def gms(path, File, template, sysData, jobTemp):
import re
from supercomp import host
from templates import gms_rjnJob
from templates import gms_mgsJob
from templates import gms_gaiJob
from templates import gms_masJob
from templates import gms_monJob
from templates import gms_stmJob
from write import write_gmsInp
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDir(path, File, template)
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
# CREATE xyzData
xyzData = []
for frag in fragList:
for atm in atmList:
if atm['id'] in frag['ids']:
xyzData.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# GET TEMPLATE LINES WITH COORDS
input = xyzTemp(path, template, xyzData)
# CHARGE AND MULT
for ind in range(len(input)):
if 'ICHARG' in input[ind]:
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
else:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'ICHARG':
oldChrg = spl_line[val + 1]
input[ind] = input[ind].replace('ICHARG=' + \
oldChrg, 'ICHARG=' + str(totChrg))
if totMult != 0:
if 'CONTRL' in input[ind]:
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
elif not 'MULT' in input[ind]:
input[ind] = input[ind].\
replace(' RUN',' MULT=' + str(totMult) + ' RUN')
# MEMORY USED IN INPUT
if 'MWORDS' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MWORDS' in input[ind]:
memory = spl_line[val + 1]
# MEMORY USED IN INPUT
ddi = False
if 'MEMDDI' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MEMDDI' in input[ind]:
ddi = spl_line[val + 1]
# WRITE INP
write_gmsInp(npath, name, input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = gms_rjnJob(name)
elif hw == 'mgs':
lines = gms_mgsJob(name)
elif hw == 'gai':
lines = gms_gaiJob(name)
elif hw == 'mas':
lines = gms_masJob(name)
elif hw == 'mon':
lines = gms_monJob(name)
elif hw == 'stm':
lines = gms_stmJob(name)
if lines:
write_job(npath, name, lines)
def fmo(path, File, template, sysData, jobTemp):
import os, re
from supercomp import host
from chemData import pTable
from templates import fmo_rjnJob
from templates import fmo_mgsJob
from templates import fmo_stmJob
from templates import fmo_gaiJob
from templates import fmo_monJob
from templates import fmo_masJob
from templates import gms_rjnJob
from templates import gms_mgsJob
from templates import gms_masJob
from templates import gms_monJob
from templates import gms_gaiJob
from templates import gms_stmJob
from tempInp import fmo_ions
from write import write_xyz
from write import write_gmsInp
from write import write_job
# NAME FOR WRITING FILE, DIRS
ions = False
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDir(path, File, template)
# UNPACK sysData
mp2 = False
fragList, atmList, totChrg, totMult = sysData
# NUMBER OF FRAGS
nfrags = len(fragList)
# CREATE xyzData
xyzData = []
for frag in fragList:
for atm in atmList:
if atm['id'] in frag['ids']:
xyzData.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# TEMPLATE LINES
input = xyzTemp(path, template, xyzData)
fmo_input = []
# IF RUNTYP IS ENERGY MAKE ION JOBS
for ind in range(len(input)):
if 'NGROUP' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'NGROUP':
in_grp = spl_line[val + 1]
if in_grp != str(nfrags):
#print('Changing NGROUP to', nfrags)
input[ind] = input[ind].\
replace('NGROUP=' + in_grp, 'NGROUP=' + str(nfrags))
