def read(filename,silent=False):
"""
This method reads Q-Chem input files, output files, and coordinate files (xyz,zmat,txyz).
"""
extension = (filename.split("."))[-1]
# Do we have an inputfile?
if extension in ("inp","in","IN","INP","qcin","QCIN"):
seperator = []
with open(filename) as infile:
for num, line in enumerate(infile):
if "@@@"==line.strip() or "@@@@"==line.strip():
seperator.append(num)
N_jobs = len(seperator)
# Does the file contain multiple jobs?
if N_jobs>0:
if not silent:
print "Batch Jobfile detected."
joblist = []
infile = open(filename,"r")
content = infile.readlines()
seperator.insert(0,-1)
seperator.append(len(content))
# Create batch jobfile object
re_file = multifile()
# Populate it with jobs
for k in range(N_jobs+1):
start=seperator[k]+1
end=seperator[k+1]
dummylines = content[start:end]
dummy = _readinput(dummylines,silent)
re_file.add(dummy)
return re_file
# No, it's a single job file
else:
if not silent:
print "Jobfile detected."
return _readinput(filename,silent)
# Is it a z-matrix file?
elif extension in ("zmat","ZMAT","Z","z"):
if not silent:
print "Z-matrix file detected."
return _readzmat(filename)
# Is it a cartesian coordinates file?
elif extension in ("xyz","XYZ"):
if not silent:
print "Cartesian coordinates file detected."
return _readcartesian(filename)
# Is it a tinker coordinates file?
elif extension in ("txyz","TXYZ"):
if not silent:
print "Tinker coordinates file detected."
return _readtinker(filename)
# Do we have a Q-Chem outputfile?
if extension.lower() in ("out", "qcout", "qchem"):
seperator = []
with open(filename) as infile:
for num, line in enumerate(infile):
if "Welcome to Q-Chem" in line:
seperator.append(num)
N_jobs = len(seperator)
# Does the file contain multiple jobs?
if N_jobs>1:
if not silent:
print "Batch-Outputfile detected."
joblist = []
infile = open(filename,"r")
content = infile.readlines()
#seperator.insert(0,-1)
seperator.append(len(content))
# Create batch jobfile object
re_file = _multioutput()
# Populate it with jobs
for k in range(N_jobs):
start=seperator[k]+1
end=seperator[k+1]
dummylines = content[start:end]
dummy = _outputfile(dummylines,silent)
re_file.add(dummy)
return re_file
# No, it's a single job file
else:
if not silent:
print "Outputfile detected."
return _outputfile(filename,silent)
# What the heck? This is not a valid file.
else:
if not silent:
print "Error: File type not recognized."
def __init__(self, file_input, silent=False):
#Check input type
if type(file_input) == list:
content = file_input
else:
infile = open(file_input, "r")
content = infile.readlines()
spin = '0'
energy = 'undetermined'
jobtype = 'undetermined'
version = 'undetermined'
basis_size = 'undetermined'
status = 'unfinished'
wall_time = -99
cpu_time = -99
# flag for detection of basis2 job
basis2_flag = False
mm_type = ""
self.aifdem = 0
self.N_Fragments = 1
self.N_SET = 0
switch = 0
for line in content:
if "JOBTYPE" in line:
jobtype = ((line.split())[-1]).lower()
if "jobtype" in line:
jobtype = ((line.split())[-1]).lower()
if "JOB_TYPE" in line:
jobtype = ((line.split())[-1]).lower()
if "basis2" in line.lower():
basis2_flag = True
if ("QM_MM_INTERFACE" in line) or ("qm_mm_interface" in line):
mm_type = ((line.split())[-1]).lower()
if ("AIFDEM" in line) or ("aifdem" in line):
self.aifdem = ((line.split())[-1]).lower()
if ("CIS_N_ROOTS" in line):
self.N_SET = ((line.split())[-1]).lower()
if "Q-Chem, Version" in line:
version = (((line.split(","))[1]).split())[1]
if "<S^2> =" in line:
spin = (line.split())[2]
if ("Total energy in the final basis set"
) in line and mm_type != "mm":
energy = (line.split())[8]
if ("Convergence criterion met") in line and basis2_flag:
energy = (line.split())[1]
if ("Etot:" in line) and (mm_type == "mm"):
energy = (line.split())[4]
if ("There are" in line) and ("shells" in line):
basis_size = (line.split())[5]
if ("Total job time:" in line):
wall_time = float(line.split()[3].split("s")[0])
cpu_time = float(line.split()[4].split("s")[0])
if "MISSION" in line:
status = 'finished'
if "--fragment" in line:
ifrgm = int((line.split())[-1])
if ifrgm + 1 > self.N_Fragments:
self.N_Fragments = ifrgm + 1
if "TIME STEPS COMPLETED" in line and jobtype == "aimd":
status = 'time steps completed'
# Create corresponding inputfile:
if switch == 0 and "User input:" in line:
switch = 1
infile_content = []
if switch == 1:
infile_content.append(line)
if switch == 1 and "Standard Nuclear Orientation" in line:
switch = 2
initial_cartesian = cartesian(
"sp job - initial geometry in standard orientation")
continue
if switch == 2 and ("Repulsion" in line or "Molecular" in line):
switch = 3
elif switch == 2 and "Atom" not in line and "---" not in line:
dummy = (line.split())[1:]
initial_cartesian.add_atom(dummy[0], dummy[1], dummy[2],
