def open_stream(self, mode):
"""Opens the output stream(s)."""
# prepare format string for zero-padded number of beads,
# including underscpre
fmt_bead = "{0:0" + str(int(1 + np.floor(np.log(self.system.beads.nbeads) / np.log(10)))) + "d}"
if getkey(self.what) in ["positions", "velocities", "forces", "extras", "forces_sc", "momenta"]:
# must write out trajectories for each bead, so must create b streams
# prepare format string for file name
if getkey(self.what) == "extras":
fmt_fn = self.filename + "_" + fmt_bead
else:
fmt_fn = self.filename + "_" + fmt_bead + "." + self.format
# open all files
self.out = []
for b in range(self.system.beads.nbeads):
if (self.ibead < 0 and (b % (-self.ibead) == 0)) or (self.ibead == b):
self.out.append(open_backup(fmt_fn.format(b), mode))
else:
# Create null outputs if a single bead output is chosen.
self.out.append(None)
else:
# open one file
filename = self.filename + "." + self.format
self.out = open_backup(filename, mode)
def open_stream(self):
"""Opens the output stream(s)."""
if getkey(self.what) in [ "positions", "velocities", "forces", "extras" ]:
# must write out trajectories for each bead, so must create b streams
self.out = []
for b in range(self.simul.beads.nbeads):
# zero-padded bead number
padb = ( ("%0" + str(int(1 + np.floor(np.log(self.simul.beads.nbeads)/np.log(10)))) + "d") % (b) )
try:
if (self.ibead < 0 or self.ibead == b):
if getkey(self.what) == "extras":
self.out.append(open(self.filename + "_" + padb, "a"))
else:
self.out.append(open(self.filename + "_" + padb + "." + self.format, "a"))
else:
self.out.append(None) # creates null outputs if a
# single bead output is chosen
except:
raise ValueError("Could not open file " + self.filename + "_" + padb + "." + self.format + " for output")
else:
try:
self.out = ( open(self.filename + "." + self.format, "a") )
except:
raise ValueError("Could not open file " + self.filename + "." + self.format + " for output")
def open_stream(self):
"""Opens the output stream."""
# Is this the start of the simulation?
is_start = self.system.simul.step == 0
# Only open a new file if this is a new run, otherwise append.
if is_start:
mode = "w"
else:
mode = "a"
self.out = open_backup(self.filename, mode)
# print nice header if information is available on the properties
if is_start:
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.system.properties.property_dict[key]
if "size" in prop and prop["size"] > 1:
ohead += "cols. %3d-%-3d" % (icol,
icol + prop["size"] - 1)
icol += prop["size"]
else:
ohead += "column %3d " % (icol)
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def open_stream(self):
"""Opens the output stream."""
try:
self.out = open(self.filename, "a")
except:
raise ValueError("Could not open file " + self.filename +
" for output")
# print nice header if information is available on the properties
if (self.simul.step == 0):
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.simul.properties.property_dict[key]
if "size" in prop and prop["size"] > 1:
ohead += "cols. %3d-%-3d" % (icol,
icol + prop["size"] - 1)
icol += prop["size"]
else:
ohead += "column %3d " % (icol)
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def write(self):
"""Writes out the required trajectories."""
if softexit.triggered: return # don't write if we are about to exit!
if not (self.system.simul.step + 1) % self.stride == 0:
return
doflush = False
self.nout += 1
if self.flush > 0 and self.nout >= self.flush:
doflush = True
self.nout = 0
data, dimension, units = self.system.trajs[self.what] # gets the trajectory data that must be printed
# quick-and-dirty way to check if a trajectory is "global" or per-bead
# Checks to see if there is a list of files or just a single file.
if hasattr(self.out, "__getitem__"):
if self.ibead < 0:
for b in range(len(self.out)):
if self.out[b] is not None:
self.write_traj(data, self.what, self.out[b], b, format=self.format, dimension=dimension, units=units, cell_units=self.cell_units, flush=doflush)
elif self.ibead < len(self.out):
self.write_traj(data, self.what, self.out[self.ibead], self.ibead, format=self.format, dimension=dimension, units=units, cell_units=self.cell_units, flush=doflush)
else:
raise ValueError("Selected bead index " + str(self.ibead) + " does not exist for trajectory " + self.what)
else:
self.write_traj(data, getkey(self.what), self.out, b=0, format=self.format, dimension=dimension, units=units, cell_units=self.cell_units, flush=doflush)
def open_stream(self):
"""Opens the output stream."""
try:
self.out = open(self.filename, "a")
except:
raise ValueError("Could not open file " + self.filename + " for output")
# print nice header if information is available on the properties
if (self.simul.step == 0) :
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.simul.properties.property_dict[key]
if "size" in prop and prop["size"] > 1:
ohead += "cols. %3d-%-3d" % ( icol, icol+prop["size"] - 1 )
icol += prop["size"]
else:
ohead += "column %3d " % ( icol )
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def open_stream(self):
"""Opens the output stream."""
# Is this the start of the simulation?
is_start = self.system.simul.step == 0
# Only open a new file if this is a new run, otherwise append.
if is_start:
mode = "w"
else:
mode = "a"
self.out = open_backup(self.filename, mode)
# print nice header if information is available on the properties
if is_start:
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.system.properties.property_dict[key]
if "size" in prop and prop["size"] > 1:
ohead += "cols. %3d-%-3d" % (icol, icol + prop["size"] - 1)
icol += prop["size"]
else:
ohead += "column %3d " % (icol)
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def write(self):
"""Writes out the required trajectories."""
if softexit.triggered:
return # don't write if we are about to exit!
if not (self.system.simul.step + 1) % self.stride == 0:
return
doflush = False
self.nout += 1
if self.flush > 0 and self.nout >= self.flush:
doflush = True
self.nout = 0
data, dimension, units = self.system.trajs[
self.what] # gets the trajectory data that must be printed
# quick-and-dirty way to check if a trajectory is "global" or per-bead
# Checks to see if there is a list of files or just a single file.
if hasattr(self.out, "__getitem__"):
if self.ibead < 0:
for b in range(len(self.out)):
if self.out[b] is not None:
self.write_traj(
data,
self.what,
self.out[b],
b,
format=self.format,
dimension=dimension,
units=units,
cell_units=self.cell_units,
flush=doflush,
)
elif self.ibead < len(self.out):
self.write_traj(
data,
self.what,
self.out[self.ibead],
self.ibead,
format=self.format,
dimension=dimension,
units=units,
cell_units=self.cell_units,
flush=doflush,
)
else:
raise ValueError("Selected bead index " + str(self.ibead) +
" does not exist for trajectory " + self.what)
else:
self.write_traj(
data,
getkey(self.what),
self.out,
b=0,
format=self.format,
dimension=dimension,
units=units,
cell_units=self.cell_units,
flush=doflush,
)
def open_stream(self):
"""Opens the output stream(s)."""
