A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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# CMMDE function for xTB standalone program
import os
def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,alp,distance,angle,dihedral,scanmode,maxiter,scan,solvent,charge,mult,method,fixedatoms,fixedelements):
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD""".format(nproc),file=fout)
meth = ''
if 'GFN-FF' in method or 'gfnff' in method:
meth += '--gfnff'
if 'XTB2' in method or 'xtb2' in method:
meth += '--gfn2'
if 'XTB1' in method or 'xtb1' in method:
meth += '--gfn1'
if 'XTB0' in method or 'xtb0' in method:
meth += '--gfn0'
if 'opt' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout)
else:
print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout)
if 'fix' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} --input cmmd.in > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout)
else:
print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} --input cmmd.in > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout)
if 'freq' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout)
else:
print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth), file=fout)
if 'opt' in job and 'freq' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge, mult-1,meth),file=fout)
else:
print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout)
if 'path' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --alpb {} --chrg {} --uhf {} ,method > cmmd.out".format(geom,product,nproc,solvent,charge,mult-1,meth),file=fout)
else:
print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --chrg {} --uhf {} {} > cmmd.out".format(geom,product,nproc,charge,mult-1,meth),file=fout)
if 'scan' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout)
else:
print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth), file=fout)
if 'freq' in job:
with open('cmmd.in', 'w') as f:
print("""$thermo
temp={}""".format(temperature),file=f)
if 'path' in job:
with open("cmmd.in", 'w') as f:
print("""$path
nrun={}
npoint={}
anopt={}
kpush={}
kpull={}
ppull={}
alp={}
$end""".format(nrun,npoint,anopt,kpush,kpull,ppull,alp),file=f)
if 'fix' in job:
with open("cmmd.in",'w') as f:
print("$fix",file=f)
if distance != 'None':
distance = distance.split(";")
for index, i in enumerate(distance):
print("distance: {}".format(i),file=f)
if angle != 'None':
angle = angle.split(";")
for index, i in enumerate(angle):
print("angle: {}".format(i),file=f)
if dihedral != 'None':
dihedral = dihedral.split(";")
for index, i in enumerate(dihedral):
print("dihedral: {}".format(i),file=f)
if fixedatoms != 'None':
print("atoms: {}".format(fixedatoms),file=f)
if fixedelements != 'None':
print("elements: {}".format(fixedelements),file=f)
if 'scan' in job:
with open("cmmd.in",'w') as f:
print("$constrain",file=f)
if distance != 'None':
distance = distance.split(";")
for index, i in enumerate(distance):
print("distance: {}".format(i),file=f)
if angle != 'None':
angle = angle.split(";")
for index, i in enumerate(angle):
print("angle: {}".format(i),file=f)
if dihedral != 'None':
dihedral = dihedral.split(";")
for index, i in enumerate(dihedral):
print("dihedral: {}".format(i),file=f)
print("$scan",file=f)
if scanmode != 'None':
print("mode = {}".format(scanmode),file=f)
scan = scan.split(";")
for index, i in enumerate(scan):
print("{}: {}".format(index+1,i),file=f)
print("""$opt
maxcycle = {}""".format(maxiter),file=f)
os.system('sbatch run.sh')