def init_chk(filename):
"""Reads a checkpoint file and returns the data contained in it.
Args:
filename: A string giving the name of the checkpoint file to be read from.
Returns:
A Beads object, Cell object and Thermostat object as read from the
checkpoint file.
"""
# reads configuration from a checkpoint file
rfile = open(filename, "r")
xmlchk = xml_parse_file(rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
sim = simchk.fetch()
if len(sim.syslist) > 1:
warning("Restart from checkpoint with " + str(len(sim.syslist)) + " systems will fetch data from the first system.")
rcell = sim.syslist[0].cell
rbeads = sim.syslist[0].beads
rmotion = sim.syslist[0].motion
return (rbeads, rcell, rmotion)
def init_chk(filename):
"""Reads a checkpoint file and returns the data contained in it.
Args:
filename: A string giving the name of the checkpoint file to be read from.
Returns:
A Beads object, Cell object and Thermostat object as read from the
checkpoint file.
"""
# reads configuration from a checkpoint file
rfile = open(filename, "r")
xmlchk = xml_parse_file(rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
sim = simchk.fetch()
if len(sim.syslist) > 1:
warning("Restart from checkpoint with " + str(len(sim.syslist)) +
" systems will fetch data from the first system.")
rcell = sim.syslist[0].cell
rbeads = sim.syslist[0].beads
rmotion = sim.syslist[0].motion
return (rbeads, rcell, rmotion)
def step(self, step=None):
"""Does one replay time step."""
self.ptime = 0.0
self.ttime = 0.0
self.qtime = -time.time()
while True:
self.rstep += 1
try:
if self.intraj.mode == "xyz":
for b in self.beads:
myframe = read_file("xyz", self.rfile)
myatoms = myframe["atoms"]
mycell = myframe["cell"]
myatoms.q *= unit_to_internal("length",
self.intraj.units, 1.0)
mycell.h *= unit_to_internal("length",
self.intraj.units, 1.0)
b.q[:] = myatoms.q
self.cell.h[:] = mycell.h
elif self.intraj.mode == "pdb":
for b in self.beads:
myatoms, mycell = read_file("pdb", self.rfile)
myatoms.q *= unit_to_internal("length",
self.intraj.units, 1.0)
mycell.h *= unit_to_internal("length",
self.intraj.units, 1.0)
b.q[:] = myatoms.q
self.cell.h[:] = mycell.h
elif self.intraj.mode == "chk" or self.intraj.mode == "checkpoint":
# TODO: Adapt the new `Simulation.load_from_xml`?
# reads configuration from a checkpoint file
xmlchk = xml_parse_file(self.rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
mycell = simchk.cell.fetch()
mybeads = simchk.beads.fetch()
self.cell.h[:] = mycell.h
self.beads.q[:] = mybeads.q
softexit.trigger(" # Read single checkpoint")
except EOFError:
softexit.trigger(" # Finished reading re-run trajectory")
if (step is None) or (self.rstep > step):
break
self.qtime += time.time()
def gleacf(path2iipi, path2ivvac, oprefix, action, nrows, stride, dparam):
# opens & parses the i-pi input file
ifile = open(path2iipi, "r")
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
# parses the drift and diffusion matrices of the GLE thermostat.
ttype = str(type(simul.syslist[0].motion.thermostat).__name__)
kbT = float(simul.syslist[0].ensemble.temp)
simul.syslist[0].motion.thermostat.temp = kbT
if (ttype == "ThermoGLE"):
Ap = simul.syslist[0].motion.thermostat.A * unit_to_internal(
"time", dt[1], float(dt[0]))
Cp = simul.syslist[0].motion.thermostat.C / kbT
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
elif (ttype == "ThermoLangevin"):
Ap = np.asarray(
[1.0 / simul.syslist[0].motion.thermostat.tau]).reshape(
(1, 1)) * unit_to_internal("time", dt[1], float(dt[0]))
Cp = np.asarray([1.0]).reshape((1, 1))
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
# imports the vvac function.
ivvac = input_vvac(path2ivvac, nrows, stride)
ix = ivvac[:, 0]
iy = ivvac[:, 1]
# computes the vvac kernel
print "# computing the kernel."
ker = gleKernel(ix, Ap, Dp)
# (de-)convolutes the spectrum
if (action == "conv"):
print "# printing the output spectrum."
output_vvac((ix, np.dot(iy, ker.T)), oprefix,
input_vvac(path2ivvac, nrows, 1))
elif (action == "deconv"):
print "# deconvoluting the input spectrum."
oy = ISRA(ix, ker, iy, dparam, oprefix)
def gleacf(path2iipi, path2ivvac, oprefix, action, nrows, stride, dparam):
# opens & parses the i-pi input file
ifile = open(path2iipi, "r")
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
# parses the drift and diffusion matrices of the GLE thermostat.
ttype = str(type(simul.syslist[0].motion.thermostat).__name__)
kbT = float(simul.syslist[0].ensemble.temp)
simul.syslist[0].motion.thermostat.temp = kbT
if(ttype == "ThermoGLE"):
Ap = simul.syslist[0].motion.thermostat.A * unit_to_internal("time", dt[1], float(dt[0]))
Cp = simul.syslist[0].motion.thermostat.C / kbT
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
elif(ttype == "ThermoLangevin"):
Ap = np.asarray([1.0 / simul.syslist[0].motion.thermostat.tau]).reshape((1, 1)) * unit_to_internal("time", dt[1], float(dt[0]))
Cp = np.asarray([1.0]).reshape((1, 1))
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
# imports the vvac function.
ivvac = input_vvac(path2ivvac, nrows, stride)
ix = ivvac[:, 0]
iy = ivvac[:, 1]
# computes the vvac kernel
print "# computing the kernel."