# Is this the start of the simulation?
is_start = self.system.simul.step == 0
# Only open a new file if this is a new run, otherwise append.
if is_start:
mode = "w"
else:
mode = "a"
# prepare format string for zero-padded number of beads,
# including underscpre
fmt_bead = "{0:0" + str(
int(1 + np.floor(np.log(self.system.beads.nbeads) /
np.log(10)))) + "d}"
if getkey(self.what) in [
"positions", "velocities", "forces", "extras", "forces_sc",
"momenta"
]:
# must write out trajectories for each bead, so must create b streams
# prepare format string for file name
if getkey(self.what) == "extras":
fmt_fn = self.filename + "_" + fmt_bead
else:
fmt_fn = self.filename + "_" + fmt_bead + "." + self.format
# open all files
self.out = []
for b in range(self.system.beads.nbeads):
if (self.ibead < 0 and
(b % (-self.ibead) == 0)) or (self.ibead == b):
self.out.append(open_backup(fmt_fn.format(b), mode))
else:
# Create null outputs if a single bead output is chosen.
self.out.append(None)
else:
# open one file
filename = self.filename + "." + self.format
self.out = open_backup(filename, mode)
def open_stream(self, mode):
"""Opens the output stream(s)."""
# prepare format string for zero-padded number of beads,
# including underscore
fmt_bead = ("{0:0" + str(
int(1 + np.floor(np.log(self.system.beads.nbeads) / np.log(10)))) +
"d}")
if getkey(self.what) in [
"positions",
"velocities",
"forces",
"extras",
"extras_component",
"forces_sc",
"momenta",
]:
# must write out trajectories for each bead, so must create b streams
# prepare format string for file name
if getkey(self.what) == "extras" or getkey(
self.what) == "extras_component":
fmt_fn = self.filename + "_" + fmt_bead
else:
fmt_fn = self.filename + "_" + fmt_bead + "." + self.format
# open all files
self.out = []
for b in range(self.system.beads.nbeads):
if (self.ibead < 0 and
(b % (-self.ibead) == 0)) or (self.ibead == b):
self.out.append(open_backup(fmt_fn.format(b), mode))
else:
# Create null outputs if a single bead output is chosen.
self.out.append(None)
else:
# open one file
filename = self.filename + "." + self.format
self.out = open_backup(filename, mode)
def write_traj(self, data, what, stream, b=0, format="xyz", dimension="", units="automatic", cell_units="automatic", flush=True):
"""Prints out a frame of a trajectory for the specified quantity and bead.
Args:
what: A string specifying what to print.
b: The bead index. Defaults to 0.
stream: A reference to the stream on which data will be printed.
format: The output file format.
cell_units: The units used to specify the cell parameters.
flush: A boolean which specifies whether to flush the output buffer
after each write to file or not.
"""
key = getkey(what)
if key in ["extras"]:
stream.write(" #*EXTRAS*# Step: %10d Bead: %5d \n" % (self.system.simul.step + 1, b))
stream.write(data[b])
stream.write("\n")
if flush:
stream.flush()
os.fsync(stream)
return
elif getkey(what) in ["positions", "velocities", "forces", "forces_sc", "momenta"]:
fatom = Atoms(self.system.beads.natoms)
fatom.names[:] = self.system.beads.names
fatom.q[:] = data[b]
else:
fatom = Atoms(self.system.beads.natoms)
fatom.names[:] = self.system.beads.names
fatom.q[:] = data
fcell = Cell()
fcell.h = self.system.cell.h
if units == "": units = "automatic"
if cell_units == "": cell_units = "automatic"
io.print_file(format, fatom, fcell, stream, title=("Step: %10d Bead: %5d " % (self.system.simul.step + 1, b)), key=key, dimension=dimension, units=units, cell_units=cell_units)
if flush:
stream.flush()
os.fsync(stream)
def bind(self, system, mode="w"):
"""Binds output proxy to System object.
Args:
system: A System object to be bound.
"""
self.system = system
# Checks as soon as possible if some asked-for trajs are missing or mispelled
key = getkey(self.what)
if not key in self.system.trajs.traj_dict.keys():
print "Computable trajectories list: ", self.system.trajs.traj_dict.keys()
raise KeyError(key + " is not a recognized output trajectory")
super(TrajectoryOutput,self).bind( mode)
def open_stream(self):
"""Opens the output stream(s)."""
if getkey(
self.what) in ["positions", "velocities", "forces", "extras"]:
# must write out trajectories for each bead, so must create b streams
self.out = []
for b in range(self.simul.beads.nbeads):
# zero-padded bead number
padb = (("%0" + str(
int(1 +
np.floor(np.log(self.simul.beads.nbeads) /
np.log(10)))) + "d") % (b))
try:
if (self.ibead < 0 or self.ibead == b):
if getkey(self.what) == "extras":
self.out.append(
open(self.filename + "_" + padb, "a"))
else:
self.out.append(
open(
self.filename + "_" + padb + "." +
self.format, "a"))
else:
self.out.append(None) # creates null outputs if a
# single bead output is chosen
except:
raise ValueError("Could not open file " + self.filename +
"_" + padb + "." + self.format +
" for output")
else:
try:
self.out = (open(self.filename + "." + self.format, "a"))
except:
raise ValueError("Could not open file " + self.filename + "." +
self.format + " for output")
def bind(self, system, mode="w"):
"""Binds output proxy to System object.
Args:
system: A System object to be bound.
"""
self.system = system
# Checks as soon as possible if some asked-for trajs are missing or mispelled
key = getkey(self.what)
if not key in self.system.trajs.traj_dict.keys():
print "Computable trajectories list: ", self.system.trajs.traj_dict.keys(
)
raise KeyError(key + " is not a recognized output trajectory")
super(TrajectoryOutput, self).bind(mode)
def bind(self, simul):
"""Binds output proxy to simulation object.
