Source code for pyne.mcnp

#!/usr/bin/env python
"""Module for parsing MCNP output data. MCNP is a general-purpose Monte Carlo
N-Particle code developed at Los Alamos National Laboratory that can be used
for neutron, photon, electron, or coupled neutron/photon/electron transport.
Further information on MCNP can be obtained from

Mctal and Runtpe classes still need work. Also should add Meshtal and Outp

If PyMOAB is not installed, then Wwinp, Meshtal, and Meshtally will not be
available to use.

from __future__ import print_function, division
from pyne.mesh import Mesh, StatMesh, HAVE_PYMOAB
import sys
import struct
import math
import os
import linecache
import datetime
from warnings import warn

import numpy as np
import tables

from pyne.utils import QAWarning
from pyne.material import Material
from pyne.material import MultiMaterial
from pyne import nucname
from pyne.binaryreader import _BinaryReader, _FortranRecord

warn(__name__ + " is not yet QA compliant.", QAWarning)

# Mesh specific imports

    from pyne.mesh import NativeMeshTag
    warn("The PyMOAB optional dependency could not be imported. "
         "Some aspects of the mcnp module may be incomplete.",

if sys.version_info[0] > 2:
    def cmp(a, b):
        return (a > b) - (a < b)

class Mctal(object):
    def __init__(self):

    def read(self, filename):
        """Parses a 'mctal' tally output file from MCNP. Currently this
        only supports reading the kcode data- the remaining tally data
        will not be read.

        # open file
        self.f = open(filename, 'r')

        # get code name, version, date/time, etc
        words = self.f.readline().split()
        self.code_name = words[0]
        self.code_version = words[1]
        self.code_date = words[2]
        self.code_time = words[3]
        self.n_dump = words[4]
        self.n_histories = int(words[5])
        self.n_prn = int(words[6])

        # comment line of input file
        self.comment = self.f.readline().strip()

        # read tally line
        words = self.f.readline().split()
        self.n_tallies = words[1]
        if len(words) > 2:
            # perturbation tallies present

        # read tally numbers
        tally_nums = [int(i) for i in self.f.readline().split()]

        # read tallies
        for i_tal in tally_nums:

        # read kcode information
        words = self.f.readline().split()
        self.n_cycles = int(words[1])
        self.n_inactive = int(words[2])
        vars_per_cycle = int(words[3])

        self.k_col = []
        self.k_abs = []
        self.k_path = []
        self.prompt_life_col = []
        self.prompt_life_path = []
        self.avg_k_col = []
        self.avg_k_abs = []
        self.avg_k_path = []
        self.avg_k_combined = []
        self.avg_k_combined_active = []
        self.prompt_life_combined = []
        self.cycle_histories = []
        self.avg_k_combined_FOM = []

        for cycle in range(self.n_cycles):
            # read keff and prompt neutron lifetimes
            if vars_per_cycle == 0 or vars_per_cycle == 5:
                values = [float(i) for i in get_words(self.f, lines=1)]
            elif vars_per_cycle == 19:
                values = [float(i) for i in get_words(self.f, lines=4)]


            if vars_per_cycle <= 5:

            avg, stdev = (values[5], values[6])
            self.avg_k_col.append((avg, stdev))
            avg, stdev = (values[7], values[8])
            self.avg_k_abs.append((avg, stdev))
            avg, stdev = (values[9], values[10])
            self.avg_k_path.append((avg, stdev))
            avg, stdev = (values[11], values[12])
            self.avg_k_combined.append((avg, stdev))
            avg, stdev = (values[13], values[14])
            self.avg_k_combined_active.append((avg, stdev))
            avg, stdev = (values[15], values[16])
            self.prompt_life_combined.append((avg, stdev))

def get_words(f, lines=1):
    words = []
    for i in range(lines):
        local_words = f.readline().split()
        words += local_words
    return words

class SourceSurf(object):
    def __init__(self):

class TrackData(object):
    def __init__(self):

