diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index bcffc30549db4198f907cfbd88700dd0d63449ea..0fbab732c88736e982e17f3d86fa55aa1a84bc0a 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -1073,7 +1073,7 @@ package"_Section_start.html#start_3.
"table/rx"_pair_table_rx.html,
"tersoff/table (o)"_pair_tersoff.html,
"thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
+"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
:line
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 579cb684740513eba174adfa2e07c68ddee50ee5..f2f2561af84cc944ad7635f10366f006e64ffbaf 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -1938,7 +1938,7 @@ documentation in the src/library.cpp file for details, including
which quantities can be queried by name:
void *lammps_extract_global(void *, char *)
-void lammps_extract_box(void *, double *, double *,
+void lammps_extract_box(void *, double *, double *,
double *, double *, double *, int *, int *)
void *lammps_extract_atom(void *, char *)
void *lammps_extract_compute(void *, char *, int, int)
@@ -2682,14 +2682,14 @@ bond_coeff 2 25.724 0.0 :pre
When running dynamics with the adiabatic core/shell model, the
following issues should be considered. The relative motion of
-the core and shell particles corresponds to the polarization,
-hereby an instantaneous relaxation of the shells is approximated
+the core and shell particles corresponds to the polarization,
+hereby an instantaneous relaxation of the shells is approximated
and a fast core/shell spring frequency ensures a nearly constant
-internal kinetic energy during the simulation.
+internal kinetic energy during the simulation.
Thermostats can alter this polarization behaviour, by scaling the
-internal kinetic energy, meaning the shell will not react freely to
-its electrostatic environment.
-Therefore it is typically desirable to decouple the relative motion of
+internal kinetic energy, meaning the shell will not react freely to
+its electrostatic environment.
+Therefore it is typically desirable to decouple the relative motion of
the core/shell pair, which is an imaginary degree of freedom, from the
real physical system. To do that, the "compute
temp/cs"_compute_temp_cs.html command can be used, in conjunction with
@@ -2721,13 +2721,13 @@ fix thermostatequ all nve # integrator as needed f
fix_modify thermoberendsen temp CSequ
thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
-The pressure for the core/shell system is computed via the regular
-LAMMPS convention by "treating the cores and shells as individual
-particles"_#MitchellFincham2. For the thermo output of the pressure
-as well as for the application of a barostat, it is necessary to
-use an additional "pressure"_compute_pressure compute based on the
-default "temperature"_compute_temp and specifying it as a second
-argument in "fix modify"_fix_modify.html and
+The pressure for the core/shell system is computed via the regular
+LAMMPS convention by "treating the cores and shells as individual
+particles"_#MitchellFincham2. For the thermo output of the pressure
+as well as for the application of a barostat, it is necessary to
+use an additional "pressure"_compute_pressure compute based on the
+default "temperature"_compute_temp and specifying it as a second
+argument in "fix modify"_fix_modify.html and
"thermo_modify"_thermo_modify.html resulting in:
(...)
@@ -2757,18 +2757,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
velocity all create 1427 134 bias yes temp CSequ
velocity all scale 1427 temp CSequ :pre
-To maintain the correct polarizability of the core/shell pairs, the
-kinetic energy of the internal motion shall remain nearly constant.
-Therefore the choice of spring force and mass ratio need to ensure
-much faster relative motion of the 2 atoms within the core/shell pair
-than their center-of-mass velocity. This allows the shells to
-effectively react instantaneously to the electrostatic environment and
+To maintain the correct polarizability of the core/shell pairs, the
+kinetic energy of the internal motion shall remain nearly constant.
+Therefore the choice of spring force and mass ratio need to ensure
+much faster relative motion of the 2 atoms within the core/shell pair
+than their center-of-mass velocity. This allows the shells to
+effectively react instantaneously to the electrostatic environment and
limits energy transfer to or from the core/shell oscillators.
This fast movement also dictates the timestep that can be used.
The primary literature of the adiabatic core/shell model suggests that
the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment.
+energy transfer to the environment.
The mentioned energy transfer will typically lead to a small drift
in total energy over time. This internal energy can be monitored
using the "compute chunk/atom"_compute_chunk_atom.html and "compute
@@ -2790,7 +2790,7 @@ pairs as chunks.
For example if core/shell pairs are the only molecules:
-read_data NaCl_CS_x0.1_prop.data
+read_data NaCl_CS_x0.1_prop.data
compute prop all property/atom molecule
compute cs_chunk all chunk/atom c_prop
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 14b2c0baa32e9387974718fc6b6d7043589ce996..24506379c374dce7b0af027ae0d1e269fbf648e5 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -585,7 +585,7 @@ do not recommend building with other acceleration packages installed
make yes-kokkos
make machine :pre
-
+
make no-kokkos
make machine :pre
@@ -839,13 +839,13 @@ written and read in parallel.
Note that MPIIO is part of the standard message-passing interface
(MPI) library, so you should not need any additional compiler or link
settings, beyond what LAMMPS normally uses for MPI on your system.
-
+
make yes-mpiio
make machine :pre
-
+
make no-mpiio
make machine :pre
-
+
[Supporting info:]
src/MPIIO: filenames -> commands
@@ -855,7 +855,7 @@ src/MPIIO: filenames -> commands
"read_restart"_read_restart.html :ul
:line
-
+
MSCG package :link(mscg),h4
[Contents:]
@@ -914,7 +914,7 @@ lib/mscg/README
examples/mscg :ul
:line
-
+
OPT package :link(OPT),h4
[Contents:]
@@ -1387,7 +1387,7 @@ atomic information to continuum fields.
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
[Install or un-install:]
-
+
Before building LAMMPS with this package, you must first build the ATC
library in lib/atc. You can do this manually if you prefer; follow
the instructions in lib/atc/README. You can also do it in one step
@@ -1420,10 +1420,10 @@ usual manner:
make yes-user-atc
make machine :pre
-
+
make no-user-atc
make machine :pre
-
+
[Supporting info:]
src/USER-ATC: filenames -> commands
@@ -1446,7 +1446,7 @@ model.
[Author:] Ilya Valuev (JIHT, Russia).
[Install or un-install:]
-
+
Before building LAMMPS with this package, you must first build the
AWPMD library in lib/awpmd. You can do this manually if you prefer;
follow the instructions in lib/awpmd/README. You can also do it in
@@ -1479,10 +1479,10 @@ usual manner:
make yes-user-awpmd
make machine :pre
-
+
make no-user-awpmd
make machine :pre
-
+
[Supporting info:]
src/USER-AWPMD: filenames -> commands
@@ -1505,13 +1505,13 @@ stability.
[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
[Install or un-install:]
-
+
make yes-user-cgdna
make machine :pre
-
+
make no-user-cgdna
make machine :pre
-
+
[Supporting info:]
src/USER-CGDNA: filenames -> commands
@@ -1536,13 +1536,13 @@ acids.
[Author:] Axel Kohlmeyer (Temple U).
[Install or un-install:]
-
+
make yes-user-cgsdk
make machine :pre
-
+
make no-user-cgsdk
make machine :pre
-
+
[Supporting info:]
src/USER-CGSDK: filenames -> commands
@@ -1570,7 +1570,7 @@ by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
Jerome Henin (LISM, CNRS, Marseille, France).
[Install or un-install:]
-
+
Before building LAMMPS with this package, you must first build the
COLVARS library in lib/colvars. You can do this manually if you
prefer; follow the instructions in lib/colvars/README. You can also
@@ -1594,10 +1594,10 @@ usual manner:
make yes-user-colvars
make machine :pre
-
+
make no-user-colvars
make machine :pre
-
+
[Supporting info:]
src/USER-COLVARS: filenames -> commands
@@ -1619,13 +1619,13 @@ intensities based on kinematic diffraction theory.
[Author:] Shawn Coleman while at the U Arkansas.
[Install or un-install:]
-
+
make yes-user-diffraction
make machine :pre
-
+
make no-user-diffraction
make machine :pre
-
+
[Supporting info:]
src/USER-DIFFRACTION: filenames -> commands
@@ -1654,13 +1654,13 @@ algorithm.
Brennan (ARL).
[Install or un-install:]
-
+
make yes-user-dpd
make machine :pre
-
+
make no-user-dpd
make machine :pre
-
+
[Supporting info:]
src/USER-DPD: filenames -> commands
@@ -1696,13 +1696,13 @@ tools/drude.
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
[Install or un-install:]
-
+
make yes-user-drude
make machine :pre
-
+
make no-user-drude
make machine :pre
-
+
[Supporting info:]
src/USER-DRUDE: filenames -> commands
@@ -1734,13 +1734,13 @@ tools/eff; see its README file.
[Author:] Andres Jaramillo-Botero (CalTech).
[Install or un-install:]
-
+
make yes-user-eff
make machine :pre
-
+
make no-user-eff
make machine :pre
-
+
[Supporting info:]
src/USER-EFF: filenames -> commands
@@ -1773,13 +1773,13 @@ for using this package in tools/fep; see its README file.
[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
[Install or un-install:]
-
+
make yes-user-fep
make machine :pre
-
+
make no-user-fep
make machine :pre
-
+
[Supporting info:]
src/USER-FEP: filenames -> commands
@@ -1836,13 +1836,13 @@ file.
You can then install/un-install the package and build LAMMPS in the
usual manner:
-
+
make yes-user-h5md
make machine :pre
-
+
make no-user-h5md
make machine :pre
-
+
[Supporting info:]
src/USER-H5MD: filenames -> commands
@@ -1908,7 +1908,7 @@ explained in "Section 5.3.2"_accelerate_intel.html.
make yes-user-intel yes-user-omp
make machine :pre
-
+
make no-user-intel no-user-omp
make machine :pre
@@ -1938,13 +1938,13 @@ can be used to model MD particles influenced by hydrodynamic forces.
Ontario).
[Install or un-install:]
-
+
make yes-user-lb
make machine :pre
-
+
make no-user-lb
make machine :pre
-
+
[Supporting info:]
src/USER-LB: filenames -> commands
@@ -1972,13 +1972,13 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
[Install or un-install:]
-
+
make yes-user-mgpt
make machine :pre
-
+
make no-user-mgpt
make machine :pre
-
+
[Supporting info:]
src/USER-MGPT: filenames -> commands
@@ -2000,13 +2000,13 @@ dihedral, improper, or command style.
src/USER-MISC/README file.
[Install or un-install:]
-
+
make yes-user-misc
make machine :pre
-
+
make no-user-misc
make machine :pre
-
+
[Supporting info:]
src/USER-MISC: filenames -> commands
@@ -2031,13 +2031,13 @@ n = grad(g).
Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
[Install or un-install:]
-
+
make yes-user-manifold
make machine :pre
-
+
make no-user-manifold
make machine :pre
-
+
[Supporting info:]
src/USER-MANIFOLD: filenames -> commands
@@ -2080,7 +2080,7 @@ at
[Author:] Axel Kohlmeyer (Temple U).
[Install or un-install:]
-
+
Note that the lib/molfile/Makefile.lammps file has a setting for a
dynamic loading library libdl.a that should is typically present on
all systems, which is required for LAMMPS to link with this package.
@@ -2090,10 +2090,10 @@ lib/molfile/Makefile.lammps for details.
make yes-user-molfile
make machine :pre
-
+
make no-user-molfile
make machine :pre
-
+
[Supporting info:]
src/USER-MOLFILE: filenames -> commands
@@ -2128,7 +2128,7 @@ tools:
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
[Install or un-install:]
-
+
Note that to follow these steps, you need the standard NetCDF software
package installed on your system. The lib/netcdf/Makefile.lammps file
has settings for NetCDF include and library files that LAMMPS needs to
@@ -2138,7 +2138,7 @@ lib/netcdf/README for details.
make yes-user-netcdf
make machine :pre
-
+
make no-user-netcdf
make machine :pre
@@ -2178,10 +2178,10 @@ Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
[Install or un-install:]
-
+
make yes-user-omp
make machine :pre
-
+
make no-user-omp
make machine :pre
@@ -2213,13 +2213,13 @@ relations, directly from molecular dynamics simulations.
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
[Install or un-install:]
-
+
make yes-user-phonon
make machine :pre
-
+
make no-user-phonon
make machine :pre
-
+
[Supporting info:]
src/USER-PHONON: filenames -> commands
@@ -2235,7 +2235,7 @@ USER-QMMM package :link(USER-QMMM),h4
A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
QM/MM simulation, currently only in combination with the "Quantum
-ESPRESSO"_espresso package.
+ESPRESSO"_espresso package.
:link(espresso,http://www.quantum-espresso.org)
@@ -2275,7 +2275,7 @@ usual manner:
make yes-user-qmmm
make machine :pre
-
+
make no-user-qmmm
make machine :pre
@@ -2284,7 +2284,7 @@ for a QM/MM simulation. You must also build Quantum ESPRESSO and
create a new executable which links LAMMPS and Quanutm ESPRESSO
together. These are steps 3 and 4 described in the lib/qmmm/README
file.
-
+
[Supporting info:]
src/USER-QMMM: filenames -> commands
@@ -2312,13 +2312,13 @@ simulation.
[Author:] Yuan Shen (Stanford U).
[Install or un-install:]
-
+
make yes-user-qtb
make machine :pre
-
+
make no-user-qtb
make machine :pre
-
+
[Supporting info:]
src/USER-QTB: filenames -> commands
@@ -2362,10 +2362,10 @@ usual manner:
make yes-user-quip
make machine :pre
-
+
make no-user-quip
make machine :pre
-
+
[Supporting info:]
src/USER-QUIP: filenames -> commands
@@ -2388,13 +2388,13 @@ for monitoring molecules as bonds are created and destroyed.
[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
[Install or un-install:]
-
+
make yes-user-reaxc
make machine :pre
-
+
make no-user-reaxc
make machine :pre
-
+
[Supporting info:]
src/USER-REAXC: filenames -> commands
@@ -2451,10 +2451,10 @@ usual manner:
make yes-user-smd
make machine :pre
-
+
make no-user-smd
make machine :pre
-
+
[Supporting info:]
src/USER-SMD: filenames -> commands
@@ -2477,13 +2477,13 @@ ionocovalent bonds in oxides.
Tetot (LAAS-CNRS, France).
[Install or un-install:]
-
+
make yes-user-smtbq
make machine :pre
-
+
make no-user-smtbq
make machine :pre
-
+
[Supporting info:]
src/USER-SMTBQ: filenames -> commands
@@ -2516,13 +2516,13 @@ property/atom"_compute_property_atom.html command.
Dynamics, Ernst Mach Institute, Germany).
[Install or un-install:]
-
+
make yes-user-sph
make machine :pre
-
+
make no-user-sph
make machine :pre
-
+
[Supporting info:]
src/USER-SPH: filenames -> commands
@@ -2544,13 +2544,13 @@ stress, etc) about individual interactions.
[Author:] Axel Kohlmeyer (Temple U).
[Install or un-install:]
-
+
make yes-user-tally
make machine :pre
-
+
make no-user-tally
make machine :pre
-
+
[Supporting info:]
src/USER-TALLY: filenames -> commands
@@ -2577,7 +2577,7 @@ system.
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
[Install or un-install:]
-
+
The lib/vtk/Makefile.lammps file has settings for accessing VTK files
and its library, which are required for LAMMPS to build and link with
this package. If the settings are not valid for your system, check if
@@ -2590,10 +2590,10 @@ usual manner:
make yes-user-vtk
make machine :pre
-
+
make no-user-vtk
make machine :pre
-
+
[Supporting info:]
src/USER-VTK: filenames -> commands
diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt
index 718e9e229c80816f368eaf4a3f215a6555f6b593..1e67fca321aa58a5fef7f71cb7d7b061e0326ae2 100644
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@@ -714,7 +714,7 @@ stored in the "image" property. All three image flags are stored in
a packed format in a single integer, so count would be 1 to retrieve
that integer, however also a count value of 3 can be used and then
the image flags will be unpacked into 3 individual integers, ordered
-in a similar fashion as coordinates.
+in a similar fashion as coordinates.
Note that the data structure gather_atoms("x") returns is different
from the data structure returned by extract_atom("x") in four ways.
diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt
index ed9e4ae833afeac0bbc59c105ce2ad67fea137d7..f5bd66aebaf7ec6c640f1fbe08fb5e844a4ca8ea 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@@ -42,11 +42,11 @@ precision mode. Performance improvements are shown compared to
LAMMPS {without using other acceleration packages} as these are
under active development (and subject to performance changes). The
measurements were performed using the input files available in
-the src/USER-INTEL/TEST directory with the provided run script.
-These are scalable in size; the results given are with 512K
-particles (524K for Liquid Crystal). Most of the simulations are
+the src/USER-INTEL/TEST directory with the provided run script.
+These are scalable in size; the results given are with 512K
+particles (524K for Liquid Crystal). Most of the simulations are
standard LAMMPS benchmarks (indicated by the filename extension in
-parenthesis) with modifications to the run length and to add a
+parenthesis) with modifications to the run length and to add a
warmup run (for use with offload benchmarks).
:c,image(JPG/user_intel.png)
@@ -64,30 +64,30 @@ simulation rates and instructions to reproduce.
In most molecular dynamics software, parallelization parameters
(# of MPI, OpenMP, and vectorization) can change the results due
-to changing the order of operations with finite-precision
+to changing the order of operations with finite-precision
calculations. The USER-INTEL package is deterministic. This means
that the results should be reproducible from run to run with the
-{same} parallel configurations and when using determinstic
+{same} parallel configurations and when using determinstic
libraries or library settings (MPI, OpenMP, FFT). However, there
are differences in the USER-INTEL package that can change the
order of operations compared to LAMMPS without acceleration:
Neighbor lists can be created in a different order :ulb,l
Bins used for sorting atoms can be oriented differently :l
-The default stencil order for PPPM is 7. By default, LAMMPS will
-calculate other PPPM parameters to fit the desired acuracy with
+The default stencil order for PPPM is 7. By default, LAMMPS will
+calculate other PPPM parameters to fit the desired acuracy with
this order :l
The {newton} setting applies to all atoms, not just atoms shared
between MPI tasks :l
Vectorization can change the order for adding pairwise forces :l
:ule
-The precision mode (described below) used with the USER-INTEL
-package can change the {accuracy} of the calculations. For the
-default {mixed} precision option, calculations between pairs or
-triplets of atoms are performed in single precision, intended to
+The precision mode (described below) used with the USER-INTEL
+package can change the {accuracy} of the calculations. For the
+default {mixed} precision option, calculations between pairs or
+triplets of atoms are performed in single precision, intended to
be within the inherent error of MD simulations. All accumulation
-is performed in double precision to prevent the error from growing
+is performed in double precision to prevent the error from growing
with the number of atoms in the simulation. {Single} precision
mode should not be used without appropriate validation.
@@ -106,7 +106,7 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
For some of the simple 2-body potentials without long-range
electrostatics, performance and scalability can be better with
the "newton off" setting added to the input script :l
-If using {kspace_style pppm} in the input script, add
+If using {kspace_style pppm} in the input script, add
"kspace_modify diff ad" for better performance :l
:ule
@@ -115,12 +115,12 @@ For Intel Xeon Phi CPUs:
Runs should be performed using MCDRAM. :ulb,l
:ule
-For simulations using {kspace_style pppm} on Intel CPUs
+For simulations using {kspace_style pppm} on Intel CPUs
supporting AVX-512:
Add "kspace_modify diff ad" to the input script :ulb,l
-The command-line option should be changed to
-"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
+The command-line option should be changed to
+"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
threads minus 1. :l
Do not use thread affinity (set KMP_AFFINITY=none) :l
The "newton off" setting may provide better scalability :l
@@ -352,7 +352,7 @@ follow in the input script.
NOTE: The USER-INTEL package will perform better with modifications
to the input script when "PPPM"_kspace_style.html is used:
-"kspace_modify diff ad"_kspace_modify.html should be added to the
+"kspace_modify diff ad"_kspace_modify.html should be added to the
input script.
