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Merge remote-tracking branch 'akohlmey/integration' into ipython-update-and-cleanup

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This commit is contained in:
Richard Berger
2016-09-26 11:59:30 -04:00
parent d3406df6a0 b97b9dd661
commit c87f9aeb9f
71 changed files with 5485 additions and 665 deletions
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2
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@ -1 +1 @@
/html

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@ -1,4 +1,6 @@
# Makefile for LAMMPS documentation # Makefile for LAMMPS documentation
SHELL = /bin/bash
SHA1 = $(shell echo $USER-$PWD | python utils/sha1sum.py) SHA1 = $(shell echo $USER-$PWD | python utils/sha1sum.py)
BUILDDIR = /tmp/lammps-docs-$(SHA1) BUILDDIR = /tmp/lammps-docs-$(SHA1)
RSTDIR = $(BUILDDIR)/rst RSTDIR = $(BUILDDIR)/rst
@ -18,15 +20,21 @@ endif
SOURCES=$(wildcard src/*.txt) SOURCES=$(wildcard src/*.txt)
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
.PHONY: help clean-all clean html pdf venv .PHONY: help clean-all clean html pdf old venv
# ------------------------------------------
help: help:
@echo "Please use \`make <target>' where <target> is one of" @echo "Please use \`make <target>' where <target> is one of"
@echo " html to make HTML version of documentation using Sphinx" @echo " html create HTML doc pages in html dir"
@echo " pdf to make Manual.pdf" @echo " pdf create Manual.pdf and Developer.pdf in this dir"
@echo " txt2html to build txt2html tool" @echo " old create old-style HTML doc pages in old dir"
@echo " clean to remove all generated RST files" @echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " clean-all to reset the entire build environment" @echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment"
@echo " txt2html build txt2html tool"
# ------------------------------------------
clean-all: clean-all:
rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
@ -34,8 +42,6 @@ clean-all:
clean: clean:
rm -rf $(RSTDIR) rm -rf $(RSTDIR)
txt2html: utils/txt2html/txt2html.exe
html: $(OBJECTS) html: $(OBJECTS)
@(\ @(\
. $(VENV)/bin/activate ;\ . $(VENV)/bin/activate ;\
@ -44,20 +50,53 @@ html: $(OBJECTS)
deactivate ;\ deactivate ;\
) )
-rm html/searchindex.js -rm html/searchindex.js
-rm -rf html/_sources @rm -rf html/_sources
@rm -rf html/PDF
@rm -rf html/USER
@cp -r src/PDF html/PDF
@cp -r src/USER html/USER
@rm -rf html/PDF/.[sg]*
@rm -rf html/USER/.[sg]*
@rm -rf html/USER/*/.[sg]*
@rm -rf html/USER/*/*.[sg]*
@echo "Build finished. The HTML pages are in doc/html." @echo "Build finished. The HTML pages are in doc/html."
pdf: utils/txt2html/txt2html.exe pdf: utils/txt2html/txt2html.exe
@(\ @(\
cd src; \ cd src; \
../utils/txt2html/txt2html.exe -b *.txt; \ ../utils/txt2html/txt2html.exe -b *.txt; \
htmldoc --batch ../lammps.book; \ htmldoc --batch lammps.book; \
for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \ for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
do grep -q $$s ../lammps.book || \ do grep -q $$s lammps.book || \
echo doc file $$s missing in lammps.book; done; \ echo doc file $$s missing in src/lammps.book; done; \
rm *.html; \ rm *.html; \
cd Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
) )
old: utils/txt2html/txt2html.exe
@rm -rf old
@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
mv *.html ../old; \
cp Eqs/*.jpg ../old/Eqs; \
cp JPG/* ../old/JPG; \
cp PDF/* ../old/PDF;
fetch:
@rm -rf html_www Manual_www.pdf Developer_www.pdf
@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
@tar xzf lammps-doc.tar.gz
@rm -f lammps-doc.tar.gz
txt2html: utils/txt2html/txt2html.exe
# ------------------------------------------
utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
g++ -O -Wall -o $@ $< g++ -O -Wall -o $@ $<

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Generation of LAMMPS Documentation
The generation of all documentation is managed by the Makefile in this
dir.
----------------
Options:
make html # generate HTML in html dir using Sphinx
make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
# in this dir via htmldoc and pdflatex
make old # generate old-style HTML pages in old dir via txt2html
make fetch # fetch HTML doc pages and 2 PDF files from web site
# as a tarball and unpack into html dir and 2 PDFs
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data
----------------
Installing prerequisites for HTML build
To run the HTML documention build toolchain, Python 3 and virtualenv
have to be installed. Here are instructions for common setups:
# Ubuntu
sudo apt-get install python-virtualenv
# Fedora (up to version 21)
# Red Hat Enterprise Linux or CentOS (up to version 7.x)
sudo yum install python3-virtualenv
# Fedora (since version 22)
sudo dnf install python3-virtualenv
# MacOS X
## Python 3
Download the latest Python 3 MacOS X package from
https://www.python.org and install it. This will install both Python
3 and pip3.
## virtualenv
Once Python 3 is installed, open a Terminal and type
pip3 install virtualenv
This will install virtualenv from the Python Package Index.

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doc/README.md
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@ -1,48 +0,0 @@
# Generation of LAMMPS Documentation
The generation of all the documentation is managed by the Makefile inside the
`doc/` folder.
## Usage:
```bash
make html # generate HTML using Sphinx
make pdf # generate PDF using htmldoc
make clean # remove generated RST files
make clean-all # remove entire build folder and any cached data
```
## Installing prerequisites
To run the documention build toolchain, Python 3 and virtualenv have
to be installed. Here are instructions for common setups:
### Ubuntu
```bash
sudo apt-get install python-virtualenv
```
### Fedora (up to version 21), Red Hat Enterprise Linux or CentOS (up to version 7.x)
```bash
sudo yum install python3-virtualenv
```
### Fedora (since version 22)
```bash
sudo dnf install python3-virtualenv
```
### MacOS X
## Python 3
Download the latest Python 3 MacOS X package from https://www.python.org and install it.
This will install both Python 3 and pip3.
## virtualenv
Once Python 3 is installed, open a Terminal and type `pip3 install virtualenv`. This will
install virtualenv from the Python Package Index.

4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="20 Sep 2016 version"> <META NAME="docnumber" CONTENT="26 Sep 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
20 Sep 2016 version :c,h4 26 Sep 2016 version :c,h4
Version info: :h4 Version info: :h4

1
doc/src/Section_commands.txt
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@ -501,6 +501,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"bond/create"_fix_bond_create.html, "bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html, "bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html, "box/relax"_fix_box_relax.html,
"cmap"_fix_cmap.html,
"controller"_fix_controller.html, "controller"_fix_controller.html,
"deform (k)"_fix_deform.html, "deform (k)"_fix_deform.html,
"deposit"_fix_deposit.html, "deposit"_fix_deposit.html,

6
doc/src/Section_example.txt
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@ -105,8 +105,8 @@ web site.
If you uncomment the "dump image"_dump_image.html line(s) in the input If you uncomment the "dump image"_dump_image.html line(s) in the input
script a series of JPG images will be produced by the run (assuming script a series of JPG images will be produced by the run (assuming
you built LAMMPS with JPG support; see "Section start you built LAMMPS with JPG support; see "Section
2.2"_Section_start.html for details). These can be viewed 2.2"_Section_start.html#start_2 for details). These can be viewed
individually or turned into a movie or animated by tools like individually or turned into a movie or animated by tools like
ImageMagick or QuickTime or various Windows-based tools. See the ImageMagick or QuickTime or various Windows-based tools. See the
"dump image"_dump_image.html doc page for more details. E.g. this "dump image"_dump_image.html doc page for more details. E.g. this
@ -136,5 +136,5 @@ The USER directory has a large number of sub-directories which
correspond by name to a USER package. They contain scripts that correspond by name to a USER package. They contain scripts that
illustrate how to use the command(s) provided in that package. Many illustrate how to use the command(s) provided in that package. Many
of the sub-directories have their own README files which give further of the sub-directories have their own README files which give further
instructions. See the "Section packages"_Section_packages.html doc instructions. See the "Section 4"_Section_packages.html doc
page for more info on specific USER packages. page for more info on specific USER packages.

109
doc/src/Section_packages.txt
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@ -71,16 +71,16 @@ Package, Description, Author(s), Doc page, Example, Library
"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, - "COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, - "CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
"DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, - "DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu "GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section 5.3.1"_accelerate_gpu.html, gpu, lib/gpu
"GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, - "GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM "KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5"_accelerate_kokkos.html, kokkos, lib/kokkos "KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5.3.3"_accelerate_kokkos.html, kokkos, lib/kokkos
"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, - "KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, - "MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam "MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, - "MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, - "MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, - "OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section 5.3.5"_accelerate_opt.html, -, -
"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, - "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
@ -127,7 +127,6 @@ of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution. it is a third-party library not included in the LAMMPS distribution.
See details on all of this below for individual packages. See details on all of this below for individual packages.
p.s.: are we ever going to get commit messages from you? ;-)
:line :line
@ -150,7 +149,7 @@ make machine :pre
Make.py -p ^asphere -a machine :pre Make.py -p ^asphere -a machine :pre
Supporting info: "Section howto 6.14"_Section_howto.html#howto_14, Supporting info: "Section 6.14"_Section_howto.html#howto_14,
"pair_style gayberne"_pair_gayberne.html, "pair_style "pair_style gayberne"_pair_gayberne.html, "pair_style
resquared"_pair_resquared.html, resquared"_pair_resquared.html,
"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf, "doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,
@ -279,9 +278,8 @@ Contents: Compute and pair styles that implement the adiabatic
core/shell model for polarizability. The compute temp/cs command core/shell model for polarizability. The compute temp/cs command
measures the temperature of a system with core/shell particles. The measures the temperature of a system with core/shell particles. The
pair styles augment Born, Buckingham, and Lennard-Jones styles with pair styles augment Born, Buckingham, and Lennard-Jones styles with
core/shell capabilities. See "Section howto core/shell capabilities. See "Section 6.26"_Section_howto.html#howto_26
6.26"_Section_howto.html#howto_26 for an overview of how to use the for an overview of how to use the package.
package.
To install via make or Make.py: To install via make or Make.py:
@ -297,8 +295,8 @@ make machine :pre
Make.py -p ^coreshell -a machine :pre Make.py -p ^coreshell -a machine :pre
Supporting info: "Section howto Supporting info: "Section 6.26"_Section_howto.html#howto_26,
6.26"_Section_howto.html#howto_26, "compute temp/cs"_compute_temp_cs.html, "compute temp/cs"_compute_temp_cs.html,
"pair_style born/coul/long/cs"_pair_cs.html, "pair_style "pair_style born/coul/long/cs"_pair_cs.html, "pair_style
buck/coul/long/cs"_pair_cs.html, pair_style buck/coul/long/cs"_pair_cs.html, pair_style
lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell
@ -335,7 +333,7 @@ GPU package :link(GPU),h5
Contents: Dozens of pair styles and a version of the PPPM long-range Contents: Dozens of pair styles and a version of the PPPM long-range
Coulombic solver for NVIDIA GPUs. All of them have a "gpu" in their Coulombic solver for NVIDIA GPUs. All of them have a "gpu" in their
style name. "Section accelerate gpu"_accelerate_gpu.html gives style name. "Section 5.3.1"_accelerate_gpu.html gives
details of what hardware and Cuda software is required on your system, details of what hardware and Cuda software is required on your system,
and how to build and use this package. See the KOKKOS package, which and how to build and use this package. See the KOKKOS package, which
also has GPU-enabled styles. also has GPU-enabled styles.
@ -380,10 +378,11 @@ make machine :pre
Make.py -p ^gpu -a machine :pre Make.py -p ^gpu -a machine :pre
Supporting info: src/GPU/README, lib/gpu/README, "Section Supporting info: src/GPU/README, lib/gpu/README,
acclerate"_Section_accelerate.html, "Section accelerate "Section 5.3"_Section_accelerate.html#acc_3,
gpu"_accelerate_gpu.html, Pair Styles section of "Section commands "Section 5.3.1"_accelerate_gpu.html,
3.5"_Section_commands.html#cmd_5 for any pair style listed with a (g), Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
for any pair style listed with a (g),
"kspace_style"_kspace_style.html, "package gpu"_package.html, "kspace_style"_kspace_style.html, "package gpu"_package.html,
examples/accelerate, bench/FERMI, bench/KEPLER examples/accelerate, bench/FERMI, bench/KEPLER
@ -409,7 +408,7 @@ make machine :pre
Make.py -p ^granular -a machine :pre Make.py -p ^granular -a machine :pre
Supporting info: "Section howto 6.6"_Section_howto.html#howto_6, "fix Supporting info: "Section 6.6"_Section_howto.html#howto_6, "fix
pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style
gran/hooke"_pair_gran.html, "pair_style gran/hooke"_pair_gran.html, "pair_style
gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
@ -453,7 +452,7 @@ Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
which run with the Kokkos library to provide optimization for which run with the Kokkos library to provide optimization for
multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
native mode). All of them have a "kk" in their style name. "Section native mode). All of them have a "kk" in their style name. "Section
accelerate kokkos"_accelerate_kokkos.html gives details of what 5.3.3"_accelerate_kokkos.html gives details of what
hardware and software is required on your system, and how to build and hardware and software is required on your system, and how to build and
use this package. See the GPU, OPT, USER-INTEL, USER-OMP packages, use this package. See the GPU, OPT, USER-INTEL, USER-OMP packages,
which also provide optimizations for the same range of hardware. which also provide optimizations for the same range of hardware.
@ -473,9 +472,8 @@ the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
below, you can use the Make.py script with its "-kokkos" option to below, you can use the Make.py script with its "-kokkos" option to
choose which hardware to build for. Type "python src/Make.py -h choose which hardware to build for. Type "python src/Make.py -h
-kokkos" to see the details. If these methods do not work on your -kokkos" to see the details. If these methods do not work on your
system, you will need to read the "Section accelerate system, you will need to read the "Section 5.3.3"_accelerate_kokkos.html
kokkos"_accelerate_kokkos.html doc page for details of what doc page for details of what Makefile.machine settings are needed.
Makefile.machine settings are needed.
To install via make or Make.py for each of 3 hardware options: To install via make or Make.py for each of 3 hardware options:
@ -495,11 +493,11 @@ make machine :pre
Make.py -p ^kokkos -a machine :pre Make.py -p ^kokkos -a machine :pre
Supporting info: src/KOKKOS/README, lib/kokkos/README, "Section Supporting info: src/KOKKOS/README, lib/kokkos/README,
acclerate"_Section_accelerate.html, "Section accelerate "Section 5.3"_Section_accelerate.html#acc_3,
kokkos"_accelerate_kokkos.html, Pair Styles section of "Section "Section 5.3.3"_accelerate_kokkos.html,
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
with a (k), "package kokkos"_package.html, for any pair style listed with a (k), "package kokkos"_package.html,
examples/accelerate, bench/FERMI, bench/KEPLER examples/accelerate, bench/FERMI, bench/KEPLER
:line :line
@ -514,7 +512,7 @@ particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
Building with the KSPACE package requires a 1d FFT library be present Building with the KSPACE package requires a 1d FFT library be present
on your system for use by the PPPM solvers. This can be the KISS FFT on your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, or 3rd party libraries like FFTW or a library provided with LAMMPS, or 3rd party libraries like FFTW or a
vendor-supplied FFT library. See step 6 of "Section start vendor-supplied FFT library. See step 6 of "Section
2.2.2"_Section_start.html#start_2_2 of the manual for details of how 2.2.2"_Section_start.html#start_2_2 of the manual for details of how
to select different FFT options in your machine Makefile. The Make.py to select different FFT options in your machine Makefile. The Make.py
tool has an "-fft" option which can insert these settings into your tool has an "-fft" option which can insert these settings into your
@ -536,12 +534,13 @@ make machine :pre
Make.py -p ^kspace -a machine :pre Make.py -p ^kspace -a machine :pre
Supporting info: "kspace_style"_kspace_style.html, Supporting info: "kspace_style"_kspace_style.html,
"doc/PDF/kspace.pdf"_PDF/kspace.pdf, "Section howto "doc/PDF/kspace.pdf"_PDF/kspace.pdf,
6.7"_Section_howto.html#howto_7, "Section howto "Section 6.7"_Section_howto.html#howto_7,
6.8"_Section_howto.html#howto_8, "Section howto "Section 6.8"_Section_howto.html#howto_8,
6.9"_Section_howto.html#howto_9, "pair_style coul"_pair_coul.html, "Section 6.9"_Section_howto.html#howto_9,
other pair style command doc pages which have "long" or "msm" in their "pair_style coul"_pair_coul.html, other pair style command doc pages
style name, examples/peptide, bench/in.rhodo which have "long" or "msm" in their style name,
examples/peptide, bench/in.rhodo
:line :line
@ -568,7 +567,7 @@ Make.py -p ^manybody -a machine :pre
Supporting info: Supporting info:
Examples: Pair Styles section of "Section commands Examples: Pair Styles section of "Section
3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim, 3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
examples/nb3d, examples/vashishta examples/nb3d, examples/vashishta
@ -700,9 +699,9 @@ Supporting info:"atom_style"_atom_style.html,
"dihedral_style"_dihedral_style.html, "dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html, "pair_style "improper_style"_improper_style.html, "pair_style
hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style
lj/charmm/coul/charmm"_pair_charmm.html, "Section howto lj/charmm/coul/charmm"_pair_charmm.html,
6.3"_Section_howto.html#howto_3, examples/micelle, examples/peptide, "Section 6.3"_Section_howto.html#howto_3,
bench/in.chain, bench/in.rhodo examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo
:line :line
@ -738,7 +737,7 @@ OPT package :link(OPT),h5
Contents: A handful of pair styles with an "opt" in their style name Contents: A handful of pair styles with an "opt" in their style name
which are optimized for improved CPU performance on single or multiple which are optimized for improved CPU performance on single or multiple
cores. These include EAM, LJ, CHARMM, and Morse potentials. "Section cores. These include EAM, LJ, CHARMM, and Morse potentials. "Section
accelerate opt"_accelerate_opt.html gives details of how to build and 5.3.5"_accelerate_opt.html gives details of how to build and
use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages, use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages,
which also have styles optimized for CPU performance. which also have styles optimized for CPU performance.
@ -763,10 +762,10 @@ make machine :pre
Make.py -p ^opt -a machine :pre Make.py -p ^opt -a machine :pre
Supporting info: "Section acclerate"_Section_accelerate.html, "Section Supporting info: "Section 5.3"_Section_accelerate.html#acc_3,
accelerate opt"_accelerate_opt.html, Pair Styles section of "Section "Section 5.3.5"_accelerate_opt.html, Pair Styles section of
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed "Section 3.5"_Section_commands.html#cmd_5 for any pair style
with an (o), examples/accelerate, bench/KEPLER listed with an (t), examples/accelerate, bench/KEPLER
:line :line
@ -845,14 +844,14 @@ PYTHON package :link(PYTHON),h5
Contents: A "python"_python.html command which allow you to execute Contents: A "python"_python.html command which allow you to execute
Python code from a LAMMPS input script. The code can be in a separate Python code from a LAMMPS input script. The code can be in a separate
file or embedded in the input script itself. See "Section python file or embedded in the input script itself. See "Section
11.2"_Section_python.html" for an overview of using Python from 11.2"_Section_python.html#py-2 for an overview of using Python from
LAMMPS and for other ways to use LAMMPS and Python together. LAMMPS and for other ways to use LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python shared Building with the PYTHON package assumes you have a Python shared
library available on your system, which needs to be a Python 2 library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not supported. The build uses the version, 2.6 or later. Python 3 is not yet supported. The build uses
contents of the lib/python/Makefile.lammps file to find all the Python the contents of the lib/python/Makefile.lammps file to find all the Python
files required in the build/link process. See the lib/python/README files required in the build/link process. See the lib/python/README
file if the settings in that file do not work on your system. Note file if the settings in that file do not work on your system. Note
that the Make.py script has a "-python" option to allow an alternate that the Make.py script has a "-python" option to allow an alternate
@ -950,7 +949,7 @@ REPLICA package :link(REPLICA),h5
Contents: A collection of multi-replica methods that are used by Contents: A collection of multi-replica methods that are used by
invoking multiple instances (replicas) of LAMMPS invoking multiple instances (replicas) of LAMMPS
simulations. Communication between individual replicas is performed in simulations. Communication between individual replicas is performed in
different ways by the different methods. See "Section howto different ways by the different methods. See "Section
6.5"_Section_howto.html#howto_5 for an overview of how to run 6.5"_Section_howto.html#howto_5 for an overview of how to run
multi-replica simulations in LAMMPS. Multi-replica methods included multi-replica simulations in LAMMPS. Multi-replica methods included
in the package are nudged elastic band (NEB), parallel replica in the package are nudged elastic band (NEB), parallel replica
@ -973,7 +972,7 @@ make machine :pre
Make.py -p ^replica -a machine :pre Make.py -p ^replica -a machine :pre
Supporting info: "Section howto 6.5"_Section_howto.html#howto_5, Supporting info: "Section 6.5"_Section_howto.html#howto_5,
"neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html, "neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html,
"run_style verlet/split"_run_style.html, examples/neb, examples/prd, "run_style verlet/split"_run_style.html, examples/neb, examples/prd,
examples/tad examples/tad
@ -1148,13 +1147,13 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
"USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, - "USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
"USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, - "USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
"USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md "USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, - "USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section 5.3.2"_accelerate_intel.html, examples/intel, -, -
"USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, - "USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, - "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, - "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, - "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, - "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, - "USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -
@ -1353,12 +1352,12 @@ USER-DRUDE package :link(USER-DRUDE),h5
Contents: This package contains methods for simulating polarizable Contents: This package contains methods for simulating polarizable
systems using thermalized Drude oscillators. It has computes, fixes, systems using thermalized Drude oscillators. It has computes, fixes,
and pair styles for this purpose. See "Section howto and pair styles for this purpose. See "Section
6.27"_Section_howto.html#howto_27 for an overview of how to use the 6.27"_Section_howto.html#howto_27 for an overview of how to use the
package. See src/USER-DRUDE/README for additional details. There are package. See src/USER-DRUDE/README for additional details. There are
auxiliary tools for using this package in tools/drude. auxiliary tools for using this package in tools/drude.
Supporting info: "Section howto 6.27"_Section_howto.html#howto_27, Supporting info: "Section 6.27"_Section_howto.html#howto_27,
src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix
drude/transform/*"_fix_drude_transform.html, "compute drude/transform/*"_fix_drude_transform.html, "compute
temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html, temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,
@ -1432,7 +1431,7 @@ USER-INTEL package :link(USER-INTEL),h5
Contents: Dozens of pair, bond, angle, dihedral, and improper styles Contents: Dozens of pair, bond, angle, dihedral, and improper styles
that are optimized for Intel CPUs and the Intel Xeon Phi (in offload that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
mode). All of them have an "intel" in their style name. "Section mode). All of them have an "intel" in their style name. "Section
accelerate intel"_accelerate_intel.html gives details of what hardware 5.3.2"_accelerate_intel.html gives details of what hardware
and compilers are required on your system, and how to build and use and compilers are required on your system, and how to build and use
this package. Also see src/USER-INTEL/README for more details. See this package. Also see src/USER-INTEL/README for more details. See
the KOKKOS, OPT, and USER-OMP packages, which also have CPU and the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
@ -1440,7 +1439,7 @@ Phi-enabled styles.
Supporting info: examples/accelerate, src/USER-INTEL/TEST Supporting info: examples/accelerate, src/USER-INTEL/TEST
"Section 5"_Section_accelerate.html#acc_3 "Section 5.3"_Section_accelerate.html#acc_3
Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
him directly if you have questions. him directly if you have questions.
@ -1532,7 +1531,7 @@ More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows: input script commands is as follows:
"Section 3"_Section_commands.html#cmd_5 "Section 3.5"_Section_commands.html#cmd_5
User-contributed features are listed at the bottom of the fix, User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections. compute, pair, etc sections.
@ -1609,7 +1608,7 @@ styles, and fix styles.
See this section of the manual to get started: See this section of the manual to get started:
"Section 5"_Section_accelerate.html#acc_3 "Section 5.3"_Section_accelerate.html#acc_3
The person who created this package is Axel Kohlmeyer at Temple U The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions. (akohlmey at gmail.com). Contact him directly if you have questions.

