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update README files to have more conventional options and settings

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This commit is contained in:
Axel Kohlmeyer
2023-03-22 20:42:54 -04:00
parent 737ef160d2
commit 667ba0febb
3 changed files with 76 additions and 58 deletions
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42
examples/QUANTUM/LATTE/README
View File

@ -77,24 +77,23 @@ NOTE: It should be fine to leave off the version number for the python
module installs, to just grab the latest MDI version. 1.4.16 is the module installs, to just grab the latest MDI version. 1.4.16 is the
version of MDI LAMMPS is currently using. version of MDI LAMMPS is currently using.
(option 1) Install MDI python module via conda: (option 1) Install MDI python module via pip:
% conda install -c conda-forge pymdi=1.4.16
(option 2) Install MDI python module via pip:
% pip install 'pymdi>=1.4.14' % pip install 'pymdi>=1.4.14'
(option 2) Install MDI python module via conda:
% conda install -c conda-forge pymdi=1.4.16
(option 3) Download/build MDI code coupling package (option 3) Download/build MDI code coupling package
(a) clone the MDI Git repo (a) clone the MDI Git repo
% mkdir mdi; cd mdi % git clone https://github.com/MolSSI-MDI/MDI_Library.git mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git
(b) build MDI (b) build MDI
% cd mdi/git % cd mdi
% mkdir build; cd build % mkdir build; cd build
% cmake .. % cmake ..
% make -j % make -j
@ -104,12 +103,12 @@ Python can find MDI:
For bash: For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/mdi/git/build/MDI_Library" % export PYTHONPATH="${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
% hash -r % hash -r
For (t)csh: For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git/build/MDI_Library % setenv PYTHONPATH "${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
% rehash % rehash
(d) Check import of 3 Python modules which the script that wraps (d) Check import of 3 Python modules which the script that wraps
@ -132,12 +131,11 @@ page will be updated when that happens.
(a) clone the ECP branch of the LATTE Git repo (a) clone the ECP branch of the LATTE Git repo
% mkdir latte; cd latte % git clone -b ECP https://github.com/lanl/LATTE.git latte
% git clone -b ECP git@github.com:lanl/LATTE.git git
(b) build LATTE as a shared library (b) build LATTE as a shared library
% cd ~/latte/git % cd ~/latte
% mkdir build; cd build % mkdir build; cd build
% cmake -DBUILD_SHARED_LIBS=on ../cmake % cmake -DBUILD_SHARED_LIBS=on ../cmake
% make -j # should produce liblatte.so in build % make -j # should produce liblatte.so in build
@ -147,12 +145,12 @@ the liblatte.so file can be found:
For bash: For bash:
% export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/home/sjplimp/latte/git/build" % export LD_LIBRARY_PATH="${HOME}/latte/build:${LD_LIBRARY_PATH}"
% hash -r % hash -r
For (t)csh: For (t)csh:
% setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/latte/git/build % setenv LD_LIBRARY_PATH "${HOME}/latte/build:${LD_LIBRARY_PATH}"
% rehash % rehash
--------------------------------- ---------------------------------
@ -198,16 +196,16 @@ mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.m
** run LATTE as plugin MDI engine, 1 proc ** run LATTE as plugin MDI engine, 1 proc
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.water.plugin.1 -in in.water.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.water.plugin.1 -in in.water.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.water.min.plugin.1 -in in.water.min.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.water.min.plugin.1 -in in.water.min.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.uo2.plugin.1 -in in.uo2.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.uo2.plugin.1 -in in.uo2.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.ch4.plugin.1 -in in.ch4.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.ch4.plugin.1 -in in.ch4.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.sucrose.plugin.1 -in in.sucrose.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.sucrose.plugin.1 -in in.sucrose.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.graphene.plugin.1 -in in.graphene.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.graphene.plugin.1 -in in.graphene.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/LATTE" -log log.series.plugin.1 -in in.series.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.series.plugin.1 -in in.series.plugin