ker = gleKernel(ix, Ap, Dp)
# (de-)convolutes the spectrum
if(action == "conv"):
print "# printing the output spectrum."
output_vvac((ix, np.dot(iy, ker.T)), oprefix, input_vvac(path2ivvac, nrows, 1))
elif(action == "deconv"):
print "# deconvoluting the input spectrum."
oy = ISRA(ix, ker, iy, dparam, oprefix)
def step(self):
"""Does one simulation time step."""
self.ptime = self.ttime = 0
self.qtime = -time.time()
try:
if (self.intraj.mode == "xyz"):
for b in self.beads:
myatoms = read_xyz(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units,
1.0)
b.q[:] = myatoms.q
elif (self.intraj.mode == "pdb"):
for b in self.beads:
myatoms, mycell = read_pdb(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units,
1.0)
mycell.h *= unit_to_internal("length", self.intraj.units,
1.0)
b.q[:] = myatoms.q
self.cell.h[:] = mycell.h
elif (self.intraj.mode == "chk"
or self.intraj.mode == "checkpoint"):
# reads configuration from a checkpoint file
xmlchk = xml_parse_file(self.rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
mycell = simchk.cell.fetch()
mybeads = simchk.beads.fetch()
self.cell.h[:] = mycell.h
self.beads.q[:] = mybeads.q
softexit.trigger(" # Read single checkpoint")
except EOFError:
softexit.trigger(" # Finished reading re-run trajectory")
self.qtime += time.time()
def init_chk(filename):
"""Reads an checkpoint file and returns the data contained in it.
Args:
filename: A string giving the name of the checkpoint file to be read from.
Returns:
A Beads object, Cell object and Thermostat object as read from the
checkpoint file.
"""
# reads configuration from a checkpoint file
rfile = open(filename, "r")
xmlchk = xml_parse_file(rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
rcell = simchk.cell.fetch()
rbeads = simchk.beads.fetch()
rthermo = simchk.ensemble.thermostat.fetch()
return (rbeads, rcell, rthermo)
def init_chk(filename):
"""Reads an checkpoint file and returns the data contained in it.
Args:
filename: A string giving the name of the checkpoint file to be read from.
Returns:
A Beads object, Cell object and Thermostat object as read from the
checkpoint file.
"""
# reads configuration from a checkpoint file
rfile = open(filename,"r")
xmlchk = xml_parse_file(rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
rcell = simchk.cell.fetch()
rbeads = simchk.beads.fetch()
rthermo = simchk.ensemble.thermostat.fetch()
return (rbeads, rcell, rthermo)
def step(self):
"""Does one simulation time step."""
self.ptime = self.ttime = 0
self.qtime = -time.time()
try:
if self.intraj.mode == "xyz":
for b in self.beads:
myatoms = read_xyz(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units, 1.0)
b.q[:] = myatoms.q
elif self.intraj.mode == "pdb":
for b in self.beads:
myatoms, mycell = read_pdb(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units, 1.0)
mycell.h *= unit_to_internal("length", self.intraj.units, 1.0)
b.q[:] = myatoms.q
self.cell.h[:] = mycell.h
elif self.intraj.mode == "chk" or self.intraj.mode == "checkpoint":
# reads configuration from a checkpoint file
xmlchk = xml_parse_file(self.rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
mycell = simchk.cell.fetch()
mybeads = simchk.beads.fetch()
self.cell.h[:] = mycell.h
self.beads.q[:] = mybeads.q
softexit.trigger(" # Read single checkpoint")
except EOFError:
softexit.trigger(" # Finished reading re-run trajectory")
self.qtime += time.time()
def step(self, step=None):
"""Does one replay time step."""
self.ptime = 0.0
self.ttime = 0.0
self.qtime = -time.time()
# If wildcard is used, check that it is consistent with Nbeads
wildcard_used = False
if any(char in self.intraj.value for char in "*?[]"):
wildcard_used = True
if len(self.rfile) != len(self.beads):
info(
"Error: if a wildcard is used for replay, then "
"the number of files should be equal to the number of beads.",
verbosity.low,
)
softexit.trigger(" # Error in replay input.")
while True:
self.rstep += 1
try:
if self.intraj.mode == "xyz":
for bindex, b in enumerate(self.beads):
if wildcard_used:
myframe = read_file("xyz", self.rfile[bindex])
else:
myframe = read_file("xyz", self.rfile)
myatoms = myframe["atoms"]
mycell = myframe["cell"]
myatoms.q *= unit_to_internal("length",
self.intraj.units, 1.0)
mycell.h *= unit_to_internal("length",
self.intraj.units, 1.0)
b.q[:] = myatoms.q
elif self.intraj.mode == "pdb":
for bindex, b in enumerate(self.beads):
if wildcard_used:
myatoms, mycell = read_file(
"pdb", self.rfile[bindex])
else:
myatoms, mycell = read_file("pdb", self.rfile)
myatoms.q *= unit_to_internal("length",
self.intraj.units, 1.0)
mycell.h *= unit_to_internal("length",
self.intraj.units, 1.0)
b.q[:] = myatoms.q
elif self.intraj.mode == "chk" or self.intraj.mode == "checkpoint":
