diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index fdee6325d0f65c04fa76eec1cfa58ee90012c8c9..3d73ffc63ee4c719f751d19c9607e261acbabcc8 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -9,13 +9,37 @@ lib/kokkos/* @stanmoore1
lib/molfile/* @akohlmey
lib/qmmm/* @akohlmey
lib/vtk/* @rbberger
+lib/kim/* @ellio167
-# packages
-src/KOKKOS @stanmoore1
-src/USER-CGSDK @akohlmey
-src/USER-COLVARS @giacomofiorin
-src/USER-OMP @akohlmey
-src/USER-QMMM @akohlmey
+# whole packages
+src/COMPRESS/* @akohlmey
+src/GPU/* @ndtrung81
+src/KOKKOS/* @stanmoore1
+src/KIM/* @ellio167
+src/USER-CGDNA/* @ohenrich
+src/USER-CGSDK/* @akohlmey
+src/USER-COLVARS/* @giacomofiorin
+src/USER-DPD/* @timattox
+src/USER-INTEL/* @wmbrownintel
+src/USER-MANIFOLD/* @Pakketeretet2
+src/USER-MEAMC/* @martok
+src/USER-MOFFF/* @hheenen
+src/USER-MOLFILE/* @akohlmey
+src/USER-NETCDF/* @pastewka
+src/USER-PHONON/* @lingtikong
+src/USER-OMP/* @akohlmey
+src/USER-QMMM/* @akohlmey
+src/USER-REAXC/* @hasanmetin
+src/USER-TALLY/* @akohlmey
+src/USER-UEF/* @danicholson
+src/USER-VTK/* @rbberger
+
+# individual files in packages
+src/GPU/pair_vashishta_gpu.* @andeplane
+src/KOKKOS/pair_vashishta_kokkos.* @andeplane
+src/MANYBODY/pair_vashishta_table.* @andeplane
+src/USER-MISC/fix_bond_react.* @jrgissing
+src/USER-MISC/*_grem.* @dstelter92
# tools
tools/msi2lmp/* @akohlmey
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index a4988611563ad8e681ae2ff39f3f7eeaad524ff6..71070aff450fa41a03a759746d2bc7187255d24c 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -101,7 +101,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANU
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
REAX REPLICA RIGID SHOCK SNAP SRD)
set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
- USER-ATC USER-AWPMD USER-CGDNA USER-MESO
+ USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
@@ -128,10 +128,6 @@ pkg_depends(USER-LB MPI)
pkg_depends(USER-MISC MANYBODY)
pkg_depends(USER-PHONON KSPACE)
-if(ENABLE_BODY AND ENABLE_POEMS)
- message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
-endif()
-
######################################################
# packages with special compiler needs or external libs
######################################################
diff --git a/doc/src/PDF/USER-CGDNA-overview.pdf b/doc/src/PDF/USER-CGDNA-overview.pdf
deleted file mode 100644
index e329877bc2cc5953574ea8fbd65789158a050879..0000000000000000000000000000000000000000
Binary files a/doc/src/PDF/USER-CGDNA-overview.pdf and /dev/null differ
diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/USER-CGDNA.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..843bba00d5c5a707577d07dda1929ba4c8a07987
Binary files /dev/null and b/doc/src/PDF/USER-CGDNA.pdf differ
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index ade75c588f071fc75fb85e35b9e28e304f693070..e9387fe35fb41758089081bed202e832029c25df 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
Package, Description, Doc page, Example, Library
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
@@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul
:line
+USER-BOCS package :link(USER-BOCS),h4
+
+[Contents:]
+
+This package provides "fix bocs"_fix_bocs.html, a modified version
+of "fix npt"_fix_nh.html which includes the pressure correction to
+the barostat as outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
+
+[Install or un-install:]
+
+make yes-user-bocs
+make machine :pre
+
+make no-user-bocs
+make machine :pre
+
+[Supporting info:]
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
+
+:line
+
USER-CGDNA package :link(USER-CGDNA),h4
[Contents:]
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index 2add6f4c2f0fb1f31aabaccca596cddbb41c5687..927fea64031d5422615d1251b9332e4e66120d3a 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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/.
-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.
+
+Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation.
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
+:link(Henrich2)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index b75d100112b9f3a9a5e49d1ec282f275e56a9014..3fd838d95775ae9e97f7ad8da792112b9890d80d 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -10,19 +10,29 @@ compute ackland/atom command :h3
[Syntax:]
-compute ID group-ID ackland/atom :pre
+compute ID group-ID ackland/atom keyword/value :pre
-ID, group-ID are documented in "compute"_compute.html command
-ackland/atom = style name of this compute command :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+ackland/atom = style name of this compute command :l
+
+zero or more keyword/value pairs may be appended :l
+keyword = {legacy} :l
+ {legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre
+:ule
[Examples:]
-compute 1 all ackland/atom :pre
+compute 1 all ackland/atom
+compute 1 all ackland/atom legacy yes :pre
[Description:]
Defines a computation that calculates the local lattice structure
according to the formulation given in "(Ackland)"_#Ackland.
+Historically, LAMMPS had two, slightly different implementations of
+the algorithm from the paper. With the {legacy} keyword, it is
+possible to switch between the pre-2015 ({legacy yes}) and post-2015
+implemention ({legacy no}). The post-2015 variant is the default.
In contrast to the "centro-symmetry
parameter"_compute_centro_atom.html this method is stable against
@@ -66,7 +76,8 @@ integers defined above.
"compute centro/atom"_compute_centro_atom.html
-[Default:] none
+[Default:]
+The keyword {legacy} defaults to {no}.
:line
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f53b7c785c251240a0d325b820545f342ce21c06
--- /dev/null
+++ b/doc/src/fix_bocs.txt
@@ -0,0 +1,112 @@
+<"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
+
+fix bocs command :h3
+
+[Syntax:]
+
+fix ID group-ID bocs keyword values ... :pre
+
+keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
+ {temp} values = Tstart Tstop Tdamp
+ {cgiso} values = Pstart Pstop Pdamp
+ {basis set}
+ {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
+ {linear_spline} values = input_filename
+ {cubic_spline} values = input_filename :pre
+:ule
+
+[Examples:]
+
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
+
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
+
+thermo_modify press 1_press :pre
+
+
+[Description:]
+
+These commands incorporate a pressure correction as described by
+Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
+barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
+The first half of the command mimics a standard fix npt command:
+
+fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
+
+The two differences are replacing {npt} with {bocs}, and replacing
+{iso}/{aniso}/{etc} with {cgiso}.
+The rest of the command details what form you would like to use for
+the pressure correction equation. The choices are: {analytic}, {linear_spline},
+or {cubic_spline}.
+
+With either spline method, the only argument that needs to follow it
+is the name of a file that contains the desired pressure correction
+as a function of volume. The file should be formatted so each line has:
+
+Volume_i, PressureCorrection_i :pre
+
+Note both the COMMA and the SPACE separating the volume's
+value and its corresponding pressure correction. The volumes in the file
+should be uniformly spaced. Both the volumes and the pressure corrections
+should be provided in the proper units, e.g. if you are using {units real},
+the volumes should all be in cubic angstroms, and the pressure corrections
+should all be in atomspheres. Furthermore, the table should start/end at a
+volume considerably smaller/larger than you expect your system to sample
+during the simulation. If the system ever reaches a volume outside of the
+range provided, the simulation will stop.
+
+With the {analytic} option, the arguments are as follows:
+
+... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
+
+Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
+are using {units real}, {V_avg} should be in cubic angstroms, and the
+coefficients should all be in atmospheres * cubic angstroms.
+
+[Restrictions:]
+
+As this is computing a (modified) pressure, group-ID should be {all}.
+
+The pressure correction has only been tested for use with an isotropic
+pressure coupling in 3 dimensions.
+
+By default, LAMMPS will still report the normal value for the pressure
+if the pressure is printed via a {thermo} command, or if the pressures
+are written to a file every so often. In order to have LAMMPS report the
+modified pressure, you must include the {thermo_modify} command given in
+the examples. For the last argument in the command, you should put
+XXXX_press, where XXXX is the ID given to the fix bocs command (in the
+example, the ID of the fix bocs command is 1 ).
+
+This fix is part of the USER-BOCS 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:]
+
+For more details about the pressure correction and the entire BOCS software
+package, visit the "BOCS package on github"_bocsgithub and read the release
+paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
+
+
+:link(bocsgithub,https://github.com/noid-group/BOCS)
+
+:line
+
+:link(bocs-Dunn1)
+[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
+
+:link(bocs-Martyna)
+[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
+
+:link(bocs-Dunn2)
+[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
+
+
+
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index b5f9a730842b73805d146d4dc07b2ee0b2c00062..4a7c2428c16aa050a24f71d685960d9d952b65a4 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -11,9 +11,9 @@ fix bond/react command :h3
[Syntax:]
fix ID group-ID bond/react common_keyword values ...
- react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
- react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
- react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
... :pre
ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
@@ -24,12 +24,13 @@ common_keyword = {stabilization}
{stabilization} values = group-ID xmax
group-ID = user-assigned ID of an internally-created dynamic group that excludes reacting atoms, and can be used by a subsequent time integration fix such as nvt, npt, or nve (cannot be 'all')
{xmax} value = distance
- distance = xmax value that is used by an internally created "nve/limit"_nve_limit.html integrator
+ distance = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator
react = mandatory argument indicating new reaction specification
react-ID = user-assigned name for the reaction
react-group-ID = only atoms in this group are available for the reaction
Nevery = attempt reaction every this many steps :l
- Rmin = bonding pair atoms separated by less than Rmin can initiate reaction (distance units) :l
+ Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
+ Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
@@ -46,15 +47,15 @@ react = mandatory argument indicating new reaction specification
molecule mol1 pre_reacted_topology.txt
molecule mol2 post_reacted_topology.txt
-fix 5 all bond/react stabilization no react myrxn1 all 1 3.25 mol1 mol2 map_file.txt
+fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt
molecule mol1 pre_reacted_rxn1.txt
molecule mol2 post_reacted_rxn1.txt
molecule mol3 pre_reacted_rxn2.txt
molecule mol4 post_reacted_rxn2.txt
fix 5 all bond/react stabilization yes nvt_grp .03 &
- react myrxn1 all 1 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
- react myrxn2 all 1 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
+ react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
+ react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
fix 6 nvt_grp nvt temp 300 300 100 # system-wide thermostat must be defined after bond/react :pre
[Description:]
@@ -101,9 +102,14 @@ The group-ID set using the {stabilization} keyword should be a
previously unused group-ID. The fix bond/react command creates a
"dynamic group"_group.html of this name that excludes reacting atoms.
This dynamic group-ID should then be used by a subsequent system-wide
-time integrator, as shown in the second example above. It is necessary
-to place the time integration command after the fix bond/react command
-due to the internal dynamic grouping performed by fix bond/react.
+time integrator, as shown in the second example above. It is currently
+necessary to place the time integration command after the fix
+bond/react command due to the internal dynamic grouping performed by
+fix bond/react.
+
+NOTE: The internally created group currently applies to all atoms in
+the system, i.e. you should generally not have a separate thermostat
+which acts on the 'all' group.
The following comments pertain to each 'react' argument:
@@ -118,21 +124,20 @@ modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
First, a pair of atoms within the specified react-group-ID of type
-typei and typej must be within a distance Rmin of each other. The atom
-types typei and typej are specified in the pre- and post-reaction
-templates. The distance calculation uses the pair neighbor list,
-therefore bonded neighbor exclusions may prevent a reaction between
-1st, 2nd or 3rd bonded neighbor atoms. If multiple bonding atom pairs
-are identified for an atom, the closest bonding atom partner is set as
-its "nearest" bonding partner. Then, if both an atomi and atomj have
-each other as their nearest bonding partners, these two atoms are
-identified as the bonding atom pair of the reaction site. Once this
-unique bonding atom pair is identified for each reaction, there could
-two or more reactions that involve a given atom on the same timestep.
-If this is the case, only one such reaction is permitted to occur.
-This reaction is chosen randomly from all potential reactions. This
-capability allows e.g. for different reaction pathways to proceed from
-identical reaction sites with user-specified probabilities.
+typei and typej must separated by a distance between Rmin and Rmax. It
+is possible that multiple bonding atom pairs are identified: if the
+bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4
+neighbors, the closest bonding atom partner is set as its bonding
+partner; otherwise, the farthest potential partner is chosen. Then, if
+both an atomi and atomj have each other as their nearest bonding
+partners, these two atoms are identified as the bonding atom pair of
+the reaction site. Once this unique bonding atom pair is identified
+for each reaction, there could two or more reactions that involve a
+given atom on the same timestep. If this is the case, only one such
+reaction is permitted to occur. This reaction is chosen randomly from
+all potential reactions. This capability allows e.g. for different
+reaction pathways to proceed from identical reaction sites with
+user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its
@@ -262,9 +267,11 @@ angles, dihedrals or impropers are supported.
A few capabilities to note: 1) You may specify as many 'react'
arguments as desired. For example, you could break down a complicated
reaction mechanism into several reaction steps, each defined by its
-own 'react' argument. 2) While typically a bond is formed between the
-bonding atom pairs specified in the pre-reacted molecule template,
-this is not required.
+own 'react' argument. 2) While typically a bond is formed or removed
+between the bonding atom pairs specified in the pre-reacted molecule
+template, this is not required. 3) By reversing the order of the pre-
+and post- reacted molecule templates in another 'react' argument, you
+can allow for the possibility of one or more reverse reactions.
The optional keywords deal with the probability of a given reaction
occurring as well as the stable equilibration of each reaction site as
@@ -300,14 +307,14 @@ reaction:
fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1
NOTE: This command must be added after the fix bond/react command, and
-will apply to all reaction steps.
+will apply to all reactions.
Computationally, each timestep this fix operates, it loops over
-neighbor lists and computes distances between pairs of atoms in the
-list. It also communicates between neighboring processors to
-coordinate which bonds are created. All of these operations increase
-the cost of a timestep. Thus you should be cautious about invoking
-this fix too frequently.
+neighbor lists (for bond-forming reactions) and computes distances
+between pairs of atoms in the list. It also communicates between
+neighboring processors to coordinate which bonds are created and/or
+removed. All of these operations increase the cost of a timestep. Thus
+you should be cautious about invoking this fix too frequently.
You can dump out snapshots of the current bond topology via the dump
local command.
diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt
index afc9c5f257523646906966d89464da26a070023e..c85ff24c96d2982439d67c4ac52fd3bea5083044 100644
--- a/doc/src/fix_langevin_drude.txt
+++ b/doc/src/fix_langevin_drude.txt
@@ -154,7 +154,7 @@ Note: The temperature thermostating the core-Drude particle pairs
should be chosen low enough, so as to mimic as closely as possible the
self-consistent minimization. It must however be high enough, so that
the dipoles can follow the local electric field exerted by the
-neighbouring atoms. The optimal value probably depends on the
+neighboring atoms. The optimal value probably depends on the
temperature of the centers of mass and on the mass of the Drude
particles.
diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt
index 1c7dcf77a5dd0c72db2dea22873e0728417e8048..308bba1ac31fdf9a7cbd45ec1da50122cd46bcb9 100644
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@@ -14,14 +14,16 @@ fix_modify fix-ID keyword value ... :pre
fix-ID = ID of the fix to modify :ulb,l
one or more keyword/value pairs may be appended :l
-keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l
+keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :l
{temp} value = compute ID that calculates a temperature
{press} value = compute ID that calculates a pressure
{energy} value = {yes} or {no}
{virial} value = {yes} or {no}
{respa} value = {1} to {max respa level} or {0} (for outermost level)
{dynamic/dof} value = {yes} or {no}
- yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
+ yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+ {bodyforces} value = {early} or {late}
+ early/late = compute rigid-body forces/torques early or late in the timestep :pre
:ule
[Examples:]
@@ -84,9 +86,8 @@ if you want virial contribution of the fix to be part of the
relaxation criteria, although this seems unlikely.
NOTE: This option is only supported by fixes that explicitly say
-so. For some of these (e.g. the
-"fix shake"_fix_shake.html command) the default setting is
-{virial yes}, for others it is {virial no}.
+so. For some of these (e.g. the "fix shake"_fix_shake.html command)
+the default setting is {virial yes}, for others it is {virial no}.
For fixes that set or modify forces, it may be possible to select at
which "r-RESPA"_run_style.html level the fix operates via the {respa}
@@ -120,6 +121,28 @@ compute to calculate temperature. See the "compute_modify
dynamic/dof"_compute_modify.html command for a similar way to insure
correct temperature normalization for those thermostats.
+The {bodyforces} keyword determines whether the forces and torques
+acting on rigid bodies are computed {early} at the post-force stage of
+each timestep (right after per-atom forces have been computed and
+communicated among processors), or {late} at the final-integrate stage
+of each timestep (after any other fixes have finished their post-force
+tasks). Only the rigid-body integration fixes use this option, which
+includes "fix rigid"_fix_rigid.html and "fix
+rigid/small"_fix_rigid.html, and their variants, and also "fix
+poems"_fix_poems.html.
+
+The default is {late}. If there are other fixes that add forces to
+individual atoms, then the rigid-body constraints will include these
+forces when time-integrating the rigid bodies. If {early} is
+specified, then new fixes can be written that use or modify the
+per-body force and torque, before time-integration of the rigid bodies
+occurs. Note however this has the side effect, that fixes such as
+"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,
+"fix spring"_fix_spring.html, which add forces to individual atoms
+will have no effect on the motion of the rigid bodies if they are
+specified in the input script after the fix rigid command. LAMMPS
+will give a warning if that is the case.
+
[Restrictions:] none
[Related commands:]
@@ -130,4 +153,5 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
[Default:]
The option defaults are temp = ID defined by fix, press = ID defined
-by fix, energy = no, virial = different for each fix style, respa = 0.
+by fix, energy = no, virial = different for each fix style, respa = 0,
+bodyforce = late.
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index d90d832cb8e2deed341771ea00e9f0b294e55c8b..03abc058b8b0d6e982f6291e1fecbb887cf2ad9a 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -106,12 +106,18 @@ off, and there is only a single fix poems defined.
[Restart, fix_modify, output, run start/stop, minimize info:]
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. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. 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 minimization"_minimize.html.
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {bodyforces} option is supported by
+this fix style to set whether per-body forces and torques are computed
+early or late in a timestep, i.e. at the post-force stage or at the
+final-integrate stage, respectively.
+
+No global or per-atom quantities are stored by this fix for access by
+various "output commands"_Section_howto.html#howto_15. 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
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt
index c8ec20daaa4ae3953b2660a2770607b15610533e..1a7c7b6ba5df11d6c9331de0963e2bc562131e42 100644
--- a/doc/src/fix_restrain.txt
+++ b/doc/src/fix_restrain.txt
@@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
theta0 = equilibrium angle theta (degrees)
- {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
+ {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
- phi0 = equilibrium dihedral angle phi (degrees) :pre
+ phi0 = equilibrium dihedral angle phi (degrees)
+ keyword/value = optional keyword value pairs. supported keyword/value pairs:
+ {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre
:ule
[Examples:]
@@ -155,11 +157,13 @@ associated with the restraint is
with the following coefficients:
K (energy)
-n = 1
+n (multiplicity, >= 0)
d (degrees) = phi0 + 180 :ul
-K and phi0 are specified with the fix. Note that the value of n is
-hard-wired to 1. Also note that the energy will be a minimum when the
+K and phi0 are specified with the fix. Note that the value of the
+dihedral multiplicity {n} is set by default to 1. You can use the
+optional {mult} keyword to set it to a different positive integer.
+Also note that the energy will be a minimum when the
current dihedral angle phi is equal to phi0.
:line
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index eced602c4b3540bf95ef8fe17278e7baf697e4c0..ec7ed4f2b1e16374b0dd318a75cf31b3618711ce 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -223,10 +223,10 @@ via several options.
NOTE: With the {rigid/small} styles, which require that {bodystyle} be
specified as {molecule} or {custom}, you can define a system that has
-no rigid bodies initially. This is useful when you are using the {mol}
-keyword in conjunction with another fix that is adding rigid bodies
-on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
-"fix pour"_fix_pour.html.
+no rigid bodies initially. This is useful when you are using the
+{mol} keyword in conjunction with another fix that is adding rigid
+bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html
+or "fix pour"_fix_pour.html.
For bodystyle {single} the entire fix group of atoms is treated as one
rigid body. This option is only allowed for the {rigid} styles.
@@ -742,6 +742,11 @@ used to calculate the instantaneous pressure tensor. Note that the 2
NVT rigid fixes do not use any external compute to compute
instantaneous temperature.
+The "fix_modify"_fix_modify.html {bodyforces} option is supported by
+all rigid styles to set whether per-body forces and torques are
+computed early or late in a timestep, i.e. at the post-force stage or
+at the final-integrate stage or the timestep, respectively.
+
The 2 NVE rigid fixes compute a global scalar which can be accessed by
various "output commands"_Section_howto.html#howto_15. The scalar
value calculated by these fixes is "intensive". The scalar is the
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index fca442cc13836eb33ad422ec2e0a7cfe3b88a948..79c2f75b8ba46f2924c2e34ed98c81edd6fe71b8 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -20,6 +20,7 @@ Fixes :h1
fix_ave_time
fix_aveforce
fix_balance
+ fix_bocs
fix_bond_break
fix_bond_create
fix_bond_swap
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 73f8d005be530d4039912f8d6c4d171471bb5b92..1f4bf157f4829df2446970b8c9550f7098b765f8 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -135,6 +135,7 @@ fix_ave_histo.html
fix_ave_time.html
fix_aveforce.html
fix_balance.html
+fix_bocs.html
fix_bond_break.html
fix_bond_create.html
fix_bond_react.html
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index c7e005a591c04b712f0bb2ed3a640b1ea8e3e5e1..97f132eacd41e00cd4318cfde24b09e29b4a6ae1 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -38,7 +38,7 @@ 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.
+be computed between atom types of neighboring 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},
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index 26a205bcf9b449ee20eea88ce5aff6a3feca024b..f272d15a8680d6499df5f7164186789426589413 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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/.
-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.
+
+Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
+:link(Henrich1)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
:link(Sulc1)
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index 2408c02d101135639561652db8f5e74dae7e037f..1b55031b2c97dc8c935c0ddb83a567f24d64ab6f 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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/.
-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.
+
+Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
+:link(Henrich)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
:link(Sulc2)
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
diff --git a/examples/USER/bocs/README b/examples/USER/bocs/README
new file mode 100644
index 0000000000000000000000000000000000000000..ae1739f8c0378256a7232290ecdd6a3a238bc7e9
--- /dev/null
+++ b/examples/USER/bocs/README
@@ -0,0 +1,6 @@
+This folder contains the files to run a NPT simulation of 1 site CG methanol
+while employing a correction to the barostat.
+The pair force was computed via the Multi-Scale Coarse-Graining method.
+The resulting model was then iteratively pressure matched.
+The model accurately reproduces both structural (RDF) and thermodynamic
+(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol.
diff --git a/examples/USER/bocs/in.methanol b/examples/USER/bocs/in.methanol
new file mode 100644
index 0000000000000000000000000000000000000000..e7c80e014d04de182615de67dd142c54034beccf
--- /dev/null
+++ b/examples/USER/bocs/in.methanol
@@ -0,0 +1,69 @@
+units real
+dimension 3
+boundary p p p
+atom_style atomic
+
+newton on
+timestep 1.0
+
+read_data methanol.data
+
+velocity all create 300.0 16802 dist gaussian
+
+pair_style table spline 15000
+
+pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+
+neigh_modify delay 0 every 1 check yes one 10000
+neighbor 12.0 bin
+
+thermo 500
+thermo_style custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+##### SPECIAL COMMANDS FOR FIX_BOCS #####
+# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
+
+# Report the modified pressure
+thermo_modify press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump 1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style verlet
+run 10000
+
diff --git a/examples/USER/bocs/lammps_nb_MET-MET.table b/examples/USER/bocs/lammps_nb_MET-MET.table
new file mode 100644
index 0000000000000000000000000000000000000000..c6d9fc6ca251cd012c78f50b1e86bc03c72cc6be
--- /dev/null
+++ b/examples/USER/bocs/lammps_nb_MET-MET.table
@@ -0,0 +1,2505 @@
+#Converted from table.xvg
+
+nb_METMET
+N 2500
+
+1 0.010000 573.151769 380.122371
+2 0.020000 569.356836 378.855163
+3 0.030000 565.574570 377.588193
+4 0.040000 561.805210 376.320985
+5 0.050000 558.048279 375.053776
+6 0.060000 554.304015 373.786807
+7 0.070000 550.572419 372.519598
+8 0.080000 546.853728 371.252390
+9 0.090000 543.147467 369.985421
+10 0.100000 539.453872 368.718212
+11 0.110000 535.773184 367.451004
+12 0.120000 532.104924 366.184034
+13 0.130000 528.449331 364.916826
+14 0.140000 524.806644 363.649618
+15 0.150000 521.176386 362.382648
+16 0.160000 517.559034 361.115440
+17 0.170000 513.954111 359.848231
+18 0.180000 510.361855 358.581262
+19 0.190000 506.782505 357.314054
+20 0.200000 503.215583 356.046845
+21 0.210000 499.661568 354.779876
+22 0.220000 496.119981 353.512667
+23 0.230000 492.591300 352.245459
+24 0.240000 489.075287 350.978489
+25 0.250000 485.571702 349.711281
+26 0.260000 482.081023 348.444073
+27 0.270000 478.602772 347.177103
+28 0.280000 475.137428 345.909895
+29 0.290000 471.684751 344.642686
+30 0.300000 468.244503 343.375717
+31 0.310000 464.817161 342.108509
+32 0.320000 461.402486 340.841300
+33 0.330000 458.000239 339.574331
+34 0.340000 454.610899 338.307122
+35 0.350000 451.234226 337.039914
+36 0.360000 447.870220 335.772945
+37 0.370000 444.518642 334.505736
+38 0.380000 441.179971 333.238528
+39 0.390000 437.853967 331.971558
+40 0.400000 434.540631 330.704350
+41 0.410000 431.239962 329.437141
+42 0.420000 427.951721 328.170172
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+44 0.440000 421.413719 325.635755
+45 0.450000 418.163719 324.368786
+46 0.460000 414.926386 323.101577
+47 0.470000 411.701721 321.834369
+48 0.480000 408.489723 320.567400
+49 0.490000 405.290392 319.300191
+50 0.500000 402.103728 318.032983
+51 0.510000 398.929732 316.766013
+52 0.520000 395.768403 315.498805
+53 0.530000 392.619742 314.231597
+54 0.540000 389.483748 312.964627
+55 0.550000 386.360421 311.697419
+56 0.560000 383.249761 310.430210
+57 0.570000 380.151769 309.163241
+58 0.580000 377.066444 307.896033
+59 0.590000 373.993786 306.628824
+60 0.600000 370.934034 305.361855
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+68 0.680000 346.910373 295.224904
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+70 0.700000 341.031310 292.690488
+71 0.710000 338.110660 291.423518
+72 0.720000 335.202916 290.156310
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+80 0.800000 312.395793 280.019359
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+100 1.000000 258.926147 254.676625
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+108 1.080000 238.957600 244.539675
+109 1.090000 236.518523 243.272467
+110 1.100000 234.092137 242.005497
+111 1.110000 231.678418 240.738289
+112 1.120000 229.277366 239.471080
+113 1.130000 226.889006 238.204039
+114 1.140000 224.513289 236.936926
+115 1.150000 222.150263 235.669790
+116 1.160000 219.799904 234.402653
+117 1.170000 217.462213 233.135540
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+119 1.190000 212.824833 230.601267
+120 1.200000 210.525167 229.334154
+121 1.210000 208.238145 228.067017
+122 1.220000 205.963815 226.799904
+123 1.230000 203.702151 225.532768
+124 1.240000 201.453155 224.265631
+125 1.250000 199.216850 222.998518
+126 1.260000 196.993188 221.731381
+127 1.270000 194.782218 220.464269
+128 1.280000 192.583915 219.197132
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+131 1.310000 186.065010 215.395746
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+134 1.340000 179.660158 211.594359
+135 1.350000 177.550550 210.327247
+136 1.360000 175.453609 209.060110
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+138 1.380000 171.297753 206.525860
+139 1.390000 169.238838 205.258724
+140 1.400000 167.192591 203.991587
+141 1.410000 165.159011 202.724474
+142 1.420000 163.138098 201.457337
+143 1.430000 161.129852 200.190225
+144 1.440000 159.134297 198.923088
+145 1.450000 157.151386 197.655951
+146 1.460000 155.181166 196.388838
+147 1.470000 153.223614 195.121702
+148 1.480000 151.278728 193.854565
+149 1.490000 149.346534 192.587452
+150 1.500000 147.426984 191.320315
+151 1.510000 145.520124 190.053203
+152 1.520000 143.625932 188.786066
+153 1.530000 141.744407 187.518929
+154 1.540000 139.875550 186.251816
+155 1.550000 138.019359 184.984680
+156 1.560000 136.175860 183.717567
+157 1.570000 134.345005 182.450430
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diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.1 b/examples/USER/bocs/log.20Apr18.methanol.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..a94bd959c816c3cb1faa1b03ee9dc176b5301950
--- /dev/null
+++ b/examples/USER/bocs/log.20Apr18.methanol.g++.1
@@ -0,0 +1,143 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+units real
+dimension 3
+boundary p p p
+atom_style atomic
+
+newton on
+timestep 1.0
+
+read_data methanol.data
+ orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 968 atoms
+
+velocity all create 300.0 16802 dist gaussian
+
+pair_style table spline 15000
+
+pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
+ Should only be flagged at inflection points (../pair_table.cpp:481)
+
+neigh_modify delay 0 every 1 check yes one 10000
+neighbor 12.0 bin
+
+thermo 500
+thermo_style custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+##### SPECIAL COMMANDS FOR FIX_BOCS #####
+# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
+
+# Report the modified pressure
+thermo_modify press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump 1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style verlet
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 10000, page size: 100000
+ master list distance cutoff = 24
+ ghost atom cutoff = 24
+ binsize = 12, bins = 4 4 4
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair table, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
+Step Temp PotEng TotEng Press Volume
+ 0 300 1061.5961 1926.3291 107.006 66250.679
+ 500 314.54728 1034.1091 1940.7738 194.42689 65660.282
+ 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
+ 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
+ 2000 294.78476 1046.8207 1896.521 50.592942 66316.735
+ 2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
+ 3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
+ 3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
+ 4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
+ 4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
+ 5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
+ 5500 292.23444 1029.5558 1871.905 20.764579 66683.876
+ 6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
+ 6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
+ 7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
+ 7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
+ 8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
+ 8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
+ 9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
+ 9500 297.46127 1034.5547 1891.97 54.23428 66892.627
+ 10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
+Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
+
+Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
+Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
+Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
+Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
+Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
+Other | | 0.1252 | | | 0.36
+
+Nlocal: 968 ave 968 max 968 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 9112 ave 9112 max 9112 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 404392 ave 404392 max 404392 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 404392
+Ave neighs/atom = 417.76
+Neighbor list builds = 13
+Dangerous builds = 0
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:34
diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.4 b/examples/USER/bocs/log.20Apr18.methanol.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..cf5891f97cbf6fee1cc998fb40fb4e8e7cb04a24
--- /dev/null
+++ b/examples/USER/bocs/log.20Apr18.methanol.g++.4
@@ -0,0 +1,143 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+units real
+dimension 3
+boundary p p p
+atom_style atomic
+
+newton on
+timestep 1.0
+
+read_data methanol.data
+ orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 968 atoms
+
+velocity all create 300.0 16802 dist gaussian
+
+pair_style table spline 15000
+
+pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
+ Should only be flagged at inflection points (../pair_table.cpp:481)
+
+neigh_modify delay 0 every 1 check yes one 10000
+neighbor 12.0 bin
+
+thermo 500
+thermo_style custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+##### SPECIAL COMMANDS FOR FIX_BOCS #####
+# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
+
+# Report the modified pressure
+thermo_modify press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump 1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style verlet
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 10000, page size: 100000
+ master list distance cutoff = 24
+ ghost atom cutoff = 24
+ binsize = 12, bins = 4 4 4
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair table, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
+Step Temp PotEng TotEng Press Volume
+ 0 300 1061.5961 1926.3291 107.006 66250.679
+ 500 314.54728 1034.1091 1940.7738 194.42689 65660.282
+ 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
+ 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
+ 2000 294.78476 1046.8207 1896.521 50.592942 66316.735
+ 2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
+ 3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
+ 3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
+ 4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
+ 4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
+ 5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
+ 5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
+ 6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
+ 6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
+ 7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
+ 7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
+ 8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
+ 8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
+ 9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
+ 9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
+ 10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
+Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
+
+Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
+95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
+Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
+Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
+Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
+Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
+Other | | 0.3112 | | | 1.08
+
+Nlocal: 242 ave 244 max 239 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost: 5718.5 ave 5736 max 5702 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 100703 ave 108064 max 93454 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 402813
+Ave neighs/atom = 416.129
+Neighbor list builds = 14
+Dangerous builds = 0
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:28
diff --git a/examples/USER/bocs/methanol.data b/examples/USER/bocs/methanol.data
new file mode 100644
index 0000000000000000000000000000000000000000..01f66de6f62294929f87497522ae541b567596a0
--- /dev/null
+++ b/examples/USER/bocs/methanol.data
@@ -0,0 +1,991 @@
+LAMMPS Description
+
+ 968 atoms
+ 0 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+
+ 1 atom types
+ 0 bond types
+ 0 angle types
+ 0 dihedral types
+
+ 0 40.4635 xlo xhi
+ 0 40.4635 ylo yhi
+ 0 40.4635 zlo zhi
+
+Masses
+
+ 1 32.0424
+
+Atoms
+
+1 1 36.39 8.05 27.55
+2 1 18.38 15.72 26.03
+3 1 3.52 1.77 23.57
+4 1 31.09 11.38 12.17
+5 1 13.3 34.8 2.89
+6 1 1.72 38.55 10.36
+7 1 38.6 23.16 6.19
+8 1 0.74 33.21 0.17
+9 1 26.97 9.53 11.24
+10 1 31.68 12.19 17.04
+11 1 15.19 9.06 0.2
+12 1 34.39 20.63 35.71
+13 1 21.79 4.93 6.49
+14 1 28.08 33.01 24.51
+15 1 37.03 20.52 32.9
+16 1 32.69 20 30.11
+17 1 23.77 38.59 18.79
+18 1 16.01 2.31 20.15
+19 1 5.65 15.5 28.5
+20 1 8.35 17.35 20.48
+21 1 31.24 24.68 27.4
+22 1 29.41 16.64 19.79
+23 1 37.42 31.93 26.68
+24 1 18.76 39.06 30.68
+25 1 22.97 35 20.81
+26 1 39.47 18.28 29.6
+27 1 34.37 19.4 0.17
+28 1 5.94 9.53 10.95
+29 1 11.45 38.44 14.64
+30 1 39.57 11.04 1.57
+31 1 25.91 20.97 12.79
+32 1 36.3 22.1 1.68
+33 1 21.87 22.49 3.43
+34 1 5.77 18.66 3.97
+35 1 7 7.59 18.42
+36 1 39.76 27.63 17.98
+37 1 10.26 23.18 5.11
+38 1 23.23 21.37 17.38
+39 1 7.47 37.37 5.57
+40 1 0.73 21.6 14.78
+41 1 2.27 30.22 14.93
+42 1 7.39 28.22 14.88
+43 1 27.48 1.11 25.02
+44 1 8.37 13.19 14.64
+45 1 7.11 33.57 0.65
+46 1 34.19 35.11 3.17
+47 1 7.52 3.2 20.33
+48 1 1.02 17.69 37.85
+49 1 8.59 6.21 10.26
+50 1 2.89 16.81 30.02
+51 1 27.05 9.07 32.8
+52 1 12.32 14.79 21.11
+53 1 26.63 22.69 16.75
+54 1 31.6 2.79 20.45
+55 1 35.11 0.74 12.16
+56 1 29.71 31.23 37.63
+57 1 38.22 19.02 18.12
+58 1 10.95 17.4 0.39
+59 1 1.65 19.87 6.67
+60 1 5.15 1.94 14.61
+61 1 8.2 31.43 15.72
+62 1 0.55 20.85 2.45
+63 1 15.27 31.74 0.33
+64 1 17.9 9.84 23.87
+65 1 1.46 8.39 19.24
+66 1 37.79 25.11 12.24
+67 1 14.11 27.19 30.7
+68 1 29.39 24.12 38.92
+69 1 39.15 20.32 39.86
+70 1 11.79 11.38 30.6
+71 1 29.87 30.18 32.5
+72 1 11.06 37.8 30.18
+73 1 20.11 4.59 35.57
+74 1 37.19 27.23 1.44
+75 1 18.83 26.13 35.26
+76 1 29.27 7.86 36.75
+77 1 34.83 29.59 37.82
+78 1 22.16 34.68 25.27
+79 1 5.95 14.65 25.55
+80 1 -0.04 3.48 29.91
+81 1 14.69 6.75 38.06
+82 1 16.8 23.69 3.14
+83 1 14.52 38.72 21.61
+84 1 37.36 15.13 27.98
+85 1 29.79 17.03 27.55
+86 1 21.01 0.39 0.9
+87 1 35.3 6.45 14.41
+88 1 13.74 34.69 10.01
+89 1 13.83 7.92 31.88
+90 1 26.88 37.81 22.36
+91 1 31.76 7.34 10.03
+92 1 11.98 37.49 19.61
+93 1 29.19 31.74 20.69
+94 1 39.15 10.97 21.06
+95 1 1.47 5 22.21
+96 1 -0.1 1.33 16.26
+97 1 34.74 34.78 30.66
+98 1 22.09 26.78 2.27
+99 1 36.58 34.8 16.19
+100 1 19.09 24.88 15.75
+101 1 2.21 31.42 38.32
+102 1 28.02 8.18 29.77
+103 1 15.99 16.78 17.61
+104 1 32.43 12.2 35.3
+105 1 26.54 38.8 30.88
+106 1 35.58 22.23 18.31
+107 1 28.3 30.81 2.96
+108 1 8.95 32.9 9.02
+109 1 28.51 30.02 29.39
+110 1 13 5.35 34.26
+111 1 37.9 36.79 1.37
+112 1 12.78 1.99 40.66
+113 1 21.19 34.55 17.45
+114 1 10.5 20 5.07
+115 1 16.19 21.64 18.49
+116 1 14.62 26.41 19.88
+117 1 27.97 2.89 28.03
+118 1 29.44 14.35 39.04
+119 1 2.29 24.16 33.8
+120 1 39.22 15.81 32.02
+121 1 7.31 19.66 18.18
+122 1 27.67 7.98 15.53
+123 1 31.23 4.04 33
+124 1 29.52 39.44 28.71
+125 1 30.86 20.28 15.84
+126 1 32.25 7.44 19.79
+127 1 34.68 15.68 1.18
+128 1 16.58 27.98 27.97
+129 1 32.27 24.24 15.82
+130 1 3.86 6.57 39.8
+131 1 9.1 2.88 13.12
+132 1 17.84 27.8 11.79
+133 1 4.77 10.88 6.75
+134 1 16.58 24.21 24.5
+135 1 10.17 19.31 38.32
+136 1 6.27 7.81 36.44
+137 1 34.76 37.89 29.76
+138 1 40.99 38.22 35.21
+139 1 25.04 21.79 36.88
+140 1 4.78 15.35 16.44
+141 1 19.24 5.77 40.18
+142 1 13.59 11.27 37.14
+143 1 1.61 23.83 39.61
+144 1 6.02 33.07 3.77
+145 1 0.85 7.4 35.42
+146 1 6.47 40.34 4.65
+147 1 16.45 36.52 15.44
+148 1 19.58 9.5 1.64
+149 1 1.36 1.72 35.53
+150 1 11.74 5.48 4.98
+151 1 25.45 40.36 15.44
+152 1 19.09 0.74 36.18
+153 1 31.78 37.98 1.84
+154 1 23.26 18.47 38.56
+155 1 7.29 22.87 25.86
+156 1 2.36 7.83 8.78
+157 1 39.61 25.94 21.12
+158 1 7.78 18.97 25.29
+159 1 36.56 19.61 26.7
+160 1 4.64 12.06 19.9
+161 1 21.05 33.08 0.87
+162 1 33.93 22.87 39.71
+163 1 33.62 29.48 20.83
+164 1 0.64 18.79 9.52
+165 1 27.53 16.7 22.51
+166 1 17.66 9.84 14.61
+167 1 31.23 22.44 24.98
+168 1 39.3 34.88 11.03
+169 1 24.01 10.56 0.09
+170 1 15.81 33.44 18.52
+171 1 19.92 30.61 19.25
+172 1 16.49 3.95 38.28
+173 1 18.6 38.87 24.98
+174 1 33.04 25.55 8.57
+175 1 16.9 35.09 22.94
+176 1 15.18 6.74 2.33
+177 1 40.54 12.58 31.65
+178 1 21.21 37.62 14.35
+179 1 33.52 38.19 14.89
+180 1 22.06 12.49 29.81
+181 1 19.49 29.03 2.52
+182 1 26.97 18.55 38.45
+183 1 24.1 11.86 17.22
+184 1 12.02 0.55 10.39
+185 1 3.8 35.94 19.94
+186 1 8.31 14.31 37.4
+187 1 29.03 8.28 22.92
+188 1 18.92 0.22 27.87
+189 1 26.79 24.9 24.62
+190 1 36.59 18.86 21.13
+191 1 33.06 13.58 30.17
+192 1 32.37 2.02 39.69
+193 1 22.65 25.97 32.59
+194 1 21.81 38.04 33.85
+195 1 36.82 37.68 19.22
+196 1 32.48 31.43 33.66
+197 1 8.75 36.66 20.34
+198 1 14.88 15.11 28.76
+199 1 22.83 28.55 29.5
+200 1 2.98 12.06 2.88
+201 1 3.01 37 6.91
+202 1 14.79 16.69 3.66
+203 1 12.62 38.28 0.97
+204 1 40.07 21.27 25.25
+205 1 34.58 6.14 39.48
+206 1 11.51 30.52 33.53
+207 1 32.22 9.28 30.52
+208 1 0.7 4.01 38.87
+209 1 32.66 39.86 36.84
+210 1 27.34 34.57 21.76
+211 1 13.7 23.12 8.34
+212 1 28 9.71 6.29
+213 1 31.69 26.39 38.19
+214 1 2.04 20.93 36.95
+215 1 30.31 26.61 12.31
+216 1 25.37 20.63 9.4
+217 1 16.29 5.62 14.04
+218 1 1.36 1.95 4.97
+219 1 38.75 26.8 5.62
+220 1 40.28 29.89 12.27
+221 1 0.52 31.22 7.58
+222 1 15.64 21.64 14.71
+223 1 10.11 28.8 9.67
+224 1 19.03 37.3 38.87
+225 1 12.07 6.46 19.25
+226 1 36.22 21.11 15.02
+227 1 12.49 15.69 7.21
+228 1 25.2 30.8 19.71
+229 1 8.24 35.22 23.02
+230 1 9.94 4.1 1.86
+231 1 4.31 19.07 26.23
+232 1 22.03 19.99 14.19
+233 1 30.84 5.24 2.75
+234 1 35.51 30.52 32.3
+235 1 3.88 20.41 39.48
+236 1 30.86 0.39 31.56
+237 1 25.91 27.12 39.04
+238 1 33.39 5.37 4.51
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+240 1 11.83 21.81 39.11
+241 1 39.94 5.2 5.73
+242 1 29.89 33.21 15.44
+243 1 23.42 15.38 30.98
+244 1 28.66 11.56 16.13
+245 1 16.74 20.43 21.72
+246 1 9.31 0.26 22.42
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+248 1 13.86 4.65 16.99
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+285 1 8.29 29.61 6.81
+286 1 7.13 17.36 -0.19
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+289 1 27.18 22.49 5.69
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+299 1 18.55 5.87 9.15
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+314 1 10.78 17.11 34.38
+315 1 13.58 14.89 0.34
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+317 1 12.68 29.51 17.07
+318 1 9.45 27 4.98
+319 1 29.02 19.27 6.45
+320 1 19.09 36.35 19.84
+321 1 23.13 6.75 19.78
+322 1 8.02 34.1 26.95
+323 1 26.03 14.18 1.57
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+353 1 3.95 4.33 20.25
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+355 1 21.35 2.88 17.26
+356 1 32.92 22.68 6.56
+357 1 21.72 4.62 12.02
+358 1 37.6 6.04 25.2
+359 1 22.22 23.78 7.36
+360 1 12.53 19.53 10.6
+361 1 17.87 26.05 19.32
+362 1 20.94 30.75 31.23
+363 1 22.33 11.87 35.79
+364 1 28.54 6.88 10.52
+365 1 29.58 26.13 8.56
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+368 1 18.66 40.35 4.69
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+371 1 8.97 24.7 0.61
+372 1 26.89 1.52 31.33
+373 1 6.88 22.51 14.06
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+375 1 0.95 14.53 10
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+377 1 6.1 35.16 11.28
+378 1 10.2 15.91 28.7
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+381 1 22.48 2.17 5.2
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+389 1 37.45 26.58 32.25
+390 1 2.8 8.96 32.35
+391 1 5.29 39.84 30.1
+392 1 29.2 26.49 31.18
+393 1 33.91 27.39 12.89
+394 1 3.37 14.19 39.34
+395 1 30.68 28.7 27
+396 1 2.59 18.45 19.38
+397 1 13.55 0.75 27.35
+398 1 3.82 20.12 16.1
+399 1 37.72 0.72 34.29
+400 1 23.85 3.32 19.46
+401 1 4.78 0.67 38.23
+402 1 22.78 23.26 38.6
+403 1 11.56 39.29 4.23
+404 1 21.38 32.45 5.39
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+406 1 28.43 31.07 17.8
+407 1 11.02 5.75 39.84
+408 1 27.36 36.71 7.62
+409 1 34.22 16.74 27.88
+410 1 3.22 22.01 27.42
+411 1 29.2 15.76 32.33
+412 1 25.29 23.44 2.2
+413 1 10.8 32.43 39.96
+414 1 32.2 1.41 4.44
+415 1 32.94 15.59 37.21
+416 1 6.8 8.08 0.84
+417 1 10.42 9.91 37.73
+418 1 1.18 31.39 3.93
+419 1 10.1 36.38 38.57
+420 1 32.89 26.96 35.07
+421 1 28.12 11.93 25.96
+422 1 4.9 29.15 -0.25
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+424 1 11.33 3.94 25.55
+425 1 3.3 30.26 10.78
+426 1 11.57 27.26 19.31
+427 1 21.79 32.67 13.3
+428 1 4.96 26.53 33.78
+429 1 33.41 32.87 18.46
+430 1 13.92 30.37 20.3
+431 1 16.91 3.5 11.57
+432 1 -0.06 4.42 34.05
+433 1 7.04 24.33 16.85
+434 1 28.66 11.93 19.73
+435 1 30.21 1.75 36.36
+436 1 3.91 6.2 6.26
+437 1 7.01 25.6 27.34
+438 1 34 1.06 18.12
+439 1 29.14 8.5 3.09
+440 1 40.13 23.52 16.94
+441 1 21.69 22.38 26.78
+442 1 18.44 32.85 39.84
+443 1 38.87 1.99 27.63
+444 1 10.47 12.02 33.68
+445 1 9.65 19.94 21.88
+446 1 25.04 8.12 27.89
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diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
index 072a8e3c456af5547403b35d859b08a5c512f941..f2dc506ddef28d978d48eb90569302e0de27124b 100644
--- a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
@@ -32,8 +32,8 @@ thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
- react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map &
- react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+ react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+ react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
index f3b3840a925573ab1b83db1402cd68c5579dab35..653c7582f8d7aba4c8800e5fcfff5ebb22d44a15 100644
--- a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
@@ -84,7 +84,9 @@ thermo 50
# dump 1 all xyz 100 test_vis.xyz
-fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
@@ -132,39 +134,42 @@ Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
- 100 693.69241 -4696.4359 0.80366765 57 22
- 150 715.44689 -14740.892 0.80366765 77 50
- 200 721.16898 -1411.95 0.80366765 84 66
-Loop time of 107.389 on 1 procs for 200 steps with 35200 atoms
+ 100 697.22819 -4624.0512 0.80366765 57 22
+ 150 723.60507 -17175.571 0.80366765 76 48
+ 200 736.71277 -12961.963 0.80366765 84 64
+Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
-Performance: 0.161 ns/day, 149.151 hours/ns, 1.862 timesteps/s
+Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 27.191 | 27.191 | 27.191 | 0.0 | 25.32
-Bond | 11.46 | 11.46 | 11.46 | 0.0 | 10.67
-Kspace | 4.2507 | 4.2507 | 4.2507 | 0.0 | 3.96
-Neigh | 55.544 | 55.544 | 55.544 | 0.0 | 51.72
-Comm | 0.41715 | 0.41715 | 0.41715 | 0.0 | 0.39
-Output | 0.0011044 | 0.0011044 | 0.0011044 | 0.0 | 0.00
-Modify | 8.4756 | 8.4756 | 8.4756 | 0.0 | 7.89
-Other | | 0.04897 | | | 0.05
+Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45
+Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01
+Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07
+Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22
+Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40
+Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00
+Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81
+Other | | 0.04545 | | | 0.04
Nlocal: 35200 ave 35200 max 35200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 38406 ave 38406 max 38406 min
+Nghost: 38403 ave 38403 max 38403 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 6.92787e+06 ave 6.92787e+06 max 6.92787e+06 min
+Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 6927872
-Ave neighs/atom = 196.815
-Ave special neighs/atom = 9.83489
+Total # of neighbors = 6928101
+Ave neighs/atom = 196.821
+Ave special neighs/atom = 9.83727
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
-Total wall time: 0:01:48
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:43
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
index 992a97e77ef920433575efd080df965045460154..cc0dda60c7dcec4b775d0d5cd6cdad4f6b751124 100644
--- a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
@@ -84,7 +84,9 @@ thermo 50
# dump 1 all xyz 100 test_vis.xyz
-fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
@@ -132,39 +134,42 @@ Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
- 100 693.69241 -4696.4359 0.80366765 57 22
- 150 715.43654 -14742.205 0.80366765 77 50
- 200 721.1906 -1411.4303 0.80366765 84 66
-Loop time of 56.2311 on 4 procs for 200 steps with 35200 atoms
+ 100 697.22819 -4624.0512 0.80366765 57 22
+ 150 724.40407 -17166.729 0.80366765 76 49
+ 200 737.28582 -12968.224 0.80366765 84 65
+Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
-Performance: 0.307 ns/day, 78.099 hours/ns, 3.557 timesteps/s
-99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 13.86 | 14.034 | 14.406 | 5.8 | 24.96
-Bond | 5.5592 | 5.5952 | 5.6492 | 1.4 | 9.95
-Kspace | 2.3969 | 2.7523 | 2.9203 | 12.5 | 4.89
-Neigh | 27.265 | 27.268 | 27.271 | 0.0 | 48.49
-Comm | 0.75523 | 0.77355 | 0.79381 | 1.7 | 1.38
-Output | 0.00051904 | 0.0007363 | 0.0013669 | 0.0 | 0.00
-Modify | 5.7629 | 5.7634 | 5.7641 | 0.0 | 10.25
-Other | | 0.04441 | | | 0.08
-
-Nlocal: 8800 ave 8912 max 8666 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-Nghost: 18358.8 ave 18432 max 18189 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-Neighs: 1.73197e+06 ave 1.77209e+06 max 1.68475e+06 min
+Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89
+Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31
+Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19
+Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68
+Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47
+Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00
+Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39
+Other | | 0.03995 | | | 0.08
+
+Nlocal: 8800 ave 8913 max 8652 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 18366 ave 18461 max 18190 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2
-Total # of neighbors = 6927873
-Ave neighs/atom = 196.815
-Ave special neighs/atom = 9.83489
+Total # of neighbors = 6928132
+Ave neighs/atom = 196.822
+Ave special neighs/atom = 9.83608
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
-Total wall time: 0:00:57
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:52
diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
index 3e21f69331c46b9527f224d58b1d03ca941705a3..1f7e9c42b7b4098fd355dec8afc696e42631321c 100644
--- a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
+++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
@@ -33,8 +33,8 @@ thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
- react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map &
- react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+ react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+ react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
fix 1 statted_grp nvt temp 300 300 100
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
index a65a5306f3d8fd89ad5d6b2c4fcb757a6a90a395..344439f94c5906e1fc7417921b89434ae0a7b8b5 100644
--- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
@@ -85,7 +85,9 @@ thermo 50
# dump 1 all xyz 1 test_vis.xyz
-fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
@@ -131,235 +133,238 @@ Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
- 100 275.26011 39.120329 0.0034851739 1 1
- 150 438.68516 35.257539 0.0034851739 1 1
- 200 394.48971 15.444537 0.0034851739 1 1
- 250 356.00369 50.185792 0.0034851739 1 1
- 300 301.25816 -26.891497 0.0034851739 1 1
- 350 279.17264 12.694513 0.0034851739 1 1
- 400 248.71641 10.684558 0.0034851739 1 1
- 450 240.30602 12.963034 0.0034851739 1 1
- 500 252.71279 0.91620356 0.0034851739 1 1
- 550 300.56824 18.541436 0.0034851739 1 1
- 600 306.46441 -1.9736081 0.0034851739 1 1
- 650 336.4537 21.474831 0.0034851739 1 1
- 700 323.46217 8.486376 0.0034851739 1 1
- 750 271.87146 5.9615231 0.0034851739 1 1
- 800 268.43041 36.676068 0.0034851739 1 1
- 850 269.02683 7.6295416 0.0034851739 1 1
- 900 282.03605 -1.4688833 0.0034851739 1 1
- 950 243.69136 -22.771489 0.0034851739 1 1
- 1000 285.01348 17.925748 0.0034851739 1 1
- 1050 383.47985 0.70536985 0.0034851739 1 1
- 1100 368.97167 -4.3046933 0.0034851739 1 1
- 1150 373.64459 6.3491837 0.0034851739 1 1
- 1200 332.90575 -36.501095 0.0034851739 1 1
- 1250 314.04078 -13.382767 0.0034851739 1 1
- 1300 305.84166 4.7713641 0.0034851739 1 1
- 1350 286.22145 37.621803 0.0034851739 1 1
- 1400 265.52855 23.621002 0.0034851739 1 1
- 1450 281.807 -31.266828 0.0034851739 1 1
- 1500 275.33855 33.495565 0.0034851739 1 1
- 1550 273.04973 -22.913871 0.0034851739 1 1
- 1600 308.18478 -17.98151 0.0034851739 1 1
- 1650 333.27664 28.987529 0.0034851739 1 1
- 1700 296.16091 -1.1440455 0.0034851739 1 1
- 1750 365.75611 34.574845 0.0034851739 1 1
- 1800 292.83503 -33.199654 0.0034851739 1 1
- 1850 261.50282 42.608703 0.0034851739 1 1
- 1900 315.14188 -31.058803 0.0034851739 1 1
- 1950 335.12895 12.40597 0.0034851739 1 1
- 2000 278.08586 -5.3178633 0.0034851739 1 1
- 2050 283.23847 -3.3974302 0.0034851739 1 1
- 2100 281.38904 0.70263324 0.0034851739 1 1
- 2150 302.23197 23.372316 0.0034851739 1 1
- 2200 337.49259 -4.8716803 0.0034851739 1 1
- 2250 409.64134 -12.043721 0.0034851739 1 1
- 2300 309.21764 -21.824645 0.0034851739 1 1
- 2350 290.97879 18.690281 0.0034851739 1 1
- 2400 341.816 -16.967741 0.0034851739 1 1
- 2450 310.28034 27.375518 0.0034851739 1 1
- 2500 248.89429 17.061192 0.0034851739 1 1
- 2550 273.10927 0.10481657 0.0034851739 1 1
- 2600 289.56101 -9.7239939 0.0034851739 1 1
- 2650 298.99719 -33.140576 0.0034851739 1 1
- 2700 326.05198 -24.509827 0.0034851739 1 1
- 2750 319.20612 24.305526 0.0034851739 1 1
- 2800 304.8715 -15.076941 0.0034851739 1 1
- 2850 374.38923 2.0874883 0.0034851739 1 1
- 2900 354.01554 -20.595102 0.0034851739 1 1
- 2950 289.89296 48.39731 0.0034851739 1 1
- 3000 312.10013 -8.5105997 0.0034851739 1 1
- 3050 296.97004 -31.008446 0.0034851739 1 1
- 3100 251.72228 35.710197 0.0034851739 1 1
- 3150 315.35895 -43.331536 0.0034851739 1 1
- 3200 334.67773 13.331058 0.0034851739 1 1