33
examples/QUANTUM/NWChem/README
View File

@ -59,24 +59,23 @@ NOTE: It should be fine to leave off the version number for the python
module installs, to just grab the latest MDI version. 1.4.16 is the module installs, to just grab the latest MDI version. 1.4.16 is the
version of MDI LAMMPS is currently using. version of MDI LAMMPS is currently using.
(option 1) Install MDI python module via conda: (option 1) Install MDI python module via pip:
% conda install -c conda-forge pymdi=1.4.16
(option 2) Install MDI python module via pip:
% pip install 'pymdi>=1.4.14' % pip install 'pymdi>=1.4.14'
(option 2) Install MDI python module via conda:
% conda install -c conda-forge pymdi=1.4.16
(option 3) Download/build MDI code coupling package (option 3) Download/build MDI code coupling package
(a) clone the MDI Git repo (a) clone the MDI Git repo
% mkdir mdi; cd mdi % git clone https://github.com/MolSSI-MDI/MDI_Library.git mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git
(b) build MDI (b) build MDI
% cd mdi/git % cd mdi
% mkdir build; cd build % mkdir build; cd build
% cmake .. % cmake ..
% make -j % make -j
@ -86,12 +85,12 @@ Python can find MDI:
For bash: For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/mdi/git/build/MDI_Library" % export PYTHONPATH="${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
% hash -r % hash -r
For (t)csh: For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git/build/MDI_Library % setenv PYTHONPATH "${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
% rehash % rehash
(d) Check import of 3 Python modules which the script that wraps (d) Check import of 3 Python modules which the script that wraps
@ -115,7 +114,7 @@ updated when that happens.
(a) clone the PWDFT Git repo (a) clone the PWDFT Git repo
% mkdir nwchem; cd nwchem % mkdir nwchem; cd nwchem
% git clone git@github.com:ebylaska/PWDFT.git PWDFT % git clone https://github.com/ebylaska/PWDFT.git PWDFT
(b) build PWDFT (b) build PWDFT
@ -124,17 +123,17 @@ updated when that happens.
% cmake -DMAKE_LIBRARY=true -DCMAKE_POSITION_INDEPENDENT_CODE=ON ../Nwpw % cmake -DMAKE_LIBRARY=true -DCMAKE_POSITION_INDEPENDENT_CODE=ON ../Nwpw
% make -j # should produce libpwdft.so in build_library % make -j # should produce libpwdft.so in build_library
(c) Add a line like this to your ~/.bashrc or !/.cshrc (c) Add a line like this to your ~/.bashrc or ~/.cshrc
file so that the libpwdft.so file can be found: file so that the libpwdft.so file can be found:
For bash: For bash:
% export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/home/sjplimp/nwchem/PWDFT/build_library" % export LD_LIBRARY_PATH="${HOME}/nwchem/PWDFT/build_library:${LD_LIBRARY_PATH}"
% hash -r % hash -r
For (t)csh: For (t)csh:
% setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/nwchem/PWDFT/build_library % setenv LD_LIBRARY_PATH "${HOME}/nwchem/PWDFT/build_library:${LD_LIBRARY_PATH}"
% rehash % rehash
--------------------------------- ---------------------------------
@ -175,8 +174,8 @@ mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.zeolite.
** run PWDFT as plugin MDI engine, 1 or more procs ** run PWDFT as plugin MDI engine, 1 or more procs
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.series.plugin.1 -in in.series.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/NWChem" -log log.series.plugin.1 -in in.series.plugin
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.water.qmmm.plugin.2 -in in.water.qmmm.plugin mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/NWChem" -log log.water.qmmm.plugin.2 -in in.water.qmmm.plugin
mpirun -np 8 lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.zeolite.qmmm.plugin.8 -in in.zeolite.qmmm.plugin mpirun -np 8 lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/NWChem" -log log.zeolite.qmmm.plugin.8 -in in.zeolite.qmmm.plugin