Args:
simul: A simulation object to be bound.
"""
self.simul = simul
# Checks as soon as possible if some asked-for trajs are missing or mispelled
key = getkey(self.what)
if not key in self.simul.trajs.traj_dict.keys():
print "Computable trajectories list: ", self.simul.trajs.traj_dict.keys()
raise KeyError(key + " is not a recognized output trajectory")
self.open_stream()
def bind(self, simul):
"""Binds output proxy to simulation object.
Args:
simul: A simulation object to be bound.
"""
self.simul = simul
# Checks as soon as possible if some asked-for trajs are missing or mispelled
key = getkey(self.what)
if not key in self.simul.trajs.traj_dict.keys():
print "Computable trajectories list: ", self.simul.trajs.traj_dict.keys(
)
raise KeyError(key + " is not a recognized output trajectory")
self.open_stream()
def bind(self, system):
"""Binds output proxy to System object.
Args:
system: A System object to be bound.
"""
self.system = system
# Checks as soon as possible if some asked-for trajs are missing or mispelled
key = getkey(self.what)
if not key in self.system.trajs.traj_dict.keys():
print "Computable trajectories list: ", self.system.trajs.traj_dict.keys()
raise KeyError(key + " is not a recognized output trajectory")
self.open_stream()
softexit.register_function(self.softexit)
def bind(self, system, mode="w"):
"""Binds output proxy to System object.
Args:
system: A System object to be bound.
"""
# Checks as soon as possible if some asked-for properties are
# missing or mispelled
self.system = system
for what in self.outlist:
key = getkey(what)
if not key in system.properties.property_dict.keys():
print "Computable properties list: ", system.properties.property_dict.keys(
)
raise KeyError(key + " is not a recognized property")
super(PropertyOutput, self).bind(mode)
def bind(self, simul):
"""Binds output proxy to simulation object.
Args:
simul: A simulation object to be bound.
"""
self.simul = simul
# Checks as soon as possible if some asked-for properties are
# missing or mispelled
for what in self.outlist:
key = getkey(what)
if not key in self.simul.properties.property_dict.keys():
print "Computable properties list: ", self.simul.properties.property_dict.keys()
raise KeyError(key + " is not a recognized property")
self.open_stream()
def bind(self, system, mode="w"):
"""Binds output proxy to System object.
Args:
system: A System object to be bound.
"""
# Checks as soon as possible if some asked-for properties are
# missing or mispelled
self.system = system
for what in self.outlist:
key = getkey(what)
if not key in system.properties.property_dict.keys():
print "Computable properties list: ", system.properties.property_dict.keys()
raise KeyError(key + " is not a recognized property")
super(PropertyOutput,self).bind(mode)
def print_header(self):
# print nice header if information is available on the properties
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.system.properties.property_dict[key]
if "size" in prop and prop["size"] > 1:
ohead += "cols. %3d-%-3d" % (icol, icol + prop["size"] - 1)
icol += prop["size"]
else:
ohead += "column %3d " % (icol)
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def print_header(self):
# print nice header if information is available on the properties
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.system.properties.property_dict[key]
if "size" in prop and prop["size"] > 1:
ohead += "cols. %3d-%-3d" % (icol, icol + prop["size"] - 1)
icol += prop["size"]
else:
ohead += "column %3d " % (icol)
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def bind(self, simul):
"""Binds output proxy to simulation object.
Args:
simul: A simulation object to be bound.
"""
self.simul = simul
# Checks as soon as possible if some asked-for properties are
# missing or mispelled
for what in self.outlist:
key = getkey(what)
if not key in self.simul.properties.property_dict.keys():
print "Computable properties list: ", self.simul.properties.property_dict.keys(
)
raise KeyError(key + " is not a recognized property")
self.open_stream()
def bind(self, system):
"""Binds output proxy to System object.
Args:
system: A System object to be bound.
"""
self.system = system
# Checks as soon as possible if some asked-for properties are
# missing or mispelled
for what in self.outlist:
key = getkey(what)
if not key in self.system.properties.property_dict.keys():
print "Computable properties list: ", self.system.properties.property_dict.keys()
raise KeyError(key + " is not a recognized property")
self.open_stream()
softexit.register_function(self.softexit)
def print_header(self):
# print nice header if information is available on the properties
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.system.properties.property_dict[key]
if "size" in prop:
if (type(prop["size"]) is str) or (prop["size"] <= 0):
raise RuntimeError(
"ERROR: property %s has undefined size." % key)
elif prop["size"] > 1:
ohead += "cols. %3d-%-3d" % (icol,
icol + prop["size"] - 1)
icol += prop["size"]
else:
ohead += "column %3d " % (icol)
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def main(inputfile, outdir="trim"):
# opens & parses the input file
ifile = open(inputfile, "r")
xmlrestart = io_xml.xml_parse_file(ifile) # Parses the file.
