def next(self):
while True:
# skip to the next frame
self._secfile.get_next("Frame Number")
if slice_match(self._sub, self._counter):
self._counter += 1
frame = ATRJFrame()
# Read the time and energy
energy_lines = self._secfile.get_next("Time/Energy")
energy_words = energy_lines[0].split()
frame.time = float(energy_words[0])*ps
frame.step = int(energy_words[1])
frame.total_energy = float(energy_words[2])*kcalmol
# Read the coordinates
coord_lines = self._secfile.get_next("Coordinates")
frame.coordinates = numpy.zeros((self.num_atoms, 3), float)
for index, line in enumerate(coord_lines):
words = line.split()
frame.coordinates[index,0] = float(words[1])
frame.coordinates[index,1] = float(words[2])
frame.coordinates[index,2] = float(words[3])
frame.coordinates *= angstrom
# Done
return frame
else:
self._counter += 1
def next(self):
while True:
# skip to the next frame
self._secfile.get_next("Frame Number")
if slice_match(self._sub, self._counter):
self._counter += 1
frame = ATRJFrame()
# Read the time and energy
energy_lines = self._secfile.get_next("Time/Energy")
energy_words = energy_lines[0].split()
frame.time = float(energy_words[0]) * ps
frame.step = int(energy_words[1])
frame.total_energy = float(energy_words[2]) * kcalmol
# Read the coordinates
coord_lines = self._secfile.get_next("Coordinates")
frame.coordinates = numpy.zeros((self.num_atoms, 3), float)
for index, line in enumerate(coord_lines):
words = line.split()
frame.coordinates[index, 0] = float(words[1])
frame.coordinates[index, 1] = float(words[2])
frame.coordinates[index, 2] = float(words[3])
frame.coordinates *= angstrom
# Done
return frame
else:
self._counter += 1
def next(self):
# skip frames as requested
while not slice_match(self._sub, self._counter):
self._counter += 1
self.skip_frame()
self._counter += 1
return self.read_frame()
def next(self):
def goto_next_frame():
marked = False
while True:
line = self._f.next()[:-1]
if marked and len(line) > 0 and not line.startswith(
" --------"):
try:
step = int(line[:10])
return step, line
except ValueError:
pass
marked = (len(line) == 131 and line == self._marker)
while True:
step, line = goto_next_frame()
if (not self.skip_equi_period or step >= self.equi_period) and \
step != self.last_step:
break
# skip frames as requested
while not slice_match(self._sub, self._counter):
step, line = goto_next_frame()
self._counter += 1
# now really read these three lines
try:
row = [step]
for i in xrange(9):
row.append(float(line[10 + i * 12:10 + (i + 1) * 12]))
line = self._f.next()[:-1]
row.append(float(line[:10]))
for i in xrange(9):
row.append(float(line[10 + i * 12:10 + (i + 1) * 12]))
line = self._f.next()[:-1]
row.append(float(line[:10]))
for i in xrange(9):
row.append(float(line[10 + i * 12:10 + (i + 1) * 12]))
except ValueError:
raise Error(
"Some numbers in the output file could not be read. (expecting floating point numbers)"
)
# convert all the numbers to atomic units
for i in xrange(30):
row[i] *= self._conv[i]
# done
self.last_step = step
return row
def next(self):
def goto_next_frame():
marked = False
while True:
line = self._f.next()[:-1]
if marked and len(line) > 0 and not line.startswith(" --------"):
try:
step = int(line[:10])
return step, line
except ValueError:
pass
marked = (len(line) == 131 and line == self._marker)
while True:
step, line = goto_next_frame()
if (not self.skip_equi_period or step >= self.equi_period) and \
step != self.last_step:
break
# skip frames as requested
while not slice_match(self._sub, self._counter):
step, line = goto_next_frame()
self._counter += 1
# now really read these three lines
try:
row = [step]
for i in xrange(9):
row.append(float(line[10+i*12:10+(i+1)*12]))
line = self._f.next()[:-1]
row.append(float(line[:10]))
for i in xrange(9):
row.append(float(line[10+i*12:10+(i+1)*12]))
line = self._f.next()[:-1]
row.append(float(line[:10]))
for i in xrange(9):
row.append(float(line[10+i*12:10+(i+1)*12]))
except ValueError:
raise Error("Some numbers in the output file could not be read. (expecting floating point numbers)")
# convert all the numbers to atomic units
for i in xrange(30):
row[i] *= self._conv[i]
# done
self.last_step = step
return row
def _read(self):
def read_size():
try:
