def expand(path, File, sysData, dists):
from write import write_xyz
import numpy as np
fragList, atmList, totChrg, totMult = sysData
# GET SMALLEST INTERIONIC DISTANCE
# a, b ARE INDEX OF SMALLEST DIST ATOMS
dmin = get_min_interionic_dist(atmList)
atmList, fragList = rearrange_list(atmList, fragList)
relxyz, coords = get_relative_coords(atmList, fragList)
# FIND NEW ORIGIN // MEAN OF ALL POINTS
d_origin = np.mean(coords, axis=0)
# REDEFINE POINTS W.R.T NEW ORIGIN
coords = coords - d_origin
# FOR EACH DISTANCE
for dist in dists:
scale = dist / dmin
# SCALE
coords_new = scale * coords
# PLUS POSITION OF EACH TO ALL RELATIVE POSITIONS TO GET NEW XYZ
coords_new = coords_new + relxyz
# RELXYZ AND COORDS IN ORDER OF APPEARANCE IN FRAGLIST
i = 0
newxyz = []
for frag in fragList:
for atm in atmList:
if atm["id"] in frag['ids_by_int_dist']:
newxyz.append([
atm["sym"], coords_new[i][0], coords_new[i][1],
coords_new[i][2]
])
i += 1
name = File.replace('.xyz', '_' + str(dist) + 'A')
write_xyz(path, name, newxyz)
def separate_mols(path, File, sysData):
from write import write_xyz
# NAME FOR WRITING FILE, DIRS
name = File.replace('.xyz', '').split('_')[0]
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
# 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"]])
# WRITE XYZ
write_xyz(path, name + '-' + frag["name"], ifrag)
def separate_mols(path, File, sysData):
from write import write_xyz
# NAME FOR WRITING FILE, DIRS
name = File.replace('.xyz','').split('_')[0]
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
ncat, nani, nntr, nunk = 0, 0, 0, 0
# 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"]])
# 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(nntr)
nntr += 1
except:
if frag['chrg'] == '?':
ion = 'unknown' + str(nunk)
nunk += 1
# WRITE XYZ
write_xyz(path, name + '-' + ion, ifrag)
def sort(path, File, soft):
import os, re
from shutil import copyfile
from general import software
from general import gms_check_spec
from general import g09_check_spec
from general import psi_check_spec
from pprint import stat_print
from write import write_xyz
if soft:
# CHECK IF SPEC AND CHECK IF LOG TERMINA
if soft == 'gms':
spec = gms_check_spec(path, File)
err, ext, stat = gms_log(path, File, spec)
elif soft == 'g09':
spec = g09_check_spec(path, File)
err, ext, stat = g09_log(path, File, spec)
elif soft == 'psi':
spec = psi_check_spec(path, File)
err, ext, stat = psi_log(path, File, spec)
# NAME WITH EXTENSION
name = File.replace('.log', ext).replace('.out', ext)
# PRINT MESSAGE
if spec and not err:
stat_print(path, File, 2)
if not spec:
# SUCCESSFUL JOB
if not err:
stat_print(path, File, stat)
# GET GEOMETRY
id = "spec/"
if soft == 'gms':
geom = gms_geom(path, File, True)
elif soft == 'g09':
geom = g09_geom(path, File, True)
elif soft == 'psi':
geom = psi_geom(path, File, True)
if not os.path.isdir(path + id):
os.makedirs(path + id)
#copyfile(path + File, path + id +'c-'+ File)
# WRITE XYZ
write_xyz(path + id, name, geom)
# FOR ALL UNFINISHED
else:
# GET GEOMETRY
if soft == 'gms':
geom = gms_geom(path, File, False)
elif soft == 'g09':
geom = g09_geom(path, File, False)
elif soft == 'psi':
