def prepareFirstInput(coordinate, stepSize):
#read the first file
gmsFile = GMSFile(sys.argv[1])
# increase MAXIT
gmsFile["CONTRL"]["MAXIT"]=200
if "MCSCF" in gmsFile:
gmsFile["MCSCF"]["MAXIT"]=200
# add the freeze point
gmsFile["STATPT"]["IFREEZ(1)"] = coordinate
#increment the coordinate
gmsFile["DATA"][coordinate-1] = float(gmsFile["DATA"][coordinate-1]) +stepSize
# read the vec
VEC=GAMESS.readVECGroupsFromFile(re.sub("\.inp",".dat",sys.argv[1]))[-1]
# prepare GUESS group
if "GUESS" not in gmsFile:
gmsFile["GUESS"] = GMSFile.parse_group("$GUESS GUESS=MOREAD $END")
else:
gmsFile["GUESS"]["GUESS"]="MOREAD"
gmsFile["GUESS"]["NORB"]= GAMESS.numberOfOrbitalsinVEC(VEC)
# add VEC group
try:
del gmsFile["VEC"]
except:
pass
gmsFile["VEC"]=VEC.strip()
if gmsFile["CONTRL"]["SCFTYP"] == "UHF":
del gmsFile["GUESS"]
#add the 1 postfix before file type e.g. test.inp > test1.inp
nextInFileName = re.sub("\.inp","1.inp",sys.argv[1])
#write the file
nextInFile = open(nextInFileName, 'w')
nextInFile.write(str(gmsFile))
nextInFile.close()
return nextInFileName
def askForCoordinateStepAndStepCount():
#open the input file
inFile = open(sys.argv[1], 'r')
print("The Data section of the input file is listed below:")
dataRow = 0
for line in inFile:
#check for $DATA group
datagroup = re.compile(r'\$DATA')
dataMatch = datagroup.search(line)
#if line begins $DATA section
if dataMatch:
dataRow += 1
#check for $END token
datagroup = re.compile(r'\$END')
endMatch = datagroup.search(line)
#if the $END token is for the $DATA group then stop counting
if dataRow and endMatch:
sys.stdout.write(line)
dataRow = 0
#if inside the data group
if dataRow:
sys.stdout.write(line)
dataRow += 1
inFile.close()
print("")
coordinateIndex = int(input("which coordinate do you want to scan over? "))
#define coordinate type and number
number = GAMESS.coordinateNumber(coordinateIndex)
type = GAMESS.ZMATCoordinateType(coordinateIndex)
print("")
numberOfSteps = int(input("numberOfSteps? "))
print("")
stepSize = float(input("stepSize? "))
print("")
print("You have selected to scan " + type + " " + str(number) + " over " + str(numberOfSteps) + " steps in increments of " + str(stepSize))
abort = input("Do you wish to confirm or abort?(C/A) ")
if abort.lower() == "a":
sys.exit()
else:
return [coordinateIndex,numberOfSteps,stepSize]
def prepareNextFile(LastInputFileName, coordinate, stepSize):
#read the first file
gmsFile = GMSFile(LastInputFileName)
# increase MAXIT
gmsFile["CONTRL"]["MAXIT"]=200
if "MCSCF" in gmsFile:
gmsFile["MCSCF"]["MAXIT"]=200
# add the freeze point
gmsFile["STATPT"]["IFREEZ(1)"] = coordinate
#read the optimized geometry
gmsFile["DATA"] = GMSFile.parse_group(GMSFileReader.read_data_group(re.sub("\.inp",".log",LastInputFileName)))
#increment the coordinate
gmsFile["DATA"][coordinate-1] = float(gmsFile["DATA"][coordinate-1]) +stepSize
# read the vec
VEC=GAMESS.readVECGroupsFromFile(re.sub("\.inp",".dat",sys.argv[1]))[-1]
# add VEC group
try:
del gmsFile["VEC"]
except:
pass
gmsFile["VEC"]=VEC.strip()
#add the 1 postfix before file type e.g. test.inp > test1.inp
nextInFileName = nextInputFleNameFromLastInputFileName(LastInputFileName)
#write the file
nextInFile = open(nextInFileName, 'w')
nextInFile.write(str(gmsFile))
nextInFile.close()
return nextInFileName
def readCoordinateFromLastFile(lastFileName,coordinate):
try:
lastOutFile = open(re.sub("\.inp", ".out",lastFileName))
except IOError as e:
try:
lastOutFile = open(re.sub("\.inp", ".log",lastFileName))
except IOError as e:
print("I was unable to find the output for the lastFile")
print(lastFileName)
print(re.sub("\.inp", ".log",lastFileName))
sys.exit()
##Two competing file types
coordinateLineNumber = GAMESS.coordinateLine(coordinate)
coordinateType = GAMESS.ZMATCoordinateType(coordinate)
lineNumber=0
flag=False
returnLine=""
ZMATMode=False
COORDMode=False
dashedLineCount=0
coordinateLineCount=0
for line in lastOutFile:
if re.search("fail",line.lower()):
print("WARNING:The last file failed to converged")
# found equilibrium geometry
if re.search("EQUILIBRIUM GEOMETRY LOCATED",line):
flag=True
dashedLineCount=1
# if the coordinates in ZMatrix mode use this
if flag and re.search("THE CURRENT FULLY SUBSTITUTED Z-MATRIX IS",line):
ZMATMode=True
flag = False
lineNumber=FIRST_COORD_LINE-2
if lineNumber == coordinateLineNumber and ZMATMode:
if lineNumber == FIRST_COORD_LINE:
returnLine = re.match(".*(\d+\.\d+)",line).group(1)
elif lineNumber == FIRST_COORD_LINE + 1:
if coordinateType == "bond":
returnLine = re.match(".*(\d+\.\d+).* +(-?\d+\.\d+)",line).group(1)
else:
returnLine = re.match(".*(\d+\.\d+).* +(-?\d+\.\d+)",line).group(2)
elif lineNumber >= FIRST_COORD_LINE + 2:
if coordinateType == "bond":
returnLine = re.match(".* +(\d+\.\d+).* +(-?\d+\.\d+).* +(-?\d+\.\d+)",line).group(1)
elif coordinateType == "angle":
returnLine = re.match(".* +(\d+\.\d+).* +(-?\d+\.\d+).* +(-?\d+\.\d+)",line).group(2)
else:
returnLine = re.match(".* +(\d+\.\d+).* +(-?\d+\.\d+).* +(-?\d+\.\d+)",line).group(3)
if lineNumber:
lineNumber+=1
#if the coordinates are given in list mode
if flag and re.search("INTERNAL COORDINATES",line):
COORMode = True
flag = False
if dashedLineCount == 5:
if re.match(" *\d.*\d+\.\d+ +(-?\d+\.\d+)",line):
coordinateLineCount+=1
if coordinateLineCount==coordinate:
returnLine = re.match(" *\d.*\d+\.\d+ +(-?\d+\.\d+)",line).group(1)
else:
dashedLineCount = 0
if dashedLineCount> 0 and dashedLineCount<5:
if re.search("-+\n",line):
dashedLineCount+=1
if returnLine == "":
print("ERROR: No minimum was found in the last file")
sys.exit()
else:
lastOutFile.close()
return returnLine