def sep_mol(coords, distca, Type):
import math
import numpy as np
from pprint import detec
from chemData import pTable
atmList = []
for ID, line in enumerate(coords):
#print(line)
atmDict = {}
atmDict["id"] = ID
atmDict["sym"] = line[0]
atmDict["x"] = float(line[1])
atmDict["y"] = float(line[2])
atmDict["z"] = float(line[3])
atmDict["con"] = []
atmDict["grp_dist"] = False
atmDict["grp_vdw"] = False
for sym, data in pTable.items():
if atmDict["sym"] == sym:
atmDict["nu"] = data[0]
atmDict["mas"] = data[1]
atmDict["vdw"] = data[2]
atmList.append(atmDict)
natoms = len(atmList)
dist = np.zeros((natoms,natoms))
# FIND DISTS BETWEEN ALL ATOMS i & j
group_dist = 0
group_vdw = 0
for val, i in enumerate(atmList):
con_vwd = False
con_dist = False
# SECOND ATOM < DISTCA
for vals, j in enumerate(atmList):
if i != j:
a = (i["x"]-j["x"])**2 + (i["y"]-j["y"])**2\
+ (i["z"]-j["z"])**2
dist[val,vals] = math.sqrt(a)
# IF UNDER DISTCA ---------------------------------------
if dist[val, vals] < distca:
con_dist = True
# IF NEITHER I NOR J PART OF A GROUP
# ADD THEM TO A NEW GROUP
if i["grp_dist"] is False and j["grp_dist"] is False:
i["grp_dist"], j["grp_dist"] = group_dist, group_dist
group_dist += 1
# IF BOTH HAVE BEEN ASSIGNED TO A DIFF GROUP
elif not i["grp_dist"] is False and not j["grp_dist"] is False:
if i["grp_dist"] != j["grp_dist"]:
grp_chng = j["grp_dist"]
for k in atmList:
if k["grp_dist"] is grp_chng:
k["grp_dist"] = i["grp_dist"]
# IF j NOT ASSIGNED
elif not i["grp_dist"] is False and j["grp_dist"] is False:
j["grp_dist"] = i["grp_dist"]
# IF i NOT ASSIGNED
elif not j["grp_dist"] is False and i["grp_dist"] is False:
i["grp_dist"] = j["grp_dist"]
# CHECK IF CONNECTED USING VDW DATA -----------------------
#print(i["vdw"] + j["vdw"])
if dist[val, vals] < i["vdw"] + j["vdw"]:
# ADD TO ATOM LIST
if not j["id"] in i["con"]:
i["con"].append(j["id"])
j["con"].append(i["id"])
con_vwd = True
# IF NEITHER I NOR J PART OF A GROUP
# ADD THEM TO A NEW GROUP
if i["grp_vdw"] is False and j["grp_vdw"] is False:
i["grp_vdw"], j["grp_vdw"] = group_vdw, group_vdw
group_vdw += 1
# IF BOTH HAVE BEEN ASSIGNED TO A DIFF GROUP
elif not i["grp_vdw"] is False and not j["grp_vdw"] is False:
if i["grp_vdw"] != j["grp_vdw"]:
grp_chng = j["grp_vdw"]
for k in atmList:
if k["grp_vdw"] is grp_chng:
k["grp_vdw"] = i["grp_vdw"]
# IF j NOT ASSIGNED
elif not i["grp_vdw"] is False and j["grp_vdw"] is False:
j["grp_vdw"] = i["grp_vdw"]
# IF i NOT ASSIGNED
elif not j["grp_vdw"] is False and i["grp_vdw"] is False:
i["grp_vdw"] = j["grp_vdw"]
# IF LONER ATOM PUT IN ITS OWN GROUP
if not con_dist:
i["grp_dist"] = group_dist
group_dist += 1
if not con_vwd:
i["grp_vdw"] = group_vdw
group_vdw += 1
# REORDER GROUPS STARTING FROM 0
# CREATE fragList ----------------------------------------------------------------
if Type == 'check_dist':
