag is passed recursively to deps of this feature
- bool toplevel /* default: true */)
- // toplevel: false if this is called as part of a chain of dependency resolution
- // this is used to diagnose failed dependencies by displaying the full stack
- // only the toplevel dependency will throw a fatal error
+ bool dry_run /* default: false */,
+ // dry_run: fail silently, do not enable if available
+ // flag is passed recursively to deps of this feature
+ bool toplevel /* default: true */)
+// toplevel: false if this is called as part of a chain of dependency resolution
+// this is used to diagnose failed dependencies by displaying the full stack
+// only the toplevel dependency will throw a fatal error
{
int res;
size_t i, j;
bool ok;
feature *f = features()[feature_id];
- feature_state *fs = feature_states[feature_id];
+ feature_state *fs = &feature_states[feature_id];
if (cvm::debug()) {
cvm::log("DEPS: " + description +
@@ -88,6 +103,14 @@ int colvardeps::enable(int feature_id,
return COLVARS_ERROR;
}
+ if (!toplevel && !is_dynamic(feature_id)) {
+ if (!dry_run) {
+ cvm::log("Non-dynamic feature : \"" + f->description
+ + "\" in " + description + " may not be enabled as a dependency.\n");
+ }
+ return COLVARS_ERROR;
+ }
+
// 1) enforce exclusions
for (i=0; i<f->requires_exclude.size(); i++) {
feature *g = features()[f->requires_exclude[i]];
@@ -168,9 +191,9 @@ int colvardeps::enable(int feature_id,
if (res != COLVARS_OK) {
if (!dry_run) {
cvm::log("...required by \"" + f->description + "\" in " + description);
- }
- if (toplevel) {
- cvm::error("Error: Failed dependency in " + description + ".");
+ if (toplevel) {
+ cvm::error("Error: Failed dependency in " + description + ".");
+ }
}
return res;
}
@@ -194,9 +217,12 @@ int colvardeps::enable(int feature_id,
// // we need refs to parents to walk up the deps tree!
// // or refresh
// }
+void colvardeps::init_feature(int feature_id, const char *description, feature_type type) {
+ features()[feature_id]->description = description;
+ features()[feature_id]->type = type;
+}
- // Shorthand macros for describing dependencies
-#define f_description(f, d) features()[f]->description = d
+// Shorthand macros for describing dependencies
#define f_req_self(f, g) features()[f]->requires_self.push_back(g)
// This macro ensures that exclusions are symmetric
#define f_req_exclude(f, g) features()[f]->requires_exclude.push_back(g); \
@@ -216,35 +242,31 @@ void colvardeps::init_cvb_requires() {
for (i = 0; i < f_cvb_ntot; i++) {
features().push_back(new feature);
}
- }
- f_description(f_cvb_active, "active");
- f_req_children(f_cvb_active, f_cv_active);
+ init_feature(f_cvb_active, "active", f_type_dynamic);
+ f_req_children(f_cvb_active, f_cv_active);
+
+ init_feature(f_cvb_apply_force, "apply force", f_type_user);
+ f_req_children(f_cvb_apply_force, f_cv_gradient);
- f_description(f_cvb_apply_force, "apply force");
- f_req_children(f_cvb_apply_force, f_cv_gradient);
+ init_feature(f_cvb_get_total_force, "obtain total force");
+ f_req_children(f_cvb_get_total_force, f_cv_total_force);
- f_description(f_cvb_get_total_force, "obtain total force");
- f_req_children(f_cvb_get_total_force, f_cv_total_force);
+ init_feature(f_cvb_history_dependent, "history-dependent", f_type_static);
- f_description(f_cvb_history_dependent, "history-dependent");
+ init_feature(f_cvb_scalar_variables, "require scalar variables", f_type_static);
+ f_req_children(f_cvb_scalar_variables, f_cv_scalar);
- f_description(f_cvb_scalar_variables, "require scalar variables");
- f_req_children(f_cvb_scalar_variables, f_cv_scalar);
+ init_feature(f_cvb_calc_pmf, "calculate a PMF", f_type_static);
+ }
// Initialize feature_states for each instance
feature_states.reserve(f_cvb_ntot);
for (i = 0; i < f_cvb_ntot; i++) {
- feature_states.push_back(new feature_state(true, false));
+ feature_states.push_back(feature_state(true, false));
// Most features are available, so we set them so
// and list exceptions below
}
-
- // some biases are not history-dependent
- feature_states[f_cvb_history_dependent]->available = false;
-
- // by default, biases should work with vector variables, too
- feature_states[f_cvb_scalar_variables]->available = false;
}
@@ -255,117 +277,111 @@ void colvardeps::init_cv_requires() {
features().push_back(new feature);
}
- f_description(f_cv_active, "active");
+ init_feature(f_cv_active, "active", f_type_dynamic);
f_req_children(f_cv_active, f_cvc_active);
// Colvars must be either a linear combination, or scalar (and polynomial) or scripted
f_req_alt3(f_cv_active, f_cv_scalar, f_cv_linear, f_cv_scripted);
- f_description(f_cv_gradient, "gradient");
+ init_feature(f_cv_gradient, "gradient", f_type_dynamic);
f_req_children(f_cv_gradient, f_cvc_gradient);
- f_description(f_cv_collect_gradient, "collect gradient");
+ init_feature(f_cv_collect_gradient, "collect gradient", f_type_dynamic);
f_req_self(f_cv_collect_gradient, f_cv_gradient);
f_req_self(f_cv_collect_gradient, f_cv_scalar);
- f_description(f_cv_fdiff_velocity, "fdiff_velocity");
+ init_feature(f_cv_fdiff_velocity, "fdiff_velocity", f_type_dynamic);
// System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly
- f_description(f_cv_total_force, "total force");
+ init_feature(f_cv_total_force, "total force", f_type_dynamic);
f_req_alt2(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);
// Deps for explicit total force calculation
- f_description(f_cv_total_force_calc, "total force calculation");
+ init_feature(f_cv_total_force_calc, "total force calculation", f_type_dynamic);
f_req_self(f_cv_total_force_calc, f_cv_scalar);
f_req_self(f_cv_total_force_calc, f_cv_linear);
f_req_children(f_cv_total_force_calc, f_cvc_inv_gradient);
f_req_self(f_cv_total_force_calc, f_cv_Jacobian);
- f_description(f_cv_Jacobian, "Jacobian derivative");
+ init_feature(f_cv_Jacobian, "Jacobian derivative", f_type_dynamic);
f_req_self(f_cv_Jacobian, f_cv_scalar);
f_req_self(f_cv_Jacobian, f_cv_linear);
f_req_children(f_cv_Jacobian, f_cvc_Jacobian);
- f_description(f_cv_hide_Jacobian, "hide Jacobian force");
+ init_feature(f_cv_hide_Jacobian, "hide Jacobian force", f_type_user);
f_req_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated
- f_description(f_cv_extended_Lagrangian, "extended Lagrangian");
+ init_feature(f_cv_extended_Lagrangian, "extended Lagrangian", f_type_user);
+ f_req_self(f_cv_extended_Lagrangian, f_cv_scalar);
+ f_req_self(f_cv_extended_Lagrangian, f_cv_gradient);
- f_description(f_cv_Langevin, "Langevin dynamics");
+ init_feature(f_cv_Langevin, "Langevin dynamics", f_type_user);
f_req_self(f_cv_Langevin, f_cv_extended_Lagrangian);
- f_description(f_cv_linear, "linear");
+ init_feature(f_cv_linear, "linear", f_type_static);
- f_description(f_cv_scalar, "scalar");
+ init_feature(f_cv_scalar, "scalar", f_type_static);
- f_description(f_cv_output_energy, "output energy");
+ init_feature(f_cv_output_energy, "output energy", f_type_user);
- f_description(f_cv_output_value, "output value");
+ init_feature(f_cv_output_value, "output value", f_type_user);
- f_description(f_cv_output_velocity, "output velocity");
+ init_feature(f_cv_output_velocity, "output velocity", f_type_user);
f_req_self(f_cv_output_velocity, f_cv_fdiff_velocity);
- f_description(f_cv_output_applied_force, "output applied force");
+ init_feature(f_cv_output_applied_force, "output applied force", f_type_user);
- f_description(f_cv_output_total_force, "output total force");
+ init_feature(f_cv_output_total_force, "output total force", f_type_user);
f_req_self(f_cv_output_total_force, f_cv_total_force);
- f_description(f_cv_subtract_applied_force, "subtract applied force from total force");
+ init_feature(f_cv_subtract_applied_force, "subtract applied force from total force", f_type_user);
f_req_self(f_cv_subtract_applied_force, f_cv_total_force);
- f_description(f_cv_lower_boundary, "lower boundary");
+ init_feature(f_cv_lower_boundary, "lower boundary", f_type_user);
f_req_self(f_cv_lower_boundary, f_cv_scalar);
- f_description(f_cv_upper_boundary, "upper boundary");
+ init_feature(f_cv_upper_boundary, "upper boundary", f_type_user);
f_req_self(f_cv_upper_boundary, f_cv_scalar);
- f_description(f_cv_grid, "grid");
+ init_feature(f_cv_grid, "grid", f_type_user);
f_req_self(f_cv_grid, f_cv_lower_boundary);
f_req_self(f_cv_grid, f_cv_upper_boundary);
- f_description(f_cv_lower_wall, "lower wall");
- f_req_self(f_cv_lower_wall, f_cv_lower_boundary);
- f_req_self(f_cv_lower_wall, f_cv_gradient);
-
- f_description(f_cv_upper_wall, "upper wall");
- f_req_self(f_cv_upper_wall, f_cv_upper_boundary);
- f_req_self(f_cv_upper_wall, f_cv_gradient);
+ init_feature(f_cv_runave, "running average", f_type_user);
- f_description(f_cv_runave, "running average");
+ init_feature(f_cv_corrfunc, "correlation function", f_type_user);
- f_description(f_cv_corrfunc, "correlation function");
-
- // The features below are set programmatically
- f_description(f_cv_scripted, "scripted");
- f_description(f_cv_periodic, "periodic");
+ init_feature(f_cv_scripted, "scripted", f_type_static);
+ init_feature(f_cv_periodic, "periodic", f_type_static);
f_req_self(f_cv_periodic, f_cv_homogeneous);
- f_description(f_cv_scalar, "scalar");
- f_description(f_cv_linear, "linear");
- f_description(f_cv_homogeneous, "homogeneous");
+ init_feature(f_cv_scalar, "scalar", f_type_static);
+ init_feature(f_cv_linear, "linear", f_type_static);
+ init_feature(f_cv_homogeneous, "homogeneous", f_type_static);
}
// Initialize feature_states for each instance
feature_states.reserve(f_cv_ntot);
for (i = 0; i < f_cv_ntot; i++) {
- feature_states.push_back(new feature_state(true, false));
+ feature_states.push_back(feature_state(true, false));
// Most features are available, so we set them so
// and list exceptions below
}
- // properties that may NOT be enabled as a dependency
- int unavailable_deps[] = {
- f_cv_lower_boundary,
- f_cv_upper_boundary,
- f_cv_extended_Lagrangian,
- f_cv_Langevin,
- f_cv_scripted,
- f_cv_periodic,
- f_cv_scalar,
- f_cv_linear,
- f_cv_homogeneous
- };
- for (i = 0; i < sizeof(unavailable_deps) / sizeof(unavailable_deps[0]); i++) {
- feature_states[unavailable_deps[i]]->available = false;
- }
+// // properties that may NOT be enabled as a dependency
+// // This will be deprecated by feature types
+// int unavailable_deps[] = {
+// f_cv_lower_boundary,
+// f_cv_upper_boundary,
+// f_cv_extended_Lagrangian,
+// f_cv_Langevin,
+// f_cv_scripted,
+// f_cv_periodic,
+// f_cv_scalar,
+// f_cv_linear,
+// f_cv_homogeneous
+// };
+// for (i = 0; i < sizeof(unavailable_deps) / sizeof(unavailable_deps[0]); i++) {
+// feature_states[unavailable_deps[i]].available = false;
+// }
}
@@ -377,34 +393,34 @@ void colvardeps::init_cvc_requires() {
features().push_back(new feature);
}
- f_description(f_cvc_active, "active");
+ init_feature(f_cvc_active, "active", f_type_dynamic);
// The dependency below may become useful if we use dynamic atom groups
// f_req_children(f_cvc_active, f_ag_active);
- f_description(f_cvc_scalar, "scalar");
+ init_feature(f_cvc_scalar, "scalar", f_type_static);
- f_description(f_cvc_gradient, "gradient");
+ init_feature(f_cvc_gradient, "gradient", f_type_dynamic);
- f_description(f_cvc_inv_gradient, "inverse gradient");
+ init_feature(f_cvc_inv_gradient, "inverse gradient", f_type_dynamic);
f_req_self(f_cvc_inv_gradient, f_cvc_gradient);
- f_description(f_cvc_debug_gradient, "debug gradient");
+ init_feature(f_cvc_debug_gradient, "debug gradient", f_type_user);
f_req_self(f_cvc_debug_gradient, f_cvc_gradient);
- f_description(f_cvc_Jacobian, "Jacobian derivative");
+ init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic);
f_req_self(f_cvc_Jacobian, f_cvc_inv_gradient);
- f_description(f_cvc_com_based, "depends on group centers of mass");
+ init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static);
// Compute total force on first site only to avoid unwanted
// coupling to other colvars (see e.g. Ciccotti et al., 2005)
- f_description(f_cvc_one_site_total_force, "compute total collective force only from one group center");
+ init_feature(f_cvc_one_site_total_force, "compute total collective force only from one group center", f_type_user);
f_req_self(f_cvc_one_site_total_force, f_cvc_com_based);
- f_description(f_cvc_scalable, "scalable calculation");
+ init_feature(f_cvc_scalable, "scalable calculation", f_type_static);
f_req_self(f_cvc_scalable, f_cvc_scalable_com);
- f_description(f_cvc_scalable_com, "scalable calculation of centers of mass");
+ init_feature(f_cvc_scalable_com, "scalable calculation of centers of mass", f_type_static);
f_req_self(f_cvc_scalable_com, f_cvc_com_based);
@@ -414,23 +430,25 @@ void colvardeps::init_cvc_requires() {
}
// Initialize feature_states for each instance
- // default as unavailable, not enabled
+ // default as available, not enabled
+ // except dynamic features which default as unavailable
feature_states.reserve(f_cvc_ntot);
for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
- feature_states.push_back(new feature_state(false, false));
+ bool avail = is_dynamic(i) ? false : true;
+ feature_states.push_back(feature_state(avail, false));
}
// Features that are implemented by all cvcs by default
// Each cvc specifies what other features are available
- feature_states[f_cvc_active]->available = true;
- feature_states[f_cvc_gradient]->available = true;
+ feature_states[f_cvc_active].available = true;
+ feature_states[f_cvc_gradient].available = true;
// Features that are implemented by default if their requirements are
- feature_states[f_cvc_one_site_total_force]->available = true;
+ feature_states[f_cvc_one_site_total_force].available = true;
// Features That are implemented only for certain simulation engine configurations
- feature_states[f_cvc_scalable_com]->available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
- feature_states[f_cvc_scalable]->available = feature_states[f_cvc_scalable_com]->available;
+ feature_states[f_cvc_scalable_com].available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
+ feature_states[f_cvc_scalable].available = feature_states[f_cvc_scalable_com].available;
}
@@ -442,21 +460,21 @@ void colvardeps::init_ag_requires() {
features().push_back(new feature);
}
- f_description(f_ag_active, "active");
- f_description(f_ag_center, "translational fit");
- f_description(f_ag_rotate, "rotational fit");
- f_description(f_ag_fitting_group, "reference positions group");
- f_description(f_ag_fit_gradient_group, "fit gradient for main group");
- f_description(f_ag_fit_gradient_ref, "fit gradient for reference group");
- f_description(f_ag_atom_forces, "atomic forces");
+ init_feature(f_ag_active, "active", f_type_dynamic);
+ init_feature(f_ag_center, "translational fit", f_type_static);
+ init_feature(f_ag_rotate, "rotational fit", f_type_static);
+ init_feature(f_ag_fitting_group, "reference positions group", f_type_static);
+ init_feature(f_ag_fit_gradient_group, "fit gradient for main group", f_type_static);
+ init_feature(f_ag_fit_gradient_ref, "fit gradient for reference group", f_type_static);
+ init_feature(f_ag_atom_forces, "atomic forces", f_type_dynamic);
// parallel calculation implies that we have at least a scalable center of mass,
// but f_ag_scalable is kept as a separate feature to deal with future dependencies
- f_description(f_ag_scalable, "scalable group calculation");
- f_description(f_ag_scalable_com, "scalable group center of mass calculation");
+ init_feature(f_ag_scalable, "scalable group calculation", f_type_static);
+ init_feature(f_ag_scalable_com, "scalable group center of mass calculation", f_type_static);
f_req_self(f_ag_scalable, f_ag_scalable_com);
-// f_description(f_ag_min_msd_fit, "minimum MSD fit")
+// init_feature(f_ag_min_msd_fit, "minimum MSD fit")
// f_req_self(f_ag_min_msd_fit, f_ag_center)
// f_req_self(f_ag_min_msd_fit, f_ag_rotate)
// f_req_exclude(f_ag_min_msd_fit, f_ag_fitting_group)
@@ -466,15 +484,15 @@ void colvardeps::init_ag_requires() {
// default as unavailable, not enabled
feature_states.reserve(f_ag_ntot);
for (i = 0; i < colvardeps::f_ag_ntot; i++) {
- feature_states.push_back(new feature_state(false, false));
+ feature_states.push_back(feature_state(false, false));
}
// Features that are implemented (or not) by all atom groups
- feature_states[f_ag_active]->available = true;
+ feature_states[f_ag_active].available = true;
// f_ag_scalable_com is provided by the CVC iff it is COM-based
- feature_states[f_ag_scalable_com]->available = false;
+ feature_states[f_ag_scalable_com].available = false;
// TODO make f_ag_scalable depend on f_ag_scalable_com (or something else)
- feature_states[f_ag_scalable]->available = true;
+ feature_states[f_ag_scalable].available = true;
}
@@ -482,7 +500,7 @@ void colvardeps::print_state() {
size_t i;
cvm::log("Enabled features of " + description);
for (i = 0; i < feature_states.size(); i++) {
- if (feature_states[i]->enabled)
+ if (feature_states[i].enabled)
cvm::log("- " + features()[i]->description);
}
for (i=0; i<children.size(); i++) {
diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h
index 4ef27ded85a5b2a1bbcaaad54933a9294e11c51a..fd07cb645715eac8a8e367d654b6fbd06735a633 100644
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@@ -13,17 +13,16 @@
#include "colvarmodule.h"
#include "colvarparse.h"
-/// Parent class for a member object of a bias, cv or cvc etc. containing dependencies
-/// (features) and handling dependency resolution
-
-// Some features like colvar::f_linear have no dependencies, require() doesn't enable anything but fails if unavailable
-// Policy: those features are unavailable at all times
-// Other features are under user control
-// They are unavailable unless requested by the user, then they may be enabled subject to
-// satisfied dependencies
-
-// It seems important to have available default to false (for safety) and enabled to false (for efficiency)
-
+/// \brief Parent class for a member object of a bias, cv or cvc etc. containing features and
+/// their dependencies, and handling dependency resolution
+///
+/// There are 3 kinds of features:
+/// 1. Dynamic features are under the control of the dependency resolution
+/// system. They may be enabled or disabled depending on dependencies.
+/// 2. User features may be enabled based on user input (they may trigger a failure upon dependency resolution, though)
+/// 3. Static features are static properties of the object, determined
+/// programatically at initialization time.
+///
class colvardeps {
public:
@@ -39,12 +38,7 @@ public:
feature_state(bool a, bool e)
: available(a), enabled(e) {}
- /// Available means: supported, subject to dependencies as listed,
- /// MAY BE ENABLED AS A RESULT OF DEPENDENCY SOLVING
- /// Remains false for passive flags that are set based on other object properties,
- /// eg. f_cv_linear
- /// Is set to true upon user request for features that are implemented by the user
- /// or under his/her direct control, e.g. f_cv_scripted or f_cv_extended_Lagrangian
+ /// Feature may be enabled, subject to possible dependencies
bool available;
/// Currently enabled - this flag is subject to change dynamically
/// TODO consider implications for dependency solving: anyone who disables
@@ -53,8 +47,22 @@ public:
// bool enabledOnce; // this should trigger an update when object is evaluated
};
- /// List of the state of all features
- std::vector<feature_state *> feature_states;
+
+private:
+ /// List of the states of all features
+ std::vector<feature_state> feature_states;
+
+ /// Enum of possible feature types
+ enum feature_type {
+ f_type_not_set,
+ f_type_dynamic,
+ f_type_user,
+ f_type_static
+ };
+
+public:
+ /// Pair a numerical feature ID with a description and type
+ void init_feature(int feature_id, const char *description, feature_type type = f_type_not_set);
/// Describes a feature and its dependecies
/// used in a static array within each subclass
@@ -83,8 +91,18 @@ public:
// features that this feature requires in children
std::vector<int> requires_children;
+
+ inline bool is_dynamic() { return type == f_type_dynamic; }
+ inline bool is_static() { return type == f_type_static; }
+ inline bool is_user() { return type == f_type_user; }
+ /// Type of this feature, from the enum feature_type
+ feature_type type;
};
+ inline bool is_dynamic(int id) { return features()[id]->type == f_type_dynamic; }
+ inline bool is_static(int id) { return features()[id]->type == f_type_static; }
+ inline bool is_user(int id) { return features()[id]->type == f_type_user; }
+
// Accessor to array of all features with deps, static in most derived classes
// Subclasses with dynamic dependency trees may override this
// with a non-static array
@@ -100,9 +118,8 @@ public:
/// (useful for cvcs because their children are member objects)
void remove_all_children();
-
-
private:
+
// pointers to objects this object depends on
// list should be maintained by any code that modifies the object
// this could be secured by making lists of colvars / cvcs / atom groups private and modified through accessor functions
@@ -130,16 +147,28 @@ public:
// Checks whether given feature is enabled
// Defaults to querying f_*_active
inline bool is_enabled(int f = f_cv_active) const {
- return feature_states[f]->enabled;
+ return feature_states[f].enabled;
}
// Checks whether given feature is available
// Defaults to querying f_*_active
inline bool is_available(int f = f_cv_active) const {
- return feature_states[f]->available;
+ return feature_states[f].available;
}
- void provide(int feature_id); // set the feature's flag to available in local object
+ /// Set the feature's available flag, without checking
+ /// To be used for dynamic properties
+ /// dependencies will be checked by enable()
+ void provide(int feature_id, bool truefalse = true);
+
+ /// Set the feature's enabled flag, without dependency check or resolution
+ /// To be used for static properties only
+ /// Checking for availability is up to the caller
+ void set_enabled(int feature_id, bool truefalse = true);
+
+protected:
+
+
/// Parse a keyword and enable a feature accordingly
bool get_keyval_feature(colvarparse *cvp,
@@ -147,6 +176,8 @@ public:
int feature_id, bool const &def_value,
colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal);
+public:
+
int enable(int f, bool dry_run = false, bool toplevel = true); // enable a feature and recursively solve its dependencies
// dry_run is set to true to recursively test if a feature is available, without enabling it
// int disable(int f);
@@ -165,6 +196,7 @@ public:
f_cvb_get_total_force, // requires total forces
f_cvb_history_dependent, // depends on simulation history
f_cvb_scalar_variables, // requires scalar colvars
+ f_cvb_calc_pmf, // whether this bias will compute a PMF
f_cvb_ntot
};
@@ -216,12 +248,6 @@ public:
/// be used by the biases or in analysis (needs lower and upper
/// boundary)
f_cv_grid,
- /// \brief Apply a restraining potential (|x-xb|^2) to the colvar
- /// when it goes below the lower wall
- f_cv_lower_wall,
- /// \brief Apply a restraining potential (|x-xb|^2) to the colvar
- /// when it goes above the upper wall
- f_cv_upper_wall,
/// \brief Compute running average
f_cv_runave,
/// \brief Compute time correlation function
diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp
index b9a435152b2cc56b50987b08adb7cf2bd75e4362..10cd3c0e4737905dabb664bcaa0d159608fd16f7 100644
--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.cpp
@@ -36,6 +36,9 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
"variable module twice.\n");
return;
}
+
+ depth_s = 0;
+
cvm::log(cvm::line_marker);
cvm::log("Initializing the collective variables module, version "+
cvm::to_str(COLVARS_VERSION)+".\n");
@@ -71,6 +74,48 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
}
+colvarmodule * colvarmodule::main()
+{
+ return proxy->colvars;
+}
+
+
+std::vector<colvar *> *colvarmodule::variables()
+{
+ return &colvars;
+}
+
+
+std::vector<colvar *> *colvarmodule::variables_active()
+{
+ return &colvars_active;
+}
+
+
+std::vector<colvar *> *colvarmodule::variables_active_smp()
+{
+ return &colvars_smp;
+}
+
+
+std::vector<int> *colvarmodule::variables_active_smp_items()
+{
+ return &colvars_smp_items;
+}
+
+
+std::vector<colvarbias *> *colvarmodule::biases_active()
+{
+ return &(biases_active_);
+}
+
+
+size_t colvarmodule::size() const
+{
+ return colvars.size() + biases.size();
+}
+
+
int colvarmodule::read_config_file(char const *config_filename)
{
cvm::log(cvm::line_marker);
@@ -118,8 +163,29 @@ int colvarmodule::read_config_string(std::string const &config_str)
}
+std::istream & colvarmodule::getline(std::istream &is, std::string &line)
+{
+ std::string l;
+ if (std::getline(is, l)) {
+ size_t const sz = l.size();
+ if (sz > 0) {
+ if (l[sz-1] == '\r' ) {
+ line = l.substr(0, sz-1);
+ } else {
+ line = l;
+ }
+ } else {
+ line.clear();
+ }
+ }
+ return is;
+}
+
+
int colvarmodule::parse_config(std::string &conf)
{
+ extra_conf.clear();
+
// parse global options
if (catch_input_errors(parse_global_params(conf))) {
return get_error();
@@ -140,6 +206,15 @@ int colvarmodule::parse_config(std::string &conf)
return get_error();
}
+ if (extra_conf.size()) {
+ catch_input_errors(parse_global_params(extra_conf));
+ catch_input_errors(parse_colvars(extra_conf));
+ catch_input_errors(parse_biases(extra_conf));
+ parse->check_keywords(extra_conf, "colvarmodule");
+ extra_conf.clear();
+ if (get_error() != COLVARS_OK) return get_error();
+ }
+
cvm::log(cvm::line_marker);
cvm::log("Collective variables module (re)initialized.\n");
cvm::log(cvm::line_marker);
@@ -156,11 +231,20 @@ int colvarmodule::parse_config(std::string &conf)
}
+int colvarmodule::append_new_config(std::string const &new_conf)
+{
+ extra_conf += new_conf;
+ return COLVARS_OK;
+}
+
+
int colvarmodule::parse_global_params(std::string const &conf)
{
+ colvarmodule *cvm = cvm::main();
+
std::string index_file_name;
if (parse->get_keyval(conf, "indexFile", index_file_name)) {
- read_index_file(index_file_name.c_str());
+ cvm->read_index_file(index_file_name.c_str());
}
if (parse->get_keyval(conf, "smp", proxy->b_smp_active, proxy->b_smp_active)) {
@@ -216,8 +300,8 @@ int colvarmodule::parse_colvars(std::string const &conf)
if (colvar_conf.size()) {
cvm::log(cvm::line_marker);
cvm::increase_depth();
- colvars.push_back(new colvar(colvar_conf));
- if (cvm::get_error() ||
+ colvars.push_back(new colvar());
+ if (((colvars.back())->init(colvar_conf) != COLVARS_OK) ||
((colvars.back())->check_keywords(colvar_conf, "colvar") != COLVARS_OK)) {
cvm::log("Error while constructing colvar number " +
cvm::to_str(colvars.size()) + " : deleting.");
@@ -262,8 +346,7 @@ bool colvarmodule::check_new_bias(std::string &conf, char const *key)
template <class bias_type>
int colvarmodule::parse_biases_type(std::string const &conf,
- char const *keyword,
- size_t &bias_count)
+ char const *keyword)
{
std::string bias_conf = "";
size_t conf_saved_pos = 0;
@@ -277,7 +360,6 @@ int colvarmodule::parse_biases_type(std::string const &conf,
return COLVARS_ERROR;
}
cvm::decrease_depth();
- bias_count++;
} else {
cvm::error("Error: keyword \""+std::string(keyword)+"\" found without configuration.\n",
INPUT_ERROR);
@@ -295,28 +377,28 @@ int colvarmodule::parse_biases(std::string const &conf)
cvm::log("Initializing the collective variables biases.\n");
/// initialize ABF instances
- parse_biases_type<colvarbias_abf>(conf, "abf", n_abf_biases);
+ parse_biases_type<colvarbias_abf>(conf, "abf");
/// initialize adaptive linear biases
- parse_biases_type<colvarbias_alb>(conf, "ALB", n_rest_biases);
+ parse_biases_type<colvarbias_alb>(conf, "ALB");
/// initialize harmonic restraints
- parse_biases_type<colvarbias_restraint_harmonic>(conf, "harmonic", n_rest_biases);
+ parse_biases_type<colvarbias_restraint_harmonic>(conf, "harmonic");
/// initialize harmonic walls restraints
- parse_biases_type<colvarbias_restraint_harmonic_walls>(conf, "harmonicWalls", n_rest_biases);
+ parse_biases_type<colvarbias_restraint_harmonic_walls>(conf, "harmonicWalls");
/// initialize histograms
- parse_biases_type<colvarbias_histogram>(conf, "histogram", n_histo_biases);
+ parse_biases_type<colvarbias_histogram>(conf, "histogram");
/// initialize histogram restraints
- parse_biases_type<colvarbias_restraint_histogram>(conf, "histogramRestraint", n_rest_biases);
+ parse_biases_type<colvarbias_restraint_histogram>(conf, "histogramRestraint");
/// initialize linear restraints
- parse_biases_type<colvarbias_restraint_linear>(conf, "linear", n_rest_biases);
+ parse_biases_type<colvarbias_restraint_linear>(conf, "linear");
/// initialize metadynamics instances
- parse_biases_type<colvarbias_meta>(conf, "metadynamics", n_meta_biases);
+ parse_biases_type<colvarbias_meta>(conf, "metadynamics");
if (use_scripted_forces) {
cvm::log(cvm::line_marker);
@@ -363,6 +445,36 @@ int colvarmodule::parse_biases(std::string const &conf)
}
+int colvarmodule::num_biases_feature(int feature_id)
+{
+ colvarmodule *cv = cvm::main();
+ size_t n = 0;
+ for (std::vector<colvarbias *>::iterator bi = cv->biases.begin();
+ bi != cv->biases.end();
+ bi++) {
+ if ((*bi)->is_enabled(feature_id)) {
+ n++;
+ }
+ }
+ return n;
+}
+
+
+int colvarmodule::num_biases_type(std::string const &type)
+{
+ colvarmodule *cv = cvm::main();
+ size_t n = 0;
+ for (std::vector<colvarbias *>::iterator bi = cv->biases.begin();
+ bi != cv->biases.end();
+ bi++) {
+ if ((*bi)->bias_type == type) {
+ n++;
+ }
+ }
+ return n;
+}
+
+
int colvarmodule::catch_input_errors(int result)
{
if (result != COLVARS_OK || get_error()) {
@@ -376,8 +488,9 @@ int colvarmodule::catch_input_errors(int result)
colvarbias * colvarmodule::bias_by_name(std::string const &name) {
- for (std::vector<colvarbias *>::iterator bi = biases.begin();
- bi != biases.end();
+ colvarmodule *cv = cvm::main();
+ for (std::vector<colvarbias *>::iterator bi = cv->biases.begin();
+ bi != cv->biases.end();
bi++) {
if ((*bi)->name == name) {
return (*bi);
@@ -388,8 +501,9 @@ colvarbias * colvarmodule::bias_by_name(std::string const &name) {
colvar *colvarmodule::colvar_by_name(std::string const &name) {
- for (std::vector<colvar *>::iterator cvi = colvars.begin();
- cvi != colvars.end();
+ colvarmodule *cv = cvm::main();
+ for (std::vector<colvar *>::iterator cvi = cv->colvars.begin();
+ cvi != cv->colvars.end();
cvi++) {
if ((*cvi)->name == name) {
return (*cvi);
@@ -555,9 +669,15 @@ int colvarmodule::calc_colvars()
int error_code = COLVARS_OK;
std::vector<colvar *>::iterator cvi;
- // Determine which colvars are active at this time step
- for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
- (*cvi)->feature_states[colvardeps::f_cv_active]->enabled = (step_absolute() % (*cvi)->get_time_step_factor() == 0);
+ // Determine which colvars are active at this iteration
+ variables_active()->resize(0);
+ variables_active()->reserve(variables()->size());
+ for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
+ // This is a dynamic feature - the next call should be to enable()
+ // or disable() when dynamic dependency resolution is fully implemented
+ (*cvi)->set_enabled(colvardeps::f_cv_active,
+ step_absolute() % (*cvi)->get_time_step_factor() == 0);
+ variables_active()->push_back(*cvi);
}
// if SMP support is available, split up the work
@@ -565,25 +685,24 @@ int colvarmodule::calc_colvars()
// first, calculate how much work (currently, how many active CVCs) each colvar has
- colvars_smp.resize(0);
- colvars_smp_items.resize(0);
+ variables_active_smp()->resize(0);
+ variables_active_smp_items()->resize(0);
- colvars_smp.reserve(colvars.size());
- colvars_smp_items.reserve(colvars.size());
+ variables_active_smp()->reserve(variables_active()->size());
+ variables_active_smp_items()->reserve(variables_active()->size());
// set up a vector containing all components
cvm::increase_depth();
- for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
+ for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
- if (!(*cvi)->is_enabled()) continue;
error_code |= (*cvi)->update_cvc_flags();
size_t num_items = (*cvi)->num_active_cvcs();
- colvars_smp.reserve(colvars_smp.size() + num_items);
- colvars_smp_items.reserve(colvars_smp_items.size() + num_items);
+ variables_active_smp()->reserve(variables_active_smp()->size() + num_items);
+ variables_active_smp_items()->reserve(variables_active_smp_items()->size() + num_items);
for (size_t icvc = 0; icvc < num_items; icvc++) {
- colvars_smp.push_back(*cvi);
- colvars_smp_items.push_back(icvc);
+ variables_active_smp()->push_back(*cvi);
+ variables_active_smp_items()->push_back(icvc);
}
}
cvm::decrease_depth();
@@ -592,8 +711,7 @@ int colvarmodule::calc_colvars()
error_code |= proxy->smp_colvars_loop();
cvm::increase_depth();
- for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
- if (!(*cvi)->is_enabled()) continue;
+ for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
error_code |= (*cvi)->collect_cvc_data();
}
cvm::decrease_depth();
@@ -602,8 +720,7 @@ int colvarmodule::calc_colvars()
// calculate colvars one at a time
cvm::increase_depth();
- for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
- if (!(*cvi)->is_enabled()) continue;
+ for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
error_code |= (*cvi)->calc();
if (cvm::get_error()) {
return COLVARS_ERROR;
@@ -627,6 +744,18 @@ int colvarmodule::calc_biases()
std::vector<colvarbias *>::iterator bi;
int error_code = COLVARS_OK;
+ // Total bias energy is reset before calling scripted biases
+ total_bias_energy = 0.0;
+
+ // update the list of active biases
+ biases_active()->resize(0);
+ biases_active()->reserve(biases.size());
+ for (bi = biases.begin(); bi != biases.end(); bi++) {
+ if ((*bi)->is_enabled()) {
+ biases_active()->push_back(*bi);
+ }
+ }
+
// if SMP support is available, split up the work
if (proxy->smp_enabled() == COLVARS_OK) {
@@ -645,7 +774,7 @@ int colvarmodule::calc_biases()
}
cvm::increase_depth();
- for (bi = biases.begin(); bi != biases.end(); bi++) {
+ for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
error_code |= (*bi)->update();
if (cvm::get_error()) {
return error_code;
@@ -654,12 +783,10 @@ int colvarmodule::calc_biases()
cvm::decrease_depth();
}
- cvm::real total_bias_energy = 0.0;
- for (bi = biases.begin(); bi != biases.end(); bi++) {
+ for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
total_bias_energy += (*bi)->get_energy();
}
- proxy->add_energy(total_bias_energy);
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@@ -675,7 +802,7 @@ int colvarmodule::update_colvar_forces()
if (cvm::debug() && biases.size())
cvm::log("Collecting forces from all biases.\n");
cvm::increase_depth();
- for (bi = biases.begin(); bi != biases.end(); bi++) {
+ for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
(*bi)->communicate_forces();
if (cvm::get_error()) {
return COLVARS_ERROR;
@@ -687,6 +814,11 @@ int colvarmodule::update_colvar_forces()
error_code |= calc_scripted_forces();
}
+ // Now we have collected energies from both built-in and scripted biases
+ if (cvm::debug())
+ cvm::log("Adding total bias energy: " + cvm::to_str(total_bias_energy) + "\n");
+ proxy->add_energy(total_bias_energy);
+
cvm::real total_colvar_energy = 0.0;
// sum up the forces for each colvar, including wall forces
// and integrate any internal
@@ -695,7 +827,7 @@ int colvarmodule::update_colvar_forces()
cvm::log("Updating the internal degrees of freedom "
"of colvars (if they have any).\n");
cvm::increase_depth();
- for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
+ for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
// Here we call even inactive colvars, so they accumulate biasing forces
// as well as update their extended-system dynamics
total_colvar_energy += (*cvi)->update_forces_energy();
@@ -704,6 +836,8 @@ int colvarmodule::update_colvar_forces()
}
}
cvm::decrease_depth();
+ if (cvm::debug())
+ cvm::log("Adding total colvar energy: " + cvm::to_str(total_colvar_energy) + "\n");
proxy->add_energy(total_colvar_energy);
// make collective variables communicate their forces to their
@@ -711,9 +845,8 @@ int colvarmodule::update_colvar_forces()
if (cvm::debug())
cvm::log("Communicating forces from the colvars to the atoms.\n");
cvm::increase_depth();
- for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
+ for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
if ((*cvi)->is_enabled(colvardeps::f_cv_gradient)) {
- if (!(*cvi)->is_enabled()) continue;
(*cvi)->communicate_forces();
if (cvm::get_error()) {
return COLVARS_ERROR;
@@ -800,8 +933,8 @@ int colvarmodule::analyze()
cvm::log("Performing analysis.\n");
// perform colvar-specific analysis
- for (std::vector<colvar *>::iterator cvi = colvars.begin();
- cvi != colvars.end();
+ for (std::vector<colvar *>::iterator cvi = variables_active()->begin();
+ cvi != variables_active()->end();
cvi++) {
cvm::increase_depth();
(*cvi)->analyze();
@@ -825,8 +958,8 @@ int colvarmodule::setup()
{
if (this->size() == 0) return cvm::get_error();
// loop over all components of all colvars to reset masses of all groups
- for (std::vector<colvar *>::iterator cvi = colvars.begin();
- cvi != colvars.end(); cvi++) {
+ for (std::vector<colvar *>::iterator cvi = variables()->begin();
+ cvi != variables()->end(); cvi++) {
(*cvi)->setup();
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@@ -934,18 +1067,18 @@ int colvarmodule::setup_output()
cvm::log("The restart output state file will be \""+restart_out_name+"\".\n");
}
- output_prefix = proxy->output_prefix();
- if (output_prefix.size()) {
+ output_prefix() = proxy->output_prefix();
+ if (output_prefix().size()) {
cvm::log("The final output state file will be \""+
- (output_prefix.size() ?