Long-Range Thread (LRT) mode is an option to the "package
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index f9b35a167c5f82275cf47e605f9eb8504e8f4757..2add6f4c2f0fb1f31aabaccca596cddbb41c5687 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -30,7 +30,7 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
to define a modified finite extensible nonlinear elastic (FENE) potential
"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
-in the oxDNA force field for coarse-grained modelling of DNA.
+in the oxDNA force field for coarse-grained modelling of DNA.
The following coefficients must be defined for the bond type via the
"bond_coeff"_bond_coeff.html command as given in the above example, or in
@@ -43,8 +43,8 @@ r0 (distance) :ul
NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles
for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
-and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
-"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
+and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
+"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
style {oxdna2/dh} have to be defined.
The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
@@ -66,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
-"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
+"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
[Default:] none
diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt
index 9aa63c84de2be20dbdb5e4494427404f637e664e..16a51f5241f16ee058553a6e4634ec578219712c 100644
--- a/doc/src/compute_cnp_atom.txt
+++ b/doc/src/compute_cnp_atom.txt
@@ -42,7 +42,7 @@ where the index {j} goes over the {n}i nearest neighbors of atom
{i}, and the index {k} goes over the {n}ij common nearest neighbors
between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom
{k} to atoms {i} and {j}. The quantity in the double sum is computed
-for each atom.
+for each atom.
The CNP calculation is sensitive to the specified cutoff value.
You should ensure that the appropriate nearest neighbors of an atom are
diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt
index 012121099454b45d3ea43fa025aba16de6257f22..16aaba4667396dfc038c9f7625fdca532a8cd04b 100644
--- a/doc/src/compute_pair_local.txt
+++ b/doc/src/compute_pair_local.txt
@@ -76,7 +76,9 @@ command for the types of the two atoms is used. For the {radius}
setting, the sum of the radii of the two particles is used as a
cutoff. For example, this is appropriate for granular particles which
only interact when they are overlapping, as computed by "granular pair
-styles"_pair_gran.txt.
+styles"_pair_gran.txt. Note that if a granular model defines atom
+types such that all particles of a specific type are monodisperse
+(same diameter), then the two settings are effectively identical.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt
index f7851e864bfbb14cef1a8e055592018a00ba609c..39106a39c890cae655d635216bbe93876f43fc74 100644
--- a/doc/src/compute_property_local.txt
+++ b/doc/src/compute_property_local.txt
@@ -79,6 +79,9 @@ the two atoms is used. For the {radius} setting, the sum of the radii
of the two particles is used as a cutoff. For example, this is
appropriate for granular particles which only interact when they are
overlapping, as computed by "granular pair styles"_pair_gran.html.
+Note that if a granular model defines atom types such that all
+particles of a specific type are monodisperse (same diameter), then
+the two settings are effectively identical.
If the inputs are bond, angle, etc attributes, the local data is
generated by looping over all the atoms owned on a processor and
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 918755ec3889678eacc5625f5b43bc401fb1a301..73dc67cdefef9bf3d853be18e4f4032b62e767d7 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -138,7 +138,15 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This dihedral style can only be used if LAMMPS was built with the
+When using run_style "respa"_run_style.html, these dihedral styles
+must be assigned to the same r-RESPA level as {pair} or {outer}.
+
+When used in combination with CHARMM pair styles, the 1-4
+"special_bonds"_special_bonds.html scaling factors must be set to 0.0.
+Otherwise non-bonded contributions for these 1-4 pairs will be
+computed multiple times.
+
+These dihedral styles can only be used if LAMMPS was built with the
MOLECULE package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt
index 21502e7f491dd32a774509644ee4b6267f14d259..d4d28c81fca69cea2fb65d72e940acf4de0fdcb0 100644
--- a/doc/src/dump_vtk.txt
+++ b/doc/src/dump_vtk.txt
@@ -16,7 +16,7 @@ ID = user-assigned name for the dump
group-ID = ID of the group of atoms to be dumped
vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page)
N = dump every this many timesteps
-file = name of file to write dump info to
+file = name of file to write dump info to
args = same as arguments for "dump_style custom"_dump.html :ul
[Examples:]
@@ -83,7 +83,7 @@ Triclinic simulation boxes (non-orthogonal) are saved as
hexahedrons in either legacy .vtk or .vtu XML format.
Style {vtk} allows you to specify a list of atom attributes to be
-written to the dump file for each atom. The list of possible attributes
+written to the dump file for each atom. The list of possible attributes
is the same as for the "dump_style custom"_dump.html command; see
its doc page for a listing and an explanation of each attribute.
diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt
index 54decd6282b972f7282b009e52d8f0131988ccac..e3d75ee858ea82013a59441cbc1fe016fcd19670 100644
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@@ -245,7 +245,7 @@ appear the system is converging to your specified pressure. The
solution for this is to either (a) zero the velocities of all atoms
before performing the minimization, or (b) make sure you are
monitoring the pressure without its kinetic component. The latter can
-be done by outputting the pressure from the pressure compute this
+be done by outputting the pressure from the pressure compute this
command creates (see below) or a pressure compute you define yourself.
NOTE: Because pressure is often a very sensitive function of volume,
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index e8d515e1f32f76f09d966d3d4910997c68108af1..e5e4f772f6d36dc7d2e86f0b2460bc9bd64fbb55 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -45,14 +45,14 @@ species {j} in particle {i}, {u_j} is the internal energy of species j,
{DeltaH_f,j} is the heat of formation of species {j}, N is the number of
molecules represented by the coarse-grained particle, kb is the
Boltzmann constant, and T is the temperature of the system. Additionally,
-it is possible to modify the concentration-dependent particle internal
-energy relation by adding an energy correction, temperature-dependent
+it is possible to modify the concentration-dependent particle internal
+energy relation by adding an energy correction, temperature-dependent
correction, and/or a molecule-dependent correction. An energy correction can
-be specified as a constant (in energy units). A temperature correction can be
-specified by multiplying a temperature correction coefficient by the
-internal temperature. A molecular correction can be specified by
-by multiplying a molecule correction coefficient by the average number of
-product gas particles in the coarse-grain particle.
+be specified as a constant (in energy units). A temperature correction can be
+specified by multiplying a temperature correction coefficient by the
+internal temperature. A molecular correction can be specified by
+by multiplying a molecule correction coefficient by the average number of
+product gas particles in the coarse-grain particle.
Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
internal energy values of each species {u_j} listed in a file as a
@@ -72,12 +72,12 @@ The second filename specifies a file containing heat of formation
{DeltaH_f,j} for each species.
In cases where the coarse-grain particle represents a single molecular
-species (i.e., no reactions occur and fix {rx} is not present in the input file),
-fix {eos/table/rx} can be applied in a similar manner to fix {eos/table}
-within a non-reactive DPD simulation. In this case, the heat of formation
+species (i.e., no reactions occur and fix {rx} is not present in the input file),
+fix {eos/table/rx} can be applied in a similar manner to fix {eos/table}
+within a non-reactive DPD simulation. In this case, the heat of formation
filename is replaced with the heat of formation value for the single species.
-Additionally, the energy correction and temperature correction coefficients may
-also be specified as fix arguments.
+Additionally, the energy correction and temperature correction coefficients may
+also be specified as fix arguments.
:line
@@ -138,8 +138,8 @@ used as the species name must correspond with the tags used to define
the reactions with the "fix rx"_fix_rx.html command.
Alternatively, corrections to the EOS can be included by specifying
-three additional columns that correspond to the energy correction,
-the temperature correction coefficient and molecule correction
+three additional columns that correspond to the energy correction,
+the temperature correction coefficient and molecule correction
coefficient. In this case, the format of the file is as follows:
# HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index a3339648fa8199a1689f11dfaa11a08cf3bf059e..b782d285c768ec6f4b25eaf29037cef6695e7613 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -70,8 +70,8 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Currently, it does not support "molecule templates"_molecule.html.
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 7ac607a2f1e146e1f24e68cf69797402dbda4044..41ec38cffb18c674575a884543fcaa3eb04b705c 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -406,7 +406,7 @@ the user for each subsequent fix gcmc command.
[Default:]
The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
-fugacity_coeff = 1, and full_energy = no,
+fugacity_coeff = 1, and full_energy = no,
except for the situations where full_energy is required, as
listed above.
diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt
index 3fc5c1a10e8a1299d11dbf6fbabe4ab1f1509a34..661f68ed99cf21d5c5a08514d78dff411a28880e 100644
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@@ -85,13 +85,13 @@ No information about this fix is written to "binary restart
files"_restart.html.
The "thermo_modify"_thermo_modify.html {press} option is supported
-by this fix to add the rescaled kinetic pressure as part of
+by this fix to add the rescaled kinetic pressure as part of
"thermodynamic output"_thermo_style.html.
[Restrictions:]
-This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index b1533830bcbd31c35eccfda7279825400be64c82..07e8025d77061db6e41fd3c3e765898664f2ffcd 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -58,14 +58,14 @@ input are listed in the same order as in the data file of LAMMPS. The
initial configuration is ignored, as it will be substituted with the
coordinates received from i-PI before forces are ever evaluated.
-A note of caution when using potentials that contain long-range
+A note of caution when using potentials that contain long-range
electrostatics, or that contain parameters that depend on box size:
all of these options will be initialized based on the cell size in the
-LAMMPS-side initial configuration and kept constant during the run.
-This is required to e.g. obtain reproducible and conserved forces.
-If the cell varies too wildly, it may be advisable to reinitialize
-these interactions at each call. This behavior can be requested by
-setting the {reset} switch.
+LAMMPS-side initial configuration and kept constant during the run.
+This is required to e.g. obtain reproducible and conserved forces.
+If the cell varies too wildly, it may be advisable to reinitialize
+these interactions at each call. This behavior can be requested by
+setting the {reset} switch.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt
index 0e09f8a9c56f1ef73b34ae6bf6f82bbce6912978..7d16967955d1d9988636092d721fe40902386054 100644
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@@ -57,7 +57,7 @@ simulations is as follows:
Perform all-atom simulations on the system to be coarse grained.
Generate a trajectory mapped to the coarse-grained model.
Create input files for the MS-CG library.
-Run the range finder functionality of the MS-CG library.
+Run the range finder functionality of the MS-CG library.
Run the force matching functionality of the MS-CG library.
Check the results of the force matching.
Run coarse-grained simulations using the new coarse-grained potentials. :ol
@@ -70,7 +70,7 @@ Step 2 can be performed using a Python script (what is the name?)
provided with the MS-CG library which defines the coarse-grained model
and converts a standard LAMMPS dump file for an all-atom simulation
(step 1) into a LAMMPS dump file which has the positions of and forces
-on the coarse-grained beads.
+on the coarse-grained beads.
In step 3, an input file named "control.in" is needed by the MS-CG
library which sets parameters for the range finding and force matching
diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt
index b1c00cd25ce56fa4eb2cbfcec2727c8c2622f0dd..7ad51f37685d7da8347dab99a937ad4b5cca3ce5 100644
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@@ -23,13 +23,13 @@ fix 1 all nve/dot :pre
[Description:]
Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
-to a group of atoms, but without Langevin dynamics.
+to a group of atoms, but without Langevin dynamics.
This command performs Molecular dynamics (MD)
-via a velocity-Verlet algorithm and an evolution operator that rotates
-the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
+via a velocity-Verlet algorithm and an evolution operator that rotates
+the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-without damping and noise and can be used to determine the stability range
+without damping and noise and can be used to determine the stability range
in a NVE ensemble prior to using the Langevin-type DOTC-integrator
(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
The command is equivalent to the "fix nve"_fix_nve.html.
diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt
index 19d5b233ce95595b8df29d50200616aaff50aed6..5de8e663c43166d19e1ae88db2a679d8623c0e63 100644
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@@ -28,20 +28,20 @@ fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
[Description:]
-Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
+Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
as described in "(Davidchack)"_#Davidchack2
to a group of atoms, which models an interaction with an implicit background
solvent. This command performs Brownian dynamics (BD)
-via a technique that splits the integration into a deterministic Hamiltonian
-part and the Ornstein-Uhlenbeck process for noise and damping.
+via a technique that splits the integration into a deterministic Hamiltonian
+part and the Ornstein-Uhlenbeck process for noise and damping.
The quaternion degrees of freedom are updated though an evolution
operator which performs a rotation in quaternion space, preserves
the quaternion norm and is akin to "(Miller)"_#Miller2.
-In terms of syntax this command has been closely modelled on the
-"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
-the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
-one single command. The main feature is improved stability
+In terms of syntax this command has been closely modelled on the
+"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
+the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
+one single command. The main feature is improved stability
over the standard integrator, permitting slightly larger timestep sizes.
NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
@@ -57,7 +57,7 @@ Fc is the conservative force computed via the usual inter-particle
interactions ("pair_style"_pair_style.html,
"bond_style"_bond_style.html, etc).
-The Ff and Fr terms are implicitly taken into account by this fix
+The Ff and Fr terms are implicitly taken into account by this fix
on a per-particle basis.
Ff is a frictional drag or viscous damping term proportional to the
@@ -77,7 +77,7 @@ a Gaussian random number) for speed.
:line
-{Tstart} and {Tstop} have to be constant values, i.e. they cannot
+{Tstart} and {Tstop} have to be constant values, i.e. they cannot
be variables.
The {damp} parameter is specified in time units and determines how
@@ -98,16 +98,16 @@ different numbers of processors.
The keyword/value option has to be used in the following way:
-This fix has to be used together with the {angmom} keyword. The
-particles are always considered to have a finite size.
-The keyword {angmom} enables thermostatting of the rotational degrees of
-freedom in addition to the usual translational degrees of freedom.
+This fix has to be used together with the {angmom} keyword. The
+particles are always considered to have a finite size.
+The keyword {angmom} enables thermostatting of the rotational degrees of
+freedom in addition to the usual translational degrees of freedom.
-The scale factor after the {angmom} keyword gives the ratio of the rotational to
+The scale factor after the {angmom} keyword gives the ratio of the rotational to
the translational friction coefficient.
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-A technical report with more information on this integrator can be found
+A technical report with more information on this integrator can be found
"here"_PDF/USER-CGDNA-overview.pdf.
:line
@@ -120,7 +120,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
+"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
[Default:] none
diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt
index 271483b44188f04a503777c20d1a0c01a6dc0c6e..49fd8217ab7a88b90c23afc7ca56295e906ec245 100644
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@@ -27,7 +27,7 @@ timestep. V is volume; K is kinetic energy. This creates a system
trajectory consistent with the isokinetic ensemble.
The equations of motion used are those of Minary et al in
-"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in
+"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in
"(Zhang)"_#nvk-Zhang.
The kinetic energy will be held constant at its value given when fix
diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt
index 5f94f4cdae00fbc51bbb81433edf49dd812fc36f..014a43aacc706e03b37ceb37ca906a1fb248f275 100644
--- a/doc/src/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@@ -89,7 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
group can straddle a periodic boundary. See the "dump"_dump.html doc
page for a discussion of unwrapped coordinates. It also means that a
spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly.
+a periodic boundary and its length be calculated correctly.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
index 40e595e21e41d4a901d9d2afd78e97d771413371..afb1dcf8fffe855b41ac19f62e6504afd8b13540 100644
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@@ -144,7 +144,11 @@ this fix.
"fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html
-[Restrictions:] none
+[Restrictions:]
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
[Default:]
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index a4afc2fe6d529e4efa4507e141ec5ef769775acc..d2e8be3f03298e9bfd9bde20f56ede4ed7675277 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -344,7 +344,7 @@ informations can help understanding what is going wrong. For instance
when the path angle becomes accute the definition of tangent used in
the NEB calculation is questionable and the NEB cannot may diverge
"(Maras)"_#Maras2.
-
+
When running on multiple partitions, LAMMPS produces additional log
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 27fb6c10fe09c622b9599146a93aae7ca3c6ade2..06dcccb9d9fc932b3e7664b1fffbdcc466ce7894 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -40,8 +40,8 @@ vectorial atomic forces.
Only a single pair_coeff command is used with the {agni} style which
specifies an AGNI potential file containing the parameters of the
-force field for the needed elements. These are mapped to LAMMPS atom
-types by specifying N additional arguments after the filename in the
+force field for the needed elements. These are mapped to LAMMPS atom
+types by specifying N additional arguments after the filename in the
pair_coeff command, where N is the number of LAMMPS atom types:
filename
@@ -52,13 +52,13 @@ to specify the path for the force field file.
An AGNI force field is fully specified by the filename which contains the
parameters of the force field, i.e., the reference training environments
-used to construct the machine learning force field. Example force field
-and input files are provided in the examples/USER/misc/agni directory.
+used to construct the machine learning force field. Example force field
+and input files are provided in the examples/USER/misc/agni directory.
:line
-Styles with {omp} suffix is functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster, depending
+Styles with {omp} suffix is functionally the same as the corresponding
+style without the suffix. They have been optimized to run faster, depending
on your available hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated style takes the same arguments and
should produce the same results, except for round-off and precision
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index 49161404c3dd370f97f922079864dd5eeddebd9b..e705e735fb78340795c8e1b2c6b9364e47322aec 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -75,7 +75,7 @@ Lennard-Jones 12/6) given by
:c,image(Eqs/pair_buck.jpg)
where rho is an ionic-pair dependent length parameter, and Rc is the
-cutoff on both terms.
+cutoff on both terms.
The styles with {coul/cut} or {coul/long} or {coul/msm} add a
Coulombic term as described for the "lj/cut"_pair_lj.html pair styles.
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index 47045a5933cef253d1d5c47b1af097d5c0b92139..cbc17d357d398222b23e5431ffbf2b0cbc7c113f 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -55,33 +55,33 @@ defined in the reaction kinetics files specified with the "fix
rx"_fix_rx.html command or they must correspond to the tag "1fluid",
signifying interaction with a product species mixture determined
through a one-fluid approximation. The interaction potential is
-weighted by the geometric average of either the mole fraction concentrations
-or the number of molecules associated with the interacting coarse-grained
-particles (see the {fractional} or {molecular} weighting pair style options).
+weighted by the geometric average of either the mole fraction concentrations
+or the number of molecules associated with the interacting coarse-grained
+particles (see the {fractional} or {molecular} weighting pair style options).
The coarse-grained potential is stored before and after the
reaction kinetics solver is applied, where the difference is defined
to be the internal chemical energy (uChem).
-The fourth argument specifies the type of scaling that will be used
+The fourth argument specifies the type of scaling that will be used
to scale the EXP-6 parameters as reactions occur. Currently, there
are three scaling options: {exponent}, {polynomial} and {none}.
-Exponent scaling requires two additional arguments for scaling
+Exponent scaling requires two additional arguments for scaling
the {Rm} and {epsilon} parameters, respectively. The scaling factor
-is computed by phi^exponent, where phi is the number of molecules
-represented by the coarse-grain particle and exponent is specified
+is computed by phi^exponent, where phi is the number of molecules
+represented by the coarse-grain particle and exponent is specified
as a pair coefficient argument for {Rm} and {epsilon}, respectively.
-The {Rm} and {epsilon} parameters are multiplied by the scaling
+The {Rm} and {epsilon} parameters are multiplied by the scaling
factor to give the scaled interaction parameters for the CG particle.
-Polynomial scaling requires a filename to be specified as a pair
+Polynomial scaling requires a filename to be specified as a pair
coeff argument. The file contains the coefficients to a fifth order
-polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend
-upon phi (the number of molecules represented by the CG particle).
+polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend
+upon phi (the number of molecules represented by the CG particle).
The format of a polynomial file is provided below.
The {none} option to the scaling does not have any additional pair coeff
-arguments. This is equivalent to specifying the {exponent} option with
+arguments. This is equivalent to specifying the {exponent} option with
{Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.
The final argument specifies the interaction cutoff (optional).
@@ -102,7 +102,7 @@ parenthesized comments):
# POLYNOMIAL FILE (one or more comment or blank lines) :pre
# General Functional Form:
-# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F
+# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F
#
# Parameter A B C D E F
(blank)
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index 0879dc34d02a87fe9f928b23fed62cbf0a1eeade..c7a6d4194f0be32b336d72ff99abca4a65ee22f8 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -24,25 +24,25 @@ pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
[Description:]
-The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
-potential as described in "(KC05)"_#KC05. An important simplification is made,
-which is to take all normals along the z-axis.
+The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
+potential as described in "(KC05)"_#KC05. An important simplification is made,
+which is to take all normals along the z-axis.
:c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
-It is important to have a suffiently large cutoff to ensure smooth forces.
-Energies are shifted so that they go continously to zero at the cutoff assuming
+It is important to have a suffiently large cutoff to ensure smooth forces.
+Energies are shifted so that they go continously to zero at the cutoff assuming
that the exponential part of {Vij} (first term) decays sufficiently fast.
This shift is achieved by the last term in the equation for {Vij} above.
-This potential is intended for interactions between two layers of graphene.
-Therefore, to avoid interaction between layers in multi-layered materials,
-each layer should have a separate atom type and interactions should only
+This potential is intended for interactions between two layers of graphene.
+Therefore, to avoid interaction between layers in multi-layered materials,
+each layer should have a separate atom type and interactions should only
be computed between atom types of neighbouring layers.
-The parameter file (e.g. CC.KC), is intended for use with metal
-"units"_units.html, with energies in meV. An additional parameter, {S},
-is available to facilitate scaling of energies in accordance with
+The parameter file (e.g. CC.KC), is intended for use with metal
+"units"_units.html, with energies in meV. An additional parameter, {S},
+is available to facilitate scaling of energies in accordance with
"(vanWijk)"_#vanWijk.
This potential must be used in combination with hybrid/overlay.
@@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
:line
-:link(KC05)
+:link(KC05)
[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
:link(vanWijk)
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt
index bf5d5636fe81f82863f34ce94980350c24a1e538..77ed223e2aa8b4bdf196b66fba72462db77aed55 100644
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@@ -97,9 +97,9 @@ tags must either correspond to the species defined in the reaction
kinetics files specified with the "fix rx"_fix_rx.html command or they
must correspond to the tag "1fluid", signifying interaction with a
product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of
-either the mole fraction concentrations or the number of molecules
-associated with the interacting coarse-grained particles (see the
+The interaction potential is weighted by the geometric average of
+either the mole fraction concentrations or the number of molecules
+associated with the interacting coarse-grained particles (see the
{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
stored before and after the reaction kinetics solver is applied, where
the difference is defined to be the internal chemical energy (uChem).
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index 0a07417fd0aa5b0c36faf78245cfdb395d984c3e..d9734f122df4ff18498fd7490262db8fd649270b 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -39,17 +39,17 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
[Description:]
-The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
+The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
and coaxial stacking interaction {oxdna/coaxstk} as well
as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
opposite strands.
-The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
-in the above example. The individual potentials consist of products of modulation factors,
-which themselves are constructed from a number of more basic potentials
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
+The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
+in the above example. The individual potentials consist of products of modulation factors,
+which themselves are constructed from a number of more basic potentials
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
for a detailed description of the oxDNA force field.
@@ -57,8 +57,8 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
-When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
+The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
+When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
the temperature coefficients have to be matched to the one used in the fix.
@@ -79,7 +79,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
-"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
+"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
[Default:] none
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index 1cc562d5f1b11769b5909642132cf7f491b29c4a..1728a0bc7b0b57019b2d8eca96abdd3a223ba59e 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -45,17 +45,17 @@ pair_coeff * * oxdna2/dh 0.1 1.0 0.815 :pre
[Description:]
-The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
+The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
opposite strands.
-The exact functional form of the pair styles is rather complex.
-The individual potentials consist of products of modulation factors,
-which themselves are constructed from a number of more basic potentials
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
+The exact functional form of the pair styles is rather complex.
+The individual potentials consist of products of modulation factors,
+which themselves are constructed from a number of more basic potentials
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
@@ -63,7 +63,7 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
+Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
the temperature coefficients have to be matched to the one used in the fix.
@@ -86,7 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
-"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
+"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
[Default:] none
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index d089a4f9da057858b8708a2695f8c45d582177c1..f93af21da4172f5b24186c20217b1d82f4d9df2b 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -85,9 +85,9 @@ tags must either correspond to the species defined in the reaction
kinetics files specified with the "fix rx"_fix_rx.html command or they
must correspond to the tag "1fluid", signifying interaction with a
product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of
-either the mole fraction concentrations or the number of molecules
-associated with the interacting coarse-grained particles (see the
+The interaction potential is weighted by the geometric average of
+either the mole fraction concentrations or the number of molecules
+associated with the interacting coarse-grained particles (see the
{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
stored before and after the reaction kinetics solver is applied, where
the difference is defined to be the internal chemical energy (uChem).
diff --git a/doc/src/python.txt b/doc/src/python.txt
index e00b90234c55c9dc44be9d86bd81d5ec5dda25b8..c6538ded45e084e75aa9540737c90224ba5bef2b 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -489,7 +489,7 @@ python"_Section_python.html. Note that it is important that the
stand-alone LAMMPS executable and the LAMMPS shared library be
consistent (built from the same source code files) in order for this
to work. If the two have been built at different times using
-different source files, problems may occur.
+different source files, problems may occur.
[Related commands:]
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 0e3c1a939f9c55602fa4ffe0d62a12231008976e..a67899420bdb1569a3250314ab0ef93600dbde22 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -17,7 +17,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
{verlet/split} args = none
{respa} args = N n1 n2 ... keyword values ...
N = # of levels of rRESPA
- n1, n2, ... = loop factor between rRESPA levels (N-1 values)
+ n1, n2, ... = loop factors between rRESPA levels (N-1 values)
zero or more keyword/value pairings may be appended to the loop factors
keyword = {bond} or {angle} or {dihedral} or {improper} or
{pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
@@ -55,7 +55,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
run_style verlet
run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
-run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 :pre
+run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 :pre
[Description:]
diff --git a/doc/src/tutorial_github.txt b/doc/src/tutorial_github.txt
index d6ec22589b23d52f94b31e7701d9081b2499fca4..3e10b821aecf3b8bce1f1f9e54198720bd521ce5 100644
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/tutorial_github.txt
@@ -86,7 +86,7 @@ machine via HTTPS:
or, if you have set up your GitHub account for using SSH keys, via SSH:
$ git clone git@github.com:<your user name>/lammps.git :pre
-
+
You can find the proper URL by clicking the "Clone or download"-button:
:c,image(JPG/tutorial_https_block.png)
diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt
index 0b4fb32ed2f0ee330432360aa532b6c645573224..78cdd241fb7fec2e81f2e5aa30ce74f99073c116 100644
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/tutorial_pylammps.txt
@@ -36,7 +36,7 @@ lammps.PyLammps :h4
higher-level abstraction built on top of original C-Types interface
manipulation of Python objects
-communication with LAMMPS is hidden from API user
+communication with LAMMPS is hidden from API user
shorter, more concise Python
better IPython integration, designed for quick prototyping :ul
@@ -328,7 +328,7 @@ IPyLammps Examples :h2
Examples of IPython notebooks can be found in the python/examples/pylammps
subdirectory. To open these notebooks launch {jupyter notebook} inside this
-directory and navigate to one of them. If you compiled and installed
+directory and navigate to one of them. If you compiled and installed
a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.
@@ -399,19 +399,19 @@ natoms = L.system.natoms :pre
for i in range(niterations):
iatom = random.randrange(0, natoms)
current_atom = L.atoms\[iatom\] :pre
-
+
x0, y0 = current_atom.position :pre
-
+
dx = deltamove * random.uniform(-1, 1)
dy = deltamove * random.uniform(-1, 1) :pre
-
+
current_atom.position = (x0+dx, y0+dy) :pre
-
+
L.run(1, "pre no post no") :pre
-
+
e = L.eval("pe")
energies.append(e) :pre
-
+
if e <= elast:
naccept += 1
elast = e
@@ -460,4 +460,4 @@ Feedback and Contributing :h2
If you find this Python interface useful, please feel free to provide feedback
and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
-and maybe their latest research results.
+and maybe their latest research results.
diff --git a/examples/USER/misc/filter_corotate/in.bpti b/examples/USER/misc/filter_corotate/in.bpti
index 6507a78704700a7b9ffa754103b279bf6c886ce3..2e4d8dda6f2d55b2a49d557da184cd40cd2f7440 100644
--- a/examples/USER/misc/filter_corotate/in.bpti
+++ b/examples/USER/misc/filter_corotate/in.bpti
@@ -28,7 +28,7 @@ thermo 100
thermo_style multi
timestep 8
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
velocity all create 200.0 12345678 dist uniform
#dump dump1 all atom 100 4pti.dump
diff --git a/examples/USER/misc/filter_corotate/in.peptide b/examples/USER/misc/filter_corotate/in.peptide
index 0a17f995b3c58324d190cb46072ca3a0c54633b3..e10dc09f0d1281a6c6107e47666d36d01d230509 100644
--- a/examples/USER/misc/filter_corotate/in.peptide
+++ b/examples/USER/misc/filter_corotate/in.peptide
@@ -20,7 +20,7 @@ thermo 50
timestep 8
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
fix cor all filter/corotate m 1.0
diff --git a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1 b/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1
deleted file mode 100644
index 5253b47b2da56967e3950869f253c1b8939a50c8..0000000000000000000000000000000000000000
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1
+++ /dev/null
@@ -1,240 +0,0 @@
-LAMMPS (10 Mar 2017)
- using 1 OpenMP thread(s) per MPI task
-
-units real
-
-atom_style full
-bond_style harmonic
-angle_style charmm
-dihedral_style charmm
-improper_style harmonic
-
-pair_style lj/charmm/coul/long 8 10
-pair_modify mix arithmetic
-kspace_style pppm 1e-4
-
-read_data data.bpti
- orthogonal box = (-10 -10 -30) to (50 50 30)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 892 atoms
- scanning bonds ...
- 4 = max bonds/atom
- scanning angles ...
- 6 = max angles/atom
- scanning dihedrals ...
- 18 = max dihedrals/atom
- scanning impropers ...
- 2 = max impropers/atom
- reading bonds ...
- 906 bonds
- reading angles ...
- 1626 angles
- reading dihedrals ...
- 2501 dihedrals
- reading impropers ...
- 137 impropers
- 4 = max # of 1-2 neighbors
- 9 = max # of 1-3 neighbors
- 19 = max # of 1-4 neighbors
- 21 = max # of special neighbors
-
-special_bonds charmm
-neigh_modify delay 2 every 1
-
-
-# ------------- MINIMIZE ----------
-
-minimize 1e-4 1e-6 1000 10000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
-PPPM initialization ...
-WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.203272
- grid = 16 16 16
- stencil order = 5
- estimated absolute RMS force accuracy = 0.0316399
- estimated relative force accuracy = 9.52826e-05
- using double precision FFTs
- 3d grid and FFT values/proc = 9261 4096
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12
- ghost atom cutoff = 12
- binsize = 6, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair lj/charmm/coul/long, perpetual
- attributes: half, newton on
- pair build: half/bin/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -3075.6498 943.91164 -2131.7381 -380.67776
- 241 0 -4503.313 749.58662 -3753.7264 -29.045104
-Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms
-
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-Minimization stats:
- Stopping criterion = energy tolerance
- Energy initial, next-to-last, final =
- -2131.73812515 -3753.43984087 -3753.72636847
- Force two-norm initial, final = 1086.21 26.3688
- Force max component initial, final = 310.811 3.92748
- Final line search alpha, max atom move = 0.00596649 0.0234333
- Iterations, force evaluations = 241 463
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 2.5003 | 2.5003 | 2.5003 | 0.0 | 74.48
-Bond | 0.24287 | 0.24287 | 0.24287 | 0.0 | 7.23
-Kspace | 0.53428 | 0.53428 | 0.53428 | 0.0 | 15.91
-Neigh | 0.069765 | 0.069765 | 0.069765 | 0.0 | 2.08
-Comm | 0.00065374 | 0.00065374 | 0.00065374 | 0.0 | 0.02
-Output | 0 | 0 | 0 | 0.0 | 0.00
-Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0.009358 | | | 0.28
-
-Nlocal: 892 ave 892 max 892 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 31 ave 31 max 31 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 148891 ave 148891 max 148891 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 148891
-Ave neighs/atom = 166.918
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 15
-Dangerous builds = 0
-reset_timestep 0
-
-# ------------- RUN ---------------
-
-thermo 100
-thermo_style multi
-timestep 8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
- 1 = bond angle dihedral improper
- 2 = pair
- 3 = kspace
-
-velocity all create 200.0 12345678 dist uniform
-#dump dump1 all atom 100 4pti.dump
-
-fix 1 all nvt temp 200 300 25
-fix cor all filter/corotate m 1.0
- 163 = # of size 2 clusters
- 0 = # of size 3 clusters
- 25 = # of size 4 clusters
- 0 = # of size 5 clusters
- 100 = # of frozen angles
-
-run 1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.203272
- grid = 16 16 16
- stencil order = 5
- estimated absolute RMS force accuracy = 0.0316399
- estimated relative force accuracy = 9.52826e-05
- using double precision FFTs
- 3d grid and FFT values/proc = 9261 4096
-Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes
----------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
-TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
-PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592
-E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
-E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283
----------------- Step 100 ----- CPU = 3.9414 (sec) ----------------
-TotEng = -2718.8970 KinEng = 538.6206 Temp = 202.8014
-PotEng = -3257.5176 E_bond = 203.3367 E_angle = 566.5317
-E_dihed = 397.6202 E_impro = 34.6623 E_vdwl = -248.7451
-E_coul = -874.5122 E_long = -3336.4111 Press = 135.8662
----------------- Step 200 ----- CPU = 7.9028 (sec) ----------------
-TotEng = -2660.1406 KinEng = 626.3319 Temp = 235.8265
-PotEng = -3286.4725 E_bond = 209.5147 E_angle = 591.7773
-E_dihed = 388.9591 E_impro = 29.4992 E_vdwl = -243.5808
-E_coul = -923.5115 E_long = -3339.1306 Press = 88.9000
----------------- Step 300 ----- CPU = 11.8246 (sec) ----------------
-TotEng = -2673.8090 KinEng = 616.7924 Temp = 232.2346
-PotEng = -3290.6014 E_bond = 202.8254 E_angle = 568.6860
-E_dihed = 378.4182 E_impro = 38.2399 E_vdwl = -221.3236
-E_coul = -915.3004 E_long = -3342.1468 Press = 78.8527
----------------- Step 400 ----- CPU = 15.7990 (sec) ----------------
-TotEng = -2614.9416 KinEng = 649.3474 Temp = 244.4922
-PotEng = -3264.2890 E_bond = 211.6116 E_angle = 617.2026
-E_dihed = 399.8744 E_impro = 40.2678 E_vdwl = -211.7790
-E_coul = -978.1624 E_long = -3343.3041 Press = -4.1958
----------------- Step 500 ----- CPU = 19.8146 (sec) ----------------
-TotEng = -2588.6772 KinEng = 660.1424 Temp = 248.5568
-PotEng = -3248.8196 E_bond = 218.4786 E_angle = 620.8605
-E_dihed = 390.3220 E_impro = 41.6794 E_vdwl = -226.3657
-E_coul = -953.1676 E_long = -3340.6269 Press = 99.3200
----------------- Step 600 ----- CPU = 23.8587 (sec) ----------------
-TotEng = -2550.4618 KinEng = 693.3384 Temp = 261.0557
-PotEng = -3243.8002 E_bond = 232.3563 E_angle = 606.2922
-E_dihed = 396.2469 E_impro = 37.1980 E_vdwl = -235.8425
-E_coul = -937.1208 E_long = -3342.9303 Press = -21.7737
----------------- Step 700 ----- CPU = 27.8381 (sec) ----------------
-TotEng = -2554.4355 KinEng = 692.8951 Temp = 260.8888
-PotEng = -3247.3306 E_bond = 216.3395 E_angle = 637.7785
-E_dihed = 391.5940 E_impro = 43.1426 E_vdwl = -187.6159
-E_coul = -1008.1694 E_long = -3340.3998 Press = 75.1484
----------------- Step 800 ----- CPU = 31.8039 (sec) ----------------
-TotEng = -2508.3551 KinEng = 699.0766 Temp = 263.2163
-PotEng = -3207.4317 E_bond = 241.9936 E_angle = 641.3631
-E_dihed = 386.2198 E_impro = 43.7793 E_vdwl = -217.7523
-E_coul = -964.6070 E_long = -3338.4282 Press = -127.7337
----------------- Step 900 ----- CPU = 35.7700 (sec) ----------------
-TotEng = -2452.7644 KinEng = 762.1842 Temp = 286.9776
-PotEng = -3214.9485 E_bond = 243.9191 E_angle = 649.8664
-E_dihed = 382.4351 E_impro = 39.0029 E_vdwl = -221.3389
-E_coul = -970.8965 E_long = -3337.9366 Press = 122.7720
----------------- Step 1000 ----- CPU = 39.7695 (sec) ----------------
-TotEng = -2386.6805 KinEng = 799.0253 Temp = 300.8490
-PotEng = -3185.7058 E_bond = 265.3649 E_angle = 661.7543
-E_dihed = 374.6843 E_impro = 38.6877 E_vdwl = -229.2030
-E_coul = -960.7041 E_long = -3336.2899 Press = -17.9910
-Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms
-
-Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 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 | 29.169 | 29.169 | 29.169 | 0.0 | 73.34
-Bond | 7.6249 | 7.6249 | 7.6249 | 0.0 | 19.17
-Kspace | 1.1525 | 1.1525 | 1.1525 | 0.0 | 2.90
-Neigh | 0.87606 | 0.87606 | 0.87606 | 0.0 | 2.20
-Comm | 0.01563 | 0.01563 | 0.01563 | 0.0 | 0.04
-Output | 0.00048423 | 0.00048423 | 0.00048423 | 0.0 | 0.00
-Modify | 0.80446 | 0.80446 | 0.80446 | 0.0 | 2.02
-Other | | 0.1266 | | | 0.32
-
-Nlocal: 892 ave 892 max 892 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 27 ave 27 max 27 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 146206 ave 146206 max 146206 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 146206
-Ave neighs/atom = 163.908
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 186
-Dangerous builds = 0
-
-unfix cor
-unfix 1
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:43
diff --git a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4 b/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4
deleted file mode 100644
index 4300c1caf50be1ac16de30c251d27a31c41e3e1e..0000000000000000000000000000000000000000
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4
+++ /dev/null
@@ -1,240 +0,0 @@
-LAMMPS (10 Mar 2017)
- using 1 OpenMP thread(s) per MPI task
-
-units real
-
-atom_style full
-bond_style harmonic
-angle_style charmm
-dihedral_style charmm
-improper_style harmonic
-
-pair_style lj/charmm/coul/long 8 10
-pair_modify mix arithmetic
-kspace_style pppm 1e-4
-
-read_data data.bpti
- orthogonal box = (-10 -10 -30) to (50 50 30)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 892 atoms
- scanning bonds ...
- 4 = max bonds/atom
- scanning angles ...
- 6 = max angles/atom
- scanning dihedrals ...
- 18 = max dihedrals/atom
- scanning impropers ...
- 2 = max impropers/atom
- reading bonds ...
- 906 bonds
- reading angles ...
- 1626 angles
- reading dihedrals ...
- 2501 dihedrals
- reading impropers ...