59
examples/QUANTUM/PySCF/README
View File

@ -78,24 +78,23 @@ NOTE: It should be fine to leave off the version number for the python
module installs, to just grab the latest MDI version. 1.4.16 is the module installs, to just grab the latest MDI version. 1.4.16 is the
version of MDI LAMMPS is currently using. version of MDI LAMMPS is currently using.
(option 1) Install MDI python module via conda: (option 1) Install MDI python module via pip:
% conda install -c conda-forge pymdi=1.4.16
(option 2) Install MDI python module via pip:
% pip install 'pymdi>=1.4.14' % pip install 'pymdi>=1.4.14'
(option 2) Install MDI python module via conda:
% conda install -c conda-forge pymdi=1.4.16
(option 3) Download/build MDI code coupling package (option 3) Download/build MDI code coupling package
(a) clone the MDI Git repo (a) clone the MDI Git repo
% mkdir mdi; cd mdi % git clone https://github.com/MolSSI-MDI/MDI_Library.git mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git
(b) build MDI (b) build MDI
% cd mdi/git % cd mdi
% mkdir build; cd build % mkdir build; cd build
% cmake .. % cmake ..
% make -j % make -j
@ -105,12 +104,12 @@ Python can find MDI:
For bash: For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/mdi/git/build/MDI_Library" % export PYTHONPATH="${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
% hash -r % hash -r
For (t)csh: For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git/build/MDI_Library % setenv PYTHONPATH "${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
% rehash % rehash
--------------------------------- ---------------------------------
@ -128,35 +127,57 @@ See https://pyscf.org/install.html for other options.
(a) clone the PySCF Git repo (a) clone the PySCF Git repo
% mkdir pyscf; cd pyscf % git clone https://github.com/MoleOrbitalHybridAnalyst/pyscf.git pyscf
% git clone git@github.com:MoleOrbitalHybridAnalyst/pyscf.git git
(option 1) build using Python
(b) create and install a wheel file
% cd pyscf
% python -m pip install --user --upgrade pip
% python -m pip install --user build wheel
% python -m build -n --wheel -o .
% python -m pip install --user pyscf-2.*.whl
(c) no setting of envionment variables needed
(d) Check import of 4 Python modules which the script that wraps PySCF
will need:
% python -i
>>> import numpy as np
>>> from mpi4py import MPI
>>> import mdi
>>> import pyscf
(option 2) build using CMake and use in place
(b) build PySCF (b) build PySCF
NOTE: you will also need numpy, scipy, h5py in your python NOTE: you will also need numpy, scipy, h5py in your python
% cd pyscf/git/pyscf/git/lib % cd pyscf/pyscf/lib
% mkdir build; cd build % mkdir build; cd build
% cmake .. % cmake ..
% make -j % make -j
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that (c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
Python can find PySCF: Python can find PySCF where you compiled it:
For bash: For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/pyscf/git" % export PYTHONPATH="${HOME}/pyscf:${PYTHONPATH}"
% hash -r % hash -r
For (t)csh: For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/pyscf/git % setenv PYTHONPATH "${HOME}/pyscf:${PYTHONPATH}"
% rehash % rehash
(d) Check import of 4 Python modules which the script that wraps PySCF (d) Check import of 4 Python modules which the script that wraps PySCF
will need: will need:
% python % python -i
>>> import numpy as np >>> import numpy as np
>>> from mpi4py import MPI >>> from mpi4py import MPI
>>> import mdi >>> import mdi
@ -192,6 +213,6 @@ mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.mixture.
** run PySCF as plugin MDI engine, 1 proc ** run PySCF as plugin MDI engine, 1 proc
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/PySCF" -log log.water.qmmm.plugin.1 -in in.water.qmmm.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/PySCF" -log log.water.qmmm.plugin.1 -in in.water.qmmm.plugin
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/PySCF" -log log.mixture.qmmm.plugin.1 -in in.mixture.qmmm.plugin lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/PySCF" -log log.mixture.qmmm.plugin.1 -in in.mixture.qmmm.plugin