- std::string(output_prefix+".colvars.state") :
+ (output_prefix().size() ?
+ std::string(output_prefix()+".colvars.state") :
std::string("colvars.state"))+"\".\n");
// cvm::log (cvm::line_marker);
}
cv_traj_name =
- (output_prefix.size() ?
- std::string(output_prefix+".colvars.traj") :
+ (output_prefix().size() ?
+ std::string(output_prefix()+".colvars.traj") :
std::string(""));
if (cv_traj_freq && cv_traj_name.size()) {
@@ -1077,14 +1210,14 @@ continue the previous simulation.\n\n");
cvm::log(cvm::line_marker);
// update this ahead of time in this special case
- output_prefix = proxy->input_prefix();
- cvm::log("All output files will now be saved with the prefix \""+output_prefix+".tmp.*\".\n");
+ output_prefix() = proxy->input_prefix();
+ cvm::log("All output files will now be saved with the prefix \""+output_prefix()+".tmp.*\".\n");
cvm::log(cvm::line_marker);
cvm::log("Please review the important warning above. After that, you may rename:\n\
-\""+output_prefix+".tmp.colvars.state\"\n\
+\""+output_prefix()+".tmp.colvars.state\"\n\
to:\n\
\""+ proxy->input_prefix()+".colvars.state\"\n");
- output_prefix = output_prefix+".tmp";
+ output_prefix() = output_prefix()+".tmp";
write_output_files();
cvm::error("Exiting with error until issue is addressed.\n", FATAL_ERROR);
}
@@ -1104,8 +1237,8 @@ int colvarmodule::write_output_files()
// if this is a simulation run (i.e. not a postprocessing), output data
// must be written to be able to restart the simulation
std::string const out_name =
- (output_prefix.size() ?
- std::string(output_prefix+".colvars.state") :
+ (output_prefix().size() ?
+ std::string(output_prefix()+".colvars.state") :
std::string("colvars.state"));
cvm::log("Saving collective variables state to \""+out_name+"\".\n");
@@ -1340,7 +1473,8 @@ std::ostream & colvarmodule::write_traj(std::ostream &os)
void cvm::log(std::string const &message)
{
- size_t const d = depth();
+ // allow logging when the module is not fully initialized
+ size_t const d = (cvm::main() != NULL) ? depth() : 0;
if (d > 0)
proxy->log((std::string(2*d, ' '))+message);
else
@@ -1365,19 +1499,20 @@ void cvm::decrease_depth()
size_t & cvm::depth()
{
// NOTE: do not call log() or error() here, to avoid recursion
- size_t const nt = proxy->smp_num_threads();
+ colvarmodule *cv = cvm::main();
if (proxy->smp_enabled() == COLVARS_OK) {
- if (depth_v.size() != nt) {
- // update array of depths
+ int const nt = proxy->smp_num_threads();
+ if (int(cv->depth_v.size()) != nt) {
proxy->smp_lock();
- if (depth_v.size() > 0) { depth_s = depth_v[0]; }
- depth_v.clear();
- depth_v.assign(nt, depth_s);
+ // update array of depths
+ if (cv->depth_v.size() > 0) { cv->depth_s = cv->depth_v[0]; }
+ cv->depth_v.clear();
+ cv->depth_v.assign(nt, cv->depth_s);
proxy->smp_unlock();
}
- return depth_v[proxy->smp_thread_id()];
+ return cv->depth_v[proxy->smp_thread_id()];
}
- return depth_s;
+ return cv->depth_s;
}
@@ -1451,8 +1586,8 @@ int cvm::read_index_file(char const *filename)
FILE_ERROR);
}
}
- cvm::index_group_names.push_back(group_name);
- cvm::index_groups.push_back(std::vector<int> ());
+ index_group_names.push_back(group_name);
+ index_groups.push_back(std::vector<int>());
} else {
cvm::error("Error: in parsing index file \""+
std::string(filename)+"\".\n",
@@ -1462,7 +1597,7 @@ int cvm::read_index_file(char const *filename)
int atom_number = 1;
size_t pos = is.tellg();
while ( (is >> atom_number) && (atom_number > 0) ) {
- (cvm::index_groups.back()).push_back(atom_number);
+ (index_groups.back()).push_back(atom_number);
pos = is.tellg();
}
is.clear();
@@ -1532,8 +1667,8 @@ int cvm::load_coords_xyz(char const *filename,
+ std::string(filename) + ".\n", INPUT_ERROR);
}
// skip comment line
- std::getline(xyz_is, line);
- std::getline(xyz_is, line);
+ cvm::getline(xyz_is, line);
+ cvm::getline(xyz_is, line);
xyz_is.width(255);
std::vector<atom_pos>::iterator pos_i = pos.begin();
@@ -1543,7 +1678,7 @@ int cvm::load_coords_xyz(char const *filename,
for ( ; pos_i != pos.end() ; pos_i++, index++) {
while ( next < *index ) {
- std::getline(xyz_is, line);
+ cvm::getline(xyz_is, line);
next++;
}
xyz_is >> symbol;
@@ -1558,15 +1693,9 @@ int cvm::load_coords_xyz(char const *filename,
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
-// static pointers
-std::vector<colvar *> colvarmodule::colvars;
-std::vector<colvarbias *> colvarmodule::biases;
-size_t colvarmodule::n_abf_biases = 0;
-size_t colvarmodule::n_rest_biases = 0;
-size_t colvarmodule::n_histo_biases = 0;
-size_t colvarmodule::n_meta_biases = 0;
-colvarproxy *colvarmodule::proxy = NULL;
+// shared pointer to the proxy object
+colvarproxy *colvarmodule::proxy = NULL;
// static runtime data
cvm::real colvarmodule::debug_gradients_step_size = 1.0e-07;
@@ -1575,14 +1704,9 @@ long colvarmodule::it = 0;
long colvarmodule::it_restart = 0;
size_t colvarmodule::restart_out_freq = 0;
size_t colvarmodule::cv_traj_freq = 0;
-size_t colvarmodule::depth_s = 0;
-std::vector<size_t> colvarmodule::depth_v(0);
bool colvarmodule::b_analysis = false;
-std::list<std::string> colvarmodule::index_group_names;
-std::list<std::vector<int> > colvarmodule::index_groups;
-bool colvarmodule::use_scripted_forces = false;
-bool colvarmodule::scripting_after_biases = true;
-std::string colvarmodule::output_prefix = "";
+bool colvarmodule::use_scripted_forces = false;
+bool colvarmodule::scripting_after_biases = true;
// i/o constants
size_t const colvarmodule::it_width = 12;
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index 0e98709adb79c7e746d76ed3fa331a65c2809e65..b4f80e0b5e47bcd0dd4475ebe9a22ddc90981ed5 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -11,7 +11,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2016-12-27"
+#define COLVARS_VERSION "2017-03-09"
#endif
#ifndef COLVARS_DEBUG
@@ -161,12 +161,37 @@ public:
/// dt)
static real debug_gradients_step_size;
+private:
+
/// Prefix for all output files for this run
- static std::string output_prefix;
+ std::string cvm_output_prefix;
+
+public:
+ /// Accessor for the above
+ static inline std::string &output_prefix()
+ {
+ colvarmodule *cv = colvarmodule::main();
+ return cv->cvm_output_prefix;
+ }
+private:
+
+ /// Array of collective variables
+ std::vector<colvar *> colvars;
/// Array of collective variables
- static std::vector<colvar *> colvars;
+ std::vector<colvar *> colvars_active;
+
+ /// Collective variables to be calculated on different threads;
+ /// colvars with multple items (e.g. multiple active CVCs) are duplicated
+ std::vector<colvar *> colvars_smp;
+ /// Indexes of the items to calculate for each colvar
+ std::vector<int> colvars_smp_items;
+
+public:
+
+ /// Array of collective variables
+ std::vector<colvar *> *variables();
/* TODO: implement named CVCs
/// Array of named (reusable) collective variable components
@@ -177,26 +202,31 @@ public:
}
*/
+ /// Collective variables with the active flag on
+ std::vector<colvar *> *variables_active();
+
/// Collective variables to be calculated on different threads;
/// colvars with multple items (e.g. multiple active CVCs) are duplicated
- std::vector<colvar *> colvars_smp;
+ std::vector<colvar *> *variables_active_smp();
+
/// Indexes of the items to calculate for each colvar
- std::vector<int> colvars_smp_items;
+ std::vector<int> *variables_active_smp_items();
/// Array of collective variable biases
- static std::vector<colvarbias *> biases;
- /// \brief Number of ABF biases initialized (in normal conditions
- /// should be 1)
- static size_t n_abf_biases;
- /// \brief Number of metadynamics biases initialized (in normal
- /// conditions should be 1)
- static size_t n_meta_biases;
- /// \brief Number of restraint biases initialized (no limit on the
- /// number)
- static size_t n_rest_biases;
- /// \brief Number of histograms initialized (no limit on the
- /// number)
- static size_t n_histo_biases;
+ std::vector<colvarbias *> biases;
+
+ /// Energy of built-in and scripted biases, summed per time-step
+ real total_bias_energy;
+
+private:
+
+ /// Array of active collective variable biases
+ std::vector<colvarbias *> biases_active_;
+
+public:
+
+ /// Array of active collective variable biases
+ std::vector<colvarbias *> *biases_active();
/// \brief Whether debug output should be enabled (compile-time option)
static inline bool debug()
@@ -205,10 +235,7 @@ public:
}
/// \brief How many objects are configured yet?
- inline size_t size() const
- {
- return colvars.size() + biases.size();
- }
+ size_t size() const;
/// \brief Constructor \param config_name Configuration file name
/// \param restart_name (optional) Restart file name
@@ -230,9 +257,12 @@ public:
/// \brief Parse a "clean" config string (no comments)
int parse_config(std::string &conf);
-
// Parse functions (setup internal data based on a string)
+ /// Allow reading from Windows text files using using std::getline
+ /// (which can still be used when the text is produced by Colvars itself)
+ static std::istream & getline(std::istream &is, std::string &line);
+
/// Parse the few module's global parameters
int parse_global_params(std::string const &conf);
@@ -242,14 +272,33 @@ public:
/// Parse and initialize collective variable biases
int parse_biases(std::string const &conf);
+ /// \brief Add new configuration during parsing (e.g. to implement
+ /// back-compatibility); cannot be nested, i.e. conf should not contain
+ /// anything that triggers another call
+ int append_new_config(std::string const &conf);
+
+private:
+
+ /// Auto-generated configuration during parsing (e.g. to implement
+ /// back-compatibility)
+ std::string extra_conf;
+
/// Parse and initialize collective variable biases of a specific type
template <class bias_type>
- int parse_biases_type(std::string const &conf, char const *keyword, size_t &bias_count);
+ int parse_biases_type(std::string const &conf, char const *keyword);
/// Test error condition and keyword parsing
/// on error, delete new bias
bool check_new_bias(std::string &conf, char const *key);
+public:
+
+ /// Return how many biases have this feature enabled
+ static int num_biases_feature(int feature_id);
+
+ /// Return how many biases are defined with this type
+ static int num_biases_type(std::string const &type);
+
private:
/// Useful wrapper to interrupt parsing if any error occurs
int catch_input_errors(int result);
@@ -449,13 +498,13 @@ public:
/// \brief Names of groups from a Gromacs .ndx file to be read at startup
- static std::list<std::string> index_group_names;
+ std::list<std::string> index_group_names;
/// \brief Groups from a Gromacs .ndx file read at startup
- static std::list<std::vector<int> > index_groups;
+ std::list<std::vector<int> > index_groups;
/// \brief Read a Gromacs .ndx file
- static int read_index_file(char const *filename);
+ int read_index_file(char const *filename);
/// \brief Create atoms from a file \param filename name of the file
@@ -515,13 +564,13 @@ protected:
/// Output restart file
colvarmodule::ofstream restart_out_os;
-protected:
+private:
/// Counter for the current depth in the object hierarchy (useg e.g. in output)
- static size_t depth_s;
+ size_t depth_s;
/// Thread-specific depth
- static std::vector<size_t> depth_v;
+ std::vector<size_t> depth_v;
public:
@@ -552,6 +601,10 @@ public:
/// from the hosting program; it is static in order to be accessible
/// from static functions in the colvarmodule class
static colvarproxy *proxy;
+
+ /// \brief Accessor for the above
+ static colvarmodule *main();
+
};
diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp
index 4d2e17f098dbb55457e5b1d8bc44f2cab79fdf70..8055d925dbbd3a403649c091563eb6e4e5e1cd0e 100644
--- a/lib/colvars/colvarparse.cpp
+++ b/lib/colvars/colvarparse.cpp
@@ -503,7 +503,7 @@ int colvarparse::check_keywords(std::string &conf, char const *key)
std::string line;
std::istringstream is(conf);
- while (std::getline(is, line)) {
+ while (cvm::getline(is, line)) {
if (line.size() == 0)
continue;
if (line.find_first_not_of(white_space) ==
@@ -539,10 +539,9 @@ int colvarparse::check_keywords(std::string &conf, char const *key)
std::istream & colvarparse::getline_nocomments(std::istream &is,
- std::string &line,
- char const delim)
+ std::string &line)
{
- std::getline(is, line, delim);
+ cvm::getline(is, line);
size_t const comment = line.find('#');
if (comment != std::string::npos) {
line.erase(comment);
diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h
index acdc46ddc9ee42d39f5889f2ebf4ab01c1781156..9f116caafdf8a5b96ec19ccc21469d2abc60741c 100644
--- a/lib/colvars/colvarparse.h
+++ b/lib/colvars/colvarparse.h
@@ -304,8 +304,7 @@ public:
/// \brief Works as std::getline() but also removes everything
/// between a comment character and the following newline
static std::istream & getline_nocomments(std::istream &is,
- std::string &s,
- char const delim = '\n');
+ std::string &s);
/// Check if the content of the file has matching braces
bool brace_check(std::string const &conf,
diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h
index bdf65c0b1f0a617a09427769e151a6db688dd154..5b216c9d41528f390f3f99dfd86184cd847e1186 100644
--- a/lib/colvars/colvarproxy.h
+++ b/lib/colvars/colvarproxy.h
@@ -336,8 +336,6 @@ public:
/// Are total forces being used?
virtual bool total_forces_enabled() const
{
- cvm::error("Error: total forces are currently not implemented.\n",
- COLVARS_NOT_IMPLEMENTED);
return false;
}
diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp
index ffb83e97801df0d4bb448b75747925e729fdb4ff..f192dcb7c05e377ba2dc44e8cd7ebf6e98481f73 100644
--- a/lib/colvars/colvarscript.cpp
+++ b/lib/colvars/colvarscript.cpp
@@ -12,6 +12,7 @@
#include <string.h>
#include "colvarscript.h"
+#include "colvardeps.h"
colvarscript::colvarscript(colvarproxy *p)
@@ -221,6 +222,16 @@ int colvarscript::run(int argc, char const *argv[]) {
}
}
+ if (cmd == "addenergy") {
+ if (argc == 3) {
+ colvars->total_bias_energy += strtod(argv[2], NULL);
+ return COLVARS_OK;
+ } else {
+ result = "Wrong arguments to command \"addenergy\"\n" + help_string();
+ return COLVARSCRIPT_ERROR;
+ }
+ }
+
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
@@ -263,10 +274,11 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
}
if (subcmd == "delete") {
- if (cv->biases.size() > 0) {
- result = "Cannot delete a colvar currently used by biases, delete those biases first";
- return COLVARSCRIPT_ERROR;
+ size_t i;
+ for (i = 0; i < cv->biases.size(); i++) {
+ delete cv->biases[i];
}
+ cv->biases.resize(0);
// colvar destructor is tasked with the cleanup
delete cv;
// TODO this could be done by the destructors
@@ -338,9 +350,8 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
return COLVARS_OK;
}
- if (subcmd == "state") {
- cv->print_state();
- return COLVARS_OK;
+ if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) {
+ return proc_features(cv, argc, argv);
}
result = "Syntax error\n" + help_string();
@@ -379,11 +390,6 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
return COLVARS_OK;
}
- if (subcmd == "state") {
- b->print_state();
- return COLVARS_OK;
- }
-
// Subcommands for MW ABF
if (subcmd == "bin") {
int r = b->current_bin();
@@ -420,6 +426,10 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
return COLVARS_OK;
}
+ if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) {
+ return proc_features(b, argc, argv);
+ }
+
if (argc >= 4) {
std::string param = argv[3];
if (subcmd == "count") {
@@ -441,6 +451,83 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
}
+int colvarscript::proc_features(colvardeps *obj,
+ int argc, char const *argv[]) {
+ // size was already checked before calling
+ std::string subcmd = argv[2];
+
+ if (argc == 3) {
+ if (subcmd == "state") {
+ // TODO make this returned as result?
+ obj->print_state();
+ return COLVARS_OK;
+ }
+
+ // get and set commands require more arguments
+ result = "Syntax error\n" + help_string();
+ return COLVARSCRIPT_ERROR;
+ }
+
+ if ((subcmd == "get") || (subcmd == "set")) {
+ std::vector<colvardeps::feature *> &features = obj->features();
+ std::string const req_feature(argv[3]);
+ colvardeps::feature *f = NULL;
+ int fid = 0;
+ for (fid = 0; fid < int(features.size()); fid++) {
+ if (features[fid]->description ==
+ colvarparse::to_lower_cppstr(req_feature)) {
+ f = features[fid];
+ break;
+ }
+ }
+
+ if (f == NULL) {
+
+ result = "Error: feature \""+req_feature+"\" does not exist.\n";
+ return COLVARSCRIPT_ERROR;
+
+ } else {
+
+ if (! obj->is_available(fid)) {
+ result = "Error: feature \""+req_feature+"\" is unavailable.\n";
+ return COLVARSCRIPT_ERROR;
+ }
+
+ if (subcmd == "get") {
+ result = cvm::to_str(obj->is_enabled(fid) ? 1 : 0);
+ return COLVARS_OK;
+ }
+
+ if (subcmd == "set") {
+ if (argc == 5) {
+ std::string const yesno =
+ colvarparse::to_lower_cppstr(std::string(argv[4]));
+ if ((yesno == std::string("yes")) ||
+ (yesno == std::string("on")) ||
+ (yesno == std::string("1"))) {
+ obj->enable(fid);
+ return COLVARS_OK;
+ } else if ((yesno == std::string("no")) ||
+ (yesno == std::string("off")) ||
+ (yesno == std::string("0"))) {
+ // TODO disable() function does not exist yet,
+ // dependencies will not be resolved
+ // obj->disable(fid);
+ obj->set_enabled(fid, false);
+ return COLVARS_OK;
+ }
+ }
+ result = "Syntax error\n" + help_string();
+ return COLVARSCRIPT_ERROR;
+ }
+ }
+ }
+
+ result = "Syntax error\n" + help_string();
+ return COLVARSCRIPT_ERROR;
+}
+
+
std::string colvarscript::help_string()
{
std::string buf;
@@ -459,6 +546,7 @@ Input and output:\n\
load <file name> -- load a state file (requires configuration)\n\
save <file name> -- save a state file (requires configuration)\n\
update -- recalculate colvars and biases\n\
+ addenergy <E> -- add <E> to the total bias energy\n\
printframe -- return a summary of the current frame\n\
printframelabels -- return labels to annotate printframe's output\n";
@@ -478,12 +566,17 @@ Accessing collective variables:\n\
colvar <name> addforce <F> -- apply given force on colvar <name>\n\
colvar <name> getconfig -- return config string of colvar <name>\n\
colvar <name> cvcflags <fl> -- enable or disable cvcs according to 0/1 flags\n\
+ colvar <name> get <f> -- get the value of the colvar feature <f>\n\
+ colvar <name> set <f> <val> -- set the value of the colvar feature <f>\n\
\n\
Accessing biases:\n\
bias <name> energy -- return the current energy of bias <name>\n\
bias <name> update -- recalculate bias <name>\n\
bias <name> delete -- delete bias <name>\n\
- bias <name> getconfig -- return config string of bias <name>\n";
+ bias <name> getconfig -- return config string of bias <name>\n\
+ bias <name> get <f> -- get the value of the bias feature <f>\n\
+ bias <name> set <f> <val> -- set the value of the bias feature <f>\n\
+";
return buf;
}
diff --git a/lib/colvars/colvarscript.h b/lib/colvars/colvarscript.h
index bfb8381e3b6c72bec02d3b6fe41e5037ab969bed..46b1ddd203afdcf72beb5da2e1ff2ffc2f01c65b 100644
--- a/lib/colvars/colvarscript.h
+++ b/lib/colvars/colvarscript.h
@@ -51,6 +51,10 @@ private:
/// Run subcommands on bias
int proc_bias(int argc, char const *argv[]);
+ /// Run subcommands on base colvardeps object (colvar, bias, ...)
+ int proc_features(colvardeps *obj,
+ int argc, char const *argv[]);
+
/// Builds and return a short help
std::string help_string(void);
};
diff --git a/potentials/Al_jpc.agni b/potentials/Al_jpc.agni
new file mode 100644
index 0000000000000000000000000000000000000000..0a82a3c8f42549407f8a6d955c93d8842f7378fb
--- /dev/null
+++ b/potentials/Al_jpc.agni
@@ -0,0 +1,3020 @@
+# DATE: 2017-02-24 CONTRIBUTOR: Venkatesh Botu <botuvenkatesh@gmail.com> CITATION: Botu, V., Batra, R., Chapman, J., and Ramprasad, R., J. Phys. Chem. C, 121 (1), 511 (2017).
+# This potential is an updated version of Al_prb.agni, which is now deprecated.
+# This potential file is parameterized for metal units
+
+generation 1
+n_elements 1
+
+element Al
+
+interaction Al
+Rc 8.0
+Rs 0.0
+neighbors 500
+eta 0.0036 0.0357 0.0715 0.1251 0.2144 0.3573 0.7147 1.4294
+sigma 13.8949549437
+lambda 1e-08
+b 102.870264493
+n_train 3000
+endVar
+
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+2.997000000000000000e+03 1.967759462537168158e+00 9.589785121656022593e-01 4.791637789432864336e-01 1.989710751744056538e-01 6.028611385465709738e-02 1.279376927015190950e-02 5.858362188501415203e-04 2.579993112555058013e-06 -1.666729999999999878e-01 -8.674934976012550294e+06
+2.998000000000000000e+03 -4.240566127251100603e+00 -2.408721967279218390e+00 -1.465757028659624428e+00 -8.229633782799549158e-01 -3.841838551044692851e-01 -1.316934500744013359e-01 -1.037225776008762756e-02 -7.684660981513854680e-05 -5.277910000000000101e-01 5.487369837599623017e+06
+2.999000000000000000e+03 -2.508963294584926285e+00 -1.271853999635049970e+00 -6.688038121713064665e-01 -3.034735449894066517e-01 -1.097891762892281714e-01 -3.107214352266277069e-02 -2.003404157198208305e-03 -8.003620864648185393e-06 -9.880500000000000393e-02 -7.476938723918542266e+06
diff --git a/potentials/Al_prb.agni b/potentials/Al_prb.agni
index a191b222206b876546114b9bf88358eb50a14219..1fca89f25f5769b3ba8daa572748d7c9b48736b0 100644
--- a/potentials/Al_prb.agni
+++ b/potentials/Al_prb.agni
@@ -1,4 +1,5 @@
# DATE: 2016-11-11 CONTRIBUTOR: Venkatesh Botu <botuvenkatesh@gmail.com> CITATION: Botu, V. and Ramprasad, R., Phys. Rev. B, 92, 094306 (2015)
+# This potential is deprecated. Please use Al_jpc.agni instead.
# This potential file is parameterized for metal units
generation 1
diff --git a/potentials/CC.KC b/potentials/CC.KC
new file mode 100644
index 0000000000000000000000000000000000000000..6559eb41209f1d9299ecd2aa920049d019d37fd3
--- /dev/null
+++ b/potentials/CC.KC
@@ -0,0 +1,8 @@
+# Kolmogorov-Crespi Potential
+#
+# Cite as A.N. Kolmogorov & V. H. Crespi,
+# Registry-dependent interlayer potential for graphitic systems
+# Physical Review B 71, 235415 (2005)
+#
+# z0 C0 C2 C4 C delta lambda A S
+C C 3.34 15.71 12.29 4.933 3.030 0.578 3.629 10.238 1.0
diff --git a/examples/snap/Ta06A_pot.snap b/potentials/Ta06A.snap
similarity index 86%
rename from examples/snap/Ta06A_pot.snap
rename to potentials/Ta06A.snap
index 7c86c24641f83b2611167c95b479f9df8dd5105a..edcc0025248e3cc5385180bac602cf6ba79dad6e 100644
--- a/examples/snap/Ta06A_pot.snap
+++ b/potentials/Ta06A.snap
@@ -9,9 +9,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL
-pair_style hybrid/overlay snap &
-zbl ${zblcutinner} ${zblcutouter}
-
+pair_style hybrid/overlay &
+zbl ${zblcutinner} ${zblcutouter} &
+snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
diff --git a/examples/snap/W_2940_2017_2.pot.snap b/potentials/W_2940_2017_2.snap
similarity index 77%
rename from examples/snap/W_2940_2017_2.pot.snap
rename to potentials/W_2940_2017_2.snap
index ea98d65c9e5b07f83a6da98df4bb3e2461d79fd8..51eee41a0a00be9c1f34ec77c5b8e25be4c70924 100644
--- a/examples/snap/W_2940_2017_2.pot.snap
+++ b/potentials/W_2940_2017_2.snap
@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
diff --git a/potentials/W_2940_2017_2.snapcoeff b/potentials/W_2940_2017_2.snapcoeff
index 98a5c5063500cbb249f0755dd59b00589d8b38cc..dcfea3feafd3ef8f305c3504476473fa5cf8df2a 100644
--- a/potentials/W_2940_2017_2.snapcoeff
+++ b/potentials/W_2940_2017_2.snapcoeff
@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# LAMMPS SNAP coefficients for W
diff --git a/potentials/W_2940_2017_2.snapparam b/potentials/W_2940_2017_2.snapparam
index 7ff57c905d146dabab2bc52b37fd7f2f5095801e..e0b20005e6a50d4a264b91995cbb1ffe96d2fcd7 100644
--- a/potentials/W_2940_2017_2.snapparam
+++ b/potentials/W_2940_2017_2.snapparam
@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# required
rcutfac 4.73442
diff --git a/potentials/W.SNAP_HePair.pot b/potentials/W_2940_2017_2_He_JW2013.snap
similarity index 82%
rename from potentials/W.SNAP_HePair.pot
rename to potentials/W_2940_2017_2_He_JW2013.snap
index eb5ee4dfbe3cc970eb825788998494c908ae5748..45a31955b3a1c21138bcb6a62dbd877804909fdc 100644
--- a/potentials/W.SNAP_HePair.pot
+++ b/potentials/W_2940_2017_2_He_JW2013.snap
@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
diff --git a/python/README b/python/README
index f0e95d3c4536cb5cdd4fd69b517f01f2bef5d6a3..6b13959f4d3b3f132f03aa095542d45e18705ecc 100644
--- a/python/README
+++ b/python/README
@@ -23,7 +23,7 @@ of LAMMPS:
>>> from lammps import lammps
>>> lmp = lammps()
-If that gives no errors, you have succesfully wrapped LAMMPS with
+If that gives no errors, you have successfully wrapped LAMMPS with
Python. See doc/Section_python.html#py_7 for tests you can then use
to run LAMMPS both in serial or parallel thru Python.