- 137 impropers
- 4 = max # of 1-2 neighbors
- 9 = max # of 1-3 neighbors
- 19 = max # of 1-4 neighbors
- 21 = max # of special neighbors
-
-special_bonds charmm
-neigh_modify delay 2 every 1
-
-
-# ------------- MINIMIZE ----------
-
-minimize 1e-4 1e-6 1000 10000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
-PPPM initialization ...
-WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.203272
- grid = 16 16 16
- stencil order = 5
- estimated absolute RMS force accuracy = 0.0316399
- estimated relative force accuracy = 9.52826e-05
- using double precision FFTs
- 3d grid and FFT values/proc = 3549 1024
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12
- ghost atom cutoff = 12
- binsize = 6, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair lj/charmm/coul/long, perpetual
- attributes: half, newton on
- pair build: half/bin/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory usage (min/avg/max) = 16.9693/0.981879/0 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -3075.6498 943.91164 -2131.7381 -380.67776
- 241 0 -4503.3131 749.58666 -3753.7264 -29.045153
-Loop time of 1.26594 on 4 procs for 241 steps with 892 atoms
-
-99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-Minimization stats:
- Stopping criterion = energy tolerance
- Energy initial, next-to-last, final =
- -2131.73812515 -3753.43983927 -3753.72640137
- Force two-norm initial, final = 1086.21 26.3688
- Force max component initial, final = 310.811 3.92751
- Final line search alpha, max atom move = 0.00596649 0.0234334
- Iterations, force evaluations = 241 463
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.34267 | 0.63792 | 0.90268 | 25.2 | 50.39
-Bond | 0.025776 | 0.063318 | 0.095631 | 10.8 | 5.00
-Kspace | 0.21904 | 0.51601 | 0.84895 | 31.3 | 40.76
-Neigh | 0.023185 | 0.023363 | 0.023538 | 0.1 | 1.85
-Comm | 0.012025 | 0.014189 | 0.016335 | 1.4 | 1.12
-Output | 0 | 0 | 0 | 0.0 | 0.00
-Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0.01114 | | | 0.88
-
-Nlocal: 223 ave 323 max 89 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-Nghost: 613 ave 675 max 557 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs: 37222.8 ave 50005 max 20830 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-
-Total # of neighbors = 148891
-Ave neighs/atom = 166.918
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 15
-Dangerous builds = 0
-reset_timestep 0
-
-# ------------- RUN ---------------
-
-thermo 100
-thermo_style multi
-timestep 8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
- 1 = bond angle dihedral improper
- 2 = pair
- 3 = kspace
-
-velocity all create 200.0 12345678 dist uniform
-#dump dump1 all atom 100 4pti.dump
-
-fix 1 all nvt temp 200 300 25
-fix cor all filter/corotate m 1.0
- 163 = # of size 2 clusters
- 0 = # of size 3 clusters
- 25 = # of size 4 clusters
- 0 = # of size 5 clusters
- 100 = # of frozen angles
-
-run 1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.203272
- grid = 16 16 16
- stencil order = 5
- estimated absolute RMS force accuracy = 0.0316399
- estimated relative force accuracy = 9.52826e-05
- using double precision FFTs
- 3d grid and FFT values/proc = 3549 1024
-Per MPI rank memory usage (min/avg/max) = 17.142/0.97212/0 Mbytes
----------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
-TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
-PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2592
-E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
-E_coul = -886.3622 E_long = -3326.2088 Press = 83.2282
----------------- Step 100 ----- CPU = 1.5457 (sec) ----------------
-TotEng = -2718.9184 KinEng = 538.6205 Temp = 202.8014
-PotEng = -3257.5389 E_bond = 203.3365 E_angle = 566.5311
-E_dihed = 397.6202 E_impro = 34.6621 E_vdwl = -248.7451
-E_coul = -874.5326 E_long = -3336.4111 Press = 135.8435
----------------- Step 200 ----- CPU = 3.0720 (sec) ----------------
-TotEng = -2660.1146 KinEng = 626.3474 Temp = 235.8323
-PotEng = -3286.4620 E_bond = 209.5168 E_angle = 591.7735
-E_dihed = 388.9615 E_impro = 29.5000 E_vdwl = -243.5840
-E_coul = -923.4998 E_long = -3339.1299 Press = 88.8857
----------------- Step 300 ----- CPU = 4.5597 (sec) ----------------
-TotEng = -2669.7442 KinEng = 619.3625 Temp = 233.2023
-PotEng = -3289.1067 E_bond = 203.4405 E_angle = 569.5281
-E_dihed = 378.3314 E_impro = 38.2880 E_vdwl = -221.1904
-E_coul = -915.3396 E_long = -3342.1646 Press = 79.3780
----------------- Step 400 ----- CPU = 5.9808 (sec) ----------------
-TotEng = -2618.9975 KinEng = 644.6145 Temp = 242.7102
-PotEng = -3263.6119 E_bond = 209.5864 E_angle = 618.8954
-E_dihed = 401.3798 E_impro = 39.9064 E_vdwl = -212.1271
-E_coul = -977.1589 E_long = -3344.0940 Press = -7.8938
----------------- Step 500 ----- CPU = 7.4159 (sec) ----------------
-TotEng = -2579.7486 KinEng = 666.4643 Temp = 250.9371
-PotEng = -3246.2129 E_bond = 219.2549 E_angle = 620.3474
-E_dihed = 388.4395 E_impro = 41.4499 E_vdwl = -225.9686
-E_coul = -949.3689 E_long = -3340.3672 Press = 113.2543
----------------- Step 600 ----- CPU = 8.9252 (sec) ----------------
-TotEng = -2535.8235 KinEng = 708.5919 Temp = 266.7990
-PotEng = -3244.4154 E_bond = 243.9451 E_angle = 606.0866
-E_dihed = 400.0562 E_impro = 33.9708 E_vdwl = -223.1319
-E_coul = -964.9940 E_long = -3340.3482 Press = -102.4475
----------------- Step 700 ----- CPU = 10.4022 (sec) ----------------
-TotEng = -2552.6681 KinEng = 702.3080 Temp = 264.4330
-PotEng = -3254.9761 E_bond = 250.8834 E_angle = 639.0977
-E_dihed = 386.4014 E_impro = 42.3004 E_vdwl = -224.4816
-E_coul = -1011.8551 E_long = -3337.3222 Press = 10.6424
----------------- Step 800 ----- CPU = 11.8699 (sec) ----------------
-TotEng = -2423.5415 KinEng = 772.1254 Temp = 290.7206
-PotEng = -3195.6670 E_bond = 238.5831 E_angle = 640.9180
-E_dihed = 377.7994 E_impro = 40.3135 E_vdwl = -216.5705
-E_coul = -935.1087 E_long = -3341.6019 Press = -38.2479
----------------- Step 900 ----- CPU = 13.3548 (sec) ----------------
-TotEng = -2394.4779 KinEng = 766.6895 Temp = 288.6739
-PotEng = -3161.1673 E_bond = 284.8428 E_angle = 671.0959
-E_dihed = 380.3406 E_impro = 51.2975 E_vdwl = -219.5211
-E_coul = -990.6305 E_long = -3338.5925 Press = -15.2279
----------------- Step 1000 ----- CPU = 14.7908 (sec) ----------------
-TotEng = -2340.1471 KinEng = 799.0198 Temp = 300.8469
-PotEng = -3139.1669 E_bond = 271.0389 E_angle = 683.8278
-E_dihed = 407.0795 E_impro = 39.6209 E_vdwl = -230.5355
-E_coul = -974.2981 E_long = -3335.9003 Press = -94.3420
-Loop time of 14.7909 on 4 procs for 1000 steps with 892 atoms
-
-Performance: 46.732 ns/day, 0.514 hours/ns, 67.609 timesteps/s
-99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 4.4184 | 7.5543 | 10.133 | 74.2 | 51.07
-Bond | 0.94027 | 1.9781 | 2.7492 | 54.4 | 13.37
-Kspace | 0.45487 | 0.45887 | 0.46343 | 0.4 | 3.10
-Neigh | 0.28145 | 0.28339 | 0.28539 | 0.3 | 1.92
-Comm | 0.7515 | 4.1484 | 8.3861 | 135.5 | 28.05
-Output | 0.00049973 | 0.00055474 | 0.00066924 | 0.0 | 0.00
-Modify | 0.26165 | 0.31142 | 0.35023 | 6.7 | 2.11
-Other | | 0.05572 | | | 0.38
-
-Nlocal: 223 ave 313 max 122 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-Nghost: 584.5 ave 605 max 553 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Neighs: 35448 ave 42093 max 25175 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 141792
-Ave neighs/atom = 158.96
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 186
-Dangerous builds = 0
-
-unfix cor
-unfix 1
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:16
diff --git a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1 b/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1
deleted file mode 100644
index 23dd4c8a89982174b72613ce0a14dde3e0d96bf0..0000000000000000000000000000000000000000
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1
+++ /dev/null
@@ -1,146 +0,0 @@
-LAMMPS (10 Mar 2017)
- using 1 OpenMP thread(s) per MPI task
-# Solvated 5-mer peptide, run for 8ps in NVT
-
-units real
-atom_style full
-
-pair_style lj/charmm/coul/long 8.0 10.0 10.0
-bond_style harmonic
-angle_style charmm
-dihedral_style charmm
-improper_style harmonic
-kspace_style pppm 0.0001
-
-read_data data.peptide
- orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 2004 atoms
- reading velocities ...
- 2004 velocities
- scanning bonds ...
- 3 = max bonds/atom
- scanning angles ...
- 6 = max angles/atom
- scanning dihedrals ...
- 14 = max dihedrals/atom
- scanning impropers ...
- 1 = max impropers/atom
- reading bonds ...
- 1365 bonds
- reading angles ...
- 786 angles
- reading dihedrals ...
- 207 dihedrals
- reading impropers ...
- 12 impropers
- 4 = max # of 1-2 neighbors
- 7 = max # of 1-3 neighbors
- 14 = max # of 1-4 neighbors
- 18 = max # of special neighbors
-
-neighbor 2.0 bin
-neigh_modify delay 5
-
-thermo 50
-#dump dump1 all atom 100 peptide.dump
-
-timestep 8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
- 1 = bond angle dihedral improper
- 2 = pair
- 3 = kspace
-
-fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
-fix cor all filter/corotate m 1.0
- 19 = # of size 2 clusters
- 0 = # of size 3 clusters
- 3 = # of size 4 clusters
- 0 = # of size 5 clusters
- 646 = # of frozen angles
-run 1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.268725
- grid = 15 15 15
- stencil order = 5
- estimated absolute RMS force accuracy = 0.0228209
- estimated relative force accuracy = 6.87243e-05
- using double precision FFTs
- 3d grid and FFT values/proc = 10648 3375
-Neighbor list info ...
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12
- ghost atom cutoff = 12
- binsize = 6, bins = 5 5 5
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair lj/charmm/coul/long, perpetual
- attributes: half, newton on
- pair build: half/bin/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
- 50 239.46028 -7546.5667 1092.8874 -5023.9668 -24643.891
- 100 242.81799 -7125.5527 416.0788 -5259.7139 15525.465
- 150 235.97108 -7531.9334 932.35464 -5190.6987 -14838.489
- 200 252.06415 -7195.6011 568.02993 -5122.6064 8841.332
- 250 249.99431 -7586.5092 881.83491 -5212.0676 -9330.345
- 300 240.3382 -7333.0933 633.29951 -5264.8395 5137.9757
- 350 255.34529 -7568.2413 856.46371 -5187.2226 -6206.063
- 400 242.99276 -7419.9031 713.23943 -5255.8602 2447.0091
- 450 251.10653 -7622.061 844.20584 -5278.6079 -4906.6559
- 500 255.59314 -7439.253 710.84907 -5202.3691 1571.0032
- 550 253.2025 -7660.5101 823.05373 -5325.695 -4551.399
- 600 249.05313 -7509.6729 741.48104 -5281.2046 992.87
- 650 251.75984 -7593.6589 847.08244 -5243.4286 -3510.1176
- 700 249.25027 -7601.9112 794.0912 -5319.6557 305.76021
- 750 255.415 -7602.2674 822.98524 -5254.3109 -2333.421
- 800 241.99621 -7643.8878 796.53352 -5402.5008 -298.66565
- 850 253.6428 -7598.3764 816.45457 -5267.5316 -1905.3478
- 900 247.20231 -7690.2806 789.75999 -5424.5838 -1331.7228
- 950 255.92583 -7634.7505 831.18272 -5275.5466 -2186.5117
- 1000 253.2126 -7647.9526 823.93602 -5312.195 -1189.9659
-Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms
-
-Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 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 | 135.81 | 135.81 | 135.81 | 0.0 | 90.14
-Bond | 2.5889 | 2.5889 | 2.5889 | 0.0 | 1.72
-Kspace | 2.0379 | 2.0379 | 2.0379 | 0.0 | 1.35
-Neigh | 5.893 | 5.893 | 5.893 | 0.0 | 3.91
-Comm | 1.6998 | 1.6998 | 1.6998 | 0.0 | 1.13
-Output | 0.00077915 | 0.00077915 | 0.00077915 | 0.0 | 0.00
-Modify | 2 | 2 | 2 | 0.0 | 1.33
-Other | | 0.6352 | | | 0.42
-
-Nlocal: 2004 ave 2004 max 2004 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 11197 ave 11197 max 11197 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 707779 ave 707779 max 707779 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 707779
-Ave neighs/atom = 353.183
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 200
-Dangerous builds = 200
-unfix cor
-unfix 1
-
-
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:02:30
diff --git a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4 b/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4
deleted file mode 100644
index 2cdd645fe3e1b97ef2ae934445e97cad92ad2a7d..0000000000000000000000000000000000000000
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4
+++ /dev/null
@@ -1,146 +0,0 @@
-LAMMPS (10 Mar 2017)
- using 1 OpenMP thread(s) per MPI task
-# Solvated 5-mer peptide, run for 8ps in NVT
-
-units real
-atom_style full
-
-pair_style lj/charmm/coul/long 8.0 10.0 10.0
-bond_style harmonic
-angle_style charmm
-dihedral_style charmm
-improper_style harmonic
-kspace_style pppm 0.0001
-
-read_data data.peptide
- orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 2004 atoms
- reading velocities ...
- 2004 velocities
- scanning bonds ...
- 3 = max bonds/atom
- scanning angles ...
- 6 = max angles/atom
- scanning dihedrals ...
- 14 = max dihedrals/atom
- scanning impropers ...
- 1 = max impropers/atom
- reading bonds ...
- 1365 bonds
- reading angles ...
- 786 angles
- reading dihedrals ...
- 207 dihedrals
- reading impropers ...
- 12 impropers
- 4 = max # of 1-2 neighbors
- 7 = max # of 1-3 neighbors
- 14 = max # of 1-4 neighbors
- 18 = max # of special neighbors
-
-neighbor 2.0 bin
-neigh_modify delay 5
-
-thermo 50
-#dump dump1 all atom 100 peptide.dump
-
-timestep 8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
- 1 = bond angle dihedral improper
- 2 = pair
- 3 = kspace
-
-fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
-fix cor all filter/corotate m 1.0
- 19 = # of size 2 clusters
- 0 = # of size 3 clusters
- 3 = # of size 4 clusters
- 0 = # of size 5 clusters
- 646 = # of frozen angles
-run 1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.268725
- grid = 15 15 15
- stencil order = 5
- estimated absolute RMS force accuracy = 0.0228209
- estimated relative force accuracy = 6.87243e-05
- using double precision FFTs
- 3d grid and FFT values/proc = 4312 960
-Neighbor list info ...
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12
- ghost atom cutoff = 12
- binsize = 6, bins = 5 5 5
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair lj/charmm/coul/long, perpetual
- attributes: half, newton on
- pair build: half/bin/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory usage (min/avg/max) = 16.8394/0.98826/0 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
- 50 239.46028 -7546.5668 1092.8874 -5023.9668 -24643.891
- 100 242.81819 -7125.5629 416.08082 -5259.7209 15525.244
- 150 235.94928 -7531.9186 932.50658 -5190.6621 -14842.431
- 200 255.85551 -7254.4065 568.8803 -5157.9249 8936.8651
- 250 247.8705 -7607.4583 858.06087 -5269.4711 -9926.0442
- 300 257.64176 -7267.424 618.5573 -5110.6004 5173.3307
- 350 251.65439 -7572.3806 821.15745 -5248.7049 -7092.327
- 400 256.87927 -7414.2145 655.33178 -5225.169 4119.4095
- 450 257.12393 -7576.5541 853.39773 -5187.9819 -5224.8823
- 500 242.42371 -7524.705 705.75357 -5371.5455 2111.3878
- 550 248.97188 -7541.076 792.86994 -5261.7038 -2278.4185
- 600 249.81862 -7592.0499 767.17722 -5333.3149 -1149.4759
- 650 253.31349 -7578.2665 813.75975 -5252.0827 -2915.5706
- 700 256.61152 -7588.1475 761.03356 -5294.9988 -747.88089
- 750 248.3606 -7660.457 837.71615 -5339.8883 -3072.8311
- 800 253.81464 -7638.6089 782.4229 -5340.7698 -1025.909
- 850 245.69185 -7660.9036 795.66792 -5398.3172 -2717.5851
- 900 249.13156 -7589.4769 806.43464 -5295.5867 -761.63361
- 950 251.11482 -7691.4981 869.34937 -5322.852 -3282.3031
- 1000 241.9195 -7630.9899 828.59107 -5358.0033 -95.962685
-Loop time of 45.5507 on 4 procs for 1000 steps with 2004 atoms
-
-Performance: 15.174 ns/day, 1.582 hours/ns, 21.954 timesteps/s
-99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 35.545 | 36.674 | 38.004 | 15.8 | 80.51
-Bond | 0.51302 | 0.67796 | 0.86345 | 18.6 | 1.49
-Kspace | 0.66031 | 0.68459 | 0.70506 | 2.1 | 1.50
-Neigh | 1.5605 | 1.5627 | 1.5649 | 0.1 | 3.43
-Comm | 3.4611 | 4.9841 | 6.294 | 47.2 | 10.94
-Output | 0.00079799 | 0.00086641 | 0.0010369 | 0.0 | 0.00
-Modify | 0.67341 | 0.69059 | 0.71186 | 1.7 | 1.52
-Other | | 0.2762 | | | 0.61
-
-Nlocal: 501 ave 523 max 473 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Nghost: 6643.25 ave 6708 max 6566 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Neighs: 176977 ave 185765 max 164931 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-
-Total # of neighbors = 707908
-Ave neighs/atom = 353.248
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 200
-Dangerous builds = 200
-unfix cor
-unfix 1
-
-
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:45
diff --git a/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1 b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..1e708a9d396f162b7b63d86e676e6308a4a166aa
--- /dev/null
+++ b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1
@@ -0,0 +1,241 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+
+units real
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+
+pair_style lj/charmm/coul/long 8 10
+pair_modify mix arithmetic
+kspace_style pppm 1e-4
+
+read_data data.bpti
+ orthogonal box = (-10 -10 -30) to (50 50 30)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 892 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 18 = max dihedrals/atom
+ scanning impropers ...
+ 2 = max impropers/atom
+ reading bonds ...
+ 906 bonds
+ reading angles ...
+ 1626 angles
+ reading dihedrals ...
+ 2501 dihedrals
+ reading impropers ...