2
doc/src/Section_perf.txt
View File

@ -51,7 +51,7 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI
and bench/KEPLER dirs have input files and scripts and instructions and bench/KEPLER dirs have input files and scripts and instructions
for running the same (or similar) problems using OpenMP or GPU or Xeon for running the same (or similar) problems using OpenMP or GPU or Xeon
Phi acceleration options. See the README files in those dirs and the Phi acceleration options. See the README files in those dirs and the
"Section accelerate"_Section_accelerate.html doc pages for "Section 5.3"_Section_accelerate.html#acc_3 doc pages for
instructions on how to build LAMMPS and run on that kind of hardware. instructions on how to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the The bench/POTENTIALS directory has input files which correspond to the

56
doc/src/Section_start.txt
View File

@ -21,7 +21,6 @@ experienced users.
2.8 "Screen output"_#start_8 2.8 "Screen output"_#start_8
2.9 "Tips for users of previous versions"_#start_9 :all(b) 2.9 "Tips for users of previous versions"_#start_9 :all(b)
:line
:line :line
2.1 What's in the LAMMPS distribution :h4,link(start_1) 2.1 What's in the LAMMPS distribution :h4,link(start_1)
@ -70,12 +69,12 @@ launch a LAMMPS Windows executable on a Windows box.
This section has the following sub-sections: This section has the following sub-sections:
"Read this first"_#start_2_1 2.2.1 "Read this first"_#start_2_1
"Steps to build a LAMMPS executable"_#start_2_2 2.2.1 "Steps to build a LAMMPS executable"_#start_2_2
"Common errors that can occur when making LAMMPS"_#start_2_3 2.2.3 "Common errors that can occur when making LAMMPS"_#start_2_3
"Additional build tips"_#start_2_4 2.2.4 "Additional build tips"_#start_2_4
"Building for a Mac"_#start_2_5 2.2.5 "Building for a Mac"_#start_2_5
"Building for Windows"_#start_2_6 :ul 2.2.6 "Building for Windows"_#start_2_6 :all(b)
:line :line
@ -559,8 +558,7 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
files created when LAMMPS is built, for either all builds or for a files created when LAMMPS is built, for either all builds or for a
particular machine. particular machine.
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
As explained above, any of these 3 settings can be specified on the As explained above, any of these 3 settings can be specified on the
LMP_INC line in your low-level src/MAKE/Makefile.foo. LMP_INC line in your low-level src/MAKE/Makefile.foo.
@ -612,7 +610,7 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
Building for a Mac :h5,link(start_2_5) Building for a Mac :h5,link(start_2_5)
OS X is BSD Unix, so it should just work. See the OS X is a derivative of BSD Unix, so it should just work. See the
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files. src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
:line :line
@ -637,9 +635,9 @@ happy to distribute contributed instructions and modifications, but
we cannot provide support for those. we cannot provide support for those.
With the so-called "Anniversary Update" to Windows 10, there is a With the so-called "Anniversary Update" to Windows 10, there is a
Ubuntu subsystem available for Windows, that can be installed and Ubuntu Linux subsystem available for Windows, that can be installed
then it can be used to compile/install LAMMPS as if you are running and then used to compile/install LAMMPS as if you are running on a
on a Ubuntu Linux system. Ubuntu Linux system instead of Windows.
As an alternative, you can download "daily builds" (and some older As an alternative, you can download "daily builds" (and some older
versions) of the installer packages from versions) of the installer packages from
@ -654,10 +652,10 @@ many examples, but no source code.
This section has the following sub-sections: This section has the following sub-sections:
"Package basics"_#start_3_1 2.3.1 "Package basics"_#start_3_1
"Including/excluding packages"_#start_3_2 2.3.2 "Including/excluding packages"_#start_3_2
"Packages that require extra libraries"_#start_3_3 2.3.3 "Packages that require extra libraries"_#start_3_3
"Packages that require Makefile.machine settings"_#start_3_4 :ul 2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
Note that the following "Section 2.4"_#start_4 describes the Make.py Note that the following "Section 2.4"_#start_4 describes the Make.py
tool which can be used to install/un-install packages and build the tool which can be used to install/un-install packages and build the
@ -673,7 +671,7 @@ are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. fields for molecular systems or granular systems are in packages.
"Section packages"_Section_packages.html in the manual has details "Section 4"_Section_packages.html in the manual has details
about all the packages, including specific instructions for building about all the packages, including specific instructions for building
LAMMPS with each package, which are covered in a more general manner LAMMPS with each package, which are covered in a more general manner
below. below.
@ -727,15 +725,15 @@ before building LAMMPS. From the src directory, this is typically as
simple as: simple as:
make yes-colloid make yes-colloid
make g++ :pre make mpi :pre
or or
make no-manybody make no-manybody
make g++ :pre make mpi :pre
NOTE: You should NOT include/exclude packages and build LAMMPS in a NOTE: You should NOT include/exclude packages and build LAMMPS in a
single make command using multiple targets, e.g. make yes-colloid g++. single make command using multiple targets, e.g. make yes-colloid mpi.
This is because the make procedure creates a list of source files that This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes will be out-of-date for the build if the package configuration changes
within the same command. within the same command.
@ -826,7 +824,7 @@ where to find them.
For libraries with provided code, the sub-directory README file For libraries with provided code, the sub-directory README file
(e.g. lib/atc/README) has instructions on how to build that library. (e.g. lib/atc/README) has instructions on how to build that library.
This information is also summarized in "Section This information is also summarized in "Section
packages"_Section_packages.html. Typically this is done by typing 4"_Section_packages.html. Typically this is done by typing
something like: something like:
make -f Makefile.g++ :pre make -f Makefile.g++ :pre
@ -885,17 +883,17 @@ A few packages require specific settings in Makefile.machine, to
either build or use the package effectively. These are the either build or use the package effectively. These are the
USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
code performance on CPUs or other hardware, as discussed in "Section code performance on CPUs or other hardware, as discussed in "Section
acclerate"_Section_accelerate.html. 5.3"_Section_accelerate.html#acc_3.
A summary of what Makefile.machine changes are needed for each of A summary of what Makefile.machine changes are needed for each of
these packages is given in "Section packages"_Section_packages.html. these packages is given in "Section 4"_Section_packages.html.
The details are given on the doc pages that describe each of these The details are given on the doc pages that describe each of these
accelerator packages in detail: accelerator packages in detail:
"USER-INTEL package"_accelerate_intel.html 5.3.1 "USER-INTEL package"_accelerate_intel.html
"KOKKOS package"_accelerate_kokkos.html 5.3.3 "KOKKOS package"_accelerate_kokkos.html
"USER-OMP package"_accelerate_omp.html 5.3.4 "USER-OMP package"_accelerate_omp.html
"OPT package"_accelerate_opt.html :ul 5.3.5 "OPT package"_accelerate_opt.html :all(b)
You can also look at the following machine Makefiles in You can also look at the following machine Makefiles in
src/MAKE/OPTIONS, which include the changes. Note that the USER-INTEL src/MAKE/OPTIONS, which include the changes. Note that the USER-INTEL
@ -1367,7 +1365,7 @@ Note that the keywords do not use a leading minus sign. I.e. the
keyword is "t", not "-t". Also note that each of the keywords has a keyword is "t", not "-t". Also note that each of the keywords has a
default setting. Example of when to use these options and what default setting. Example of when to use these options and what
settings to use on different platforms is given in "Section settings to use on different platforms is given in "Section
5.8"_Section_accelerate.html#acc_3. 5.3"_Section_accelerate.html#acc_3.
d or device d or device
g or gpus g or gpus

7
doc/src/Section_tools.txt
View File

@ -107,9 +107,10 @@ The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS. back-and-forth between the CHARMM MD code and LAMMPS.
They are intended to make it easy to use CHARMM as a builder and as a They are intended to make it easy to use CHARMM as a builder and as a
post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
ensemble built in CHARMM into its LAMMPS equivalent. Using PDB file with associated CHARMM info, including CHARMM force field
lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files. data, into its LAMMPS equivalent. Using lammps2pdb.pl you can convert
LAMMPS atom dumps into PDB files.
See the README file in the ch2lmp sub-directory for more information. See the README file in the ch2lmp sub-directory for more information.

38
doc/src/accelerate_kokkos.txt
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@ -156,19 +156,25 @@ CPU-only (run all-MPI or with OpenMP threading):
cd lammps/src cd lammps/src
make yes-kokkos make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP :pre make kokkos_omp :pre
Intel Xeon Phi: CPU-only (only MPI, no threading):
cd lammps/src cd lammps/src
make yes-kokkos make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC :pre make kokkos_mpi :pre
CPUs and GPUs: Intel Xeon Phi (Intel Compiler, Intel MPI):
cd lammps/src cd lammps/src
make yes-kokkos make yes-kokkos
make cuda KOKKOS_DEVICES=Cuda :pre make kokkos_phi :pre
CPUs and GPUs (with MPICH):
cd lammps/src
make yes-kokkos
make kokkos_cuda_mpich :pre
These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try make command line which requires a GNU-compatible make command. Try
@ -180,26 +186,6 @@ first two examples above, then you *must* perform a "make clean-all"
or "make clean-machine" before each build. This is to force all the or "make clean-machine" before each build. This is to force all the
KOKKOS-dependent files to be re-compiled with the new options. KOKKOS-dependent files to be re-compiled with the new options.
You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
with a line like:
KOKKOS_ARCH = KNC :pre
Note that if you build LAMMPS multiple times in this manner, using
different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a "clean" in between. This is
because the targets will be different.
NOTE: The 3rd example above for a GPU, uses a different machine
makefile, in this case src/MAKE/Makefile.cuda, which is included in
the LAMMPS distribution. To build the KOKKOS package for a GPU, this
makefile must use the NVIDA "nvcc" compiler. And it must have a
KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and
installed software. Typical values for KOKKOS_ARCH are given below,
as well as other settings that must be included in the machine
makefile, if you create your own.
NOTE: Currently, there are no precision options with the KOKKOS NOTE: Currently, there are no precision options with the KOKKOS
package. All compilation and computation is performed in double package. All compilation and computation is performed in double
precision. precision.
@ -246,7 +232,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is threads to hardware cores. More info on binding threads to cores is
given in "this section"_Section_accelerate.html#acc_3. given in "Section 5.3"_Section_accelerate.html#acc_3.
KOKKOS_ARCH=KNC enables compiler switches needed when compling for an KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor. Intel Phi processor.

6
doc/src/accelerate_omp.txt
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@ -7,7 +7,7 @@
:line :line
"Return to Section accelerate overview"_Section_accelerate.html "Return to Section 5 overview"_Section_accelerate.html
5.3.4 USER-OMP package :h5 5.3.4 USER-OMP package :h5
@ -103,8 +103,8 @@ USER-OMP style (in serial or parallel) with a single thread per MPI
task, versus running standard LAMMPS with its standard un-accelerated task, versus running standard LAMMPS with its standard un-accelerated
styles (in serial or all-MPI parallelization with 1 task/core). This styles (in serial or all-MPI parallelization with 1 task/core). This
is because many of the USER-OMP styles contain similar optimizations is because many of the USER-OMP styles contain similar optimizations
to those used in the OPT package, described in "Section accelerate to those used in the OPT package, described in "Section
5.3.6"_accelerate_opt.html. 5.3.5"_accelerate_opt.html.
With multiple threads/task, the optimal choice of number of MPI With multiple threads/task, the optimal choice of number of MPI
tasks/node and OpenMP threads/task can vary a lot and should always be tasks/node and OpenMP threads/task can vary a lot and should always be

9
doc/src/compute_tally.txt
View File

@ -35,7 +35,12 @@ group/group"_compute_group_group.html only that the data is
accumulated directly during the non-bonded force computation. The accumulated directly during the non-bonded force computation. The
computes {force/tally}, {pe/tally}, {stress/tally}, and computes {force/tally}, {pe/tally}, {stress/tally}, and
{heat/flux/tally} are primarily provided as example how to program {heat/flux/tally} are primarily provided as example how to program
additional, more sophisticated computes using the tally mechanism. additional, more sophisticated computes using the tally callback
mechanism. Compute {pe/mol/tally} is one such style, that can
- through using this mechanism - separately tally intermolecular
and intramolecular energies. Something that would otherwise be
impossible without integrating this as a core functionality into
the based classes of LAMMPS.
:line :line
@ -56,7 +61,7 @@ atom scalar (the contributions of the single atom to the global
scalar). Compute {pe/mol/tally} calculates a global 4-element vector scalar). Compute {pe/mol/tally} calculates a global 4-element vector
containing (in this order): {evdwl} and {ecoul} for intramolecular pairs containing (in this order): {evdwl} and {ecoul} for intramolecular pairs
and {evdwl} and {ecoul} for intermolecular pairs. Since molecules are and {evdwl} and {ecoul} for intermolecular pairs. Since molecules are
identified my their molecule IDs, the partitioning does not have to be identified by their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or slots depending on whether the molecule IDs of a pair are the same or
different. Compute {force/tally} calculates a global scalar (the force different. Compute {force/tally} calculates a global scalar (the force

8
doc/src/dump.txt
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@ -328,8 +328,8 @@ bonds and colors.
Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
popular molecular viewing program. See "Section popular molecular viewing program. See
tools"_Section_tools.html#vmd of the manual and the "Section 9"_Section_tools.html#vmd of the manual and the
tools/lmp2vmd/README.txt file for more information about support in tools/lmp2vmd/README.txt file for more information about support in
VMD for reading and visualizing LAMMPS dump files. VMD for reading and visualizing LAMMPS dump files.
@ -390,7 +390,7 @@ Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
package installed, e.g. package installed, e.g.
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre make mpi # build LAMMPS for your platform :pre
Second, use a dump filename which contains ".mpiio". Note that it Second, use a dump filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters. does not have to end in ".mpiio", just contain those characters.
@ -531,7 +531,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. (tilted), then all atom coords will still be between 0.0 and 1.0.
I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
the non-orthogonal vectors of the simulation box edges, as discussed the non-orthogonal vectors of the simulation box edges, as discussed
in "Section howto 6.12"_Section_howto.html#howto_12. in "Section 6.12"_Section_howto.html#howto_12.
Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
image flags for each atom. Unwrapped means that if the atom has image flags for each atom. Unwrapped means that if the atom has

2
doc/src/dump_molfile.txt
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@ -34,7 +34,7 @@ to one or more files every N timesteps in one of several formats.
Only information for atoms in the specified group is dumped. This Only information for atoms in the specified group is dumped. This
specific dump style uses molfile plugins that are bundled with the specific dump style uses molfile plugins that are bundled with the
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
analysis program. See "Section tools"_Section_tools.html#vmd of the analysis program. See "Section 9"_Section_tools.html#vmd of the
manual and the tools/lmp2vmd/README.txt file for more information manual and the tools/lmp2vmd/README.txt file for more information
about support in VMD for reading and visualizing native LAMMPS dump about support in VMD for reading and visualizing native LAMMPS dump
files. files.