# TODO: Adapt the new `Simulation.load_from_xml`?
# reads configuration from a checkpoint file
xmlchk = xml_parse_file(self.rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
mycell = simchk.cell.fetch()
mybeads = simchk.beads.fetch()
self.beads.q[:] = mybeads.q
softexit.trigger(" # Read single checkpoint")
# do not assign cell if it contains an invalid value (typically missing cell in the input)
if mycell.V > 0:
self.cell.h[:] = mycell.h
except EOFError:
softexit.trigger(" # Finished reading re-run trajectory")
if (step is None) or (self.rstep > step):
break
self.qtime += time.time()
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 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 main(inputfile, prefix="PTW-", ttemp="300.0", skip="2000"):
txtemp = ttemp
ttemp = unit_to_internal("energy", "kelvin", float(ttemp))
skip = int(skip)
# opens & parses the input file
ifile = open(inputfile, "r")
verbosity.level = "quiet"
verbosity.lock = True
xmlrestart = io_xml.xml_parse_file(ifile) # Parses the file.
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
verbosity.level = "quiet"
banner()
print(
"# Printing out temperature re-weighing factors for a parallel tempering simulation"
)
simul = isimul.fetch()
if simul.mode != "paratemp":
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
tlist = simul.paratemp.temp_list
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 + (("%0" + str(
int(1 + np.floor(np.log(len(simul.syslist)) / np.log(10))))
+ "d") % (isys)) + "_" + o.filename)
nprop.append({
"filename": filename,
"ofilename": ofilename,
"stride": o.stride,
"ifile": open(filename, "r"),
"ofile": None,
})
isys += 1
lprop.append(nprop)
ptfile = open("PARATEMP", "r")
# these are variables used to compute the weighting factors
tprops = []
vfields = []
refpots = []
vunits = []
nw = []
tw = []
tw2 = []
repot = re.compile(" ([0-9]*) *--> potential")
reunit = re.compile("{(.*)}")
# now reads files one frame at a time, and re-direct output to the appropriate location
irep = np.zeros(nsys, int)
while True:
# reads one line from PARATEMP index file
line = ptfile.readline()
line = line.split()
try:
if len(line) == 0:
raise EOFError
step = int(line[0])
irep[:] = line[1:]
wk = 0
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
while iline[
0] == "#": # fast forward if line is a comment
# checks if we have one single file with potential energies
rm = repot.search(iline)
if not (rm is None) and not (prop in tprops):
tprops.append(prop)
for p in prop:
p["ofile"] = open(p["ofilename"], "w")
p["ofile"].write(
"# column 1 --> ptlogweight: ln of re-weighing factor with target temperature %s K\n"
% (txtemp))
vfields.append(int(rm.group(1)) - 1)
refpots.append(np.zeros(nsys))
nw.append(np.zeros(nsys))
tw.append(np.zeros(nsys))
tw2.append(np.zeros(nsys))
rm = reunit.search(iline)
if rm:
vunits.append(rm.group(1))
else:
vunits.append("atomic_unit")
iline = sprop["ifile"].readline()
if prop in tprops: # do temperature weighing
pot = unit_to_internal(
"energy", vunits[wk],
float(iline.split()[vfields[wk]]))
ir = irep[isys]
if nw[wk][ir] == 0:
refpots[wk][
ir] = pot # picks the first value as a reference potential to avoid insane absolute values of the logweight
temp = tlist[ir]
lw = (pot - refpots[wk][ir]) * (1 / temp -
1 / ttemp)
if (
step > skip
): # computes trajectory weights avoiding the initial - possibly insane - values
if nw[wk][ir] == 0:
tw[wk][ir] = lw
tw2[wk][ir] = lw
else:
tw[wk][ir] = logsumlog((tw[wk][ir], 1),
(lw, 1))[0]
tw2[wk][ir] = logsumlog((tw2[wk][ir], 1),
(2 * lw, 1))[0]
nw[wk][ir] += 1
prop[ir]["ofile"].write("%15.7e\n" % (lw))
if isys == nsys - 1:
wk += 1
except EOFError:
# print out trajectory weights based on PRSA 2011, assuming that observables and weights are weakly correlated
wk = 0
fpw = open(prefix + "WEIGHTS", "w")
fpw.write("# Global trajectory weights for temperature %s K\n" %
(txtemp))
fpw.write(
"# Please cite M. Ceriotti, G. A. Brain, O. Riordan, D.E. Manolopoulos, "
+
"The inefficiency of re-weighted sampling and the curse of system size in high-order path integration. "
+
"Proceedings of the Royal Society A, 468(2137), 2-17 (2011) \n"
)
for prop in lprop:
if prop in tprops:
for ir in range(nsys):
fpw.write("%s %15.7e \n" % (
prop[ir]["ofilename"],
1.0 / (np.exp(tw2[wk][ir] - 2 * tw[wk][ir]) *
nw[wk][ir]),
))
wk += 1
break
def get_A(path2iipi):
"""
Parses the i-PI input to read the relevant data files
and returns the Helmholtz free energy obtained within the
self consitent phonons (SCP) approximation.