+ 137 impropers
+ 4 = max # of 1-2 neighbors
+ 9 = max # of 1-3 neighbors
+ 19 = max # of 1-4 neighbors
+ 21 = max # of special neighbors
+
+special_bonds charmm
+neigh_modify delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 1e-4 1e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.203272
+ grid = 16 16 16
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0316399
+ estimated relative force accuracy = 9.52826e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 9261 4096
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/charmm/coul/long, 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) = 17.86 | 17.86 | 17.86 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -3075.6498 943.91164 -2131.7381 -380.67776
+ 241 0 -4503.313 749.58662 -3753.7264 -29.045104
+Loop time of 7.63279 on 1 procs for 241 steps with 892 atoms
+
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -2131.73812515 -3753.43984087 -3753.72636847
+ Force two-norm initial, final = 1086.21 26.3688
+ Force max component initial, final = 310.811 3.92748
+ Final line search alpha, max atom move = 0.00596649 0.0234333
+ Iterations, force evaluations = 241 463
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.8395 | 5.8395 | 5.8395 | 0.0 | 76.51
+Bond | 0.46414 | 0.46414 | 0.46414 | 0.0 | 6.08
+Kspace | 1.1535 | 1.1535 | 1.1535 | 0.0 | 15.11
+Neigh | 0.14908 | 0.14908 | 0.14908 | 0.0 | 1.95
+Comm | 0.001932 | 0.001932 | 0.001932 | 0.0 | 0.03
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.02465 | | | 0.32
+
+Nlocal: 892 ave 892 max 892 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 31 ave 31 max 31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 148891 ave 148891 max 148891 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 148891
+Ave neighs/atom = 166.918
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 15
+Dangerous builds = 0
+reset_timestep 0
+
+# ------------- RUN ---------------
+
+thermo 100
+thermo_style multi
+timestep 8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+ 1 = bond angle
+ 2 = dihedral improper pair
+ 3 = kspace
+
+velocity all create 200.0 12345678 dist uniform
+#dump dump1 all atom 100 4pti.dump
+
+fix 1 all nvt temp 200 300 25
+fix cor all filter/corotate m 1.0
+ 163 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 25 = # of size 4 clusters
+ 0 = # of size 5 clusters
+ 100 = # of frozen angles
+
+run 1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.203272
+ grid = 16 16 16
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0316399
+ estimated relative force accuracy = 9.52826e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 9261 4096
+Per MPI rank memory allocation (min/avg/max) = 19.55 | 19.55 | 19.55 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
+PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592
+E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
+E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283
+---------------- Step 100 ----- CPU = 8.4380 (sec) ----------------
+TotEng = -2718.4258 KinEng = 539.6265 Temp = 203.1802
+PotEng = -3258.0524 E_bond = 203.2307 E_angle = 566.1893
+E_dihed = 397.6759 E_impro = 34.7696 E_vdwl = -248.6577
+E_coul = -874.8466 E_long = -3336.4135 Press = 135.8640
+---------------- Step 200 ----- CPU = 16.9012 (sec) ----------------
+TotEng = -2661.9611 KinEng = 625.0674 Temp = 235.3503
+PotEng = -3287.0285 E_bond = 208.1804 E_angle = 590.8462
+E_dihed = 389.1482 E_impro = 30.5882 E_vdwl = -240.5448
+E_coul = -926.3091 E_long = -3338.9378 Press = 103.4738
+---------------- Step 300 ----- CPU = 25.3046 (sec) ----------------
+TotEng = -2662.4139 KinEng = 622.2647 Temp = 234.2951
+PotEng = -3284.6785 E_bond = 202.4210 E_angle = 573.6793
+E_dihed = 382.8919 E_impro = 41.8973 E_vdwl = -218.9895
+E_coul = -924.8414 E_long = -3341.7372 Press = 40.6746
+---------------- Step 400 ----- CPU = 33.8063 (sec) ----------------
+TotEng = -2604.9431 KinEng = 662.9890 Temp = 249.6286
+PotEng = -3267.9321 E_bond = 195.9116 E_angle = 616.1383
+E_dihed = 407.8502 E_impro = 43.3560 E_vdwl = -219.0377
+E_coul = -966.3118 E_long = -3345.8387 Press = -91.8856
+---------------- Step 500 ----- CPU = 42.3470 (sec) ----------------
+TotEng = -2609.3867 KinEng = 657.0939 Temp = 247.4090
+PotEng = -3266.4806 E_bond = 236.4955 E_angle = 570.6256
+E_dihed = 390.5111 E_impro = 41.9250 E_vdwl = -223.9927
+E_coul = -939.5249 E_long = -3342.5201 Press = 236.7471
+---------------- Step 600 ----- CPU = 50.9590 (sec) ----------------
+TotEng = -2564.7161 KinEng = 701.8494 Temp = 264.2603
+PotEng = -3266.5655 E_bond = 223.5820 E_angle = 582.7722
+E_dihed = 394.6196 E_impro = 43.8581 E_vdwl = -201.7759
+E_coul = -967.4136 E_long = -3342.2079 Press = 26.6595
+---------------- Step 700 ----- CPU = 59.4791 (sec) ----------------
+TotEng = -2510.1142 KinEng = 689.5931 Temp = 259.6455
+PotEng = -3199.7072 E_bond = 254.6476 E_angle = 611.9715
+E_dihed = 403.0624 E_impro = 44.1360 E_vdwl = -205.6377
+E_coul = -964.7455 E_long = -3343.1416 Press = 60.5789
+---------------- Step 800 ----- CPU = 67.9330 (sec) ----------------
+TotEng = -2452.7408 KinEng = 777.5962 Temp = 292.7805
+PotEng = -3230.3370 E_bond = 250.4950 E_angle = 656.6738
+E_dihed = 382.4702 E_impro = 39.5378 E_vdwl = -225.0375
+E_coul = -994.4519 E_long = -3340.0244 Press = -19.6463
+---------------- Step 900 ----- CPU = 76.3690 (sec) ----------------
+TotEng = -2339.9766 KinEng = 808.7116 Temp = 304.4961
+PotEng = -3148.6883 E_bond = 247.7657 E_angle = 679.0658
+E_dihed = 398.2984 E_impro = 43.7890 E_vdwl = -230.2498
+E_coul = -945.8152 E_long = -3341.5422 Press = -64.4343
+---------------- Step 1000 ----- CPU = 84.8757 (sec) ----------------
+TotEng = -2329.1819 KinEng = 822.9820 Temp = 309.8691
+PotEng = -3152.1639 E_bond = 264.9609 E_angle = 691.7104
+E_dihed = 385.9914 E_impro = 40.5525 E_vdwl = -230.5182
+E_coul = -954.6203 E_long = -3350.2405 Press = -146.6649
+Loop time of 84.8758 on 1 procs for 1000 steps with 892 atoms
+
+Performance: 8.144 ns/day, 2.947 hours/ns, 11.782 timesteps/s
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 68.548 | 68.548 | 68.548 | 0.0 | 80.76
+Bond | 10.263 | 10.263 | 10.263 | 0.0 | 12.09
+Kspace | 2.4528 | 2.4528 | 2.4528 | 0.0 | 2.89
+Neigh | 1.9041 | 1.9041 | 1.9041 | 0.0 | 2.24
+Comm | 0.044126 | 0.044126 | 0.044126 | 0.0 | 0.05
+Output | 0.000983 | 0.000983 | 0.000983 | 0.0 | 0.00
+Modify | 1.4113 | 1.4113 | 1.4113 | 0.0 | 1.66
+Other | | 0.2516 | | | 0.30
+
+Nlocal: 892 ave 892 max 892 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 38 ave 38 max 38 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 144068 ave 144068 max 144068 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 144068
+Ave neighs/atom = 161.511
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 190
+Dangerous builds = 0
+
+unfix cor
+unfix 1
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:32
diff --git a/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4 b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..5367f0e624094f484b4b35d8b57aeea1975df3fc
--- /dev/null
+++ b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4
@@ -0,0 +1,241 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+
+units real
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+
+pair_style lj/charmm/coul/long 8 10
+pair_modify mix arithmetic
+kspace_style pppm 1e-4
+
+read_data data.bpti
+ orthogonal box = (-10 -10 -30) to (50 50 30)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 892 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 18 = max dihedrals/atom
+ scanning impropers ...
+ 2 = max impropers/atom
+ reading bonds ...
+ 906 bonds
+ reading angles ...
+ 1626 angles
+ reading dihedrals ...
+ 2501 dihedrals
+ reading impropers ...
+ 137 impropers
+ 4 = max # of 1-2 neighbors
+ 9 = max # of 1-3 neighbors
+ 19 = max # of 1-4 neighbors
+ 21 = max # of special neighbors
+
+special_bonds charmm
+neigh_modify delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 1e-4 1e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.203272
+ grid = 16 16 16
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0316399
+ estimated relative force accuracy = 9.52826e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 3549 1024
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/charmm/coul/long, 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) = 16.97 | 17.2 | 17.52 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -3075.6498 943.91164 -2131.7381 -380.67776
+ 241 0 -4503.3131 749.58665 -3753.7264 -29.044989
+Loop time of 3.06327 on 4 procs for 241 steps with 892 atoms
+
+31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -2131.73812515 -3753.4398752 -3753.72640446
+ Force two-norm initial, final = 1086.21 26.3687
+ Force max component initial, final = 310.811 3.92765
+ Final line search alpha, max atom move = 0.0059665 0.0234343
+ Iterations, force evaluations = 241 463
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.91458 | 1.6235 | 2.2701 | 38.2 | 53.00
+Bond | 0.055164 | 0.13173 | 0.19487 | 15.1 | 4.30
+Kspace | 0.48966 | 1.1993 | 1.9847 | 48.7 | 39.15
+Neigh | 0.053297 | 0.053442 | 0.053576 | 0.0 | 1.74
+Comm | 0.031677 | 0.035006 | 0.038061 | 1.5 | 1.14
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.02021 | | | 0.66
+
+Nlocal: 223 ave 323 max 89 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 613 ave 675 max 557 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs: 37222.8 ave 50005 max 20830 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+
+Total # of neighbors = 148891
+Ave neighs/atom = 166.918
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 15
+Dangerous builds = 0
+reset_timestep 0
+
+# ------------- RUN ---------------
+
+thermo 100
+thermo_style multi
+timestep 8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+ 1 = bond angle
+ 2 = dihedral improper pair
+ 3 = kspace
+
+velocity all create 200.0 12345678 dist uniform
+#dump dump1 all atom 100 4pti.dump
+
+fix 1 all nvt temp 200 300 25
+fix cor all filter/corotate m 1.0
+ 163 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 25 = # of size 4 clusters
+ 0 = # of size 5 clusters
+ 100 = # of frozen angles
+
+run 1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.203272
+ grid = 16 16 16
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0316399
+ estimated relative force accuracy = 9.52826e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 3549 1024
+Per MPI rank memory allocation (min/avg/max) = 17.14 | 17.63 | 18.14 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
+PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2593
+E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
+E_coul = -886.3622 E_long = -3326.2088 Press = 83.2284
+---------------- Step 100 ----- CPU = 3.4639 (sec) ----------------
+TotEng = -2718.4266 KinEng = 539.6246 Temp = 203.1794
+PotEng = -3258.0513 E_bond = 203.2306 E_angle = 566.1887
+E_dihed = 397.6756 E_impro = 34.7695 E_vdwl = -248.6577
+E_coul = -874.8446 E_long = -3336.4135 Press = 135.8653
+---------------- Step 200 ----- CPU = 6.8898 (sec) ----------------
+TotEng = -2662.0450 KinEng = 625.0178 Temp = 235.3317
+PotEng = -3287.0628 E_bond = 208.1691 E_angle = 590.8259
+E_dihed = 389.1424 E_impro = 30.5879 E_vdwl = -240.5397
+E_coul = -926.3110 E_long = -3338.9375 Press = 103.4843
+---------------- Step 300 ----- CPU = 10.2791 (sec) ----------------
+TotEng = -2661.8829 KinEng = 623.0352 Temp = 234.5852
+PotEng = -3284.9181 E_bond = 203.0274 E_angle = 573.6583
+E_dihed = 383.0124 E_impro = 41.9015 E_vdwl = -218.0696
+E_coul = -926.5806 E_long = -3341.8675 Press = 45.6868
+---------------- Step 400 ----- CPU = 13.5874 (sec) ----------------
+TotEng = -2594.5220 KinEng = 672.8693 Temp = 253.3487
+PotEng = -3267.3914 E_bond = 201.3378 E_angle = 612.7099
+E_dihed = 410.1920 E_impro = 44.0201 E_vdwl = -217.9714
+E_coul = -971.6203 E_long = -3346.0595 Press = -121.1015
+---------------- Step 500 ----- CPU = 16.9047 (sec) ----------------
+TotEng = -2603.9306 KinEng = 668.2122 Temp = 251.5952
+PotEng = -3272.1428 E_bond = 238.1081 E_angle = 578.3310
+E_dihed = 399.1305 E_impro = 41.4314 E_vdwl = -216.9664
+E_coul = -969.4047 E_long = -3342.7729 Press = 156.7851
+---------------- Step 600 ----- CPU = 20.1970 (sec) ----------------
+TotEng = -2531.1096 KinEng = 728.1698 Temp = 274.1705
+PotEng = -3259.2794 E_bond = 232.8396 E_angle = 621.3323
+E_dihed = 398.1952 E_impro = 37.0914 E_vdwl = -241.6350
+E_coul = -963.1540 E_long = -3343.9488 Press = 58.6784
+---------------- Step 700 ----- CPU = 23.4360 (sec) ----------------
+TotEng = -2499.9495 KinEng = 742.1211 Temp = 279.4234
+PotEng = -3242.0705 E_bond = 240.5622 E_angle = 582.9270
+E_dihed = 396.6246 E_impro = 36.6510 E_vdwl = -228.4925
+E_coul = -926.8734 E_long = -3343.4695 Press = -60.7458
+---------------- Step 800 ----- CPU = 26.6709 (sec) ----------------
+TotEng = -2426.0217 KinEng = 760.1083 Temp = 286.1959
+PotEng = -3186.1300 E_bond = 266.5863 E_angle = 652.3401
+E_dihed = 380.7407 E_impro = 34.6861 E_vdwl = -225.3729
+E_coul = -953.2382 E_long = -3341.8721 Press = -57.9824
+---------------- Step 900 ----- CPU = 29.8152 (sec) ----------------
+TotEng = -2419.4636 KinEng = 780.8361 Temp = 294.0004
+PotEng = -3200.2996 E_bond = 269.3237 E_angle = 665.7171
+E_dihed = 408.3527 E_impro = 43.7811 E_vdwl = -254.0696
+E_coul = -1002.0694 E_long = -3331.3352 Press = -52.0169
+---------------- Step 1000 ----- CPU = 32.8748 (sec) ----------------
+TotEng = -2398.7244 KinEng = 811.9856 Temp = 305.7288
+PotEng = -3210.7099 E_bond = 258.2207 E_angle = 639.3671
+E_dihed = 379.3353 E_impro = 41.7602 E_vdwl = -207.2654
+E_coul = -983.9330 E_long = -3338.1948 Press = 89.4870
+Loop time of 32.8751 on 4 procs for 1000 steps with 892 atoms
+
+Performance: 21.025 ns/day, 1.141 hours/ns, 30.418 timesteps/s
+31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 12.449 | 19.023 | 24.612 | 99.6 | 57.86
+Bond | 1.4547 | 2.8768 | 3.9098 | 61.4 | 8.75
+Kspace | 1.0537 | 1.0778 | 1.0992 | 2.1 | 3.28
+Neigh | 0.67542 | 0.67994 | 0.68323 | 0.3 | 2.07
+Comm | 1.8602 | 8.4515 | 16.516 | 182.9 | 25.71
+Output | 0.000839 | 0.00147 | 0.003293 | 2.7 | 0.00
+Modify | 0.56658 | 0.63186 | 0.69304 | 6.8 | 1.92
+Other | | 0.133 | | | 0.40
+
+Nlocal: 223 ave 339 max 136 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost: 590 ave 626 max 552 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs: 36488.2 ave 41965 max 29054 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 145953
+Ave neighs/atom = 163.624
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 189
+Dangerous builds = 0
+
+unfix cor
+unfix 1
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:36
diff --git a/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1 b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..22c5483c9e23dd879f68802b0221b6693e75021b
--- /dev/null
+++ b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1
@@ -0,0 +1,147 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units real
+atom_style full
+
+pair_style lj/charmm/coul/long 8.0 10.0 10.0
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+kspace_style pppm 0.0001
+
+read_data data.peptide
+ orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 2004 atoms
+ reading velocities ...
+ 2004 velocities
+ scanning bonds ...
+ 3 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 14 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 1365 bonds
+ reading angles ...
+ 786 angles
+ reading dihedrals ...
+ 207 dihedrals
+ reading impropers ...
+ 12 impropers
+ 4 = max # of 1-2 neighbors
+ 7 = max # of 1-3 neighbors
+ 14 = max # of 1-4 neighbors
+ 18 = max # of special neighbors
+
+neighbor 2.0 bin
+neigh_modify delay 5
+
+thermo 50
+#dump dump1 all atom 100 peptide.dump
+
+timestep 8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+ 1 = bond angle
+ 2 = dihedral improper pair
+ 3 = kspace
+
+fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix cor all filter/corotate m 1.0
+ 19 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 3 = # of size 4 clusters
+ 0 = # of size 5 clusters
+ 646 = # of frozen angles
+run 1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.268725
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0228209
+ estimated relative force accuracy = 6.87243e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 5 5 5
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/charmm/coul/long, 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) = 22.72 | 22.72 | 22.72 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984
+ 50 239.47667 -7205.1006 1092.7664 -4682.5237 -23733.122
+ 100 244.63086 -6788.0793 422.97204 -4904.5234 16458.011
+ 150 240.79042 -7267.0791 966.31411 -4863.1107 -13554.894
+ 200 254.77122 -6868.5713 591.00071 -4756.4431 10532.563
+ 250 241.87417 -7264.9349 856.9357 -4963.8743 -9043.4359
+ 300 251.37775 -6976.8 650.55612 -4825.3773 6986.2021
+ 350 250.81494 -7286.7011 880.11184 -4909.0829 -6392.4665
+ 400 247.55673 -7104.4036 701.89555 -4924.4551 4720.7811
+ 450 258.54988 -7215.3011 832.23692 -4839.3759 -3446.3859
+ 500 246.80928 -7151.2468 715.61007 -4962.0464 2637.5769
+ 550 246.20721 -7159.0464 805.24974 -4883.8011 -2725.227
+ 600 250.62483 -7201.7688 806.10076 -4899.2968 770.22352
+ 650 247.59777 -7260.1607 802.97277 -4978.8899 -430.42309
+ 700 246.86951 -7286.2971 825.99865 -4986.3486 -427.88651
+ 750 252.79268 -7307.8572 833.4822 -4965.0605 -614.74372
+ 800 251.73191 -7315.2457 839.59859 -4972.666 952.56448
+ 850 246.75844 -7303.6221 816.67112 -5013.6642 -2055.2823
+ 900 251.00123 -7317.4219 825.12165 -4993.6817 -356.53166
+ 950 259.20822 -7252.3466 854.62611 -4850.1016 -1719.5267
+ 1000 245.72486 -7347.5547 811.48146 -5068.9576 -717.6136
+Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms
+
+Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 328.2 | 328.2 | 328.2 | 0.0 | 91.80
+Bond | 4.4815 | 4.4815 | 4.4815 | 0.0 | 1.25
+Kspace | 3.9448 | 3.9448 | 3.9448 | 0.0 | 1.10
+Neigh | 12.457 | 12.457 | 12.457 | 0.0 | 3.48
+Comm | 3.2147 | 3.2147 | 3.2147 | 0.0 | 0.90
+Output | 0.001689 | 0.001689 | 0.001689 | 0.0 | 0.00
+Modify | 3.937 | 3.937 | 3.937 | 0.0 | 1.10
+Other | | 1.289 | | | 0.36
+
+Nlocal: 2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 11191 ave 11191 max 11191 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 708610 ave 708610 max 708610 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 708610
+Ave neighs/atom = 353.598
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 200
+unfix cor
+unfix 1
+
+
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:05:57
diff --git a/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4 b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..eec3843bd0ea170ef43347cc2dc29c7ef4a25e71
--- /dev/null
+++ b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4
@@ -0,0 +1,147 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units real
+atom_style full
+
+pair_style lj/charmm/coul/long 8.0 10.0 10.0
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+kspace_style pppm 0.0001
+
+read_data data.peptide
+ orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 2004 atoms
+ reading velocities ...
