def readGulpOutput(system, fileName):
"""
Reads the gulp output and updates atoms' positions and systems energy
"""
system_Type = _costSystemBox
success = False
error = ""
if not os.path.isfile(fileName):
error = "File [%s] doesn't exist." % (fileName)
return success, error, system
try:
f = open(fileName)
except:
error = "Cannot read file [%s]" % (fileName)
return success, error, system
# optimisation achieved?
success = Utilities.stringInFile(_constOutOptiAchieved, f)
success = True
if not success:
error = "Optimisation has not been achieved"
optiAchievedSection = False
finalEnergy_eV = None
iniParamsSectionSt = False
iniParamsCount = 0
finalCoordsSectionSt = False
finalParamsSectionSt = False
finalParamsSectionBreakCount = 0
finalParamsCount = 0
i = 0
# saving name and path
name_array = fileName.split("/")
name_array_len = len(name_array)
name_array = name_array[name_array_len-1].split(".")
system.name = name_array[0]
system.path = fileName
# read in final atom positions
if success:
for line in f:
line = line.strip()
# Looking for the final energy
if optiAchievedSection:
if _constOutFinalEnergy in line:
energyArray = line.split()
finalEnergy_eV = float(energyArray[3])
# updating the final energy value
system.totalEnergy = finalEnergy_eV
system.energyDefinition = "Gulp"
optiAchievedSection = False
# Found the end of the section
if ((_constOutFinalDerivs in line) or (_constOutFinalDerivsPoly in line)):
finalParamsSectionSt = False
# Found the end of the section
if ((_constIniParamsCellVol in line) or (_constIniParamsCellParamPoly in line)):
iniParamsSectionSt = False
if finalCoordsSectionSt:
array = line.split()
if (len(array) == 7):
no_str = array[0]
try:
no_int = np.int16(no_str)
except:
no_int = -1
if no_int == -1:
finalCoordsSectionSt = False
else:
atomSpecie = array[1]
atomType = array[2]
# Do atom speces and types match?
if ((not system.specieList[system.specie[i]].lower() == atomSpecie.lower()) or
(not system.gulpAtomType[i] == atomType)):
error = "atom types do not match %d : %s != %s" % (i, system.specieList[system.specie[i]], atomSpecie)
return False, error
# Reading the atom positions
posx = float(array[3])
posy = float(array[4])
posz = float(array[5])
# Updating the atom positions
system.pos[3*i] = posx
system.pos[3*i+1] = posy
system.pos[3*i+2] = posz
i += 1
if i == system.NAtoms:
finalCoordsSectionSt = False
if finalParamsSectionSt:
if "-----" in line:
finalParamsSectionBreakCount += 1
if finalParamsSectionBreakCount < 2:
array = line.split()
if len(array) == 6:
# new cell dimensions
if finalParamsCount == 0:
system.cellDims_final[0] = np.float64(array[1])
elif finalParamsCount == 1:
system.cellDims_final[1] = np.float64(array[1])
elif finalParamsCount == 2:
system.cellDims_final[2] = np.float64(array[1])
# new cell angles:
elif finalParamsCount == 3:
system.cellAngles_final[0] = np.float64(array[1])
elif finalParamsCount == 4:
system.cellAngles_final[1] = np.float64(array[1])
elif finalParamsCount == 5:
system.cellAngles_final[2] = np.float64(array[1])
finalParamsCount += 1
else:
finalParamsSectionSt = False
if iniParamsSectionSt:
array = line.split()
if system_Type == _costSystemPolymer:
if len(array) == 3:
system.cellDims_ini[0] = np.float64(array[0])
system.cellDims_ini[1] = np.float64(array[1])
system.cellDims_ini[2] = np.float64(array[2])
else:
if len(array) == 6:
# new cell dimensions
if iniParamsCount == 0:
system.cellDims_ini[0] = np.float64(array[2])
system.cellAngles_ini[0] = np.float64(array[5])
elif iniParamsCount == 1:
system.cellDims_ini[1] = np.float64(array[2])
system.cellAngles_ini[1] = np.float64(array[5])
elif iniParamsCount == 2:
system.cellDims_ini[2] = np.float64(array[2])
system.cellAngles_ini[2] = np.float64(array[5])
iniParamsCount += 1
# Found the beginning of the section
if ((_constOutFinalCartCoords in line) or (_constOutFinalFracCoords in line) or
(_constOutFinalFracCartCoords in line)):
finalCoordsSectionSt = True
# Found the beginning of the section
if ((_constOutFinalParams in line) or (_constOutFinalDerivsPoly in line)):
finalParamsSectionSt = True
# Found the beginning of the section
if (_constIniParams in line):
iniParamsSectionSt = True
if (_constIniParamsPoly in line):
iniParamsSectionSt = True
system_Type = _costSystemPolymer
if _constOutOptiAchieved in line:
optiAchievedSection = True
success = True
return success, error
def readGulpOutputPolymerOutput(polymer, fileName):
"""
Reads the gulp output as polymer
"""
success = False
error = ""
if not os.path.isfile(fileName):
error = "File [%s] doesn't exist." % (fileName)
return success, error, polymer
try:
f = open(fileName)
except:
error = "Cannot read file [%s]" % (fileName)