[docs]class SurfSrc(_BinaryReader): """Enables manipulating both the header and tracklists in surface source files. Example use cases include adding source particles from other codes, and combining multiple files together. Note that typically additional code will be needed to supplement this class in order to modify the header or track information in a way suitable to the use case. Parameters ---------- filename : str Path to surface source file being read or written. mode : str, optional String indicating file opening mode to be used (defaults to 'rb'). """ def __init__(self, filename, mode="rb"): super(SurfSrc, self).__init__(filename, mode) def __str__(self): return self.print_header()
[docs] def print_header(self): """Returns contents of SurfSrc's header as an informative string. Returns ------- header_string : str A line-by-line listing of the contents of the SurfSrc's header. """ header_string = "Code: {0} (version: {1}) [{2}]\n".format( self.kod, self.ver, self.loddat) header_string += "Problem info: ({0}) {1}\n{2}\n".format( self.idtm, self.probid, self.aid) header_string += "Showing dump #{0}\n".format(self.knod) header_string += ( "{0} histories, {1} tracks, {2} record size, " "{0} surfaces, {1} histories\n").format( self.np1, self.nrss, self.ncrd, self.njsw, self.niss) header_string += ( "{0} cells, source particle: {1}," " macrobody facet flag: {2}\n").format( self.niwr, self.mipts, self.kjaq) for i in self.surflist: header_string += ( "Surface {0}: facet {1}," " type {2} with {3} parameters: (").format(, i.facet_id, i.type, i.num_params) if i.num_params > 1: for j in i.surf_params: header_string += " {0}".format(j) else: header_string += " {0}".format(i.surf_params) header_string += ")\n" header_string += "Summary Table: " + str(self.summary_table) return header_string
[docs] def print_tracklist(self, max_tracks=None): """Returns tracklists in SurfSrc as a string. Parameters ---------- max_tracks : int, optional Maximum number of tracks to print. Defaults to all tracks. Returns ------- track_data : str Single string with data for one track on each line. """ if max_tracks is None: max_tracks = self.nrss track_data = "Track Data\n" track_data += \ " nps BITARRAY WGT ERG TME" \ " X Y Z" \ " U V COSINE | W\n" for cnt, j in enumerate(self.tracklist): format_string = "%10d %10g %10.5g %10.5g %10.5g" \ " %13.5e %13.5e %13.5e" \ " %10.5f %10.5f %10.5f | %10.5f " track_data += format_string % ( j.nps, j.bitarray, j.wgt, j.erg, j.tme, j.x, j.y, j.z, j.u, j.v, j.cs, j.w) + "\n" if cnt > max_tracks: break return track_data
def __eq__(self, other): rtn = self.__cmp__(other) return rtn == 0 def __cmp__(self, other): """ Comparison is not completely robust. Tracklists are not compared!!! """ if other.kod != self.kod: # kod does not match return cmp(other.kod, self.kod) if other.ver != self.ver: # ver does not match return cmp(other.ver, self.ver) if other.loddat != self.loddat: # loddat does not match return cmp(other.loddat, self.loddat) if other.ncrd != self.ncrd: # ncrd does not match return cmp(other.nrcd, self.nrcd) if other.njsw != self.njsw: # njsw does not match return cmp(other.njsw, self.njsw) if other.np1 != self.np1: # np1 does not match return cmp(other.np1, self.np1) if other.nrss != self.nrss: # nrss does not match return cmp(other.nrss, self.nrss) if other.niss != self.niss: # nrss does not match return cmp(other.niss, self.niss) if other.niwr != self.niwr: # niwr does not match return cmp(other.niwr, self.niwr) if other.mipts != self.mipts: # mipts does not match return cmp(other.mipts, self.mipts) if other.kjaq != self.kjaq: # kjaq does not match return cmp(other.kjaq, self.kjaq) for surf in range(len(self.surflist)): if other.surflist[surf].id != self.surflist[surf].id: # ID doesn't match return cmp(other.surflist[surf].id, self.surflist[surf].id) if other.surflist[surf].facet_id != self.surflist[surf].facet_id: # facet_id doesn't match return cmp(other.surflist[surf].facet_id, self.surflist[surf].facet_id) if other.surflist[surf].type != self.surflist[surf].type: # type doesn't match return cmp(other.surflist[surf].type, self.surflist[surf].type) if other.surflist[surf].num_params != \ self.surflist[surf].num_params: # num_params ddoesn't match return cmp(other.surflist[surf].num_params, self.surflist[surf].num_params) if other.surflist[surf].surf_params != \ self.surflist[surf].surf_params: # surf_params doesn't match return cmp(other.surflist[surf].surf_params, self.surflist[surf].surf_params) return 0
[docs] def read_header(self): """Read in the header block data. This block comprises 4 fortran records which we refer to as: header, table1, table2, summary. """ # read header record header = self.get_fortran_record() # interpret header self.kod = header.get_string(8)[0] # code identifier if 'SF_00001' not in self.kod: self.ver = header.get_string(5)[0] # code version identifier if '2.6.0' in self.ver: self.loddat = header.get_string(28)[0] # code version date elif '5 ' in self.ver: self.loddat = header.get_string(8)[0] # code version date else: raise NotImplementedError("MCNP5/X Version:" + self.ver.rstrip() + " not supported") self.idtm = header.get_string(19)[0] # current date and time self.probid = header.get_string(19)[0] # problem id string self.aid = header.get_string(80)[0] # title card of initial run self.knod = header.get_int()[0] # dump number # read table 1 record; various counts and sizes tablelengths = self.get_fortran_record() # interpret table lengths if '2.6.0' in self.ver: self.np1 = tablelengths.get_int()[0] # hist used to gen. src self.nrss = tablelengths.get_int()[0] # #tracks to surf src else: self.np1 = tablelengths.get_long()[0] # hist used to gen. src self.nrss = tablelengths.get_long()[0] # #tracks to surf src # values in surf src record # 6 for a spherical source # 11 otherwise self.ncrd = tablelengths.get_int()[0] self.njsw = tablelengths.get_int()[0] # number of surfaces self.niss = tablelengths.get_int()[0] # #histories to surf src self.table1extra = list() while tablelengths.num_bytes > tablelengths.pos: self.table1extra += tablelengths.get_int() elif 'SF_00001' in self.kod: header = self.get_fortran_record() self.ver = header.get_string(12)[0] # code version identifier self.loddat = header.get_string(9)[0] # code version date self.idtm = header.get_string(19)[0] # current date and time self.probid = header.get_string(19)[0] # problem id string self.aid = header.get_string(80)[0] # title card of initial run self.knod = header.get_int()[0] # dump number # read table 1 record; various counts and sizes tablelengths = self.get_fortran_record() # interpret table lengths self.np1 = tablelengths.get_int()[0] # hist used to gen.source self.notsure0 = tablelengths.get_int()[0] # vals in surf src rec. self.nrss = tablelengths.get_int()[0] # tracks writ. to surf.src self.notsure1 = tablelengths.get_int()[0] # number of surfaces self.ncrd = tablelengths.get_int()[0] # histories to surf.src self.njsw = tablelengths.get_int()[0] # number of surfaces self.niss = tablelengths.get_int()[0] # histories to surf.src self.table1extra = list() while tablelengths.num_bytes > tablelengths.pos: self.table1extra += tablelengths.get_int() if self.np1 < 0: # read table 2 record; more size info tablelengths = self.get_fortran_record() self.niwr = tablelengths.get_int()[0] # #cells in surf.src card self.mipts = tablelengths.get_int()[0] # source particle type self.kjaq = tablelengths.get_int()[0] # macrobody facet flag self.table2extra = list() while tablelengths.num_bytes > tablelengths.pos: self.table2extra += tablelengths.get_int() else: pass # Since np1 can be negative, preserve the actual np1 value while # taking the absolute value so that np1 can be used mathematically self.orignp1 = self.np1 self.np1 = abs(self.np1) # get info for each surface self.surflist = list() for j in range(self.njsw): # read next surface info record self.surfaceinfo = self.get_fortran_record() surfinfo = SourceSurf() = self.surfaceinfo.get_int() # surface ID if self.kjaq == 1: surfinfo.facet_id = self.surfaceinfo.get_int() # facet ID else: surfinfo.facet_id = -1 # dummy facet ID surfinfo.type = self.surfaceinfo.get_int() # surface type surfinfo.num_params = self.surfaceinfo.get_int()[0] # #surface prm surfinfo.surf_params = \ self.surfaceinfo.get_double(surfinfo.num_params) self.surflist.append(surfinfo) # we read any extra records as determined by njsw+niwr... # no known case of their actual utility is known currently for j in range(self.njsw, self.njsw+self.niwr): self.get_fortran_record() warn("Extra info in header not handled: {0}".format(j), RuntimeWarning) # read summary table record summary_info = self.get_fortran_record() self.summary_table = summary_info.get_int( (2+4*self.mipts)*(self.njsw+self.niwr)+1) self.summary_extra = list() while summary_info.num_bytes > summary_info.pos: self.summary_extra += summary_info.get_int()
[docs] def read_tracklist(self): """Reads in track records for individual particles.""" self.tracklist = [] for j in range(self.nrss): track_info = self.get_fortran_record() track_data = TrackData() track_data.record = track_info.get_double(abs(self.ncrd)) track_data.nps = track_data.record[0] track_data.bitarray = track_data.record[1] track_data.cell = abs(track_data.bitarray) // 8 % 100000000 track_data.wgt = track_data.record[2] track_data.erg = track_data.record[3] track_data.tme = track_data.record[4] track_data.x = track_data.record[5] track_data.y = track_data.record[6] track_data.z = track_data.record[7] track_data.u = track_data.record[8] track_data.v = track_data.record[9] track_data.cs = track_data.record[10] track_data.w = math.copysign( math.sqrt(1 - track_data.u*track_data.u - track_data.v*track_data.v), track_data.bitarray) # track_data.bitarray = abs(track_data.bitarray) self.tracklist.append(track_data) return
[docs] def put_header(self): """Write the header part of the header to the surface source file""" if 'SF_00001' in self.kod: rec = [self.kod] joinrec = "".join(rec) newrecord = _FortranRecord(joinrec, len(joinrec)) self.put_fortran_record(newrecord) rec = [self.ver, self.loddat, self.idtm, self.probid, self.aid] joinrec = "".join(rec) newrecord = _FortranRecord(joinrec, len(joinrec)) newrecord.put_int([self.knod]) self.put_fortran_record(newrecord) else: rec = [self.kod, self.ver, self.loddat, self.idtm, self.probid, self.aid] joinrec = "".join(rec) newrecord = _FortranRecord(joinrec, len(joinrec)) newrecord.put_int([self.knod]) self.put_fortran_record(newrecord) return
[docs] def put_table_1(self): """Write the table1 part of the header to the surface source file""" newrecord = _FortranRecord("", 0) if '2.6.0' in self.ver: newrecord.put_int([self.np1]) newrecord.put_int([self.nrss]) else: newrecord.put_long([self.np1]) newrecord.put_long([self.nrss]) newrecord.put_int([self.ncrd]) newrecord.put_int([self.njsw]) newrecord.put_int([self.niss]) # MCNP needs 'int', could be 'long' ? newrecord.put_int(self.table1extra) self.put_fortran_record(newrecord) return
[docs] def put_table_2(self): """Write the table2 part of the header to the surface source file""" newrecord = _FortranRecord("", 0) newrecord.put_int([self.niwr]) newrecord.put_int([self.mipts]) newrecord.put_int([self.kjaq]) newrecord.put_int(self.table2extra) self.put_fortran_record(newrecord) return
[docs] def put_surface_info(self): """Write the record for each surface to the surface source file""" for cnt, s in enumerate(self.surflist): newrecord = _FortranRecord("", 0) newrecord.put_int( if self.kjaq == 1: newrecord.put_int(s.facet_id) # don't add a 'dummy facet ID' # else no macrobody flag byte in the record newrecord.put_int(s.type) newrecord.put_int(s.num_params) newrecord.put_double(s.surf_params) self.put_fortran_record(newrecord) return
[docs] def put_summary(self): """Write the summary part of the header to the surface source file""" newrecord = _FortranRecord("", 0) newrecord.put_int(list(self.summary_table)) newrecord.put_int(list(self.summary_extra)) self.put_fortran_record(newrecord) return
[docs] def write_header(self): """Write the first part of the MCNP surface source file. The header content comprises five parts shown below. """ self.put_header() self.put_table_1() self.put_table_2() self.put_surface_info() self.put_summary()
[docs] def write_tracklist(self): """Write track records for individual particles. Second part of the MCNP surface source file. Tracklist is also known as a 'phase space'. """ for j in range(self.nrss): # nrss is the size of tracklist newrecord = _FortranRecord("", 0) # 11 records comprising particle information newrecord.put_double(self.tracklist[j].nps) newrecord.put_double(self.tracklist[j].bitarray) newrecord.put_double(self.tracklist[j].wgt) newrecord.put_double(self.tracklist[j].erg) newrecord.put_double(self.tracklist[j].tme) newrecord.put_double(self.tracklist[j].x) newrecord.put_double(self.tracklist[j].y) newrecord.put_double(self.tracklist[j].z) newrecord.put_double(self.tracklist[j].u) newrecord.put_double(self.tracklist[j].v) newrecord.put_double(self.tracklist[j].cs) self.put_fortran_record(newrecord) return
[docs] def update_tracklist(self, surf_src): """ Update tracklist from another surface source. This updates the surface source in-place. """ # Catch for improper non-SurfSrc type if type(surf_src) != SurfSrc: raise TypeError('Surface Source is not of type SurfSrc') # Because 'kod' is the first header attribute elif not hasattr(surf_src, 'kod'): raise AttributeError( 'No header attributes for surface source argument') elif not hasattr(self, 'kod'): raise AttributeError( 'No header attributes read for surface source') # Because 'tracklist' forms the non-header portion elif not hasattr(surf_src, 'tracklist'): raise AttributeError( 'No tracklist read for surface source argument') elif not hasattr(self, 'tracklist'): raise AttributeError( 'No tracklist read for surface source') # No point in updating with self elif self == surf_src: raise ValueError('Tracklist cannot be updated with itself') self.tracklist = surf_src.tracklist self.nrss = surf_src.nrss
def __del__(self): """Destructor. The only thing to do is close the file.""" self.f.close()
[docs]class Srctp(_BinaryReader): """This class stores source site data from a 'srctp' file written by MCNP. The source sites are stored in the 'fso' array in MCNP. Parameters ---------- filename : str Path to Srctp file being worked with. """ def __init__(self, filename): super(Srctp, self).__init__(filename) def read(self): # read header block header = self.get_fortran_record() # interpret header block # NOTUSED k = header.get_int() # unique code (947830) self.loc_next = header.get_int() # loc. of next site in FSO arr (ixak) self.n_run = header.get_int() # source particles yet to be run (nsa) self.loc_store = header.get_int() # where to put nxt src neutron (ist) self.n_source = header.get_int() # # of source points in fso (mrl) # read source site array fso = self.get_fortran_record() self.sites = [] for i in range(self.n_source): vals = fso.get_double(11) site = SourceSite() site.x = vals[0] site.y = vals[1] site.z = vals[2] site.E = vals[3] self.sites.append(site) def remaining_sites(self): index = self.loc_next - 1 if (self.loc_next + self.n_run) >= self.n_source: return (self.sites[index:] + self.sites[:self.n_run - (self.n_source - index)]) else: return self.sites[index: index + self.n_run] def __repr__(self): return "<Srctp: {0}>".format(
class SourceSite(object): def __init__(self): pass def __repr__(self): return "<SourceSite: ({0.x},{0.y},{0.z})>".format(self)
[docs]class Runtpe(_BinaryReader): def __init__(self, filename): super(Runtpe, self).__init__(filename) def read(self, filename): # read identification block header = self.get_fortran_record() # parse identification block self.code_name = header.get_string(8) self.code_version = header.get_string(5) self.code_date = header.get_string(8) header.get_string(19) # machine designator, date and time self.charge_code = header.get_string(10) self.problem_ID = header.get_string(19) self.problem_ID_surf = header.get_string(19) self.title = header.get_string(80) header.pos += 3*6*11 # skip user file characteristics self.n_tables = header.get_int() # read cross-section tables self.tables = [] for i in range(self.n_tables): self.tables.append(self.get_fortran_record()) def __repr__(self): return "<Runtpe: {0}>".format(
[docs]class Xsdir(object): """This class stores the information contained in a single MCNP xsdir file. Attributes ---------- f : file handle The xsdir file. filename : str Path to the xsdir file. directory : str Path to the directory containing the xsdir file. datapath : str The data path specified in the first line of the xsdir file, if it exists. awr : dict Maps material ids to their atomic weight ratios. tables : list Entries are XsdirTable objects, that appear in the same order as the xsdir table lines. Notes ----- See MCNP5 User's Guide Volume 3 Appendix K for more information. """ def __init__(self, filename): """Parameters ---------- filename : str Path to xsdir file. """ self.f = open(filename, 'r') self.filename = os.path.abspath(filename) = os.path.dirname(filename) self.awr = {} self.tables = []
[docs] def read(self): """Populate the Xsdir object by reading the file. """ # Go to beginning of file # Read first section (DATAPATH) line = self.f.readline() words = line.split() if words: if words[0].lower().startswith('datapath'): index = line.index('=') self.datapath = line[index+1:].strip() # Read second section line = self.f.readline() words = line.split() assert len(words) == 3 assert words[0].lower() == 'atomic' assert words[1].lower() == 'weight' assert words[2].lower() == 'ratios' while True: line = self.f.readline() words = line.split() # Check for end of second section if len(words) % 2 != 0 or words[0] == 'directory': break for zaid, awr in zip(words[::2], words[1::2]): self.awr[zaid] = awr # Read third section while words[0] != 'directory': words = self.f.readline().split() while True: words = self.f.readline().split() if not words: break # Handle continuation lines while words[-1] == '+': extraWords = self.f.readline().split() words = words + extraWords assert len(words) >= 7 # Create XsdirTable object and add to line table = XsdirTable() self.tables.append(table) # All tables have at least 7 attributes = words[0] table.awr = float(words[1]) table.filename = words[2] table.access = words[3] table.filetype = int(words[4]) table.address = int(words[5]) table.tablelength = int(words[6]) if len(words) > 7: table.recordlength = int(words[7]) if len(words) > 8: table.entries = int(words[8]) if len(words) > 9: table.temperature = float(words[9]) if len(words) > 10: table.ptable = (words[10] == 'ptable')
[docs] def find_table(self, name): """Find all tables for a given ZIAD. Parameters ---------- name : str The ZIAD name. Returns ------- tables : list All XsdirTable objects for a given ZIAD. """ tables = [] for table in self: if name in tables.append(table) return tables
[docs] def to_xsdata(self, filename): """Writes a Serpent xsdata file for all continuous energy xs tables. Parameters ---------- filename : str The output filename. """ xsdata = open(filename, 'w') for table in self.tables: if table.serpent_type == 1: xsdata.write(table.to_serpent() + '\n') xsdata.close()
def __iter__(self): for table in self.tables: yield table
[docs] def nucs(self): """Provides a set of the valid nuclide ids for nuclides contained in the xsdir. Returns ------- valid_nucs : set The valid nuclide ids. """ valid_nucs = set('.')[0]) for table in self.tables if nucname.isnuclide('.')[0])) return valid_nucs
[docs]class XsdirTable(object): """Stores all information that describes a xsdir table entry, which appears as a single line in xsdir file. Attribute names are based off of those found in the MCNP5 User's Guide Volume 3, appendix K. Attributes ---------- name : str The ZAID and library identifier, delimited by a '.'. awr : float The atomic mass ratio of the nuclide. filename : str The relative path of the file containing the xs table. access : str Additional string to specify an access route, such as UNIX directory. This entry is typically 0. filetype : int Describes whether the file contains formated (1) or unformated (2) file. address : int If filetype is 1, address is the line number of the xsdir table. If filetype is 2, address is the record number. tablelength : int Length of the second block of a data table. recordlength : int Unused for filetype = 1. For filetype = 2, recordlength is the number of entires per record times the size (in bytes) of each entry. entries : int Unused for filetype = 1. For filetype = 2, it is the number of entries per record temperature : float Temperature in MeV for neutron data only. ptable : bool True if xs table describes continuous energy neutron data with unresolved resonance range probability tables. """ def __init__(self): = None self.awr = None self.filename = None self.access = None self.filetype = None self.address = None self.tablelength = None self.recordlength = None self.entries = None self.temperature = None self.ptable = False @property def alias(self): """Returns the name of the table entry <ZIAD>.<library id>. """ return @property def serpent_type(self): """Converts cross section table type to Serpent format: :1: continuous energy (c). :2: dosimetry table (y). :3: termal (t). """ if'c'): return 1 elif'y'): return 2 elif't'): return 3 else: return None @property def metastable(self): """Returns 1 is xsdir table nuclide is metastable. Returns zero otherwise. """ # Only valid for neutron cross-sections if not'c'): return # Handle special case of Am-242 and Am-242m if self.zaid == '95242': return 1 elif self.zaid == '95642': return 0 # All other cases A = int('.')[0]) % 1000 if A > 600: return 1 else: return 0 @property def zaid(self): """Returns the ZIAD of the nuclide. """ return['.')]
[docs] def to_serpent(self, directory=''): """Converts table to serpent format. Parameters ---------- directory : str The directory where Serpent data is to be stored. """ # Adjust directory if directory: if not directory.endswith('/'): directory = directory.strip() + '/' return "{0} {0} {1} {2} {3} {4} {5:.11e} {6} {7}".format(, self.serpent_type, self.zaid, 1 if self.metastable else 0, self.awr, self.temperature/8.6173423e-11, self.filetype - 1, directory + self.filename)
def __repr__(self): return "<XsDirTable: {0}>".format(
class PtracEvent(tables.IsDescription): """This class holds one Ptrac event and serves as a table definition for saving Ptrac data to a HDF5 file. """ event_type = tables.Int32Col() node = tables.Float32Col() nsr = tables.Float32Col() nsf = tables.Float32Col() nxs = tables.Float32Col() ntyn = tables.Float32Col() ipt = tables.Float32Col() ncl = tables.Float32Col() mat = tables.Float32Col() ncp = tables.Float32Col() xxx = tables.Float32Col() yyy = tables.Float32Col() zzz = tables.Float32Col() uuu = tables.Float32Col() vvv = tables.Float32Col() www = tables.Float32Col() erg = tables.Float32Col() wgt = tables.Float32Col() tme = tables.Float32Col()
[docs]class PtracReader(object): """Class to read _binary_ PTRAC files generated by MCNP. """ def __init__(self, filename): """Construct a new Ptrac reader for a given filename, determine the number format and read the file's headers. """ self.variable_mappings = { 1: "nps", 3: "ncl", 4: "nsf", # surface id 8: "node", 9: "nsr", 10: "nxs", 11: "ntyn", 12: "nsf", 16: "ipt", 17: "ncl", 18: "mat", 19: "ncp", 20: "xxx", # position x 21: "yyy", # position y 22: "zzz", # position z 23: "uuu", # cos(x-direction) 24: "vvv", # cos(y-direction) 25: "www", # cos(z-direction) 26: "erg", # energy 27: "wgt", # mass 28: "tme" } self.eightbytes = False self.f = open(filename, 'rb') self.determine_endianness() self.read_headers() self.read_variable_ids() self.next_event = 0 def __del__(self): """Destructor. The only thing to do is close the Ptrac file. """ self.f.close()
[docs] def determine_endianness(self): """Determine the number format (endianness) used in the Ptrac file. For this, the file's first entry is used. It is always minus one and has a length of 4 bytes. """ # read and unpack first 4 bytes b = should_be_4 = struct.unpack('<i', b)[0] if should_be_4 == 4: self.endianness = '<' else: self.endianness = '>' # discard the next 8 bytes (the value -1 und another 4)
[docs] def read_next(self, format, number=1, auto=False, raw_format=False): """Helper method for reading records from the Ptrac file. All binary records consist of the record content's length in bytes, the content itself and then the length again. format can be one of the struct module's format characters (i.e. i for an int, f for a float, s for a string). The length of the record can either be hard-coded by setting the number parameter (e.g. to read 10 floats) or determined automatically by setting auto=True. Setting the parameter raw_format to True means that the format string will not be expanded by number, but will be used directly. """ if self.eightbytes and (not raw_format) and format == 'f': format = 'd' if self.eightbytes and (not raw_format) and format == 'i': format = 'q' # how long is one field of the read values format_length = 1 if format in ['h', 'H'] and not raw_format: format_length = 2 elif format in ['i', 'I', 'l', 'L', 'f'] and not raw_format: format_length = 4 elif format in ['d', 'q', 'Q'] and not raw_format: format_length = 8 if auto and not raw_format: b = if b == b'': raise EOFError length = struct.unpack(self.endianness.encode() + b'i', b)[0] number = length // format_length b = + 4) tmp = struct.unpack(b"".join([self.endianness.encode(), (format*number).encode(), b'i']), b) length2 = tmp[-1] tmp = tmp[:-1] else: bytes_to_read = number * format_length + 8 b = if b == b'': raise EOFError fmt_string = self.endianness + "i" if raw_format: fmt_string += format + "i" else: fmt_string += format * number + "i" tmp = struct.unpack(fmt_string.encode(), b) length = tmp[0] length2 = tmp[-1] tmp = tmp[1:-1] assert length == length2 if format == 's': # return just one string return b''.join(tmp).decode() elif number == 1: # just return the number and not a tuple containing just the number return tmp[0] else: # convert tuple to list return list(tmp)
[docs] def read_headers(self): """Read and save the MCNP version and problem description from the Ptrac file. """ # mcnp version info self.mcnp_version_info = self.read_next('s', auto=True) # problem title self.problem_title = self.read_next('s', auto=True).strip() # ptrac input data. can be omitted for now, # but has to be parsed, because it has variable length. # Also, this is the first difference between a file generated # with 4-byte and 8-byte numbers. line = self.read_next('f', auto=True) # if this line doesn't consist of 10 floats, then we've read them with # the wrong byte length and re have to re-read them (and every # following float) with 8 bytes length. if len(line) != 10: self.eightbytes = True tmp = struct.pack(self.endianness + "f"*20, *line) line = list(struct.unpack(self.endianness + "d"*10, tmp)) # the first item is always 13. afterwards, there is 13 times the # following scheme: # N x_0 ... x_N, # where N is the number of values for the current input variable and # the x_i are its N values. num_variables = int(line[0]) # should always be 13. current_pos = 1 current_variable = 1 while current_variable <= num_variables: n = int(line[current_pos]) if current_variable < num_variables and (current_pos + n + 1) >= \ len(line): line += self.read_next('f', 10) current_pos += n + 1 current_variable += 1
[docs] def read_variable_ids(self): """Read the list of variable IDs that each record type in the Ptrac file is comprised of. The variables can vary for different problems. Consult the MCNP manual for details. """ variable_nums = dict() variable_ids = dict() if self.eightbytes: variable_info = self.read_next( "qqqqqqqqqqqiiiiiiiii", 124, raw_format=True) else: variable_info = self.read_next('i', 20) variable_nums["nps"] = variable_info[0] variable_nums["src"] = variable_info[1] + variable_info[2] variable_nums["bnk"] = variable_info[3] + variable_info[4] variable_nums["sur"] = variable_info[5] + variable_info[6] variable_nums["col"] = variable_info[7] + variable_info[8] variable_nums["ter"] = variable_info[9] + variable_info[10] num_vars_total = sum(variable_info[:11]) if self.eightbytes: # only the NPS vars are in 8 byte, the other ones are still 4 fmt_string = "q" * variable_info[0] + \ "i" * sum(variable_info[1:11]) fmt_length = 8 * variable_info[0] + 4 * sum(variable_info[1:11]) all_var_ids = self.read_next( fmt_string, fmt_length, raw_format=True) else: all_var_ids = self.read_next('i', num_vars_total) for l in ["nps", "src", "bnk", "sur", "col", "ter"]: variable_ids[l] = all_var_ids[:variable_nums[l]] all_var_ids = all_var_ids[variable_nums[l]:] self.variable_nums = variable_nums self.variable_ids = variable_ids
[docs] def read_nps_line(self): """Read an NPS record and save the type of the next event. """ nps_line = self.read_next('i', self.variable_nums["nps"]) self.next_event = nps_line[1]