+ 2004 velocities
+ scanning bonds ...
+ 3 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 14 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 1365 bonds
+ reading angles ...
+ 786 angles
+ reading dihedrals ...
+ 207 dihedrals
+ reading impropers ...
+ 12 impropers
+ 4 = max # of 1-2 neighbors
+ 7 = max # of 1-3 neighbors
+ 14 = max # of 1-4 neighbors
+ 18 = max # of special neighbors
+
+neighbor 2.0 bin
+neigh_modify delay 5
+
+thermo 50
+#dump dump1 all atom 100 peptide.dump
+
+timestep 8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+ 1 = bond angle
+ 2 = dihedral improper pair
+ 3 = kspace
+
+fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix cor all filter/corotate m 1.0
+ 19 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 3 = # of size 4 clusters
+ 0 = # of size 5 clusters
+ 646 = # of frozen angles
+run 1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.268725
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0228209
+ estimated relative force accuracy = 6.87243e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 5 5 5
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/charmm/coul/long, 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) = 16.87 | 17.05 | 17.26 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984
+ 50 239.47667 -7205.1005 1092.7664 -4682.5237 -23733.122
+ 100 244.63889 -6788.1152 422.96733 -4904.5161 16457.756
+ 150 239.36917 -7258.7053 967.87775 -4861.6589 -13526.261
+ 200 255.14702 -6864.0525 604.58036 -4736.1009 11013.1
+ 250 252.72919 -7303.0966 898.11178 -4896.0494 -8480.8766
+ 300 250.66477 -6989.2603 652.83649 -4839.8141 6209.3375
+ 350 243.30794 -7218.8575 838.31977 -4927.8525 -5180.4928
+ 400 256.3573 -7090.677 706.24197 -4853.8377 3302.577
+ 450 246.15776 -7274.574 834.31676 -4970.557 -3427.971
+ 500 256.28473 -7082.1447 735.42828 -4816.5524 2846.086
+ 550 251.32327 -7341.739 812.64934 -5028.5484 -1786.9277
+ 600 254.57737 -7152.3448 740.52534 -4891.8494 825.91675
+ 650 244.95305 -7207.1136 790.67659 -4953.9295 -520.79769
+ 700 249.4984 -7204.2699 779.06969 -4935.5544 -940.75384
+ 750 248.46962 -7232.1037 791.6642 -4956.9361 -548.12171
+ 800 260.2974 -7293.1982 793.23282 -4945.8435 -1171.26
+ 850 249.79023 -7258.3759 823.56789 -4943.4198 -499.76275
+ 900 249.97237 -7267.0584 784.57992 -4990.0028 -271.33531
+ 950 251.29018 -7261.0642 823.467 -4937.2534 -538.7168
+ 1000 246.05777 -7285.0948 847.90892 -4968.0826 -2613.1854
+Loop time of 94.6835 on 4 procs for 1000 steps with 2004 atoms
+
+Performance: 7.300 ns/day, 3.288 hours/ns, 10.562 timesteps/s
+37.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 33.389 | 78.508 | 94.639 | 294.1 | 82.92
+Bond | 0.39957 | 1.104 | 1.4443 | 40.6 | 1.17
+Kspace | 0.53324 | 1.2631 | 1.5137 | 37.5 | 1.33
+Neigh | 1.2668 | 3.011 | 3.5942 | 58.0 | 3.18
+Comm | 3.4563 | 8.8707 | 11.494 | 107.9 | 9.37
+Output | 0.000435 | 0.0017425 | 0.004136 | 3.4 | 0.00
+Modify | 0.59335 | 1.4123 | 1.6921 | 39.8 | 1.49
+Other | | 0.5129 | | | 0.54
+
+Nlocal: 501 ave 515 max 476 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Nghost: 6681.5 ave 6740 max 6634 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs: 176872 ave 182642 max 168464 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 707486
+Ave neighs/atom = 353.037
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 200
+unfix cor
+unfix 1
+
+
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:53
diff --git a/src/CORESHELL/compute_temp_cs.h b/src/CORESHELL/compute_temp_cs.h
index 5a1d1434c3b2a5f86334d5c4f68a75787e4322bc..3e93e4a68c51c6e468ecffb31ac5747371ba419b 100644
--- a/src/CORESHELL/compute_temp_cs.h
+++ b/src/CORESHELL/compute_temp_cs.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/CORESHELL/pair_born_coul_long_cs.h b/src/CORESHELL/pair_born_coul_long_cs.h
index d2c8c04849b0eb86beca6331a83ab4448c2131f7..68c29e4fc22164c62fa06c68450707636f1e58cf 100644
--- a/src/CORESHELL/pair_born_coul_long_cs.h
+++ b/src/CORESHELL/pair_born_coul_long_cs.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/CORESHELL/pair_buck_coul_long_cs.h b/src/CORESHELL/pair_buck_coul_long_cs.h
index 7f0bc149c1ac3152c1e7ff08ba8e04814024b420..d6b117d6774bb9751ac664989fa6d1294f88f102 100644
--- a/src/CORESHELL/pair_buck_coul_long_cs.h
+++ b/src/CORESHELL/pair_buck_coul_long_cs.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/GPU/pair_lj_cubic_gpu.h b/src/GPU/pair_lj_cubic_gpu.h
index 1591eb8b9e8dae3a1ef0c6a793fb00b7e97f0cc7..cdfc157e8e7cf94a72550253c3ac1fe1798505ab 100644
--- a/src/GPU/pair_lj_cubic_gpu.h
+++ b/src/GPU/pair_lj_cubic_gpu.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/GPU/pair_tersoff_gpu.h b/src/GPU/pair_tersoff_gpu.h
index 4fa358a6b1da1ab7d95fa41065c2b4dbcdba9398..ed3dadef5d5f2122a1adfc75edc5b3d158e0702a 100644
--- a/src/GPU/pair_tersoff_gpu.h
+++ b/src/GPU/pair_tersoff_gpu.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/GPU/pair_tersoff_mod_gpu.h b/src/GPU/pair_tersoff_mod_gpu.h
index 6d3017669a9a9781031d3052add1f64427077a88..3967e90a70aab0ef8e9a443cce8dc159a471a840 100644
--- a/src/GPU/pair_tersoff_mod_gpu.h
+++ b/src/GPU/pair_tersoff_mod_gpu.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/GPU/pair_tersoff_zbl_gpu.h b/src/GPU/pair_tersoff_zbl_gpu.h
index 003e037bba4c844451e07dc6b813abcc1782726c..ba923ffd2ff5b28a51017e0bd17b123462944d47 100644
--- a/src/GPU/pair_tersoff_zbl_gpu.h
+++ b/src/GPU/pair_tersoff_zbl_gpu.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/GPU/pair_zbl_gpu.h b/src/GPU/pair_zbl_gpu.h
index 950fe952dd776825602afaee1eadae79b618776c..3e6ac373943eb2e05ce06960e7b0aa90ecc986fa 100644
--- a/src/GPU/pair_zbl_gpu.h
+++ b/src/GPU/pair_zbl_gpu.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/KOKKOS/pair_buck_kokkos.h b/src/KOKKOS/pair_buck_kokkos.h
index d57e320e993f7074079962296eccefcfea0eb284..2691f10929bafefac91fb80f5cfaa1f045c6f5aa 100644
--- a/src/KOKKOS/pair_buck_kokkos.h
+++ b/src/KOKKOS/pair_buck_kokkos.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/KOKKOS/pair_sw_kokkos.h b/src/KOKKOS/pair_sw_kokkos.h
index d899edfc1b4167b1b8c672997253026646d8f257..b94e39335f639832acef58b4f44f18a2fba1cfff 100644
--- a/src/KOKKOS/pair_sw_kokkos.h
+++ b/src/KOKKOS/pair_sw_kokkos.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/KOKKOS/pair_vashishta_kokkos.h b/src/KOKKOS/pair_vashishta_kokkos.h
index 49c936185d4b15874e999357f69e14522ea1bce6..174db2cb946521c0f72115f20f4e319f20a98553 100644
--- a/src/KOKKOS/pair_vashishta_kokkos.h
+++ b/src/KOKKOS/pair_vashishta_kokkos.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp
index d2a6b801fc58d2f515b8fc3cf5c7adf16d0307c4..1dc1ca1cb451f0a09fa30e7925efae444bacd98f 100644
--- a/src/KSPACE/pair_lj_long_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp
@@ -1337,8 +1337,8 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
- xH1 = x[jH1];
- xH2 = x[jH2];
+ xH1 = x[iH1];
+ xH2 = x[iH2];
v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index d83f5a39a8414e7358a68cb4d8d9a25d47602201..0ca80c6b7647a95d160d8dc5782208e1c075412c 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -1271,7 +1271,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
double cross321[3],cross234[3],prefactor,SpN;
double fcijpc,fcikpc,fcjlpc,fcjkpc,fcilpc;
- double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
+ double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa2,at2,cw,cwnum,cwnom;
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
double dctik,dctjk,dctjl,dctij,dctji,dctil,rik2i,rjl2i,sink2i,sinl2i;
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil,dt1dij;
@@ -1856,8 +1856,6 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
- aaa1 = -prefactor*(1.0-square(om1234)) *
- (1.0-tspjik)*(1.0-tspijl);
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
at2 = aa*cwnum;
@@ -2107,7 +2105,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
double cross321[3],cross234[3],prefactor,SpN;
double fcikpc,fcjlpc,fcjkpc,fcilpc;
- double dt2dik[3],dt2djl[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
+ double dt2dik[3],dt2djl[3],aa,aaa2,at2,cw,cwnum,cwnom;
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
double dctik,dctjk,dctjl,dctil,rik2i,rjl2i,sink2i,sinl2i;
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil;
@@ -2800,8 +2798,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
- aaa1 = -prefactor*(1.0-square(om1234)) *
- (1.0-tspjik)*(1.0-tspijl);
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
at2 = aa*cwnum;
diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h
index d55d9a79a4fb5c7362fbb9e266e989bc383d7cf5..f50c5edd00f7d73c90f2419319de6026a6937641 100644
--- a/src/MANYBODY/pair_bop.h
+++ b/src/MANYBODY/pair_bop.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h
index 9b7fe761bbc5482c0e2bcfa3d9b4b8f28d21db2b..9917bcd96df565ec9ec5953fe5b135a5d50ac7e8 100644
--- a/src/MANYBODY/pair_polymorphic.h
+++ b/src/MANYBODY/pair_polymorphic.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/MANYBODY/pair_vashishta_table.h b/src/MANYBODY/pair_vashishta_table.h
index a45cac5ae1c719407c3faeaf0885f5f2aa7ef1b4..8c52f967cb55892e2a4f230d1937393466816ddf 100644
--- a/src/MANYBODY/pair_vashishta_table.h
+++ b/src/MANYBODY/pair_vashishta_table.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h
index 25208a2b5a221776b8b33734b56d69220ac4f248..74720d6222e1dcdf9cfc3a4d054c60a609cd9c43 100644
--- a/src/MC/fix_atom_swap.h
+++ b/src/MC/fix_atom_swap.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h
index 8a5375eed70ad12bd72c12744bd8f55b5cd3c161..3656a1df58f7e5dade999cc2e48d36dedba3e5a4 100644
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/MC/fix_tfmc.h b/src/MC/fix_tfmc.h
index fee3a944cdbc72cfd59c5a768c751be84a12c789..d4f121eb906a519b1f70ad87750d0a26effee4f9 100644
--- a/src/MC/fix_tfmc.h
+++ b/src/MC/fix_tfmc.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index b9d1c440d44cbb7ef5acb06a219ef1007191be9b..35953a6ac456185b8b87a49b5b7c5be772e2d3e5 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -18,6 +18,7 @@
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
+#include <string.h>
#include "dihedral_charmm.h"
#include "atom.h"
#include "comm.h"
@@ -26,6 +27,7 @@
#include "force.h"
#include "pair.h"
#include "update.h"
+#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
@@ -368,10 +370,26 @@ void DihedralCharmm::coeff(int narg, char **arg)
void DihedralCharmm::init_style()
{
+ if (strstr(update->integrate_style,"respa")) {
+ Respa *r = (Respa *) update->integrate;
+ if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
+ error->all(FLERR,"Dihedral style charmm must be set to same"
+ " r-RESPA level as 'pair'");
+ if (r->level_outer >= 0 && (r->level_outer != r->level_dihedral))
+ error->all(FLERR,"Dihedral style charmm must be set to same"
+ " r-RESPA level as 'outer'");
+ }
+
// insure use of CHARMM pair_style if any weight factors are non-zero
// set local ptrs to LJ 14 arrays setup by Pair
+ // also verify that the correct 1-4 scaling is set
if (weightflag) {
+
+ if ((force->special_lj[3] != 0.0) || (force->special_coul[3] != 0.0))
+ error->all(FLERR,"Must use 'special_bonds charmm' with"
+ " dihedral style charmm for use with CHARMM pair styles");
+
int itmp;
if (force->pair == NULL)
error->all(FLERR,"Dihedral charmm is incompatible with Pair style");
diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp
index 613170bbfab6c7eff157a9c97951c371b5a0bf8e..feb3e02bd42135ca5ac82b416d0043431dc7b1b5 100644
--- a/src/MOLECULE/dihedral_charmmfsw.cpp
+++ b/src/MOLECULE/dihedral_charmmfsw.cpp
@@ -21,6 +21,7 @@
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
+#include <string.h>
#include "dihedral_charmmfsw.h"
#include "atom.h"
#include "comm.h"
@@ -29,6 +30,7 @@
#include "force.h"
#include "pair.h"
#include "update.h"
+#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
@@ -386,10 +388,26 @@ void DihedralCharmmfsw::coeff(int narg, char **arg)
void DihedralCharmmfsw::init_style()
{
+ if (strstr(update->integrate_style,"respa")) {
+ Respa *r = (Respa *) update->integrate;
+ if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
+ error->all(FLERR,"Dihedral style charmmfsw must be set to same"
+ " r-RESPA level as 'pair'");
+ if (r->level_outer >= 0 && (r->level_outer != r->level_dihedral))
+ error->all(FLERR,"Dihedral style charmmfsw must be set to same"
+ " r-RESPA level as 'outer'");
+ }
+
// insure use of CHARMM pair_style if any weight factors are non-zero
// set local ptrs to LJ 14 arrays setup by Pair
+ // also verify that the correct 1-4 scaling is set
if (weightflag) {
+
+ if ((force->special_lj[3] != 0.0) || (force->special_coul[3] != 0.0))
+ error->all(FLERR,"Must use 'special_bonds charmm' with"
+ " dihedral style charmm for use with CHARMM pair styles");
+
int itmp;
if (force->pair == NULL)
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h
index 3220b771954d1b32579b1df7d47c3e46741d0928..02f83df1af696a4bb69854636fceb59e520832be 100644
--- a/src/RIGID/fix_ehex.h
+++ b/src/RIGID/fix_ehex.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h
index 642c325af91b23c58138fd7fc10fcd9fef3a0a45..56055d5facab082760d899473fec3cbe667b5f8f 100644
--- a/src/USER-CGDNA/mf_oxdna.h
+++ b/src/USER-CGDNA/mf_oxdna.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.h b/src/USER-CGDNA/pair_oxdna2_coaxstk.h
index 477b35ee1306727a1bac874c44eabdeb883c04c4..be8d6d6b3752474e6d32936c0c20e0c27496908f 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.h
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/USER-CGDNA/pair_oxdna2_dh.h
index 3af355d5036947fbea739bf337574ca28d2edfc0..b40346e1cf130e935ffe7497096dae72dc73c030 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.h
+++ b/src/USER-CGDNA/pair_oxdna2_dh.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna2_excv.h b/src/USER-CGDNA/pair_oxdna2_excv.h
index 94e39a0fa269f5fa290aa865b4d3b750165d1c6f..f59daf8361d01c709724b35fd538e6500b26154d 100644
--- a/src/USER-CGDNA/pair_oxdna2_excv.h
+++ b/src/USER-CGDNA/pair_oxdna2_excv.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna2_stk.h b/src/USER-CGDNA/pair_oxdna2_stk.h
index b78fc89d5e0fdde7c89b4d71692d17f82c290f3c..7654e5db2fe134ac8a7c756aa88fe71e26fbfdc7 100644
--- a/src/USER-CGDNA/pair_oxdna2_stk.h
+++ b/src/USER-CGDNA/pair_oxdna2_stk.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/USER-CGDNA/pair_oxdna_coaxstk.h
index b12ef6e77b2ac39211d31290a72c0dab121759b3..f9228c94a213b78d11c5e9d14c20c16f38bcde54 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.h
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna_excv.h b/src/USER-CGDNA/pair_oxdna_excv.h
index 0308c1f48e52b7194a021d0bd6fc31dec88b53a2..ec9ddee3ece9a545c09e12f1b10417e4a905dbdb 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.h
+++ b/src/USER-CGDNA/pair_oxdna_excv.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.h b/src/USER-CGDNA/pair_oxdna_hbond.h
index 409241710be7d2f88296c9a90466bb5dd0066ac5..1c9f37bf50a1bc25a788ff0fb6989bb914b053ae 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.h
+++ b/src/USER-CGDNA/pair_oxdna_hbond.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna_stk.h b/src/USER-CGDNA/pair_oxdna_stk.h
index fd0c27d38c5150316165755d45f19016fee0c59c..950c2762289efc8b71848c398344e1b9fb240aea 100644
--- a/src/USER-CGDNA/pair_oxdna_stk.h
+++ b/src/USER-CGDNA/pair_oxdna_stk.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.h b/src/USER-CGDNA/pair_oxdna_xstk.h
index c71962ab5206e529c948382288fbe4e8a9b70994..5c443a4dac28459528b33cc0b1828892742b4e2b 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.h
+++ b/src/USER-CGDNA/pair_oxdna_xstk.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DIFFRACTION/compute_saed.h b/src/USER-DIFFRACTION/compute_saed.h