132
doc/src/fix_cmap.txt Normal file
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@ -0,0 +1,132 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix cmap command :h3
[Syntax:]
fix ID group-ID cmap filename :pre
ID, group-ID are documented in "fix"_fix.html command
cmap = style name of this fix command
filename = force-field file with CMAP coefficients :ul
[Examples:]
fix myCMAP all cmap ../potentials/cmap36.data
read_data proteinX.data fix myCMAP crossterm CMAP
fix_modify myCMAP energy yes :pre
[Description:]
This command enables CMAP crossterms to be added to simulations which
use the CHARMM force field. These are relevant for any CHARMM model
of a peptide or protein sequences that is 3 or more amino-acid
residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks for details,
including the analytic energy expressions for CMAP interactions. The
CMAP crossterms add additional potential energy contributions to pairs
of overlapping phi-psi dihedrals of amino-acids, which are important
to properly represent their conformational behavior.
The examples/cmap directory has a sample input script and data file
for a small peptide, that illustrates use of the fix cmap command.
As in the example above, this fix should be used before reading a data
file that contains a listing of CMAP interactions. The {filename}
specified should contain the CMAP parameters for a particular version
of the CHARMM force field. Two such files are including in the
lammps/potentials directory: charmm22.cmap and charmm36.cmap.
The data file read by the "read_data" must contain the topology of all
the CMAP interactions, similar to the topology data for bonds, angles,
dihedrals, etc. Specically it should have a line like this
in its header section:
N crossterms :pre
where N is the number of CMAP crossterms. It should also have a section
in the body of the data file like this with N lines:
CMAP :pre
1 1 8 10 12 18 20
2 5 18 20 22 25 27
...
N 3 314 315 317 318 330 :pre
The first column is an index from 1 to N to enumerate the CMAP terms;
it is ignored by LAMMPS. The 2nd column is the "type" of the
interaction; it is an index into the CMAP force field file. The
remaining 5 columns are the atom IDs of the atoms in the two 4-atom
dihedrals that overlap to create the CMAP 5-body interaction. Note
that the "crossterm" and "CMAP" keywords for the header and body
sections match those specified in the read_data command following the
data file name; see the "read_data"_doc/read_data.html doc page for
more details.
A data file containing CMAP crossterms can be generated from a PDB
file using the charmm2lammps.pl script in the tools/ch2lmp directory
of the LAMMPS distribution. The script must be invoked with the
optional "-cmap" flag to do this; see the tools/ch2lmp/README file for
more information.
The potential energy associated with CMAP interactions can be output
as described below. It can also be included in the total potential
energy of the system, as output by the
"thermo_style"_thermo_style.html command, if the "fix_modify
energy"_fix_modify.html command is used, as in the example above. See
the note below about how to include the CMAP energy when performing an
"energy minimization"_minimize.html.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential "energy" of the CMAP interactions system's
potential energy as part of "thermodynamic output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
potential energy discussed above. The scalar value calculated by this
fix is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
NOTE: If you want the potential energy associated with the CMAP terms
forces to be included in the total potential energy of the system (the
quantity being minimized), you MUST enable the
"fix_modify"_fix_modify.html {energy} option for this fix.
[Restrictions:]
This fix can only be used if LAMMPS was built with the MOLECULE
package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"fix_modify"_fix_modify.html, "read_data"_read_data.html
[Default:] none
:line
(Buck)
Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
(2006).
(Brooks)
Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).

52
doc/src/fix_phonon.txt
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@ -43,10 +43,11 @@ fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 :pre
Calculate the dynamical matrix from molecular dynamics simulations Calculate the dynamical matrix from molecular dynamics simulations
based on fluctuation-dissipation theory for a group of atoms. based on fluctuation-dissipation theory for a group of atoms.
Consider a crystal with \(N\) unit cells in three dimensions labelled \(l = (l_1, l_2, l_3)\) where \(l_i\) Consider a crystal with \(N\) unit cells in three dimensions labelled
are integers. Each unit cell is defined by three linearly independent \(l = (l_1, l_2, l_3)\) where \(l_i\) are integers. Each unit cell is
vectors \(\mathbf\{a\}_1\), \(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a defined by three linearly independent vectors \(\mathbf\{a\}_1\),
parallelipiped, containing \(K\) basis atoms labeled \(k\). \(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelipiped,
containing \(K\) basis atoms labeled \(k\).
Based on fluctuation-dissipation theory, the force constant Based on fluctuation-dissipation theory, the force constant
coefficients of the system in reciprocal space are given by coefficients of the system in reciprocal space are given by
@ -62,18 +63,16 @@ where \(\mathbf\{G\}\) is the Green's functions coefficients given by
\mathbf\{G\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) = \left< \mathbf\{u\}_\{k\alpha\}(\mathbf\{q\}) \bullet \mathbf\{u\}_\{k^\prime \beta\}^*(\mathbf\{q\}) \right> \mathbf\{G\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) = \left< \mathbf\{u\}_\{k\alpha\}(\mathbf\{q\}) \bullet \mathbf\{u\}_\{k^\prime \beta\}^*(\mathbf\{q\}) \right>
\end\{equation\} \end\{equation\}
where \(\left< \ldots \right>\) denotes the ensemble average, and where \(\left< \ldots \right>\) denotes the ensemble average, and
\begin\{equation\} \begin\{equation\}
\mathbf\{u\}_\{k\alpha\}(\mathbf\{q\}) = \sum_l \mathbf\{u\}_\{l k \alpha\} \exp\{(i\mathbf\{qr\}_l)\} \mathbf\{u\}_\{k\alpha\}(\mathbf\{q\}) = \sum_l \mathbf\{u\}_\{l k \alpha\} \exp\{(i\mathbf\{qr\}_l)\}
\end\{equation\} \end\{equation\}
is the \(\alpha\) component of the atomic displacement for the \(k\)
is the \(\alpha\) component of the atomic displacement for the \(k\) th atom th atom in the unit cell in reciprocal space at \(\mathbf\{q\}\). In
in the unit cell in reciprocal space at \(\mathbf\{q\}\). In practice, the Green's practice, the Green's functions coefficients can also be measured
functions coefficients can also be measured according to the following according to the following formula,
formula,
\begin\{equation\} \begin\{equation\}
\mathbf\{G\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) = \mathbf\{G\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) =
@ -81,12 +80,13 @@ formula,
- \left<\mathbf\{R\}\right>_\{k \alpha\}(\mathbf\{q\}) \bullet \left<\mathbf\{R\}\right>^*_\{k^\prime \beta\}(\mathbf\{q\}) - \left<\mathbf\{R\}\right>_\{k \alpha\}(\mathbf\{q\}) \bullet \left<\mathbf\{R\}\right>^*_\{k^\prime \beta\}(\mathbf\{q\})
\end\{equation\} \end\{equation\}
where \(\mathbf\{R\}\) is the instantaneous positions of atoms, and \(\left<\mathbf\{R\}\right>\) is the where \(\mathbf\{R\}\) is the instantaneous positions of atoms, and
averaged atomic positions. It gives essentially the same results as \(\left<\mathbf\{R\}\right>\) is the averaged atomic positions. It
the displacement method and is easier to implement in an MD code. gives essentially the same results as the displacement method and is
easier to implement in an MD code.
Once the force constant matrix is known, the dynamical matrix \(\mathbf\{D\}\) can Once the force constant matrix is known, the dynamical matrix
then be obtained by \(\mathbf\{D\}\) can then be obtained by
\begin\{equation\} \begin\{equation\}
\mathbf\{D\}_\{k\alpha, k^\prime\beta\}(\mathbf\{q\}) = \mathbf\{D\}_\{k\alpha, k^\prime\beta\}(\mathbf\{q\}) =
@ -100,10 +100,11 @@ two-point correlations. To achieve this. the positions of the atoms
are examined every {Nevery} steps and are Fourier-transformed into are examined every {Nevery} steps and are Fourier-transformed into
reciprocal space, where the averaging process and correlation reciprocal space, where the averaging process and correlation
computation is then done. After every {Noutput} measurements, the computation is then done. After every {Noutput} measurements, the
matrix \(\mathbf\{G\}(\mathbf\{q\})\) is calculated and inverted to obtain the elastic matrix \(\mathbf\{G\}(\mathbf\{q\})\) is calculated and inverted to
stiffness coefficients. The dynamical matrices are then constructed obtain the elastic stiffness coefficients. The dynamical matrices are
and written to {prefix}.bin.timestep files in binary format and to the then constructed and written to {prefix}.bin.timestep files in binary
file {prefix}.log for each wavevector \(\mathbf\{q\}\). format and to the file {prefix}.log for each wavevector
\(\mathbf\{q\}\).
A detailed description of this method can be found in A detailed description of this method can be found in
("Kong2011"_#Kong2011). ("Kong2011"_#Kong2011).
@ -126,12 +127,13 @@ which lattice point; the lattice indices start from 0. An auxiliary
code, "latgen"_http://code.google.com/p/latgen, can be employed to code, "latgen"_http://code.google.com/p/latgen, can be employed to
generate the compatible map file for various crystals. generate the compatible map file for various crystals.
In case one simulates an aperiodic system, where the whole simulation box In case one simulates an aperiodic system, where the whole simulation
is treated as a unit cell, one can set {map_file} as {GAMMA}, so that the mapping box is treated as a unit cell, one can set {map_file} as {GAMMA}, so
info will be generated internally and a file is not needed. In this case, the that the mapping info will be generated internally and a file is not
dynamical matrix at only the gamma-point will/can be evaluated. Please keep in needed. In this case, the dynamical matrix at only the gamma-point
mind that fix-phonon is designed for cyrstals, it will be inefficient and will/can be evaluated. Please keep in mind that fix-phonon is designed
even degrade the performance of lammps in case the unit cell is too large. for cyrstals, it will be inefficient and even degrade the performance
of lammps in case the unit cell is too large.
The calculated dynamical matrix elements are written out in The calculated dynamical matrix elements are written out in
"energy/distance^2/mass"_units.html units. The coordinates for {q} "energy/distance^2/mass"_units.html units. The coordinates for {q}

4
doc/src/fix_ti_spring.txt
View File

@ -99,8 +99,8 @@ center-of-mass fixed during the thermodynamic integration. A nonzero
total velocity will result in divergences during the integration due total velocity will result in divergences during the integration due
to the fact that the atoms are 'attached' to their equilibrium to the fact that the atoms are 'attached' to their equilibrium
positions by the Einstein crystal. Check the option {zero} of "fix positions by the Einstein crystal. Check the option {zero} of "fix
langevin"_fix_langevin_html and "velocity"_velocity.html. The use of langevin"_fix_langevin.html and "velocity"_velocity.html. The use of
the Nose-Hoover thermostat ("fix nvt"_fix_nvt.html) is {NOT} the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT}
recommended due to its well documented issues with the canonical recommended due to its well documented issues with the canonical
sampling of harmonic degrees of freedom (notice that the {chain} sampling of harmonic degrees of freedom (notice that the {chain}
option will {NOT} solve this problem). The Langevin thermostat ("fix option will {NOT} solve this problem). The Langevin thermostat ("fix

6
doc/src/fix_wall_region.txt
View File

@ -85,8 +85,10 @@ to feel no force (they don't "see" the wall) when in one location,
then move a distance epsilon, and suddenly feel a large force because then move a distance epsilon, and suddenly feel a large force because
they now "see" the wall. In a worst-case scenario, this can blow they now "see" the wall. In a worst-case scenario, this can blow
particles out of the simulation box. Thus, as a general rule you particles out of the simulation box. Thus, as a general rule you
should not use the fix wall/region command with {union} or should not use the fix wall/gran/region command with {union} or
{interesect} regions that have convex points or edges. {interesect} regions that have convex points or edges resulting from
the union/intersection (convex points/edges in the union/intersection
due to a single sub-region are still OK).
NOTE: Similarly, you should not define {union} or {intersert} regions NOTE: Similarly, you should not define {union} or {intersert} regions
for use with this command that share an overlapping common face that for use with this command that share an overlapping common face that

1
doc/src/fixes.txt
View File

@ -138,7 +138,6 @@ Fixes :h1
fix_temp_rescale_eff fix_temp_rescale_eff
fix_tfmc fix_tfmc
fix_thermal_conductivity fix_thermal_conductivity
fix_ti_rs
fix_ti_spring fix_ti_spring
fix_tmd fix_tmd
fix_ttm fix_ttm

2
doc/lammps.book → doc/src/lammps.book
View File

@ -247,7 +247,6 @@ fix_smd_integrate_tlsph.html
fix_smd_integrate_ulsph.html fix_smd_integrate_ulsph.html
fix_smd_move_triangulated_surface.html fix_smd_move_triangulated_surface.html
fix_smd_setvel.html fix_smd_setvel.html
fix_smd_tlsph_reference_configuration.html
fix_smd_wall_surface.html fix_smd_wall_surface.html
fix_spring.html fix_spring.html
fix_spring_chunk.html fix_spring_chunk.html
@ -262,7 +261,6 @@ fix_temp_rescale.html
fix_temp_rescale_eff.html fix_temp_rescale_eff.html
fix_tfmc.html fix_tfmc.html
fix_thermal_conductivity.html fix_thermal_conductivity.html
fix_ti_rs.html
fix_ti_spring.html fix_ti_spring.html
fix_tmd.html fix_tmd.html
fix_ttm.html fix_ttm.html

2
doc/src/package.txt
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@ -142,7 +142,7 @@ the style options are set, either to default values or to specified
settings. I.e. settings from previous invocations do not persist settings. I.e. settings from previous invocations do not persist
across multiple invocations. across multiple invocations.
See the "Section Accelerate"_Section_accelerate.html section of the See the "Section 5.3"_Section_accelerate.html#acc_3 section of the
manual for more details about using the various accelerator packages manual for more details about using the various accelerator packages
for speeding up LAMMPS simulations. for speeding up LAMMPS simulations.

8
doc/src/pair_gauss.txt
View File

@ -63,7 +63,7 @@ solvent simulations of salt ions "(Lenart)"_#Lenart and of surfactants
"(Jusufi)"_#Jusufi. In these instances the Gaussian potential mimics "(Jusufi)"_#Jusufi. In these instances the Gaussian potential mimics
the hydration barrier between a pair of particles. The hydration the hydration barrier between a pair of particles. The hydration
barrier is located at r_mh and has a width of sigma_h. The prefactor barrier is located at r_mh and has a width of sigma_h. The prefactor
determines the hight of the potential barrier. determines the height of the potential barrier.
The following coefficients must be defined for each pair of atom types The following coefficients must be defined for each pair of atom types
via the "pair_coeff"_pair_coeff.html command as in the example above, via the "pair_coeff"_pair_coeff.html command as in the example above,
@ -73,9 +73,11 @@ commands:
H (energy * distance units) H (energy * distance units)
r_mh (distance units) r_mh (distance units)
sigma_h (distance units) :ul sigma_h (distance units)
cutoff (distance units) :ul
The global cutoff (r_c) specified in the pair_style command is used. The last coefficient is optional. If not specified, the global cutoff
is used.
:line :line

2
doc/src/python.txt
View File

@ -97,7 +97,7 @@ be passed to various commands as arguments, so that the variable is
evaluated during a simulation run. evaluated during a simulation run.
A broader overview of how Python can be used with LAMMPS is A broader overview of how Python can be used with LAMMPS is
given in "Section python"_Section_python.html. There is an given in "Section 11"_Section_python.html. There is an
examples/python directory which illustrates use of the python examples/python directory which illustrates use of the python
command. command.

2
doc/src/read_restart.txt
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@ -124,7 +124,7 @@ MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g. installed, e.g.
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre make mpi # build LAMMPS for your platform :pre
Second, use a restart filename which contains ".mpiio". Note that it Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters. does not have to end in ".mpiio", just contain those characters.

6
doc/src/region.txt
View File

@ -186,7 +186,7 @@ functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent radius. time. Thus it is easy to specify a time-dependent radius.
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS, for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used and how to transform these parameters to and from other commonly used
triclinic representations. triclinic representations.
@ -361,7 +361,7 @@ sub-regions can be defined with the {open} keyword.
Styles with a {kk} suffix are functionally the same as the Styles with a {kk} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in run faster, depending on your available hardware, as discussed in
"Section_accelerate"_Section_accelerate.html of the manual. The "Section 5"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues. results, except for round-off and precision issues.
@ -378,7 +378,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script. use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively. more instructions on how to use the accelerated styles effectively.
:line :line

2
doc/src/restart.txt
View File

@ -82,7 +82,7 @@ versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g. build LAMMPS with its MPIIO package installed, e.g.
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre make mpi # build LAMMPS for your platform :pre
Second, use a restart filename which contains ".mpiio". Note that it Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters. does not have to end in ".mpiio", just contain those characters.