# CHECK NFRAG = NO. OF FOUND FRAGMENTS
if 'NFRAG' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'NFRAG':
in_nfrags = spl_line[val + 1]
if in_nfrags != str(nfrags):
#print('Changing NFRAG to', nfrags)
input[ind] = input[ind].\
replace('NFRAG=' + in_nfrags, 'NFRAG=' + str(nfrags))
# LIST OF CHARGES FOR FRAGMENTS
if 'ICHARG' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if 'ICHARG' in bit:
in_chrg = spl_line[val + 1]
chrgs = []
for frag in fragList:
chrgs.append(frag['chrg'])
input[ind] = input[ind].replace('ICHARG(1)=' + in_chrg, \
'ICHARG(1)=' + ','.join(str(p) for p in chrgs) + '\n')
# MULT
if 'MULT' in input[ind]:
spl_line = re.split('=', input[ind])
for val, bit in enumerate(spl_line):
if 'MULT' in bit:
mults = []
for frag in fragList:
mults.append(frag['mult'])
in_chrg = spl_line[val + 1]
input[ind] = input[ind].replace('MULT(1)=' + in_chrg,\
'MULT(1)=' + ','.join(str(p) for p in mults) + '\n')
# CHECK IF SPEC FOR ION CALCS
if 'RUNTYP' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if 'RUNTYP' in bit:
if spl_line[val + 1] == 'ENERGY':
ions = True
# MEMORY USED IN INPUT USED FOR JOB MEMORY
if 'MWORDS' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MWORDS' in input[ind]:
memory = spl_line[val + 1]
# MEMORY USED IN INPUT FOR JOB MEMORY
ddi = False
if 'MEMDDI' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MEMDDI' in input[ind]:
ddi = spl_line[val + 1]
# FOR FMO_IONS
if '$MP2' in input[ind]:
mp2 = input[ind]
if "GBASIS" in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'GBASIS' in input[ind]:
bset = spl_line[val + 1]
# REMOVE LINES FROM INPUT WITH NEW LIST
# FOR MANY LINE CHANGES - COORDS, INDAT, ATM LIST
atmUniq = []
numUniq = []
seenA = False
for line in input:
if type(line) != list:
# INDAT MAY BE DIFF NUMBER OF LINES TO NEW INDAT
if 'INDAT' in line:
fmo_input.append(' INDAT(1)=0,1,-' +
str(len(fragList[0]['ids'])) + ',\n')
# REMEMBER WHERE LAST FRAG FINISHED
n = len(fragList[0]['ids']) + 1
for frag in fragList:
if not frag is fragList[0]:
fmo_input.append(' '*13 + '0,' + str(n) + \
',-' + str(n + len(frag['ids']) - 1) + ',\n')
n += len(frag['ids'])
fmo_input.append(' ' * 13 + '0\n')
# SO NOT PASSED TO ELSE // EXTRA LINES TO DETERMINE FRAGMENT
elif re.search('^\s*0,[0-9]{1,3},-[0-9]{1,3},\s*$', line) or \
re.search('^\s*0\s*$', line):
pass
# ATOM LIST MAY BE DIFF NUMBER OF LINES TO NEW ATOM LIST
elif re.search('^\s*[A-Za-z]*\s*[0-9]*\.0*$', line):
if not seenA:
for i in xyzData:
atmUniq.append(i[0])
numUniq.append(i[1])
atmUniq = list(set(atmUniq))
for i in range(len(atmUniq)):
for sym, data in pTable.items():
if sym == atmUniq[i]:
fmo_input.append(' ' + str(atmUniq[i]) + ' ' + \
str(data[0]) + '\n')
seenA = True
# EVERY OTHER LINE AS IS
else:
fmo_input.append(line)
else:
fmo_input.append(line)
# HARDWARE FOR WRITING
hw = host()
if ions:
# FOR EACH FRAGMENT
for frag in fragList:
ifrag = []
for ID in frag['ids']:
atm = atmList[ID]
ifrag.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDER AND XYZ
if not os.path.isdir(npath + name + '-' + frag["name"]):
os.mkdir(npath + name + '-' + frag["name"])
write_xyz(npath + name + '-' + frag["name"] + '/',
name + '-' + frag["name"], ifrag)
# INPUT AND OUTPUT FOR JOB
input = fmo_ions(str(frag['chrg']), ifrag, bset, mp2)
write_gmsInp(npath + name + '-' + frag["name"] + '/',