- 3250 308.1669 37.236121 0.0034851739 1 1
- 3300 329.47601 30.798598 0.0034851739 1 1
- 3350 299.40055 2.0785585 0.0034851739 1 1
- 3400 272.41031 32.744922 0.0034851739 1 1
- 3450 279.34594 -26.181793 0.0034851739 1 1
- 3500 288.89969 8.935052 0.0034851739 1 1
- 3550 253.4967 9.7244709 0.0034851739 1 1
- 3600 294.83266 19.33305 0.0034851739 1 1
- 3650 290.23794 -5.4939069 0.0034851739 1 1
- 3700 332.5222 -29.834229 0.0034851739 1 1
- 3750 364.63024 20.706191 0.0034851739 1 1
- 3800 295.3842 -6.9434004 0.0034851739 1 1
- 3850 346.84424 37.796066 0.0034851739 1 1
- 3900 265.67286 -0.31628068 0.0034851739 1 1
- 3950 260.455 -2.2571902 0.0034851739 1 1
- 4000 259.82636 -2.2286205 0.0034851739 1 1
- 4050 257.79848 24.520293 0.0034851739 1 1
- 4100 295.58626 -0.42318936 0.0034851739 1 1
- 4150 265.81353 -49.092436 0.0034851739 1 1
- 4200 302.10333 51.715259 0.0034851739 1 1
- 4250 258.98448 -4.8516655 0.0034851739 1 1
- 4300 327.83401 33.717282 0.0034851739 1 1
- 4350 311.59571 23.580382 0.0034851739 1 1
- 4400 300.64237 -31.866661 0.0034851739 1 1
- 4450 294.15643 -0.11927421 0.0034851739 1 1
- 4500 299.83605 -17.560873 0.0034851739 1 1
- 4550 326.83265 32.818482 0.0034851739 1 1
- 4600 260.39068 -8.0567902 0.0034851739 1 1
- 4650 247.93553 19.462991 0.0034851739 1 1
- 4700 214.22252 -34.118303 0.0034851739 1 1
- 4750 203.15329 27.356205 0.0034851739 1 1
- 4800 257.761 -10.407989 0.0034851739 1 1
- 4850 307.1923 11.71101 0.0034851739 1 1
- 4900 319.00942 4.7808306 0.0034851739 1 1
- 4950 282.23989 24.996151 0.0034851739 1 1
- 5000 311.53284 -3.0012665 0.0034851739 1 1
- 5050 317.58212 32.567832 0.0034851739 1 1
- 5100 267.51501 -47.695087 0.0034851739 1 1
- 5150 260.19048 29.046388 0.0034851739 1 1
- 5200 239.83552 -5.4890385 0.0034851739 1 1
- 5250 234.8852 -18.172633 0.0034851739 1 1
- 5300 236.43277 -39.06212 0.0034851739 1 1
- 5350 280.90079 -2.6932923 0.0034851739 1 1
- 5400 316.65266 23.071362 0.0034851739 1 1
- 5450 345.63226 19.573323 0.0034851739 1 1
- 5500 384.57334 41.507217 0.0034851739 1 1
- 5550 317.14278 9.6992897 0.0034851739 1 1
- 5600 279.93243 -12.076895 0.0034851739 1 1
- 5650 268.06471 1.6196401 0.0034851739 1 1
- 5700 271.85714 -40.378455 0.0034851739 1 1
- 5750 313.88363 10.722639 0.0034851739 1 1
- 5800 281.54495 31.914889 0.0034851739 1 1
- 5850 293.34821 -8.3154922 0.0034851739 1 1
- 5900 249.25216 -17.307353 0.0034851739 1 1
- 5950 268.18639 -4.7222512 0.0034851739 1 1
- 6000 302.99398 -52.615528 0.0034851739 1 1
- 6050 314.57931 34.51318 0.0034851739 1 1
- 6100 345.70348 30.334721 0.0034851739 1 1
- 6150 316.59329 31.862519 0.0034851739 1 1
- 6200 317.85346 -32.235221 0.0034851739 1 1
- 6250 282.97676 0.2936745 0.0034851739 1 1
- 6300 267.91814 19.265567 0.0034851739 1 1
- 6350 226.20967 -13.093547 0.0034851739 1 1
- 6400 307.73316 17.439598 0.0034851739 1 1
- 6450 292.16253 -23.275163 0.0034851739 1 1
- 6500 335.05939 26.936463 0.0034851739 1 1
- 6550 380.73546 19.532416 0.0034851739 1 1
- 6600 373.0103 30.879532 0.0034851739 1 1
- 6650 335.37975 -2.1762828 0.0034851739 1 1
- 6700 298.94272 -10.578587 0.0034851739 1 1
- 6750 255.11531 -50.576215 0.0034851739 1 1
- 6800 222.87459 3.0499548 0.0034851739 1 1
- 6850 268.57213 -43.675945 0.0034851739 1 1
- 6900 260.3024 4.7483005 0.0034851739 1 1
- 6950 289.15855 31.62106 0.0034851739 1 1
- 7000 289.11874 21.635533 0.0034851739 1 1
- 7050 361.08776 22.445996 0.0034851739 1 1
- 7100 368.95003 4.8383881 0.0034851739 1 1
- 7150 331.47448 -36.200495 0.0034851739 1 1
- 7200 304.7251 13.982693 0.0034851739 1 1
- 7250 284.09747 0.53758275 0.0034851739 1 1
- 7300 269.17023 -41.571482 0.0034851739 1 1
- 7350 222.07071 25.564662 0.0034851739 1 1
- 7400 304.09598 15.482955 0.0034851739 1 1
- 7450 298.78752 -7.4335841 0.0034851739 1 1
- 7500 328.78697 14.666097 0.0034851739 1 1
- 7550 347.07038 -37.165295 0.0034851739 1 1
- 7600 362.85673 20.52268 0.0034851739 1 1
- 7650 347.15141 2.3383775 0.0034851739 1 1
- 7700 262.10132 33.898374 0.0034851739 1 1
- 7750 275.84724 -33.534813 0.0034851739 1 1
- 7800 281.14075 -18.284372 0.0034851739 1 1
- 7850 264.83337 -30.580199 0.0034851739 1 1
- 7900 257.35275 -35.080567 0.0034851739 1 1
- 7950 286.32446 26.594779 0.0034851739 1 1
- 8000 248.36889 15.605894 0.0034851739 1 1
- 8050 292.55015 28.811985 0.0034851739 1 1
- 8100 312.47888 0.83990451 0.0034851739 1 1
- 8150 285.58532 -15.258185 0.0034851739 1 1
- 8200 292.22819 -38.233195 0.0034851739 1 1
- 8250 321.6208 -19.052143 0.0034851739 1 1
- 8300 319.41332 54.97437 0.0034851739 1 1
- 8350 307.95647 32.009591 0.0034851739 1 1
- 8400 345.58105 8.8535539 0.0034851739 1 1
- 8450 357.75168 12.416896 0.0034851739 1 1
- 8500 370.049 4.3288665 0.0034851739 1 1
- 8550 360.62882 12.618614 0.0034851739 1 1
- 8600 290.10834 -4.8081765 0.0034851739 1 1
- 8650 297.7575 -5.1976816 0.0034851739 1 1
- 8700 286.57505 -31.469549 0.0034851739 1 1
- 8750 307.77059 19.338001 0.0034851739 1 1
- 8800 231.68316 12.159459 0.0034851739 1 1
- 8850 329.13623 -8.7262592 0.0034851739 1 1
- 8900 286.40715 10.326025 0.0034851739 1 1
- 8950 339.43101 2.7809618 0.0034851739 1 1
- 9000 402.53799 19.481869 0.0034851739 1 1
- 9050 349.56449 -4.8450179 0.0034851739 1 1
- 9100 307.64739 16.889327 0.0034851739 1 1
- 9150 276.54451 -34.808372 0.0034851739 1 1
- 9200 233.18668 4.9409791 0.0034851739 1 1
- 9250 266.48384 -19.850366 0.0034851739 1 1
- 9300 289.14808 13.520201 0.0034851739 1 1
- 9350 295.08335 17.156468 0.0034851739 1 1
- 9400 338.08757 -31.112278 0.0034851739 1 1
- 9450 336.64739 -25.697747 0.0034851739 1 1
- 9500 338.10622 1.9241797 0.0034851739 1 1
- 9550 294.82158 -12.043972 0.0034851739 1 1
- 9600 268.9836 12.235553 0.0034851739 1 1
- 9650 279.6269 28.710734 0.0034851739 1 1
- 9700 279.88562 -10.865604 0.0034851739 1 1
- 9750 287.56565 12.975819 0.0034851739 1 1
- 9800 278.39949 4.2088595 0.0034851739 1 1
- 9850 307.61259 9.341169 0.0034851739 1 1
- 9900 317.53581 2.3948493 0.0034851739 1 1
- 9950 332.52938 -14.809185 0.0034851739 1 1
- 10000 401.93365 -7.637581 0.0034851739 1 1
-Loop time of 1.94139 on 1 procs for 10000 steps with 44 atoms
+ 100 274.25324 46.715512 0.0034851739 1 1
+ 150 471.61579 31.321598 0.0034851739 1 1
+ 200 362.87766 42.061118 0.0034851739 1 1
+ 250 367.58058 65.303109 0.0034851739 1 1
+ 300 372.38236 -52.421725 0.0034851739 1 1
+ 350 297.69957 17.869945 0.0034851739 1 1
+ 400 258.30433 49.19156 0.0034851739 1 1
+ 450 253.34384 -5.8162637 0.0034851739 1 1
+ 500 269.96465 -43.337517 0.0034851739 1 1
+ 550 303.23718 10.180246 0.0034851739 1 1
+ 600 329.59579 -48.97461 0.0034851739 1 1
+ 650 350.42568 50.983183 0.0034851739 1 1
+ 700 342.03272 35.43465 0.0034851739 1 1
+ 750 269.23405 -41.873166 0.0034851739 1 1
+ 800 245.15025 13.953092 0.0034851739 1 1
+ 850 257.85421 -3.1492141 0.0034851739 1 1
+ 900 316.15644 7.7798301 0.0034851739 1 1
+ 950 299.9124 -15.77014 0.0034851739 1 1
+ 1000 302.89968 -17.049693 0.0034851739 1 1
+ 1050 308.91651 71.84632 0.0034851739 1 1
+ 1100 348.43932 -18.742012 0.0034851739 1 1
+ 1150 309.03036 50.536311 0.0034851739 1 1
+ 1200 318.9761 -16.905746 0.0034851739 1 1
+ 1250 320.42806 -0.057975092 0.0034851739 1 1
+ 1300 289.7824 18.200772 0.0034851739 1 1
+ 1350 284.79836 -9.1978427 0.0034851739 1 1
+ 1400 325.43292 42.082833 0.0034851739 1 1
+ 1450 261.5041 -37.823325 0.0034851739 1 1
+ 1500 298.88723 -5.1647385 0.0034851739 1 1
+ 1550 291.37403 -7.7764201 0.0034851739 1 1
+ 1600 293.83475 22.2458 0.0034851739 1 1
+ 1650 293.80611 24.202512 0.0034851739 1 1
+ 1700 291.70205 -23.397884 0.0034851739 1 1
+ 1750 292.32437 -10.671214 0.0034851739 1 1
+ 1800 302.01367 -11.671025 0.0034851739 1 1
+ 1850 322.1651 24.438331 0.0034851739 1 1
+ 1900 310.45076 45.343592 0.0034851739 1 1
+ 1950 325.91745 -19.847809 0.0034851739 1 1
+ 2000 276.89662 63.387098 0.0034851739 1 1
+ 2050 311.33783 -24.683247 0.0034851739 1 1
+ 2100 346.2336 -27.526891 0.0034851739 1 1
+ 2150 345.30604 -15.722411 0.0034851739 1 1
+ 2200 346.7718 -17.857633 0.0034851739 1 1
+ 2250 304.28676 -1.9965581 0.0034851739 1 1
+ 2300 322.56372 -31.786868 0.0034851739 1 1
+ 2350 282.64326 6.1982735 0.0034851739 1 1
+ 2400 286.65759 -63.207781 0.0034851739 1 1
+ 2450 257.05528 32.931491 0.0034851739 1 1
+ 2500 283.64386 26.912373 0.0034851739 1 1
+ 2550 299.54005 27.277039 0.0034851739 1 1
+ 2600 283.92503 14.660972 0.0034851739 1 1
+ 2650 321.93453 -18.977358 0.0034851739 1 1
+ 2700 376.7189 31.826935 0.0034851739 1 1
+ 2750 372.20075 -32.821697 0.0034851739 1 1
+ 2800 361.40604 83.035183 0.0034851739 1 1
+ 2850 332.27269 -23.927452 0.0034851739 1 1
+ 2900 331.14638 -0.12328446 0.0034851739 1 1
+ 2950 303.67489 -24.078857 0.0034851739 1 1
+ 3000 311.40462 21.563537 0.0034851739 1 1
+ 3050 284.72849 -23.849667 0.0034851739 1 1
+ 3100 303.48477 39.347763 0.0034851739 1 1
+ 3150 264.2739 -0.22299879 0.0034851739 1 1
+ 3200 300.03351 31.545323 0.0034851739 1 1
+ 3250 288.56663 5.7225228 0.0034851739 1 1
+ 3300 200.13238 -31.239655 0.0034851739 1 1
+ 3350 231.32512 16.631728 0.0034851739 1 1
+ 3400 260.57402 2.1717992 0.0034851739 1 1
+ 3450 301.47128 -42.210623 0.0034851739 1 1
+ 3500 321.77414 40.074365 0.0034851739 1 1
+ 3550 353.21858 28.387783 0.0034851739 1 1
+ 3600 331.45989 -57.800858 0.0034851739 1 1
+ 3650 303.88123 44.86596 0.0034851739 1 1
+ 3700 329.73833 -0.80615652 0.0034851739 1 1
+ 3750 297.55588 -0.49626039 0.0034851739 1 1
+ 3800 286.38794 -10.010003 0.0034851739 1 1
+ 3850 290.17417 -43.51187 0.0034851739 1 1
+ 3900 247.88933 51.23735 0.0034851739 1 1
+ 3950 332.31324 -18.194985 0.0034851739 1 1
+ 4000 325.56802 18.402825 0.0034851739 1 1
+ 4050 338.37593 36.430977 0.0034851739 1 1
+ 4100 370.95478 39.290285 0.0034851739 1 1
+ 4150 348.47859 -7.0779678 0.0034851739 1 1
+ 4200 241.30632 -33.371788 0.0034851739 1 1
+ 4250 242.17258 -9.986197 0.0034851739 1 1
+ 4300 300.85311 -7.9244294 0.0034851739 1 1
+ 4350 273.15684 -21.257283 0.0034851739 1 1
+ 4400 305.77463 -5.8720722 0.0034851739 1 1
+ 4450 314.97697 45.0373 0.0034851739 1 1
+ 4500 310.77723 16.958773 0.0034851739 1 1
+ 4550 302.1742 12.156862 0.0034851739 1 1
+ 4600 319.74799 6.84889 0.0034851739 1 1
+ 4650 270.86805 -13.767905 0.0034851739 1 1
+ 4700 249.81731 -31.197487 0.0034851739 1 1
+ 4750 285.86481 -9.8916364 0.0034851739 1 1
+ 4800 233.98321 7.1338571 0.0034851739 1 1
+ 4850 302.60551 49.262889 0.0034851739 1 1
+ 4900 316.55056 34.663247 0.0034851739 1 1
+ 4950 357.32741 11.583006 0.0034851739 1 1
+ 5000 400.21045 -8.1781061 0.0034851739 1 1
+ 5050 390.01845 -20.490275 0.0034851739 1 1
+ 5100 378.84247 -41.328757 0.0034851739 1 1
+ 5150 324.02038 -15.023862 0.0034851739 1 1
+ 5200 262.08429 10.937354 0.0034851739 1 1
+ 5250 255.75508 16.381455 0.0034851739 1 1
+ 5300 277.84989 40.68232 0.0034851739 1 1
+ 5350 302.92832 9.1989494 0.0034851739 1 1
+ 5400 283.7196 -1.6584671 0.0034851739 1 1
+ 5450 300.71266 -4.7030295 0.0034851739 1 1
+ 5500 343.5499 -0.30550044 0.0034851739 1 1
+ 5550 369.51271 21.691649 0.0034851739 1 1
+ 5600 372.69789 -38.67994 0.0034851739 1 1
+ 5650 327.41266 11.352137 0.0034851739 1 1
+ 5700 278.98614 -23.827304 0.0034851739 1 1
+ 5750 308.30054 -20.756187 0.0034851739 1 1
+ 5800 341.45594 28.058441 0.0034851739 1 1
+ 5850 322.97844 -10.731921 0.0034851739 1 1
+ 5900 304.53591 32.825279 0.0034851739 1 1
+ 5950 287.1752 -36.780091 0.0034851739 1 1
+ 6000 296.52681 18.781896 0.0034851739 1 1
+ 6050 314.25442 15.992829 0.0034851739 1 1
+ 6100 313.86576 3.4342714 0.0034851739 1 1
+ 6150 325.64196 32.392039 0.0034851739 1 1
+ 6200 367.42931 -27.160706 0.0034851739 1 1
+ 6250 369.30798 39.020934 0.0034851739 1 1
+ 6300 328.92285 -23.175157 0.0034851739 1 1
+ 6350 305.63077 4.9024453 0.0034851739 1 1
+ 6400 241.70341 -13.676629 0.0034851739 1 1
+ 6450 265.66717 2.40612 0.0034851739 1 1
+ 6500 249.36037 13.420255 0.0034851739 1 1
+ 6550 294.53814 10.853462 0.0034851739 1 1
+ 6600 308.2025 18.995308 0.0034851739 1 1
+ 6650 305.43797 -49.56785 0.0034851739 1 1
+ 6700 320.27344 11.336281 0.0034851739 1 1
+ 6750 321.78666 -23.463899 0.0034851739 1 1
+ 6800 303.40388 7.6224553 0.0034851739 1 1
+ 6850 297.18966 51.52256 0.0034851739 1 1
+ 6900 284.18909 -8.4947203 0.0034851739 1 1
+ 6950 331.03663 13.233655 0.0034851739 1 1
+ 7000 311.37928 -43.265479 0.0034851739 1 1
+ 7050 286.81661 -14.174683 0.0034851739 1 1
+ 7100 302.84119 12.048954 0.0034851739 1 1
+ 7150 297.19357 -43.111968 0.0034851739 1 1
+ 7200 332.47359 26.048249 0.0034851739 1 1
+ 7250 262.70677 41.176242 0.0034851739 1 1
+ 7300 250.61405 -23.413982 0.0034851739 1 1
+ 7350 296.91117 35.88133 0.0034851739 1 1
+ 7400 245.09229 -13.447194 0.0034851739 1 1
+ 7450 272.28131 -23.322585 0.0034851739 1 1
+ 7500 209.04985 13.871239 0.0034851739 1 1
+ 7550 255.00955 4.9325621 0.0034851739 1 1
+ 7600 312.30937 -37.368274 0.0034851739 1 1
+ 7650 305.65903 55.245496 0.0034851739 1 1
+ 7700 325.09504 -18.347711 0.0034851739 1 1
+ 7750 363.28282 -22.479686 0.0034851739 1 1
+ 7800 350.17429 26.849547 0.0034851739 1 1
+ 7850 271.70853 -17.764575 0.0034851739 1 1
+ 7900 272.66484 -11.701967 0.0034851739 1 1
+ 7950 298.60202 -12.765675 0.0034851739 1 1
+ 8000 274.58852 49.641532 0.0034851739 1 1
+ 8050 304.72347 -0.55414183 0.0034851739 1 1
+ 8100 328.30757 -39.861301 0.0034851739 1 1
+ 8150 406.67601 2.8999409 0.0034851739 1 1
+ 8200 332.20083 -51.217399 0.0034851739 1 1
+ 8250 354.50609 53.128769 0.0034851739 1 1
+ 8300 337.2758 20.68562 0.0034851739 1 1
+ 8350 361.89708 -54.185869 0.0034851739 1 1
+ 8400 305.63496 24.058529 0.0034851739 1 1
+ 8450 303.27461 4.304683 0.0034851739 1 1
+ 8500 253.53694 -10.909021 0.0034851739 1 1
+ 8550 277.03017 23.241479 0.0034851739 1 1
+ 8600 291.41844 -22.240665 0.0034851739 1 1
+ 8650 307.85368 31.919587 0.0034851739 1 1
+ 8700 309.19724 0.53529642 0.0034851739 1 1
+ 8750 354.6583 11.565515 0.0034851739 1 1
+ 8800 329.78598 19.5996 0.0034851739 1 1
+ 8850 240.79198 21.803515 0.0034851739 1 1
+ 8900 318.40749 -59.816923 0.0034851739 1 1
+ 8950 308.47211 -57.808635 0.0034851739 1 1
+ 9000 271.51207 50.943482 0.0034851739 1 1
+ 9050 249.4005 6.7529187 0.0034851739 1 1
+ 9100 221.8772 47.196092 0.0034851739 1 1
+ 9150 297.9351 4.0058184 0.0034851739 1 1
+ 9200 274.85051 -24.774393 0.0034851739 1 1
+ 9250 336.04757 5.3799028 0.0034851739 1 1
+ 9300 380.44956 -22.389381 0.0034851739 1 1
+ 9350 336.9824 23.050616 0.0034851739 1 1
+ 9400 304.46425 32.530218 0.0034851739 1 1
+ 9450 317.55591 -22.265425 0.0034851739 1 1
+ 9500 323.70901 -7.0159787 0.0034851739 1 1
+ 9550 316.07308 28.062131 0.0034851739 1 1
+ 9600 262.74608 -0.78519192 0.0034851739 1 1
+ 9650 271.55045 -21.430123 0.0034851739 1 1
+ 9700 239.6022 14.483637 0.0034851739 1 1
+ 9750 338.1437 -0.72765302 0.0034851739 1 1
+ 9800 334.50189 19.495144 0.0034851739 1 1
+ 9850 354.87554 19.272719 0.0034851739 1 1
+ 9900 334.02141 -22.393457 0.0034851739 1 1
+ 9950 293.63651 19.178873 0.0034851739 1 1
+ 10000 319.81736 21.904414 0.0034851739 1 1
+Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
-Performance: 445.042 ns/day, 0.054 hours/ns, 5150.945 timesteps/s
-99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.26479 | 0.26479 | 0.26479 | 0.0 | 13.64
-Bond | 0.76875 | 0.76875 | 0.76875 | 0.0 | 39.60
-Kspace | 0.32111 | 0.32111 | 0.32111 | 0.0 | 16.54
-Neigh | 0.41333 | 0.41333 | 0.41333 | 0.0 | 21.29
-Comm | 0.025956 | 0.025956 | 0.025956 | 0.0 | 1.34
-Output | 0.0043445 | 0.0043445 | 0.0043445 | 0.0 | 0.22
-Modify | 0.12526 | 0.12526 | 0.12526 | 0.0 | 6.45
-Other | | 0.01786 | | | 0.92
+Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14
+Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04
+Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49
+Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62
+Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22
+Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19
+Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40
+Other | | 0.01666 | | | 0.90
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 62 ave 62 max 62 min
+Nghost: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 812 ave 812 max 812 min
+Neighs: 823 ave 823 max 823 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 812
-Ave neighs/atom = 18.4545
+Total # of neighbors = 823
+Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
Total wall time: 0:00:01
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
index dddc9f2801e6c62482640b4bed730d57e324854b..377781f48f7091dbc910d9ce1ab0f98723abb7bb 100644
--- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
@@ -85,7 +85,9 @@ thermo 50
# dump 1 all xyz 1 test_vis.xyz
-fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
@@ -131,235 +133,238 @@ Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
- 100 275.26011 39.120329 0.0034851739 1 1
- 150 438.68516 35.257539 0.0034851739 1 1
- 200 394.48971 15.444537 0.0034851739 1 1
- 250 356.00369 50.185792 0.0034851739 1 1
- 300 301.25816 -26.891497 0.0034851739 1 1
- 350 279.17264 12.694513 0.0034851739 1 1
- 400 248.71641 10.684558 0.0034851739 1 1
- 450 240.30602 12.963034 0.0034851739 1 1
- 500 252.71279 0.91620356 0.0034851739 1 1
- 550 300.56824 18.541436 0.0034851739 1 1
- 600 306.46441 -1.9736081 0.0034851739 1 1
- 650 336.4537 21.474831 0.0034851739 1 1
- 700 323.46217 8.486376 0.0034851739 1 1
- 750 271.87146 5.9615231 0.0034851739 1 1
- 800 268.43041 36.676068 0.0034851739 1 1
- 850 269.02683 7.6295416 0.0034851739 1 1
- 900 282.03605 -1.4688833 0.0034851739 1 1
- 950 243.69136 -22.771489 0.0034851739 1 1
- 1000 285.01348 17.925748 0.0034851739 1 1
- 1050 383.47985 0.70536985 0.0034851739 1 1
- 1100 368.97167 -4.3046933 0.0034851739 1 1
- 1150 373.64459 6.3491837 0.0034851739 1 1
- 1200 332.90575 -36.501095 0.0034851739 1 1
- 1250 314.04078 -13.382767 0.0034851739 1 1
- 1300 305.84166 4.7713641 0.0034851739 1 1
- 1350 286.22145 37.621803 0.0034851739 1 1
- 1400 265.52855 23.621002 0.0034851739 1 1
- 1450 281.807 -31.266828 0.0034851739 1 1
- 1500 275.33855 33.495565 0.0034851739 1 1
- 1550 273.04973 -22.913871 0.0034851739 1 1
- 1600 308.18478 -17.98151 0.0034851739 1 1
- 1650 333.27664 28.987529 0.0034851739 1 1
- 1700 296.16091 -1.1440455 0.0034851739 1 1
- 1750 365.75611 34.574845 0.0034851739 1 1
- 1800 292.83503 -33.199654 0.0034851739 1 1
- 1850 261.50282 42.608703 0.0034851739 1 1
- 1900 315.14188 -31.058803 0.0034851739 1 1
- 1950 335.12895 12.40597 0.0034851739 1 1
- 2000 278.08586 -5.3178633 0.0034851739 1 1
- 2050 283.23847 -3.3974302 0.0034851739 1 1
- 2100 281.38904 0.70263324 0.0034851739 1 1
- 2150 302.23197 23.372316 0.0034851739 1 1
- 2200 337.49259 -4.8716803 0.0034851739 1 1
- 2250 409.64134 -12.043721 0.0034851739 1 1
- 2300 309.21764 -21.824645 0.0034851739 1 1
- 2350 290.97879 18.690281 0.0034851739 1 1
- 2400 341.816 -16.967741 0.0034851739 1 1
- 2450 310.28034 27.375518 0.0034851739 1 1
- 2500 248.89429 17.061192 0.0034851739 1 1
- 2550 273.10927 0.1048166 0.0034851739 1 1
- 2600 289.56101 -9.7239939 0.0034851739 1 1
- 2650 298.99719 -33.140576 0.0034851739 1 1
- 2700 326.05198 -24.509827 0.0034851739 1 1
- 2750 319.20612 24.305526 0.0034851739 1 1
- 2800 304.8715 -15.076941 0.0034851739 1 1
- 2850 374.38923 2.0874883 0.0034851739 1 1
- 2900 354.01554 -20.595102 0.0034851739 1 1
- 2950 289.89296 48.39731 0.0034851739 1 1
- 3000 312.10013 -8.5105996 0.0034851739 1 1
- 3050 296.97004 -31.008446 0.0034851739 1 1
- 3100 251.72228 35.710197 0.0034851739 1 1
- 3150 315.35895 -43.331536 0.0034851739 1 1
- 3200 334.67773 13.331058 0.0034851739 1 1
- 3250 308.1669 37.236121 0.0034851739 1 1
- 3300 329.47601 30.798598 0.0034851739 1 1
- 3350 299.40055 2.0785585 0.0034851739 1 1
- 3400 272.41031 32.744921 0.0034851739 1 1
- 3450 279.34594 -26.181793 0.0034851739 1 1
- 3500 288.89969 8.935052 0.0034851739 1 1
- 3550 253.4967 9.724471 0.0034851739 1 1
- 3600 294.83266 19.33305 0.0034851739 1 1
- 3650 290.23794 -5.493907 0.0034851739 1 1
- 3700 332.5222 -29.83423 0.0034851739 1 1
- 3750 364.63024 20.706191 0.0034851739 1 1
- 3800 295.3842 -6.9434003 0.0034851739 1 1
- 3850 346.84424 37.796066 0.0034851739 1 1
- 3900 265.67286 -0.3162804 0.0034851739 1 1
- 3950 260.455 -2.2571901 0.0034851739 1 1
- 4000 259.82636 -2.2286207 0.0034851739 1 1
- 4050 257.79848 24.520293 0.0034851739 1 1
- 4100 295.58626 -0.42318895 0.0034851739 1 1
- 4150 265.81352 -49.092436 0.0034851739 1 1
- 4200 302.10333 51.715258 0.0034851739 1 1
- 4250 258.98448 -4.8516657 0.0034851739 1 1
- 4300 327.83401 33.717283 0.0034851739 1 1
- 4350 311.59571 23.580382 0.0034851739 1 1
- 4400 300.64237 -31.866661 0.0034851739 1 1
- 4450 294.15642 -0.11927262 0.0034851739 1 1
- 4500 299.83605 -17.560872 0.0034851739 1 1
- 4550 326.83265 32.818481 0.0034851739 1 1
- 4600 260.39068 -8.0567907 0.0034851739 1 1
- 4650 247.93553 19.462991 0.0034851739 1 1
- 4700 214.22252 -34.118304 0.0034851739 1 1
- 4750 203.15329 27.356204 0.0034851739 1 1
- 4800 257.761 -10.407986 0.0034851739 1 1
- 4850 307.1923 11.711008 0.0034851739 1 1
- 4900 319.00942 4.7808342 0.0034851739 1 1
- 4950 282.2399 24.996151 0.0034851739 1 1
- 5000 311.53284 -3.0012669 0.0034851739 1 1
- 5050 317.58213 32.56782 0.0034851739 1 1
- 5100 267.51502 -47.695103 0.0034851739 1 1
- 5150 260.19047 29.046394 0.0034851739 1 1
- 5200 239.8355 -5.4890372 0.0034851739 1 1
- 5250 234.88522 -18.172649 0.0034851739 1 1
- 5300 236.43278 -39.062111 0.0034851739 1 1
- 5350 280.90083 -2.6932604 0.0034851739 1 1
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- 5450 345.6322 19.573305 0.0034851739 1 1
- 5500 384.57334 41.50729 0.0034851739 1 1
- 5550 317.14286 9.6992981 0.0034851739 1 1
- 5600 279.93246 -12.076859 0.0034851739 1 1
- 5650 268.06471 1.6196502 0.0034851739 1 1
- 5700 271.85714 -40.378489 0.0034851739 1 1
- 5750 313.88361 10.722652 0.0034851739 1 1
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- 5850 293.34819 -8.3155887 0.0034851739 1 1
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- 6100 345.70342 30.33474 0.0034851739 1 1
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- 6200 317.85341 -32.23511 0.0034851739 1 1
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- 6400 307.73307 17.439662 0.0034851739 1 1
- 6450 292.16311 -23.275251 0.0034851739 1 1
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- 6950 289.15739 31.622589 0.0034851739 1 1
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- 7050 361.08905 22.442487 0.0034851739 1 1
- 7100 368.95006 4.8393179 0.0034851739 1 1
- 7150 331.47878 -36.202032 0.0034851739 1 1
- 7200 304.72518 13.982604 0.0034851739 1 1
- 7250 284.0996 0.53900966 0.0034851739 1 1
- 7300 269.17156 -41.572215 0.0034851739 1 1
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- 7500 328.78217 14.672853 0.0034851739 1 1
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- 7700 262.09822 33.901831 0.0034851739 1 1
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- 7800 281.16159 -18.288414 0.0034851739 1 1
- 7850 264.83553 -30.566284 0.0034851739 1 1
- 7900 257.35224 -35.087067 0.0034851739 1 1
- 7950 286.30756 26.586163 0.0034851739 1 1
- 8000 248.38175 15.601961 0.0034851739 1 1
- 8050 292.59171 28.784541 0.0034851739 1 1
- 8100 312.52852 0.87995053 0.0034851739 1 1
- 8150 285.62346 -15.337252 0.0034851739 1 1
- 8200 292.24175 -38.192576 0.0034851739 1 1
- 8250 321.61618 -19.030398 0.0034851739 1 1
- 8300 319.42189 55.078305 0.0034851739 1 1
- 8350 308.00357 32.050518 0.0034851739 1 1
- 8400 345.68186 8.7983733 0.0034851739 1 1
- 8450 358.00849 12.434592 0.0034851739 1 1
- 8500 370.14359 4.2184721 0.0034851739 1 1
- 8550 360.6511 12.580836 0.0034851739 1 1
- 8600 290.04938 -4.8422589 0.0034851739 1 1
- 8650 297.95745 -5.3185591 0.0034851739 1 1
- 8700 286.54284 -31.490479 0.0034851739 1 1
- 8750 308.08791 19.24417 0.0034851739 1 1
- 8800 231.72534 12.262217 0.0034851739 1 1
- 8850 329.2349 -8.9133933 0.0034851739 1 1
- 8900 287.64023 10.525164 0.0034851739 1 1
- 8950 341.08296 2.80127 0.0034851739 1 1
- 9000 403.71266 17.88418 0.0034851739 1 1
- 9050 348.95132 -4.5813611 0.0034851739 1 1
- 9100 307.98322 16.707575 0.0034851739 1 1
- 9150 276.75719 -35.563923 0.0034851739 1 1
- 9200 230.15547 3.8091656 0.0034851739 1 1
- 9250 264.64479 -20.97438 0.0034851739 1 1
- 9300 285.70467 13.881735 0.0034851739 1 1
- 9350 297.515 13.599319 0.0034851739 1 1
- 9400 341.45203 -28.494544 0.0034851739 1 1
- 9450 319.29703 -27.907344 0.0034851739 1 1
- 9500 332.50473 4.9891138 0.0034851739 1 1
- 9550 293.10499 -8.3244772 0.0034851739 1 1
- 9600 255.31174 2.2568315 0.0034851739 1 1
- 9650 250.01932 5.7005159 0.0034851739 1 1
- 9700 278.37409 -8.5970424 0.0034851739 1 1
- 9750 294.86737 17.686447 0.0034851739 1 1
- 9800 277.07345 -2.0856886 0.0034851739 1 1
- 9850 295.54707 2.8365471 0.0034851739 1 1
- 9900 311.51074 29.885116 0.0034851739 1 1
- 9950 296.01363 12.206068 0.0034851739 1 1
- 10000 341.35187 -3.0045464 0.0034851739 1 1
-Loop time of 3.64332 on 4 procs for 10000 steps with 44 atoms
+ 100 274.25324 46.715512 0.0034851739 1 1
+ 150 471.61579 31.321598 0.0034851739 1 1
+ 200 362.87766 42.061118 0.0034851739 1 1
+ 250 367.58058 65.303109 0.0034851739 1 1
+ 300 372.38236 -52.421725 0.0034851739 1 1
+ 350 297.69957 17.869945 0.0034851739 1 1
+ 400 258.30433 49.19156 0.0034851739 1 1
+ 450 253.34384 -5.8162637 0.0034851739 1 1
+ 500 269.96465 -43.337517 0.0034851739 1 1
+ 550 303.23718 10.180246 0.0034851739 1 1
+ 600 329.59579 -48.97461 0.0034851739 1 1
+ 650 350.42568 50.983183 0.0034851739 1 1
+ 700 342.03272 35.43465 0.0034851739 1 1
+ 750 269.23405 -41.873166 0.0034851739 1 1
+ 800 245.15025 13.953092 0.0034851739 1 1
+ 850 257.85421 -3.1492141 0.0034851739 1 1
+ 900 316.15644 7.7798301 0.0034851739 1 1
+ 950 299.9124 -15.77014 0.0034851739 1 1
+ 1000 302.89968 -17.049693 0.0034851739 1 1
+ 1050 308.91651 71.84632 0.0034851739 1 1
+ 1100 348.43932 -18.742012 0.0034851739 1 1
+ 1150 309.03036 50.536311 0.0034851739 1 1
+ 1200 318.9761 -16.905746 0.0034851739 1 1
+ 1250 320.42806 -0.057975092 0.0034851739 1 1
+ 1300 289.7824 18.200772 0.0034851739 1 1
+ 1350 284.79836 -9.1978427 0.0034851739 1 1
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+ 1450 261.5041 -37.823325 0.0034851739 1 1
+ 1500 298.88723 -5.1647385 0.0034851739 1 1
+ 1550 291.37403 -7.7764201 0.0034851739 1 1
+ 1600 293.83475 22.2458 0.0034851739 1 1
+ 1650 293.80611 24.202512 0.0034851739 1 1
+ 1700 291.70205 -23.397884 0.0034851739 1 1
+ 1750 292.32437 -10.671214 0.0034851739 1 1
+ 1800 302.01367 -11.671025 0.0034851739 1 1
+ 1850 322.1651 24.438331 0.0034851739 1 1
+ 1900 310.45076 45.343592 0.0034851739 1 1
+ 1950 325.91745 -19.847809 0.0034851739 1 1
+ 2000 276.89662 63.387098 0.0034851739 1 1
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+ 2100 346.2336 -27.526891 0.0034851739 1 1
+ 2150 345.30604 -15.722411 0.0034851739 1 1
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+ 2250 304.28676 -1.9965581 0.0034851739 1 1
+ 2300 322.56372 -31.786868 0.0034851739 1 1
+ 2350 282.64326 6.1982735 0.0034851739 1 1
+ 2400 286.65759 -63.207781 0.0034851739 1 1
+ 2450 257.05528 32.931491 0.0034851739 1 1
+ 2500 283.64386 26.912373 0.0034851739 1 1
+ 2550 299.54005 27.277039 0.0034851739 1 1
+ 2600 283.92503 14.660972 0.0034851739 1 1
+ 2650 321.93453 -18.977358 0.0034851739 1 1
+ 2700 376.7189 31.826935 0.0034851739 1 1
+ 2750 372.20075 -32.821697 0.0034851739 1 1
+ 2800 361.40604 83.035183 0.0034851739 1 1
+ 2850 332.27269 -23.927452 0.0034851739 1 1
+ 2900 331.14638 -0.12328446 0.0034851739 1 1
+ 2950 303.67489 -24.078857 0.0034851739 1 1
+ 3000 311.40462 21.563537 0.0034851739 1 1
+ 3050 284.72849 -23.849667 0.0034851739 1 1
+ 3100 303.48477 39.347763 0.0034851739 1 1
+ 3150 264.2739 -0.22299878 0.0034851739 1 1
+ 3200 300.03351 31.545323 0.0034851739 1 1
+ 3250 288.56663 5.7225229 0.0034851739 1 1
+ 3300 200.13238 -31.239655 0.0034851739 1 1
+ 3350 231.32512 16.631728 0.0034851739 1 1
+ 3400 260.57402 2.1717992 0.0034851739 1 1
+ 3450 301.47128 -42.210623 0.0034851739 1 1
+ 3500 321.77414 40.074365 0.0034851739 1 1
+ 3550 353.21858 28.387783 0.0034851739 1 1
+ 3600 331.45989 -57.800858 0.0034851739 1 1
+ 3650 303.88123 44.86596 0.0034851739 1 1
+ 3700 329.73833 -0.8061567 0.0034851739 1 1
+ 3750 297.55588 -0.49626022 0.0034851739 1 1
+ 3800 286.38794 -10.010003 0.0034851739 1 1
+ 3850 290.17417 -43.51187 0.0034851739 1 1
+ 3900 247.88933 51.23735 0.0034851739 1 1
+ 3950 332.31324 -18.194985 0.0034851739 1 1
+ 4000 325.56802 18.402825 0.0034851739 1 1
+ 4050 338.37594 36.430977 0.0034851739 1 1
+ 4100 370.95478 39.290285 0.0034851739 1 1
+ 4150 348.47859 -7.0779683 0.0034851739 1 1
+ 4200 241.30632 -33.371789 0.0034851739 1 1
+ 4250 242.17258 -9.9861962 0.0034851739 1 1
+ 4300 300.85311 -7.924429 0.0034851739 1 1
+ 4350 273.15684 -21.257282 0.0034851739 1 1
+ 4400 305.77464 -5.8720712 0.0034851739 1 1
+ 4450 314.97697 45.037299 0.0034851739 1 1
+ 4500 310.77723 16.958771 0.0034851739 1 1
+ 4550 302.17421 12.156862 0.0034851739 1 1
+ 4600 319.74799 6.8488914 0.0034851739 1 1
+ 4650 270.86805 -13.767907 0.0034851739 1 1
+ 4700 249.81731 -31.197484 0.0034851739 1 1
+ 4750 285.86481 -9.8916332 0.0034851739 1 1
+ 4800 233.98321 7.1338518 0.0034851739 1 1
+ 4850 302.60551 49.262886 0.0034851739 1 1
+ 4900 316.55055 34.663238 0.0034851739 1 1
+ 4950 357.32741 11.583013 0.0034851739 1 1
+ 5000 400.21044 -8.1780861 0.0034851739 1 1
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+ 5100 378.84249 -41.328772 0.0034851739 1 1
+ 5150 324.02039 -15.023852 0.0034851739 1 1
+ 5200 262.08427 10.937367 0.0034851739 1 1
+ 5250 255.75506 16.381495 0.0034851739 1 1
+ 5300 277.84991 40.682283 0.0034851739 1 1
+ 5350 302.92834 9.1989644 0.0034851739 1 1
+ 5400 283.71964 -1.6583895 0.0034851739 1 1
+ 5450 300.71261 -4.703054 0.0034851739 1 1
+ 5500 343.54987 -0.30546396 0.0034851739 1 1
+ 5550 369.51272 21.691639 0.0034851739 1 1
+ 5600 372.69786 -38.679919 0.0034851739 1 1
+ 5650 327.41256 11.352201 0.0034851739 1 1
+ 5700 278.9861 -23.82728 0.0034851739 1 1
+ 5750 308.30037 -20.756238 0.0034851739 1 1
+ 5800 341.4559 28.058314 0.0034851739 1 1
+ 5850 322.9786 -10.731862 0.0034851739 1 1
+ 5900 304.53598 32.825105 0.0034851739 1 1
+ 5950 287.17515 -36.780057 0.0034851739 1 1
+ 6000 296.52688 18.782156 0.0034851739 1 1
+ 6050 314.25411 15.99272 0.0034851739 1 1
+ 6100 313.86572 3.4344108 0.0034851739 1 1
+ 6150 325.64197 32.39212 0.0034851739 1 1
+ 6200 367.4298 -27.161154 0.0034851739 1 1
+ 6250 369.30937 39.020881 0.0034851739 1 1
+ 6300 328.92245 -23.175612 0.0034851739 1 1
+ 6350 305.6293 4.9011587 0.0034851739 1 1
+ 6400 241.70456 -13.675247 0.0034851739 1 1
+ 6450 265.66574 2.4049735 0.0034851739 1 1
+ 6500 249.3592 13.420453 0.0034851739 1 1
+ 6550 294.5367 10.856753 0.0034851739 1 1
+ 6600 308.20246 18.992923 0.0034851739 1 1
+ 6650 305.43756 -49.57151 0.0034851739 1 1
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+ 7750 363.24898 -22.473126 0.0034851739 1 1
+ 7800 350.19254 26.792307 0.0034851739 1 1
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+ 8100 328.29239 -39.901891 0.0034851739 1 1
+ 8150 406.52096 2.8669076 0.0034851739 1 1
+ 8200 332.17309 -51.168754 0.0034851739 1 1
+ 8250 354.68419 53.003157 0.0034851739 1 1
+ 8300 337.28934 20.766408 0.0034851739 1 1
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+ 8400 305.59597 24.011667 0.0034851739 1 1
+ 8450 303.25823 4.423341 0.0034851739 1 1
+ 8500 253.50747 -11.026949 0.0034851739 1 1
+ 8550 277.13504 23.204625 0.0034851739 1 1
+ 8600 291.40211 -22.253861 0.0034851739 1 1
+ 8650 307.93765 32.14162 0.0034851739 1 1
+ 8700 309.1529 0.36279434 0.0034851739 1 1
+ 8750 355.10326 11.677219 0.0034851739 1 1
+ 8800 330.21328 19.235269 0.0034851739 1 1
+ 8850 241.29109 21.707386 0.0034851739 1 1
+ 8900 319.15363 -60.010115 0.0034851739 1 1
+ 8950 308.88552 -57.637014 0.0034851739 1 1
+ 9000 272.22373 51.15837 0.0034851739 1 1
+ 9050 248.84947 7.3390565 0.0034851739 1 1
+ 9100 221.91564 48.387079 0.0034851739 1 1
+ 9150 298.03506 2.9058639 0.0034851739 1 1
+ 9200 274.25114 -24.597819 0.0034851739 1 1
+ 9250 334.08373 5.1079577 0.0034851739 1 1
+ 9300 383.07285 -23.274763 0.0034851739 1 1
+ 9350 335.00581 20.94212 0.0034851739 1 1
+ 9400 309.23862 34.074744 0.0034851739 1 1
+ 9450 312.62262 -28.468057 0.0034851739 1 1
+ 9500 324.54274 2.851136 0.0034851739 1 1
+ 9550 313.32781 22.468182 0.0034851739 1 1
+ 9600 269.04372 4.064934 0.0034851739 1 1
+ 9650 270.98476 -21.520127 0.0034851739 1 1
+ 9700 236.8736 16.250728 0.0034851739 1 1
+ 9750 333.94686 1.6864148 0.0034851739 1 1
+ 9800 330.91875 12.150018 0.0034851739 1 1
+ 9850 343.8603 25.338853 0.0034851739 1 1
+ 9900 330.93364 -28.292992 0.0034851739 1 1
+ 9950 291.25518 25.795948 0.0034851739 1 1
+ 10000 319.25565 25.323846 0.0034851739 1 1
+Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
-Performance: 237.146 ns/day, 0.101 hours/ns, 2744.751 timesteps/s
-94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
+93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0029962 | 0.10426 | 0.34564 | 43.9 | 2.86
-Bond | 0.005929 | 0.29803 | 0.95305 | 71.2 | 8.18
-Kspace | 0.83969 | 1.5992 | 1.9344 | 35.6 | 43.89
-Neigh | 0.65468 | 0.66443 | 0.67431 | 0.9 | 18.24
-Comm | 0.1727 | 0.23754 | 0.2745 | 8.0 | 6.52
-Output | 0.0048738 | 0.010774 | 0.028434 | 9.8 | 0.30
-Modify | 0.62478 | 0.70376 | 0.779 | 6.5 | 19.32
-Other | | 0.02531 | | | 0.69
+Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94
+Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22
+Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39
+Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51
+Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91
+Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33
+Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03
+Other | | 0.02359 | | | 0.66
-Nlocal: 11 ave 40 max 0 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-Nghost: 36 ave 47 max 7 min
+Nlocal: 11 ave 44 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost: 33 ave 44 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 3
-Neighs: 203 ave 809 max 0 min
+Neighs: 205.75 ave 823 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
-Total # of neighbors = 812
-Ave neighs/atom = 18.4545
+Total # of neighbors = 823
+Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
Total wall time: 0:00:03
diff --git a/examples/rigid/in.rigid-atomfile b/examples/rigid/in.rigid.atomfile
similarity index 100%
rename from examples/rigid/in.rigid-atomfile
rename to examples/rigid/in.rigid.atomfile
diff --git a/examples/rigid/in.rigid-atomvar b/examples/rigid/in.rigid.atomvar
similarity index 100%
rename from examples/rigid/in.rigid-atomvar
rename to examples/rigid/in.rigid.atomvar
diff --git a/examples/rigid/in.rigid.early b/examples/rigid/in.rigid.early
new file mode 100644
index 0000000000000000000000000000000000000000..6f04ba40f4fb3ca879f9955c964cdc7716014656
--- /dev/null
+++ b/examples/rigid/in.rigid.early
@@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
+ clump6 clump7 clump8 clump9
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/examples/rigid/in.rigid.nve b/examples/rigid/in.rigid.nve
new file mode 100644
index 0000000000000000000000000000000000000000..d61cdecfe8ac021110939746c5d908fe741d7523
--- /dev/null
+++ b/examples/rigid/in.rigid.nve
@@ -0,0 +1,81 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
+ clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/examples/rigid/in.rigid.nve.early b/examples/rigid/in.rigid.nve.early
new file mode 100644
index 0000000000000000000000000000000000000000..86e970ee75151de0d51f253585b80b9dc2a081f0
--- /dev/null
+++ b/examples/rigid/in.rigid.nve.early
@@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
+ clump6 clump7 clump8 clump9
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/examples/rigid/in.rigid-property b/examples/rigid/in.rigid.property
similarity index 100%
rename from examples/rigid/in.rigid-property
rename to examples/rigid/in.rigid.property
diff --git a/examples/rigid/log.20Apr18.rigid.atomfile.g++.1 b/examples/rigid/log.20Apr18.rigid.atomfile.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c66711c41c26e15490051359a8990e3c6fbd402b
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.atomfile.g++.1
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+variable bodies atomfile bodies.txt
+fix 1 all rigid custom v_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
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+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
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+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
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+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
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+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934367 0 5269.4889 12.025288
+ 3750 16737.731 0.20706557 0 5269.4927 12.061948
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+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
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+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
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+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.140447 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 615179.112 tau/day, 71201.286 timesteps/s
+98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010351 | 0.010351 | 0.010351 | 0.0 | 7.37
+Neigh | 0.036597 | 0.036597 | 0.036597 | 0.0 | 26.06
+Comm | 0.0092356 | 0.0092356 | 0.0092356 | 0.0 | 6.58
+Output | 0.0023856 | 0.0023856 | 0.0023856 | 0.0 | 1.70
+Modify | 0.07586 | 0.07586 | 0.07586 | 0.0 | 54.01
+Other | | 0.006017 | | | 4.28
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 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
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.atomfile.g++.4 b/examples/rigid/log.20Apr18.rigid.atomfile.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..70f86f32bbee23abe600df2cf540dd2624d5292e
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.atomfile.g++.4
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+variable bodies atomfile bodies.txt
+fix 1 all rigid custom v_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934368 0 5269.4889 12.025288
+ 3750 16737.731 0.20706558 0 5269.4927 12.061948
+ 3800 16738.578 -0.05582043 0 5269.4965 12.035665
+ 3850 16738.471 -0.016307928 0 5269.5024 12.035302
+ 3900 16738.449 -0.0058182199 0 5269.5059 12.035401
+ 3950 16738.439 -0.0012027325 0 5269.5074 12.035461
+ 4000 16738.436 -0.00020698452 0 5269.5075 12.035469
+ 4050 16738.437 0 0 5269.5078 12.035454
+ 4100 16738.437 0 0 5269.508 12.035435
+ 4150 16738.438 0 0 5269.5081 12.035426
+ 4200 16738.438 0 0 5269.5083 12.035432
+ 4250 16738.439 0 0 5269.5085 12.035447
+ 4300 16738.439 0 0 5269.5086 12.035463
+ 4350 16738.44 0 0 5269.5087 12.035474
+ 4400 16738.44 0 0 5269.5088 12.035478
+ 4450 16738.44 0 0 5269.5089 12.035474
+ 4500 16738.44 0 0 5269.509 12.035462
+ 4550 16738.441 0 0 5269.5092 12.035449
+ 4600 16738.441 0 0 5269.5093 12.035445
+ 4650 16738.442 0 0 5269.5095 12.035451
+ 4700 16738.442 0 0 5269.5096 12.03546
+ 4750 16738.443 0 0 5269.5097 12.035465
+ 4800 16738.443 0 0 5269.5098 12.035466
+ 4850 16738.443 0 0 5269.51 12.035463
+ 4900 16738.444 0 0 5269.5101 12.035456
+ 4950 16738.444 0 0 5269.5102 12.035447
+ 5000 16738.445 0 0 5269.5104 12.03544
+ 5050 16738.445 0 0 5269.5105 12.035442
+ 5100 16738.446 0 0 5269.5107 12.035455
+ 5150 16738.446 0 0 5269.5108 12.03547
+ 5200 16738.446 0 0 5269.5109 12.035479
+ 5250 16738.447 0 0 5269.511 12.035479
+ 5300 16738.447 0 0 5269.5111 12.03547
+ 5350 16738.447 0 0 5269.5112 12.035454
+ 5400 16738.448 0 0 5269.5113 12.035434
+ 5450 16738.448 0 0 5269.5115 12.03542
+ 5500 16738.449 0 0 5269.5117 12.035422
+ 5550 16738.457 -0.0030919234 0 5269.5111 12.035383
+ 5600 16738.51 -0.021618357 0 5269.5092 12.035106
+ 5650 16738.622 -0.059214788 0 5269.507 12.035694
+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
+ 5800 16738.456 -0.0037013529 0 5269.5102 12.011675
+ 5850 16738.451 0 0 5269.5123 12.011709
+ 5900 16738.451 -0.0002211587 0 5269.5122 12.011687
+ 5950 16738.452 -0.00024253349 0 5269.5124 12.011678
+ 6000 16738.452 0 0 5269.5128 12.011688
+ 6050 16738.453 0 0 5269.513 12.011702
+ 6100 16738.453 0 0 5269.5131 12.011716
+ 6150 16738.454 0 0 5269.5132 12.011725
+ 6200 16738.454 0 0 5269.5133 12.011728
+ 6250 16738.454 0 0 5269.5134 12.011723
+ 6300 16738.455 0 0 5269.5135 12.011712
+ 6350 16738.455 0 0 5269.5137 12.0117
+ 6400 16738.456 0 0 5269.5138 12.011697
+ 6450 16738.456 0 0 5269.514 12.011704
+ 6500 16738.456 0 0 5269.5141 12.011714
+ 6550 16738.457 0 0 5269.5142 12.011719
+ 6600 16738.457 0 0 5269.5143 12.011718
+ 6650 16738.458 0 0 5269.5144 12.011713
+ 6700 16738.458 0 0 5269.5146 12.011705
+ 6750 16738.459 0 0 5269.5147 12.011696
+ 6800 16738.459 0 0 5269.5149 12.01169
+ 6850 16738.46 0 0 5269.515 12.011695
+ 6900 16738.46 0 0 5269.5152 12.01171
+ 6950 16738.46 0 0 5269.5153 12.011726
+ 7000 16738.461 0 0 5269.5154 12.011736
+ 7050 16738.461 0 0 5269.5155 12.011737
+ 7100 16738.461 0 0 5269.5155 12.011728
+ 7150 16738.461 0 0 5269.5156 12.011712
+ 7200 16738.462 0 0 5269.5158 12.011691
+ 7250 16738.463 0 0 5269.516 12.011676
+ 7300 16738.463 0 0 5269.5162 12.011677
+ 7350 16738.464 0 0 5269.5164 12.011693
+ 7400 16738.464 0 0 5269.5165 12.011713
+ 7450 16738.465 0 0 5269.5166 12.011729
+ 7500 16738.465 0 0 5269.5167 12.011736
+ 7550 16738.465 0 0 5269.5168 12.011734
+ 7600 16738.465 0 0 5269.5168 12.011722
+ 7650 16738.466 0 0 5269.517 12.011704
+ 7700 16738.466 0 0 5269.5171 12.011687
+ 7750 16738.467 0 0 5269.5173 12.011681
+ 7800 16738.467 0 0 5269.5175 12.011687
+ 7850 16738.468 0 0 5269.5176 12.0117
+ 7900 16738.468 0 0 5269.5178 12.011712
+ 7950 16738.469 0 0 5269.5179 12.011721
+ 8000 16738.469 0 0 5269.518 12.011724
+ 8050 16738.469 0 0 5269.5181 12.01172
+ 8100 16738.47 0 0 5269.5182 12.011709
+ 8150 16738.47 0 0 5269.5183 12.0117
+ 8200 16738.47 0 0 5269.5185 12.0117
+ 8250 16738.471 0 0 5269.5186 12.011709
+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690664 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532811 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.191483 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 451214.099 tau/day, 52223.854 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0024264 | 0.0036595 | 0.0042815 | 1.2 | 1.91
+Neigh | 0.011347 | 0.012011 | 0.013367 | 0.7 | 6.27
+Comm | 0.081701 | 0.083476 | 0.087947 | 0.9 | 43.59
+Output | 0.0042565 | 0.0045614 | 0.0053556 | 0.7 | 2.38
+Modify | 0.075719 | 0.078165 | 0.080737 | 0.7 | 40.82
+Other | | 0.009611 | | | 5.02
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.atomvar.g++.1 b/examples/rigid/log.20Apr18.rigid.atomvar.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..99098d04d21db9221011b9f511c469eb180e213f
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.atomvar.g++.1
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
+fix 1 all rigid custom v_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
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+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652438 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814371 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589893 0 5269.4979 12.062708
+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.139024 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 621477.474 tau/day, 71930.263 timesteps/s
+99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010292 | 0.010292 | 0.010292 | 0.0 | 7.40
+Neigh | 0.036968 | 0.036968 | 0.036968 | 0.0 | 26.59
+Comm | 0.0091348 | 0.0091348 | 0.0091348 | 0.0 | 6.57
+Output | 0.0024047 | 0.0024047 | 0.0024047 | 0.0 | 1.73
+Modify | 0.074017 | 0.074017 | 0.074017 | 0.0 | 53.24
+Other | | 0.006207 | | | 4.46
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 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
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.atomvar.g++.4 b/examples/rigid/log.20Apr18.rigid.atomvar.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..76344d09952c3346a80847688e6398edebf5d765
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.atomvar.g++.4
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
+fix 1 all rigid custom v_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
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+ 200 16733.929 1.372872 0 5269.4617 14.569267
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+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
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+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.202733 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 426175.966 tau/day, 49325.922 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0025222 | 0.0037088 | 0.0044038 | 1.2 | 1.83
+Neigh | 0.01135 | 0.012003 | 0.013654 | 0.9 | 5.92
+Comm | 0.088217 | 0.089948 | 0.091659 | 0.4 | 44.37
+Output | 0.0044014 | 0.0047023 | 0.0055132 | 0.7 | 2.32
+Modify | 0.080218 | 0.082638 | 0.084872 | 0.6 | 40.76
+Other | | 0.009733 | | | 4.80
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.early.g++.1 b/examples/rigid/log.20Apr18.rigid.early.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..5402647b9814753bbcfd831d54d12823586a59f1
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.early.g++.1
@@ -0,0 +1,337 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
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+ 8050 16738.469 0 0 5269.5181 12.01172
+ 8100 16738.47 0 0 5269.5182 12.011709
+ 8150 16738.47 0 0 5269.5183 12.0117
+ 8200 16738.47 0 0 5269.5185 12.0117
+ 8250 16738.471 0 0 5269.5186 12.011709
+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690663 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646802 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532813 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652438 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814371 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589893 0 5269.4979 12.062708
+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.142284 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 607236.588 tau/day, 70282.013 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010693 | 0.010693 | 0.010693 | 0.0 | 7.52
+Neigh | 0.037908 | 0.037908 | 0.037908 | 0.0 | 26.64
+Comm | 0.0087049 | 0.0087049 | 0.0087049 | 0.0 | 6.12
+Output | 0.0025849 | 0.0025849 | 0.0025849 | 0.0 | 1.82
+Modify | 0.076329 | 0.076329 | 0.076329 | 0.0 | 53.65
+Other | | 0.006064 | | | 4.26
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 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
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.early.g++.4 b/examples/rigid/log.20Apr18.rigid.early.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c9513a211e9fbc42cfb70bea162e3791cbd98abc
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.early.g++.4
@@ -0,0 +1,337 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934368 0 5269.4889 12.025288
+ 3750 16737.731 0.20706558 0 5269.4927 12.061948
+ 3800 16738.578 -0.05582043 0 5269.4965 12.035665
+ 3850 16738.471 -0.016307928 0 5269.5024 12.035302
+ 3900 16738.449 -0.0058182199 0 5269.5059 12.035401
+ 3950 16738.439 -0.0012027325 0 5269.5074 12.035461
+ 4000 16738.436 -0.00020698452 0 5269.5075 12.035469
+ 4050 16738.437 0 0 5269.5078 12.035454
+ 4100 16738.437 0 0 5269.508 12.035435
+ 4150 16738.438 0 0 5269.5081 12.035426
+ 4200 16738.438 0 0 5269.5083 12.035432
+ 4250 16738.439 0 0 5269.5085 12.035447
+ 4300 16738.439 0 0 5269.5086 12.035463
+ 4350 16738.44 0 0 5269.5087 12.035474
+ 4400 16738.44 0 0 5269.5088 12.035478
+ 4450 16738.44 0 0 5269.5089 12.035474
+ 4500 16738.44 0 0 5269.509 12.035462
+ 4550 16738.441 0 0 5269.5092 12.035449
+ 4600 16738.441 0 0 5269.5093 12.035445
+ 4650 16738.442 0 0 5269.5095 12.035451
+ 4700 16738.442 0 0 5269.5096 12.03546
+ 4750 16738.443 0 0 5269.5097 12.035465
+ 4800 16738.443 0 0 5269.5098 12.035466
+ 4850 16738.443 0 0 5269.51 12.035463
+ 4900 16738.444 0 0 5269.5101 12.035456
+ 4950 16738.444 0 0 5269.5102 12.035447
+ 5000 16738.445 0 0 5269.5104 12.03544
+ 5050 16738.445 0 0 5269.5105 12.035442
+ 5100 16738.446 0 0 5269.5107 12.035455
+ 5150 16738.446 0 0 5269.5108 12.03547
+ 5200 16738.446 0 0 5269.5109 12.035479
+ 5250 16738.447 0 0 5269.511 12.035479
+ 5300 16738.447 0 0 5269.5111 12.03547
+ 5350 16738.447 0 0 5269.5112 12.035454
+ 5400 16738.448 0 0 5269.5113 12.035434
+ 5450 16738.448 0 0 5269.5115 12.03542
+ 5500 16738.449 0 0 5269.5117 12.035422
+ 5550 16738.457 -0.0030919234 0 5269.5111 12.035383
+ 5600 16738.51 -0.021618357 0 5269.5092 12.035106
+ 5650 16738.622 -0.059214788 0 5269.507 12.035694
+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
+ 5800 16738.456 -0.0037013529 0 5269.5102 12.011675
+ 5850 16738.451 0 0 5269.5123 12.011709
+ 5900 16738.451 -0.0002211587 0 5269.5122 12.011687
+ 5950 16738.452 -0.00024253349 0 5269.5124 12.011678
+ 6000 16738.452 0 0 5269.5128 12.011688
+ 6050 16738.453 0 0 5269.513 12.011702
+ 6100 16738.453 0 0 5269.5131 12.011716
+ 6150 16738.454 0 0 5269.5132 12.011725
+ 6200 16738.454 0 0 5269.5133 12.011728
+ 6250 16738.454 0 0 5269.5134 12.011723
+ 6300 16738.455 0 0 5269.5135 12.011712
+ 6350 16738.455 0 0 5269.5137 12.0117
+ 6400 16738.456 0 0 5269.5138 12.011697
+ 6450 16738.456 0 0 5269.514 12.011704
+ 6500 16738.456 0 0 5269.5141 12.011714
+ 6550 16738.457 0 0 5269.5142 12.011719
+ 6600 16738.457 0 0 5269.5143 12.011718
+ 6650 16738.458 0 0 5269.5144 12.011713
+ 6700 16738.458 0 0 5269.5146 12.011705
+ 6750 16738.459 0 0 5269.5147 12.011696
+ 6800 16738.459 0 0 5269.5149 12.01169
+ 6850 16738.46 0 0 5269.515 12.011695
+ 6900 16738.46 0 0 5269.5152 12.01171
+ 6950 16738.46 0 0 5269.5153 12.011726
+ 7000 16738.461 0 0 5269.5154 12.011736
+ 7050 16738.461 0 0 5269.5155 12.011737
+ 7100 16738.461 0 0 5269.5155 12.011728
+ 7150 16738.461 0 0 5269.5156 12.011712
+ 7200 16738.462 0 0 5269.5158 12.011691
+ 7250 16738.463 0 0 5269.516 12.011676
+ 7300 16738.463 0 0 5269.5162 12.011677
+ 7350 16738.464 0 0 5269.5164 12.011693
+ 7400 16738.464 0 0 5269.5165 12.011713
+ 7450 16738.465 0 0 5269.5166 12.011729
+ 7500 16738.465 0 0 5269.5167 12.011736
+ 7550 16738.465 0 0 5269.5168 12.011734
+ 7600 16738.465 0 0 5269.5168 12.011722
+ 7650 16738.466 0 0 5269.517 12.011704
+ 7700 16738.466 0 0 5269.5171 12.011687
+ 7750 16738.467 0 0 5269.5173 12.011681
+ 7800 16738.467 0 0 5269.5175 12.011687
+ 7850 16738.468 0 0 5269.5176 12.0117
+ 7900 16738.468 0 0 5269.5178 12.011712
+ 7950 16738.469 0 0 5269.5179 12.011721
+ 8000 16738.469 0 0 5269.518 12.011724
+ 8050 16738.469 0 0 5269.5181 12.01172
+ 8100 16738.47 0 0 5269.5182 12.011709
+ 8150 16738.47 0 0 5269.5183 12.0117
+ 8200 16738.47 0 0 5269.5185 12.0117
+ 8250 16738.471 0 0 5269.5186 12.011709
+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690664 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532811 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.170899 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 505560.431 tau/day, 58513.939 timesteps/s
+96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0024047 | 0.0038016 | 0.0044513 | 1.3 | 2.22
+Neigh | 0.011313 | 0.012043 | 0.013355 | 0.7 | 7.05
+Comm | 0.066761 | 0.069035 | 0.071617 | 0.7 | 40.40
+Output | 0.0038884 | 0.0041398 | 0.0048923 | 0.7 | 2.42
+Modify | 0.071143 | 0.072567 | 0.074478 | 0.4 | 42.46
+Other | | 0.009313 | | | 5.45
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.5Oct16.rigid.g++.4 b/examples/rigid/log.20Apr18.rigid.g++.1
similarity index 91%
rename from examples/rigid/log.5Oct16.rigid.g++.4
rename to examples/rigid/log.20Apr18.rigid.g++.1
index 968f3a2d99bab33a911e22007e3ebc8548aba0ab..ca76376e320f83b2172b8d71b901e500c6b9314f 100644
--- a/examples/rigid/log.5Oct16.rigid.g++.4
+++ b/examples/rigid/log.20Apr18.rigid.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
@@ -8,7 +9,7 @@ pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 2 by 2 MPI processor grid
+ 1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
@@ -91,13 +92,18 @@ timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 3.62803 Mbytes
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
@@ -151,7 +157,7 @@ Step Temp E_pair E_mol TotEng Press
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
- 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
+ 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
@@ -173,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
- 3700 16738.602 -0.070934368 0 5269.4889 12.025288
+ 3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
@@ -269,7 +275,7 @@ Step Temp E_pair E_mol TotEng Press
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
- 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
+ 8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
@@ -290,37 +296,37 @@ Step Temp E_pair E_mol TotEng Press
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
- 9550 16738.493 -0.0053156163 0 5269.5203 12.011611
+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
- 9700 16735.041 1.0589894 0 5269.4979 12.062708
- 9750 16738.013 0.13550109 0 5269.5101 11.407246
- 9800 16738.512 -0.011620327 0 5269.5201 11.394974
- 9850 16738.489 -0.00067270507 0 5269.5237 11.395098
- 9900 16738.489 -0.00024984555 0 5269.5242 11.395085
+ 9700 16735.041 1.0589893 0 5269.4979 12.062708
+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
-Loop time of 0.169479 on 4 procs for 10000 steps with 81 atoms
+Loop time of 0.155936 on 1 procs for 10000 steps with 81 atoms
-Performance: 509796.561 tau/day, 59004.232 timesteps/s
-98.1% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 554075.151 tau/day, 64129.068 timesteps/s
+98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0024633 | 0.0031875 | 0.0039403 | 0.9 | 1.88
-Neigh | 0.010975 | 0.011817 | 0.013459 | 0.9 | 6.97
-Comm | 0.072126 | 0.074024 | 0.076456 | 0.7 | 43.68
-Output | 0.0034711 | 0.0036327 | 0.0040615 | 0.4 | 2.14
-Modify | 0.069286 | 0.070574 | 0.073233 | 0.6 | 41.64
-Other | | 0.006244 | | | 3.68
+Pair | 0.013007 | 0.013007 | 0.013007 | 0.0 | 8.34
+Neigh | 0.041885 | 0.041885 | 0.041885 | 0.0 | 26.86
+Comm | 0.0094752 | 0.0094752 | 0.0094752 | 0.0 | 6.08
+Output | 0.002636 | 0.002636 | 0.002636 | 0.0 | 1.69
+Modify | 0.082249 | 0.082249 | 0.082249 | 0.0 | 52.75
+Other | | 0.006683 | | | 4.29
-Nlocal: 20.25 ave 38 max 3 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Nghost: 27.25 ave 48 max 13 min
-Histogram: 1 0 1 1 0 0 0 0 0 1
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
+Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
diff --git a/examples/rigid/log.5Oct16.rigid.g++.1 b/examples/rigid/log.20Apr18.rigid.g++.4
similarity index 89%
rename from examples/rigid/log.5Oct16.rigid.g++.1
rename to examples/rigid/log.20Apr18.rigid.g++.4
index 9b84f89c95e3182a0875dedd6ef0d13aa131af08..ff72c213edb53af7c1d29d67f70410453e144ca6 100644
--- a/examples/rigid/log.5Oct16.rigid.g++.1
+++ b/examples/rigid/log.20Apr18.rigid.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
@@ -8,7 +9,7 @@ pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 1 by 1 MPI processor grid
+ 1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
@@ -91,13 +92,18 @@ timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 3.65531 Mbytes
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
@@ -151,8 +157,8 @@ Step Temp E_pair E_mol TotEng Press
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
- 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
- 2650 16733.017 1.7051479 0 5269.5067 14.596295
+ 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
@@ -160,7 +166,7 @@ Step Temp E_pair E_mol TotEng Press
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
- 3050 16715.332 7.2419352 0 5269.476 14.870305
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
@@ -170,7 +176,7 @@ Step Temp E_pair E_mol TotEng Press
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
- 3550 16713.405 7.8460621 0 5269.4737 12.389816
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
@@ -268,8 +274,8 @@ Step Temp E_pair E_mol TotEng Press
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
- 8450 16738.473 -0.00039690666 0 5269.5189 12.011706
- 8500 16738.481 -0.0034646804 0 5269.5182 12.011643
+ 8450 16738.473 -0.00039690664 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
@@ -289,38 +295,38 @@ Step Temp E_pair E_mol TotEng Press
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
- 9500 16738.481 -0.00037652434 0 5269.5216 12.011692
- 9550 16738.493 -0.005315616 0 5269.5203 12.011611
- 9600 16738.549 -0.026814368 0 5269.5163 12.011415
+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
- 9700 16735.041 1.0589885 0 5269.4979 12.062708
- 9750 16738.013 0.13550123 0 5269.5101 11.407245
- 9800 16738.512 -0.011620328 0 5269.5201 11.394974
- 9850 16738.489 -0.00067270523 0 5269.5237 11.395098
- 9900 16738.489 -0.00024984554 0 5269.5242 11.395085
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
-Loop time of 0.125672 on 1 procs for 10000 steps with 81 atoms
+Loop time of 0.194532 on 4 procs for 10000 steps with 81 atoms
-Performance: 687503.421 tau/day, 79572.155 timesteps/s
-100.2% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 444142.918 tau/day, 51405.430 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0097554 | 0.0097554 | 0.0097554 | 0.0 | 7.76
-Neigh | 0.038657 | 0.038657 | 0.038657 | 0.0 | 30.76
-Comm | 0.0074 | 0.0074 | 0.0074 | 0.0 | 5.89
-Output | 0.0010791 | 0.0010791 | 0.0010791 | 0.0 | 0.86
-Modify | 0.064604 | 0.064604 | 0.064604 | 0.0 | 51.41
-Other | | 0.004176 | | | 3.32
+Pair | 0.0025368 | 0.003831 | 0.0045376 | 1.2 | 1.97
+Neigh | 0.011299 | 0.012014 | 0.013005 | 0.6 | 6.18
+Comm | 0.081939 | 0.084112 | 0.087817 | 0.8 | 43.24
+Output | 0.0044608 | 0.0047221 | 0.0053811 | 0.6 | 2.43
+Modify | 0.078212 | 0.080219 | 0.082467 | 0.7 | 41.24
+Other | | 0.009634 | | | 4.95
-Nlocal: 81 ave 81 max 81 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 84 ave 84 max 84 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
+Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
diff --git a/examples/rigid/log.20Apr18.rigid.nve.early.g++.1 b/examples/rigid/log.20Apr18.rigid.nve.early.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..7e92b4e6ef4efd96d7d3e1077f54cfc42e36a93c
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.nve.early.g++.1
@@ -0,0 +1,337 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.69 571.70921 0 5265.8153 32.005816
