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correct nonPBC vs PBC calls to PySCF

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This commit is contained in:
Steve Plimpton
2023-01-31 13:31:42 -07:00
parent b4ac95b225
commit 7c9068c34a
3 changed files with 14 additions and 15 deletions
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4
examples/QUANTUM/PySCF/README
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@ -107,8 +107,8 @@ Step 4: run the 2-water QMMM problem for a few steps
# 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 yes
% 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/work_qm" -log log.water.pyscf.qmmm.plugin.1 -in in.water.pyscf.qmmm.plugin
% 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

2
examples/QUANTUM/PySCF/in.water.pyscf.qmmm.plugin
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@ -46,4 +46,4 @@ thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
thermo 1
mdi plugin pyscf_mdi mdi "-role ENGINE -name PySCF -method LINK" &
extra "-pbc yes" command "run 2"
extra "-pbc no" command "run 2"

23
examples/QUANTUM/PySCF/pyscf_mdi.py
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@ -1,9 +1,11 @@
# MDI wrapper on PySCF quantum code
# NOTE: Qs or issues to still address
# mm_radii is input to PySCF in Angstroms?
# Todo:
# allow for changes in box size on driver side, e.g. NPT
# should just work for PySCF
# NOTE: Qs or issues to still address for PySCF support
# add list of radii for all elements
# allow for changes in box size, e.g. every step for NPT
# PySCF can do DIRECT mode (LATTICE commands) for QMMM
# can it also do POTENTIAL mode (Coulomb potential at QM atoms)
# if so, add PySCF logic in evaluate()
@ -12,8 +14,6 @@
# any other PySCF settings for users to set
# are the 3 below good default values
# is wiping out dm_previous sufficient to make it a new system
# should max_memory=10000 depend on # of MM or QM atoms
# doc what "mf" is in evaluate()
# add PySCF code for AIMD (no MM atoms)
# how to specify box for mixed BC, i.e. cell.dimension = 2 or 1
# also need command-line options for those cases ?
@ -28,7 +28,8 @@ import MDI_Library as mdi
from pyscf.gto import Mole
from pyscf.pbc.gto import Cell
from pyscf import qmmm
from pyscf.dft import RKS
from pyscf.dft import RKS as RKS_nonpbc
from pyscf.pbc.dft import RKS as RKS_pbc
# --------------------------------------------
@ -529,9 +530,9 @@ def evaluate():
box_str = "%s\n%s\n%s" % (edge_vec,edge_vec,edge_vec)
box_str = box_str % \
(box_A[0],box_A[1],box_A[2],box_A[3],box_A[4],box_A[5],box_A[6],box_A[7],box_A[8])
print("BOX STR:",box_str)
print("ATOM STR:",atom_str)
print("BOX STR:",box_str)
print("MM COORDS:",mm_coords)
print("MM CHARGES:",mm_charges)
print("MM RADII:",mm_radii)
@ -543,18 +544,16 @@ def evaluate():
cell = Cell()
cell.atom = atom_str
cell.a = box_str
cell.max_memory = 10000
cell.basis = basis
cell.build()
else:
mol = Mole()
mol.atom = atom_str
mol.max_memory = 10000
mol.basis = basis
mol.build()
# QMMM with QM and MM atoms
# mf = ???
# mf = mean-field object
# qm_pe = QM energy + QM/MM energy
# QM energy = QM_nuclear/QM_nuclear + electron/QM_nuclear + electron/electron
# QM/MM energy = QM_nuclear/MM_charges + electron/MM_charges
@ -563,8 +562,8 @@ def evaluate():
# dm = molecular orbitals (wave functions) for system
if mode == QMMM:
if periodic: mf = RKS(cell,xc=xcstr)
else: mf = RKS(mol,xc=xcstr)
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)
if dm_previous_exists: