def loadConfiguration(energyLog, geomLog, statesLog, extSymmetry, spinMultiplicity, freqScaleFactor, linear, rotors, atoms, bonds, E0=None, TS=False):
logging.debug(' Reading optimized geometry...')
log = GaussianLog(geomLog)
geom = log.loadGeometry()
logging.debug(' Reading energy...')
if E0 is None:
if energyLog is not None: log = GaussianLog(energyLog)
E0 = log.loadEnergy()
else:
E0 *= 4.35974394e-18 * constants.Na # Hartree/particle to J/mol
E0 = applyEnergyCorrections(E0, modelChemistry, atoms, bonds)
logging.debug(' E0 (0 K) = %g kcal/mol' % (E0 / 4184))
logging.debug(' Reading molecular degrees of freedom...')
log = GaussianLog(statesLog)
states = log.loadStates(symmetry=extSymmetry)
states.spinMultiplicity = spinMultiplicity
F = log.loadForceConstantMatrix()
if F is not None and len(geom.mass) > 1 and len(rotors) > 0:
logging.debug(' Fitting %i hindered rotors...' % len(rotors))
for scanLog, pivots, top, symmetry in rotors:
log = GaussianLog(scanLog)
fourier = log.fitFourierSeriesPotential()
inertia = geom.getInternalReducedMomentOfInertia(pivots, top)
rotor = HinderedRotor(inertia=(inertia*constants.Na*1e23,"amu*angstrom^2"), symmetry=symmetry, fourier=(fourier,"J/mol"))
states.modes.append(rotor)
#import numpy
#import pylab
#import math
#Vlist = log.loadScanEnergies()
#Vlist = Vlist[:-1]
#angle = numpy.arange(0.0, 2*math.pi+0.00001, 2*math.pi/(len(Vlist)-1), numpy.float64)
#phi = numpy.arange(0, 6.3, 0.02, numpy.float64)
#pylab.plot(angle, Vlist / 4184, 'ok')
#pylab.plot(phi, rotor.getPotential(phi) / 4184, '-k')
#pylab.show()
logging.debug(' Determining frequencies from reduced force constant matrix...')
frequencies = list(projectRotors(geom, F, rotors, linear, TS))
elif len(states.modes) > 2:
frequencies = states.modes[2].frequencies.values
rotors = []
else:
frequencies = []
rotors = []
for mode in states.modes:
if isinstance(mode, HarmonicOscillator):
mode.frequencies.values = numpy.array(frequencies, numpy.float) * freqScaleFactor
return E0, geom, states
def loadTransitionState(label, geomLog, statesLog, extSymmetry, spinMultiplicity, freqScaleFactor, linear, rotors, atoms, bonds, directory=None, E0=None, energyLog=None):
global modelChemistry
logging.info('Loading transition state %s...' % label)
if directory:
geomLog = os.path.join(directory, geomLog)
statesLog = os.path.join(directory, statesLog)
if energyLog: energyLog = os.path.join(directory, energyLog)
E0, geom, states = loadConfiguration(energyLog, geomLog, statesLog, extSymmetry, spinMultiplicity, freqScaleFactor, linear, rotors, atoms, bonds, E0, TS=True)
log = GaussianLog(statesLog)
frequency = log.loadNegativeFrequency()
transitionStateDict[label] = TransitionState(label=label, states=states, frequency=(frequency,"cm^-1"), E0=(E0/1000.,"kJ/mol"))
geometryDict[label] = geom
def loadConfiguration(energyLog, geomLog, statesLog, extSymmetry, spinMultiplicity, freqScaleFactor, linear, rotors, atoms, bonds, E0=None, TS=False):
logging.debug(' Reading optimized geometry...')
log = GaussianLog(geomLog)
geom = log.loadGeometry()
logging.debug(' Reading energy...')
if E0 is None:
if energyLog is not None: log = GaussianLog(energyLog)
E0 = log.loadEnergy()
else:
E0 *= 4.35974394e-18 * constants.Na # Hartree/particle to J/mol
E0 = applyEnergyCorrections(E0, modelChemistry, atoms, bonds)
logging.debug(' E0 (0 K) = %g kcal/mol' % (E0 / 4184))
logging.debug(' Reading molecular degrees of freedom...')
log = GaussianLog(statesLog)
states = log.loadStates(symmetry=extSymmetry)
states.spinMultiplicity = spinMultiplicity
F = log.loadForceConstantMatrix()
if F is not None and len(geom.mass) > 1 and len(rotors) > 0:
logging.debug(' Fitting %i hindered rotors...' % len(rotors))
for scanLog, pivots, top, symmetry in rotors:
log = GaussianLog(scanLog)
Vlist, angle = log.loadScanEnergies()
inertia = geom.getInternalReducedMomentOfInertia(pivots, top)
barr, symm = log.fitCosinePotential()
cosineRotor = HinderedRotor(inertia=(inertia*constants.Na*1e23,"amu*angstrom^2"), symmetry=symm, barrier=(barr/4184.,"kcal/mol"))
fourier = log.fitFourierSeriesPotential()
fourierRotor = HinderedRotor(inertia=(inertia*constants.Na*1e23,"amu*angstrom^2"), symmetry=symmetry, fourier=(fourier,"J/mol"))
Vlist_cosine = cosineRotor.getPotential(angle)
Vlist_fourier = fourierRotor.getPotential(angle)
rms_cosine = numpy.sqrt(numpy.sum((Vlist_cosine - Vlist) * (Vlist_cosine - Vlist)) / (len(Vlist) - 1)) / 4184.
rms_fourier = numpy.sqrt(numpy.sum((Vlist_fourier - Vlist) * (Vlist_fourier - Vlist))/ (len(Vlist) - 1)) / 4184.
print rms_cosine, rms_fourier, symm, symmetry
# Keep the rotor with the most accurate potential
rotor = cosineRotor if rms_cosine < rms_fourier else fourierRotor
# However, keep the cosine rotor if it is accurate enough, the
# fourier rotor is not significantly more accurate, and the cosine
# rotor has the correct symmetry
if rms_cosine < 0.05 and rms_cosine / rms_fourier > 0.25 and rms_cosine / rms_fourier < 4.0 and symmetry == symm:
rotor = cosineRotor
states.modes.append(rotor)
import pylab
phi = numpy.arange(0, 6.3, 0.02, numpy.float64)
fig = pylab.figure()
pylab.plot(angle, Vlist / 4184, 'ok')
linespec = '-r' if rotor is cosineRotor else '--r'
pylab.plot(phi, cosineRotor.getPotential(phi) / 4184, linespec)
linespec = '-b' if rotor is fourierRotor else '--b'
pylab.plot(phi, fourierRotor.getPotential(phi) / 4184, linespec)
pylab.legend(['scan', 'cosine', 'fourier'], loc=1)
pylab.xlim(0, 2*math.pi)
axes = fig.get_axes()[0]
axes.set_xticks([float(j*math.pi/4) for j in range(0,9)])
axes.set_xticks([float(j*math.pi/8) for j in range(0,17)], minor=True)
axes.set_xticklabels(['$0$', '$\pi/4$', '$\pi/2$', '$3\pi/4$', '$\pi$', '$5\pi/4$', '$3\pi/2$', '$7\pi/4$', '$2\pi$'])
pylab.show()
logging.debug(' Determining frequencies from reduced force constant matrix...')
frequencies = list(projectRotors(geom, F, rotors, linear, TS))
elif len(states.modes) > 2:
frequencies = states.modes[2].frequencies.values
rotors = []
else:
frequencies = []
rotors = []
for mode in states.modes:
if isinstance(mode, HarmonicOscillator):
mode.frequencies.values = numpy.array(frequencies, numpy.float) * freqScaleFactor
return E0, geom, states
from gaussian import GaussianCom, GaussianLog
print("Trying to read qm_modred_gen.com, a simple gassian.com file")
gaussian_file_name = "qm_modred_gen.com"
gaussian_com = GaussianCom(gaussian_file_name)
print("List of atoms:\n", gaussian_com.atoms_list)
print("Everything seems ok\n\n")
print("Trying to read oniom.com, a simple ONIOM gassian.com file")
gaussian_file_name = "oniom.com"
gaussian_com = GaussianCom(gaussian_file_name)
print("List of atoms:\n", gaussian_com.atoms_list[0:100], " ... ")
print("Everything seems ok\n\n")
print("Trying to read oniom_pdb.com, a ONIOM gassian.com file with pdb info")
gaussian_file_name = "oniom_pdb.com"
gaussian_com = GaussianCom(gaussian_file_name)
print("List of atoms:\n", gaussian_com.atoms_list[0:100], " ... ")
print("Everything seems ok\n\n")
print("Trying to read oniom_pdb.log, a ONIOM gassian.log file with pdb info")
gaussian_file_name = "oniom_pdb.log"
gaussian_log = GaussianLog(gaussian_file_name)
print("Everything seems ok\n\n")
print("Trying to read big_scan_oniom.log, a 1.2 GB ONIOM gassian.log file")
gaussian_file_name = "big_scan_oniom.log"
gaussian_log = GaussianLog(gaussian_file_name)
print("Everything seems ok\n\n")
if len(sys.argv) == 1 or sys.argv[1] in ["-h", "--help"]:
print("Como usar: {0} file.log ").format(sys.argv[0])
sys.exit()
#ficheiro entrada (output do gaussian)
global filein
filein = sys.argv[1]
#transformar o ficheiro log aberto numa variavel global (ler com o GaussianLog)
############## INICIO ##############
main()
#ler os bytes de todo o ficheiro e fazer todos os atributos d
gaussianlog = GaussianLog(filein)
for i, scan_step in enumerate( gaussianlog.grep_bytes['Step number'] ):
print( "Scan", i, ": ", len(gaussianlog.grep_bytes['Step number'][i]), "opt steps" )
scan_step = input('Type "scan_step" that you which to extract. Options: scan_step="all": ')
opt_step = input('Type "opt_step" that you which to extract. Options: opt_step="all": ')
#verificar se existe o ficheiro
output = input('Type the name of the output file: ')
if path.exists(output + '.pdb'):
raise RuntimeError('%s already exists' %(str(output)+".pdb"))
open_output = open(str(output) + ".pdb", "w")
#casos em que extraio todos os scans
if str(scan_step) == 'all':
print(len(gaussianlog.grep_bytes['orientation:']))
distpair = tuple([int(x) for x in line.split()])
dists.append(distpair)
input_file_list = sys.argv[2:] #com files
results_dict = OrderedDict([])
for input_file in input_file_list:
input_file_no_suf = input_file[:-4]
results_dict[input_file_no_suf] = []
#print(input_file)
if input_file.endswith(".com"):
gaussian_file = GaussianCom(input_file)
structure = gaussian_file.atoms_list
else:
gaussian_file = GaussianLog(input_file)
structure = gaussian_file.final_geometry
for pair in dists:
atom_a = structure[pair[0] - 1]
atom_b = structure[pair[1] - 1]
this_dist = atom_a.distance(atom_b)
if len(pair) == 2:
results_dict[input_file_no_suf].append(
"{0:7.5f}".format(this_dist))
#print("{0:>3}{2[0]:<4}-{1:>3}{2[1]:<4} : {3:7.3f}".format(atom_a,atom_b,pair,this_dist))
elif len(pair) == 3:
atom_c = structure[pair[2] - 1]
this_angle = atom_b.angle(atom_a, atom_c)
this_angle = math.degrees(this_angle)
results_dict[input_file_no_suf].append(
"{0:7.3f}".format(this_angle))
from elements_database import ATOMIC_NUMBER_DICT
try:
reactants_folder = sys.argv[1]
ts_folder = sys.argv[2]
original_ts_energy = float(sys.argv[3])
except:
print(
"Usage: residel_energies.py <reactants_folder> <ts_folder> <ts_energy>"
)
sys.exit()
for reactants_filename in os.listdir(reactants_folder):
if reactants_filename.endswith(".log"):
try:
reactants_energy = GaussianLog("{0}/{1}"\
.format(reactants_folder,reactants_filename)).energies_list[-1][-1]
except IndexError:
reactants_energy = None
try:
ts_filenames = os.listdir(ts_folder)
ts_filename_end = "_".join(reactants_filename.split("_")[-2:])
ts_filename = ts_folder + "_" + ts_filename_end
ts_energy = GaussianLog("{0}/{1}"\
.format(ts_folder,ts_filename)).energies_list[-1][-1]
except IndexError:
ts_energy = None
if reactants_energy and ts_energy:
print(
ts_filename_end[:-4],
