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sjplimp 2012-05-23 16:19:50 +00:00
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6
doc/Section_commands.html
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@ -356,9 +356,9 @@ of each style or click on the style itself for a full description:
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_reaxc_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
<TR ALIGN="center"><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_reaxc_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated fix styles, which can be used if LAMMPS is

1
doc/Section_commands.txt
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@ -495,6 +495,7 @@ package"_Section_start.html#start_3.
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"colvars"_fix_colvars.html,
"imd"_fix_imd.html,
"langevin/eff"_fix_langevin_eff.html,
"meso"_fix_meso.html,

38
doc/Section_packages.html
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@ -105,6 +105,7 @@ E.g. "peptide" refers to the examples/peptide directory.
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (2)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (3)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-EWALDN</TD><TD > Ewald for 1/R^n</TD><TD > Pieter in' t Veld (BASF)</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
@ -125,7 +126,12 @@ E.g. "peptide" refers to the examples/peptide directory.
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
</P>
<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia).
<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
</P>
<P>(3) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
@ -216,6 +222,36 @@ have questions.
</P>
<HR>
<H4>USER-COLVARS package
</H4>
<P>This package implements the "fix colvars" command which can be
used in a LAMMPS input script.
</P>
<P>This fix allows to use "collective variables" to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:
</P>
<UL><LI>A portable collective variable module library written and maintained by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS, Marseille, France). This code is located in the directory lib/colvars and needs to be compiled first.
<LI>The colvars fix and an interface layer, exchanges information between LAMMPS and the collective variable module.
</UL>
<P>See the doc page of <A HREF = "fix_colvars.html">fix colvars</A> for more details.
</P>
<P>There are example scripts for using this package in
examples/USER/colvars
</P>
<P>This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-CG-CMM package
</H4>
<P>This package implements 3 commands which can be used in a LAMMPS input

38
doc/Section_packages.txt
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@ -97,6 +97,7 @@ USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -,
USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (2), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_Section_accelerate.html#acc_4, USER/cuda, -, lib/cuda
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-EWALDN, Ewald for 1/R^n, Pieter in' t Veld (BASF), "kspace_style"_kspace_style.html, -, -, -
@ -113,7 +114,12 @@ USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
(2) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia).
(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
(3) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).
The "Doc page" column links to either a portion of the
"Section_howto"_Section_howto.html of the manual, or an input script
@ -204,6 +210,36 @@ have questions.
:line
USER-COLVARS package :h4
This package implements the "fix colvars" command which can be
used in a LAMMPS input script.
This fix allows to use "collective variables" to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:
A portable collective variable module library written and maintained by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS, Marseille, France). This code is located in the directory lib/colvars and needs to be compiled first.
The colvars fix and an interface layer, exchanges information between LAMMPS and the collective variable module. :ul
See the doc page of "fix colvars"_fix_colvars.html for more details.
There are example scripts for using this package in
examples/USER/colvars
This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-CG-CMM package :h4
This package implements 3 commands which can be used in a LAMMPS input