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
trimstep = isimul.step.fetch()
os.makedirs(outdir)
# reconstructs the list of the property and trajectory files that have been output
# and that should be re-ordered
lprop = [] # list of property files
ltraj = [] # list of trajectory files
nsys = len(simul.syslist)
for o in simul.outtemplate:
o = deepcopy(o) # avoids overwriting the actual filename
if simul.outtemplate.prefix != "":
o.filename = simul.outtemplate.prefix + "." + o.filename
if type(o) is CheckpointOutput: # properties and trajectories are output per system
pass
elif type(o) is PropertyOutput:
nprop = []
isys = 0
for s in simul.syslist: # create multiple copies
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
ofilename = outdir + "/" + filename
nprop.append({"filename": filename, "ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
lprop.append(nprop)
elif type(o) is TrajectoryOutput: # trajectories are more complex, as some have per-bead output
if getkey(o.what) in ["positions", "velocities", "forces", "extras"]: # multiple beads
nbeads = simul.syslist[0].beads.nbeads
for b in range(nbeads):
ntraj = []
isys = 0
# zero-padded bead number
padb = (("%0" + str(int(1 + np.floor(np.log(nbeads) / np.log(10)))) + "d") % (b))
for s in simul.syslist:
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
ofilename = outdir + "/" + filename
if (o.ibead < 0 or o.ibead == b):
if getkey(o.what) == "extras":
filename = filename + "_" + padb
ofilename = ofilename + "_" + padb
else:
filename = filename + "_" + padb + "." + o.format
ofilename = ofilename + "_" + padb + "." + o.format
ntraj.append({"filename": filename, "format": o.format,
"ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
if ntraj != []:
ltraj.append(ntraj)
else:
ntraj = []
isys = 0
for s in simul.syslist: # create multiple copies
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
filename = filename + "." + o.format
ofilename = outdir + "/" + filename
ntraj.append({"filename": filename, "format": o.format,
"ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
ltraj.append(ntraj)
ptfile = None
wtefile = None
if os.path.isfile("PARATEMP"):
ptfile = open("PARATEMP", "r")
optfile = open(outdir + "/PARATEMP", "w")
if os.path.isfile("PARAWTE"):
wtefile = open("PARAWTE", "r")
owtefile = open(outdir + "/PARAWTE", "w")
# now reads files one frame at a time, and re-direct output to the appropriate location
for step in range(trimstep + 1):
# reads one line from PARATEMP index file
if not ptfile is None:
line = ptfile.readline()
optfile.write(line)
if not wtefile is None:
line = wtefile.readline()
owtefile.write(line)
try:
for prop in lprop:
for isys in range(nsys):
sprop = prop[isys]
if step % sprop["stride"] == 0: # property transfer
iline = sprop["ifile"].readline()
while iline[0] == "#": # fast forward if line is a comment
prop[isys]["ofile"].write(iline)
iline = sprop["ifile"].readline()
prop[isys]["ofile"].write(iline)
for traj in ltraj:
for isys in range(nsys):
straj = traj[isys]
if step % straj["stride"] == 0: # property transfer
# reads one frame from the input file
ibuffer = []
if straj["format"] == "xyz":
iline = straj["ifile"].readline()
nat = int(iline)
ibuffer.append(iline)
ibuffer.append(straj["ifile"].readline())
for i in range(nat):
ibuffer.append(straj["ifile"].readline())
traj[isys]["ofile"].write(''.join(ibuffer))
elif straj["format"] == "pdb":
iline = straj["ifile"].readline()
while (iline.strip() != "" and iline.strip() != "END"):
ibuffer.append(iline)
iline = straj["ifile"].readline()
ibuffer.append(iline)
traj[isys]["ofile"].write(''.join(ibuffer))
except EOFError:
break
def main(inputfile, prefix="SRT_"):
verbosity.level = "low"
# opens & parses the input file
ifile = open(inputfile, "r")
xmlrestart = io_xml.xml_parse_file(ifile) # Parses the file.
ifile.close()
# ugly hack to remove ffplumed objects to avoid messing up with plumed output files
newfields = [
f for f in xmlrestart.fields[0][1].fields if f[0] != "ffplumed"
]
xmlrestart.fields[0][1].fields = newfields
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
swapfile = ""
if simul.smotion is None or (simul.smotion.mode != "remd"
and simul.smotion.mode != "multi"):
raise ValueError(
"Simulation does not look like a parallel tempering one.")
else:
if simul.smotion.mode == "remd":
swapfile = simul.smotion.swapfile
else:
for sm in simul.smotion.mlist:
if sm.mode == "remd":
if swapfile != "":
raise ValueError(
"I'm not equipped to deal with multiple REMD outputs, sorry"
)
swapfile = sm.swapfile
if swapfile == "":
raise ValueError("Could not determine the REMD swapfile name. \
Sorry, you'll have to look carefully at your inputs.")
# reconstructs the list of the property and trajectory files that have been output
# and that should be re-ordered
lprop = [] # list of property files
ltraj = [] # list of trajectory files
nsys = len(simul.syslist)
for o in simul.outtemplate:
o = deepcopy(o) # avoids overwriting the actual filename
if simul.outtemplate.prefix != "":
o.filename = simul.outtemplate.prefix + "." + o.filename
if (type(o) is CheckpointOutput
): # properties and trajectories are output per system
pass
elif type(o) is PropertyOutput:
nprop = []
isys = 0
for s in simul.syslist: # create multiple copies
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else:
filename = o.filename
ofilename = prefix + filename
nprop.append({
"filename": filename,
"ofilename": ofilename,
"stride": o.stride,
"ifile": open(filename, "r"),
"ofile": open(ofilename, "w"),
})
isys += 1
lprop.append(nprop)
elif (type(o) is TrajectoryOutput
): # trajectories are more complex, as some have per-bead output
if getkey(o.what) in [
"positions",
"velocities",
"forces",
"extras",
]: # multiple beads
nbeads = simul.syslist[0].beads.nbeads
for b in range(nbeads):
ntraj = []
isys = 0
# zero-padded bead number
padb = ("%0" + str(
int(1 + np.floor(np.log(nbeads) / np.log(10)))) +
"d") % (b)
for s in simul.syslist:
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else:
filename = o.filename
ofilename = prefix + filename
if o.ibead < 0 or o.ibead == b:
if getkey(o.what) == "extras":
filename = filename + "_" + padb
ofilename = ofilename + "_" + padb
# Sets format of extras as None
ntraj.append({
"filename": filename,
"format": None,
"ofilename": ofilename,
"stride": o.stride,
"ifile": open(filename, "r"),
"ofile": open(ofilename, "w"),
})
else:
filename = filename + "_" + padb + "." + o.format
ofilename = ofilename + "_" + padb + "." + o.format
ntraj.append({
"filename": filename,
"format": o.format,
"ofilename": ofilename,
"stride": o.stride,
"ifile": open(filename, "r"),
"ofile": open(ofilename, "w"),
})
isys += 1
if ntraj != []:
ltraj.append(ntraj)
else:
ntraj = []
isys = 0
for s in simul.syslist: # create multiple copies
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else:
filename = o.filename
filename = filename + "." + o.format
ofilename = prefix + filename
ntraj.append({
"filename": filename,
"format": o.format,
"ofilename": ofilename,
"stride": o.stride,
"ifile": open(filename, "r"),
"ofile": open(ofilename, "w"),
})
isys += 1
ltraj.append(ntraj)
ptfile = open(simul.outtemplate.prefix + "." + swapfile, "r")
# now reads files one frame at a time,
# and re-direct output to the appropriate location
line = ptfile.readline().split()
irep = list(range(nsys)) # Could this be harmful?