dummy[3])
inputfile = _readinput(infile_content, silent)
# Creating geometry objects under 'general' for convenience, final geometry will be overwritten later if different
# Final geometry is NOT read directly from inputfile, but from Q-Chem standard orientation output in order to
# avoid issues with molecule 'read' in batch jobs
initial_geometry = inputfile.molecule.geometry()
final_geometry = initial_cartesian
# The info object 'general' will be created after ALL OTHER objects are finished with parsing
# Make another round if we have an MM or a QM/MM Janus job (just one MM per step)
if mm_type == "mm" or mm_type == "janus":
etot = []
ecoulomb = []
etorsion = []
eimptors = []
eureybrad = []
eangle = []
ebond = []
evdw = []
first_bond = 1
for line in content:
if ("MM bonds to file" in line) and (first_bond == 1):
nbonds = int((line.split())[1])
first_bond = 0
if "Ebond:" in line:
ebond.append(float((line.split())[1]))
if "Eangle:" in line:
eangle.append(float((line.split())[1]))
if "EUreyBrad:" in line:
eureybrad.append(float((line.split())[1]))
if "Eimptors:" in line:
eimptors.append(float((line.split())[1]))
if "Etorsion:" in line:
etorsion.append(float((line.split())[1]))
if "Evdw:" in line:
evdw.append(float((line.split())[1]))
if "Ecoulomb:" in line:
ecoulomb.append(float((line.split())[1]))
if "Etot:" in line:
etot.append(float((line.split())[1]))
self.mm = _mm([
etot, ecoulomb, evdw, etorsion, eimptors, eureybrad, eangle,
ebond, nbonds
]) # Create MM info object
# Make another round if we have an QM/MM ONIOM job (has two MM calulations per step)
elif mm_type == "oniom":
etot = []
ecoulomb = []
etorsion = []
eimptors = []
eureybrad = []
eangle = []
ebond = []
evdw = []
etot2 = []
ecoulomb2 = []
etorsion2 = []
eimptors2 = []
eureybrad2 = []
eangle2 = []
ebond2 = []
evdw2 = []
mm_step = 0
first_bond = 1
first_bond2 = 1
for line in content:
if "Step 1: MM calculation on the entire system" in line:
mm_step = 1
if "Step 2: MM calculation on the model system" in line:
mm_step = 2
if ("MM bonds to file" in line) and (first_bond
== 1) and (mm_step == 1):
nbonds = int((line.split())[1])
first_bond = 0
if "Ebond:" in line and (mm_step == 1):
ebond.append(float((line.split())[1]))
if "Eangle:" in line and (mm_step == 1):
eangle.append(float((line.split())[1]))
if "EUreyBrad:" in line and (mm_step == 1):
eureybrad.append(float((line.split())[1]))
if "Eimptors:" in line and (mm_step == 1):
eimptors.append(float((line.split())[1]))
if "Etorsion:" in line and (mm_step == 1):
etorsion.append(float((line.split())[1]))
if "Evdw:" in line and (mm_step == 1):
evdw.append(float((line.split())[1]))
if "Ecoulomb:" in line and (mm_step == 1):
ecoulomb.append(float((line.split())[1]))
if "Etot:" in line and (mm_step == 1):
etot.append(float((line.split())[1]))
if ("n_qm_bonds =" in line) and (first_bond2 == 1) and (mm_step
== 2):
nbonds2 = int((line.split())[2])
first_bond2 = 0
if "Ebond:" in line and (mm_step == 2):
ebond2.append(float((line.split())[1]))
if "Eangle:" in line and (mm_step == 2):
eangle2.append(float((line.split())[1]))
if "EUreyBrad:" in line and (mm_step == 2):
eureybrad2.append(float((line.split())[1]))
if "Eimptors:" in line and (mm_step == 2):
eimptors2.append(float((line.split())[1]))
if "Etorsion:" in line and (mm_step == 2):
etorsion2.append(float((line.split())[1]))
if "Evdw:" in line and (mm_step == 2):
evdw2.append(float((line.split())[1]))
if "Ecoulomb:" in line and (mm_step == 2):
ecoulomb2.append(float((line.split())[1]))
if "Etot:" in line and (mm_step == 2):
etot2.append(float((line.split())[1]))
# Create MM info object for entire system
self.mm_total = _mm([
etot, ecoulomb, evdw, etorsion, eimptors, eureybrad, eangle,
ebond, nbonds
])
# Create MM info object for model system
self.mm_model = _mm([
etot2, ecoulomb2, evdw2, etorsion2, eimptors2, eureybrad2,
eangle2, ebond2, nbonds2
])
if jobtype == "sp":
# Retrieve rem object from input file
index = inputfile.list_of_content.index("rem")
rem = inputfile.list_of_arrays[index]
adc_variant = ''
if "METHOD" in rem.dict_of_keywords:
if "adc" in rem.dict_of_keywords["METHOD"]:
adc_variant = rem.dict_of_keywords["METHOD"]
elif "ADC_ORDER" in rem.dict_of_keywords:
adc_order = int(rem.dict_of_keywords["ADC_ORDER"])
adc_ext = False
if adc_order == 2 and "ADC_EXTENDED" in rem.dict_of_keywords:
if int(rem.dict_of_keywords["ADC_EXTENDED"] == 1):
adc_ext = True
adc_variant = "adc(" + str(adc_order) + ")"
if adc_ext:
adc_variant += "-x"
if adc_variant:
if "ADC_SOS" in rem.dict_of_keywords:
if int(rem.dict_of_keywords("ADC_SOS")) != 0:
if "adc(2)" in adc_variant and not "sos" in adc_variant:
adc_variant = "sos-" + adc_variant
if "ADC_CVS" in rem.dict_of_keywords:
if int(rem.dict_of_keywords("ADC_CVS")) != 0:
if not "cvs" in adc_variant:
adc_variant = "cvs-" + adc_variant
self.adc = _parse_adc(adc_variant, content, silent)
if jobtype == "freq":
H2kcal = constants.hartree_to_kcal_pro_mole
E = float(energy)
temp = []
press = []
R_T = []
enth_corr = []
entr_corr = []
zero_point = []
mass = []
mom_inertia = []
rot_sym = []
switch = 0
frequencies = []
intensities = []
loop = 0
linear_switch = 0
for line in content:
if "STANDARD THERMODYNAMIC QUANTITIES AT" in line:
temp.append(float((line.split())[4]))
press.append(1.01325e5 * float((line.split())[7]))
if "Zero point vibrational energy" in line:
zero_point.append(float((line.split())[4]) / H2kcal)
if "gas constant (RT):" in line:
R_T.append(float((line.split())[3]) / H2kcal)
if "Total Enthalpy:" in line:
enth_corr.append(float((line.split())[2]) / H2kcal)
if "Total Entropy:" in line:
entr_corr.append(float((line.split())[2]) / 1000 / H2kcal)
if "We detect a D*h symmetry" in line:
linear_switch = 1
if "We detect a C*v symmetry" in line:
linear_switch = 1
if "We detect a C*h symmetry" in line: # necessary because of wrong nomenclature in Q-chem (thermodyn.F)
linear_switch = 1
if "Molecular Mass:" in line:
loop += 1
if "*" in line:
if not silent:
print "Warning: Molecular mass in loop " + str(
loop
) + " is unphysically large. Will use mass of first loop instead."
mass.append(mass[0])
else:
dummy = float((line.split())[2])
mass.append(dummy)
if "Rotational Symmetry Number is" in line:
rot_sym.append(float((line.split())[4]))
if "Eigenvalues --" in line:
if "*" in line:
if not silent:
print "Warning: Moment of inertia in loop " + str(
loop
) + " is unphysically large. Will use values of first loop instead."
mom_inertia.append(mom_inertia[0])
else:
dummy = [
float((line.split())[2]),
float((line.split())[3]),
float((line.split())[4])
]
mom_inertia.append(dummy)
if "VIBRATIONAL ANALYSIS" in line:
loop1 = []
loop2 = []
switch = 1
infile_content = []
if switch == 1:
if "Frequency:" in line:
dummy = line.split()
del dummy[0]
for k in dummy:
loop1.append(float(k))
if "IR Intens:" in line:
dummy = line.split()
del dummy[0]
del dummy[0]
for k in dummy:
loop2.append(float(k))
if switch == 1 and "STANDARD THERMODYNAMIC" in line:
switch = 0
frequencies.append(loop1)
intensities.append(loop2)
T = _np.asarray(temp)
p = _np.asarray(press)
ZPE = _np.asarray(zero_point)
H = E + _np.asarray(enth_corr)
S = _np.asarray(entr_corr)
ITE = _np.asarray(
enth_corr
) - R_T # RT = pV is subtracted from H to obtain the ZPE corrected ITE
F = E + ITE - (T * S)
G = H - (T * S)
self.thermo = _thermo(E, ZPE, ITE, T, p, S, H, F, G, frequencies,
intensities, mass, mom_inertia, rot_sym,
linear_switch)
if jobtype == "opt" or jobtype == "optimization" or jobtype == "ts":
energies = []
gradient_vector = []
gradient = [0.0]
displacement = []
change = []
geometries = []
optstat = "no convergence"
N_step = 1
switch = 0
for line in content:
if "Energy is" in line:
dummy = float((line.split())[-1])
energies.append(dummy)
if "Gradient " in line:
try:
dummy = float((line.split())[1])
except:
dummy = 0.0
gradient.append(dummy)
if "Displacement " in line:
dummy = float((line.split())[1])
displacement.append(dummy)
if "Energy change " in line:
try:
dummy = float((line.split())[2])
except:
dummy = 0.0
change.append(dummy)
if "** OPTIMIZATION CONVERGED **" in line:
optstat = "converged"
if "ATOM X Y Z" in line:
switch = 1
cycle_name = "Optimization step " + str(N_step)
cart_dummy = cartesian(cycle_name)
if switch == 1 and "ATOM" not in line and "Point Group" not in line:
con = line.split()
cart_dummy.add_atom(con[1], con[2], con[3], con[4])
if "Point Group" in line and switch == 1:
geometries.append(deepcopy(cart_dummy))
N_step += 1
switch = 0
if "Gradient of SCF Energy" in line:
switch = 2
grad_dummy = []
elif "Max gradient component" in line and switch == 2:
# Assuming that the array will always have a 3xN structure:
matrix = [[], [], []]
for i, sp in enumerate(grad_dummy):
if not i % 4 == 0:
matrix[i % 4 - 1].extend(
[float(si) for si in sp[1:]])
switch = 0
gradient_vector.append(_np.array(matrix))
elif switch == 2:
grad_dummy.append(line.split())
# The geometry has changed, so let's update a variable in the 'general' info object
final_geometry = deepcopy(geometries[-1])
if jobtype == "opt" or jobtype == "optimization":
self.opt = _opt(geometries, energies, gradient,
gradient_vector, displacement, change, optstat)
else:
self.ts = _opt(geometries, energies, gradient, gradient_vector,
displacement, change, optstat)
if jobtype == "aimd":
drift = []
kinetic_energies = []
time = []
energies = []
geometries = []
aimdstat = "steps not completed"
temp = 0
aimd_step = 0
drift_switch = 0
geom_switch = 0
for line in content:
if "Simulation temperature" in line:
temp = float((line.split())[3])
if "AIMD will take" in line:
N_steps = int((line.split())[3])
if "Time step =" in line:
time_step = float((line.split())[7]) # use fs units
if "Total simulation time requested" in line:
total_time = float((line.split())[5]) # use fs units
if "TIME STEP #" in line: # AIMD starts
aimd_step += 1
time.append(float((line.split())[5]))
if ("Drift factor =" in line) and (aimd_step > 0):
drift_switch = 1
if ("Total" in line) and (drift_switch
== 1) and (aimd_step > 0):
drift.append(float((line.split())[2]))
kinetic_energies.append(float((line.split())[1]))
drift_switch = 0
if ("Total energy in the final" in line) and (aimd_step > 0):
dummy = float((line.split())[8])
energies.append(dummy)
#if "Atom X Y Z" in line and (aimd_step>0):
if "Standard Nuclear Orientation (Angstroms)" in line and (
aimd_step > 0):
geom_switch = 1
cycle_name = "time step " + str(aimd_step)
cart_dummy = cartesian(cycle_name)
if (geom_switch == 1) and ("------" not in line) and (
"Atom" not in line) and ("Nuclear" not in line):
con = line.split()
cart_dummy.add_atom(con[1], con[2], con[3], con[4])
if geom_switch == 1 and "Nuclear Repulsion Energy" in line:
geometries.append(deepcopy(cart_dummy))
geom_switch = 0
if "TIME STEPS COMPLETED" in line:
aimdstat = "steps completed"
# The geometry has changed, so let's update a variable in the 'general' info object
final_geometry = deepcopy(geometries[-1])
self.aimd = _aimd(temp, N_steps, time_step, total_time, time,
energies, drift, kinetic_energies, geometries,
aimdstat)
if self.aifdem != 0:
self.EvalStrng = ""
self.aifdem_E_Excite = 0.0
self.aifdem_Time = 0.0
EvalSwitch = 0
for line in content:
if ("AIFDEM Time:" in line):
self.aifdem_Time = float(line.split()[6])
if (" EigenVectors " in line) and (EvalSwitch == 1):
EvalSwitch = 0
if EvalSwitch == 1:
self.EvalStrng += line
if " EigenValues \n" in line:
EvalSwitch = 1
_ierr = 0
for i in range(len(self.EvalStrng.split())):
_ierr += 1
if _ierr > 7:
print "Possible Error finding AIFDEM Excitation Energy in output_classes.py"
if len(self.EvalStrng.split()[i]) > 1:
_iFirstline = i
break
_EvalStrngFirstline = self.EvalStrng.split()[_iFirstline]
self.aifdem_E_Excite = float(
(_EvalStrngFirstline.split("-"))[1]) - float(
(_EvalStrngFirstline.split("-"))[2])
self.aifdem_E_Excite = round(self.aifdem_E_Excite, 7)
if self.N_SET > 0 and self.aifdem == 0:
self.excited_states = []
self.cis_time = 0
_N_SET = 0
for line in content:
if ("Excited state" in line):
_E_Exc_eV = float(line.split()[-1])
_N_SET += 1
if ("Total energy for state" in line):
_E_Exc_total = float(line.split()[-1])
if ("Multiplicity:" in line):
_Mult = line.split()[-1]
if ("Trans. Mom.:" in line):
_momX = line.split()[2]
_momY = line.split()[4]
_momZ = line.split()[6]
if ("Strength" in line):
_osc = line.split()[-1]
self.excited_states.append({
"Exc_eV": _E_Exc_eV,
"Tot": _E_Exc_total,
"Mult": _Mult,
"X": _momX,
"Y": _momY,
"Z": _momZ,
"Strength": _osc
})
if ("CPU time" in line):
self.cis_time = line.split()[-1]
self.N_SET = _N_SET
if self.N_SET > 0 and self.aifdem == 0:
self.excited_states = []
self.cis_time = 0
_N_SET = 0
for line in content:
if ("Excited state" in line):
_E_Exc_eV = float(line.split()[-1])
_N_SET += 1
if ("Total energy for state" in line):
_E_Exc_total = float(line.split()[-1])
if ("Multiplicity:" in line):
_Mult = line.split()[-1]
if ("Trans. Mom.:" in line):
_momX = line.split()[2]
_momY = line.split()[4]
_momZ = line.split()[6]
if ("Strength" in line):
_osc = line.split()[-1]
self.excited_states.append({
"Exc_eV": _E_Exc_eV,
"Tot": _E_Exc_total,
"Mult": _Mult,
"X": _momX,
"Y": _momY,
"Z": _momZ,
"Strength": _osc
})
if ("CPU time" in line):
self.cis_time = line.split()[-1]
self.N_SET = _N_SET
# Finally, we create the global info object 'general'
self.general = _general(jobtype, version, spin, basis_size, energy,
status, inputfile, mm_type, initial_geometry,
final_geometry, wall_time, cpu_time)
def __init__(self,file_input,silent=False):
#Check input type
if type(file_input)==list:
content = file_input
else:
infile = open(file_input, "r")
content = infile.readlines()
spin = '0'
energy = 'undetermined'
jobtype = 'undetermined'
version = 'undetermined'
basis_size = 'undetermined'
status = 'unfinished'
# flag for detection of basis2 job
basis2_flag = False
mm_type = ""
switch = 0
for line in content:
if "JOBTYPE" in line:
jobtype = ((line.split())[-1]).lower()
if "jobtype" in line:
jobtype = ((line.split())[-1]).lower()
if "JOB_TYPE" in line:
jobtype = ((line.split())[-1]).lower()
if "basis2" in line.lower():
basis2_flag = True
if ("QM_MM_INTERFACE" in line) or ("qm_mm_interface" in line):
mm_type = ((line.split())[-1]).lower()
if "Q-Chem, Version" in line:
version = (((line.split(","))[1]).split())[1]
if "<S^2> =" in line:
spin = (line.split())[2]
if ("Total energy in the final basis set") in line and mm_type!="mm":
energy = (line.split())[8]
if ("Convergence criterion met") in line and basis2_flag:
energy = (line.split())[1]
if ("Etot:" in line) and (mm_type=="mm"):
energy = (line.split())[4]
if ("There are" in line) and ("shells" in line):
basis_size = (line.split())[5]
if "MISSION" in line:
status = 'finished'
if "TIME STEPS COMPLETED" in line and jobtype=="aimd":
status = 'time steps completed'
# Create corresponding inputfile:
if "User input:" in line:
switch = 1
infile_content = []
if switch == 1:
infile_content.append(line)
if switch == 1 and "Standard Nuclear Orientation" in line:
switch = 0
inputfile = _readinput(infile_content,silent)
self.general = _general(jobtype,version,spin,basis_size,energy,status,inputfile,mm_type)
# Make another round if we have an MM or a QM/MM Janus job (just one MM per step)
if mm_type=="mm" or mm_type=="janus":
etot = []
ecoulomb = []
etorsion = []
eimptors = []
eureybrad = []
eangle = []
ebond = []
evdw = []
first_bond=1
for line in content:
if ("MM bonds to file" in line) and (first_bond==1):
nbonds = int((line.split())[1])
first_bond = 0
if "Ebond:" in line:
ebond.append(float((line.split())[1]))
if "Eangle:" in line:
eangle.append(float((line.split())[1]))
if "EUreyBrad:" in line:
eureybrad.append(float((line.split())[1]))
if "Eimptors:" in line:
eimptors.append(float((line.split())[1]))
if "Etorsion:" in line:
etorsion.append(float((line.split())[1]))
if "Evdw:" in line:
evdw.append(float((line.split())[1]))
if "Ecoulomb:" in line:
ecoulomb.append(float((line.split())[1]))
if "Etot:" in line:
etot.append(float((line.split())[1]))
self.mm = _mm([etot,ecoulomb,evdw,etorsion,eimptors,eureybrad,eangle,ebond,nbonds]) # Create MM info object
# Make another round if we have an QM/MM ONIOM job (has two MM calulations per step)
elif mm_type=="oniom":
etot = []
ecoulomb = []
etorsion = []
eimptors = []
eureybrad = []
eangle = []
ebond = []
evdw = []
etot2 = []
ecoulomb2 = []
etorsion2 = []
eimptors2 = []
eureybrad2 = []
eangle2 = []
ebond2 = []
evdw2 = []
mm_step = 0
first_bond=1
first_bond2=1
for line in content:
if "Step 1: MM calculation on the entire system" in line:
mm_step = 1
if "Step 2: MM calculation on the model system" in line:
mm_step = 2
if ("MM bonds to file" in line) and (first_bond==1) and (mm_step==1):
nbonds = int((line.split())[1])
first_bond = 0
if "Ebond:" in line and (mm_step==1):
ebond.append(float((line.split())[1]))
if "Eangle:" in line and (mm_step==1):
eangle.append(float((line.split())[1]))
if "EUreyBrad:" in line and (mm_step==1):
eureybrad.append(float((line.split())[1]))
if "Eimptors:" in line and (mm_step==1):
eimptors.append(float((line.split())[1]))
if "Etorsion:" in line and (mm_step==1):
etorsion.append(float((line.split())[1]))
if "Evdw:" in line and (mm_step==1):
evdw.append(float((line.split())[1]))
if "Ecoulomb:" in line and (mm_step==1):
ecoulomb.append(float((line.split())[1]))
if "Etot:" in line and (mm_step==1):
etot.append(float((line.split())[1]))
if ("n_qm_bonds =" in line) and (first_bond2==1) and (mm_step==2):
nbonds2 = int((line.split())[2])
first_bond2 = 0
if "Ebond:" in line and (mm_step==2):
ebond2.append(float((line.split())[1]))
if "Eangle:" in line and (mm_step==2):
eangle2.append(float((line.split())[1]))
if "EUreyBrad:" in line and (mm_step==2):
eureybrad2.append(float((line.split())[1]))
if "Eimptors:" in line and (mm_step==2):
eimptors2.append(float((line.split())[1]))
if "Etorsion:" in line and (mm_step==2):
etorsion2.append(float((line.split())[1]))
if "Evdw:" in line and (mm_step==2):
evdw2.append(float((line.split())[1]))
if "Ecoulomb:" in line and (mm_step==2):
ecoulomb2.append(float((line.split())[1]))
if "Etot:" in line and (mm_step==2):
etot2.append(float((line.split())[1]))
# Create MM info object for entire system
self.mm_total = _mm([etot,ecoulomb,evdw,etorsion,eimptors,eureybrad,eangle,ebond,nbonds])
# Create MM info object for model system
self.mm_model = _mm([etot2,ecoulomb2,evdw2,etorsion2,eimptors2,eureybrad2,eangle2,ebond2,nbonds2])
if jobtype=="freq":
H2kcal=constants.hartree_to_kcal_pro_mole
E = float(energy)
temp = []
press = []
R_T = []
enth_corr = []
entr_corr = []
zero_point = []
mass = []
mom_inertia = []
rot_sym = []
switch = 0
frequencies = []
intensities = []
loop = 0
linear_switch = 0
for line in content:
if "STANDARD THERMODYNAMIC QUANTITIES AT" in line:
temp.append(float((line.split())[4]))
press.append(1.01325e5*float((line.split())[7]))
if "Zero point vibrational energy" in line:
zero_point.append(float((line.split())[4])/H2kcal)
if "gas constant (RT):" in line:
R_T.append(float((line.split())[3])/H2kcal)
if "Total Enthalpy:" in line:
enth_corr.append(float((line.split())[2])/H2kcal)
if "Total Entropy:" in line:
entr_corr.append(float((line.split())[2])/1000/H2kcal)
if "We detect a D*h symmetry" in line:
linear_switch = 1
if "We detect a C*v symmetry" in line:
linear_switch = 1
if "We detect a C*h symmetry" in line: # necessary because of wrong nomenclature in Q-chem (thermodyn.F)
linear_switch = 1
if "Molecular Mass:" in line:
loop += 1
if "*" in line:
if not silent:
print "Warning: Molecular mass in loop " + str(loop) + " is unphysically large. Will use mass of first loop instead."
mass.append(mass[0])
else:
dummy = float((line.split())[2])
mass.append(dummy)
if "Rotational Symmetry Number is" in line:
rot_sym.append(float((line.split())[4]))
if "Eigenvalues --" in line:
if "*" in line:
if not silent:
print "Warning: Moment of inertia in loop " + str(loop) + " is unphysically large. Will use values of first loop instead."
mom_inertia.append(mom_inertia[0])
else:
dummy = [float((line.split())[2]),float((line.split())[3]),float((line.split())[4])]
mom_inertia.append(dummy)
if "VIBRATIONAL ANALYSIS" in line:
loop1 = []
loop2 = []
switch = 1
infile_content = []
if switch == 1:
if "Frequency:" in line:
dummy = line.split()
del dummy[0]
for k in dummy:
loop1.append(float(k))
if "IR Intens:" in line:
dummy = line.split()
del dummy[0]
del dummy[0]
for k in dummy:
loop2.append(float(k))
if switch == 1 and "STANDARD THERMODYNAMIC" in line:
switch = 0
frequencies.append(loop1)
intensities.append(loop2)
T = _np.asarray(temp)
p = _np.asarray(press)
ZPE = _np.asarray(zero_point)
H = E + _np.asarray(enth_corr)
S = _np.asarray(entr_corr)
ITE = _np.asarray(enth_corr) - R_T # RT = pV is subtracted from H to obtain the ZPE corrected ITE
F = E + ITE - (T*S)
G = H - (T*S)
self.thermo = _thermo(E,ZPE,ITE,T,p,S,H,F,G,frequencies,intensities,mass,mom_inertia,rot_sym,linear_switch)
if jobtype=="opt" or jobtype=="optimization" or jobtype=="ts":
energies = []
gradient = [0.0]
displacement = []
change = []
geometries = []
optstat = "no convergence"
N_step = 1
switch = 0
for line in content:
if "Energy is" in line:
dummy = float((line.split())[2])
energies.append(dummy)
if "Gradient " in line:
try:
dummy = float((line.split())[1])
except:
dummy = 0.0
gradient.append(dummy)
if "Displacement " in line:
dummy = float((line.split())[1])
displacement.append(dummy)
if "Energy change " in line:
try:
dummy = float((line.split())[2])
except:
dummy = 0.0
change.append(dummy)
if "** OPTIMIZATION CONVERGED **" in line:
optstat = "converged"
if "ATOM X Y Z" in line:
switch = 1
cycle_name = "Optimization step " + str(N_step)
cart_dummy = cartesian(cycle_name)
if "ATOM X Y Z" in line:
switch = 1
cycle_name = "Optimization step " + str(N_step)
cart_dummy = cartesian(cycle_name)
if switch == 1 and "ATOM" not in line and "Point Group" not in line:
con = line.split()
cart_dummy.add_atom(con[1],con[2],con[3],con[4])
if "Point Group" in line and switch == 1:
geometries.append(deepcopy(cart_dummy))
N_step += 1
switch = 0
if jobtype=="opt" or jobtype=="optimization":
self.opt = _opt(geometries,energies,gradient,displacement,change,optstat)
else:
self.ts = _opt(geometries,energies,gradient,displacement,change,optstat)
if jobtype=="aimd":
drift = []
kinetic_energies = []
time = []
energies = []
geometries = []
aimdstat = "steps not completed"
aimd_step = 0
drift_switch = 0
geom_switch = 0
for line in content:
if "Simulation temperature" in line:
temp = float((line.split())[3])
if "AIMD will take" in line:
N_steps = int((line.split())[3])
if "Time step =" in line:
time_step = float((line.split())[7]) # use fs units
if "Total simulation time requested" in line:
total_time = float((line.split())[5]) # use fs units
if "TIME STEP #" in line: # AIMD starts
aimd_step += 1
time.append(float((line.split())[5]))
if ("Drift factor =" in line) and (aimd_step>0):
drift_switch = 1
if ("Total" in line) and (drift_switch==1) and (aimd_step>0):
drift.append(float((line.split())[2]))
kinetic_energies.append(float((line.split())[1]))
drift_switch = 0
if ("Total energy in the final" in line) and (aimd_step>0):
dummy = float((line.split())[8])
energies.append(dummy)
if "Atom X Y Z" in line and (aimd_step>0):
geom_switch = 1
cycle_name = "time step " + str(aimd_step)
cart_dummy = cartesian(cycle_name)
if (geom_switch == 1) and ("------" not in line) and ("Atom" not in line) and ("Nuclear" not in line):
con = line.split()
cart_dummy.add_atom(con[1],con[2],con[3],con[4])
if geom_switch==1 and "Nuclear Repulsion Energy" in line:
geometries.append(deepcopy(cart_dummy))
geom_switch = 0
if "TIME STEPS COMPLETED" in line:
aimdstat = "steps completed"
self.aimd = _aimd(temp,N_steps,time_step,total_time,time,energies,drift,kinetic_energies,geometries,aimdstat)
def read(filename, silent=False):
"""
This method reads Q-Chem input files, output files, and coordinate files (xyz,zmat,txyz).
"""
extension = (filename.split("."))[-1]
#catchall pybel list
pybel_inlist = [
'txyz', 'text', 'alc', 'castep', 'nwo', 'cdx', 'xml', 'pwscf', 'rsmi',
'xtc', 'g09', 'pcm', 'mopin', 'mopcrt', 'xyz', 'fchk', 'g03', 'cube',
'axsf', 'mpc', 'mpo', 'mop', 'pos', 'dat', 'moo', 'dx', 'mol', 'inchi',
'hin', 'cml', 'outmol', 'xsf', 'qcout', 'output', 'mdl', 'unixyz',
'pdbqt', 'gzmat', 'arc', 'out', 'c09out', 'feat', 'crk3d', 'got',
'mopout', 'tdd', 'mmod', 'bs', 'mmd', 'box', 'bgf', 'vmol', 'acr',
'pqs', 'crk2d', 'CONFIG', 'pdb', 'ck', 'c3d2', 't41', 'c3d1',
'CONTCAR', 'gamout', 'mmcif', 'txt', 'ct', 'therm', 'log', 'pc',
'dmol', 'molden', 'ml2', 'fract', 'msi', 'cdxml', 'g98', 'prep', 'gpr',
'cub', 'gam', 'gukin', 'cmlr', 'abinit', 'POSCAR', 'ins', 'tmol',
'png', 'cif', 'gamess', 'car', 'mcif', 'smi', 'can', 'caccrt',
'fhiaims', 'inp', 'gukout', 'sy2', 'fasta', 'mpqc', 'mold', 'molf',
'jout', 'yob', 'mcdl', 'ent', 'adfout', 'gro', 'smiles', 'fs', 'mol2',
'fa', 'pqr', 'g94', 'g92', 'fch', 'VASP', 'fck', 'HISTORY', 'fsa',
'gamin', 'rxn', 'mrv', 'sdf', 'gal', 'res', 'sd', 'ccc', 'acesout'
]
# Do we have an inputfile?
if extension in ("inp", "in", "IN", "INP", "qcin", "QCIN"):
seperator = []
with open(filename) as infile:
for num, line in enumerate(infile):
if "@@@" == line.strip() or "@@@@" == line.strip():
seperator.append(num)
N_jobs = len(seperator)
# Does the file contain multiple jobs?
if N_jobs > 0:
if not silent:
print "Batch Jobfile detected."
joblist = []
infile = open(filename, "r")
content = infile.readlines()
seperator.insert(0, -1)
seperator.append(len(content))
# Create batch jobfile object
re_file = multifile()
# Populate it with jobs
for k in range(N_jobs + 1):
start = seperator[k] + 1
end = seperator[k + 1]
dummylines = content[start:end]
dummy = _readinput(dummylines, silent)
re_file.add(dummy)
return re_file
# No, it's a single job file
else:
if not silent:
print "Jobfile detected."
return _readinput(filename, silent)
# Is it a z-matrix file?
elif extension in ("zmat", "ZMAT", "Z", "z"):
if not silent:
print "Z-matrix file detected."
return _readzmat(filename)
# Is it a cartesian coordinates file?
elif extension in ("xyz", "XYZ"):
if not silent:
print "Cartesian coordinates file detected."
return _readcartesian(filename)
# Is it a tinker coordinates file?
elif extension in ("txyz", "TXYZ"):
if not silent:
print "Tinker coordinates file detected."
return _readtinker(filename)
# Do we have a Q-Chem outputfile?
if extension.lower() in ("out", "qcout", "qchem"):
seperator = []
with open(filename) as infile:
for num, line in enumerate(infile):
if "Welcome to Q-Chem" in line:
seperator.append(num)
N_jobs = len(seperator)
# Does the file contain multiple jobs?
if N_jobs > 1:
if not silent:
print "Batch-Outputfile detected."
joblist = []
infile = open(filename, "r")
content = infile.readlines()
#seperator.insert(0,-1)
seperator.append(len(content))
# Create batch jobfile object
re_file = _multioutput()
# Populate it with jobs
for k in range(N_jobs):
start = seperator[k] + 1
end = seperator[k + 1]
dummylines = content[start:end]
dummy = _outputfile(dummylines, silent)
re_file.add(dummy)
return re_file
# No, it's a single job file
else:
if not silent:
print "Outputfile detected."
return _outputfile(filename, silent)
# Is it anything pybel can read?
elif extension in pybel_inlist:
try:
import pybel
except:
print "Error: File type not recognized."
return
if not silent:
print pybel.informats[extension], " detected"
return _readpybel(extension, filename)
# What the heck? This is not a valid file.
else:
if not silent:
print "Error: File type not recognized."
def read(filename,silent=False):
"""
This method reads Q-Chem input files, output files, and coordinate files (xyz,zmat,txyz).
"""
extension = (filename.split("."))[-1]
#catchall pybel list
pybel_inlist=['txyz', 'text', 'alc', 'castep', 'nwo', 'cdx', 'xml', 'pwscf', 'rsmi', 'xtc', 'g09', 'pcm', 'mopin', 'mopcrt', 'xyz', 'fchk', 'g03', 'cube', 'axsf', 'mpc', 'mpo', 'mop', 'pos', 'dat', 'moo', 'dx', 'mol', 'inchi', 'hin', 'cml', 'outmol', 'xsf', 'qcout', 'output', 'mdl', 'unixyz', 'pdbqt', 'gzmat', 'arc', 'out', 'c09out', 'feat', 'crk3d', 'got', 'mopout', 'tdd', 'mmod', 'bs', 'mmd', 'box', 'bgf', 'vmol', 'acr', 'pqs', 'crk2d', 'CONFIG', 'pdb', 'ck', 'c3d2', 't41', 'c3d1', 'CONTCAR', 'gamout', 'mmcif', 'txt', 'ct', 'therm', 'log', 'pc', 'dmol', 'molden', 'ml2', 'fract', 'msi', 'cdxml', 'g98', 'prep', 'gpr', 'cub', 'gam', 'gukin', 'cmlr', 'abinit', 'POSCAR', 'ins', 'tmol', 'png', 'cif', 'gamess', 'car', 'mcif', 'smi', 'can', 'caccrt', 'fhiaims', 'inp', 'gukout', 'sy2', 'fasta', 'mpqc', 'mold', 'molf', 'jout', 'yob', 'mcdl', 'ent', 'adfout', 'gro', 'smiles', 'fs', 'mol2', 'fa', 'pqr', 'g94', 'g92', 'fch', 'VASP', 'fck', 'HISTORY', 'fsa', 'gamin', 'rxn', 'mrv', 'sdf', 'gal', 'res', 'sd', 'ccc', 'acesout']
# Do we have an inputfile?
if extension in ("inp","in","IN","INP","qcin","QCIN"):
seperator = []
with open(filename) as infile:
for num, line in enumerate(infile):
if "@@@"==line.strip() or "@@@@"==line.strip():
seperator.append(num)
N_jobs = len(seperator)
# Does the file contain multiple jobs?
if N_jobs>0:
if not silent:
print "Batch Jobfile detected."
joblist = []
infile = open(filename,"r")
content = infile.readlines()
seperator.insert(0,-1)
seperator.append(len(content))
# Create batch jobfile object
re_file = multifile()
# Populate it with jobs
for k in range(N_jobs+1):
start=seperator[k]+1
end=seperator[k+1]
dummylines = content[start:end]
dummy = _readinput(dummylines,silent)
re_file.add(dummy)
return re_file
# No, it's a single job file
else:
if not silent:
print "Jobfile detected."
return _readinput(filename,silent)
# Is it a z-matrix file?
elif extension in ("zmat","ZMAT","Z","z"):
if not silent:
print "Z-matrix file detected."
return _readzmat(filename)
# Is it a cartesian coordinates file?
elif extension in ("xyz","XYZ"):
if not silent:
print "Cartesian coordinates file detected."
return _readcartesian(filename)
# Is it a tinker coordinates file?
elif extension in ("txyz","TXYZ"):
if not silent:
print "Tinker coordinates file detected."
return _readtinker(filename)
# Do we have a Q-Chem outputfile?
if extension.lower() in ("out", "qcout", "qchem"):
seperator = []
with open(filename) as infile:
for num, line in enumerate(infile):
if "Welcome to Q-Chem" in line:
seperator.append(num)
N_jobs = len(seperator)
# Does the file contain multiple jobs?
if N_jobs>1:
if not silent:
print "Batch-Outputfile detected."
joblist = []
infile = open(filename,"r")
content = infile.readlines()
#seperator.insert(0,-1)
seperator.append(len(content))
# Create batch jobfile object
re_file = _multioutput()
# Populate it with jobs
for k in range(N_jobs):
start=seperator[k]+1
end=seperator[k+1]
dummylines = content[start:end]
dummy = _outputfile(dummylines,silent)
re_file.add(dummy)
return re_file
# No, it's a single job file
else:
if not silent:
print "Outputfile detected."
return _outputfile(filename,silent)
# Is it anything pybel can read?
elif extension in pybel_inlist:
try:
import pybel
except:
print "Error: File type not recognized."
return
if not silent:
print pybel.informats[extension], " detected"
return _readpybel(extension,filename)
# What the heck? This is not a valid file.
else:
if not silent:
print "Error: File type not recognized."