@@ -43,7 +43,7 @@ simple.py parallel example, mimicing examples/COUPLE/simple/simple.cpp
split.py parallel example
mc.py Monte Carlo energy relaxation wrapper on LAMMPS
gui.py GUI go/stop/temperature-slider to control LAMMPS
-plot.py real-time temeperature plot with GnuPlot via Pizza.py
+plot.py real-time temperature plot with GnuPlot via Pizza.py
viz_tool.py real-time viz via some viz package
vizplotgui_tool.py combination of viz.py and plot.py and gui.py
diff --git a/python/examples/demo.py b/python/examples/demo.py
index 958ebcd04bf91b48c04c6c34e0e6141a7d0a9baf..5d2b62fee38071dc51756b84aa545910a5a3b78b 100755
--- a/python/examples/demo.py
+++ b/python/examples/demo.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# demo.py
# Purpose: illustrate use of many library interface commands
diff --git a/python/examples/gui.py b/python/examples/gui.py
index 3fc1d7e36c6603a4b1102e6f5823da8559fc94f1..ac96448b437123c32275bfcdaa862d98b32f6201 100755
--- a/python/examples/gui.py
+++ b/python/examples/gui.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# gui.py
# Purpose: control a continuously running LAMMPS simulation via a Tkinter GUI
diff --git a/python/examples/mc.py b/python/examples/mc.py
index 9e7317218baa04cdb4df33fb4696b3e809b518ef..fb2bfabab984c61599ce9a1731b391341a9da5b2 100755
--- a/python/examples/mc.py
+++ b/python/examples/mc.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# mc.py
# Purpose: mimic operation of example/MC/in.mc via Python
diff --git a/python/examples/plot.py b/python/examples/plot.py
index efb9ecaa688a52aef8daefe82346e393b1dd3e0c..c67509f6501f92f9898ac98b14bd3f8696cca10d 100755
--- a/python/examples/plot.py
+++ b/python/examples/plot.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# plot.py
# Purpose: plot Temp of running LAMMPS simulation via GnuPlot in Pizza.py
diff --git a/python/examples/simple.py b/python/examples/simple.py
index 6336c89de3e6171d16ed82968a99ed2bf8d39a3d..da07a699970c27ce63a262c1bb36ca5dc9fd5350 100755
--- a/python/examples/simple.py
+++ b/python/examples/simple.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# simple.py
# Purpose: mimic operation of examples/COUPLE/simple/simple.cpp via Python
diff --git a/python/examples/split.py b/python/examples/split.py
index 719877d82698ca8e8fde1d6d5dcb9b9a6bf4d80e..77e605092e3bcb95a3f8a09af63e6fd5063a24ea 100755
--- a/python/examples/split.py
+++ b/python/examples/split.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# split.py
# Purpose: similar to simple.py, but first the world communicator
diff --git a/python/examples/trivial.py b/python/examples/trivial.py
index 0e3d6b91af5fdbfa8a65df2e2f4c42b610754aa6..e52f1745e04f5795f83d15b0af7368ef2b8f6646 100755
--- a/python/examples/trivial.py
+++ b/python/examples/trivial.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# trivial.py
# Purpose: run a LAMMPS input script via Python
diff --git a/python/examples/viz_atomeye.py b/python/examples/viz_atomeye.py
index 3803b2e79c616d50590e80c8da887afcacb6dfcc..d9cf4dcef274f3675d8891d6f64608893d0165a4 100755
--- a/python/examples/viz_atomeye.py
+++ b/python/examples/viz_atomeye.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# viz_atomeye.py
# Purpose: viz running LAMMPS simulation via AtomEye
diff --git a/python/examples/viz_gl.py b/python/examples/viz_gl.py
index 476509ad43b753f52ee7209fbc1489bf55bb1d83..5878b68502be2ac89675fdab26be5f18df1b7435 100755
--- a/python/examples/viz_gl.py
+++ b/python/examples/viz_gl.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# viz_gl.py
# Purpose: viz running LAMMPS simulation via GL tool in Pizza.py
diff --git a/python/examples/viz_pymol.py b/python/examples/viz_pymol.py
index 02178a0fb00415d94c74a124c68d79a69ee12475..0950b3668b4a0075b14d0141b3fe4fd854aa3995 100755
--- a/python/examples/viz_pymol.py
+++ b/python/examples/viz_pymol.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# viz_pymol.py
# Purpose: viz running LAMMPS simulation via PyMol
diff --git a/python/examples/viz_vmd.py b/python/examples/viz_vmd.py
index 807a8c9d55b50aff997a86f95c1475266399a585..f5928575666c8f954276102586a5972744e98f25 100755
--- a/python/examples/viz_vmd.py
+++ b/python/examples/viz_vmd.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# viz_vmd.py
# Purpose: viz running LAMMPS simulation via VMD
diff --git a/python/examples/vizplotgui_atomeye.py b/python/examples/vizplotgui_atomeye.py
index 71730974df54e199c981eb1f8188ef8a6bb56ff7..02f119b7260c0411316f13270c65d53aa642b306 100755
--- a/python/examples/vizplotgui_atomeye.py
+++ b/python/examples/vizplotgui_atomeye.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# vizplotgui_atomeye.py
# Purpose: viz running LAMMPS simulation via AtomEye with plot and GUI
diff --git a/python/examples/vizplotgui_gl.py b/python/examples/vizplotgui_gl.py
index 937670e5112326f07619e4c3477c473ddf473817..c4847667fd6848bc906d043d6b63ca54fa572781 100755
--- a/python/examples/vizplotgui_gl.py
+++ b/python/examples/vizplotgui_gl.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# vizplotgui_gl.py
# Purpose: viz running LAMMPS simulation via GL tool with plot and GUI
diff --git a/python/examples/vizplotgui_pymol.py b/python/examples/vizplotgui_pymol.py
index c7a8a00c6d69ab818d11da616f8719118c908433..11be498741a10a22d7f1319b4cdfa51b58ce154f 100755
--- a/python/examples/vizplotgui_pymol.py
+++ b/python/examples/vizplotgui_pymol.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# vizplotgui_pymol.py
# Purpose: viz running LAMMPS simulation via PyMol with plot and GUI
diff --git a/python/examples/vizplotgui_vmd.py b/python/examples/vizplotgui_vmd.py
index 9eab0865e2bfcfd4beada0cbdc4969bed2896940..0003ebc929b9e32a3e44333a229c43da7a409607 100755
--- a/python/examples/vizplotgui_vmd.py
+++ b/python/examples/vizplotgui_vmd.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python -i
-# preceeding line should have path for Python on your machine
+# preceding line should have path for Python on your machine
# vizplotgui_vmd.py
# Purpose: viz running LAMMPS simulation via VMD with plot and GUI
diff --git a/src/ASPHERE/compute_erotate_asphere.h b/src/ASPHERE/compute_erotate_asphere.h
index be1c5349234c53246e27772b32dacd7f1d7bdb23..23e30d7c93b612533cb9c6379531cbce44800509 100644
--- a/src/ASPHERE/compute_erotate_asphere.h
+++ b/src/ASPHERE/compute_erotate_asphere.h
@@ -56,6 +56,6 @@ Self-explanatory.
E: Compute erotate/asphere requires extended particles
-This compute cannot be used with point paritlces.
+This compute cannot be used with point particles.
*/
diff --git a/src/ASPHERE/compute_temp_asphere.h b/src/ASPHERE/compute_temp_asphere.h
index 4688a5612d35c8d9cd1c2b15b97d56091bcf459d..d1cce3802589854738f421924da686bbeab1f637 100644
--- a/src/ASPHERE/compute_temp_asphere.h
+++ b/src/ASPHERE/compute_temp_asphere.h
@@ -65,7 +65,7 @@ Self-explanatory.
E: Compute temp/asphere requires extended particles
-This compute cannot be used with point paritlces.
+This compute cannot be used with point particles.
E: Could not find compute ID for temperature bias
diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp
index eafa57973ca135404c90fdbe086d28acc93f38f1..a50473a194fb653a6af52800ca0c1aec0e1b2e6c 100644
--- a/src/COLLOID/pair_lubricateU.cpp
+++ b/src/COLLOID/pair_lubricateU.cpp
@@ -153,7 +153,7 @@ void PairLubricateU::compute(int eflag, int vflag)
}
// Stage one of Midpoint method
- // Solve for velocities based on intial positions
+ // Solve for velocities based on initial positions
stage_one();
@@ -651,7 +651,7 @@ void PairLubricateU::compute_Fh(double **x)
jnum = numneigh[i];
// Find the contribution to stress from isotropic RS0
- // Set psuedo force to obtain the required contribution
+ // Set pseudo force to obtain the required contribution
// need to set delx and fy only
fx = 0.0; delx = radi;
diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp
index 30ad42ea60d68e9349218d0ff009b6c18c1d233c..29e192cd94a8bd3cdf7987ebb7c5c3fcad0b3015 100644
--- a/src/COLLOID/pair_lubricateU_poly.cpp
+++ b/src/COLLOID/pair_lubricateU_poly.cpp
@@ -122,7 +122,7 @@ void PairLubricateUPoly::compute(int eflag, int vflag)
}
// Stage one of Midpoint method
- // Solve for velocities based on intial positions
+ // Solve for velocities based on initial positions
iterate(atom->x,1);
@@ -421,7 +421,7 @@ void PairLubricateUPoly::compute_Fh(double **x)
pre[0] *= 6.0;
// Find the contribution to stress from isotropic RS0
- // Set psuedo force to obtain the required contribution
+ // Set pseudo force to obtain the required contribution
// need to set delx and fy only
fx = 0.0; delx = radi;
diff --git a/src/COLLOID/pair_yukawa_colloid.h b/src/COLLOID/pair_yukawa_colloid.h
index f22c9654be37a529180ec36befdb0626b144ab53..ac15d535b3a1da9ae07891f383189cbf7c65f767 100644
--- a/src/COLLOID/pair_yukawa_colloid.h
+++ b/src/COLLOID/pair_yukawa_colloid.h
@@ -43,10 +43,10 @@ class PairYukawaColloid : public PairYukawa {
E: Pair yukawa/colloid requires atom style sphere
-Self-explantory.
+Self-explanatory.
E: Pair yukawa/colloid requires atoms with same type have same radius
-Self-explantory.
+Self-explanatory.
*/
diff --git a/src/DEPEND/fastdep.c b/src/DEPEND/fastdep.c
index 2f4927abce88f6f5691631205f81b772fd863021..3a6d3a017355b5f860589085beed8f1e27851d37 100644
--- a/src/DEPEND/fastdep.c
+++ b/src/DEPEND/fastdep.c
@@ -178,7 +178,7 @@ typedef struct {
* linked list functions
************************************************************************/
-/* allocate and intitialize linked list */
+/* allocate and initialize linked list */
static llist_t *llist_init()
{
llist_t *ll;
diff --git a/src/GPU/README b/src/GPU/README
index ea1fa702853bfd5881fede970be51ae3444a8211..792fc1a8b9ecf6cc9918884dd25f112693a7f0c4 100644
--- a/src/GPU/README
+++ b/src/GPU/README
@@ -1,11 +1,16 @@
This package implements GPU optimizations of various LAMMPS styles.
-This package uses an external library in lib/gpu which must be
-compiled before making LAMMPS. See the lib/gpu/README file and the
+Section 5.3.1 on the manual gives details of what hardware and Cuda
+software is required on your system, and full details on how to build
+and use this package. See the KOKKOS package, which also has
+GPU-enabled styles.
+
+This package uses an external library provided in lib/gpu which must
+be compiled before making LAMMPS. See the lib/gpu/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries. The settings in the Makefile.lammps file in that directory
must be correct for LAMMPS to build correctly with this package
installed.
-The people who created this package are Mike Brown (while at Sandia
-and ORNL) and Trung Nguyen (while at ORNL).
+The GPU package and its associated library was created by Mike Brown
+while at Sandia and ORNL, and by Trung Nguyen while at ORNL.
diff --git a/src/GPU/pair_born_gpu.h b/src/GPU/pair_born_gpu.h
index 49c76fadf62676e0ef844a43637def04d6e6054a..d8ccbe0029b3b90c8adea9ca486a3c4a1b2b0e54 100644
--- a/src/GPU/pair_born_gpu.h
+++ b/src/GPU/pair_born_gpu.h
@@ -54,6 +54,6 @@ package
E: Cannot use newton pair with born/gpu pair style
-Self-explantory.
+Self-explanatory.
*/
diff --git a/src/GPU/pair_zbl_gpu.h b/src/GPU/pair_zbl_gpu.h
index 0939dafaaabbf4e65161afa8919b99507d5df5a6..950fe952dd776825602afaee1eadae79b618776c 100644
--- a/src/GPU/pair_zbl_gpu.h
+++ b/src/GPU/pair_zbl_gpu.h
@@ -53,6 +53,6 @@ package
E: Cannot use newton pair with zbl/gpu pair style
-Self-explantory.
+Self-explanatory.
*/
diff --git a/src/KIM/README b/src/KIM/README
index e450d7dfd12671c758232e874d3291224180f976..496db92cf23471109cce0c30d0a03aa2cf06ac03 100644
--- a/src/KIM/README
+++ b/src/KIM/README
@@ -1,5 +1,3 @@
--*- fill-column: 70; -*-
-
This package provides a pair_style kim command which is a wrapper on
the Knowledge Base for Interatomic Models (KIM) repository of
interatomic potentials, so that they can be used by LAMMPS scripts.
diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h
index 843fb6db2aa65766591b7c0fc20866715d5d716c..07947f9d189843c65c4ee335aef16df7e84d00cb 100644
--- a/src/KIM/pair_kim.h
+++ b/src/KIM/pair_kim.h
@@ -126,7 +126,7 @@ namespace LAMMPS_NS {
int lmps_maxalloc; // max allocated memory value
int* kim_particleSpecies; // array of KIM particle species
double** lmps_force_tmp; // temp storage for f, when running in
- // hybrid mode needed to avoid reseting
+ // hybrid mode needed to avoid resetting
// f to zero in each object
int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS
// is in molecular mode
diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp
index e2a605b80260bfb8191c05dcf5eec74ca8024cff..346077e07119c4b3f5f45eb535f5ca698083ce30 100644
--- a/src/KOKKOS/angle_charmm_kokkos.cpp
+++ b/src/KOKKOS/angle_charmm_kokkos.cpp
@@ -64,7 +64,7 @@ void AngleCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp
index 0232571bcc5f066be7a0ccebdbab2985b8857779..e851e9d500b10246571210a6c38daae5d472528a 100644
--- a/src/KOKKOS/angle_class2_kokkos.cpp
+++ b/src/KOKKOS/angle_class2_kokkos.cpp
@@ -64,7 +64,7 @@ void AngleClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp
index 0d3110f9049c61f3f99b8213bfda590107f35f86..9fd237ddb3e90404aa9e9a979be2ccaba3953e6d 100644
--- a/src/KOKKOS/angle_harmonic_kokkos.cpp
+++ b/src/KOKKOS/angle_harmonic_kokkos.cpp
@@ -64,7 +64,7 @@ void AngleHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp
index 82dc3f382a65826d4666313620baa76ea3a3f21d..b01af92b5fddfdecf00ab2d00ec709a14c6a3741 100644
--- a/src/KOKKOS/bond_class2_kokkos.cpp
+++ b/src/KOKKOS/bond_class2_kokkos.cpp
@@ -60,7 +60,7 @@ void BondClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp
index b10469b45e340406d207c62e09737b9e1acba7f6..cfc37bfa9f6e26afb65d97e985580d485bb65a91 100644
--- a/src/KOKKOS/bond_fene_kokkos.cpp
+++ b/src/KOKKOS/bond_fene_kokkos.cpp
@@ -69,7 +69,7 @@ void BondFENEKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp
index aead60274734c6b6e65070a82d3b40f856f9fa66..408f59c5632b87c6177f41d7b623dbc852370eee 100644
--- a/src/KOKKOS/bond_harmonic_kokkos.cpp
+++ b/src/KOKKOS/bond_harmonic_kokkos.cpp
@@ -61,7 +61,7 @@ void BondHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index 3ec22c42fafbe4c55575df02511a1c5d9b97fc46..f38a6c21c91191f9a004c3e86d79a1762bdb68c6 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -71,6 +71,10 @@ CommKokkos::CommKokkos(LAMMPS *lmp) : CommBrick(lmp)
maxsendlist[i] = BUFMIN;
}
memory->create_kokkos(k_sendlist,sendlist,maxswap,BUFMIN,"comm:sendlist");
+
+ max_buf_pair = 0;
+ k_buf_send_pair = DAT::tdual_xfloat_1d("comm:k_buf_send_pair",1);
+ k_buf_recv_pair = DAT::tdual_xfloat_1d("comm:k_recv_send_pair",1);
}
/* ---------------------------------------------------------------------- */
@@ -89,6 +93,9 @@ CommKokkos::~CommKokkos()
void CommKokkos::init()
{
+ maxsend = BUFMIN;
+ maxrecv = BUFMIN;
+
grow_send_kokkos(maxsend+bufextra,0,Host);
grow_recv_kokkos(maxrecv,Host);
@@ -300,9 +307,13 @@ void CommKokkos::forward_comm_pair_device(Pair *pair)
int nsize = pair->comm_forward;
for (iswap = 0; iswap < nswap; iswap++) {
+ int n = MAX(max_buf_pair,nsize*sendnum[iswap]);
+ n = MAX(n,nsize*recvnum[iswap]);
+ if (n > max_buf_pair)
+ grow_buf_pair(n);
+ }
- DAT::tdual_xfloat_1d k_buf_send_pair = DAT::tdual_xfloat_1d("comm:k_buf_send_pair",nsize*sendnum[iswap]);
- DAT::tdual_xfloat_1d k_buf_recv_pair = DAT::tdual_xfloat_1d("comm:k_recv_send_pair",nsize*recvnum[iswap]);
+ for (iswap = 0; iswap < nswap; iswap++) {
// pack buffer
@@ -327,6 +338,12 @@ void CommKokkos::forward_comm_pair_device(Pair *pair)
}
}
+void CommKokkos::grow_buf_pair(int n) {
+ max_buf_pair = n * BUFFACTOR;
+ k_buf_send_pair.resize(max_buf_pair);
+ k_buf_recv_pair.resize(max_buf_pair);
+}
+
void CommKokkos::reverse_comm_pair(Pair *pair)
{
k_sendlist.sync<LMPHostType>();
diff --git a/src/KOKKOS/comm_kokkos.h b/src/KOKKOS/comm_kokkos.h
index 587b0305958ffbd8c0a6988091c2d40adf48df86..71d5e59595361cd4fc4af1a19b736ce34604149c 100644
--- a/src/KOKKOS/comm_kokkos.h
+++ b/src/KOKKOS/comm_kokkos.h
@@ -59,6 +59,11 @@ class CommKokkos : public CommBrick {
//double *buf_send; // send buffer for all comm
//double *buf_recv; // recv buffer for all comm
+ int max_buf_pair;
+ DAT::tdual_xfloat_1d k_buf_send_pair;
+ DAT::tdual_xfloat_1d k_buf_recv_pair;
+ void grow_buf_pair(int);
+
void grow_send(int, int);
void grow_recv(int);
void grow_send_kokkos(int, int, ExecutionSpace space = Host);
diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp
index 0af9fc4e835305d526be3f64dc0c460cfec526ba..ee9e3d1244b0c4c22bddee191751471803c4a08e 100644
--- a/src/KOKKOS/dihedral_charmm_kokkos.cpp
+++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp
@@ -69,7 +69,7 @@ void DihedralCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// insure pair->ev_tally() will use 1-4 virial contribution
diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index 9f7ef52cb085ca04795838cc87fdd27beac97a63..edfd1b3395ba909aec568fdd86d5867665efcad1 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -69,7 +69,7 @@ void DihedralClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp
index 5406a6daafa108bceb0223a31129da776d954229..8e222ad86083e762df7e698be81b6e080d42fcbf 100644
--- a/src/KOKKOS/dihedral_opls_kokkos.cpp
+++ b/src/KOKKOS/dihedral_opls_kokkos.cpp
@@ -69,7 +69,7 @@ void DihedralOPLSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp
index 60e21339849ed469b98c019209527baeb5e3f4c1..25bd2c732f6621278661e3fb891338a263992466 100644
--- a/src/KOKKOS/improper_class2_kokkos.cpp
+++ b/src/KOKKOS/improper_class2_kokkos.cpp
@@ -71,7 +71,7 @@ void ImproperClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp
index cde7d60e8edd213f8a8d95e399437f43f3606dcc..9c99b35bd9ec374953985eeec173dcea58d40c76 100644
--- a/src/KOKKOS/improper_harmonic_kokkos.cpp
+++ b/src/KOKKOS/improper_harmonic_kokkos.cpp
@@ -71,7 +71,7 @@ void ImproperHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp
index 2a85255e12aa7c282ade0ef87b7e2a696104fdc4..e40e6a238c6f06fc7d8d5db58d7520b97f8e3e31 100644
--- a/src/KOKKOS/neighbor_kokkos.cpp
+++ b/src/KOKKOS/neighbor_kokkos.cpp
@@ -64,6 +64,7 @@ NeighborKokkos::~NeighborKokkos()
memory->destroy_kokkos(k_ex1_bit,ex1_bit);
memory->destroy_kokkos(k_ex2_bit,ex2_bit);
memory->destroy_kokkos(k_ex_mol_bit,ex_mol_bit);
+ memory->destroy_kokkos(k_ex_mol_intra,ex_mol_intra);
memory->destroy_kokkos(k_bondlist,bondlist);
memory->destroy_kokkos(k_anglelist,anglelist);
@@ -133,6 +134,14 @@ void NeighborKokkos::init_ex_mol_bit_kokkos()
k_ex_mol_bit.modify<LMPHostType>();
}
+/* ---------------------------------------------------------------------- */
+
+void NeighborKokkos::grow_ex_mol_intra_kokkos()
+{
+ memory->grow_kokkos(k_ex_mol_intra, ex_mol_intra, maxex_mol, "neigh:ex_mol_intra");
+ k_ex_mol_intra.modify<LMPHostType>();
+}
+
/* ----------------------------------------------------------------------
if any atom moved trigger distance (half of neighbor skin) return 1
shrink trigger distance if box size has changed
@@ -348,6 +357,12 @@ void NeighborKokkos::modify_mol_group_grow_kokkos(){
k_ex_mol_group.modify<LMPHostType>();
}
+/* ---------------------------------------------------------------------- */
+void NeighborKokkos::modify_mol_intra_grow_kokkos(){
+ memory->grow_kokkos(k_ex_mol_intra,ex_mol_intra,maxex_mol,"neigh:ex_mol_intra");
+ k_ex_mol_intra.modify<LMPHostType>();
+}
+
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_topology() {
diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h
index 244de19dcecbfe9415c1ffb6dfd97b5a1f66b118..137c071e87a7f078647f34ca43c73254c9ab916b 100644
--- a/src/KOKKOS/neighbor_kokkos.h
+++ b/src/KOKKOS/neighbor_kokkos.h
@@ -54,6 +54,7 @@ class NeighborKokkos : public Neighbor {
DAT::tdual_int_1d k_ex1_bit,k_ex2_bit;
DAT::tdual_int_1d k_ex_mol_group;
DAT::tdual_int_1d k_ex_mol_bit;
+ DAT::tdual_int_1d k_ex_mol_intra;
NeighBondKokkos<LMPHostType> neighbond_host;
NeighBondKokkos<LMPDeviceType> neighbond_device;
@@ -76,6 +77,7 @@ class NeighborKokkos : public Neighbor {
void init_ex_type_kokkos(int);
void init_ex_bit_kokkos();
void init_ex_mol_bit_kokkos();
+ void grow_ex_mol_intra_kokkos();
virtual int check_distance();
template<class DeviceType> int check_distance_kokkos();
virtual void build(int);
@@ -84,6 +86,7 @@ class NeighborKokkos : public Neighbor {
void modify_ex_type_grow_kokkos();
void modify_ex_group_grow_kokkos();
void modify_mol_group_grow_kokkos();
+ void modify_mol_intra_grow_kokkos();
};
}
diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp
index f49e44c3522e05a066ab630274798687becb27de..3614a82cfed29a3e9d55988a0c57c553ad37aeea 100644
--- a/src/KOKKOS/npair_kokkos.cpp
+++ b/src/KOKKOS/npair_kokkos.cpp
@@ -56,6 +56,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::copy_neighbor_info()
k_ex2_bit = neighborKK->k_ex2_bit;
k_ex_mol_group = neighborKK->k_ex_mol_group;
k_ex_mol_bit = neighborKK->k_ex_mol_bit;
+ k_ex_mol_intra = neighborKK->k_ex_mol_intra;
}
/* ----------------------------------------------------------------------
@@ -147,6 +148,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::build(NeighList *list_)
nex_mol,
k_ex_mol_group.view<DeviceType>(),
k_ex_mol_bit.view<DeviceType>(),
+ k_ex_mol_intra.view<DeviceType>(),
bboxhi,bboxlo,
domain->xperiodic,domain->yperiodic,domain->zperiodic,
domain->xprd_half,domain->yprd_half,domain->zprd_half);
@@ -161,6 +163,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::build(NeighList *list_)
k_ex2_bit.sync<DeviceType>();
k_ex_mol_group.sync<DeviceType>();
k_ex_mol_bit.sync<DeviceType>();
+ k_ex_mol_intra.sync<DeviceType>();
k_bincount.sync<DeviceType>(),
k_bins.sync<DeviceType>(),
atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
@@ -284,8 +287,12 @@ int NeighborKokkosExecute<DeviceType>::exclusion(const int &i,const int &j,
if (nex_mol) {
for (m = 0; m < nex_mol; m++)
- if (mask(i) & ex_mol_bit(m) && mask(j) & ex_mol_bit(m) &&
- molecule(i) == molecule(j)) return 1;
+ if (ex_mol_intra[m]) { // intra-chain: exclude i-j pair if on same molecule
+ if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+ molecule[i] == molecule[j]) return 1;
+ } else // exclude i-j pair if on different molecules
+ if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+ molecule[i] != molecule[j]) return 1;
}
return 0;
diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h
index 54726cb9716abcbfe01adee464286318ef440d92..52cdfe0d53bdfde4c5aa2cf6dab82c78209609da 100644
--- a/src/KOKKOS/npair_kokkos.h
+++ b/src/KOKKOS/npair_kokkos.h
@@ -98,6 +98,7 @@ class NPairKokkos : public NPair {
DAT::tdual_int_1d k_ex1_bit,k_ex2_bit;
DAT::tdual_int_1d k_ex_mol_group;
DAT::tdual_int_1d k_ex_mol_bit;
+ DAT::tdual_int_1d k_ex_mol_intra;
// data from NBin class
@@ -139,6 +140,7 @@ class NeighborKokkosExecute
const int nex_mol;
const typename AT::t_int_1d_const ex_mol_group;
const typename AT::t_int_1d_const ex_mol_bit;
+ const typename AT::t_int_1d_const ex_mol_intra;
// data from NBin class
@@ -216,6 +218,7 @@ class NeighborKokkosExecute
const int & _nex_mol,
const typename AT::t_int_1d_const & _ex_mol_group,
const typename AT::t_int_1d_const & _ex_mol_bit,
+ const typename AT::t_int_1d_const & _ex_mol_intra,
const X_FLOAT *_bboxhi, const X_FLOAT* _bboxlo,
const int & _xperiodic, const int & _yperiodic, const int & _zperiodic,
const int & _xprd_half, const int & _yprd_half, const int & _zprd_half):
@@ -235,6 +238,7 @@ class NeighborKokkosExecute
ex1_group(_ex1_group),ex2_group(_ex2_group),
ex1_bit(_ex1_bit),ex2_bit(_ex2_bit),nex_mol(_nex_mol),
ex_mol_group(_ex_mol_group),ex_mol_bit(_ex_mol_bit),
+ ex_mol_intra(_ex_mol_intra),
xperiodic(_xperiodic),yperiodic(_yperiodic),zperiodic(_zperiodic),
xprd_half(_xprd_half),yprd_half(_yprd_half),zprd_half(_zprd_half) {
diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
index afe2d14fcc15e67cc7420ed9383e3d220c1b3c0c..34fd4272267333e8333776b0739685c8192f20c8 100644
--- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
@@ -92,7 +92,7 @@ void PairBuckCoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
index fa05c99995dccc4cf4c06638292788a484101ca1..243bac5ab70805134d0c48d359ca7959f9db5054 100644
--- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
@@ -111,7 +111,7 @@ void PairBuckCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp
index 02f767fa03baeca2e33a32b9bf1615627ea0cfe4..d8534f79005eec2ed926659e80e2eded9c7aefaa 100644
--- a/src/KOKKOS/pair_buck_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_kokkos.cpp
@@ -81,7 +81,7 @@ void PairBuckKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp
index a770d55be9e50c6a0ff7d32b73e8e31a51847a47..80ab01d91a52a77294852155cfe57494079456b3 100644
--- a/src/KOKKOS/pair_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp
@@ -80,7 +80,7 @@ void PairCoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp
index e9314c2a0ad7086d5edadd4de2641ffd52e65d4d..dc85c39832cd0028c864f842b99f9047ae9bf25e 100644
--- a/src/KOKKOS/pair_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp
@@ -87,7 +87,7 @@ void PairCoulDebyeKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
index 948a234a4ac56503ecdef29ff3d5a68505b3242c..f2063bdc08cf6a722c376aa4c64547cfcfbeb458 100644
--- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
@@ -80,7 +80,7 @@ void PairCoulDSFKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp
index dcf4943104d349d9b52d63a2dd66b680b11c229f..7dbadf4834f27f1cca2c0ea2db956cf01bc104ad 100644
--- a/src/KOKKOS/pair_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_long_kokkos.cpp
@@ -104,7 +104,7 @@ void PairCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
index 55b19958a348b545446b37d4c32fcdd8715ef530..8049ba00310a1e932257e51a4e3fc51b077eae6f 100644
--- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
@@ -75,7 +75,7 @@ void PairCoulWolfKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index 491ec10f6631b733c94c29d3deabffd433a50901..45c320bc516fcfd13816a6dfe809ec7296d035c5 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -74,7 +74,7 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index 006db6abc2ba5394d05098d5ce960bc7c4b994f0..b9fa82740aeb0d59bba5e1c5d5d9f6e762292941 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -74,7 +74,7 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 656dd11c62c9ceab881ba8e21ea1e92755842f04..e4128de72265b609e9d86723d8acc9100e446346 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -69,7 +69,7 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
index a4e0fa963d3f92eba02ef7a1b7f93660463441c0..c00b1fbae43684b720a655b6a53597d0bf3a7330 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
@@ -112,7 +112,7 @@ void PairLJCharmmCoulCharmmImplicitKokkos<DeviceType>::compute(int eflag_in, int
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
index 1e5509c39c6b238b22021f1371094c1b1c3c166f..c88c7db2e3f614a97b57d0db6b8d9d9992b70fb2 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
@@ -112,7 +112,7 @@ void PairLJCharmmCoulCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_i
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
index 2f94c47baeb345ce75c2796b95168e1eb3f2e5ed..8ebc5f87f3beb0e1266e4c8039ae43f29e028c1f 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
@@ -112,7 +112,7 @@ void PairLJCharmmCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
index 4283cfa981e276b0fd21c557e4ab3ec4da3669de..936eae79d518e1735243209916ffee90e71112e2 100644
--- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
@@ -89,7 +89,7 @@ void PairLJClass2CoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
index adbffff50ff5921d93b0b3c8fbc1bf8eacd341ce..268213cdbcbc66e9565efa7a1917104c28911fa1 100644
--- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
@@ -97,7 +97,7 @@ void PairLJClass2CoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp
index c26aa4f467d3246403ebe6c1d8cc2ff64261662d..c899327d7c993802bf0655106aaa452f1e4726f6 100644
--- a/src/KOKKOS/pair_lj_class2_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp
@@ -89,7 +89,7 @@ void PairLJClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
index e9f587d0ccf309902fcda93acb4e520c00b4717f..f4de48f176de8b9467075f0001cfe9fae555a503 100644
--- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
@@ -89,7 +89,7 @@ void PairLJCutCoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
index 0af781affddb3e6f91b3be47ca332f6997aa54a3..ad51dd0a889dc2a74bfc5699df7de9daae94e2eb 100644
--- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
@@ -93,7 +93,7 @@ void PairLJCutCoulDebyeKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
index 5ddf035b62fefe1e7af5f5aca61afcaad1a6e59b..89f263113eca976e1327793575c5743202928b56 100644
--- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
@@ -101,7 +101,7 @@ void PairLJCutCoulDSFKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
index e3754cdb5d59a46460aefe69213ba4211e8e85f2..4de51ca8d2f5ef64e5ab864d4a5599a738d8609f 100644
--- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
@@ -101,7 +101,7 @@ void PairLJCutCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp
index 9a2a7e23a985e622ba36e5e602f56d8859990a08..ea78b73711423e8ec268a638aefda6c73814ddc9 100644
--- a/src/KOKKOS/pair_lj_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp
@@ -89,7 +89,7 @@ void PairLJCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp
index cdede8bd52a5859a7c26fb37856f26cbcca9bbc3..6b62150632de7b1a563a6a6a1918a52d7017beb8 100644
--- a/src/KOKKOS/pair_lj_expand_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp
@@ -88,7 +88,7 @@ void PairLJExpandKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
index 0ca8375657b50137ad020e0e6a21877414ff1066..0c492131dd6dcaf83f415cb6d029052b2a04c567 100644
--- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
@@ -103,7 +103,7 @@ void PairLJGromacsCoulGromacsKokkos<DeviceType>::compute(int eflag_in, int vflag
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
index e6606d30cff23673d5b0c08e34ab7934eff25eff..76d7abbe289e5dd2ce4b811cfc5ae888740e0375 100644
--- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
@@ -100,7 +100,7 @@ void PairLJGromacsKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
index 2d74e37192ac7d72ceda9adf939ccc71da2bc7d2..41561c29889e6d991400e3249e22f578739c7509 100644
--- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
@@ -88,7 +88,7 @@ void PairLJSDKKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp
index e0685f13762cda8109ad544c700f261d4de6b1c3..3201fad215f5587b115402d1fe481c7f9f385180 100644
--- a/src/KOKKOS/pair_morse_kokkos.cpp
+++ b/src/KOKKOS/pair_morse_kokkos.cpp
@@ -93,7 +93,7 @@ void PairMorseKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_reax_c_kokkos.cpp b/src/KOKKOS/pair_reax_c_kokkos.cpp
index 5490268e561ccbe0992df27df4996697ba30a75e..acf9c754cdc70367e4f7bc96311291e92d6fe46a 100644
--- a/src/KOKKOS/pair_reax_c_kokkos.cpp
+++ b/src/KOKKOS/pair_reax_c_kokkos.cpp
@@ -633,7 +633,7 @@ void PairReaxCKokkos<DeviceType>::LR_vdW_Coulomb( int i, int j, double r_ij, LR_
}
if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
- { // innner wall
+ { // inner wall
e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
lr->e_vdW += Tap * e_core;
diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp
index 6b2c1ca04bb277db1dd1e59a5238eaf345345738..a8950a0c79c542e3a98a91ceb5b094ceb0b5da1b 100644
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
@@ -80,7 +80,7 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp
index 93556635c203ecfc064bcc1e10c2863bdefbb257..7f763baae6fe7b40eb4830d243c0b714a6bcf2b1 100644
--- a/src/KOKKOS/pair_table_kokkos.cpp
+++ b/src/KOKKOS/pair_table_kokkos.cpp
@@ -86,7 +86,7 @@ void PairTableKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index 0f5e93979490ea5bc401155562b46ac692b26e45..75280c8f7c381c668fa0cd1d41c48917d166dfc1 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -164,7 +164,7 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index 1f66da409d08a52029d2b4a7ee2bd3a63dcd33f6..d16a7fc4d79b5572552dcf8d955c7c2a4a7e6233 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -164,7 +164,7 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index 264b769df311e93800ca509558f10ef57c3533d8..e9bae49fb77ca55530e280df9e391a58e7c85715 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -178,7 +178,7 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp
index 0e972d24640bba5f62a96c451d3084405305c86b..f81af0b149659994e68ccf93a25ddd6beb57b314 100644
--- a/src/KOKKOS/pair_vashishta_kokkos.cpp
+++ b/src/KOKKOS/pair_vashishta_kokkos.cpp
@@ -79,7 +79,7 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == FULL) no_virial_fdotr_compute = 1;
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp
index 7b88563cbb2569fd5198ded0551f21ed6dbf89bf..c59bd89e51303784efef00d44be83c84b3960a7c 100644
--- a/src/KOKKOS/pppm_kokkos.cpp
+++ b/src/KOKKOS/pppm_kokkos.cpp
@@ -615,7 +615,7 @@ void PPPMKokkos<DeviceType>::compute(int eflag, int vflag)
// set energy/virial flags
// invoke allocate_peratom() if needed for first time
- if (eflag || vflag) ev_setup(eflag,vflag);
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
diff --git a/src/KSPACE/pair_buck_long_coul_long.h b/src/KSPACE/pair_buck_long_coul_long.h
index 736742a77aef352be6ea7af590a92947cc640f43..cf752a09b0604c4c676b6d309b7ed3c0a248e089 100644
--- a/src/KSPACE/pair_buck_long_coul_long.h
+++ b/src/KSPACE/pair_buck_long_coul_long.h
@@ -80,15 +80,15 @@ command-line option when running LAMMPS to see the offending line.