name + '-' + frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
# lines = job_replace(name, jobTemp)
lines = job_replace(name + '-' + frag["name"], jobTemp)
else:
if hw == 'rjn':
lines = gms_rjnJob(name + '-' + frag["name"])
elif hw == 'mgs':
lines = gms_mgsJob(name + '-' + frag["name"])
elif hw == 'gai':
lines = gms_gaiJob(name + '-' + frag["name"])
elif hw == 'mas':
lines = gms_masJob(name + '-' + frag["name"])
elif hw == 'mon':
lines = gms_monJob(name + '-' + frag["name"])
elif hw == 'stm':
lines = gms_stmJob(name + '-' + frag["name"])
if lines:
write_job(npath + name + '-' + frag["name"] + '/',
name + '-' + frag["name"], lines)
# -------------------------------------------------
# WRITE INP
write_gmsInp(npath, name, fmo_input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
if hw == 'rjn':
lines = fmo_rjnJob(name, nfrags, memory, ddi)
elif hw == 'mgs':
lines = fmo_mgsJob(name, nfrags, memory, ddi)
elif hw == 'stm':
lines = fmo_stmJob(name, nfrags, memory, ddi)
elif hw == 'gai':
lines = fmo_gaiJob(name) #, nfrags, memory, ddi)
elif hw == 'mon':
lines = fmo_monJob(name, nfrags, memory, ddi)
elif hw == 'mas':
lines = fmo_masJob(name, nfrags, memory, ddi)
if lines:
write_job(npath, name, lines)
def fmo(path, File, template, sysData, jobTemp):
import os, re
from general import hardware
from chemData import pTable
from templates import fmo_rjnJob
from templates import fmo_mgsJob
from templates import fmo_gaiJob
from templates import gms_rjnJob
from templates import gms_mgsJob
from templates import gms_gaiJob
from tempInp import fmo_ions
from write import write_xyz
from write import write_gmsInp
from write import write_job
# NAME FOR WRITING FILE, DIRS
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDir(path, File, template)
# UNPACK sysData
fmo = True
mp2 = False
fragList, atmList, totChrg, totMult = sysData
# NUMBER OF FRAGS
nfrags = len(fragList)
# MAKE xyzData
xyzData = []
# USE LIST OF IDS TO APPEND
for frag in fragList:
for ID in frag['ids']:
atm = atmList[ID]
xyzData.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# TEMPLATE LINES
input = xyzTemp(path, template, xyzData)
#print(input)
fmo_input = []
# ONE LINE REPLACEMENTS - NO MULT YET ***
# IF RUNTYP IS ENERGY MAKE ION JOBS
ions = False
for ind in range(len(input)):
if 'NGROUP' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'NGROUP':
in_grp = spl_line[val + 1]
if in_grp != str(nfrags):
#print('Changing NGROUP to', nfrags)
input[ind] = input[ind].\
replace('NGROUP=' + in_grp, 'NGROUP=' + str(nfrags))
# CHECK NFRAG = NO. OF FOUND FRAGMENTS
if 'NFRAG' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'NFRAG':
in_nfrags = spl_line[val + 1]
if in_nfrags != str(nfrags):
#print('Changing NFRAG to', nfrags)
input[ind] = input[ind].\
replace('NFRAG=' + in_nfrags, 'NFRAG=' + str(nfrags))
# LIST OF CHARGES FOR FRAGMENTS
if 'ICHARG' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if 'ICHARG' in bit:
in_chrg = spl_line[val + 1]
chrgs = []
for frag in fragList:
chrgs.append(frag['chrg'])
input[ind] = input[ind].replace('ICHARG(1)=' + in_chrg, \
'ICHARG(1)=' + ','.join(str(p) for p in chrgs) + '\n')
# MULT
if 'MULT' in input[ind]:
spl_line = re.split('=', input[ind])
for val, bit in enumerate(spl_line):
if 'MULT' in bit:
mults = []
for frag in fragList:
mults.append(frag['mult'])