+ 100 16298.128 136.75661 0 5267.6488 16.449029
+ 150 16682.532 17.504156 0 5269.4124 14.901186
+ 200 16733.906 1.3755079 0 5269.4571 14.571305
+ 250 16738.861 -0.15272039 0 5269.4886 14.498342
+ 300 16738.608 -0.055216883 0 5269.5066 14.498
+ 350 16738.5 -0.017457072 0 5269.5104 14.498392
+ 400 16738.451 -0.0060161309 0 5269.5063 14.49851
+ 450 16738.435 -0.001271965 0 5269.5059 14.498571
+ 500 16738.443 -0.00081074175 0 5269.509 14.498598
+ 550 16738.452 -0.00083208965 0 5269.5118 14.498618
+ 600 16738.45 -0.00058358431 0 5269.5116 14.498617
+ 650 16738.443 -0.00047228525 0 5269.5093 14.4986
+ 700 16738.444 0 0 5269.5102 14.498612
+ 750 16738.461 0 0 5269.5157 14.498654
+ 800 16738.479 0 0 5269.521 14.498697
+ 850 16738.473 0 0 5269.5192 14.498683
+ 900 16738.449 0 0 5269.5116 14.498624
+ 950 16738.438 -0.0035324203 0 5269.5046 14.498537
+ 1000 16738.562 -0.051134242 0 5269.4963 14.498093
+ 1050 16737.343 0.32970192 0 5269.4934 14.527634
+ 1100 16737.878 0.16213235 0 5269.4941 14.533864
+ 1150 16738.682 -0.089236256 0 5269.4959 14.511765
+ 1200 16738.444 -0.0075446558 0 5269.5025 14.512479
+ 1250 16738.45 0 0 5269.5119 14.512611
+ 1300 16738.475 0 0 5269.5199 14.512673
+ 1350 16738.484 0 0 5269.5228 14.512696
+ 1400 16738.469 -0.00044683992 0 5269.5175 14.512651
+ 1450 16738.45 -0.0010933363 0 5269.511 14.512595
+ 1500 16738.445 -0.00057484239 0 5269.51 14.512591
+ 1550 16738.451 0 0 5269.5123 14.512615
+ 1600 16738.452 0 0 5269.5127 14.512618
+ 1650 16738.443 0 0 5269.5099 14.512596
+ 1700 16738.433 0 0 5269.5068 14.512572
+ 1750 16738.438 0 0 5269.5084 14.512584
+ 1800 16738.459 0 0 5269.5149 14.512635
+ 1850 16738.473 0 0 5269.5193 14.51267
+ 1900 16738.462 0 0 5269.5159 14.512644
+ 1950 16738.446 -0.0032069962 0 5269.5076 14.512539
+ 2000 16738.463 -0.013425408 0 5269.5027 14.512382
+ 2050 16738.535 -0.036964311 0 5269.5017 14.512152
+ 2100 16738.621 -0.063490509 0 5269.5023 14.512108
+ 2150 16738.594 -0.056143934 0 5269.5012 14.512117
+ 2200 16738.536 -0.038486645 0 5269.5007 14.512277
+ 2250 16738.496 -0.023712406 0 5269.503 14.51242
+ 2300 16738.488 -0.013209094 0 5269.5109 14.51255
+ 2350 16738.486 -0.0045244524 0 5269.519 14.512693
+ 2400 16738.475 -0.00051678325 0 5269.5194 14.512743
+ 2450 16738.456 -0.0023209272 0 5269.5115 14.512659
+ 2500 16738.442 -0.0052101787 0 5269.5042 14.512594
+ 2550 16738.552 -0.04420046 0 5269.4998 14.512177
+ 2600 16738.42 -0.004347531 0 5269.4982 14.512783
+ 2650 16734.241 1.3131302 0 5269.5 14.577195
+ 2700 16738.737 -0.10612056 0 5269.4961 14.503874
+ 2750 16732.705 1.7939719 0 5269.4974 14.629294
+ 2800 16738.558 -0.042867033 0 5269.5032 14.519893
+ 2850 16738.499 -0.01271227 0 5269.5146 14.518524
+ 2900 16738.486 -0.0032778045 0 5269.52 14.518712
+ 2950 16738.482 -0.0089544631 0 5269.5133 14.518629
+ 3000 16738.647 -0.070862542 0 5269.5031 14.51803
+ 3050 16678.313 18.829038 0 5269.409 15.533426
+ 3100 16632.312 33.399217 0 5269.4975 14.588597
+ 3150 16739.318 -0.31388148 0 5269.4715 13.520782
+ 3200 16727.951 3.26736 0 5269.4741 12.288358
+ 3250 16686.364 16.353793 0 5269.4682 14.152517
+ 3300 16738.532 -0.031574462 0 5269.5064 13.310615
+ 3350 16738.454 -0.0062292918 0 5269.5071 13.308187
+ 3400 16738.445 -0.0049349125 0 5269.5055 13.308178
+ 3450 16738.489 -0.021623738 0 5269.5026 13.308001
+ 3500 16737.78 0.19719043 0 5269.4983 13.325999
+ 3550 16658.578 25.116206 0 5269.4834 13.778249
+ 3600 16738.51 -0.032864725 0 5269.4981 12.392389
+ 3650 16738.899 -0.15952703 0 5269.4938 12.383503
+ 3700 16738.879 -0.16025994 0 5269.487 12.382575
+ 3750 16738.878 -0.16608251 0 5269.4806 12.382765
+ 3800 16738.591 -0.078679341 0 5269.4776 12.383227
+ 3850 16738.429 -0.024729409 0 5269.4807 12.382942
+ 3900 16738.399 -0.0062729967 0 5269.4897 12.383192
+ 3950 16738.428 -0.002521266 0 5269.5027 12.383324
+ 4000 16738.467 -0.0002068506 0 5269.5173 12.383474
+ 4050 16738.488 0 0 5269.5241 12.383531
+ 4100 16738.468 0 0 5269.5178 12.383482
+ 4150 16738.422 0 0 5269.5033 12.383369
+ 4200 16738.387 0 0 5269.4921 12.383281
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+ 8700 16738.446 0.00084613367 0 5269.5116 10.591358
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+ 9100 16738.477 0 0 5269.5205 10.590519
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+ 9200 16738.502 0 0 5269.5285 10.590583
+ 9250 16738.493 0 0 5269.5254 10.590559
+ 9300 16738.482 0 0 5269.522 10.590532
+ 9350 16738.46 0 0 5269.5151 10.590478
+ 9400 16738.48 0 0 5269.5216 10.590528
+ 9450 16738.509 0 0 5269.5306 10.590599
+ 9500 16738.49 0 0 5269.5247 10.590554
+ 9550 16738.484 0 0 5269.5226 10.590536
+ 9600 16738.483 0 0 5269.5223 10.590534
+ 9650 16738.464 0 0 5269.5165 10.590489
+ 9700 16738.484 0 0 5269.5228 10.590537
+ 9750 16738.507 0 0 5269.53 10.590595
+ 9800 16738.482 0 0 5269.522 10.590532
+ 9850 16738.478 0 0 5269.5207 10.590521
+ 9900 16738.487 -0.00030979882 0 5269.5233 10.590538
+ 9950 16738.476 -0.00095967357 0 5269.5193 10.590496
+ 10000 16738.494 -0.00062714625 0 5269.5253 10.590548
+Loop time of 0.166298 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 519549.516 tau/day, 60133.046 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 | 0.011685 | 0.011685 | 0.011685 | 0.0 | 7.03
+Neigh | 0.038539 | 0.038539 | 0.038539 | 0.0 | 23.17
+Comm | 0.0086315 | 0.0086315 | 0.0086315 | 0.0 | 5.19
+Output | 0.0026531 | 0.0026531 | 0.0026531 | 0.0 | 1.60
+Modify | 0.098759 | 0.098759 | 0.098759 | 0.0 | 59.39
+Other | | 0.00603 | | | 3.63
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 49 ave 49 max 49 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3 ave 3 max 3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3
+Ave neighs/atom = 0.037037
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.nve.early.g++.4 b/examples/rigid/log.20Apr18.rigid.nve.early.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..1c3592990bbae7b9871d3557490358b33bd2dcb9
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.nve.early.g++.4
@@ -0,0 +1,337 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.69 571.70921 0 5265.8153 32.005816
+ 100 16298.128 136.75661 0 5267.6488 16.449029
+ 150 16682.532 17.504156 0 5269.4124 14.901186
+ 200 16733.906 1.3755079 0 5269.4571 14.571305
+ 250 16738.861 -0.15272039 0 5269.4886 14.498342
+ 300 16738.608 -0.055216883 0 5269.5066 14.498
+ 350 16738.5 -0.017457072 0 5269.5104 14.498392
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+ 550 16738.452 -0.00083208965 0 5269.5118 14.498618
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+ 7800 16738.398 0 0 5269.4958 12.521267
+ 7850 16738.407 -0.00021180715 0 5269.4982 12.521283
+ 7900 16738.441 -0.0002167946 0 5269.509 12.521367
+ 7950 16738.446 -0.0002384787 0 5269.5107 12.52138
+ 8000 16738.423 0 0 5269.5035 12.521327
+ 8050 16738.423 0 0 5269.5034 12.521325
+ 8100 16738.478 -0.00069624484 0 5269.52 12.521448
+ 8150 16738.523 -0.0040058183 0 5269.531 12.521494
+ 8200 16738.486 -0.0092298512 0 5269.5142 12.521328
+ 8250 16738.458 -0.023189661 0 5269.4914 12.521008
+ 8300 16738.513 -0.045847765 0 5269.4861 12.520773
+ 8350 16723.735 4.5720344 0 5269.4516 12.849543
+ 8400 16738.466 -0.02019859 0 5269.497 12.835812
+ 8450 16738.437 -0.012822198 0 5269.4952 12.829979
+ 8500 16738.408 -0.0016833646 0 5269.4972 12.830104
+ 8550 16738.464 -0.00097382606 0 5269.5155 12.830258
+ 8600 16738.669 -0.050581176 0 5269.5304 12.829977
+ 8650 15918.073 250.131 0 5261.3761 24.542327
+ 8700 16738.446 0.00085039409 0 5269.5116 10.59114
+ 8750 16738.472 -0.010146632 0 5269.5089 10.590059
+ 8800 16738.468 0 0 5269.5176 10.590278
+ 8850 16738.508 0 0 5269.5303 10.590378
+ 8900 16738.509 0 0 5269.5306 10.590381
+ 8950 16738.496 0 0 5269.5266 10.590349
+ 9000 16738.477 0 0 5269.5204 10.590302
+ 9050 16738.455 0 0 5269.5135 10.590247
+ 9100 16738.477 0 0 5269.5205 10.590301
+ 9150 16738.512 0 0 5269.5315 10.590388
+ 9200 16738.502 0 0 5269.5285 10.590364
+ 9250 16738.493 0 0 5269.5254 10.59034
+ 9300 16738.482 0 0 5269.522 10.590314
+ 9350 16738.46 0 0 5269.5151 10.59026
+ 9400 16738.48 0 0 5269.5216 10.59031
+ 9450 16738.509 0 0 5269.5306 10.590381
+ 9500 16738.49 0 0 5269.5247 10.590335
+ 9550 16738.484 0 0 5269.5226 10.590318
+ 9600 16738.483 0 0 5269.5223 10.590316
+ 9650 16738.464 0 0 5269.5165 10.590271
+ 9700 16738.484 0 0 5269.5228 10.590319
+ 9750 16738.507 0 0 5269.53 10.590376
+ 9800 16738.482 0 0 5269.522 10.590314
+ 9850 16738.478 0 0 5269.5207 10.590303
+ 9900 16738.487 -0.00030979874 0 5269.5233 10.59032
+ 9950 16738.476 -0.00095967134 0 5269.5192 10.590278
+ 10000 16738.494 -0.00062714318 0 5269.5253 10.590329
+Loop time of 0.224811 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 384323.005 tau/day, 44481.829 timesteps/s
+95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0032673 | 0.0039269 | 0.0048387 | 1.1 | 1.75
+Neigh | 0.010401 | 0.012159 | 0.015022 | 1.6 | 5.41
+Comm | 0.087584 | 0.08909 | 0.090645 | 0.4 | 39.63
+Output | 0.0042956 | 0.0045624 | 0.0052695 | 0.6 | 2.03
+Modify | 0.10208 | 0.10506 | 0.10697 | 0.6 | 46.73
+Other | | 0.01001 | | | 4.45
+
+Nlocal: 20.25 ave 34 max 9 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 38.5 ave 43 max 26 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs: 0.75 ave 2 max 0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 3
+Ave neighs/atom = 0.037037
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.nve.g++.1 b/examples/rigid/log.20Apr18.rigid.nve.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..26fa4e7f680fb2a016cb0ea0c4ec195855ca4224
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.nve.g++.1
@@ -0,0 +1,335 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.69 571.70921 0 5265.8153 32.005816
+ 100 16298.128 136.75661 0 5267.6488 16.449029
+ 150 16682.532 17.504156 0 5269.4124 14.901186
+ 200 16733.906 1.3755079 0 5269.4571 14.571305
+ 250 16738.861 -0.15272039 0 5269.4886 14.498342
+ 300 16738.608 -0.055216883 0 5269.5066 14.498
+ 350 16738.5 -0.017457072 0 5269.5104 14.498392
+ 400 16738.451 -0.0060161309 0 5269.5063 14.49851
+ 450 16738.435 -0.001271965 0 5269.5059 14.498571
+ 500 16738.443 -0.00081074175 0 5269.509 14.498598
+ 550 16738.452 -0.00083208965 0 5269.5118 14.498618
+ 600 16738.45 -0.00058358431 0 5269.5116 14.498617
+ 650 16738.443 -0.00047228525 0 5269.5093 14.4986
+ 700 16738.444 0 0 5269.5102 14.498612
+ 750 16738.461 0 0 5269.5157 14.498654
+ 800 16738.479 0 0 5269.521 14.498697
+ 850 16738.473 0 0 5269.5192 14.498683
+ 900 16738.449 0 0 5269.5116 14.498624
+ 950 16738.438 -0.0035324203 0 5269.5046 14.498537
+ 1000 16738.562 -0.051134242 0 5269.4963 14.498093
+ 1050 16737.343 0.32970192 0 5269.4934 14.527634
+ 1100 16737.878 0.16213235 0 5269.4941 14.533864
+ 1150 16738.682 -0.089236256 0 5269.4959 14.511765
+ 1200 16738.444 -0.0075446558 0 5269.5025 14.512479
+ 1250 16738.45 0 0 5269.5119 14.512611
+ 1300 16738.475 0 0 5269.5199 14.512673
+ 1350 16738.484 0 0 5269.5228 14.512696
+ 1400 16738.469 -0.00044683992 0 5269.5175 14.512651
+ 1450 16738.45 -0.0010933363 0 5269.511 14.512595
+ 1500 16738.445 -0.00057484239 0 5269.51 14.512591
+ 1550 16738.451 0 0 5269.5123 14.512615
+ 1600 16738.452 0 0 5269.5127 14.512618
+ 1650 16738.443 0 0 5269.5099 14.512596
+ 1700 16738.433 0 0 5269.5068 14.512572
+ 1750 16738.438 0 0 5269.5084 14.512584
+ 1800 16738.459 0 0 5269.5149 14.512635
+ 1850 16738.473 0 0 5269.5193 14.51267
+ 1900 16738.462 0 0 5269.5159 14.512644
+ 1950 16738.446 -0.0032069962 0 5269.5076 14.512539
+ 2000 16738.463 -0.013425408 0 5269.5027 14.512382
+ 2050 16738.535 -0.036964311 0 5269.5017 14.512152
+ 2100 16738.621 -0.063490509 0 5269.5023 14.512108
+ 2150 16738.594 -0.056143934 0 5269.5012 14.512117
+ 2200 16738.536 -0.038486645 0 5269.5007 14.512277
+ 2250 16738.496 -0.023712406 0 5269.503 14.51242
+ 2300 16738.488 -0.013209094 0 5269.5109 14.51255
+ 2350 16738.486 -0.0045244524 0 5269.519 14.512693
+ 2400 16738.475 -0.00051678325 0 5269.5194 14.512743
+ 2450 16738.456 -0.0023209272 0 5269.5115 14.512659
+ 2500 16738.442 -0.0052101787 0 5269.5042 14.512594
+ 2550 16738.552 -0.04420046 0 5269.4998 14.512177
+ 2600 16738.42 -0.004347531 0 5269.4982 14.512783
+ 2650 16734.241 1.3131302 0 5269.5 14.577195
+ 2700 16738.737 -0.10612056 0 5269.4961 14.503874
+ 2750 16732.705 1.7939719 0 5269.4974 14.629294
+ 2800 16738.558 -0.042867033 0 5269.5032 14.519893
+ 2850 16738.499 -0.01271227 0 5269.5146 14.518524
+ 2900 16738.486 -0.0032778045 0 5269.52 14.518712
+ 2950 16738.482 -0.0089544631 0 5269.5133 14.518629
+ 3000 16738.647 -0.070862542 0 5269.5031 14.51803
+ 3050 16678.313 18.829038 0 5269.409 15.533426
+ 3100 16632.312 33.399217 0 5269.4975 14.588597
+ 3150 16739.318 -0.31388148 0 5269.4715 13.520782
+ 3200 16727.951 3.26736 0 5269.4741 12.288358
+ 3250 16686.364 16.353793 0 5269.4682 14.152517
+ 3300 16738.532 -0.031574462 0 5269.5064 13.310615
+ 3350 16738.454 -0.0062292918 0 5269.5071 13.308187
+ 3400 16738.445 -0.0049349125 0 5269.5055 13.308178
+ 3450 16738.489 -0.021623738 0 5269.5026 13.308001
+ 3500 16737.78 0.19719043 0 5269.4983 13.325999
+ 3550 16658.578 25.116206 0 5269.4834 13.778249
+ 3600 16738.51 -0.032864725 0 5269.4981 12.392389
+ 3650 16738.899 -0.15952703 0 5269.4938 12.383503
+ 3700 16738.879 -0.16025994 0 5269.487 12.382575
+ 3750 16738.878 -0.16608251 0 5269.4806 12.382765
+ 3800 16738.591 -0.078679341 0 5269.4776 12.383227
+ 3850 16738.429 -0.024729409 0 5269.4807 12.382942
+ 3900 16738.399 -0.0062729967 0 5269.4897 12.383192
+ 3950 16738.428 -0.002521266 0 5269.5027 12.383324
+ 4000 16738.467 -0.0002068506 0 5269.5173 12.383474
+ 4050 16738.488 0 0 5269.5241 12.383531
+ 4100 16738.468 0 0 5269.5178 12.383482
+ 4150 16738.422 0 0 5269.5033 12.383369
+ 4200 16738.387 0 0 5269.4921 12.383281
+ 4250 16738.383 0 0 5269.4908 12.38327
+ 4300 16738.4 0 0 5269.4964 12.383314
+ 4350 16738.423 0 0 5269.5036 12.38337
+ 4400 16738.441 0 0 5269.5092 12.383414
+ 4450 16738.45 0 0 5269.5121 12.383437
+ 4500 16738.45 0 0 5269.5122 12.383438
+ 4550 16738.442 0 0 5269.5095 12.383417
+ 4600 16738.425 0 0 5269.5042 12.383376
+ 4650 16738.404 -0.0014438316 0 5269.4961 12.383299
+ 4700 16738.444 -0.024020551 0 5269.4862 12.382975
+ 4750 16738.49 -0.048521421 0 5269.4761 12.385777
+ 4800 16735.057 1.0347219 0 5269.4786 12.43543
+ 4850 16735.441 0.92650928 0 5269.4913 12.418653
+ 4900 16723.839 4.5908971 0 5269.5033 13.410103
+ 4950 16738.531 -0.021537669 0 5269.5159 13.089982
+ 5000 16738.45 -0.0042589693 0 5269.5077 13.090062
+ 5050 16738.409 -0.00024692474 0 5269.4987 13.090038
+ 5100 16738.404 0 0 5269.4976 13.090032
+ 5150 16738.421 0 0 5269.5029 13.090073
+ 5200 16738.44 0 0 5269.5087 13.090119
+ 5250 16738.448 -0.0012793921 0 5269.5102 13.090114
+ 5300 16738.456 -0.0064376397 0 5269.5075 13.090026
+ 5350 16738.479 -0.020383842 0 5269.5007 13.089898
+ 5400 16735.845 0.79889481 0 5269.4909 13.136244
+ 5450 16735.558 0.87619898 0 5269.4778 12.324482
+ 5500 16711.494 8.47243 0 5269.4984 12.65658
+ 5550 16454.525 89.074845 0 5269.2031 16.996503
+ 5600 16713.084 7.9801091 0 5269.5065 13.774971
+ 5650 16738.676 -0.079987812 0 5269.5033 13.168292
+ 5700 16446.281 91.866085 0 5269.399 23.764658
+ 5750 16738.549 -0.039869082 0 5269.5034 13.378117
+ 5800 16738.487 -0.014994464 0 5269.5086 13.378394
+ 5850 16738.466 -0.0051267378 0 5269.512 13.378555
+ 5900 16738.462 -0.0043689966 0 5269.5113 13.378568
+ 5950 16738.528 -0.032727396 0 5269.5039 13.378192
+ 6000 16702.774 10.969422 0 5269.2502 13.788847
+ 6050 16682.271 17.483217 0 5269.3092 13.353098
+ 6100 16738.508 -0.028838289 0 5269.5016 12.521077
+ 6150 16738.425 -0.0067595568 0 5269.4974 12.521216
+ 6200 16738.401 -0.0011499904 0 5269.4955 12.521247
+ 6250 16738.455 0 0 5269.5136 12.521403
+ 6300 16738.523 0 0 5269.5352 12.521573
+ 6350 16738.503 0 0 5269.5287 12.521525
+ 6400 16738.427 0 0 5269.5047 12.521337
+ 6450 16738.399 0 0 5269.496 12.521268
+ 6500 16738.425 0 0 5269.5042 12.521331
+ 6550 16738.441 0 0 5269.5093 12.521372
+ 6600 16738.42 0 0 5269.5025 12.521319
+ 6650 16738.398 0 0 5269.4957 12.521266
+ 6700 16738.435 0 0 5269.5074 12.521355
+ 6750 16738.505 0 0 5269.5293 12.521527
+ 6800 16738.508 0 0 5269.5303 12.521536
+ 6850 16738.446 0 0 5269.5108 12.521384
+ 6900 16738.414 0 0 5269.5009 12.521306
+ 6950 16738.432 0 0 5269.5063 12.521348
+ 7000 16738.444 0 0 5269.5102 12.521378
+ 7050 16738.421 0 0 5269.5029 12.521322
+ 7100 16738.393 0 0 5269.4941 12.521253
+ 7150 16738.419 0 0 5269.5022 12.521315
+ 7200 16738.489 0 0 5269.5244 12.521489
+ 7250 16738.505 0 0 5269.5293 12.521528
+ 7300 16738.443 0 0 5269.5098 12.521376
+ 7350 16738.404 0 0 5269.4976 12.521281
+ 7400 16738.43 0 0 5269.5058 12.521343
+ 7450 16738.461 0 0 5269.5156 12.521421
+ 7500 16738.447 0 0 5269.5109 12.521385
+ 7550 16738.407 0 0 5269.4986 12.521288
+ 7600 16738.412 0 0 5269.5002 12.5213
+ 7650 16738.478 0 0 5269.5208 12.52146
+ 7700 16738.51 0 0 5269.5309 12.521541
+ 7750 16738.454 0 0 5269.5135 12.521405
+ 7800 16738.398 0 0 5269.4958 12.521267
+ 7850 16738.407 -0.0002118068 0 5269.4982 12.521283
+ 7900 16738.441 -0.00021679441 0 5269.509 12.521366
+ 7950 16738.446 -0.00023847865 0 5269.5107 12.52138
+ 8000 16738.423 0 0 5269.5035 12.521326
+ 8050 16738.423 0 0 5269.5034 12.521325
+ 8100 16738.478 -0.00069624411 0 5269.52 12.521447
+ 8150 16738.523 -0.0040058094 0 5269.531 12.521494
+ 8200 16738.486 -0.0092298399 0 5269.5142 12.521327
+ 8250 16738.458 -0.023189572 0 5269.4914 12.521008
+ 8300 16738.513 -0.045847775 0 5269.4861 12.520773
+ 8350 16723.734 4.5722877 0 5269.4516 12.849562
+ 8400 16738.466 -0.020202622 0 5269.497 12.835807
+ 8450 16738.437 -0.012822209 0 5269.4952 12.829975
+ 8500 16738.408 -0.001683355 0 5269.4972 12.8301
+ 8550 16738.464 -0.00097382251 0 5269.5155 12.830254
+ 8600 16738.669 -0.050581166 0 5269.5304 12.829973
+ 8650 15918.256 250.07455 0 5261.3774 24.539208
+ 8700 16738.446 0.00084613367 0 5269.5116 10.591358
+ 8750 16738.472 -0.010145611 0 5269.5089 10.590277
+ 8800 16738.468 0 0 5269.5176 10.590497
+ 8850 16738.508 0 0 5269.5303 10.590596
+ 8900 16738.509 0 0 5269.5306 10.590599
+ 8950 16738.496 0 0 5269.5266 10.590568
+ 9000 16738.477 0 0 5269.5204 10.59052
+ 9050 16738.455 0 0 5269.5135 10.590465
+ 9100 16738.477 0 0 5269.5205 10.590519
+ 9150 16738.512 0 0 5269.5315 10.590606
+ 9200 16738.502 0 0 5269.5285 10.590583
+ 9250 16738.493 0 0 5269.5254 10.590559
+ 9300 16738.482 0 0 5269.522 10.590532
+ 9350 16738.46 0 0 5269.5151 10.590478
+ 9400 16738.48 0 0 5269.5216 10.590528
+ 9450 16738.509 0 0 5269.5306 10.590599
+ 9500 16738.49 0 0 5269.5247 10.590554
+ 9550 16738.484 0 0 5269.5226 10.590536
+ 9600 16738.483 0 0 5269.5223 10.590534
+ 9650 16738.464 0 0 5269.5165 10.590489
+ 9700 16738.484 0 0 5269.5228 10.590537
+ 9750 16738.507 0 0 5269.53 10.590595
+ 9800 16738.482 0 0 5269.522 10.590532
+ 9850 16738.478 0 0 5269.5207 10.590521
+ 9900 16738.487 -0.00030979882 0 5269.5233 10.590538
+ 9950 16738.476 -0.00095967357 0 5269.5193 10.590496
+ 10000 16738.494 -0.00062714625 0 5269.5253 10.590548
+Loop time of 0.166547 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 518773.777 tau/day, 60043.261 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.011439 | 0.011439 | 0.011439 | 0.0 | 6.87
+Neigh | 0.038572 | 0.038572 | 0.038572 | 0.0 | 23.16
+Comm | 0.0085464 | 0.0085464 | 0.0085464 | 0.0 | 5.13
+Output | 0.0025046 | 0.0025046 | 0.0025046 | 0.0 | 1.50
+Modify | 0.099479 | 0.099479 | 0.099479 | 0.0 | 59.73
+Other | | 0.006005 | | | 3.61
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 49 ave 49 max 49 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3 ave 3 max 3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3
+Ave neighs/atom = 0.037037
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.nve.g++.4 b/examples/rigid/log.20Apr18.rigid.nve.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..782457b42795a959c6a2dfbfcd003226e40bba24
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.nve.g++.4
@@ -0,0 +1,335 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.69 571.70921 0 5265.8153 32.005816
+ 100 16298.128 136.75661 0 5267.6488 16.449029
+ 150 16682.532 17.504156 0 5269.4124 14.901186
+ 200 16733.906 1.3755079 0 5269.4571 14.571305
+ 250 16738.861 -0.15272039 0 5269.4886 14.498342
+ 300 16738.608 -0.055216883 0 5269.5066 14.498
+ 350 16738.5 -0.017457072 0 5269.5104 14.498392
+ 400 16738.451 -0.0060161309 0 5269.5063 14.49851
+ 450 16738.435 -0.001271965 0 5269.5059 14.498571
+ 500 16738.443 -0.00081074175 0 5269.509 14.498598
+ 550 16738.452 -0.00083208965 0 5269.5118 14.498618
+ 600 16738.45 -0.00058358431 0 5269.5116 14.498617
+ 650 16738.443 -0.00047228525 0 5269.5093 14.4986
+ 700 16738.444 0 0 5269.5102 14.498612
+ 750 16738.461 0 0 5269.5157 14.498654
+ 800 16738.479 0 0 5269.521 14.498697
+ 850 16738.473 0 0 5269.5192 14.498683
+ 900 16738.449 0 0 5269.5116 14.498624
+ 950 16738.438 -0.0035324203 0 5269.5046 14.498537
+ 1000 16738.562 -0.051134242 0 5269.4963 14.498093
+ 1050 16737.343 0.32970192 0 5269.4934 14.527634
+ 1100 16737.878 0.16213235 0 5269.4941 14.533864
+ 1150 16738.682 -0.089236256 0 5269.4959 14.511765
+ 1200 16738.444 -0.0075446558 0 5269.5025 14.512479
+ 1250 16738.45 0 0 5269.5119 14.512611
+ 1300 16738.475 0 0 5269.5199 14.512673
+ 1350 16738.484 0 0 5269.5228 14.512696
+ 1400 16738.469 -0.00044683992 0 5269.5175 14.512651
+ 1450 16738.45 -0.0010933363 0 5269.511 14.512595
+ 1500 16738.445 -0.00057484239 0 5269.51 14.512591
+ 1550 16738.451 0 0 5269.5123 14.512615
+ 1600 16738.452 0 0 5269.5127 14.512618
+ 1650 16738.443 0 0 5269.5099 14.512596
+ 1700 16738.433 0 0 5269.5068 14.512572
+ 1750 16738.438 0 0 5269.5084 14.512584
+ 1800 16738.459 0 0 5269.5149 14.512635
+ 1850 16738.473 0 0 5269.5193 14.51267
+ 1900 16738.462 0 0 5269.5159 14.512644
+ 1950 16738.446 -0.0032069962 0 5269.5076 14.512539
+ 2000 16738.463 -0.013425408 0 5269.5027 14.512382
+ 2050 16738.535 -0.036964311 0 5269.5017 14.512152
+ 2100 16738.621 -0.063490509 0 5269.5023 14.512108
+ 2150 16738.594 -0.056143934 0 5269.5012 14.512117
+ 2200 16738.536 -0.038486645 0 5269.5007 14.512277
+ 2250 16738.496 -0.023712406 0 5269.503 14.51242
+ 2300 16738.488 -0.013209094 0 5269.5109 14.51255
+ 2350 16738.486 -0.0045244524 0 5269.519 14.512693
+ 2400 16738.475 -0.00051678325 0 5269.5194 14.512743
+ 2450 16738.456 -0.0023209272 0 5269.5115 14.512659
+ 2500 16738.442 -0.0052101787 0 5269.5042 14.512594
+ 2550 16738.552 -0.04420046 0 5269.4998 14.512177
+ 2600 16738.42 -0.004347531 0 5269.4982 14.512783
+ 2650 16734.241 1.3131302 0 5269.5 14.577195
+ 2700 16738.737 -0.10612056 0 5269.4961 14.503874
+ 2750 16732.705 1.7939719 0 5269.4974 14.629294
+ 2800 16738.558 -0.042867033 0 5269.5032 14.519893
+ 2850 16738.499 -0.01271227 0 5269.5146 14.518524
+ 2900 16738.486 -0.0032778045 0 5269.52 14.518712
+ 2950 16738.482 -0.0089544631 0 5269.5133 14.518629
+ 3000 16738.647 -0.070862542 0 5269.5031 14.51803
+ 3050 16678.313 18.829038 0 5269.409 15.533426
+ 3100 16632.312 33.399217 0 5269.4975 14.588597
+ 3150 16739.318 -0.31388148 0 5269.4715 13.520782
+ 3200 16727.951 3.26736 0 5269.4741 12.288358
+ 3250 16686.364 16.353793 0 5269.4682 14.152517
+ 3300 16738.532 -0.031574462 0 5269.5064 13.310615
+ 3350 16738.454 -0.0062292918 0 5269.5071 13.308187
+ 3400 16738.445 -0.0049349125 0 5269.5055 13.308178
+ 3450 16738.489 -0.021623738 0 5269.5026 13.308001
+ 3500 16737.78 0.19719043 0 5269.4983 13.325999
+ 3550 16658.578 25.116206 0 5269.4834 13.778249
+ 3600 16738.51 -0.032864725 0 5269.4981 12.392389
+ 3650 16738.899 -0.15952703 0 5269.4938 12.383503
+ 3700 16738.879 -0.16025994 0 5269.487 12.382575
+ 3750 16738.878 -0.16608251 0 5269.4806 12.382765
+ 3800 16738.591 -0.078679341 0 5269.4776 12.383227
+ 3850 16738.429 -0.024729409 0 5269.4807 12.382942
+ 3900 16738.399 -0.0062729967 0 5269.4897 12.383192
+ 3950 16738.428 -0.002521266 0 5269.5027 12.383324
+ 4000 16738.467 -0.0002068506 0 5269.5173 12.383474
+ 4050 16738.488 0 0 5269.5241 12.383531
+ 4100 16738.468 0 0 5269.5178 12.383482
+ 4150 16738.422 0 0 5269.5033 12.383369
+ 4200 16738.387 0 0 5269.4921 12.383281
+ 4250 16738.383 0 0 5269.4908 12.38327
+ 4300 16738.4 0 0 5269.4964 12.383314
+ 4350 16738.423 0 0 5269.5036 12.38337
+ 4400 16738.441 0 0 5269.5092 12.383414
+ 4450 16738.45 0 0 5269.5121 12.383437
+ 4500 16738.45 0 0 5269.5122 12.383438
+ 4550 16738.442 0 0 5269.5095 12.383417
+ 4600 16738.425 0 0 5269.5042 12.383376
+ 4650 16738.404 -0.0014438316 0 5269.4961 12.383299
+ 4700 16738.444 -0.024020551 0 5269.4862 12.382975
+ 4750 16738.49 -0.048521424 0 5269.4761 12.385777
+ 4800 16735.057 1.0347218 0 5269.4786 12.43543
+ 4850 16735.441 0.92650925 0 5269.4913 12.418653
+ 4900 16723.839 4.5908973 0 5269.5033 13.410103
+ 4950 16738.531 -0.021537669 0 5269.5159 13.089982
+ 5000 16738.45 -0.0042589693 0 5269.5077 13.090062
+ 5050 16738.409 -0.00024692474 0 5269.4987 13.090038
+ 5100 16738.404 0 0 5269.4976 13.090032
+ 5150 16738.421 0 0 5269.5029 13.090073
+ 5200 16738.44 0 0 5269.5087 13.090119
+ 5250 16738.448 -0.0012793921 0 5269.5102 13.090114
+ 5300 16738.456 -0.0064376396 0 5269.5075 13.090026
+ 5350 16738.479 -0.020383843 0 5269.5007 13.089898
+ 5400 16735.845 0.79889489 0 5269.4909 13.136244
+ 5450 16735.558 0.87619907 0 5269.4778 12.324482
+ 5500 16711.494 8.4724273 0 5269.4984 12.656579
+ 5550 16454.525 89.074821 0 5269.2031 16.996502
+ 5600 16713.084 7.9801107 0 5269.5065 13.774972
+ 5650 16738.676 -0.079987805 0 5269.5033 13.168292
+ 5700 16446.281 91.866085 0 5269.399 23.764659
+ 5750 16738.549 -0.039869082 0 5269.5034 13.378118
+ 5800 16738.487 -0.014994465 0 5269.5086 13.378394
+ 5850 16738.466 -0.0051267396 0 5269.512 13.378555
+ 5900 16738.462 -0.004368998 0 5269.5113 13.378568
+ 5950 16738.528 -0.032727397 0 5269.5039 13.378192
+ 6000 16702.774 10.969422 0 5269.2502 13.788847
+ 6050 16682.271 17.483223 0 5269.3092 13.353098
+ 6100 16738.508 -0.028838294 0 5269.5016 12.521077
+ 6150 16738.425 -0.0067595586 0 5269.4974 12.521216
+ 6200 16738.401 -0.0011499906 0 5269.4955 12.521248
+ 6250 16738.455 0 0 5269.5136 12.521404
+ 6300 16738.523 0 0 5269.5352 12.521573
+ 6350 16738.503 0 0 5269.5287 12.521525
+ 6400 16738.427 0 0 5269.5047 12.521337
+ 6450 16738.399 0 0 5269.496 12.521268
+ 6500 16738.425 0 0 5269.5042 12.521331
+ 6550 16738.441 0 0 5269.5093 12.521372
+ 6600 16738.42 0 0 5269.5025 12.521319
+ 6650 16738.398 0 0 5269.4957 12.521266
+ 6700 16738.435 0 0 5269.5074 12.521355
+ 6750 16738.505 0 0 5269.5293 12.521527
+ 6800 16738.508 0 0 5269.5303 12.521536
+ 6850 16738.446 0 0 5269.5108 12.521384
+ 6900 16738.414 0 0 5269.5009 12.521306
+ 6950 16738.432 0 0 5269.5063 12.521348
+ 7000 16738.444 0 0 5269.5102 12.521379
+ 7050 16738.421 0 0 5269.5029 12.521322
+ 7100 16738.393 0 0 5269.4941 12.521253
+ 7150 16738.419 0 0 5269.5022 12.521315
+ 7200 16738.489 0 0 5269.5244 12.521489
+ 7250 16738.505 0 0 5269.5293 12.521528
+ 7300 16738.443 0 0 5269.5098 12.521377
+ 7350 16738.404 0 0 5269.4976 12.521281
+ 7400 16738.43 0 0 5269.5058 12.521344
+ 7450 16738.461 0 0 5269.5156 12.521421
+ 7500 16738.447 0 0 5269.5109 12.521385
+ 7550 16738.407 0 0 5269.4986 12.521288
+ 7600 16738.412 0 0 5269.5002 12.5213
+ 7650 16738.478 0 0 5269.5208 12.521461
+ 7700 16738.51 0 0 5269.5309 12.521541
+ 7750 16738.454 0 0 5269.5135 12.521406
+ 7800 16738.398 0 0 5269.4958 12.521267
+ 7850 16738.407 -0.00021180715 0 5269.4982 12.521283
+ 7900 16738.441 -0.0002167946 0 5269.509 12.521367
+ 7950 16738.446 -0.0002384787 0 5269.5107 12.52138
+ 8000 16738.423 0 0 5269.5035 12.521327
+ 8050 16738.423 0 0 5269.5034 12.521325
+ 8100 16738.478 -0.00069624484 0 5269.52 12.521448
+ 8150 16738.523 -0.0040058183 0 5269.531 12.521494
+ 8200 16738.486 -0.0092298512 0 5269.5142 12.521328
+ 8250 16738.458 -0.023189661 0 5269.4914 12.521008
+ 8300 16738.513 -0.045847765 0 5269.4861 12.520773
+ 8350 16723.735 4.5720344 0 5269.4516 12.849543
+ 8400 16738.466 -0.02019859 0 5269.497 12.835812
+ 8450 16738.437 -0.012822198 0 5269.4952 12.829979
+ 8500 16738.408 -0.0016833646 0 5269.4972 12.830104
+ 8550 16738.464 -0.00097382606 0 5269.5155 12.830258
+ 8600 16738.669 -0.050581176 0 5269.5304 12.829977
+ 8650 15918.073 250.131 0 5261.3761 24.542327
+ 8700 16738.446 0.00085039409 0 5269.5116 10.59114
+ 8750 16738.472 -0.010146632 0 5269.5089 10.590059
+ 8800 16738.468 0 0 5269.5176 10.590278
+ 8850 16738.508 0 0 5269.5303 10.590378
+ 8900 16738.509 0 0 5269.5306 10.590381
+ 8950 16738.496 0 0 5269.5266 10.590349
+ 9000 16738.477 0 0 5269.5204 10.590302
+ 9050 16738.455 0 0 5269.5135 10.590247
+ 9100 16738.477 0 0 5269.5205 10.590301
+ 9150 16738.512 0 0 5269.5315 10.590388
+ 9200 16738.502 0 0 5269.5285 10.590364
+ 9250 16738.493 0 0 5269.5254 10.59034
+ 9300 16738.482 0 0 5269.522 10.590314
+ 9350 16738.46 0 0 5269.5151 10.59026
+ 9400 16738.48 0 0 5269.5216 10.59031
+ 9450 16738.509 0 0 5269.5306 10.590381
+ 9500 16738.49 0 0 5269.5247 10.590335
+ 9550 16738.484 0 0 5269.5226 10.590318
+ 9600 16738.483 0 0 5269.5223 10.590316
+ 9650 16738.464 0 0 5269.5165 10.590271
+ 9700 16738.484 0 0 5269.5228 10.590319
+ 9750 16738.507 0 0 5269.53 10.590376
+ 9800 16738.482 0 0 5269.522 10.590314
+ 9850 16738.478 0 0 5269.5207 10.590303
+ 9900 16738.487 -0.00030979874 0 5269.5233 10.59032
+ 9950 16738.476 -0.00095967134 0 5269.5192 10.590278
+ 10000 16738.494 -0.00062714318 0 5269.5253 10.590329
+Loop time of 0.22441 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 385008.767 tau/day, 44561.200 timesteps/s
+97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0032785 | 0.0039999 | 0.0052714 | 1.3 | 1.78
+Neigh | 0.010548 | 0.012524 | 0.016082 | 1.9 | 5.58
+Comm | 0.082771 | 0.087847 | 0.091037 | 1.1 | 39.15
+Output | 0.0042846 | 0.0045864 | 0.0054133 | 0.7 | 2.04
+Modify | 0.10401 | 0.10533 | 0.10736 | 0.4 | 46.94
+Other | | 0.01013 | | | 4.51
+
+Nlocal: 20.25 ave 34 max 9 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 38.5 ave 43 max 26 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs: 0.75 ave 2 max 0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 3
+Ave neighs/atom = 0.037037
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.poems.g++.1 b/examples/rigid/log.20Apr18.rigid.poems.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..0cba72a2dd681d8b47f54984e93b6e8b280bbcd3
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.poems.g++.1
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 36 45
+10 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+1 clusters, 9 bodies, 8 joints, 81 atoms
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 217.7783 3430.3907 0 3466.6871 -2.7403788
+ 50 13679.637 1404.2468 0 3684.1863 12.446066
+ 100 16777.225 888.87665 0 3685.0808 -31.828677
+ 150 19595.365 418.45042 0 3684.3446 40.709078
+ 200 18524.188 596.47273 0 3683.8375 -0.8159371
+ 250 21015.789 180.96521 0 3683.5967 -10.042469
+ 300 20785.513 219.25314 0 3683.5053 2.6452719
+ 350 21072.46 171.2554 0 3683.3321 7.0609024
+ 400 19956.414 356.36381 0 3682.4328 19.320259
+ 450 20724.42 227.73284 0 3681.8028 8.1259249
+ 500 20152.578 322.71466 0 3681.4777 5.4929878
+ 550 20017.022 345.29701 0 3681.4673 5.4661666
+ 600 17897.743 698.72196 0 3681.6791 3.2854742
+ 650 17297.758 796.60256 0 3679.5623 15.191113
+ 700 18581.934 584.29715 0 3681.2861 5.1588289
+ 750 21774.158 52.821062 0 3681.8474 -10.775664
+ 800 21604.055 81.188546 0 3681.8644 -3.2045743
+ 850 17821.483 711.53827 0 3681.7854 7.4384277
+ 900 21033.292 175.98127 0 3681.5299 -16.345167
+ 950 20968.166 186.59847 0 3681.2929 -2.330456
+ 1000 20490.66 266.19375 0 3681.3037 11.787983
+ 1050 20222.396 310.94072 0 3681.34 -8.3459539
+ 1100 21321.687 127.61533 0 3681.2299 -1.2184717
+ 1150 20849.582 206.01695 0 3680.9472 -0.86699146
+ 1200 21815.003 45.317414 0 3681.1512 1.5988314
+ 1250 18655.437 572.41453 0 3681.654 10.064078
+ 1300 20780.781 217.36506 0 3680.8286 6.0538615
+ 1350 20558.971 254.36482 0 3680.8601 -3.6773954
+ 1400 21485.029 99.812918 0 3680.6511 -16.185473
+ 1450 21771.107 52.159607 0 3680.6775 -2.4756675
+ 1500 21520.948 93.503927 0 3680.3286 2.1023577
+ 1550 21351.418 121.68138 0 3680.2511 5.515995
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+ 1750 18563.642 587.3479 0 3681.2882 33.532211
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+ 1900 20146.627 322.14849 0 3679.9197 5.7313175
+ 1950 20692.671 231.25345 0 3680.0319 4.297772
+ 2000 20943.905 189.11218 0 3679.7629 -22.64509
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+ 2100 20280.434 299.76289 0 3679.8353 7.4807805
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+ 2250 20486.914 266.64414 0 3681.1299 -8.6458025
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+ 2450 20100.204 332.25468 0 3682.2886 35.739592
+ 2500 20764.513 221.64794 0 3682.4001 -12.46688
+ 2550 20436.771 276.13128 0 3682.2598 -22.419404
+ 2600 21466.252 104.57185 0 3682.2806 -10.080362
+ 2650 20817.269 212.81674 0 3682.3615 5.1374497
+ 2700 18565.157 588.46125 0 3682.6541 22.283866
+ 2750 20780.743 218.76366 0 3682.2208 -8.0046411
+ 2800 21032.22 176.82368 0 3682.1936 -7.078895
+ 2850 16817.729 879.49153 0 3682.4464 33.140849
+ 2900 19309.511 463.89319 0 3682.145 7.9225025
+ 2950 20544.978 257.86831 0 3682.0314 2.0523059
+ 3000 20616.438 246.0975 0 3682.1706 -0.2824889
+ 3050 18648.596 574.37266 0 3682.4721 -5.8677065
+ 3100 19147.135 490.76826 0 3681.9574 -1.9922835
+ 3150 18568.022 587.36965 0 3682.0399 14.694505
+ 3200 19720.841 395.38315 0 3682.1899 5.9162402
+ 3250 19008.557 514.50687 0 3682.5998 -3.4702895
+ 3300 21708.937 64.231264 0 3682.3874 -5.4808611
+ 3350 20548.477 257.62974 0 3682.3759 9.7818301
+ 3400 20508.84 264.0153 0 3682.1553 -12.578182
+ 3450 18736.579 559.11222 0 3681.8754 21.920437
+ 3500 21444.82 107.82706 0 3681.9638 0.093050651
+ 3550 20439.241 275.31015 0 3681.8503 -3.0785302
+ 3600 21547.1 90.778361 0 3681.9617 -5.9189729
+ 3650 15623.305 1079.996 0 3683.8802 36.064752
+ 3700 19912.452 363.09483 0 3681.8368 5.4802367
+ 3750 21289.7 133.2258 0 3681.5091 -10.884642
+ 3800 20214.875 312.09245 0 3681.2382 8.6419893
+ 3850 19853.031 372.13835 0 3680.9769 2.6229234
+ 3900 17863.409 703.8716 0 3681.1064 -1.4250404
+ 3950 19926.351 359.87227 0 3680.9307 -14.60997
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+ 4050 18408.194 611.80934 0 3679.8416 4.4236034
+ 4100 17506.503 762.1286 0 3679.8792 5.0526379
+ 4150 18479.134 600.76034 0 3680.6159 -6.6523095
+ 4200 18475.322 601.95797 0 3681.1783 1.3292995
+ 4250 18301.378 630.34119 0 3680.5709 2.5387332
+ 4300 19384.541 449.98455 0 3680.7414 5.8750989
+ 4350 18717.888 561.31715 0 3680.9651 3.7948584
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+ 4450 20269.613 302.15984 0 3680.4286 -10.145642
+ 4500 19151.762 489.32407 0 3681.2845 21.695364
+ 4550 19914.708 361.54065 0 3680.6587 -4.2298372
+ 4600 21153.44 154.99598 0 3680.5693 2.3172078
+ 4650 21021.611 176.81454 0 3680.4164 1.9128023
+ 4700 21707.966 62.767734 0 3680.762 -5.2080189
+ 4750 16517.674 927.53839 0 3680.484 17.329608
+ 4800 21654.604 71.574174 0 3680.6749 -6.0650166
+ 4850 18135.978 657.28622 0 3679.9493 5.4803307
+ 4900 20389.048 282.49215 0 3680.6668 -2.8570431
+ 4950 17159.074 820.81472 0 3680.6604 31.273877
+ 5000 20788.159 215.88415 0 3680.5773 4.6345196
+ 5050 21366.767 119.68693 0 3680.8148 -9.9482889
+ 5100 20668.21 236.17655 0 3680.8782 3.8118334
+ 5150 20468.573 269.83696 0 3681.2657 -26.625943
+ 5200 19493.142 432.49135 0 3681.3483 -7.6677112
+ 5250 19626.594 410.09767 0 3681.1967 7.3622341
+ 5300 20771.914 219.12484 0 3681.1105 -7.0871793
+ 5350 21152.459 155.26401 0 3680.6738 5.9030557
+ 5400 21376.189 117.91075 0 3680.6088 -1.2004513
+ 5450 21455.06 105.15166 0 3680.995 -9.1675471
+ 5500 21227.896 143.35739 0 3681.3401 -6.646305
+ 5550 21149.831 156.61404 0 3681.5858 -12.953136
+ 5600 21364.198 120.94695 0 3681.6466 1.0372254
+ 5650 20219.777 311.34588 0 3681.3088 6.5026316
+ 5700 21163.024 154.3001 0 3681.4708 -0.47587262
+ 5750 19583.077 418.40745 0 3682.2535 24.609517
+ 5800 18801.324 548.79742 0 3682.3515 -12.082631
+ 5850 20875.4 203.07604 0 3682.3093 -8.1191161
+ 5900 20737.053 226.2734 0 3682.4489 -7.6845943
+ 5950 21260.028 139.21888 0 3682.5568 -2.2977046
+ 6000 19823.84 378.71803 0 3682.6914 -1.1163373
+ 6050 20487.214 268.03474 0 3682.5704 4.313979
+ 6100 17853.211 707.10918 0 3682.6443 16.762322
+ 6150 21322.705 129.06 0 3682.8441 2.7500936
+ 6200 21609.008 81.580972 0 3683.0823 0.37062555
+ 6250 20364.115 289.30707 0 3683.3262 13.176034
+ 6300 20201.9 316.16558 0 3683.149 -1.6318339
+ 6350 21151.879 157.75018 0 3683.0634 -23.337621
+ 6400 21453.129 107.45563 0 3682.9772 -0.60776225
+ 6450 21105.382 165.1926 0 3682.7562 4.244932
+ 6500 20746.748 224.6945 0 3682.4859 0.2929158
+ 6550 20913.725 197.29847 0 3682.9194 -15.792862
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+ 6650 20270.609 303.60078 0 3682.0357 -0.26503277
+ 6700 21442.931 109.08904 0 3682.9109 -2.8409166
+ 6750 20907.994 198.30695 0 3682.9726 0.91664072
+ 6800 20431.208 277.98326 0 3683.1845 -1.8537161
+ 6850 20312.052 297.88656 0 3683.2285 3.1028547
+ 6900 19458.401 439.97157 0 3683.0385 -4.1856293
+ 6950 20507.759 264.99217 0 3682.952 -1.4597973
+ 7000 20782.356 219.47456 0 3683.2006 -7.1967021
+ 7050 20560.324 256.07109 0 3682.7917 -10.720013
+ 7100 21652.145 74.086415 0 3682.7772 -0.61455054
+ 7150 20134.823 326.40272 0 3682.2065 11.689827
+ 7200 20778.071 219.16459 0 3682.1765 -1.796567
+ 7250 20153.065 323.13721 0 3681.9814 -0.1215538
+ 7300 19524.938 427.99711 0 3682.1534 -3.1139903
+ 7350 20554.595 256.63855 0 3682.4044 10.023083
+ 7400 18778.53 552.29852 0 3682.0534 -1.7145222
+ 7450 18972.509 520.15393 0 3682.2388 1.4489874
+ 7500 17680.668 736.20139 0 3682.9794 15.096954
+ 7550 19070.785 504.65403 0 3683.1182 2.2707533
+ 7600 20805.541 214.54957 0 3682.1398 -3.4306308
+ 7650 18473.262 604.25322 0 3683.1301 2.2083367
+ 7700 19294.016 466.99211 0 3682.6615 2.2666382
+ 7750 20995.664 183.47108 0 3682.7484 -13.935938
+ 7800 21042.433 175.06619 0 3682.1384 0.49855811
+ 7850 19343.054 459.21955 0 3683.0618 7.9049312
+ 7900 18382.898 619.01969 0 3682.8361 1.7996366
+ 7950 16092.435 1000.6563 0 3682.7287 29.993154
+ 8000 17551.635 757.47719 0 3682.7498 8.1753011
+ 8050 20309.875 298.25877 0 3683.2379 -1.9545317
+ 8100 21746.174 59.002125 0 3683.3645 -2.6980678
+ 8150 21478.427 103.44202 0 3683.1799 -10.930392
+ 8200 20986.729 185.46995 0 3683.2581 -14.298403
+ 8250 20744.064 225.47546 0 3682.8194 -6.4982356
+ 8300 19887.982 368.35069 0 3683.0143 1.5899179
+ 8350 21871.414 37.899202 0 3683.1348 -2.0554107
+ 8400 20002.858 348.98887 0 3682.7985 8.2963084
+ 8450 21553.861 90.985193 0 3683.2953 2.8575186
+ 8500 21605.143 82.347635 0 3683.2048 -4.711565
+ 8550 20151.76 324.4703 0 3683.097 -8.5109459
+ 8600 20564.158 255.77814 0 3683.1378 -1.3815408
+ 8650 19316.602 463.61706 0 3683.0507 -2.6895635
+ 8700 18157.859 656.69518 0 3683.0051 19.428927
+ 8750 18752.43 557.67555 0 3683.0805 1.9765973
+ 8800 20903.812 199.07408 0 3683.0428 1.9011523
+ 8850 20132.963 327.56826 0 3683.0621 3.0389961
+ 8900 21667.171 71.80023 0 3682.9954 -2.0042246
+ 8950 20346.973 292.00907 0 3683.1712 7.5582361
+ 9000 17889.448 695.59406 0 3677.1688 7.5315391
+ 9050 19446.144 441.90609 0 3682.9302 5.9819228
+ 9100 20384.34 285.05862 0 3682.4486 9.8610378
+ 9150 20023.515 344.98587 0 3682.2384 -0.40175043
+ 9200 17786.795 718.76166 0 3683.2275 10.984317
+ 9250 20843.023 208.42263 0 3682.2597 -7.4709344
+ 9300 21670.622 70.503925 0 3682.2742 -6.2303366
+ 9350 20642.313 241.21277 0 3681.5983 4.7423898
+ 9400 19228.566 476.44753 0 3681.2085 10.836639
+ 9450 21215.705 146.40003 0 3682.3509 -9.091421
+ 9500 21543.685 91.725901 0 3682.3401 -1.0608492
+ 9550 20143.22 324.98532 0 3682.1887 -5.995164
+ 9600 21234.294 142.96512 0 3682.0142 0.004838125
+ 9650 21025.207 177.8801 0 3682.0813 -5.4857701
+ 9700 20638.235 242.46577 0 3682.1716 -1.6014085
+ 9750 18374.191 620.54322 0 3682.9084 13.864712
+ 9800 19730.262 393.89083 0 3682.2679 5.7601754
+ 9850 21547.855 91.283379 0 3682.5926 2.1989329
+ 9900 20959.935 189.28821 0 3682.6108 2.1174676
+ 9950 21191.026 150.79441 0 3682.6321 8.3829825
+ 10000 20776.574 220.03769 0 3682.8 -1.8404787
+Loop time of 3.0852 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 28004.636 tau/day, 3241.277 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.17336 | 0.17336 | 0.17336 | 0.0 | 5.62
+Neigh | 0.1094 | 0.1094 | 0.1094 | 0.0 | 3.55
+Comm | 0.010163 | 0.010163 | 0.010163 | 0.0 | 0.33
+Output | 0.0030687 | 0.0030687 | 0.0030687 | 0.0 | 0.10
+Modify | 2.7782 | 2.7782 | 2.7782 | 0.0 | 90.05
+Other | | 0.01105 | | | 0.36
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 82 ave 82 max 82 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 887 ave 887 max 887 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 887
+Ave neighs/atom = 10.9506
+Neighbor list builds = 992
+Dangerous builds = 939
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.20Apr18.rigid.poems.g++.4 b/examples/rigid/log.20Apr18.rigid.poems.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..e2fb6b65b6602bd72ac74b5d0719836f459cd25d
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.poems.g++.4
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 36 45
+10 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+1 clusters, 9 bodies, 8 joints, 81 atoms
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 217.7783 3430.3907 0 3466.6871 -2.7403788
+ 50 13679.637 1404.2468 0 3684.1863 12.446066
+ 100 16777.225 888.87665 0 3685.0808 -31.828677
+ 150 19595.365 418.45042 0 3684.3446 40.709078
+ 200 18524.188 596.47273 0 3683.8375 -0.8159371
+ 250 21015.789 180.96521 0 3683.5967 -10.042469
+ 300 20785.513 219.25314 0 3683.5053 2.6452719
+ 350 21072.46 171.2554 0 3683.3321 7.0609024
+ 400 19956.414 356.36381 0 3682.4328 19.320259
+ 450 20724.42 227.73284 0 3681.8028 8.1259249
+ 500 20152.578 322.71466 0 3681.4777 5.4929878
+ 550 20017.022 345.29701 0 3681.4673 5.4661666
+ 600 17897.743 698.72196 0 3681.6791 3.2854742
+ 650 17297.758 796.60256 0 3679.5623 15.191113
+ 700 18581.934 584.29715 0 3681.2861 5.1588289
+ 750 21774.158 52.821062 0 3681.8474 -10.775664
+ 800 21604.055 81.188546 0 3681.8644 -3.2045743
+ 850 17821.483 711.53827 0 3681.7854 7.4384277
+ 900 21033.292 175.98127 0 3681.5299 -16.345167
+ 950 20968.166 186.59847 0 3681.2929 -2.330456
+ 1000 20490.66 266.19375 0 3681.3037 11.787983
+ 1050 20222.396 310.94072 0 3681.34 -8.3459539
+ 1100 21321.687 127.61533 0 3681.2299 -1.2184717
+ 1150 20849.582 206.01695 0 3680.9472 -0.86699147
+ 1200 21815.003 45.317414 0 3681.1512 1.5988314
+ 1250 18655.437 572.41453 0 3681.654 10.064078
+ 1300 20780.781 217.36506 0 3680.8286 6.0538614
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+ 3600 19265.519 471.27582 0 3682.1956 2.3506222
+ 3650 20351.848 290.65727 0 3682.6319 3.5445062
+ 3700 18507.473 597.72931 0 3682.3082 -21.283074
+ 3750 20344.017 291.60622 0 3682.2757 6.5366987
+ 3800 20672.372 237.18966 0 3682.585 6.7310703
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+ 3900 20890.294 201.69901 0 3683.4147 -9.5644117
+ 3950 20684.181 235.91733 0 3683.2809 -4.8913079
+ 4000 21499.086 100.67563 0 3683.8566 1.1969651
+ 4050 18549.152 590.04529 0 3681.5707 -9.1914883
+ 4100 18436.457 604.2601 0 3677.003 3.6486137
+ 4150 19332.655 462.03124 0 3684.1404 -11.280758
+ 4200 21199.837 150.66602 0 3683.9722 0.14505208
+ 4250 19088.228 501.77395 0 3683.1453 1.6869973
+ 4300 16617.942 913.86736 0 3683.5244 9.1792322
+ 4350 19765.761 388.52744 0 3682.821 -4.1982973
+ 4400 20181.964 320.06096 0 3683.7216 5.3685715
+ 4450 20132.04 328.29106 0 3683.631 6.3340995
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+ 4650 19821.01 380.27685 0 3683.7784 11.857115
+ 4700 18724.367 563.42963 0 3684.1575 13.250333
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+ 5050 20750.212 226.15635 0 3684.525 -0.73974419
+ 5100 20569.533 255.21358 0 3683.4691 -18.332775
+ 5150 21447.046 109.3048 0 3683.8124 -2.5745966
+ 5200 18985.753 519.77191 0 3684.0641 9.7821968
+ 5250 21334.568 128.16597 0 3683.9273 -0.61310451
+ 5300 18836.476 544.54018 0 3683.9528 -17.979429
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+ 5900 21566.123 89.588216 0 3683.9421 -7.8944316
+ 5950 21591.695 85.284975 0 3683.9009 -2.4895203
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+ 6350 20509.459 264.29515 0 3682.5383 2.5335834
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+ 7200 21014.278 182.97687 0 3685.3566 1.044649
+ 7250 18588.789 587.96259 0 3686.094 22.707132
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+ 7400 20967.579 190.67822 0 3685.2747 -0.94800692
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+ 7500 19056.583 507.18197 0 3683.2791 3.2026014
+ 7550 18542.455 594.92944 0 3685.3386 -27.908724
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+ 7700 20683.189 235.46294 0 3682.6611 10.876437
+ 7750 20729.325 228.204 0 3683.0915 3.8844308
+ 7800 21667.475 71.752748 0 3682.9985 -15.457992
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+ 7900 21079.827 169.61123 0 3682.9158 -1.3216223
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+ 8000 20606.41 248.06357 0 3682.4652 4.2844844
+ 8050 20284.503 302.0469 0 3682.7973 6.3402329
+ 8100 21859.537 39.514865 0 3682.7711 -13.302141
+ 8150 18495.181 600.26329 0 3682.7934 9.9318242
+ 8200 21458.549 105.63828 0 3682.0631 -7.7419285
+ 8250 18704.511 564.30958 0 3681.728 14.680489
+ 8300 20689.366 233.57049 0 3681.7982 2.3067527
+ 8350 20692.974 232.67005 0 3681.499 4.2743386
+ 8400 20240.086 307.5395 0 3680.8872 1.9694217
+ 8450 19075.969 501.34689 0 3680.6751 11.056078
+ 8500 21456.727 103.36067 0 3679.4818 -3.4512371
+ 8550 20393.16 279.84781 0 3678.7078 6.3282998
+ 8600 20898.88 195.43751 0 3678.5842 -14.393947
+ 8650 20297.482 295.3169 0 3678.2306 -0.96829147
+ 8700 21079.56 164.72934 0 3677.9893 -8.339122
+ 8750 21142.519 154.18527 0 3677.9384 -4.6169442
+ 8800 20143.871 320.23161 0 3677.5435 6.5710426
+ 8850 21030.065 172.88831 0 3677.8992 1.3973883
+ 8900 19814.648 375.22097 0 3677.6624 2.6996208
+ 8950 17392.382 778.87517 0 3677.6055 11.963975
+ 9000 19209.163 476.44659 0 3677.9738 8.7050034
+ 9050 20143.824 320.17051 0 3677.4745 -5.8044332
+ 9100 21400.78 110.99404 0 3677.7908 -3.0027429
+ 9150 21834.471 38.970732 0 3678.0493 -2.5838117
+ 9200 21344.715 120.55831 0 3678.0108 4.8187829
+ 9250 20998.277 178.31959 0 3678.0324 -1.2009012
+ 9300 21141.788 154.4658 0 3678.0971 -21.693564
+ 9350 21439.398 105.00432 0 3678.2374 -16.113694
+ 9400 21296.282 128.83877 0 3678.2191 -2.9990284
+ 9450 19050.623 503.10319 0 3678.207 15.622525
+ 9500 20845.847 203.77117 0 3678.079 -1.7504827
+ 9550 18808.956 543.38757 0 3678.2135 -2.6611868
+ 9600 20612.559 242.57373 0 3678.0002 -0.1650541
+ 9650 20522.637 257.28926 0 3677.7288 6.8876074
+ 9700 20970.074 182.75754 0 3677.7699 -4.5350279
+ 9750 18297.505 625.06808 0 3674.6522 32.429153
+ 9800 21042.472 170.78969 0 3677.8684 5.4901963
+ 9850 20444.092 270.84839 0 3678.197 6.9444494
+ 9900 21597.787 78.901871 0 3678.533 2.3445932
+ 9950 18376.854 616.35469 0 3679.1636 -8.55063
+ 10000 21490.054 97.234379 0 3678.9101 -0.36115606
+Loop time of 3.38095 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 25554.943 tau/day, 2957.748 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.015775 | 0.043664 | 0.1024 | 16.8 | 1.29
+Neigh | 0.012822 | 0.029038 | 0.061576 | 11.5 | 0.86
+Comm | 0.18256 | 0.2516 | 0.30898 | 10.5 | 7.44
+Output | 0.0063725 | 0.0069898 | 0.0081069 | 0.8 | 0.21
+Modify | 2.9608 | 3.0171 | 3.0947 | 2.8 | 89.24
+Other | | 0.03255 | | | 0.96
+
+Nlocal: 20.25 ave 81 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost: 45.5 ave 82 max 12 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 218.75 ave 875 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 875
+Ave neighs/atom = 10.8025
+Neighbor list builds = 993
+Dangerous builds = 945
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.20Apr18.rigid.poems2.g++.1 b/examples/rigid/log.20Apr18.rigid.poems2.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..9062b78def3407178b062603c2a74207cac6e611
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.poems2.g++.1
@@ -0,0 +1,342 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4
+1 clusters, 4 bodies, 3 joints, 36 atoms
+fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+1 clusters, 5 bodies, 4 joints, 45 atoms
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems2
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+WARNING: More than one fix poems (../fix_poems.cpp:363)
+WARNING: More than one fix poems (../fix_poems.cpp:363)
+WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.854 | 3.854 | 3.854 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 196.00047 3632.2347 0 3668.5311 -2.7403788
+ 50 12167.633 1505.5478 0 3758.8133 35.125973
+ 100 17556.978 512.66277 0 3763.9549 11.137534
+ 150 19579.586 138.04942 0 3763.8987 -29.953971
+ 200 19757.51 105.30542 0 3764.1036 -0.030645317
+ 250 18218.374 390.10747 0 3763.8804 13.711001
+ 300 19383.039 174.40688 0 3763.8586 5.7240693
+ 350 20125.986 36.972611 0 3764.0071 1.9559205
+ 400 18888.816 266.10975 0 3764.0386 9.6362168
+ 450 19307.656 188.2511 0 3763.743 1.9326206
+ 500 16331.197 738.56392 0 3762.8597 9.1715579
+ 550 19318.722 186.16172 0 3763.7027 3.0115336
+ 600 19455.268 161.20621 0 3764.0336 0.55208034
+ 650 18487.011 340.03216 0 3763.5528 -8.0359122
+ 700 17321.201 556.32471 0 3763.9545 -13.631751
+ 750 18979.187 249.04389 0 3763.7082 -2.6072455
+ 800 19342.456 181.85552 0 3763.7918 8.1918726
+ 850 19070.641 232.19342 0 3763.7936 7.3148472
+ 900 19478.873 156.65987 0 3763.8586 2.4284987
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+ 6150 16487.861 707.08907 0 3760.3967 32.53899
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+ 7150 17739.189 478.35458 0 3763.3896 11.976827
+ 7200 19492.829 153.62536 0 3763.4084 -8.6815909
+ 7250 18797.718 282.17319 0 3763.232 -19.897633
+ 7300 18353.871 364.09362 0 3762.9585 5.4538454
+ 7350 19040.053 237.34144 0 3763.2772 6.5600248
+ 7400 19452.586 160.98629 0 3763.317 -9.0542585
+ 7450 19033.845 238.45033 0 3763.2365 3.2654681
+ 7500 18137.358 404.80969 0 3763.5796 -7.2639486
+ 7550 16863.391 642.47654 0 3765.3267 31.248679
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+ 7700 15593.154 876.08807 0 3763.7093 -9.7668717
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+ 8100 18749.745 291.57889 0 3763.7538 -14.015057
+ 8150 19411.326 169.05845 0 3763.7485 -4.3392799
+ 8200 17994.991 431.56932 0 3763.9751 6.8158642
+ 8250 19325.923 185.1137 0 3763.9883 9.4923883
+ 8300 17354.302 550.33316 0 3764.0927 6.1636399
+ 8350 19900.895 78.431831 0 3763.7828 -4.5224196
+ 8400 17775.757 471.62915 0 3763.4361 12.949899
+ 8450 19909.324 76.935162 0 3763.8471 -2.950115
+ 8500 18601.933 318.79405 0 3763.5965 6.0173542
+ 8550 18685.758 303.59497 0 3763.9205 2.7277487
+ 8600 19297.521 190.12606 0 3763.741 4.8998933
+ 8650 17396.37 542.14326 0 3763.6932 39.937715
+ 8700 17134.714 590.99465 0 3764.0898 10.37328
+ 8750 14348.104 1106.7544 0 3763.8106 -3.8604659
+ 8800 19830.924 90.929138 0 3763.3225 0.26603444
+ 8850 18551.537 326.53747 0 3762.0072 -1.5369982
+ 8900 20040.322 52.066026 0 3763.2367 -12.667979
+ 8950 19314.585 186.54793 0 3763.3228 -0.64755555
+ 9000 19117.66 222.84553 0 3763.153 5.2990011
+ 9050 19072.016 231.26038 0 3763.1152 -1.6513695
+ 9100 19284.933 191.73976 0 3763.0237 -3.932358
+ 9150 17356.576 548.61808 0 3762.7988 1.3659056
+ 9200 18939.549 255.43703 0 3762.761 3.3037106
+ 9250 19621.961 129.5012 0 3763.1976 1.667
+ 9300 16898.033 633.79921 0 3763.0647 7.5941845
+ 9350 19662.75 122.10836 0 3763.3584 -3.3144828
+ 9400 16118.338 778.70243 0 3763.5799 9.8684537
+ 9450 17362.374 548.18847 0 3763.443 6.8117548
+ 9500 17873.057 453.37389 0 3763.1993 9.5651746
+ 9550 19282.305 192.593 0 3763.3901 -4.987757
+ 9600 18236.48 386.36263 0 3763.4886 8.8658343
+ 9650 17695.571 486.6517 0 3763.6093 12.471421
+ 9700 19044.003 237.04652 0 3763.7138 0.84430497
+ 9750 17937.299 442.4372 0 3764.1592 3.981475
+ 9800 18179.761 396.86987 0 3763.4923 -11.397273
+ 9850 19157.292 215.8937 0 3763.5404 -7.7648682
+ 9900 19719.066 111.98124 0 3763.6602 5.5378968
+ 9950 18103.235 410.65473 0 3763.1056 28.201374
+ 10000 18479.903 341.32548 0 3763.5297 -5.0581298
+Loop time of 3.14341 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 27486.104 tau/day, 3181.262 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.12201 | 0.12201 | 0.12201 | 0.0 | 3.88
+Neigh | 0.077269 | 0.077269 | 0.077269 | 0.0 | 2.46
+Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 0.39
+Output | 0.0032048 | 0.0032048 | 0.0032048 | 0.0 | 0.10
+Modify | 2.9172 | 2.9172 | 2.9172 | 0.0 | 92.80
+Other | | 0.01151 | | | 0.37
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 67 ave 67 max 67 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 599 ave 599 max 599 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 599
+Ave neighs/atom = 7.39506
+Neighbor list builds = 993
+Dangerous builds = 945
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.20Apr18.rigid.poems2.g++.4 b/examples/rigid/log.20Apr18.rigid.poems2.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..812b101841c6a9260eb4fad1a39b26a07c2dd64a
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.poems2.g++.4
@@ -0,0 +1,342 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4
+1 clusters, 4 bodies, 3 joints, 36 atoms
+fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+1 clusters, 5 bodies, 4 joints, 45 atoms
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems2
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+WARNING: More than one fix poems (../fix_poems.cpp:363)
+WARNING: More than one fix poems (../fix_poems.cpp:363)
+WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.919 | 4.201 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 196.00047 3632.2347 0 3668.5311 -2.7403788
+ 50 12167.633 1505.5478 0 3758.8133 35.125973
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+ 300 19383.039 174.40688 0 3763.8586 5.7240693
+ 350 20125.986 36.972611 0 3764.0071 1.9559205
+ 400 18888.816 266.10975 0 3764.0386 9.6362168
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+ 500 16331.197 738.56392 0 3762.8597 9.1715579
+ 550 19318.722 186.16172 0 3763.7027 3.0115336
+ 600 19455.268 161.20621 0 3764.0336 0.55208034
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+ 9850 20094.73 43.013036 0 3764.2593 -8.9770288
+ 9900 18988.815 247.63984 0 3764.087 -6.3990966
+ 9950 18290.808 377.34967 0 3764.5363 7.7453525
+ 10000 19558.326 142.47047 0 3764.3828 3.4110829
+Loop time of 3.53831 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 24418.438 tau/day, 2826.208 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0096724 | 0.035349 | 0.063574 | 10.3 | 1.00
+Neigh | 0.0091243 | 0.022333 | 0.037608 | 6.9 | 0.63
+Comm | 0.18063 | 0.2494 | 0.33202 | 12.6 | 7.05
+Output | 0.0060797 | 0.0065744 | 0.0074706 | 0.7 | 0.19
+Modify | 3.0943 | 3.1895 | 3.2828 | 4.0 | 90.14
+Other | | 0.0352 | | | 0.99
+
+Nlocal: 20.25 ave 36 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost: 17.5 ave 37 max 1 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 154.25 ave 393 max 0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 617
+Ave neighs/atom = 7.61728
+Neighbor list builds = 993
+Dangerous builds = 948
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.20Apr18.rigid.property.g++.1 b/examples/rigid/log.20Apr18.rigid.property.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..76ef36825b00775073409ad7d4c97c9e9261e4c3
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.property.g++.1
@@ -0,0 +1,340 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+fix 0 all property/atom i_bodies
+
+read_data data.rigid-property fix 0 NULL Bodies
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+# assemble bodies from per-atom custom integer property bodies
+fix 1 all rigid custom i_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
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+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934367 0 5269.4889 12.025288
+ 3750 16737.731 0.20706557 0 5269.4927 12.061948
+ 3800 16738.578 -0.05582043 0 5269.4965 12.035665
+ 3850 16738.471 -0.016307928 0 5269.5024 12.035302
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+ 3950 16738.439 -0.0012027325 0 5269.5074 12.035461
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+ 5600 16738.51 -0.021618357 0 5269.5092 12.035106
+ 5650 16738.622 -0.059214788 0 5269.507 12.035694
+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
+ 5800 16738.456 -0.0037013529 0 5269.5102 12.011675
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+ 8000 16738.469 0 0 5269.518 12.011724
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+ 8500 16738.481 -0.0034646802 0 5269.5182 12.011643
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+ 8600 16738.474 -0.00076532813 0 5269.5189 12.011681
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+ 8800 16738.475 0 0 5269.52 12.011743
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+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652438 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814371 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589893 0 5269.4979 12.062708
+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.140719 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 613990.898 tau/day, 71063.761 timesteps/s
+97.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010882 | 0.010882 | 0.010882 | 0.0 | 7.73
+Neigh | 0.037245 | 0.037245 | 0.037245 | 0.0 | 26.47
+Comm | 0.0092154 | 0.0092154 | 0.0092154 | 0.0 | 6.55
+Output | 0.0024879 | 0.0024879 | 0.0024879 | 0.0 | 1.77
+Modify | 0.074702 | 0.074702 | 0.074702 | 0.0 | 53.09
+Other | | 0.006187 | | | 4.40
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 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
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.property.g++.4 b/examples/rigid/log.20Apr18.rigid.property.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c34324b19c8d5928fd0bee8e128ff88555f65d92
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.property.g++.4
@@ -0,0 +1,340 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+fix 0 all property/atom i_bodies
+
+read_data data.rigid-property fix 0 NULL Bodies
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+# assemble bodies from per-atom custom integer property bodies