"""
blockPrint()
# Parses the i-PI input file.
ifile = open(path2iipi, "r")
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
# Initializes the simulation class.
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
enablePrint()
# Obtains various parameters and relevant filenames.
prefix = simul.outtemplate.prefix + "." + simul.syslist[0].motion.prefix
max_iter = simul.syslist[0].motion.max_iter
batch_exp = simul.syslist[0].motion.batch_weight_exponent
kbT = float(simul.syslist[0].ensemble.temp)
beta = 1.0 / kbT
# Checks for ASR type to skip
# over zero modes.
asr = simul.syslist[0].motion.asr
if asr == "crystal":
nz = 3
elif asr == "poly":
nz = 6
iD_list = []
q_list = []
K_list = []
V_list = []
hw_list = []
x_list = []
v_list = []
for i in range(max_iter):
try:
# Imports the q, iD, x, f from the i^th SCP iteration.
# "0" stands for the SCP trial Hamiltonian.
# iD -> the covariance matrix of the canonical density in position representation.
# q -> the position at minimum potential energy.
# K -> the force constant matrix.
# V -> the minimum potential energy.
# hw -> the frequencies.
# vH -> the ensemble average of the potential w.r.t the canonical density.
# AH -> the free energy.
iD_list.append(np.loadtxt(prefix + ".iD." + str(i)))
q_list.append(np.loadtxt(prefix + ".q." + str(i)))
K_list.append(np.loadtxt(prefix + ".K." + str(i)))
V_list.append(np.loadtxt(prefix + ".V0." + str(i)))
hw_list.append(np.loadtxt(prefix + ".w." + str(i))[nz:])
# x -> the samples drawn from the canonical density of the trial distribution.
# v -> the potential enegry of the samples.
x_list.append(np.loadtxt(prefix + ".x." + str(i)))
v_list.append(np.loadtxt(prefix + ".v." + str(i)))
except IOError:
break
print("# Finished Import")
for i in range(max_iter):
try:
# Imports the q, iD, x, f from the i^th SCP iteration.
iD0 = iD_list[i]
q0 = q_list[i]
K0 = K_list[i]
V0 = V_list[i]
hw0 = hw_list[i]
betahw0 = beta * hw0
vH0 = np.sum(hw0 * np.cosh(betahw0 / 2.0) /
np.sinh(betahw0 / 2.0) * 0.250)
AH0 = np.sum(hw0 * 0.5 + kbT * np.log(1 - np.exp(-betahw0)))
except IOError:
break
# Stores the potential /free energy of the initial harmonic trail Hamiltonian.
if i == 0:
A_harm = AH0
v_harm = vH0
V0_harm = V0
print(("%23s %23s %23s %23s %23s %23s %23s" % (
"# ITERATION",
"A_SCP",
"A_SCP-A_HARM",
"ERROR",
"E_SCP",
"E_SCP-E_HARM",
"ERROR",
)))
# Initializes the average and the error in the difference between the physical
# and the SCP potential.
avg_dv = 0.0
err_dv = 0.0
norm = 0
# Inner loop over previous SCP steps
for j in range(i + 1):
try:
# Imports the q, iD of the j^th trial Hamiltonian.
# The idea is to reweight using samples drawn from the j <= i trial Hamiltonians.
iD = iD_list[j]
q = q_list[j]
# x -> the samples drawn from the canonical density of the trial distribution.
# v -> the potential enegry of the samples.
x = x_list[j]
v = v_list[j]
except IOError:
break
# vh -> the harmonic component of the potential energy.
# Note that the harmonic Hamiltonian is the i^th one
# while the samples are drawn from the j^th one.
vh = 0.5 * np.sum(np.dot(x - q0, K0.T) * (x - q0), axis=1)
# Calculates the statistical weight of each sample.
w = np.exp(-(0.50 * np.dot(iD0, (x - q0).T).T *
(x - q0)).sum(axis=1) +
(0.50 * np.dot(iD, (x - q).T).T * (x - q)).sum(axis=1))
V1 = np.sum(w)
V2 = np.sum(w**2)
# Calculates the average amd error (over the samples from the j^th batch of samples)
# associated with the "anharmonic" component of the potential.
avg_dv_j = np.nan_to_num(np.sum(w * (v - vh)) / V1)
err_dv_j = np.nan_to_num(
np.sum(w * (v - vh - avg_dv_j)**2) / (V1 - V2 / V1))
# Calculates the "batch" weight.
c = np.nan_to_num(np.exp(-np.var(np.log(w))))**batch_exp
# Accumulates the contribution to the average (and error) from the j^th batch.
avg_dv += c * avg_dv_j
err_dv += c**2 * err_dv_j
norm += c
avg_dv = np.nan_to_num(avg_dv / norm)
err_dv = np.nan_to_num(err_dv / norm**2 / len(w))
# Calculates the SCP potential / free energy.
A_scp = AH0 + avg_dv
A_scp_err = np.sqrt(err_dv)
E_scp = 2.0 * vH0 + avg_dv
E_scp_err = np.sqrt(err_dv)
# Calculates the SCP potential / free energy correction
# w.r.t the initial trial Hamiltonian.
A_scp_corr = A_scp - A_harm - V0_harm
E_scp_corr = E_scp - 2.0 * v_harm - V0_harm
print(
("%23d %23.8e %23.8e %23.8e %23.8e %23.8e %23.8e" %
(i, A_scp, A_scp_corr, A_scp_err, E_scp, E_scp_corr, E_scp_err)))
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 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 main(inputfile, prefix="PTW-", ttemp="300.0", skip="2000"):
txtemp = ttemp
ttemp = unit_to_internal("energy", "kelvin", float(ttemp))
skip = int(skip)
# opens & parses the input file
ifile = open(inputfile, "r")
verbosity.level = "quiet"
verbosity.lock = True
xmlrestart = io_xml.xml_parse_file(ifile) # Parses the file.
