ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update for more recent MDI and PySCF versions

Browse Source
This commit is contained in:
Axel Kohlmeyer
2023-03-14 13:52:56 -04:00
parent 04dfda9952
commit c3dba53040
3 changed files with 22 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files

46
examples/QUANTUM/PySCF/README
View File

@ -11,11 +11,11 @@ Step 4: Perform test runs in any of 3 modes
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.
PySCF can be used with fix mdi/qmmm for QM/MM simulations, but not with fix
mdi/qm to perform QM calculations of an entire system. For QM/MM it can use
the direct mode of fix mdi/qmmm, but not the plugin mode. PySCF can calculate
a QM energy and QM forces on each atom, but it cannot compute a QM stress
tensor.
PySCF does not support MPI parallelism, so run it on a single MPI task.
But it does support multi-threading via OpenMP. By default it will use
@ -66,32 +66,18 @@ CMake:
---------------------------------
---------------------------------
Step 2: Download/build MDI code coupling package
Step 2: Install MDI code coupling python module
(a) clone the MDI Git repo
You can install MDI in your Python environment via conda:
% mkdir mdi; cd mdi
% git clone git@github.com:MolSSI-MDI/MDI_Library.git git
% conda install -c conda-forge pymdi=1.4.16
(b) build MDI
or via pip:
% cd mdi/git
% mkdir build; cd build
% cmake ..
% make -j
% pip install 'pymdi>=1.4.14'
(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
It is likely fine to leave off the version number, to get the latest
MDI version. 1.4.16 is the version LAMMPS is currently using.
---------------------------------
---------------------------------
@ -101,7 +87,7 @@ 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
(a) clone the PySCF Git repo
% mkdir pyscf; cd pyscf
% git clone https://github.com/pyscf/pyscf.git git
@ -134,7 +120,7 @@ will need:
% python
>>> import numpy as np
>>> from mpi4py import MPI
>>> import MDI_Library as mdi
>>> import mdi
>>> import pyscf
---------------------------------
@ -149,9 +135,9 @@ 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
lmp_mpi -log log.mixture.mm.1 -in in.mixture.mm
** run LAMMPS and LATTE with TCP/IP, 1 proc each
** run LAMMPS and PySCF 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"

4
examples/QUANTUM/PySCF/pyscf_mdi.py
View File

@ -532,12 +532,14 @@ def evaluate():
if periodic:
cell = Cell()
cell.verbose = 4
cell.atom = atom_str
cell.a = box_str
cell.basis = basis
cell.build()
else:
mol = Mole()
mol.verbose = 4
mol.atom = atom_str
mol.basis = basis
#mol.max_memory = 10000
@ -555,7 +557,7 @@ def evaluate():
if mode == QMMM:
if periodic: mf = RKS_pbc(cell,xc=xcstr)
else: mf = RKS_nonpbc(mol,xc=xcstr)
mf = qmmm.mm_charge(mf,mm_coords,mm_charges,mm_radii)
mf = qmmm.mm_charge(mf,mm_coords,mm_charges)
if dm_previous_exists:
qm_pe = mf.kernel(dm0=dm_previous)