# NUMBER FRAG
ncat, nani, nnrt, nunk, nrad = 0, 0, 0, 0, 0
print("-"*40)
print("SYSTEM USING CUTOFF DISTANCE:")
totChrg = 0
totMult = 1
nfrags_dist = 0
fragList = []
# FIND DISTANCES
for grp_dist in range(group_dist):
fragDict_dist = {}
fragDict_dist['ids'] = []
fragDict_dist['syms'] = []
foundnew = False
for atm in atmList:
if atm["grp_dist"] == grp_dist:
foundnew = True
atm["grp_dist"] = nfrags_dist
fragDict_dist['syms'].append(atm['sym'])
fragDict_dist['ids'].append(atm['id'])
if foundnew:
fragDict_dist['grp'] = nfrags_dist
# FIND CHARGE/MULT
if isCation(fragDict_dist['syms'], fragDict_dist['ids']):
fragDict_dist["chrg"] = 1
fragDict_dist["mult"] = 1
fragDict_dist["name"] = "cation" + str(ncat)
ncat += 1
if totChrg != '?':
totChrg += 1
elif isAnion(fragDict_dist['syms'], fragDict_dist['ids']):
fragDict_dist["chrg"] = -1
fragDict_dist["mult"] = 1
fragDict_dist["name"] = "anion" + str(nani)
nani += 1
if totChrg != '?':
totChrg += -1
elif isNeutral(fragDict_dist['syms'], fragDict_dist['ids']):
fragDict_dist["chrg"] = 0
fragDict_dist["mult"] = 1
fragDict_dist["name"] = "neutral" + str(nnrt)
nnrt += 1
elif isRadical(fragDict_dist['syms'], fragDict_dist['ids']):
fragDict_dist["chrg"] = 0
fragDict_dist["mult"] = 2
fragDict_dist["name"] = "radical" + str(nrad)
nrad += 1
totMult = 2
else:
# FIND CHEMICAL FORMULA
syms = []
chemForm = ''
for sym in fragDict_dist['syms']:
if sym not in syms:
numTimes = fragDict_dist['syms'].count(sym)
chemForm += sym + str(numTimes)
syms.append(sym)
detec("unknown", chemForm, " ".join(str(x+1) for x in fragDict_dist['ids']))
fragDict_dist["chrg"] = '?'
fragDict_dist["mult"] = '?'
fragDict_dist["name"] = "unknown" + str(nunk)
nunk += 1
totChrg = '?'
totMult = '?'
# FOR NEXT FRAGMENT
fragList.append(fragDict_dist)
nfrags_dist += 1
elif Type == 'check_vdw':
# CREATE fragList --------------------------------------------------------
print("-"*40)
print("SYSTEM USING VDW's RADII:")
# PROPERTIES
totChrg = 0
totMult = 1
nfrags_vdw = 0
fragList = []
# NAMING
ncat, nani, nntr, nunk, nrad = 0, 0, 0, 0, 0
for grp_vdw in range(group_vdw):
fragDict_vdw = {}
fragDict_vdw['ids'] = []
fragDict_vdw['syms'] = []
foundnew = False
for atm in atmList:
if atm["grp_vdw"] == grp_vdw:
foundnew = True
atm["grp_vdw"] = nfrags_vdw
fragDict_vdw['syms'].append(atm['sym'])
fragDict_vdw['ids'].append(atm['id'])
if foundnew:
fragDict_vdw['grp'] = nfrags_vdw
# FIND CHARGE/MULT
if isCation(fragDict_vdw['syms'], fragDict_vdw['ids']):
fragDict_vdw["chrg"] = 1
fragDict_vdw["mult"] = 1
fragDict_vdw["name"] = "cation" + str(ncat)
ncat += 1
if totChrg != '?':
totChrg += 1
elif isAnion(fragDict_vdw['syms'], fragDict_vdw['ids']):
fragDict_vdw["chrg"] = -1
fragDict_vdw["mult"] = 1