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
verbosity.level = "quiet"
banner()
print "# Printing out temperature re-weighing factors for a parallel tempering simulation"
simul = isimul.fetch()
if simul.mode != "paratemp":
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
tlist = simul.paratemp.temp_list
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 + (("%0" + str(int(1 + np.floor(np.log(len(simul.syslist)) / np.log(10)))) + "d") % (isys)) + "_" + o.filename
nprop.append({"filename": filename, "ofilename": ofilename, "stride": o.stride,
"ifile": open(filename, "r"), "ofile": None
})
isys += 1
lprop.append(nprop)
ptfile = open("PARATEMP", "r")
# these are variables used to compute the weighting factors
tprops = []
vfields = []
refpots = []
vunits = []
nw = []
tw = []
tw2 = []
repot = re.compile(' ([0-9]*) *--> potential')
reunit = re.compile('{(.*)}')
# now reads files one frame at a time, and re-direct output to the appropriate location
irep = np.zeros(nsys, int)
while True:
# reads one line from PARATEMP index file
line = ptfile.readline()
line = line.split()
try:
if len(line) == 0: raise EOFError
step = int(line[0])
irep[:] = line[1:]
wk = 0
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
while iline[0] == "#": # fast forward if line is a comment
# checks if we have one single file with potential energies
rm = repot.search(iline)
if not (rm is None) and not (prop in tprops):
tprops.append(prop)
for p in prop:
p["ofile"] = open(p["ofilename"], "w")
p["ofile"].write("# column 1 --> ptlogweight: ln of re-weighing factor with target temperature %s K\n" % (txtemp))
vfields.append(int(rm.group(1)) - 1)
refpots.append(np.zeros(nsys))
nw.append(np.zeros(nsys))
tw.append(np.zeros(nsys))
tw2.append(np.zeros(nsys))
rm = reunit.search(iline)
if rm: vunits.append(rm.group(1))
else: vunits.append("atomic_unit")
iline = sprop["ifile"].readline()
if prop in tprops: # do temperature weighing
pot = unit_to_internal("energy", vunits[wk], float(iline.split()[vfields[wk]]))
ir = irep[isys]
if (nw[wk][ir] == 0):
refpots[wk][ir] = pot # picks the first value as a reference potential to avoid insane absolute values of the logweight
temp = tlist[ir]
lw = (pot - refpots[wk][ir]) * (1 / temp - 1 / ttemp)
if step > skip: # computes trajectory weights avoiding the initial - possibly insane - values
if nw[wk][ir] == 0:
tw[wk][ir] = lw
tw2[wk][ir] = lw
else:
tw[wk][ir] = logsumlog((tw[wk][ir], 1), (lw, 1))[0]
tw2[wk][ir] = logsumlog((tw2[wk][ir], 1), (2 * lw, 1))[0]
nw[wk][ir] += 1
prop[ir]["ofile"].write("%15.7e\n" % (lw))
if isys == nsys - 1: wk += 1
except EOFError:
# print out trajectory weights based on PRSA 2011, assuming that observables and weights are weakly correlated
wk = 0
fpw = open(prefix + "WEIGHTS", "w")
fpw.write("# Global trajectory weights for temperature %s K\n" % (txtemp))
fpw.write("# Please cite M. Ceriotti, G. A. Brain, O. Riordan, D.E. Manolopoulos, " +
"The inefficiency of re-weighted sampling and the curse of system size in high-order path integration. " +
"Proceedings of the Royal Society A, 468(2137), 2-17 (2011) \n")
for prop in lprop:
if prop in tprops:
for ir in range(nsys):
fpw.write("%s %15.7e \n" % (prop[ir]["ofilename"], 1.0 / (np.exp(tw2[wk][ir] - 2 * tw[wk][ir]) * nw[wk][ir])))
wk += 1
break
def gleacf(path2ixml, path2iA, path2iC, path2ifacf, oprefix, action, nrows,
stride, tscale, dparam):
if path2ixml != None and path2iA != None:
raise Exception(
"The drift and covariance matrices have to be provided either through the i-pi xml file or manually. Can not use both forms of input simultaneously. "
)
elif path2ixml != None and path2iA == None:
# opens & parses the i-pi input file
ifile = open(path2ixml, "r")
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
# parses the drift and diffusion matrices of the GLE thermostat.
ttype = str(type(simul.syslist[0].motion.thermostat).__name__)
P = float(simul.syslist[0].init.nbeads)
kbT = float(simul.syslist[0].ensemble.temp) * P
simul.syslist[0].motion.thermostat.temp = kbT
if (ttype == "ThermoGLE"):
Ap = simul.syslist[0].motion.thermostat.A * tscale
Cp = simul.syslist[0].motion.thermostat.C / kbT
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
elif (ttype == "ThermoNMGLE"):
Ap = simul.syslist[0].motion.thermostat.A[0] * tscale
Cp = simul.syslist[0].motion.thermostat.C[0] / kbT
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
elif (ttype == "ThermoLangevin" or ttype == "ThermoPILE_L"):
Ap = np.asarray([1.0 / simul.syslist[0].motion.thermostat.tau
]).reshape((1, 1)) * tscale
Cp = np.asarray([1.0]).reshape((1, 1))
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
else:
raise Exception(
"GLE thermostat not found. The allowed thermostats are gle, nm_gle, langevin and pile_l."