W: Using largest cutoff for buck/long/coul/long
-Self-exlanatory.
+Self-explanatory.
E: Cutoffs missing in pair_style buck/long/coul/long
-Self-exlanatory.
+Self-explanatory.
E: LJ6 off not supported in pair_style buck/long/coul/long
-Self-exlanatory.
+Self-explanatory.
E: Coulomb cut not supported in pair_style buck/long/coul/coul
diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h
index ae07ea9e07b3f762df77c827b2cc28d3e9a8f3f8..6993ad6c91bcd2584a3627b5f256dbba058d5a71 100644
--- a/src/KSPACE/pppm_disp.h
+++ b/src/KSPACE/pppm_disp.h
@@ -513,7 +513,7 @@ E: Cannot compute initial g_ewald_disp
LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6
factor that partitions the computation between real space and k-space
-for Disptersion interactions.
+for Dispersion interactions.
E: Could not compute grid size for Dispersion
diff --git a/src/MAKE/OPTIONS/Makefile.omp b/src/MAKE/OPTIONS/Makefile.omp
index 5c25c8e41c6fe8fd90a8f6941189179f59a1a852..fd485d541695bc10470223b30eed8487d938139b 100644
--- a/src/MAKE/OPTIONS/Makefile.omp
+++ b/src/MAKE/OPTIONS/Makefile.omp
@@ -7,7 +7,7 @@ SHELL = /bin/sh
# specify flags and libraries needed for your compiler
CC = mpicxx
-CCFLAGS = -g -O3 -fopenmp
+CCFLAGS = -g -O3 -restrict -fopenmp
SHFLAGS = -fPIC
DEPFLAGS = -M
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 51cf2216680a3747c00b6791e459cbb5ddfb4983..cacc8b3416cbc0b2bc3d1b0d0ace04cbcd75a3b2 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -753,7 +753,7 @@ void PairAIREBO::FLJ(int eflag, int vflag)
tee = drij / swidth;
tee2 = tee*tee;
slw = 1.0 - tee2 * (3.0 - 2.0 * tee);
- dslw = 6.0 * tee * (1.0 - tee) / rij / swidth;
+ dslw = -6.0 * tee * (1.0 - tee) / swidth;
} else {
slw = 1.0;
dslw = 0.0;
@@ -2104,6 +2104,9 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
double F12[3],F23[3],F34[3],F31[3],F24[3];
double fi[3],fj[3],fk[3],fl[3],f1[3],f2[3],f3[3],f4[4];
double rji[3],rki[3],rlj[3],r13[3],r43[3];
+ double realrij[3], realrijmag;
+ double rjkmag, rilmag, dctdjk, dctdik, dctdil, dctdjl;
+ double fjk[3], fil[3], rijmbr;
double **x = atom->x;
int *type = atom->type;
@@ -2130,6 +2133,12 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
Stb = 0.0;
dStb = 0.0;
+ realrij[0] = x[atomi][0] - x[atomj][0];
+ realrij[1] = x[atomi][1] - x[atomj][1];
+ realrij[2] = x[atomi][2] - x[atomj][2];
+ realrijmag = sqrt(realrij[0] * realrij[0] + realrij[1] * realrij[1]
+ + realrij[2] * realrij[2]);
+
REBO_neighs = REBO_firstneigh[i];
for (k = 0; k < REBO_numneigh[i]; k++) {
atomk = REBO_neighs[k];
@@ -2319,50 +2328,53 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
lamdajik = 4.0*kronecker(itype,1) *
((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
- (rijmag*rikmag);
+ rjk[0] = rik[0] - rij[0];
+ rjk[1] = rik[1] - rij[1];
+ rjk[2] = rik[2] - rij[2];
+ rjkmag = sqrt(rjk[0] * rjk[0] + rjk[1] * rjk[1] + rjk[2] * rjk[2]);
+ rijrik = 2 * rijmag * rikmag;
+ rr = rijmag * rijmag - rikmag * rikmag;
+ cosjik = (rijmag * rijmag + rikmag * rikmag - rjkmag * rjkmag) / rijrik;
cosjik = MIN(cosjik,1.0);
cosjik = MAX(cosjik,-1.0);
-
- dcosjikdri[0] = ((rij[0]+rik[0])/(rijmag*rikmag)) -
- (cosjik*((rij[0]/(rijmag*rijmag))+(rik[0]/(rikmag*rikmag))));
- dcosjikdri[1] = ((rij[1]+rik[1])/(rijmag*rikmag)) -
- (cosjik*((rij[1]/(rijmag*rijmag))+(rik[1]/(rikmag*rikmag))));
- dcosjikdri[2] = ((rij[2]+rik[2])/(rijmag*rikmag)) -
- (cosjik*((rij[2]/(rijmag*rijmag))+(rik[2]/(rikmag*rikmag))));
- dcosjikdrk[0] = (-rij[0]/(rijmag*rikmag)) +
- (cosjik*(rik[0]/(rikmag*rikmag)));
- dcosjikdrk[1] = (-rij[1]/(rijmag*rikmag)) +
- (cosjik*(rik[1]/(rikmag*rikmag)));
- dcosjikdrk[2] = (-rij[2]/(rijmag*rikmag)) +
- (cosjik*(rik[2]/(rikmag*rikmag)));
- dcosjikdrj[0] = (-rik[0]/(rijmag*rikmag)) +
- (cosjik*(rij[0]/(rijmag*rijmag)));
- dcosjikdrj[1] = (-rik[1]/(rijmag*rikmag)) +
- (cosjik*(rij[1]/(rijmag*rijmag)));
- dcosjikdrj[2] = (-rik[2]/(rijmag*rikmag)) +
- (cosjik*(rij[2]/(rijmag*rijmag)));
+ dctdjk = -2 / rijrik;
+ dctdik = (-rr + rjkmag * rjkmag) / (rijrik * rikmag * rikmag);
+ // evaluate splines g and derivatives dg
g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik));
- fj[0] = -tmp2*dcosjikdrj[0];
- fj[1] = -tmp2*dcosjikdrj[1];
- fj[2] = -tmp2*dcosjikdrj[2];
- fi[0] = -tmp2*dcosjikdri[0];
- fi[1] = -tmp2*dcosjikdri[1];
- fi[2] = -tmp2*dcosjikdri[2];
- fk[0] = -tmp2*dcosjikdrk[0];
- fk[1] = -tmp2*dcosjikdrk[1];
- fk[2] = -tmp2*dcosjikdrk[2];
+
+ fi[0] = -tmp2 * dctdik * rik[0];
+ fi[1] = -tmp2 * dctdik * rik[1];
+ fi[2] = -tmp2 * dctdik * rik[2];
+ fk[0] = tmp2 * dctdik * rik[0];
+ fk[1] = tmp2 * dctdik * rik[1];
+ fk[2] = tmp2 * dctdik * rik[2];
+ fj[0] = 0;
+ fj[1] = 0;
+ fj[2] = 0;
+ fjk[0] = -tmp2 * dctdjk * rjk[0];
+ fjk[1] = -tmp2 * dctdjk * rjk[1];
+ fjk[2] = -tmp2 * dctdjk * rjk[2];
+ fi[0] += fjk[0];
+ fi[1] += fjk[1];
+ fi[2] += fjk[2];
+ fk[0] -= fjk[0];
+ fk[1] -= fjk[1];
+ fk[2] -= fjk[2];
+ rijmbr = rcmin[itype][jtype] / realrijmag;
+ fj[0] += rijmbr * (fjk[0] - (realrij[0] * realrij[0] * fjk[0] + realrij[0] * realrij[1] * fjk[1] + realrij[0] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
+ fj[1] += rijmbr * (fjk[1] - (realrij[1] * realrij[0] * fjk[0] + realrij[1] * realrij[1] * fjk[1] + realrij[1] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
+ fj[2] += rijmbr * (fjk[2] - (realrij[2] * realrij[0] * fjk[0] + realrij[2] * realrij[1] * fjk[1] + realrij[2] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
+ fi[0] -= rijmbr * (fjk[0] - (realrij[0] * realrij[0] * fjk[0] + realrij[0] * realrij[1] * fjk[1] + realrij[0] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
+ fi[1] -= rijmbr * (fjk[1] - (realrij[1] * realrij[0] * fjk[0] + realrij[1] * realrij[1] * fjk[1] + realrij[1] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
+ fi[2] -= rijmbr * (fjk[2] - (realrij[2] * realrij[0] * fjk[0] + realrij[2] * realrij[1] * fjk[1] + realrij[2] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
tmp2 = VA*.5*(tmp*wik*g*exp(lamdajik)*4.0*kronecker(itype,1));
- fj[0] -= tmp2*(-rij[0]/rijmag);
- fj[1] -= tmp2*(-rij[1]/rijmag);
- fj[2] -= tmp2*(-rij[2]/rijmag);
- fi[0] -= tmp2*((-rik[0]/rikmag)+(rij[0]/rijmag));
- fi[1] -= tmp2*((-rik[1]/rikmag)+(rij[1]/rijmag));
- fi[2] -= tmp2*((-rik[2]/rikmag)+(rij[2]/rijmag));
+ fi[0] += tmp2*(rik[0]/rikmag);
+ fi[1] += tmp2*(rik[1]/rikmag);
+ fi[2] += tmp2*(rik[2]/rikmag);
fk[0] -= tmp2*(rik[0]/rikmag);
fk[1] -= tmp2*(rik[1]/rikmag);
fk[2] -= tmp2*(rik[2]/rikmag);
@@ -2427,51 +2439,53 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
lamdaijl = 4.0*kronecker(jtype,1) *
((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) /
- (rijmag*rjlmag);
+ ril[0] = rij[0] + rjl[0];
+ ril[1] = rij[1] + rjl[1];
+ ril[2] = rij[2] + rjl[2];
+ rilmag = sqrt(ril[0] * ril[0] + ril[1] * ril[1] + ril[2] * ril[2]);
+ rijrjl = 2 * rijmag * rjlmag;
+ rr = rijmag * rijmag - rjlmag * rjlmag;
+ cosijl = (rijmag * rijmag + rjlmag * rjlmag - rilmag * rilmag) / rijrjl;
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
-
- dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
- (cosijl*rij[0]/(rijmag*rijmag));
- dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
- (cosijl*rij[1]/(rijmag*rijmag));
- dcosijldri[2] = (-rjl[2]/(rijmag*rjlmag)) -
- (cosijl*rij[2]/(rijmag*rijmag));
- dcosijldrj[0] = ((-rij[0]+rjl[0])/(rijmag*rjlmag)) +
- (cosijl*((rij[0]/square(rijmag))-(rjl[0]/(rjlmag*rjlmag))));
- dcosijldrj[1] = ((-rij[1]+rjl[1])/(rijmag*rjlmag)) +
- (cosijl*((rij[1]/square(rijmag))-(rjl[1]/(rjlmag*rjlmag))));
- dcosijldrj[2] = ((-rij[2]+rjl[2])/(rijmag*rjlmag)) +
- (cosijl*((rij[2]/square(rijmag))-(rjl[2]/(rjlmag*rjlmag))));
- dcosijldrl[0] = (rij[0]/(rijmag*rjlmag)) +
- (cosijl*rjl[0]/(rjlmag*rjlmag));
- dcosijldrl[1] = (rij[1]/(rijmag*rjlmag)) +
- (cosijl*rjl[1]/(rjlmag*rjlmag));
- dcosijldrl[2] = (rij[2]/(rijmag*rjlmag)) +
- (cosijl*rjl[2]/(rjlmag*rjlmag));
+ dctdil = -2 / rijrjl;
+ dctdjl = (-rr + rilmag * rilmag) / (rijrjl * rjlmag * rjlmag);
// evaluate splines g and derivatives dg
g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl));
- fi[0] = -tmp2*dcosijldri[0];
- fi[1] = -tmp2*dcosijldri[1];
- fi[2] = -tmp2*dcosijldri[2];
- fj[0] = -tmp2*dcosijldrj[0];
- fj[1] = -tmp2*dcosijldrj[1];
- fj[2] = -tmp2*dcosijldrj[2];
- fl[0] = -tmp2*dcosijldrl[0];
- fl[1] = -tmp2*dcosijldrl[1];
- fl[2] = -tmp2*dcosijldrl[2];
-
+ fj[0] = -tmp2 * dctdjl * rjl[0];
+ fj[1] = -tmp2 * dctdjl * rjl[1];
+ fj[2] = -tmp2 * dctdjl * rjl[2];
+ fl[0] = tmp2 * dctdjl * rjl[0];
+ fl[1] = tmp2 * dctdjl * rjl[1];
+ fl[2] = tmp2 * dctdjl * rjl[2];
+ fi[0] = 0;
+ fi[1] = 0;
+ fi[2] = 0;
+ fil[0] = -tmp2 * dctdil * ril[0];
+ fil[1] = -tmp2 * dctdil * ril[1];
+ fil[2] = -tmp2 * dctdil * ril[2];
+ fj[0] += fil[0];
+ fj[1] += fil[1];
+ fj[2] += fil[2];
+ fl[0] -= fil[0];
+ fl[1] -= fil[1];
+ fl[2] -= fil[2];
+ rijmbr = rcmin[itype][jtype] / realrijmag;
+ fi[0] += rijmbr * (fil[0] - (realrij[0] * realrij[0] * fil[0] + realrij[0] * realrij[1] * fil[1] + realrij[0] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
+ fi[1] += rijmbr * (fil[1] - (realrij[1] * realrij[0] * fil[0] + realrij[1] * realrij[1] * fil[1] + realrij[1] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
+ fi[2] += rijmbr * (fil[2] - (realrij[2] * realrij[0] * fil[0] + realrij[2] * realrij[1] * fil[1] + realrij[2] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
+ fj[0] -= rijmbr * (fil[0] - (realrij[0] * realrij[0] * fil[0] + realrij[0] * realrij[1] * fil[1] + realrij[0] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
+ fj[1] -= rijmbr * (fil[1] - (realrij[1] * realrij[0] * fil[0] + realrij[1] * realrij[1] * fil[1] + realrij[1] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
+ fj[2] -= rijmbr * (fil[2] - (realrij[2] * realrij[0] * fil[0] + realrij[2] * realrij[1] * fil[1] + realrij[2] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
+
+
tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
- fi[0] -= tmp2*(rij[0]/rijmag);
- fi[1] -= tmp2*(rij[1]/rijmag);
- fi[2] -= tmp2*(rij[2]/rijmag);
- fj[0] -= tmp2*((-rjl[0]/rjlmag)-(rij[0]/rijmag));
- fj[1] -= tmp2*((-rjl[1]/rjlmag)-(rij[1]/rijmag));
- fj[2] -= tmp2*((-rjl[2]/rjlmag)-(rij[2]/rijmag));
+ fj[0] += tmp2*(rjl[0]/rjlmag);
+ fj[1] += tmp2*(rjl[1]/rjlmag);
+ fj[2] += tmp2*(rjl[2]/rjlmag);
fl[0] -= tmp2*(rjl[0]/rjlmag);
fl[1] -= tmp2*(rjl[1]/rjlmag);
fl[2] -= tmp2*(rjl[2]/rjlmag);
@@ -2654,14 +2668,14 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
dN3[2] = dN3Tij[2];
atom2 = atomi;
atom3 = atomj;
- r32[0] = x[atom3][0]-x[atom2][0];
- r32[1] = x[atom3][1]-x[atom2][1];
- r32[2] = x[atom3][2]-x[atom2][2];
- r32mag = sqrt((r32[0]*r32[0])+(r32[1]*r32[1])+(r32[2]*r32[2]));
- r23[0] = -r32[0];
- r23[1] = -r32[1];
- r23[2] = -r32[2];
- r23mag = r32mag;
+ r32[0] = -rij[0];
+ r32[1] = -rij[1];
+ r32[2] = -rij[2];
+ r23[0] = rij[0];
+ r23[1] = rij[1];
+ r23[2] = rij[2];
+ r32mag = rijmag;
+ r23mag = rijmag;
REBO_neighs_i = REBO_firstneigh[i];
for (k = 0; k < REBO_numneigh[i]; k++) {
@@ -2690,7 +2704,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
rijrik = 2.0*rijmag*r21mag;
rik2 = r21mag*r21mag;
dctik = (-rr+rjk2)/(rijrik*rik2);
- dctij = (rr+rjk2)/(rijrik*rijmag*rijmag);
dctjk = -2.0/rijrik;
w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
rikmag = r21mag;
@@ -2729,7 +2742,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
rijrjl = 2.0*r23mag*r34mag;
rjl2 = r34mag*r34mag;
dctjl = (-rr+ril2)/(rijrjl*rjl2);
- dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
dctil = -2.0/rijrjl;
rjlmag = r34mag;
rjl2 = r34mag*r34mag;
@@ -2750,15 +2762,11 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
om1234 = cwnum/cwnom;
cw = om1234;
- Etmp += ((1.0-square(om1234))*w21*w34) *
- (1.0-tspjik)*(1.0-tspijl);
dt1dik = (rik2i)-(dctik*sink2i*cos321);
dt1djk = (-dctjk*sink2i*cos321);
dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
dt1dil = (-dctil*sinl2i*cos234);
- dt1dij = (2.0/(r23mag*r23mag)) -
- (dctij*sink2i*cos321)-(dctji*sinl2i*cos234);
dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
@@ -2768,16 +2776,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
- dt2dij[0] = (r21[2]*cross234[1]) -
- (r34[2]*cross321[1])-(r21[1]*cross234[2]) +
- (r34[1]*cross321[2]);
- dt2dij[1] = (r21[0]*cross234[2]) -
- (r34[0]*cross321[2])-(r21[2]*cross234[0]) +
- (r34[2]*cross321[0]);
- dt2dij[2] = (r21[1]*cross234[0]) -
- (r34[1]*cross321[0])-(r21[0]*cross234[1]) +
- (r34[0]*cross321[1]);
-
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
aaa1 = -prefactor*(1.0-square(om1234)) *
@@ -2785,17 +2783,11 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
aaa2 = aaa1*w21*w34;
at2 = aa*cwnum;
- fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
- (aaa2*dtsijl*dctji*(1.0-tspjik));
fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
- F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
- F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
- F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
-
F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
@@ -2815,16 +2807,31 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
f1[0] = -F12[0]-F31[0];
f1[1] = -F12[1]-F31[1];
f1[2] = -F12[2]-F31[2];
- f2[0] = F23[0]+F12[0]+F24[0];
- f2[1] = F23[1]+F12[1]+F24[1];
- f2[2] = F23[2]+F12[2]+F24[2];
- f3[0] = -F23[0]+F34[0]+F31[0];
- f3[1] = -F23[1]+F34[1]+F31[1];
- f3[2] = -F23[2]+F34[2]+F31[2];
+ f2[0] = F12[0]+F31[0];
+ f2[1] = F12[1]+F31[1];
+ f2[2] = F12[2]+F31[2];
+ f3[0] = F34[0]+F24[0];
+ f3[1] = F34[1]+F24[1];
+ f3[2] = F34[2]+F24[2];
f4[0] = -F34[0]-F24[0];
f4[1] = -F34[1]-F24[1];
f4[2] = -F34[2]-F24[2];
+ rijmbr = rcmin[itype][jtype] / realrijmag;
+ f2[0] += rijmbr * (F24[0] - (realrij[0] * realrij[0] * F24[0] + realrij[0] * realrij[1] * F24[1] + realrij[0] * realrij[2] * F24[2]) / (realrijmag * realrijmag));
+ f2[1] += rijmbr * (F24[1] - (realrij[1] * realrij[0] * F24[0] + realrij[1] * realrij[1] * F24[1] + realrij[1] * realrij[2] * F24[2]) / (realrijmag * realrijmag));
+ f2[2] += rijmbr * (F24[2] - (realrij[2] * realrij[0] * F24[0] + realrij[2] * realrij[1] * F24[1] + realrij[2] * realrij[2] * F24[2]) / (realrijmag * realrijmag));
+ f3[0] -= rijmbr * (F24[0] - (realrij[0] * realrij[0] * F24[0] + realrij[0] * realrij[1] * F24[1] + realrij[0] * realrij[2] * F24[2]) / (realrijmag * realrijmag));
+ f3[1] -= rijmbr * (F24[1] - (realrij[1] * realrij[0] * F24[0] + realrij[1] * realrij[1] * F24[1] + realrij[1] * realrij[2] * F24[2]) / (realrijmag * realrijmag));
+ f3[2] -= rijmbr * (F24[2] - (realrij[2] * realrij[0] * F24[0] + realrij[2] * realrij[1] * F24[1] + realrij[2] * realrij[2] * F24[2]) / (realrijmag * realrijmag));
+
+ f2[0] -= rijmbr * (F31[0] - (realrij[0] * realrij[0] * F31[0] + realrij[0] * realrij[1] * F31[1] + realrij[0] * realrij[2] * F31[2]) / (realrijmag * realrijmag));
+ f2[1] -= rijmbr * (F31[1] - (realrij[1] * realrij[0] * F31[0] + realrij[1] * realrij[1] * F31[1] + realrij[1] * realrij[2] * F31[2]) / (realrijmag * realrijmag));
+ f2[2] -= rijmbr * (F31[2] - (realrij[2] * realrij[0] * F31[0] + realrij[2] * realrij[1] * F31[1] + realrij[2] * realrij[2] * F31[2]) / (realrijmag * realrijmag));
+ f3[0] += rijmbr * (F31[0] - (realrij[0] * realrij[0] * F31[0] + realrij[0] * realrij[1] * F31[1] + realrij[0] * realrij[2] * F31[2]) / (realrijmag * realrijmag));
+ f3[1] += rijmbr * (F31[1] - (realrij[1] * realrij[0] * F31[0] + realrij[1] * realrij[1] * F31[1] + realrij[1] * realrij[2] * F31[2]) / (realrijmag * realrijmag));
+ f3[2] += rijmbr * (F31[2] - (realrij[2] * realrij[0] * F31[0] + realrij[2] * realrij[1] * F31[1] + realrij[2] * realrij[2] * F31[2]) / (realrijmag * realrijmag));
+
// coordination forces
tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h
index a0408d55dd4c64dfb7b6c2a4bf93219060bf1a5e..d55d9a79a4fb5c7362fbb9e266e989bc383d7cf5 100644
--- a/src/MANYBODY/pair_bop.h
+++ b/src/MANYBODY/pair_bop.h
@@ -274,7 +274,7 @@ atomic structure to ensure that it is realistic.
E: Too many atom triplets for pair bop
The number of three atom groups for angle determinations exceeds the
-expected number. Check your atomic structrure to ensure that it is
+expected number. Check your atomic structure to ensure that it is
realistic.
E: Cannot open BOP potential file %s
diff --git a/src/MISC/fix_ttm.h b/src/MISC/fix_ttm.h
index 34629fb538bd20c30434d105a76aaca380d6b0e1..57d18bcb3ac971ff2fbcdfaad81fb64a5abfec44 100644
--- a/src/MISC/fix_ttm.h
+++ b/src/MISC/fix_ttm.h
@@ -148,7 +148,7 @@ Self-explanatory.
E: Initial temperatures not all set in fix ttm
-Self-explantory.
+Self-explanatory.
W: Too many inner timesteps in fix ttm
diff --git a/src/PYTHON/python.cpp b/src/PYTHON/python.cpp
index 6c89be69229d159a059e643ef790f311762584dd..11bb848b334f6f177c25506f17b7ea35f5f94ee0 100644
--- a/src/PYTHON/python.cpp
+++ b/src/PYTHON/python.cpp
@@ -146,7 +146,7 @@ void Python::command(int narg, char **arg)
int ifunc = create_entry(arg[0]);
- // one-time intitialization of Python interpreter
+ // one-time initialization of Python interpreter
// Py_SetArgv() enables finding of *.py module files in current dir
// only needed for module load, not for direct file read into __main__
// pymain stores pointer to main module
diff --git a/src/PYTHON/python.h b/src/PYTHON/python.h
index 61e5f015e200e5f1fd2255d36e3b875bd1d9dc17..5f65e3970bea5a860d311a55c2b8701e82193d9d 100644
--- a/src/PYTHON/python.h
+++ b/src/PYTHON/python.h
@@ -94,12 +94,12 @@ path and name are correct.
E: Could not process Python file
-The Python code in the specified file was not run sucessfully by
+The Python code in the specified file was not run successfully by
Python, probably due to errors in the Python code.
E: Could not process Python string
-The Python code in the here string was not run sucessfully by Python,
+The Python code in the here string was not run successfully by Python,
probably due to errors in the Python code.
E: Could not find Python function
@@ -123,7 +123,7 @@ Self-explanatory.
E: Python function evaluation failed
-The Python function did not run succesfully and/or did not return a
+The Python function did not run successfully and/or did not return a
value (if it is supposed to return a value). This is probably due to
some error condition in the function.
diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h
index dc7c6d389e829e751f5781ee6d2c7aa5be2fe822..99237d839702e5f25e48054bbb7dd4321e1618ce 100644
--- a/src/REAX/fix_reax_bonds.h
+++ b/src/REAX/fix_reax_bonds.h
@@ -63,7 +63,7 @@ Check that the path and name are correct.
E: Cannot use fix reax/bonds without pair_style reax
-Self-explantory.
+Self-explanatory.
E: Fix reax/bonds numbonds > nsbmax_most
diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h
index 00719dcc95fa5ae1456448c0129e08375956b7ea..afedf0cdc5cb79ff891978fc4e20a0caa30cdc4c 100644
--- a/src/REPLICA/neb.h
+++ b/src/REPLICA/neb.h
@@ -106,7 +106,7 @@ for NEB.
E: Too many timesteps
-The cummulative timesteps must fit in a 64-bit integer.
+The cumulative timesteps must fit in a 64-bit integer.
E: Unexpected end of neb file
diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h
index cc866007d2b439f21f223a877a1a8a8858489a13..be09af496562599151069feddacb87d60e08577f 100644
--- a/src/REPLICA/prd.h
+++ b/src/REPLICA/prd.h
@@ -122,7 +122,7 @@ after the PRD simulation.
E: Too many timesteps
-The cummulative timesteps must fit in a 64-bit integer.
+The cumulative timesteps must fit in a 64-bit integer.
E: Cannot use PRD with a changing box
diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h
index 8b8b22552a6137b90d556290b23205885c1cebc0..d44b22664372a924082b1d609e7b1699b83df66f 100644
--- a/src/REPLICA/tad.h
+++ b/src/REPLICA/tad.h
@@ -145,7 +145,7 @@ after the PRD simulation.
E: Too many timesteps
-The cummulative timesteps must fit in a 64-bit integer.
+The cumulative timesteps must fit in a 64-bit integer.
E: Too many iterations
diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h
index 832e36e491d388e0665b9e646cb15458eca58995..3d24fdbc69c879413d9441be4b04d078e27af361 100644
--- a/src/REPLICA/temper.h
+++ b/src/REPLICA/temper.h
@@ -96,7 +96,7 @@ temperature (nvt or langevin).
E: Too many timesteps
-The cummulative timesteps must fit in a 64-bit integer.
+The cumulative timesteps must fit in a 64-bit integer.
E: Tempering could not find thermo_pe compute
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 4358793a332578ef6e0a0b0163baa835f7002e61..2d8e736a1eef1ebf811c555259695ace712b8038 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -2488,7 +2488,7 @@ void FixRigidSmall::write_restart_file(char *file)
{
FILE *fp;
- // do not write file if bodies have not yet been intialized
+ // do not write file if bodies have not yet been initialized
if (!setupflag) return;
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 5907a69b1fcb9ecd9c9958ad523e433a34cecc43..6d5d470545f2867ad0b12a90ed2a60aae9589535 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -447,7 +447,6 @@ void FixShake::setup(int vflag)
next_output = (ntimestep/output_every)*output_every + output_every;
} else next_output = -1;
-
// set respa to 0 if verlet is used and to 1 otherwise
if (strstr(update->integrate_style,"verlet"))
@@ -476,7 +475,6 @@ void FixShake::setup(int vflag)
// precalculate constraining forces for first integration step
shake_end_of_step(vflag);
-
}
/* ----------------------------------------------------------------------
@@ -592,6 +590,7 @@ void FixShake::post_force(int vflag)
}
// store vflag for coordinate_constraints_end_of_step()
+
vflag_post_force = vflag;
}
diff --git a/src/RIGID/fix_shake.h b/src/RIGID/fix_shake.h
index afd3868cb4e90fe5aba61260eeb808f4f07116e0..ff12b9e120cb54f17111e7df618fc971dba39507 100644
--- a/src/RIGID/fix_shake.h
+++ b/src/RIGID/fix_shake.h
@@ -184,7 +184,7 @@ Self-explanatory.
W: Molecule template for fix shake has multiple molecules
-The fix shake command will only recoginze molecules of a single
+The fix shake command will only recognize molecules of a single
type, i.e. the first molecule in the template.
E: Fix shake molecule template must have shake info
diff --git a/src/SHOCK/fix_append_atoms.h b/src/SHOCK/fix_append_atoms.h
index d9885998bea9f68fa3894b36d7c2d7d1643436f6..cc26acc8b8b34948d84a6e7c2e70360133b34131 100644
--- a/src/SHOCK/fix_append_atoms.h
+++ b/src/SHOCK/fix_append_atoms.h
@@ -94,7 +94,7 @@ type p (periodic).
E: Cannot append atoms to a triclinic box
-The simulation box must be defined with edges alligned with the
+The simulation box must be defined with edges aligned with the
Cartesian axes.
E: Fix ID for fix ave/spatial does not exist
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index d3f132bd046e88d084ea7aa33373d4c537d26765..dc84b0be055a41ba2dfd400e605aadd803256b12 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -700,7 +700,7 @@ double PairSNAP::extra_cutoff()
// Note that at most one atom is exchanged per processor pair.
-// Also note that the local atom assignement
+// Also note that the local atom assignment
// doesn't change. This load balancer will cause
// some ghost atoms to have full neighborlists
// which are unique to PairSNAP.
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index ef93ce9ff6319e19767027f3f4b649d6f8abdeb3..8b16b89336d35aadf4d5452e4e7d6e677457bf29 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -815,7 +815,7 @@ void SNA::compute_dbidrj()
// for mb1 = 0,...,j1mid
// for ma1 = 0,...,j1
// zdb +=
- // Conj(dudr(j1,ma1,mb1))*z(j1,j2,j,ma1,mb1)
+ // Conj(dudr(j1,ma1,mb1))*z(j,j2,j1,ma1,mb1)
// dbdr(j1,j2,j) += 2*zdb*(j+1)/(j1+1)
// zdb = 0
// for mb2 = 0,...,j2mid
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 736b10d83f2d94943d9e63896585b45c8141a516..7e43901dc950dd5667b04889d64d0cd417c4e97e 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -811,7 +811,7 @@ void FixSRD::post_force(int vflag)
}
// if wall has moved too far, trigger reneigh on next step
- // analagous to neighbor check for big particle moving 1/2 of skin distance
+ // analogous to neighbor check for big particle moving 1/2 of skin distance
if (wallexist) {
for (m = 0; m < nwall; m++)
diff --git a/src/SRD/fix_srd.h b/src/SRD/fix_srd.h
index fae9780b8926e498545cf1fd75fe15336f8d291c..e14652e526996f8075e99069158e45882b4097e2 100644
--- a/src/SRD/fix_srd.h
+++ b/src/SRD/fix_srd.h
@@ -361,11 +361,11 @@ warning.
E: Bad quadratic solve for particle/line collision
-This is an internal error. It should nornally not occur.
+This is an internal error. It should normally not occur.
E: Bad quadratic solve for particle/tri collision
-This is an internal error. It should nornally not occur.
+This is an internal error. It should normally not occur.
W: Fix srd particle moved outside valid domain
@@ -377,7 +377,7 @@ Big particles must be extended spheriods or ellipsoids.
E: Cannot use lines with fix srd unless overlap is set
-This is because line segements are connected to each other.
+This is because line segments are connected to each other.
E: Cannot use tris with fix srd unless overlap is set
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.h b/src/USER-AWPMD/atom_vec_wavepacket.h
index e43c093ca3d91fc4fa24d7eb58499d8432c71d9e..d1a0c7c7f28c9c2907d302249d6cc9dd2395ce8f 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.h
+++ b/src/USER-AWPMD/atom_vec_wavepacket.h
@@ -95,9 +95,9 @@ private:
// AWPMD- specific:
///\en electron tag: must be the same for the WPs belonging to the same electron
int *etag;
- ///\en wavepacket split coeffcients: cre, cim, size is 2*N
+ ///\en wavepacket split coefficients: cre, cim, size is 2*N
double *cs;
- ///\en force on wavepacket split coeffcients: re, im, size is 2*N
+ ///\en force on wavepacket split coefficients: re, im, size is 2*N
double *csforce;
///\en (generalized) force on velocity, size is 3*N
double *vforce;
diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp
index 7320263ba7b27f3d6a79caf40002934405df1e91..89453ded9be77b795ea1b005e2262927442a1088 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.cpp
+++ b/src/USER-COLVARS/colvarproxy_lammps.cpp
@@ -352,12 +352,17 @@ int colvarproxy_lammps::smp_enabled()
int colvarproxy_lammps::smp_colvars_loop()
{
colvarmodule *cv = this->colvars;
+ colvarproxy_lammps *proxy = (colvarproxy_lammps *) cv->proxy;
#pragma omp parallel for
- for (size_t i = 0; i < cv->colvars_smp.size(); i++) {
+ for (size_t i = 0; i < cv->variables_active_smp()->size(); i++) {
+ colvar *x = (*(cv->variables_active_smp()))[i];
+ int x_item = (*(cv->variables_active_smp_items()))[i];
if (cvm::debug()) {
- cvm::log("Calculating colvar \""+cv->colvars_smp[i]->name+"\" on thread "+cvm::to_str(smp_thread_id())+"\n");
+ cvm::log("["+cvm::to_str(proxy->smp_thread_id())+"/"+cvm::to_str(proxy->smp_num_threads())+
+ "]: calc_colvars_items_smp(), i = "+cvm::to_str(i)+", cv = "+
+ x->name+", cvc = "+cvm::to_str(x_item)+"\n");
}
- cv->colvars_smp[i]->calc_cvcs(cv->colvars_smp_items[i], 1);
+ x->calc_cvcs(x_item, 1);
}
return cvm::get_error();
}
@@ -367,11 +372,13 @@ int colvarproxy_lammps::smp_biases_loop()
{
colvarmodule *cv = this->colvars;
#pragma omp parallel for
- for (size_t i = 0; i < cv->biases.size(); i++) {
+ for (size_t i = 0; i < cv->biases_active()->size(); i++) {
+ colvarbias *b = (*(cv->biases_active()))[i];
if (cvm::debug()) {
- cvm::log("Calculating bias \""+cv->biases[i]->name+"\" on thread "+cvm::to_str(smp_thread_id())+"\n");
+ cvm::log("Calculating bias \""+b->name+"\" on thread "+
+ cvm::to_str(smp_thread_id())+"\n");
}
- cv->biases[i]->update();
+ b->update();
}
return cvm::get_error();
}
diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h
index c0b4ea20fecb37dfad428b0e7058b4fa885652bc..ad63eb2f9eb6b740131d38aaac641b6f25df23e5 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.h
+++ b/src/USER-COLVARS/colvarproxy_lammps.h
@@ -29,7 +29,7 @@
#endif
#ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2016-12-27"
+#define COLVARPROXY_VERSION "2017-01-09"
#endif
/* struct for packed data communication of coordinates and forces. */
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h
index b8cee21c3534a1e1a0d23e6570e55e23f2affda8..294b003b0c119b7007afedaa1bf05d4a8f301e82 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.h
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.h
@@ -106,15 +106,15 @@ Self-explanatory.
