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fix typo and reformat

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Axel Kohlmeyer 2018-11-02 21:08:45 -04:00
parent ea9746f26d
commit b7e507a258
1 changed files with 60 additions and 47 deletions
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107
doc/src/fix_plumed.txt
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@ -12,82 +12,95 @@ fix plumed command :h3
fix ID group-ID plumed keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
plumed = style name of this fix command :1
keyword = {plumedfile} or {outfile} :1
ID, group-ID are documented in "fix"_fix.html command :ulb,l
plumed = style name of this fix command :l
keyword = {plumedfile} or {outfile} :l
{plumedfile} arg = name of PLUMED input file to use (default: NULL)
{outfile} arg = name of file on which to write the PLUMED log (default: NULL)
:ule
{outfile} arg = name of file on which to write the PLUMED log (default: NULL) :pre
:ule
[Examples:]
fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
[Description:]
This fix instructs LAMMPS to call the PLUMED library, which allows one
to perform various forms of trajectory analysis on the fly and to also use
methods such as umbrella sampling and metadynamics to enhance the sampling of
phase space.
This fix instructs LAMMPS to call the PLUMED library, which allows one
to perform various forms of trajectory analysis on the fly and to also
use methods such as umbrella sampling and metadynamics to enhance the
sampling of phase space.
The documentation included here only describes the fix plumed command. This command
is LAMMPS specific whereas most of the functionality implemented in PLUMED will work with a
range of MD codes and also when PLUMED is used as a stand alone code. The full documentation
for PLUMED is available at "this website"_http://www.plumed.org/documentation
The documentation included here only describes the fix plumed command.
This command is LAMMPS specific whereas most of the functionality
implemented in PLUMED will work with a range of MD codes and also when
PLUMED is used as a stand alone code. The full documentation for PLUMED
is available at "this website"_http://www.plumed.org/documentation
The PLUMED library is developed at "https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
The PLUMED library is developed at
"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2 A
detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
There are some example scripts for using this package with LAMMPS in the
examples/USER/plumed directory.
:line
The command to call PLUMED above is reasonably self explanatory. Within the input file
for lammps the user is required to specify the input file for PLUMED and a file on which
to output the PLUMED log. The user must specify both of these arguments every time
PLUMED is to be used. Furthermore, the fix plumed command should appear in the LAMMPS input
file after the relevant input paramters (e.g. the timestep) have been set.
The command to call PLUMED above is reasonably self explanatory. Within
the input file for lammps the user is required to specify the input file
for PLUMED and a file on which to output the PLUMED log. The user must
specify both of these arguments every time PLUMED is to be used.
Furthermore, the fix plumed command should appear in the LAMMPS input
file after the relevant input paramters (e.g. the timestep) have been
set.
The {group-ID} entry is ignored. LAMMPS will always pass all the atoms to PLUMED
and there can only be one instance of the plumed fix at a time. The plumed fix communicates
the minimum amount of information required and the PLUMED supports multiple, completely
independent collective variables, multiple independent biases and multiple independent forms of analysis.
There is thus really no restriction in functionality by only allowing only one plumed fix in the LAMMPS input.
The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
to PLUMED and there can only be one instance of the plumed fix at a
time. The plumed fix communicates the minimum amount of information
required and the PLUMED supports multiple, completely independent
collective variables, multiple independent biases and multiple
independent forms of analysis. There is thus really no restriction in
functionality by only allowing only one plumed fix in the LAMMPS input.
The {plumedfile} keyword allows the user to specify the name of the PLUMED input file.
Instructions as to what should be included in a plumed input file can be found in the
"documentation for PLUMED"_http://www.plumed.org/documentation.
The {plumedfile} keyword allows the user to specify the name of the
PLUMED input file. Instructions as to what should be included in a
plumed input file can be found in the "documentation for
PLUMED"_http://www.plumed.org/documentation.
The {outfile} keyword allows the user to specify the name of a file on which to output
the PLUMED log. This log file normally just parots the information that is contained in the input
file. The names of the files on which the results from the various analyses that have been performed
using PLUMED will be specified by the user in the PLUMED input file.
The {outfile} keyword allows the user to specify the name of a file on
which to output the PLUMED log. This log file normally just parots the
information that is contained in the input file. The names of the files
on which the results from the various analyses that have been performed
using PLUMED will be specified by the user in the PLUMED input file.
[Restart, fix_modify, output, run start/stop, minimize info:]
When performing a restart of a calculation that involves PLUMED you must include a RESTART command
in the PLUMED input file as detailed in the "PLUMED documentation"_http://www.plumed.org/documentation. When the restart
command is found in the PLUMED input PLUMED will append to the files that were generated in the run
that was performed previously. Furthermore, any history dependent bias potentials that were accumulated in
previous calculations will be read in when the restart command is included in the PLUMED input.
When performing a restart of a calculation that involves PLUMED you must
include a RESTART command in the PLUMED input file as detailed in the
"PLUMED documentation"_http://www.plumed.org/documentation. When the
restart command is found in the PLUMED input PLUMED will append to the
files that were generated in the run that was performed previously.
Furthermore, any history dependent bias potentials that were accumulated
in previous calculations will be read in when the restart command is
included in the PLUMED input.
The "fix_modify"_fix_modify.html {energy} option is not supported by this fix.
The "fix_modify"_fix_modify.html {energy} option is not supported by
this fix.
Nothing is computed by this fix that can be accessed by any of the
Nothing is computed by this fix that can be accessed by any of the
"output commands"_Howto_output.html within LAMMPS. All the quantities
of interest can be output by commands that are native to PLUMED, however.
of interest can be output by commands that are native to PLUMED,
however.
[Restrictions:]
This fix is part of the USER-PLUMED package. It is only enabled if
LAMMPS was built with that package. See the "Build
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
There can only be one plumed fix active at a time. Since the interface
communicates only the minimum amount of information and since the PLUMED module
itself can handle an arbitrary number of analysis and biasing methods, this is
not a limitation of functionality.
communicates only the minimum amount of information and since the PLUMED
module itself can handle an arbitrary number of analysis and biasing
methods, this is not a limitation of functionality.
[Related commands:]
@ -96,9 +109,9 @@ not a limitation of functionality.
[Default:]
The default options are plumedfile = NULL and outfile = NULL
The default options are plumedfile = NULL and outfile = NULL
:line
:link(PLUMED)
[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) DOI:https://doi.org/10.1016/j.cpc.2013.09.018
[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)