def psi_log(path, File, spec):
import os
from general import eof
err = False
ext = False
stat = False
# CHECK FOR RAIJIN WALLTIME EXCEEDED
err, ext, stat = rjn_wall(path, File, err, ext, stat)
if not ext:
# LINES AT END OF FILE
lines = eof(path, File, 0.1)
#for line in lines:
if '4 exiting successfully' in lines[len(lines) - 1]:
stat = 7
ext = '_eGeom'
#break
# COMMON ERRORS
if not ext:
stat = 10
err = 'unk'
ext = '_unknown'
return err, ext, stat
def gms_log(path, File, spec):
import os
from general import eof
from pprint import stat_print
err = False
ext = False
stat = False
# CHECK FOR RAIJIN WALLTIME EXCEEDED
err, ext, stat = rjn_wall(path, File, err, ext, stat)
# IF NOT WALLTIME EXCEEDED
if not ext:
# LINES AT END OF FILE
lines = eof(path, File, 0.2)
for line in lines:
if "CHECK YOUR INPUT CHARGE AND MULT" in line:
stat = 8
err = 'inp'
ext = '_inpError'
break
elif "ERROR READING VARIABLE IDUM" in line:
stat = 9
err = 'inp'
ext = '_inpError'
break
elif "FAILURE TO LOCATE STATIONARY" in line:
stat = 4
err = 'max'
ext = '_maxIters'
break
elif "DDI Process" in line:
stat = 10
err = 'mem'
ext = '_memError'
break
elif "CORRUPTION OF THE HESSIAN" in line:
stat = 17
err = 'hes'
ext = '_hesError'
break
elif "DUE TO TIME LIMIT" in line:
stat = 11
err = 'time'
ext = '_timeLimit'
elif "ION OF GAMESS TERMINATED NORMA" in line:
stat = 7
ext = '_eGeom'
break
if not ext:
stat = 10
err = 'unk'
ext = '_unknown'
return err, ext, stat
def energy_psi(path, File, energy):
from logFile import psi_log
from general import psi_check_spec
from general import eof
HF = ''
ZP = ''
MP2 = ''
MP2_opp = ''
MP2_same = ''
sysDict = {}
spec = psi_check_spec(path, File)
err, ext, stat = psi_log(path, File, spec)
if spec:
typ = 'spe'
else:
typ = 'opt'
if not err:
lines = eof(path, File, 0.1)
for line in lines:
if "Total Energy =" in line:
MP2 = line.split()
MP2 = MP2[len(MP2) - 2]
elif 'Reference Energy' in line:
HF = line.split()
HF = HF[len(HF) - 2]
elif "Same-Spin Energy =" in line:
MP2_same = line.split()
MP2_same = MP2_same[len(MP2_same) - 2]
elif "Opposite-Spin Energy =" in line:
MP2_opp = line.split()
MP2_opp = MP2_opp[len(MP2_opp) - 2]
# FINDING ZP NOT INCLUDED
# CREATE DICTIONARY OF FILE
sysDict["Path"] = path
sysDict["File"] = File
sysDict["Type"] = typ
sysDict["HF" ] = HF
sysDict["ZP" ] = ZP
sysDict["MP2" ] = MP2
sysDict["MP2_same"] = MP2_same
sysDict["MP2_opp"] = MP2_opp
energy.append(sysDict)
return energy
def g09_log(path, File, spec):
import os, re
from general import eof
err = False
ext = False
stat = False
# CHECK FOR RAIJIN WALLTIME EXCEEDED
err, ext, stat = rjn_wall(path, File, err, ext, stat)
# IF NOT WALLTIME EXCEEDED
if not ext:
# LINES AT END OF FILE
lines = eof(path, File, 0.3)
for line in lines:
if 'Normal termination' in line:
stat = 7
ext = '_eGeom'
break
# COMMON ERRORS
if "Erroneous write" in line:
stat = 13
err = 'mem'
ext = '_diskError'
break
elif "link 9999" in line:
stat = 14
err = 'conv'
ext = '_convError'
break
elif "NtrErr" in line:
stat = 13
err = 'mem'
ext = '_diskError'
break
elif "Convergence fail" in line:
stat = 14
err = 'conv'
