def orc(path, File, template, sysData, jobTemp):
import re
from supercomp import host
from templates import orc_rjnJob
from write import write_inp
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"]])
# PUT XYZ IN TEMPLATE
input = xyzTemp(path, template, xyzData)
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\*xyzfile\s*-?[0-9]\s*-?[0-9]\s*', input[i]):
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
line = input[i].split()
if '.xyz' in line[-1]:
input[i] = '*xyzfile ' + str(totChrg) + ' ' + str(
totMult) + ' ' + line[-1]
if re.search('.xyz', input[i]):
line = input[i].strip()
line = line.rsplit(' ', 1)[0]
input[i] = line + ' ' + name + '.xyz\n'
# WRITE INP
write_inp(npath, name, input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = orc_rjnJob(name)
if lines:
write_job(npath, name, lines)
def psi(path, File, template, sysData, jobTemp):
import re
from general import xyzPull
from general import hardware
from system import systemData
from templates import psi_rjnJob
from templates import psi_gaiJob
from write import write_inp
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 ID in frag['ids']:
atm = atmList[ID]
xyzData.append([atm['sym'], atm["x"], atm["y"], atm["z"]])
# PUT XYZ IN TEMPLATE
input = xyzTemp(path, template, xyzData)
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
input[i] = ' ' + str(totChrg) + ' ' + str(totMult) + '\n'
# WRITE INP
write_inp(npath, name, input)
# MEMORY
for line in input:
if 'memory' in line:
line = line.split()
memory = int(line[1])
# WRITE JOB
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = hardware()
if hw == 'rjn':
lines = psi_rjnJob(name)
if hw == 'gai':
lines = psi_gaiJob(name)
write_job(npath, name, lines)
def g09(path, File, template, sysData):
# CREATES JOB FILE FROM TEMPLATE AND .xyz
import re
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# FOR MORE THAN ONE TEMPLATE IN DIR
temp = numTemp(path)
if temp > 1:
name = name + '-' + template.replace('.template', '')\
.replace('template', '')
# UNPACK LIST
fragList, atmList, totChrg, totMult = sysData
# CREATE xyzData
xyzData = []
for frag in fragList:
for atm in atmList:
if atm['id'] in frag['ids']:
xyzData.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# PUT XYZ COORDS IN TEMPLATE
input = xyzTemp(path, template, xyzData)
# ADD COORDS IN TEMPLATE
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE NAMES BEFORE LOG ETC.
input[i] = job_replace(name, input[i])
# CHANGE CHARGE AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# DON'T CHANGE IF NOT KNOWN
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
input[i] = str(totChrg) + ' ' + str(totMult) + '\n'
write_job(path, name, input)
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 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 g09(path, File, template, sysData):
# CREATES JOB FILE FROM TEMPLATE AND .xyz
import re
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# FOR MORE THAN ONE TEMPLATE IN DIR
temp = numTemp(path)
if temp > 1:
name = name + '-' + template.replace('.template', '')\
.replace('template', '')
# UNPACK LIST
fragList, atmList, totChrg, totMult = sysData
# CREATE xyzData
xyzData = []
for frag in fragList:
for ID in frag['ids']:
atm = atmList[ID]
xyzData.append([atm['sym'], atm["x"], atm["y"], atm["z"]])
# PUT XYZ COORDS IN TEMPLATE
input = xyzTemp(path, template, xyzData)
# ADD COORDS IN TEMPLATE
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE NAMES BEFORE LOG Ect.
