def getRelaxStepsEnergies(outputFile):
"""
Counts the number of relaxation steps
"""
relax_steps = []
error = None
success = IO.checkFile(outputFile)
if not success:
error = __name__ + ": Cannot locate: " + outputFile
return success, error, relax_steps
try:
fout = open(outputFile, "r")
except:
success = False
error = __name__ + ": Cannot open: " + outputFile
return success, error, relax_steps
for line in fout:
# checks if the run was successful
if _const_nice_day_line in line:
success = True
# reads in energy
if _const_total_energy_corrected in line:
energy = np.float128((line.split(":")[1]).split("eV")[0].strip())
relax_steps.append(energy)
fout.close()
return success, error, relax_steps
def _readAimsOutput(inputFile, system, relaxed=True, eigenvalues=False):
"""
Reads in FHI-aims output as a system.
"""
error = ""
success = True
have_nice_day = False
readAtoms = False
readCompleted = False
readEigenvalues = False
read_evs_up = False
read_evs_down = False
initial_energy_read = False
initial_energy = 0.0
eigen_values_array = []
eigen_values_up_array = []
eigen_values_down_array = []
atomsLineCnt = 0
noOfAtoms = 0
energy = 0.0
version = ''
noOfcores = 0
runTime = 0.0
success = IO.checkFile(inputFile)
if not success:
error = __name__ + ": Cannot locate: " + inputFile
return success, error
try:
fin = open(inputFile, "r")
except:
success = False
error = __name__ + ": Cannot open: " + inputFile
return success, error
# initialising spin values
spin_N = _const_def_value
spin_S = _const_def_value
spin_J = _const_def_value
vbm = _const_def_value
vbm_occ_num = _const_def_value
vbm_spin_chan = _const_def_value
cbm = _const_def_value
cbm_occ_num = _const_def_value
cbm_spin_chan = _const_def_value
homo_lumo_gap = _const_def_value
for line in fin:
fields = line.strip().split()
# reading the final atoms positions
if (readAtoms and (system is not None)):
if atomsLineCnt >= noOfAtoms:
readCompleted = True
readAtoms = False
# ignoring the first line
if atomsLineCnt > 0:
#print fields
sym = fields[4].strip()
if sym not in system.specieList:
system.addSpecie(sym)
specInd = system.specieIndex(sym)
system.specieCount[specInd] += 1
system.specie[atomsLineCnt-1] = specInd
for j in range(3):
system.pos[(atomsLineCnt-1)*3 + j] = float(fields[j+1])
system.charge[atomsLineCnt-1] = 0.0
atomsLineCnt += 1
if ((len(fields) > 1) and (fields[0] == "Version")):
version = fields[1]
if ((len(fields) > 5) and (' '.join(fields[1:4]) == "Number of atoms")):
noOfAtoms = int(fields[5])
if (system.NAtoms != noOfAtoms):
success = False
error = __name__ + ": the number of atoms does not match the original number of atoms"
if ((len(fields) > 5) and (' '.join(fields[1:4]) == "Total energy uncorrected")):
energy = float(fields[5])
if not initial_energy_read:
initial_energy = copy.copy(energy)
initial_energy_read = True
# reset values
if _const_scf_iter in line:
vbm = _const_def_value
vbm_occ_num = _const_def_value
vbm_spin_chan = _const_def_value
cbm = _const_def_value
cbm_occ_num = _const_def_value
cbm_spin_chan = _const_def_value
if _const_spin_N in line:
spin_N = float(fields[7])
if _const_spin_S in line:
spin_S = float(fields[3])
if _const_spin_J in line:
spin_J = float(fields[3])
if _const_vbm in line:
vbm = float(fields[5])
# stop reading eigenvalues
readEigenvalues = False
if _const_cbm in line:
cbm = float(fields[5])
if _const_homo_lumo in line:
homo_lumo_gap = float(fields[3])
# Highest occupied state (VBM)
if vbm != _const_def_value and cbm == _const_def_value:
if _const_occ_num in line:
vbm_occ_num = float(fields[3])
if _const_spin_chan in line:
vbm_spin_chan = float(fields[3])
# Lowest unoccupied state (CBM)
if vbm != _const_def_value and cbm != _const_def_value:
if _const_occ_num in line:
cbm_occ_num = float(fields[3])
if _const_spin_chan in line:
cbm_spin_chan = float(fields[3])
# reading the eigenvalues
if (eigenvalues and readEigenvalues and (system is not None)):
if read_evs_up and (_const_evs_down in line):
read_evs_up = False
if read_evs_down and (_const_curr_spin in line):
read_evs_down = False
readEigenvalues = False
if len(fields) == 4:
if read_evs_up:
eigen_values_up_array.append(fields[3])
elif read_evs_down:
eigen_values_down_array.append(fields[3])
else:
eigen_values_array.append(fields[3])
# reading in spin ups?
if _const_evs_up in line:
read_evs_up = True
# reading in spin downs?
if _const_evs_up in line:
read_evs_down = True
# Checking whether geometry relaxation was performed
if relaxed:
if ((len(fields) > 2) and (' '.join(fields[0:3]) == "Final atomic structure:")):
readAtoms = True
if ((len(fields) == 4) and (fields[0] == "Using")):
noOfcores = int(fields[1])
if ((len(fields) > 5) and (' '.join(fields[1:4]) == "Total time :")):
runTime = float(fields[6])
# Checks whether the have a nice day is in the output file. It indicates that the simulation was successful.
if _const_nice_day_line in line:
have_nice_day = True
# Start reading eigenvalues
if _const_eigenvalues in line:
readEigenvalues = True
eigen_values_array = []
eigen_values_up_array = []
eigen_values_down_array = []
fin.close()
# saving the eigenvalues
if eigenvalues:
if (len(eigen_values_array) > 0):
system.eigenvalues = np.array(eigen_values_array, np.float128)
if (len(eigen_values_up_array) > 0) :
system.evs_up = np.array(eigen_values_up_array, np.float128)
if (len(eigen_values_down_array) > 0):
system.evs_down = np.array(eigen_values_down_array, np.float128)
if not have_nice_day:
system.totalEnergy = 99999999.99
success = False
error = __name__ + ": it seems that we are not having a good day"
if not success:
return success, error
if relaxed and not readCompleted:
success = False
error = __name__ + ": data has not been read from: " + inputFile + ". It seems FHIaims encountered an error."
elif system is not None:
system.homo_lumo_gap = homo_lumo_gap
system.vbm = vbm
system.vbm_occ_num =vbm_occ_num
system.cbm = cbm
system.cbm_occ_num = cbm_occ_num
if spin_N != _const_def_value:
system.spin_N = spin_N
system.spin_S = spin_S
system.spin_J = spin_J
system.vbm_spin_chan = vbm_spin_chan
system.cbm_spin_chan = cbm_spin_chan
system.totalEnergy_initial = initial_energy
system.totalEnergy = energy
system.energyDefinition = "FHI-aims_" + version
system.noOfcores = noOfcores
system.runTime = runTime
else:
success = False
error = __name__ + ": data has not been read from: " + inputFile
return success, error