return int(self._file.readline().strip())
except ValueError:
raise StopIteration
while not slice_match(self._sub, self._counter):
size = read_size()
for i in xrange(size + 1):
line = self._file.readline()
if len(line) == 0:
raise StopIteration
self._counter += 1
size = read_size()
title = self._file.readline()[:-1]
symbols = []
coordinates = numpy.zeros((size, 3), float)
for counter in xrange(size):
line = self._file.readline()
if len(line) == 0:
raise StopIteration
words = line.split()
if len(words) < 4:
raise StopIteration
symbols.append(words[0])
try:
coordinates[counter, 0] = float(words[1])
coordinates[counter, 1] = float(words[2])
coordinates[counter, 2] = float(words[3])
except ValueError:
raise StopIteration
coordinates *= self.file_unit
self._counter += 1
return symbols, title, coordinates
def _read(self):
def read_size():
try:
return int(self._file.readline().strip())
except ValueError:
raise StopIteration
while not slice_match(self._sub, self._counter):
size = read_size()
for i in xrange(size+1):
line = self._file.readline()
if len(line) == 0:
raise StopIteration
self._counter += 1
size = read_size()
title = self._file.readline()[:-1]
symbols = []
coordinates = numpy.zeros((size, 3), float)
for counter in xrange(size):
line = self._file.readline()
if len(line) == 0:
raise StopIteration
words = line.split()
if len(words) < 4:
raise StopIteration
symbols.append(words[0])
try:
coordinates[counter,0] = float(words[1])
coordinates[counter,1] = float(words[2])
coordinates[counter,2] = float(words[3])
except ValueError:
raise StopIteration
coordinates *= self.file_unit
self._counter += 1
return symbols, title, coordinates
def next(self):
# auxiliary read function
def read_three(msg):
# read three words as floating point numbers
line = self._f.next()
try:
return [float(line[:12]), float(line[12:24]), float(line[24:])]
except ValueError:
raise Error(msg)
# skip frames as requested
while not slice_match(self._sub, self._counter):
for i in xrange(self._frame_size):
self._f.next()
self._counter += 1
frame = {}
# read the frame header line
words = self._f.next().split()
if len(words) != 6:
raise Error("The first line of each time frame must contain 6 words. (%i'th frame)" % self._counter)
if words[0] != "timestep":
raise Error("The first word of the first line of each time frame must be 'timestep'. (%i'th frame)" % self._counter)
try:
step = int(words[1])
frame["step"] = step
if int(words[2]) != self.num_atoms:
raise Error("The number of atoms has changed. (%i'th frame, %i'th step)" % (self._counter, step))
if int(words[3]) != self.keytrj:
raise Error("keytrj has changed. (%i'th frame, %i'th step)" % (self._counter, step))
if int(words[4]) != self.imcon:
raise Error("imcon has changed. (%i'th frame, %i'th step)" % (self._counter, step))
frame["timestep"] = float(words[5])*self.time_unit
frame["time"] = frame["timestep"]*step # this is ugly, or wait ... dlpoly is a bit ugly. we are not to blame!
except ValueError:
raise Error("Could not convert all numbers on the first line of the current time frame. (%i'th frame)" % self._counter)
# the three cell lines
cell = numpy.zeros((3,3), float)
frame["cell"] = cell
cell_msg = "The cell lines must consist of three floating point values. (%i'th frame, %i'th step)" % (self._counter, step)
for i in xrange(3):
cell[:,i] = read_three(cell_msg)
cell *= self.pos_unit
# the atoms
symbols = []
frame["symbols"] = symbols
masses = numpy.zeros(self.num_atoms, float)
frame["masses"] = masses
charges = numpy.zeros(self.num_atoms, float)
frame["charges"] = charges
pos = numpy.zeros((self.num_atoms,3), float)
frame["pos"] = pos
if self.keytrj > 0:
vel = numpy.zeros((self.num_atoms,3), float)
frame["vel"] = vel
if self.keytrj > 1:
frc = numpy.zeros((self.num_atoms,3), float)
frame["frc"] = frc
for i in xrange(self.num_atoms):
# the atom header line
words = self._f.next().split()
if len(words) != 4:
raise Error("The atom header line must contain 4 words. (%i'th frame, %i'th step, %i'th atom)" % (self._counter, step, i+1))
symbols.append(words[0])
try:
masses[i] = float(words[2])*self.mass_unit
charges[i] = float(words[3])
except ValueError:
raise Error("The numbers in the atom header line could not be interpreted.")
