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 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)