[docs] def read_event_line(self, ptrac_event): """Read an event record and save it to a given PtracParticle instance. """ # save for current event, because this record # contains only the next event's type event_type = self.next_event if event_type == 1000: e = "src" elif event_type == 3000: e = "sur" elif event_type == 4000: e = "col" elif event_type == 5000: e = "ter" else: e = "bnk" evt_line = self.read_next('f', self.variable_nums[e]) self.next_event = evt_line[0] for i in range(1, len(self.variable_ids[e])): if self.variable_ids[e][i] in self.variable_mappings: ptrac_event[self.variable_mappings[ self.variable_ids[e][i]]] = \ evt_line[i] ptrac_event["event_type"] = event_type
[docs] def write_to_hdf5_table(self, hdf5_table, print_progress=0): """Writes the events contained in this Ptrac file to a given HDF5 table. The table must already exist and have rows that match the PtracEvent definition. If desired, the number of processed events can be printed to the console each N events by passing the print_progress=N parameter. """ ptrac_event = hdf5_table.row counter = 0 while True: try: self.read_nps_line() except EOFError: break # no more entries while self.next_event != 9000: self.read_event_line(ptrac_event) ptrac_event.append() counter += 1 if print_progress > 0 and counter % print_progress == 0: print("processing event {0}".format(counter))
def _is_cell_line(line): is_cell = False if len(line.split()) > 3: if line.split()[0].isdigit() and \ line.split()[1].isdigit() and \ not line.split()[2][0].isalpha() and \ line[0:5] != ' ' and \ line.split()[1] != '0': is_cell = True return is_cell
[docs]def mats_from_inp(inp): """This function reads an MCNP inp file and returns a mapping of material numbers to material objects. Parameters ---------- inp : str MCNP input file Returns -------- materials : dict Keys are MCNP material numbers and values are PyNE material objects (for single density materials) and MultiMaterial objects (for multiple density materials). """ mat_lines = [] # line of lines that begin material cards densities = {} # dictionary to be populuated with material # and densities mat_nums = [] # list of material numbers to be printed to stdout materials = {} # to be populated with material objectes and returned line_count = 1 line = linecache.getline(inp, line_count) # scroll through every line of the mcnp inp file while line != '': line = linecache.getline(inp, line_count) # check to see if line contains a cell card. If so, grab the density. # information is stored in a dictionary where: # key = material number, value = list of densities if _is_cell_line(line): mat_num = int(line.split()[1]) den = float(line.split()[2]) if mat_num not in densities.keys(): densities[mat_num] = [den] else: same_bool = False for j in range(0, len(densities[mat_num])): if abs((den - densities[mat_num][j])/den) < 1E-4: same_bool = True if same_bool is False: densities[mat_num].append(den) # check line to see if it contain a material card, in the form # m* where * is a digit. If so store the line num. and material number if line.split() != []: if line.split()[0][0] == 'm' or line.split()[0][0] == 'M': if line.split()[0][1].isdigit() is True: mat_lines.append(line_count) mat_nums.append(int(line.split()[0][1:])) line_count += 1 line = linecache.getline(inp, line_count) for i in range(0, len(mat_nums)): if mat_nums[i] in densities.keys(): materials[mat_nums[i]] = mat_from_inp_line(inp, mat_lines[i], densities[mat_nums[i]]) else: materials[mat_nums[i]] = mat_from_inp_line(inp, mat_lines[i]) return materials
[docs]def mat_from_inp_line(filename, mat_line, densities='None'): """ This function reads an MCNP material card from a file and returns a Material or Multimaterial object for the material described by the card. This function is used by :func:`mats_from_inp`. Parameters ---------- filename : str Name of the MCNP input file mat_line : int Line number of the material card or interest densities : list of floats The densities associated with the material Returns ------- finished_mat : Material or MultiMaterial A Material object is returned if there is 1 density supplied. If multiple densities are supplied a MultiMaterial is returned. """ data_string = linecache.getline(filename, mat_line).split('$')[0] # collect all material card data on one string line_index = 1 line = linecache.getline(filename, mat_line + line_index) # people sometimes put comments in materials and then this loop breaks # so we need to keep reading if we encounter comments while len(line.split()) > 0 and (line[0:5] == ' ' or line[0].lower() == 'c'): # make sure element/isotope is not commented out if line.split()[0][0] != 'c' and line.split()[0][0] != 'C': data_string += line.split('$')[0] line_index += 1 line = linecache.getline(filename, mat_line + line_index) # otherwise this not a line we care about, move on and # skip lines that start with c or C else: line_index += 1 line = linecache.getline(filename, mat_line + line_index) # create dictionaries nucvec and table_ids nucvec = {} table_ids = {} for i in range(1, len(data_string.split())): if i & 1 == 1: zzzaaam = str(nucname.zzaaam( nucname.mcnp_to_id(data_string.split()[i].split('.')[0]))) # this allows us to read nuclides that are repeated if zzzaaam in nucvec.keys(): nucvec[zzzaaam] += float(data_string.split()[i+1]) else: nucvec[zzzaaam] = float(data_string.split()[i+1]) if len(data_string.split()[i].split('.')) > 1: table_ids[str(zzzaaam)] = data_string.split()[i].split('.')[1] # Check to see it material is definted my mass or atom fracs. # Do this by comparing the first non-zero fraction to the rest # If atom fracs, convert. nucvecvals = list(nucvec.values()) n = 0 isatom = 0 < nucvecvals[n] while 0 == nucvecvals[n]: n += 1 isatom = 0 < nucvecvals[n] for value in nucvecvals[n+1:]: if isatom != (0 <= value): msg = 'Mixed atom and mass fractions not supported.' ' See material defined on line {0}'.format(mat_line) warn(msg) # apply all data to material object if isatom: mat = Material() mat.from_atom_frac(nucvec) else: # set nucvec attribute to the nucvec dict from above mat = Material(nucvec=nucvec) mat.metadata['table_ids'] = table_ids mat.metadata['mat_number'] = data_string.split()[0][1:] # collect metadata, if present mds = ['source', 'comments', 'name'] line_index = 1 mds_line = linecache.getline(filename, mat_line - line_index) # while reading non-empty comment lines while mds_line.strip() not in set('cC') \ and mds_line.split()[0] in ['c', 'C']: if mds_line.split()[0] in ['c', 'C'] \ and len(mds_line.split()) > 1: possible_md = mds_line.split()[1].split(':')[0].lower() if possible_md in mds: if possible_md.lower() == 'comments': comments_string = str( ''.join(mds_line.split(':')[1:]).split('\n')[0]) comment_index = 1 comment_line = linecache.getline( filename, mat_line - line_index + comment_index) while comment_line.split()[0] in ['c', 'C']: if comment_line.split()[1].split(':')[0].lower() in mds: break comments_string += ' ' + ' '.join( comment_line.split()[1:]) comment_index += 1 comment_line = \ linecache.getline(filename, mat_line - line_index + comment_index) mat.metadata[possible_md] = comments_string else: mat.metadata[possible_md] = ''.join( mds_line.split(':')[1:]).split('\n')[0] # set metadata line_index += 1 mds_line = linecache.getline(filename, mat_line - line_index) # Check all the densities. If they are atom densities, convert them to mass # densities. If they are mass densities they willl be negative, so make # them positive. if densities != 'None': converted_densities = [] for den in densities: if den <= 0: converted_densities.append(-1*float(den)) else: converted_densities.append(mat.mass_density(float(den)*1E24)) # check to see how many densities are associated with this material. # if there is more than one, create a multimaterial""" if len(converted_densities) == 1: mat.density = converted_densities[0] finished_mat = mat elif len(converted_densities) > 1: mat_dict = {} for density in converted_densities: mat2 = Material() mat2.comp = mat.comp mat2.atoms_per_molecule = mat.atoms_per_molecule mat2.mass = mat.mass mat2.metadata = mat.metadata mat2.density = density mat_dict[mat2] = 1 finished_mat = MultiMaterial(mat_dict) else: finished_mat = mat return finished_mat
[docs]class Wwinp(Mesh): """A Wwinp object stores all of the information from a single MCNP WWINP file. Weight window lower bounds are stored on a structured mesh. Only Cartesian mesh WWINP files are supported. Neutron, photon, and simotaneous neutron and photon WWINP files are supported. Attributes ---------- ni : number of integers on card 2. ni = 1 for neutron WWINPs, ni = 2 for photon WWINPs or neutron + photon WWINPs. nr : int 10 for rectangular, 16 for cylindrical. ne : list of number of energy groups for neutrons and photons. If ni = 1 the list is only 1 value long, to represent the number of neutron energy groups nf : list of numbers of fine mesh points in the i, j, k dimensions nft : int total number of fine mesh points origin : list of i, j, k minimums. nc : list number of coarse mesh points in the i, j, k dimensions nwg : int 1 for rectangular, 2 for cylindrical. cm : list of lists of coarse mesh points in the i, j, k dimensions. Note the origin is not considered a coarse mesh point (as in MCNP). fm : list of lists of number of fine mesh points between the coarses mesh points in the i, j, k dimensions. e : list of lists of energy upper bounds for neutrons, photons. If ni = 1, the e will look like [[]]. If ni = 2, e will look like [[], []]. bounds : list of lists of spacial bounds in the i, j, k dimensions. mesh : Mesh object with a structured mesh containing all the neutron and/or photon weight window lower bounds. These tags have the form "ww_X" where X is n or p The mesh has rootSet tags in the form X_e_upper_bounds. Notes ----- Attribute names are identical to names speficied in WWINP file description in the MCNP5 User's Guide Volume 3 Appendix J. """ def __init__(self): if not HAVE_PYMOAB: raise RuntimeError("PyMOAB is not available, " "unable to create Wwinp Mesh.") pass
[docs] def read_wwinp(self, filename): """This method creates a Wwinp object from the WWINP file <filename>. """ with open(filename, 'r') as f: self._read_block1(f) self._read_block2(f) self._read_block3(f)
def _read_block1(self, f): # Retrieves all of the information from block 1 of a wwinp file. line_1 = f.readline() = int(line_1.split()[2]) = int(line_1.split()[3]) line_2 = f.readline() = [int(x) for x in line_2.split()] if == 10: # Cartesian line_3 = f.readline() = [int(float(x)) for x in line_3.split()[0:3]] self.nft =[0]*[1]*[2] self.origin = [float(x) for x in line_3.split()[3:6]] line_4 = f.readline() = [int(float(x)) for x in line_4.split()[0:3]] self.nwg = int(float(line_4.split()[3])) if == 16: # Cylindrical raise ValueError('Cylindrical WWINP not currently supported') def _read_block2(self, f): # Retrieves all of the information from block 2 of a wwinp file. self.bounds = [[], [], []] = [[], [], []] = [[], [], []] for i in [0, 1, 2]: # Create a list of raw block 2 values. raw = [] while len(raw) < 3*[i] + 1: raw += [float(x) for x in f.readline().split()] # Remove all the rx(i), ry(i), rz(i) values that # contaminated the raw list. removed_values = [raw[0]] for j in range(1, len(raw)): if j % 3 != 0: removed_values.append(raw[j]) # Expaned out nfx/nfy/nfx values to get structured mesh bounds. for j in range(0, len(removed_values)): if j % 2 == 0: self.bounds[i].append(removed_values[j]) if j != 0:[i].append(removed_values[j]) else:[i].append(removed_values[j]) for k in range(1, int(removed_values[j])): self.bounds[i].append( (removed_values[j+1] - removed_values[j-1]) * k / removed_values[j] + removed_values[j-1]) def _read_block3(self, f): # Retrives all the information of the block 3 of a wwinp file. self.e = [[]] if[0] != 0: while len(self.e[0]) <[0]: self.e[0] += [float(x) for x in f.readline().split()] self._read_wwlb('n', f) if len( == 2 and[1] != 0: self.e.append([]) while len(self.e[-1]) <[1]: self.e[-1] += [float(x) for x in f.readline().split()] self._read_wwlb('p', f) def _read_wwlb(self, particle, f): # Reads the weight window lower bounds from block 3 and returns a # mesh. # If this is the first time this method is called then created a mesh, # otherwise (in the case of n and p in the same WWINP) add to the # preexisting mesh. if not hasattr(self, 'mesh'): super(Wwinp, self).__init__(structured_coords=[self.bounds[0], self.bounds[1], self.bounds[2]], structured=True) volume_elements = list(self.structured_iterate_hex('zyx')) if particle == 'n': particle_index = 0 elif particle == 'p': particle_index = 1 # read in WW data for a single particle type ww_data = np.empty(shape=([particle_index], self.nft)) for i in range(0,[particle_index]): count = 0 ww_row = [] while count < self.nft: ww_row += [float(x) for x in f.readline().split()] count += 6 # number of entries per row in WWINP ww_data[i] = ww_row # create vector tags for data ww_tag_name = "ww_{0}".format(particle) self.tag(ww_tag_name,[particle_index], dtype=float, tagtype='nat_mesh') tag_ww = self.get_tag(ww_tag_name) # tag vector data to mesh for i, volume_element in enumerate(volume_elements): tag_ww[volume_element] = ww_data[:, i] # Save energy upper bounds to rootset. e_bounds_tag_name = '{0}_e_upper_bounds'.format(particle) self.tag(e_bounds_tag_name, size=len(self.e[particle_index]), dtype=float, tagtype='nat_mesh') tag_e_bounds = self.get_tag(e_bounds_tag_name) tag_e_bounds[self] = self.e[particle_index]
[docs] def write_wwinp(self, filename): """This method writes a complete WWINP file to <filename>. """ with open(filename, 'w') as f: self._write_block1(f) self._write_block2(f) self._write_block3(f)