# the pos line
pos_msg = "The position lines must consist of three floating point values. (%i'th frame, %i'th step, %i'th atom)" % (self._counter, step, i+1)
pos[i] = read_three(pos_msg)
if self.keytrj > 0:
vel_msg = "The velocity lines must consist of three floating point values. (%i'th frame, %i'th step, %i'th atom)" % (self._counter, step, i+1)
vel[i] = read_three(vel_msg)
if self.keytrj > 1:
frc_msg = "The force lines must consist of three floating point values. (%i'th frame, %i'th step, %i'th atom)" % (self._counter, step, i+1)
frc[i] = read_three(frc_msg)
pos *= self.pos_unit # convert to au
if self.keytrj > 0:
vel *= self.vel_unit # convert to au
if self.keytrj > 1:
frc *= self.frc_unit # convert to au
# done
self._counter += 1
return frame
def next(self):
# auxiliary read function
def read_three(msg):
# read three words as floating point numbers
line = self._f.next()
try:
return [float(line[:12]), float(line[12:24]), float(line[24:])]
except ValueError:
raise Error(msg)
# skip frames as requested
while not slice_match(self._sub, self._counter):
for i in xrange(self._frame_size):
self._f.next()
self._counter += 1
frame = {}
# read the frame header line
words = self._f.next().split()
if len(words) != 6:
raise Error(
"The first line of each time frame must contain 6 words. (%i'th frame)"
% self._counter)
if words[0] != "timestep":
raise Error(
"The first word of the first line of each time frame must be 'timestep'. (%i'th frame)"
% self._counter)
try:
step = int(words[1])
frame["step"] = step
if int(words[2]) != self.num_atoms:
raise Error(
"The number of atoms has changed. (%i'th frame, %i'th step)"
% (self._counter, step))
if int(words[3]) != self.keytrj:
raise Error("keytrj has changed. (%i'th frame, %i'th step)" %
(self._counter, step))
if int(words[4]) != self.imcon:
raise Error("imcon has changed. (%i'th frame, %i'th step)" %
(self._counter, step))
frame["timestep"] = float(words[5]) * self.time_unit
frame["time"] = frame[
"timestep"] * step # this is ugly, or wait ... dlpoly is a bit ugly. we are not to blame!
except ValueError:
raise Error(
"Could not convert all numbers on the first line of the current time frame. (%i'th frame)"
% self._counter)
# the three cell lines
cell = numpy.zeros((3, 3), float)
frame["cell"] = cell
cell_msg = "The cell lines must consist of three floating point values. (%i'th frame, %i'th step)" % (
self._counter, step)
for i in xrange(3):
cell[:, i] = read_three(cell_msg)
cell *= self.pos_unit
# the atoms
symbols = []
frame["symbols"] = symbols
masses = numpy.zeros(self.num_atoms, float)
frame["masses"] = masses
charges = numpy.zeros(self.num_atoms, float)
frame["charges"] = charges
pos = numpy.zeros((self.num_atoms, 3), float)
frame["pos"] = pos
if self.keytrj > 0:
vel = numpy.zeros((self.num_atoms, 3), float)
frame["vel"] = vel
if self.keytrj > 1:
frc = numpy.zeros((self.num_atoms, 3), float)
frame["frc"] = frc
for i in xrange(self.num_atoms):
# the atom header line
words = self._f.next().split()
if len(words) != 4:
raise Error(
"The atom header line must contain 4 words. (%i'th frame, %i'th step, %i'th atom)"
% (self._counter, step, i + 1))
symbols.append(words[0])
try:
masses[i] = float(words[2]) * self.mass_unit
charges[i] = float(words[3])
except ValueError:
raise Error(
"The numbers in the atom header line could not be interpreted."
)
# the pos line
pos_msg = "The position lines must consist of three floating point values. (%i'th frame, %i'th step, %i'th atom)" % (
self._counter, step, i + 1)
pos[i] = read_three(pos_msg)
if self.keytrj > 0:
vel_msg = "The velocity lines must consist of three floating point values. (%i'th frame, %i'th step, %i'th atom)" % (
self._counter, step, i + 1)
vel[i] = read_three(vel_msg)
if self.keytrj > 1:
frc_msg = "The force lines must consist of three floating point values. (%i'th frame, %i'th step, %i'th atom)" % (
self._counter, step, i + 1)
frc[i] = read_three(frc_msg)
pos *= self.pos_unit # convert to au
if self.keytrj > 0:
vel *= self.vel_unit # convert to au
if self.keytrj > 1:
frc *= self.frc_unit # convert to au
# done
self._counter += 1
return frame