lammps/examples/QUANTUM/PySCF

# Test runs of QMMM with LAMMPS and PySCF

Step 1: build LAMMPS
Step 2: download/build the MDI code coupling package
Step 3: download/build or install PySCF
Step 4: run 2-water QMMM problem for a few steps

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Step 1: build LAMMPS

The molecule and kspace packages are needed for the 2-water test
problem.  Copy the final LAMMPS executable into the
examples/QUANTUM/PySCF directory.

Traditional make:

% cd ~/lammps/lib/mdi
% python Install.py -m mpi
% cd ~/lammps/src
% make yes-mdi yes-molecule yes-kspace
% make -j mpi
% cp lmp_mpi ~/lammps/examples/QUANTUM/PySCF

CMake:

% cd ~/lammps
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes -D PKG_KSPACE=yes ../cmake
% make -j
% cp lmp ~/lammps/examples/QUANTUM/PySCF/lmp_mpi

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Step 2: install the MDI code coupling package

(a) grab the MDI Git repo

% mkdir git; cd mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git

(b) build MDI

% cd mdi/git
% mkdir build; cd build
% cmake ..
% make -j

(c) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find MDI:

For bash:

% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/mdi/git"
% hash -r

For (t)csh:

% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git
% rehash

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Step 3: install PySCF

(a) download/build or install PySCF on your box

NOTE: add instructions here

(b) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find PySCF:

For bash:

% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/pyscf/git"
% hash -r

For (t)csh:

% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/pyscf/git
% rehash

(c) Check that you can import the 4 Python modules which the script
that wraps PySCF will need:

% python
>>> import numpy as np
>>> from mpi4py import MPI
>>> import MDI_Library as mdi
>>> import pyscf

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Step 4: run the 2-water QMMM problem for a few steps

% cd ~/lammps/examples/QUANTUM/PySCF

# Run with TCP: 1 proc each

% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.pyscf.qmmm.tcp.1 -in in.water.pyscf.qmmm &

% python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method TCP -port 8021 -hostname localhost"

# Run with MPI: 1 proc each

% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.pyscf.qmmm.mpi.1 -in in.water.pyscf.qmmm : -np 1 python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method MPI" -pbc no

# Run in plugin mode: 1 proc

% lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/PySCF" -log log.water.pyscf.qmmm.plugin.1 -in in.water.pyscf.qmmm.plugin

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Step 5: run the mixture QMMM problem for a few steps

% cd ~/lammps/examples/QUANTUM/PySCF

# Run with TCP: 1 proc each

% lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.mixture.pyscf.qmmm.tcp.1 -in in.mixture.pyscf.qmmm &

% python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method TCP -port 8021 -hostname localhost"

# Run with MPI: 1 proc each

% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.mixture.pyscf.qmmm.mpi.1 -in in.mixture.pyscf.qmmm : -np 1 python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method MPI" -pbc no

# Run in plugin mode: 1 proc

% lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/PySCF" -log log.mixture.pyscf.qmmm.plugin.1 -in in.mixture.pyscf.qmmm.plugin