# Test runs with copuling of LAMMPS and PySCF
Step 0: What PySCF currently supports
Step 1: Build LAMMPS
Step 2: Download/build MDI code coupling package
Step 3: Download/build PySCF
Step 4: Perform test runs in any of 3 modes
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Step 0: What PySCF currently supports
LATTE can be used with fix mdi/qmmm for QMMM simulations, but not with
fix mdi/qm to perform QM calculations of an entire system. For QMMM
it can use the direct mode of fix mdi/qmmm, but not the potential
mode. PySCF can calculate a QM energy and QM forces on each atom, but
it cannot compute a QM stress tensor.
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Step 1: Build LAMMPS
The MDI, molecule, and kspace packages are needed. 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 -DPKG_MDI=yes -DPKG_MOLECULE=yes -DPKG_KSPACE=yes ../cmake
% make -j
% cp lmp ~/lammps/examples/QUANTUM/PySCF/lmp_mpi
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Step 2: Download/build MDI code coupling package
(a) clone the MDI Git repo
% mkdir mdi; 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 a line like this to your ~/.bashrc or ~/.cshrc file so that
Python can find MDI:
For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/mdi/git/build"
% hash -r
For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git/build
% rehash
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Step 3: Download/build PySCF
See https://pyscf.org/install.html for install options.
This describes building PySCF from source code.
(a) clone the PySCI Git repo
% mkdir pyscf; cd pyscf
% git clone https://github.com/pyscf/pyscf.git git
(b) build PySCF
NOTE: you will also need numpy, scipy, h5py in your python
% cd pyscf/git/lib
% mkdir build; cd build
% cmake ..
% make -j
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
Python can find PySCF:
For bash:
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/pyscf/git"
% hash -r
For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/pyscf/git
% rehash
(d) Check import of 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: Perform test runs in any of 3 modes
These tests are in lammps/examples/QUANTUM/PySCF
in.water = QMMM of two-water system, 1 QM + 1 MM
in.mixture = QMMM of mixture, QM small molecule in MM water
** run LAMMPS-only versions of mixture problem
lmp_mpi -log log.mixture.mm.1 < in.mixture.mm
** run LAMMPS and LATTE with TCP/IP, 1 proc each
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.qmmm.tcp.1 -in in.water.qmmm &
python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method TCP -port 8021 -hostname localhost"
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.mixture.qmmm.tcp.1 -in in.mixture.qmmm &
python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method TCP -port 8021 -hostname localhost"
** run LAMMPS and PySCF with MPI, 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.qmmm.mpi.1 -in in.water.qmmm : -np 1 python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method MPI" -pbc no
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.mixture.qmmm.mpi.1 -in in.mixture.qmmm : -np 1 python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method MPI" -pbc no
** 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/sjplimp/lammps/git/examples/QUANTUM/PySCF" -log log.mixture.qmmm.plugin.1 -in in.mixture.qmmm.plugin