)
elif path2ixml == None and path2iA != None:
Ap = np.loadtxt(path2iA, dtype=float, ndmin=2) * tscale
if path2iC != None:
Cp = np.loadtxt(path2iC)
else:
Cp = np.eye(len(Ap))
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
else:
raise Exception(
"The drift and covariance matrixes have to be provided either through the i-pi xml file or manually."
)
# imports the facf function.
ifacf = input_facf(path2ifacf, nrows, stride)
ix = ifacf[:, 0]
iy = ifacf[:, 1]
# computes the facf kernel
print "# computing the kernel."
ker = gleKernel(ix, Ap, Dp)
# (de-)convolutes the spectrum
if (action == "conv"):
print "# printing the output spectrum."
output_facf((ix, np.dot(iy, ker.T)), oprefix,
input_facf(path2ifacf, nrows, 1))
elif (action == "deconv"):
print "# deconvoluting the input spectrum."
oy = ISRA(ix, ker, iy, dparam, oprefix)
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_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_np(path2iipi, bsize=20000, nskip=300, si=15.0, sf=-15.0, ns=10000):
# opens & parses the i-pi input file
ifile = open(path2iipi, "r")
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
# parses the temperature, the number of beads, the number of atoms, the number of target species and their masses.
T = float(simul.syslist[0].ensemble.temp)
P = simul.syslist[0].beads.nbeads
open_paths = simul.syslist[0].nm.open_paths[-1]
m = simul.syslist[0].beads.m[open_paths]
# initialises the data files.
dq = np.zeros((bsize, 3), float)
dqxgrid = np.linspace(si, sf, ns)
dqygrid = np.linspace(si, sf, ns)
dqzgrid = np.linspace(si, sf, ns)
nplistx = []
nplisty = []
nplistz = []
# Read the end to end distances from file
data_path = (
"/home/cuzzocre/source/i-pi-mc/examples/lammps/ice-nst/P32-T269/endtoend.data"
)
delta = np.loadtxt(data_path)
step = np.shape(delta)[0]
n_block = int(step / bsize)
for x in range(n_block):
dq = delta[x * bsize:(x + 1) * bsize]
hx = histo(np.concatenate((dq.T[0], -dq.T[0])), dqxgrid, kernel, 0,
np.sqrt(T * P * m))
hy = histo(np.concatenate((dq.T[1], -dq.T[1])), dqygrid, kernel, 0,
np.sqrt(T * P * m))
hz = histo(np.concatenate((dq.T[2], -dq.T[2])), dqzgrid, kernel, 0,
np.sqrt(T * P * m))
# Defines the grid for momentum.
pxi = -np.pi / (dqxgrid[1] - dqxgrid[0])
pxf = +np.pi / (dqxgrid[1] - dqxgrid[0])
pxstep = 2 * np.pi / np.abs(dqxgrid[-1] - dqxgrid[0])
pxgrid = np.linspace(pxi, pxf, ns)
pyi = -np.pi / (dqygrid[1] - dqygrid[0])
pyf = +np.pi / (dqygrid[1] - dqygrid[0])
pystep = 2 * np.pi / np.abs(dqygrid[-1] - dqygrid[0])
pygrid = np.linspace(pyi, pyf, ns)
pzi = -np.pi / (dqzgrid[1] - dqzgrid[0])
pzf = +np.pi / (dqzgrid[1] - dqzgrid[0])
pzstep = 2 * np.pi / np.abs(dqzgrid[-1] - dqzgrid[0])
pzgrid = np.linspace(pzi, pzf, ns)
# Computes the Fourier transform of the end to end vector.
npx = np.abs(np.fft.fftshift(np.fft.fft(hx)))
npy = np.abs(np.fft.fftshift(np.fft.fft(hy)))
npz = np.abs(np.fft.fftshift(np.fft.fft(hz)))
nplistx.append(npx)
nplisty.append(npy)
nplistz.append(npz)
avgnpx = np.mean(np.asarray(nplistx), axis=0)
avgnpy = np.mean(np.asarray(nplisty), axis=0)
avgnpz = np.mean(np.asarray(nplistz), axis=0)
normx = np.sum(avgnpx)
normy = np.sum(avgnpy)
normz = np.sum(avgnpz)
errnpx = np.std(np.asarray(nplistx), axis=0) / np.sqrt(n_block) / normx
avgnpx = avgnpx / normx
errnpy = np.std(np.asarray(nplisty), axis=0) / np.sqrt(n_block) / normy
avgnpy = avgnpy / normy
errnpz = np.std(np.asarray(nplistz), axis=0) / np.sqrt(n_block) / normz
avgnpz = avgnpz / normz
avgpsqnpx = pxgrid**2 * avgnpx / pxstep
errpsqnpx = pxgrid**2 * errnpx / pxstep
avgpsqnpy = pygrid**2 * avgnpy / pystep
errpsqnpy = pygrid**2 * errnpy / pystep
avgpsqnpz = pzgrid**2 * avgnpz / pzstep
errpsqnpz = pzgrid**2 * errnpz / pzstep
np.savetxt("np.data", np.c_[pxgrid, avgnpx, errnpx, avgnpy, errnpy, avgnpz,
errnpz])
np.savetxt(
"psq-np.data",
np.c_[pxgrid, avgpsqnpx, errpsqnpx, avgpsqnpy, errpsqnpy, avgpsqnpz,
errpsqnpz],
)
psqmedx = 0.0
psqmed2x = 0.0
psqmedy = 0.0
psqmed2y = 0.0
psqmedz = 0.0
psqmed2z = 0.0
for i in range(n_block):
psqmedx = psqmedx + np.dot(pxgrid**2,
np.asarray(nplistx)[i, :]) / normx
psqmed2x = (psqmed2x + (np.dot(pxgrid**2,
np.asarray(nplistx)[i, :]) / normx)**2)
psqmedy = psqmedy + np.dot(pygrid**2,
np.asarray(nplisty)[i, :]) / normy
psqmed2y = (psqmed2y + (np.dot(pygrid**2,
np.asarray(nplisty)[i, :]) / normy)**2)
psqmedz = psqmedz + np.dot(pzgrid**2,
np.asarray(nplistz)[i, :]) / normz
psqmed2z = (psqmed2z + (np.dot(pzgrid**2,
np.asarray(nplistz)[i, :]) / normz)**2)
print("number of blocks", n_block)
print(
"av_px^2",
psqmedx / n_block,
"sigmax",
np.sqrt((psqmed2x / n_block) - (psqmedx / n_block)**2) /
np.sqrt(n_block),
)
print(
"av_py^2",
psqmedy / n_block,
"sigmay",
np.sqrt((psqmed2y / n_block) - (psqmedy / n_block)**2) /
np.sqrt(n_block),
)
print(
"av_pz^2",
psqmedz / n_block,
"sigmaz",
np.sqrt((psqmed2z / n_block) - (psqmedz / n_block)**2) /
np.sqrt(n_block),
)
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 gleacf(path2ixml, path2iA, path2iC, path2ifacf, oprefix, action, nrows, stride, tscale, dparam):
if path2ixml != None and path2iA != None:
raise Exception("The drift and covariance matrices have to be provided either through the i-pi xml file or manually. Can not use both forms of input simultaneously. ")
elif path2ixml != None and path2iA == None:
# opens & parses the i-pi input file
ifile = open(path2ixml, "r")
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
# parses the drift and diffusion matrices of the GLE thermostat.
ttype = str(type(simul.syslist[0].motion.thermostat).__name__)
P = float(simul.syslist[0].init.nbeads)
kbT = float(simul.syslist[0].ensemble.temp) * P
simul.syslist[0].motion.thermostat.temp = kbT
if(ttype == "ThermoGLE"):
Ap = simul.syslist[0].motion.thermostat.A * tscale
Cp = simul.syslist[0].motion.thermostat.C / kbT
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
elif(ttype == "ThermoNMGLE"):
Ap = simul.syslist[0].motion.thermostat.A[0] * tscale
Cp = simul.syslist[0].motion.thermostat.C[0] / kbT
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
elif(ttype == "ThermoLangevin" or ttype == "ThermoPILE_L"):
Ap = np.asarray([1.0 / simul.syslist[0].motion.thermostat.tau]).reshape((1, 1)) * tscale
Cp = np.asarray([1.0]).reshape((1, 1))
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
else:
raise Exception("GLE thermostat not found. The allowed thermostats are gle, nm_gle, langevin and pile_l.")
elif path2ixml == None and path2iA != None:
Ap = np.loadtxt(path2iA, dtype=float, ndmin=2) * tscale
if path2iC != None:
Cp = np.loadtxt(path2iC)
else:
Cp = np.eye(len(Ap))
Dp = np.dot(Ap, Cp) + np.dot(Cp, Ap.T)
else:
raise Exception("The drift and covariance matrixes have to be provided either through the i-pi xml file or manually.")
# imports the facf function.
ifacf = input_facf(path2ifacf, nrows, stride)
ix = ifacf[:, 0]
iy = ifacf[:, 1]
# computes the facf kernel
print "# computing the kernel."
ker = gleKernel(ix, Ap, Dp)
# (de-)convolutes the spectrum
if(action == "conv"):
print "# printing the output spectrum."
output_facf((ix, np.dot(iy, ker.T)), oprefix, input_facf(path2ifacf, nrows, 1))
elif(action == "deconv"):
print "# deconvoluting the input spectrum."
oy = ISRA(ix, ker, iy, dparam, oprefix)
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 get_np(path2iipi, bsize=20000, nskip=300, si=15.0, sf=-15.0, ns=10000):
# opens & parses the i-pi input file
ifile = open(path2iipi, "r")
xmlrestart = io_xml.xml_parse_file(ifile)
ifile.close()
isimul = InputSimulation()
isimul.parse(xmlrestart.fields[0][1])
simul = isimul.fetch()