index 89e57f5097fc473867be477e48876d0950ceac5e..87785c493679395186b6afb2c7c1970c7d2af948 100644
--- a/src/USER-DIFFRACTION/compute_saed.h
+++ b/src/USER-DIFFRACTION/compute_saed.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DIFFRACTION/compute_saed_consts.h b/src/USER-DIFFRACTION/compute_saed_consts.h
index 0cce0abfc2b7d9c0ccc2e2088439adc2b95c4b67..0c07ae13ad9aeb7bdddde49515f75b9ec119c456 100644
--- a/src/USER-DIFFRACTION/compute_saed_consts.h
+++ b/src/USER-DIFFRACTION/compute_saed_consts.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DIFFRACTION/compute_xrd.h b/src/USER-DIFFRACTION/compute_xrd.h
index 92a59fcf23f779628900aee25524a0ef1c06ff92..61e1dae1bdc9d26b6f00fe0d192eb62d305c5d6f 100644
--- a/src/USER-DIFFRACTION/compute_xrd.h
+++ b/src/USER-DIFFRACTION/compute_xrd.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DIFFRACTION/compute_xrd_consts.h b/src/USER-DIFFRACTION/compute_xrd_consts.h
index 1ca0d6bd669cd1c9816dd813526124da507577ae..582cecae014902f5f874b2500658f21aadb52baf 100644
--- a/src/USER-DIFFRACTION/compute_xrd_consts.h
+++ b/src/USER-DIFFRACTION/compute_xrd_consts.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h
index 294b003b0c119b7007afedaa1bf05d4a8f301e82..fa379e7216ca9dfdb366969e3aca3c481559d3b4 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.h
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DPD/fix_dpd_energy.h b/src/USER-DPD/fix_dpd_energy.h
index 9be41c3b9a4e93fa61b8a195dc43bc6c0ddfffab..89ba84c08bd40acfeb57ebe34b4519fa05e7b22a 100644
--- a/src/USER-DPD/fix_dpd_energy.h
+++ b/src/USER-DPD/fix_dpd_energy.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DPD/fix_rx.h b/src/USER-DPD/fix_rx.h
index c35c9afabfb930290b888a2ac85aa6817353a36c..35998963e2fbe1fd946d19a7f8d392cb30e4f971 100644
--- a/src/USER-DPD/fix_rx.h
+++ b/src/USER-DPD/fix_rx.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DPD/pair_exp6_rx.h b/src/USER-DPD/pair_exp6_rx.h
index c16875c96021702ecb532aed737b688daf8d7303..33bd6e6623880dba0ea280d9b976ed903ad2698e 100644
--- a/src/USER-DPD/pair_exp6_rx.h
+++ b/src/USER-DPD/pair_exp6_rx.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DPD/pair_multi_lucy_rx.h b/src/USER-DPD/pair_multi_lucy_rx.h
index 87d2ed7ae8194f9fa0f03dfd85fdc0312461458d..092f40f1d11fd7053c77465401d3cd1e9f21c19d 100644
--- a/src/USER-DPD/pair_multi_lucy_rx.h
+++ b/src/USER-DPD/pair_multi_lucy_rx.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-DPD/pair_table_rx.h b/src/USER-DPD/pair_table_rx.h
index c6afe6a8d59eea99f021add838112be13250683d..34b9fd75ce739012053f2c63d70ce399db6e1785 100644
--- a/src/USER-DPD/pair_table_rx.h
+++ b/src/USER-DPD/pair_table_rx.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h
index 71aa1aed9a4a7b5a67cbe550de6991577fa360df..2bc821ab04fc37e2ad7f275954fae78f161bf4ba 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h
index a9d3e3122f976c50e37c1123e06f0762a9b858e6..144cda3799064e521eceff85849e11081e047683 100644
--- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h
+++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h
index b89e765a6eab068f99194cd492d867fe456fa4f8..f0d56ffd82efd240526bbe204181206cbf2d2400 100644
--- a/src/USER-MANIFOLD/manifold.h
+++ b/src/USER-MANIFOLD/manifold.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h
index a2f21861ebc9e197b551440e3e411a6a7e522887..7fdd0a6de555f23c146849d67909a9367d74c5ea 100644
--- a/src/USER-MANIFOLD/manifold_factory.h
+++ b/src/USER-MANIFOLD/manifold_factory.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.h b/src/USER-MANIFOLD/manifold_gaussian_bump.h
index f3401a4a33d0d1a9082d13a6e9d201ed0f8e05fd..f31e2a4bf4f4863bdbc911eea2e64bf5a502afdc 100644
--- a/src/USER-MANIFOLD/manifold_gaussian_bump.h
+++ b/src/USER-MANIFOLD/manifold_gaussian_bump.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp
index 89568c6731a85c05bfc5d621cd04807f10c37f00..f479486b79cc18f48fe7032f0c15ba3e9509f2df 100644
--- a/src/USER-MISC/compute_cnp_atom.cpp
+++ b/src/USER-MISC/compute_cnp_atom.cpp
@@ -50,7 +50,7 @@ enum{NCOMMON};
ComputeCNPAtom::ComputeCNPAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- nearest(NULL), nnearest(NULL), cnpv(NULL)
+ list(NULL), nearest(NULL), nnearest(NULL), cnpv(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal compute cnp/atom command");
diff --git a/src/USER-MISC/fix_filter_corotate.h b/src/USER-MISC/fix_filter_corotate.h
index 3f8e8bba43a75cd110b8c69489261399f9517850..67e3fb4f01dfd6e9d2edaf567700f7746d1256e7 100644
--- a/src/USER-MISC/fix_filter_corotate.h
+++ b/src/USER-MISC/fix_filter_corotate.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/fix_ti_spring.h b/src/USER-MISC/fix_ti_spring.h
index 57c0d3299a84dd3f6e2e65232096348b8f38028c..13f1236a8a42a646575211ae4192545552fe0339 100644
--- a/src/USER-MISC/fix_ti_spring.h
+++ b/src/USER-MISC/fix_ti_spring.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/fix_ttm_mod.h b/src/USER-MISC/fix_ttm_mod.h
index 3415baf5b10f13f8cfc1cbffe13cb68cfd0da5f4..21f6e57e043938c7421d36587ee344f7cde6acb2 100644
--- a/src/USER-MISC/fix_ttm_mod.h
+++ b/src/USER-MISC/fix_ttm_mod.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h
index 6301e6897a95c7f45333e6150ca4bf496bf31e67..cff96c6d9d7b096f3481730d23e354ad31cd6190 100644
--- a/src/USER-MISC/improper_distance.h
+++ b/src/USER-MISC/improper_distance.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/pair_buck_mdf.h b/src/USER-MISC/pair_buck_mdf.h
index c0ecceeea8ce3f8ef7bb261ed460becb19bae34b..4f9bac634163a55d8da4e3a2bcc06d93d7d8dff8 100644
--- a/src/USER-MISC/pair_buck_mdf.h
+++ b/src/USER-MISC/pair_buck_mdf.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/pair_edip_multi.h b/src/USER-MISC/pair_edip_multi.h
index e55916f79b62254923f018c0eb52a2cb57440214..fd94594d931d550fe9673d3ba2e77f654dd9751f 100644
--- a/src/USER-MISC/pair_edip_multi.h
+++ b/src/USER-MISC/pair_edip_multi.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.h b/src/USER-MISC/pair_kolmogorov_crespi_z.h
index 3a81e571ef511d54f5c1d4b5ac855a1dab3d2f8d..caa5dac8683247e71df5cdab837f463a55edbb16 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_z.h
+++ b/src/USER-MISC/pair_kolmogorov_crespi_z.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/pair_lennard_mdf.h b/src/USER-MISC/pair_lennard_mdf.h
index 6fefe6fc3f1bcde1147ca1e5f21d203bbbd46b3f..c4ffc80cd676f9ab3fe9873ca53335f5301cbad7 100644
--- a/src/USER-MISC/pair_lennard_mdf.h
+++ b/src/USER-MISC/pair_lennard_mdf.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/pair_lj_mdf.h b/src/USER-MISC/pair_lj_mdf.h
index f49020bf2d2ea2e958d5ae75d17279f86f42cf99..c6236a923c5e809e535edf0f70c6387c38f565b0 100644
--- a/src/USER-MISC/pair_lj_mdf.h
+++ b/src/USER-MISC/pair_lj_mdf.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/pair_meam_spline.h b/src/USER-MISC/pair_meam_spline.h
index 62002546749ae71d6edf1b2716d8af20cdde6ffb..d3554f056e198923f6dd754fb852a9632a18d5b4 100644
--- a/src/USER-MISC/pair_meam_spline.h
+++ b/src/USER-MISC/pair_meam_spline.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-MISC/pair_momb.h b/src/USER-MISC/pair_momb.h
index 95b750cb2c4e2f1be450c1b94a6af5bf2240ef55..e08b81aa3eead79307478888fae85d9ca1ffd215 100644
--- a/src/USER-MISC/pair_momb.h
+++ b/src/USER-MISC/pair_momb.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-NETCDF/dump_netcdf.h b/src/USER-NETCDF/dump_netcdf.h
index 036df3f058398a53c9f55df4f1fab79f7a477b8e..b86f294d3084d41ff7116ef995b7852a55f31bc5 100644
--- a/src/USER-NETCDF/dump_netcdf.h
+++ b/src/USER-NETCDF/dump_netcdf.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.h b/src/USER-NETCDF/dump_netcdf_mpiio.h
index 10b0e800d2347d561d42073c1b3c196275fd9ca5..3ca52449a5f2de1b888706c3cfba1f58b247cf53 100644
--- a/src/USER-NETCDF/dump_netcdf_mpiio.h
+++ b/src/USER-NETCDF/dump_netcdf_mpiio.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-OMP/fix_qeq_reax_omp.h b/src/USER-OMP/fix_qeq_reax_omp.h
index 078ba3b9af55171d61efec56d84b2e2c121da4d7..7565f0aff090be62ab65d2da53c441c99ada0b95 100644
--- a/src/USER-OMP/fix_qeq_reax_omp.h
+++ b/src/USER-OMP/fix_qeq_reax_omp.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index 206e8e86e69374f920b12719ee0d7887ca62db8f..13df133585f3ac551e117831e975d493f3416b5d 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -1038,7 +1038,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
double cross321[3],cross234[3],prefactor,SpN;
double fcijpc,fcikpc,fcjlpc,fcjkpc,fcilpc;
- double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
+ double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa2,at2,cw,cwnum,cwnom;
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
double dctik,dctjk,dctjl,dctij,dctji,dctil,rik2i,rjl2i,sink2i,sinl2i;
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil,dt1dij;
@@ -1628,8 +1628,6 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
- aaa1 = -prefactor*(1.0-square(om1234)) *
- (1.0-tspjik)*(1.0-tspijl);
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
at2 = aa*cwnum;
@@ -1879,7 +1877,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
double cross321[3],cross234[3],prefactor,SpN;
double fcikpc,fcjlpc,fcjkpc,fcilpc;
- double dt2dik[3],dt2djl[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
+ double dt2dik[3],dt2djl[3],aa,aaa2,at2,cw,cwnum,cwnom;
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
double dctik,dctjk,dctjl,dctil,rik2i,rjl2i,sink2i,sinl2i;
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil;
@@ -2572,8 +2570,6 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
(1.0-tspjik)*(1.0-tspijl);
- aaa1 = -prefactor*(1.0-square(om1234)) *
- (1.0-tspjik)*(1.0-tspijl);
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
at2 = aa*cwnum;
diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp
index 0fb24ed5f212ac7840cab36cd17a5b53f2de6fa7..91fa3d38c7f3d0310fb5e7e69729ff4c3bdc90e6 100644
--- a/src/USER-OMP/pair_reaxc_omp.cpp
+++ b/src/USER-OMP/pair_reaxc_omp.cpp
@@ -572,17 +572,18 @@ void PairReaxCOMP::read_reax_forces(int vflag)
void PairReaxCOMP::FindBond()
{
- int i, ii, j, pj, jtag, nj, jtmp, jj;
- double bo_tmp, bo_cut, rij, rsq;
-
- bond_data *bo_ij;
- bo_cut = 0.10;
+ const double bo_cut = 0.10;
+ int i;
#if defined(_OPENMP)
#pragma omp parallel for schedule(static) default(shared) \
- private(i, nj, pj, bo_ij, j, bo_tmp)
+ private(i)
#endif
for (i = 0; i < system->n; i++) {
+ int j, pj, nj;
+ double bo_tmp;
+ bond_data *bo_ij;
+
nj = 0;
for( pj = Start_Index(i, lists); pj < End_Index(i, lists); ++pj ) {
bo_ij = &( lists->select.bond_list[pj] );
diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h
index a5e077c309601a59bd71f9b659eb5af34b1e6468..156627ece0a29b67d753ec51101af9f850cb11ab 100644
--- a/src/USER-OMP/pair_reaxc_omp.h
+++ b/src/USER-OMP/pair_reaxc_omp.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp
index 222c00980ec53e04e8140ab68f13b924480c81c0..85755a39a306a014eff4d4839f356acff1f8c984 100644
--- a/src/USER-OMP/reaxc_bond_orders_omp.cpp
+++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp
@@ -55,7 +55,6 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
long reductionOffset = (system->N * tid);
/* Virial Tallying variables */
- double f_scaler;
rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp;
/* Initializations */
@@ -229,14 +228,11 @@ void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_
ivec rel_box;
int pk, k, j;
- PairReaxCOMP *pair_reax_ptr = static_cast<class PairReaxCOMP*>(system->pair_ptr);
-
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
int tid = 0;
#endif
- ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);
long reductionOffset = (system->N * tid);
/* Initializations */
@@ -430,12 +426,9 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
#endif
double p_lp1 = system->reax_param.gp.l[15];
- int num_bonds = 0;
double p_boc1 = system->reax_param.gp.l[0];
double p_boc2 = system->reax_param.gp.l[1];
reax_list *bonds = (*lists) + BONDS;
- int natoms = system->N;
- int nthreads = control->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(shared)
@@ -454,11 +447,6 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
two_body_parameters *twbp;
bond_order_data *bo_ij, *bo_ji;
-#if defined(_OPENMP)
- int tid = omp_get_thread_num();
-#else
- int tid = 0;
-#endif
/* Calculate Deltaprime, Deltaprime_boc values */
#if defined(_OPENMP)
#pragma omp for schedule(static)
diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp
index dcf788a79c228d8b9dacfba56058262933841a2f..9e169190079900d49dccbbc0955f2f1c1678553a 100644
--- a/src/USER-OMP/reaxc_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_bonds_omp.cpp
@@ -49,14 +49,13 @@ void BondsOMP( reax_system *system, control_params *control,
startTimeBase = MPI_Wtime();
#endif
- int natoms = system->n;
- int nthreads = control->nthreads;
+ const int natoms = system->n;
reax_list *bonds = (*lists) + BONDS;
- double gp3 = system->reax_param.gp.l[3];
- double gp4 = system->reax_param.gp.l[4];
- double gp7 = system->reax_param.gp.l[7];
- double gp10 = system->reax_param.gp.l[10];
- double gp37 = (int) system->reax_param.gp.l[37];
+ const double gp3 = system->reax_param.gp.l[3];
+ const double gp4 = system->reax_param.gp.l[4];
+ const double gp7 = system->reax_param.gp.l[7];
+ const double gp10 = system->reax_param.gp.l[10];
+ const int gp37 = (int) system->reax_param.gp.l[37];
double total_Ebond = 0.0;
#if defined(_OPENMP)
@@ -66,9 +65,8 @@ void BondsOMP( reax_system *system, control_params *control,
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
- double ebond, ebond_thr=0.0, pow_BOs_be2, exp_be12, CEbo;
- double gp3, gp4, gp7, gp10, gp37;
- double exphu, exphua1, exphub1, exphuov, hulpov, estriph, estriph_thr=0.0;
+ double ebond, pow_BOs_be2, exp_be12, CEbo;
+ double exphu, exphua1, exphub1, exphuov, hulpov, estriph;
double decobdbo, decobdboua, decobdboub;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp
index 4e37dac38dfb319b1ca8d85b542713a36f2044cf..5e93f31125582ea5785ae47ed712591ad1cf7d0f 100644
--- a/src/USER-OMP/reaxc_forces_omp.cpp
+++ b/src/USER-OMP/reaxc_forces_omp.cpp
@@ -265,7 +265,6 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
- reallocate_data *realloc = &(workspace->realloc);
double saferzone = system->saferzone;
#if defined(_OPENMP)
@@ -335,25 +334,21 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
startTimeBase = MPI_Wtime();
#endif
- int i, j, pi, pj;
- int start_i, end_i, start_j, end_j;
+ int i, j, pj;
+ int start_i, end_i;
int type_i, type_j;
int ihb, jhb, ihb_top, jhb_top;
- int local, flag;
- double r_ij, cutoff;
+ double cutoff;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
- bond_data *ibond, *jbond;
reax_list *far_nbrs = *lists + FAR_NBRS;
reax_list *bonds = *lists + BONDS;
reax_list *hbonds = *lists + HBONDS;
int num_bonds = 0;
int num_hbonds = 0;
int btop_i = 0;
- int btop_j = 0;
- int renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
// We will use CdDeltaReduction as a temporary (double) buffer to accumulate total_bond_order
// This is safe because CdDeltaReduction is currently zeroed and its accumulation doesn't start until BondsOMP()
@@ -368,8 +363,8 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
#if defined(_OPENMP)
#pragma omp parallel default(shared) \
- private(i, atom_i, type_i, pi, start_i, end_i, sbp_i, btop_i, ibond, ihb, ihb_top, \
- j, atom_j, type_j, pj, start_j, end_j, sbp_j, nbr_pj, jbond, jhb, twbp)
+ private(i, atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \
+ j, atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp)
#endif
{
@@ -417,7 +412,6 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
// outside of critical section.
