# Test runs with coupling of LAMMPS and NWChem PWDFT
Step 0: What NWChem/PWDF currently supports
Step 1: Build LAMMPS
Step 2: Install or download/build MDI code coupling package
Step 3: Download/build NWChem PWDFT
Step 4: Perform test runs in any of 3 modes
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Step 0: What NWChem/PWDFT currently supports
PWDFT can be used with fix mdi/qm to perform QM calculations of an
entire system and with fix mdi/qmmm for QMMM simulations. For QMMM it
can use the potential mode of fix mdi/qmmm, but not the direct mode.
PWDFT can calculate a QM energy and QM forces on each atom, but it
cannot compute a QM stress tensor.
PWDFT supports MPI parallelism, but not threading parallelism.
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Step 1: Build LAMMPS
The MDI and molecule packags are needed. Copy the final LAMMPS
executable into the examples/QUANTUM/NWChem directory.
Traditional make:
% cd ~/lammps/lib/mdi
% python Install.py -m mpi
% cd ~/lammps/src
% make yes-mdi yes-molecule
% make -j mpi
% cp lmp_mpi ~/lammps/examples/QUANTUM/NWChem
CMake:
% cd ~/lammps
% mkdir build; cd build
% cmake -DPKG_MDI=yes -DPKG_MOLECULE=yes ../cmake
% make -j
% cp lmp ~/lammps/examples/QUANTUM/NWChem/lmp_mpi
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Step 2: Install or download/build MDI code coupling package
To simply use the MDI python module for the example scripts in this
dir, you only need to install the MDI python module in your
environment. Alternatively, you can download/build MDI itself, which
will include its documentation and examples (as well as libraries and
Python interface).
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
version of MDI LAMMPS is currently using.
(option 1) Install MDI python module via pip:
% 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
(a) clone the MDI Git repo
% git clone https://github.com/MolSSI-MDI/MDI_Library.git mdi
(b) build MDI
% cd mdi
% 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="${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
% hash -r
For (t)csh:
% setenv PYTHONPATH "${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
% rehash
(d) Check import of 3 Python modules which the script that wraps
NWChem will need:
% python
>>> import numpy as np
>>> from mpi4py import MPI
>>> import mdi
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Step 3: Download/build NWChem PWDFT
NOTE: As of March 2023, this PWDFT-only repo is part of the new
NWChemEx (exascale) version of NWChem. It will be included in the
NWChemEx repo when it is publicly released. This doc page will be
updated when that happens.
(a) clone the PWDFT Git repo
% mkdir nwchem; cd nwchem
% git clone https://github.com/ebylaska/PWDFT.git PWDFT
(b) build PWDFT
% cd ~/nwchem/PWDFT
% cd build_library; rm -r *
% cmake -DMAKE_LIBRARY=true -DCMAKE_POSITION_INDEPENDENT_CODE=ON ../Nwpw
% make -j # should produce libpwdft.so in build_library
(c) Add a line like this to your ~/.bashrc or ~/.cshrc
file so that the libpwdft.so file can be found:
For bash:
% export LD_LIBRARY_PATH="${HOME}/nwchem/PWDFT/build_library:${LD_LIBRARY_PATH}"
% hash -r
For (t)csh:
% setenv LD_LIBRARY_PATH "${HOME}/nwchem/PWDFT/build_library:${LD_LIBRARY_PATH}"
% rehash
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Step 4: Perform test runs in any of 3 modes
These tests are in lammps/examples/QUANTUM/NWChem
in.series = series of several W conformations
in.water.qmmm = QMMM of two-water system, 1 QM + 1 MM
in.zeolite.qmmm = QMMM of zeolite, MM zeolite + QM methane molecule
** run LAMMPS-only versions of water and zeolite problems
lmp_mpi -log log.water.mm.1 < in.water.mm
lmp_mpi -log log.zeolite.mm.1 < in.zeolite.mm
** run LAMMPS and PWDFT with TCP/IP, 1 or more procs each
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.series.tcp.1 -in in.series &
python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.w.nw w.nw log.series.pwdft.tcp.1
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.qmmm.tcp.1 -in in.water.qmmm &
mpirun -np 2 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.water.nw water.nw log.water.pwdft.qmmm.tcp.2
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.zeolite.qmmm.tcp.1 -in in.zeolite.qmmm &
mpirun -np 8 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.tcp.8
** run LAMMPS and PWDFT with MPI, 1 or more procs each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.mpi.1 -in in.series : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.w.nw w.nw log.series.pwdft.mpi.1
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.qmmm.mpi.1 -in in.water.qmmm : -np 2 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.water.nw water.nw log.water.pwdft.qmmm.mpi.2
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.zeolite.qmmm.mpi.1 -in in.zeolite.qmmm : -np 8 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.mpi.8
** run PWDFT as plugin MDI engine, 1 or more procs
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}/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}/lammps/examples/QUANTUM/NWChem" -log log.zeolite.qmmm.plugin.8 -in in.zeolite.qmmm.plugin