E: Invalid fix ave/time off column
-Self-explantory.
+Self-explanatory.
E: Fix ave/time compute does not calculate a scalar
-Self-explantory.
+Self-explanatory.
E: Fix ave/time compute does not calculate a vector
-Self-explantory.
+Self-explanatory.
E: Fix ave/time compute vector is accessed out-of-range
diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp
index 399383ec18715a153abb3d90a1f753476cd3dc58..477ed05e3f04c85cd0ba864bb56b0bd76200df5b 100644
--- a/src/USER-DPD/atom_vec_dpd.cpp
+++ b/src/USER-DPD/atom_vec_dpd.cpp
@@ -488,8 +488,6 @@ int AtomVecDPD::pack_comm_hybrid(int n, int *list, double *buf)
buf[m++] = uCond[j];
buf[m++] = uMech[j];
buf[m++] = uChem[j];
- buf[m++] = uCG[j];
- buf[m++] = uCGnew[j];
}
return m;
}
@@ -589,8 +587,6 @@ int AtomVecDPD::unpack_comm_hybrid(int n, int first, double *buf)
uCond[i] = buf[m++];
uMech[i] = buf[m++];
uChem[i] = buf[m++];
- uCG[i] = buf[m++];
- uCGnew[i] = buf[m++];
}
return m;
}
diff --git a/src/USER-DPD/fix_eos_table_rx.h b/src/USER-DPD/fix_eos_table_rx.h
index 8c26d133a52e364bf34bce6c4d7a7b9009adde57..9de7c5fbc70ab083122fca8ea463562eab007692 100644
--- a/src/USER-DPD/fix_eos_table_rx.h
+++ b/src/USER-DPD/fix_eos_table_rx.h
@@ -157,6 +157,6 @@ Self-explanatory.
E: Maxit exceeded in secant solver
-The maximum number of interations was exceeded in the secant solver
+The maximum number of iterations was exceeded in the secant solver
*/
diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp
index 1a07fb9d3894a7c32c4b71f3aba29244650d10ae..deff0d34e98251789d1ee6028dd46a606c5af13a 100644
--- a/src/USER-DPD/pair_exp6_rx.cpp
+++ b/src/USER-DPD/pair_exp6_rx.cpp
@@ -1098,7 +1098,7 @@ void PairExp6rx::getMixingWeights(int id,double &epsilon1,double &alpha1,double
fraction2 = atom->dvector[ispecies][id]/nTotal;
}
- // If Site1 or Site2 matches is a fluid, then compute the paramters
+ // If Site1 or Site2 matches is a fluid, then compute the parameters
if (isOneFluidApprox(isite1) || isOneFluidApprox(isite2)) {
if (isite1 == params[iparam].ispecies || isite2 == params[iparam].ispecies) continue;
rmi = params[iparam].rm;
diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp
index 6e20f206d5b81a114e10e3997044bb6b60adb876..43d41147416bc6ffd28fcfea29d48b02cae0bb29 100644
--- a/src/USER-DPD/pair_multi_lucy_rx.cpp
+++ b/src/USER-DPD/pair_multi_lucy_rx.cpp
@@ -385,11 +385,11 @@ void PairMultiLucyRX::coeff(int narg, char **arg)
nspecies = atom->nspecies_dpd;
int n;
- n = strlen(arg[3]) + 1;
+ n = strlen(arg[4]) + 1;
site1 = new char[n];
strcpy(site1,arg[4]);
- n = strlen(arg[4]) + 1;
+ n = strlen(arg[5]) + 1;
site2 = new char[n];
strcpy(site2,arg[5]);
@@ -923,15 +923,15 @@ void PairMultiLucyRX::computeLocalDensity()
rho_i += factor;
if (newton_pair || j < nlocal)
rho[j] += factor;
- } else if (rsq < cutsq[itype][jtype]) {
- const double rcut = sqrt(cutsq[itype][jtype]);
- const double tmpFactor = 1.0-sqrt(rsq)/rcut;
- const double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor;
- const double factor = (84.0/(5.0*pi*rcut*rcut*rcut))*(1.0+3.0*sqrt(rsq)/(2.0*rcut))*tmpFactor4;
- rho_i += factor;
- if (newton_pair || j < nlocal)
- rho[j] += factor;
}
+ } else if (rsq < cutsq[itype][jtype]) {
+ const double rcut = sqrt(cutsq[itype][jtype]);
+ const double tmpFactor = 1.0-sqrt(rsq)/rcut;
+ const double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor;
+ const double factor = (84.0/(5.0*pi*rcut*rcut*rcut))*(1.0+3.0*sqrt(rsq)/(2.0*rcut))*tmpFactor4;
+ rho_i += factor;
+ if (newton_pair || j < nlocal)
+ rho[j] += factor;
}
}
diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp
index 8498d752e31396b79101c362568beb06659d8b24..2529d33f918629b606d11bc6e54e1dca85ec4fd4 100644
--- a/src/USER-DPD/pair_table_rx.cpp
+++ b/src/USER-DPD/pair_table_rx.cpp
@@ -351,7 +351,7 @@ void PairTableRX::coeff(int narg, char **arg)
nspecies = atom->nspecies_dpd;
if(nspecies==0) error->all(FLERR,"There are no rx species specified.");
int n;
- n = strlen(arg[3]) + 1;
+ n = strlen(arg[4]) + 1;
site1 = new char[n];
strcpy(site1,arg[4]);
@@ -362,7 +362,7 @@ void PairTableRX::coeff(int narg, char **arg)
if (ispecies == nspecies && strcmp(site1,"1fluid") != 0)
error->all(FLERR,"Site1 name not recognized in pair coefficients");
- n = strlen(arg[4]) + 1;
+ n = strlen(arg[5]) + 1;
site2 = new char[n];
strcpy(site2,arg[5]);
diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp
index 5b4463631f130a5be7c13f4846f20ee558885c14..d6c3e23ab42632dbef0b573692bc2b2867e0e2ec 100644
--- a/src/USER-LB/fix_lb_fluid.cpp
+++ b/src/USER-LB/fix_lb_fluid.cpp
@@ -50,7 +50,7 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
// where: nevery: call this fix every nevery timesteps.
// (keep this set to 1 for now).
// typeLB: there are two different integrators
- // in the code labelled "1" and "2".
+ // in the code labeled "1" and "2".
// viscosity: the viscosity of the fluid.
// densityinit_real: the density of the fluid.
//
diff --git a/src/USER-MANIFOLD/README b/src/USER-MANIFOLD/README
index 36563916413c74adb597f59ac7d5a2aa0b932daa..f55a9bb8e32de355a75d7f3506ef7d848ff833db 100644
--- a/src/USER-MANIFOLD/README
+++ b/src/USER-MANIFOLD/README
@@ -31,7 +31,7 @@ To add a new manifold, do the following in the "USER-MANIFOLD" directory:
e. The header file has to contain somewhere the macro ManifoldStyle with as
first argument the name of the manifold and as second argument the name
of the class implementing this manifold. The macro expands into some code
- that registers the manifold during static initialisation, before main is
+ that registers the manifold during static initialization, before main is
entered.
2. In the source file, make sure you implement the following (of course,
@@ -51,7 +51,7 @@ To add a new manifold, do the following in the "USER-MANIFOLD" directory:
| | manifold in LAMMPS input scripts. |
| const char *id() | Should return whatever type() returns. |
| static int expected_argc() | Returns the number of arguments needed |
-| | for the construction/initialisation of |
+| | for the construction/initialization of |
| | your manifold. Example: Sphere only |
| | needs a radius, so it returns 1. The |
| | spine needs 5 parameters, so it |
diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp
index c3bbc935af33ba195390e29766e6b88bc583343b..2fac8e40df5756decae59dbc195b04a957496aec 100644
--- a/src/USER-MANIFOLD/fix_manifoldforce.cpp
+++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp
@@ -104,7 +104,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) :
}
- // Perform any further initialisation for the manifold that depends on params:
+ // Perform any further initialization for the manifold that depends on params:
ptr_m->post_param_init();
}
diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h
index 82a565af38b3b2ebcdd33bbe0a5de134df6514c5..85692a8b6b8cd0110941877fd4e6405ed855f143 100644
--- a/src/USER-MANIFOLD/manifold.h
+++ b/src/USER-MANIFOLD/manifold.h
@@ -65,7 +65,7 @@ namespace user_manifold {
virtual int nparams() = 0;
double **get_params(){ return ¶ms; };
- // Overload if any initialisation depends on params:
+ // Overload if any initialization depends on params:
virtual void post_param_init(){}
virtual void checkup(){} // Some diagnostics...
protected:
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 8aed7972355e348e32d03484670a6abad28490f4..52ee6cad9467af17133a9d4ad86e61dddc3931bc 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -63,6 +63,7 @@ pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
+pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17
pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16
diff --git a/src/USER-MISC/fix_grem.h b/src/USER-MISC/fix_grem.h
index 5e828a8b9f30fc5b9eb9ac463a6a0ae9ee28cd6d..4806505f613616b70a8f3405c85177ce65d600fe 100644
--- a/src/USER-MISC/fix_grem.h
+++ b/src/USER-MISC/fix_grem.h
@@ -77,7 +77,7 @@ in energy directly.
E: Must use variable energy with fix grem
-Must define an energy vartiable when applyting a dynamic
+Must define an energy variable when applying a dynamic
force during minimization.
*/
diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp
index 5b5341f5061b3cf113aed66fb668121aaa037b83..5a7937e4ee974caf6441da75c5e8b8fa92c8e0b4 100644
--- a/src/USER-MISC/improper_ring.cpp
+++ b/src/USER-MISC/improper_ring.cpp
@@ -26,7 +26,7 @@
(2002)
This potential does not affect small amplitude vibrations
but is used in an ad hoc way to prevent the onset of
- accidentially large amplitude fluctuations leading to
+ accidentally large amplitude fluctuations leading to
the occurrence of a planar conformation of the three
bonds i, i + 1 and i', an intermediate conformation
toward the chiral inversion of a methine carbon.
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 03bb22c71346c29a07d0647a72c493ac0d82daa1..9cd2cf57b883175f5f8b50a1439f8fbed7bd9b8e 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -60,6 +60,14 @@ static const char cite_pair_agni[] =
" pages = {094306},\n"
" year = {2015},\n"
" publisher = {APS}\n"
+ "}\n\n"
+ "@article{botu2017jpc,\n"
+ " author = {Botu, V. and Batra, R. and Chapman, J. and Ramprasad, Rampi},\n"
+ " journal = {J. Phys. Chem. C},\n"
+ " volume = {121},\n"
+ " number = {1},\n"
+ " pages = {511},\n"
+ " year = {2017},\n"
"}\n\n";
#define AGNI_VERSION 1
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index f3a599dbdb6168e295af820fb8bddc6cac001d82..6ce84ab767e61da53a6f54efc25a11f2ec8875d7 100644
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -1034,7 +1034,7 @@ void PairEDIP::setup_params()
if (rtmp > cutmax) cutmax = rtmp;
}
- // this should be removed for multi species parametrizations
+ // this should be removed for multi species parameterization
A = params[0].A;
B = params[0].B;
diff --git a/src/USER-MISC/pair_edip.h b/src/USER-MISC/pair_edip.h
index 6a55992f1f74423681d7bef2213188af77ad9f91..6c4a37d795f66495900478083cdf78bf0dbe6562 100644
--- a/src/USER-MISC/pair_edip.h
+++ b/src/USER-MISC/pair_edip.h
@@ -64,7 +64,7 @@ class PairEDIP : public Pair {
double *tauFunctionGrid;
double *tauFunctionDerivedGrid;
- // this should be removed for multi species parametrizations
+ // this should be removed for multi species parameterization
// since these parameters should be addressed through indexes
// see also the PairEDIP::setup()
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..ddb39f6870ad0a9968d739e32bf137207640150b
--- /dev/null
+++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
@@ -0,0 +1,441 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Jaap Kroes (Radboud Universiteit)
+ e-mail: jaapkroes at gmail dot com
+ based on previous versions by Merel van Wijk and by Marco Raguzzoni
+
+ This is a simplified version of the potential described in
+ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
+ The simplification is that all normals are taken along the z-direction
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_kolmogorov_crespi_z.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define MAXLINE 1024
+#define DELTA 4
+
+/* ---------------------------------------------------------------------- */
+
+PairKolmogorovCrespiZ::PairKolmogorovCrespiZ(LAMMPS *lmp) : Pair(lmp)
+{
+ writedata = 1;
+
+ // initialize element to parameter maps
+ nelements = 0;
+ elements = NULL;
+ nparams = maxparam = 0;
+ params = NULL;
+ elem2param = NULL;
+ map = NULL;
+
+ // always compute energy offset
+ offset_flag = true;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairKolmogorovCrespiZ::~PairKolmogorovCrespiZ()
+{
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ memory->destroy(cut);
+ memory->destroy(offset);
+ }
+
+ if (elements)
+ for (int i = 0; i < nelements; i++) delete [] elements[i];
+ delete [] elements;
+ memory->destroy(params);
+ memory->destroy(elem2param);
+ if (allocated) delete [] map;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiZ::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair, fpair1;
+ double rsq,r,rhosq,exp1,exp2,r6,r8;
+ double frho,sumC,sumC2,sumCff,fsum,rdsq;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ jtype = type[j];
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ // rho^2 = r^2 - (n,r) = r^2 - z^2
+ rhosq = delx*delx + dely*dely;
+ rsq = rhosq + delz*delz;
+
+ if (rsq < cutsq[itype][jtype]) {
+
+ int iparam_ij = elem2param[map[itype]][map[jtype]];
+ Param& p = params[iparam_ij];
+
+ r = sqrt(rsq);
+ r6 = rsq*rsq*rsq;
+ r8 = r6*rsq;
+ rdsq = rhosq*p.delta2inv; // (rho/delta)^2
+
+ // store exponents
+ exp1 = exp(-p.lambda*(r-p.z0));
+ exp2 = exp(-rdsq);
+
+ // note that f(rho_ij) equals f(rho_ji) as normals are all along z
+ sumC = p.C0+p.C2*rdsq+p.C4*rdsq*rdsq;
+ sumC2 = (2*p.C2+4*p.C4*rdsq)*p.delta2inv;
+ frho = exp2*sumC;
+ sumCff = p.C + 2*frho;
+
+ // derivatives
+ fpair = -6.0*p.A*p.z06/r8+p.lambda*exp1/r*sumCff;
+ fpair1 = exp1*exp2*(4.0*p.delta2inv*sumC-2.0*sumC2);
+ fsum = fpair + fpair1;
+
+ f[i][0] += delx*fsum;
+ f[i][1] += dely*fsum;
+ // fi_z does not contain contributions from df/dr
+ // because rho_ij does not depend on z_i or z_j
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fsum;
+ f[j][1] -= dely*fsum;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = -p.A*p.z06/r6+ exp1*sumCff - offset[itype][jtype];
+ }
+
+ if (evflag){
+ ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,
+ fsum,fsum,fpair,delx,dely,delz);
+ }
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiZ::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+ memory->create(cut,n+1,n+1,"pair:cut");
+ memory->create(offset,n+1,n+1,"pair:offset");
+ map = new int[atom->ntypes+1];
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiZ::settings(int narg, char **arg)
+{
+ if (narg != 1) error->all(FLERR,"Illegal pair_style command");
+ if (strcmp(force->pair_style,"hybrid/overlay")!=0)
+ error->all(FLERR,"ERROR: requires hybrid/overlay pair_style");
+
+ cut_global = force->numeric(FLERR,arg[0]);
+
+ // reset cutoffs that have been explicitly set
+
+ if (allocated) {
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i+1; j <= atom->ntypes; j++)
+ if (setflag[i][j]) cut[i][j] = cut_global;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiZ::coeff(int narg, char **arg)
+{
+ int i,j,n;
+
+ if (narg != 3 + atom->ntypes)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+ // read args that map atom types to elements in potential file
+ // map[i] = which element the Ith atom type is, -1 if NULL
+ // nelements = # of unique elements
+ // elements = list of element names
+
+ if (elements) {
+ for (i = 0; i < nelements; i++) delete [] elements[i];
+ delete [] elements;
+ }
+ elements = new char*[atom->ntypes];
+ for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
+
+ nelements = 0;
+ for (i = 3; i < narg; i++) {
+ if (strcmp(arg[i],"NULL") == 0) {
+ map[i-2] = -1;
+ continue;
+ }
+ for (j = 0; j < nelements; j++)
+ if (strcmp(arg[i],elements[j]) == 0) break;
+ map[i-2] = j;
+ if (j == nelements) {
+ n = strlen(arg[i]) + 1;
+ elements[j] = new char[n];
+ strcpy(elements[j],arg[i]);
+ nelements++;
+ }
+ }
+
+
+ read_file(arg[2]);
+
+ double cut_one = cut_global;
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ cut[i][j] = cut_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairKolmogorovCrespiZ::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+ if (offset_flag) {
+ int iparam_ij = elem2param[map[i]][map[j]];
+ Param& p = params[iparam_ij];
+ offset[i][j] = -p.A*pow(p.z0/cut[i][j],6);
+ } else offset[i][j] = 0.0;
+ offset[j][i] = offset[i][j];
+
+ return cut[i][j];
+}
+
+/* ----------------------------------------------------------------------
+ read Kolmogorov-Crespi potential file
+------------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiZ::read_file(char *filename)
+{
+ int params_per_line = 11;
+ char **words = new char*[params_per_line+1];
+ memory->sfree(params);
+ params = NULL;
+ nparams = maxparam = 0;
+
+ // open file on proc 0
+
+ FILE *fp;
+ if (comm->me == 0) {
+ fp = force->open_potential(filename);
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open KC potential file %s",filename);
+ error->one(FLERR,str);
+ }
+ }
+
+ // read each line out of file, skipping blank lines or leading '#'
+ // store line of params if all 3 element tags are in element list
+
+ int i,j,n,m,nwords,ielement,jelement;
+ char line[MAXLINE],*ptr;
+ int eof = 0;
+
+ while (1) {
+ if (comm->me == 0) {
+ ptr = fgets(line,MAXLINE,fp);
+ if (ptr == NULL) {
+ eof = 1;
+ fclose(fp);
+ } else n = strlen(line) + 1;
+ }
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
+ if (eof) break;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+
+ // strip comment, skip line if blank
+
+ if ((ptr = strchr(line,'#'))) *ptr = '\0';
+ nwords = atom->count_words(line);
+ if (nwords == 0) continue;
+
+ // concatenate additional lines until have params_per_line words
+
+ while (nwords < params_per_line) {
+ n = strlen(line);
+ if (comm->me == 0) {
+ ptr = fgets(&line[n],MAXLINE-n,fp);
+ if (ptr == NULL) {
+ eof = 1;
+ fclose(fp);
+ } else n = strlen(line) + 1;
+ }
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
+ if (eof) break;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+ if ((ptr = strchr(line,'#'))) *ptr = '\0';
+ nwords = atom->count_words(line);
+ }
+
+ if (nwords != params_per_line)
+ error->all(FLERR,"Insufficient format in KC potential file");
+
+ // words = ptrs to all words in line
+
+ nwords = 0;
+ words[nwords++] = strtok(line," \t\n\r\f");
+ while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
+
+ // ielement,jelement = 1st args
+ // if these 2 args are in element list, then parse this line
+ // else skip to next line (continue)
+
+ for (ielement = 0; ielement < nelements; ielement++)
+ if (strcmp(words[0],elements[ielement]) == 0) break;
+ if (ielement == nelements) continue;
+ for (jelement = 0; jelement < nelements; jelement++)
+ if (strcmp(words[1],elements[jelement]) == 0) break;
+ if (jelement == nelements) continue;
+
+ // load up parameter settings and error check their values
+
+ if (nparams == maxparam) {
+ maxparam += DELTA;
+ params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
+ "pair:params");
+ }
+
+ params[nparams].ielement = ielement;
+ params[nparams].jelement = jelement;
+ params[nparams].z0 = atof(words[2]);
+ params[nparams].C0 = atof(words[3]);
+ params[nparams].C2 = atof(words[4]);
+ params[nparams].C4 = atof(words[5]);
+ params[nparams].C = atof(words[6]);
+ params[nparams].delta = atof(words[7]);
+ params[nparams].lambda = atof(words[8]);
+ params[nparams].A = atof(words[9]);
+ // S provides a convenient scaling of all energies
+ params[nparams].S = atof(words[10]);
+
+ // energies in meV further scaled by S
+ double meV = 1.0e-3*params[nparams].S;
+ params[nparams].C *= meV;
+ params[nparams].A *= meV;
+ params[nparams].C0 *= meV;
+ params[nparams].C2 *= meV;
+ params[nparams].C4 *= meV;
+
+ // precompute some quantities
+ params[nparams].delta2inv = pow(params[nparams].delta,-2);
+ params[nparams].z06 = pow(params[nparams].z0,6);
+
+ nparams++;
+ if(nparams >= pow(atom->ntypes,3)) break;
+ }
+ memory->destroy(elem2param);
+ memory->create(elem2param,nelements,nelements,"pair:elem2param");
+ for (i = 0; i < nelements; i++) {
+ for (j = 0; j < nelements; j++) {
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ if (i == params[m].ielement && j == params[m].jelement) {
+ if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+ n = m;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j] = n;
+ }
+ }
+ delete [] words;
+}
+
+/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.h b/src/USER-MISC/pair_kolmogorov_crespi_z.h
new file mode 100644
index 0000000000000000000000000000000000000000..3a81e571ef511d54f5c1d4b5ac855a1dab3d2f8d
--- /dev/null
+++ b/src/USER-MISC/pair_kolmogorov_crespi_z.h
@@ -0,0 +1,83 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(kolmogorov/crespi/z,PairKolmogorovCrespiZ)
+
+#else
+
+#ifndef LMP_PAIR_KolmogorovCrespiZ_H
+#define LMP_PAIR_KolmogorovCrespiZ_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairKolmogorovCrespiZ : public Pair {
+ public:
+ PairKolmogorovCrespiZ(class LAMMPS *);
+ virtual ~PairKolmogorovCrespiZ();
+
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ double init_one(int, int);
+
+ protected:
+ int me;
+
+ struct Param {
+ double z0,C0,C2,C4,C,delta,lambda,A,S;
+ double delta2inv,z06;
+ int ielement,jelement;
+ };
+ Param *params; // parameter set for I-J interactions
+ char **elements; // names of unique elements
+ int **elem2param; // mapping from element pairs to parameters
+ int *map; // mapping from atom types to elements
+ int nelements; // # of unique elements
+ int nparams; // # of stored parameter sets
+ int maxparam; // max # of parameter sets
+
+ double cut_global;
+ double **cut;
+ double **offset;
+ void read_file( char * );
+ void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+*/
+
diff --git a/src/USER-MISC/temper_grem.h b/src/USER-MISC/temper_grem.h
index 53b8a91446c2fcc28c35f93dd75ac3a472f23fe8..f379814c616b930e7b71172a087742531bb81527 100644
--- a/src/USER-MISC/temper_grem.h
+++ b/src/USER-MISC/temper_grem.h
@@ -101,7 +101,7 @@ temperature (nvt or npt).
E: Too many timesteps
-The cummulative timesteps must fit in a 64-bit integer.
+The cumulative timesteps must fit in a 64-bit integer.
E: Grem could not find thermo_pe compute
diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp
index b9ee2238a981d8a0c9b83a4b07f982dd9bc5d942..37f343736d6ae05f34695304e9d1219e45a6121c 100644
--- a/src/USER-MOLFILE/molfile_interface.cpp
+++ b/src/USER-MOLFILE/molfile_interface.cpp
@@ -464,7 +464,7 @@ int MolfileInterface::load_plugin(const char *filename)
return E_SYMBOL;
}
- // intialize plugin. skip plugin if it fails.
+ // initialize plugin. skip plugin if it fails.
if (((initfunc)(ifunc))()) {
my_dlclose(dso);
return E_SYMBOL;
diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.h b/src/USER-OMP/pair_buck_long_coul_long_omp.h
index 2dc017d8fbd98d53b0ef7e79bd9ed50fcf3b7680..f874dd9b6875e7ecf8cbdf54c23d59e3269943c3 100644
--- a/src/USER-OMP/pair_buck_long_coul_long_omp.h
+++ b/src/USER-OMP/pair_buck_long_coul_long_omp.h
@@ -70,15 +70,15 @@ Self-explanatory.
W: Using largest cutoff for buck/long/coul/long
-Self-exlanatory.
+Self-explanatory.
E: Cutoffs missing in pair_style buck/long/coul/long
-Self-exlanatory.
+Self-explanatory.
E: LJ6 off not supported in pair_style buck/long/coul/long
-Self-exlanatory.
+Self-explanatory.
E: Coulomb cut not supported in pair_style buck/long/coul/coul
diff --git a/src/USER-OMP/thr_data.cpp b/src/USER-OMP/thr_data.cpp
index 0e9eafb2f58886df226a80e5b3e23fd1c0d2c966..28fd27f9b8bc2700a13da7622ce66f9479e9b576 100644
--- a/src/USER-OMP/thr_data.cpp
+++ b/src/USER-OMP/thr_data.cpp
@@ -312,7 +312,7 @@ void LAMMPS_NS::data_reduce_thr(double *dall, int nall, int nthreads, int ndim,
int m = 0;
// for architectures that have L1 D-cache line sizes of 64 bytes
- // (8 doubles) wide, explictly unroll this loop to compute 8
+ // (8 doubles) wide, explicitly unroll this loop to compute 8
// contiguous values in the array at a time
// -- modify this code based on the size of the cache line
double t0, t1, t2, t3, t4, t5, t6, t7;
diff --git a/src/USER-QTB/fix_qbmsst.h b/src/USER-QTB/fix_qbmsst.h
index 0ed210c9951fc3e4d8376b6be5391022e09dbbfa..3484076abf995e7421a962b261061d9db2ff05d7 100644
--- a/src/USER-QTB/fix_qbmsst.h
+++ b/src/USER-QTB/fix_qbmsst.h
@@ -89,7 +89,7 @@ class FixQBMSST : public Fix {
int seed; // seed for the random number generator
double f_max; // frequency cutoff
int N_f; // number of frequency grid
- double eta; // coupling coefficient bewteen shock and the qtb
+ double eta; // coupling coefficient between shock and the qtb
int beta; // average beta steps before updating the qtb temperature
double t_init; // initial qtb temperature
int qtb_set; // 1 if its a restarting qbmsst, 0 if not
diff --git a/src/USER-REAXC/README b/src/USER-REAXC/README
index cdcfb17603c72546281c1fc34b89c3e1b3d3277b..86803957b80c3ffd08a5074a8d50b138e378d402 100644
--- a/src/USER-REAXC/README
+++ b/src/USER-REAXC/README
@@ -14,7 +14,7 @@ particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
-For technical details about this implemention of ReaxFF, see
+For technical details about this implementation of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp
index fff046ba7c96dda90581a829444ac2f507dff162..cb24e2dc3704f8fa28008e336224b6352b185ecc 100644
--- a/src/USER-REAXC/reaxc_nonbonded.cpp
+++ b/src/USER-REAXC/reaxc_nonbonded.cpp
@@ -139,7 +139,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
}
if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
- { // innner wall
+ { // inner wall
e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
data->my_en.e_vdW += Tap * e_core;
@@ -398,7 +398,7 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
}
if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
- { // innner wall
+ { // inner wall
e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
lr->e_vdW += Tap * e_core;
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index e4a7ea1c126ddf65532b7c65b0138525cc9a8fd8..eec9e517ead642ef79d89372f454f38728e7bed6 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -249,7 +249,7 @@ void PairTriSurf::compute(int eflag, int vflag) {
}
/*
- * if particle comes too close to triangle, reflect its velocity and explicitely move it away
+ * if particle comes too close to triangle, reflect its velocity and explicitly move it away
*/
touch_distance = 1.0 * radius[particle];
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
index 5ab12aed6b9dea9d47da63ae63f841596c2e8a42..5e24ced35cafb72a3db2fbfb41469d645d079c4a 100644
--- a/src/USER-SMTBQ/pair_smtbq.cpp
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -548,7 +548,7 @@ void PairSMTBQ::read_file(char *file)
// ---------------------------------
m += 1;
- // Ligne 5 - parametre des potentiels
+ // Ligne 5 - parametre des potentials
fgets(ptr,MAXLINE,fp); if (verbose) printf ("%s",ptr);
// Lecture des protagonistes
@@ -615,7 +615,7 @@ void PairSMTBQ::read_file(char *file)
if (verbose) printf (" %s %f %f %f %f\n",words[0],
intparams[m].a,intparams[m].p,intparams[m].ksi,intparams[m].q);
- // Ligne 6 - rayon de coupure potentiel SM
+ // Ligne 6 - rayon de coupure potential SM
fgets( ptr, MAXLINE, fp);
Tokenize( ptr, &words );
@@ -1724,7 +1724,7 @@ void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng)
{
/* ===================================================================
- Coulombian potentiel energy calcul between i and j atoms
+ Coulombian potential energy calcul between i and j atoms
with fafb table make in sm_table().
fafb[i][j] : i is the table's step (r)
j is the interaction's # (in intype[itype][jtype])
@@ -2655,7 +2655,7 @@ void PairSMTBQ::Charge()
forward(q) ; // reverse(q);
- // Calcul des potentiel
+ // Calcul des potential
// ----------------------
QForce_charge(iloop);
@@ -2736,7 +2736,7 @@ void PairSMTBQ::Charge()
//:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
// ==========================================
- // Ecriture des potentiels dans un fichier
+ // Ecriture des potentials dans un fichier
// ==========================================
if (strcmp(writepot,"true") == 0 && fmod(static_cast<double>(step), Neverypot) == 0.0) {
diff --git a/src/USER-VTK/dump_custom_vtk.h b/src/USER-VTK/dump_custom_vtk.h
index 189e96aa990a9a85d4b37b6ac1b72ba4cb5b0c33..f3b4a8b63e63cad24849ed30ae8cfc7ccb24473e 100644
--- a/src/USER-VTK/dump_custom_vtk.h
+++ b/src/USER-VTK/dump_custom_vtk.h
@@ -147,7 +147,7 @@ output to dump file.
E: Invalid attribute in dump custom command
-Self-explantory.
+Self-explanatory.
E: Dump_modify format string is too short
@@ -186,7 +186,7 @@ cannot be used in a dump between runs.
E: Threshhold for an atom property that isn't allocated
-A dump threshhold has been requested on a quantity that is
+A dump threshold has been requested on a quantity that is
not defined by the atom style used in this simulation.
E: Dumping an atom property that isn't allocated
@@ -255,7 +255,7 @@ Number of element names must equal number of atom types.
E: Invalid attribute in dump modify command
-Self-explantory.
+Self-explanatory.
E: Could not find dump modify compute ID
@@ -313,7 +313,7 @@ E: Could not find dump modify custom atom integer property ID
Self-explanatory.
-E: Invalid dump_modify threshhold operator
+E: Invalid dump_modify threshold operator
Operator keyword used for threshold specification in not recognized.
diff --git a/src/angle.cpp b/src/angle.cpp
index 14433fc44d78eaf09d4594663ac72b4e7329fde9..1366c48865b5daa516b58bba254aa0171eaf3da0 100644
--- a/src/angle.cpp
+++ b/src/angle.cpp
@@ -76,7 +76,7 @@ void Angle::init()
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
-void Angle::ev_setup(int eflag, int vflag)
+void Angle::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
@@ -94,25 +94,29 @@ void Angle::ev_setup(int eflag, int vflag)
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
- memory->destroy(eatom);
- memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom");
+ if (alloc) {
+ memory->destroy(eatom);
+ memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom");
+ }
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
- memory->destroy(vatom);
- memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom");
+ if (alloc) {
+ memory->destroy(vatom);
+ memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom");
+ }
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (eflag_atom) {
+ if (eflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
- if (vflag_atom) {
+ if (vflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) {
diff --git a/src/angle.h b/src/angle.h
index 119f206c36ee9ef2d3817841f995230068a8df6b..000c3fe916d84c1766eeb4dd09dbd082fba61387 100644
--- a/src/angle.h
+++ b/src/angle.h
@@ -27,7 +27,7 @@ class Angle : protected Pointers {
int *setflag;
int writedata; // 1 if writes coeffs to data file
double energy; // accumulated energies
- double virial[6]; // accumlated virial
+ double virial[6]; // accumulated virial
double *eatom,**vatom; // accumulated per-atom energy/virial
// KOKKOS host/device flag and data masks
@@ -58,7 +58,7 @@ class Angle : protected Pointers {
int vflag_either,vflag_global,vflag_atom;
int maxeatom,maxvatom;
- void ev_setup(int, int);
+ void ev_setup(int, int, int alloc = 1);
void ev_tally(int, int, int, int, int, double, double *, double *,
double, double, double, double, double, double);
};
diff --git a/src/atom.cpp b/src/atom.cpp
index 6b3427c04ee5ed3aeb2d1ed22c2eac3cdf981c7b..4df2bc2194abccdd3198ec525c42e5b0b9424c28 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1634,7 +1634,7 @@ int Atom::find_molecule(char *id)
/* ----------------------------------------------------------------------
add info to current atom ilocal from molecule template onemol and its iatom
- offset = atom ID preceeding IDs of atoms in this molecule
+ offset = atom ID preceding IDs of atoms in this molecule
called by fixes and commands that add molecules
------------------------------------------------------------------------- */
diff --git a/src/atom.h b/src/atom.h
index 9abbb495698e43025ae9e15242e1f24c679b4c0d..0f84c8242fb86ece27b4abe2f6722ab667e1315d 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -97,7 +97,7 @@ class Atom : protected Pointers {
// molecular info
- int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
+ int **nspecial; // 0,1,2 = cumulative # of 1-2,1-3,1-4 neighs
tagint **special; // IDs of 1-2,1-3,1-4 neighs of each atom
int maxspecial; // special[nlocal][maxspecial]
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index 54bd78a83c6a063d700b2f3151c8ab26470486f6..40c744afc5461bb83822053291f01e0701f341e3 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -82,7 +82,7 @@ void AtomVecHybrid::process_args(int narg, char **arg)
delete [] allstyles;
// hybrid settings are MAX or MIN of sub-style settings
- // hybrid sizes are minimial values plus extra values for each sub-style
+ // hybrid sizes are minimal values plus extra values for each sub-style
molecular = 0;
comm_x_only = comm_f_only = 1;
diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h
index b5dc2cfde003d0f9202127bc0aeb44abae287a9d..390efc7c10f27b136f8a2420fe9d6ac6e009fee2 100644
--- a/src/atom_vec_tri.h
+++ b/src/atom_vec_tri.h
@@ -140,7 +140,7 @@ the atom coordinate.
