def load_from_xml(fn_input,
custom_verbosity=None,
request_banner=False,
read_only=False):
"""Load an XML input file and return a `Simulation` object.
Arguments:
fn_input (str): Name of the input file.
custom_verbosity (str): If not `None`, overrides the verbosity
specified by the input file.
request_banner (bool): Whether to print the i-PI banner,
if verbosity is higher than 'quiet'.
"""
# parse the file
xmlrestart = xml_parse_file(open(fn_input))
# prepare the simulation input object
input_simulation = isimulation.InputSimulation()
# check the input and partition it appropriately
input_simulation.parse(xmlrestart.fields[0][1])
# override verbosity if requested
if custom_verbosity is None:
# Get from the input file
custom_verbosity = input_simulation.verbosity.fetch()
input_simulation.verbosity.value = custom_verbosity
# print banner if not suppressed and simulation verbose enough
if request_banner and input_simulation.verbosity.value != "quiet":
banner()
# create the simulation object
simulation = input_simulation.fetch()
# pipe between the components of the simulation
simulation.bind(read_only)
# echo the input file if verbose enough
if verbosity.level > 0:
print(" # i-PI loaded input file: ", fn_input)
if verbosity.level > 1:
print(" --- begin input file content ---")
ifile = open(fn_input, "r")
for line in ifile.readlines():
print(line, end=" ")
print(" --- end input file content ---")
ifile.close()
return simulation
def load_from_xml(fn_input, custom_verbosity=None, request_banner=False):
"""Load an XML input file and return a `Simulation` object.
Arguments:
fn_input (str): Name of the input file.
custom_verbosity (str): If not `None`, overrides the verbosity
specified by the input file.
request_banner (bool): Whether to print the i-PI banner,
if verbosity is higher than 'quiet'.
"""
# parse the file
xmlrestart = xml_parse_file(open(fn_input))
# prepare the simulation input object
input_simulation = isimulation.InputSimulation()
# check the input and partition it appropriately
input_simulation.parse(xmlrestart.fields[0][1])
# override verbosity if requested
if custom_verbosity is None:
# Get from the input file
custom_verbosity = input_simulation.verbosity.fetch()
input_simulation.verbosity.value = custom_verbosity
# print banner if not suppressed and simulation verbose enough
if request_banner and input_simulation.verbosity.value != 'quiet':
banner()
# create the simulation object
simulation = input_simulation.fetch()
# pipe between the components of the simulation
simulation.bind()
# echo the input file if verbose enough
if verbosity.level > 0:
print " # i-PI loaded input file: ", fn_input
if verbosity.level > 1:
print " --- begin input file content ---"
ifile = open(fn_input, "r")
for line in ifile.readlines():
print line,
print " --- end input file content ---"
ifile.close()
return simulation
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 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