geom = psi_geom(path, File, False)
# IF NO STEPS IN OPTIMISATION
if len(geom) == 0:
stat_print(path, File, 6)
name = File.replace('.out', '').replace('.log', '')
nam1 = name + '.xyz'
nam2 = name + '_'
nam3 = name + '_Fail.xyz'
# REGULAR XYZ NAME
try:
copyfile(path + nam1, path + "rerun/" + nam3)
except:
# IF XYZ NAME WITH EXTENTION
for fILE in os.listdir(path):
if nam2 in fILE:
if not os.path.exists(path + 'rerun'):
os.mkdir(path + 'rerun')
try:
copyfile(path + fILE,
path + "rerun/" + nam3)
except:
print(File +
": could not pull geom, zero steps")
# RETURNED GEOMETRY
else:
stat_print(path, File, stat)
if err in ['conv', 'hes']:
id = 'notConv/'
elif err in ['inp', 'max', 'mem', 'time']:
id = 'rerun/'
elif err in ['unk']:
id = 'unknown/'
if not os.path.isdir(path + id):
os.makedirs(path + id)
copyfile(path + File, path + id + 'f-' + File)
write_xyz(path + id, name, geom)
# IF FAILED SPEC
elif spec and err:
xyz = File.replace('.out', '.xyz') \
.replace('.log', '.xyz')
xyz_ = File.replace('.out', '_.+xyz') \
.replace('.log', '_.+xyz')
found = False
for file in os.listdir(path):
if xyz == file or re.search(xyz_, file):
if not os.path.exists(path + "rerun"):
os.mkdir(path + "rerun")
newExt = file.split('_')[0] + ext + '.xyz'
copyfile(path + file, path + "rerun/" + newExt)
stat_print(path, File, 16)
found = True
if not found:
stat_print(path, File, 15)
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)
def xyzShell(path, File, sysData, dist, returnList=False):
"""Uses a distance to create a shell of molecules
around each fragment."""
import math
from write import write_xyz
fragList, atmList, totChrg, totMult = sysData
# FOR EACH FRAGMENT
for val, frag in enumerate(fragList):
# GET ATOMS IN THE FRAGMENT
mol = []
# FOR EACH ATOM
for atm in atmList:
# IF ATOM IN THIS FRAG ADD TO mol
if atm["id"] in frag["ids"]:
mol.append(atm)
# GET CENTER OF MASS OF FRAGMENT
fragList[val]["com"] = get_center_of_mass(mol)
# FOR EACH FRAG
xyzs = []
for frag in fragList:
# ADD ORIGIN FRAG TO coordList
firstMol = []
otherMol = []
for atm in atmList:
if atm["id"] in frag["ids"]:
firstMol.append(atm)
# PAIR WITH SECOND FRAG
for frag2 in fragList:
if frag != frag2:
# GET DISTANCE BETWEEN REFERENCE FRAG AND EACH FRAG
s = (frag["com"][0] - frag2["com"][0]) ** 2 + \
(frag["com"][1] - frag2["com"][1]) ** 2 + \
(frag["com"][2] - frag2["com"][2]) ** 2
s = math.sqrt(s)
# CHECK IF CENTER OF MASS IS WITHIN DIST
if s < float(dist):
# ADD TO coordList
for atm in atmList:
if atm["id"] in frag2["ids"]:
otherMol.append(atm)
xyzs.append([frag, firstMol, otherMol])
# PRINT NUMBER OF ATOMS INCLUDED FOR EACH CALCULATION
print(frag["name"], ':', len(firstMol + otherMol))
# RETURN LIST
if returnList:
return xyzs
# ADD MOLECULE TOGETHER AND WRITE TO FILE
for xyz_parts in xyzs:
xyz = []
for atm in xyz_parts[1]:
xyz.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
for atm in xyz_parts[2]:
xyz.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# WRITE FRAGS WITHIN DIST TO XYZ IF NOT returnList
name = File.replace('.xyz',
'') + '-' + xyz_parts[0]["name"] + '-' + dist
# WRITE
write_xyz(path, name, xyz)
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)
