Esempio n. 1
0
    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
Esempio n. 2
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    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
Esempio n. 3
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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
Esempio n. 4
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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