step = 0
while True:
# reads one line from index file
try:
for prop in lprop:
for isys in range(nsys):
sprop = prop[isys]
if step % sprop["stride"] == 0: # property transfer
iline = sprop["ifile"].readline()
if len(iline) == 0:
raise EOFError # useful if line is blank
while iline[
0] == "#": # fast forward if line is a comment
prop[irep[isys]]["ofile"].write(iline)
iline = sprop["ifile"].readline()
prop[irep[isys]]["ofile"].write(iline)
for traj in ltraj:
for isys in range(nsys):
straj = traj[isys]
if step % straj["stride"] == 0: # property transfer
# reads one frame from the input file
ibuffer = []
if straj["format"] is None:
ibuffer.append(straj["ifile"].readline())
ibuffer.append(straj["ifile"].readline())
traj[irep[isys]]["ofile"].write("".join(ibuffer))
if straj["format"] == "xyz":
iline = straj["ifile"].readline()
nat = int(iline)
ibuffer.append(iline)
ibuffer.append(straj["ifile"].readline())
for i in range(nat):
ibuffer.append(straj["ifile"].readline())
traj[irep[isys]]["ofile"].write("".join(ibuffer))
elif straj["format"] == "pdb":
iline = straj["ifile"].readline()
while iline.strip() != "" and iline.strip(
) != "END":
ibuffer.append(iline)
iline = straj["ifile"].readline()
ibuffer.append(iline)
traj[irep[isys]]["ofile"].write("".join(ibuffer))
except EOFError:
break
if len(line) > 0 and step == int(line[0]):
irep = [int(i) for i in line[1:]]
line = ptfile.readline()
line = line.split()
step += 1
def write_traj(
self,
data,
what,
stream,
b=0,
format="xyz",
dimension="",
units="automatic",
cell_units="automatic",
flush=True,
):
"""Prints out a frame of a trajectory for the specified quantity and bead.
Args:
what: A string specifying what to print.
b: The bead index. Defaults to 0.
stream: A reference to the stream on which data will be printed.
format: The output file format.
cell_units: The units used to specify the cell parameters.
flush: A boolean which specifies whether to flush the output buffer
after each write to file or not.
"""
key = getkey(what)
if key in ["extras", "extras_component"]:
stream.write(" #*EXTRAS*# Step: %10d Bead: %5d \n" %
(self.system.simul.step + 1, b))
if self.extra_type in data:
if np.array(data[self.extra_type][b]).ndim == 2:
stream.write("\n".join([
" ".join(
["{:15.8f}".format(item) for item in row])
for row in data[self.extra_type][b]
]))
elif np.array(data[self.extra_type][b]).ndim == 1:
stream.write(" ".join(
"%15.8f" % el
for el in np.asarray(data[self.extra_type][b])))
else:
stream.write("%s" % data[self.extra_type][b])
stream.write("\n")
else:
raise KeyError(
"Extra type '" + self.extra_type +
"' is not among the quantities returned by any of the forcefields."
)
if flush:
stream.flush()
os.fsync(stream)
return
elif getkey(what) in [
"positions",
"velocities",
"forces",
"forces_sc",
"momenta",
]:
fatom = Atoms(self.system.beads.natoms)
fatom.names[:] = self.system.beads.names
fatom.q[:] = data[b]
else:
fatom = Atoms(self.system.beads.natoms)
fatom.names[:] = self.system.beads.names
fatom.q[:] = data
fcell = Cell()
fcell.h = self.system.cell.h
if units == "":
units = "automatic"
if cell_units == "":
cell_units = "automatic"
io.print_file(
format,
fatom,
fcell,
stream,
title=("Step: %10d Bead: %5d " %
(self.system.simul.step + 1, b)),
key=key,
dimension=dimension,
units=units,
cell_units=cell_units,
)
if flush:
stream.flush()
os.fsync(stream)
def main(inputfile, outdir="trim"):
# opens & parses the input file
ifile = open(inputfile, "r")
xmlrestart = io_xml.xml_parse_file(ifile) # Parses the file.
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
trimstep = isimul.step.fetch()
os.makedirs(outdir)
# reconstructs the list of the property and trajectory files that have been output
# and that should be re-ordered
lprop = [] # list of property files
ltraj = [] # list of trajectory files
nsys = len(simul.syslist)
for o in simul.outtemplate:
if type(o) is CheckpointOutput: # properties and trajectories are output per system
pass
elif type(o) is PropertyOutput:
nprop = []
isys = 0
for s in simul.syslist: # create multiple copies
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
ofilename = outdir + "/" + filename
nprop.append({"filename": filename, "ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
lprop.append(nprop)
elif type(o) is TrajectoryOutput: # trajectories are more complex, as some have per-bead output
if getkey(o.what) in ["positions", "velocities", "forces", "extras"]: # multiple beads
nbeads = simul.syslist[0].beads.nbeads
for b in range(nbeads):
ntraj = []
isys = 0
# zero-padded bead number
padb = (("%0" + str(int(1 + np.floor(np.log(nbeads) / np.log(10)))) + "d") % (b))
for s in simul.syslist:
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
ofilename = outdir + "/" + filename
if (o.ibead < 0 or o.ibead == b):
if getkey(o.what) == "extras":
filename = filename + "_" + padb
ofilename = ofilename + "_" + padb
else:
filename = filename + "_" + padb + "." + o.format
ofilename = ofilename + "_" + padb + "." + o.format
ntraj.append({"filename": filename, "format": o.format,
"ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
if ntraj != []:
ltraj.append(ntraj)
else:
ntraj = []
isys = 0
for s in simul.syslist: # create multiple copies
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
filename = filename + "." + o.format
ofilename = outdir + "/" + filename
ntraj.append({"filename": filename, "format": o.format,
"ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
ltraj.append(ntraj)
ptfile = None
wtefile = None
if os.path.isfile("PARATEMP"):
ptfile = open("PARATEMP", "r")
optfile = open(outdir + "/PARATEMP", "w")
if os.path.isfile("PARAWTE"):
wtefile = open("PARAWTE", "r")
owtefile = open(outdir + "/PARAWTE", "w")
# now reads files one frame at a time, and re-direct output to the appropriate location
for step in range(trimstep + 1):
# reads one line from PARATEMP index file
if not ptfile is None:
line = ptfile.readline()
optfile.write(line)
if not wtefile is None:
line = wtefile.readline()
owtefile.write(line)
try:
for prop in lprop:
for isys in range(nsys):
sprop = prop[isys]
if step % sprop["stride"] == 0: # property transfer
iline = sprop["ifile"].readline()
while iline[0] == "#": # fast forward if line is a comment
prop[isys]["ofile"].write(iline)
iline = sprop["ifile"].readline()
prop[isys]["ofile"].write(iline)
for traj in ltraj:
for isys in range(nsys):
straj = traj[isys]
if step % straj["stride"] == 0: # property transfer
# reads one frame from the input file
ibuffer = []
if straj["format"] == "xyz":
iline = straj["ifile"].readline()
nat = int(iline)
ibuffer.append(iline)
ibuffer.append(straj["ifile"].readline())
for i in range(nat):
ibuffer.append(straj["ifile"].readline())
traj[isys]["ofile"].write(''.join(ibuffer))
elif straj["format"] == "pdb":
iline = straj["ifile"].readline()
while (iline.strip() != "" and iline.strip() != "END"):
ibuffer.append(iline)
iline = straj["ifile"].readline()
ibuffer.append(iline)
traj[isys]["ofile"].write(''.join(ibuffer))
except EOFError:
break
def get_output_filenames(xml_path):
"""
Predicts ipi output filenames based on I-PI input file.