input[i] = job_replace(name, input[i])
# CHANGE CHARGE AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# DON'T CHANGE IF NOT KNOWN
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
input[i] = str(totChrg) + ' ' + str(totMult) + '\n'
# CHANGE OUTPUT NAME
# if re.search('\.log', input[i]) \
# or re.search('\.out', input[i]):
# # KEEP LINE TO REPLACE
# chng = input[i].split()
# for val, bit in enumerate(chng):
# print(chng)
# if '.log' in bit:
# print(bit)
# n = val
# # chng[n] = a1b3d2.log
# input[i] = input[i].replace(chng[n], name + '.log')
#
# # CHANGE CHECKPOINT NAME
# if re.search('%chk', input[i]): # %chk=reactant.chk
# # KEEP LINE TO REPLACE
# chng = input[i].split('=')
# for val, bit in enumerate(chng):
# if '%chk' in bit:
# n = val + 1
# # chng[n] = a1b3d2.log
# input[i] = input[i].replace(chng[n], name + '.chk\n')
write_job(path, name, input)
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)
def orc_cpoise(path, File, template, sysData, jobTemp, dist):
import os, re
from supercomp import host
from genJob import xyzTemp
from genJob import job_replace
from templates import orc_rjnJob
from write import write_inp
from write import write_xyz
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDirCP(path, File, template)
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
# IF NOT RADIAL CUTOFF FOR MOLS INCLUDED DO ALL
if not dist:
# FOR EACH FRAGMENT
for frag in fragList:
ifrag = []
for atm in atmList:
if atm['id'] in frag['ids']:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
else:
# MAKE OTHER FRAGS GHOST
ifrag.append([atm['sym'] + ':'] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDERS
if not os.path.isdir(npath + frag["name"]):
os.mkdir(npath + frag["name"])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\*xyzfile\s*-?[0-9]\s*-?[0-9]\s*', input[i]):
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
line = input[i].split()
if '.xyz' in line[-1]:
input[i] = '*xyz ' + str(frag["chrg"]) + ' ' + str(frag["mult"]) + '\n'
# ADD XYZ AS GHOST ATOMS
for atm in ifrag:
i += 1
input.insert(i, atm)
# END XYZ
input.insert(i+1, '*')
# WILL CHANGE NUMBER OF LINES - DO NOT CONTINUE THIS LOOP
break
# WRITE INPUT FILE FOR EACH FRAG
write_inp(npath + frag["name"] + '/', name +'-'+ frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name +'-'+ frag["name"], jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = orc_rjnJob(name +'-'+ frag["name"])
if lines:
write_job(npath + frag["name"] + '/', name +'-'+ frag["name"], lines)
# IF RADIAL CUTOFF FOR MOLS INCLUDED IN EACH FILE
else:
from xyzGenerate import xyzShell
# GET < DIST SEPARATED FRAGS
# xyzList = [frag, mol, ghost atoms]
xyzList = xyzShell(path, File, sysData, dist, returnList=True)
# FOR EACH FRAGMENT CENTER
for frag, firstMol, otherMol in xyzList:
ifrag = []
for atm in firstMol:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
for atm in otherMol:
ifrag.append([atm['sym'] + ":"] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDERS
if not os.path.isdir(npath + frag["name"]):
os.mkdir(npath + frag["name"])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
# MEMORY OF INPUT NEEDS TO BE >>> MEM JOB
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\*xyzfile\s*-?[0-9]\s*-?[0-9]\s*', input[i]):
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
line = input[i].split()
if '.xyz' in line[-1]:
input[i] = '*xyzfile ' + str(totChrg) + ' ' + str(totMult) + ' ' +line[-1]
if re.search('.xyz', input[i]):
line = input[i].strip()
line = line.rsplit(' ', 1)[0]
input[i] = line+' '+name+'-ghost.xyz\n'
# WRITE GHOST FILE XYZ
write_xyz(npath + frag["name"] + '/', frag["name"] + "-ghost", ifrag)
# WRITE INPUT FILE FOR EACH FRAG
write_inp(npath + frag["name"] + '/', frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(frag["name"], jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = orc_rjnJob(frag["name"])
if lines:
write_job(npath + frag["name"] + '/', frag["name"], lines)
def psi_cpoise(path, File, template, sysData, jobTemp, dist):
import os, re
from supercomp import host
from genJob import xyzTemp
from genJob import job_replace
from templates import psi_rjnJob
from templates import psi_gaiJob
from templates import psi_masJob
from write import write_inp
