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add instructions for running 2-water QMMM PySCF problem

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Steve Plimpton
2023-01-31 07:43:20 -07:00
parent 3b2647917f
commit e7bcdc63e5
3 changed files with 26 additions and 15 deletions
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37
examples/QUANTUM/PySCF/README
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@ -10,8 +10,14 @@ Step 4: run 2-water QMMM problem for a few steps
Step 1: build LAMMPS 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: Traditional make:
% cd ~/lammps/lib/mdi
% python Install.py -m mpi
% cd ~/lammps/src % cd ~/lammps/src
% make yes-mdi yes-molecule yes-kspace % make yes-mdi yes-molecule yes-kspace
% make -j mpi % make -j mpi
@ -21,17 +27,14 @@ CMake:
% cd ~/lammps % cd ~/lammps
% mkdir build_test; cd build_test % mkdir build_test; cd build_test
% cmake ../cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes -D PKG_KSPACE=yes % cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes -D PKG_KSPACE=yes ../cmake
% make -j % make -j
% cp lmp_mpi ~/lammps/examples/QUANTUM/PySCF % cp lmp ~/lammps/examples/QUANTUM/PySCF/lmp_mpi
Note: the molecule and kspace packages are needed for the water test
problem.
--------------------------------- ---------------------------------
--------------------------------- ---------------------------------
Step 2: download/build the MDI code coupling package Step 2: install the MDI code coupling package
(a) grab the MDI Git repo (a) grab the MDI Git repo
@ -42,20 +45,28 @@ Step 2: download/build the MDI code coupling package
% cd mdi/git % cd mdi/git
% mkdir build; cd build % mkdir build; cd build
% cmake .. # include support for all langauges % cmake ..
% make -j % make -j
(c) install mdi.py into your Python: (c) Add something similar to the following to your .bashrc or .cshrc
file so that Python can find MDI:
% cd mdi/git For bash:
% pip3 install .
% export PYTHONPATH="$PYTHONPATH:/home/sjplimp/mdi/git"
% hash -r
For (t)csh:
% setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/mdi/git
% rehash
--------------------------------- ---------------------------------
--------------------------------- ---------------------------------
Step 3: download/build or install PySCF Step 3: install PySCF
(a) install PySCF on your box (a) download/build or install PySCF on your box
NOTE: add instructions here NOTE: add instructions here
@ -84,7 +95,7 @@ that wraps PySCF will need:
--------------------------------- ---------------------------------
--------------------------------- ---------------------------------
Step 4: run 2-water QMMM problem for a few steps Step 4: run the 2-water QMMM problem for a few steps
% cd ~/lammps/examples/QUANTUM/PySCF % cd ~/lammps/examples/QUANTUM/PySCF

2
examples/README
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@ -190,7 +190,7 @@ corresponding doc page in the manual for more info. See the
https://docs.lammps.org/Build_package.html page for more info about https://docs.lammps.org/Build_package.html page for more info about
installing and building packages. installing and building packages.
The QM directory has examples of how to use LAMMPS in tandem with The QUANTUM directory has examples of how to use LAMMPS in tandem with
several quantum codes. several quantum codes.
The TIP4P directory has an example for testing forces computed on a The TIP4P directory has an example for testing forces computed on a

2
lib/mdi/Install.py
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@ -32,7 +32,7 @@ make lib-mdi args="-m mpi" # build MDI lib with same settings as in the mpi Make
# settings # settings
version = "1.4.12" version = "1.4.14"
url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
# known checksums for different MDI versions. used to validate the download. # known checksums for different MDI versions. used to validate the download.