return success, error, polymer
# optimisation achieved?
success = Utilities.stringInFile(_constOutOptiAchieved, f)
success = True
if not success:
error = "Optimisation has not been achieved"
optiAchievedSection = False
finalEnergy_eV = None
finalCoordsSectionSt = False
finalParamsSectionSt = False
finalParamsSectionBreakCount = 0
finalParamsCount = 0
i = 0
# read in final atom positions
if success:
for line in f:
line = line.strip()
# Looking for the final energy
if optiAchievedSection:
if _constOutFinalEnergy in line:
energyArray = line.split()
finalEnergy_eV = float(energyArray[3])
# updating the final energy value
polymer.totalEnergy = finalEnergy_eV
polymer.energyDefinition = "Gulp"
optiAchievedSection = False
# Found the end of the section
if ((_constOutFinalDerivs in line) or (_constOutFinalDerivsPoly in line)):
finalParamsSectionSt = False
# Found the end of the section
if finalCoordsSectionSt:
array = line.split()
if (len(array) == 7):
no_str = array[0]
try:
no_int = np.int16(no_str)
except:
no_int = -1
if no_int == -1:
finalCoordsSectionSt = False
else:
atomSpecie = array[1]
atomType = array[2]
# Do atom speces and types match?
if ((not polymer.specieList[polymer.specie[i]].lower() == atomSpecie.lower()) or
(not polymer.gulpAtomType[i] == atomType)):
error = "atom types do not match %d : %s != %s" % (i, polymer.specieList[polymer.specie[i]], atomSpecie)
return False, error
# Reading the atom positions
posx = float(array[3])
posy = float(array[4])
posz = float(array[5])
# Updating the atom positions
polymer.pos[3*i] = posx
polymer.pos[3*i+1] = posy
polymer.pos[3*i+2] = posz
i += 1
if i == polymer.NAtoms:
finalCoordsSectionSt = False
if finalParamsSectionSt:
if "-----" in line:
finalParamsSectionBreakCount += 1
if finalParamsSectionBreakCount < 2:
array = line.split()
if len(array) == 6:
# new cell dimensions
if finalParamsCount == 0:
polymer.cellDims_final[0] = np.float64(array[1])
elif finalParamsCount == 1:
polymer.cellDims_final[1] = np.float64(array[1])
elif finalParamsCount == 2:
polymer.cellDims_final[2] = np.float64(array[1])
# new cell angles:
elif finalParamsCount == 3:
polymer.cellAngles_final[0] = np.float64(array[1])
elif finalParamsCount == 4:
polymer.cellAngles_final[1] = np.float64(array[1])
elif finalParamsCount == 5:
polymer.cellAngles_final[2] = np.float64(array[1])
finalParamsCount += 1
else:
finalParamsSectionSt = False
# Found the beginning of the section
if ((_constOutFinalCartCoords in line) or (_constOutFinalFracCoords in line) or
(_constOutFinalFracCartCoords in line)):
finalCoordsSectionSt = True
# Found the beginning of the section
if _constOutFinalDerivsPoly in line:
finalParamsSectionSt = True
if _constOutOptiAchieved in line:
optiAchievedSection = True
# saving name and path
name_array = fileName.split("/")
name_array_len = len(name_array)
polymer.name = name_array[name_array_len-1].split(".")[0]
polymer.path = fileName
if success:
# multiplying the fractional coordinate of the polymer with the cell parameter
for i in range(polymer.NAtoms):
polymer.pos[i*3] *= polymer.cellDims_final[0]
polymer.cellDims = copy.deepcopy(polymer.cellDims_final)
polymer.cellAngles = copy.deepcopy(polymer.cellAngles_final)
success = True
return success, error