// Start top portion of BOp()
- int jj = nbr_pj->nbr;
double C12, C34, C56;
double BO, BO_s, BO_pi, BO_pi2;
double bo_cut = control->bo_cut;
@@ -602,7 +596,6 @@ void Compute_ForcesOMP( reax_system *system, control_params *control,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data )
{
- int qeq_flag;
MPI_Comm comm = mpi_data->world;
// Init Forces
diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp
index acbe4ec268e74f7af165c082ad4c4299cccad96f..ff8baa3c1a7f4954faa7c5ba4cf050eaadc19cc6 100644
--- a/src/USER-OMP/reaxc_multi_body_omp.cpp
+++ b/src/USER-OMP/reaxc_multi_body_omp.cpp
@@ -50,16 +50,14 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
#endif
/* Initialize parameters */
- double p_lp1 = system->reax_param.gp.l[15];
- double p_lp3 = system->reax_param.gp.l[5];
- double p_ovun3 = system->reax_param.gp.l[32];
- double p_ovun4 = system->reax_param.gp.l[31];
- double p_ovun6 = system->reax_param.gp.l[6];
- double p_ovun7 = system->reax_param.gp.l[8];
- double p_ovun8 = system->reax_param.gp.l[9];
-
- int natoms = system->n;
- int nthreads = control->nthreads;
+ const double p_lp3 = system->reax_param.gp.l[5];
+ const double p_ovun3 = system->reax_param.gp.l[32];
+ const double p_ovun4 = system->reax_param.gp.l[31];
+ const double p_ovun6 = system->reax_param.gp.l[6];
+ const double p_ovun7 = system->reax_param.gp.l[8];
+ const double p_ovun8 = system->reax_param.gp.l[9];
+
+ const int natoms = system->n;
reax_list *bonds = (*lists) + BONDS;
double total_Elp = 0.0;
@@ -79,11 +77,11 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
double exp_ovun2n, exp_ovun6, exp_ovun8;
double inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
double e_un, CEunder1, CEunder2, CEunder3, CEunder4;
- double eng_tmp, f_tmp;
+ double eng_tmp;
double p_lp2, p_ovun2, p_ovun5;
int numbonds;
- single_body_parameters *sbp_i, *sbp_j;
+ single_body_parameters *sbp_i;
two_body_parameters *twbp;
bond_data *pbond;
bond_order_data *bo_ij;
diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp
index 38a6d9e860178602cc4da1cc94d6f3d43663b2b1..c509be8a26305ee7c165c7f3a53b652ec486af8f 100644
--- a/src/USER-OMP/reaxc_nonbonded_omp.cpp
+++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp
@@ -48,8 +48,6 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
reax_list **lists, output_controls *out_control ) {
int natoms = system->n;
- int nthreads = control->nthreads;
- long totalReductionSize = system->N * nthreads;
reax_list *far_nbrs = (*lists) + FAR_NBRS;
double p_vdW1 = system->reax_param.gp.l[28];
double p_vdW1i = 1.0 / p_vdW1;
@@ -71,7 +69,8 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
double tmp, r_ij, fn13, exp1, exp2;
double Tap, dTap, dfn13, CEvd, CEclmb, de_core;
double dr3gamij_1, dr3gamij_3;
- double e_ele, e_ele_thr, e_vdW, e_vdW_thr, e_core, SMALL = 0.0001;
+ double e_ele, e_vdW, e_core;
+ const double SMALL = 0.0001;
double e_lg, de_lg, r_ij5, r_ij6, re6;
rvec temp, ext_press;
two_body_parameters *twbp;
@@ -92,7 +91,6 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
system->pair_ptr->vatom, thr);
e_core = 0;
e_vdW = 0;
- e_vdW_thr = 0;
e_lg = 0;
de_lg = 0.0;
@@ -263,8 +261,6 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro
double SMALL = 0.0001;
int natoms = system->n;
reax_list *far_nbrs = (*lists) + FAR_NBRS;
- int nthreads = control->nthreads;
- long totalReductionSize = system->N * nthreads;
double total_EvdW = 0.;
double total_Eele = 0.;
diff --git a/src/USER-QTB/fix_qbmsst.h b/src/USER-QTB/fix_qbmsst.h
index 3484076abf995e7421a962b261061d9db2ff05d7..cec54e40d8d2a40394fabf5f5ad80b7f5ffb6fdb 100644
--- a/src/USER-QTB/fix_qbmsst.h
+++ b/src/USER-QTB/fix_qbmsst.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-QTB/fix_qtb.h b/src/USER-QTB/fix_qtb.h
index e2b76345373c39e7e311b36eddf53703ae3f7418..5537ecb56ef7219032d112b63f87167542e875b8 100644
--- a/src/USER-QTB/fix_qtb.h
+++ b/src/USER-QTB/fix_qtb.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-QUIP/pair_quip.h b/src/USER-QUIP/pair_quip.h
index 15e143aee75c7ddb9f75d31800b5fb649fe332ca..f86df015ea7fe3f922a2ca91e6097b732bb33f56 100644
--- a/src/USER-QUIP/pair_quip.h
+++ b/src/USER-QUIP/pair_quip.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index df28a34fe884bbe28a02f5c6058cccf53e521fbf..62b3bff93edbe770bfd3db1bcda1cf9303a49b94 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -514,8 +514,6 @@ void FixReaxCSpecies::FindMolecule ()
int *ilist;
double bo_tmp,bo_cut;
double **spec_atom = f_SPECBOND->array_atom;
- const double * const * const x = atom->x;
- const int nlocal = atom->nlocal;
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
diff --git a/src/USER-SMD/atom_vec_smd.h b/src/USER-SMD/atom_vec_smd.h
index cea9a31f863f17d556faf455a638d88402b04829..34fdfc1f76fbb7ce3ffb9265a979a009eaf7d5ca 100644
--- a/src/USER-SMD/atom_vec_smd.h
+++ b/src/USER-SMD/atom_vec_smd.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_contact_radius.h b/src/USER-SMD/compute_smd_contact_radius.h
index 46034f2f113a577a209f5325a5ee5f7950b71055..f22dce1bab1e405bf076b5369ac778529138acbd 100644
--- a/src/USER-SMD/compute_smd_contact_radius.h
+++ b/src/USER-SMD/compute_smd_contact_radius.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_damage.h b/src/USER-SMD/compute_smd_damage.h
index 1259788ec405b1cf1256de925efce41ac3f6af02..c8447872c7ed0feeaafd6c54ec3e03e93f5c0ddd 100644
--- a/src/USER-SMD/compute_smd_damage.h
+++ b/src/USER-SMD/compute_smd_damage.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_hourglass_error.h b/src/USER-SMD/compute_smd_hourglass_error.h
index d4e39ce25f5a4404417b29dc50cfea9f490123e9..a6d1d1a1e25db2ba0e42b7e68810a7f18f957ae0 100644
--- a/src/USER-SMD/compute_smd_hourglass_error.h
+++ b/src/USER-SMD/compute_smd_hourglass_error.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_internal_energy.h b/src/USER-SMD/compute_smd_internal_energy.h
index 0754f6fe6c807ffad7b2aab259ebadea64554e96..fbccfbfb7edec980e908409392f3af30bfee3c38 100644
--- a/src/USER-SMD/compute_smd_internal_energy.h
+++ b/src/USER-SMD/compute_smd_internal_energy.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_plastic_strain.h b/src/USER-SMD/compute_smd_plastic_strain.h
index cdc322e4cf5d6fabc70071e1b25c86f35ca03276..d2e64e31a1e7fef2ddeede51d8111cdec1a8b382 100644
--- a/src/USER-SMD/compute_smd_plastic_strain.h
+++ b/src/USER-SMD/compute_smd_plastic_strain.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.h b/src/USER-SMD/compute_smd_plastic_strain_rate.h
index efc4f0c67c7d75bfa470ba0d785fa4d0ff77c937..03445e92f8f56e79a4629d69ad9962a490bdde59 100644
--- a/src/USER-SMD/compute_smd_plastic_strain_rate.h
+++ b/src/USER-SMD/compute_smd_plastic_strain_rate.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_rho.h b/src/USER-SMD/compute_smd_rho.h
index ce749c6466bbf6042ce5703935ba0a8197ebb5f8..35dfdf8e91de1864d4bc34467110862b6747b558 100644
--- a/src/USER-SMD/compute_smd_rho.h
+++ b/src/USER-SMD/compute_smd_rho.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.h b/src/USER-SMD/compute_smd_tlsph_defgrad.h
index 654403e7a388b19b4b1a07aca87c9f64c5c59ec6..5dfa502991423c504ac9c39fd928a50e83fc0cc2 100644
--- a/src/USER-SMD/compute_smd_tlsph_defgrad.h
+++ b/src/USER-SMD/compute_smd_tlsph_defgrad.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_tlsph_dt.h b/src/USER-SMD/compute_smd_tlsph_dt.h
index 16969a05be394702d363a2502f26ef0262dbfcd6..09bf6c9727b4e569d0d40759de1a581cf8ead8fd 100644
--- a/src/USER-SMD/compute_smd_tlsph_dt.h
+++ b/src/USER-SMD/compute_smd_tlsph_dt.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.h b/src/USER-SMD/compute_smd_tlsph_num_neighs.h
index 77e4c5838c61a4675bae8e32b08221ba92ac0504..da649fbce20a52cc26ae7cd326e5876093c1b950 100644
--- a/src/USER-SMD/compute_smd_tlsph_num_neighs.h
+++ b/src/USER-SMD/compute_smd_tlsph_num_neighs.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_tlsph_shape.h b/src/USER-SMD/compute_smd_tlsph_shape.h
index 167e2b67e401a02dc06f4e6a13163cb7f3842b16..193657870c99052fd6b09831e842cf4fc1c55514 100644
--- a/src/USER-SMD/compute_smd_tlsph_shape.h
+++ b/src/USER-SMD/compute_smd_tlsph_shape.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_tlsph_strain.h b/src/USER-SMD/compute_smd_tlsph_strain.h
index 199190c8b9208d995339c801adc95a3b14b41867..1294af2f458d5779b0928232bd8e9fa3a3a0b382 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain.h
+++ b/src/USER-SMD/compute_smd_tlsph_strain.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.h b/src/USER-SMD/compute_smd_tlsph_strain_rate.h
index 9924f5e1cc0552f2daadad32402e7d728bdc693f..cc4ed9f5eef125ab4bbb366dea16f12039dd6b64 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain_rate.h
+++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_tlsph_stress.h b/src/USER-SMD/compute_smd_tlsph_stress.h
index 3a8f6610b1b76c8ef2147e31130f62a5eaa1066a..bf9079bb4f6d398a6202df577ff2b8acbf8245e0 100644
--- a/src/USER-SMD/compute_smd_tlsph_stress.h
+++ b/src/USER-SMD/compute_smd_tlsph_stress.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.h b/src/USER-SMD/compute_smd_triangle_mesh_vertices.h
index 1a4ff295bbd261402e00a7d493a7e5e5bd4ec4de..54c6055b98272dd4152eb55fba2f3e58e08fe484 100644
--- a/src/USER-SMD/compute_smd_triangle_mesh_vertices.h
+++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_ulsph_effm.h b/src/USER-SMD/compute_smd_ulsph_effm.h
index 3c2abd851df96c94f818a55e21f3445999832a2f..68981fe76d3d02def73c27bc0e45f57d20daa8a5 100644
--- a/src/USER-SMD/compute_smd_ulsph_effm.h
+++ b/src/USER-SMD/compute_smd_ulsph_effm.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.h b/src/USER-SMD/compute_smd_ulsph_num_neighs.h
index 5af3bd93028a8e1bd49d08985d0f77d19219fad3..57340f01b6c83990c667cbeb9326dcdb740d553f 100644
--- a/src/USER-SMD/compute_smd_ulsph_num_neighs.h
+++ b/src/USER-SMD/compute_smd_ulsph_num_neighs.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_ulsph_strain.h b/src/USER-SMD/compute_smd_ulsph_strain.h
index 2e266f4e251024434079cf0faf3ffdfbe85311bb..a5796f34e29984881cfd1b3c3ca623666d7fde7d 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain.h
+++ b/src/USER-SMD/compute_smd_ulsph_strain.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.h b/src/USER-SMD/compute_smd_ulsph_strain_rate.h
index d2d43ef972c69364de6b5da5f3e0af9929b2d462..fc6df758e639c283ac62ecab3e053fbea181c680 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain_rate.h
+++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_ulsph_stress.h b/src/USER-SMD/compute_smd_ulsph_stress.h
index c96244970355ad6e9731ce1b0845f2498925c286..4e27a517233042adee0d88e1ebe2e45bc29bd3e5 100644
--- a/src/USER-SMD/compute_smd_ulsph_stress.h
+++ b/src/USER-SMD/compute_smd_ulsph_stress.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/compute_smd_vol.h b/src/USER-SMD/compute_smd_vol.h
index e946ed85ca8d40030f14105ea9b915c27a8d15cf..5525ce57cbd2f84f59218181202c53b9dfcf353a 100644
--- a/src/USER-SMD/compute_smd_vol.h
+++ b/src/USER-SMD/compute_smd_vol.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/fix_smd_adjust_dt.h b/src/USER-SMD/fix_smd_adjust_dt.h
index 3b96d76d760491a1e9407f11914f6bb157e3b366..d7d8c922f2a9c37ace33bee301103b2f2a3b4d2d 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.h
+++ b/src/USER-SMD/fix_smd_adjust_dt.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.h b/src/USER-SMD/fix_smd_integrate_tlsph.h
index 7119f8d919355ca3a03d01980c59e08e9fce71cd..ca047f2dfde2847345b16c23b5ab4dd81c3792d0 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.h
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/USER-SMD/fix_smd_integrate_ulsph.h
index 19ae31a59e6c5f5af1079090f527b765e2884642..ea4f46ce530ea0d40606c1c3aa157707f2a91e5a 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.h
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.h b/src/USER-SMD/fix_smd_move_triangulated_surface.h
index ce4eaed88ea8e05e13ab097697a4c34a5c672832..c851d490c5c81ea95e8549946f57f88b9e78a79e 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.h
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h
index 9e5fe642eb806ce5a5a1cb54de0942a653316a6c..b987a56f6cc1bc9603d72113139f0d27986d3d58 100644
--- a/src/USER-SMD/fix_smd_setvel.h
+++ b/src/USER-SMD/fix_smd_setvel.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
index ede06151ee16e4f2413fad8b49dc1803b4e8cca9..3ff693e9bb115ee576c370ace23dabadd52eb7c1 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/fix_smd_wall_surface.h b/src/USER-SMD/fix_smd_wall_surface.h
index 8bd7002a9e42ffa6f284f16ec2f5fac4d146ebcc..a32319f48f5fa1121e4d565d27d3316037968b1b 100644
--- a/src/USER-SMD/fix_smd_wall_surface.h
+++ b/src/USER-SMD/fix_smd_wall_surface.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-SMD/pair_smd_hertz.h b/src/USER-SMD/pair_smd_hertz.h
index 6b40b6bb5cdd86f25fc532ca2a7edf11f7deed2c..0866ef74868e6e693fed022a0f3a75062c21e877 100644
--- a/src/USER-SMD/pair_smd_hertz.h
+++ b/src/USER-SMD/pair_smd_hertz.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/pair_smd_tlsph.h b/src/USER-SMD/pair_smd_tlsph.h
index 17db11b816a17fe47541da016f4364476f6d4cab..4c9db9209bcb1368f317316de2b53d1da258e05c 100644
--- a/src/USER-SMD/pair_smd_tlsph.h
+++ b/src/USER-SMD/pair_smd_tlsph.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.h b/src/USER-SMD/pair_smd_triangulated_surface.h
index 6332313646de03c772256e2077bf35406e677701..c1eba7804ef69fa769a203107453383c9727cd6e 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.h
+++ b/src/USER-SMD/pair_smd_triangulated_surface.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/pair_smd_ulsph.h b/src/USER-SMD/pair_smd_ulsph.h
index 40ccc37e93b82e6c3a99d8d8942aa0233fe1f0b1..032079072ee82788371befd3aadb736e17ebf715 100644
--- a/src/USER-SMD/pair_smd_ulsph.h
+++ b/src/USER-SMD/pair_smd_ulsph.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/smd_kernels.h b/src/USER-SMD/smd_kernels.h
index ba40699fc7696d71f8243e6fbe2ba26c0e743fbd..6621881f4b295e808f5ac7757a0ef42cd6bb5451 100644
--- a/src/USER-SMD/smd_kernels.h
+++ b/src/USER-SMD/smd_kernels.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/smd_material_models.h b/src/USER-SMD/smd_material_models.h
index 858c5bbbdf66e1ee3bc2a653d14cc4e09c193df5..c6b6f8d94c8031b6a7cfcef5b1e3c7fb2690f212 100644
--- a/src/USER-SMD/smd_material_models.h
+++ b/src/USER-SMD/smd_material_models.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMD/smd_math.h b/src/USER-SMD/smd_math.h
index 5352cfccf98658968ba401a58120e77e4c385609..b7bf9c112d72ac1308aba49e58e645cd95489b78 100644
--- a/src/USER-SMD/smd_math.h
+++ b/src/USER-SMD/smd_math.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/USER-SMTBQ/pair_smtbq.h
index 49fbe8768b1194e683de81af8b91cdd10c2dbe74..25dfe98888325ee3be02f211796c79ee01d2aa7a 100644
--- a/src/USER-SMTBQ/pair_smtbq.h
+++ b/src/USER-SMTBQ/pair_smtbq.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp
index 65f57b7678096e5a066f3710a54f2c4f70faedd3..b366b92be39442cb98208171e64494425eea9fe5 100644
--- a/src/USER-TALLY/compute_heat_flux_tally.cpp
+++ b/src/USER-TALLY/compute_heat_flux_tally.cpp
@@ -246,7 +246,7 @@ void ComputeHeatFluxTally::compute_vector()
double ke_i;
if (rmass) ke_i = pfactor * rmass[i];
- else ke_i *= pfactor * mass[type[i]];
+ else ke_i = pfactor * mass[type[i]];
ke_i *= (vi[0]*vi[0] + vi[1]*vi[1] + vi[2]*vi[2]);
ke_i += eatom[i];
diff --git a/src/USER-VTK/dump_vtk.h b/src/USER-VTK/dump_vtk.h
index 603ca114ba6ddc33938b76d6c05cfb1aa9556056..8df14c7f34b4ed001c4b5d05f0ae1ea5eb73fcc5 100644
--- a/src/USER-VTK/dump_vtk.h
+++ b/src/USER-VTK/dump_vtk.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index 9680921e5f17dcbe84baa38071b918cc7bad58dc..bd24e06cae4e289893e48f19affed911f74cdb1e 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -43,7 +43,7 @@ enum{NCOMMON,NBOND,MAXBOND,MINBOND};
ComputeCNAAtom::ComputeCNAAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- nearest(NULL), nnearest(NULL), pattern(NULL)
+ list(NULL), nearest(NULL), nnearest(NULL), pattern(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal compute cna/atom command");
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index 4595175503d610f9b658ad9df0234e63600c05d1..adac486bef34567c9245813bf7712dcd18fa1883 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -126,11 +126,15 @@ void ComputePairLocal::init()
" requested by compute pair/local");
// need an occasional half neighbor list
+ // set size to same value as request made by force->pair
+ // this should enable it to always be a copy list (e.g. for granular pstyle)
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
+ NeighRequest *pairrequest = neighbor->find_request((void *) force->pair);
+ if (pairrequest) neighbor->requests[irequest]->size = pairrequest->size;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index 90faa88921271c6e8810617f306fa28954fa9107..27b31979c9885e797314c09ec23bef5fc4c45bd7 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -280,12 +280,16 @@ void ComputePropertyLocal::init()
}
// for NEIGH/PAIR need an occasional half neighbor list
+ // set size to same value as request made by force->pair
+ // this should enable it to always be a copy list (e.g. for granular pstyle)
if (kindflag == NEIGH || kindflag == PAIR) {
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
+ NeighRequest *pairrequest = neighbor->find_request((void *) force->pair);
+ if (pairrequest) neighbor->requests[irequest]->size = pairrequest->size;
}
// do initial memory allocation so that memory_usage() is correct
diff --git a/src/dump.h b/src/dump.h
index 3c1450854ecb4eb0df1cd6216c9b84931b91bb0f..a5582ce5a50e28e46f99f23a64cf965de4f3b805 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -33,7 +33,7 @@ class Dump : protected Pointers {
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
-#if defined(LMP_USE_LIBC_QSORT)
+#if defined(LMP_QSORT)
// static variable across all Dump objects
static Dump *dumpptr; // holds a ptr to Dump currently being used
#endif
@@ -135,7 +135,7 @@ class Dump : protected Pointers {
void pbc_allocate();
void sort();
-#if defined(LMP_USE_LIBC_QSORT)
+#if defined(LMP_QSORT)
static int idcompare(const void *, const void *);
static int bufcompare(const void *, const void *);
static int bufcompare_reverse(const void *, const void *);
diff --git a/src/irregular.h b/src/irregular.h
index 5b2a7718472dc6d35d8af16eaaf360cae77d6f33..1f74fe801b616d2c763d35a6c962e0602729536c 100644
--- a/src/irregular.h
+++ b/src/irregular.h
@@ -21,7 +21,7 @@ namespace LAMMPS_NS {
class Irregular : protected Pointers {
public:
-#if defined(LMP_USE_LIBC_QSORT)
+#if defined(LMP_QSORT)
// static variable across all Irregular objects, for qsort callback
static int *proc_recv_copy;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 62a9143226333455a55d1c61928a53d44d03dd8a..487b860c92a33752a847147f9ed8aa18aa662154 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -1268,6 +1268,12 @@ void Neighbor::morph_copy()
if (irq->ghost && !jrq->ghost) continue;
+ // do not copy from a history list or a respa middle/inner list
+
+ if (jrq->history) continue;
+ if (jrq->respamiddle) continue;
+ if (jrq->respainner) continue;
+
// these flags must be same,
// else 2 lists do not store same pairs
// or their data structures are different
@@ -1619,6 +1625,21 @@ void Neighbor::requests_new2old()
old_oneatom = oneatom;
}
+/* ----------------------------------------------------------------------
+ find and return request made by classptr
+ if not found or classpt = NULL, return NULL
+------------------------------------------------------------------------- */
+
+NeighRequest *Neighbor::find_request(void *classptr)
+{
+ if (classptr == NULL) return NULL;
+
+ for (int i = 0; i < nrequest; i++)
+ if (requests[i]->requestor == classptr) return requests[i];
+
+ return NULL;
+}
+
/* ----------------------------------------------------------------------
assign NBin class to a NeighList
use neigh request settings to build mask
diff --git a/src/neighbor.h b/src/neighbor.h
index 16a80b599179500477f712cdb9c82b3720cd43ec..64bced2293daec3bf040092a5097701ed0de1f8a 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -122,6 +122,7 @@ class Neighbor : protected Pointers {
void exclusion_group_group_delete(int, int); // rm a group-group exclusion
int exclude_setting(); // return exclude value to accelerator pkg
+ class NeighRequest *find_request(void *); // find a neighbor request
bigint memory_usage();
diff --git a/src/pair_coul_streitz.h b/src/pair_coul_streitz.h
index 5f02d29c119322623e596f7f213783b06aa57c4a..8e713997f5710a64d100c3e3c4949b0c8c1a477f 100644
--- a/src/pair_coul_streitz.h
+++ b/src/pair_coul_streitz.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov