def _read_energies(self):
oniom_loc_bytes = self.bytedict['ONIOM: calculating energy.']
scf_loc_bytes = self.bytedict['SCF Done:']
ONIOM_extrapol = []
ONIOM_model_high = []
ONIOM_model_low = []
ONIOM_real_low = []
ONIOM_lowlayer_low = []
SCF_energy = []
f = open(self.name)
for complete_opt in oniom_loc_bytes:
ONIOM_model_high.append([])
ONIOM_model_low.append([])
ONIOM_real_low.append([])
ONIOM_lowlayer_low.append([])
ONIOM_extrapol.append([])
for location_byte in complete_opt:
f.seek(location_byte)
f.readline() # discard this line
model_low = misc.starfloat(
f.readline().split('low system: model energy:')[1])
ONIOM_model_low[-1].append(model_low)
model_high = misc.starfloat(
f.readline().split('high system: model energy:')[1])
ONIOM_model_high[-1].append(model_high)
real_low = misc.starfloat(
f.readline().split('low system: real energy:')[1])
ONIOM_real_low[-1].append(real_low)
extrapol = misc.starfloat(
f.readline().split('extrapolated energy =')[1])
ONIOM_extrapol[-1].append(extrapol)
ONIOM_lowlayer_low[-1].append(real_low - model_low)
for complete_opt in scf_loc_bytes:
SCF_energy.append([])
for location_byte in complete_opt:
f.seek(location_byte)
SCF_energy[-1].append(
float(f.readline().split('=')[1].split()[0]))
energies = {}
energies['ONIOM_extrapol'] = ONIOM_extrapol
energies['ONIOM_model_high'] = ONIOM_model_high
energies['ONIOM_lowlayer_low'] = ONIOM_lowlayer_low
energies['SCF_energy'] = SCF_energy
return energies
def read_converged(self, byte):
OFF = 60
LINE_OFF = 56
LABEL_START = 1
VALUE_START = 26
THRESH_START = 39
NCHARS_LABEL = 20
NCHARS_FLOAT = 8
stop_label = 'Predicted change in '
short_labels = {
'Maximum Force ': 'Max F',
'RMS Force ': 'rms F',
'Maximum Displacement': 'Max D',
'RMS Displacement': 'rms D',
'Maximum MM Force ': 'MaxMM',
'RMS MM Force ': 'rmsMM'
}
labels = []
values = []
thresholds = []
# correct byte
f = open(self.name)
f.seek(byte - 1)
if f.read(1) != '\n':
byte = byte - 1
stderr.write('WARTING: grep -b 1 byte ahead\n')
for i in range(7):
off = byte + OFF + i * LINE_OFF
f.seek(off + LABEL_START)
label = f.read(NCHARS_LABEL)
if label == stop_label:
f.close()
return (labels, values, thresholds)
labels.append(short_labels[label])
f.seek(off + VALUE_START)
values.append(misc.starfloat(f.read(NCHARS_FLOAT)))
f.seek(off + THRESH_START)
thresholds.append(misc.starfloat(f.read(NCHARS_FLOAT)))
# if here, stop_label not found
f.close()
error_msg = 'Expected %s after Converged section' % stop_label
print(labels, values, thresholds)
raise RuntimeError(error_msg)
def read_converged(self, byte):
OFF = 60
LINE_OFF = 56
LABEL_START = 1
VALUE_START = 26
THRESH_START = 39
NCHARS_LABEL = 20
NCHARS_FLOAT = 8
stop_label = 'Predicted change in '
short_labels = {
'Maximum Force ': 'Max F',
'RMS Force ': 'rms F',
'Maximum Displacement': 'Max D',
'RMS Displacement': 'rms D',
'Maximum MM Force ': 'MaxMM',
'RMS MM Force ': 'rmsMM'
}
labels = []
values = []
thresholds = []
# correct byte
f = open(self.name)
f.seek(byte-1)
if f.read(1) != '\n':
byte = byte - 1
stderr.write('WARTING: grep -b 1 byte ahead\n')
for i in range(7):
off = byte + OFF + i*LINE_OFF
f.seek(off + LABEL_START)
label = f.read(NCHARS_LABEL)
if label == stop_label:
f.close()
return (labels, values, thresholds)
labels.append(short_labels[label])
f.seek(off + VALUE_START)
values.append(misc.starfloat(f.read(NCHARS_FLOAT)))
f.seek(off + THRESH_START)
thresholds.append(misc.starfloat(f.read(NCHARS_FLOAT)))
# if here, stop_label not found
f.close()
error_msg = 'Expected %s after Converged section' % stop_label
print(labels, values, thresholds)
raise RuntimeError(error_msg)
def _read_energies(self):
oniom_loc_bytes = self.bytedict['ONIOM: calculating energy.']
scf_loc_bytes = self.bytedict['SCF Done:']
ONIOM_extrapol = []
ONIOM_model_high= []
ONIOM_model_low = []
ONIOM_real_low = []
ONIOM_lowlayer_low = []
SCF_energy = []
f = open(self.name)
for complete_opt in oniom_loc_bytes:
ONIOM_model_high.append([])
ONIOM_model_low.append([])
ONIOM_real_low.append([])
ONIOM_lowlayer_low.append([])
ONIOM_extrapol.append([])
for location_byte in complete_opt:
f.seek(location_byte)
f.readline() # discard this line
model_low = misc.starfloat(f.readline().split('low system: model energy:')[1])
ONIOM_model_low[-1].append(model_low)
model_high = misc.starfloat(f.readline().split('high system: model energy:')[1])
ONIOM_model_high[-1].append(model_high)
real_low = misc.starfloat(f.readline().split('low system: real energy:')[1])
ONIOM_real_low[-1].append(real_low)
extrapol = misc.starfloat(f.readline().split('extrapolated energy =')[1])
ONIOM_extrapol[-1].append(extrapol)
ONIOM_lowlayer_low[-1].append(real_low-model_low)
for complete_opt in scf_loc_bytes:
SCF_energy.append([])
for location_byte in complete_opt:
f.seek(location_byte)
SCF_energy[-1].append(float(f.readline().split('=')[1].split()[0]))
energies = {}
energies['ONIOM_extrapol'] = ONIOM_extrapol
energies['ONIOM_model_high'] = ONIOM_model_high
energies['ONIOM_lowlayer_low'] = ONIOM_lowlayer_low
energies['SCF_energy'] = SCF_energy
return energies