in_chrg = spl_line[val + 1]
input[ind] = input[ind].replace('MULT(1)=' + in_chrg,\
'MULT(1)=' + ','.join(str(p) for p in mults) + '\n')
# CHECK IF SPEC FOR ION CALCS
if 'RUNTYP' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if 'RUNTYP' in bit:
if spl_line[val + 1] == 'ENERGY':
ions = True
# MEMORY USED IN INPUT USED FOR JOB MEMORY
if 'MWORDS' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MWORDS' in input[ind]:
memory = spl_line[val + 1]
# MEMORY USED IN INPUT FOR JOB MEMORY
ddi = False
if 'MEMDDI' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MEMDDI' in input[ind]:
ddi = spl_line[val + 1]
# FOR FMO_IONS
if '$MP2' in input[ind]:
mp2 = input[ind]
if "GBASIS" in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'GBASIS' in input[ind]:
bset = spl_line[val + 1]
# REMOVE LINES FROM INPUT WITH NEW LIST
# FOR MANY LINE CHANGES - COORDS, INDAT, ATM LIST
atmUniq = []
numUniq = []
seenA = False
for line in input:
if type(line) != list:
# INDAT MAY BE DIFF NUMBER OF LINES TO NEW INDAT
if 'INDAT' in line:
fmo_input.append(' INDAT(1)=0,1,-' +
str(fragList[0]['ids'][-1] + 1) + ',\n')
for frag in fragList:
if not frag is fragList[0]:
fmo_input.append(' '*13 + '0,' + str(frag['ids'][0] + 1) + \
',-' + str(frag['ids'][-1] + 1) + ',\n')
fmo_input.append(' ' * 13 + '0\n')
# SO NOT PASSED TO ELSE // EXTRA LINES TO DETERMINE FRAGMENT
elif re.search('^\s*0,[0-9]{1,3},-[0-9]{1,3},\s*$', line) or \
re.search('^\s*0\s*$', line):
pass
# ATOM LIST MAY BE DIFF NUMBER OF LINES TO NEW ATOM LIST
elif re.search('^\s*[A-Za-z]*\s*[0-9]*\.0*$', line):
if not seenA:
for i in xyzData:
atmUniq.append(i[0])
numUniq.append(i[1])
atmUniq = list(set(atmUniq))
for i in range(len(atmUniq)):
for sym, data in pTable.items():
if sym == atmUniq[i]:
fmo_input.append(' ' + str(atmUniq[i]) + ' ' + \
str(data[0]) + '\n')
seenA = True
# EVERY OTHER LINE AS IS
else:
fmo_input.append(line)
else:
fmo_input.append(line)
# HARDWARE FOR WRITING
hw = hardware()
# XYZ OF IONS ------------------------------------
if ions:
ncat = 0
nani = 0
nnrt = 0
nunk = 0
# FOR EACH FRAGMENT
for i, frag in enumerate(fragList):
ifrag = []
for val, atm in enumerate(xyzData):
if val in frag['ids']:
ifrag.append(atm)
# IN CASE QUESTION MARK
try:
if frag['chrg'] < 0:
ion = 'anion' + str(nani)
nani += 1
elif frag['chrg'] > 0:
ion = 'cation' + str(ncat)
ncat += 1
else:
ion = 'neutral' + str(nnrt)
nnrt += 1
except:
if frag['chrg'] == '?':
ion = 'unknown' + str(nunk)
nunk += 1
# MAKE FOLDER AND XYZ
if not os.path.isdir(npath + ion):
os.mkdir(npath + ion)
write_xyz(npath + ion + '/', ion, ifrag)
# INPUT AND OUTPUT FOR JOB
input = fmo_ions(str(frag['chrg']), ifrag, bset, mp2)
write_gmsInp(npath + ion + '/', ion, input)
# WRITE JOB
if hw == 'rjn':
lines = gms_rjnJob(ion, memory, ddi)
if hw == 'mgs':
lines = gms_mgsJob(ion, memory, ddi)
if hw == 'gai':
lines = gms_gaiJob(ion, memory, ddi)
write_job(npath + fol + '/', ion, lines)
# -------------------------------------------------
# WRITE INP
write_gmsInp(npath, name, fmo_input)
# WRITE JOB
if jobTemp:
lines = job_replace(name, jobTemp)
else:
if hw == 'rjn':
lines = fmo_rjnJob(name, nfrags, memory, ddi)
if hw == 'mgs':
lines = fmo_mgsJob(name, nfrags, memory, ddi)
if hw == 'gai':
lines = fmo_gaiJob(name) #, nfrags, memory, ddi)
write_job(npath, name, lines)