# parses the temperature, the number of beads, the number of atoms, the number of target species and their masses.
T = float(simul.syslist[0].ensemble.temp)
P = simul.syslist[0].beads.nbeads
natoms = simul.syslist[0].beads.natoms
open_paths = simul.syslist[0].nm.open_paths[-1]
m = simul.syslist[0].beads.m[open_paths]
# initialises the data files.
data_1 = np.zeros((bsize, 3), float)
data_2 = np.zeros((bsize, 3), float)
dq = np.zeros((bsize, 3), float)
dqxgrid = np.linspace(si, sf, ns)
dqygrid = np.linspace(si, sf, ns)
dqzgrid = np.linspace(si, sf, ns)
nplistx = []
nplisty = []
nplistz = []
# Read the end to end distances from file
data_path = '/home/cuzzocre/source/i-pi-mc/examples/lammps/ice-nst/P32-T269/endtoend.data'
delta = np.loadtxt(data_path)
step = np.shape(delta)[0]
n_block = int(step / bsize)
for x in xrange(n_block):
dq = delta[x * bsize: (x + 1) * bsize]
hx = histo(np.concatenate((dq.T[0], -dq.T[0])), dqxgrid, kernel, 0, np.sqrt(T * P * m))
hy = histo(np.concatenate((dq.T[1], -dq.T[1])), dqygrid, kernel, 0, np.sqrt(T * P * m))
hz = histo(np.concatenate((dq.T[2], -dq.T[2])), dqzgrid, kernel, 0, np.sqrt(T * P * m))
# Defines the grid for momentum.
pxi = -np.pi / (dqxgrid[1] - dqxgrid[0])
pxf = +np.pi / (dqxgrid[1] - dqxgrid[0])
pxstep = 2 * np.pi / np.abs(dqxgrid[-1] - dqxgrid[0])
pxgrid = np.linspace(pxi, pxf, ns)
pyi = -np.pi / (dqygrid[1] - dqygrid[0])
pyf = +np.pi / (dqygrid[1] - dqygrid[0])
pystep = 2 * np.pi / np.abs(dqygrid[-1] - dqygrid[0])
pygrid = np.linspace(pyi, pyf, ns)
pzi = -np.pi / (dqzgrid[1] - dqzgrid[0])
pzf = +np.pi / (dqzgrid[1] - dqzgrid[0])
pzstep = 2 * np.pi / np.abs(dqzgrid[-1] - dqzgrid[0])
pzgrid = np.linspace(pzi, pzf, ns)
# Computes the Fourier transform of the end to end vector.
npx = np.abs(np.fft.fftshift(np.fft.fft(hx)))
npy = np.abs(np.fft.fftshift(np.fft.fft(hy)))
npz = np.abs(np.fft.fftshift(np.fft.fft(hz)))
nplistx.append(npx)
nplisty.append(npy)
nplistz.append(npz)
avgnpx = np.mean(np.asarray(nplistx), axis=0)
avgnpy = np.mean(np.asarray(nplisty), axis=0)
avgnpz = np.mean(np.asarray(nplistz), axis=0)
normx = np.sum(avgnpx)
normy = np.sum(avgnpy)
normz = np.sum(avgnpz)
errnpx = np.std(np.asarray(nplistx), axis=0) / np.sqrt(n_block) / normx
avgnpx = avgnpx / normx
errnpy = np.std(np.asarray(nplisty), axis=0) / np.sqrt(n_block) / normy
avgnpy = avgnpy / normy
errnpz = np.std(np.asarray(nplistz), axis=0) / np.sqrt(n_block) / normz
avgnpz = avgnpz / normz
avgpsqnpx = pxgrid**2 * avgnpx / pxstep
errpsqnpx = pxgrid**2 * errnpx / pxstep
avgpsqnpy = pygrid**2 * avgnpy / pystep
errpsqnpy = pygrid**2 * errnpy / pystep
avgpsqnpz = pzgrid**2 * avgnpz / pzstep
errpsqnpz = pzgrid**2 * errnpz / pzstep
np.savetxt("np.data", np.c_[pxgrid, avgnpx, errnpx, avgnpy, errnpy, avgnpz, errnpz])
np.savetxt("psq-np.data", np.c_[pxgrid, avgpsqnpx, errpsqnpx, avgpsqnpy, errpsqnpy, avgpsqnpz, errpsqnpz])
psqmedx = 0.
psqmed2x = 0.
psqmedy = 0.
psqmed2y = 0.
psqmedz = 0.
psqmed2z = 0.
for i in range(n_block):
psqmedx = psqmedx + np.dot(pxgrid**2, np.asarray(nplistx)[i, :]) / normx
psqmed2x = psqmed2x + (np.dot(pxgrid**2, np.asarray(nplistx)[i, :]) / normx)**2
psqmedy = psqmedy + np.dot(pygrid**2, np.asarray(nplisty)[i, :]) / normy
psqmed2y = psqmed2y + (np.dot(pygrid**2, np.asarray(nplisty)[i, :]) / normy)**2
psqmedz = psqmedz + np.dot(pzgrid**2, np.asarray(nplistz)[i, :]) / normz
psqmed2z = psqmed2z + (np.dot(pzgrid**2, np.asarray(nplistz)[i, :]) / normz)**2
print 'number of blocks', n_block
print 'av_px^2', psqmedx / n_block, 'sigmax', np.sqrt((psqmed2x / n_block) - (psqmedx / n_block)**2) / np.sqrt(n_block)
print 'av_py^2', psqmedy / n_block, 'sigmay', np.sqrt((psqmed2y / n_block) - (psqmedy / n_block)**2) / np.sqrt(n_block)
print 'av_pz^2', psqmedz / n_block, 'sigmaz', np.sqrt((psqmed2z / n_block) - (psqmedz / n_block)**2) / np.sqrt(n_block)