2
doc/src/variable.txt
View File

@ -1121,7 +1121,7 @@ with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_"
(e.g. v_x or v_abc). The former can be used in any input script (e.g. v_x or v_abc). The former can be used in any input script
command, including a variable command. The input script parser command, including a variable command. The input script parser
evaluates the reference variable immediately and substitutes its value evaluates the reference variable immediately and substitutes its value
into the command. As explained in "Section commands into the command. As explained in "Section
3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use 3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use
un-named "immediate" variables for this purpose. For example, a un-named "immediate" variables for this purpose. For example, a
string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script

6
doc/src/velocity.txt
View File

@ -139,7 +139,7 @@ if rot = yes, the angular momentum is zeroed.
If specified, the {temp} keyword is used by {create} and {scale} to If specified, the {temp} keyword is used by {create} and {scale} to
specify a "compute"_compute.html that calculates temperature in a specify a "compute"_compute.html that calculates temperature in a
desired way, e.g. by first subtracting out a velocity bias, as desired way, e.g. by first subtracting out a velocity bias, as
discussed in "Section howto 16"_Section_howto.html#howto_15 of the doc discussed in "Section 6.16"_Section_howto.html#howto_16 of the doc
pages. If this keyword is not specified, {create} and {scale} pages. If this keyword is not specified, {create} and {scale}
calculate temperature using a compute that is defined internally as calculate temperature using a compute that is defined internally as
follows: follows:
@ -161,8 +161,8 @@ The {bias} keyword with a {yes} setting is used by {create} and
If the temperature compute also calculates a velocity bias, the the If the temperature compute also calculates a velocity bias, the the
bias is subtracted from atom velocities before the {create} and bias is subtracted from atom velocities before the {create} and
{scale} operations are performed. After the operations, the bias is {scale} operations are performed. After the operations, the bias is
added back to the atom velocities. See "Section howto added back to the atom velocities. See "Section
16"_Section_howto.html#howto_15 of the doc pages for more discussion 6.16"_Section_howto.html#howto_16 of the doc pages for more discussion
of temperature computes with biases. Note that the velocity bias is of temperature computes with biases. Note that the velocity bias is
only applied to atoms in the temperature compute specified with the only applied to atoms in the temperature compute specified with the
{temp} keyword. {temp} keyword.

2
doc/src/write_restart.txt
View File

@ -55,7 +55,7 @@ versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g. build LAMMPS with its MPIIO package installed, e.g.
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre make mpi # build LAMMPS for your platform :pre
Second, use a restart filename which contains ".mpiio". Note that it Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters. does not have to end in ".mpiio", just contain those characters.

1
examples/README
View File

@ -61,6 +61,7 @@ sub-directories:
accelerate: use of all the various accelerator packages accelerate: use of all the various accelerator packages
balance: dynamic load balancing, 2d system balance: dynamic load balancing, 2d system
body: body particles, 2d system body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
colloid: big colloid particles in a small particle solvent, 2d system colloid: big colloid particles in a small particle solvent, 2d system
coreshell: adiabatic core/shell model coreshell: adiabatic core/shell model
comb: models using the COMB potential comb: models using the COMB potential

0
examples/USER/misc/ti/in.ti_spring Executable file → Normal file
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1022
examples/cmap/charmm22.cmap Normal file
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File diff suppressed because it is too large Load Diff

380
examples/cmap/gagg.data Normal file
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@ -0,0 +1,380 @@
Created by charmm2lammps v1.8.2.6 beta on Sun Mar 20 00:26:35 EDT 2016
34 atoms
33 bonds
57 angles
75 dihedrals
7 impropers
2 crossterms
13 atom types
15 bond types
30 angle types
42 dihedral types
5 improper types
-34.414709 45.585291 xlo xhi
-36.134827 43.865173 ylo yhi
-39.349142 40.650858 zlo zhi
Masses
1 1.008 # H
2 1.008 # HC
3 1.008 # HA
4 1.008 # HB
5 12.011 # C
6 12.011 # CT1
7 12.011 # CT2
8 12.011 # CT3
9 12.011 # CC
10 14.007 # NH1
11 14.007 # NH3
12 15.999 # O
13 15.999 # OC
Pair Coeffs
1 0.046 0.400013524445 0.046 0.400013524445 # H
2 0.046 0.400013524445 0.046 0.400013524445 # HC
3 0.022 2.35197261589 0.022 2.35197261589 # HA
4 0.022 2.35197261589 0.022 2.35197261589 # HB
5 0.11 3.56359487256 0.11 3.56359487256 # C
6 0.02 4.05358916754 0.01 3.38541512893 # CT1
7 0.055 3.87540942391 0.01 3.38541512893 # CT2
8 0.08 3.67050271874 0.01 3.38541512893 # CT3
9 0.07 3.56359487256 0.07 3.56359487256 # CC
10 0.2 3.29632525712 0.2 2.76178602624 # NH1
11 0.2 3.29632525712 0.2 3.29632525712 # NH3
12 0.12 3.02905564168 0.12 2.49451641079 # O
13 0.12 3.02905564168 0.12 3.02905564168 # OC
Atoms
1 1 11 -0.3 0.0088076654 -0.0395361015 -0.0125765907 # NH3
2 1 2 0.33 -0.3781208354 -1.0038773849 -0.01724272 # HC
3 1 2 0.33 -0.3448285543 0.4901827566 -0.8403800387 # HC
4 1 2 0.33 -0.3306420078 0.4732826156 0.8294424358 # HC
5 1 7 0.13 1.526230489 -0.0164860529 -0.0402820599 # CT2
6 1 4 0.09 1.8596639218 -0.5263587482 -0.9333647137 # HB
7 1 4 0.09 1.8904342902 -0.4510777655 0.8809945249 # HB
8 1 5 0.51 2.0135471936 1.4020233344 -0.1137107587 # C
9 1 12 -0.51 1.1818164992 2.2781068718 -0.313197467 # O
10 2 10 -0.47 3.3194424268 1.666672014 0.0713249543 # NH1
11 2 1 0.31 4.0409429153 0.9783582555 0.1693897169 # H
12 2 6 0.07 3.8529467728 3.0161771739 0.0690818527 # CT1
13 2 4 0.09 3.5315723829 3.5134434764 -0.8378950509 # HB
14 2 8 -0.27 3.3981217437 3.8178727883 1.3071600161 # CT3
15 2 3 0.09 2.2921877645 3.9163330652 1.3111957959 # HA
16 2 3 0.09 3.7142964083 3.3104118688 2.2424399743 # HA
17 2 3 0.09 3.8238672849 4.8446179852 1.2978564897 # HA
18 2 5 0.51 5.3731873136 2.946062408 0.0042414688 # C
19 2 12 -0.51 5.9268816775 1.8488403755 0.0011766847 # O
20 3 10 -0.47 6.0445386951 4.1111769168 -0.0636349698 # NH1
21 3 1 0.31 5.5768514013 4.9972489389 -0.0653583036 # H
22 3 7 -0.02 7.4911642129 4.2772062416 -0.0346088891 # CT2
23 3 4 0.09 7.9218377956 3.8786283786 -0.9407244447 # HB
24 3 4 0.09 7.8877470687 3.8607990619 0.8803359097 # HB
25 3 5 0.51 7.7351287723 5.7597169026 -0.0088736611 # C
26 3 12 -0.51 6.7657462979 6.5189223559 0.005150418 # O
27 4 10 -0.47 9.0014031015 6.1940849758 -0.0045995102 # NH1
28 4 1 0.31 9.8272711181 5.6225413025 -0.008448093 # H
29 4 7 -0.02 9.4067557288 7.5845263022 0.0016383819 # CT2
30 4 4 0.09 9.0736276253 8.0578903151 0.9119901724 # HB
31 4 4 0.09 9.0736165596 8.064051906 -0.9055419386 # HB
32 4 9 0.34 10.9382207556 7.612479283 0.0008762597 # CC
33 4 13 -0.67 11.5487033003 6.5062943609 -0.0007524693 # OC
34 4 13 -0.67 11.5055524841 8.734223435 0.0013684148 # OC
Bond Coeffs
1 250 1.49 # C CT1
2 250 1.49 # C CT2
3 370 1.345 # C NH1
4 620 1.23 # C O
5 200 1.522 # CC CT2
6 525 1.26 # CC OC
7 222.5 1.538 # CT1 CT3
8 330 1.08 # CT1 HB
9 320 1.43 # CT1 NH1
10 330 1.08 # CT2 HB
11 320 1.43 # CT2 NH1
12 200 1.48 # CT2 NH3
13 322 1.111 # CT3 HA
14 440 0.997 # H NH1
15 403 1.04 # HC NH3
Bonds
1 15 2 1 # HC NH3
2 15 3 1 # HC NH3
3 15 4 1 # HC NH3
4 12 1 5 # CT2 NH3
5 2 8 5 # C CT2
6 3 8 10 # C NH1
7 10 5 6 # CT2 HB
8 10 5 7 # CT2 HB
9 4 9 8 # C O
10 7 14 12 # CT1 CT3
11 14 10 11 # H NH1
12 9 10 12 # CT1 NH1
13 1 18 12 # C CT1
14 3 18 20 # C NH1
15 8 12 13 # CT1 HB
16 13 14 15 # CT3 HA
17 13 14 16 # CT3 HA
18 13 14 17 # CT3 HA
19 4 19 18 # C O
20 14 20 21 # H NH1
21 11 20 22 # CT2 NH1
22 2 25 22 # C CT2
23 3 25 27 # C NH1
24 10 22 23 # CT2 HB
25 10 22 24 # CT2 HB
26 4 26 25 # C O
27 14 27 28 # H NH1
28 11 27 29 # CT2 NH1
29 5 32 29 # CC CT2
30 10 29 30 # CT2 HB
31 10 29 31 # CT2 HB
32 6 32 34 # CC OC
33 6 32 33 # CC OC
Angle Coeffs
1 52 108 0 0 # C CT1 CT3
2 50 109.5 0 0 # C CT1 HB
3 50 107 0 0 # C CT1 NH1
4 50 109.5 0 0 # C CT2 HB
5 50 107 0 0 # C CT2 NH1
6 43.7 110 0 0 # C CT2 NH3
7 50 120 0 0 # C NH1 CT1
8 50 120 0 0 # C NH1 CT2
9 34 123 0 0 # C NH1 H
10 50 109.5 0 0 # CC CT2 HB
11 50 107 0 0 # CC CT2 NH1
12 80 116.5 0 0 # CT1 C NH1
13 80 121 0 0 # CT1 C O
14 33.43 110.1 22.53 2.179 # CT1 CT3 HA
15 35 117 0 0 # CT1 NH1 H
16 80 116.5 0 0 # CT2 C NH1
17 80 121 0 0 # CT2 C O
18 40 118 50 2.388 # CT2 CC OC
19 35 117 0 0 # CT2 NH1 H
20 30 109.5 20 2.074 # CT2 NH3 HC
21 35 111 0 0 # CT3 CT1 HB
22 70 113.5 0 0 # CT3 CT1 NH1
23 35.5 108.4 5.4 1.802 # HA CT3 HA
24 48 108 0 0 # HB CT1 NH1
25 36 115 0 0 # HB CT2 HB
26 48 108 0 0 # HB CT2 NH1
27 51.5 107.5 0 0 # HB CT2 NH3
28 44 109.5 0 0 # HC NH3 HC
29 80 122.5 0 0 # NH1 C O
30 100 124 70 2.225 # OC CC OC
Angles
1 28 2 1 3 # HC NH3 HC
2 28 2 1 4 # HC NH3 HC
3 20 2 1 5 # CT2 NH3 HC
4 28 3 1 4 # HC NH3 HC
5 20 3 1 5 # CT2 NH3 HC
6 20 4 1 5 # CT2 NH3 HC
7 27 1 5 6 # HB CT2 NH3
8 27 1 5 7 # HB CT2 NH3
9 6 1 5 8 # C CT2 NH3
10 25 6 5 7 # HB CT2 HB
11 4 6 5 8 # C CT2 HB
12 4 7 5 8 # C CT2 HB
13 17 5 8 9 # CT2 C O
14 16 5 8 10 # CT2 C NH1
15 29 9 8 10 # NH1 C O
16 9 8 10 11 # C NH1 H
17 7 8 10 12 # C NH1 CT1
18 15 11 10 12 # CT1 NH1 H
19 24 10 12 13 # HB CT1 NH1
20 22 10 12 14 # CT3 CT1 NH1
21 3 10 12 18 # C CT1 NH1
22 21 13 12 14 # CT3 CT1 HB
23 2 13 12 18 # C CT1 HB
24 1 14 12 18 # C CT1 CT3
25 14 12 14 15 # CT1 CT3 HA
26 14 12 14 16 # CT1 CT3 HA
27 14 12 14 17 # CT1 CT3 HA
28 23 15 14 16 # HA CT3 HA
29 23 15 14 17 # HA CT3 HA
30 23 16 14 17 # HA CT3 HA
31 13 12 18 19 # CT1 C O
32 12 12 18 20 # CT1 C NH1
33 29 19 18 20 # NH1 C O
34 9 18 20 21 # C NH1 H
35 8 18 20 22 # C NH1 CT2
36 19 21 20 22 # CT2 NH1 H
37 26 20 22 23 # HB CT2 NH1
38 26 20 22 24 # HB CT2 NH1
39 5 20 22 25 # C CT2 NH1
40 25 23 22 24 # HB CT2 HB
41 4 23 22 25 # C CT2 HB
42 4 24 22 25 # C CT2 HB
43 17 22 25 26 # CT2 C O
44 16 22 25 27 # CT2 C NH1
45 29 26 25 27 # NH1 C O
46 9 25 27 28 # C NH1 H
47 8 25 27 29 # C NH1 CT2
48 19 28 27 29 # CT2 NH1 H
49 26 27 29 30 # HB CT2 NH1
50 26 27 29 31 # HB CT2 NH1
51 11 27 29 32 # CC CT2 NH1
52 25 30 29 31 # HB CT2 HB
53 10 30 29 32 # CC CT2 HB
54 10 31 29 32 # CC CT2 HB
55 18 29 32 33 # CT2 CC OC
56 18 29 32 34 # CT2 CC OC
57 30 33 32 34 # OC CC OC
Dihedral Coeffs
1 0.2 3 0 1 # C CT1 CT3 HA
2 0.2 1 180 1 # C CT1 NH1 C
3 0 1 0 1 # C CT1 NH1 H
4 0.2 1 180 1 # C CT2 NH1 C
5 0 1 0 1 # C CT2 NH1 H
6 0.1 3 0 1 # C CT2 NH3 HC
7 1.8 1 0 1 # C NH1 CT1 CT3
8 0 1 0 1 # C NH1 CT1 HB
9 0.2 1 180 1 # C NH1 CT2 CC
10 0 1 0 1 # C NH1 CT2 HB
11 0 1 0 1 # CC CT2 NH1 H
12 1.6 1 0 1 # CT1 C NH1 CT2
13 2.5 2 180 0 # CT1 C NH1 CT2
14 2.5 2 180 1 # CT1 C NH1 H
15 1.6 1 0 1 # CT1 NH1 C CT2
16 2.5 2 180 0 # CT1 NH1 C CT2
17 2.5 2 180 1 # CT1 NH1 C O
18 1.6 1 0 1 # CT2 C NH1 CT2
19 2.5 2 180 0 # CT2 C NH1 CT2
20 2.5 2 180 1 # CT2 C NH1 H
21 2.5 2 180 1 # CT2 NH1 C O
22 0 1 0 1 # CT3 CT1 C NH1
23 1.4 1 0 1 # CT3 CT1 C O
24 0 1 0 1 # CT3 CT1 NH1 H
25 2.5 2 180 1 # H NH1 C O
26 0 1 0 1 # H NH1 CT1 HB
27 0 1 0 1 # H NH1 CT2 HB
28 0.2 3 0 1 # HA CT3 CT1 HB
29 0.2 3 0 1 # HA CT3 CT1 NH1
30 0 1 0 1 # HB CT1 C NH1
31 0 1 0 1 # HB CT1 C O
32 0 1 0 1 # HB CT2 C NH1
33 0 1 0 1 # HB CT2 C O
34 0.05 6 180 1 # HB CT2 CC OC
35 0.1 3 0 1 # HB CT2 NH3 HC
36 0.6 1 0 1 # NH1 C CT1 NH1
37 0.6 1 0 1 # NH1 C CT2 NH1
38 0.4 1 0 1 # NH1 C CT2 NH3
39 0 1 0 1 # NH1 CT1 C O
40 0 1 0 1 # NH1 CT2 C O
41 0.05 6 180 1 # NH1 CT2 CC OC
42 0 1 0 1 # NH3 CT2 C O
Dihedrals
1 42 1 5 8 9 # NH3 CT2 C O
2 38 1 5 8 10 # NH1 C CT2 NH3
3 35 2 1 5 6 # HB CT2 NH3 HC
4 35 2 1 5 7 # HB CT2 NH3 HC
5 6 2 1 5 8 # C CT2 NH3 HC
6 35 3 1 5 6 # HB CT2 NH3 HC
7 35 3 1 5 7 # HB CT2 NH3 HC
8 6 3 1 5 8 # C CT2 NH3 HC
9 35 4 1 5 6 # HB CT2 NH3 HC
10 35 4 1 5 7 # HB CT2 NH3 HC
11 6 4 1 5 8 # C CT2 NH3 HC
12 20 5 8 10 11 # CT2 C NH1 H
13 15 5 8 10 12 # CT1 NH1 C CT2
14 16 5 8 10 12 # CT1 NH1 C CT2
15 33 6 5 8 9 # HB CT2 C O
16 32 6 5 8 10 # HB CT2 C NH1
17 33 7 5 8 9 # HB CT2 C O
18 32 7 5 8 10 # HB CT2 C NH1
19 8 8 10 12 13 # C NH1 CT1 HB
20 7 8 10 12 14 # C NH1 CT1 CT3
21 2 8 10 12 18 # C CT1 NH1 C
22 25 9 8 10 11 # H NH1 C O
23 17 9 8 10 12 # CT1 NH1 C O
24 29 10 12 14 15 # HA CT3 CT1 NH1
25 29 10 12 14 16 # HA CT3 CT1 NH1
26 29 10 12 14 17 # HA CT3 CT1 NH1
27 39 10 12 18 19 # NH1 CT1 C O
28 36 10 12 18 20 # NH1 C CT1 NH1
29 26 11 10 12 13 # H NH1 CT1 HB
30 24 11 10 12 14 # CT3 CT1 NH1 H
31 3 11 10 12 18 # C CT1 NH1 H
32 14 12 18 20 21 # CT1 C NH1 H
33 12 12 18 20 22 # CT1 C NH1 CT2
34 13 12 18 20 22 # CT1 C NH1 CT2
35 28 13 12 14 15 # HA CT3 CT1 HB
36 28 13 12 14 16 # HA CT3 CT1 HB
37 28 13 12 14 17 # HA CT3 CT1 HB
38 31 13 12 18 19 # HB CT1 C O
39 30 13 12 18 20 # HB CT1 C NH1
40 23 14 12 18 19 # CT3 CT1 C O
41 22 14 12 18 20 # CT3 CT1 C NH1
42 1 15 14 12 18 # C CT1 CT3 HA
43 1 16 14 12 18 # C CT1 CT3 HA
44 1 17 14 12 18 # C CT1 CT3 HA
45 10 18 20 22 23 # C NH1 CT2 HB
46 10 18 20 22 24 # C NH1 CT2 HB
47 4 18 20 22 25 # C CT2 NH1 C
48 25 19 18 20 21 # H NH1 C O
49 21 19 18 20 22 # CT2 NH1 C O
50 40 20 22 25 26 # NH1 CT2 C O
51 37 20 22 25 27 # NH1 C CT2 NH1
52 27 21 20 22 23 # H NH1 CT2 HB
53 27 21 20 22 24 # H NH1 CT2 HB
54 5 21 20 22 25 # C CT2 NH1 H
55 20 22 25 27 28 # CT2 C NH1 H
56 18 22 25 27 29 # CT2 C NH1 CT2
57 19 22 25 27 29 # CT2 C NH1 CT2
58 33 23 22 25 26 # HB CT2 C O
59 32 23 22 25 27 # HB CT2 C NH1
60 33 24 22 25 26 # HB CT2 C O
61 32 24 22 25 27 # HB CT2 C NH1
62 10 25 27 29 30 # C NH1 CT2 HB
63 10 25 27 29 31 # C NH1 CT2 HB
64 9 25 27 29 32 # C NH1 CT2 CC
65 25 26 25 27 28 # H NH1 C O
66 21 26 25 27 29 # CT2 NH1 C O
67 41 27 29 32 33 # NH1 CT2 CC OC
68 41 27 29 32 34 # NH1 CT2 CC OC
69 27 28 27 29 30 # H NH1 CT2 HB
70 27 28 27 29 31 # H NH1 CT2 HB
71 11 28 27 29 32 # CC CT2 NH1 H
72 34 30 29 32 33 # HB CT2 CC OC
73 34 30 29 32 34 # HB CT2 CC OC
74 34 31 29 32 33 # HB CT2 CC OC
75 34 31 29 32 34 # HB CT2 CC OC
Improper Coeffs
1 120 0 # C CT1 NH1 O
2 120 0 # C CT2 NH1 O
3 96 0 # CC CT2 OC OC
4 20 0 # H CT1 C NH1
5 20 0 # H CT2 C NH1
Impropers
1 2 8 5 10 9 # C CT2 NH1 O
2 4 10 8 12 11 # H CT1 C NH1
3 1 18 12 20 19 # C CT1 NH1 O
4 5 20 18 22 21 # H CT2 C NH1
5 2 25 22 27 26 # C CT2 NH1 O
6 5 27 25 29 28 # H CT2 C NH1
7 3 32 29 34 33 # CC CT2 OC OC
CMAP
1 1 8 10 12 18 20
2 5 18 20 22 25 27