E: Insufficient Jacobi rotations for triangle
-The calculation of the intertia tensor of the triangle failed. This
+The calculation of the inertia tensor of the triangle failed. This
should not happen if it is a reasonably shaped triangle.
*/
diff --git a/src/balance.cpp b/src/balance.cpp
index 7780b5207c82dfc84e3aa50b94348314d9cd9beb..52f6072a6c014a229ab05973927bf4e6b106052d 100644
--- a/src/balance.cpp
+++ b/src/balance.cpp
@@ -276,7 +276,7 @@ void Balance::command(int narg, char **arg)
set_weights();
double imbinit = imbalance_factor(maxinit);
- // no load-balance if imbalance doesn't exceed threshhold
+ // no load-balance if imbalance doesn't exceed threshold
// unless switching from tiled to non tiled layout, then force rebalance
if (comm->layout == LAYOUT_TILED && style != BISECTION) {
@@ -456,6 +456,7 @@ void Balance::options(int iarg, int narg, char **arg)
wtflag = 0;
varflag = 0;
+ oldrcb = 0;
outflag = 0;
int outarg = 0;
fp = NULL;
@@ -491,6 +492,9 @@ void Balance::options(int iarg, int narg, char **arg)
}
iarg += 2+nopt;
+ } else if (strcmp(arg[iarg],"old") == 0) {
+ oldrcb = 1;
+ iarg++;
} else if (strcmp(arg[iarg],"out") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal (fix) balance command");
outflag = 1;
@@ -640,13 +644,22 @@ int *Balance::bisection(int sortflag)
double *shrinkhi = &shrinkall[3];
// invoke RCB
- // then invert() to create list of proc assignements for my atoms
-
- if (wtflag) {
- weight = fixstore->vstore;
- rcb->compute(dim,atom->nlocal,atom->x,weight,shrinklo,shrinkhi);
- } else rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
+ // then invert() to create list of proc assignments for my atoms
+ // NOTE: (3/2017) can remove undocumented "old" option at some point
+ // ditto in rcb.cpp
+ if (oldrcb) {
+ if (wtflag) {
+ weight = fixstore->vstore;
+ rcb->compute_old(dim,atom->nlocal,atom->x,weight,shrinklo,shrinkhi);
+ } else rcb->compute_old(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
+ } else {
+ if (wtflag) {
+ weight = fixstore->vstore;
+ rcb->compute(dim,atom->nlocal,atom->x,weight,shrinklo,shrinkhi);
+ } else rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
+ }
+
rcb->invert(sortflag);
// reset RCB lo/hi bounding box to full simulation box as needed
@@ -776,7 +789,7 @@ int Balance::shift()
bigint natoms = atom->natoms;
if (natoms == 0) return 0;
- // set delta for 1d balancing = root of threshhold
+ // set delta for 1d balancing = root of threshold
// root = # of dimensions being balanced on
double delta = pow(stopthresh,1.0/ndim) - 1.0;
@@ -865,7 +878,7 @@ int Balance::shift()
// stop if all split sums are within delta of targets
// this is a 1d test of particle count per slice
// assumption is that this is sufficient accuracy
- // for 3d imbalance factor to reach threshhold
+ // for 3d imbalance factor to reach threshold
doneflag = 1;
for (i = 1; i < np; i++)
@@ -918,7 +931,7 @@ int Balance::shift()
}
*/
- // stop at this point in bstr if imbalance factor < threshhold
+ // stop at this point in bstr if imbalance factor < threshold
// this is a true 3d test of particle count per processor
double imbfactor = imbalance_splits(max);
@@ -937,7 +950,7 @@ int Balance::shift()
N = # of slices
split = N+1 cuts between N slices
return updated count = particles per slice
- return updated sum = cummulative count below each of N+1 splits
+ return updated sum = cumulative count below each of N+1 splits
use binary search to find which slice each atom is in
------------------------------------------------------------------------- */
@@ -972,8 +985,8 @@ void Balance::tally(int dim, int n, double *split)
/* ----------------------------------------------------------------------
adjust cuts between N slices in a dim via recursive multisectioning method
split = current N+1 cuts, with 0.0 and 1.0 at end points
- sum = cummulative count up to each split
- target = desired cummulative count up to each split
+ sum = cumulative count up to each split
+ target = desired cumulative count up to each split
lo/hi = split values that bound current split
update lo/hi to reflect sums at current split values
overwrite split with new cuts
diff --git a/src/balance.h b/src/balance.h
index 7ca03540236facfda48717a5e662950eb582fbc8..0f2f79bb151cc755755988af2490239ae5ea8aad 100644
--- a/src/balance.h
+++ b/src/balance.h
@@ -49,10 +49,11 @@ class Balance : protected Pointers {
private:
int me,nprocs;
- double thresh; // threshhold to perform LB
+ double thresh; // threshold to perform LB
int style; // style of LB
int xflag,yflag,zflag; // xyz LB flags
double *user_xsplit,*user_ysplit,*user_zsplit; // params for xyz LB
+ int oldrcb; // use old-style RCB compute
int nitermax; // params for shift LB
double stopthresh;
@@ -63,10 +64,10 @@ class Balance : protected Pointers {
int *bdim; // XYZ for each character in bstr
double *onecost; // work vector of counts in one dim
double *allcost; // counts for slices in one dim
- double *sum; // cummulative count for slices in one dim
+ double *sum; // cumulative count for slices in one dim
double *target; // target sum for slices in one dim
double *lo,*hi; // lo/hi split coords that bound each target
- double *losum,*hisum; // cummulative counts at lo/hi coords
+ double *losum,*hisum; // cumulative counts at lo/hi coords
int rho; // 0 for geometric recursion
// 1 for density weighted recursion
diff --git a/src/bond.cpp b/src/bond.cpp
index 8074d9767766c9524008ed4bd9c1794760daf720..5a33f107cf44ade599dff8b5a9a9b81f00d04386 100644
--- a/src/bond.cpp
+++ b/src/bond.cpp
@@ -79,7 +79,7 @@ void Bond::init()
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
-void Bond::ev_setup(int eflag, int vflag)
+void Bond::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
@@ -97,25 +97,29 @@ void Bond::ev_setup(int eflag, int vflag)
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
- memory->destroy(eatom);
- memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom");
+ if (alloc) {
+ memory->destroy(eatom);
+ memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom");
+ }
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
- memory->destroy(vatom);
- memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom");
+ if (alloc) {
+ memory->destroy(vatom);
+ memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom");
+ }
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (eflag_atom) {
+ if (eflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
- if (vflag_atom) {
+ if (vflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) {
diff --git a/src/bond.h b/src/bond.h
index 06e05a7265d169b7a5b68320c0c8085def614f2e..41604387a3f8e056a92e7b08a25007a062ca3021 100644
--- a/src/bond.h
+++ b/src/bond.h
@@ -27,7 +27,7 @@ class Bond : protected Pointers {
int *setflag;
int writedata; // 1 if writes coeffs to data file
double energy; // accumulated energies
- double virial[6]; // accumlated virial
+ double virial[6]; // accumulated virial
double *eatom,**vatom; // accumulated per-atom energy/virial
// KOKKOS host/device flag and data masks
@@ -60,7 +60,7 @@ class Bond : protected Pointers {
int vflag_either,vflag_global,vflag_atom;
int maxeatom,maxvatom;
- void ev_setup(int, int);
+ void ev_setup(int, int, int alloc = 1);
void ev_tally(int, int, int, int, double, double, double, double, double);
};
diff --git a/src/citeme.h b/src/citeme.h
index 80b642ab6d7a889b73443688950f280b1a2ae16d..18e9a712db81a1ce5fed2f5f2ca4d26867a15688 100644
--- a/src/citeme.h
+++ b/src/citeme.h
@@ -42,7 +42,7 @@ E: Cannot open log.cite file
This file is created when you use some LAMMPS features, to indicate
what paper you should cite on behalf of those who implemented
-the feature. Check that you have write priveleges into the directory
+the feature. Check that you have write privileges into the directory
you are running in.
*/
diff --git a/src/compute_angle.h b/src/compute_angle.h
index d50e3e21d783b72022e0e9ab2d7e8b0187cca1e4..c39a2c3d2772a4739968aef80e141480fba235f8 100644
--- a/src/compute_angle.h
+++ b/src/compute_angle.h
@@ -52,7 +52,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute bond must use group all
-Bond styles accumlate energy on all atoms.
+Bond styles accumulate energy on all atoms.
E: Unrecognized bond style in compute bond command
diff --git a/src/compute_bond.h b/src/compute_bond.h
index 0f3c8112188888c7b5ed623bcf5766d9cbc3f59d..0f6c088f1dca5a8e9c092f8296276771302a62e4 100644
--- a/src/compute_bond.h
+++ b/src/compute_bond.h
@@ -52,7 +52,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute bond must use group all
-Bond styles accumlate energy on all atoms.
+Bond styles accumulate energy on all atoms.
E: Unrecognized bond style in compute bond command
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index 925c5fbf81ff1c6340670bf00b8abf34044a9091..ac35629d08109324c9a117f4c7b997a5cbae7f94 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -616,6 +616,7 @@ void ComputeChunkAtom::setup()
{
if (nchunkflag == ONCE) setup_chunks();
if (idsflag == ONCE) compute_ichunk();
+ else invoked_ichunk = -1;
}
/* ----------------------------------------------------------------------
@@ -1298,7 +1299,7 @@ int ComputeChunkAtom::setup_sphere_bins()
}
// if pbcflag set, sradmax must be < 1/2 box in any periodic dim
- // treat orthongonal and triclinic the same
+ // treat orthogonal and triclinic the same
// check every time bins are created
if (pbcflag) {
@@ -1363,7 +1364,7 @@ int ComputeChunkAtom::setup_cylinder_bins()
}
// if pbcflag set, sradmax must be < 1/2 box in any periodic non-axis dim
- // treat orthongonal and triclinic the same
+ // treat orthogonal and triclinic the same
// check every time bins are created
if (pbcflag) {
diff --git a/src/compute_chunk_atom.h b/src/compute_chunk_atom.h
index cbec221048a1a7df7d26b5e84ab495ff2c04bf7e..9c64e9bc7a37587c5f3647f6bdb388a1ebd18f82 100644
--- a/src/compute_chunk_atom.h
+++ b/src/compute_chunk_atom.h
@@ -248,11 +248,11 @@ The lo/hi values are inconsistent.
E: Compute chunk/atom bin/sphere radius is too large for periodic box
-Radius cannot be bigger than 1/2 of any periodic dimention.
+Radius cannot be bigger than 1/2 of any periodic dimension.
E: Compute chunk/atom bin/cylinder radius is too large for periodic box
-Radius cannot be bigger than 1/2 of a non-axis periodic dimention.
+Radius cannot be bigger than 1/2 of a non-axis periodic dimension.
E: Cannot use compute chunk/atom bin z for 2d model
diff --git a/src/compute_cna_atom.h b/src/compute_cna_atom.h
index 77ea5951dce924c80538a570716d1630f8354ede..82cf8df608d058a734367aaa6c345eefc37fef3e 100644
--- a/src/compute_cna_atom.h
+++ b/src/compute_cna_atom.h
@@ -57,11 +57,11 @@ command-line option when running LAMMPS to see the offending line.
E: Compute cna/atom requires a pair style be defined
-Self-explantory.
+Self-explanatory.
E: Compute cna/atom cutoff is longer than pairwise cutoff
-Self-explantory.
+Self-explanatory.
W: Compute cna/atom cutoff may be too large to find ghost atom neighbors
diff --git a/src/compute_contact_atom.h b/src/compute_contact_atom.h
index bf2f1314d9b4bf061a06833d515b03184b602da8..2ce7678f5611dec88dd676998c0a9676558283e6 100644
--- a/src/compute_contact_atom.h
+++ b/src/compute_contact_atom.h
@@ -60,7 +60,7 @@ Self-explanatory.
E: Compute contact/atom requires a pair style be defined
-Self-explantory.
+Self-explanatory.
W: More than one compute contact/atom
diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h
index 2ad46fa854b233e461cd0bc0d53fc7b017a8006e..6c60c8626605375f5af30a8f6f5e886d685b6160 100644
--- a/src/compute_coord_atom.h
+++ b/src/compute_coord_atom.h
@@ -67,7 +67,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute coord/atom requires a pair style be defined
-Self-explantory.
+Self-explanatory.
E: Compute coord/atom cutoff is longer than pairwise cutoff
diff --git a/src/compute_dihedral.h b/src/compute_dihedral.h
index 80b78aba9850204918d9d867eecb928c5aa728db..041e1f6eaed13720ceaa1a4a08f708a6bc46354a 100644
--- a/src/compute_dihedral.h
+++ b/src/compute_dihedral.h
@@ -52,7 +52,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute bond must use group all
-Bond styles accumlate energy on all atoms.
+Bond styles accumulate energy on all atoms.
E: Unrecognized bond style in compute bond command
diff --git a/src/compute_group_group.h b/src/compute_group_group.h
index 906a185cf2c0f63d0025712a319f51bfd7ccca72..c7443bda5cb375c57ecdbf88c8c02b882dc86364 100644
--- a/src/compute_group_group.h
+++ b/src/compute_group_group.h
@@ -72,7 +72,7 @@ Cannot calculate group interactions without a pair style defined.
E: Pair style does not support compute group/group
The pair_style does not have a single() function, so it cannot be
-invokded by the compute group/group command.
+invoked by the compute group/group command.
E: No Kspace style defined for compute group/group
@@ -84,6 +84,6 @@ Self-explanatory.
W: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero
-Self-explantory.
+Self-explanatory.
*/
diff --git a/src/compute_hexorder_atom.h b/src/compute_hexorder_atom.h
index 84c80abc5749273c686958218358099c1ebdf587..39af576cb7bc9555750d87719f4764b4eb0e9c2c 100644
--- a/src/compute_hexorder_atom.h
+++ b/src/compute_hexorder_atom.h
@@ -62,7 +62,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute hexorder/atom requires a pair style be defined
-Self-explantory.
+Self-explanatory.
E: Compute hexorder/atom cutoff is longer than pairwise cutoff
diff --git a/src/compute_improper.h b/src/compute_improper.h
index 6f92f068e309793e264ecb21bf432db1978bfdbe..d3602677a6b8524b8ba86f176122eb2a1a750a62 100644
--- a/src/compute_improper.h
+++ b/src/compute_improper.h
@@ -52,7 +52,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute bond must use group all
-Bond styles accumlate energy on all atoms.
+Bond styles accumulate energy on all atoms.
E: Unrecognized bond style in compute bond command
diff --git a/src/compute_orientorder_atom.h b/src/compute_orientorder_atom.h
index 81b08dbddc17740538545d8ea7b6add7cd90ed7a..eb814e9c1c639bd021523bcd641e52b42b7cfc43 100644
--- a/src/compute_orientorder_atom.h
+++ b/src/compute_orientorder_atom.h
@@ -72,7 +72,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute orientorder/atom requires a pair style be defined
-Self-explantory.
+Self-explanatory.
E: Compute orientorder/atom cutoff is longer than pairwise cutoff
diff --git a/src/compute_pair.h b/src/compute_pair.h
index 37f026f1eeae9d476731210f25d72f7b6184e752..91702748a6530379f79a65241084178c4b3a146e 100644
--- a/src/compute_pair.h
+++ b/src/compute_pair.h
@@ -54,7 +54,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute pair must use group all
-Pair styles accumlate energy on all atoms.
+Pair styles accumulate energy on all atoms.
E: Unrecognized pair style in compute pair command
diff --git a/src/compute_property_chunk.h b/src/compute_property_chunk.h
index 077129a06ead44ced9d8ef2026e8bce2c84702a5..48211ec91bec831c0a5e38829f43db49c44f3266 100644
--- a/src/compute_property_chunk.h
+++ b/src/compute_property_chunk.h
@@ -81,15 +81,15 @@ It will only store IDs if its compress option is enabled.
E: Compute chunk/atom stores no coord1 for compute property/chunk
-Only certain binning options for comptue chunk/atom store coordinates.
+Only certain binning options for compute chunk/atom store coordinates.
E: Compute chunk/atom stores no coord2 for compute property/chunk
-Only certain binning options for comptue chunk/atom store coordinates.
+Only certain binning options for compute chunk/atom store coordinates.
E: Compute chunk/atom stores no coord3 for compute property/chunk
-Only certain binning options for comptue chunk/atom store coordinates.
+Only certain binning options for compute chunk/atom store coordinates.
E: Invalid keyword in compute property/chunk command
diff --git a/src/compute_property_local.h b/src/compute_property_local.h
index fbc1ea3097b3669864351d9a4e2c5155f75669d3..2b0dda5a10e5388c03e37cdfc02c67a4115fe126 100644
--- a/src/compute_property_local.h
+++ b/src/compute_property_local.h
@@ -99,7 +99,7 @@ command-line option when running LAMMPS to see the offending line.
E: Compute property/local cannot use these inputs together
Only inputs that generate the same number of datums can be used
-togther. E.g. bond and angle quantities cannot be mixed.
+together. E.g. bond and angle quantities cannot be mixed.
E: Invalid keyword in compute property/local command
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 776a94c8b933d58960cecf5ac6ba1178f780ba75..04a2df91f8b252586705d8418cc774afb4cc448c 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -806,7 +806,7 @@ void CreateAtoms::add_molecule(double *center, double *quat_user)
onemol->quat_external = quat;
// create atoms in molecule with atom ID = 0 and mol ID = 0
- // reset in caller after all moleclues created by all procs
+ // reset in caller after all molecules created by all procs
// pass add_molecule_atom an offset of 0 since don't know
// max tag of atoms in previous molecules at this point
diff --git a/src/create_atoms.h b/src/create_atoms.h
index 721b31e8c547c20627736b415a089f09b32092e1..56e9c65b89ad5f5a929c1a97615e80ea78fcc625 100644
--- a/src/create_atoms.h
+++ b/src/create_atoms.h
@@ -88,7 +88,7 @@ is the number of atom types.
E: Molecule template ID for create_atoms does not exist
-Self-explantory.
+Self-explanatory.
W: Molecule template for create_atoms has multiple molecules
diff --git a/src/dihedral.cpp b/src/dihedral.cpp
index 4c941d7225c47e0094d950933caf30be80172496..f5c1c6c44c143604cec5ec3aa9b1bbd8ea03688d 100644
--- a/src/dihedral.cpp
+++ b/src/dihedral.cpp
@@ -76,7 +76,7 @@ void Dihedral::init()
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
-void Dihedral::ev_setup(int eflag, int vflag)
+void Dihedral::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
@@ -94,25 +94,29 @@ void Dihedral::ev_setup(int eflag, int vflag)
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
- memory->destroy(eatom);
- memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom");
+ if (alloc) {
+ memory->destroy(eatom);
+ memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom");
+ }
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
- memory->destroy(vatom);
- memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom");
+ if (alloc) {
+ memory->destroy(vatom);
+ memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom");
+ }
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (eflag_atom) {
+ if (eflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
- if (vflag_atom) {
+ if (vflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) {
diff --git a/src/dihedral.h b/src/dihedral.h
index 68167eb86f413deb8214d96473af4e6014bf8eb7..d27810c4d6e79ede7d5875daced83861f2461346 100644
--- a/src/dihedral.h
+++ b/src/dihedral.h
@@ -27,7 +27,7 @@ class Dihedral : protected Pointers {
int *setflag;
int writedata; // 1 if writes coeffs to data file
double energy; // accumulated energy
- double virial[6]; // accumlated virial
+ double virial[6]; // accumulated virial
double *eatom,**vatom; // accumulated per-atom energy/virial
// KOKKOS host/device flag and data masks
@@ -56,7 +56,7 @@ class Dihedral : protected Pointers {
int vflag_either,vflag_global,vflag_atom;
int maxeatom,maxvatom;
- void ev_setup(int, int);
+ void ev_setup(int, int, int alloc = 1);
void ev_tally(int, int, int, int, int, int, double,
double *, double *, double *, double, double, double,
double, double, double, double, double, double);
diff --git a/src/domain.cpp b/src/domain.cpp
index 1dede69729cad6d13bdcb959eab7cd27f7c84802..31fb3b855955e15126bb2e881ac6cfa68872e1ca 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -514,7 +514,7 @@ void Domain::pbc()
double *coord;
int n3 = 3*nlocal;
- coord = &x[0][0]; // note: x is always initialzed to at least one element.
+ coord = &x[0][0]; // note: x is always initialized to at least one element.
int flag = 0;
for (i = 0; i < n3; i++)
if (!ISFINITE(*coord++)) flag = 1;
diff --git a/src/dump_custom.h b/src/dump_custom.h
index 38567b7523c181fd07de02f2d6c0f7993339df4a..80674158342e3d68850392f5f05693f7e2e8364c 100644
--- a/src/dump_custom.h
+++ b/src/dump_custom.h
@@ -206,7 +206,7 @@ output to dump file.
E: Invalid attribute in dump custom command
-Self-explantory.
+Self-explanatory.
E: Dump_modify format string is too short
@@ -314,7 +314,7 @@ Number of element names must equal number of atom types.
E: Invalid attribute in dump modify command
-Self-explantory.
+Self-explanatory.
E: Could not find dump modify compute ID
diff --git a/src/dump_local.h b/src/dump_local.h
index 6f8dc09f578a3321bd647956db6918177f537394..ffca02b381075fecf1d0667f35193e941de02e4c 100644
--- a/src/dump_local.h
+++ b/src/dump_local.h
@@ -125,7 +125,7 @@ Every column of output must be the same length.
E: Invalid attribute in dump local command
-Self-explantory.
+Self-explanatory.
E: Dump local compute does not compute local info
diff --git a/src/fix.h b/src/fix.h
index bd3189afe7624a47eaff7f949103d28257aa8ca9..8005da1addca8956991c283111901016f551d544 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -89,7 +89,7 @@ class Fix : protected Pointers {
int comm_reverse; // size of reverse communication (0 if none)
int comm_border; // size of border communication (0 if none)
- double virial[6]; // accumlated virial
+ double virial[6]; // accumulated virial
double *eatom,**vatom; // accumulated per-atom energy/virial
int restart_reset; // 1 if restart just re-initialized fix
diff --git a/src/fix_addforce.h b/src/fix_addforce.h
index d19c0db0d1d170206a0e6873f4e8807a69d00a3e..f06ed5ed4c310802483d56955a7ed557cd1df722 100644
--- a/src/fix_addforce.h
+++ b/src/fix_addforce.h
@@ -85,7 +85,7 @@ in energy directly.
E: Must use variable energy with fix addforce
-Must define an energy vartiable when applyting a dynamic
+Must define an energy variable when applying a dynamic
force during minimization.
*/
diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h
index 18622699de84d969382a89378fae0ae9b77bfeef..eb51043e0f6a7221c965be741dfd05eb301756d9 100644
--- a/src/fix_ave_chunk.h
+++ b/src/fix_ave_chunk.h
@@ -162,7 +162,7 @@ Self-explanatory.
E: Fix ave/chunk does not use chunk/atom compute
-The specified conpute is not for a compute chunk/atom command.
+The specified compute is not for a compute chunk/atom command.
E: Error writing file header
diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp
index 277a57a48da99ddae6eb5fb4f6701670668cb93b..37dd8c9898c74f16f5bea3d52aff364a12ab8d15 100644
--- a/src/fix_ave_histo_weight.cpp
+++ b/src/fix_ave_histo_weight.cpp
@@ -126,7 +126,7 @@ void FixAveHistoWeight::end_of_step()
modify->clearstep_compute();
- // calcualte weight factors which are 2nd value (i = 1)
+ // calculate weight factors which are 2nd value (i = 1)
double weight = 0.0;
double *weights = NULL;
diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
index d771036530da9b2f33e34b3905d2187080f6a7c9..0357815f0ce76a9e8fe76da6e65bed6b6673867e 100644
--- a/src/fix_ave_time.h
+++ b/src/fix_ave_time.h
@@ -101,15 +101,15 @@ Self-explanatory.
E: Invalid fix ave/time off column
-Self-explantory.
+Self-explanatory.
E: Fix ave/time compute does not calculate a scalar
-Self-explantory.
+Self-explanatory.
E: Fix ave/time compute does not calculate a vector
-Self-explantory.
+Self-explanatory.
E: Fix ave/time compute vector is accessed out-of-range
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index 33054e0e3bbcb5a19825c02cc22ba9df82b397ce..7e0aa681bbfb942f1c81304be9f497aabc2d6702 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -189,7 +189,7 @@ void FixBalance::setup_pre_exchange()
domain->reset_box();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
- // perform a rebalance if threshhold exceeded
+ // perform a rebalance if threshold exceeded
balance->set_weights();
imbnow = balance->imbalance_factor(maxloadperproc);
@@ -224,7 +224,7 @@ void FixBalance::pre_exchange()
domain->reset_box();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
- // perform a rebalance if threshhold exceeded
+ // perform a rebalance if threshold exceeded
// if weight variable is used, wrap weight setting in clear/add compute
if (balance->varflag) modify->clearstep_compute();
diff --git a/src/fix_deform.h b/src/fix_deform.h
index efbecfd6368f340d340d7a6954ad90f244a345b8..cdda1b8547c0eb735b5e17e00957f14d915bb74f 100644
--- a/src/fix_deform.h
+++ b/src/fix_deform.h
@@ -107,7 +107,7 @@ Only one fix deform can be defined at a time.
E: Variable name for fix deform does not exist
-Self-explantory.
+Self-explanatory.
E: Variable for fix deform is invalid style
diff --git a/src/fix_group.h b/src/fix_group.h
index 5815d314591968ac6870bd90705155ddcd317e89..6ed842578d5ea1834c84c74e3804c2b43f0416b6 100644
--- a/src/fix_group.h
+++ b/src/fix_group.h
@@ -77,10 +77,10 @@ The variable must be an atom-style variable.
W: One or more dynamic groups may not be updated at correct point in timestep
-If there are other fixes that act immediately after the intitial stage
+If there are other fixes that act immediately after the initial stage
of time integration within a timestep (i.e. after atoms move), then
the command that sets up the dynamic group should appear after those
-fixes. This will insure that dynamic group assignements are made
+fixes. This will insure that dynamic group assignments are made
after all atoms have moved.
*/
diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp
index ca74efa4546341de44c72a0b132ce70e740d7a24..2a4af4dc66d42d9ac76a22163f6a1e66543834a8 100644
--- a/src/fix_halt.cpp
+++ b/src/fix_halt.cpp
@@ -30,9 +30,10 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-enum{BONDMAX,VARIABLE};
+enum{BONDMAX,TLIMIT,VARIABLE};
enum{LT,LE,GT,GE,EQ,NEQ,XOR};
enum{HARD,SOFT,CONTINUE};
+enum{NOMSG,YESMSG};
/* ---------------------------------------------------------------------- */
@@ -47,7 +48,8 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) :
idvar = NULL;
- if (strcmp(arg[4],"bondmax") == 0) attribute = BONDMAX;
+ if (strcmp(arg[4],"tlimit") == 0) attribute = TLIMIT;
+ else if (strcmp(arg[4],"bondmax") == 0) attribute = BONDMAX;
else if (strncmp(arg[4],"v_",2) == 0) {
attribute = VARIABLE;
int n = strlen(arg[4]);
@@ -73,6 +75,7 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) :
// parse optional args
eflag = SOFT;
+ msgflag = YESMSG;
int iarg = 7;
while (iarg < narg) {
@@ -83,6 +86,12 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"continue") == 0) eflag = CONTINUE;
else error->all(FLERR,"Illegal fix halt command");
iarg += 2;
+ } else if (strcmp(arg[iarg],"message") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix halt command");
+ if (strcmp(arg[iarg+1],"no") == 0) msgflag = NOMSG;
+ else if (strcmp(arg[iarg+1],"yes") == 0) msgflag = YESMSG;
+ else error->all(FLERR,"Illegal fix halt command");
+ iarg += 2;
} else error->all(FLERR,"Illegal fix halt command");
}
@@ -125,6 +134,11 @@ void FixHalt::init()
if (input->variable->equalstyle(ivar) == 0)
error->all(FLERR,"Fix halt variable is not equal-style variable");
}
+
+ // settings used by TLIMIT
+
+ nextstep = (update->ntimestep/nevery)*nevery + nevery;
+ tratio = 0.5;
}
/* ---------------------------------------------------------------------- */
@@ -135,8 +149,12 @@ void FixHalt::end_of_step()
double attvalue;
- if (attribute == BONDMAX) attvalue = bondmax();
- else {
+ if (attribute == TLIMIT) {
+ if (update->ntimestep != nextstep) return;
+ attvalue = tlimit();
+ } else if (attribute == BONDMAX) {
+ attvalue = bondmax();
+ } else {
modify->clearstep_compute();
attvalue = input->variable->compute_equal(ivar);
modify->addstep_compute(update->ntimestep + nevery);
@@ -169,9 +187,10 @@ void FixHalt::end_of_step()
sprintf(str,"Fix halt %s condition met on step %ld with value %g",
id,update->ntimestep,attvalue);
- if (eflag == HARD) error->all(FLERR,str);
- else if (eflag == SOFT || eflag == CONTINUE) {
- if (comm->me == 0) error->message(FLERR,str);
+ if (eflag == HARD) {
+ error->all(FLERR,str);
+ } else if (eflag == SOFT || eflag == CONTINUE) {
+ if (comm->me == 0 && msgflag == YESMSG) error->message(FLERR,str);
timer->force_timeout();
}
}
@@ -218,3 +237,27 @@ double FixHalt::bondmax()
return sqrt(maxall);
}
+
+/* ----------------------------------------------------------------------
+ compute synced elapsed time
+ reset nextstep = estimate of timestep when run will end
+ first project to 1/2 the run time, thereafter to end of run
+------------------------------------------------------------------------- */
+
+double FixHalt::tlimit()
+{
+ double cpu = timer->elapsed(Timer::TOTAL);
+ MPI_Bcast(&cpu,1,MPI_DOUBLE,0,world);
+
+ if (cpu < value) {
+ bigint elapsed = update->ntimestep - update->firststep;
+ bigint final = update->firststep +
+ static_cast<bigint> (tratio*value/cpu * elapsed);
+ nextstep = (final/nevery)*nevery + nevery;
+ tratio = 1.0;
+ }
+
+ //printf("EVAL %ld %g %d\n",update->ntimestep,cpu,nevery);
+
+ return cpu;
+}
diff --git a/src/fix_halt.h b/src/fix_halt.h
index 156397a4b5a76cb979e3b524bbf544edbcf446db..52d2f95d2f5c24333b5b6e54bd7f0e44f89f989a 100644
--- a/src/fix_halt.h
+++ b/src/fix_halt.h
@@ -35,11 +35,13 @@ class FixHalt : public Fix {
void post_run();
private:
- int attribute,operation,eflag,ivar;
- double value;
+ int attribute,operation,eflag,msgflag,ivar;
+ bigint nextstep;
+ double value,tratio;
char *idvar;
double bondmax();
+ double tlimit();
};
}
diff --git a/src/fix_langevin.h b/src/fix_langevin.h
index 863c0f554c4d2272068491e98b26fef4d7986b9d..34eec639871072c719919278464598b97f2bbb7f 100644
--- a/src/fix_langevin.h
+++ b/src/fix_langevin.h
@@ -132,7 +132,7 @@ One of the particles has radius 0.0.
E: Fix langevin angmom requires extended particles
-This fix option cannot be used with point paritlces.
+This fix option cannot be used with point particles.
