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reformatting and simplification of fix plumed docs

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Axel Kohlmeyer 2018-11-15 10:53:38 -05:00
parent 82d6aa9add
commit 8a4983e4bc
1 changed files with 33 additions and 33 deletions
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doc/src/fix_plumed.txt
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@ -25,33 +25,32 @@ 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"_plumedhome 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
itself. This command is LAMMPS specific, whereas most of the
functionality implemented in PLUMED, however, will work with a range of
MD codes, and when PLUMED is used as a stand alone code for analysis.
The full "documentation for PLUMED"_plumeddocs is available online and
included in the PLUMED source code. The PLUMED library development is
hosted 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
There is an example input 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 make LAMMPS call PLUMED during a run requires two keyword
value pairs pointing to the PLUMED input file and an output file for the
PLUMED log. The user must specify these arguments every time PLUMED is
to be used. Furthermore, the fix plumed command should appear in the
LAMMPS input file [after] 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
@ -64,10 +63,10 @@ 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.
PLUMED"_plumeddocs
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
which to output the PLUMED log. This log file normally just parrots 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.
@ -76,12 +75,13 @@ using PLUMED will be specified by the user in the PLUMED input file.
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.
"PLUMED documentation"_plumeddocs. 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. No part of the PLUMED restart
data is included in the LAMMPS restart files. 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.
@ -97,10 +97,7 @@ This fix is part of the USER-PLUMED package. It is only enabled if
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.
There can only be one plumed fix active at a time.
[Related commands:]
@ -115,3 +112,6 @@ The default options are plumedfile = NULL and outfile = NULL
:link(PLUMED)
[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
:link(plumeddocs,http://www.plumed.org/documentation)
:link(plumedhome,http://www.plumed.org/)