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDirCP(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"]])
# PUT XYZ IN TEMPLATE
input = xyzTemp(path, template, xyzData)
# IF bsse_type='cp' PSI4 ONLY ONE CALC
cp_type = False
for line in input:
if "bsse_type=" in line and "'cp'" in line:
cp_type = True
# IF bsse_type='cp' PSI4 ONLY ONE CALC
if cp_type:
# REMOVE EXTRA '--' AND CHARGE MULTIPLICITY
cp_input = []
for line in input:
if type(line) != list:
if '--' in line:
pass
elif re.search('\s*-?[0-9]\s*[0-9]\s*', line):
pass
else:
cp_input.append(line)
else:
cp_input.append(line)
# COUNT WHICH ATOM UP TO
count = 0
input = []
for i in range(len(cp_input)):
# IF ATOM LINE
if type(cp_input[i]) is list:
# FOR EACH FRAG
put = False
for frag in fragList:
# IF ATOM NUMBER LAST ATOMS OF FRAG
if count == frag['ids'][0]:
# IF NOT FIRST FRAG
if not count == fragList[0]['ids'][0]:
input.append('--\n')
input.append(str(frag['chrg'])+' '+str(frag['mult'])+'\n')
input.append(cp_input[i])
put = True
if not put:
input.append(cp_input[i])
count += 1
else:
input.append(cp_input[i])
# WRITE INP
write_inp(npath, name, input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = psi_rjnJob(name)
elif hw == 'gai':
lines = psi_gaiJob(name)
elif hw == 'mas':
lines = psi_masJob(name)
if lines:
write_job(npath, name, lines)
# NORMAL INPUT -------------------------
else:
# IF NOT RADIAL CUTOFF FOR MOLS INCLUDED DO ALL
if not dist:
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE MEMORY to 64
#if 'memory' in input[i]:
# line = input[i].split()
# memory = line[1]
# input[i] = input[i].replace(memory, '64')
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(totChrg) + ' ' + str(totMult) + '\n'
# WRITE INP
write_inp(npath, name, input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = psi_rjnJob(name)
elif hw == 'gai':
lines = psi_gaiJob(name)
elif hw == 'mas':
lines = psi_masJob(name)
if lines:
write_job(npath, name, lines)
# FOR EACH FRAGMENT
for frag in fragList:
ifrag = []
for atm in atmList:
if atm['id'] in frag['ids']:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
else:
# MAKE OTHER FRAGS GHOST
ifrag.append(['@' + atm['sym']] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDERS
if not os.path.isdir(npath + frag["name"]):
os.mkdir(npath + frag["name"])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
# MEMORY OF INPUT NEEDS TO BE >>> MEM JOB
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(frag['chrg']) + ' ' + str(totMult) + '\n'
# WRITE INPUT FILE FOR EACH FRAG
write_inp(npath + frag["name"] + '/', frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(frag["name"], jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = psi_rjnJob(frag["name"])
elif hw == 'gai':
lines = psi_gaiJob(frag["name"])
elif hw == 'mas':
lines = psi_masJob(frag["name"])
if lines:
write_job(npath + frag["name"] + '/', frag["name"], lines)
# IF RADIAL CUTOFF FOR MOLS INCLUDED IN EACH FILE
else:
from xyzGenerate import xyzShell
# GET < DIST SEPARATED FRAGS
# xyzList = [frag, mol, ghost atoms]
xyzList = xyzShell(path, File, sysData, dist, returnList=True)
# FOR EACH FRAGMENT CENTER
for frag, firstMol, otherMol in xyzList:
ifrag = []
for atm in firstMol:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
for atm in otherMol:
ifrag.append(['@' + atm['sym']] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDERS
if not os.path.isdir(npath + frag["name"]):
os.mkdir(npath + frag["name"])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
# MEMORY OF INPUT NEEDS TO BE >>> MEM JOB
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(frag['chrg']) + ' ' + str(totMult) + '\n'
# CHANGE MEMORY
if re.search('memory', input[i]):
line = re.split(' |G|g', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '64')
break
# WRITE INPUT FILE FOR EACH FRAG
write_inp(npath + frag["name"] + '/', frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(frag["name"], jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = psi_rjnJob(frag["name"])
elif hw == 'gai':
lines = psi_gaiJob(frag["name"])
elif hw == 'mas':
lines = psi_masJob(frag["name"])
if lines:
write_job(npath + frag["name"] + '/', frag["name"], lines)
def g09_cpoise(path, File, template, sysData, dist):
# CREATES JOB FILE FROM TEMPLATE AND .xyz
import re
from genJob import xyzTemp