E: Cannot zero Langevin force of 0 atoms
diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp
index e885392c413cb13e464f23aa1445d73c0c282f12..21942d753fc4fb35c383ca1b7e0104152ebb5f57 100644
--- a/src/fix_shear_history.cpp
+++ b/src/fix_shear_history.cpp
@@ -38,7 +38,7 @@ FixShearHistory::FixShearHistory(LAMMPS *lmp, int narg, char **arg) :
npartner(NULL), partner(NULL), shearpartner(NULL), pair(NULL),
ipage(NULL), dpage(NULL)
{
- if (narg != 4) error->all(FLERR,"Illegal fix SHEAR_HISTORY commmand");
+ if (narg != 4) error->all(FLERR,"Illegal fix SHEAR_HISTORY command");
restart_peratom = 1;
create_attribute = 1;
diff --git a/src/improper.cpp b/src/improper.cpp
index e20d0d2666aa8cccd63efb75fbe4543b793fc204..089fc43aad09205a0e72aecaa886ef3b78a87d50 100644
--- a/src/improper.cpp
+++ b/src/improper.cpp
@@ -74,7 +74,7 @@ void Improper::init()
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
-void Improper::ev_setup(int eflag, int vflag)
+void Improper::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
@@ -92,25 +92,29 @@ void Improper::ev_setup(int eflag, int vflag)
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
- memory->destroy(eatom);
- memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom");
+ if (alloc) {
+ memory->destroy(eatom);
+ memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom");
+ }
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
- memory->destroy(vatom);
- memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom");
+ if (alloc) {
+ memory->destroy(vatom);
+ memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom");
+ }
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (eflag_atom) {
+ if (eflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
- if (vflag_atom) {
+ if (vflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) {
diff --git a/src/improper.h b/src/improper.h
index b20bc732dfb4e0f84f1de8084f474f3720db1ce6..df3c966cdc4704b5d91c03332274fabd0e3ab9b5 100644
--- a/src/improper.h
+++ b/src/improper.h
@@ -27,7 +27,7 @@ class Improper : protected Pointers {
int *setflag;
int writedata; // 1 if writes coeffs to data file
double energy; // accumulated energies
- double virial[6]; // accumlated virial
+ double virial[6]; // accumulated virial
double *eatom,**vatom; // accumulated per-atom energy/virial
// KOKKOS host/device flag and data masks
@@ -56,7 +56,7 @@ class Improper : protected Pointers {
int vflag_either,vflag_global,vflag_atom;
int maxeatom,maxvatom;
- void ev_setup(int, int);
+ void ev_setup(int, int, int alloc = 1);
void ev_tally(int, int, int, int, int, int, double,
double *, double *, double *, double, double, double,
double, double, double, double, double, double);
diff --git a/src/kspace.cpp b/src/kspace.cpp
index 48626346b185a76a712f20715f3471a16451b3a1..c2113cdf767c899d733ed9dc3d44162ff140563f 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -206,7 +206,7 @@ void KSpace::pair_check()
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
-void KSpace::ev_setup(int eflag, int vflag)
+void KSpace::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
@@ -227,25 +227,29 @@ void KSpace::ev_setup(int eflag, int vflag)
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
- memory->destroy(eatom);
- memory->create(eatom,maxeatom,"kspace:eatom");
+ if (alloc) {
+ memory->destroy(eatom);
+ memory->create(eatom,maxeatom,"kspace:eatom");
+ }
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
- memory->destroy(vatom);
- memory->create(vatom,maxvatom,6,"kspace:vatom");
+ if (alloc) {
+ memory->destroy(vatom);
+ memory->create(vatom,maxvatom,6,"kspace:vatom");
+ }
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (eflag_atom) {
+ if (eflag_atom && alloc) {
n = atom->nlocal;
if (tip4pflag) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
- if (vflag_atom) {
+ if (vflag_atom && alloc) {
n = atom->nlocal;
if (tip4pflag) n += atom->nghost;
for (i = 0; i < n; i++) {
diff --git a/src/kspace.h b/src/kspace.h
index 95fb6ffaf25abf86612acc79e679a3059e6a7adf..ad29c214728f56eb0eec5739aeac18b076c752b9 100644
--- a/src/kspace.h
+++ b/src/kspace.h
@@ -33,7 +33,7 @@ class KSpace : protected Pointers {
public:
double energy; // accumulated energies
double energy_1,energy_6;
- double virial[6]; // accumlated virial
+ double virial[6]; // accumulated virial
double *eatom,**vatom; // accumulated per-atom energy/virial
double e2group; // accumulated group-group energy
double f2group[3]; // accumulated group-group force
@@ -62,14 +62,14 @@ class KSpace : protected Pointers {
int order,order_6,order_allocated;
double accuracy; // accuracy of KSpace solver (force units)
- double accuracy_absolute; // user-specifed accuracy in force units
+ double accuracy_absolute; // user-specified accuracy in force units
double accuracy_relative; // user-specified dimensionless accuracy
// accurary = acc_rel * two_charge_force
double accuracy_real_6; // real space accuracy for
// dispersion solver (force units)
double accuracy_kspace_6; // reciprocal space accuracy for
// dispersion solver (force units)
- int auto_disp_flag; // use automatic paramter generation for pppm/disp
+ int auto_disp_flag; // use automatic parameter generation for pppm/disp
double two_charge_force; // force in user units of two point
// charges separated by 1 Angstrom
@@ -197,7 +197,7 @@ class KSpace : protected Pointers {
int kx_ewald,ky_ewald,kz_ewald; // kspace settings for Ewald sum
void pair_check();
- void ev_setup(int, int);
+ void ev_setup(int, int, int alloc = 1);
double estimate_table_accuracy(double, double);
};
diff --git a/src/library.cpp b/src/library.cpp
index 992b8ba100d62209f607654baf999c78fa95d039..5980b135eb1bd8ee00f417b662e63339a9f9b0c2 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -140,7 +140,7 @@ void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
/* ----------------------------------------------------------------------
create an instance of LAMMPS and return pointer to it
caller doesn't know MPI communicator, so use MPI_COMM_WORLD
- intialize MPI if needed
+ initialize MPI if needed
------------------------------------------------------------------------- */
void lammps_open_no_mpi(int argc, char **argv, void **ptr)
@@ -646,7 +646,7 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
/* ----------------------------------------------------------------------
reset simulation box parameters
see domain.h for definition of these arguments
- assumes domain->set_intiial_box() has been invoked previously
+ assumes domain->set_initial_box() has been invoked previously
------------------------------------------------------------------------- */
void lammps_reset_box(void *ptr, double *boxlo, double *boxhi,
@@ -761,6 +761,10 @@ void lammps_gather_atoms(void *ptr, char *name,
int i,j,offset;
void *vptr = lmp->atom->extract(name);
+ if(vptr == NULL) {
+ lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name");
+ return;
+ }
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
@@ -857,6 +861,10 @@ void lammps_scatter_atoms(void *ptr, char *name,
int i,j,m,offset;
void *vptr = lmp->atom->extract(name);
+ if(vptr == NULL) {
+ lmp->error->warning(FLERR,"lammps_scatter_atoms: unknown property name");
+ return;
+ }
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
diff --git a/src/lmptype.h b/src/lmptype.h
index a8c09bd2adbec12cb9c86016702935f7813f786f..253f9a7470a400ef4330e7619c9d89a6e60e7a7f 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -13,7 +13,7 @@
// define integer data types used by LAMMPS and associated size limits
-// smallint = variables for on-procesor system (nlocal, nmax, etc)
+// smallint = variables for on-processor system (nlocal, nmax, etc)
// imageint = variables for atom image flags (image)
// tagint = variables for atom IDs and molecule IDs (tag,molecule)
// bigint = variables for total system (natoms, ntimestep, etc)
diff --git a/src/molecule.cpp b/src/molecule.cpp
index 2253e86af0d789eb80dab35164e5a9d606c94da8..76b28e3d470611f56c9f33d367a6a8f6b53736fc 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -1395,7 +1395,7 @@ void Molecule::check_attributes(int flag)
if (atom->maxspecial < onemol->maxspecial) mismatch = 1;
if (mismatch)
- error->all(FLERR,"Molecule toplogy/atom exceeds system topology/atom");
+ error->all(FLERR,"Molecule topology/atom exceeds system topology/atom");
}
// warn if molecule topology defined but no special settings
diff --git a/src/molecule.h b/src/molecule.h
index 0bbe6846365755a4ea64f153e8a40bfc524a002e..bfc9da1857cf12bd32a6b332c88b45038e16da3c 100644
--- a/src/molecule.h
+++ b/src/molecule.h
@@ -406,7 +406,7 @@ The number of bond, angle, etc types in the molecule exceeds the
system setting. See the create_box command for how to specify these
values.
-E: Molecule toplogy/atom exceeds system topology/atom
+E: Molecule topology/atom exceeds system topology/atom
The number of bonds, angles, etc per-atom in the molecule exceeds the
system setting. See the create_box command for how to specify these
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index e0b84cc4109ba83bee4c47bc948ba85abf14ad0c..8da6c1b9d25452ffe5659bdc0c6aa54d2cf1573c 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -166,7 +166,7 @@ pairclass(NULL), pairnames(NULL), pairmasks(NULL)
ex1_group = ex2_group = ex1_bit = ex2_bit = NULL;
nex_mol = maxex_mol = 0;
- ex_mol_group = ex_mol_bit = NULL;
+ ex_mol_group = ex_mol_bit = ex_mol_intra = NULL;
// Kokkos setting
@@ -234,6 +234,7 @@ Neighbor::~Neighbor()
memory->destroy(ex_mol_group);
delete [] ex_mol_bit;
+ memory->destroy(ex_mol_intra);
}
/* ---------------------------------------------------------------------- */
@@ -918,7 +919,7 @@ void Neighbor::morph_other()
requests[i-1]->historylist = i;
}
- // if respaouter, point all asociated rRESPA lists at each other
+ // if respaouter, point all associated rRESPA lists at each other
if (irq->respaouter) {
if (requests[i-1]->respainner) {
@@ -1128,6 +1129,11 @@ void Neighbor::morph_halffull()
if (!irq->half) continue;
+ // Kokkos doesn't yet support half from full
+
+ if (irq->kokkos_host) continue;
+ if (irq->kokkos_device) continue;
+
// these lists are created other ways, no need for halffull
// do want to process skip lists
@@ -1153,8 +1159,6 @@ void Neighbor::morph_halffull()
// this includes custom cutoff set by requestor
// no need to check respaouter b/c it stores same pairs
// no need to check dnum b/c only set for history
- // NOTE: need check for 2 Kokkos flags?
- // Kokkos doesn't yet support half from full?
if (irq->ghost != jrq->ghost) continue;
if (irq->size != jrq->size) continue;
@@ -2323,7 +2327,8 @@ void Neighbor::modify_params(int narg, char **arg)
nex_group++;
iarg += 4;
- } else if (strcmp(arg[iarg+1],"molecule") == 0) {
+ } else if (strcmp(arg[iarg+1],"molecule/inter") == 0 ||
+ strcmp(arg[iarg+1],"molecule/intra") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (atom->molecule_flag == 0)
error->all(FLERR,"Neigh_modify exclude molecule "
@@ -2331,13 +2336,21 @@ void Neighbor::modify_params(int narg, char **arg)
if (nex_mol == maxex_mol) {
maxex_mol += EXDELTA;
memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group");
+ if (lmp->kokkos)
+ grow_ex_mol_intra_kokkos();
+ else
+ memory->grow(ex_mol_intra,maxex_mol,"neigh:ex_mol_intra");
}
ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
if (ex_mol_group[nex_mol] == -1)
error->all(FLERR,"Invalid group ID in neigh_modify command");
+ if (strcmp(arg[iarg+1],"molecule/intra") == 0)
+ ex_mol_intra[nex_mol] = 1;
+ else
+ ex_mol_intra[nex_mol] = 0;
nex_mol++;
iarg += 3;
-
+
} else if (strcmp(arg[iarg+1],"none") == 0) {
nex_type = nex_group = nex_mol = 0;
iarg += 2;
diff --git a/src/neighbor.h b/src/neighbor.h
index 8e2fad1f1b2cc26a396eba9092b4b5f67f5828b4..16a80b599179500477f712cdb9c82b3720cd43ec 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -71,6 +71,8 @@ class Neighbor : protected Pointers {
int nex_mol; // # of entries in molecule exclusion list
int *ex_mol_group; // molecule group #'s to exclude
int *ex_mol_bit; // molecule group bits to exclude
+ int *ex_mol_intra; // 0 = exclude if in 2 molecules (inter)
+ // 1 = exclude if in same molecule (intra)
// special info, used by NeighPair
@@ -229,6 +231,7 @@ class Neighbor : protected Pointers {
virtual void init_ex_type_kokkos(int) {}
virtual void init_ex_bit_kokkos() {}
virtual void init_ex_mol_bit_kokkos() {}
+ virtual void grow_ex_mol_intra_kokkos() {}
};
namespace NeighConst {
diff --git a/src/npair.cpp b/src/npair.cpp
index 9fe326cbd1f77c269e05024c1dd2918a6c8a3a95..6c3f8ac05e3545ca61b6087c64fa0dbb9a86b1ee 100644
--- a/src/npair.cpp
+++ b/src/npair.cpp
@@ -86,6 +86,7 @@ void NPair::copy_neighbor_info()
nex_mol = neighbor->nex_mol;
ex_mol_group = neighbor->ex_mol_group;
ex_mol_bit = neighbor->ex_mol_bit;
+ ex_mol_intra = neighbor->ex_mol_intra;
// special info
@@ -180,8 +181,17 @@ int NPair::exclusion(int i, int j, int itype, int jtype,
if (nex_mol) {
for (m = 0; m < nex_mol; m++)
- if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
- molecule[i] == molecule[j]) return 1;
+
+ // intra-chain: exclude i-j pair if in same molecule
+ // inter-chain: exclude i-j pair if in different molecules
+
+ if (ex_mol_intra[m]) {
+ if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+ molecule[i] == molecule[j]) return 1;
+ } else {
+ if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+ molecule[i] != molecule[j]) return 1;
+ }
}
return 0;
diff --git a/src/npair.h b/src/npair.h
index cdb8b3061d8588bee7ee46df9a78e604736b6ae4..8f2bcb13bc8d26f7fbb15f317b4bee7ec78e648f 100644
--- a/src/npair.h
+++ b/src/npair.h
@@ -61,8 +61,10 @@ class NPair : protected Pointers {
int *ex1_bit,*ex2_bit; // pairs of group bits to exclude
int nex_mol; // # of entries in molecule exclusion list
- int *ex_mol_group; // molecule group #'s to exclude
int *ex_mol_bit; // molecule group bits to exclude
+ int *ex_mol_group; // molecule group #'s to exclude
+ int *ex_mol_intra; // 0 = exclude if in 2 molecules (inter)
+ // 1 = exclude if in same molecule (intra)
// special data from Neighbor class
diff --git a/src/output.h b/src/output.h
index cc282cbeddb9b7eed8ac65c0353b262eba49d567..de5eaaa70b708fa61a3e95fd3f40cd86cad57009 100644
--- a/src/output.h
+++ b/src/output.h
@@ -172,7 +172,7 @@ W: New thermo_style command, previous thermo_modify settings will be lost
If a thermo_style command is used after a thermo_modify command, the
settings changed by the thermo_modify command will be reset to their
-default values. This is because the thermo_modify commmand acts on
+default values. This is because the thermo_modify command acts on
the currently defined thermo style, and a thermo_style command creates
a new style.
diff --git a/src/pair.cpp b/src/pair.cpp
index 5d73a592e8bea96cfe4b16939cdde484a3ee1fa9..d90ed8bb43a90e422dccf6b39a296b092d2e938f 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -749,7 +749,7 @@ void Pair::del_tally_callback(Compute *ptr)
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
-void Pair::ev_setup(int eflag, int vflag)
+void Pair::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
@@ -767,13 +767,17 @@ void Pair::ev_setup(int eflag, int vflag)
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
- memory->destroy(eatom);
- memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom");
+ if (alloc) {
+ memory->destroy(eatom);
+ memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom");
+ }
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
- memory->destroy(vatom);
- memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom");
+ if (alloc) {
+ memory->destroy(vatom);
+ memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom");
+ }
}
// zero accumulators
@@ -782,12 +786,12 @@ void Pair::ev_setup(int eflag, int vflag)
if (eflag_global) eng_vdwl = eng_coul = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (eflag_atom) {
+ if (eflag_atom && alloc) {
n = atom->nlocal;
if (force->newton) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
- if (vflag_atom) {
+ if (vflag_atom && alloc) {
n = atom->nlocal;
if (force->newton) n += atom->nghost;
for (i = 0; i < n; i++) {
@@ -1534,7 +1538,7 @@ void Pair::virial_fdotr_compute()
void Pair::write_file(int narg, char **arg)
{
- if (narg < 8) error->all(FLERR,"Illegal pair_write command");
+ if (narg != 8 && narg != 10) error->all(FLERR,"Illegal pair_write command");
if (single_enable == 0)
error->all(FLERR,"Pair style does not support pair_write");
diff --git a/src/pair.h b/src/pair.h
index 16746a29a8798d15017ad3f28400d8bf8bf4e809..3f66c6095a8199b8b4530761af014854efce0914 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -221,7 +221,7 @@ class Pair : protected Pointers {
int copymode; // if set, do not deallocate during destruction
// required when classes are used as functors by Kokkos
- virtual void ev_setup(int, int);
+ virtual void ev_setup(int, int, int alloc = 1);
void ev_unset();
void ev_tally_full(int, double, double, double, double, double, double);
void ev_tally_xyz_full(int, double, double,
diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp
index c7b77c32709af9e5a854fc671bfa6143dc5ac5d3..c8f6afdacc6853e7df8b697d46958e2053015131 100644
--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@@ -168,7 +168,7 @@ void PairGauss::settings(int narg, char **arg)
cut_global = force->numeric(FLERR,arg[0]);
- // reset cutoffs that have been explicity set
+ // reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
diff --git a/src/procmap.cpp b/src/procmap.cpp
index 088939b21828fe708da302722d652542a6bad727..f54ac1915c4b4c934d18d3ae0e848c57df856808 100644
--- a/src/procmap.cpp
+++ b/src/procmap.cpp
@@ -216,7 +216,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
best_factors(numapossible,numafactors,numagrid,1,1,1);
- // user_nodegrid = implied user contraints on nodes
+ // user_nodegrid = implied user constraints on nodes
int user_nodegrid[3];
user_nodegrid[0] = user_procgrid[0] / numagrid[0];
diff --git a/src/rcb.cpp b/src/rcb.cpp
index 7223e4616aa94c805533bab34115596173cfeff1..1aca015dafb00232abcf59217510fe7f45026b74 100644
--- a/src/rcb.cpp
+++ b/src/rcb.cpp
@@ -42,7 +42,7 @@ RCB::RCB(LAMMPS *lmp) : Pointers(lmp)
dots = NULL;
nlist = maxlist = 0;
- dotlist = dotmark = NULL;
+ dotlist = dotmark = dotmark_select = NULL;
maxbuf = 0;
buf = NULL;
@@ -73,6 +73,7 @@ RCB::~RCB()
memory->sfree(dots);
memory->destroy(dotlist);
memory->destroy(dotmark);
+ memory->destroy(dotmark_select);
memory->sfree(buf);
memory->destroy(recvproc);
@@ -91,6 +92,9 @@ RCB::~RCB()
/* ----------------------------------------------------------------------
perform RCB balancing of N particles at coords X in bounding box LO/HI
+ NEW version: each RCB cut is tested in all dimensions
+ dimeension that produces 2 boxes with largest min size is selected
+ this is to prevent very narrow boxes from being produced
if wt = NULL, ignore per-particle weights
if wt defined, per-particle weights > 0.0
dimension = 2 or 3
@@ -103,6 +107,523 @@ RCB::~RCB()
void RCB::compute(int dimension, int n, double **x, double *wt,
double *bboxlo, double *bboxhi)
+{
+ int i,j,k;
+ int keep,outgoing,incoming,incoming2;
+ int dim,markactive;
+ int indexlo,indexhi;
+ int first_iteration,breakflag;
+ double wttot,wtlo,wthi,wtsum,wtok,wtupto,wtmax;
+ double targetlo,targethi;
+ double valuemin,valuemax,valuehalf,valuehalf_select,smaller;
+ double tolerance;
+ MPI_Comm comm,comm_half;
+ MPI_Request request,request2;
+ Median med,medme;
+
+ // create list of my Dots
+
+ ndot = nkeep = noriginal = n;
+
+ if (ndot > maxdot) {
+ maxdot = ndot;
+ memory->sfree(dots);
+ dots = (Dot *) memory->smalloc(ndot*sizeof(Dot),"RCB:dots");
+ }
+
+ for (i = 0; i < ndot; i++) {
+ dots[i].x[0] = x[i][0];
+ dots[i].x[1] = x[i][1];
+ dots[i].x[2] = x[i][2];
+ dots[i].proc = me;
+ dots[i].index = i;
+ }
+
+ if (wt)
+ for (i = 0; i < ndot; i++) dots[i].wt = wt[i];
+ else
+ for (i = 0; i < ndot; i++) dots[i].wt = 1.0;
+
+ // initial bounding box = simulation box
+ // includes periodic or shrink-wrapped boundaries
+
+ lo = bbox.lo;
+ hi = bbox.hi;
+
+ lo[0] = bboxlo[0];
+ lo[1] = bboxlo[1];
+ lo[2] = bboxlo[2];
+ hi[0] = bboxhi[0];
+ hi[1] = bboxhi[1];
+ hi[2] = bboxhi[2];
+
+ cut = 0.0;
+ cutdim = -1;
+
+ // initialize counters
+
+ counters[0] = 0;
+ counters[1] = 0;
+ counters[2] = 0;
+ counters[3] = ndot;
+ counters[4] = maxdot;
+ counters[5] = 0;
+ counters[6] = 0;
+
+ // create communicator for use in recursion
+
+ MPI_Comm_dup(world,&comm);
+
+ // recurse until partition is a single proc = me
+ // proclower,procupper = lower,upper procs in partition
+ // procmid = 1st proc in upper half of partition
+
+ int procpartner,procpartner2;
+
+ int procmid;
+ int proclower = 0;
+ int procupper = nprocs - 1;
+
+ while (proclower != procupper) {
+
+ // if odd # of procs, lower partition gets extra one
+
+ procmid = proclower + (procupper - proclower) / 2 + 1;
+
+ // determine communication partner(s)
+ // readnumber = # of proc partners to read from
+
+ if (me < procmid)
+ procpartner = me + (procmid - proclower);
+ else
+ procpartner = me - (procmid - proclower);
+
+ int readnumber = 1;
+ if (procpartner > procupper) {
+ readnumber = 0;
+ procpartner--;
+ }
+ if (me == procupper && procpartner != procmid - 1) {
+ readnumber = 2;
+ procpartner2 = procpartner + 1;
+ }
+
+ // wttot = summed weight of entire partition
+ // search tolerance = largest single weight (plus epsilon)
+ // targetlo = desired weight in lower half of partition
+ // targethi = desired weight in upper half of partition
+
+ wtmax = wtsum = 0.0;
+
+ if (wt) {
+ for (i = 0; i < ndot; i++) {
+ wtsum += dots[i].wt;
+ if (dots[i].wt > wtmax) wtmax = dots[i].wt;
+ }
+ } else {
+ for (i = 0; i < ndot; i++) wtsum += dots[i].wt;
+ wtmax = 1.0;
+ }
+
+ MPI_Allreduce(&wtsum,&wttot,1,MPI_DOUBLE,MPI_SUM,comm);
+ if (wt) MPI_Allreduce(&wtmax,&tolerance,1,MPI_DOUBLE,MPI_MAX,comm);
+ else tolerance = 1.0;
+
+ tolerance *= 1.0 + TINY;
+ targetlo = wttot * (procmid - proclower) / (procupper + 1 - proclower);
+ targethi = wttot - targetlo;
+
+ // attempt a cut in each dimension
+ // each cut produces 2 boxes, each with a reduced box length in that dim
+ // smaller = the smaller of the 2 reduced box lengths in that dimension
+ // choose to cut in dimension which produces largest smaller value
+ // this should induce final proc sub-boxes to be as cube-ish as possible
+ // dim_select = selected cut dimension
+ // valuehalf_select = valuehalf in that dimension
+ // dotmark_select = dot markings in that dimension
+
+ int dim_select = -1;
+ double largest = 0.0;
+
+ for (dim = 0; dim < dimension; dim++) {
+
+ // create active list and mark array for dots
+ // initialize active list to all dots
+
+ if (ndot > maxlist) {
+ memory->destroy(dotlist);
+ memory->destroy(dotmark);
+ memory->destroy(dotmark_select);
+ maxlist = maxdot;
+ memory->create(dotlist,maxlist,"RCB:dotlist");
+ memory->create(dotmark,maxlist,"RCB:dotmark");
+ memory->create(dotmark_select,maxlist,"RCB:dotmark_select");
+ }
+
+ nlist = ndot;
+ for (i = 0; i < nlist; i++) dotlist[i] = i;
+
+ // median iteration
+ // zoom in on bisector until correct # of dots in each half of partition
+ // as each iteration of median-loop begins, require:
+ // all non-active dots are marked with 0/1 in dotmark
+ // valuemin <= every active dot <= valuemax
+ // wtlo, wthi = total wt of non-active dots
+ // when leave median-loop, require only:
+ // valuehalf = correct cut position
+ // all dots <= valuehalf are marked with 0 in dotmark
+ // all dots >= valuehalf are marked with 1 in dotmark
+ // markactive = which side of cut is active = 0/1
+ // indexlo,indexhi = indices of dot closest to median
+
+ wtlo = wthi = 0.0;
+ valuemin = lo[dim];
+ valuemax = hi[dim];
+ first_iteration = 1;
+ indexlo = indexhi = 0;
+
+ while (1) {
+
+ // choose bisector value
+ // use old value on 1st iteration if old cut dimension is the same
+ // on 2nd option: could push valuehalf towards geometric center
+ // with "1.0-factor" to force overshoot
+
+ if (first_iteration && reuse && dim == tree[procmid].dim) {
+ counters[5]++;
+ valuehalf = tree[procmid].cut;
+ if (valuehalf < valuemin || valuehalf > valuemax)
+ valuehalf = 0.5 * (valuemin + valuemax);
+ } else if (wt)
+ valuehalf = valuemin + (targetlo - wtlo) /
+ (wttot - wtlo - wthi) * (valuemax - valuemin);
+ else
+ valuehalf = 0.5 * (valuemin + valuemax);
+
+ first_iteration = 0;
+
+ // initialize local median data structure
+
+ medme.totallo = medme.totalhi = 0.0;
+ medme.valuelo = -MYHUGE;
+ medme.valuehi = MYHUGE;
+ medme.wtlo = medme.wthi = 0.0;
+ medme.countlo = medme.counthi = 0;
+ medme.proclo = medme.prochi = me;
+
+ // mark all active dots on one side or other of bisector
+ // also set all fields in median data struct
+ // save indices of closest dots on either side
+
+ for (j = 0; j < nlist; j++) {
+ i = dotlist[j];
+ if (dots[i].x[dim] <= valuehalf) { // in lower part
+ medme.totallo += dots[i].wt;
+ dotmark[i] = 0;
+ if (dots[i].x[dim] > medme.valuelo) { // my closest dot
+ medme.valuelo = dots[i].x[dim];
+ medme.wtlo = dots[i].wt;
+ medme.countlo = 1;
+ indexlo = i;
+ } else if (dots[i].x[dim] == medme.valuelo) { // tied for closest
+ medme.wtlo += dots[i].wt;
+ medme.countlo++;
+ }
+ }
+ else { // in upper part
+ medme.totalhi += dots[i].wt;
+ dotmark[i] = 1;
+ if (dots[i].x[dim] < medme.valuehi) { // my closest dot
+ medme.valuehi = dots[i].x[dim];
+ medme.wthi = dots[i].wt;
+ medme.counthi = 1;
+ indexhi = i;
+ } else if (dots[i].x[dim] == medme.valuehi) { // tied for closest
+ medme.wthi += dots[i].wt;
+ medme.counthi++;
+ }
+ }
+ }
+
+ // combine median data struct across current subset of procs
+
+ counters[0]++;
+ MPI_Allreduce(&medme,&med,1,med_type,med_op,comm);
+
+ // test median guess for convergence
+ // move additional dots that are next to cut across it
+
+ if (wtlo + med.totallo < targetlo) { // lower half TOO SMALL
+
+ wtlo += med.totallo;
+ valuehalf = med.valuehi;
+
+ if (med.counthi == 1) { // only one dot to move
+ if (wtlo + med.wthi < targetlo) { // move it, keep iterating
+ if (me == med.prochi) dotmark[indexhi] = 0;
+ }
+ else { // only move if beneficial
+ if (wtlo + med.wthi - targetlo < targetlo - wtlo)
+ if (me == med.prochi) dotmark[indexhi] = 0;
+ break; // all done
+ }
+ }
+ else { // multiple dots to move
+ breakflag = 0;
+ wtok = 0.0;
+ if (medme.valuehi == med.valuehi) wtok = medme.wthi;
+ if (wtlo + med.wthi >= targetlo) { // all done
+ MPI_Scan(&wtok,&wtupto,1,MPI_DOUBLE,MPI_SUM,comm);
+ wtmax = targetlo - wtlo;
+ if (wtupto > wtmax) wtok = wtok - (wtupto - wtmax);
+ breakflag = 1;
+ } // wtok = most I can move
+ for (j = 0, wtsum = 0.0; j < nlist && wtsum < wtok; j++) {
+ i = dotlist[j];
+ if (dots[i].x[dim] == med.valuehi) { // only move if better
+ if (wtsum + dots[i].wt - wtok < wtok - wtsum)
+ dotmark[i] = 0;
+ wtsum += dots[i].wt;
+ }
+ }
+ if (breakflag) break; // done if moved enough
+ }
+
+ wtlo += med.wthi;
+ if (targetlo-wtlo <= tolerance) break; // close enough
+
+ valuemin = med.valuehi; // iterate again
+ markactive = 1;
+ }
+
+ else if (wthi + med.totalhi < targethi) { // upper half TOO SMALL
+
+ wthi += med.totalhi;
+ valuehalf = med.valuelo;
+
+ if (med.countlo == 1) { // only one dot to move
+ if (wthi + med.wtlo < targethi) { // move it, keep iterating
+ if (me == med.proclo) dotmark[indexlo] = 1;
+ }
+ else { // only move if beneficial
+ if (wthi + med.wtlo - targethi < targethi - wthi)
+ if (me == med.proclo) dotmark[indexlo] = 1;
+ break; // all done
+ }
+ }
+ else { // multiple dots to move
+ breakflag = 0;
+ wtok = 0.0;
+ if (medme.valuelo == med.valuelo) wtok = medme.wtlo;
+ if (wthi + med.wtlo >= targethi) { // all done
+ MPI_Scan(&wtok,&wtupto,1,MPI_DOUBLE,MPI_SUM,comm);
+ wtmax = targethi - wthi;
+ if (wtupto > wtmax) wtok = wtok - (wtupto - wtmax);
+ breakflag = 1;
+ } // wtok = most I can move
+ for (j = 0, wtsum = 0.0; j < nlist && wtsum < wtok; j++) {
+ i = dotlist[j];
+ if (dots[i].x[dim] == med.valuelo) { // only move if better
+ if (wtsum + dots[i].wt - wtok < wtok - wtsum)
+ dotmark[i] = 1;
+ wtsum += dots[i].wt;
+ }
+ }
+ if (breakflag) break; // done if moved enough
+ }
+
+ wthi += med.wtlo;
+ if (targethi-wthi <= tolerance) break; // close enough
+
+ valuemax = med.valuelo; // iterate again
+ markactive = 0;
+ }
+
+ else // Goldilocks result: both partitions just right
+ break;
+
+ // shrink the active list
+
+ k = 0;
+ for (j = 0; j < nlist; j++) {
+ i = dotlist[j];
+ if (dotmark[i] == markactive) dotlist[k++] = i;
+ }
+ nlist = k;
+ }
+
+ // cut produces 2 sub-boxes with reduced size in dim
+ // compare smaller of the 2 sizes to previous dims
+ // keep dim that has the largest smaller
+
+ smaller = MIN(valuehalf-lo[dim],hi[dim]-valuehalf);
+ if (smaller > largest) {
+ largest = smaller;
+ dim_select = dim;
+ valuehalf_select = valuehalf;
+ memcpy(dotmark_select,dotmark,ndot*sizeof(int));
+ }
+ }
+
+ // copy results for best dim cut into dim,valuehalf,dotmark
+
+ dim = dim_select;
+ valuehalf = valuehalf_select;
+ memcpy(dotmark,dotmark_select,ndot*sizeof(int));
+
+ // found median
+ // store cut info only if I am procmid
+
+ if (me == procmid) {
+ cut = valuehalf;
+ cutdim = dim;
+ }
+
+ // use cut to shrink my RCB bounding box
+
+ if (me < procmid) hi[dim] = valuehalf;
+ else lo[dim] = valuehalf;
+
+ // outgoing = number of dots to ship to partner
+ // nkeep = number of dots that have never migrated
+
+ markactive = (me < procpartner);
+ for (i = 0, keep = 0, outgoing = 0; i < ndot; i++)
+ if (dotmark[i] == markactive) outgoing++;
+ else if (i < nkeep) keep++;
+ nkeep = keep;
+
+ // alert partner how many dots I'll send, read how many I'll recv
+
+ MPI_Send(&outgoing,1,MPI_INT,procpartner,0,world);
+ incoming = 0;
+ if (readnumber) {
+ MPI_Recv(&incoming,1,MPI_INT,procpartner,0,world,MPI_STATUS_IGNORE);
+ if (readnumber == 2) {
+ MPI_Recv(&incoming2,1,MPI_INT,procpartner2,0,world,MPI_STATUS_IGNORE);
+ incoming += incoming2;
+ }
+ }
+
+ // check if need to alloc more space
+
+ int ndotnew = ndot - outgoing + incoming;
+ if (ndotnew > maxdot) {
+ while (maxdot < ndotnew) maxdot += DELTA;
+ dots = (Dot *) memory->srealloc(dots,maxdot*sizeof(Dot),"RCB::dots");
+ counters[6]++;
+ }
+
+ counters[1] += outgoing;
+ counters[2] += incoming;
+ if (ndotnew > counters[3]) counters[3] = ndotnew;
+ if (maxdot > counters[4]) counters[4] = maxdot;
+
+ // malloc comm send buffer
+
+ if (outgoing > maxbuf) {
+ memory->sfree(buf);
+ maxbuf = outgoing;
+ buf = (Dot *) memory->smalloc(maxbuf*sizeof(Dot),"RCB:buf");
+ }
+
+ // fill buffer with dots that are marked for sending
+ // pack down the unmarked ones
+
+ keep = outgoing = 0;
+ for (i = 0; i < ndot; i++) {
+ if (dotmark[i] == markactive)
+ memcpy(&buf[outgoing++],&dots[i],sizeof(Dot));
+ else
+ memcpy(&dots[keep++],&dots[i],sizeof(Dot));
+ }
+
+ // post receives for dots
+
+ if (readnumber > 0) {
+ MPI_Irecv(&dots[keep],incoming*sizeof(Dot),MPI_CHAR,
+ procpartner,1,world,&request);
+ if (readnumber == 2) {
+ keep += incoming - incoming2;
+ MPI_Irecv(&dots[keep],incoming2*sizeof(Dot),MPI_CHAR,
+ procpartner2,1,world,&request2);
+ }
+ }
+
+ // handshake before sending dots to insure recvs have been posted
+
+ if (readnumber > 0) {
+ MPI_Send(NULL,0,MPI_INT,procpartner,0,world);
+ if (readnumber == 2) MPI_Send(NULL,0,MPI_INT,procpartner2,0,world);
+ }
+ MPI_Recv(NULL,0,MPI_INT,procpartner,0,world,MPI_STATUS_IGNORE);
+
+ // send dots to partner
+
+ MPI_Rsend(buf,outgoing*sizeof(Dot),MPI_CHAR,procpartner,1,world);
+
+ // wait until all dots are received
+
+ if (readnumber > 0) {
+ MPI_Wait(&request,MPI_STATUS_IGNORE);
+ if (readnumber == 2) MPI_Wait(&request2,MPI_STATUS_IGNORE);
+ }
+
+ ndot = ndotnew;
+
+ // cut partition in half, create new communicators of 1/2 size
+
+ int split;
+ if (me < procmid) {
+ procupper = procmid - 1;
+ split = 0;
+ } else {
+ proclower = procmid;
+ split = 1;
+ }
+
+ MPI_Comm_split(comm,split,me,&comm_half);
+ MPI_Comm_free(&comm);
+ comm = comm_half;
+ }
+
+ // clean up
+
+ MPI_Comm_free(&comm);
+
+ // set public variables with results of rebalance
+
+ nfinal = ndot;
+
+ if (nfinal > maxrecv) {
+ memory->destroy(recvproc);
+ memory->destroy(recvindex);
+ maxrecv = nfinal;
+ memory->create(recvproc,maxrecv,"RCB:recvproc");
+ memory->create(recvindex,maxrecv,"RCB:recvindex");
+ }
+
+ for (i = 0; i < nfinal; i++) {
+ recvproc[i] = dots[i].proc;
+ recvindex[i] = dots[i].index;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform RCB balancing of N particles at coords X in bounding box LO/HI
+ OLD version: each RCB cut is made in longest dimension of sub-box
+ if wt = NULL, ignore per-particle weights
+ if wt defined, per-particle weights > 0.0
+ dimension = 2 or 3
+ as documented in rcb.h:
+ sets noriginal,nfinal,nkeep,recvproc,recvindex,lo,hi
+ all proc particles will be inside or on surface of 3-d box
+ defined by final lo/hi
+ // NOTE: worry about re-use of data structs for fix balance?
+------------------------------------------------------------------------- */
+
+void RCB::compute_old(int dimension, int n, double **x, double *wt,
+ double *bboxlo, double *bboxhi)
{
int i,j,k;
int keep,outgoing,incoming,incoming2;
diff --git a/src/rcb.h b/src/rcb.h
index 7a82d42f93b1fe96b402f45c29a2f583d8ec0eaa..90b82f5952df5761500c7f5392900847e009f19d 100644
--- a/src/rcb.h
+++ b/src/rcb.h
@@ -42,6 +42,7 @@ class RCB : protected Pointers {
RCB(class LAMMPS *);
~RCB();
void compute(int, int, double **, double *, double *, double *);
+ void compute_old(int, int, double **, double *, double *, double *);
void invert(int sortflag = 0);
bigint memory_usage();
@@ -99,6 +100,7 @@ class RCB : protected Pointers {
int maxlist;
int *dotlist;
int *dotmark;
+ int *dotmark_select;
int maxbuf;
Dot *buf;
diff --git a/src/region_block.cpp b/src/region_block.cpp
index f1787d2ca2f2ee403ff880120315461bb799f5ad..769edb14899e2e3835d30b579229888e853c7beb 100644
--- a/src/region_block.cpp
+++ b/src/region_block.cpp
@@ -401,7 +401,7 @@ double RegBlock::find_closest_point(int i, double *x,
zc = p[2];
}
- point_on_line_segment(corners[i][3],corners[i][4],x,p);
+ point_on_line_segment(corners[i][3],corners[i][0],x,p);
d2 = (p[0]-x[0])*(p[0]-x[0]) + (p[1]-x[1])*(p[1]-x[1]) +
(p[2]-x[2])*(p[2]-x[2]);
if (d2 < d2min) {
diff --git a/src/region_cylinder.h b/src/region_cylinder.h
index bc5255b343019d5c312758c98d4c5bffffc210cc..e065c7d3f1bfdddda42b7db2cd193e07cc2b5d28 100644
--- a/src/region_cylinder.h
+++ b/src/region_cylinder.h
@@ -78,6 +78,6 @@ Self-explanatory.
E: Variable for region cylinder is invalid style
-Only equal-style varaibles are allowed.
+Only equal-style variables are allowed.
*/
diff --git a/src/region_sphere.h b/src/region_sphere.h
index 9e1fb4e739ce56b696ed9bfc462a716f6e192215..c003a9165128108efcb1ac0b65b868bdafb957fe 100644
--- a/src/region_sphere.h
+++ b/src/region_sphere.h
@@ -69,6 +69,6 @@ Self-explanatory.
E: Variable for region sphere is invalid style
-Only equal-style varaibles are allowed.
+Only equal-style variables are allowed.
*/
diff --git a/src/rerun.cpp b/src/rerun.cpp
index 493e5dca10e7966593c72afc37799ee063f34ae6..6081a6fc4721026ba3c89db20a3098cb7718735c 100644
--- a/src/rerun.cpp
+++ b/src/rerun.cpp
@@ -124,7 +124,7 @@ void Rerun::command(int narg, char **arg)
if (nremain) rd->setup_reader(nremain,&arg[narg-nremain]);
else rd->setup_reader(0,NULL);
- // perform the psuedo run
+ // perform the pseudo run
// invoke lmp->init() only once
// read all relevant snapshots
// use setup_minimal() since atoms are already owned by correct procs
diff --git a/src/run.h b/src/run.h
index 5f6accbfac32383298602e1b79d02a0db56ef152..727b23f1c4ec82ee9017664c605fe767d436dbb0 100644
--- a/src/run.h
+++ b/src/run.h
@@ -71,6 +71,6 @@ Self-explanatory.
E: Too many timesteps
-The cummulative timesteps must fit in a 64-bit integer.
+The cumulative timesteps must fit in a 64-bit integer.
*/
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 3d3a28cde8a6d47e18cbfb568d995d2a320ab8d9..dbbeff4998524443e3084651a99a3ca9a4ea445b 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -55,7 +55,8 @@ using namespace MathConst;
// customize a new keyword by adding to this list:
-// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain, part, timeremain
+// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain,
+// part, timeremain
// atoms, temp, press, pe, ke, etotal, enthalpy
// evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail
// vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz,
@@ -394,6 +395,11 @@ void Thermo::compute(int flag)
if (flushflag) fflush(logfile);
}
}
+
+ // set to 1, so that subsequent invocations of CPU time will be non-zero
+ // e.g. via variables in print command
+
+ firststep = 1;
}
/* ----------------------------------------------------------------------
@@ -1054,7 +1060,7 @@ int Thermo::add_variable(const char *id)
compute a single thermodynamic value, word is any keyword in custom list
called when a variable is evaluated by Variable class
return value as double in answer
- return 0 if str is recoginzed keyword, 1 if unrecognized
+ return 0 if str is recognized keyword, 1 if unrecognized
customize a new keyword by adding to if statement
------------------------------------------------------------------------- */
diff --git a/src/thermo.h b/src/thermo.h
index ddbe3cc95b7ef1eff7ade1f48417a0610c4a1981..d87e8fce3d9e98cb26be277ea9aeeaf5e2f6984f 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -95,7 +95,7 @@ class Thermo : protected Pointers {
char **id_fix; // their IDs
class Fix **fixes; // list of ptrs to the Fix objects
- int nvariable; // # of variables evaulated by thermo
+ int nvariable; // # of variables evaluated by thermo
char **id_variable; // list of variable names
int *variables; // list of Variable indices
@@ -236,7 +236,7 @@ E: Lost atoms: original %ld current %ld
Lost atoms are checked for each time thermo output is done. See the
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved futher than one processor's sub-domain away before
+box, or moved further than one processor's sub-domain away before
reneighboring.
W: Lost atoms: original %ld current %ld
@@ -244,7 +244,7 @@ W: Lost atoms: original %ld current %ld
Lost atoms are checked for each time thermo output is done. See the
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved futher than one processor's sub-domain away before
+box, or moved further than one processor's sub-domain away before
reneighboring.
E: Thermo style does not use temp
diff --git a/src/variable.cpp b/src/variable.cpp
index 67c89519746ce238d467f3960820e382c8a69782..3eea50a463cf2f99720238cdbb3a25793e60e885 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -1004,7 +1004,7 @@ void Variable::compute_atom(int ivar, int igroup,
return length of vector and result pointer to vector values
if length == 0 or -1 (mismatch), generate an error
if variable already computed on this timestep, just return
- else evaulate the formula and its length, store results in VecVar entry
+ else evaluate the formula and its length, store results in VecVar entry
------------------------------------------------------------------------- */
int Variable::compute_vector(int ivar, double **result)
@@ -2747,7 +2747,7 @@ double Variable::collapse_tree(Tree *tree)
/* ----------------------------------------------------------------------
evaluate an atom-style or vector-style variable parse tree
index I = atom I or vector index I
- tree was created by one-time parsing of formula string via evaulate()
+ tree was created by one-time parsing of formula string via evaluate()
customize by adding a function:
sqrt(),exp(),ln(),log(),sin(),cos(),tan(),asin(),acos(),atan(),
atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),
diff --git a/src/variable.h b/src/variable.h
index 042ce5b3fe448577b2b7265814bf5c40132aa5ef..76607e96b404ab3ade4ec4cb9fe134bdc0f396ed 100644
--- a/src/variable.h
+++ b/src/variable.h
@@ -210,7 +210,7 @@ This is to insure they stay in sync.
E: Variable has circular dependency
A circular dependency is when variable "a" in used by variable "b" and
-variable "b" is also used by varaible "a". Circular dependencies with
+variable "b" is also used by variable "a". Circular dependencies with
longer chains of dependence are also not allowed.
E: Python variable does not match Python function
@@ -355,7 +355,7 @@ Self-explanatory.
E: Non digit character between brackets in variable
-Self-explantory.
+Self-explanatory.
E: Mismatched brackets in variable
diff --git a/src/version.h b/src/version.h
index 9f6021787c1871f25f6ca2419359b94ef45c3cc2..e0aa18371ccee56ed85a2ef6455314d70f954c41 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "21 Feb 2017"
+#define LAMMPS_VERSION "10 Mar 2017"
diff --git a/tools/eff/cfg2lammps.py b/tools/eff/cfg2lammps.py
index 1bf364aa93e7dd010fe7be04a436d385a4518b26..49830dbb097bf6e9e9a66f95a8de4784e25fea05 100644
--- a/tools/eff/cfg2lammps.py
+++ b/tools/eff/cfg2lammps.py
@@ -217,7 +217,7 @@ def generate_lammps_input(infile):
if line.find("e_field_packet_duration")>=0:
continue
if line.find("set_limit")>=0:
- continue # need to add this contraint
+ continue # need to add this constraint
if line.find("set_limit_stiffness")>=0:
continue
if line.find("output_position")>=0:
diff --git a/tools/i-pi/drivers/driver.f90 b/tools/i-pi/drivers/driver.f90
index 9ff992dab329c8d6c09ad98e52ae58348174cfb7..646f1e9addbae368d6edada3ee73242fe2cddc22 100644
--- a/tools/i-pi/drivers/driver.f90
+++ b/tools/i-pi/drivers/driver.f90
@@ -67,7 +67,7 @@
INTEGER i
! parse the command line parameters
- ! intialize defaults
+ ! initialize defaults
ccmd = 0
inet = 1
host = "localhost"//achar(0)
diff --git a/tools/i-pi/ipi/engine/atoms.py b/tools/i-pi/ipi/engine/atoms.py
index 02ffcd75515197215e4f33b7be1884352cd81c1a..fd52ccf96bdd8c39ff3e818dca7e02e3fac6e1ba 100644
--- a/tools/i-pi/ipi/engine/atoms.py
+++ b/tools/i-pi/ipi/engine/atoms.py
@@ -120,7 +120,7 @@ class Atoms(dobject):
Each replica and the centroid coordinate are all held as Atoms objects,
and so slices of the global position and momentum arrays must be used in
- the initialisation so that they always agree with each other.
+ the initialization so that they always agree with each other.
Args:
natoms: An integer giving the number of atoms.
diff --git a/tools/i-pi/ipi/engine/initializer.py b/tools/i-pi/ipi/engine/initializer.py
index 466677938a18de1030c123cfc234fa6f973020bb..de629c7f964055a2738e6b27ed2f68d4d3e240e8 100644
--- a/tools/i-pi/ipi/engine/initializer.py
+++ b/tools/i-pi/ipi/engine/initializer.py
@@ -70,7 +70,7 @@ class InitBase(dobject):
Args:
value: A string which specifies what value to initialize the
simulation property to.
- mode: A string specifiying what style of initialization should be
+ mode: A string specifying what style of initialization should be
used to read the data.
units: A string giving which unit the value is in.
"""
@@ -97,7 +97,7 @@ class InitIndexed(InitBase):
Args:
value: A string which specifies what value to initialize the
simulation property to.
- mode: A string specifiying what style of initialization should be
+ mode: A string specifying what style of initialization should be
used to read the data.
units: A string giving which unit the value is in.
index: Which atom to initialize the value of.
diff --git a/tools/i-pi/ipi/engine/properties.py b/tools/i-pi/ipi/engine/properties.py
index 1ea07bda87b3a79f43b24fad16308e437b0ec564..a76aca1fafe9f4741c209e3ea9dc1e5708be52d8 100644
--- a/tools/i-pi/ipi/engine/properties.py
+++ b/tools/i-pi/ipi/engine/properties.py
@@ -460,7 +460,7 @@ class Properties(dobject):
key: A string contained in property_dict.
Returns:
- The property labelled by the keyword key, along with its unit
+ The property labeled by the keyword key, along with its unit
keyword, and the argument lists for the function used to calculate
the property specified by the keyword key.
"""
@@ -1216,7 +1216,7 @@ class Trajectories(dobject):
key: A string contained in trajectory_dict.
Returns:
- The trajectory labelled by the keyword key, along with its unit
+ The trajectory labeled by the keyword key, along with its unit
keyword, and the argument lists for the function used to calculate
the trajectory specified by the keyword key.
"""
diff --git a/tools/i-pi/ipi/engine/simulation.py b/tools/i-pi/ipi/engine/simulation.py
index 42645939ee994c82611f302b8eb57f41bfdc1464..3c16a99621b4789c84cd4afc924d673896036620 100644
--- a/tools/i-pi/ipi/engine/simulation.py
+++ b/tools/i-pi/ipi/engine/simulation.py
@@ -49,7 +49,7 @@ class Simulation(dobject):
"""Main simulation object.
Contains all the references and the main dynamics loop. Also handles the
- initialisation and output.
+ initialization and output.
Attributes:
beads: A beads object giving the atom positions.
diff --git a/tools/i-pi/ipi/engine/thermostats.py b/tools/i-pi/ipi/engine/thermostats.py
index 5375bb917e4349d3b550200f24c759d3bfa0a6c3..1fb048ec27c8becd0c96f6d526bf97fce0f3f0c9 100644
--- a/tools/i-pi/ipi/engine/thermostats.py
+++ b/tools/i-pi/ipi/engine/thermostats.py
@@ -691,7 +691,7 @@ class ThermoNMGLE(Thermostat):
"""
def get_C(self):
- """Calculates C from temp (if C is not set explicitely)."""
+ """Calculates C from temp (if C is not set explicitly)."""
rv = np.ndarray((self.nb, self.ns+1, self.ns+1), float)
for b in range(0,self.nb):
diff --git a/tools/i-pi/ipi/interfaces/sockets.py b/tools/i-pi/ipi/interfaces/sockets.py
index 998a87d113455d36019007425de7cdaf5a20e1cf..2783d31e06a56b9e573348a8d4e1dc09c1822b03 100644
--- a/tools/i-pi/ipi/interfaces/sockets.py
+++ b/tools/i-pi/ipi/interfaces/sockets.py
@@ -243,7 +243,7 @@ class DriverSocket(socket.socket):
return np.fromstring(self._buf[0:blen], dest.dtype).reshape(dest.shape)
def initialize(self, rid, pars):
- """Sends the initialisation string to the driver.
+ """Sends the initialization string to the driver.
Args:
rid: The index of the request, i.e. the replica that
@@ -456,13 +456,13 @@ class InterfaceSocket(object):
"""Adds a request.
Note that the pars dictionary need to be sent as a string of a
- standard format so that the initialisation of the driver can be done.
+ standard format so that the initialization of the driver can be done.
Args:
atoms: An Atoms object giving the atom positions.
cell: A Cell object giving the system box.
pars: An optional dictionary giving the parameters to be sent to the
- driver for initialisation. Defaults to {}.
+ driver for initialization. Defaults to {}.
reqid: An optional integer that identifies requests of the same type,
e.g. the bead index
diff --git a/tools/i-pi/ipi/utils/depend.py b/tools/i-pi/ipi/utils/depend.py
index 1ca361f781109db2754ec28c8638c491c2edfcbc..4b87323533f5eb180de71d5d82c576bcf8c223f9 100644
--- a/tools/i-pi/ipi/utils/depend.py
+++ b/tools/i-pi/ipi/utils/depend.py
@@ -115,7 +115,7 @@ class depend_base(object):
def __init__(self, name, synchro=None, func=None, dependants=None, dependencies=None, tainted=None):
"""Initialises depend_base.
- An unusual initialisation routine, as it has to be able to deal with the
+ An unusual initialization routine, as it has to be able to deal with the
depend array mechanism for returning slices as new depend arrays.
This is the reason for the penultimate if statement; it automatically
diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT
index b57d0e76c87e69f017754bc77492cb2280d4eef9..6ec463efab12ac8e4da7b3a1f991e4ffba475e16 100644
--- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT
+++ b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT
@@ -2,7 +2,7 @@ The simulation consists of a mixture of isobutane and water.
Over time (less than 1 ns), the two molecules phase-separate.
The GAFF parameters are applied only to the isobutane molecule.
-(The water molecule paramters are defined explicitly in
+(The water molecule parameters are defined explicitly in
src/moltemplate_force_fields/tip3p_2004.lt)
WARNING: THIS IS A PRELIMINARY EXAMPLE WHICH USES AMBER'S GAFF FORCE FIELD.
diff --git a/tools/moltemplate/src/bonds_by_type.py b/tools/moltemplate/src/bonds_by_type.py
index 786a6a8a864b169aba48aa25839036a03ee9f7e0..919cfa51af7369094d92d642d333099a4de96a74 100644
--- a/tools/moltemplate/src/bonds_by_type.py
+++ b/tools/moltemplate/src/bonds_by_type.py
@@ -315,7 +315,7 @@ if __name__ == "__main__":
elif argv[i][0] == '-':
raise ttree_lex.InputError('Error('+g_program_name+'):\n'
- 'Unrecogized command line argument \"'+argv[i]+'\"\n')
+ 'Unrecognized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
diff --git a/tools/moltemplate/src/chargepairs_by_type.py b/tools/moltemplate/src/chargepairs_by_type.py
index 0d006abd5a9e481e654e620cbd703a5b91469dea..3de8131141ee9342ade0b81c3a30dd39bc786ce7 100644
--- a/tools/moltemplate/src/chargepairs_by_type.py
+++ b/tools/moltemplate/src/chargepairs_by_type.py
@@ -328,7 +328,7 @@ if __name__ == "__main__":
elif argv[i][0] == '-':
raise ttree_lex.InputError('Error('+g_program_name+'):\n'
- 'Unrecogized command line argument \"'+argv[i]+'\"\n')
+ 'Unrecognized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
diff --git a/tools/moltemplate/src/dump2data.py b/tools/moltemplate/src/dump2data.py
index adcb5a03695fea9cb65dfe615e66d0e9e5db720e..25c73219dd04226859dcccdb260825689e601b65 100644
--- a/tools/moltemplate/src/dump2data.py
+++ b/tools/moltemplate/src/dump2data.py
@@ -458,7 +458,7 @@ def ParseArgs(argv,
del(argv[i:i+2])
elif ((argv[i][0] == '-') and (__name__ == "__main__")):
- raise InputError('Error(dump2data): Unrecogized command line argument \"'+argv[i]+'\"\n')
+ raise InputError('Error(dump2data): Unrecognized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py
index c77d82043403cd748bb324297c08fa9a88f30897..743419eb2b9dde0e0d3ab41cf73860e945838c3e 100644
--- a/tools/moltemplate/src/lttree.py
+++ b/tools/moltemplate/src/lttree.py
@@ -165,7 +165,7 @@ def LttreeParseArgs(argv, settings):
elif ((argv[i][0] == '-') and (__name__ == "__main__")):
#elif (__name__ == "__main__"):
raise InputError('Error('+g_program_name+'):\n'
- 'Unrecogized command line argument \"'+argv[i]+'\"\n')
+ 'Unrecognized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
diff --git a/tools/moltemplate/src/moltemplate.sh b/tools/moltemplate/src/moltemplate.sh
index 3a8d17bcd631eee0ecdcc12ae9f4fae1c5931fd5..d6f76a2483d04af9fce6b3ea7521b58137275d83 100755
--- a/tools/moltemplate/src/moltemplate.sh
+++ b/tools/moltemplate/src/moltemplate.sh
@@ -57,7 +57,7 @@ ERR_INTERNAL()
echo " !!!!!! Possible internal error !!!!!!" >&2
echo "This could be a bug in moltemplate." >&2
echo "Please report this error." >&2
- echo "(And please include the last few lines of moltemplate output preceeding this.)" >&2
+ echo "(And please include the last few lines of moltemplate output preceding this.)" >&2
echo " Thank you." >&2
exit 100
}
diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh
index 7ef489d5f099cbcee119390b39de97905b73475b..92e7e2c42a71203c4a2131c3ab72cf99c0694676 100755
--- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh
+++ b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh
@@ -159,7 +159,7 @@ echo " # ----------------------------------------------------------------------
#echo " # This file was automatically generated by \"common/amber/amberparm2lt.sh\""
echo " # The basic atom nomenclature and conventions are explained here:"
echo " # http://ambermd.org/antechamber/gaff.pdf"
-echo " # For reference, the original gaff.dat file and format documenation are here:"
+echo " # For reference, the original gaff.dat file and format documentation are here:"
echo " # http://ambermd.org/AmberTools-get.html"
echo " # http://ambermd.org/formats.html#parm.dat"
echo " # ----------------------------------------------------------------------"
diff --git a/tools/moltemplate/src/moltemplate_force_fields/gaff.lt b/tools/moltemplate/src/moltemplate_force_fields/gaff.lt
index 82063a721b635519b8e80dc792ff44095506f02a..683dbf4ee42e01d7556487963fa1a659809b2b53 100644
--- a/tools/moltemplate/src/moltemplate_force_fields/gaff.lt
+++ b/tools/moltemplate/src/moltemplate_force_fields/gaff.lt
@@ -44,7 +44,7 @@ GAFF {
# ----------------------------------------------------------------------
# The basic atom nomenclature and conventions are explained here:
# http://ambermd.org/antechamber/gaff.pdf
- # For reference, the original gaff.dat file and format documenation are here:
+ # For reference, the original gaff.dat file and format documentation are here:
# http://ambermd.org/AmberTools-get.html
# http://ambermd.org/formats.html#parm.dat
# ----------------------------------------------------------------------
diff --git a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT b/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT
index 3bb903968ae2cc3cb9e22cb7c0b2050c20123311..ab7c32530a2732902407bcd87b6506ea14d35954 100644
--- a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT
+++ b/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT
@@ -5,7 +5,7 @@ NOTE: THE "oplsaa_moltemplate.py" SCRIPT HAS MOVED TO THE "../src/" DIRECTORY.
Description:
Unfortunately, moltemplate does not come with a file containing OPLSAA
-paramters which is ready to use. You must build it yourself.
+parameters which is ready to use. You must build it yourself.
This directory has tools and instructions to explain how to do this.
-----------------------------
diff --git a/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py b/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py
index 059aacaafb487a1f72fd7f7b7c02b046f2695785..5a2ce05c4a1ce26479d313e2de6d1d6068baf673 100755
--- a/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py
+++ b/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py
@@ -109,7 +109,7 @@ atom_lookup={} #this dictionary contains all the atom ffid's as a key and the nu
#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms
atom=[[-10000,-10000] for i in range(0,max_atomType+1)]
#charge_by_type={} # lookup charge by atom type
-#vdw_by_type={} # lookup epsilon & sigma paramters by atom type
+#vdw_by_type={} # lookup epsilon & sigma parameters by atom type
charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom
vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma
diff --git a/tools/moltemplate/src/nbody_by_type.py b/tools/moltemplate/src/nbody_by_type.py
index ee9884302befb8991fd21dfd3a7bdc4f60efc5b4..13fc012015d5a7678c7ff6c77ff90cc85cb1e040 100644
--- a/tools/moltemplate/src/nbody_by_type.py
+++ b/tools/moltemplate/src/nbody_by_type.py
@@ -524,7 +524,7 @@ if __name__ == "__main__":
elif argv[i][0] == '-':
raise InputError('Error('+g_program_name+'):\n'
- 'Unrecogized command line argument \"'+argv[i]+'\"\n')
+ 'Unrecognized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
diff --git a/tools/moltemplate/src/ttree.py b/tools/moltemplate/src/ttree.py
index 87c385f27bfb98ce4c6b96b4d561ab2a964334be..dda1880c1d41ba3e4abc9b6b1487a1819a2861d2 100644
--- a/tools/moltemplate/src/ttree.py
+++ b/tools/moltemplate/src/ttree.py
@@ -2489,7 +2489,7 @@ class StaticObj(object):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' new '+class_name_str+'\n'
- 'Bracketed number should be preceeded by a class name.')
+ 'Bracketed number should be preceded by a class name.')
class_names = []
weights = []
num_by_type = []
@@ -2979,7 +2979,7 @@ class StaticObj(object):
# Dots in class names can appear for 2 reasons:
# 1) as part of a path like "../" describing the location
# where this class was defined relative to the caller.
- # In that case it will be preceeded or followed by
+ # In that case it will be preceded or followed by
# either another dot '.', or a slash '/'
# 2) as part of a "suffix" which appears after the name
# containing instructions which modify how to
@@ -4434,7 +4434,7 @@ def ExtractFormattingCommands(suffix):
if suffix[-1] != ')': # Format functions are always followed by parens
return None, None
else:
- idot = suffix.find('.') # Format functions usually preceeded by '.'
+ idot = suffix.find('.') # Format functions usually preceded by '.'
ioparen = suffix.find('(')
icparen = suffix.find(')')
format_fname = suffix[idot+1:ioparen]
@@ -5113,7 +5113,7 @@ def BasicUIParseArgs(argv, settings):
elif ((argv[i][0] == '-') and (__name__ == "__main__")):
#elif (__name__ == "__main__"):
raise InputError('Error('+g_filename+'):\n'
- 'Unrecogized command line argument \"'+argv[i]+'\"\n')
+ 'Unrecognized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
@@ -5177,7 +5177,7 @@ def BasicUI(settings,
# Parsing, and compiling is a multi-pass process.
- # Step 1: Read in the StaticObj (class) defintions, without checking
+ # Step 1: Read in the StaticObj (class) definitions, without checking
# whether or not the instance_children refer to valid StaticObj types.
sys.stderr.write('parsing the class definitions...')
static_tree_root.Parse(settings.lex)
diff --git a/tools/moltemplate/src/ttree_lex.py b/tools/moltemplate/src/ttree_lex.py
index a8bb10a73c69ea6ba3b9b6bb38501ea499cb0742..d0938047c7a471b55b55ac9bfacca3aa38c626f9 100644
--- a/tools/moltemplate/src/ttree_lex.py
+++ b/tools/moltemplate/src/ttree_lex.py
@@ -1107,7 +1107,7 @@ def _DeleteLineFromTemplate(tmpl_list,
tmpl_list is an alternating list of VarRefs and TextBlocks.
To identify the line, the index corresponding to one of the
entries in the tmpl_list is used. (Usually it is a VarRef)
- The text after the preceeding newline, and the text up to the next newline
+ The text after the preceding newline, and the text up to the next newline
(starting from the beginning of the current entry, if a TextBlock)
is deleted, including any VarRef (variables) located in between.
@@ -1505,7 +1505,7 @@ class TemplateLexer(TtreeShlex):
new member function (ReadTemplate()), which can read in a block of raw text,
(halting at an (non-escaped) terminal character), and split the text into
alternating blocks of text and variables. (As far as this lexer is
- concerned, "variables" are simply tokens preceeded by $ or @ characters,
+ concerned, "variables" are simply tokens preceded by $ or @ characters,
and surrounded by optional curly-brackets {}.)
"""
@@ -1652,7 +1652,7 @@ class TemplateLexer(TtreeShlex):
(for example, '}' in "\}" does not cause terminate parsing).
In that case, the text is considered normal text. (However the
'\' character is also stripped out. It is also stripped out if it
- preceeds any characters in "other_esc_chars", which is
+ precedes any characters in "other_esc_chars", which is
the second argument. Otherwise it is left in the text block.)
"""
diff --git a/tools/msi2lmp/frc_files/cvff_aug.frc b/tools/msi2lmp/frc_files/cvff_aug.frc
index 9fcdd300688e0e1c03c81b02656a58c1a346ab60..75af9ace24d44241c171a4272c4a378be0ec556f 100644
--- a/tools/msi2lmp/frc_files/cvff_aug.frc
+++ b/tools/msi2lmp/frc_files/cvff_aug.frc
@@ -209,7 +209,7 @@
#define cvff_aug
-> This specifes the use of the ionic parameter types
+> This specifies the use of the ionic parameter types
!Ver Ref Function Label
!---- --- --------------------------------- ------
diff --git a/tools/msi2lmp/frc_files/pcff.frc b/tools/msi2lmp/frc_files/pcff.frc
index ce24f000cb7196b38563b331ad41e69316ac7404..a06b04202a4f9e641d1c8c702ae42301ea38c7f4 100644
--- a/tools/msi2lmp/frc_files/pcff.frc
+++ b/tools/msi2lmp/frc_files/pcff.frc
@@ -158,7 +158,7 @@
1.0 1 op 15.99940 O 2 sp2 aromatic in 5 membered ring
3.0 10 osh 15.99491 O 2 oxygen atom in terminal hydroxyl group on silicon
1.0 1 osi 16.00000 O 2 siloxane oxygen
- 3.0 10 oss 15.99491 O 2 oxygen atom betweem two silicons
+ 3.0 10 oss 15.99491 O 2 oxygen atom between two silicons
2.0 5 oz 15.99940 O 2 ester oxygen in carbonate
1.0 1 p 30.97380 P 4 general phosphorous atom
1.0 1 p= 30.97380 P 5 phosphazene phosphorous atom
diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h
index e07a4486dbd10e42178a305c51670b25b8d77358..377ab1a6c32586207895d6ce43852b8055a411d7 100644
--- a/tools/msi2lmp/src/msi2lmp.h
+++ b/tools/msi2lmp/src/msi2lmp.h
@@ -172,7 +172,7 @@ extern int periodic; /* 0= nonperiodic 1= 3-D periodic */
extern int TriclinicFlag; /* 0= Orthogonal 1= Triclinic */
extern int forcefield; /* BitMask: the value FF_TYPE_COMMON is set for common components of the options below,
* FF_TYPE_CLASS1 = ClassI, FF_TYPE_CLASS2 = ClassII, FF_TYPE_OPLSAA = OPLS-AA*/
-extern int ljtypeflag; /* how LJ paramters are stored: 0 = A-B, 1 = r-eps */
+extern int ljtypeflag; /* how LJ parameters are stored: 0 = A-B, 1 = r-eps */
extern int centerflag; /* 1= center box 0= keep box */
extern int hintflag; /* 1= print style hint comments 0= no hints */
extern int pflag; /* print level: 0, 1, 2, 3 */
diff --git a/tools/phonon/dynmat.cpp b/tools/phonon/dynmat.cpp
index eb91647ed203a735641ac75dd9928afa5e73c281..e82f473130eb3a63822436c2ca3ae2527e66146e 100644
--- a/tools/phonon/dynmat.cpp
+++ b/tools/phonon/dynmat.cpp
@@ -3,7 +3,7 @@
#include "version.h"
#include "global.h"
-// to intialize the class
+// to initialize the class
DynMat::DynMat(int narg, char **arg)
{
attyp = NULL;
diff --git a/tools/pymol_asphere/src/cartesian.cpp b/tools/pymol_asphere/src/cartesian.cpp
index 38550db0e728bf3517762fad0eec8517f9289972..a244d07dac40bd3ca95404446fe92d1a9d8c7afb 100644
--- a/tools/pymol_asphere/src/cartesian.cpp
+++ b/tools/pymol_asphere/src/cartesian.cpp
@@ -4,7 +4,7 @@
* Also contains quaternion structures and operations
*
* Cartesian point of doubles: cPt
- * Cartesian point of intergers: iPt
+ * Cartesian point of integers: iPt
* Vector of doubles: vectorPt
* Color of doubles: colorPt
* Quaternion: Quaternion
diff --git a/tools/pymol_asphere/src/cartesian.h b/tools/pymol_asphere/src/cartesian.h
index a486b5163ec5f845ffbf10346c21c1d7b19e16be..a5acd70b339cd307e5712696045f0addffc85e82 100644
--- a/tools/pymol_asphere/src/cartesian.h
+++ b/tools/pymol_asphere/src/cartesian.h
@@ -4,7 +4,7 @@
* Also contains quaternion structures and operations
*
* Cartesian point of doubles: cPt
- * Cartesian point of intergers: iPt
+ * Cartesian point of integers: iPt
* Vector of doubles: vectorPt
* Color of doubles: colorPt
* Quaternion: Quaternion
diff --git a/tools/python/pizza/dump.py b/tools/python/pizza/dump.py
index 3b7e7c46c77a7090602b797ce066c711d35b5b65..36a24dcd39f0f15053710da5a8957468a1d74c4b 100644
--- a/tools/python/pizza/dump.py
+++ b/tools/python/pizza/dump.py
@@ -448,7 +448,7 @@ class dump:
# --------------------------------------------------------------------
# scale coords to 0-1 for all snapshots or just one
- # use 6 params as h-matrix to treat orthongonal or triclinic boxes
+ # use 6 params as h-matrix to treat orthogonal or triclinic boxes
def scale(self,*list):
if len(list) == 0:
@@ -512,7 +512,7 @@ class dump:
# --------------------------------------------------------------------
# unscale coords from 0-1 to box size for all snapshots or just one
- # use 6 params as h-matrix to treat orthongonal or triclinic boxes
+ # use 6 params as h-matrix to treat orthogonal or triclinic boxes
def unscale(self,*list):
if len(list) == 0: