jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8166 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-05-23 16:35:55 +00:00
parent 5ea3c4d23a
commit 032819687c
2 changed files with 238 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

124
doc/fix_colvars.html Normal file
View File

@ -0,0 +1,124 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix colvars command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID colvars configfile keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>colvars = style name of this fix command
<LI>configfile = the configuration file for the colvars module
<LI>keyword = <I>input</I> or <I>output</I> or <I>seed</I> or <I>tstat</I>
<PRE> <I>input</I> arg = colvars.state file name or prefix or NULL (default: NULL)
<I>output</I> arg = output filename prefix (default: out)
<I>seed</I> arg = seed for random number generator (default: 1966)
<I>tstat</I> arg = fix id of a thermostat or NULL (default: NULL)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
fix colvars all colvars.inp
</PRE>
<P><B>Description:</B>
</P>
<P>This fix interfaces LAMMPS to a "collective variables" or "colvars"
module library which allows to calculate potentials of mean force
(PMFs) for any set of colvars, using different sampling methods:
currently implemented are the Adaptive Biasing Force (ABF) method,
metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
(US) via a flexible harmonic restraint bias. This documentation
describes only the colvars fix itself and LAMMPS specific parts of the
code. The documentation of the colvars implementation itself is
available as part of the <A HREF = "http://www.ks.uiuc.edu/Research/namd/2.8/ug/node53.html">NAMD online
documentation</A>
</P>
<P>There are example scripts for using this package with LAMMPS in
examples/USER/colvars.
</P>
<P>The implementation of the portable collective variable library is also
documented in <A HREF = "#Henin">(Henin)</A>
</P>
<HR>
<P>The only mandatory argument to the fix is the filename to the colvars
input file that contains all input that is independent from the MD
program in which the colvars library has been integrated.
</P>
<P>The <I>group-ID</I> entry is ignored. The collective variable module will
always apply to the entire system, i.e. use the group <I>all</I>.
</P>
<P>The <I>input</I> keyword allows to specify a state file that would contain
the information required in order to continue a calculation, e.g.
from a restart. Setting it to NULL will start a new colvars run.
</P>
<P>The <I>output</I> keyword allows to specify the output prefix. All output
files generated will use this prefix followed by the ".colvars." and
a word like "state" or "traj".
</P>
<P>The <I>seed</I> keyword contains the seed for the random number generator
that will be used in the colvars module.
</P>
<P>The <I>tstat</I> keyword can be either NULL or the label of a thermostating
fix that thermostats all atoms in the fix colvars group. This will be
used to provide the colvars module with the current thermostat target
temperature.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change from the biasing force added by the fix
to the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>There can only be one colvars fix active at a time. Since the
colvars module itself can handle an arbitrary number of collective
variables and always applies to the entire system, this is not
really a deficit in practice.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_smd.html">fix smd</A>
</P>
<P><B>Default:</B>
</P>
<P>The default options are input = NULL, output = out, seed = 1966, and
tstat = NULL.
</P>
<HR>
<A NAME = "Henin"></A>
<P><B>(Henin)</B> Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
35-47 (2010)
</P>
</HTML>

114
doc/fix_colvars.txt Normal file
View File

@ -0,0 +1,114 @@
"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 colvars command :h3
[Syntax:]
fix ID group-ID colvars configfile keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
colvars = style name of this fix command :l
configfile = the configuration file for the colvars module :l
keyword = {input} or {output} or {seed} or {tstat} :l
{input} arg = colvars.state file name or prefix or NULL (default: NULL)
{output} arg = output filename prefix (default: out)
{seed} arg = seed for random number generator (default: 1966)
{tstat} arg = fix id of a thermostat or NULL (default: NULL) :pre
:ule
[Examples:]
fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
fix colvars all colvars.inp :pre
[Description:]
This fix interfaces LAMMPS to a "collective variables" or "colvars"
module library which allows to calculate potentials of mean force
(PMFs) for any set of colvars, using different sampling methods:
currently implemented are the Adaptive Biasing Force (ABF) method,
metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
(US) via a flexible harmonic restraint bias. This documentation
describes only the colvars fix itself and LAMMPS specific parts of the
code. The documentation of the colvars implementation itself is
available as part of the "NAMD online
documentation"_http://www.ks.uiuc.edu/Research/namd/2.8/ug/node53.html
There are example scripts for using this package with LAMMPS in
examples/USER/colvars.
The implementation of the portable collective variable library is also
documented in "(Henin)"_#Henin
:line
The only mandatory argument to the fix is the filename to the colvars
input file that contains all input that is independent from the MD
program in which the colvars library has been integrated.
The {group-ID} entry is ignored. The collective variable module will
always apply to the entire system, i.e. use the group {all}.
The {input} keyword allows to specify a state file that would contain
the information required in order to continue a calculation, e.g.
from a restart. Setting it to NULL will start a new colvars run.
The {output} keyword allows to specify the output prefix. All output
files generated will use this prefix followed by the ".colvars." and
a word like "state" or "traj".
The {seed} keyword contains the seed for the random number generator
that will be used in the colvars module.
The {tstat} keyword can be either NULL or the label of a thermostating
fix that thermostats all atoms in the fix colvars group. This will be
used to provide the colvars module with the current thermostat target
temperature.
[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 energy change from the biasing force added by the fix
to the 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
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
[Restrictions:]
This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
There can only be one colvars fix active at a time. Since the
colvars module itself can handle an arbitrary number of collective
variables and always applies to the entire system, this is not
really a deficit in practice.
[Related commands:]
"fix smd"_fix_smd.html
[Default:]
The default options are input = NULL, output = out, seed = 1966, and
tstat = NULL.
:line
:link(Henin)
[(Henin)] Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
35-47 (2010)