Args:
xml_path: absolute path to I-PI input file
Returns:
list of I-PI output files that will be generated
running I-PI using this input
TODO A more elegant solution. This function launches I-PI
in the directory of the input file and dumps output to dev/null,
which would make potential bugs hard to detect.
"""
# Avoid to print i-pi output
devnull = open('/dev/null', 'w')
oldstdout_fno = os.dup(sys.stdout.fileno())
os.dup2(devnull.fileno(), 1)
xml_path = os.path.abspath(xml_path)
os.chdir(os.path.dirname(xml_path))
# i-pi xml file parser
ifile = open(xml_path, 'r')
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
# reconstructs the list of the property and trajectory files
lprop = [] # list of property files
ltraj = [] # list of trajectory files
for o in simul.outtemplate:
# properties and trajectories are output per system
if isinstance(o, CheckpointOutput):
pass
elif isinstance(o, PropertyOutput):
for _ss in simul.syslist: # create multiple copies
filename = o.filename
if _ss.prefix != "":
filename = _ss.prefix + "_" + filename
lprop.append(filename)
# trajectories are more complex, as some have per-bead output
elif isinstance(o, TrajectoryOutput):
if getkey(o.what) in ['positions', 'velocities',
'forces', 'forces_sc', 'extras']: # multiple beads
nbeads = simul.syslist[0].beads.nbeads
for _bi in range(nbeads):
# zero-padded bead number
padb = (('%0' + str(int(1 +
np.floor(np.log(nbeads) /
np.log(10)))) +
'd') % (_bi))
for _ss in simul.syslist:
if (o.ibead < 0 and ((_bi % (-o.ibead) == 0))) or o.ibead == _bi:
filename = o.filename
if _ss.prefix != "":
filename = _ss.prefix + "_" + filename
if getkey(o.what) == 'extras':
filename += "_" + padb
else:
filename += "_" + padb + "." + o.format
ltraj.append(filename)
else:
for _ss in simul.syslist: # create multiple copies
filename = o.filename
if _ss.prefix != "":
filename = _ss.prefix + "_" + filename
filename += "." + o.format
ltraj.append(filename)
os.dup2(oldstdout_fno, 1)
return (ltraj + lprop)
def get_output_filenames(xml_path):
"""
Predicts ipi output filenames based on I-PI input file.
Args:
xml_path: absolute path to I-PI input file
Returns:
list of I-PI output files that will be generated
running I-PI using this input
TODO A more elegant solution. This function launches I-PI
in the directory of the input file and dumps output to dev/null,
which would make potential bugs hard to detect.
"""
# Avoid to print i-pi output
devnull = open('/dev/null', 'w')
oldstdout_fno = os.dup(sys.stdout.fileno())
os.dup2(devnull.fileno(), 1)
xml_path = os.path.abspath(xml_path)
os.chdir(os.path.dirname(xml_path))
# i-pi xml file parser
ifile = open(xml_path, 'r')
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
# reconstructs the list of the property and trajectory files
lprop = [] # list of property files
ltraj = [] # list of trajectory files
for o in simul.outtemplate:
# properties and trajectories are output per system
if isinstance(o, CheckpointOutput):
pass
elif isinstance(o, PropertyOutput):
for _ss in simul.syslist: # create multiple copies
filename = o.filename
if _ss.prefix != "":
filename = _ss.prefix + "_" + filename
lprop.append(filename)
# trajectories are more complex, as some have per-bead output
elif isinstance(o, TrajectoryOutput):
if getkey(o.what) in [
'positions', 'velocities', 'forces', 'forces_sc', 'extras'
]: # multiple beads
nbeads = simul.syslist[0].beads.nbeads
for _bi in range(nbeads):
# zero-padded bead number
padb = (('%0' + str(
int(1 + np.floor(np.log(nbeads) / np.log(10)))) + 'd')
% (_bi))
for _ss in simul.syslist:
if (o.ibead < 0 and
((_bi % (-o.ibead) == 0))) or o.ibead == _bi:
filename = o.filename
if _ss.prefix != "":
filename = _ss.prefix + "_" + filename
if getkey(o.what) == 'extras':
filename += "_" + padb
else:
filename += "_" + padb + "." + o.format
ltraj.append(filename)
else:
for _ss in simul.syslist: # create multiple copies
filename = o.filename
if _ss.prefix != "":
filename = _ss.prefix + "_" + filename
filename += "." + o.format
ltraj.append(filename)
os.dup2(oldstdout_fno, 1)
return (ltraj + lprop)
def get_filesname(self, xml_path, olddir, newdir):
""" The test results should be analyzed number by numbers.
The idea is that the testing input should never change, then the files
should be always the same. It would probably be better, anyway, to use
the i-pi infrastructure to retrieve the right position of the data. In
fact, this would work as a further testing.
Args:
olddir: The path used for the 'old_filename' in the returned
dictionary.
newdir: The path used for the 'new_filename' in the returned
dictionary.