fragDict_vdw["name"] = "anion" + str(nani)
nani += 1
if totChrg != '?':
totChrg += -1
elif isNeutral(fragDict_vdw['syms'], fragDict_vdw['ids']):
fragDict_vdw["chrg"] = 0
fragDict_vdw["mult"] = 1
fragDict_vdw["name"] = "neutral" + str(nntr)
nntr += 1
elif isRadical(fragDict_vdw['syms'], fragDict_vdw['ids']):
fragDict_vdw["chrg"] = 0
fragDict_vdw["mult"] = 2
fragDict_vdw["name"] = "radical" + str(nrad)
nrad += 1
totMult = 2
else:
# FIND CHEMICAL FORMULA
syms = []
chemForm = ''
for sym in fragDict_vdw['syms']:
if sym not in syms:
numTimes = fragDict_vdw['syms'].count(sym)
chemForm += sym + str(numTimes)
syms.append(sym)
detec("unknown", chemForm, " ".join(str(x+1) for x in fragDict_vdw['ids']))
fragDict_vdw["chrg"] = '?'
fragDict_vdw["mult"] = '?'
fragDict_vdw["name"] = "unknown" + str(nunk)
nunk += 1
totChrg = '?'
totMult = '?'
# FOR NEXT FRAGMENT
fragList.append(fragDict_vdw)
nfrags_vdw += 1
print('-'*40)
### fragList = {'ids': [21], 'syms': ['Cl'], 'grp_dist': 1, 'chrg': -1, 'mult': 1}
#for i in fragList:
# print(i)
### atmList = {'id': 710, 'sym': 'H', 'x': 11.5282, 'y': 7.0276, 'z': -18.5563, 'grp_dist': 80, 'nu': 1.0}
#for i in atmList:
# print(i)
#print(fragList, atmList, totChrg, totMult)
return atmList, fragList, totChrg, totMult
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 g09_geom(path, File, opt):
import os, re
from general import eof
from chemData import pTable
ginc = False
vals = False
end = False
coords = []
geom = []
hold = []
pattern = "-?[0-9]*\.[0-9]*\s*"
lines = eof(path, File, 0.4)
# GRAB GINC VALUES
if opt:
for line in lines:
if re.search("GINC", line):
# FINDS LAST CASE OF 'GINC'
coords = []
ginc = True
if ginc:
coords.append(line)
j = ''
# FOR ALL LINES
for i in coords:
# SUM ALL LINES TOGETHER AS CONTINUOUR STRING
j = j + i
j = j.replace('\n', '')
j = j.replace(' ', '')
j = j.split('\\')
# AND OPT GEOM
geom = []
pat = ",-?[0-9]*\.[0-9]*"
for line in j:
if re.search("^[A-Z]{1,2},?[a-z]?[0-9]*" + \
pat + pat + pat + "$", line):
line = line.split(',')
# SOMETIMES AN EXTRA COLUMN RETRIEVED?
geom.append([line[0], line[len(line) - 3],\
line[len(line) - 2], line[len(line) - 1]])
# FIND SECOND LAST STEP; LAST MAY NOT BE FINISHED
else:
with open(path + File, 'r+') as f:
try:
for line in f:
if vals:
if end:
if re.search("------------*", line):
vals = False
if re.search(pattern + pattern + pattern, line):
hold.append(line)
end = True
if "Coordinates" in line:
vals = True
end = False
coords = hold
hold = []
except:
print("Corrupt line passed in file ", File)
hold = []
for i in coords:
i = i.split()
hold.append([i[1], i[3], i[4], i[5]])
for i in hold:
for el, data in pTable.items():
if data[0] == int(i[0]):
geom.append([el, i[1], i[2], i[3]])
break
return geom
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)