from write import write_job
# NAME AFTER COUNTERPOISE
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDirCP(path, File, template)
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
nfrags = len(fragList)
if not dist:
# 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"]])
# PUT XYZ IN TEMPLATE
input = xyzTemp(path, template, xyzData)
input_cp = input[:]
# CHANGE INPUT LINES
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(totChrg) + ' ' + str(totMult) + '\n'
# CHANGE OUTPUT NAME
if re.search('\.log', input[i]) \
or re.search('\.out', input[i]):
# KEEP LINE TO REPLACE
chng = input[i].split()
for val, bit in enumerate(chng):
if '.log' in bit:
n = val
# chng[n] = a1b3d2.log
input[i] = input[i].replace(chng[n], name + '.log')
# WRITE JOB FOR TOTAL CALC
write_job(npath, name, input)
# WRITE JOB FOR CPOISE CORRECTION
# MAKE SURE INTO INPUT
inInput = False
# COUNT PLACE IN COORDS
t = 0
for i in range(len(input_cp)):
if "module load" in input_cp[i]:
inInput = True
if inInput and type(input_cp[i]) != list:
if "#" in input_cp[i]:
if 'counterpoise' in input_cp[i]:
input_cp[i] = input_cp[i].replace("counterpoise=*",'')
else:
input_cp[i] = input_cp[i].\
replace('\n'," counterpoise=" + str(nfrags) + '\n')
elif re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input_cp[i]):
# IF CHRG = MULT COULD BE TRICKY
input_cp[i] = str(totChrg) + ',' + str(totMult)
for frag in fragList:
input_cp[i] += ' ' + str(frag['chrg']) + ',' + str(frag['mult'])
input_cp[i] = input_cp[i] + '\n'
# CHANGE OUTPUT NAME
if re.search('\.log', input_cp[i]) or re.search('\.out', input_cp[i]):
# KEEP LINE TO REPLACE
chng = input_cp[i].split()
for val, bit in enumerate(chng):
if '.log' in bit:
n = val
# chng[n] = blahblah.log
input_cp[i] = input_cp[i].replace(chng[n], 'cp-' + name + '.log')
# FIND WHICH FRAG ATOM PART OF
elif inInput and type(input_cp[i]) == list:
atm = atmList[t]
input_cp[i] = [atm['sym'], atm["x"], atm["y"], atm["z"], str(int(atm["grp"]) + 1)]
# NUMBER ATOM
t += 1
# WRITE COUNTERPOISE JOB
write_job(npath, 'CP-'+ name, input_cp, cp = True)
# FOR EACH FRAGMENT
for frag in fragList:
ifrag = []
for atm in atmList:
if atm['id'] in frag['ids']:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
else:
# MAKE OTHER FRAGS GHOST
ifrag.append([atm['sym']+ '-Bq'] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
# MEMORY OF INPUT NEEDS TO BE >>> MEM JOB
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(frag['chrg']) + ' ' + str(totMult) + '\n'
# CHANGE MEMORY
elif re.search(' mem', input[i]):
line = re.split('=|G|g', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '16')
break
elif re.search('%mem', input[i]):
line = re.split('=|G|g', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '14')
break
elif re.search('ncpus', input[i]):
line = re.split('=', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '8\n')
break
elif re.search('nprocshared', input[i]):
line = re.split('=', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '8\n')
break
# WRITE INPUT FILE FOR EACH FRAG
write_job(npath, frag["name"], input)
# DIST RADIUS TO EXCLUDE MOLS FROM CP CORRECTION
else:
from xyzGenerate import xyzShell
# GET < DIST SEPARATED FRAGS
# xyzList = [frag, mol, ghost atoms]
xyzList = xyzShell(path, File, sysData, dist)
# FOR EACH FRAGMENT CENTER
for frag, firstMol, otherMol in xyzList:
ifrag = []
for atm in firstMol:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
for atm in otherMol:
ifrag.append([atm['sym'] + '-Bq'] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
# MEMORY OF INPUT NEEDS TO BE >>> MEM JOB
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(frag['chrg']) + ' ' + str(totMult) + '\n'
# CHANGE MEMORY
elif re.search(' mem', input[i]):
line = re.split('=|G|g', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '16')
break
elif re.search('%mem', input[i]):
line = re.split('=|G|g', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '14')
break
elif re.search('ncpus', input[i]):
line = re.split('=', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '8\n')
break
elif re.search('nprocshared', input[i]):
line = re.split('=', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '8\n')
break
# WRITE INPUT FILE FOR EACH FRAG
write_job(npath, frag["name"], input)