ext = '_convError'
break
elif "NtrErr Called from FileIO" in line:
stat = 14
err = 'conv'
ext = '_convError'
break
elif "galloc" in line or "GetChg" in line:
stat = 10
err = 'mem'
ext = '_memError'
break
elif "Out-of-memory" in line:
stat = 10
err = 'mem'
ext = '_memError'
break
if not ext:
stat = 12
err = 'unk'
ext = '_unknown'
return err, ext, stat
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 energy_g09(path, File, energy):
import re
from logFile import g09_log
from general import g09_check_spec
from general import eof
HF = ''
ZP = ''
MP2 = ''
sysDict = {}
spec = g09_check_spec(path, File)
err, ext, stat = g09_log(path, File, spec)
if spec:
typ = 'spe'
else:
typ = 'opt'
coords = []
if not err:
lines = eof(path, File, 0.1)
ginc = False
for line in lines:
if re.search("GINC", line):
# FINDS LAST CASE OF 'GINC'
ginc = True
if ginc:
coords.append(line)
if not coords:
lines = eof(path, File, 0.4)
for line in lines:
if re.search("GINC", line):
# FINDS LAST CASE OF 'GINC'
ginc = True
if ginc:
coords.append(line)
j = ''
# FOR ALL LINES
for i in coords:
# SUM ALL LINES TOGETHER AS CONTINUOUS STRING
j = j + i
j = j.replace('\n', '')
j = j.replace(' ','')
j = j.split('\\')
# FIND HF AND ZPVE
for line in j:
if 'HF=' in line:
HF = line.split('=')
HF = HF[1]
pass
if 'ZeroPoint' in line:
ZP = line.split('=')
ZP = line.split('=')
ZP = ZP[1]
if 'MP2' in line:
MP2 = line.split('=')
MP2 = MP2[1]
# CREATE DICTIONARY OF FILE
sysDict["Path"] = path
sysDict["File"] = File
sysDict["Type"] = typ
sysDict["HF" ] = HF
sysDict["ZP" ] = ZP
sysDict["MP2" ] = MP2
### A bit hacky
sysDict["MP2_opp"] = ''
sysDict["MP2_same"] = ''
energy.append(sysDict)
return energy
def energy_gms(path, File, energy):
from logFile import gms_log
from general import gms_check_spec
from general import eof
spec = gms_check_spec(path, File)
err, ext, stat = gms_log(path, File, spec)
scs = False
HF = ''
ZP = ''
MP2 = ''
sysDict = {}
if spec:
typ = 'spe'
else:
typ = 'opt'
if not err:
# CHECK IF FMO
fmo = False
with open(path + File) as f:
for line in f:
if 'FMO' in line:
fmo = True
elif 'SCSOPO' in line:
scs = True
elif 'THE POINT GROUP OF THE M' in line:
break
lines = eof(path, File, 0.2)
if scs:
for line in lines:
if "E corr SCS" in line:
MP2 = line.split()
MP2 = MP2[len(MP2) - 1]
elif 'Euncorr HF' in line:
HF = line.split()
HF = HF[len(HF) - 1]
if fmo and HF == '':
for line in lines:
if "Ecorr" in line:
MP2 = line.split()
MP2 = MP2[len(MP2) - 1]
elif 'Euncorr' in line:
HF = line.split()
HF = HF[len(HF) - 1]
if not fmo:
for line in lines:
if "SCS-MP2" in line:
MP2 = line.split()
if 'E=' not in MP2[1]:
MP2 = MP2[1]
# E(MP2)= -76.2919350192 ACTUALLY, THIS IS THE SCS-MP2 ENERGY
else:
# SCS-MP2 E= -1161.8759377385 (magnus, massive)
MP2 = MP2[-1]
elif 'E(0)=' in line:
HF = line.split()
HF = HF[len(HF) - 1]
# FINDING ZP NOT INCLUDED
# CREATE DICTIONARY OF FILE
sysDict["Path"] = path
sysDict["File"] = File
sysDict["Type"] = typ
sysDict["HF" ] = HF
sysDict["ZP" ] = ZP
sysDict["MP2" ] = MP2
### A bit hacky
sysDict["MP2_opp"] = ''
sysDict["MP2_same"] = ''
energy.append(sysDict)
return energy