Returns:
lprop
nprop
"""
# Avoid to print i-pi output
devnull = open('/dev/null', 'w')
oldstdout_fno = os.dup(sys.stdout.fileno())
os.dup2(devnull.fileno(), 1)
# opens & parses the input file
# get in the input file location so it can find other input files for initialization
cwd = os.getcwd()
iodir = os.path.dirname(os.path.realpath(xml_path))
os.chdir(iodir)
# print "READING FILE FROM ", iodir
# print " WHILE RUNNING IN ", cwd
# print "I have changed directory to ", os.getcwd()
ifile = open(xml_path, "r")
xmlrestart = io_xml.xml_parse_file(ifile) # Parses the file.
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
os.chdir(cwd)
# reconstructs the list of the property and trajectory files
lprop = [] # list of property files
ltraj = [] # list of trajectory files
for o in simul.outtemplate:
# properties and trajectories are output per system
if isinstance(o, CheckpointOutput):
pass
elif isinstance(o, PropertyOutput):
nprop = []
isys = 0
for _ss in simul.syslist: # create multiple copies
filename = _ss.prefix + o.filename
nprop.append({"old_filename": os.path.join(olddir,
filename),
"new_filename": os.path.join(newdir,
filename),
"stride": o.stride,
"properties": o.outlist, })
isys += 1
lprop.append(nprop)
# trajectories are more complex, as some have per-bead output
elif isinstance(o, TrajectoryOutput):
if getkey(o.what) in ["positions", "velocities",
"forces", "forces_sc", "extras"]: # multiple beads
nbeads = simul.syslist[0].beads.nbeads
for _bi in range(nbeads):
ntraj = []
isys = 0
# zero-padded bead number
padb = (("%0" + str(int(1 +
np.floor(np.log(nbeads) /
np.log(10)))) +
"d") % (_bi))
for _ss in simul.syslist:
if o.ibead < 0 or o.ibead == _bi:
if getkey(o.what) == "extras":
filename = _ss.prefix + o.filename + "_" + padb
else:
filename = _ss.prefix + o.filename + "_" + padb + \
"." + o.format
ntraj.append({"old_filename": os.path.join(olddir, filename),
"format": o.format,
"new_filename": os.path.join(newdir, filename),
"stride": o.stride,
"what": o.what, })
isys += 1
if ntraj != []:
ltraj.append(ntraj)
else:
ntraj = []
isys = 0
for _ss in simul.syslist: # create multiple copies
filename = _ss.prefix + o.filename
filename = filename + "." + o.format
ntraj.append({"old_filename": os.path.join(olddir,
filename),
"new_filename": os.path.join(newdir,
filename),
"format": o.format,
"stride": o.stride, })
isys += 1
ltraj.append(ntraj)
os.dup2(oldstdout_fno, 1)
return ltraj, lprop
def main(inputfile, prefix="PT"):
verbosity.level = "low"
# opens & parses the input file
ifile = open(inputfile, "r")
xmlrestart = io_xml.xml_parse_file(ifile) # Parses the file.
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
if simul.smotion.mode != "remd":
raise ValueError("Simulation does not look like a parallel tempering one.")
# reconstructs the list of the property and trajectory files that have been output
# and that should be re-ordered
lprop = [] # list of property files
ltraj = [] # list of trajectory files
nsys = len(simul.syslist)
for o in simul.outtemplate:
if type(o) is CheckpointOutput: # properties and trajectories are output per system
pass
elif type(o) is PropertyOutput:
nprop = []
isys = 0
for s in simul.syslist: # create multiple copies
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
ofilename = prefix + str(isys) + "_" + o.filename
nprop.append({"filename": filename, "ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
lprop.append(nprop)
elif type(o) is TrajectoryOutput: # trajectories are more complex, as some have per-bead output
if getkey(o.what) in ["positions", "velocities", "forces", "extras"]: # multiple beads
nbeads = simul.syslist[0].beads.nbeads
for b in range(nbeads):
ntraj = []
isys = 0
# zero-padded bead number
padb = (("%0" + str(int(1 + np.floor(np.log(nbeads) / np.log(10)))) + "d") % (b))
for s in simul.syslist:
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
ofilename = prefix + str(isys) + "_" + o.filename
if (o.ibead < 0 or o.ibead == b):
if getkey(o.what) == "extras":
filename = filename + "_" + padb
ofilename = ofilename + "_" + padb
else:
filename = filename + "_" + padb + "." + o.format
ofilename = ofilename + "_" + padb + "." + o.format
ntraj.append({"filename": filename, "format": o.format,
"ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
if ntraj != []:
ltraj.append(ntraj)
else:
ntraj = []
isys = 0
for s in simul.syslist: # create multiple copies
if s.prefix != "":
filename = s.prefix + "_" + o.filename
else: filename = o.filename
filename = filename + "." + o.format
ofilename = prefix + str(isys) + "_" + o.filename + "." + o.format
ntraj.append({"filename": filename, "format": o.format,
"ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": open(ofilename, "w")
})
isys += 1
ltraj.append(ntraj)
ptfile = open("PARATEMP", "r")
# now reads files one frame at a time, and re-direct output to the appropriate location
line = ptfile.readline().split()
irep = range(nsys) # Could this be harmful?
step = 0
while True:
# reads one line from PARATEMP index file
try:
for prop in lprop:
for isys in range(nsys):
sprop = prop[isys]
if step % sprop["stride"] == 0: # property transfer
iline = sprop["ifile"].readline()
if len(iline) == 0: raise EOFError # useful if line is blank
while iline[0] == "#": # fast forward if line is a comment
prop[irep[isys]]["ofile"].write(iline)
iline = sprop["ifile"].readline()
prop[irep[isys]]["ofile"].write(iline)
for traj in ltraj:
for isys in range(nsys):
straj = traj[isys]
if step % straj["stride"] == 0: # property transfer
# reads one frame from the input file
ibuffer = []
if straj["format"] == "xyz":
iline = straj["ifile"].readline()
nat = int(iline)
ibuffer.append(iline)
ibuffer.append(straj["ifile"].readline())
for i in range(nat):
ibuffer.append(straj["ifile"].readline())
traj[irep[isys]]["ofile"].write(''.join(ibuffer))
elif straj["format"] == "pdb":
iline = straj["ifile"].readline()
while (iline.strip() != "" and iline.strip() != "END"):
ibuffer.append(iline)
iline = straj["ifile"].readline()
ibuffer.append(iline)
traj[irep[isys]]["ofile"].write(''.join(ibuffer))
except EOFError:
break
if len(line) > 0 and step == int(line[0]):
irep = [int(i) for i in line[1:]]
line = ptfile.readline()
line = line.split()
step += 1
def get_filesname(self, xml_path, olddir, newdir):
""" The test results should be analyzed number by numbers.