36
examples/cmap/in.cmap Normal file
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@ -0,0 +1,36 @@
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
units real
neigh_modify delay 2 every 1
#newton off
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/charmm 8 12
#pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap
fix_modify cmap energy yes
read_data gagg.data fix cmap crossterm CMAP
special_bonds charmm
fix 1 all nve
#fix 1 all nvt temp 300 300 100.0
#fix 2 all shake 1e-9 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform
thermo 1000
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
timestep 2.0
run 100000

200
examples/cmap/log.23Sep16.cmap.g++.1 Normal file
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@ -0,0 +1,200 @@
LAMMPS (21 Sep 2016)
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
units real
neigh_modify delay 2 every 1
#newton off
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/charmm 8 12
#pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap
fix_modify cmap energy yes
read_data gagg.data fix cmap crossterm CMAP
orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
1 by 1 by 1 MPI processor grid
reading atoms ...
34 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
33 bonds
reading angles ...
57 angles
reading dihedrals ...
75 dihedrals
reading impropers ...
7 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
13 = max # of 1-4 neighbors
16 = max # of special neighbors
special_bonds charmm
fix 1 all nve
#fix 1 all nvt temp 300 300 100.0
#fix 2 all shake 1e-9 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform
thermo 1000
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
timestep 2.0
run 100000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 12 12 12
Memory usage per processor = 14.6355 Mbytes
Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792664 -2.3185572 0.088366962
6000 29.214175 -0.95299225 0.81926009 3.6805429 4.6742897 -2.9343577 0.26697813
7000 27.018614 -0.52423475 0.72502764 3.8840137 4.7780956 -2.3916009 0.24952584
8000 29.682167 -1.0939711 0.76111486 3.1090116 4.9359719 -2.5662984 0.1411154
9000 27.909695 -0.80905986 0.78952533 4.203187 4.1301204 -2.000402 0.088859259
10000 27.480298 -0.86273377 1.1293962 4.3857421 4.899282 -3.3895621 0.12126215
11000 28.303203 -1.0221152 0.62762348 4.055414 4.5863024 -2.5842816 0.17996907
12000 28.311127 -0.94227367 0.91859012 3.6673926 4.7018632 -3.902715 0.30065704
13000 30.818607 -1.5220116 0.95710386 3.3364371 4.543427 -3.0423067 0.16712905
14000 27.643736 -1.0144117 0.95806952 4.1046912 4.800236 -4.0534389 0.29293405
15000 27.660491 -1.0390086 0.78061056 4.1139174 4.7197202 -2.3670379 0.22126985
16000 27.845157 -0.63654502 0.78007478 3.9365994 4.949418 -3.1470214 0.22335355
17000 28.44772 -1.0255112 0.70402007 4.0573343 4.2887527 -2.2099596 0.048050962
18000 27.128323 -0.96218536 1.1327159 4.3222585 4.326607 -2.2881766 0.13491257
19000 27.337633 -0.78999574 0.80152298 4.2239689 4.7073478 -2.2924164 0.12710292
20000 27.780537 -0.46458072 0.79707671 3.7232618 4.943417 -2.5290628 0.26191223
21000 26.435484 -0.7803224 1.0753217 4.4196051 5.9945933 -2.3340925 0.16448475
22000 28.619429 -1.1623149 0.9401731 3.8508844 5.1636737 -2.5551846 0.25318434
23000 28.399338 -0.79700962 0.85575503 4.488526 4.5975422 -2.5663549 0.13601693
24000 29.645532 -1.158744 0.83180313 3.8193399 4.60319 -2.6847864 0.24260466
25000 28.695339 -1.4802204 0.76583757 3.6786272 4.8959496 -2.3627896 0.080867326
26000 28.149711 -1.029689 0.79383806 3.7885067 4.3345813 -2.1041553 0.14598209
27000 29.580373 -1.0525813 1.0262723 3.7767318 4.6119758 -2.2802386 0.088556038
28000 28.44308 -0.93411225 0.8794395 3.948079 4.780246 -2.1814583 0.14340149
29000 29.335621 -1.6087988 0.71803091 3.7819186 4.6688385 -2.4282242 0.16061111
30000 28.706138 -1.3938241 0.67713818 4.031275 4.4756505 -2.1807056 0.11461356
31000 27.451944 0.010297225 0.65064883 3.6402029 4.3607811 -2.5511516 0.12637237
32000 27.070878 -1.103158 1.1932199 5.1329709 4.5201653 -2.2224479 0.11215427
33000 29.889976 -1.6228316 0.69407996 3.5361991 4.3502767 -1.9847454 0.09089949
34000 28.223151 -0.927208 1.043253 3.4650939 5.1028142 -2.8127219 0.10648823
35000 27.985986 -0.48153861 0.63878449 3.3724641 4.9551679 -2.6565919 0.12123115
36000 28.580688 -1.4500694 1.055762 4.0490064 4.423782 -2.3103578 0.072747638
37000 29.192947 -0.49678176 1.1146731 2.9233947 4.5738603 -2.4376144 0.22874047
38000 26.954594 -0.53812359 0.79230685 4.3356989 5.0284656 -2.3791255 0.0486081
39000 27.567555 -0.57870028 0.73614374 4.191991 4.9209556 -2.6122044 0.08635571
40000 28.494172 -0.79057135 0.79072816 4.1893209 4.4826919 -2.4179635 0.14612898
41000 28.44904 -1.1002948 0.93405654 4.3586358 4.4338415 -2.2950944 0.15705834
42000 28.95725 -1.0297067 1.1632348 4.274711 4.9979487 -2.7611464 0.15944725
43000 28.640394 -0.70938882 0.68100893 3.1844315 5.1817454 -2.2837487 0.14189233
44000 27.997558 -1.0115099 0.59125208 4.0883422 4.6033907 -2.2775964 0.094273258
45000 27.67163 -0.67992747 1.1225552 3.9020703 4.8171056 -2.1952679 0.041418433
46000 28.822607 -0.6687953 0.74160059 3.3193715 4.5546965 -2.3024572 0.047569065
47000 29.20147 -1.4456785 0.79223353 3.8288813 4.5811826 -2.5154936 0.061230141
48000 27.843026 -1.0222301 0.87322137 4.3432743 4.4266307 -2.1414153 0.06802794
49000 28.199573 -1.1887794 1.2781088 4.0779644 4.5881353 -2.319775 0.094803547
50000 28.759212 -1.354416 0.68534569 3.8394841 4.2308134 -2.1281844 0.1395951
51000 27.876455 -1.5705462 0.76557156 4.5335223 4.523708 -2.203702 0.14679803
52000 27.930587 -1.2277489 0.96071516 3.960953 5.1152188 -2.4101451 0.060949521
53000 27.031236 -1.4746477 1.2341141 5.0540975 4.3656865 -2.1288513 0.092725656
54000 28.809394 -1.1162427 0.94350207 3.4013958 4.4755547 -2.3342811 0.18855912
55000 28.948415 -1.1560418 0.6260139 3.5386373 4.5244978 -2.340212 0.17474657
56000 28.048368 -0.95784532 0.76432571 4.1404665 4.4570033 -2.0899628 0.045693628
57000 28.707642 -1.366574 0.9907873 3.729903 4.3131997 -2.2777698 0.065420213
58000 26.361663 -1.0424403 1.0452563 5.0977108 4.7035231 -2.3101244 0.13671642
59000 29.218218 -1.2210564 0.62435875 3.4236327 4.5481681 -2.1575943 0.037984042
60000 27.655546 -1.1053224 0.86323501 3.7641375 4.8946898 -2.2422249 0.077725979
61000 27.252108 -1.3744824 1.1150806 5.0444848 4.4878135 -2.2743829 0.058331257
62000 27.163469 -1.1715781 0.72099321 4.5295501 4.9509918 -2.2993961 0.050401105
63000 29.581575 -1.2238537 0.86303245 3.1194038 5.2218965 -2.5002427 0.055032632
64000 27.897822 -1.1011516 0.74540883 4.2869228 4.3394269 -2.2552393 0.1403321
65000 27.083245 -1.0633392 0.92771724 5.0805224 4.2747962 -2.2388039 0.064196692
66000 29.072723 -1.5514209 0.89798805 4.2600224 4.4261812 -2.3524752 0.15067414
67000 27.308181 -0.72224802 0.97109517 4.5074578 4.4559352 -2.1381121 0.089297603
68000 27.505686 -0.43855431 0.80785812 4.1917251 5.0157721 -2.3382145 0.11105164
69000 29.041681 -0.64735378 0.89874684 3.3891579 4.3753361 -2.2320941 0.14716747
70000 29.735756 -1.7061457 0.9206878 3.5767878 4.3851664 -2.2516304 0.097196062
71000 28.224352 -0.92217702 0.86093586 3.9507157 4.5596589 -2.2173397 0.089116669
72000 29.282336 -1.056142 0.65185725 3.8735742 4.4839333 -2.4314756 0.071909704
73000 26.257283 -0.64273826 0.98300685 5.063943 5.045958 -2.5544375 0.2180275
74000 28.825119 -0.97736616 0.87201848 3.55875 4.3653309 -2.2303567 0.098963875
75000 29.239507 -0.96508809 0.74517323 3.4306236 4.7651921 -2.6077732 0.17883654
76000 27.349841 -0.50990238 1.1183613 4.4252451 4.4097775 -2.4125794 0.18483606
77000 28.130197 -1.4081219 0.94921357 4.2572132 4.5162849 -2.4013797 0.073744606
78000 28.235774 -0.9214321 0.6324981 3.8697686 4.8092154 -2.2272847 0.092108346
79000 26.732846 -0.55949486 1.0989617 5.0088609 4.4930687 -2.277945 0.03855146
80000 28.529208 -0.94244671 0.79407482 3.961106 4.3930011 -2.3127726 0.091124948
81000 29.603852 -1.6116062 1.060847 3.7824932 4.151001 -1.9139868 0.19875986
82000 28.232876 -1.1833011 1.0182713 3.4195758 5.1394333 -2.4632697 0.28501012
83000 29.565482 -1.3479552 0.99056973 3.7851802 4.4781011 -2.7872481 0.2031991
84000 28.780274 -1.3073882 1.0512637 4.004638 4.502282 -2.3789146 0.015656202
85000 27.262312 -1.1305346 1.203524 4.7938623 4.1747105 -2.0952844 0.054240361
86000 28.157348 -1.0662817 0.81163796 3.9912709 4.8320213 -2.255237 0.14698333
87000 28.445543 -1.3365026 0.78156195 4.4767689 4.4457575 -2.5008786 0.13879386
88000 27.656717 -1.1490599 0.87974869 4.4629952 4.7023033 -2.3258145 0.081904139
89000 28.838821 -1.020709 0.85587929 3.7110705 4.4938307 -2.4914483 0.11447952
90000 27.356497 -0.59107077 0.81879666 4.5209332 4.4703836 -2.3806717 0.071307775
91000 27.780445 -0.80564513 0.94752313 3.8468943 4.2924253 -2.1011134 0.1118672
92000 28.555276 -1.3514732 0.80826674 3.9590742 4.5775954 -2.4891232 0.054254978
93000 28.747267 -1.2133243 0.75507246 4.1319789 4.9048611 -2.4913887 0.13045693
94000 27.479343 -0.69973695 0.99696121 3.5966229 4.549025 -2.4155312 0.41745762
95000 27.726945 -1.1905026 1.1120842 4.7433275 4.5386861 -2.7947142 0.33671682
96000 28.021114 -1.0341645 0.6663033 4.2397505 4.6203984 -1.9904034 0.10972565
97000 28.382022 -1.3916008 1.180588 4.0729621 4.6741792 -2.554927 0.13462346
98000 27.895969 -0.7496449 1.3072185 4.2611888 4.3726077 -2.1320701 0.15376665
99000 28.517889 -1.2183957 1.279778 3.957647 4.2638434 -2.2888407 0.042705003
100000 28.109211 -1.2538948 0.83671785 4.3734766 4.544545 -2.3076497 0.042189096
Loop time of 2.96683 on 1 procs for 100000 steps with 34 atoms
Performance: 5824.390 ns/day, 0.004 hours/ns, 33705.963 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.98759 | 0.98759 | 0.98759 | 0.0 | 33.29
Bond | 1.6463 | 1.6463 | 1.6463 | 0.0 | 55.49
Neigh | 0.007688 | 0.007688 | 0.007688 | 0.0 | 0.26
Comm | 0.012214 | 0.012214 | 0.012214 | 0.0 | 0.41
Output | 0.0010295 | 0.0010295 | 0.0010295 | 0.0 | 0.03
Modify | 0.25684 | 0.25684 | 0.25684 | 0.0 | 8.66
Other | | 0.05519 | | | 1.86
Nlocal: 34 ave 34 max 34 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 395
Ave neighs/atom = 11.6176
Ave special neighs/atom = 9.52941
Neighbor list builds = 237
Dangerous builds = 0
Total wall time: 0:00:02

200
examples/cmap/log.23Sep16.cmap.g++.4 Normal file
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@ -0,0 +1,200 @@
LAMMPS (21 Sep 2016)
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
units real
neigh_modify delay 2 every 1
#newton off
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/charmm 8 12
#pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap
fix_modify cmap energy yes
read_data gagg.data fix cmap crossterm CMAP
orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
1 by 2 by 2 MPI processor grid
reading atoms ...
34 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
33 bonds
reading angles ...
57 angles
reading dihedrals ...
75 dihedrals
reading impropers ...
7 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
13 = max # of 1-4 neighbors
16 = max # of special neighbors
special_bonds charmm
fix 1 all nve
#fix 1 all nvt temp 300 300 100.0
#fix 2 all shake 1e-9 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform
thermo 1000
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
timestep 2.0
run 100000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 12 12 12
Memory usage per processor = 15.9307 Mbytes
Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792663 -2.3185572 0.088366962
6000 29.214175 -0.95299239 0.81926011 3.6805428 4.6742897 -2.9343578 0.26697816
7000 27.018614 -0.52423469 0.72502751 3.8840141 4.7780958 -2.3916014 0.24952572
8000 29.682494 -1.0940368 0.76113051 3.1089345 4.9357863 -2.5662256 0.14112613
9000 27.853918 -0.7913741 0.79503268 4.2177256 4.146792 -2.00475 0.090585666
10000 27.13754 -0.80551128 1.1325023 4.4718283 5.2460631 -3.4947725 0.11893125
11000 28.277434 -1.4897448 0.90075953 4.1895717 4.3594269 -1.9553119 0.090222212
12000 28.630973 -1.222206 0.67796385 3.3905661 4.9691334 -2.9052721 0.13897658
13000 28.593007 -0.95684026 0.75585196 3.7242568 4.7417932 -2.3893117 0.2074121
14000 26.147115 -0.6026921 0.93591488 5.1292829 4.9821952 -2.2571835 0.11872421
15000 26.29432 -0.82424162 1.048979 4.5569495 5.1189308 -2.9750422 0.16195676
16000 29.189992 -0.80998247 0.74093508 3.8299275 4.4536688 -2.5497538 0.19155639
17000 25.878012 -0.3519646 1.0988924 4.7359591 5.3923098 -2.7211029 0.13405223
18000 27.726135 -0.28229987 0.63072344 4.1777888 4.7237271 -2.2177157 0.15939372
19000 27.153504 -0.66477422 0.77910129 4.2036117 5.113851 -2.3494315 0.094793307
20000 28.044833 -1.2835827 0.88745367 3.9955526 4.5077788 -3.0116467 0.17197859
21000 27.205696 -0.74090037 1.0023251 4.3421733 4.912671 -2.3473271 0.26089356
22000 27.385785 -0.93740972 0.84554838 4.562743 4.883866 -2.2110955 0.11573301
23000 27.05534 -0.95605442 0.96719024 3.9277618 5.0359014 -2.6135949 0.21368061
24000 28.273378 -0.97543103 0.8983443 4.2067985 4.4782971 -2.4230505 0.30311692
25000 27.477789 -0.20383849 0.8380706 3.8037992 4.8312504 -2.5831791 0.093843746
26000 30.344199 -1.9773473 0.92882437 3.7821405 4.5176677 -2.3020968 0.2194307
27000 27.32767 -0.9803839 0.92988865 3.7611603 5.0328211 -2.4647656 0.18213622
28000 27.34208 -1.037938 0.74488346 4.1727342 4.7056812 -2.2718346 0.17741362
29000 27.682777 -0.51006495 0.57074224 4.7332237 4.7080462 -2.0491512 0.2130517
30000 24.925731 0.13670248 0.84976065 4.4143762 6.0677158 -3.5479173 0.28059419
31000 28.623419 -0.90725708 1.0710501 3.6930688 4.6639301 -2.2225373 0.20988139
32000 27.732286 -1.1948367 0.89230134 4.4398373 4.8923907 -3.5849327 0.49167488
33000 28.800772 -1.5319589 0.93455495 4.1634728 4.6107706 -2.3503486 0.22636535
34000 27.374398 -1.0957453 0.89450276 3.9829508 4.991786 -2.3548834 0.15869465
35000 28.38753 -0.89261166 0.90000776 3.536864 4.4293294 -2.4218118 0.10640557
36000 27.713974 0.088038031 0.85190574 3.8969601 4.6256355 -2.7935475 0.34671662
37000 29.13007 -1.378597 0.74412556 3.131538 4.6458653 -2.9373734 0.38035616
38000 28.556573 -1.4055344 1.139984 4.0035753 4.2938358 -2.489329 0.25338326
39000 26.447036 -1.1829705 0.87032438 5.0804461 4.5772023 -2.7346466 0.32165802
40000 27.991454 -0.64295679 0.61020872 4.165871 4.4623087 -2.2244194 0.13826991
41000 29.483296 -1.2400745 0.66926627 3.3473666 4.5766617 -2.3051145 0.12171554
42000 26.948627 -1.2162288 1.1440628 4.3993073 5.1176533 -2.4734485 0.15497709
43000 28.04459 -0.26543193 0.83647367 3.5160747 4.6964397 -2.2805068 0.12618821
44000 28.213608 -1.216128 0.9132792 4.0206483 4.9483599 -2.3387049 0.10132022
45000 28.283506 -1.0390766 0.86113772 4.504509 4.7209088 -2.3043085 0.14588362
46000 27.433853 -0.57912107 0.78448334 4.5998579 5.1181394 -2.6165094 0.18722528
47000 27.552939 -1.1128925 0.80087638 4.3448001 4.8062869 -2.4296883 0.2702479
48000 28.874034 -1.3242519 0.71770727 3.5648565 4.4671824 -2.2608958 0.16115978
49000 29.216186 -1.2210307 0.76937497 3.9260628 4.7550577 -2.7316081 0.085505664
50000 28.065856 -1.1545547 0.86953819 4.4137666 4.732157 -2.4450867 0.23320539
51000 26.308975 -0.99728352 0.90408444 4.2400186 5.6340425 -2.2090554 0.079882158
52000 28.517571 -1.5027398 0.83520278 3.8176552 4.3001251 -2.0731682 0.1665375
53000 28.77579 -1.3564268 0.97253881 3.6866407 4.8532347 -2.5330776 0.17668411
54000 29.135315 -1.0994106 0.67605671 3.6819254 4.3134408 -1.9796929 0.076951331
55000 26.168938 -0.76247492 0.88784685 4.6533473 6.0484793 -2.1334561 0.036876985
56000 27.471775 -0.68648837 1.0576168 4.0354311 4.4767052 -2.2368959 0.24950568
57000 29.787083 -1.4914384 1.0702944 3.5388133 4.5173097 -2.6694464 0.27937092
58000 28.705448 -1.3016617 0.63337853 3.9552713 4.4119825 -1.8774657 0.17540021
59000 29.130155 -0.91647363 0.84384883 3.1076903 4.5346348 -2.3457338 0.16674486
60000 26.874199 -0.81598034 1.3432151 5.1322624 4.9545484 -2.9566615 0.25950486
61000 27.401306 -0.82895856 1.1636949 4.020154 4.5745928 -2.601466 0.18061051
62000 28.930313 -1.5231967 0.85173243 4.3517328 4.4878662 -2.5859205 0.1755493
63000 26.56874 0.026147233 0.60836216 4.4231618 4.4390677 -2.1721849 0.08594237
64000 26.729023 -0.76953985 0.76734633 4.5104288 5.0886456 -2.2118551 0.11339216
65000 28.900471 -1.3901477 0.86194657 4.2774976 4.498325 -2.3672362 0.20668335
66000 26.884253 -0.21198879 0.98509625 4.0843117 4.4344172 -2.3289416 0.23631017
67000 27.210888 -0.84075559 1.0396559 4.7253607 4.4314589 -2.2985702 0.19326507
68000 28.042102 -1.1898715 1.053534 3.8748712 4.4358449 -2.3998723 0.2431659
69000 28.939141 -1.6968936 0.98155912 4.0460838 5.0075204 -2.5547087 0.28645131
70000 27.15577 -0.85202797 1.1469079 4.7645212 4.6133209 -2.3410451 0.086576572
71000 25.507417 -0.27780727 0.95157881 4.8759406 4.853401 -2.9598705 0.41011008
72000 29.804703 -1.4847015 0.96345767 3.6797304 4.3678377 -2.4594626 0.14480206
73000 28.602798 -1.4906143 0.72497266 4.2442974 4.5360598 -2.3621638 0.14385651
74000 28.4928 -0.91319873 1.0377472 3.8033127 4.3991601 -2.4051911 0.095567428
75000 26.38168 -0.70733237 1.1557817 5.697939 4.5935618 -2.4285007 0.058980519
76000 27.16626 -0.83631031 0.84844246 4.7460887 4.5801472 -2.1260014 0.12845946
77000 29.040661 -1.3089499 0.80285084 4.664804 4.5215895 -2.6861939 0.13215598
78000 27.477871 -1.0600977 0.88595045 4.6264017 5.4095605 -2.474411 0.10987174
79000 26.151797 -0.55779685 0.91382436 4.99964 4.9184022 -2.2547241 0.22854038
80000 28.14523 -0.54460026 0.8982411 3.5374555 4.3785673 -2.3196807 0.088567964
81000 29.029941 -1.6467789 0.79042284 3.7269899 4.7407998 -2.3795824 0.1408727
82000 27.920287 -0.72798032 1.0076975 3.4449461 4.5621371 -2.8239074 0.25103454
83000 29.131054 -1.114367 0.76887285 3.459639 4.5163922 -2.607825 0.19991648
84000 28.249768 -0.69944068 1.0510846 4.0436296 4.6430538 -2.4213355 0.077299966
85000 28.06888 -0.62132922 0.91829312 4.1294147 4.3099557 -2.354063 0.15866186
86000 28.664264 -1.1022906 0.87831695 4.5773522 4.6045802 -2.9206875 0.33950063
87000 27.960967 -1.2852756 0.77694253 3.9011301 4.9114139 -3.2374868 0.3068138
88000 27.190678 -1.2803268 1.1545301 4.5769709 5.2404761 -2.3825838 0.10356039
89000 26.792931 -0.44516641 1.0236244 4.2007253 4.7098685 -2.3608551 0.034447062
90000 27.173991 -0.87185611 1.065719 4.1953618 4.6856408 -2.6539232 0.16957757
91000 28.626528 -1.239257 0.89524651 4.7048012 4.6344201 -2.7367901 0.43534143
92000 27.661812 -1.109044 0.92817391 5.0294489 4.3890711 -2.4108669 0.12570139
93000 28.156793 -1.0820907 0.92812693 4.938385 4.4901426 -2.4023366 0.30135781
94000 28.842149 -1.3524969 1.1451109 4.3125908 4.6959035 -2.6747199 0.2254607
95000 27.862247 -1.2119045 1.0218976 4.2614082 4.4931316 -2.6902934 0.16345201
96000 27.084973 -0.93738328 1.3984324 4.5647189 4.4232205 -2.2834097 0.11217888
97000 27.587078 -0.89397255 0.78218462 3.8944421 4.3981479 -2.4205318 0.16570942
98000 27.981746 -1.2380545 0.84847869 4.311441 4.7340377 -2.4270441 0.023565612
99000 27.476625 -0.8569146 0.82550381 4.1656963 4.4064921 -2.4169708 0.160814
100000 26.121325 -0.63610855 1.0803389 4.9257118 4.7073263 -2.4010334 0.066303044
Loop time of 2.60487 on 4 procs for 100000 steps with 34 atoms
Performance: 6633.735 ns/day, 0.004 hours/ns, 38389.667 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.066848 | 0.26055 | 0.6843 | 48.6 | 10.00
Bond | 0.067332 | 0.45486 | 0.93545 | 55.1 | 17.46
Neigh | 0.0078266 | 0.007863 | 0.0078835 | 0.0 | 0.30
Comm | 0.41829 | 1.3207 | 1.8951 | 50.8 | 50.70
Output | 0.0033038 | 0.0036355 | 0.0040481 | 0.4 | 0.14
Modify | 0.040861 | 0.15162 | 0.27091 | 27.3 | 5.82
Other | | 0.4057 | | | 15.57
Nlocal: 8.5 ave 15 max 2 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 25.5 ave 32 max 19 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 98.75 ave 257 max 18 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 395
Ave neighs/atom = 11.6176
Ave special neighs/atom = 9.52941
Neighbor list builds = 294
Dangerous builds = 0
Total wall time: 0:00:02

28
python/lammps.py
View File

@ -28,6 +28,15 @@ import os
import select import select
import re import re
class MPIAbortException(Exception):
def __init__(self, message):
self.message = message
def __str__(self):
return repr(self.message)
class lammps(object): class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator # detect if Python is using version of mpi4py that can pass a communicator
@ -43,6 +52,7 @@ class lammps(object):
# create instance of LAMMPS # create instance of LAMMPS
def __init__(self,name="",cmdargs=None,ptr=None,comm=None): def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
self.comm = comm
# determine module location # determine module location
@ -150,10 +160,14 @@ class lammps(object):
if cmd: cmd = cmd.encode() if cmd: cmd = cmd.encode()
self.lib.lammps_command(self.lmp,cmd) self.lib.lammps_command(self.lmp,cmd)
if self.lib.lammps_has_error(self.lmp): if self.uses_exceptions and self.lib.lammps_has_error(self.lmp):
sb = create_string_buffer(100) sb = create_string_buffer(100)
self.lib.lammps_get_last_error_message(self.lmp, sb, 100) error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
raise Exception(sb.value.decode().strip()) error_msg = sb.value.decode().strip()
if error_type == 2:
raise MPIAbortException(error_msg)
raise Exception(error_msg)
def extract_global(self,name,type): def extract_global(self,name,type):
if name: name = name.encode() if name: name = name.encode()
@ -286,6 +300,14 @@ class lammps(object):
if name: name = name.encode() if name: name = name.encode()
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data) self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
@property
def uses_exceptions(self):
try:
if self.lib.lammps_has_error:
return True
except(AttributeError):
return False
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------

1
src/GPU/pair_eam_alloy_gpu.h
View File

@ -33,6 +33,7 @@ public:
void init_style(); void init_style();
double single(int, int, int, int, double, double, double, double &); double single(int, int, int, int, double, double, double, double &);
double memory_usage(); double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *); int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *); void unpack_forward_comm(int, int, double *);

1
src/GPU/pair_eam_fs_gpu.h
View File

@ -33,6 +33,7 @@ public:
void init_style(); void init_style();
double single(int, int, int, int, double, double, double, double &); double single(int, int, int, int, double, double, double, double &);
double memory_usage(); double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *); int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *); void unpack_forward_comm(int, int, double *);

1
src/GPU/pair_eam_gpu.h
View File

@ -34,6 +34,7 @@ class PairEAMGPU : public PairEAM {
void init_style(); void init_style();
double single(int, int, int, int, double, double, double, double &); double single(int, int, int, int, double, double, double, double &);
double memory_usage(); double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *); int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *); void unpack_forward_comm(int, int, double *);

1
src/KOKKOS/pair_eam_alloy_kokkos.h
View File

@ -61,6 +61,7 @@ class PairEAMAlloyKokkos : public PairEAM {
virtual ~PairEAMAlloyKokkos(); virtual ~PairEAMAlloyKokkos();
virtual void compute(int, int); virtual void compute(int, int);
void init_style(); void init_style();
void *extract(const char *, int &) { return NULL; }
void coeff(int, char **); void coeff(int, char **);
KOKKOS_INLINE_FUNCTION KOKKOS_INLINE_FUNCTION

1
src/KOKKOS/pair_eam_fs_kokkos.h
View File

@ -61,6 +61,7 @@ class PairEAMFSKokkos : public PairEAM {
virtual ~PairEAMFSKokkos(); virtual ~PairEAMFSKokkos();
virtual void compute(int, int); virtual void compute(int, int);
void init_style(); void init_style();
void *extract(const char *, int &) { return NULL; }
void coeff(int, char **); void coeff(int, char **);
KOKKOS_INLINE_FUNCTION KOKKOS_INLINE_FUNCTION

1
src/KOKKOS/pair_eam_kokkos.h
View File

@ -59,6 +59,7 @@ class PairEAMKokkos : public PairEAM {
virtual ~PairEAMKokkos(); virtual ~PairEAMKokkos();
virtual void compute(int, int); virtual void compute(int, int);
void init_style(); void init_style();
void *extract(const char *, int &) { return NULL; }
KOKKOS_INLINE_FUNCTION KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMPackForwardComm, const int&) const; void operator()(TagPairEAMPackForwardComm, const int&) const;

4
src/MANYBODY/pair_eam.cpp
View File

@ -54,6 +54,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
frho = NULL; frho = NULL;
rhor = NULL; rhor = NULL;
z2r = NULL; z2r = NULL;
scale = NULL;
frho_spline = NULL; frho_spline = NULL;
rhor_spline = NULL; rhor_spline = NULL;
@ -232,6 +233,7 @@ void PairEAM::compute(int eflag, int vflag)
if (eflag) { if (eflag) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi; if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi; if (eflag_atom) eatom[i] += phi;
} }
@ -306,7 +308,7 @@ void PairEAM::compute(int eflag, int vflag)
f[j][2] -= delz*fpair; f[j][2] -= delz*fpair;
} }
if (eflag) evdwl = phi; if (eflag) evdwl = scale[itype][jtype]*phi;
if (evflag) ev_tally(i,j,nlocal,newton_pair, if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz); evdwl,0.0,fpair,delx,dely,delz);
} }

2
src/MANYBODY/pair_eam.h
View File

@ -54,7 +54,7 @@ class PairEAM : public Pair {
void init_style(); void init_style();
double init_one(int, int); double init_one(int, int);
double single(int, int, int, int, double, double, double, double &); double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &); virtual void *extract(const char *, int &);
virtual int pack_forward_comm(int, int *, double *, int, int *); virtual int pack_forward_comm(int, int *, double *, int, int *);
virtual void unpack_forward_comm(int, int, double *); virtual void unpack_forward_comm(int, int, double *);

1432
src/MOLECULE/fix_cmap.cpp Normal file
View File

File diff suppressed because it is too large Load Diff

129
src/MOLECULE/fix_cmap.h Normal file
View File

@ -0,0 +1,129 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(cmap,FixCMAP)
#else
#ifndef LMP_FIX_CMAP_H
#define LMP_FIX_CMAP_H
#include "fix.h"
namespace LAMMPS_NS {
class FixCMAP : public Fix {
public:
FixCMAP(class LAMMPS *, int, char **);
~FixCMAP();
int setmask();
void init();
void setup(int);
void setup_pre_neighbor();
void min_setup(int);
void pre_neighbor();
void pre_reverse(int, int);
void post_force(int);
void post_force_respa(int, int, int);
void min_post_force(int);
double compute_scalar();
void read_data_header(char *);
void read_data_section(char *, int, char *, tagint);
bigint read_data_skip_lines(char *);
void write_data_header(FILE *, int);
void write_data_section_size(int, int &, int &);
void write_data_section_pack(int, double **);
void write_data_section_keyword(int, FILE *);
void write_data_section(int, FILE *, int, double **, int);
void write_restart(FILE *);
void restart(char *);
int pack_restart(int, double *);
void unpack_restart(int, int);
int size_restart(int);
int maxsize_restart();
void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
double memory_usage();
private:
int nprocs,me;
int newton_bond,eflag_caller;
int ctype,nlevels_respa;
int ncrosstermtypes,crossterm_per_atom,maxcrossterm;
int ncrosstermlist;
bigint ncmap;
int **crosstermlist;
int nmax_previous;
int *num_crossterm;
int **crossterm_type;
tagint **crossterm_atom1,**crossterm_atom2,**crossterm_atom3;
tagint **crossterm_atom4,**crossterm_atom5;
double E,dEdPhi,dEdPsi;
double ecmap;
double fcmap[4],cij[4][4];
double *g_axis;
// CMAP grid points obtained from external file
double ***cmapgrid;
// partial derivatives and cross-derivatives of the grid data
double ***d1cmapgrid,***d2cmapgrid,***d12cmapgrid;
// read map grid data
void read_grid_map(char *);
// read in CMAP cross terms from LAMMPS data file
void read_cmap_data(int, char *);
// pre-compute the partial and cross-derivatives of map grid points
void set_map_derivatives(double **, double **, double **, double **);
// cubic spline interpolation functions for derivatives of map grid points
void spline(double *, double *, int);
void spl_interpolate(double, double *, double *, double &, double &);
// calculate dihedral angles
double dihedral_angle_atan2(double, double, double, double, double, double,
double, double, double, double);
// calculate bicubic interpolation coefficient matrix c_ij
void bc_coeff(double *, double *, double *, double *);
// perform bicubic interpolation at point of interest
void bc_interpol(double, double, int, int, double *, double *, double *,
double *);
};
}
#endif
#endif

7
src/OPT/pair_eam_opt.cpp
View File

@ -247,6 +247,7 @@ void PairEAMOpt::eval()
if (EFLAG) { if (EFLAG) {
double phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; double phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi; if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi; if (eflag_atom) eatom[i] += phi;
} }
@ -273,6 +274,7 @@ void PairEAMOpt::eval()
double tmpfz = 0.0; double tmpfz = 0.0;
fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr]; fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr];
double* _noalias scale_i = scale[itype1+1]+1;
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
j = jlist[jj]; j = jlist[jj];
@ -316,12 +318,13 @@ void PairEAMOpt::eval()
// psip needs both fp[i] and fp[j] terms since r_ij appears in two // psip needs both fp[i] and fp[j] terms since r_ij appears in two
// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji) // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
// scale factor can be applied by thermodynamic integration
double recip = 1.0/r; double recip = 1.0/r;
double phi = z2*recip; double phi = z2*recip;
double phip = z2p*recip - phi*recip; double phip = z2p*recip - phi*recip;
double psip = fp[i]*rhojp + fp[j]*rhoip + phip; double psip = fp[i]*rhojp + fp[j]*rhoip + phip;
double fpair = -psip*recip; double fpair = -scale_i[jtype]*psip*recip;
tmpfx += delx*fpair; tmpfx += delx*fpair;
tmpfy += dely*fpair; tmpfy += dely*fpair;
@ -332,7 +335,7 @@ void PairEAMOpt::eval()
ff[j].z -= delz*fpair; ff[j].z -= delz*fpair;
} }
if (EFLAG) evdwl = phi; if (EFLAG) evdwl = scale_i[jtype]*phi;
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR, if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz); evdwl,0.0,fpair,delx,dely,delz);

3
src/Purge.list
View File

@ -13,6 +13,9 @@ style_kspace.h
style_minimize.h style_minimize.h
style_pair.h style_pair.h
style_region.h style_region.h
# deleted on 20 Sep 2016
fix_ti_rs.cpp
fix_ti_rs.h
# deleted on 31 May 2016 # deleted on 31 May 2016
fix_ave_spatial_sphere.cpp fix_ave_spatial_sphere.cpp
fix_ave_spatial_sphere.h fix_ave_spatial_sphere.h

64
src/USER-MISC/fix_ti_spring.cpp
View File

@ -18,8 +18,8 @@
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "stdlib.h" #include <stdlib.h>
#include "string.h" #include <string.h>
#include "fix_ti_spring.h" #include "fix_ti_spring.h"
#include "atom.h" #include "atom.h"
#include "update.h" #include "update.h"
@ -27,12 +27,13 @@
#include "respa.h" #include "respa.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "citeme.h"
#include "force.h" #include "force.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
static const char cite_ti_spring[] = static const char cite_fix_ti_spring[] =
"ti/spring command:\n\n" "ti/spring command:\n\n"
"@article{freitas2016,\n" "@article{freitas2016,\n"
" author={Freitas, Rodrigo and Asta, Mark and de Koning, Maurice},\n" " author={Freitas, Rodrigo and Asta, Mark and de Koning, Maurice},\n"
@ -49,6 +50,8 @@ static const char cite_ti_spring[] =
FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) : FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) Fix(lmp, narg, arg)
{ {
if (lmp->citeme) lmp->citeme->add(cite_fix_ti_spring);
if (narg < 6 || narg > 8) if (narg < 6 || narg > 8)
error->all(FLERR,"Illegal fix ti/spring command"); error->all(FLERR,"Illegal fix ti/spring command");
@ -62,22 +65,25 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1; extscalar = 1;
extvector = 1; extvector = 1;
// disallow resetting the time step, while this fix is defined
time_depend = 1;
// Spring constant. // Spring constant.
k = force->numeric(FLERR,arg[3]); k = force->numeric(FLERR,arg[3]);
if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command"); if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
// Perform initial allocation of atom-based array. // Perform initial allocation of atom-based array
// Registar with Atom class. // Register with Atom class
xoriginal = NULL; xoriginal = NULL;
grow_arrays(atom->nmax); grow_arrays(atom->nmax);
atom->add_callback(0); atom->add_callback(0);
atom->add_callback(1); atom->add_callback(1);
// xoriginal = initial unwrapped positions of atom. // xoriginal = initial unwrapped positions of atoms
double **x = atom->x; double **x = atom->x;
int *mask = atom->mask; int *mask = atom->mask;
tagint *image = atom->image; imageint *image = atom->image;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
@ -86,16 +92,16 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
} }
// Time variables. // Time variables.
t_switch = atoi(arg[4]); // Switching time. t0 = update->ntimestep; // timestep of original/starting coordinates
t_equil = atoi(arg[5]); // Equilibration time. t_switch = force->bnumeric(FLERR,arg[4]); // Number of steps for switching
t0 = update->ntimestep; // Initial time. t_equil = force->bnumeric(FLERR,arg[5]); // Number of steps for equilibration
if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/spring command"); if ((t_switch <= 0) || (t_equil < 0))
if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/spring command"); error->all(FLERR,"Illegal fix ti/spring command");
// Coupling parameter initialization. // Coupling parameter initialization
sf = 1; sf = 1;
if (narg > 6) { if (narg > 6) {
if (strcmp(arg[6], "function") == 0) sf = atoi(arg[7]); if (strcmp(arg[6], "function") == 0) sf = force->inumeric(FLERR,arg[7]);
else error->all(FLERR,"Illegal fix ti/spring switching function"); else error->all(FLERR,"Illegal fix ti/spring switching function");
if ((sf!=1) && (sf!=2)) if ((sf!=1) && (sf!=2))
error->all(FLERR,"Illegal fix ti/spring switching function"); error->all(FLERR,"Illegal fix ti/spring switching function");
@ -163,14 +169,13 @@ void FixTISpring::min_setup(int vflag)
void FixTISpring::post_force(int vflag) void FixTISpring::post_force(int vflag)
{ {
// If on the first equilibration do not calculate forces. // do not calculate forces during equilibration
int t = update->ntimestep - t0; if ((update->ntimestep - t0) < t_equil) return;
if(t < t_equil) return;
double **x = atom->x; double **x = atom->x;
double **f = atom->f; double **f = atom->f;
int *mask = atom->mask; int *mask = atom->mask;
tagint *image = atom->image; imageint *image = atom->image;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
double dx, dy, dz; double dx, dy, dz;
@ -211,17 +216,20 @@ void FixTISpring::min_post_force(int vflag)
void FixTISpring::initial_integrate(int vflag) void FixTISpring::initial_integrate(int vflag)
{ {
// Update the coupling parameter value. // Update the coupling parameter value if needed
double t = update->ntimestep - (t0+t_equil); if ((update->ntimestep - t0) < t_equil) return;
if( (t >= 0) && (t <= t_switch) ) { const bigint t = update->ntimestep - (t0+t_equil);
lambda = switch_func(t/t_switch); const double r_switch = 1.0/t_switch;
dlambda = dswitch_func(t/t_switch);
if ( (t >= 0) && (t <= t_switch) ) {
lambda = switch_func(t*r_switch);
dlambda = dswitch_func(t*r_switch);
} }
if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) { if ( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
lambda = switch_func(1.0 - (t - t_switch - t_equil)/t_switch ); lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch);
dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch ); dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch);
} }
} }
@ -352,7 +360,7 @@ int FixTISpring::size_restart(int nlocal)
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Switching function. Switching function
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
double FixTISpring::switch_func(double t) double FixTISpring::switch_func(double t)
@ -365,7 +373,7 @@ double FixTISpring::switch_func(double t)
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Switching function derivative. Switching function derivative
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
double FixTISpring::dswitch_func(double t) double FixTISpring::dswitch_func(double t)

6
src/USER-MISC/fix_ti_spring.h
View File

@ -66,9 +66,9 @@ class FixTISpring : public Fix {
double lambda; // Coupling parameter. double lambda; // Coupling parameter.
double dlambda; // Lambda variation with t. double dlambda; // Lambda variation with t.
double linfo[2]; // Current lambda status. double linfo[2]; // Current lambda status.
int t_switch; // Total switching steps. bigint t_switch; // Total switching steps.
int t_equil; // Equilibration time. bigint t_equil; // Equilibration time.
int t0; // Initial time. bigint t0; // Initial time.
int sf; // Switching function option. int sf; // Switching function option.
int nlevels_respa; int nlevels_respa;
}; };

2
src/USER-MISC/pair_cdeam.h
View File

@ -49,6 +49,8 @@ public:
/// Reports the memory usage of this pair style to LAMMPS. /// Reports the memory usage of this pair style to LAMMPS.
double memory_usage(); double memory_usage();
void *extract(const char *, int &) { return NULL; }
/// Parses the coefficients of the h polynomial from the end of the EAM file. /// Parses the coefficients of the h polynomial from the end of the EAM file.
void read_h_coeff(char* filename); void read_h_coeff(char* filename);

7
src/USER-OMP/pair_eam_omp.cpp
View File

@ -203,7 +203,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
if (EFLAG) { if (EFLAG) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, phi, 0.0, thr); e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, scale[type[i]][type[i]]*phi, 0.0, thr);
} }
} }
@ -230,6 +230,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
ztmp = x[i].z; ztmp = x[i].z;
itype = type[i]; itype = type[i];
fxtmp = fytmp = fztmp = 0.0; fxtmp = fytmp = fztmp = 0.0;
const double * _noalias const scale_i = scale[itype];
jlist = firstneigh[i]; jlist = firstneigh[i];
jnum = numneigh[i]; jnum = numneigh[i];
@ -274,7 +275,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
phi = z2*recip; phi = z2*recip;
phip = z2p*recip - phi*recip; phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip; psip = fp[i]*rhojp + fp[j]*rhoip + phip;
fpair = -psip*recip; fpair = -scale_i[jtype]*psip*recip;
fxtmp += delx*fpair; fxtmp += delx*fpair;
fytmp += dely*fpair; fytmp += dely*fpair;
@ -285,7 +286,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j].z -= delz*fpair; f[j].z -= delz*fpair;
} }
if (EFLAG) evdwl = phi; if (EFLAG) evdwl = scale_i[jtype]*phi;
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR, if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz,thr); evdwl,0.0,fpair,delx,dely,delz,thr);
} }

27
src/error.cpp
View File

@ -22,7 +22,12 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
Error::Error(LAMMPS *lmp) : Pointers(lmp), last_error_message(NULL) {} Error::Error(LAMMPS *lmp) : Pointers(lmp) {
#ifdef LAMMPS_EXCEPTIONS
last_error_message = NULL;
last_error_type = ERROR_NONE;
#endif
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
called by all procs in universe called by all procs in universe
@ -198,6 +203,7 @@ void Error::done(int status)
exit(status); exit(status);
} }
#ifdef LAMMPS_EXCEPTIONS
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
return the last error message reported by LAMMPS (only used if return the last error message reported by LAMMPS (only used if
compiled with -DLAMMPS_EXCEPTIONS) compiled with -DLAMMPS_EXCEPTIONS)
@ -208,13 +214,22 @@ char * Error::get_last_error() const
return last_error_message; return last_error_message;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
set the last error message (only used if compiled with return the type of the last error reported by LAMMPS (only used if
-DLAMMPS_EXCEPTIONS) compiled with -DLAMMPS_EXCEPTIONS)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Error::set_last_error(const char * msg) ErrorType Error::get_last_error_type() const
{
return last_error_type;
}
/* ----------------------------------------------------------------------
set the last error message and error type
(only used if compiled with -DLAMMPS_EXCEPTIONS)
------------------------------------------------------------------------- */
void Error::set_last_error(const char * msg, ErrorType type)
{ {
delete [] last_error_message; delete [] last_error_message;
@ -224,4 +239,6 @@ void Error::set_last_error(const char * msg)
} else { } else {
last_error_message = NULL; last_error_message = NULL;
} }
last_error_type = type;
} }
#endif

46
src/error.h
View File

@ -15,41 +15,14 @@
#define LMP_ERROR_H #define LMP_ERROR_H
#include "pointers.h" #include "pointers.h"
#include <string>
#include <exception> #ifdef LAMMPS_EXCEPTIONS
#include "exceptions.h"
#endif
namespace LAMMPS_NS { namespace LAMMPS_NS {
class LAMMPSException : public std::exception
{
public:
std::string message;
LAMMPSException(std::string msg) : message(msg) {
}
~LAMMPSException() throw() {
}
virtual const char * what() const throw() {
return message.c_str();
}
};
class LAMMPSAbortException : public LAMMPSException {
public:
MPI_Comm universe;
LAMMPSAbortException(std::string msg, MPI_Comm universe) :
LAMMPSException(msg),
universe(universe)
{
}
};
class Error : protected Pointers { class Error : protected Pointers {
char * last_error_message;
public: public:
Error(class LAMMPS *); Error(class LAMMPS *);
@ -63,8 +36,15 @@ class Error : protected Pointers {
void message(const char *, int, const char *, int = 1); void message(const char *, int, const char *, int = 1);
void done(int = 0); // 1 would be fully backwards compatible void done(int = 0); // 1 would be fully backwards compatible
char * get_last_error() const; #ifdef LAMMPS_EXCEPTIONS
void set_last_error(const char * msg); char * get_last_error() const;
ErrorType get_last_error_type() const;
void set_last_error(const char * msg, ErrorType type = ERROR_NORMAL);
private:
char * last_error_message;
ErrorType last_error_type;
#endif
}; };
} }

58
src/exceptions.h Normal file
View File

@ -0,0 +1,58 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_EXCEPTIONS_H
#define LMP_EXCEPTIONS_H
#include <mpi.h>
#include <string>
#include <exception>
namespace LAMMPS_NS {
class LAMMPSException : public std::exception
{
public:
std::string message;
LAMMPSException(std::string msg) : message(msg) {
}
~LAMMPSException() throw() {
}
virtual const char * what() const throw() {
return message.c_str();
}
};
class LAMMPSAbortException : public LAMMPSException {
public:
MPI_Comm universe;
LAMMPSAbortException(std::string msg, MPI_Comm universe) :
LAMMPSException(msg),
universe(universe)
{
}
};
enum ErrorType {
ERROR_NONE = 0,
ERROR_NORMAL = 1,
ERROR_ABORT = 2
};
}
#endif

2
src/fix.cpp
View File

@ -139,7 +139,7 @@ void Fix::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"respa") == 0) { } else if (strcmp(arg[iarg],"respa") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command"); if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (!respa_level_support) error->all(FLERR,"Illegal fix_modify command"); if (!respa_level_support) error->all(FLERR,"Illegal fix_modify command");
int lvl = force->inumeric(FLERR,arg[1]); int lvl = force->inumeric(FLERR,arg[iarg+1]);
if (lvl < 0) error->all(FLERR,"Illegal fix_modify command"); if (lvl < 0) error->all(FLERR,"Illegal fix_modify command");
respa_level = lvl-1; respa_level = lvl-1;
iarg += 2; iarg += 2;

6
src/fix_move.cpp
View File

@ -48,8 +48,10 @@ enum{EQUAL,ATOM};
FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), Fix(lmp, narg, arg),
xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL), vyvarstr(NULL), vzvarstr(NULL), xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL),
xoriginal(NULL), toriginal(NULL), qoriginal(NULL), displace(NULL), velocity(NULL) vyvarstr(NULL), vzvarstr(NULL),
xoriginal(NULL), toriginal(NULL), qoriginal(NULL),
displace(NULL), velocity(NULL)
{ {
if (narg < 4) error->all(FLERR,"Illegal fix move command"); if (narg < 4) error->all(FLERR,"Illegal fix move command");

3
src/fix_nh.cpp
View File

@ -54,7 +54,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
tstat_flag(0), pstat_flag(0), tstat_flag(0), pstat_flag(0),
rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL), rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL),
tcomputeflag(0), pcomputeflag(0), eta(NULL), eta_dot(NULL), eta_dotdot(NULL), tcomputeflag(0), pcomputeflag(0), eta(NULL), eta_dot(NULL), eta_dotdot(NULL),
eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL), etap_mass(NULL), mpchain(0) eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL),
etap_mass(NULL), mpchain(0)
{ {
if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command"); if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command");

16
src/fix_store.cpp
View File

@ -40,6 +40,7 @@ vstore(NULL), astore(NULL), rbuf(NULL)
// 0/1 flag = not-store or store peratom values in restart file // 0/1 flag = not-store or store peratom values in restart file
// nvalues = # of peratom values, N = 1 is vector, N > 1 is array // nvalues = # of peratom values, N = 1 is vector, N > 1 is array
disable = 0;
nvalues = vecflag = 0; nvalues = vecflag = 0;
flavor = UNKNOWN; flavor = UNKNOWN;
@ -230,6 +231,8 @@ void FixStore::grow_arrays(int nmax)
void FixStore::copy_arrays(int i, int j, int delflag) void FixStore::copy_arrays(int i, int j, int delflag)
{ {
if (disable) return;
if (vecflag) vstore[j] = vstore[i]; if (vecflag) vstore[j] = vstore[i];
else else
for (int m = 0; m < nvalues; m++) for (int m = 0; m < nvalues; m++)
@ -242,6 +245,8 @@ void FixStore::copy_arrays(int i, int j, int delflag)
int FixStore::pack_exchange(int i, double *buf) int FixStore::pack_exchange(int i, double *buf)
{ {
if (disable) return 0;
if (vecflag) buf[0] = vstore[i]; if (vecflag) buf[0] = vstore[i];
else else
for (int m = 0; m < nvalues; m++) for (int m = 0; m < nvalues; m++)
@ -255,6 +260,8 @@ int FixStore::pack_exchange(int i, double *buf)
int FixStore::unpack_exchange(int nlocal, double *buf) int FixStore::unpack_exchange(int nlocal, double *buf)
{ {
if (disable) return 0;
if (vecflag) vstore[nlocal] = buf[0]; if (vecflag) vstore[nlocal] = buf[0];
else else
for (int m = 0; m < nvalues; m++) for (int m = 0; m < nvalues; m++)
@ -268,6 +275,11 @@ int FixStore::unpack_exchange(int nlocal, double *buf)
int FixStore::pack_restart(int i, double *buf) int FixStore::pack_restart(int i, double *buf)
{ {
if (disable) {
buf[0] = 0;
return 1;
}
buf[0] = nvalues+1; buf[0] = nvalues+1;
if (vecflag) buf[1] = vstore[i]; if (vecflag) buf[1] = vstore[i];
else else
@ -282,6 +294,8 @@ int FixStore::pack_restart(int i, double *buf)
void FixStore::unpack_restart(int nlocal, int nth) void FixStore::unpack_restart(int nlocal, int nth)
{ {
if (disable) return;
double **extra = atom->extra; double **extra = atom->extra;
// skip to Nth set of extra values // skip to Nth set of extra values
@ -302,6 +316,7 @@ void FixStore::unpack_restart(int nlocal, int nth)
int FixStore::maxsize_restart() int FixStore::maxsize_restart()
{ {
if (disable) return 1;
return nvalues+1; return nvalues+1;
} }
@ -311,6 +326,7 @@ int FixStore::maxsize_restart()
int FixStore::size_restart(int nlocal) int FixStore::size_restart(int nlocal)
{ {
if (disable) return 1;
return nvalues+1; return nvalues+1;
} }

1
src/fix_store.h
View File

@ -31,6 +31,7 @@ class FixStore : public Fix {
int nvalues; // number of per-atom values int nvalues; // number of per-atom values
double *vstore; // vector storage for GLOBAL or PERATOM double *vstore; // vector storage for GLOBAL or PERATOM
double **astore; // array storage for GLOBAL or PERATOM double **astore; // array storage for GLOBAL or PERATOM
int disable; // 1 if operations (except grow) are currently disabled
FixStore(class LAMMPS *, int, char **); FixStore(class LAMMPS *, int, char **);
~FixStore(); ~FixStore();

557
src/library.cpp
View File

@ -38,6 +38,45 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
Utility macros for optional code path which captures all exceptions
and stores the last error message. These assume there is a variable lmp
which is a pointer to the current LAMMPS instance.
Usage:
BEGIN_CAPTURE
{
// code paths which might throw exception
...
}
END_CAPTURE
------------------------------------------------------------------------- */
#ifdef LAMMPS_EXCEPTIONS
#define BEGIN_CAPTURE \
Error * error = lmp->error; \
try
#define END_CAPTURE \
catch(LAMMPSAbortException & ae) { \
int nprocs = 0; \
MPI_Comm_size(ae.universe, &nprocs ); \
\
if (nprocs > 1) { \
error->set_last_error(ae.message.c_str(), ERROR_ABORT); \
} else { \
error->set_last_error(ae.message.c_str(), ERROR_NORMAL); \
} \
} catch(LAMMPSException & e) { \
error->set_last_error(e.message.c_str(), ERROR_NORMAL); \
}
#else
#define BEGIN_CAPTURE
#define END_CAPTURE
#endif
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
create an instance of LAMMPS and return pointer to it create an instance of LAMMPS and return pointer to it
pass in command-line args and MPI communicator to run on pass in command-line args and MPI communicator to run on
@ -45,8 +84,20 @@ using namespace LAMMPS_NS;
void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr) void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
{ {
#ifdef LAMMPS_EXCEPTIONS
try
{
LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp;
}
catch(LAMMPSException & e) {
fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
*ptr = (void*) NULL;
}
#else
LAMMPS *lmp = new LAMMPS(argc,argv,communicator); LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp; *ptr = (void *) lmp;
#endif
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -68,8 +119,20 @@ void lammps_open_no_mpi(int argc, char **argv, void **ptr)
MPI_Comm communicator = MPI_COMM_WORLD; MPI_Comm communicator = MPI_COMM_WORLD;
#ifdef LAMMPS_EXCEPTIONS
try
{
LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp;
}
catch(LAMMPSException & e) {
fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
*ptr = (void*) NULL;
}
#else
LAMMPS *lmp = new LAMMPS(argc,argv,communicator); LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp; *ptr = (void *) lmp;
#endif
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -99,7 +162,12 @@ int lammps_version(void *ptr)
void lammps_file(void *ptr, char *str) void lammps_file(void *ptr, char *str)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
lmp->input->file(str);
BEGIN_CAPTURE
{
lmp->input->file(str);
}
END_CAPTURE
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -108,15 +176,16 @@ void lammps_file(void *ptr, char *str)
char *lammps_command(void *ptr, char *str) char *lammps_command(void *ptr, char *str)
{ {
LAMMPS * lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
Error * error = lmp->error; char * result = NULL;
try { BEGIN_CAPTURE
return lmp->input->one(str); {
} catch(LAMMPSException & e) { result = lmp->input->one(str);
error->set_last_error(e.message.c_str());
return NULL;
} }
END_CAPTURE
return result;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -215,58 +284,62 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id); BEGIN_CAPTURE
if (icompute < 0) return NULL; {
Compute *compute = lmp->modify->compute[icompute]; int icompute = lmp->modify->find_compute(id);
if (icompute < 0) return NULL;
Compute *compute = lmp->modify->compute[icompute];
if (style == 0) { if (style == 0) {
if (type == 0) { if (type == 0) {
if (!compute->scalar_flag) return NULL; if (!compute->scalar_flag) return NULL;
if (compute->invoked_scalar != lmp->update->ntimestep) if (compute->invoked_scalar != lmp->update->ntimestep)
compute->compute_scalar(); compute->compute_scalar();
return (void *) &compute->scalar; return (void *) &compute->scalar;
}
if (type == 1) {
if (!compute->vector_flag) return NULL;
if (compute->invoked_vector != lmp->update->ntimestep)
compute->compute_vector();
return (void *) compute->vector;
}
if (type == 2) {
if (!compute->array_flag) return NULL;
if (compute->invoked_array != lmp->update->ntimestep)
compute->compute_array();
return (void *) compute->array;
}
} }
if (type == 1) {
if (!compute->vector_flag) return NULL; if (style == 1) {
if (compute->invoked_vector != lmp->update->ntimestep) if (!compute->peratom_flag) return NULL;
compute->compute_vector(); if (type == 1) {
return (void *) compute->vector; if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
} }
if (type == 2) {
if (!compute->array_flag) return NULL; if (style == 2) {
if (compute->invoked_array != lmp->update->ntimestep) if (!compute->local_flag) return NULL;
compute->compute_array(); if (type == 1) {
return (void *) compute->array; if (compute->invoked_local != lmp->update->ntimestep)
} compute->compute_local();
} return (void *) compute->vector_local;
}
if (style == 1) { if (type == 2) {
if (!compute->peratom_flag) return NULL; if (compute->invoked_local != lmp->update->ntimestep)
if (type == 1) { compute->compute_local();
if (compute->invoked_peratom != lmp->update->ntimestep) return (void *) compute->array_local;
compute->compute_peratom(); }
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
}
if (style == 2) {
if (!compute->local_flag) return NULL;
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->vector_local;
}
if (type == 2) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->array_local;
} }
} }
END_CAPTURE
return NULL; return NULL;
} }
@ -300,40 +373,44 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id); BEGIN_CAPTURE
if (ifix < 0) return NULL; {
Fix *fix = lmp->modify->fix[ifix]; int ifix = lmp->modify->find_fix(id);
if (ifix < 0) return NULL;
Fix *fix = lmp->modify->fix[ifix];
if (style == 0) { if (style == 0) {
double *dptr = (double *) malloc(sizeof(double)); double *dptr = (double *) malloc(sizeof(double));
if (type == 0) { if (type == 0) {
if (!fix->scalar_flag) return NULL; if (!fix->scalar_flag) return NULL;
*dptr = fix->compute_scalar(); *dptr = fix->compute_scalar();
return (void *) dptr; return (void *) dptr;
}
if (type == 1) {
if (!fix->vector_flag) return NULL;
*dptr = fix->compute_vector(i);
return (void *) dptr;
}
if (type == 2) {
if (!fix->array_flag) return NULL;
*dptr = fix->compute_array(i,j);
return (void *) dptr;
}
} }
if (type == 1) {
if (!fix->vector_flag) return NULL; if (style == 1) {
*dptr = fix->compute_vector(i); if (!fix->peratom_flag) return NULL;
return (void *) dptr; if (type == 1) return (void *) fix->vector_atom;
if (type == 2) return (void *) fix->array_atom;
} }
if (type == 2) {
if (!fix->array_flag) return NULL; if (style == 2) {
*dptr = fix->compute_array(i,j); if (!fix->local_flag) return NULL;
return (void *) dptr; if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
} }
} }
END_CAPTURE
if (style == 1) {
if (!fix->peratom_flag) return NULL;
if (type == 1) return (void *) fix->vector_atom;
if (type == 2) return (void *) fix->array_atom;
}
if (style == 2) {
if (!fix->local_flag) return NULL;
if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
}
return NULL; return NULL;
} }
@ -369,23 +446,27 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
int ivar = lmp->input->variable->find(name); BEGIN_CAPTURE
if (ivar < 0) return NULL; {
int ivar = lmp->input->variable->find(name);
if (ivar < 0) return NULL;
if (lmp->input->variable->equalstyle(ivar)) { if (lmp->input->variable->equalstyle(ivar)) {
double *dptr = (double *) malloc(sizeof(double)); double *dptr = (double *) malloc(sizeof(double));
*dptr = lmp->input->variable->compute_equal(ivar); *dptr = lmp->input->variable->compute_equal(ivar);
return (void *) dptr; return (void *) dptr;
} }
if (lmp->input->variable->atomstyle(ivar)) { if (lmp->input->variable->atomstyle(ivar)) {
int igroup = lmp->group->find(group); int igroup = lmp->group->find(group);
if (igroup < 0) return NULL; if (igroup < 0) return NULL;
int nlocal = lmp->atom->nlocal; int nlocal = lmp->atom->nlocal;
double *vector = (double *) malloc(nlocal*sizeof(double)); double *vector = (double *) malloc(nlocal*sizeof(double));
lmp->input->variable->compute_atom(ivar,igroup,vector,1,0); lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
return (void *) vector; return (void *) vector;
}
} }
END_CAPTURE
return NULL; return NULL;
} }
@ -399,7 +480,14 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
int lammps_set_variable(void *ptr, char *name, char *str) int lammps_set_variable(void *ptr, char *name, char *str)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
int err = lmp->input->variable->set_string(name,str); int err = -1;
BEGIN_CAPTURE
{
err = lmp->input->variable->set_string(name,str);
}
END_CAPTURE
return err; return err;
} }
@ -414,9 +502,14 @@ int lammps_set_variable(void *ptr, char *name, char *str)
double lammps_get_thermo(void *ptr, char *name) double lammps_get_thermo(void *ptr, char *name)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
double dval; double dval = 0.0;
BEGIN_CAPTURE
{
lmp->output->thermo->evaluate_keyword(name,&dval);
}
END_CAPTURE
lmp->output->thermo->evaluate_keyword(name,&dval);
return dval; return dval;
} }
@ -449,79 +542,83 @@ void lammps_gather_atoms(void *ptr, char *name,
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
// error if tags are not defined or not consecutive BEGIN_CAPTURE
{
// error if tags are not defined or not consecutive
int flag = 0; int flag = 0;
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1; if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms"); lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
return; return;
}
int natoms = static_cast<int> (lmp->atom->natoms);
int i,j,offset;
void *vptr = lmp->atom->extract(name);
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1)
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
else
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][0];
}
MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
} else {
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][j];
}
} }
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world); int natoms = static_cast<int> (lmp->atom->natoms);
lmp->memory->destroy(copy);
int i,j,offset;
void *vptr = lmp->atom->extract(name);
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1)
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
else
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][0];
}
MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
} else {
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][j];
}
}
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
}
} }
END_CAPTURE
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -538,69 +635,74 @@ void lammps_scatter_atoms(void *ptr, char *name,
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
// error if tags are not defined or not consecutive or no atom map BEGIN_CAPTURE
{
// error if tags are not defined or not consecutive or no atom map
int flag = 0; int flag = 0;
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1; if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == 0) flag = 1; if (lmp->atom->map_style == 0) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms"); lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms");
return; return;
}
int natoms = static_cast<int> (lmp->atom->natoms);
int i,j,m,offset;
void *vptr = lmp->atom->extract(name);
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *dptr = (int *) data;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
} }
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *dptr = (double *) data;
if (count == 1) { int natoms = static_cast<int> (lmp->atom->natoms);
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0) int i,j,m,offset;
vector[m] = dptr[i]; void *vptr = lmp->atom->extract(name);
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *dptr = (int *) data;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
}
} else { } else {
for (i = 0; i < natoms; i++) { double *vector = NULL;
if ((m = lmp->atom->map(i+1)) >= 0) { double **array = NULL;
offset = count*i; if (count == 1) vector = (double *) vptr;
for (j = 0; j < count; j++) else array = (double **) vptr;
array[m][j] = dptr[offset++]; double *dptr = (double *) data;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++) {
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
} }
} }
} }
} }
END_CAPTURE
} }
#ifdef LAMMPS_EXCEPTIONS
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Check if a new error message Check if a new error message
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -613,6 +715,9 @@ int lammps_has_error(void *ptr) {
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Copy the last error message of LAMMPS into a character buffer Copy the last error message of LAMMPS into a character buffer
The return value encodes which type of error it is.
1 = normal error (recoverable)
2 = abort error (non-recoverable)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) { int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
@ -620,9 +725,11 @@ int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
Error * error = lmp->error; Error * error = lmp->error;
if(error->get_last_error()) { if(error->get_last_error()) {
int error_type = error->get_last_error_type();
strncpy(buffer, error->get_last_error(), buffer_size-1); strncpy(buffer, error->get_last_error(), buffer_size-1);
error->set_last_error(NULL); error->set_last_error(NULL, ERROR_NONE);
return 1; return error_type;
} }
return 0; return 0;
} }
#endif

2
src/library.h
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@ -45,8 +45,10 @@ int lammps_get_natoms(void *);
void lammps_gather_atoms(void *, char *, int, int, void *); void lammps_gather_atoms(void *, char *, int, int, void *);
void lammps_scatter_atoms(void *, char *, int, int, void *); void lammps_scatter_atoms(void *, char *, int, int, void *);
#ifdef LAMMPS_EXCEPTIONS
int lammps_has_error(void *); int lammps_has_error(void *);
int lammps_get_last_error_message(void *, char *, int); int lammps_get_last_error_message(void *, char *, int);
#endif
#ifdef __cplusplus #ifdef __cplusplus
} }

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "20 Sep 2016" #define LAMMPS_VERSION "26 Sep 2016"

68
tools/ch2lmp/README
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@ -13,33 +13,38 @@ In this directory, you should find:
In addition, you will need to provide the following input for In addition, you will need to provide the following input for
charmm2lammps.pl: charmm2lammps.pl:
1) a CHARMM parameter file (par_<forcefield>.prm) 1) a CHARMM parameter file (par_<forcefield>.prm)
2) a CHARMM topology file (top_<forcefield>.rtf) 2) a CHARMM topology file (top_<forcefield>.rtf)
3) a CHARMM coordinates file or pdb file (<project>.crd or <project>.pdb) 3) a CHARMM coordinates file or pdb file (<project>.crd or <project>.pdb)
(NOTE: a .pdb file is required if the -cmap option is used)
4) a CHARMM psf file (<project>.psf) 4) a CHARMM psf file (<project>.psf)
To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl
[-option[=#]] <forcefield> <project>" where <forcefield> is the name <forcefield> <project> [-option=value ...]" where <forcefield> is the
of the CHARMM FF you are using, (i.e. all22_prot), and <project> is name of the CHARMM FF you are using, (i.e. all22_prot), and <project>
the common name of your *.crd and *.psf files. The options for the is the common name of your *.crd and *.psf files. Possible options
script are listed below. If the option requires a parameter, the are listed next. If the option requires a parameter, the syntax
syntax must be [-option[=#]], (i.e. -border=5). should be -option=value (e.g. -border=5).
-help "display available options", -help display available options
-charmm "add charmm types to LAMMPS data file", -charmm add charmm types to LAMMPS data file
-water "add TIP3P water [default: 1 g/cc]", -water add TIP3P water [default: 1 g/cc]
-ions "add (counter)ions using Na+ and Cl- [default: 0 mol/l]", -ions add (counter)ions using Na+ and Cl- [default: 0 mol/l]
-center "recenter atoms", -center recenter atoms
-quiet "do not print info", -quiet do not print info
-pdb_ctrl "output project_ctrl.pdb", -pdb_ctrl output project_ctrl.pdb
-l "set x-, y-, and z-dimensions simultaneously", -l set x-, y-, and z-dimensions simultaneously
-lx "x-dimension of simulation box", -lx x-dimension of simulation box
-ly "y-dimension of simulation box", -ly y-dimension of simulation box
-lz "z-dimension of simulation box", -lz z-dimension of simulation box
-border "add border to all sides of simulation box [default: 0 A]", -border add border to all sides of simulation box [default: 0 A]
-ax "rotation around x-axis", -ax rotation around x-axis
-ay "rotation around y-axis", -ay rotation around y-axis
-az "rotation around z-axis" -az rotation around z-axis
-cd correction for dihedral for carbohydrate systems
-cmap add CMAP section to data file and fix cmap command lines in
input script" (NOTE: requires use of *.pdb file)
In the "example" folder, you will find example files that were created In the "example" folder, you will find example files that were created
by following the steps below. These steps describe how to take a by following the steps below. These steps describe how to take a
@ -102,6 +107,21 @@ can be visualized in a standard visualization package such as VMD. The
after the # sign is a comment) for user convenience in tracking atom after the # sign is a comment) for user convenience in tracking atom
types etc. according to CHARMM nomenclature. types etc. according to CHARMM nomenclature.
The example molecule provided above (i.e., 1ac7) is a DNA fragment.
If instead, a peptide longer than 2 amino acid residues or a protein
is to be modeled, the '-cmap' option should be used. This will add a
section at the end of the data file with the heading of 'CMAP' that
will contain cmap crossterm corrections for the phi-psi dihedrals for
the amino acid residues. You will then need to also copy the
appropriate file for the cmap crossterms into your directory and be
sure that you are using the appropriate cmap crossterms that go with
the respective version of the charmm force field that is being used
(e.g, cmap22.data or cmap36.data). This is necessary to account for
the fact that the CHARMM group has provided updated cmap correction
terms for use with the c36 and more recent version of the charmm
protein force field. Copies of cmap22.data and cmap36.data are
provided in the tools/ch2lmp directory.
The default timestep in the LAMMPS *.in file is set to 0.5 fs, which The default timestep in the LAMMPS *.in file is set to 0.5 fs, which
can typically be increased to 2 fs after equilibration if the bonds can typically be increased to 2 fs after equilibration if the bonds
involving H are constrained via shake. Also, after equilibration, the involving H are constrained via shake. Also, after equilibration, the
@ -109,9 +129,9 @@ delay on neigh_modify can probably increased to 5 or so to improve
speed. speed.
The -ions option allows the user to neutralize the simulation cell The -ions option allows the user to neutralize the simulation cell
with Na+ or Cl- counterions if the molecule has a net with Na+ or Cl- counterions if the molecule has a net charge
charge. Additional salt can be added by increasing the default Additional salt can be added by increasing the default concentration
concentration (i.e. -ions=0.5). (e.g. -ions=0.5).
** In the "other" file folder, you will find: ** In the "other" file folder, you will find:
@ -126,5 +146,3 @@ concentration (i.e. -ions=0.5).
3) A 3rd party perl script called "crd2pdb.pl" 3) A 3rd party perl script called "crd2pdb.pl"
4) A 3rd party fortran code called "pdb_to_crd.f" 4) A 3rd party fortran code called "pdb_to_crd.f"

1148
tools/ch2lmp/charmm2lammps.pl
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