+fix 1 all rigid custom i_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934368 0 5269.4889 12.025288
+ 3750 16737.731 0.20706558 0 5269.4927 12.061948
+ 3800 16738.578 -0.05582043 0 5269.4965 12.035665
+ 3850 16738.471 -0.016307928 0 5269.5024 12.035302
+ 3900 16738.449 -0.0058182199 0 5269.5059 12.035401
+ 3950 16738.439 -0.0012027325 0 5269.5074 12.035461
+ 4000 16738.436 -0.00020698452 0 5269.5075 12.035469
+ 4050 16738.437 0 0 5269.5078 12.035454
+ 4100 16738.437 0 0 5269.508 12.035435
+ 4150 16738.438 0 0 5269.5081 12.035426
+ 4200 16738.438 0 0 5269.5083 12.035432
+ 4250 16738.439 0 0 5269.5085 12.035447
+ 4300 16738.439 0 0 5269.5086 12.035463
+ 4350 16738.44 0 0 5269.5087 12.035474
+ 4400 16738.44 0 0 5269.5088 12.035478
+ 4450 16738.44 0 0 5269.5089 12.035474
+ 4500 16738.44 0 0 5269.509 12.035462
+ 4550 16738.441 0 0 5269.5092 12.035449
+ 4600 16738.441 0 0 5269.5093 12.035445
+ 4650 16738.442 0 0 5269.5095 12.035451
+ 4700 16738.442 0 0 5269.5096 12.03546
+ 4750 16738.443 0 0 5269.5097 12.035465
+ 4800 16738.443 0 0 5269.5098 12.035466
+ 4850 16738.443 0 0 5269.51 12.035463
+ 4900 16738.444 0 0 5269.5101 12.035456
+ 4950 16738.444 0 0 5269.5102 12.035447
+ 5000 16738.445 0 0 5269.5104 12.03544
+ 5050 16738.445 0 0 5269.5105 12.035442
+ 5100 16738.446 0 0 5269.5107 12.035455
+ 5150 16738.446 0 0 5269.5108 12.03547
+ 5200 16738.446 0 0 5269.5109 12.035479
+ 5250 16738.447 0 0 5269.511 12.035479
+ 5300 16738.447 0 0 5269.5111 12.03547
+ 5350 16738.447 0 0 5269.5112 12.035454
+ 5400 16738.448 0 0 5269.5113 12.035434
+ 5450 16738.448 0 0 5269.5115 12.03542
+ 5500 16738.449 0 0 5269.5117 12.035422
+ 5550 16738.457 -0.0030919234 0 5269.5111 12.035383
+ 5600 16738.51 -0.021618357 0 5269.5092 12.035106
+ 5650 16738.622 -0.059214788 0 5269.507 12.035694
+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
+ 5800 16738.456 -0.0037013529 0 5269.5102 12.011675
+ 5850 16738.451 0 0 5269.5123 12.011709
+ 5900 16738.451 -0.0002211587 0 5269.5122 12.011687
+ 5950 16738.452 -0.00024253349 0 5269.5124 12.011678
+ 6000 16738.452 0 0 5269.5128 12.011688
+ 6050 16738.453 0 0 5269.513 12.011702
+ 6100 16738.453 0 0 5269.5131 12.011716
+ 6150 16738.454 0 0 5269.5132 12.011725
+ 6200 16738.454 0 0 5269.5133 12.011728
+ 6250 16738.454 0 0 5269.5134 12.011723
+ 6300 16738.455 0 0 5269.5135 12.011712
+ 6350 16738.455 0 0 5269.5137 12.0117
+ 6400 16738.456 0 0 5269.5138 12.011697
+ 6450 16738.456 0 0 5269.514 12.011704
+ 6500 16738.456 0 0 5269.5141 12.011714
+ 6550 16738.457 0 0 5269.5142 12.011719
+ 6600 16738.457 0 0 5269.5143 12.011718
+ 6650 16738.458 0 0 5269.5144 12.011713
+ 6700 16738.458 0 0 5269.5146 12.011705
+ 6750 16738.459 0 0 5269.5147 12.011696
+ 6800 16738.459 0 0 5269.5149 12.01169
+ 6850 16738.46 0 0 5269.515 12.011695
+ 6900 16738.46 0 0 5269.5152 12.01171
+ 6950 16738.46 0 0 5269.5153 12.011726
+ 7000 16738.461 0 0 5269.5154 12.011736
+ 7050 16738.461 0 0 5269.5155 12.011737
+ 7100 16738.461 0 0 5269.5155 12.011728
+ 7150 16738.461 0 0 5269.5156 12.011712
+ 7200 16738.462 0 0 5269.5158 12.011691
+ 7250 16738.463 0 0 5269.516 12.011676
+ 7300 16738.463 0 0 5269.5162 12.011677
+ 7350 16738.464 0 0 5269.5164 12.011693
+ 7400 16738.464 0 0 5269.5165 12.011713
+ 7450 16738.465 0 0 5269.5166 12.011729
+ 7500 16738.465 0 0 5269.5167 12.011736
+ 7550 16738.465 0 0 5269.5168 12.011734
+ 7600 16738.465 0 0 5269.5168 12.011722
+ 7650 16738.466 0 0 5269.517 12.011704
+ 7700 16738.466 0 0 5269.5171 12.011687
+ 7750 16738.467 0 0 5269.5173 12.011681
+ 7800 16738.467 0 0 5269.5175 12.011687
+ 7850 16738.468 0 0 5269.5176 12.0117
+ 7900 16738.468 0 0 5269.5178 12.011712
+ 7950 16738.469 0 0 5269.5179 12.011721
+ 8000 16738.469 0 0 5269.518 12.011724
+ 8050 16738.469 0 0 5269.5181 12.01172
+ 8100 16738.47 0 0 5269.5182 12.011709
+ 8150 16738.47 0 0 5269.5183 12.0117
+ 8200 16738.47 0 0 5269.5185 12.0117
+ 8250 16738.471 0 0 5269.5186 12.011709
+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690664 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532811 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.206235 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 418940.303 tau/day, 48488.461 timesteps/s
+97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0026572 | 0.004187 | 0.0050838 | 1.5 | 2.03
+Neigh | 0.012115 | 0.012789 | 0.013634 | 0.5 | 6.20
+Comm | 0.084275 | 0.089969 | 0.095318 | 1.5 | 43.62
+Output | 0.0048559 | 0.0051559 | 0.0059836 | 0.7 | 2.50
+Modify | 0.077074 | 0.083586 | 0.088022 | 1.5 | 40.53
+Other | | 0.01055 | | | 5.11
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.tnr.g++.1 b/examples/rigid/log.20Apr18.rigid.tnr.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..097fd132aa7c352d4ceac0735d1f9b455ec8e002
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.tnr.g++.1
@@ -0,0 +1,458 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Tethered nanorods
+
+atom_style molecular
+
+read_data data.rigid.tnr
+ orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 5600 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 1600 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+# Specify bond parameters
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+special_bonds fene
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+# Specify initial velocities
+
+velocity all create 1.4 109345
+
+# Specify rigid components
+
+group rods type 2
+4000 atoms in group rods
+group tethers subtract all rods
+1600 atoms in group tethers
+
+neigh_modify exclude molecule/intra rods delay 0 every 1
+
+# Specify the pair potentials
+
+pair_style lj/cut 2.5
+pair_modify shift yes
+pair_coeff * * 1.0 1.0 1.122
+pair_coeff 2 2 1.0 1.0 2.5
+
+# Specify output
+
+thermo 100
+thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
+thermo_modify flush yes lost warn
+
+timestep 0.005
+
+fix 1 rods rigid molecule
+800 rigid bodies with 4000 atoms
+fix 2 tethers nve
+fix 3 all langevin 1.4 1.4 1.0 437624
+
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 45 45 45
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
+ 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
+ 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
+ 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
+ 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
+ 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
+ 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
+ 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
+ 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
+ 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
+ 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
+ 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
+ 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
+ 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
+ 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
+ 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
+ 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
+ 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
+ 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
+ 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
+ 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
+ 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
+ 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216998 -0.0032636911
+ 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
+ 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738261 0.0090537939 0.013165402
+ 2500 1.4153808 5.9421661 7.0538718 0.00015906308 7.0607216 62.244 62.244 62.244 0.0023516211 -0.0019814987 0.00010706678
+ 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
+ 2700 1.4138077 5.9369067 7.047377 0.0024268843 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960354 0.00049277379
+ 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113032 0.0047214106
+ 2900 1.3938659 5.921023 7.01583 0.0053751201 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566097 0.0064197134
+ 3000 1.390221 5.9205014 7.0124455 -0.0010750973 6.9661486 62.244 62.244 62.244 0.0019519817 -0.0041878875 -0.0009893861
+ 3100 1.4205722 5.9178284 7.0336117 0.0098735467 7.4587964 62.244 62.244 62.244 0.0040973349 0.012167268 0.013356037
+ 3200 1.398418 5.9150349 7.0134173 0.0061541837 7.278435 62.244 62.244 62.244 0.0067621825 0.011952562 -0.00025219321
+ 3300 1.4269859 5.9148727 7.0356937 0.006062387 7.2967584 62.244 62.244 62.244 0.012956233 -2.480748e-05 0.005255736
+ 3400 1.434286 5.9356705 7.0622253 0.0002731615 7.0739885 62.244 62.244 62.244 -0.00054959543 0.0052526331 -0.0038835532
+ 3500 1.4416808 5.9228153 7.0551783 0.0083383068 7.414251 62.244 62.244 62.244 0.0073994017 0.0030328023 0.014582716
+ 3600 1.4136063 5.9039442 7.0142562 0.0019711852 7.0991414 62.244 62.244 62.244 -0.00032317688 0.0035029725 0.0027337599
+ 3700 1.433382 5.91201 7.0378548 0.0071286927 7.3448378 62.244 62.244 62.244 0.0064768108 0.0046765006 0.010232767
+ 3800 1.3659481 5.9032872 6.9761663 -0.0054034056 6.7434793 62.244 62.244 62.244 -0.007394357 -0.0082833116 -0.00053254832
+ 3900 1.396322 5.9043001 7.0010362 0.005331024 7.2306062 62.244 62.244 62.244 0.0081855301 0.0048806234 0.0029269184
+ 4000 1.412548 5.906066 7.0155468 0.0028450132 7.1380616 62.244 62.244 62.244 0.0052588387 0.00072412871 0.0025520721
+ 4100 1.3943949 5.9040868 6.9993093 0.0058053193 7.2493039 62.244 62.244 62.244 0.0060583148 0.0024781972 0.0088794459
+ 4200 1.4249768 5.8906369 7.0098798 0.0030209006 7.1399689 62.244 62.244 62.244 0.0061742017 -0.0020795681 0.0049680681
+ 4300 1.3899827 5.8966327 6.9883897 0.0057278096 7.2350464 62.244 62.244 62.244 0.0049035059 0.0021868561 0.010093067
+ 4400 1.4414361 5.8986386 7.0308094 0.0050941357 7.2501783 62.244 62.244 62.244 0.0057971901 0.0037941986 0.0056910185
+ 4500 1.4093099 5.8922729 6.9992103 0.0012182325 7.0516711 62.244 62.244 62.244 0.0042896986 0.0014287789 -0.00206378
+ 4600 1.3779677 5.892894 6.9752138 0.002057623 7.0638213 62.244 62.244 62.244 0.0029271755 -0.0031752166 0.0064209102
+ 4700 1.4086418 5.9096898 7.0161024 -0.00052853259 6.9933422 62.244 62.244 62.244 -0.001862386 -0.0018129293 0.0020897176
+ 4800 1.4394 5.9146102 7.0451818 0.015326441 7.7051846 62.244 62.244 62.244 0.014754936 0.017967956 0.013256431
+ 4900 1.4496219 5.9074613 7.0460616 0.0075297868 7.370317 62.244 62.244 62.244 0.0092907193 0.0079794674 0.0053191736
+ 5000 1.4280291 5.9106136 7.032254 -0.0013249587 6.9751972 62.244 62.244 62.244 -0.0044875103 0.0020723667 -0.0015597324
+Loop time of 6.73744 on 1 procs for 5000 steps with 5600 atoms
+
+Performance: 320596.735 tau/day, 742.122 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.52635 | 0.52635 | 0.52635 | 0.0 | 7.81
+Bond | 0.26628 | 0.26628 | 0.26628 | 0.0 | 3.95
+Neigh | 1.5927 | 1.5927 | 1.5927 | 0.0 | 23.64
+Comm | 0.16011 | 0.16011 | 0.16011 | 0.0 | 2.38
+Output | 0.0040634 | 0.0040634 | 0.0040634 | 0.0 | 0.06
+Modify | 4.0145 | 4.0145 | 4.0145 | 0.0 | 59.58
+Other | | 0.1735 | | | 2.57
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1352 ave 1352 max 1352 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5257 ave 5257 max 5257 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5257
+Ave neighs/atom = 0.93875
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 766
+Dangerous builds = 0
+
+# Replace fix rigid and fix langevin with new ones
+
+unfix 1
+unfix 3
+
+fix 3 tethers langevin 1.4 1.4 1.0 198450
+
+# Test different integrators for rods
+
+fix 1 rods rigid/nve molecule
+800 rigid bodies with 4000 atoms
+print "rigid/nve"
+rigid/nve
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 5000 1.4280291 5.9106136 7.032254 0.02814128 8.2441024 62.244 62.244 62.244 0.019873502 0.039656784 0.024893554
+ 5100 1.4435659 5.8998386 7.0336823 0.0063929319 7.3089813 62.244 62.244 62.244 0.0089837757 0.0052773116 0.0049177085
+ 5200 1.3970069 5.9117164 7.0089904 0.0065245686 7.289958 62.244 62.244 62.244 0.008502047 0.0043872479 0.0066844108
+ 5300 1.433167 5.8796669 7.0053428 0.0076478538 7.3346825 62.244 62.244 62.244 0.0061384889 0.0070193789 0.0097856935
+ 5400 1.4191626 5.8830864 6.9977626 0.0026371359 7.1113257 62.244 62.244 62.244 0.0024097043 -0.00082200506 0.0063237084
+ 5500 1.409376 5.8753367 6.982326 0.010180815 7.4207427 62.244 62.244 62.244 0.010429709 0.0081711083 0.011941628
+ 5600 1.4005678 5.882485 6.9825559 0.00036705268 6.9983623 62.244 62.244 62.244 -0.0034485466 0.0031079204 0.0014417843
+ 5700 1.4116833 5.8842566 6.9930582 0.00053413233 7.0160595 62.244 62.244 62.244 0.0016669624 -0.0030741941 0.0030096286
+ 5800 1.409035 5.894902 7.0016235 4.7080816e-05 7.003651 62.244 62.244 62.244 0.0018596854 -5.3937508e-05 -0.0016645054
+ 5900 1.4150353 5.8928576 7.004292 0.0063467985 7.2776043 62.244 62.244 62.244 0.0055755751 0.0090839847 0.0043808358
+ 6000 1.4374163 5.8778036 7.0068171 0.0031890481 7.1441472 62.244 62.244 62.244 0.0067647375 0.0015458579 0.0012565488
+Loop time of 1.41082 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 306205.780 tau/day, 708.810 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.149 | 0.149 | 0.149 | 0.0 | 10.56
+Bond | 0.053873 | 0.053873 | 0.053873 | 0.0 | 3.82
+Neigh | 0.35532 | 0.35532 | 0.35532 | 0.0 | 25.19
+Comm | 0.032433 | 0.032433 | 0.032433 | 0.0 | 2.30
+Output | 0.00080752 | 0.00080752 | 0.00080752 | 0.0 | 0.06
+Modify | 0.78447 | 0.78447 | 0.78447 | 0.0 | 55.60
+Other | | 0.03491 | | | 2.47
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1347 ave 1347 max 1347 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5592 ave 5592 max 5592 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5592
+Ave neighs/atom = 0.998571
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 153
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
+800 rigid bodies with 4000 atoms
+print "rigid/nvt"
+rigid/nvt
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 6000 1.4374163 5.8778036 7.0068171 -0.0020672233 6.9177963 62.244 62.244 62.244 0.034504923 -0.030001164 -0.010705429
+ 6100 1.4393824 5.8852696 7.0158274 0.0055792227 7.2560855 62.244 62.244 62.244 0.0072602759 0.0074870643 0.0019903278
+ 6200 1.4265711 5.8853532 7.0058484 0.0019366613 7.0892468 62.244 62.244 62.244 -0.0035411799 0.0047319741 0.0046191897
+ 6300 1.4030198 5.8824874 6.9844843 0.0055760353 7.2246052 62.244 62.244 62.244 0.0031273033 0.0080002386 0.005600564
+ 6400 1.3592064 5.8924876 6.9600714 0.0051450348 7.1816321 62.244 62.244 62.244 0.0042848197 0.0044005693 0.0067497155
+ 6500 1.3946028 5.8798014 6.9751872 0.0051168754 7.1955353 62.244 62.244 62.244 0.0020473208 0.0038175566 0.0094857487
+ 6600 1.3652122 5.8985637 6.9708648 0.0065480579 7.2528439 62.244 62.244 62.244 0.0056940621 0.0062242398 0.0077258719
+ 6700 1.3808929 5.9047739 6.9893913 0.0074053719 7.308289 62.244 62.244 62.244 0.0049554161 0.012378296 0.0048824031
+ 6800 1.4140879 5.891133 7.0018233 0.001592636 7.070407 62.244 62.244 62.244 -9.4421917e-05 -0.00029455229 0.0051668821
+ 6900 1.4364121 5.8904988 7.0187235 0.00647853 7.2977086 62.244 62.244 62.244 0.0024458531 0.0073279625 0.0096617742
+ 7000 1.4370567 5.8900758 7.0188069 0.00098705898 7.0613127 62.244 62.244 62.244 0.0024436343 -0.0011032284 0.001620771
+Loop time of 1.44111 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 299769.942 tau/day, 693.912 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.14928 | 0.14928 | 0.14928 | 0.0 | 10.36
+Bond | 0.053511 | 0.053511 | 0.053511 | 0.0 | 3.71
+Neigh | 0.35946 | 0.35946 | 0.35946 | 0.0 | 24.94
+Comm | 0.033026 | 0.033026 | 0.033026 | 0.0 | 2.29
+Output | 0.00081658 | 0.00081658 | 0.00081658 | 0.0 | 0.06
+Modify | 0.80995 | 0.80995 | 0.80995 | 0.0 | 56.20
+Other | | 0.03506 | | | 2.43
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1351 ave 1351 max 1351 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5541 ave 5541 max 5541 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5541
+Ave neighs/atom = 0.989464
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 153
+Dangerous builds = 0
+unfix 1
+
+compute myTemp all temp
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt iso"
+rigid/npt iso
+fix_modify 1 temp myTemp
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 7000 1.4370567 5.8900758 7.0188069 -0.0033603557 6.8740999 62.244 62.244 62.244 -0.094745193 0.10894465 -0.024280521
+ 7100 1.485379 5.864626 7.0313116 0.018625962 7.6475425 57.008236 57.008236 57.008236 0.023222208 0.015549704 0.017105973
+ 7200 1.5367991 5.8157585 7.0228319 0.019179143 7.4580039 50.273593 50.273593 50.273593 0.019479917 0.008906575 0.029150938
+ 7300 1.5692285 5.785208 7.0177529 0.026450106 7.4560147 45.27218 45.27218 45.27218 0.029705272 0.019989987 0.029655059
+ 7400 1.5961415 5.7633541 7.0170377 0.049085262 7.6510208 41.665015 41.665015 41.665015 0.045248259 0.047932005 0.054075524
+ 7500 1.5805951 5.7223115 6.9637843 0.022024393 7.1962354 38.952791 38.952791 38.952791 0.017398546 0.0097043058 0.038970326
+ 7600 1.5679583 5.6928914 6.9244386 0.05023237 7.3717858 36.808633 36.808633 36.808633 0.029561593 0.080716323 0.040419195
+ 7700 1.5214637 5.661404 6.8564322 0.038992847 7.1614257 35.25044 35.25044 35.25044 0.013961981 0.064676103 0.038340457
+ 7800 1.5313649 5.6185256 6.8213307 0.053950562 7.1990319 33.971403 33.971403 33.971403 0.036690654 0.066107903 0.059053129
+ 7900 1.5272701 5.5732963 6.7728851 0.067896988 7.2131774 33.115109 33.115109 33.115109 0.046486851 0.073976177 0.083227936
+ 8000 1.4754162 5.5525858 6.7114461 0.036458901 6.9347086 32.48878 32.48878 32.48878 0.066065978 0.031260775 0.01204995
+Loop time of 3.09124 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 139749.554 tau/day, 323.494 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.38334 | 0.38334 | 0.38334 | 0.0 | 12.40
+Bond | 0.079063 | 0.079063 | 0.079063 | 0.0 | 2.56
+Neigh | 1.3711 | 1.3711 | 1.3711 | 0.0 | 44.35
+Comm | 0.07249 | 0.07249 | 0.07249 | 0.0 | 2.35
+Output | 0.00079656 | 0.00079656 | 0.00079656 | 0.0 | 0.03
+Modify | 1.1412 | 1.1412 | 1.1412 | 0.0 | 36.92
+Other | | 0.04324 | | | 1.40
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2922 ave 2922 max 2922 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 24639 ave 24639 max 24639 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 24639
+Ave neighs/atom = 4.39982
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 335
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt x"
+rigid/npt x
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.784 | 7.784 | 7.784 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 8000 1.4754162 5.5525858 6.7114461 -0.036273091 6.4893215 32.48878 32.48878 32.48878 -0.12886524 -0.13731772 0.15736368
+ 8100 1.4842494 5.5359706 6.701769 0.040754696 6.9494736 32.246136 32.48878 32.48878 0.0098547221 0.069850343 0.042559024
+ 8200 1.4385513 5.5252007 6.6551057 -0.0053954052 6.6228379 31.729684 32.48878 32.48878 0.029251386 -0.023427626 -0.022009975
+ 8300 1.4426011 5.5073818 6.6404676 0.034683453 6.8437384 31.093797 32.48878 32.48878 0.028287259 0.027455229 0.048307871
+ 8400 1.4194517 5.5015592 6.6164624 0.015869651 6.7074209 30.408624 32.48878 32.48878 0.020129982 0.00586219 0.021616782
+ 8500 1.4584335 5.4424151 6.5879365 0.025786252 6.7324275 29.728548 32.48878 32.48878 0.051564744 0.0046756434 0.021118368
+ 8600 1.4578973 5.4266016 6.5717019 0.061244725 6.9097759 29.286286 32.48878 32.48878 0.08652905 0.052448352 0.044756773
+ 8700 1.4158345 5.4199695 6.5320317 0.076133238 6.9466617 28.894001 32.48878 32.48878 0.078560655 0.077921379 0.071917679
+ 8800 1.4360707 5.3986549 6.5266116 0.05106059 6.7993343 28.337182 32.48878 32.48878 0.030158729 0.080651224 0.042371819
+ 8900 1.424778 5.386975 6.5060619 0.0023828771 6.5185272 27.75397 32.48878 32.48878 -0.026562751 0.0076340254 0.026077357
+ 9000 1.4273004 5.369067 6.490135 0.077698761 6.8879525 27.163833 32.48878 32.48878 0.056923916 0.050917329 0.12525504
+Loop time of 3.05599 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 141361.930 tau/day, 327.227 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.60397 | 0.60397 | 0.60397 | 0.0 | 19.76
+Bond | 0.080384 | 0.080384 | 0.080384 | 0.0 | 2.63
+Neigh | 1.1078 | 1.1078 | 1.1078 | 0.0 | 36.25
+Comm | 0.057267 | 0.057267 | 0.057267 | 0.0 | 1.87
+Output | 0.0007937 | 0.0007937 | 0.0007937 | 0.0 | 0.03
+Modify | 1.1674 | 1.1674 | 1.1674 | 0.0 | 38.20
+Other | | 0.03837 | | | 1.26
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3326 ave 3326 max 3326 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 31301 ave 31301 max 31301 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 31301
+Ave neighs/atom = 5.58946
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 168
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph iso"
+rigid/nph iso
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.787 | 7.787 | 7.787 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 9000 1.4273004 5.369067 6.490135 0.075024718 6.8742614 27.163833 32.48878 32.48878 0.020257355 0.083191009 0.12162579
+ 9100 1.425834 5.3711961 6.4911123 0.045582762 6.7236289 27.13015 32.448495 32.448495 0.047970965 0.045448278 0.043329042
+ 9200 1.4609827 5.3288319 6.4763555 0.072880923 6.8414166 26.96611 32.252298 32.252298 0.053774659 0.093193782 0.071674329
+ 9300 1.448717 5.3331013 6.4709909 0.048446002 6.7095138 26.811748 32.067676 32.067676 0.053340258 0.056657855 0.035339893
+ 9400 1.441683 5.326611 6.4589758 0.014571871 6.5288665 26.578822 31.789089 31.789089 0.043939432 -0.038654064 0.038430244
+ 9500 1.4651641 5.2943716 6.4451796 0.079668782 6.8205296 26.421077 31.600422 31.600422 0.10411792 0.075090335 0.059798087
+ 9600 1.4617024 5.2886327 6.4367216 0.01137432 6.4894218 26.274239 31.424799 31.424799 0.023318055 0.015516795 -0.0047118896
+ 9700 1.4381296 5.2798198 6.4093935 0.030371415 6.5484925 26.173039 31.303761 31.303761 0.05231569 0.025227191 0.013571362
+ 9800 1.4412744 5.2674085 6.3994523 0.076731911 6.7476559 26.092768 31.207754 31.207754 0.05712947 0.077029719 0.096036545
+ 9900 1.4427959 5.2666411 6.39988 0.034570225 6.5551479 26.003248 31.100686 31.100686 0.020955217 0.019879252 0.062876207
+ 10000 1.4337411 5.258442 6.3845688 0.011619021 6.4367617 26.004486 31.102166 31.102166 0.018666906 0.01076669 0.005423467
+Loop time of 3.23963 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 133348.758 tau/day, 308.678 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.71266 | 0.71266 | 0.71266 | 0.0 | 22.00
+Bond | 0.0805 | 0.0805 | 0.0805 | 0.0 | 2.48
+Neigh | 1.2019 | 1.2019 | 1.2019 | 0.0 | 37.10
+Comm | 0.061646 | 0.061646 | 0.061646 | 0.0 | 1.90
+Output | 0.00080585 | 0.00080585 | 0.00080585 | 0.0 | 0.02
+Modify | 1.1436 | 1.1436 | 1.1436 | 0.0 | 35.30
+Other | | 0.03849 | | | 1.19
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3617 ave 3617 max 3617 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 35834 ave 35834 max 35834 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 35834
+Ave neighs/atom = 6.39893
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 162
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph xy couple"
+rigid/nph xy couple
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.793 | 7.793 | 7.793 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 10000 1.4337411 5.258442 6.3845688 0.26156311 7.559515 26.004486 31.102166 31.102166 0.31569183 0.56043401 -0.091436513
+ 10100 1.4450694 5.2429626 6.3779872 0.026397674 6.4966895 26.018016 31.118349 31.102166 0.012890725 0.035887426 0.030414871
+ 10200 1.4603735 5.2471262 6.3941713 0.041496848 6.5804213 25.993694 31.089259 31.102166 0.043043384 0.031851909 0.04959525
+ 10300 1.4434562 5.2268279 6.3605855 0.073867581 6.6874051 25.808018 30.867184 31.102166 0.049265569 0.084151743 0.08818543
+ 10400 1.4391471 5.209772 6.3401449 0.010656841 6.3865593 25.605881 30.625422 31.102166 -0.012411333 -0.014743822 0.059125677
+ 10500 1.4239127 5.2146206 6.3330277 0.08346505 6.689122 25.342982 30.310987 31.102166 0.15420896 0.040839126 0.055347067
+ 10600 1.4524651 5.1794989 6.3203324 -0.025909515 6.2120807 25.079294 29.995608 31.102166 -0.014573849 -0.056558124 -0.0065965719
+ 10700 1.4455577 5.1721256 6.3075337 0.084888991 6.6555495 24.842844 29.712806 31.102166 0.10063515 0.067972312 0.08605951
+ 10800 1.4598996 5.15251 6.2991829 0.11430526 6.7624231 24.700034 29.542001 31.102166 0.12408423 0.12316195 0.095669606
+ 10900 1.4149128 5.1641212 6.2754594 0.045495923 6.4584246 24.605124 29.428485 31.102166 0.10001213 0.053235051 -0.016759411
+ 11000 1.3909637 5.1566933 6.2492208 0.046382806 6.433354 24.446408 29.238657 31.102166 0.091440494 0.0046064525 0.043101472
+Loop time of 3.41971 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 126326.531 tau/day, 292.423 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.78521 | 0.78521 | 0.78521 | 0.0 | 22.96
+Bond | 0.080655 | 0.080655 | 0.080655 | 0.0 | 2.36
+Neigh | 1.2846 | 1.2846 | 1.2846 | 0.0 | 37.57
+Comm | 0.064334 | 0.064334 | 0.064334 | 0.0 | 1.88
+Output | 0.00080228 | 0.00080228 | 0.00080228 | 0.0 | 0.02
+Modify | 1.1651 | 1.1651 | 1.1651 | 0.0 | 34.07
+Other | | 0.03903 | | | 1.14
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3805 ave 3805 max 3805 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 40038 ave 40038 max 40038 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40038
+Ave neighs/atom = 7.14964
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 162
+Dangerous builds = 0
+
+Total wall time: 0:00:22
diff --git a/examples/rigid/log.20Apr18.rigid.tnr.g++.4 b/examples/rigid/log.20Apr18.rigid.tnr.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..28457f51ee4fef7fbc8db5d263e0abfa27bf8e61
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.tnr.g++.4
@@ -0,0 +1,458 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Tethered nanorods
+
+atom_style molecular
+
+read_data data.rigid.tnr
+ orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 5600 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 1600 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+# Specify bond parameters
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+special_bonds fene
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+# Specify initial velocities
+
+velocity all create 1.4 109345
+
+# Specify rigid components
+
+group rods type 2
+4000 atoms in group rods
+group tethers subtract all rods
+1600 atoms in group tethers
+
+neigh_modify exclude molecule/intra rods delay 0 every 1
+
+# Specify the pair potentials
+
+pair_style lj/cut 2.5
+pair_modify shift yes
+pair_coeff * * 1.0 1.0 1.122
+pair_coeff 2 2 1.0 1.0 2.5
+
+# Specify output
+
+thermo 100
+thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
+thermo_modify flush yes lost warn
+
+timestep 0.005
+
+fix 1 rods rigid molecule
+800 rigid bodies with 4000 atoms
+fix 2 tethers nve
+fix 3 all langevin 1.4 1.4 1.0 437624
+
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 45 45 45
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
+ 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
+ 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
+ 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
+ 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
+ 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
+ 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
+ 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
+ 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
+ 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
+ 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
+ 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
+ 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
+ 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
+ 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
+ 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278431
+ 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
+ 1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
+ 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
+ 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
+ 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119435 -0.0036279901
+ 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
+ 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
+ 2300 1.4048926 5.9444129 7.0478808 0.0062444035 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
+ 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825028
+ 2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414188 0.0039571831 0.0048428539
+ 2600 1.3876469 5.9249124 7.0148347 -0.0017777223 6.9382806 62.244 62.244 62.244 -0.00047616388 -0.0025484917 -0.0023085112
+ 2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048357
+ 2800 1.4444643 5.9283432 7.0628925 0.0019400019 7.1464348 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.0003062412
+ 2900 1.3902832 5.9152516 7.0072446 -0.0021662211 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403267 -0.0046971892
+ 3000 1.3711706 5.922146 6.999127 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147658
+ 3100 1.3569137 5.9171753 6.9829583 -0.0028266781 6.861233 62.244 62.244 62.244 -0.0069507246 0.001008439 -0.0025377485
+ 3200 1.4004275 5.905939 7.0058998 0.005439464 7.2401395 62.244 62.244 62.244 0.010352181 0.0057594129 0.00020679783
+ 3300 1.3641217 5.9145275 6.985972 -0.0027212797 6.8687855 62.244 62.244 62.244 -0.00065933477 -0.0057712994 -0.0017332048
+ 3400 1.3868722 5.9059546 6.9952684 0.0092591181 7.3939939 62.244 62.244 62.244 0.010690872 0.01075251 0.0063339724
+ 3500 1.3939168 5.8992292 6.9940762 0.0074340103 7.3142071 62.244 62.244 62.244 0.010137319 0.0044252681 0.0077394433
+ 3600 1.3982507 5.921946 7.020197 0.0056794467 7.2647712 62.244 62.244 62.244 0.0023367139 0.0080592038 0.0066424225
+ 3700 1.4019908 5.9059954 7.007184 0.0065915246 7.291035 62.244 62.244 62.244 0.0049554227 0.010827006 0.0039921455
+ 3800 1.3960735 5.9020788 6.9986197 0.0027763543 7.1181779 62.244 62.244 62.244 -0.0015907599 0.0025861989 0.007333624
+ 3900 1.4352827 5.8986213 7.025959 0.0034983366 7.1766079 62.244 62.244 62.244 0.0030418079 0.002773833 0.0046793689
+ 4000 1.4121839 5.9079032 7.017098 0.0050464926 7.2344152 62.244 62.244 62.244 0.0045546986 0.0064116168 0.0041731626
+ 4100 1.3989613 5.9082377 7.0070468 0.00042898744 7.0255203 62.244 62.244 62.244 0.0025736361 0.0025182434 -0.0038049172
+ 4200 1.3998851 5.8998106 6.9993454 0.0042770066 7.1835262 62.244 62.244 62.244 0.0013728904 0.0064694548 0.0049886746
+ 4300 1.4076016 5.9044534 7.0100491 0.0066777871 7.2976147 62.244 62.244 62.244 0.0073579039 0.0048129651 0.0078624924
+ 4400 1.3948857 5.9101851 7.0057931 0.0013429373 7.063624 62.244 62.244 62.244 -0.00084288143 0.0061856571 -0.0013139638
+ 4500 1.4356157 5.8855608 7.01316 -0.0013707942 6.9541295 62.244 62.244 62.244 -0.0018523205 -0.0050195956 0.0027595334
+ 4600 1.4148397 5.8957564 7.0070372 0.0072212968 7.318008 62.244 62.244 62.244 0.011376867 0.0074399971 0.0028470263
+ 4700 1.3695106 5.8936708 6.969348 0.0017509017 7.0447471 62.244 62.244 62.244 -0.0061975951 0.0044076775 0.0070426225
+ 4800 1.4142735 5.8887578 6.9995939 0.0081923232 7.35238 62.244 62.244 62.244 0.013343877 0.0054560473 0.0057770449
+ 4900 1.4300042 5.8867398 7.0099315 0.0070875112 7.3151411 62.244 62.244 62.244 0.0080416381 0.0042409901 0.0089799056
+ 5000 1.4286039 5.8964609 7.0185527 -0.003158533 6.8825368 62.244 62.244 62.244 0.0024975808 -0.0097503027 -0.0022228771
+Loop time of 3.4608 on 4 procs for 5000 steps with 5600 atoms
+
+Performance: 624133.913 tau/day, 1444.754 timesteps/s
+98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.083226 | 0.13336 | 0.18611 | 13.0 | 3.85
+Bond | 0.045169 | 0.066142 | 0.087486 | 7.8 | 1.91
+Neigh | 0.57772 | 0.57997 | 0.58211 | 0.3 | 16.76
+Comm | 0.19402 | 0.26217 | 0.32776 | 12.2 | 7.58
+Output | 0.0027087 | 0.0035715 | 0.0041978 | 0.9 | 0.10
+Modify | 2.1223 | 2.2156 | 2.2842 | 4.2 | 64.02
+Other | | 0.2 | | | 5.78
+
+Nlocal: 1400 ave 1844 max 907 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 642 ave 714 max 581 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs: 1307.25 ave 1883 max 682 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 5229
+Ave neighs/atom = 0.93375
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 762
+Dangerous builds = 0
+
+# Replace fix rigid and fix langevin with new ones
+
+unfix 1
+unfix 3
+
+fix 3 tethers langevin 1.4 1.4 1.0 198450
+
+# Test different integrators for rods
+
+fix 1 rods rigid/nve molecule
+800 rigid bodies with 4000 atoms
+print "rigid/nve"
+rigid/nve
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 5000 1.4286039 5.8964609 7.0185527 -0.017900244 6.2477142 62.244 62.244 62.244 -0.017934885 -0.027283526 -0.0084823215
+ 5100 1.4251274 5.887521 7.0068821 0.0066290394 7.2923486 62.244 62.244 62.244 0.0033173534 0.0056467845 0.01092298
+ 5200 1.4246222 5.8928547 7.0118192 -0.00025763331 7.0007247 62.244 62.244 62.244 -0.001891953 -0.0031121381 0.0042311911
+ 5300 1.3905023 5.9024119 6.994577 0.0026824588 7.1100918 62.244 62.244 62.244 0.003106008 0.0040692376 0.00087213068
+ 5400 1.4139617 5.8906493 7.0012405 0.003175173 7.137973 62.244 62.244 62.244 0.0034546577 0.003858524 0.0022123373
+ 5500 1.4160473 5.8891813 7.0014106 0.0032907848 7.1431217 62.244 62.244 62.244 0.0014909385 0.0067546452 0.0016267707
+ 5600 1.4185962 5.8932473 7.0074786 0.013015823 7.5679792 62.244 62.244 62.244 0.011297248 0.011426835 0.016323387
+ 5700 1.4115847 5.892193 7.0009171 0.0080660065 7.3482637 62.244 62.244 62.244 0.0096534077 0.004127271 0.010417341
+ 5800 1.3920238 5.8874957 6.9808558 0.0087013878 7.3555639 62.244 62.244 62.244 0.0070865796 0.0093328615 0.0096847223
+ 5900 1.389416 5.8996657 6.9909775 0.0053218583 7.2201528 62.244 62.244 62.244 0.0050547275 0.0054113274 0.0054995198
+ 6000 1.4079053 5.8795437 6.9853779 0.0066005053 7.2696156 62.244 62.244 62.244 0.0087434104 0.0013589366 0.0096991689
+Loop time of 0.793224 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 544612.641 tau/day, 1260.677 timesteps/s
+98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.018101 | 0.036068 | 0.051689 | 7.6 | 4.55
+Bond | 0.0083735 | 0.013206 | 0.017318 | 3.6 | 1.66
+Neigh | 0.12864 | 0.1293 | 0.13002 | 0.1 | 16.30
+Comm | 0.037184 | 0.056407 | 0.077999 | 7.4 | 7.11
+Output | 0.00048971 | 0.00072509 | 0.00083923 | 0.0 | 0.09
+Modify | 0.49526 | 0.51293 | 0.52997 | 2.2 | 64.66
+Other | | 0.04459 | | | 5.62
+
+Nlocal: 1400 ave 1844 max 884 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 713.5 ave 818 max 656 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+Neighs: 1315 ave 1956 max 573 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 5260
+Ave neighs/atom = 0.939286
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 156
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
+800 rigid bodies with 4000 atoms
+print "rigid/nvt"
+rigid/nvt
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 6000 1.4079053 5.8795437 6.9853779 0.010184208 7.4239406 62.244 62.244 62.244 0.0015995549 0.064769849 -0.035816779
+ 6100 1.4031886 5.8721732 6.9743027 0.0039601 7.1448365 62.244 62.244 62.244 0.0019177243 0.0048575488 0.005105027
+ 6200 1.4078378 5.8813987 6.9871798 -0.0019043091 6.9051745 62.244 62.244 62.244 -0.0012543967 -0.0035545317 -0.00090399881
+ 6300 1.3898748 5.8818577 6.97353 0.0050781011 7.1922083 62.244 62.244 62.244 0.0037642013 0.0035169519 0.0079531499
+ 6400 1.3901345 5.8620878 6.953964 -0.0013161864 6.897285 62.244 62.244 62.244 0.0024166375 -0.0023907165 -0.0039744801
+ 6500 1.3990792 5.8647534 6.9636551 0.0025190902 7.0721348 62.244 62.244 62.244 0.003080505 -0.00072200043 0.0051987659
+ 6600 1.3802747 5.8639204 6.9480523 0.0030906745 7.0811461 62.244 62.244 62.244 0.0041979458 0.0059358092 -0.00086173155
+ 6700 1.392968 5.8692368 6.9633385 0.00060394401 6.9893462 62.244 62.244 62.244 0.0037955666 0.00058857296 -0.0025723075
+ 6800 1.4139599 5.8777321 6.9883218 0.0064457022 7.2658932 62.244 62.244 62.244 0.0066202313 0.0077537688 0.0049631066
+ 6900 1.3913822 5.8914016 6.9842578 0.0012411779 7.0377066 62.244 62.244 62.244 -0.0029791199 0.0027656154 0.0039370381
+ 7000 1.4203244 5.8676225 6.9832112 0.0053040447 7.2116194 62.244 62.244 62.244 0.0024159021 0.0053958945 0.0081003375
+Loop time of 0.812983 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 531376.713 tau/day, 1230.039 timesteps/s
+98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.020489 | 0.038507 | 0.054352 | 7.9 | 4.74
+Bond | 0.0086164 | 0.013153 | 0.017908 | 3.5 | 1.62
+Neigh | 0.13205 | 0.13275 | 0.13353 | 0.1 | 16.33
+Comm | 0.039251 | 0.05774 | 0.079146 | 7.7 | 7.10
+Output | 0.00057149 | 0.00076026 | 0.00087905 | 0.0 | 0.09
+Modify | 0.51332 | 0.52873 | 0.54512 | 2.1 | 65.04
+Other | | 0.04134 | | | 5.09
+
+Nlocal: 1400 ave 1861 max 953 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 732.5 ave 799 max 634 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Neighs: 1478.5 ave 2087 max 852 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 5914
+Ave neighs/atom = 1.05607
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 154
+Dangerous builds = 0
+unfix 1
+
+compute myTemp all temp
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt iso"
+rigid/npt iso
+fix_modify 1 temp myTemp
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 7000 1.4203244 5.8676225 6.9832112 -0.040722281 5.2295869 62.244 62.244 62.244 -0.12474488 0.041369653 -0.038791619
+ 7100 1.4820526 5.8454198 7.0094927 0.013935005 7.4687465 56.934813 56.934813 56.934813 0.011753675 0.011015866 0.019035475
+ 7200 1.5504398 5.8024995 7.0202869 0.023075447 7.5454178 50.323226 50.323226 50.323226 0.02128889 0.024383628 0.023553823
+ 7300 1.5422614 5.7803177 6.9916814 0.022398755 7.3670099 45.442117 45.442117 45.442117 0.011815608 0.027421849 0.027958808
+ 7400 1.5762224 5.7500188 6.988057 0.044637382 7.5673845 41.732187 41.732187 41.732187 0.045858714 0.035776277 0.052277154
+ 7500 1.5734284 5.7222605 6.9581042 0.029862564 7.2743396 38.996336 38.996336 38.996336 0.024440229 0.034455527 0.030691934
+ 7600 1.5572312 5.6929606 6.9160823 0.050216724 7.366563 36.898208 36.898208 36.898208 0.059366814 0.056376093 0.034907266
+ 7700 1.5225653 5.659289 6.8551824 0.042054552 7.1814902 35.15611 35.15611 35.15611 0.043735305 0.039349247 0.043079104
+ 7800 1.5081978 5.629903 6.8145116 0.057013188 7.2106251 33.885255 33.885255 33.885255 0.055017894 0.053733429 0.062288242
+ 7900 1.4721367 5.5821237 6.7384082 0.067262555 7.1645957 32.860322 32.860322 32.860322 0.097134972 0.066643481 0.03800921
+ 8000 1.4710105 5.5302806 6.6856805 0.054118027 7.0029681 32.020862 32.020862 32.020862 0.039052412 0.059044234 0.064257435
+Loop time of 1.47728 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 292430.022 tau/day, 676.921 timesteps/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.064968 | 0.10073 | 0.1395 | 10.5 | 6.82
+Bond | 0.014031 | 0.019927 | 0.02572 | 3.7 | 1.35
+Neigh | 0.52043 | 0.52145 | 0.52214 | 0.1 | 35.30
+Comm | 0.069327 | 0.11344 | 0.15499 | 11.3 | 7.68
+Output | 0.00045276 | 0.00050163 | 0.00058174 | 0.0 | 0.03
+Modify | 0.65598 | 0.67559 | 0.69898 | 2.4 | 45.73
+Other | | 0.04563 | | | 3.09
+
+Nlocal: 1400 ave 1711 max 1074 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 1617 ave 1748 max 1514 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Neighs: 6221.75 ave 8875 max 3829 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 24887
+Ave neighs/atom = 4.44411
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 340
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt x"
+rigid/npt x
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.408 | 7.596 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 8000 1.4710105 5.5302806 6.6856805 0.19181859 7.81029 32.020862 32.020862 32.020862 0.26866704 0.14123342 0.16555531
+ 8100 1.47531 5.5300767 6.6888537 0.072844262 7.1138998 31.868578 32.020862 32.020862 0.090224787 0.062332105 0.065975895
+ 8200 1.448408 5.51143 6.6490768 0.069870568 7.0519422 31.491082 32.020862 32.020862 0.087940256 0.058037199 0.063634249
+ 8300 1.4057002 5.4923673 6.5964694 0.065508742 6.9688194 31.043742 32.020862 32.020862 0.079268242 0.048811269 0.068446714
+ 8400 1.3991297 5.4626242 6.5615657 -0.017027709 6.4660067 30.650474 32.020862 32.020862 0.0088006578 -0.001632039 -0.058251747
+ 8500 1.4126457 5.4676374 6.5771949 0.012615987 6.6471389 30.279686 32.020862 32.020862 0.010145607 0.017449486 0.010252867
+ 8600 1.4250925 5.4367644 6.5560982 0.057260287 6.8682646 29.775194 32.020862 32.020862 0.05660339 0.10551068 0.0096667873
+ 8700 1.4259617 5.431439 6.5514555 0.060058224 6.8743509 29.36374 32.020862 32.020862 0.059243843 0.040552126 0.080378702
+ 8800 1.4336545 5.3949149 6.5209738 0.052324111 6.7965365 28.763424 32.020862 32.020862 0.02607362 0.067534725 0.063363987
+ 8900 1.4228767 5.3718196 6.489413 0.04039784 6.6975045 28.133143 32.020862 32.020862 0.038493401 0.059136317 0.023563801
+ 9000 1.3840335 5.3851579 6.4722421 0.055356171 6.7513156 27.534332 32.020862 32.020862 0.067391117 0.061540537 0.03713686
+Loop time of 1.41644 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 304989.819 tau/day, 705.995 timesteps/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.111 | 0.15928 | 0.20768 | 11.1 | 11.25
+Bond | 0.014816 | 0.020169 | 0.024592 | 3.1 | 1.42
+Neigh | 0.40146 | 0.40175 | 0.40221 | 0.0 | 28.36
+Comm | 0.063586 | 0.11635 | 0.16698 | 14.1 | 8.21
+Output | 0.00045538 | 0.00050312 | 0.00063586 | 0.0 | 0.04
+Modify | 0.66405 | 0.67875 | 0.69575 | 1.6 | 47.92
+Other | | 0.03963 | | | 2.80
+
+Nlocal: 1400 ave 1641 max 1120 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost: 1593.5 ave 1674 max 1480 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs: 7766.25 ave 10004 max 5618 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 31065
+Ave neighs/atom = 5.54732
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 168
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph iso"
+rigid/nph iso
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.228 | 7.409 | 7.596 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 9000 1.3840335 5.3851579 6.4722421 0.16503405 7.3042475 27.534332 32.020862 32.020862 0.18505216 0.10781406 0.20223595
+ 9100 1.3884253 5.3614209 6.4519546 -0.00091586458 6.4474179 27.373411 31.83372 31.83372 0.022761165 -0.0041100422 -0.021398716
+ 9200 1.420492 5.3303864 6.4461068 0.059143817 6.7274082 27.005021 31.405303 31.405303 0.083033013 0.062389471 0.032008967
+ 9300 1.4715513 5.2993502 6.4551749 -0.0012173753 6.4496031 26.66115 31.005402 31.005402 3.6757409e-05 -0.035942133 0.03225325
+ 9400 1.446323 5.2997487 6.4357579 0.089723486 6.8324557 26.355721 30.650205 30.650205 0.074549411 0.091827859 0.10279319
+ 9500 1.4429552 5.2778071 6.4111711 0.074185245 6.7328342 26.184941 30.451597 30.451597 0.081909739 0.072238574 0.068407422
+ 9600 1.4570864 5.2601352 6.4045984 0.0580315 6.6544318 26.122769 30.379295 30.379295 0.060115487 0.027228888 0.086750125
+ 9700 1.4421488 5.2741205 6.4068511 0.044711738 6.5981759 26.069954 30.317874 30.317874 0.093367845 0.025219144 0.015548226
+ 9800 1.4305027 5.2831767 6.4067599 0.064007051 6.6787519 26.009567 30.247648 30.247648 0.1207317 0.021857174 0.049432283
+ 9900 1.4457473 5.2513943 6.3869514 0.016264617 6.4551575 25.895064 30.114487 30.114487 0.055652525 0.015908352 -0.022767026
+ 10000 1.4739193 5.2108898 6.3685744 0.066079547 6.6416503 25.768894 29.967759 29.967759 0.059174033 0.048716715 0.090347892
+Loop time of 1.47405 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 293069.938 tau/day, 678.403 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.14109 | 0.19261 | 0.2429 | 10.7 | 13.07
+Bond | 0.015511 | 0.020164 | 0.023957 | 2.5 | 1.37
+Neigh | 0.43698 | 0.43723 | 0.43759 | 0.0 | 29.66
+Comm | 0.064379 | 0.1184 | 0.17429 | 14.5 | 8.03
+Output | 0.00053048 | 0.00056964 | 0.00067139 | 0.0 | 0.04
+Modify | 0.65413 | 0.66598 | 0.68039 | 1.3 | 45.18
+Other | | 0.0391 | | | 2.65
+
+Nlocal: 1400 ave 1629 max 1159 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 1760.25 ave 1871 max 1635 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs: 9467.75 ave 11967 max 6712 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 37871
+Ave neighs/atom = 6.76268
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 163
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph xy couple"
+rigid/nph xy couple
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 10000 1.4739193 5.2108898 6.3685744 0.15675952 7.0163882 25.768894 29.967759 29.967759 0.15485552 -0.045372029 0.36079506
+ 10100 1.450711 5.2108741 6.3503298 0.0083383764 6.3849239 25.819477 30.026584 29.967759 0.0025039775 -0.0028716599 0.025382812
+ 10200 1.4627819 5.2187046 6.3676414 0.031215755 6.4961258 25.717327 29.907789 29.967759 0.04657158 0.0023172248 0.044758461
+ 10300 1.4689915 5.2231223 6.3769364 0.094530779 6.7645053 25.667024 29.84929 29.967759 0.10402187 0.089461211 0.090109255
+ 10400 1.465366 5.211321 6.3622875 0.057765151 6.5976168 25.585426 29.754396 29.967759 0.025724468 0.03148259 0.1160884
+ 10500 1.4206144 5.2096595 6.325476 0.029618225 6.4439115 25.348314 29.478648 29.967759 0.016757876 -0.021974627 0.094071428
+ 10600 1.4490516 5.1686358 6.3067882 0.10186675 6.705618 25.082174 29.169143 29.967759 0.13985672 0.13649813 0.029245401
+ 10700 1.42637 5.1516578 6.271995 0.12577606 6.7554051 24.851151 28.900476 29.967759 0.099699897 0.11678127 0.16084703
+ 10800 1.4675204 5.1334029 6.2860615 0.054610838 6.494291 24.752517 28.78577 29.967759 0.018006539 0.090588468 0.055237507
+ 10900 1.4312627 5.1332052 6.2573854 -0.0020120377 6.2496947 24.782913 28.821119 29.967759 -0.0035770106 0.047436898 -0.049896
+ 11000 1.3986074 5.1272068 6.225738 0.045641244 6.3993661 24.72401 28.752618 29.967759 0.052336235 0.073561738 0.011025759
+Loop time of 1.50406 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 287222.965 tau/day, 664.868 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.16856 | 0.21287 | 0.26569 | 9.4 | 14.15
+Bond | 0.016815 | 0.020397 | 0.023304 | 1.9 | 1.36
+Neigh | 0.44152 | 0.44161 | 0.44172 | 0.0 | 29.36
+Comm | 0.067729 | 0.1232 | 0.16886 | 13.0 | 8.19
+Output | 0.00045419 | 0.00048572 | 0.0005734 | 0.0 | 0.03
+Modify | 0.6568 | 0.66799 | 0.6841 | 1.3 | 44.41
+Other | | 0.0375 | | | 2.49
+
+Nlocal: 1400 ave 1605 max 1229 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Nghost: 1859 ave 1964 max 1718 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs: 10208.2 ave 13091 max 7670 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 40833
+Ave neighs/atom = 7.29161
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 160
+Dangerous builds = 0
+
+Total wall time: 0:00:10
diff --git a/examples/rigid/log.5Oct16.rigid.poems.g++.1 b/examples/rigid/log.5Oct16.rigid.poems.g++.1
deleted file mode 100644
index 8b5e47c00a078b92f4a66c0fb0a4cf30229c1949..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.poems.g++.1
+++ /dev/null
@@ -1,332 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Simple rigid body system
-
-units lj
-atom_style atomic
-
-pair_style lj/cut 2.5
-
-read_data data.rigid
- orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 81 atoms
-
-velocity all create 100.0 4928459
-
-# unconnected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 10 18
-#group clump3 id <> 19 27
-#group clump4 id <> 28 36
-#group clump5 id <> 37 45
-#group clump6 id <> 46 54
-#group clump7 id <> 55 63
-#group clump8 id <> 64 72
-#group clump9 id <> 73 81
-
-#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 1 chain of connected bodies
-
-group clump1 id <> 1 9
-9 atoms in group clump1
-group clump2 id <> 9 18
-10 atoms in group clump2
-group clump3 id <> 18 27
-10 atoms in group clump3
-group clump4 id <> 27 36
-10 atoms in group clump4
-group clump5 id <> 36 45
-10 atoms in group clump5
-group clump6 id <> 45 54
-10 atoms in group clump6
-group clump7 id <> 54 63
-10 atoms in group clump7
-group clump8 id <> 63 72
-10 atoms in group clump8
-group clump9 id <> 72 81
-10 atoms in group clump9
-
-fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
-1 clusters, 9 bodies, 8 joints, 81 atoms
-
-# 2 chains of connected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 9 18
-#group clump3 id <> 18 27
-#group clump4 id <> 27 36
-#group clump5 id <> 37 45
-#group clump6 id <> 45 54
-#group clump7 id <> 54 63
-#group clump8 id <> 63 72
-#group clump9 id <> 72 81
-
-#fix 1 all poems group clump1 clump2 clump3 clump4
-#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
-
-neigh_modify exclude group clump1 clump1
-neigh_modify exclude group clump2 clump2
-neigh_modify exclude group clump3 clump3
-neigh_modify exclude group clump4 clump4
-neigh_modify exclude group clump5 clump5
-neigh_modify exclude group clump6 clump6
-neigh_modify exclude group clump7 clump7
-neigh_modify exclude group clump8 clump8
-neigh_modify exclude group clump9 clump9
-
-thermo 100
-
-#dump 1 all atom 50 dump.rigid.poems
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
-
-timestep 0.0001
-thermo 50
-run 10000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 2.96781 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 217.7783 3430.3907 0 3466.6871 -2.7403788
- 50 13679.637 1404.2468 0 3684.1863 12.446066
- 100 16777.225 888.87665 0 3685.0808 -31.828677
- 150 19595.365 418.45042 0 3684.3446 40.709078
- 200 18524.188 596.47273 0 3683.8375 -0.8159371
- 250 21015.789 180.96521 0 3683.5967 -10.042469
- 300 20785.513 219.25314 0 3683.5053 2.6452719
- 350 21072.46 171.2554 0 3683.3321 7.0609024
- 400 19956.414 356.36381 0 3682.4328 19.320259
- 450 20724.42 227.73284 0 3681.8028 8.1259249
- 500 20152.578 322.71466 0 3681.4777 5.4929878
- 550 20017.022 345.29701 0 3681.4673 5.4661666
- 600 17897.743 698.72196 0 3681.6791 3.2854742
- 650 17297.758 796.60256 0 3679.5623 15.191113
- 700 18581.934 584.29715 0 3681.2861 5.1588289
- 750 21774.158 52.821062 0 3681.8474 -10.775664
- 800 21604.055 81.188546 0 3681.8644 -3.2045743
- 850 17821.483 711.53827 0 3681.7854 7.4384277
- 900 21033.292 175.98127 0 3681.5299 -16.345167
- 950 20968.166 186.59847 0 3681.2929 -2.330456
- 1000 20490.66 266.19375 0 3681.3037 11.787983
- 1050 20222.396 310.94072 0 3681.34 -8.3459539
- 1100 21321.687 127.61533 0 3681.2299 -1.2184717
- 1150 20849.582 206.01695 0 3680.9472 -0.86699149
- 1200 21815.003 45.317414 0 3681.1512 1.5988314
- 1250 18655.437 572.41453 0 3681.654 10.064078
- 1300 20780.781 217.36506 0 3680.8286 6.0538616
- 1350 20558.971 254.36482 0 3680.8601 -3.6773952
- 1400 21485.029 99.812921 0 3680.6511 -16.185473
- 1450 21771.107 52.15961 0 3680.6775 -2.4756673
- 1500 21520.948 93.503927 0 3680.3286 2.1023576
- 1550 21351.418 121.68137 0 3680.2511 5.5159947
- 1600 20778.805 216.92177 0 3680.0559 15.089188
- 1650 21477.638 100.21836 0 3679.8247 -1.1045746
- 1700 18501.339 596.47914 0 3680.0357 -15.679679
- 1750 18563.642 587.34785 0 3681.2882 33.532209
- 1800 19110.185 494.8234 0 3679.8543 18.024046
- 1850 21364.191 119.23545 0 3679.9339 2.5291103
- 1900 20146.626 322.14867 0 3679.9197 5.7313218
- 1950 20692.672 231.25325 0 3680.0319 4.2977763
- 2000 20943.904 189.11235 0 3679.7629 -22.645121
- 2050 19668.057 401.82994 0 3679.8394 3.6251916
- 2100 20280.442 299.76155 0 3679.8353 7.4807949
- 2150 19181.86 483.522 0 3680.4987 22.620507
- 2200 21300.161 130.70534 0 3680.7322 4.7102665
- 2250 20486.943 266.63931 0 3681.1299 -8.6456512
- 2300 18653.122 572.24819 0 3681.1018 -5.2637122
- 2350 21513.523 95.614901 0 3681.2021 -9.3621767
- 2400 21466.272 103.56446 0 3681.2765 -29.561368
- 2450 20100.105 332.27123 0 3682.2887 35.744287
- 2500 20764.395 221.6677 0 3682.4001 -12.468906
- 2550 20435.699 276.31055 0 3682.2603 -22.413697
- 2600 21466.467 104.53618 0 3682.2807 -10.078508
- 2650 20814.737 213.23892 0 3682.3617 5.1390411
- 2700 18565.761 588.3578 0 3682.6513 22.27664
- 2750 20772.36 220.1607 0 3682.2206 -7.9448198
- 2800 21018.563 179.10058 0 3682.1945 -7.0717829
- 2850 16789.412 884.21472 0 3682.4501 33.279015
- 2900 19304.363 464.75282 0 3682.1466 7.947554
- 2950 20513.758 263.07578 0 3682.0355 2.2361434
- 3000 20617.309 245.95251 0 3682.1706 -0.75213689
- 3050 18567.52 587.90473 0 3682.4914 -4.0112006
- 3100 18696.577 566.20617 0 3682.3023 -1.4814167
- 3150 19864.606 371.56078 0 3682.3284 8.9362836
- 3200 18902.643 532.04614 0 3682.4867 0.76630303
- 3250 21110.454 163.86212 0 3682.271 -1.6253894
- 3300 19369.939 454.05833 0 3682.3816 4.9066544
- 3350 19082.603 501.69905 0 3682.133 3.5982292
- 3400 19527.779 426.918 0 3681.5478 6.9612143
- 3450 19892.953 366.19989 0 3681.6921 3.0050426
- 3500 19708.981 396.84552 0 3681.6756 7.0757635
- 3550 20256.096 306.23937 0 3682.2554 -1.752138
- 3600 21289.889 133.93823 0 3682.253 -3.7462615
- 3650 18333.877 627.18028 0 3682.8264 -15.276791
- 3700 19829.133 377.33753 0 3682.1931 -6.269648
- 3750 20771.635 220.07171 0 3682.0109 -28.479036
- 3800 18373.813 619.79253 0 3682.0947 29.594781
- 3850 19320.99 461.92786 0 3682.0928 -5.3212101
- 3900 16119.825 995.68064 0 3682.3182 -8.4683118
- 3950 15556.948 1091.3655 0 3684.1902 20.98273
- 4000 20000.464 348.24891 0 3681.6596 7.1589745
- 4050 18870.219 536.59924 0 3681.6358 -3.7997025
- 4100 19889.518 367.49253 0 3682.4122 -14.091266
- 4150 15789.623 1051.3399 0 3682.9438 -4.4152389
- 4200 20548.889 256.83493 0 3681.6498 0.92234153
- 4250 20681.925 235.46113 0 3682.4487 -11.515773
- 4300 19330.404 460.80975 0 3682.5437 -22.351775
- 4350 19369.443 453.35405 0 3681.5945 29.418242
- 4400 20762.165 222.24133 0 3682.6021 2.6627047
- 4450 19984.657 350.71294 0 3681.4891 28.88731
- 4500 21167.58 154.25344 0 3682.1834 -3.0784322
- 4550 18133.576 660.73671 0 3682.9995 2.5305835
- 4600 19935.069 360.36826 0 3682.8798 2.4575034
- 4650 21413.76 113.86464 0 3682.8246 -5.1271547
- 4700 21716.333 63.609419 0 3682.9982 -2.4708049
- 4750 21352.947 124.36961 0 3683.1941 -0.29026265
- 4800 19043.788 508.8617 0 3682.8264 14.797006
- 4850 20516.121 263.78758 0 3683.1411 7.1348281
- 4900 20624.5 245.81827 0 3683.235 0.34708051
- 4950 20317.197 296.68937 0 3682.8889 -0.55065946
- 5000 18346.865 625.37246 0 3683.1832 7.3371413
- 5050 18867.53 538.49153 0 3683.0799 1.9249866
- 5100 18790.276 551.17224 0 3682.885 2.2333017
- 5150 20241.365 311.84683 0 3685.4076 -3.998004
- 5200 17685.058 739.76418 0 3687.2739 3.2835025
- 5250 18496.626 604.58166 0 3687.3526 -10.185776
- 5300 18420.042 617.82026 0 3687.8273 -16.392458
- 5350 18767.338 559.0349 0 3686.9246 4.5320767
- 5400 20423.245 284.90517 0 3688.7794 -8.6356656
- 5450 21080.398 176.18494 0 3689.5846 -16.450038
- 5500 16684.424 909.12643 0 3689.8637 49.94555
- 5550 20132.31 335.03663 0 3690.4216 -16.018038
- 5600 20430.923 285.17562 0 3690.3295 -5.0773675
- 5650 20479.943 276.55962 0 3689.8834 5.4334564
- 5700 20061.532 345.95553 0 3689.5441 -16.230658
- 5750 20523.759 268.92217 0 3689.5487 -4.4128812
- 5800 18900.356 537.65462 0 3687.7139 13.605549
- 5850 20280.502 310.27193 0 3690.3556 -4.7884959
- 5900 19050.26 515.66087 0 3690.7042 7.8864722
- 5950 19566.917 430.2997 0 3691.4525 31.715268
- 6000 18878.118 544.75449 0 3691.1076 -4.2415329
- 6050 19308.682 471.70734 0 3689.821 -10.561614
- 6100 18776.194 560.04764 0 3689.4133 -7.7286747
- 6150 21475.064 110.1508 0 3689.3281 -3.6506391
- 6200 19975 360.82675 0 3689.9934 10.282021
- 6250 21396.341 123.5341 0 3689.5909 -5.7215163
- 6300 18533.423 600.87422 0 3689.778 15.408027
- 6350 20653.152 247.19253 0 3689.3846 8.5607784
- 6400 19716.537 403.41487 0 3689.5044 13.165575
- 6450 21120.66 168.79838 0 3688.9084 -0.50382728
- 6500 19700.345 404.7155 0 3688.1064 13.941375
- 6550 10818.393 1892.037 0 3695.1025 38.423155
- 6600 18684.478 574.84755 0 3688.9273 5.9176985
- 6650 19219.732 486.04269 0 3689.3314 18.287659
- 6700 20058.587 344.88255 0 3687.9804 6.5372086
- 6750 21279.318 142.77333 0 3689.3264 2.498188
- 6800 20671.545 244.25024 0 3689.5078 -4.1356416
- 6850 21203.598 155.82001 0 3689.753 -0.0083061182
- 6900 21699.344 73.301497 0 3689.8588 -8.0309898
- 6950 20951.212 197.19403 0 3689.0627 0.76668303
- 7000 20166.275 329.02869 0 3690.0746 2.0083318
- 7050 21554.944 97.465792 0 3689.9564 -3.2420086
- 7100 20817.494 220.25476 0 3689.8372 0.17206182
- 7150 21481.11 109.84029 0 3690.0253 -3.6814741
- 7200 21266.824 145.53099 0 3690.0016 -2.060543
- 7250 19434.684 450.81331 0 3689.9273 9.4822765
- 7300 21246.525 148.96573 0 3690.0532 3.3208839
- 7350 19749.269 398.60049 0 3690.1454 1.0929662
- 7400 20354.792 297.70261 0 3690.168 1.547159
- 7450 19996.859 357.16723 0 3689.977 -0.68412025
- 7500 20179.628 326.53243 0 3689.8038 -2.4805507
- 7550 18765.184 561.65039 0 3689.1811 -1.7976428
- 7600 19457.496 447.04428 0 3689.9603 -1.9055522
- 7650 18206.823 655.57276 0 3690.0433 1.2797964
- 7700 19152.344 497.77422 0 3689.8315 18.145069
- 7750 21387.484 125.48654 0 3690.0673 -2.9915772
- 7800 18127.052 668.61425 0 3689.7896 9.044869
- 7850 21419.557 120.08889 0 3690.015 6.2651717
- 7900 21817.182 53.739819 0 3689.9368 -4.2387416
- 7950 18215.195 654.15494 0 3690.0208 -54.628049
- 8000 21523.503 102.58018 0 3689.8307 -4.84236
- 8050 20720.799 236.28689 0 3689.7535 -9.3725225
- 8100 21196.483 157.3232 0 3690.0704 -7.7222497
- 8150 20869.667 211.65308 0 3689.9309 -6.8438295
- 8200 17790.052 725.72497 0 3690.7336 -25.697688
- 8250 19634.94 417.71929 0 3690.2094 8.861604
- 8300 19135.784 500.92443 0 3690.2218 -3.1245167
- 8350 20191.718 324.93312 0 3690.2195 6.5736107
- 8400 20695.239 241.02378 0 3690.2302 -14.592221
- 8450 21793.857 57.609525 0 3689.9191 -11.509747
- 8500 21271.088 144.43102 0 3689.6124 -0.091587085
- 8550 20064.337 345.21754 0 3689.2737 9.5058471
- 8600 20282.86 308.2307 0 3688.7074 2.265529
- 8650 21223.055 151.24306 0 3688.419 1.7296834
- 8700 18875.342 542.42055 0 3688.3108 6.367148
- 8750 20922.65 201.55122 0 3688.6595 3.4208578
- 8800 21406.54 120.8539 0 3688.6106 1.8253729
- 8850 19868.524 377.05623 0 3688.477 16.327796
- 8900 20025.322 348.94892 0 3686.5025 17.063406
- 8950 21224.374 151.3567 0 3688.7524 -0.11028753
- 9000 21318.309 135.862 0 3688.9135 -0.50826819
- 9050 17538.618 768.00136 0 3691.1043 37.978645
- 9100 21247.861 147.84641 0 3689.1566 -6.7773259
- 9150 18455.677 613.08767 0 3689.0339 -3.4844751
- 9200 19486.859 441.03829 0 3688.8482 -18.602827
- 9250 21774.926 59.710446 0 3688.8648 -13.379919
- 9300 17628.877 750.72321 0 3688.8694 27.797974
- 9350 19827.334 383.85708 0 3688.4128 6.5459021
- 9400 20020.126 351.61742 0 3688.3051 -14.332562
- 9450 21596.338 88.904175 0 3688.2939 1.5779716
- 9500 18981.418 524.60141 0 3688.1711 5.4352409
- 9550 18652.616 579.05144 0 3687.8208 25.600729
- 9600 21198.037 155.23097 0 3688.2371 -3.3586596
- 9650 19958.317 361.32544 0 3687.7115 4.2910178
- 9700 19129.101 499.5993 0 3687.7828 13.267102
- 9750 21913.967 35.689587 0 3688.0174 -7.3222905
- 9800 21314.694 135.43794 0 3687.8869 -9.5613518
- 9850 20899.743 204.82802 0 3688.1185 -2.6321428
- 9900 20288.244 306.5013 0 3687.8753 3.6196618
- 9950 19271.015 475.88527 0 3687.7211 -1.8196764
- 10000 21122.24 167.82714 0 3688.2005 -3.8464842
-Loop time of 3.6648 on 1 procs for 10000 steps with 81 atoms
-
-Performance: 23575.670 tau/day, 2728.665 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.15599 | 0.15599 | 0.15599 | 0.0 | 4.26
-Neigh | 0.099093 | 0.099093 | 0.099093 | 0.0 | 2.70
-Comm | 0.0088665 | 0.0088665 | 0.0088665 | 0.0 | 0.24
-Output | 0.0016377 | 0.0016377 | 0.0016377 | 0.0 | 0.04
-Modify | 3.392 | 3.392 | 3.392 | 0.0 | 92.56
-Other | | 0.007194 | | | 0.20
-
-Nlocal: 81 ave 81 max 81 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 95 ave 95 max 95 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 744 ave 744 max 744 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 744
-Ave neighs/atom = 9.18519
-Neighbor list builds = 992
-Dangerous builds = 941
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/rigid/log.5Oct16.rigid.poems.g++.4 b/examples/rigid/log.5Oct16.rigid.poems.g++.4
deleted file mode 100644
index 06610ea5c8e9ece3f154dc4c9d1730e592c7bc69..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.poems.g++.4
+++ /dev/null
@@ -1,332 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Simple rigid body system
-
-units lj
-atom_style atomic
-
-pair_style lj/cut 2.5
-
-read_data data.rigid
- orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 81 atoms
-
-velocity all create 100.0 4928459
-
-# unconnected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 10 18
-#group clump3 id <> 19 27
-#group clump4 id <> 28 36
-#group clump5 id <> 37 45
-#group clump6 id <> 46 54
-#group clump7 id <> 55 63
-#group clump8 id <> 64 72
-#group clump9 id <> 73 81
-
-#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 1 chain of connected bodies
-
-group clump1 id <> 1 9
-9 atoms in group clump1
-group clump2 id <> 9 18
-10 atoms in group clump2
-group clump3 id <> 18 27
-10 atoms in group clump3
-group clump4 id <> 27 36
-10 atoms in group clump4
-group clump5 id <> 36 45
-10 atoms in group clump5
-group clump6 id <> 45 54
-10 atoms in group clump6
-group clump7 id <> 54 63
-10 atoms in group clump7
-group clump8 id <> 63 72
-10 atoms in group clump8
-group clump9 id <> 72 81
-10 atoms in group clump9
-
-fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
-1 clusters, 9 bodies, 8 joints, 81 atoms
-
-# 2 chains of connected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 9 18
-#group clump3 id <> 18 27
-#group clump4 id <> 27 36
-#group clump5 id <> 37 45
-#group clump6 id <> 45 54
-#group clump7 id <> 54 63
-#group clump8 id <> 63 72
-#group clump9 id <> 72 81
-
-#fix 1 all poems group clump1 clump2 clump3 clump4
-#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
-
-neigh_modify exclude group clump1 clump1
-neigh_modify exclude group clump2 clump2
-neigh_modify exclude group clump3 clump3
-neigh_modify exclude group clump4 clump4
-neigh_modify exclude group clump5 clump5
-neigh_modify exclude group clump6 clump6
-neigh_modify exclude group clump7 clump7
-neigh_modify exclude group clump8 clump8
-neigh_modify exclude group clump9 clump9
-
-thermo 100
-
-#dump 1 all atom 50 dump.rigid.poems
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
-
-timestep 0.0001
-thermo 50
-run 10000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 2.94053 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 217.7783 3430.3907 0 3466.6871 -2.7403788
- 50 13679.637 1404.2468 0 3684.1863 12.446066
- 100 16777.225 888.87665 0 3685.0808 -31.828677
- 150 19595.365 418.45042 0 3684.3446 40.709078
- 200 18524.188 596.47273 0 3683.8375 -0.8159371
- 250 21015.789 180.96521 0 3683.5967 -10.042469
- 300 20785.513 219.25314 0 3683.5053 2.6452719
- 350 21072.46 171.2554 0 3683.3321 7.0609024
- 400 19956.414 356.36381 0 3682.4328 19.320259
- 450 20724.42 227.73284 0 3681.8028 8.1259249
- 500 20152.578 322.71466 0 3681.4777 5.4929878
- 550 20017.022 345.29701 0 3681.4673 5.4661666
- 600 17897.743 698.72196 0 3681.6791 3.2854742
- 650 17297.758 796.60256 0 3679.5623 15.191113
- 700 18581.934 584.29715 0 3681.2861 5.1588289
- 750 21774.158 52.821062 0 3681.8474 -10.775664
- 800 21604.055 81.188546 0 3681.8644 -3.2045743
- 850 17821.483 711.53827 0 3681.7854 7.4384276
- 900 21033.292 175.98127 0 3681.5299 -16.345167
- 950 20968.166 186.59847 0 3681.2929 -2.330456
- 1000 20490.66 266.19375 0 3681.3037 11.787983
- 1050 20222.396 310.94072 0 3681.34 -8.3459539
- 1100 21321.687 127.61533 0 3681.2299 -1.2184718
- 1150 20849.582 206.01695 0 3680.9472 -0.8669916
- 1200 21815.003 45.317417 0 3681.1512 1.5988314
- 1250 18655.437 572.41453 0 3681.654 10.064076
- 1300 20780.781 217.36504 0 3680.8286 6.0538619
- 1350 20558.972 254.3648 0 3680.8601 -3.6773987
- 1400 21485.029 99.812949 0 3680.6511 -16.185471
- 1450 21771.108 52.15959 0 3680.6775 -2.4756681
- 1500 21520.948 93.503949 0 3680.3286 2.1023578
- 1550 21351.418 121.6814 0 3680.2511 5.5159978
- 1600 20778.805 216.92171 0 3680.0559 15.089182
- 1650 21477.639 100.2182 0 3679.8247 -1.1045944
- 1700 18501.343 596.47853 0 3680.0357 -15.67963
- 1750 18563.643 587.34767 0 3681.2882 33.532167
- 1800 19110.19 494.82264 0 3679.8543 18.024034
- 1850 21364.196 119.23454 0 3679.9339 2.5291491
- 1900 20146.643 322.14595 0 3679.9197 5.731152
- 1950 20692.67 231.25357 0 3680.0319 4.2977641
- 2000 20943.904 189.11223 0 3679.763 -22.645645
- 2050 19668.152 401.81407 0 3679.8394 3.6255896
- 2100 20280.572 299.73976 0 3679.8351 7.4809355
- 2150 19182.121 483.47905 0 3680.4992 22.615309
- 2200 21299.76 130.77281 0 3680.7327 4.7114154
- 2250 20487.784 266.4995 0 3681.1302 -8.6406776
- 2300 18655.125 571.91487 0 3681.1023 -5.2671669
- 2350 21512.614 95.766913 0 3681.2025 -9.3523428
- 2400 21467.773 103.31519 0 3681.2773 -29.600307
- 2450 20096.937 332.80159 0 3682.2911 35.890912
- 2500 20761.446 222.16118 0 3682.4022 -12.528127
- 2550 20409.6 280.67234 0 3682.2723 -22.277373
- 2600 21469.964 103.95529 0 3682.2826 -10.038267
- 2650 20708.138 231.00516 0 3682.3615 5.3659502
- 2700 18584.743 585.07862 0 3682.5357 21.785261
- 2750 20503.019 264.91491 0 3682.0847 -4.5583917
- 2800 20584.075 251.44664 0 3682.1258 -6.5084595
- 2850 17277.076 802.33356 0 3681.8462 15.519513
- 2900 19392.956 449.92915 0 3682.0885 -4.3829957
- 2950 18371.786 620.29835 0 3682.2626 7.2117592
- 3000 20412.015 280.25302 0 3682.2555 0.32492606
- 3050 20858.248 205.65269 0 3682.0273 4.5055715
- 3100 21561.094 88.438447 0 3681.9541 -3.7523733
- 3150 15471.278 1103.4497 0 3681.9961 -14.576367
- 3200 15386.973 1117.8815 0 3682.377 15.051163
- 3250 19741.037 392.04755 0 3682.2204 -2.6610995
- 3300 20870.191 203.58229 0 3681.9475 -4.7795545
- 3350 16648.228 907.66571 0 3682.3704 -8.9242511
- 3400 20104.016 331.58603 0 3682.2554 6.4783858
- 3450 21421.316 112.28228 0 3682.5015 -8.3484987
- 3500 19284.533 467.80739 0 3681.8962 -12.835452
- 3550 20160.125 322.4476 0 3682.4684 1.6574827
- 3600 16682.415 902.73752 0 3683.14 22.383296
- 3650 16762.19 890.14636 0 3683.8446 16.119412
- 3700 17858.568 707.37212 0 3683.8 -1.6582504
- 3750 20029.881 345.15986 0 3683.4733 -3.1415889
- 3800 20734 227.99158 0 3683.6582 -7.9580418
- 3850 20741.089 226.39408 0 3683.2423 8.3055765
- 3900 18671.251 571.42296 0 3683.2981 -3.7468858
- 3950 19547.209 423.14256 0 3681.0108 5.8312279
- 4000 19739.799 393.58799 0 3683.5544 18.604884
- 4050 20014.121 347.8176 0 3683.5044 9.93387
- 4100 20503.654 266.08691 0 3683.3626 8.1304118
- 4150 18309.702 632.29807 0 3683.9151 -0.0021480359
- 4200 20509.423 265.60353 0 3683.8408 -2.1658857
- 4250 21805.541 50.325935 0 3684.5828 1.082842
- 4300 21420.551 114.90431 0 3684.9962 -1.7985998
- 4350 20256.928 308.74187 0 3684.8966 -11.669472
- 4400 21633.488 79.629274 0 3685.2106 -0.96131785
- 4450 20793.327 219.66955 0 3685.2241 1.3752349
- 4500 18719.484 564.86754 0 3684.7816 2.6308699
- 4550 20966.335 190.68308 0 3685.0722 -18.587627
- 4600 19428.962 446.59618 0 3684.7565 -4.4051672
- 4650 18408.956 616.85009 0 3685.0095 2.777272
- 4700 19215.779 482.57562 0 3685.2054 19.441016
- 4750 20155.927 326.13401 0 3685.4553 6.1734993
- 4800 20918.085 199.31832 0 3685.6659 3.4407437
- 4850 20236.958 312.07276 0 3684.899 3.2612893
- 4900 21419.89 115.36879 0 3685.3505 -4.675951
- 4950 19707.901 401.14828 0 3685.7985 -10.730734
- 5000 19407.201 450.64394 0 3685.1775 17.518981
- 5050 21527.598 97.655186 0 3685.5882 -9.2294707
- 5100 21581.933 88.595517 0 3685.5843 -20.669485
- 5150 21161.214 158.48503 0 3685.3541 -2.7587502
- 5200 21166.679 157.24762 0 3685.0275 -18.180044
- 5250 20909.576 200.23507 0 3685.1644 -16.617303
- 5300 21911.746 33.236563 0 3685.1942 -5.8313967
- 5350 20857.303 208.87453 0 3685.0916 12.176312
- 5400 20958.96 191.96694 0 3685.1269 3.6116429
- 5450 20433.179 279.61178 0 3685.1415 13.324529
- 5500 19604.675 416.88499 0 3684.3308 21.536484
- 5550 18171.145 655.92915 0 3684.4534 -9.2269804
- 5600 19799.907 385.12116 0 3685.1056 22.202165
- 5650 19711.882 399.30581 0 3684.6194 15.93063
- 5700 17908.833 699.52405 0 3684.3295 0.35530356
- 5750 18606.518 583.538 0 3684.6243 -4.4540843
- 5800 21814.053 48.974627 0 3684.6501 -1.5206358
- 5850 18029.107 679.9357 0 3684.7868 12.137677
- 5900 21090.739 169.64502 0 3684.7682 -1.5051545
- 5950 21086.26 170.29075 0 3684.6674 -2.8164474
- 6000 21285.771 136.95608 0 3684.5846 -26.582739
- 6050 21203.994 150.87822 0 3684.8772 -2.6617226
- 6100 21481.553 104.57796 0 3684.8368 -16.524974
- 6150 20354.4 292.57675 0 3684.9767 2.7960207
- 6200 21326.591 130.75243 0 3685.1843 -1.5929194
- 6250 21505.087 101.07817 0 3685.2593 -3.7821931
- 6300 21296.273 135.6593 0 3685.0382 -0.55635908
- 6350 21295.389 135.86485 0 3685.0964 5.6614093
- 6400 16552.242 926.02655 0 3684.7336 14.177218
- 6450 20148.951 327.1151 0 3685.2736 7.4561085
- 6500 20962.151 191.79415 0 3685.486 -4.5436711
- 6550 21710.328 67.433972 0 3685.8219 -5.7678572
- 6600 20698.571 234.79099 0 3684.5528 -2.1984068
- 6650 17892.287 704.05484 0 3686.1026 11.525836
- 6700 21272.999 141.26589 0 3686.7657 0.44088069
- 6750 19558.993 426.46448 0 3686.2966 -16.907401
- 6800 20350.247 295.23951 0 3686.9474 1.1284348
- 6850 18665.05 573.5326 0 3684.3742 17.088712
- 6900 19769.199 392.1551 0 3687.0216 6.7562425
- 6950 19439.159 446.99138 0 3686.8512 -6.0105763
- 7000 19379.907 456.53471 0 3686.5192 -9.0505095
- 7050 19983.754 356.02523 0 3686.651 -5.6274314
- 7100 19867.737 375.47627 0 3686.7658 17.315482
- 7150 19258.794 477.47344 0 3687.2724 14.316676
- 7200 21282.428 139.96051 0 3687.0318 -0.77043459
- 7250 19828.603 381.98919 0 3686.7564 6.5142869
- 7300 20574.582 257.8245 0 3686.9215 -3.6547118
- 7350 21613.467 84.771568 0 3687.0161 -7.5188826
- 7400 21817.009 50.844944 0 3687.0131 -14.888864
- 7450 14937.538 1197.4257 0 3687.0154 1.7540499
- 7500 18326.914 632.40374 0 3686.8894 8.3397357
- 7550 13611.007 1418.4727 0 3686.9739 -19.379482
- 7600 19173.985 491.9482 0 3687.6123 17.229001
- 7650 16911.504 867.33649 0 3685.9204 -21.042834
- 7700 21752.116 61.143705 0 3686.4963 -10.344487
- 7750 20208.337 318.26355 0 3686.3197 13.385814
- 7800 21649.909 77.950987 0 3686.2692 -1.7911084
- 7850 20139.64 329.50319 0 3686.1098 -5.5805093
- 7900 21355.026 126.7642 0 3685.9352 -7.7062172
- 7950 21336.178 129.88925 0 3685.9188 -2.059298
- 8000 21047.596 177.71546 0 3685.6482 0.37963466
- 8050 19217.351 482.62331 0 3685.5152 6.5582595
- 8100 20499.057 268.7173 0 3685.2268 -1.1959737
- 8150 21494.301 102.83829 0 3685.2219 -1.6427647
- 8200 20074.928 339.19817 0 3685.0195 6.285123
- 8250 17335.157 793.47566 0 3682.6685 22.877381
- 8300 17340.544 794.62619 0 3684.7168 3.9147755
- 8350 20529.345 262.51162 0 3684.0691 4.031768
- 8400 18884.747 537.47827 0 3684.9361 22.853404
- 8450 20341.86 293.10484 0 3683.4148 0.33856656
- 8500 19300.282 467.58127 0 3684.2949 12.35507
- 8550 21631.936 78.254534 0 3683.5772 -10.992959
- 8600 20204.913 316.83233 0 3684.3178 20.74228
- 8650 21018.189 181.32054 0 3684.352 1.8412068
- 8700 20161.304 323.97907 0 3684.1964 -2.646629
- 8750 19081.79 504.00155 0 3684.2998 -10.088053
- 8800 20834.489 211.76247 0 3684.1773 14.896336
- 8850 20929.355 196.18335 0 3684.4092 -1.2602398
- 8900 21491.074 102.47788 0 3684.3235 -1.4696758
- 8950 20474.735 271.69461 0 3684.1504 -6.9489258
- 9000 21128.641 162.40732 0 3683.8474 -7.7928168
- 9050 18421.801 614.46442 0 3684.7646 24.40313
- 9100 19301.292 466.98873 0 3683.8707 4.4687046
- 9150 21575.705 88.213763 0 3684.1646 -0.94696984
- 9200 20004.776 350.05448 0 3684.1838 -7.3466605
- 9250 21384.079 120.14472 0 3684.1578 -8.3773844
- 9300 21980.599 20.702393 0 3684.1356 -12.666293
- 9350 21686.606 69.517984 0 3683.9524 -8.8366533
- 9400 20732.704 228.46247 0 3683.9131 -6.4080307
- 9450 19798.859 384.34696 0 3684.1568 7.6198484
- 9500 20270.695 305.22664 0 3683.6758 1.5862486
- 9550 16496.156 935.28481 0 3684.6441 15.001468
- 9600 20642.429 241.08853 0 3681.4934 -9.2159382
- 9650 21292.587 135.4474 0 3684.2119 -0.54770976
- 9700 18888.158 536.60518 0 3684.6315 5.3236926
- 9750 18750.018 559.35922 0 3684.3623 -9.9424949
- 9800 20544.772 259.71076 0 3683.8394 8.732202
- 9850 16698.125 901.90076 0 3684.9216 9.9553329
- 9900 21450.963 109.58687 0 3684.7474 -4.8001999
- 9950 20664.461 240.66995 0 3684.7468 -3.4840781
- 10000 18951.367 526.45428 0 3685.0155 21.512727
-Loop time of 3.89095 on 4 procs for 10000 steps with 81 atoms
-
-Performance: 22205.346 tau/day, 2570.063 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.012426 | 0.039516 | 0.089301 | 15.3 | 1.02
-Neigh | 0.012618 | 0.027118 | 0.055113 | 10.4 | 0.70
-Comm | 0.16629 | 0.21469 | 0.26329 | 8.2 | 5.52
-Output | 0.0051188 | 0.0053029 | 0.0055087 | 0.2 | 0.14
-Modify | 3.5241 | 3.5783 | 3.6729 | 3.0 | 91.96
-Other | | 0.02605 | | | 0.67
-
-Nlocal: 20.25 ave 81 max 0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-Nghost: 46.25 ave 95 max 14 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-Neighs: 249.25 ave 997 max 0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 997
-Ave neighs/atom = 12.3086
-Neighbor list builds = 993
-Dangerous builds = 943
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/rigid/log.5Oct16.rigid.poems2.g++.1 b/examples/rigid/log.5Oct16.rigid.poems2.g++.1
deleted file mode 100644
index edbef2d5b691d05bff1f665704301a72079aadc0..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.poems2.g++.1
+++ /dev/null
@@ -1,336 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Simple rigid body system
-
-units lj
-atom_style atomic
-
-pair_style lj/cut 2.5
-
-read_data data.rigid
- orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 81 atoms
-
-velocity all create 100.0 4928459
-
-# unconnected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 10 18
-#group clump3 id <> 19 27
-#group clump4 id <> 28 36
-#group clump5 id <> 37 45
-#group clump6 id <> 46 54
-#group clump7 id <> 55 63
-#group clump8 id <> 64 72
-#group clump9 id <> 73 81
-
-#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 1 chain of connected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 9 18
-#group clump3 id <> 18 27
-#group clump4 id <> 27 36
-#group clump5 id <> 36 45
-#group clump6 id <> 45 54
-#group clump7 id <> 54 63
-#group clump8 id <> 63 72
-#group clump9 id <> 72 81
-
-#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 2 chains of connected bodies
-
-group clump1 id <> 1 9
-9 atoms in group clump1
-group clump2 id <> 9 18
-10 atoms in group clump2
-group clump3 id <> 18 27
-10 atoms in group clump3
-group clump4 id <> 27 36
-10 atoms in group clump4
-group clump5 id <> 37 45
-9 atoms in group clump5
-group clump6 id <> 45 54
-10 atoms in group clump6
-group clump7 id <> 54 63
-10 atoms in group clump7
-group clump8 id <> 63 72
-10 atoms in group clump8
-group clump9 id <> 72 81
-10 atoms in group clump9
-
-fix 1 all poems group clump1 clump2 clump3 clump4
-1 clusters, 4 bodies, 3 joints, 36 atoms
-fix 2 all poems group clump5 clump6 clump7 clump8 clump9
-1 clusters, 5 bodies, 4 joints, 45 atoms
-
-neigh_modify exclude group clump1 clump1
-neigh_modify exclude group clump2 clump2
-neigh_modify exclude group clump3 clump3
-neigh_modify exclude group clump4 clump4
-neigh_modify exclude group clump5 clump5
-neigh_modify exclude group clump6 clump6
-neigh_modify exclude group clump7 clump7
-neigh_modify exclude group clump8 clump8
-neigh_modify exclude group clump9 clump9
-
-thermo 100
-
-#dump 1 all atom 50 dump.rigid.poems2
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
-
-timestep 0.0001
-thermo 50
-run 10000
-WARNING: More than one fix poems (../fix_poems.cpp:352)
-WARNING: More than one fix poems (../fix_poems.cpp:352)
-WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 3.53031 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 196.00047 3632.2347 0 3668.5311 -2.7403788
- 50 12167.633 1505.5478 0 3758.8133 35.125973
- 100 17556.978 512.66277 0 3763.9549 11.137534
- 150 19579.586 138.04942 0 3763.8987 -29.953971
- 200 19757.51 105.30542 0 3764.1036 -0.030645317
- 250 18218.374 390.10747 0 3763.8804 13.711001
- 300 19383.039 174.40688 0 3763.8586 5.7240693
- 350 20125.986 36.972611 0 3764.0071 1.9559205
- 400 18888.816 266.10975 0 3764.0386 9.6362168
- 450 19307.656 188.2511 0 3763.743 1.9326206
- 500 16331.197 738.56392 0 3762.8597 9.1715579
- 550 19318.722 186.16172 0 3763.7027 3.0115336
- 600 19455.268 161.20621 0 3764.0336 0.55208034
- 650 18487.011 340.03216 0 3763.5528 -8.0359122
- 700 17321.201 556.32471 0 3763.9545 -13.631751
- 750 18979.187 249.04389 0 3763.7082 -2.6072455
- 800 19342.456 181.85552 0 3763.7918 8.1918726
- 850 19070.641 232.19342 0 3763.7936 7.3148472
- 900 19478.873 156.65987 0 3763.8586 2.4284987
- 950 19912.415 76.437437 0 3763.9216 -1.4667227
- 1000 16003.749 802.39753 0 3766.0548 46.642188
- 1050 19859.583 86.64176 0 3764.3424 -2.1961943
- 1100 19229.575 203.61488 0 3764.6473 -10.632365
- 1150 18821.6 279.15861 0 3764.64 -0.89495035
- 1200 19392.695 173.59744 0 3764.8373 1.8508753
- 1250 16459.624 717.32104 0 3765.3995 33.478127
- 1300 19343.863 182.59043 0 3764.7874 0.75890736
- 1350 20019.643 57.503573 0 3764.8448 0.31444671
- 1400 18549.582 329.31436 0 3764.4221 10.738303
- 1450 15163.926 957.47585 0 3765.6103 -17.923459
- 1500 19223.688 204.15175 0 3764.0939 -1.6134531
- 1550 18147.996 404.12677 0 3764.8668 8.4194779
- 1600 18615.043 317.42467 0 3764.6548 -2.3288934
- 1650 20120.654 38.887913 0 3764.935 -8.7620277
- 1700 19450.907 162.98272 0 3765.0025 2.3254731
- 1750 19374.632 177.37966 0 3765.2744 8.9328774
- 1800 19424.404 167.93966 0 3765.0514 0.081230261
- 1850 17936.249 442.84231 0 3764.3699 6.6010636
- 1900 19982.595 64.406198 0 3764.8868 -2.9529813
- 1950 16215.852 761.91287 0 3764.8485 13.994708
- 2000 18584.422 322.12049 0 3763.68 7.1654003
- 2050 20107.965 41.025754 0 3764.723 -0.3109069
- 2100 20002.333 60.593017 0 3764.7288 -6.7919784
- 2150 16949.762 626.59623 0 3765.441 3.508941
- 2200 20010.953 58.808279 0 3764.5403 -10.862172
- 2250 18982.73 247.00892 0 3762.3292 -0.53807815
- 2300 18401.298 354.87973 0 3762.5274 1.0920554
- 2350 19390.524 172.9415 0 3763.7793 -3.3524932
- 2400 16080.801 786.38838 0 3764.3146 -16.200514
- 2450 18870.412 268.74976 0 3763.2705 11.197736
- 2500 19688.29 117.58223 0 3763.5618 4.382644
- 2550 18870.825 268.78678 0 3763.384 -5.6623656
- 2600 17019.35 611.70808 0 3763.4395 6.3109641
- 2650 18753.285 291.0596 0 3763.8902 2.4120296
- 2700 19742.456 107.20901 0 3763.2193 -0.33061303
- 2750 19522.438 148.16759 0 3763.4339 -1.6254851
- 2800 18304.801 372.55152 0 3762.3295 22.6368
- 2850 18465.36 343.48495 0 3762.9961 4.4169272
- 2900 20151.999 31.372926 0 3763.2245 1.2013699
- 2950 15498.143 892.80071 0 3762.8272 13.263724
- 3000 18728.301 294.65113 0 3762.855 8.1897838
- 3050 18538.466 330.25223 0 3763.3015 8.5865739
- 3100 19081.409 229.5907 0 3763.1849 -4.8573813
- 3150 18498.802 337.11548 0 3762.8195 1.0555321
- 3200 19925.897 73.358029 0 3763.339 -7.7325108
- 3250 19780.108 100.23785 0 3763.2209 -5.5974972
- 3300 19221.043 203.82387 0 3763.2763 4.2703251
- 3350 19025.292 240.11329 0 3763.3156 5.7708328
- 3400 18153.696 401.52086 0 3763.3164 21.076943
- 3450 18611.375 316.50396 0 3763.0548 -3.5484945
- 3500 19931.319 71.969274 0 3762.9543 1.8764978
- 3550 19747.562 106.05439 0 3763.0103 -2.5506186
- 3600 18491.39 338.4134 0 3762.7449 -4.0527808
- 3650 19757.998 104.19207 0 3763.0806 1.4865598
- 3700 20108.003 39.345514 0 3763.0498 0.062827129
- 3750 19222.505 203.28065 0 3763.0039 0.33719277
- 3800 19286.383 191.08831 0 3762.6406 -0.1826802
- 3850 19450.083 161.09138 0 3762.9587 -0.2708263
- 3900 18002.304 429.25655 0 3763.0166 -4.6832439
- 3950 17186.829 582.26502 0 3765.0111 55.816834
- 4000 16826.434 645.84974 0 3761.856 19.675962
- 4050 19227.526 202.18151 0 3762.8344 -0.2596098
- 4100 19908.792 76.084531 0 3762.8978 -2.796813
- 4150 17821.329 462.63065 0 3762.8768 13.069155
- 4200 19917.133 74.574998 0 3762.9329 -6.4181155
- 4250 19012.618 241.96787 0 3762.823 4.0847974
- 4300 19077.34 229.98133 0 3762.8221 4.324323
- 4350 19361.128 177.47406 0 3762.8681 -7.377974
- 4400 18565.044 324.95107 0 3762.9223 2.5229032
- 4450 19352.406 178.98756 0 3762.7665 0.10862717
- 4500 18482.218 340.15496 0 3762.788 12.518301
- 4550 18359.732 362.83749 0 3762.7879 3.7500902
- 4600 19623.618 128.71624 0 3762.7196 -1.1328521
- 4650 17565.707 509.99904 0 3762.9078 1.7135935
- 4700 19876.052 81.892814 0 3762.6431 0.32476108
- 4750 19022.676 239.92262 0 3762.6403 -0.24613022
- 4800 18862.685 269.24248 0 3762.3324 6.2733979
- 4850 19899.174 77.426145 0 3762.4584 0.42535238
- 4900 18250.865 382.72867 0 3762.5185 23.308462
- 4950 18895.847 263.22651 0 3762.4575 8.0634675
- 5000 19096.705 225.69358 0 3762.1204 3.6816481
- 5050 16546.294 698.91312 0 3763.0416 17.453618
- 5100 19501.208 151.20999 0 3762.5449 -1.1231291
- 5150 19479.879 155.00669 0 3762.3917 -3.983378
- 5200 17397.818 541.23039 0 3763.0485 6.1109992
- 5250 18564.869 324.10557 0 3762.0442 9.2244762
- 5300 16271.663 747.52374 0 3760.7947 -6.5256602
- 5350 19831.418 89.851887 0 3762.3367 -2.3453958
- 5400 18723.697 294.67435 0 3762.0256 4.6822081
- 5450 19547.28 142.21934 0 3762.086 -5.5243408
- 5500 19415.447 166.68729 0 3762.1404 -9.5658991
- 5550 18492.721 337.54773 0 3762.1256 6.5184903
- 5600 19391.389 171.14375 0 3762.1416 -0.53835361
- 5650 18503.465 334.62751 0 3761.1951 4.6580363
- 5700 18153.344 399.91064 0 3761.6409 12.851587
- 5750 18342.297 365.14769 0 3761.8694 2.7148176
- 5800 19583.241 135.64969 0 3762.1758 -1.089608
- 5850 15967.283 804.18382 0 3761.088 11.278762
- 5900 19040.271 235.35509 0 3761.3312 5.1352158
- 5950 17920.962 443.17951 0 3761.8762 4.9621366
- 6000 19100.92 224.3946 0 3761.602 -9.537589
- 6050 17982.119 432.3251 0 3762.3472 -2.851617
- 6100 16233.096 755.46191 0 3761.5908 25.113316
- 6150 18316.543 370.01118 0 3761.9635 -1.7445703
- 6200 18483.464 339.13282 0 3761.9966 -2.0857447
- 6250 18609.406 315.56032 0 3761.7467 -12.289208
- 6300 17167.919 582.68212 0 3761.9264 -3.8263397
- 6350 17870.329 452.58116 0 3761.9013 -3.3843134
- 6400 19309.717 186.11786 0 3761.9913 -4.9462739
- 6450 17964.073 435.39924 0 3762.0794 12.272972
- 6500 18772.847 285.61959 0 3762.0727 6.7928648
- 6550 18915.116 259.41365 0 3762.213 -4.1449761
- 6600 19446.628 161.18763 0 3762.415 -2.1906581
- 6650 16348.787 734.99282 0 3762.546 -9.9624546
- 6700 19066.684 231.43863 0 3762.3061 -5.362833
- 6750 14890.323 1004.547 0 3762.0143 37.373013
- 6800 18235.19 385.253 0 3762.1401 0.21012662
- 6850 16447.997 716.11276 0 3762.0382 -9.2095411
- 6900 18343.362 364.81902 0 3761.7379 10.417932
- 6950 16014.084 797.13348 0 3762.7046 6.7906777
- 7000 19120.393 221.29236 0 3762.1059 -1.3461375
- 7050 18055.409 418.30136 0 3761.8957 1.5772317
- 7100 18407.231 353.41868 0 3762.1652 0.61071769
- 7150 18728.136 293.64021 0 3761.8136 5.1649654
- 7200 17706.628 483.07628 0 3762.0815 18.000708
- 7250 19349.505 178.89673 0 3762.1385 2.540201
- 7300 20016.293 55.389159 0 3762.1101 -1.5793163
- 7350 19398.573 169.86661 0 3762.1949 -5.060123
- 7400 19466.526 157.37407 0 3762.2862 1.7158273
- 7450 18440.348 347.09196 0 3761.9712 12.781963
- 7500 19989.907 60.555934 0 3762.3906 -1.5033319
- 7550 19667.28 120.27403 0 3762.363 -3.3502366
- 7600 18497.707 336.15863 0 3761.66 1.7887539
- 7650 17901.957 447.17282 0 3762.3501 0.016725252
- 7700 19758.725 103.3129 0 3762.3361 -23.534448
- 7750 19443.957 161.6532 0 3762.386 -10.323924
- 7800 19776.178 100.1773 0 3762.4324 6.0854422
- 7850 19242.512 198.86705 0 3762.2952 5.2823659
- 7900 19499.929 151.30366 0 3762.4017 12.299911
- 7950 19630.317 127.19541 0 3762.4393 8.0799632
- 8000 19872.384 82.421129 0 3762.4923 2.2126691
- 8050 17747.038 476.27982 0 3762.7683 -7.7042786
- 8100 18832.654 274.78106 0 3762.3095 13.882157
- 8150 19949.814 68.09711 0 3762.5072 -0.54410896
- 8200 17555.866 511.02517 0 3762.1115 6.2471175
- 8250 17800.1 465.9992 0 3762.314 13.583485
- 8300 19755.224 103.89732 0 3762.2721 -1.487243
- 8350 17583.61 506.17539 0 3762.3995 -9.7819128
- 8400 18529.003 330.75623 0 3762.0532 14.731228
- 8450 20155.902 29.797078 0 3762.3716 -8.5711085
- 8500 18047.548 420.54645 0 3762.685 7.3875118
- 8550 19790.794 97.493375 0 3762.4553 -3.3427911
- 8600 19997.902 59.172074 0 3762.4874 3.3479688
- 8650 19987.319 61.148363 0 3762.5037 -1.889232
- 8700 19363.91 176.41833 0 3762.3276 -9.4291288
- 8750 18712.689 296.3979 0 3761.7107 5.9221369
- 8800 19783.17 98.860518 0 3762.4105 -3.5262066
- 8850 18796.049 281.60057 0 3762.3504 -8.2913002
- 8900 16738.277 662.62261 0 3762.3035 8.5838631
- 8950 17869.613 452.25006 0 3761.4377 11.561101
- 9000 18682.512 302.27997 0 3762.0043 3.8878724
- 9050 17513.759 518.50265 0 3761.7914 23.05778
- 9100 17500.686 521.57944 0 3762.4473 -2.8435751
- 9150 19645.683 124.43597 0 3762.5254 -3.0193092
- 9200 18898.897 262.76552 0 3762.5612 3.5891701
- 9250 20114.279 37.614866 0 3762.4813 -0.58120871
- 9300 19562.613 139.54073 0 3762.2468 -3.2630158
- 9350 19679.811 118.05865 0 3762.468 -3.4644363
- 9400 19297.384 188.84527 0 3762.4349 0.40498037
- 9450 18267.029 379.52581 0 3762.309 -0.13762867
- 9500 19951.072 67.63844 0 3762.2814 -7.575539
- 9550 19134.562 218.46835 0 3761.9057 -1.9626244
- 9600 19089.093 227.29178 0 3762.3089 -1.94158
- 9650 16964.603 620.71289 0 3762.3061 16.987042
- 9700 18846.881 271.3129 0 3761.4761 3.4458802
- 9750 19309.225 186.0142 0 3761.7966 9.4048627
- 9800 16359.704 733.51007 0 3763.0849 15.870164
- 9850 19958.532 66.203725 0 3762.2282 6.0043645
- 9900 19864.564 83.502384 0 3762.1253 -0.65360617
- 9950 18996.789 244.25101 0 3762.1749 -2.4961826
- 10000 17933.494 441.33587 0 3762.3532 -6.0731708
-Loop time of 3.80061 on 1 procs for 10000 steps with 81 atoms
-
-Performance: 22733.175 tau/day, 2631.155 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.11276 | 0.11276 | 0.11276 | 0.0 | 2.97
-Neigh | 0.075881 | 0.075881 | 0.075881 | 0.0 | 2.00
-Comm | 0.011113 | 0.011113 | 0.011113 | 0.0 | 0.29
-Output | 0.0016332 | 0.0016332 | 0.0016332 | 0.0 | 0.04
-Modify | 3.5918 | 3.5918 | 3.5918 | 0.0 | 94.51
-Other | | 0.007383 | | | 0.19
-
-Nlocal: 81 ave 81 max 81 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 71 ave 71 max 71 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 612 ave 612 max 612 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 612
-Ave neighs/atom = 7.55556
-Neighbor list builds = 989
-Dangerous builds = 906
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/rigid/log.5Oct16.rigid.poems2.g++.4 b/examples/rigid/log.5Oct16.rigid.poems2.g++.4
deleted file mode 100644
index b408fb6f098ec6b74d06d4b9f44cf19efdbf47fc..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.poems2.g++.4
+++ /dev/null
@@ -1,336 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Simple rigid body system
-
-units lj
-atom_style atomic
-
-pair_style lj/cut 2.5
-
-read_data data.rigid
- orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 81 atoms
-
-velocity all create 100.0 4928459
-
-# unconnected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 10 18
-#group clump3 id <> 19 27
-#group clump4 id <> 28 36
-#group clump5 id <> 37 45
-#group clump6 id <> 46 54
-#group clump7 id <> 55 63
-#group clump8 id <> 64 72
-#group clump9 id <> 73 81
-
-#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 1 chain of connected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 9 18
-#group clump3 id <> 18 27
-#group clump4 id <> 27 36
-#group clump5 id <> 36 45
-#group clump6 id <> 45 54
-#group clump7 id <> 54 63
-#group clump8 id <> 63 72
-#group clump9 id <> 72 81
-
-#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 2 chains of connected bodies
-
-group clump1 id <> 1 9
-9 atoms in group clump1
-group clump2 id <> 9 18
-10 atoms in group clump2
-group clump3 id <> 18 27
-10 atoms in group clump3
-group clump4 id <> 27 36
-10 atoms in group clump4
-group clump5 id <> 37 45
-9 atoms in group clump5
-group clump6 id <> 45 54
-10 atoms in group clump6
-group clump7 id <> 54 63
-10 atoms in group clump7
-group clump8 id <> 63 72
-10 atoms in group clump8
-group clump9 id <> 72 81
-10 atoms in group clump9
-
-fix 1 all poems group clump1 clump2 clump3 clump4
-1 clusters, 4 bodies, 3 joints, 36 atoms
-fix 2 all poems group clump5 clump6 clump7 clump8 clump9
-1 clusters, 5 bodies, 4 joints, 45 atoms
-
-neigh_modify exclude group clump1 clump1
-neigh_modify exclude group clump2 clump2
-neigh_modify exclude group clump3 clump3
-neigh_modify exclude group clump4 clump4
-neigh_modify exclude group clump5 clump5
-neigh_modify exclude group clump6 clump6
-neigh_modify exclude group clump7 clump7
-neigh_modify exclude group clump8 clump8
-neigh_modify exclude group clump9 clump9
-
-thermo 100
-
-#dump 1 all atom 50 dump.rigid.poems2
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
-
-timestep 0.0001
-thermo 50
-run 10000
-WARNING: More than one fix poems (../fix_poems.cpp:352)
-WARNING: More than one fix poems (../fix_poems.cpp:352)
-WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 3.50303 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 196.00047 3632.2347 0 3668.5311 -2.7403788
- 50 12167.633 1505.5478 0 3758.8133 35.125973
- 100 17556.978 512.66277 0 3763.9549 11.137534
- 150 19579.586 138.04942 0 3763.8987 -29.953971
- 200 19757.51 105.30542 0 3764.1036 -0.030645317
- 250 18218.374 390.10747 0 3763.8804 13.711001
- 300 19383.039 174.40688 0 3763.8586 5.7240693
- 350 20125.986 36.972611 0 3764.0071 1.9559205
- 400 18888.816 266.10975 0 3764.0386 9.6362168
- 450 19307.656 188.2511 0 3763.743 1.9326206
- 500 16331.197 738.56392 0 3762.8597 9.1715579
- 550 19318.722 186.16172 0 3763.7027 3.0115336
- 600 19455.268 161.20621 0 3764.0336 0.55208034
- 650 18487.011 340.03216 0 3763.5528 -8.0359122
- 700 17321.201 556.32471 0 3763.9545 -13.631751
- 750 18979.187 249.04389 0 3763.7082 -2.6072455
- 800 19342.456 181.85552 0 3763.7918 8.1918726
- 850 19070.641 232.19342 0 3763.7936 7.3148472
- 900 19478.873 156.65987 0 3763.8586 2.4284987
- 950 19912.415 76.437437 0 3763.9216 -1.4667227
- 1000 16003.749 802.39753 0 3766.0548 46.642188
- 1050 19859.583 86.64176 0 3764.3424 -2.1961943
- 1100 19229.575 203.61488 0 3764.6473 -10.632365
- 1150 18821.6 279.15861 0 3764.64 -0.89495035
- 1200 19392.695 173.59744 0 3764.8373 1.8508753
- 1250 16459.624 717.32104 0 3765.3995 33.478127
- 1300 19343.863 182.59043 0 3764.7874 0.75890736
- 1350 20019.643 57.503573 0 3764.8448 0.31444671
- 1400 18549.582 329.31436 0 3764.4221 10.738303
- 1450 15163.926 957.47585 0 3765.6103 -17.923459
- 1500 19223.688 204.15176 0 3764.0939 -1.6134529
- 1550 18147.996 404.12677 0 3764.8668 8.4194781
- 1600 18615.043 317.42468 0 3764.6548 -2.3288926
- 1650 20120.654 38.887908 0 3764.935 -8.7620288
- 1700 19450.907 162.98267 0 3765.0025 2.3254739
- 1750 19374.631 177.3797 0 3765.2744 8.9328773
- 1800 19424.404 167.93965 0 3765.0514 0.081228843
- 1850 17936.227 442.84645 0 3764.3699 6.6011251
- 1900 19982.595 64.406244 0 3764.8868 -2.952971
- 1950 16215.818 761.91942 0 3764.8486 13.994877
- 2000 18584.433 322.11846 0 3763.6801 7.1653695
- 2050 20107.965 41.025796 0 3764.723 -0.31089763
- 2100 20002.329 60.593879 0 3764.7288 -6.7919882
- 2150 16949.817 626.58598 0 3765.4409 3.5087505
- 2200 20010.954 58.8082 0 3764.5403 -10.862143
- 2250 18982.732 247.00854 0 3762.3293 -0.53812607
- 2300 18401.276 354.88369 0 3762.5274 1.0921058
- 2350 19390.535 172.93951 0 3763.7793 -3.3524354
- 2400 16080.475 786.44896 0 3764.3146 -16.201558
- 2450 18870.293 268.77171 0 3763.2704 11.199749
- 2500 19688.508 117.54164 0 3763.5617 4.3806994
- 2550 18870.328 268.87896 0 3763.3841 -5.6641099
- 2600 17020.211 611.54841 0 3763.4394 6.3081434
- 2650 18748.838 291.88478 0 3763.8917 2.4175163
- 2700 19743.991 106.92945 0 3763.224 -0.33916964
- 2750 19525.446 147.60906 0 3763.4324 -1.6251174
- 2800 18257.411 381.40184 0 3762.4038 23.39495
- 2850 18496.796 337.65425 0 3762.9868 4.3657735
- 2900 20163.418 29.253902 0 3763.2203 1.4431917
- 2950 16823.317 646.69817 0 3762.1273 4.9041552
- 3000 19223.007 203.2529 0 3763.069 4.0414458
- 3050 17391.02 542.93746 0 3763.4968 15.139863
- 3100 19205.6 206.57791 0 3763.1705 4.8519241
- 3150 19835.659 90.247763 0 3763.5179 -14.900053
- 3200 18962.776 251.5838 0 3763.2089 -13.706561
- 3250 19418.837 167.29058 0 3763.3716 -2.0866468
- 3300 18628.291 313.69067 0 3763.3742 5.9919715
- 3350 17465.974 529.14439 0 3763.5841 14.122593
- 3400 18488.661 339.6186 0 3763.4448 21.526798
- 3450 19163.152 214.26098 0 3762.9928 4.1888096
- 3500 18000.27 429.81789 0 3763.2011 5.4734485
- 3550 19582.423 136.71887 0 3763.0935 -2.5335675
- 3600 19634.325 127.2219 0 3763.208 -1.9728322
- 3650 19428.114 165.40707 0 3763.2059 -2.3318779
- 3700 19861.116 85.356944 0 3763.3414 -3.9097609
- 3750 19337.239 182.43992 0 3763.4102 -3.3559651
- 3800 19493.146 153.40349 0 3763.2453 -0.71089657
- 3850 18607.616 317.74889 0 3763.6037 3.475832
- 3900 19719.59 111.5553 0 3763.3313 0.58876668
- 3950 19756.661 104.5522 0 3763.1931 3.7526698
- 4000 17904.708 447.1673 0 3762.854 12.270654
- 4050 19588.087 135.80435 0 3763.2279 0.94578945
- 4100 19065.901 232.38235 0 3763.1048 -2.7495195
- 4150 18775.075 286.2257 0 3763.0915 -3.7039858
- 4200 18800.725 281.46601 0 3763.0817 0.15619543
- 4250 19732.687 108.90618 0 3763.1075 3.0865861
- 4300 18278.151 377.63653 0 3762.4794 1.5768601
- 4350 17915.757 445.4804 0 3763.2133 -3.7040484
- 4400 15987.794 802.41575 0 3763.1183 22.252078
- 4450 19302.37 188.69495 0 3763.2079 0.91081327
- 4500 20039.32 52.304099 0 3763.2893 -2.0828905
- 4550 19535.953 145.4374 0 3763.2064 -3.3804255
- 4600 19700.723 114.79823 0 3763.0803 -1.1761163
- 4650 17804.641 465.85788 0 3763.0136 7.5947192
- 4700 19913.881 75.240289 0 3762.996 -2.1100557
- 4750 19982.484 62.535995 0 3762.996 -4.5821237
- 4800 17400.76 540.21707 0 3762.58 -5.8418778
- 4850 19199.88 206.90989 0 3762.4433 3.4536341
- 4900 19173.92 212.11327 0 3762.8392 5.0387071
- 4950 19236.635 200.57537 0 3762.9152 -1.4932783
- 5000 19077.616 230.04967 0 3762.9415 4.3742655
- 5050 19893.763 78.909747 0 3762.94 -1.5796711
- 5100 18884.746 265.68301 0 3762.8583 2.2767949
- 5150 17417.096 537.54036 0 3762.9286 -2.8632555
- 5200 18247.844 383.60092 0 3762.8312 10.384179
- 5250 19494.107 152.60532 0 3762.6251 -4.7617287
- 5300 18739.781 292.46206 0 3762.7919 23.210048
- 5350 19310.938 186.62363 0 3762.7232 14.895327
- 5400 19540.39 144.14287 0 3762.7336 6.094624
- 5450 20074.459 45.247888 0 3762.7403 -2.0871835
- 5500 19986.377 61.668045 0 3762.849 -2.4551918
- 5550 19038.904 237.07578 0 3762.7987 5.4250813
- 5600 19439.124 163.1438 0 3762.9816 4.1291468
- 5650 19480.321 155.58325 0 3763.0501 -3.5308058
- 5700 19869.291 83.651379 0 3763.1497 -7.8661592
- 5750 19991.447 61.068554 0 3763.1884 -6.8473586
- 5800 19454.072 160.36805 0 3762.9739 1.527662
- 5850 17994.409 430.95597 0 3763.2539 -5.6078082
- 5900 19209.794 205.74997 0 3763.1193 8.4113055
- 5950 19046.427 236.06321 0 3763.1793 10.463356
- 6000 19409.899 168.95271 0 3763.3785 2.542067
- 6050 18068.174 417.35443 0 3763.3125 10.498199
- 6100 19549.253 143.21885 0 3763.4509 2.3075797
- 6150 18464.719 344.0303 0 3763.4228 0.46469762
- 6200 19811.205 94.62725 0 3763.3689 1.2382763
- 6250 18715.36 297.26445 0 3763.0718 -3.4541762
- 6300 17115.664 594.09913 0 3763.6666 4.2065564
- 6350 18155.927 400.71764 0 3762.9264 1.1521258
- 6400 19873.093 83.169067 0 3763.3716 0.16383592
- 6450 19991.88 61.13218 0 3763.3321 -1.3008128
- 6500 19434.416 164.40698 0 3763.3728 -13.593422
- 6550 19855.253 86.645329 0 3763.544 -0.85704037
- 6600 19251.141 198.41152 0 3763.4376 4.3027745
- 6650 19741.815 107.69047 0 3763.582 4.994835
- 6700 19633.466 127.69333 0 3763.5203 6.3677145
- 6750 16231.353 757.83705 0 3763.6431 -1.5978692
- 6800 18863.396 270.1114 0 3763.3329 -11.915909
- 6850 19644.779 125.29421 0 3763.2163 -1.151217
- 6900 18883.642 266.06889 0 3763.0397 -4.3950749
- 6950 19042.364 236.54144 0 3762.9052 5.5718878
- 7000 18351.868 364.38028 0 3762.8743 7.8958273
- 7050 19981.031 62.840667 0 3763.0316 -5.8572298
- 7100 19796.372 97.073665 0 3763.0685 -3.5178361
- 7150 19805.385 95.235221 0 3762.899 -2.5481726
- 7200 18722.055 295.86113 0 3762.9084 13.826356
- 7250 19537.304 144.54234 0 3762.5616 1.2288666
- 7300 18787.328 283.49504 0 3762.6299 9.0044469
- 7350 18886.005 265.52121 0 3762.9295 6.6791881
- 7400 19891.864 79.239278 0 3762.9178 -2.3882842
- 7450 18164.752 399.07065 0 3762.9137 3.9400481
- 7500 18702.612 299.582 0 3763.0286 4.7987316
- 7550 19884.986 80.231665 0 3762.6365 -0.75016515
- 7600 19549.059 142.16243 0 3762.3586 -2.1035756
- 7650 18223.668 387.9047 0 3762.658 -17.064339
- 7700 19428.4 164.79531 0 3762.6473 -2.8342541
- 7750 19239.584 199.93029 0 3762.8163 3.1746033
- 7800 19458.005 159.46176 0 3762.7961 1.714515
- 7850 18320.308 369.77051 0 3762.4202 2.1422976
- 7900 18817.415 278.04812 0 3762.7546 0.94492621
- 7950 19892.761 79.115928 0 3762.9606 1.4948501
- 8000 19592.344 134.7639 0 3762.9758 -1.8520224
- 8050 19316.109 185.70579 0 3762.7631 -4.8061205
- 8100 19867.017 83.850395 0 3762.9277 -3.496391
- 8150 19129.936 220.29802 0 3762.8789 -2.8357376
- 8200 18449.554 346.30415 0 3762.8883 1.4417837
- 8250 18405.197 354.49049 0 3762.8602 6.7020283
- 8300 18310.437 372.25376 0 3763.0755 3.9043508
- 8350 18842.702 273.55075 0 3762.94 -10.987272
- 8400 18574.308 323.33378 0 3763.0204 12.008785
- 8450 15368.628 918.21692 0 3764.2591 34.80292
- 8500 18432.887 349.54013 0 3763.0378 0.00064258465
- 8550 15777.73 841.79263 0 3763.5945 15.473699
- 8600 17205.381 576.4515 0 3762.6331 2.3985544
- 8650 19773.742 101.48276 0 3763.2869 2.3978892
- 8700 19059.824 232.99716 0 3762.5941 5.2611349
- 8750 19006.086 243.41125 0 3763.0568 4.7880403
- 8800 19492.691 153.0188 0 3762.7763 1.9118755
- 8850 19625.883 128.44474 0 3762.8675 3.4157389
- 8900 19916.97 74.635094 0 3762.9629 -10.157254
- 8950 16012.956 798.16801 0 3763.5302 16.904998
- 9000 19364.051 177.00354 0 3762.9389 -13.373346
- 9050 19133.929 219.61882 0 3762.9389 -7.3824392
- 9100 18657.168 307.85939 0 3762.8905 9.3071421
- 9150 17975.904 434.21548 0 3763.0867 6.9609506
- 9200 19075.282 230.41699 0 3762.8767 7.0961232
- 9250 20115.276 37.578674 0 3762.6298 1.8678552
- 9300 18195.486 393.20682 0 3762.7413 13.272552
- 9350 19617.155 129.85893 0 3762.6653 -2.0849447
- 9400 19276.325 193.03425 0 3762.724 -2.8963555
- 9450 18642.803 310.4759 0 3762.8467 3.407984
- 9500 19175.951 211.72785 0 3762.8298 -0.39025564
- 9550 17669.191 490.85942 0 3762.9319 5.3867954
- 9600 18481.199 340.29485 0 3762.7391 8.9004886
- 9650 20091.442 42.504743 0 3763.1422 -1.3206133
- 9700 19651.405 124.04835 0 3763.1975 1.4000525
- 9750 19138.245 219.03637 0 3763.1558 5.8352794
- 9800 19189.146 209.67958 0 3763.2251 6.214691
- 9850 19899.376 78.096337 0 3763.166 -0.75102404
- 9900 19447.247 161.27279 0 3762.6149 -6.4166376
- 9950 19807.083 95.152663 0 3763.1309 -0.88933698
- 10000 18972.157 249.56342 0 3762.9258 1.9189241
-Loop time of 3.99472 on 4 procs for 10000 steps with 81 atoms
-
-Performance: 21628.565 tau/day, 2503.306 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0090363 | 0.029554 | 0.05092 | 8.8 | 0.74
-Neigh | 0.0090437 | 0.021045 | 0.034359 | 6.3 | 0.53
-Comm | 0.1326 | 0.17829 | 0.2132 | 7.3 | 4.46
-Output | 0.0044832 | 0.0048217 | 0.0053875 | 0.5 | 0.12
-Modify | 3.6632 | 3.7381 | 3.8211 | 2.9 | 93.58
-Other | | 0.02291 | | | 0.57
-
-Nlocal: 20.25 ave 37 max 0 min
-Histogram: 1 0 1 0 0 0 0 0 0 2
-Nghost: 17.75 ave 33 max 4 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 144.75 ave 356 max 0 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 579
-Ave neighs/atom = 7.14815
-Neighbor list builds = 994
-Dangerous builds = 958
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/rigid/log.5Oct16.rigid.tnr.g++.1 b/examples/rigid/log.5Oct16.rigid.tnr.g++.1
deleted file mode 100644
index 935b7eaf073db00214c230a128fc1e43153dad2e..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.tnr.g++.1
+++ /dev/null
@@ -1,452 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Tethered nanorods
-
-atom_style molecular
-
-read_data data.rigid.tnr
- orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 5600 atoms
- scanning bonds ...
- 1 = max bonds/atom
- reading bonds ...
- 1600 bonds
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 1 = max # of 1-4 neighbors
- 2 = max # of special neighbors
-
-# Specify bond parameters
-
-bond_style fene
-bond_coeff 1 30.0 1.5 1.0 1.0
-
-special_bonds fene
- 2 = max # of 1-2 neighbors
- 2 = max # of special neighbors
-
-# Specify initial velocities
-
-velocity all create 1.4 109345
-
-# Specify rigid components
-
-group rods type 2
-4000 atoms in group rods
-group tethers subtract all rods
-1600 atoms in group tethers
-
-neigh_modify exclude molecule rods delay 0 every 1
-
-# Specify the pair potentials
-
-pair_style lj/cut 2.5
-pair_modify shift yes
-pair_coeff * * 1.0 1.0 1.122
-pair_coeff 2 2 1.0 1.0 2.5
-
-# Specify output
-
-thermo 100
-thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
-thermo_modify flush yes lost warn
-
-timestep 0.005
-
-fix 1 rods rigid molecule
-800 rigid bodies with 4000 atoms
-fix 2 tethers nve
-fix 3 all langevin 1.4 1.4 1.0 437624
-
-run 5000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 45 45 45
-Memory usage per processor = 7.32042 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
- 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
- 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
- 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
- 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
- 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
- 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
- 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
- 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
- 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
- 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
- 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
- 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
- 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
- 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
- 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
- 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
- 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
- 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
- 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
- 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
- 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
- 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
- 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
- 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
- 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
- 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
- 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
- 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
- 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
- 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
- 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
- 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
- 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
- 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
- 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
- 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
- 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
- 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
- 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
- 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
- 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
- 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
- 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
- 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
- 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
- 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
- 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
- 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
- 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
- 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
-Loop time of 6.51777 on 1 procs for 5000 steps with 5600 atoms
-
-Performance: 331401.531 tau/day, 767.133 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.51894 | 0.51894 | 0.51894 | 0.0 | 7.96
-Bond | 0.24096 | 0.24096 | 0.24096 | 0.0 | 3.70
-Neigh | 1.8769 | 1.8769 | 1.8769 | 0.0 | 28.80
-Comm | 0.16548 | 0.16548 | 0.16548 | 0.0 | 2.54
-Output | 0.0032616 | 0.0032616 | 0.0032616 | 0.0 | 0.05
-Modify | 3.5349 | 3.5349 | 3.5349 | 0.0 | 54.23
-Other | | 0.1774 | | | 2.72
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1351 ave 1351 max 1351 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5254 ave 5254 max 5254 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5254
-Ave neighs/atom = 0.938214
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 766
-Dangerous builds = 0
-
-# Replace fix rigid and fix langevin with new ones
-
-unfix 1
-unfix 3
-
-fix 3 tethers langevin 1.4 1.4 1.0 198450
-
-# Test different integrators for rods
-
-fix 1 rods rigid/nve molecule
-800 rigid bodies with 4000 atoms
-print "rigid/nve"
-rigid/nve
-run 1000
-Memory usage per processor = 7.32042 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
- 5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041
- 5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551
- 5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518
- 5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493
- 5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038
- 5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751
- 5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035
- 5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927
- 5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509
- 6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075
-Loop time of 1.37139 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 315008.398 tau/day, 729.186 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.1443 | 0.1443 | 0.1443 | 0.0 | 10.52
-Bond | 0.049211 | 0.049211 | 0.049211 | 0.0 | 3.59
-Neigh | 0.40564 | 0.40564 | 0.40564 | 0.0 | 29.58
-Comm | 0.033721 | 0.033721 | 0.033721 | 0.0 | 2.46
-Output | 0.00065017 | 0.00065017 | 0.00065017 | 0.0 | 0.05
-Modify | 0.70225 | 0.70225 | 0.70225 | 0.0 | 51.21
-Other | | 0.03562 | | | 2.60
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1347 ave 1347 max 1347 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5399 ave 5399 max 5399 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5399
-Ave neighs/atom = 0.964107
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 153
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
-800 rigid bodies with 4000 atoms
-print "rigid/nvt"
-rigid/nvt
-run 1000
-Memory usage per processor = 7.32042 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547
- 6100 1.4199699 5.8764035 6.9917138 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644
- 6200 1.3976825 5.8924426 6.9902474 0.0004390082 7.0091524 62.244 62.244 62.244 -0.0023073118 -0.00049925474 0.0041235912
- 6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018933 0.0091933882 0.0049242089
- 6400 1.3749203 5.8817073 6.9616336 0.0074967166 7.2844648 62.244 62.244 62.244 0.012281889 0.0039781604 0.0062301007
- 6500 1.3467096 5.8881263 6.9458946 -0.00011926206 6.9407588 62.244 62.244 62.244 0.0030721983 -0.0013265855 -0.002103399
- 6600 1.3646558 5.8739857 6.9458497 0.0056064173 7.1872789 62.244 62.244 62.244 0.0059660118 0.0057680329 0.0050852071
- 6700 1.392725 5.8836119 6.9775228 0.0025583772 7.0876942 62.244 62.244 62.244 0.0030974509 0.0018499704 0.0027277104
- 6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295
- 6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161
- 7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587
-Loop time of 1.38662 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 311550.061 tau/day, 721.181 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.14525 | 0.14525 | 0.14525 | 0.0 | 10.48
-Bond | 0.048966 | 0.048966 | 0.048966 | 0.0 | 3.53
-Neigh | 0.40266 | 0.40266 | 0.40266 | 0.0 | 29.04
-Comm | 0.033521 | 0.033521 | 0.033521 | 0.0 | 2.42
-Output | 0.00064969 | 0.00064969 | 0.00064969 | 0.0 | 0.05
-Modify | 0.71998 | 0.71998 | 0.71998 | 0.0 | 51.92
-Other | | 0.03559 | | | 2.57
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1284 ave 1284 max 1284 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5677 ave 5677 max 5677 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5677
-Ave neighs/atom = 1.01375
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 151
-Dangerous builds = 0
-unfix 1
-
-compute myTemp all temp
-
-fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/npt iso"
-rigid/npt iso
-fix_modify 1 temp myTemp
-
-run 1000
-Memory usage per processor = 7.32042 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105
- 7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125
- 7200 1.5163014 5.8421234 7.0330969 0.018918793 7.4624535 50.277182 50.277182 50.277182 0.017832308 0.02668088 0.012243191
- 7300 1.5675512 5.7752788 7.0065063 0.02287049 7.3825189 45.15491 45.15491 45.15491 0.019317818 0.024266569 0.025027083
- 7400 1.5432894 5.7512252 6.9633963 0.024351591 7.2723284 41.416611 41.416611 41.416611 0.032039305 0.022247464 0.018768005
- 7500 1.5510339 5.7073864 6.9256404 0.030706866 7.2413185 38.612893 38.612893 38.612893 0.04157713 0.012507079 0.038036388
- 7600 1.5435609 5.6657445 6.8781288 0.03187398 7.1535577 36.440727 36.440727 36.440727 0.036502896 0.022097075 0.037021969
- 7700 1.5862733 5.6141666 6.8600993 0.053474714 7.2612259 34.762178 34.762178 34.762178 0.035691782 0.06016314 0.064569222
- 7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539
- 7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293
- 8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532
-Loop time of 3.05773 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 141281.224 tau/day, 327.040 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.37231 | 0.37231 | 0.37231 | 0.0 | 12.18
-Bond | 0.07144 | 0.07144 | 0.07144 | 0.0 | 2.34
-Neigh | 1.3968 | 1.3968 | 1.3968 | 0.0 | 45.68
-Comm | 0.071773 | 0.071773 | 0.071773 | 0.0 | 2.35
-Output | 0.00065684 | 0.00065684 | 0.00065684 | 0.0 | 0.02
-Modify | 1.0951 | 1.0951 | 1.0951 | 0.0 | 35.82
-Other | | 0.04962 | | | 1.62
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 2963 ave 2963 max 2963 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 25797 ave 25797 max 25797 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 25797
-Ave neighs/atom = 4.60661
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 334
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/npt x"
-rigid/npt x
-run 1000
-Memory usage per processor = 7.32428 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422
- 8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751
- 8200 1.4061729 5.5008938 6.6053673 0.038080967 6.8240633 31.398913 32.003919 32.003919 0.041554276 0.038085252 0.034603372
- 8300 1.4225542 5.4730766 6.5904167 0.071241779 6.992772 30.878537 32.003919 32.003919 0.068190354 0.076631686 0.068903297
- 8400 1.4344356 5.4772885 6.6039608 0.044141975 6.8495696 30.421029 32.003919 32.003919 0.031058774 0.039890974 0.061476178
- 8500 1.4377845 5.4485066 6.5778092 0.04242205 6.8099428 29.91769 32.003919 32.003919 0.053013546 0.050003453 0.02424915
- 8600 1.4339418 5.4280263 6.5543108 0.0048261176 6.58031 29.453954 32.003919 32.003919 -0.0020411927 0.005967365 0.010552181
- 8700 1.4284879 5.4273043 6.549305 0.058717611 6.8609844 29.021604 32.003919 32.003919 0.09927212 0.02309782 0.053782894
- 8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909
- 8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701
- 9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594
-Loop time of 2.94424 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 146727.069 tau/day, 339.646 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.57781 | 0.57781 | 0.57781 | 0.0 | 19.63
-Bond | 0.072705 | 0.072705 | 0.072705 | 0.0 | 2.47
-Neigh | 1.0768 | 1.0768 | 1.0768 | 0.0 | 36.57
-Comm | 0.052799 | 0.052799 | 0.052799 | 0.0 | 1.79
-Output | 0.00064921 | 0.00064921 | 0.00064921 | 0.0 | 0.02
-Modify | 1.1247 | 1.1247 | 1.1247 | 0.0 | 38.20
-Other | | 0.03878 | | | 1.32
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 3244 ave 3244 max 3244 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 30929 ave 30929 max 30929 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 30929
-Ave neighs/atom = 5.52304
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 165
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/nph iso"
-rigid/nph iso
-run 1000
-Memory usage per processor = 7.32428 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468
- 9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506
- 9200 1.4790176 5.3498933 6.5115824 0.068306349 6.8531758 27.642255 31.829623 31.829623 0.057719204 0.083928825 0.063271019
- 9300 1.4685339 5.3439444 6.4973991 0.012381058 6.5578428 27.421331 31.575232 31.575232 0.018937907 0.0065076203 0.011697646
- 9400 1.4675871 5.3321417 6.4848528 0.056515448 6.7525582 27.146928 31.259261 31.259261 0.035834387 0.047161137 0.086550819
- 9500 1.4464119 5.3137665 6.4498455 0.043906827 6.6517871 26.881604 30.953745 30.953745 0.031891513 0.065507153 0.034321816
- 9600 1.4541889 5.284445 6.4266325 0.046471589 6.6332098 26.578003 30.604153 30.604153 0.0041035598 0.071274602 0.064036606
- 9700 1.4577034 5.2493866 6.3943346 0.045073503 6.5909605 26.41175 30.412715 30.412715 0.018293408 0.069031147 0.047895953
- 9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761
- 9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473
- 10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177
-Loop time of 3.13351 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 137864.384 tau/day, 319.131 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.68 | 0.68 | 0.68 | 0.0 | 21.70
-Bond | 0.073233 | 0.073233 | 0.073233 | 0.0 | 2.34
-Neigh | 1.1775 | 1.1775 | 1.1775 | 0.0 | 37.58
-Comm | 0.057102 | 0.057102 | 0.057102 | 0.0 | 1.82
-Output | 0.00068927 | 0.00068927 | 0.00068927 | 0.0 | 0.02
-Modify | 1.1058 | 1.1058 | 1.1058 | 0.0 | 35.29
-Other | | 0.03924 | | | 1.25
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 3635 ave 3635 max 3635 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 38235 ave 38235 max 38235 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 38235
-Ave neighs/atom = 6.82768
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 165
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/nph xy couple"
-rigid/nph xy couple
-run 1000
-Memory usage per processor = 7.32811 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455
- 10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324
- 10200 1.4231669 5.2080497 6.3258711 0.086173671 6.682435 25.959905 29.892423 29.859779 0.11480457 0.12471881 0.018997629
- 10300 1.4334516 5.1992954 6.3251949 -0.0076414301 6.2932457 26.095439 30.048488 29.859779 0.00870511 -0.0049134764 -0.026715924
- 10400 1.4408912 5.1980613 6.3298041 0.070774329 6.6314048 26.345108 30.335978 29.859779 0.061559356 0.075929557 0.074834076
- 10500 1.4299517 5.1990298 6.3221802 0.077553868 6.6569567 26.515356 30.532016 29.859779 0.11568876 0.063812738 0.053160106
- 10600 1.439113 5.1937953 6.3241415 0.024333431 6.4286629 26.449816 30.456548 29.859779 0.035925567 0.023132021 0.013942706
- 10700 1.4379108 5.1704548 6.2998567 0.06126476 6.5597578 26.285754 30.267632 29.859779 0.074214186 0.040233796 0.069346299
- 10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395
- 10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071
- 11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746
-Loop time of 3.22377 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 134004.591 tau/day, 310.196 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.74959 | 0.74959 | 0.74959 | 0.0 | 23.25
-Bond | 0.073572 | 0.073572 | 0.073572 | 0.0 | 2.28
-Neigh | 1.1793 | 1.1793 | 1.1793 | 0.0 | 36.58
-Comm | 0.057446 | 0.057446 | 0.057446 | 0.0 | 1.78
-Output | 0.00065088 | 0.00065088 | 0.00065088 | 0.0 | 0.02
-Modify | 1.1241 | 1.1241 | 1.1241 | 0.0 | 34.87
-Other | | 0.03903 | | | 1.21
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 3799 ave 3799 max 3799 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 39646 ave 39646 max 39646 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 39646
-Ave neighs/atom = 7.07964
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 158
-Dangerous builds = 0
-
-Total wall time: 0:00:21
diff --git a/examples/rigid/log.5Oct16.rigid.tnr.g++.4 b/examples/rigid/log.5Oct16.rigid.tnr.g++.4
deleted file mode 100644
index 2a27702446e57a6adc0b139c69592a1b3594b6ed..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.tnr.g++.4
+++ /dev/null
@@ -1,452 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Tethered nanorods
-
-atom_style molecular
-
-read_data data.rigid.tnr
- orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 5600 atoms
- scanning bonds ...
- 1 = max bonds/atom
- reading bonds ...
- 1600 bonds
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 1 = max # of 1-4 neighbors
- 2 = max # of special neighbors
-
-# Specify bond parameters
-
-bond_style fene
-bond_coeff 1 30.0 1.5 1.0 1.0
-
-special_bonds fene
- 2 = max # of 1-2 neighbors
- 2 = max # of special neighbors
-
-# Specify initial velocities
-
-velocity all create 1.4 109345
-
-# Specify rigid components
-
-group rods type 2
-4000 atoms in group rods
-group tethers subtract all rods
-1600 atoms in group tethers
-
-neigh_modify exclude molecule rods delay 0 every 1
-
-# Specify the pair potentials
-
-pair_style lj/cut 2.5
-pair_modify shift yes
-pair_coeff * * 1.0 1.0 1.122
-pair_coeff 2 2 1.0 1.0 2.5
-
-# Specify output
-
-thermo 100
-thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
-thermo_modify flush yes lost warn
-
-timestep 0.005
-
-fix 1 rods rigid molecule
-800 rigid bodies with 4000 atoms
-fix 2 tethers nve
-fix 3 all langevin 1.4 1.4 1.0 437624
-
-run 5000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 45 45 45
-Memory usage per processor = 6.96454 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
- 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
- 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
- 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
- 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
- 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
- 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
- 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
- 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
- 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
- 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
- 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
- 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
- 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
- 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
- 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
- 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
- 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
- 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
- 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
- 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
- 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
- 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
- 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
- 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026
- 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
- 2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
- 2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
- 2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
- 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
- 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
- 3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
- 3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
- 3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
- 3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
- 3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
- 3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
- 3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
- 3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
- 3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
- 4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
- 4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
- 4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
- 4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
- 4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
- 4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
- 4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
- 4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
- 4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
- 4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
- 5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
-Loop time of 3.14543 on 4 procs for 5000 steps with 5600 atoms
-
-Performance: 686709.553 tau/day, 1589.605 timesteps/s
-99.2% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.081628 | 0.12747 | 0.17984 | 12.8 | 4.05
-Bond | 0.037502 | 0.057149 | 0.076595 | 7.6 | 1.82
-Neigh | 0.65705 | 0.6588 | 0.66084 | 0.2 | 20.94
-Comm | 0.1653 | 0.23616 | 0.29975 | 12.9 | 7.51
-Output | 0.0021076 | 0.0028133 | 0.003227 | 0.9 | 0.09
-Modify | 1.8231 | 1.8972 | 1.9713 | 5.2 | 60.32
-Other | | 0.1658 | | | 5.27
-
-Nlocal: 1400 ave 1868 max 905 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Nghost: 648.25 ave 688 max 598 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-Neighs: 1202.5 ave 1821 max 698 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 4810
-Ave neighs/atom = 0.858929
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 759
-Dangerous builds = 0
-
-# Replace fix rigid and fix langevin with new ones
-
-unfix 1
-unfix 3
-
-fix 3 tethers langevin 1.4 1.4 1.0 198450
-
-# Test different integrators for rods
-
-fix 1 rods rigid/nve molecule
-800 rigid bodies with 4000 atoms
-print "rigid/nve"
-rigid/nve
-run 1000
-Memory usage per processor = 6.98553 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
- 5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
- 5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
- 5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
- 5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
- 5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
- 5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
- 5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
- 5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
- 5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
- 6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
-Loop time of 0.74555 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 579437.739 tau/day, 1341.291 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.020915 | 0.033416 | 0.047822 | 6.7 | 4.48
-Bond | 0.0076883 | 0.011506 | 0.015239 | 3.3 | 1.54
-Neigh | 0.14225 | 0.14262 | 0.14297 | 0.1 | 19.13
-Comm | 0.030192 | 0.0485 | 0.064376 | 7.2 | 6.51
-Output | 0.00039148 | 0.0005275 | 0.00062299 | 0.4 | 0.07
-Modify | 0.46557 | 0.47773 | 0.49051 | 1.7 | 64.08
-Other | | 0.03125 | | | 4.19
-
-Nlocal: 1400 ave 1868 max 935 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 633.75 ave 695 max 541 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Neighs: 1263 ave 1799 max 710 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 5052
-Ave neighs/atom = 0.902143
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 153
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
-800 rigid bodies with 4000 atoms
-print "rigid/nvt"
-rigid/nvt
-run 1000
-Memory usage per processor = 6.98553 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
- 6100 1.3829575 5.9055308 6.9917699 0.0022904847 7.0904051 62.244 62.244 62.244 -0.00045870152 0.004055647 0.0032745086
- 6200 1.3942692 5.90506 7.0001838 0.0046406767 7.2000253 62.244 62.244 62.244 0.0042263478 0.0051632788 0.0045324035
- 6300 1.4009885 5.902399 7.0028005 0.0077682485 7.3373247 62.244 62.244 62.244 0.0071636925 0.0098268465 0.0063142066
- 6400 1.3627532 5.9075587 6.9779284 0.0093180812 7.3791931 62.244 62.244 62.244 0.0062401482 0.013022619 0.0086914761
- 6500 1.3341203 5.9012967 6.9491767 0.010108056 7.3844601 62.244 62.244 62.244 0.0031876333 0.011099549 0.016036984
- 6600 1.3572847 5.8915298 6.9576041 -0.00034416741 6.9427833 62.244 62.244 62.244 0.0025578983 -0.0011308804 -0.0024595201
- 6700 1.3663741 5.8985276 6.9717412 0.002947281 7.09866 62.244 62.244 62.244 0.0022469396 -0.00042872124 0.0070236245
- 6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922
- 6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422
- 7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504
-Loop time of 0.761012 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 567665.504 tau/day, 1314.041 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.022122 | 0.034862 | 0.048912 | 6.6 | 4.58
-Bond | 0.0078702 | 0.011574 | 0.015191 | 3.2 | 1.52
-Neigh | 0.1398 | 0.14013 | 0.14044 | 0.1 | 18.41
-Comm | 0.029736 | 0.047586 | 0.064077 | 7.3 | 6.25
-Output | 0.00039291 | 0.00053465 | 0.00063396 | 0.4 | 0.07
-Modify | 0.48838 | 0.49907 | 0.50959 | 1.4 | 65.58
-Other | | 0.02726 | | | 3.58
-
-Nlocal: 1400 ave 1832 max 970 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 652.5 ave 749 max 561 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Neighs: 1407.5 ave 2071 max 748 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 5630
-Ave neighs/atom = 1.00536
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 149
-Dangerous builds = 0
-unfix 1
-
-compute myTemp all temp
-
-fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/npt iso"
-rigid/npt iso
-fix_modify 1 temp myTemp
-
-run 1000
-Memory usage per processor = 6.98553 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 7000 1.3973667 5.8867951 6.9843517 0.0026559416 7.0987246 62.244 62.244 62.244 0.033713637 -0.0068647989 -0.018881013
- 7100 1.4639139 5.8611823 7.0110083 0.011521251 7.3924625 57.022152 57.022152 57.022152 0.010787531 0.0093708984 0.014405322
- 7200 1.4950463 5.8177011 6.9919798 0.023101297 7.5163969 50.281647 50.281647 50.281647 0.023242216 0.018105116 0.02795656
- 7300 1.5103331 5.7757714 6.9620571 0.022650056 7.3366292 45.243 45.243 45.243 0.023573421 0.022300241 0.022076507
- 7400 1.5582095 5.7578511 6.9817412 0.028508467 7.3477691 41.582392 41.582392 41.582392 0.02740467 0.030003113 0.028117619
- 7500 1.5992723 5.6927269 6.9488696 0.046538335 7.4419099 39.001967 39.001967 39.001967 0.057728057 0.030859627 0.05102732
- 7600 1.5572154 5.6717168 6.894826 0.032055597 7.184009 36.967405 36.967405 36.967405 0.034785798 0.033408508 0.027972486
- 7700 1.541013 5.6302838 6.840667 0.046629681 7.2052858 35.246953 35.246953 35.246953 0.051145184 0.022437926 0.066305932
- 7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623
- 7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184
- 8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909
-Loop time of 1.40621 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 307209.818 tau/day, 711.134 timesteps/s
-99.5% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.057011 | 0.094542 | 0.13471 | 11.0 | 6.72
-Bond | 0.012043 | 0.017356 | 0.022935 | 3.8 | 1.23
-Neigh | 0.50655 | 0.50716 | 0.50781 | 0.1 | 36.07
-Comm | 0.060325 | 0.10627 | 0.14985 | 12.0 | 7.56
-Output | 0.0003705 | 0.00040978 | 0.00051475 | 0.3 | 0.03
-Modify | 0.60798 | 0.63453 | 0.65863 | 2.9 | 45.12
-Other | | 0.04594 | | | 3.27
-
-Nlocal: 1400 ave 1820 max 1010 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Nghost: 1576 ave 1694 max 1470 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs: 6543 ave 9989 max 3497 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 26172
-Ave neighs/atom = 4.67357
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 337
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/npt x"
-rigid/npt x
-run 1000
-Memory usage per processor = 7.00192 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 8000 1.498932 5.5307653 6.708096 0.044418732 6.9660307 31.918601 31.918601 31.918601 0.033240642 0.090981355 0.0090341992
- 8100 1.4932748 5.5104122 6.6832996 0.078824127 7.1379335 31.703188 31.918601 31.918601 0.046668046 0.090499077 0.099305258
- 8200 1.4783774 5.4958482 6.6570345 0.024180825 6.7956092 31.500184 31.918601 31.918601 -0.01991799 0.022036912 0.070423554
- 8300 1.4699766 5.468569 6.6231569 0.050331767 6.9062762 30.919162 31.918601 31.918601 0.030889484 0.091318073 0.028787743
- 8400 1.4423945 5.4591749 6.5920985 0.034769472 6.7835475 30.266023 31.918601 31.918601 0.031838545 0.067297532 0.0051723374
- 8500 1.4478469 5.4405027 6.5777089 0.061608005 6.9111775 29.752136 31.918601 31.918601 0.056987338 0.064105062 0.063731616
- 8600 1.4216004 5.443144 6.5597349 0.031739807 6.7291722 29.343028 31.918601 31.918601 0.047008356 0.040197385 0.0080136813
- 8700 1.3993468 5.4199487 6.5190607 0.055753353 6.8130189 28.981104 31.918601 31.918601 0.038071725 0.050746074 0.078442261
- 8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108
- 8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314
- 9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783
-Loop time of 1.3981 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 308990.110 tau/day, 715.255 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.090644 | 0.15054 | 0.22186 | 13.5 | 10.77
-Bond | 0.013196 | 0.017756 | 0.022439 | 2.9 | 1.27
-Neigh | 0.40253 | 0.40269 | 0.40288 | 0.0 | 28.80
-Comm | 0.057128 | 0.13282 | 0.1979 | 15.4 | 9.50
-Output | 0.00036597 | 0.00040632 | 0.0004673 | 0.2 | 0.03
-Modify | 0.62613 | 0.65125 | 0.67228 | 2.1 | 46.58
-Other | | 0.04265 | | | 3.05
-
-Nlocal: 1400 ave 1770 max 1095 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-Nghost: 1578.5 ave 1693 max 1493 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs: 7868 ave 12041 max 4579 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 31472
-Ave neighs/atom = 5.62
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 167
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/nph iso"
-rigid/nph iso
-run 1000
-Memory usage per processor = 7.00192 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 9000 1.4147254 5.3571794 6.4683705 0.026540417 6.6005164 27.368213 31.918601 31.918601 -0.25291277 0.19881452 0.1337195
- 9100 1.4143578 5.3349724 6.4458747 0.032533861 6.6070914 27.324726 31.867884 31.867884 0.031965858 0.023737907 0.041897818
- 9200 1.4489265 5.3126352 6.4506893 0.020125553 6.5486389 27.161226 31.6772 31.6772 0.024138053 0.045983015 -0.0097444101
- 9300 1.4434983 5.3100314 6.4438219 0.071722015 6.7864703 26.993744 31.481872 31.481872 0.081599435 0.059208723 0.074357889
- 9400 1.4179009 5.3170886 6.4307738 0.020348306 6.5262516 26.832169 31.293432 31.293432 0.070733237 -0.0042808269 -0.0054074919
- 9500 1.455947 5.2941589 6.4377273 0.0066330065 6.4680826 26.60963 31.033892 31.033892 -0.026145193 -0.017478757 0.06352297
- 9600 1.4322198 5.2747171 6.399649 0.079157317 6.755508 26.452091 30.85016 30.85016 0.09770091 0.095143096 0.044627945
- 9700 1.4366074 5.2650795 6.3934576 0.052444405 6.6264505 26.347873 30.728614 30.728614 0.043301655 0.043720535 0.070311026
- 9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122
- 9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308
- 10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946
-Loop time of 1.38185 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 312625.215 tau/day, 723.669 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.11291 | 0.17289 | 0.23942 | 12.0 | 12.51
-Bond | 0.013814 | 0.017709 | 0.022031 | 2.5 | 1.28
-Neigh | 0.40444 | 0.4048 | 0.40511 | 0.0 | 29.29
-Comm | 0.055045 | 0.12527 | 0.18875 | 14.9 | 9.07
-Output | 0.0003531 | 0.00038058 | 0.00045681 | 0.2 | 0.03
-Modify | 0.60769 | 0.62523 | 0.64283 | 1.7 | 45.25
-Other | | 0.03557 | | | 2.57
-
-Nlocal: 1400 ave 1669 max 1139 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost: 1761.5 ave 1898 max 1632 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 9311.75 ave 12525 max 5959 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 37247
-Ave neighs/atom = 6.65125
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 165
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/nph xy couple"
-rigid/nph xy couple
-run 1000
-Memory usage per processor = 7.00192 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 10000 1.4627878 5.2272205 6.376162 0.087181735 6.7375684 25.746677 30.02746 30.02746 0.01077504 0.047196696 0.20357347
- 10100 1.461932 5.2277217 6.3759909 0.045218386 6.5623932 25.674625 29.943429 30.02746 0.029664553 0.034940919 0.071049687
- 10200 1.4394425 5.2183968 6.3490017 0.064139003 6.6129181 25.651225 29.916138 30.02746 0.063541799 0.099454655 0.029420554
- 10300 1.445679 5.2124787 6.3479821 0.073611235 6.6513251 25.670301 29.938385 30.02746 0.09678342 0.1092442 0.01480609
- 10400 1.4289478 5.2082727 6.3306346 -0.00091064043 6.3268902 25.642317 29.905748 30.02746 -0.021792005 0.043173882 -0.024113799
- 10500 1.4138512 5.191318 6.3018224 0.051274311 6.5114152 25.566672 29.817526 30.02746 0.087657762 0.022098862 0.04406631
- 10600 1.4101298 5.2048433 6.3124247 0.032021085 6.442127 25.450236 29.681731 30.02746 0.032483644 0.022737859 0.040841754
- 10700 1.4527253 5.1827275 6.3237654 0.045295082 6.5054661 25.327296 29.53835 30.02746 0.082847312 0.0364514 0.016586533
- 10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992
- 10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683
- 11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165
-Loop time of 1.36647 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 316143.197 tau/day, 731.813 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.13847 | 0.19365 | 0.24916 | 9.9 | 14.17
-Bond | 0.014236 | 0.017841 | 0.02132 | 2.2 | 1.31
-Neigh | 0.37634 | 0.37662 | 0.37685 | 0.0 | 27.56
-Comm | 0.057297 | 0.11588 | 0.17429 | 13.5 | 8.48
-Output | 0.00035167 | 0.00037664 | 0.00044203 | 0.2 | 0.03
-Modify | 0.61282 | 0.62929 | 0.64128 | 1.4 | 46.05
-Other | | 0.03282 | | | 2.40
-
-Nlocal: 1400 ave 1607 max 1199 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost: 1819.25 ave 1940 max 1712 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs: 9882 ave 12628 max 7201 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 39528
-Ave neighs/atom = 7.05857
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 156
-Dangerous builds = 0
-
-Total wall time: 0:00:10
diff --git a/lib/colvars/Makefile.deps b/lib/colvars/Makefile.deps
index 9a7de0647db57eeb3d62ee866e71f6e363b6c802..a0d8515bc104f985584d18726c79914c67227cdf 100644
--- a/lib/colvars/Makefile.deps
+++ b/lib/colvars/Makefile.deps
@@ -1,9 +1,9 @@
$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarparse.h colvaratoms.h colvardeps.h
$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
colvarparse.h colvardeps.h lepton/include/Lepton.h \
lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
@@ -29,7 +29,7 @@ $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvarbias_alb.h
$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvarbias.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvarbias.h \
colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \
lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
@@ -42,8 +42,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
- colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \
- colvartypes.h colvar.h colvarparse.h colvardeps.h \
+ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h \
lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
lepton/include/lepton/windowsIncludes.h \
@@ -55,7 +55,7 @@ $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvarbias_histogram.h colvarbias.h colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
colvarparse.h colvardeps.h lepton/include/Lepton.h \
lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
@@ -68,8 +68,8 @@ $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvarbias_meta.h colvarbias.h colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
- colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \
- colvartypes.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
+ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
+ colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
colvardeps.h lepton/include/Lepton.h \
lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
@@ -171,7 +171,7 @@ $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvarcomp.h colvaratoms.h colvarproxy.h colvarscript.h colvarbias.h
$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvardeps.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \
colvarparse.h
$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h colvar.h \
@@ -204,7 +204,7 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h
$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \
lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp
index c717e8f4c678a5e22f204942805fe894d22cbc28..39b84b26d195dc59eae8bbced3ef40ef14f4cbb9 100644
--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@@ -77,6 +77,8 @@ int colvar::cvc::init(std::string const &conf)
if (cvm::debug())
cvm::log("Done initializing cvc base object.\n");
+
+ return error_code;
}
diff --git a/lib/latte/.gitignore b/lib/latte/.gitignore
index a4c2a2362e959e7672e6289f0b9cbade4b6156a5..2c9ff6be9e655db4bf7c02b5b639e398ac8781ad 100644
--- a/lib/latte/.gitignore
+++ b/lib/latte/.gitignore
@@ -2,4 +2,4 @@
/filelink
/liblink
/includelink
-/LATTE-master
+/LATTE-*
diff --git a/lib/vtk/Makefile.lammps.fedora28_vtk7 b/lib/vtk/Makefile.lammps.fedora28_vtk7
new file mode 100644
index 0000000000000000000000000000000000000000..6919dd36b96c37cedd912ba5b0dad1f88dba0ded
--- /dev/null
+++ b/lib/vtk/Makefile.lammps.fedora28_vtk7
@@ -0,0 +1,8 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+# settings for VTK 7.1.1 on Fedora 28. This seems to work with Fedora versions going back to at least 23 and VTK version 6.x.
+# You need to install vtk-devel and all its dependencies using "dnf install vtk-devel"
+vtk_SYSINC = -I/usr/include/vtk
+vtk_SYSLIB = -lvtkCommonCore -lvtkIOCore -lvtkCommonDataModel -lvtkIOXML -lvtkIOLegacy -lvtkIOParallelXML
+vtk_SYSPATH = -L/usr/lib64/vtk
+
diff --git a/src/.gitignore b/src/.gitignore
index 46c8f1ca080b4bb909a3653da1ad827cda6bcf91..1ff66859e86cb6c1f920439aa4e2fa25e799c61d 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -734,6 +734,8 @@
/pair_hbond_dreiding_morse.h
/pair_ilp_graphene_hbn.cpp
/pair_ilp_graphene_hbn.h
+/pair_kim.cpp
+/pair_kim.h
/pair_kolmogorov_crespi_full.cpp
/pair_kolmogorov_crespi_full.h
/pair_kolmogorov_crespi_z.cpp
diff --git a/src/Depend.sh b/src/Depend.sh
index a83a99ffb5da5bf320b8a28a151b33af4eb189f6..9fe30e658325bbbf385e33e543065a1ab32eff44 100644
--- a/src/Depend.sh
+++ b/src/Depend.sh
@@ -134,6 +134,7 @@ fi
if (test $1 = "USER-MISC") then
depend GPU
depend USER-OMP
+ depend USER-INTEL
fi
if (test $1 = "USER-REAXC") then
diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h
index ddb0b5ceaa51cf1bae036d014f6aa24220bdc98d..56a4f15f1bff5a18ee050badf8acfb420c97b28b 100644
--- a/src/GPU/gpu_extra.h
+++ b/src/GPU/gpu_extra.h
@@ -61,13 +61,13 @@ namespace GPU_EXTRA {
else
error->all(FLERR,"Unknown error in GPU library");
}
- };
+ }
inline void gpu_ready(LAMMPS_NS::Modify *modify, LAMMPS_NS::Error *error) {
int ifix = modify->find_fix("package_gpu");
if (ifix < 0)
error->all(FLERR,"The package gpu command is required for gpu styles");
- };
+ }
}
#endif
diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index 46e843158abe6649ba751b7480bba01e4ba94ebe..fe638214baabe8205172d78d898bd21ee75096e5 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -1264,15 +1264,15 @@ void *PairKIM::extract(const char *str, int &dim)
int ier;
int dummyint;
int isIndexed = 0;
- int maxLine = 1024;
+ const int MAXLINE = 1024;
int rank;
int validParam = 0;
int numParams;
- int *speciesIndex = new int[maxLine];
- char *paramStr = new char[maxLine];
+ int *speciesIndex = new int[MAXLINE];
+ char *paramStr = new char[MAXLINE];
char *paramName;
char *indexStr;
- char message[maxLine];
+ char message[MAXLINE];
int offset;
double* paramPtr;
@@ -1354,7 +1354,7 @@ void *PairKIM::extract(const char *str, int &dim)
}
kim_error(__LINE__,"get_rank",kimerror);
- int *shape = new int[maxLine];
+ int *shape = new int[MAXLINE];
dummyint = (*pkim).get_shape(paramName, shape, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp
index cc1ea027eec3a115ebc58400663863194ca3b93e..9f3221449bb2329923cfa9ed987beb6f26e58e3f 100644
--- a/src/KSPACE/msm.cpp
+++ b/src/KSPACE/msm.cpp
@@ -2261,7 +2261,7 @@ void MSM::restriction(int n)
double ***qgrid2 = qgrid[n+1];
int k = 0;
- int index[p+2];
+ int *index = new int[p+2];
for (int nu=-p; nu<=p; nu++) {
if (nu%2 == 0 && nu != 0) continue;
phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]);
@@ -2317,7 +2317,7 @@ void MSM::restriction(int n)
}
qgrid2[kp][jp][ip] += q2sum;
}
-
+ delete[] index;
}
/* ----------------------------------------------------------------------
@@ -2348,7 +2348,7 @@ void MSM::prolongation(int n)
double ***v5grid2 = v5grid[n+1];
int k = 0;
- int index[p+2];
+ int *index = new int[p+2];
for (int nu=-p; nu<=p; nu++) {
if (nu%2 == 0 && nu != 0) continue;
phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]);
@@ -2420,7 +2420,7 @@ void MSM::prolongation(int n)
}
}
-
+ delete[] index;
}
/* ----------------------------------------------------------------------
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index e38a05c6edffb4eab8a6e34089c86762d94971de..b4f9c02206f926d39307b19317bd7e00b9cd16eb 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -310,10 +310,10 @@ double PairComb3::init_one(int i, int j)
void PairComb3::read_lib()
{
- unsigned int maxlib = 1024;
+ const unsigned int MAXLIB = 1024;
int i,j,k,l,nwords,m;
int ii,jj,kk,ll,mm,iii;
- char s[maxlib];
+ char s[MAXLIB];
char **words = new char*[80];
// open libraray file on proc 0
@@ -327,8 +327,8 @@ void PairComb3::read_lib()
}
// read and store at the same time
- fgets(s,maxlib,fp);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -339,7 +339,7 @@ void PairComb3::read_lib()
ccutoff[4] = atof(words[4]);
ccutoff[5] = atof(words[5]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -351,7 +351,7 @@ void PairComb3::read_lib()
ch_a[5] = atof(words[5]);
ch_a[6] = atof(words[6]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -359,7 +359,7 @@ void PairComb3::read_lib()
nsplrad = atoi(words[1]);
nspltor = atoi(words[2]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -367,7 +367,7 @@ void PairComb3::read_lib()
maxy = atoi(words[1]);
maxz = atoi(words[2]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -376,7 +376,7 @@ void PairComb3::read_lib()
maxconj = atoi(words[2]);
for (l=0; l<nsplpcn; l++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -385,14 +385,14 @@ void PairComb3::read_lib()
dvmaxxcn[l] = atof(words[3]);
}
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
ntab = atoi(words[0]);
for (i=0; i<ntab+1; i++){
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -405,7 +405,7 @@ void PairComb3::read_lib()
for (i=0; i<maxx+1; i++)
for (j=0; j<maxy+1; j++)
for (k=0; k<maxz+1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -423,7 +423,7 @@ void PairComb3::read_lib()
for (i=0; i<maxx; i++)
for (j=0; j<maxy; j++)
for (k=0; k<maxz; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -432,7 +432,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3]);
for(iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -447,7 +447,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -465,7 +465,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -474,7 +474,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3])-1;
for (iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -489,7 +489,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -507,7 +507,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -516,7 +516,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3])-1;
for(iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 08fe7de5cb4a12402698e60410e9936609d8bf49..6221e6d52c26b359d9efd7d87460a1ed3ceacaf3 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -1349,7 +1349,7 @@ void FixGCMC::attempt_molecule_insertion()
MathExtra::quat_to_mat(quat,rotmat);
double insertion_energy = 0.0;
- bool procflag[natoms_per_molecule];
+ bool *procflag = new bool[natoms_per_molecule];
for (int i = 0; i < natoms_per_molecule; i++) {
MathExtra::matvec(rotmat,onemols[imol]->x[i],molcoords[i]);
@@ -1472,6 +1472,7 @@ void FixGCMC::attempt_molecule_insertion()
update_gas_atoms_list();
ninsertion_successes += 1.0;
}
+ delete[] procflag;
}
/* ----------------------------------------------------------------------
@@ -1934,7 +1935,7 @@ void FixGCMC::attempt_molecule_deletion_full()
grow_molecule_arrays(nmolq);
int m = 0;
- int tmpmask[atom->nlocal];
+ int *tmpmask = new int[atom->nlocal];
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == deletion_molecule) {
tmpmask[i] = atom->mask[i];
@@ -1982,6 +1983,7 @@ void FixGCMC::attempt_molecule_deletion_full()
if (force->kspace) force->kspace->qsum_qsq();
}
update_gas_atoms_list();
+ delete[] tmpmask;
}
/* ----------------------------------------------------------------------
@@ -2426,9 +2428,9 @@ void FixGCMC::update_gas_atoms_list()
for (int i = 0; i < nlocal; i++) maxmol = MAX(maxmol,molecule[i]);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
- double comx[maxmol_all];
- double comy[maxmol_all];
- double comz[maxmol_all];
+ double *comx = new double[maxmol_all];
+ double *comy = new double[maxmol_all];
+ double *comz = new double[maxmol_all];
for (int imolecule = 0; imolecule < maxmol_all; imolecule++) {
for (int i = 0; i < nlocal; i++) {
if (molecule[i] == imolecule) {
@@ -2458,7 +2460,9 @@ void FixGCMC::update_gas_atoms_list()
}
}
}
-
+ delete[] comx;
+ delete[] comy;
+ delete[] comz;
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp
index 2e9e03c941af82e82225f4676d88d75e58bc36b6..b28259524071672463f17051e5a388e0d89d133d 100644
--- a/src/MSCG/fix_mscg.cpp
+++ b/src/MSCG/fix_mscg.cpp
@@ -21,6 +21,7 @@
#include "fix_mscg.h"
#include "mscg.h"
#include "atom.h"
+#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
@@ -284,11 +285,9 @@ void FixMSCG::end_of_step()
if (domain->triclinic == 1)
error->all(FLERR,"Fix mscg does not yet support triclinic geometries");
- int natoms = atom->natoms;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
double **x = atom->x;
- double *prd_half = domain->prd_half;
int i,ii,j;
// trajectory information
diff --git a/src/Makefile b/src/Makefile
index 03f40721324e8d1712d967481f7611484be0c558..d17a2ccbd99ecf0ff2c29b1626ebe1bdd3da39dc 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -57,10 +57,10 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
molecule mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap srd voronoi
-PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \
+PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-meamc user-meso \
- user-mgpt user-misc user-molfile \
+ user-mgpt user-misc user-mofff user-molfile \
user-netcdf user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
@@ -267,7 +267,7 @@ package:
@echo 'make yes-all install all pgks in src dir'
@echo 'make no-all remove all pkgs from src dir'
@echo 'make yes-standard (yes-std) install all standard pkgs'
- @echo 'make no-standard (no-srd) remove all standard pkgs'
+ @echo 'make no-standard (no-std) remove all standard pkgs'
@echo 'make yes-user install all user pkgs'
@echo 'make no-user remove all user pkgs'
@echo 'make yes-lib install all pkgs with libs (included or ext)'
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index ebd1729b6e02521299517a54aa68650c1da65856..edc72ea70ce953ba2fc28d21efbedcb3fd49f00c 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -267,6 +267,10 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
poems = new Workspace;
+ // compute per body forces and torques inside final_integrate() by default
+
+ earlyflag = 0;
+
// print statistics
int nsum = 0;
@@ -351,12 +355,26 @@ void FixPOEMS::init()
int i,ibody;
// warn if more than one POEMS fix
+ // if earlyflag, warn if any post-force fixes come after POEMS fix
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"poems") == 0) count++;
if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix poems");
+ if (earlyflag) {
+ int pflag = 0;
+ for (i = 0; i < modify->nfix; i++) {
+ if (strcmp(modify->fix[i]->style,"poems") == 0) pflag = 1;
+ if (pflag && (modify->fmask[i] & POST_FORCE) &&
+ !modify->fix[i]->rigid_flag) {
+ char str[128];
+ sprintf(str,"Fix %d alters forces after fix poems",modify->fix[i]->id);
+ error->warning(FLERR,str);
+ }
+ }
+ }
+
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
@@ -696,7 +714,8 @@ void FixPOEMS::setup(int vflag)
// use post_force() to compute initial fcm & torque
- post_force(vflag);
+ compute_forces_and_torques();
+ //post_force(vflag);
// setup for POEMS
@@ -727,12 +746,29 @@ void FixPOEMS::initial_integrate(int vflag)
set_xv();
}
+/* ---------------------------------------------------------------------- */
+
+void FixPOEMS::post_force(int vflag)
+{
+ if (earlyflag) compute_forces_and_torques();
+
+ /*
+ for (int ibody = 0; ibody < nbody; ibody++) {
+ if (ibody == 0) {
+ printf("PFF %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]);
+ printf("PFT %d %g %g %g\n",ibody,
+ torque[ibody][0],torque[ibody][1],torque[ibody][2]);
+ }
+ }
+ */
+}
+
/* ----------------------------------------------------------------------
compute fcm,torque on each rigid body
only count joint atoms in 1st body
------------------------------------------------------------------------- */
-void FixPOEMS::post_force(int vflag)
+void FixPOEMS::compute_forces_and_torques()
{
int i,ibody;
int xbox,ybox,zbox;
@@ -790,6 +826,18 @@ void FixPOEMS::post_force(int vflag)
void FixPOEMS::final_integrate()
{
+ if (!earlyflag) compute_forces_and_torques();
+
+ /*
+ for (int ibody = 0; ibody < nbody; ibody++) {
+ if (ibody == 0) {
+ printf("FI %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]);
+ printf("TQ %d %g %g %g\n",ibody,
+ torque[ibody][0],torque[ibody][1],torque[ibody][2]);
+ }
+ }
+ */
+
// perform POEMS integration
poems->LobattoTwo(vcm,omega,torque,fcm);
@@ -1615,6 +1663,21 @@ int FixPOEMS::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
+int FixPOEMS::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"bodyforces") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (strcmp(arg[1],"early") == 0) earlyflag = 1;
+ else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
+ else error->all(FLERR,"Illegal fix_modify command");
+ return 2;
+ }
+
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
void FixPOEMS::reset_dt()
{
dtv = update->dt;
diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h
index 4d5e5c319861398f1c4e8f2f9d92f944dd4192e9..7b2c77a1bd78deec2d9ea0a62e3bc021d79b3e05 100644
--- a/src/POEMS/fix_poems.h
+++ b/src/POEMS/fix_poems.h
@@ -47,6 +47,7 @@ class FixPOEMS : public Fix {
void pre_neighbor();
int dof(int);
void deform(int);
+ int modify_param(int, char **);
void reset_dt();
private:
@@ -55,6 +56,7 @@ class FixPOEMS : public Fix {
double *step_respa;
int nlevels_respa;
double total_ke;
+ int earlyflag; // 1 if forces and torques are computed at post_force()
// atom assignment to rigid bodies
// double count joint atoms as being in multiple bodies
@@ -96,6 +98,7 @@ class FixPOEMS : public Fix {
// internal class functions
+ void compute_forces_and_torques();
void readfile(char *);
int readline(FILE *, char **, int *);
void jointbuild();
diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp
index 7331a75db68448ed1b3dbd6a892981637e851daa..b330ab79450b805e595e6b5d52710722d962ee32 100644
--- a/src/PYTHON/fix_python_move.cpp
+++ b/src/PYTHON/fix_python_move.cpp
@@ -47,7 +47,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
PyGILState_STATE gstate = PyGILState_Ensure();
// add current directory to PYTHONPATH
- PyObject * py_path = PySys_GetObject("path");
+ PyObject * py_path = PySys_GetObject((char *)"path");
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
@@ -136,7 +136,7 @@ void FixPythonMove::init()
{
PyGILState_STATE gstate = PyGILState_Ensure();
PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_init = PyObject_GetAttrString(py_move_obj,"init");
+ PyObject *py_init = PyObject_GetAttrString(py_move_obj,(char *)"init");
if (!py_init) {
PyErr_Print();
PyErr_Clear();
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 35225b3c1e2bd6f192896a96294bc42b4477c76c..c9aedf74018409a5913ed1055d554775e4704746 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -303,7 +303,7 @@ void NEB::run()
update->minimize->setup();
if (me_universe == 0) {
- if (uscreen)
+ if (uscreen) {
if (verbose) {
fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc EBF EBR RDT "
@@ -317,7 +317,8 @@ void NEB::run()
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
- if (ulogfile)
+ }
+ if (ulogfile) {
if (verbose) {
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc EBF EBR RDT "
@@ -331,6 +332,7 @@ void NEB::run()
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
+ }
}
print_status();
@@ -588,7 +590,7 @@ void NEB::print_status()
MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots);
}
- double one[numall];
+ double one[7];
one[0] = fneb->veng;
one[1] = fneb->plen;
one[2] = fneb->nlen;
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 554412330c955fd187dbb61ee9857c849c1c65ca..07ebf884c7450cf53c4d6e028f758ace69499100 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -174,7 +174,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
molecule = new tagint[nlocal];
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) molecule[i] = (tagint)((tagint)value[i] - minval + 1);
+ if (mask[i] & groupbit)
+ molecule[i] = (tagint)((tagint)value[i] - minval + 1);
delete[] value;
} else error->all(FLERR,"Unsupported fix rigid custom property");
} else {
@@ -624,6 +625,10 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
setupflag = 0;
+ // compute per body forces and torques at final_integrate() by default
+
+ earlyflag = 0;
+
// print statistics
int nsum = 0;
@@ -711,12 +716,26 @@ void FixRigid::init()
avec_tri = (AtomVecTri *) atom->style_match("tri");
// warn if more than one rigid fix
+ // if earlyflag, warn if any post-force fixes come after POEMS fix
int count = 0;
for (i = 0; i < modify->nfix; i++)
- if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
+ if (modify->fix[i]->rigid_flag) count++;
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
+ if (earlyflag) {
+ int rflag = 0;
+ for (i = 0; i < modify->nfix; i++) {
+ if (modify->fix[i]->rigid_flag) rflag = 1;
+ if (rflag && (modify->fmask[i] & POST_FORCE) &&
+ !modify->fix[i]->rigid_flag) {
+ char str[128];
+ sprintf(str,"Fix %d alters forces after fix rigid",modify->fix[i]->id);
+ error->warning(FLERR,str);
+ }
+ }
+ }
+
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
@@ -944,7 +963,7 @@ void FixRigid::initial_integrate(int vflag)
which are added in when final_integrate() calculates a new fcm/torque
------------------------------------------------------------------------- */
-void FixRigid::post_force(int vflag)
+void FixRigid::apply_langevin_thermostat()
{
if (me == 0) {
double gamma1,gamma2;
@@ -1008,7 +1027,7 @@ void FixRigid::enforce2d()
/* ---------------------------------------------------------------------- */
-void FixRigid::final_integrate()
+void FixRigid::compute_forces_and_torques()
{
int i,ibody;
double dtfm;
@@ -1062,9 +1081,7 @@ void FixRigid::final_integrate()
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
- // update vcm and angmom
// include Langevin thermostat forces
- // fflag,tflag = 0 for some dimensions in 2d
for (ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
@@ -1073,6 +1090,31 @@ void FixRigid::final_integrate()
torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
+ }
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigid::post_force(int vflag)
+{
+ if (langflag) apply_langevin_thermostat();
+ if (earlyflag) compute_forces_and_torques();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigid::final_integrate()
+{
+ int ibody;
+ double dtfm;
+
+ if (!earlyflag) compute_forces_and_torques();
+
+ // update vcm and angmom
+ // fflag,tflag = 0 for some dimensions in 2d
+
+ for (ibody = 0; ibody < nbody; ibody++) {
// update vcm by 1/2 step
@@ -2342,7 +2384,7 @@ void FixRigid::write_restart_file(char *file)
sprintf(outfile,"%s.rigid",file);
FILE *fp = fopen(outfile,"w");
if (fp == NULL) {
- char str[128];
+ char str[192];
sprintf(str,"Cannot open fix rigid restart file %s",outfile);
error->one(FLERR,str);
}
@@ -2587,6 +2629,32 @@ void FixRigid::zero_rotation()
set_v();
}
+/* ---------------------------------------------------------------------- */
+
+int FixRigid::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"bodyforces") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (strcmp(arg[1],"early") == 0) earlyflag = 1;
+ else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
+ else error->all(FLERR,"Illegal fix_modify command");
+
+ // reset fix mask
+ // must do here and not in init,
+ // since modify.cpp::init() uses fix masks before calling fix::init()
+
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->id,id) == 0) {
+ if (earlyflag) modify->fmask[i] |= POST_FORCE;
+ else if (!langflag) modify->fmask[i] &= ~POST_FORCE;
+ break;
+ }
+ return 2;
+ }
+
+ return 0;
+}
+
/* ----------------------------------------------------------------------
return temperature of collection of rigid bodies
non-active DOF are removed by fflag/tflag and in tfactor
diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h
index 467ae56cf9e4ed88b83149064392c0fb910da475..507e4c755356686ae3b7a5f3f5c352e49932ae0f 100644
--- a/src/RIGID/fix_rigid.h
+++ b/src/RIGID/fix_rigid.h
@@ -38,7 +38,6 @@ class FixRigid : public Fix {
void final_integrate_respa(int, int);
void write_restart_file(char *);
virtual double compute_scalar();
- virtual int modify_param(int, char **) {return 0;}
double memory_usage();
void grow_arrays(int);
@@ -55,6 +54,7 @@ class FixRigid : public Fix {
void reset_dt();
void zero_momentum();
void zero_rotation();
+ virtual int modify_param(int, char **);
virtual void *extract(const char*, int &);
double extract_ke();
double extract_erotational();
@@ -70,6 +70,7 @@ class FixRigid : public Fix {
char *infile; // file to read rigid body attributes from
int rstyle; // SINGLE,MOLECULE,GROUP
int setupflag; // 1 if body properties are setup, else 0
+ int earlyflag; // 1 if forces/torques computed at post_force()
int dimension; // # of dimensions
int nbody; // # of rigid bodies
@@ -144,6 +145,8 @@ class FixRigid : public Fix {
void set_v();
void setup_bodies_static();
void setup_bodies_dynamic();
+ void apply_langevin_thermostat();
+ void compute_forces_and_torques();
void readfile(int, double *, double **, double **, double **,
imageint *, int *);
};
diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp
index 7007ba1930252740ceb7491f859ee65da9b9036b..96c44d15b5b0e1861803203e4d20e0d0e052e891 100644
--- a/src/RIGID/fix_rigid_nh.cpp
+++ b/src/RIGID/fix_rigid_nh.cpp
@@ -620,87 +620,14 @@ void FixRigidNH::final_integrate()
akin_t = akin_r = 0.0;
}
- // sum over atoms to get force and torque on rigid body
+ // late calculation of forces and torques (if requested)
- double **x = atom->x;
- double **f = atom->f;
- int nlocal = atom->nlocal;
-
- double xprd = domain->xprd;
- double yprd = domain->yprd;
- double zprd = domain->zprd;
- if (triclinic) {
- xy = domain->xy;
- xz = domain->xz;
- yz = domain->yz;
- }
-
- int xbox,ybox,zbox;
- double xunwrap,yunwrap,zunwrap,dx,dy,dz;
- for (ibody = 0; ibody < nbody; ibody++)
- for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
- for (i = 0; i < nlocal; i++) {
- if (body[i] < 0) continue;
- ibody = body[i];
-
- sum[ibody][0] += f[i][0];
- sum[ibody][1] += f[i][1];
- sum[ibody][2] += f[i][2];
-
- xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
- ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
- zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
-
- if (triclinic == 0) {
- xunwrap = x[i][0] + xbox*xprd;
- yunwrap = x[i][1] + ybox*yprd;
- zunwrap = x[i][2] + zbox*zprd;
- } else {
- xunwrap = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
- yunwrap = x[i][1] + ybox*yprd + zbox*yz;
- zunwrap = x[i][2] + zbox*zprd;
- }
-
- dx = xunwrap - xcm[ibody][0];
- dy = yunwrap - xcm[ibody][1];
- dz = zunwrap - xcm[ibody][2];
-
- sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
- sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
- sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
- }
-
- // extended particles add their torque to torque of body
-
- if (extended) {
- double **torque_one = atom->torque;
-
- for (i = 0; i < nlocal; i++) {
- if (body[i] < 0) continue;
- ibody = body[i];
-
- if (eflags[i] & TORQUE) {
- sum[ibody][3] += torque_one[i][0];
- sum[ibody][4] += torque_one[i][1];
- sum[ibody][5] += torque_one[i][2];
- }
- }
- }
-
- MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
+ if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom
- // include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
for (ibody = 0; ibody < nbody; ibody++) {
- fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
- fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
- fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
- torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
- torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
- torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
// update vcm by 1/2 step
@@ -1324,7 +1251,7 @@ int FixRigidNH::modify_param(int narg, char **arg)
return 2;
}
- return 0;
+ return FixRigid::modify_param(narg,arg);
}
/* ---------------------------------------------------------------------- */
diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp
index 874812cc69d5ed964e58271f040662493c1e84b5..135a1fb4bdb0e8ee37b8e958bb31e5b6117a1a33 100644
--- a/src/RIGID/fix_rigid_nh_small.cpp
+++ b/src/RIGID/fix_rigid_nh_small.cpp
@@ -643,80 +643,9 @@ void FixRigidNHSmall::final_integrate()
scale_r *= exp(-dtq * (pdim * mtk_term2));
}
- // sum over atoms to get force and torque on rigid body
+ // late calculation of forces and torques (if requested)
- double **x = atom->x;
- double **f = atom->f;
- int nlocal = atom->nlocal;
-
- double dx,dy,dz;
- double unwrap[3];
- double *xcm,*fcm,*tcm;
-
- for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
- fcm = body[ibody].fcm;
- fcm[0] = fcm[1] = fcm[2] = 0.0;
- tcm = body[ibody].torque;
- tcm[0] = tcm[1] = tcm[2] = 0.0;
- }
-
- for (i = 0; i < nlocal; i++) {
- if (atom2body[i] < 0) continue;
- Body *b = &body[atom2body[i]];
-
- fcm = b->fcm;
- fcm[0] += f[i][0];
- fcm[1] += f[i][1];
- fcm[2] += f[i][2];
-
- domain->unmap(x[i],xcmimage[i],unwrap);
- xcm = b->xcm;
- dx = unwrap[0] - xcm[0];
- dy = unwrap[1] - xcm[1];
- dz = unwrap[2] - xcm[2];
-
- tcm = b->torque;
- tcm[0] += dy*f[i][2] - dz*f[i][1];
- tcm[1] += dz*f[i][0] - dx*f[i][2];
- tcm[2] += dx*f[i][1] - dy*f[i][0];
- }
-
- // extended particles add their torque to torque of body
-
- if (extended) {
- double **torque = atom->torque;
-
- for (i = 0; i < nlocal; i++) {
- if (atom2body[i] < 0) continue;
-
- if (eflags[i] & TORQUE) {
- tcm = body[atom2body[i]].torque;
- tcm[0] += torque[i][0];
- tcm[1] += torque[i][1];
- tcm[2] += torque[i][2];
- }
- }
- }
-
- // reverse communicate fcm, torque of all bodies
-
- commflag = FORCE_TORQUE;
- comm->reverse_comm_fix(this,6);
-
- // include Langevin thermostat forces and torques
-
- if (langflag) {
- for (int ibody = 0; ibody < nlocal_body; ibody++) {
- fcm = body[ibody].fcm;
- fcm[0] += langextra[ibody][0];
- fcm[1] += langextra[ibody][1];
- fcm[2] += langextra[ibody][2];
- tcm = body[ibody].torque;
- tcm[0] += langextra[ibody][3];
- tcm[1] += langextra[ibody][4];
- tcm[2] += langextra[ibody][5];
- }
- }
+ if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom
// include Langevin thermostat forces
@@ -1440,7 +1369,7 @@ int FixRigidNHSmall::modify_param(int narg, char **arg)
return 2;
}
- return 0;
+ return FixRigidSmall::modify_param(narg,arg);
}
/* ---------------------------------------------------------------------- */
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index e5ccd5ec1591cca90b1a08274dd67480e980740c..d0cb596c82c8736af9a0e92457224e021c0c7f41 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -457,6 +457,10 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
avec_line = (AtomVecLine *) atom->style_match("line");
avec_tri = (AtomVecTri *) atom->style_match("tri");
+ // compute per body forces and torques inside final_integrate() by default
+
+ earlyflag = 0;
+
// print statistics
int one = 0;
@@ -555,9 +559,22 @@ void FixRigidSmall::init()
int count = 0;
for (i = 0; i < modify->nfix; i++)
- if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
+ if (modify->fix[i]->rigid_flag) count++;
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
+ if (earlyflag) {
+ int rflag = 0;
+ for (i = 0; i < modify->nfix; i++) {
+ if (modify->fix[i]->rigid_flag) rflag = 1;
+ if (rflag && (modify->fmask[i] & POST_FORCE) &&
+ !modify->fix[i]->rigid_flag) {
+ char str[128];
+ sprintf(str,"Fix %d alters forces after fix rigid",modify->fix[i]->id);
+ error->warning(FLERR,str);
+ }
+ }
+ }
+
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
@@ -770,10 +787,10 @@ void FixRigidSmall::initial_integrate(int vflag)
/* ----------------------------------------------------------------------
apply Langevin thermostat to all 6 DOF of rigid bodies I own
unlike fix langevin, this stores extra force in extra arrays,
- which are added in when final_integrate() calculates a new fcm/torque
+ which are added in when a new fcm/torque are calculated
------------------------------------------------------------------------- */
-void FixRigidSmall::post_force(int vflag)
+void FixRigidSmall::apply_langevin_thermostat()
{
double gamma1,gamma2;
@@ -850,10 +867,18 @@ void FixRigidSmall::enforce2d()
/* ---------------------------------------------------------------------- */
-void FixRigidSmall::final_integrate()
+void FixRigidSmall::post_force(int vflag)
+{
+ if (langflag) apply_langevin_thermostat();
+ if (earlyflag) compute_forces_and_torques();
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidSmall::compute_forces_and_torques()
{
int i,ibody;
- double dtfm;
//check(3);
@@ -931,6 +956,18 @@ void FixRigidSmall::final_integrate()
tcm[2] += langextra[ibody][5];
}
}
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidSmall::final_integrate()
+{
+ double dtfm;
+
+ //check(3);
+
+ if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom, recompute omega
@@ -3384,6 +3421,33 @@ void FixRigidSmall::zero_rotation()
/* ---------------------------------------------------------------------- */
+int FixRigidSmall::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"bodyforces") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (strcmp(arg[1],"early") == 0) earlyflag = 1;
+ else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
+ else error->all(FLERR,"Illegal fix_modify command");
+
+ // reset fix mask
+ // must do here and not in init,
+ // since modify.cpp::init() uses fix masks before calling fix::init()
+
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->id,id) == 0) {
+ if (earlyflag) modify->fmask[i] |= POST_FORCE;
+ else if (!langflag) modify->fmask[i] &= ~POST_FORCE;
+ break;
+ }
+
+ return 2;
+ }
+
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
void *FixRigidSmall::extract(const char *str, int &dim)
{
if (strcmp(str,"body") == 0) {
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index 493185104f8b2d9fe4b7128303a7b5f0908c9ce8..3f6826f9bb140bf131d1ccb2a4c260fee6fd01e5 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -63,6 +63,7 @@ class FixRigidSmall : public Fix {
void reset_dt();
void zero_momentum();
void zero_rotation();
+ int modify_param(int, char **);
void *extract(const char*, int &);
double extract_ke();
double extract_erotational();
@@ -78,6 +79,7 @@ class FixRigidSmall : public Fix {
char *infile; // file to read rigid body attributes from
int setupflag; // 1 if body properties are setup, else 0
+ int earlyflag; // 1 if forces/torques are computed at post_force()
int commflag; // various modes of forward/reverse comm
int customflag; // 1 if custom property/variable define bodies
int nbody; // total # of rigid bodies
@@ -191,6 +193,8 @@ class FixRigidSmall : public Fix {
void create_bodies(tagint *);
void setup_bodies_static();
void setup_bodies_dynamic();
+ void apply_langevin_thermostat();
+ void compute_forces_and_torques();
void readfile(int, double **, int *);
void grow_body();
void reset_atom2body();
diff --git a/src/USER-BOCS/README b/src/USER-BOCS/README
new file mode 100644
index 0000000000000000000000000000000000000000..adeb34c38729a3614df738333bb64c6565c3dec7
--- /dev/null
+++ b/src/USER-BOCS/README
@@ -0,0 +1,19 @@
+This user package implements the pressure correction to the barostat as
+outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+doi: 10.1063/1.4937383
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+https://github.com/noid-group/BOCS
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..fc24efab4c52e27529b225c67f37393d7c500b01
--- /dev/null
+++ b/src/USER-BOCS/compute_pressure_bocs.cpp
@@ -0,0 +1,444 @@
+/* ----------------------------------------------------------------------
+ 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.
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+ from The Pennsylvania State University
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <cstring>
+#include <cstdlib>
+#include "compute_pressure_bocs.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "force.h"
+#include "pair.h"
+#include "bond.h"
+#include "angle.h"
+#include "dihedral.h"
+#include "improper.h"
+#include "kspace.h"
+#include "error.h"
+
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg),
+ vptr(NULL), id_temp(NULL)
+{
+ if (narg < 4) error->all(FLERR,"Illegal compute pressure/bocs command");
+ if (igroup) error->all(FLERR,"Compute pressure/bocs must use group all");
+
+ scalar_flag = vector_flag = 1;
+ size_vector = 6;
+ extscalar = 0;
+ extvector = 0;
+ pressflag = 1;
+ timeflag = 1;
+
+ p_match_flag = 0;
+ phi_coeff = NULL;
+
+ // store temperature ID used by pressure computation
+ // insure it is valid for temperature computation
+
+ if (strcmp(arg[3],"NULL") == 0) id_temp = NULL;
+ else {
+ int n = strlen(arg[3]) + 1;
+ id_temp = new char[n];
+ strcpy(id_temp,arg[3]);
+
+ int icompute = modify->find_compute(id_temp);
+ if (icompute < 0)
+ error->all(FLERR,"Could not find compute pressure/bocs temperature ID");
+ if (modify->compute[icompute]->tempflag == 0)
+ error->all(FLERR,"Compute pressure/bocs temperature ID does not "
+ "compute temperature");
+ }
+
+ // process optional args
+
+ if (narg == 4) {
+ keflag = 1;
+ pairflag = 1;
+ bondflag = angleflag = dihedralflag = improperflag = 1;
+ kspaceflag = fixflag = 1;
+ } else {
+ keflag = 0;
+ pairflag = 0;
+ bondflag = angleflag = dihedralflag = improperflag = 0;
+ kspaceflag = fixflag = 0;
+ int iarg = 4;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
+ else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
+ else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
+ else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
+ else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
+ else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
+ else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
+ else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
+ else if (strcmp(arg[iarg],"virial") == 0) {
+ pairflag = 1;
+ bondflag = angleflag = dihedralflag = improperflag = 1;
+ kspaceflag = fixflag = 1;
+ } else error->all(FLERR,"Illegal compute pressure/bocs command");
+ iarg++;
+ }
+ }
+
+ // error check
+
+ if (keflag && id_temp == NULL)
+ error->all(FLERR,"Compute pressure/bocs requires temperature ID "
+ "to include kinetic energy");
+
+ vector = new double[6];
+ nvirial = 0;
+ vptr = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputePressureBocs::~ComputePressureBocs()
+{
+ delete [] id_temp;
+ delete [] vector;
+ delete [] vptr;
+ if (phi_coeff) free(phi_coeff);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePressureBocs::init()
+{
+ boltz = force->boltz;
+ nktv2p = force->nktv2p;
+ dimension = domain->dimension;
+
+ // set temperature compute, must be done in init()
+ // fixes could have changed or compute_modify could have changed it
+
+ if (keflag) {
+ int icompute = modify->find_compute(id_temp);
+ if (icompute < 0)
+ error->all(FLERR,"Could not find compute pressure/bocs temperature ID");
+ temperature = modify->compute[icompute];
+ }
+
+ // detect contributions to virial
+ // vptr points to all virial[6] contributions
+
+ delete [] vptr;
+ nvirial = 0;
+ vptr = NULL;
+
+ if (pairflag && force->pair) nvirial++;
+ if (bondflag && atom->molecular && force->bond) nvirial++;
+ if (angleflag && atom->molecular && force->angle) nvirial++;
+ if (dihedralflag && atom->molecular && force->dihedral) nvirial++;
+ if (improperflag && atom->molecular && force->improper) nvirial++;
+ if (fixflag)
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->virial_flag) nvirial++;
+
+ if (nvirial) {
+ vptr = new double*[nvirial];
+ nvirial = 0;
+ if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial;
+ if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial;
+ if (angleflag && force->angle) vptr[nvirial++] = force->angle->virial;
+ if (dihedralflag && force->dihedral)
+ vptr[nvirial++] = force->dihedral->virial;
+ if (improperflag && force->improper)
+ vptr[nvirial++] = force->improper->virial;
+ if (fixflag)
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->virial_flag)
+ vptr[nvirial++] = modify->fix[i]->virial;
+ }
+
+ // flag Kspace contribution separately, since not summed across procs
+
+ if (kspaceflag && force->kspace) kspace_virial = force->kspace->virial;
+ else kspace_virial = NULL;
+}
+
+/* Extra functions added for BOCS */
+
+/* ----------------------------------------------------------------------
+ Compute the pressure correction for the analytical basis set
+------------------------------------------------------------------------- */
+double ComputePressureBocs::get_cg_p_corr(int N_basis, double *phi_coeff,
+ int N_mol, double vavg, double vCG)
+{
+ double correction = 0.0;
+ for (int i = 1; i <= N_basis; ++i)
+ {
+ correction -= phi_coeff[i-1] * ( N_mol * i / vavg ) *
+ pow( ( 1 / vavg ) * ( vCG - vavg ),i-1);
+ }
+ return correction;
+}
+
+/* ----------------------------------------------------------------------
+ Find the relevant index position if using a spline basis set
+------------------------------------------------------------------------- */
+double ComputePressureBocs::find_index(double * grid, double value)
+{
+ int i;
+ double spacing = fabs(grid[1]-grid[0]);
+ int gridsize = spline_length;
+ for (i = 0; i < (gridsize-1); ++i)
+ {
+ if (value >= grid[i] && value <= grid[i+1]) { return i; }
+ }
+
+ if (value >= grid[i] && value <= (grid[i] + spacing)) { return i; }
+
+ for (int i = 0; i < gridsize; ++i)
+ {
+ fprintf(stderr, "grid %d: %f\n",i,grid[i]);
+ }
+ char * errmsg = (char *) calloc(100,sizeof(char));
+ sprintf(errmsg,"Value %f does not fall within spline grid.\n",value);
+ error->all(FLERR,errmsg);
+
+ exit(1);
+}
+
+/* ----------------------------------------------------------------------
+ Compute the pressure correction for a spline basis set
+------------------------------------------------------------------------- */
+
+double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
+ double vCG)
+{
+ int i = find_index(grid[0],vCG);
+ double correction, deltax = vCG - grid[0][i];
+
+ if (basis_type == 1)
+ {
+ correction = grid[1][i] + (deltax) *
+ ( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] );
+ }
+ else if (basis_type == 2)
+ {
+ correction = grid[1][i] + (grid[2][i] * deltax) +
+ (grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
+ }
+ else
+ {
+ error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n");
+ }
+ return correction;
+}
+
+/* ----------------------------------------------------------------------
+ send cg info from fix_bocs to compute_pressure_bocs for the analytical
+ basis set
+------------------------------------------------------------------------- */
+void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
+ double *sent_phi_coeff, int sent_N_mol, double sent_vavg)
+{
+ if (basis_type == 0) { p_basis_type = 0; }
+ else
+ {
+ error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
+ }
+
+ p_match_flag = 1;
+
+ N_basis = sent_N_basis;
+ if (phi_coeff) free(phi_coeff);
+ phi_coeff = ((double *) calloc(N_basis, sizeof(double)) );
+ for (int i=0; i<N_basis; i++) { phi_coeff[i] = sent_phi_coeff[i]; }
+
+ N_mol = sent_N_mol;
+ vavg = sent_vavg;
+}
+
+/* ----------------------------------------------------------------------
+ send cg info from fix_bocs to compute_pressure_bocs for a spline basis
+ set
+------------------------------------------------------------------------- */
+void ComputePressureBocs::send_cg_info(int basis_type,
+ double ** in_splines, int gridsize)
+{
+ if (basis_type == 1) { p_basis_type = 1; }
+ else if (basis_type == 2) { p_basis_type = 2; }
+ else
+ {
+ error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
+ }
+ splines = in_splines;
+ spline_length = gridsize;
+ p_match_flag = 1;
+}
+
+/* End of new functions for BOCS */
+
+/* ----------------------------------------------------------------------
+ compute total pressure, averaged over Pxx, Pyy, Pzz
+------------------------------------------------------------------------- */
+double ComputePressureBocs::compute_scalar()
+{
+ invoked_scalar = update->ntimestep;
+ if (update->vflag_global != invoked_scalar)
+ error->all(FLERR,"Virial was not tallied on needed timestep");
+
+ // invoke temperature if it hasn't been already
+
+ double t;
+ double volume, correction = 0;
+ if (keflag) {
+ if (temperature->invoked_scalar != update->ntimestep)
+ t = temperature->compute_scalar();
+ else t = temperature->scalar;
+ }
+
+ if (dimension == 3) {
+ inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+ volume = (domain->xprd * domain->yprd * domain->zprd);
+
+ /* MRD NJD if block */
+ if ( p_basis_type == 0 )
+ {
+ correction = get_cg_p_corr(N_basis,phi_coeff,N_mol,vavg,volume);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ correction = get_cg_p_corr(splines, p_basis_type, volume);
+ }
+
+ virial_compute(3,3);
+ if (keflag)
+ scalar = (temperature->dof * boltz * t +
+ virial[0] + virial[1] + virial[2]) / 3.0 *
+ inv_volume * nktv2p + (correction);
+ else
+ scalar = (virial[0] + virial[1] + virial[2]) / 3.0 *
+ inv_volume * nktv2p + (correction);
+ } else {
+ if (p_match_flag)
+ {
+ error->all(FLERR,"Pressure matching not implemented in 2-d.\n");
+ exit(1);
+ } // The rest of this can probably be deleted.
+ inv_volume = 1.0 / (domain->xprd * domain->yprd);
+ virial_compute(2,2);
+ if (keflag)
+ scalar = (temperature->dof * boltz * t +
+ virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
+ else
+ scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
+ }
+
+ return scalar;
+}
+
+/* ----------------------------------------------------------------------
+ compute pressure tensor
+ assume KE tensor has already been computed
+------------------------------------------------------------------------- */
+
+void ComputePressureBocs::compute_vector()
+{
+ invoked_vector = update->ntimestep;
+ if (update->vflag_global != invoked_vector)
+ error->all(FLERR,"Virial was not tallied on needed timestep");
+
+ if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
+ error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
+ "tensor components with kspace_style msm");
+
+ // invoke temperature if it hasn't been already
+
+ double *ke_tensor;
+ if (keflag) {
+ if (temperature->invoked_vector != update->ntimestep)
+ temperature->compute_vector();
+ ke_tensor = temperature->vector;
+ }
+
+ if (dimension == 3) {
+ inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+ virial_compute(6,3);
+ if (keflag) {
+ for (int i = 0; i < 6; i++)
+ vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
+ } else
+ for (int i = 0; i < 6; i++)
+ vector[i] = virial[i] * inv_volume * nktv2p;
+ } else {
+ inv_volume = 1.0 / (domain->xprd * domain->yprd);
+ virial_compute(4,2);
+ if (keflag) {
+ vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
+ vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
+ vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
+ vector[2] = vector[4] = vector[5] = 0.0;
+ } else {
+ vector[0] = virial[0] * inv_volume * nktv2p;
+ vector[1] = virial[1] * inv_volume * nktv2p;
+ vector[3] = virial[3] * inv_volume * nktv2p;
+ vector[2] = vector[4] = vector[5] = 0.0;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePressureBocs::virial_compute(int n, int ndiag)
+{
+ int i,j;
+ double v[6],*vcomponent;
+
+ for (i = 0; i < n; i++) v[i] = 0.0;
+
+ // sum contributions to virial from forces and fixes
+
+ for (j = 0; j < nvirial; j++) {
+ vcomponent = vptr[j];
+ for (i = 0; i < n; i++) v[i] += vcomponent[i];
+ }
+
+ // sum virial across procs
+
+ MPI_Allreduce(v,virial,n,MPI_DOUBLE,MPI_SUM,world);
+
+ // KSpace virial contribution is already summed across procs
+
+ if (kspace_virial)
+ for (i = 0; i < n; i++) virial[i] += kspace_virial[i];
+
+ // LJ long-range tail correction, only if pair contributions are included
+
+ if (force->pair && pairflag && force->pair->tail_flag)
+ for (i = 0; i < ndiag; i++) virial[i] += force->pair->ptail * inv_volume;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePressureBocs::reset_extra_compute_fix(const char *id_new)
+{
+ delete [] id_temp;
+ int n = strlen(id_new) + 1;
+ id_temp = new char[n];
+ strcpy(id_temp,id_new);
+}
diff --git a/src/USER-BOCS/compute_pressure_bocs.h b/src/USER-BOCS/compute_pressure_bocs.h
new file mode 100644
index 0000000000000000000000000000000000000000..4fb932c5082473e2b3c111774dd78c1675ad6ec4
--- /dev/null
+++ b/src/USER-BOCS/compute_pressure_bocs.h
@@ -0,0 +1,114 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ 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.
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+ from The Pennsylvania State University
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(PRESSURE/BOCS,ComputePressureBocs)
+
+#else
+
+
+#ifndef LMP_COMPUTE_PRESSURE_BOCS_H
+#define LMP_COMPUTE_PRESSURE_BOCS_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+// ComputePressure -> ComputePressureBocs MRD NJD
+class ComputePressureBocs : public Compute {
+ public:
+ ComputePressureBocs(class LAMMPS *, int, char **);
+ virtual ~ComputePressureBocs();
+ virtual void init();
+ virtual double compute_scalar();
+ virtual void compute_vector();
+ void reset_extra_compute_fix(const char *);
+
+ double compute_cg_scalar();
+ double get_cg_p_corr(int, double *, int, double, double);
+ double get_cg_fluct(double, double);
+ void send_cg_info(int, int, double*, int, double);
+ void send_cg_info(int, double **, int);
+ double get_cg_p_corr(double **, int, double);
+ double find_index(double* , double);
+
+ protected:
+ double boltz,nktv2p,inv_volume;
+ int nvirial,dimension;
+ double **vptr;
+ double *kspace_virial;
+ Compute *temperature;
+ char *id_temp;
+ double virial[6];
+ int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;
+ int fixflag,kspaceflag;
+
+// NJD MRD
+ int p_basis_type;
+ int p_match_flag;
+ double vavg;
+ int N_mol;
+ int N_basis;
+ double *phi_coeff;
+ double ** splines;
+ int spline_length;
+
+ void virial_compute(int, int);
+};
+
+}
+
+#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: Compute pressure must use group all
+
+Virial contributions computed by potentials (pair, bond, etc) are
+computed on all atoms.
+
+E: Could not find compute pressure temperature ID
+
+The compute ID for calculating temperature does not exist.
+
+E: Compute pressure temperature ID does not compute temperature
+
+The compute ID assigned to a pressure computation must compute
+temperature.
+
+E: Compute pressure requires temperature ID to include kinetic energy
+
+The keflag cannot be used unless a temperature compute is provided.
+
+E: Virial was not tallied on needed timestep
+
+You are using a thermo keyword that requires potentials to
+have tallied the virial, but they didn't on this timestep. See the
+variable doc page for ideas on how to make this work.
+
+E: Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm
+
+Otherwise MSM will compute only a scalar pressure. See the kspace_modify
+command for details on this setting.
+
+*/
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..37e128f55662a6e6c9152abb518d3233845604fd
--- /dev/null
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -0,0 +1,2431 @@
+/* ----------------------------------------------------------------------
+ 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.
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+ from The Pennsylvania State University
+------------------------------------------------------------------------- */
+
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
+#include "fix_bocs.h"
+#include "math_extra.h"
+#include "atom.h"
+#include "force.h"
+#include "group.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "irregular.h"
+#include "modify.h"
+#include "fix_deform.h"
+#include "compute.h"
+#include "kspace.h"
+#include "update.h"
+#include "respa.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+#include "citeme.h"
+
+#include "compute_pressure_bocs.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+static const char cite_user_bocs_package[] =
+ "USER-BOCS package:\n\n"
+ "@Article{Dunn2018,\n"
+ " author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n"
+ " title = {BOCS: Bottom-Up Open-Source Coarse-Graining Software},\n"
+ " journal = {J. Phys. Chem. B},\n"
+ " year = 2018,\n"
+ " volume = 122,\n"
+ " pages = {3363--3377}\n"
+ "}\n\n";
+
+
+#define DELTAFLIP 0.1
+#define TILTMAX 1.5
+
+enum{NOBIAS,BIAS};
+enum{NONE,XYZ,XY,YZ,XZ};
+enum{ISO,ANISO,TRICLINIC};
+
+/* ----------------------------------------------------------------------
+ NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
+ ---------------------------------------------------------------------- */
+
+FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg),
+ rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL),
+ eta(NULL), eta_dot(NULL), eta_dotdot(NULL),
+ eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL),
+ etap_mass(NULL)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_user_bocs_package);
+
+ if (narg < 4) error->all(FLERR,"Illegal fix bocs command");
+
+ restart_global = 1;
+ dynamic_group_allow = 1;
+ time_integrate = 1;
+ scalar_flag = 1;
+ vector_flag = 1;
+ global_freq = 1;
+ extscalar = 1;
+ extvector = 0;
+
+ // default values
+
+ pcouple = NONE;
+ drag = 0.0;
+ allremap = 1;
+ id_dilate = NULL;
+ mtchain = mpchain = 3;
+ nc_tchain = nc_pchain = 1;
+ mtk_flag = 1;
+ deviatoric_flag = 0;
+ nreset_h0 = 0;
+ eta_mass_flag = 1;
+ omega_mass_flag = 0;
+ etap_mass_flag = 0;
+ flipflag = 1;
+ dipole_flag = 0;
+ dlm_flag = 0;
+
+ tcomputeflag = 0;
+ pcomputeflag = 0;
+ id_temp = NULL;
+ id_press = NULL;
+
+ p_match_coeffs = NULL;
+
+ // turn on tilt factor scaling, whenever applicable
+
+ dimension = domain->dimension;
+
+ scaleyz = scalexz = scalexy = 0;
+ if (domain->yperiodic && domain->xy != 0.0) scalexy = 1;
+ if (domain->zperiodic && dimension == 3) {
+ if (domain->yz != 0.0) scaleyz = 1;
+ if (domain->xz != 0.0) scalexz = 1;
+ }
+
+ // set fixed-point to default = center of cell
+
+ fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
+ fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
+ fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
+
+ // used by FixNVTSllod to preserve non-default value
+
+ mtchain_default_flag = 1;
+
+ tstat_flag = 0;
+ double t_period = 0.0;
+
+ double p_period[6];
+ for (int i = 0; i < 6; i++) {
+ p_start[i] = p_stop[i] = p_period[i] = p_target[i] = 0.0;
+ p_flag[i] = 0;
+ }
+
+ // process keywords
+
+ int iarg = 3;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"temp") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix bocs command");
+ tstat_flag = 1;
+ t_start = force->numeric(FLERR,arg[iarg+1]);
+ t_target = t_start;
+ t_stop = force->numeric(FLERR,arg[iarg+2]);
+ t_period = force->numeric(FLERR,arg[iarg+3]);
+ if (t_start <= 0.0 || t_stop <= 0.0)
+ error->all(FLERR,
+ "Target temperature for fix bocs cannot be 0.0");
+ iarg += 4;
+ } else if (strcmp(arg[iarg],"iso") == 0) {
+ error->all(FLERR,"Illegal fix bocs command. Pressure fix must be "
+ "cgiso . Use regular fix bocs for iso"); // MRD NJD
+ } else if (strcmp(arg[iarg],"cgiso") == 0) { // MRD NJD the whole else if
+ if (iarg+4 > narg)
+ error->all(FLERR,"Illegal fix bocs command. cgiso must be "
+ "followed by: P_0 P_f P_coupl");
+ p_match_flag = 1;
+ pcouple = XYZ;
+ p_start[0] = p_start[1] = p_start[2] =
+ force->numeric(FLERR,arg[iarg+1]);
+ p_stop[0] = p_stop[1] = p_stop[2] =
+ force->numeric(FLERR,arg[iarg+2]);
+ p_period[0] = p_period[1] = p_period[2] =
+ force->numeric(FLERR,arg[iarg+3]);
+
+ p_flag[0] = p_flag[1] = p_flag[2] = 1;
+ p_flag[3] = p_flag[4] = p_flag[5] = 0; // MRD
+ if (dimension == 2) { // Later I force 3D... MRD
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
+ }
+ iarg += 4;
+
+ if ( strcmp(arg[iarg], "analytic") == 0 ) {
+ if (iarg + 4 > narg) {
+ error->all(FLERR,"Illegal fix bocs command. basis type analytic"
+ " must be followed by: avg_vol n_mol n_pmatch_coeff");
+ }
+ p_basis_type = 0;
+ vavg = force->numeric(FLERR,arg[iarg+1]);
+ N_mol = force->inumeric(FLERR,arg[iarg+2]);
+ N_p_match = force->inumeric(FLERR,arg[iarg+3]);
+ p_match_coeffs = (double *) (calloc(N_p_match, sizeof(double)) );
+ iarg += 4;
+ if (iarg + N_p_match > narg)
+ error->all(FLERR,"Illegal fix bocs command. Missing coeffs.");
+ for (int pmatchi = 0; pmatchi < N_p_match; pmatchi++)
+ p_match_coeffs[pmatchi] = force->numeric(FLERR,arg[iarg+pmatchi]);
+ iarg += (N_p_match);
+ } else if (strcmp(arg[iarg], "linear_spline") == 0 ) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. "
+ "Supply a file name after linear_spline.");
+ p_basis_type = 1;
+ spline_length = read_F_table( arg[iarg+1], p_basis_type );
+ iarg += 2;
+ } else if (strcmp(arg[iarg], "cubic_spline") == 0 ) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. "
+ "Supply a file name after cubic_spline.");
+ p_basis_type = 2;
+ spline_length = read_F_table( arg[iarg+1], p_basis_type );
+ iarg += 2;
+ } else
+ {
+ char * errmsg = (char *) calloc(150,sizeof(char));
+ sprintf(errmsg,"CG basis type %s is not recognized\nSupported "
+ "basis types: analytic linear_spline cubic_spline",arg[iarg]);
+ error->all(FLERR,errmsg);
+ } // END NJD MRD
+ } else if (strcmp(arg[iarg],"tchain") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ mtchain = force->inumeric(FLERR,arg[iarg+1]);
+ // used by FixNVTSllod to preserve non-default value
+ mtchain_default_flag = 0;
+ if (mtchain < 1) error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"pchain") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ mpchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (mpchain < 0) error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"mtk") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0;
+ else error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"tloop") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ nc_tchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (nc_tchain < 0) error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"ploop") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ nc_pchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (nc_pchain < 0) error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else {
+ char * errmsg = (char *) calloc(80,sizeof(char));
+ sprintf(errmsg,"Illegal fix bocs command: unrecognized keyword %s"
+ ,arg[iarg]);
+ error->all(FLERR,errmsg);
+ }
+ }
+ // error checks
+
+ if (dimension != 3) // MRD NJD
+ error->all(FLERR,"Invalid fix bocs command. Must use 3 dimensions");
+
+// With cgiso, p_flag[0] = p_flag[1] = p_flag[2] = 1
+
+ // require periodicity in tensile dimension
+
+ if (p_flag[0] && domain->xperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+ if (p_flag[1] && domain->yperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+ if (p_flag[2] && domain->zperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+
+ if (dipole_flag) {
+ if (!atom->sphere_flag)
+ error->all(FLERR,"Using update dipole flag requires atom style sphere");
+ if (!atom->mu_flag)
+ error->all(FLERR,"Using update dipole flag requires atom attribute mu");
+ }
+
+ if ((tstat_flag && t_period <= 0.0) ||
+ (p_flag[0] && p_period[0] <= 0.0) ||
+ (p_flag[1] && p_period[1] <= 0.0) ||
+ (p_flag[2] && p_period[2] <= 0.0) ||
+ (p_flag[3] && p_period[3] <= 0.0) ||
+ (p_flag[4] && p_period[4] <= 0.0) ||
+ (p_flag[5] && p_period[5] <= 0.0))
+ error->all(FLERR,"Fix bocs damping parameters must be > 0.0");
+
+ // set pstat_flag and box change and restart_pbc variables
+
+ pre_exchange_flag = 0;
+ pstat_flag = 0;
+ pstyle = ISO;
+
+ for (int i = 0; i < 6; i++)
+ if (p_flag[i]) pstat_flag = 1;
+
+ if (pstat_flag) {
+ if (p_flag[0] || p_flag[1] || p_flag[2]) box_change_size = 1;
+ if (p_flag[3] || p_flag[4] || p_flag[5]) box_change_shape = 1;
+ no_change_box = 1;
+ if (allremap == 0) restart_pbc = 1;
+
+ pstyle = ISO; // MRD this is the only one that can happen
+
+ // pre_exchange only required if flips can occur due to shape changes
+
+ if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5]))
+ pre_exchange_flag = 1;
+ if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 ||
+ domain->xy != 0.0))
+ pre_exchange_flag = 1;
+ }
+
+ // convert input periods to frequencies
+
+ t_freq = 0.0;
+ p_freq[0] = p_freq[1] = p_freq[2] = p_freq[3] = p_freq[4] = p_freq[5] = 0.0;
+
+ if (tstat_flag) t_freq = 1.0 / t_period;
+ if (p_flag[0]) p_freq[0] = 1.0 / p_period[0];
+ if (p_flag[1]) p_freq[1] = 1.0 / p_period[1];
+ if (p_flag[2]) p_freq[2] = 1.0 / p_period[2];
+ if (p_flag[3]) p_freq[3] = 1.0 / p_period[3];
+ if (p_flag[4]) p_freq[4] = 1.0 / p_period[4];
+ if (p_flag[5]) p_freq[5] = 1.0 / p_period[5];
+
+ // Nose/Hoover temp and pressure init
+
+ size_vector = 0;
+
+ if (tstat_flag) {
+ int ich;
+ eta = new double[mtchain];
+
+ // add one extra dummy thermostat, set to zero
+
+ eta_dot = new double[mtchain+1];
+ eta_dot[mtchain] = 0.0;
+ eta_dotdot = new double[mtchain];
+ for (ich = 0; ich < mtchain; ich++) {
+ eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0;
+ }
+ eta_mass = new double[mtchain];
+ size_vector += 2*2*mtchain;
+ }
+
+ if (pstat_flag) {
+ omega[0] = omega[1] = omega[2] = 0.0;
+ omega_dot[0] = omega_dot[1] = omega_dot[2] = 0.0;
+ omega_mass[0] = omega_mass[1] = omega_mass[2] = 0.0;
+ omega[3] = omega[4] = omega[5] = 0.0;
+ omega_dot[3] = omega_dot[4] = omega_dot[5] = 0.0;
+ omega_mass[3] = omega_mass[4] = omega_mass[5] = 0.0;
+ if (pstyle == ISO) size_vector += 2*2*1;
+ else if (pstyle == ANISO) size_vector += 2*2*3;
+ else if (pstyle == TRICLINIC) size_vector += 2*2*6;
+
+ if (mpchain) {
+ int ich;
+ etap = new double[mpchain];
+
+ // add one extra dummy thermostat, set to zero
+
+ etap_dot = new double[mpchain+1];
+ etap_dot[mpchain] = 0.0;
+ etap_dotdot = new double[mpchain];
+ for (ich = 0; ich < mpchain; ich++) {
+ etap[ich] = etap_dot[ich] =
+ etap_dotdot[ich] = 0.0;
+ }
+ etap_mass = new double[mpchain];
+ size_vector += 2*2*mpchain;
+ }
+
+ if (deviatoric_flag) size_vector += 1;
+ }
+
+ nrigid = 0;
+ rfix = NULL;
+
+ if (pre_exchange_flag) irregular = new Irregular(lmp);
+ else irregular = NULL;
+
+ // initialize vol0,t0 to zero to signal uninitialized
+ // values then assigned in init(), if necessary
+
+ vol0 = t0 = 0.0;
+
+ /*~ MRD I copied this from fix_npt.cpp 8/17/17 ~*/
+
+ if (!tstat_flag)
+ error->all(FLERR,"Temperature control must be used with fix bocs");
+ if (!pstat_flag)
+ error->all(FLERR,"Pressure control must be used with fix bocs");
+
+ // create a new compute temp style
+ // id = fix-ID + temp
+ // compute group = all since pressure is always global (group all)
+ // and thus its KE/temperature contribution should use group all
+
+
+ int n = strlen(id) + 6;
+ id_temp = new char[n];
+ strcpy(id_temp,id);
+ strcat(id_temp,"_temp");
+
+ char **newarg = new char*[3];
+ newarg[0] = id_temp;
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "temp";
+
+
+ modify->add_compute(3,newarg);
+ delete [] newarg;
+ tcomputeflag = 1;
+
+ // create a new compute pressure style
+ // id = fix-ID + press, compute group = all
+ // pass id_temp as 4th arg to pressure constructor
+
+ n = strlen(id) + 7;
+ id_press = new char[n];
+ strcpy(id_press,id);
+ strcat(id_press,"_press");
+
+ newarg = new char*[4];
+ newarg[0] = id_press;
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "PRESSURE/BOCS";
+ newarg[3] = id_temp;
+ modify->add_compute(4,newarg);
+ delete [] newarg;
+ pcomputeflag = 1;
+
+/*~ MRD End of stuff copied from fix_npt.cpp~*/
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixBocs::~FixBocs()
+{
+ if (copymode) return;
+
+ delete [] id_dilate;
+ delete [] rfix;
+
+ delete irregular;
+
+ // delete temperature and pressure if fix created them
+
+ if (tcomputeflag) modify->delete_compute(id_temp);
+ delete [] id_temp;
+
+ if (tstat_flag) {
+ delete [] eta;
+ delete [] eta_dot;
+ delete [] eta_dotdot;
+ delete [] eta_mass;
+ }
+
+ if (pstat_flag) {
+ if (pcomputeflag) modify->delete_compute(id_press);
+ delete [] id_press;
+ if (mpchain) {
+ delete [] etap;
+ delete [] etap_dot;
+ delete [] etap_dotdot;
+ delete [] etap_mass;
+ }
+ }
+ if (p_match_coeffs) free(p_match_coeffs);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBocs::setmask()
+{
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ mask |= THERMO_ENERGY;
+ mask |= INITIAL_INTEGRATE_RESPA;
+ mask |= FINAL_INTEGRATE_RESPA;
+ if (pre_exchange_flag) mask |= PRE_EXCHANGE;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::init()
+{
+ // recheck that dilate group has not been deleted
+ if (allremap == 0) {
+ int idilate = group->find(id_dilate);
+ if (idilate == -1)
+ error->all(FLERR,"Fix bocs dilate group ID does not exist");
+ dilate_group_bit = group->bitmask[idilate];
+ }
+
+ // ensure no conflict with fix deform
+
+ if (pstat_flag)
+ {
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->style,"deform") == 0) {
+ int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
+ if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
+ (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
+ (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
+ error->all(FLERR,"Cannot use fix bocs and fix deform on "
+ "same component of stress tensor");
+ }
+ }
+
+ // set temperature and pressure ptrs
+ int icompute = modify->find_compute(id_temp);
+ if (icompute < 0)
+ error->all(FLERR,"Temperature ID for fix bocs does not exist");
+ temperature = modify->compute[icompute];
+
+ if (temperature->tempbias) which = BIAS;
+ else which = NOBIAS;
+
+ if (pstat_flag) {
+ icompute = modify->find_compute(id_press);
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix bocs does not exist");
+ pressure = modify->compute[icompute];
+ }
+
+
+ if (pstat_flag)
+ {
+ if (p_match_flag) // MRD NJD
+ {
+ if (pressure)
+ {
+ if (p_basis_type == 0)
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
+ N_p_match, p_match_coeffs, N_mol, vavg);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
+ splines, spline_length);
+ }
+ }
+ else
+ {
+ error->all(FLERR,"Unable to find pressure. Are you sure you included"
+ " the compute bocsPress and fix_modify commands?");
+ }
+ }
+ }
+
+
+ // set timesteps and frequencies
+
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ dthalf = 0.5 * update->dt;
+ dt4 = 0.25 * update->dt;
+ dt8 = 0.125 * update->dt;
+ dto = dthalf;
+
+ p_freq_max = 0.0;
+ if (pstat_flag) {
+ p_freq_max = MAX(p_freq[0],p_freq[1]);
+ p_freq_max = MAX(p_freq_max,p_freq[2]);
+ if (pstyle == TRICLINIC) {
+ p_freq_max = MAX(p_freq_max,p_freq[3]);
+ p_freq_max = MAX(p_freq_max,p_freq[4]);
+ p_freq_max = MAX(p_freq_max,p_freq[5]);
+ }
+ pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
+ }
+
+ if (tstat_flag)
+ tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
+
+ // tally the number of dimensions that are barostatted
+ // set initial volume and reference cell, if not already done
+
+ if (pstat_flag) {
+ pdim = p_flag[0] + p_flag[1] + p_flag[2];
+ if (vol0 == 0.0) {
+ if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
+ else vol0 = domain->xprd * domain->yprd;
+ h0_inv[0] = domain->h_inv[0];
+ h0_inv[1] = domain->h_inv[1];
+ h0_inv[2] = domain->h_inv[2];
+ h0_inv[3] = domain->h_inv[3];
+ h0_inv[4] = domain->h_inv[4];
+ h0_inv[5] = domain->h_inv[5];
+ }
+ }
+
+ boltz = force->boltz;
+ nktv2p = force->nktv2p;
+
+ if (force->kspace) kspace_flag = 1;
+ else kspace_flag = 0;
+
+ if (strstr(update->integrate_style,"respa")) {
+ nlevels_respa = ((Respa *) update->integrate)->nlevels;
+ step_respa = ((Respa *) update->integrate)->step;
+ dto = 0.5*step_respa[0];
+ }
+
+ // detect if any rigid fixes exist so rigid bodies move when box is remapped
+ // rfix[] = indices to each fix rigid
+
+ delete [] rfix;
+ nrigid = 0;
+ rfix = NULL;
+
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->rigid_flag) nrigid++;
+ if (nrigid) {
+ rfix = new int[nrigid];
+ nrigid = 0;
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i;
+ }
+}
+
+// NJD MRD 2 functions
+int FixBocs::read_F_table( char *filename, int p_basis_type )
+{
+ char separator = ',';
+ FILE *fpi;
+ int N_columns = 2, n_entries = 0, i;
+ float f1, f2;
+ double n1, n2;
+ int test_sscanf;
+ double **data = (double **) calloc(N_columns,sizeof(double *));
+ char * line = (char *) calloc(200,sizeof(char));
+
+ fpi = fopen(filename,"r");
+ if (fpi)
+ {
+ while (fgets(line,199,fpi)) { ++n_entries; }
+ fclose(fpi);
+ for (i = 0; i < N_columns; ++i)
+ {
+ data[i] = (double *) calloc(n_entries,sizeof(double));
+ }
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(50,sizeof(char));
+ sprintf(errmsg,"Unable to open file: %s\n",filename);
+ error->all(FLERR,errmsg);
+ }
+
+ n_entries = 0;
+ fpi = fopen(filename,"r");
+ if (fpi)
+ {
+ while( fgets(line,199,fpi))
+ {
+ ++n_entries;
+ test_sscanf = sscanf(line," %f , %f ",&f1, &f2);
+ if (test_sscanf == 2)
+ {
+ data[0][n_entries-1] = (double) f1;
+ data[1][n_entries-1] = (double) f2;
+ }
+ else
+ {
+ fprintf(stderr,"WARNING: did not find 2 comma separated values in "
+ "line %d of file %s\n\tline: %s",n_entries,filename,line);
+ }
+ }
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(50,sizeof(char));
+ sprintf(errmsg,"Unable to open file: %s\n",filename);
+ error->all(FLERR,errmsg);
+ }
+ fclose(fpi);
+
+ if (p_basis_type == 1)
+ {
+ splines = (double **) calloc(2,sizeof(double *));
+ splines[0] = (double *) calloc(n_entries,sizeof(double));
+ splines[1] = (double *) calloc(n_entries,sizeof(double));
+ int idxa, idxb;
+ for (idxa = 0; idxa < 2; ++idxa)
+ {
+ for (idxb = 0; idxb < n_entries; ++idxb)
+ {
+ splines[idxa][idxb] = data[idxa][idxb];
+ }
+ }
+ }
+ else if (p_basis_type == 2)
+ {
+ spline_length = n_entries;
+ build_cubic_splines(data);
+ n_entries -= 1;
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(70,sizeof(char));
+ sprintf(errmsg,"ERROR: invalid p_basis_type value "
+ "of %d in read_F_table",p_basis_type);
+ error->all(FLERR,errmsg);
+ }
+ return n_entries;
+}
+
+void FixBocs::build_cubic_splines( double **data )
+{
+ double *a, *b, *d, *h, *alpha, *c, *l, *mu, *z;
+ int n = spline_length;
+ double alpha_i;
+ a = (double *) calloc(n,sizeof(double));
+ b = (double *) calloc(n+1,sizeof(double));
+ d = (double *) calloc(n+1,sizeof(double));
+ h = (double *) calloc(n,sizeof(double));
+ alpha = (double *) calloc(n,sizeof(double));
+ c = (double *) calloc(n+1,sizeof(double));
+ l = (double *) calloc(n,sizeof(double));
+ mu = (double *) calloc(n,sizeof(double));
+ z = (double *) calloc(n,sizeof(double));
+ int idx;
+ for (int i=0; i<n; i++)
+ {
+ a[i] = data[1][i];
+ b[i] = 0.0;
+ d[i] = 0.0;
+
+ if (i<(n-1))
+ {
+ h[i] = (data[0][i+1] - data[0][i]);
+ }
+
+ if (i>1 && i<(n-1))
+ {
+ alpha_i = (3.0 / h[i]) * ( data[1][i+1] - data[1][i]) - (3.0 / h[i-1] )
+ * ( data[1][i] - data[1][i-1] );
+ alpha[i-1] = alpha_i;
+ }
+ }
+ l[0] = 1.0;
+ mu[0] = 0.0;
+ z[0] = 0.0;
+
+ for (int i=1; i<n-1; i++)
+ {
+ l[i] = 2*(data[0][i+1] - data[0][i-1]) - h[i-1] * mu[i-1];
+ mu[i] = h[i]/l[i];
+ z[i] = (alpha[i] - h[i-1] * z[i-1]) / l[i];
+ }
+ l[n-1] = 1.0;
+ mu[n-1] = 0.0;
+ z[n-1] = 0.0;
+
+ c[n] = 0.0;
+ b[n] = 0.0;
+ d[n] = 0.0;
+
+ for(int j=n-1; j>=0; j--)
+ {
+ c[j] = z[j] - mu[j]*c[j+1];
+
+ b[j] = (a[j+1]-a[j])/h[j] - h[j]*(c[j+1] + 2.0 * c[j])/3.0;
+
+ d[j] = (c[j+1]-c[j])/(3.0 * h[j]);
+ }
+ splines = (double **) calloc(5,sizeof(double *));
+
+ for ( idx = 0; idx < 5; ++idx)
+ {
+ splines[idx] = (double *) calloc(n-1,sizeof(double));
+ }
+ idx = 0;
+ for ( idx = 0; idx < n - 1; ++idx)
+ {
+ splines[1][idx] = a[idx];
+ splines[2][idx] = b[idx];
+ splines[3][idx] = c[idx];
+ splines[4][idx] = d[idx];
+ splines[0][idx] = data[0][idx];
+ }
+}
+// END NJD MRD 2 functions
+
+/* ----------------------------------------------------------------------
+ compute T,P before integrator starts
+------------------------------------------------------------------------- */
+
+void FixBocs::setup(int vflag)
+{
+ // tdof needed by compute_temp_target()
+
+ t_current = temperature->compute_scalar();
+ tdof = temperature->dof;
+
+ // t_target is needed by NVT and NPT in compute_scalar()
+ // If no thermostat or using fix nphug,
+ // t_target must be defined by other means.
+
+ if (tstat_flag && strstr(style,"nphug") == NULL) {
+ compute_temp_target();
+ } else if (pstat_flag) {
+
+ // t0 = reference temperature for masses
+ // cannot be done in init() b/c temperature cannot be called there
+ // is b/c Modify::init() inits computes after fixes due to dof dependence
+ // guesstimate a unit-dependent t0 if actual T = 0.0
+ // if it was read in from a restart file, leave it be
+
+ if (t0 == 0.0) {
+ t0 = temperature->compute_scalar();
+ if (t0 == 0.0) {
+ if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
+ else t0 = 300.0;
+ }
+ }
+ t_target = t0;
+ }
+
+ if (pstat_flag) compute_press_target();
+
+ if (pstat_flag) {
+ if (pstyle == ISO) pressure->compute_scalar();
+ else pressure->compute_vector();
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ // masses and initial forces on thermostat variables
+
+ if (tstat_flag) {
+ eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++)
+ eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++) {
+ eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] -
+ boltz * t_target) / eta_mass[ich];
+ }
+ }
+
+ // masses and initial forces on barostat variables
+
+ if (pstat_flag) {
+ double kt = boltz * t_target;
+ double nkt = atom->natoms * kt;
+
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++)
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ }
+
+ // masses and initial forces on barostat thermostat variables
+
+ if (mpchain) {
+ etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz * t_target) / etap_mass[ich];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ 1st half of Verlet update
+------------------------------------------------------------------------- */
+
+void FixBocs::initial_integrate(int vflag)
+{
+ // update eta_press_dot
+
+ if (pstat_flag && mpchain) nhc_press_integrate();
+
+ // update eta_dot
+
+ if (tstat_flag) {
+ compute_temp_target();
+ nhc_temp_integrate();
+ }
+
+ // need to recompute pressure to account for change in KE
+ // t_current is up-to-date, but compute_temperature is not
+ // compute appropriately coupled elements of mvv_current
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ temperature->compute_scalar();
+ pressure->compute_scalar();
+ } else {
+ temperature->compute_vector();
+ pressure->compute_vector();
+ }
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) {
+ compute_press_target();
+ nh_omega_dot();
+ nh_v_press();
+ }
+
+ nve_v();
+
+ // remap simulation box by 1/2 step
+
+ if (pstat_flag) remap();
+
+ nve_x();
+
+ // remap simulation box by 1/2 step
+ // redo KSpace coeffs since volume has changed
+
+ if (pstat_flag) {
+ remap();
+ if (kspace_flag) force->kspace->setup();
+ }
+}
+
+/* ----------------------------------------------------------------------
+ 2nd half of Verlet update
+------------------------------------------------------------------------- */
+
+void FixBocs::final_integrate()
+{
+ nve_v();
+
+ // re-compute temp before nh_v_press()
+ // only needed for temperature computes with BIAS on reneighboring steps:
+ // b/c some biases store per-atom values (e.g. temp/profile)
+ // per-atom values are invalid if reneigh/comm occurred
+ // since temp->compute() in initial_integrate()
+
+ if (which == BIAS && neighbor->ago == 0)
+ t_current = temperature->compute_scalar();
+
+ if (pstat_flag) nh_v_press();
+
+ // compute new T,P after velocities rescaled by nh_v_press()
+ // compute appropriately coupled elements of mvv_current
+
+ t_current = temperature->compute_scalar();
+ tdof = temperature->dof;
+
+ if (pstat_flag) {
+ if (pstyle == ISO) pressure->compute_scalar();
+ else pressure->compute_vector();
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) nh_omega_dot();
+
+ // update eta_dot
+ // update eta_press_dot
+
+ if (tstat_flag) nhc_temp_integrate();
+ if (pstat_flag && mpchain) nhc_press_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop)
+{
+ // set timesteps by level
+
+ dtv = step_respa[ilevel];
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ dthalf = 0.5 * step_respa[ilevel];
+
+ // outermost level - update eta_dot and omega_dot, apply to v
+ // all other levels - NVE update of v
+ // x,v updates only performed for atoms in group
+
+ if (ilevel == nlevels_respa-1) {
+
+ // update eta_press_dot
+
+ if (pstat_flag && mpchain) nhc_press_integrate();
+
+ // update eta_dot
+
+ if (tstat_flag) {
+ compute_temp_target();
+ nhc_temp_integrate();
+ }
+
+ // recompute pressure to account for change in KE
+ // t_current is up-to-date, but compute_temperature is not
+ // compute appropriately coupled elements of mvv_current
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ temperature->compute_scalar();
+ pressure->compute_scalar();
+ } else {
+ temperature->compute_vector();
+ pressure->compute_vector();
+ }
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) {
+ compute_press_target();
+ nh_omega_dot();
+ nh_v_press();
+ }
+
+ nve_v();
+
+ } else nve_v();
+
+ // innermost level - also update x only for atoms in group
+ // if barostat, perform 1/2 step remap before and after
+
+ if (ilevel == 0) {
+ if (pstat_flag) remap();
+ nve_x();
+ if (pstat_flag) remap();
+ }
+
+ // if barostat, redo KSpace coeffs at outermost level,
+ // since volume has changed
+
+ if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag)
+ force->kspace->setup();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::final_integrate_respa(int ilevel, int iloop)
+{
+ // set timesteps by level
+
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ dthalf = 0.5 * step_respa[ilevel];
+
+ // outermost level - update eta_dot and omega_dot, apply via final_integrate
+ // all other levels - NVE update of v
+
+ if (ilevel == nlevels_respa-1) final_integrate();
+ else nve_v();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::couple()
+{
+ double *tensor = pressure->vector;
+
+ if (pstyle == ISO)
+ p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
+ else if (pcouple == XYZ) {
+ double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
+ p_current[0] = p_current[1] = p_current[2] = ave;
+ } else if (pcouple == XY) {
+ double ave = 0.5 * (tensor[0] + tensor[1]);
+ p_current[0] = p_current[1] = ave;
+ p_current[2] = tensor[2];
+ } else if (pcouple == YZ) {
+ double ave = 0.5 * (tensor[1] + tensor[2]);
+ p_current[1] = p_current[2] = ave;
+ p_current[0] = tensor[0];
+ } else if (pcouple == XZ) {
+ double ave = 0.5 * (tensor[0] + tensor[2]);
+ p_current[0] = p_current[2] = ave;
+ p_current[1] = tensor[1];
+ } else {
+ p_current[0] = tensor[0];
+ p_current[1] = tensor[1];
+ p_current[2] = tensor[2];
+ }
+
+ if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2]))
+ error->all(FLERR,"Non-numeric pressure - simulation unstable");
+
+ // switch order from xy-xz-yz to Voigt
+
+ if (pstyle == TRICLINIC) {
+ p_current[3] = tensor[5];
+ p_current[4] = tensor[4];
+ p_current[5] = tensor[3];
+
+ if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5]))
+ error->all(FLERR,"Non-numeric pressure - simulation unstable");
+ }
+}
+
+/* ----------------------------------------------------------------------
+ change box size
+ remap all atoms or dilate group atoms depending on allremap flag
+ if rigid bodies exist, scale rigid body centers-of-mass
+------------------------------------------------------------------------- */
+
+void FixBocs::remap()
+{
+ int i;
+ double oldlo,oldhi;
+ double expfac;
+
+ double **x = atom->x;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *h = domain->h;
+
+ // omega is not used, except for book-keeping
+
+ for (int i = 0; i < 6; i++) omega[i] += dto*omega_dot[i];
+
+ // convert pertinent atoms and rigid bodies to lamda coords
+
+ if (allremap) domain->x2lamda(nlocal);
+ else {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & dilate_group_bit)
+ domain->x2lamda(x[i],x[i]);
+ }
+
+ if (nrigid)
+ for (i = 0; i < nrigid; i++)
+ modify->fix[rfix[i]]->deform(0);
+
+ // reset global and local box to new size/shape
+
+ // this operation corresponds to applying the
+ // translate and scale operations
+ // corresponding to the solution of the following ODE:
+ //
+ // h_dot = omega_dot * h
+ //
+ // where h_dot, omega_dot and h are all upper-triangular
+ // 3x3 tensors. In Voigt notation, the elements of the
+ // RHS product tensor are:
+ // h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
+ //
+ // Ordering of operations preserves time symmetry.
+
+ double dto2 = dto/2.0;
+ double dto4 = dto/4.0;
+ double dto8 = dto/8.0;
+
+ // off-diagonal components, first half
+
+ if (pstyle == TRICLINIC) {
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ if (p_flag[3]) {
+ expfac = exp(dto4*omega_dot[1]);
+ h[3] *= expfac;
+ h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] *= expfac;
+ }
+
+ if (p_flag[5]) {
+ expfac = exp(dto4*omega_dot[0]);
+ h[5] *= expfac;
+ h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] *= expfac;
+ }
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+ }
+
+ // scale diagonal components
+ // scale tilt factors with cell, if set
+
+ if (p_flag[0]) {
+ oldlo = domain->boxlo[0];
+ oldhi = domain->boxhi[0];
+ expfac = exp(dto*omega_dot[0]);
+ domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0];
+ domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0];
+ }
+
+ if (p_flag[1]) {
+ oldlo = domain->boxlo[1];
+ oldhi = domain->boxhi[1];
+ expfac = exp(dto*omega_dot[1]);
+ domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1];
+ domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1];
+ if (scalexy) h[5] *= expfac;
+ }
+
+ if (p_flag[2]) {
+ oldlo = domain->boxlo[2];
+ oldhi = domain->boxhi[2];
+ expfac = exp(dto*omega_dot[2]);
+ domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2];
+ domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2];
+ if (scalexz) h[4] *= expfac;
+ if (scaleyz) h[3] *= expfac;
+ }
+
+ // off-diagonal components, second half
+
+ if (pstyle == TRICLINIC) {
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ if (p_flag[3]) {
+ expfac = exp(dto4*omega_dot[1]);
+ h[3] *= expfac;
+ h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] *= expfac;
+ }
+
+ if (p_flag[5]) {
+ expfac = exp(dto4*omega_dot[0]);
+ h[5] *= expfac;
+ h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] *= expfac;
+ }
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ }
+
+ domain->yz = h[3];
+ domain->xz = h[4];
+ domain->xy = h[5];
+
+ // tilt factor to cell length ratio can not exceed TILTMAX in one step
+
+ if (domain->yz < -TILTMAX*domain->yprd ||
+ domain->yz > TILTMAX*domain->yprd ||
+ domain->xz < -TILTMAX*domain->xprd ||
+ domain->xz > TILTMAX*domain->xprd ||
+ domain->xy < -TILTMAX*domain->xprd ||
+ domain->xy > TILTMAX*domain->xprd)
+ error->all(FLERR,"Fix bocs has tilted box too far in one step - "
+ "periodic cell is too far from equilibrium state");
+
+ domain->set_global_box();
+ domain->set_local_box();
+
+ // convert pertinent atoms and rigid bodies back to box coords
+
+ if (allremap) domain->lamda2x(nlocal);
+ else {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & dilate_group_bit)
+ domain->lamda2x(x[i],x[i]);
+ }
+
+ if (nrigid)
+ for (i = 0; i < nrigid; i++)
+ modify->fix[rfix[i]]->deform(1);
+}
+
+/* ----------------------------------------------------------------------
+ pack entire state of Fix into one write
+------------------------------------------------------------------------- */
+
+void FixBocs::write_restart(FILE *fp)
+{
+ int nsize = size_restart_global();
+
+ double *list;
+ memory->create(list,nsize,"nh:list");
+
+ pack_restart_data(list);
+
+ if (comm->me == 0) {
+ int size = nsize * sizeof(double);
+ fwrite(&size,sizeof(int),1,fp);
+ fwrite(list,sizeof(double),nsize,fp);
+ }
+
+ memory->destroy(list);
+}
+
+/* ----------------------------------------------------------------------
+ calculate the number of data to be packed
+------------------------------------------------------------------------- */
+
+int FixBocs::size_restart_global()
+{
+ int nsize = 2;
+ if (tstat_flag) nsize += 1 + 2*mtchain;
+ if (pstat_flag) {
+ nsize += 16 + 2*mpchain;
+ if (deviatoric_flag) nsize += 6;
+ }
+
+ return nsize;
+}
+
+/* ----------------------------------------------------------------------
+ pack restart data
+------------------------------------------------------------------------- */
+
+int FixBocs::pack_restart_data(double *list)
+{
+ int n = 0;
+
+ list[n++] = tstat_flag;
+ if (tstat_flag) {
+ list[n++] = mtchain;
+ for (int ich = 0; ich < mtchain; ich++)
+ list[n++] = eta[ich];
+ for (int ich = 0; ich < mtchain; ich++)
+ list[n++] = eta_dot[ich];
+ }
+
+ list[n++] = pstat_flag;
+ if (pstat_flag) {
+ list[n++] = omega[0];
+ list[n++] = omega[1];
+ list[n++] = omega[2];
+ list[n++] = omega[3];
+ list[n++] = omega[4];
+ list[n++] = omega[5];
+ list[n++] = omega_dot[0];
+ list[n++] = omega_dot[1];
+ list[n++] = omega_dot[2];
+ list[n++] = omega_dot[3];
+ list[n++] = omega_dot[4];
+ list[n++] = omega_dot[5];
+ list[n++] = vol0;
+ list[n++] = t0;
+ list[n++] = mpchain;
+ if (mpchain) {
+ for (int ich = 0; ich < mpchain; ich++)
+ list[n++] = etap[ich];
+ for (int ich = 0; ich < mpchain; ich++)
+ list[n++] = etap_dot[ich];
+ }
+
+ list[n++] = deviatoric_flag;
+ if (deviatoric_flag) {
+ list[n++] = h0_inv[0];
+ list[n++] = h0_inv[1];
+ list[n++] = h0_inv[2];
+ list[n++] = h0_inv[3];
+ list[n++] = h0_inv[4];
+ list[n++] = h0_inv[5];
+ }
+ }
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixBocs::restart(char *buf)
+{
+ int n = 0;
+ double *list = (double *) buf;
+ int flag = static_cast<int> (list[n++]);
+ if (flag) {
+ int m = static_cast<int> (list[n++]);
+ if (tstat_flag && m == mtchain) {
+ for (int ich = 0; ich < mtchain; ich++)
+ eta[ich] = list[n++];
+ for (int ich = 0; ich < mtchain; ich++)
+ eta_dot[ich] = list[n++];
+ } else n += 2*m;
+ }
+ flag = static_cast<int> (list[n++]);
+ if (flag) {
+ omega[0] = list[n++];
+ omega[1] = list[n++];
+ omega[2] = list[n++];
+ omega[3] = list[n++];
+ omega[4] = list[n++];
+ omega[5] = list[n++];
+ omega_dot[0] = list[n++];
+ omega_dot[1] = list[n++];
+ omega_dot[2] = list[n++];
+ omega_dot[3] = list[n++];
+ omega_dot[4] = list[n++];
+ omega_dot[5] = list[n++];
+ vol0 = list[n++];
+ t0 = list[n++];
+ int m = static_cast<int> (list[n++]);
+ if (pstat_flag && m == mpchain) {
+ for (int ich = 0; ich < mpchain; ich++)
+ etap[ich] = list[n++];
+ for (int ich = 0; ich < mpchain; ich++)
+ etap_dot[ich] = list[n++];
+ } else n+=2*m;
+ flag = static_cast<int> (list[n++]);
+ if (flag) {
+ h0_inv[0] = list[n++];
+ h0_inv[1] = list[n++];
+ h0_inv[2] = list[n++];
+ h0_inv[3] = list[n++];
+ h0_inv[4] = list[n++];
+ h0_inv[5] = list[n++];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBocs::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"temp") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (tcomputeflag) {
+ modify->delete_compute(id_temp);
+ tcomputeflag = 0;
+ }
+ delete [] id_temp;
+ int n = strlen(arg[1]) + 1;
+ id_temp = new char[n];
+ strcpy(id_temp,arg[1]);
+
+ int icompute = modify->find_compute(arg[1]);
+ if (icompute < 0)
+ error->all(FLERR,"Could not find fix_modify temperature ID");
+ temperature = modify->compute[icompute];
+
+ if (temperature->tempflag == 0)
+ error->all(FLERR,
+ "Fix_modify temperature ID does not compute temperature");
+ if (temperature->igroup != 0 && comm->me == 0)
+ error->warning(FLERR,"Temperature for fix modify is not for group all");
+
+ // reset id_temp of pressure to new temperature ID
+
+ if (pstat_flag) {
+ icompute = modify->find_compute(id_press);
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix modify does not exist");
+ modify->compute[icompute]->reset_extra_compute_fix(id_temp);
+ }
+
+ return 2;
+
+ } else if (strcmp(arg[0],"press") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command");
+ if (pcomputeflag) {
+ modify->delete_compute(id_press);
+ pcomputeflag = 0;
+ }
+ delete [] id_press;
+ int n = strlen(arg[1]) + 1;
+ id_press = new char[n];
+ strcpy(id_press,arg[1]);
+
+ int icompute = modify->find_compute(arg[1]);
+ if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");
+ pressure = modify->compute[icompute];
+
+ if (p_match_flag) // NJD MRD
+ {
+ if ( p_basis_type == 0 )
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, N_p_match,
+ p_match_coeffs, N_mol, vavg);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, splines,
+ spline_length );
+ }
+ }
+
+ if (pressure->pressflag == 0)
+ error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
+ return 2;
+ }
+
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixBocs::compute_scalar()
+{
+ int i;
+ double volume;
+ double energy;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+ int ich;
+ if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
+ else volume = domain->xprd * domain->yprd;
+
+ energy = 0.0;
+
+ // thermostat chain energy is equivalent to Eq. (2) in
+ // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117
+ // Sum(0.5*p_eta_k^2/Q_k,k=1,M) + L*k*T*eta_1 + Sum(k*T*eta_k,k=2,M),
+ // where L = tdof
+ // M = mtchain
+ // p_eta_k = Q_k*eta_dot[k-1]
+ // Q_1 = L*k*T/t_freq^2
+ // Q_k = k*T/t_freq^2, k > 1
+
+ if (tstat_flag) {
+ energy += ke_target * eta[0] + 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
+ for (ich = 1; ich < mtchain; ich++)
+ energy += kt * eta[ich] + 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
+ }
+
+ // barostat energy is equivalent to Eq. (8) in
+ // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117
+ // Sum(0.5*p_omega^2/W + P*V),
+ // where N = natoms
+ // p_omega = W*omega_dot
+ // W = N*k*T/p_freq^2
+ // sum is over barostatted dimensions
+
+ if (pstat_flag) {
+ for (i = 0; i < 3; i++)
+ if (p_flag[i])
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
+ p_hydro*(volume-vol0) / (pdim*nktv2p);
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i])
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ }
+
+ // extra contributions from thermostat chain for barostat
+
+ if (mpchain) {
+ energy += lkt_press * etap[0] + 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
+ for (ich = 1; ich < mpchain; ich++)
+ energy += kt * etap[ich] +
+ 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ }
+
+ // extra contribution from strain energy
+
+ if (deviatoric_flag) energy += compute_strain_energy();
+ }
+
+ return energy;
+}
+
+/* ----------------------------------------------------------------------
+ return a single element of the following vectors, in this order:
+ eta[tchain], eta_dot[tchain], omega[ndof], omega_dot[ndof]
+ etap[pchain], etap_dot[pchain], PE_eta[tchain], KE_eta_dot[tchain]
+ PE_omega[ndof], KE_omega_dot[ndof], PE_etap[pchain], KE_etap_dot[pchain]
+ PE_strain[1]
+ if no thermostat exists, related quantities are omitted from the list
+ if no barostat exists, related quantities are omitted from the list
+ ndof = 1,3,6 degrees of freedom for pstyle = ISO,ANISO,TRI
+------------------------------------------------------------------------- */
+
+double FixBocs::compute_vector(int n)
+{
+ int ilen;
+
+ if (tstat_flag) {
+ ilen = mtchain;
+ if (n < ilen) return eta[n];
+ n -= ilen;
+ ilen = mtchain;
+ if (n < ilen) return eta_dot[n];
+ n -= ilen;
+ }
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ }
+
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ }
+
+ if (mpchain) {
+ ilen = mpchain;
+ if (n < ilen) return etap[n];
+ n -= ilen;
+ ilen = mpchain;
+ if (n < ilen) return etap_dot[n];
+ n -= ilen;
+ }
+ }
+
+ double volume;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+ int ich;
+ if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
+ else volume = domain->xprd * domain->yprd;
+
+ if (tstat_flag) {
+ ilen = mtchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return ke_target * eta[0];
+ else
+ return kt * eta[ich];
+ }
+ n -= ilen;
+ ilen = mtchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
+ else
+ return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
+ }
+ n -= ilen;
+ }
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen)
+ return p_hydro*(volume-vol0) / nktv2p;
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) {
+ if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
+ }
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) {
+ if (n > 2) return 0.0;
+ else if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
+ }
+ n -= ilen;
+ }
+
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen)
+ return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) {
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
+ }
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) {
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
+ }
+ n -= ilen;
+ }
+
+ if (mpchain) {
+ ilen = mpchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0) return lkt_press * etap[0];
+ else return kt * etap[ich];
+ }
+ n -= ilen;
+ ilen = mpchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
+ else
+ return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ }
+ n -= ilen;
+ }
+
+ if (deviatoric_flag) {
+ ilen = 1;
+ if (n < ilen)
+ return compute_strain_energy();
+ n -= ilen;
+ }
+ }
+
+ return 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::reset_target(double t_new)
+{
+ t_target = t_start = t_stop = t_new;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::reset_dt()
+{
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ dthalf = 0.5 * update->dt;
+ dt4 = 0.25 * update->dt;
+ dt8 = 0.125 * update->dt;
+ dto = dthalf;
+
+ // If using respa, then remap is performed in innermost level
+
+ if (strstr(update->integrate_style,"respa"))
+ dto = 0.5*step_respa[0];
+
+ if (pstat_flag)
+ pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
+
+ if (tstat_flag)
+ tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
+}
+
+/* ----------------------------------------------------------------------
+ extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixBocs::extract(const char *str, int &dim)
+{
+ dim=0;
+ if (tstat_flag && strcmp(str,"t_target") == 0) {
+ return &t_target;
+ } else if (tstat_flag && strcmp(str,"t_start") == 0) {
+ return &t_start;
+ } else if (tstat_flag && strcmp(str,"t_stop") == 0) {
+ return &t_stop;
+ } else if (tstat_flag && strcmp(str,"mtchain") == 0) {
+ return &mtchain;
+ } else if (pstat_flag && strcmp(str,"mpchain") == 0) {
+ return &mtchain;
+ }
+ dim=1;
+ if (tstat_flag && strcmp(str,"eta") == 0) {
+ return η
+ } else if (pstat_flag && strcmp(str,"etap") == 0) {
+ return η
+ } else if (pstat_flag && strcmp(str,"p_flag") == 0) {
+ return &p_flag;
+ } else if (pstat_flag && strcmp(str,"p_start") == 0) {
+ return &p_start;
+ } else if (pstat_flag && strcmp(str,"p_stop") == 0) {
+ return &p_stop;
+ } else if (pstat_flag && strcmp(str,"p_target") == 0) {
+ return &p_target;
+ }
+ return NULL;
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of chain thermostat variables
+------------------------------------------------------------------------- */
+
+void FixBocs::nhc_temp_integrate()
+{
+ int ich;
+ double expfac;
+ double kecurrent = tdof * boltz * t_current;
+
+ // Update masses, to preserve initial freq, if flag set
+
+ if (eta_mass_flag) {
+ eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++)
+ eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
+ }
+
+ if (eta_mass[0] > 0.0)
+ eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
+ else eta_dotdot[0] = 0.0;
+
+ double ncfac = 1.0/nc_tchain;
+ for (int iloop = 0; iloop < nc_tchain; iloop++) {
+
+ for (ich = mtchain-1; ich > 0; ich--) {
+ expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
+ eta_dot[ich] *= expfac;
+ eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
+ eta_dot[ich] *= tdrag_factor;
+ eta_dot[ich] *= expfac;
+ }
+
+ expfac = exp(-ncfac*dt8*eta_dot[1]);
+ eta_dot[0] *= expfac;
+ eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
+ eta_dot[0] *= tdrag_factor;
+ eta_dot[0] *= expfac;
+
+ factor_eta = exp(-ncfac*dthalf*eta_dot[0]);
+ nh_v_temp();
+
+ // rescale temperature due to velocity scaling
+ // should not be necessary to explicitly recompute the temperature
+
+ t_current *= factor_eta*factor_eta;
+ kecurrent = tdof * boltz * t_current;
+
+ if (eta_mass[0] > 0.0)
+ eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
+ else eta_dotdot[0] = 0.0;
+
+ for (ich = 0; ich < mtchain; ich++)
+ eta[ich] += ncfac*dthalf*eta_dot[ich];
+
+ eta_dot[0] *= expfac;
+ eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
+ eta_dot[0] *= expfac;
+
+ for (ich = 1; ich < mtchain; ich++) {
+ expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
+ eta_dot[ich] *= expfac;
+ eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
+ - boltz * t_target)/eta_mass[ich];
+ eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
+ eta_dot[ich] *= expfac;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of chain thermostat variables for barostat
+ scale barostat velocities
+------------------------------------------------------------------------- */
+
+void FixBocs::nhc_press_integrate()
+{
+ int ich,i;
+ double expfac,factor_etap,kecurrent;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+
+ // Update masses, to preserve initial freq, if flag set
+
+ if (omega_mass_flag) {
+ double nkt = atom->natoms * kt;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++)
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ }
+ }
+
+ if (etap_mass_flag) {
+ if (mpchain) {
+ etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz * t_target) / etap_mass[ich];
+ }
+ }
+
+ kecurrent = 0.0;
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ }
+
+ etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
+
+ double ncfac = 1.0/nc_pchain;
+ for (int iloop = 0; iloop < nc_pchain; iloop++) {
+
+ for (ich = mpchain-1; ich > 0; ich--) {
+ expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
+ etap_dot[ich] *= expfac;
+ etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
+ etap_dot[ich] *= pdrag_factor;
+ etap_dot[ich] *= expfac;
+ }
+
+ expfac = exp(-ncfac*dt8*etap_dot[1]);
+ etap_dot[0] *= expfac;
+ etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
+ etap_dot[0] *= pdrag_factor;
+ etap_dot[0] *= expfac;
+
+ for (ich = 0; ich < mpchain; ich++)
+ etap[ich] += ncfac*dthalf*etap_dot[ich];
+
+ factor_etap = exp(-ncfac*dthalf*etap_dot[0]);
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) omega_dot[i] *= factor_etap;
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) omega_dot[i] *= factor_etap;
+ }
+
+ kecurrent = 0.0;
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ }
+
+ etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
+
+ etap_dot[0] *= expfac;
+ etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
+ etap_dot[0] *= expfac;
+
+ for (ich = 1; ich < mpchain; ich++) {
+ expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
+ etap_dot[ich] *= expfac;
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) /
+ etap_mass[ich];
+ etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
+ etap_dot[ich] *= expfac;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step barostat scaling of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_v_press()
+{
+ double factor[3];
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
+ factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
+ factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
+
+ if (which == NOBIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ }
+ }
+ } else if (which == BIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ temperature->restore_bias(i,v[i]);
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nve_v()
+{
+ double dtfm;
+ double **v = atom->v;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ if (rmass) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
+ }
+ }
+ } else {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform full-step update of positions
+-----------------------------------------------------------------------*/
+
+void FixBocs::nve_x()
+{
+ double **x = atom->x;
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ // x update by full step only for atoms in group
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step thermostat scaling of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_v_temp()
+{
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ if (which == NOBIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
+ }
+ }
+ } else if (which == BIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
+ temperature->restore_bias(i,v[i]);
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ compute sigma tensor
+ needed whenever p_target or h0_inv changes
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_sigma()
+{
+ // if nreset_h0 > 0, reset vol0 and h0_inv
+ // every nreset_h0 timesteps
+
+ if (nreset_h0 > 0) {
+ int delta = update->ntimestep - update->beginstep;
+ if (delta % nreset_h0 == 0) {
+ if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
+ else vol0 = domain->xprd * domain->yprd;
+ h0_inv[0] = domain->h_inv[0];
+ h0_inv[1] = domain->h_inv[1];
+ h0_inv[2] = domain->h_inv[2];
+ h0_inv[3] = domain->h_inv[3];
+ h0_inv[4] = domain->h_inv[4];
+ h0_inv[5] = domain->h_inv[5];
+ }
+ }
+
+ // generate upper-triangular half of
+ // sigma = vol0*h0inv*(p_target-p_hydro)*h0inv^t
+ // units of sigma are are PV/L^2 e.g. atm.A
+ //
+ // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
+ // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
+ // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
+
+ sigma[0] =
+ vol0*(h0_inv[0]*((p_target[0]-p_hydro)*h0_inv[0] +
+ p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) +
+ h0_inv[5]*(p_target[5]*h0_inv[0] +
+ (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) +
+ h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] +
+ (p_target[2]-p_hydro)*h0_inv[4]));
+ sigma[1] =
+ vol0*(h0_inv[1]*((p_target[1]-p_hydro)*h0_inv[1] +
+ p_target[3]*h0_inv[3]) +
+ h0_inv[3]*(p_target[3]*h0_inv[1] +
+ (p_target[2]-p_hydro)*h0_inv[3]));
+ sigma[2] =
+ vol0*(h0_inv[2]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[3] =
+ vol0*(h0_inv[1]*(p_target[3]*h0_inv[2]) +
+ h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[4] =
+ vol0*(h0_inv[0]*(p_target[4]*h0_inv[2]) +
+ h0_inv[5]*(p_target[3]*h0_inv[2]) +
+ h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[5] =
+ vol0*(h0_inv[0]*(p_target[5]*h0_inv[1]+p_target[4]*h0_inv[3]) +
+ h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) +
+ h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3]));
+}
+
+/* ----------------------------------------------------------------------
+ compute strain energy
+-----------------------------------------------------------------------*/
+
+double FixBocs::compute_strain_energy()
+{
+ // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
+
+ double* h = domain->h;
+ double d0,d1,d2;
+
+ d0 =
+ sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
+ sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
+ sigma[4]*( h[2]*h[4]);
+ d1 =
+ sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
+ sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
+ sigma[3]*( h[2]*h[3]);
+ d2 =
+ sigma[4]*( h[4]*h[2]) +
+ sigma[3]*( h[3]*h[2]) +
+ sigma[2]*( h[2]*h[2]);
+
+ double energy = 0.5*(d0+d1+d2)/nktv2p;
+ return energy;
+}
+
+/* ----------------------------------------------------------------------
+ compute deviatoric barostat force = h*sigma*h^t
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_deviatoric()
+{
+ // generate upper-triangular part of h*sigma*h^t
+ // units of fdev are are PV, e.g. atm*A^3
+ // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
+ // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
+ // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
+
+ double* h = domain->h;
+
+ fdev[0] =
+ h[0]*(sigma[0]*h[0]+sigma[5]*h[5]+sigma[4]*h[4]) +
+ h[5]*(sigma[5]*h[0]+sigma[1]*h[5]+sigma[3]*h[4]) +
+ h[4]*(sigma[4]*h[0]+sigma[3]*h[5]+sigma[2]*h[4]);
+ fdev[1] =
+ h[1]*( sigma[1]*h[1]+sigma[3]*h[3]) +
+ h[3]*( sigma[3]*h[1]+sigma[2]*h[3]);
+ fdev[2] =
+ h[2]*( sigma[2]*h[2]);
+ fdev[3] =
+ h[1]*( sigma[3]*h[2]) +
+ h[3]*( sigma[2]*h[2]);
+ fdev[4] =
+ h[0]*( sigma[4]*h[2]) +
+ h[5]*( sigma[3]*h[2]) +
+ h[4]*( sigma[2]*h[2]);
+ fdev[5] =
+ h[0]*( sigma[5]*h[1]+sigma[4]*h[3]) +
+ h[5]*( sigma[1]*h[1]+sigma[3]*h[3]) +
+ h[4]*( sigma[3]*h[1]+sigma[2]*h[3]);
+}
+
+/* ----------------------------------------------------------------------
+ compute target temperature and kinetic energy
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_temp_target()
+{
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ t_target = t_start + delta * (t_stop-t_start);
+ ke_target = tdof * boltz * t_target;
+}
+
+/* ----------------------------------------------------------------------
+ compute hydrostatic target pressure
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_press_target()
+{
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ p_hydro = 0.0;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i]) {
+ p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
+ p_hydro += p_target[i];
+ }
+ if (pdim > 0) p_hydro /= pdim;
+
+ if (pstyle == TRICLINIC)
+ for (int i = 3; i < 6; i++)
+ p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
+
+ // if deviatoric, recompute sigma each time p_target changes
+
+ if (deviatoric_flag) compute_sigma();
+}
+
+/* ----------------------------------------------------------------------
+ update omega_dot, omega
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_omega_dot()
+{
+ double f_omega,volume;
+
+ if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
+ else volume = domain->xprd*domain->yprd;
+
+ if (deviatoric_flag) compute_deviatoric();
+
+ mtk_term1 = 0.0;
+ if (mtk_flag) {
+ if (pstyle == ISO) {
+ mtk_term1 = tdof * boltz * t_current;
+ mtk_term1 /= pdim * atom->natoms;
+ } else {
+ double *mvv_current = temperature->vector;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ mtk_term1 += mvv_current[i];
+ mtk_term1 /= pdim * atom->natoms;
+ }
+ }
+
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i]) {
+ f_omega = (p_current[i]-p_hydro)*volume /
+ (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
+ if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
+ omega_dot[i] += f_omega*dthalf;
+ omega_dot[i] *= pdrag_factor;
+ }
+
+ mtk_term2 = 0.0;
+ if (mtk_flag) {
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ mtk_term2 += omega_dot[i];
+ if (pdim > 0) mtk_term2 /= pdim * atom->natoms;
+ }
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++) {
+ if (p_flag[i]) {
+ f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
+ if (deviatoric_flag)
+ f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
+ omega_dot[i] += f_omega*dthalf;
+ omega_dot[i] *= pdrag_factor;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ if any tilt ratios exceed limits, set flip = 1 and compute new tilt values
+ do not flip in x or y if non-periodic (can tilt but not flip)
+ this is b/c the box length would be changed (dramatically) by flip
+ if yz tilt exceeded, adjust C vector by one B vector
+ if xz tilt exceeded, adjust C vector by one A vector
+ if xy tilt exceeded, adjust B vector by one A vector
+ check yz first since it may change xz, then xz check comes after
+ if any flip occurs, create new box in domain
+ image_flip() adjusts image flags due to box shape change induced by flip
+ remap() puts atoms outside the new box back into the new box
+ perform irregular on atoms in lamda coords to migrate atoms to new procs
+ important that image_flip comes before remap, since remap may change
+ image flags to new values, making eqs in doc of Domain:image_flip incorrect
+------------------------------------------------------------------------- */
+
+void FixBocs::pre_exchange()
+{
+ double xprd = domain->xprd;
+ double yprd = domain->yprd;
+
+ // flip is only triggered when tilt exceeds 0.5 by DELTAFLIP
+ // this avoids immediate re-flipping due to tilt oscillations
+
+ double xtiltmax = (0.5+DELTAFLIP)*xprd;
+ double ytiltmax = (0.5+DELTAFLIP)*yprd;
+
+ int flipxy,flipxz,flipyz;
+ flipxy = flipxz = flipyz = 0;
+
+ if (domain->yperiodic) {
+ if (domain->yz < -ytiltmax) {
+ domain->yz += yprd;
+ domain->xz += domain->xy;
+ flipyz = 1;
+ } else if (domain->yz >= ytiltmax) {
+ domain->yz -= yprd;
+ domain->xz -= domain->xy;
+ flipyz = -1;
+ }
+ }
+
+ if (domain->xperiodic) {
+ if (domain->xz < -xtiltmax) {
+ domain->xz += xprd;
+ flipxz = 1;
+ } else if (domain->xz >= xtiltmax) {
+ domain->xz -= xprd;
+ flipxz = -1;
+ }
+ if (domain->xy < -xtiltmax) {
+ domain->xy += xprd;
+ flipxy = 1;
+ } else if (domain->xy >= xtiltmax) {
+ domain->xy -= xprd;
+ flipxy = -1;
+ }
+ }
+
+ int flip = 0;
+ if (flipxy || flipxz || flipyz) flip = 1;
+
+ if (flip) {
+ domain->set_global_box();
+ domain->set_local_box();
+
+ domain->image_flip(flipxy,flipxz,flipyz);
+
+ double **x = atom->x;
+ imageint *image = atom->image;
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
+
+ domain->x2lamda(atom->nlocal);
+ irregular->migrate_atoms();
+ domain->lamda2x(atom->nlocal);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of Irregular
+------------------------------------------------------------------------- */
+
+double FixBocs::memory_usage()
+{
+ double bytes = 0.0;
+ if (irregular) bytes += irregular->memory_usage();
+ return bytes;
+}
diff --git a/src/USER-BOCS/fix_bocs.h b/src/USER-BOCS/fix_bocs.h
new file mode 100644
index 0000000000000000000000000000000000000000..34090e4f3ac5cfc624dbc22e1ae77b905c4ee153
--- /dev/null
+++ b/src/USER-BOCS/fix_bocs.h
@@ -0,0 +1,302 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ 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.
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+ from The Pennsylvania State University
+------------------------------------------------------------------------- */
+
+
+#ifdef FIX_CLASS
+
+FixStyle(bocs,FixBocs)
+
+#else
+
+#ifndef LMP_FIX_BOCS_H
+#define LMP_FIX_BOCS_H
+
+#include "fix.h"
+
+
+namespace LAMMPS_NS {
+
+class FixBocs : public Fix {
+ public:
+ FixBocs(class LAMMPS *, int, char **); // MRD NJD
+ virtual ~FixBocs(); // MRD NJD
+ int setmask();
+ virtual void init();
+ virtual void setup(int);
+ virtual void initial_integrate(int);
+ virtual void final_integrate();
+ void initial_integrate_respa(int, int, int);
+ void final_integrate_respa(int, int);
+ virtual void pre_exchange();
+ double compute_scalar();
+ virtual double compute_vector(int);
+ void write_restart(FILE *);
+ virtual int pack_restart_data(double *); // pack restart data
+ virtual void restart(char *);
+ int modify_param(int, char **);
+ void reset_target(double);
+ void reset_dt();
+ virtual void *extract(const char*,int &);
+ double memory_usage();
+
+
+ protected:
+ int dimension,which;
+ double dtv,dtf,dthalf,dt4,dt8,dto;
+ double boltz,nktv2p,tdof;
+ double vol0; // reference volume
+ double t0; // reference temperature
+ // used for barostat mass
+ double t_start,t_stop;
+ double t_current,t_target,ke_target;
+ double t_freq;
+
+ int tstat_flag; // 1 if control T
+ int pstat_flag; // 1 if control P
+
+ int pstyle,pcouple,allremap;
+ int p_flag[6]; // 1 if control P on this dim, 0 if not
+ double p_start[6],p_stop[6];
+ double p_freq[6],p_target[6];
+ double omega[6],omega_dot[6];
+ double omega_mass[6];
+ double p_current[6];
+ double drag,tdrag_factor; // drag factor on particle thermostat
+ double pdrag_factor; // drag factor on barostat
+ int kspace_flag; // 1 if KSpace invoked, 0 if not
+ int nrigid; // number of rigid fixes
+ int dilate_group_bit; // mask for dilation group
+ int *rfix; // indices of rigid fixes
+ char *id_dilate; // group name to dilate
+ class Irregular *irregular; // for migrating atoms after box flips
+
+// MRD NJD
+ int p_basis_type;
+ int p_match_flag;
+ double vavg;
+ int N_mol;
+ int N_p_match;
+ double *p_match_coeffs;
+ double ** splines;
+ int spline_length;
+
+
+ int nlevels_respa;
+ double *step_respa;
+
+ char *id_temp,*id_press;
+ class Compute *temperature,*pressure;
+ int tcomputeflag,pcomputeflag; // 1 = compute was created by fix
+ // 0 = created externally
+
+ double *eta,*eta_dot; // chain thermostat for particles
+ double *eta_dotdot;
+ double *eta_mass;
+ int mtchain; // length of chain
+ int mtchain_default_flag; // 1 = mtchain is default
+
+ double *etap; // chain thermostat for barostat
+ double *etap_dot;
+ double *etap_dotdot;
+ double *etap_mass;
+ int mpchain; // length of chain
+
+ int mtk_flag; // 0 if using Hoover barostat
+ int pdim; // number of barostatted dims
+ double p_freq_max; // maximum barostat frequency
+
+ double p_hydro; // hydrostatic target pressure
+
+ int nc_tchain,nc_pchain;
+ double factor_eta;
+ double sigma[6]; // scaled target stress
+ double fdev[6]; // deviatoric force on barostat
+ int deviatoric_flag; // 0 if target stress tensor is hydrostatic
+ double h0_inv[6]; // h_inv of reference (zero strain) box
+ int nreset_h0; // interval for resetting h0
+
+ double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
+
+ int eta_mass_flag; // 1 if eta_mass updated, 0 if not.
+ int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
+ int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
+ int dipole_flag; // 1 if dipole is updated, 0 if not.
+ int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not
+
+ int scaleyz; // 1 if yz scaled with lz
+ int scalexz; // 1 if xz scaled with lz
+ int scalexy; // 1 if xy scaled with ly
+ int flipflag; // 1 if box flips are invoked as needed
+
+ int pre_exchange_flag; // set if pre_exchange needed for box flips
+
+ double fixedpoint[3]; // location of dilation fixed-point
+
+ void couple();
+ virtual void remap();
+ void nhc_temp_integrate();
+ void nhc_press_integrate();
+
+ int read_F_table(char *, int);
+ void build_cubic_splines(double **);
+
+ virtual void nve_x(); // may be overwritten by child classes
+ virtual void nve_v();
+ virtual void nh_v_press();
+ virtual void nh_v_temp();
+ virtual void compute_temp_target();
+ virtual int size_restart_global();
+
+ void compute_sigma();
+ void compute_deviatoric();
+ double compute_strain_energy();
+ void compute_press_target();
+ void nh_omega_dot();
+};
+
+}
+
+#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: Target temperature for fix bocs cannot be 0.0
+
+Self-explanatory.
+
+E: Invalid fix bocs command for a 2d simulation
+
+Cannot control z dimension in a 2d model.
+
+E: Fix bocs dilate group ID does not exist
+
+Self-explanatory.
+
+E: Invalid fix bocs command pressure settings
+
+If multiple dimensions are coupled, those dimensions must be
+specified.
+
+E: Cannot use fix bocs on a non-periodic dimension
+
+When specifying a diagonal pressure component, the dimension must be
+periodic.
+
+E: Cannot use fix bocs on a 2nd non-periodic dimension
+
+When specifying an off-diagonal pressure component, the 2nd of the two
+dimensions must be periodic. E.g. if the xy component is specified,
+then the y dimension must be periodic.
+
+E: Cannot use fix bocs with yz scaling when z is non-periodic dimension
+
+The 2nd dimension in the barostatted tilt factor must be periodic.
+
+E: Cannot use fix bocs with xz scaling when z is non-periodic dimension
+
+The 2nd dimension in the barostatted tilt factor must be periodic.
+
+E: Cannot use fix bocs with xy scaling when y is non-periodic dimension
+
+The 2nd dimension in the barostatted tilt factor must be periodic.
+
+E: Cannot use fix bocs with both yz dynamics and yz scaling
+
+Self-explanatory.
+
+E: Cannot use fix bocs with both xz dynamics and xz scaling
+
+Self-explanatory.
+
+E: Cannot use fix bocs with both xy dynamics and xy scaling
+
+Self-explanatory.
+
+E: Can not specify Pxy/Pxz/Pyz in fix bocs with non-triclinic box
+
+Only triclinic boxes can be used with off-diagonal pressure components.
+See the region prism command for details.
+
+E: Invalid fix bocs pressure settings
+
+Settings for coupled dimensions must be the same.
+
+E: Using update dipole flag requires atom style sphere
+
+Self-explanatory.
+
+E: Using update dipole flag requires atom attribute mu
+
+Self-explanatory.
+
+E: The dlm flag must be used with update dipole
+
+Self-explanatory.
+
+E: Fix bocs damping parameters must be > 0.0
+
+Self-explanatory.
+
+E: Cannot use fix npt and fix deform on same component of stress tensor
+
+This would be changing the same box dimension twice.
+
+E: Temperature ID for fix bocs does not exist
+
+Self-explanatory.
+
+E: Pressure ID for fix bocs does not exist
+
+Self-explanatory.
+
+E: Fix bocs has tilted box too far in one step - periodic cell is too far from equilibrium state
+
+Self-explanatory. The change in the box tilt is too extreme
+on a short timescale.
+
+E: Could not find fix_modify temperature ID
+
+The compute ID for computing temperature does not exist.
+
+E: Fix_modify temperature ID does not compute temperature
+
+The compute ID assigned to the fix must compute temperature.
+
+W: Temperature for fix modify is not for group all
+
+The temperature compute is being used with a pressure calculation
+which does operate on group all, so this may be inconsistent.
+
+E: Pressure ID for fix modify does not exist
+
+Self-explanatory.
+
+E: Could not find fix_modify pressure ID
+
+The compute ID for computing pressure does not exist.
+
+E: Fix_modify pressure ID does not compute pressure
+
+The compute ID assigned to the fix must compute pressure.
+
+*/
diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README
index 735f005f54e03e5024bdc51172453d986876f7c0..d71f3b7a43acc9df6f7c56f1077a991ce7e762e0 100644
--- a/src/USER-CGDNA/README
+++ b/src/USER-CGDNA/README
@@ -2,22 +2,29 @@ This package contains a LAMMPS implementation of coarse-grained
models of DNA, which can be used to model sequence-specific
DNA strands.
-See the doc pages and [1,2,3] for the individual bond and pair styles.
+Please cite [1] and the relevant oxDNA articles in any publication
+that uses this package.
+
+See the doc pages and [2,3,4] for the individual bond and pair styles.
The packages contains also a new Langevin-type rigid-body integrator,
-which has also its own doc page and is explained in [4].
+which has also its own doc page and is explained in [5].
+
+[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
+"Coarse-grained simulation of DNA using LAMMPS",
+Eur. Phys. J. E 41, 57 (2018).
-[1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
+[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
and thermodynamic properties of a coarse-grained DNA model",
J. Chem. Phys. 134, 085101 (2011).
-[2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
+[3] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
self-assembly, DPhil. University of Oxford (2011).
-[3] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
+[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
Improved Structural Properties and Salt Dependence into a Coarse-Grained
Model of DNA, J. Chem. Phys. 142, 234901 (2015).
-[4] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
+[5] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
144114 (2015).
@@ -28,7 +35,7 @@ well as DNA duplexes or arrays of duplexes can be found in
/examples/USER/cgdna/util/. A technical report with more information
on the models, the structure of the input and data file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA can be found
-in /doc/src/PDF/USER-CGDNA-overview.pdf.
+in /doc/src/PDF/USER-CGDNA.pdf.
IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
with the MOLECULE and ASPHERE packages. These should be included in
@@ -40,9 +47,8 @@ The creator of this package is:
Dr Oliver Henrich
University of Strathclyde, Glasgow, UK
-oliver.henrich at strath.ac.uk
-University of Edinburgh, UK
-ohenrich at staffmail.ed.ac.uk
+oliver d o t henrich a t strath d o t ac d o t uk
+
--------------------------------------------------------------------------
diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp
index da1eb38e762a3e03b01195566b3b4e91bcc08d39..47d8d8f60b3854632e13bdf7358200f596fef98c 100644
--- a/src/USER-CGDNA/bond_oxdna_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna_fene.cpp
@@ -242,7 +242,7 @@ void BondOxdnaFene::coeff(int narg, char **arg)
void BondOxdnaFene::init_style()
{
/* special bonds have to be lj = 0 1 1 and coul = 1 1 1 to exclude
- the ss excluded volume interaction between nearest neighbours */
+ the ss excluded volume interaction between nearest neighbors */
force->special_lj[1] = 0.0;
force->special_lj[2] = 1.0;
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index 3a80de436ac8759e2ccaf5cf81c9ba02261d0e88..151e7526924f508677c0c4648203b1091db9a4a0 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -157,7 +157,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -183,7 +183,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index f4f78685b74132fb3ecf9b84be5ab14887982cc7..974ade89c1230b3e6fff154855cdf8c7d13513f3 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -122,7 +122,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -145,7 +145,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
@@ -186,7 +186,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
}
- // knock out nearest-neighbour interaction between adjacent backbone sites
+ // knock out nearest-neighbor interaction between adjacent backbone sites
fpair *= factor_lj;
evdwl *= factor_lj;
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
index 11689df73888fe2cfe8dddbb28953c7916a7b801..0eb75fbb43b39b6bf29c460e2ebc0680d1cb66cb 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
@@ -163,7 +163,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -189,7 +189,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp
index 31762018a3665ef01bb49d79cdccf4b164d449e0..e2b8334078cc4c0fae3dc34dcceb6bdefc662657 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna_excv.cpp
@@ -152,7 +152,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -179,7 +179,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
@@ -222,7 +222,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
evdwl = F3(rsq_ss,cutsq_ss_ast[atype][btype],cut_ss_c[atype][btype],lj1_ss[atype][btype],
lj2_ss[atype][btype],epsilon_ss[atype][btype],b_ss[atype][btype],fpair);
- // knock out nearest-neighbour interaction between ss
+ // knock out nearest-neighbor interaction between ss
fpair *= factor_lj;
evdwl *= factor_lj;
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp
index 3d3ba9b4563d384db09f88529932ae7099ac318a..ce1bfe036a3842ae07ceb2baf3b42eef63bd3c7b 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp
@@ -168,7 +168,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -188,7 +188,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp
index d456c0117c3d7b1a15e2331795217adcc7027648..e5b9de81c09c4450584434a8dfa006c826675c0a 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp
@@ -160,7 +160,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -180,7 +180,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index b8b002a7fa11df5e5a2f5fe93ba3ad82be8f1c70..c370f8abe6ebe0fb35fae63730a909ae44dcf335 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -260,6 +260,7 @@ void FixRX::post_constructor()
error->all(FLERR,"fix rx cannot be combined with fix property/atom");
char **tmpspecies = new char*[maxspecies];
+ int tmpmaxstrlen = 0;
for(int jj=0; jj < maxspecies; jj++)
tmpspecies[jj] = NULL;
@@ -320,6 +321,7 @@ void FixRX::post_constructor()
error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx.");
tmpspecies[nUniqueSpecies] = new char[strlen(word)+1];
strcpy(tmpspecies[nUniqueSpecies],word);
+ tmpmaxstrlen = MAX(tmpmaxstrlen,strlen(word));
nUniqueSpecies++;
}
word = strtok(NULL, " \t\n\r\f");
@@ -354,9 +356,9 @@ void FixRX::post_constructor()
newarg2[0] = id_fix_species_old;
newarg2[1] = group->names[igroup];
newarg2[2] = (char *) "property/atom";
+ char *str1 = new char[tmpmaxstrlen+3];
+ char *str2 = new char[tmpmaxstrlen+6];
for(int ii=0; ii<nspecies; ii++){
- char str1[2+strlen(tmpspecies[ii])+1];
- char str2[2+strlen(tmpspecies[ii])+4];
strcpy(str1,"d_");
strcpy(str2,"d_");
strncat(str1,tmpspecies[ii],strlen(tmpspecies[ii]));
@@ -367,6 +369,8 @@ void FixRX::post_constructor()
strcpy(newarg[ii+3],str1);
strcpy(newarg2[ii+3],str2);
}
+ delete[] str1;
+ delete[] str2;
newarg[nspecies+3] = (char *) "ghost";
newarg[nspecies+4] = (char *) "yes";
newarg2[nspecies+3] = (char *) "ghost";
diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp
index 29c1ff88211085fb9769e3d292b6bc3352d9d02d..34742a0683311a8e1286b4e122897434d845209b 100644
--- a/src/USER-DRUDE/fix_drude_transform.cpp
+++ b/src/USER-DRUDE/fix_drude_transform.cpp
@@ -75,7 +75,7 @@ void FixDrudeTransform<inverse>::setup(int) {
if (!rmass) {
if (!mcoeff) mcoeff = new double[ntypes+1];
- double mcoeff_loc[ntypes+1];
+ double *mcoeff_loc = new double[ntypes+1];
for (int itype=0; itype<=ntypes; itype++) mcoeff_loc[itype] = 2.; // an impossible value: mcoeff is at most 1.
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) {
@@ -95,6 +95,7 @@ void FixDrudeTransform<inverse>::setup(int) {
// mcoeff is 2 for non polarizable
// 0 < mcoeff < 1 for drude
// mcoeff < 0 for core
+ delete[] mcoeff_loc;
}
}
@@ -313,6 +314,6 @@ void FixDrudeTransform<inverse>::unpack_forward_comm(int n, int first, double *b
}
/* ---------------------------------------------------------------------- */
-template class FixDrudeTransform<false>;
-template class FixDrudeTransform<true>;
+template class LAMMPS_NS::FixDrudeTransform<false>;
+template class LAMMPS_NS::FixDrudeTransform<true>;
diff --git a/src/USER-INTEL/Install.sh b/src/USER-INTEL/Install.sh
index da553d158ac24ff88ec9f86fd4e5b88ad7750191..8c291f0ae28da6090db92191e1ca48df7cebb8fd 100644
--- a/src/USER-INTEL/Install.sh
+++ b/src/USER-INTEL/Install.sh
@@ -38,6 +38,8 @@ for file in *_intel.h; do
action $file $dep
done
+# step 2: handle cases and tasks not handled in step 1.
+
action intel_preprocess.h
action intel_buffers.h
action intel_buffers.cpp
@@ -50,8 +52,6 @@ action intel_simd.h
action intel_intrinsics.h pair_tersoff_intel.cpp
action intel_intrinsics_airebo.h pair_airebo_intel.cpp
-# step 2: handle cases and tasks not handled in step 1.
-
if (test $mode = 1) then
if (test -e ../Makefile.package) then
diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp
index f85eb50b02dfdf9760a88f2ddf071467eedbb35b..832ce7ed50e482c787bd4e14e22d225b7b3be721 100644
--- a/src/USER-INTEL/dihedral_opls_intel.cpp
+++ b/src/USER-INTEL/dihedral_opls_intel.cpp
@@ -185,13 +185,6 @@ void DihedralOPLSIntel::eval(const int vflag,
const flt_t vb3y = x[i4].y - x[i3].y;
const flt_t vb3z = x[i4].z - x[i3].z;
- // 1-4
-
- const flt_t delx = x[i1].x - x[i4].x;
- const flt_t dely = x[i1].y - x[i4].y;
- const flt_t delz = x[i1].z - x[i4].z;
-
-
// c0 calculation
// 1st and 2nd angle
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index 1b31ec7fc2f6216497104a6edb64e64c238975b8..0f32cb48b201ca71c7181d512f241c0634db89ad 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -642,6 +642,6 @@ double IntelBuffers<flt_t, acc_t>::memory_usage(const int nthreads)
/* ---------------------------------------------------------------------- */
-template class IntelBuffers<float,float>;
-template class IntelBuffers<float,double>;
-template class IntelBuffers<double,double>;
+template class LAMMPS_NS::IntelBuffers<float,float>;
+template class LAMMPS_NS::IntelBuffers<float,double>;
+template class LAMMPS_NS::IntelBuffers<double,double>;
diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp
index 6cf2d3bfd09a5b8f857a44cc73ced2f3ad78c182..490b95ef719a132448c2925ba2879c9f1874f163 100644
--- a/src/USER-LB/fix_lb_momentum.cpp
+++ b/src/USER-LB/fix_lb_momentum.cpp
@@ -102,8 +102,8 @@ void FixLbMomentum::end_of_step()
double masslb,masslbloc;
double momentumlbloc[3],momentumlb[3];
double vcmtotal[3];
- int numvel = fix_lb_fluid->numvel;
- double etacov[numvel];
+ const int numvel = fix_lb_fluid->numvel;
+ double etacov[19]; // = double etacov[numvel]; i.e. 15 or 19
double rho;
if (linear) {
diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 8a439a2118394c01bc6bb6787152e6e4ec587d68..42fd722e016ce4dce882599cb1ff37fe24dd7422 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -255,5 +255,5 @@ static inline double fdiv_zero(const double n, const double d) {
return n / d;
}
-};
+}
#endif
diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp
index 56e855ad0c80fa7a0fec7d381976a39d685d85e3..8b03e051814ffe6f636f01d7c8e92f4b83950464 100644
--- a/src/USER-MESO/fix_edpd_source.cpp
+++ b/src/USER-MESO/fix_edpd_source.cpp
@@ -112,7 +112,7 @@ void FixEDPDSource::post_force(int vflag)
drx = x[i][0] - center[0];
dry = x[i][1] - center[1];
drz = x[i][2] - center[2];
- if(abs(drx) <= 0.5*dLx && abs(dry) <= 0.5*dLy && abs(drz) <= 0.5*dLz)
+ if(fabs(drx) <= 0.5*dLx && fabs(dry) <= 0.5*dLy && fabs(drz) <= 0.5*dLz)
edpd_flux[i] += value*edpd_cv[i];
}
}
diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp
index 21fecdf49d8c03848cbd45a89e77140c1c843468..64964a4c983ebb5ef8fb5cd27df15079f8860464 100644
--- a/src/USER-MESO/fix_tdpd_source.cpp
+++ b/src/USER-MESO/fix_tdpd_source.cpp
@@ -112,7 +112,7 @@ void FixTDPDSource::post_force(int vflag)
drx = x[i][0] - center[0];
dry = x[i][1] - center[1];
drz = x[i][2] - center[2];
- if(abs(drx) <= 0.5*dLx && abs(dry) <= 0.5*dLy && abs(drz) <= 0.5*dLz)
+ if(fabs(drx) <= 0.5*dLx && fabs(dry) <= 0.5*dLy && fabs(drz) <= 0.5*dLz)
cc_flux[i][cc_index-1] += value;
}
}
diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp
index f1d9c215b4207670e657c7fb2249b590235b23b9..351637a842018c6469c09a1929e5552487c20695 100644
--- a/src/USER-MESO/pair_edpd.cpp
+++ b/src/USER-MESO/pair_edpd.cpp
@@ -59,7 +59,6 @@ static const char cite_pair_edpd[] =
" volume = {51},\n"
" pages = {11038--11040}\n"
"}\n\n";
-;
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index 0d0d2a3a0ad5ab7f7fd6545aaa07f91e2c5f2abe..b8bbf6d622f51e16f15813cbeb1af08a692adceb 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -280,7 +280,9 @@ void PairTDPD::coeff(int narg, char **arg)
double power_one = force->numeric(FLERR,arg[4]);
double cut_one = force->numeric(FLERR,arg[5]);
double cutcc_one = force->numeric(FLERR,arg[6]);
- double kappa_one[cc_species],epsilon_one[cc_species],powercc_one[cc_species];
+ double *kappa_one = new double[cc_species];
+ double *epsilon_one = new double[cc_species];
+ double *powercc_one = new double[cc_species];
for(int k=0; k<cc_species; k++) {
kappa_one[k] = force->numeric(FLERR,arg[7+3*k]);
epsilon_one[k] = force->numeric(FLERR,arg[8+3*k]);
@@ -304,6 +306,9 @@ void PairTDPD::coeff(int narg, char **arg)
setflag[i][j] = 1;
count++;
}
+ delete[] kappa_one;
+ delete[] epsilon_one;
+ delete[] powercc_one;
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp
index dcf17ca489d49e7ffb487b0b61e803b5d6c442a7..a17aefe71b46b0dd435473c9d917eb6a74561365 100644
--- a/src/USER-MISC/compute_ackland_atom.cpp
+++ b/src/USER-MISC/compute_ackland_atom.cpp
@@ -12,8 +12,9 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing author: G. Ziegenhain, gerolf@ziegenhain.com
- Copyright (C) 2007
+ Contributing author: G. Ziegenhain, gerolf@ziegenhain.com
+ Copyright (C) 2007
+ Updated algorithm by: Brian Barnes, brian.c.barnes11.civ@mail.mil
------------------------------------------------------------------------- */
#include <cmath>
@@ -40,7 +41,8 @@ enum{UNKNOWN,BCC,FCC,HCP,ICO};
ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
- if (narg != 3) error->all(FLERR,"Illegal compute ackland/atom command");
+ if ((narg < 3) || (narg > 5))
+ error->all(FLERR,"Illegal compute ackland/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
@@ -48,10 +50,26 @@ ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS *lmp, int narg, char **arg) :
nmax = 0;
structure = NULL;
maxneigh = 0;
+ legacy = 0;
distsq = NULL;
nearest = NULL;
nearest_n0 = NULL;
nearest_n1 = NULL;
+
+ int iarg = 3;
+ while (narg > iarg) {
+ if (strcmp("legacy",arg[iarg]) == 0) {
+ ++iarg;
+ if (iarg >= narg)
+ error->all(FLERR,"Invalid compute ackland/atom command");
+ if (strcmp("yes",arg[iarg]) == 0)
+ legacy = 1;
+ else if (strcmp("no",arg[iarg]) == 0)
+ legacy = 0;
+ else error->all(FLERR,"Invalid compute ackland/atom command");
+ }
+ ++iarg;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -140,13 +158,13 @@ void ComputeAcklandAtom::compute_peratom()
// ensure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
- memory->destroy(distsq);
- memory->destroy(nearest);
+ memory->destroy(distsq);
+ memory->destroy(nearest);
memory->destroy(nearest_n0);
memory->destroy(nearest_n1);
- maxneigh = jnum;
- memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
- memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
+ maxneigh = jnum;
+ memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
+ memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
memory->create(nearest_n0,maxneigh,"compute/ackland/atom:nearest_n0");
memory->create(nearest_n1,maxneigh,"compute/ackland/atom:nearest_n1");
}
@@ -157,14 +175,14 @@ void ComputeAcklandAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
+ j = jlist[jj];
j &= NEIGHMASK;
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
distsq[n] = rsq;
nearest[n++] = j;
}
@@ -188,12 +206,12 @@ void ComputeAcklandAtom::compute_peratom()
n1_dist_sq = 1.55*r0_sq;
int n0 = 0, n1 = 0;
for (j = 0; j < n; j++) {
- if (distsq[j] < n1_dist_sq) {
- nearest_n1[n1++] = nearest[j];
- if (distsq[j] < n0_dist_sq) {
- nearest_n0[n0++] = nearest[j];
- }
- }
+ if (distsq[j] < n1_dist_sq) {
+ nearest_n1[n1++] = nearest[j];
+ if (distsq[j] < n0_dist_sq) {
+ nearest_n0[n0++] = nearest[j];
+ }
+ }
}
// Evaluate all angles <(r_ij,rik) forall n0 particles with:
@@ -231,47 +249,98 @@ void ComputeAcklandAtom::compute_peratom()
else chi[7]++;
}
}
+ if (legacy) {
- if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN;
- else if (chi[0] == 7) structure[i] = BCC;
- else if (chi[0] == 6) structure[i] = FCC;
- else if (chi[0] == 3) structure[i] = HCP;
- else {
+ // This is the original implementation by Gerolf Ziegenhain
// Deviations from the different lattice structures
+ double delta_bcc = 0.35*chi[4]/(double)(chi[5]+chi[6]-chi[4]);
double delta_cp = fabs(1.-(double)chi[6]/24.);
+ double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6.))+
+ (double)chi[2])/6.0;
+ double delta_hcp = (fabs((double)chi[0]-3.)+
+ fabs((double)chi[0]+(double)chi[1]+
+ (double)chi[2]+(double)chi[3]-9.0))/12.0;
+
+ // Identification of the local structure according to the reference
+
+ if (chi[0] == 7) { delta_bcc = 0.; }
+ else if (chi[0] == 6) { delta_fcc = 0.; }
+ else if (chi[0] <= 3) { delta_hcp = 0.; }
+
+ if (chi[7] > 0.)
+ structure[i] = UNKNOWN;
+ else
+ if (chi[4] < 3.)
+ {
+ if (n1 > 13 || n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ structure[i] = ICO;
+ } else
+ if (delta_bcc <= delta_cp)
+ {
+ if (n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ structure[i] = BCC;
+ } else
+ if (n1 > 12 || n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ if (delta_fcc < delta_hcp)
+ structure[i] = FCC;
+ else
+ structure[i] = HCP;
- // ensure we do not get divide by zero
- // and if we will, make delta_bcc irrelevant
- double delta_bcc = delta_cp + 1.0;
- int chi56m4 = chi[5]+chi[6]-chi[4];
+ } else {
- // note that chi[7] presumed zero
- if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
+ // This is the updated implementation by Brian Barnes
- double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
- +(double)chi[2])/6.0;
+ if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN;
+ else if (chi[0] == 7) structure[i] = BCC;
+ else if (chi[0] == 6) structure[i] = FCC;
+ else if (chi[0] == 3) structure[i] = HCP;
+ else {
+ // Deviations from the different lattice structures
- double delta_hcp = (fabs((double)chi[0]-3.)+fabs((double)chi[0]
- +(double)chi[1]+(double)chi[2]+(double)chi[3]
- -9.0))/12.0;
+ double delta_cp = fabs(1.-(double)chi[6]/24.);
- // Identification of the local structure according to the reference
+ // ensure we do not get divide by zero
+ // and if we will, make delta_bcc irrelevant
+ double delta_bcc = delta_cp + 1.0;
+ int chi56m4 = chi[5]+chi[6]-chi[4];
- if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
- && delta_hcp >= 0.1) structure[i] = UNKNOWN;
+ // note that chi[7] presumed zero
+ if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
- // not part of Ackland-Jones 2006; included for backward compatibility
- if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
+ double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
+ +(double)chi[2])/6.0;
+
+ double delta_hcp = (fabs((double)chi[0]-3.)
+ +fabs((double)chi[0]
+ +(double)chi[1]
+ +(double)chi[2]
+ +(double)chi[3]
+ -9.0))/12.0;
+
+ // Identification of the local structure according to the reference
+
+ if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
+ && delta_hcp >= 0.1) structure[i] = UNKNOWN;
+
+ // not part of Ackland-Jones 2006; included for backward compatibility
+ if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
- else {
- if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
else {
- if (n0 > 12) structure[i] = UNKNOWN;
+ if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
else {
- if (delta_fcc < delta_hcp) structure[i] = FCC;
- else
- structure[i] = HCP;
+ if (n0 > 12) structure[i] = UNKNOWN;
+ else {
+ if (delta_fcc < delta_hcp) structure[i] = FCC;
+ else
+ structure[i] = HCP;
+ }
}
}
}
diff --git a/src/USER-MISC/compute_ackland_atom.h b/src/USER-MISC/compute_ackland_atom.h
index 5464a10f872101fc5b07a85dab118d091ab2980e..dd70762627646080dace0fd75dfc94a11d98feaf 100644
--- a/src/USER-MISC/compute_ackland_atom.h
+++ b/src/USER-MISC/compute_ackland_atom.h
@@ -34,7 +34,7 @@ class ComputeAcklandAtom : public Compute {
double memory_usage();
private:
- int nmax,maxneigh;
+ int nmax,maxneigh,legacy;
double *distsq;
int *nearest, *nearest_n0, *nearest_n1;
double *structure;
diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp
index 1da43a6bafb18693cfbb70450d2a68a53f14820c..4d8627a11fb66534b0e982413790156d4efaf524 100644
--- a/src/USER-MISC/compute_basal_atom.cpp
+++ b/src/USER-MISC/compute_basal_atom.cpp
@@ -204,8 +204,11 @@ void ComputeBasalAtom::compute_peratom()
double bond_angle;
double norm_j, norm_k;
chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0;
- double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik,x3[n0],y3[n0],z3[n0],
- xmean5, ymean5, zmean5, xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
+ double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik, xmean5, ymean5, zmean5,
+ xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
+ double *x3 = new double[n0];
+ double *y3 = new double[n0];
+ double *z3 = new double[n0];
for (j = 0; j < n0; j++) {
x_ij = x[i][0]-x[nearest_n0[j]][0];
y_ij = x[i][1]-x[nearest_n0[j]][1];
@@ -411,9 +414,12 @@ void ComputeBasalAtom::compute_peratom()
}
}
}
- }
- //if there are less than two ~180 degree bond angles, the algorithm returns null
- else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0;
+ //if there are less than two ~180 degree bond angles, the algorithm returns null
+ } else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0;
+
+ delete[] x3;
+ delete[] y3;
+ delete[] z3;
//normalize BPV:
double Mag = sqrt(BPV[i][0]*BPV[i][0] +
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index b3c92eed67354745665760ee5b0f8bb29b68b9ef..86da8a0c4fb306297f2cbdac9575e3cd32ec1dc9 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -43,6 +43,17 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
using namespace LAMMPS_NS;
using namespace FixConst;
+static const char cite_fix_bond_react[] =
+ "fix bond/react:\n\n"
+ "@Article{Gissinger17,\n"
+ " author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
+ " title = {Modeling chemical reactions in classical molecular dynamics simulations},\n"
+ " journal = {Polymer},\n"
+ " year = 2017,\n"
+ " volume = 128,\n"
+ " pages = {211--217}\n"
+ "}\n\n";
+
#define BIG 1.0e20
#define DELTA 16
#define MAXLINE 256
@@ -62,6 +73,8 @@ enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};
FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
+ if (lmp->citeme) lmp->citeme->add(cite_fix_bond_react);
+
fix1 = NULL;
fix2 = NULL;
@@ -71,7 +84,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
MPI_Comm_size(world,&nprocs);
attempted_rxn = 0;
- ghostcheck_flag = 0;
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
@@ -127,7 +139,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
// this looks excessive
// the price of vectorization (all reactions in one command)?
memory->create(nevery,nreacts,"bond/react:nevery");
- memory->create(cutsq,nreacts,"bond/react:cutsq");
+ memory->create(cutsq,nreacts,2,"bond/react:cutsq");
memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol");
memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");
memory->create(fraction,nreacts,"bond/react:fraction");
@@ -138,6 +150,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(jatomtype,nreacts,"bond/react:jatomtype");
memory->create(ibonding,nreacts,"bond/react:ibonding");
memory->create(jbonding,nreacts,"bond/react:jbonding");
+ memory->create(closeneigh,nreacts,"bond/react:closeneigh");
memory->create(groupbits,nreacts,"bond/react:groupbits");
memory->create(reaction_count,nreacts,"bond/react:reaction_count");
memory->create(local_rxn_count,nreacts,"bond/react:local_rxn_count");
@@ -176,7 +189,11 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
double cutoff = force->numeric(FLERR,arg[iarg++]);
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.5");
- cutsq[rxn] = cutoff*cutoff;
+ cutsq[rxn][0] = cutoff*cutoff;
+
+ cutoff = force->numeric(FLERR,arg[iarg++]);
+ if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.55");
+ cutsq[rxn][1] = cutoff*cutoff;
unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]);
if (unreacted_mol[rxn] == -1) error->all(FLERR,"Unreacted molecule template ID for "
@@ -241,6 +258,23 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecular != 1)
error->all(FLERR,"Cannot use fix bond/react with non-molecular systems");
+ // check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors
+ // if so, we don't need non-bonded neighbor list
+ for (int myrxn = 0; myrxn < nreacts; myrxn++) {
+ closeneigh[myrxn] = -1; // indicates will search non-bonded neighbors
+ onemol = atom->molecules[unreacted_mol[myrxn]];
+ for (int k = 0; k < onemol->nspecial[ibonding[myrxn]-1][2]; k++) {
+ if (onemol->special[ibonding[myrxn]-1][k] == jbonding[myrxn]) {
+ closeneigh[myrxn] = 2; // index for 1-4 neighbor
+ if (k < onemol->nspecial[ibonding[myrxn]-1][1])
+ closeneigh[myrxn] = 1; // index for 1-3 neighbor
+ if (k < onemol->nspecial[ibonding[myrxn]-1][0])
+ closeneigh[myrxn] = 0; // index for 1-2 neighbor
+ break;
+ }
+ }
+ }
+
// initialize Marsaglia RNG with processor-unique seed
random = new class RanMars*[nreacts];
@@ -259,6 +293,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
nmax = 0;
partner = finalpartner = NULL;
distsq = NULL;
+ probability = NULL;
maxcreate = 0;
created = NULL;
local_ncreate = NULL;
@@ -302,6 +337,7 @@ FixBondReact::~FixBondReact()
memory->destroy(local_ncreate);
memory->destroy(ncreate);
memory->destroy(distsq);
+ memory->destroy(probability);
memory->destroy(created);
memory->destroy(edge);
memory->destroy(equivalences);
@@ -320,6 +356,7 @@ FixBondReact::~FixBondReact()
memory->destroy(jatomtype);
memory->destroy(ibonding);
memory->destroy(jbonding);
+ memory->destroy(closeneigh);
memory->destroy(groupbits);
memory->destroy(reaction_count);
memory->destroy(local_rxn_count);
@@ -372,7 +409,7 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group
void FixBondReact::post_constructor()
{
- //let's add the limit_tags per-atom property fix
+ // let's add the limit_tags per-atom property fix
int len = strlen("per_atom_props") + 1;
id_fix2 = new char[len];
strcpy(id_fix2,"per_atom_props");
@@ -521,7 +558,7 @@ void FixBondReact::init()
// check cutoff for iatomtype,jatomtype
for (int i = 0; i < nreacts; i++) {
- if (force->pair == NULL || cutsq[i] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
+ if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff");
}
@@ -548,10 +585,6 @@ void FixBondReact::init_list(int id, NeighList *ptr)
void FixBondReact::post_integrate()
{
- int inum,jnum,itype,jtype,possible;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *ilist,*jlist,*numneigh,**firstneigh;
-
// check if any reactions could occur on this timestep
int nevery_check = 1;
for (int i = 0; i < nreacts; i++) {
@@ -578,7 +611,6 @@ void FixBondReact::post_integrate()
comm->forward_comm();
// resize bond partner list and initialize it
- // probability array overlays distsq array
// needs to be atom->nmax in length
if (atom->nmax > nmax) {
@@ -587,13 +619,14 @@ void FixBondReact::post_integrate()
memory->destroy(distsq);
memory->destroy(local_ncreate);
memory->destroy(ncreate);
+ memory->destroy(probability);
nmax = atom->nmax;
memory->create(partner,nmax,"bond/react:partner");
memory->create(finalpartner,nmax,"bond/react:finalpartner");
- memory->create(distsq,nmax,"bond/react:distsq");
+ memory->create(distsq,nmax,2,"bond/react:distsq");
memory->create(local_ncreate,nreacts,"bond/react:local_ncreate");
memory->create(ncreate,nreacts,"bond/react:ncreate");
- probability = distsq;
+ memory->create(probability,nmax,"bond/react:probability");
}
// reset create counts
@@ -605,129 +638,28 @@ void FixBondReact::post_integrate()
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
- // NOTE: this might be faster if we remembered neighbor distances from
- // previous timestep and used those --JG
-
// loop over neighbors of my atoms
// each atom sets one closest eligible partner atom ID to bond with
- double **x = atom->x;
tagint *tag = atom->tag;
- int **nspecial = atom->nspecial;
- tagint **special = atom->special;
- int *mask = atom->mask;
int *type = atom->type;
neighbor->build_one(list,1);
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
- // per-atom property indicating if in bond/react master group
- int flag;
- int index1 = atom->find_custom("limit_tags",flag);
- int *i_limit_tags = atom->ivector[index1];
-
- int i,j;
+ int j;
- for (int myrxn = 0; myrxn < nreacts; myrxn++) {
+ for (rxnID = 0; rxnID < nreacts; rxnID++) {
for (int ii = 0; ii < nall; ii++) {
partner[ii] = 0;
finalpartner[ii] = 0;
- distsq[ii] = BIG;
+ distsq[ii][0] = 0.0;
+ distsq[ii][1] = BIG;
}
- for (int ii = 0; ii < inum; ii++) { // inum vs nlocal
- i = ilist[ii];
- if (!(mask[i] & groupbits[myrxn])) continue;
- if (i_limit_tags[i] != 0) continue;
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (int jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- if (!(mask[j] & groupbits[myrxn])) {
- continue;
- }
-
- if (i_limit_tags[j] != 0) {
- continue;
- }
-
- jtype = type[j];
- possible = 0;
-
- if (itype == iatomtype[myrxn] && jtype == jatomtype[myrxn]) {
- possible = 1;
- } else if (itype == jatomtype[myrxn] && jtype == iatomtype[myrxn]) {
- possible = 1;
- }
-
- if (possible == 0) continue;
-
- for (int k = 0; k < nspecial[i][0]; k++)
- if (special[i][k] == tag[j]) possible = 0;
- if (!possible) continue;
-
- // NOTE(for below): certain neighbor list settings prevent 3-cycles anyway!
- // e.g., in my examples, must use kspace command to include 1-3 neighbors for consideration here
-
- // do not allow a three-membered ring to be created (by the new bond)
- // check 1-3 neighbors of atom I
- for (int k = nspecial[i][0]; k < nspecial[i][1]; k++)
- if (special[i][k] == tag[j]) possible = 0;
- if (possible == 0) {
- continue;
- }
-
- // do not allow a four-membered ring to be created (by the new bond)
- // check 1-4 neighbors of atom I -> probably make an option
-
- /*
- for (k = nspecial[i][1]; k < nspecial[i][2]; k++)
- if (special[i][k] == tag[j]) {
- possible = 0;
- }
- if (possible == 0) continue;
- */
-
- // do not allow 5 membered rings -> probably make this an option
-
- /*
- for (k = nspecial[i][1]; k < nspecial[i][2]; k++) {
- for (m = nspecial[atom->map(special[i][k])][1]; m < nspecial[atom->map(special[i][k])][2]; m++) {
- if (special[atom->map(special[i][k])][m] == tag[j]) possible = 0;
- / }
- }
- if (possible == 0) continue;
- */
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq >= cutsq[myrxn]) {
- continue;
- }
- if (rsq < distsq[i]) {
- partner[i] = tag[j];
- distsq[i] = rsq;
- }
- if (rsq < distsq[j]) {
- partner[j] = tag[i];
- distsq[j] = rsq;
- }
- }
- }
+ // fork between far and close_partner here
+ if (closeneigh[rxnID] < 0) far_partner();
+ else close_partner();
// reverse comm of distsq and partner
// not needed if newton_pair off since I,J pair was seen by both procs
@@ -739,9 +671,9 @@ void FixBondReact::post_integrate()
// for prob check, generate random value for each atom with a bond partner
// forward comm of partner and random value, so ghosts have it
- if (fraction[myrxn] < 1.0) {
+ if (fraction[rxnID] < 1.0) {
for (int i = 0; i < nlocal; i++)
- if (partner[i]) probability[i] = random[myrxn]->uniform();
+ if (partner[i]) probability[i] = random[rxnID]->uniform();
}
commflag = 2;
@@ -764,11 +696,11 @@ void FixBondReact::post_integrate()
// apply probability constraint using RN for atom with smallest ID
- if (fraction[myrxn] < 1.0) {
+ if (fraction[rxnID] < 1.0) {
if (tag[i] < tag[j]) {
- if (probability[i] >= fraction[myrxn]) continue;
+ if (probability[i] >= fraction[rxnID]) continue;
} else {
- if (probability[j] >= fraction[myrxn]) continue;
+ if (probability[j] >= fraction[rxnID]) continue;
}
}
@@ -780,31 +712,17 @@ void FixBondReact::post_integrate()
if (tag[i] < tag[j]) temp_ncreate++;
}
- local_ncreate[myrxn] = temp_ncreate;
+ local_ncreate[rxnID] = temp_ncreate;
// break loop if no even eligible bonding atoms were found (on any proc)
int some_chance;
MPI_Allreduce(&temp_ncreate,&some_chance,1,MPI_INT,MPI_SUM,world);
- if (!some_chance) {
- continue;
- }
+ if (!some_chance) continue;
// communicate final partner
commflag = 3;
comm->forward_comm_fix(this);
-//obsolete comment block
-/*
- // I think this also simplifies for bond/react.
- // but currently unsure how to adapt it - JG
- // create list of created bonds that influence my owned atoms
- // even if between owned-ghost or ghost-ghost atoms
- // finalpartner is now set for owned and ghost atoms so loop over nall
- // OK if duplicates in created list due to ghosts duplicating owned atoms
- // check J < 0 to insure a created bond to unknown atom is included
- // i.e. a bond partner outside of skin length
-*/
-
// add instance to 'created' only if this processor
// owns the atoms with smaller global ID
// NOTE: we no longer care about ghost-ghost instances as bond/create did
@@ -816,21 +734,21 @@ void FixBondReact::post_integrate()
j = atom->map(finalpartner[i]);
// if (j < 0 || tag[i] < tag[j]) {
if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal &&
- if (ncreate[myrxn] == maxcreate) {
+ if (ncreate[rxnID] == maxcreate) {
maxcreate += DELTA;
// third column of 'created': bond/react integer ID
memory->grow(created,maxcreate,2,nreacts,"bond/react:created");
}
// to ensure types remain in same order
// unnecessary now taken from reaction map file
- if (iatomtype[myrxn] == type[i]) {
- created[ncreate[myrxn]][0][myrxn] = tag[i];
- created[ncreate[myrxn]][1][myrxn] = finalpartner[i];
+ if (iatomtype[rxnID] == type[i]) {
+ created[ncreate[rxnID]][0][rxnID] = tag[i];
+ created[ncreate[rxnID]][1][rxnID] = finalpartner[i];
} else {
- created[ncreate[myrxn]][0][myrxn] = finalpartner[i];
- created[ncreate[myrxn]][1][myrxn] = tag[i];
+ created[ncreate[rxnID]][0][rxnID] = finalpartner[i];
+ created[ncreate[rxnID]][1][rxnID] = tag[i];
}
- ncreate[myrxn]++;
+ ncreate[rxnID]++;
}
}
unlimit_bond(); //free atoms that have been relaxed
@@ -854,7 +772,152 @@ void FixBondReact::post_integrate()
superimpose_algorithm();
// free atoms that have been limited after reacting
unlimit_bond();
+}
+
+/* ----------------------------------------------------------------------
+ Search non-bonded neighbor lists if bonding atoms are not in special list
+------------------------------------------------------------------------- */
+
+void FixBondReact::far_partner()
+{
+ int inum,jnum,itype,jtype,possible;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ // loop over neighbors of my atoms
+ // each atom sets one closest eligible partner atom ID to bond with
+
+ double **x = atom->x;
+ tagint *tag = atom->tag;
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+ int *mask = atom->mask;
+ int *type = atom->type;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // per-atom property indicating if in bond/react master group
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ int i,j;
+
+ for (int ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ if (!(mask[i] & groupbits[rxnID])) continue;
+ if (i_limit_tags[i] != 0) continue;
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (int jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ if (!(mask[j] & groupbits[rxnID])) {
+ continue;
+}
+
+ if (i_limit_tags[j] != 0) {
+ continue;
+ }
+
+ jtype = type[j];
+ possible = 0;
+
+ if (itype == iatomtype[rxnID] && jtype == jatomtype[rxnID]) {
+ possible = 1;
+ } else if (itype == jatomtype[rxnID] && jtype == iatomtype[rxnID]) {
+ possible = 1;
+ }
+
+ if (possible == 0) continue;
+
+ // do not allow bonding atoms within special list
+ for (int k = 0; k < nspecial[i][2]; k++)
+ if (special[i][k] == tag[j]) possible = 0;
+ if (!possible) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) {
+ continue;
+ }
+ if (rsq < distsq[i][1]) {
+ partner[i] = tag[j];
+ distsq[i][1] = rsq;
+ }
+ if (rsq < distsq[j][1]) {
+ partner[j] = tag[i];
+ distsq[j][1] = rsq;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ Slightly simpler to find bonding partner when a close neighbor
+------------------------------------------------------------------------- */
+
+void FixBondReact::close_partner()
+{
+ int n,i1,i2,itype,jtype;
+ double delx,dely,delz,rsq;
+
+ double **x = atom->x;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+
+ // per-atom property indicating if in bond/react master group
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ // loop over special list
+ for (int ii = 0; ii < atom->nlocal; ii++) {
+ itype = type[ii];
+ n = 0;
+ if (closeneigh[rxnID] != 0)
+ n = nspecial[ii][closeneigh[rxnID]-1];
+ for (; n < nspecial[ii][closeneigh[rxnID]]; n++) {
+ i1 = ii;
+ i2 = atom->map(special[ii][n]);
+ jtype = type[i2];
+ if (!(mask[i1] & groupbits[rxnID])) continue;
+ if (!(mask[i2] & groupbits[rxnID])) continue;
+ if (i_limit_tags[i1] != 0) continue;
+ if (i_limit_tags[i2] != 0) continue;
+ if (itype != iatomtype[rxnID] || jtype != jatomtype[rxnID]) continue;
+
+ delx = x[i1][0] - x[i2][0];
+ dely = x[i1][1] - x[i2][1];
+ delz = x[i1][2] - x[i2][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue;
+
+ if (rsq > distsq[i1][0]) {
+ partner[i1] = tag[i2];
+ distsq[i1][0] = rsq;
+ }
+ if (rsq > distsq[i2][0]) {
+ partner[i2] = tag[i1];
+ distsq[i2][0] = rsq;
+ }
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -1076,8 +1139,8 @@ void FixBondReact::make_a_guess()
if (assigned_count == nfirst_neighs) status = GUESSFAIL;
// check if all neigh atom types are the same between simulation and unreacted mol
- int mol_ntypes[atom->ntypes];
- int lcl_ntypes[atom->ntypes];
+ int *mol_ntypes = new int[atom->ntypes];
+ int *lcl_ntypes = new int[atom->ntypes];
for (int i = 0; i < atom->ntypes; i++) {
mol_ntypes[i] = 0;
@@ -1096,6 +1159,9 @@ void FixBondReact::make_a_guess()
}
}
+ delete [] mol_ntypes;
+ delete [] lcl_ntypes;
+
// okay everything seems to be in order. let's assign some ID pairs!!!
neighbor_loop();
}
@@ -1384,7 +1450,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// if no edge atoms (small reacting molecule), all atoms are landlocked
// we can delete all current topology of landlocked atoms and replace
- // alwasy remove edge atoms from landlocked list
+ // always remove edge atoms from landlocked list
for (int i = 0; i < twomol->natoms; i++) {
if (edge[equivalences[i][1][myrxn]-1][myrxn] == 1) landlocked_atoms[i][myrxn] = 0;
else landlocked_atoms[i][myrxn] = 1;
@@ -1395,7 +1461,6 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
if ((force->dihedral && twomol->dihedralflag) ||
(force->improper && twomol->improperflag)) nspecial_limit = 1;
-
if (nspecial_limit != -1) {
for (int i = 0; i < twomol->natoms; i++) {
for (int j = 0; j < twomol->nspecial[i][nspecial_limit]; j++) {
@@ -1410,11 +1475,21 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// bad molecule templates check
// if atoms change types, but aren't landlocked, that's bad
-
for (int i = 0; i < twomol->natoms; i++) {
if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0)
error->one(FLERR,"Atom affected by reaction too close to template edge");
}
+
+ // also, if atoms change number of bonds, but aren't landlocked, that could be bad
+ if (me == 0)
+ for (int i = 0; i < twomol->natoms; i++) {
+ if (twomol->nspecial[i][0] != onemol->nspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
+ char str[128];
+ sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
+ error->warning(FLERR,str);
+ break;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -1438,7 +1513,8 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
dedup_size = global_megasize;
}
- tagint dedup_glove[max_natoms+1][dedup_size];
+ tagint **dedup_glove;
+ memory->create(dedup_glove,max_natoms+1,dedup_size,"bond/react:dedup_glove");
if (dedup_mode == 0) {
for (int i = 0; i < dedup_size; i++) {
@@ -1456,8 +1532,8 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
// dedup_mask is size dedup_size and filters reactions that have been deleted
// a value of 1 means this reaction instance has been deleted
- int dedup_mask[dedup_size];
- int dup_list[dedup_size];
+ int *dedup_mask = new int[dedup_size];
+ int *dup_list = new int[dedup_size];
for (int i = 0; i < dedup_size; i++) {
dedup_mask[i] = 0;
@@ -1467,14 +1543,12 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
// let's randomly mix up our reaction instances first
// then we can feel okay about ignoring ones we've already deleted (or accepted)
// based off std::shuffle
- // will produce same 'random' sequences on different processors.
- // not really an issue, as reaction lists are independent
+ int *temp_rxn = new int[max_natoms+1];
for (int i = dedup_size-1; i > 0; --i) { //dedup_size
- //choose random entry to swap current one with
- int k = rand() % (i+1);
+ // choose random entry to swap current one with
+ int k = floor(random[0]->uniform()*(i+1));
// swap entries
- int temp_rxn[max_natoms+1];
for (int j = 0; j < max_natoms+1; j++)
temp_rxn[j] = dedup_glove[j][i];
@@ -1483,6 +1557,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
dedup_glove[j][k] = temp_rxn[j];
}
}
+ delete [] temp_rxn;
for (int i = 0; i < dedup_size; i++) {
if (dedup_mask[i] == 0) {
@@ -1557,6 +1632,10 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
}
global_megasize = new_global_megasize;
}
+
+ memory->destroy(dedup_glove);
+ delete [] dedup_mask;
+ delete [] dup_list;
}
/* ----------------------------------------------------------------------
@@ -1743,9 +1822,6 @@ void FixBondReact::ghost_glovecast()
for (int j = 0; j < global_megasize; j++)
global_mega_glove[i][j] = 0;
-
- ghostcheck_flag = 1;
-
if (ghostly_num_mega > 0) {
for (int i = 0; i < max_natoms+1; i++) {
for (int j = 0; j < ghostly_num_mega; j++) {
@@ -1806,7 +1882,8 @@ void FixBondReact::update_everything()
// add check for local atoms as well
int update_num_mega;
- tagint update_mega_glove[max_natoms+1][MAX(local_num_mega,global_megasize)];
+ tagint **update_mega_glove;
+ memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
for (int pass = 0; pass < 2; pass++) {
@@ -2217,6 +2294,9 @@ void FixBondReact::update_everything()
}
}
+
+ memory->destroy(update_mega_glove);
+
// something to think about: this could done much more concisely if
// all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG
@@ -2522,7 +2602,10 @@ int FixBondReact::pack_reverse_comm(int n, int first, double *buf)
for (i = first; i < last; i++) {
buf[m++] = ubuf(partner[i]).d;
- buf[m++] = distsq[i];
+ if (closeneigh[rxnID] < 0)
+ buf[m++] = distsq[i][1];
+ else
+ buf[m++] = distsq[i][0];
}
return m;
}
@@ -2538,10 +2621,16 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf)
if (commflag != 1) {
for (i = 0; i < n; i++) {
j = list[i];
- if (buf[m+1] < distsq[j]) {
+ if (closeneigh[rxnID] < 0)
+ if (buf[m+1] < distsq[j][1]) {
partner[j] = (tagint) ubuf(buf[m++]).i;
- distsq[j] = buf[m++];
+ distsq[j][1] = buf[m++];
} else m += 2;
+ else
+ if (buf[m+1] > distsq[j][0]) {
+ partner[j] = (tagint) ubuf(buf[m++]).i;
+ distsq[j][0] = buf[m++];
+ } else m += 2;
}
}
}
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
index a0f52c02882353de6c9ddf2794b34e6a58f4b91a..e60fff37fbaa93f6e4e09136a57282cd883d9fe3 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-MISC/fix_bond_react.h
@@ -53,7 +53,7 @@ class FixBondReact : public Fix {
FILE *fp;
int *iatomtype,*jatomtype;
int *seed;
- double *cutsq,*fraction;
+ double **cutsq,*fraction;
tagint lastcheck;
int stabilization_flag;
int *stabilize_steps_flag;
@@ -66,7 +66,7 @@ class FixBondReact : public Fix {
int nmax; // max num local atoms
int max_natoms; // max natoms in a molecule template
tagint *partner,*finalpartner;
- double *distsq,*probability;
+ double **distsq,*probability;
int *ncreate;
int maxcreate;
int allncreate;
@@ -96,10 +96,9 @@ class FixBondReact : public Fix {
void superimpose_algorithm(); // main function of the superimpose algorithm
int *ibonding,*jbonding;
+ int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
int nedge,nequivalent; // number of edge, equivalent atoms in mapping file
int attempted_rxn; // there was an attempt!
- int ghostcheck_flag; // idicates whether a reaction instances contains a nonlocal atom
- int this_rxn_count; // num of local reaction occurrences
int *local_rxn_count;
int *ghostly_rxn_count;
int avail_guesses; // num of restore points available
@@ -143,6 +142,8 @@ class FixBondReact : public Fix {
void skip_lines(int, char *);
int parse(char *, char **, int);
+ void far_partner();
+ void close_partner();
void find_landlocked_atoms(int);
void glove_ghostcheck();
void ghost_glovecast();
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
index a5f0e5704116c78b88793c35722b5f208ef74269..91c70335133e4fdf6a37c0ec212d5d38dc9501fb 100644
--- a/src/USER-MISC/fix_filter_corotate.cpp
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -1527,7 +1527,10 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
//derivative:
//dn1dx:
- double sum1[3][3*N];
+
+ double **sum1;
+ memory->create(sum1,3,3*N,"filter_corotate:sum1");
+
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
sum1[i][j] = 0;
@@ -1564,10 +1567,12 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn1dx[i][j] = norm1*sum;
}
}
+ memory->destroy(sum1);
//dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
- double sum2[3][3*N];
+ double **sum2;
+ memory->create(sum2,3,3*N,"filter_corotate:sum2");
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
sum2[i][j] = 0;
@@ -1618,7 +1623,8 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
//dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
//sum3 = (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
- double sum3[3][3*N];
+ double **sum3;
+ memory->create(sum3,3,3*N,"filter_corotate:sum3");
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++) {
double sum = 0;
@@ -1627,6 +1633,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
sum3[i][j] = sum;
}
+ memory->destroy(sum2);
//dn2dx = norm2 * I3mn2n2T * sum3
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++) {
@@ -1636,6 +1643,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn2dx[i][j] = norm2*sum;
}
+ memory->destroy(sum3);
//dn3dx = norm3 * I3mn3n3T * cross
double I3mn3n3T[3][3]; //(I_3 - n3n3T)
for (int i=0; i<3; i++) {
@@ -1644,7 +1652,8 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
I3mn3n3T[i][i] += 1.0;
}
- double cross[3][3*N];
+ double **cross;
+ memory->create(cross,3,3*N,"filter_corotate:cross");
for (int j=0; j<3*N; j++) {
cross[0][j] = dn1dx[1][j]*n2[2] -dn1dx[2][j]*n2[1] +
@@ -1663,6 +1672,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn3dx[i][j] = norm3*sum;
}
+ memory->destroy(cross);
for (int l=0; l<N; l++)
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 5857bafc2ef9fb07062812b3992d1460d969fd3c..584b33bfe7da1bc93d041ee15388d7e72ebe36d5 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -44,6 +44,7 @@ using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL,ATOM};
+
//#define GLE_DEBUG 1
#define MAXLINE 1024
@@ -62,35 +63,37 @@ namespace GLE {
//"stabilized" cholesky decomposition. does a LDL^t decomposition, then sets to zero the negative diagonal elements and gets MM^t
void StabCholesky(int n, const double* MMt, double* M)
{
- double L[n*n], D[n];
-
- int i,j,k;
- for(i=0; i<n; ++i) D[i]=0.;
- for(i=0; i<n*n; ++i) L[i]=0.;
-
- for(i=0; i<n; ++i)
- {
- L[midx(n,i,i)]=1.;
- for (j=0; j<i; j++)
- {
- L[midx(n,i,j)]=MMt[midx(n,i,j)];
- for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]*L[midx(n,j,k)]*D[k];
- if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
- else L[midx(n,i,j)]=0.0;
- }
- D[i]=MMt[midx(n,i,i)];
- for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
+ double *L = new double[n*n];
+ double *D = new double[n];
+
+ int i,j,k;
+ for (i=0; i<n; ++i) D[i]=0.0;
+ for (i=0; i<n*n; ++i) L[i]=0.0;
+
+ for (i=0; i<n; ++i) {
+ L[midx(n,i,i)]=1.0;
+ for (j=0; j<i; j++) {
+ L[midx(n,i,j)]=MMt[midx(n,i,j)];
+ for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]*L[midx(n,j,k)]*D[k];
+ if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
+ else L[midx(n,i,j)]=0.0;
}
+ D[i]=MMt[midx(n,i,i)];
+ for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
+ }
- for(i=0; i<n; ++i)
- {
+ for (i=0; i<n; ++i) {
#ifdef GLE_DEBUG
- if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
+ if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
#endif
- D[i]=(D[i]>0.?sqrt(D[i]):0.);
- }
+ D[i]=(D[i]>0.0) ? sqrt(D[i]):0.0;
+ }
+
+ for (i=0; i<n; ++i)
+ for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
- for(i=0; i<n; ++i) for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
+ delete[] D;
+ delete[] L;
}
void MyMult(int n, int m, int r, const double* A, const double* B, double* C, double cf=0.0)
@@ -162,26 +165,32 @@ void MyPrint(int n, const double* A)
//matrix exponential by scaling and squaring.
void MatrixExp(int n, const double* M, double* EM, int j=8, int k=8)
{
- double tc[j+1], SM[n*n], TMP[n*n];
- double onetotwok=pow(0.5,1.0*k);
+ double *tc = new double[j+1];
+ double *SM = new double[n*n];
+ double *TMP = new double[n*n];
+ double onetotwok=pow(0.5,1.0*k);
- tc[0]=1;
- for (int i=0; i<j; ++i) tc[i+1]=tc[i]/(i+1.0);
+ tc[0]=1;
+ for (int i=0; i<j; ++i) tc[i+1]=tc[i]/(i+1.0);
- for (int i=0; i<n*n; ++i) { SM[i]=M[i]*onetotwok; EM[i]=0.0; TMP[i]=0.0; }
+ for (int i=0; i<n*n; ++i) { SM[i]=M[i]*onetotwok; EM[i]=0.0; TMP[i]=0.0; }
- for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];
+ for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];
- //taylor exp of scaled matrix
- for (int p=j-1; p>=0; p--)
- {
- MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
- for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
- }
+ //taylor exp of scaled matrix
+ for (int p=j-1; p>=0; p--) {
+ MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
+ for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
+ }
- for (int p=0; p<k; p++)
- { MyMult(n, n, n, EM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i]; }
+ for (int p=0; p<k; p++) {
+ MyMult(n, n, n, EM, EM, TMP);
+ for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
+ }
+ delete[] tc;
+ delete[] SM;
+ delete[] TMP;
}
}
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index 090a330af66ff0fed4e87bd58e1ac7363067ec97..c4750ce49e211b22c6f3b1ddc8e8d812f1843402 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -428,7 +428,7 @@ void FixIPI::final_integrate()
int nat=bsize/3;
double **f= atom->f;
- double lbuf[bsize];
+ double *lbuf = new double[bsize];
// reassembles the force vector from the local arrays
int nlocal = atom->nlocal;
@@ -440,6 +440,7 @@ void FixIPI::final_integrate()
lbuf[3*(atom->tag[i]-1)+2]=f[i][2]*forceconv;
}
MPI_Allreduce(lbuf,buffer,bsize,MPI_DOUBLE,MPI_SUM,world);
+ delete[] lbuf;
for (int i = 0; i < 9; ++i) vir[i]=0.0;
diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index cc92bfc30f9f906b7202c266df8d015163122366..523b2ca71a7b466f35939a67c7b5e9ac77501cac 100644
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -539,7 +539,7 @@ double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
double &fforce)
{
double r2inv,r6inv;
- double pdotp,pidotr,pjdotr,pre1,delx,dely,delz;
+ double pdotp,pidotr,pjdotr,delx,dely,delz;
double rinv, r3inv,r5inv, rcutlj2inv, rcutcoul2inv,rcutlj6inv;
double qtmp,xtmp,ytmp,ztmp,bfac,pqfac,qpfac, ecoul, evdwl;
diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp
index 9f25a1d0001868f58b4152b08ce3a1fd80960a5b..53d013474104725d33b9f5ad8a4e83d33cd0d140 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nh_omp.cpp
@@ -235,29 +235,9 @@ void FixRigidNHOMP::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRigidNHOMP::final_integrate()
+void FixRigidNHOMP::compute_forces_and_torques()
{
- double scale_t[3],scale_r;
-
- // compute scale variables
-
- scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
- scale_r = 1.0;
-
- if (tstat_flag) {
- double tmp = exp(-1.0 * dtq * eta_dot_t[0]);
- scale_t[0] = scale_t[1] = scale_t[2] = tmp;
- scale_r = exp(-1.0 * dtq * eta_dot_r[0]);
- }
-
- if (pstat_flag) {
- scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
- scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
- scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
- scale_r *= exp(-dtq * (pdim * mtk_term2));
-
- akin_t = akin_r = 0.0;
- }
+ int ibody;
double * const * _noalias const x = atom->x;
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
@@ -395,12 +375,53 @@ void FixRigidNHOMP::final_integrate()
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+ for (ibody = 0; ibody < nbody; ibody++) {
+ fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
+ fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
+ fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
+ torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
+ torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
+ torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidNHOMP::final_integrate()
+{
+ int ibody;
+ double scale_t[3],scale_r;
+
+ // compute scale variables
+
+ scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
+ scale_r = 1.0;
+
+ if (tstat_flag) {
+ double tmp = exp(-1.0 * dtq * eta_dot_t[0]);
+ scale_t[0] = scale_t[1] = scale_t[2] = tmp;
+ scale_r = exp(-1.0 * dtq * eta_dot_r[0]);
+ }
+
+ if (pstat_flag) {
+ scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
+ scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
+ scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
+ scale_r *= exp(-dtq * (pdim * mtk_term2));
+
+ akin_t = akin_r = 0.0;
+ }
+
+ if (!earlyflag) compute_forces_and_torques();
+
// update vcm and angmom
// include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
double akt=0.0,akr=0.0;
const double dtf2 = dtf * 2.0;
- int ibody;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr)
@@ -408,13 +429,6 @@ void FixRigidNHOMP::final_integrate()
for (ibody = 0; ibody < nbody; ibody++) {
double mbody[3],tbody[3],fquat[4];
- fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
- fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
- fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
- torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
- torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
- torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
-
// update vcm by 1/2 step
const double dtfm = dtf / masstotal[ibody];
diff --git a/src/USER-OMP/fix_rigid_nh_omp.h b/src/USER-OMP/fix_rigid_nh_omp.h
index 9210d7e5dc88f1a412f047f3d3eab5d19dc90c47..2f57b2723b8515dfb23606c45057ad742b4157e8 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.h
+++ b/src/USER-OMP/fix_rigid_nh_omp.h
@@ -28,6 +28,9 @@ class FixRigidNHOMP : public FixRigidNH {
virtual void final_integrate();
virtual void remap();
+ protected:
+ virtual void compute_forces_and_torques();
+
private: // copied from FixRigidOMP
template <int, int> void set_xv_thr();
template <int, int> void set_v_thr();
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 15e5f91c320513173bd482d0810f046b2ee6bad8..12c6362ed8bd4803e76e07c1b8e54dec5a74f8d5 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -108,7 +108,7 @@ void FixRigidOMP::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRigidOMP::final_integrate()
+void FixRigidOMP::compute_forces_and_torques()
{
double * const * _noalias const x = atom->x;
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
@@ -261,6 +261,23 @@ void FixRigidOMP::final_integrate()
torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidOMP::final_integrate()
+{
+ int ibody;
+
+ if (!earlyflag) compute_forces_and_torques();
+
+ // update vcm and angmom
+
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+ for (ibody = 0; ibody < nbody; ibody++) {
// update vcm by 1/2 step
diff --git a/src/USER-OMP/fix_rigid_omp.h b/src/USER-OMP/fix_rigid_omp.h
index 2b7b9461d2adee1b4ba327d6903e2b7f476ba845..b666a173a87c0a949ba8e8aba33f81da493f345a 100644
--- a/src/USER-OMP/fix_rigid_omp.h
+++ b/src/USER-OMP/fix_rigid_omp.h
@@ -33,6 +33,9 @@ class FixRigidOMP : public FixRigid {
virtual void initial_integrate(int);
virtual void final_integrate();
+ protected:
+ virtual void compute_forces_and_torques();
+
private:
template <int, int> void set_xv_thr();
template <int, int> void set_v_thr();
@@ -42,4 +45,3 @@ class FixRigidOMP : public FixRigid {
#endif
#endif
-
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index 7d82bd04e8d056141978c046c907a8557a339c54..a0495b3b933a4fa5a852b079dfd5936cb8b10088 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -112,7 +112,7 @@ void FixRigidSmallOMP::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRigidSmallOMP::final_integrate()
+void FixRigidSmallOMP::compute_forces_and_torques()
{
double * const * _noalias const x = atom->x;
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
@@ -201,6 +201,15 @@ void FixRigidSmallOMP::final_integrate()
tcm[2] += langextra[ibody][5];
}
}
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidSmallOMP::final_integrate()
+{
+ int ibody;
+
+ if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom, recompute omega
diff --git a/src/USER-OMP/fix_rigid_small_omp.h b/src/USER-OMP/fix_rigid_small_omp.h
index ffc4bee660ab3683498df38c9bd235cbf1522d95..298a1aa9de2ed8bc733840f4708608da9a9638a1 100644
--- a/src/USER-OMP/fix_rigid_small_omp.h
+++ b/src/USER-OMP/fix_rigid_small_omp.h
@@ -33,6 +33,9 @@ class FixRigidSmallOMP : public FixRigidSmall {
virtual void initial_integrate(int);
virtual void final_integrate();
+ protected:
+ virtual void compute_forces_and_torques();
+
private:
template <int, int> void set_xv_thr();
template <int, int> void set_v_thr();
diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh
index cfa369bb055ee2679b873535221244839cce9094..3428415443f5bc59c8486dd1e6327a50265c34e4 100644
--- a/src/USER-PHONON/Install.sh
+++ b/src/USER-PHONON/Install.sh
@@ -26,6 +26,16 @@ action () {
fi
}
+# USER-PHONON uses the parallel FFT wrapper used in PPPM,
+# so we must require the KSPACE package to be installed.
+
+if (test $1 = 1) then
+ if (test ! -e ../fft3d_wrap.h) then
+ echo "Must install KSPACE package with USER-PHONON"
+ exit 1
+ fi
+fi
+
# list of files with optional dependcies
action fix_phonon.cpp fft3d_wrap.h
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index cf561178926cb00be0740eb5fd7348d7243286e7..3a37c67a3871f1e044ba568e256c8c57a56620c8 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -668,7 +668,8 @@ void FixPhonon::postprocess( )
}
// to get Phi = KT.G^-1; normalization of FFTW data is done here
- double boltz = force->boltz, kbtsqrt[sysdim], TempAve = 0.;
+ double boltz = force->boltz, TempAve = 0.;
+ double *kbtsqrt = new double[sysdim];
double TempFac = inv_neval * inv_nTemp;
double NormFac = TempFac * double(ntotal);
@@ -692,7 +693,7 @@ void FixPhonon::postprocess( )
MPI_Gatherv(Phi_q[0],mynq*fft_dim2*2,MPI_DOUBLE,Phi_all[0],recvcnts,displs,MPI_DOUBLE,0,world);
// to collect all basis info and averaged it on root
- double basis_root[fft_dim];
+ double *basis_root = new double[fft_dim];
if (fft_dim > sysdim) MPI_Reduce(&basis[1][0], &basis_root[sysdim], fft_dim-sysdim, MPI_DOUBLE, MPI_SUM, 0, world);
if (me == 0){ // output dynamic matrix by root
@@ -772,7 +773,8 @@ void FixPhonon::postprocess( )
}
fflush(flog);
}
-
+ delete[] kbtsqrt;
+ delete[] basis_root;
} // end of postprocess
/* ----------------------------------------------------------------------
diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp
index f8968bfda2ca289c7375f3a39645d5cdc161f096..3bf12d19d2ab3217e44bea084f53523706328425 100644
--- a/src/USER-QUIP/pair_quip.cpp
+++ b/src/USER-QUIP/pair_quip.cpp
@@ -303,7 +303,7 @@ void PairQUIP::init_style()
if (force->newton_pair != 1)
error->all(FLERR,"Pair style quip requires newton pair on");
- // Initialise neighbour list
+ // Initialise neighbor list
int irequest_full = neighbor->request(this);
neighbor->requests[irequest_full]->id = 1;
neighbor->requests[irequest_full]->half = 0;
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/USER-SMD/fix_smd_integrate_ulsph.h
index ea4f46ce530ea0d40606c1c3aa157707f2a91e5a..9d954bf529aaf00ddf1df307d7f3a0b1d012538f 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.h
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.h
@@ -48,7 +48,7 @@ class FixSMDIntegrateUlsph : public Fix {
private:
class NeighList *list;
protected:
- double dtv,dtf, vlimit, vlimitsq;;
+ double dtv,dtf, vlimit, vlimitsq;
int mass_require;
bool xsphFlag;
bool adjust_radius_flag;
diff --git a/src/USER-UEF/fix_nh_uef.h b/src/USER-UEF/fix_nh_uef.h
index 43f5bb46a9f2c97c6f3a5f784506d3c9839aed56..0629db5aa176c96e74271aef1b43e08383e0279b 100644
--- a/src/USER-UEF/fix_nh_uef.h
+++ b/src/USER-UEF/fix_nh_uef.h
@@ -23,7 +23,7 @@ namespace LAMMPS_NS {
// forward declaration
namespace UEF_utils {
class UEFBox;
- };
+ }
class FixNHUef : public FixNH {
public:
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index 8b5ab60f050777cd73fa8e93c8ba3307a0e1459a..751c4746ba5286aaa39a2b9089a4e4d1ec217a49 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -323,9 +323,13 @@ void CreateBonds::single_bond()
// check that 2 atoms exist
+ const int nlocal = atom->nlocal;
+ const int idx1 = atom->map(batom1);
+ const int idx2 = atom->map(batom2);
+
int count = 0;
- if (atom->map(batom1) >= 0) count++;
- if (atom->map(batom2) >= 0) count++;
+ if ((idx1 >= 0) && (idx1 < nlocal)) count++;
+ if ((idx2 >= 0) && (idx2 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@@ -338,7 +342,7 @@ void CreateBonds::single_bond()
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
- if ((m = atom->map(batom1)) >= 0) {
+ if ((m = idx1) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
@@ -349,7 +353,7 @@ void CreateBonds::single_bond()
if (force->newton_bond) return;
- if ((m = atom->map(batom2)) >= 0) {
+ if ((m = idx2) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
@@ -366,10 +370,15 @@ void CreateBonds::single_angle()
// check that 3 atoms exist
+ const int nlocal = atom->nlocal;
+ const int idx1 = atom->map(aatom1);
+ const int idx2 = atom->map(aatom2);
+ const int idx3 = atom->map(aatom3);
+
int count = 0;
- if (atom->map(aatom1) >= 0) count++;
- if (atom->map(aatom2) >= 0) count++;
- if (atom->map(aatom3) >= 0) count++;
+ if ((idx1 >= 0) && (idx1 < nlocal)) count++;
+ if ((idx2 >= 0) && (idx2 < nlocal)) count++;
+ if ((idx3 >= 0) && (idx3 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@@ -384,7 +393,7 @@ void CreateBonds::single_angle()
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
- if ((m = atom->map(aatom2)) >= 0) {
+ if ((m = idx2) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@@ -397,7 +406,7 @@ void CreateBonds::single_angle()
if (force->newton_bond) return;
- if ((m = atom->map(aatom1)) >= 0) {
+ if ((m = idx1) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@@ -407,7 +416,7 @@ void CreateBonds::single_angle()
num_angle[m]++;
}
- if ((m = atom->map(aatom3)) >= 0) {
+ if ((m = idx3) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@@ -426,11 +435,17 @@ void CreateBonds::single_dihedral()
// check that 4 atoms exist
+ const int nlocal = atom->nlocal;
+ const int idx1 = atom->map(datom1);
+ const int idx2 = atom->map(datom2);
+ const int idx3 = atom->map(datom3);
+ const int idx4 = atom->map(datom4);
+
int count = 0;
- if (atom->map(datom1) >= 0) count++;
- if (atom->map(datom2) >= 0) count++;
- if (atom->map(datom3) >= 0) count++;
- if (atom->map(datom4) >= 0) count++;
+ if ((idx1 >= 0) && (idx1 < nlocal)) count++;
+ if ((idx2 >= 0) && (idx2 < nlocal)) count++;
+ if ((idx3 >= 0) && (idx3 < nlocal)) count++;
+ if ((idx4 >= 0) && (idx4 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@@ -446,7 +461,7 @@ void CreateBonds::single_dihedral()
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_atom4;
- if ((m = atom->map(datom2)) >= 0) {
+ if ((m = idx2) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@@ -461,7 +476,7 @@ void CreateBonds::single_dihedral()
if (force->newton_bond) return;
- if ((m = atom->map(datom1)) >= 0) {
+ if ((m = idx1) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@@ -473,7 +488,7 @@ void CreateBonds::single_dihedral()
num_dihedral[m]++;
}
- if ((m = atom->map(datom3)) >= 0) {
+ if ((m = idx3) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@@ -485,7 +500,7 @@ void CreateBonds::single_dihedral()
num_dihedral[m]++;
}
- if ((m = atom->map(datom4)) >= 0) {
+ if ((m = idx4) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
diff --git a/src/fix_group.cpp b/src/fix_group.cpp
index d316f52425bcc914a043afee82762351ae6c8954..2447002bc5202350b779d390dc31124a7f5dd5a1 100644
--- a/src/fix_group.cpp
+++ b/src/fix_group.cpp
@@ -251,3 +251,13 @@ void FixGroup::set_group()
if (varflag) memory->destroy(var);
}
+
+/* ---------------------------------------------------------------------- */
+
+void *FixGroup::extract(const char *str, int &unused)
+{
+ if (strcmp(str,"property") == 0 && propflag) return (void *) idprop;
+ if (strcmp(str,"variable") == 0 && varflag) return (void *) idvar;
+ if (strcmp(str,"region") == 0 && regionflag) return (void *) idregion;
+ return NULL;
+}
diff --git a/src/fix_group.h b/src/fix_group.h
index 070b4801bca3a9e8ab1a15379a52a2182c7bc38c..f3fecac31605a8a38b84a11b35ca2b27456dd9c8 100644
--- a/src/fix_group.h
+++ b/src/fix_group.h
@@ -33,6 +33,7 @@ class FixGroup : public Fix {
void setup(int);
void post_integrate();
void post_integrate_respa(int,int);
+ void *extract(const char *,int &);
private:
int gbit,gbitinverse;
@@ -69,7 +70,7 @@ Self-explanatory.
E: Per atom property for group dynamic does not exist
-UNDOCUMENTED
+Self-explanatory.
E: Group dynamic parent group cannot be dynamic
@@ -79,10 +80,6 @@ E: Variable for group dynamic is invalid style
The variable must be an atom-style variable.
-E: Per-atom property for group dynamic does not exist
-
-UNDOCUMENTED
-
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 initial stage
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index 0f6c86ba5bc610f6e3d63e7921a47eca9432ec2e..09cb8946e51d86692b201e4e5473f8839b0fc30a 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -45,7 +45,7 @@ enum{BOND,ANGLE,DIHEDRAL};
FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- rstyle(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),
+ rstyle(NULL), mult(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),
cos_target(NULL), sin_target(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix restrain command");
@@ -65,6 +65,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
if (nrestrain == maxrestrain) {
maxrestrain += DELTA;
memory->grow(rstyle,maxrestrain,"restrain:rstyle");
+ memory->grow(mult,maxrestrain,"restrain:mult");
memory->grow(ids,maxrestrain,4,"restrain:ids");
memory->grow(kstart,maxrestrain,"restrain:kstart");
memory->grow(kstop,maxrestrain,"restrain:kstop");
@@ -96,6 +97,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+8 > narg) error->all(FLERR,"Illegal fix restrain command");
rstyle[nrestrain] = DIHEDRAL;
+ mult[nrestrain] = 1;
ids[nrestrain][0] = force->inumeric(FLERR,arg[iarg+1]);
ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]);
ids[nrestrain][2] = force->inumeric(FLERR,arg[iarg+3]);
@@ -107,6 +109,13 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
cos_target[nrestrain] = cos(target[nrestrain]);
sin_target[nrestrain] = sin(target[nrestrain]);
iarg += 8;
+ if ((iarg < narg) && (strcmp("mult",arg[iarg]) == 0)) {
+ if (iarg+1 > narg) error->all(FLERR,"Illegal fix restrain command");
+ mult[nrestrain] = force->inumeric(FLERR,arg[iarg+1]);
+ if (mult[nrestrain] < 0)
+ error->all(FLERR,"Illegal fix restrain command");
+ iarg += 2;
+ }
} else error->all(FLERR,"Illegal fix restrain command");
nrestrain++;
@@ -123,6 +132,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
FixRestrain::~FixRestrain()
{
memory->destroy(rstyle);
+ memory->destroy(mult);
memory->destroy(ids);
memory->destroy(kstart);
memory->destroy(kstop);
@@ -410,7 +420,7 @@ void FixRestrain::restrain_angle(int m)
void FixRestrain::restrain_dihedral(int m)
{
- int i1,i2,i3,i4,i,mult;
+ int i1,i2,i3,i4,i;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
@@ -534,11 +544,10 @@ void FixRestrain::restrain_dihedral(int m)
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
- mult = 1; // multiplicity
p = 1.0;
df1 = 0.0;
- for (i = 0; i < mult; i++) {
+ for (i = 0; i < mult[m]; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
p = ddf1;
@@ -546,7 +555,7 @@ void FixRestrain::restrain_dihedral(int m)
p = p*cos_target[m] + df1*sin_target[m];
df1 = df1*cos_target[m] - ddf1*sin_target[m];
- df1 *= -mult;
+ df1 *= -mult[m];
p += 1.0;
energy += k * p;
diff --git a/src/fix_restrain.h b/src/fix_restrain.h
index a6f23f86c6c311afeee63dac0b1da5b9456e20ce..14699ed5af38965d0e42768aec6e2fc114d3deea 100644
--- a/src/fix_restrain.h
+++ b/src/fix_restrain.h
@@ -41,6 +41,7 @@ class FixRestrain : public Fix {
int ilevel_respa;
int nrestrain,maxrestrain;
int *rstyle;
+ int *mult;
int **ids;
double *kstart,*kstop,*target;
double *cos_target,*sin_target;
diff --git a/src/image.cpp b/src/image.cpp
index 599ac4a09132c1917f087cf2c89d6270dd696519..301a2af88f23588dfcdea129fe2c283ae6269cb0 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -1065,7 +1065,7 @@ void Image::write_PNG(FILE *fp)
png_set_text(png_ptr,info_ptr,text_ptr,1);
png_write_info(png_ptr,info_ptr);
- png_bytep row_pointers[height];
+ png_bytep *row_pointers = new png_bytep[height];
for (int i=0; i < height; ++i)
row_pointers[i] = (png_bytep) &writeBuffer[(height-i-1)*3*width];
@@ -1073,6 +1073,7 @@ void Image::write_PNG(FILE *fp)
png_write_end(png_ptr, info_ptr);
png_destroy_write_struct(&png_ptr, &info_ptr);
+ delete[] row_pointers;
#endif
}
diff --git a/src/library.cpp b/src/library.cpp
index 865bf2a0a5d41bda4e5f5c8ec349e1b2903b96af..0162c560cea7e21b66cc759a481aae6420c86d51 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -933,7 +933,7 @@ void lammps_gather_atoms_concat(void *ptr, char *name,
BEGIN_CAPTURE
{
- int i,j,offset;
+ int i,offset;
// error if tags are not defined
// NOTE: test that name = image or ids is not a 64-bit int in code?
@@ -975,7 +975,6 @@ void lammps_gather_atoms_concat(void *ptr, char *name,
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
@@ -1117,7 +1116,6 @@ void lammps_gather_atoms_subset(void *ptr, char *name,
lmp->memory->create(copy,count*ndata,"lib/gather:copy");
for (i = 0; i < count*ndata; i++) copy[i] = 0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
@@ -1163,7 +1161,6 @@ void lammps_gather_atoms_subset(void *ptr, char *name,
lmp->memory->create(copy,count*ndata,"lib/gather:copy");
for (i = 0; i < count*ndata; i++) copy[i] = 0.0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
diff --git a/src/molecule.cpp b/src/molecule.cpp
index b03142e98498eeffeeb106965098fc925ef89634..56e56dab2cd16ef45c9c6068161c29a4815d51ca 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -1111,7 +1111,7 @@ void Molecule::special_generate()
{
int newton_bond = force->newton_bond;
tagint atom1,atom2;
- int count[natoms];
+ int *count = new int[natoms];
// temporary array for special atoms
@@ -1197,6 +1197,7 @@ void Molecule::special_generate()
}
}
}
+ delete[] count;
maxspecial = 0;
for (int i = 0; i < natoms; i++)