The idea is that the testing input should never change, then the files
should be always the same. It would probably be better, anyway, to use
the i-pi infrastructure to retrieve the right position of the data. In
fact, this would work as a further testing.
Args:
olddir: The path used for the 'old_filename' in the returned
dictionary.
newdir: The path used for the 'new_filename' in the returned
dictionary.
Returns:
lprop
nprop
"""
# Avoid to print i-pi output
devnull = open('/dev/null', 'w')
oldstdout_fno = os.dup(sys.stdout.fileno())
os.dup2(devnull.fileno(), 1)
# opens & parses the input file
# get in the input file location so it can find other input files for initialization
cwd = os.getcwd()
iodir = os.path.dirname(os.path.realpath(xml_path))
os.chdir(iodir)
# print "READING FILE FROM ", iodir
# print " WHILE RUNNING IN ", cwd
# print "I have changed directory to ", os.getcwd()
ifile = open(xml_path, "r")
xmlrestart = io_xml.xml_parse_file(ifile) # Parses the file.
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
os.chdir(cwd)
# reconstructs the list of the property and trajectory files
lprop = [] # list of property files
ltraj = [] # list of trajectory files
for o in simul.outtemplate:
# properties and trajectories are output per system
if isinstance(o, CheckpointOutput):
pass
elif isinstance(o, PropertyOutput):
nprop = []
isys = 0
for _ss in simul.syslist: # create multiple copies
filename = _ss.prefix + o.filename
nprop.append({"old_filename": os.path.join(olddir,
filename),
"new_filename": os.path.join(newdir,
filename),
"stride": o.stride,
"properties": o.outlist, })
isys += 1
lprop.append(nprop)
# trajectories are more complex, as some have per-bead output
elif isinstance(o, TrajectoryOutput):
if getkey(o.what) in ["positions", "velocities",
"forces", "forces_sc", "extras"]: # multiple beads
nbeads = simul.syslist[0].beads.nbeads
for _bi in range(nbeads):
ntraj = []
isys = 0
# zero-padded bead number
padb = (("%0" + str(int(1 +
np.floor(np.log(nbeads) /
np.log(10)))) +
"d") % (_bi))
for _ss in simul.syslist:
if o.ibead < 0 or o.ibead == _bi:
if getkey(o.what) == "extras":
filename = _ss.prefix + o.filename + "_" + padb
else:
filename = _ss.prefix + o.filename + "_" + padb + \
"." + o.format
ntraj.append({"old_filename": os.path.join(olddir, filename),
"format": o.format,
"new_filename": os.path.join(newdir, filename),
"stride": o.stride,
"what": o.what, })
isys += 1
if ntraj != []:
ltraj.append(ntraj)
else:
ntraj = []
isys = 0
for _ss in simul.syslist: # create multiple copies
filename = _ss.prefix + o.filename
filename = filename + "." + o.format
ntraj.append({"old_filename": os.path.join(olddir,
filename),
"new_filename": os.path.join(newdir,
filename),
"format": o.format,
"stride": o.stride, })
isys += 1
ltraj.append(ntraj)
os.dup2(oldstdout_fno, 1)
return ltraj, lprop
def write_traj(
self,
data,
what,
stream,
b=0,
format="xyz",
dimension="",
units="automatic",
cell_units="automatic",
flush=True,
):
"""Prints out a frame of a trajectory for the specified quantity and bead.
Args:
what: A string specifying what to print.
b: The bead index. Defaults to 0.
stream: A reference to the stream on which data will be printed.
format: The output file format.
cell_units: The units used to specify the cell parameters.
flush: A boolean which specifies whether to flush the output buffer
after each write to file or not.
"""
key = getkey(what)
if key in ["extras"]:
stream.write(" #*EXTRAS*# Step: %10d Bead: %5d \n" %
(self.system.simul.step + 1, b))
try:
index = 0
for el, item in enumerate(data):
if self.xtratype in item[b].keys():
index = el
try:
if self.xtratype == "friction":
fatom = Atoms(self.system.beads.natoms)
fatom.names[:] = self.system.beads.names
stream.write("# %s\n" %
" ".join("%15s" % el for el in [
"xx",
"yy",
"zz",
"xy=yx",
"xz=zx",
"yz=zy",
]))
for na in range(self.system.beads.natoms):
stream.write("%3s %s\n" % (
fatom.names[na],
" ".join(
"%15.8f" % el for el in data[index][b]
[self.xtratype][na * 6:(na + 1) * 6]),
))
else:
stream.write(" ".join(
"%15.8f" % el
for el in data[index][b][self.xtratype]))
stream.write("\n")
except:
stream.write(json.dumps(data[index][b][self.xtratype]))
stream.write("\n")
except:
try:
info(
"Sorry, your specified xtratype %s is not among the available options. \n"
"The available keys are the following: %s " % (
self.xtratype,
",".join("%s" % key for key in data[0][b].keys()),
),
verbosity.low,
)
except:
info(
"Sorry, no extras string has been passed, there are no available options for the xtratype "
"attribute. \n",
verbosity.low,
)
if flush:
stream.flush()
os.fsync(stream)
return
elif getkey(what) in [
"positions",
"velocities",
"forces",
"forces_sc",
"momenta",
]:
fatom = Atoms(self.system.beads.natoms)
fatom.names[:] = self.system.beads.names
fatom.q[:] = data[b]
else:
fatom = Atoms(self.system.beads.natoms)
fatom.names[:] = self.system.beads.names
fatom.q[:] = data
fcell = Cell()
fcell.h = self.system.cell.h
if units == "":
units = "automatic"
if cell_units == "":
cell_units = "automatic"
io.print_file(
format,
fatom,
fcell,
stream,
title=("Step: %10d Bead: %5d " %
(self.system.simul.step + 1, b)),
key=key,
dimension=dimension,
units=units,
cell_units=cell_units,
)
if flush:
stream.flush()
os.fsync(stream)