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doc page additions for USER-PLUMED package

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This commit is contained in:
Steve Plimpton
2018-11-13 08:29:07 -07:00
parent 1651a21f92
commit 4805e1df22
4 changed files with 48 additions and 36 deletions
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61
doc/src/Build_extras.txt
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@ -41,11 +41,11 @@ This is the list of packages that may require additional steps.
"USER-ATC"_#user-atc,
"USER-AWPMD"_#user-awpmd,
"USER-COLVARS"_#user-colvars,
"USER-PLUMED" _#user-plumed,
"USER-H5MD"_#user-h5md,
"USER-INTEL"_#user-intel,
"USER-MOLFILE"_#user-molfile,
"USER-NETCDF"_#user-netcdf,
"USER-PLUMED"_#user-plumed,
"USER-OMP"_#user-omp,
"USER-QMMM"_#user-qmmm,
"USER-QUIP"_#user-quip,
@ -719,47 +719,52 @@ USER-PLUMED package :h4,link(user-plumed)
[Traditional make]:
Before building LAMMPS with this package, you must first build
PLUMED. We recommending building PLUMED separately to LAMMPS using
the instructions that can be found at http://plumed.github.io/doc-master/user-doc/html/_installation.html.
Before building LAMMPS with this package, you must first build PLUMED.
We recommending building PLUMED separately to LAMMPS using the
instructions that can be found at
http://plumed.github.io/doc-master/user-doc/html/_installation.html.
Before compiling LAMMPS you can then install the fix plumed command
and compile LAMMPS in the usual manner:
make yes-user-plumed
make machine :pre
Once this compilation completes you should be able to run LAMMPS in the usual
way. When running LAMMPS with an input script that contains a fix
plumed command LAMMPS will try to call the PLUMED runtime library. PLUMED
must therefore be available in your path if LAMMPS is compiled in this way.
Once this compilation completes you should be able to run LAMMPS in
the usual way. When running LAMMPS with an input script that contains
a fix plumed command LAMMPS will try to call the PLUMED runtime
library. PLUMED must therefore be available in your path if LAMMPS is
compiled in this way.
On some machines it is not possible to call runtime libraries in the way described
above. When compiling on these machines it is thus better to statically link
PLUMED when compiling LAMMPS. To do this you must either download a PLUMED
tarball from http://www.plumed.org/get-it or clone it using
git clone https://github.com/plumed/plumed2.git. If you download the tarball
unpack it in the /lib/plumed directory. Similarly if you clone
it clone it to the /lib/plumed directory as if there is a version of PLUMED within
this directory LAMMPS will always try to statically link the version of PLUMED
that this directory contains instead of dynamically linking the library.
On some machines it is not possible to call runtime libraries in the
way described above. When compiling on these machines it is thus
better to statically link PLUMED when compiling LAMMPS. To do this
you must either download a PLUMED tarball from
http://www.plumed.org/get-it or clone it using git clone
https://github.com/plumed/plumed2.git. If you download the tarball
unpack it in the /lib/plumed directory. Similarly if you clone it
clone it to the /lib/plumed directory as if there is a version of
PLUMED within this directory LAMMPS will always try to statically link
the version of PLUMED that this directory contains instead of
dynamically linking the library.
Once you have downloaded PLUMED into /lib/plumed you must again build the code
here by following the instructions that can be found at
Once you have downloaded PLUMED into /lib/plumed you must again build
the code here by following the instructions that can be found at
http://plumed.github.io/doc-master/user-doc/html/_installation.html.
You can statically link PLUMED manually and if you want to access the full
range of PLUMED functionalities this is what you should do. If you only want the
basic range of functionalities, however, (i.e. no user contributed modules) then
you can download and compile PLUMED in one step from the lammps/src dir, using a
command like like those below:
You can statically link PLUMED manually and if you want to access the
full range of PLUMED functionalities this is what you should do. If
you only want the basic range of functionalities, however, (i.e. no
user contributed modules) then you can download and compile PLUMED in
one step from the lammps/src dir, using a command like like those
below:
make lib-plumed # print help message
make lib-plumed args="-b" # download and build the latest stable version of PLUMED
These commands will simply invoke the lib/plumed/Install.py script with
args specified. Furthermore, once the script has completed you should
have a compiled version of PLUMED. With this built you can install/un-install
PLUMED and build LAMMPS in the usual manner:
These commands will simply invoke the lib/plumed/Install.py script
with args specified. Furthermore, once the script has completed you
should have a compiled version of PLUMED. With this built you can
install/un-install PLUMED and build LAMMPS in the usual manner:
make yes-user-plumed
make machine :pre

1
doc/src/Build_package.txt
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@ -56,6 +56,7 @@ packages:
"USER-INTEL"_Build_extras.html#user-intel,
"USER-MOLFILE"_Build_extras.html#user-molfile,
"USER-NETCDF"_Build_extras.html#user-netcdf,
"USER-PLUMED"_Build_extras.html#user-plumed,
"USER-OMP"_Build_extras.html#user-omp,
"USER-QMMM"_Build_extras.html#user-qmmm,
"USER-QUIP"_Build_extras.html#user-quip,

19
doc/src/Packages_details.txt
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@ -89,6 +89,7 @@ as contained in the file name.
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
"USER-PHONON"_#PKG-USER-PHONON,
"USER-PLUMED"_#PKG-USER-PLUMED,
"USER-PTM"_#PKG-USER-PTM,
"USER-QMMM"_#PKG-USER-QMMM,
"USER-QTB"_#PKG-USER-QTB,
@ -1205,14 +1206,16 @@ USER-PLUMED package :link(USER-PLUMED),h4
[Contents:]
The fix plumed command allows you to use the plugin for molecular
dynamics PLUMED to analyse and bias your LAMMPS trajectory on the fly.
In practise PLUMED is called from within the lammps input script by using
the "fix plumed _fix_plumed.html command.
The fix plumed command allows you to use the PLUMED free energy plugin
for molecular dynamics to analyse and bias your LAMMPS trajectory on
the fly. The PLUMED library is called from within the LAMMPS input
script by using the "fix plumed _fix_plumed.html command.
[Authors:] The PLUMED library is written and maintained by
Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and
Gareth Tribello.
[Authors:] The "PLUMED library"_#PLUMED is written and maintained by
Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth
Tribello.
:link(PLUMED,http://www.plumed.org)
[Install:]
@ -1224,7 +1227,7 @@ extras"_Build_extras.html doc page.
src/USER-PLUMED/README
lib/plumed/README
"fix plumed "_fix_plumed.html
"fix plumed"_fix_plumed.html
examples/USER/plumed :ul
:line

3
doc/src/Packages_user.txt
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@ -62,6 +62,7 @@ Package, Description, Doc page, Example, Library
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
"USER-PLUMED"_Packages_details.html#PKG-USER-PLUMED, "PLUMED"_#PLUMED free energy library,"fix plumed"_fix_plumed.html, USER/plumed, ext
"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
@ -75,4 +76,6 @@ Package, Description, Doc page, Example, Library
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
:link(PLUMED,http://www.plumed.org)