def _write_block1(self, f): # Writes the all block 1 data to WWINP file block1 = '' # Create a MCNP formated time string. now = time = '{0:02d}/{1}/{2} {3}:{4}:{5}'.format( now.month,, str(now.year)[2:], now.hour, now.minute, now.second) # Append line 1. block1 += \ "{0:10.0f}{1:10.0f}{2:10.0f}{3:10.0f}" \ "{4:>38}\n".format(1, 1,,, time) # Append line 2. for i in block1 += '{0:10.0f}'.format(int(i)) block1 += '\n' # Append line 3. block1 += \ '{0:13.5E}{1:13.5E}{2:13.5E}{3:13.5E}{4:13.5E}{5:13.5E}\n'\ .format([0],[1],[2], self.origin[0], self.origin[1], self.origin[2]) # Append line 4. block1 += '{0:13.5E}{1:13.5E}{2:13.5E}{3:13.5E}\n'\ .format([0],[1],[2], self.nwg) f.write(block1) def _write_block2(self, f): # Writes the all block 2 data to WWINP file # Create an array of values to be print in block 2. block2_array = [[], [], []] for i in [0, 1, 2]: block2_array[i].append(self.origin[i]) for j in range(0, len([i])): block2_array[i] += [[i][j],[i][j], 1.0000] # Translate block2 vector into a string with appropriate text wrapping. block2 = "" for i in range(0, 3): line_count = 0 # number of entries printed to current line, max=6 for j in range(0, len(block2_array[i])): block2 += '{0:13.5E}'.format(block2_array[i][j]) line_count += 1 if line_count == 6: block2 += '\n' line_count = 0 if line_count != 0: block2 += '\n' f.write(block2) def _write_block3(self, f): # Writes the all block 3 data to WWINP file if[0] != 0: self._write_block3_single('n', f) if len( == 2: self._write_block3_single('p', f) def _write_block3_single(self, particle, f): # Write all of block 3 a single time (e.g. for WWINP with only n or # p). This function is called twice in the case of the WWINP having # both n and p. if particle == 'n': particle_index = 0 elif particle == 'p': particle_index = 1 # Append energy line. block3 = '' line_count = 0 for e_upper_bound in self.e[particle_index]: block3 += '{0:13.5E}'.format(e_upper_bound) line_count += 1 if line_count == 6: block3 += '\n' line_count = 0 if line_count != 0: block3 += '\n' # Get ww_data. ww_data = np.empty(shape=(self.nft,[particle_index])) volume_elements = list(self.structured_iterate_hex('zyx')) for i, volume_element in enumerate(volume_elements): ww_data[i] = self.get_tag("ww_{0}".format(particle))[ volume_element] for i in range(0,[particle_index]): # Append ww_data to block3 string. line_count = 0 for ww in ww_data[:, i]: block3 += '{0:13.5E}'.format(ww) line_count += 1 if line_count == 6: block3 += '\n' line_count = 0 if line_count != 0: block3 += '\n' f.write(block3)
[docs] def read_mesh(self, mesh): """This method creates a Wwinp object from a structured mesh object. The mesh must have tags in the form "ww_X" where X is n or p. For every particle there must be a rootSet tag in the form X_e_upper_bounds containing a list of energy upper bounds. """ super(Wwinp, self).__init__(mesh=mesh, structured=True) # Set geometry related attributes. = 10 self.nwg = 1 # Set energy related attributes. self.e = [] = [] all_tags = [ for x in self.get_all_tags()] if 'n_e_upper_bounds' in all_tags: n_e_upper_bounds = self.n_e_upper_bounds[self] # In the single energy group case, the "E_upper_bounds" tag # returns a non-iterable float. If this is the case, put this # float into an array so that it can be iterated over if isinstance(n_e_upper_bounds, float): n_e_upper_bounds = [n_e_upper_bounds] self.e.append(n_e_upper_bounds) else: self.e.append([]) if 'p_e_upper_bounds' in all_tags: p_e_upper_bounds = self.p_e_upper_bounds[self] if isinstance(p_e_upper_bounds, float): p_e_upper_bounds = [p_e_upper_bounds] self.e.append(p_e_upper_bounds) = int(len( # Set space related attributes. self.bounds = [self.structured_get_divisions('x'), self.structured_get_divisions('y'), self.structured_get_divisions('z')] self.origin = [self.bounds[0][0], self.bounds[1][0], self.bounds[2][0]] # Cycle through the rest of bounds to get the fine/coarse information. = [[], [], []] = [[], [], []] for i, points in enumerate(self.bounds): # There exists at least 1 fine mesh point.[i].append(1) # Loop through remaining points to determine which are coarse, # and the number of fine meshes between them. j = 1 while j < len(points) - 1: # Floating point comparison characterizes coarse vs. fine. if abs((points[j] - points[j-1]) - (points[j+1] - points[j])) <= 1.01E-4:[i][len([i])] += 1 else:[i].append(points[j])[i].append(1) j += 1 # Append last point as coarse point, as this is always the case.[i].append(points[-1]) = [len([0]), len([1]), len([2])] = [sum([0]), sum([1]), sum([2])] self.nft =[0]*[1]*[2]
[docs]class Meshtal(object): """This class stores all the information from an MCNP meshtal file with single or multiple fmesh4 neutron or photon tallies. The "tally" attribute provides key/value access to invidial MeshTally objects. Attributes ---------- filename : string Path to an MCNP meshtal file version : float The MCNP verison number ld : string The MCNP verison date title : string Title card from the MCNP input histories : int Number of histories from the MCNP simulation tally : dict A dictionary with MCNP fmesh4 tally numbers (e.g. 4, 14, 24) as keys and MeshTally objects as values. tags : dict Maps integer tally numbers to iterables containing four strs, the results tag name, the relative error tag name, the total results tag name, and the total relative error tag name. If tags is None the tags are named 'x_result', 'x_rel_error', 'x_result_total', 'x_rel_error_total' where x is n or p for neutrons or photons. """ def __init__(self, filename, tags=None, meshes_have_mats=False): """Parameters ---------- filename : str MCNP meshtal file. tags : dict, optional Maps integer tally numbers to iterables containing four strs: the results tag name, the relative error tag name, the total results tag name, and the total relative error tag name. If tags is None the tags are named 'x_result', 'x_rel_error', 'x_result_total', 'x_rel_error_total' where x is n or p for neutrons or photons. meshes_have_mats : bool If false, Meshtally objects will be created without PyNE material material objects. """ if not HAVE_PYMOAB: raise RuntimeError("PyMOAB is not available, " "unable to create Meshtal.") self.tally = {} self.tags = tags self._meshes_have_mats = meshes_have_mats with open(filename, 'r') as f: self._read_meshtal_head(f) self._read_tallies(f) def _read_meshtal_head(self, f): """Get the version, ld, title card and number of histories. """ line_1 = f.readline() # set mcnp version self.version = line_1.split()[2] # get version date ("ld" in MCNP User's Manual) self.ld = line_1.split()[3][3:] line_2 = f.readline() # store title card self.title = line_2.strip() line_3 = f.readline() # get number of histories self.histories = int(float(line_3.split()[-1])) def _read_tallies(self, f): """Read in all of the mesh tallies from the meshtal file. """ line = f.readline() while line != "": if line.split()[0:3] == ['Mesh', 'Tally', 'Number']: tally_num = int(line.split()[3]) if self.tags is not None and tally_num in self.tags.keys(): self.tally[tally_num] = MeshTally(f, tally_num, self.tags[tally_num], mesh_has_mats=self._meshes_have_mats) else: self.tally[tally_num] = MeshTally(f, tally_num, mesh_has_mats=self._meshes_have_mats) line = f.readline()
[docs]class MeshTally(StatMesh): """This class stores all information from all single MCNP mesh tally that exists within some meshtal file. Header information is stored as attributes and the "mesh" attribute is a MOAB mesh with all result and relative error data tagged. This class inherits from StatMesh, exposing all statistical mesh manipulation methods. Attributes ---------- tally_number : int The MCNP tally number. Must end in 4 (e.g. 4, 14, 214). particle : string Either "neutron" for a neutron mesh tally or "photon" for a photon mesh tally. dose_response : bool True is the tally is modified by a dose response function. x_bounds : list of floats The locations of mesh vertices in the x direction. y_bounds : list of floats The locations of mesh vertices in the y direction. z_bounds : list of floats The locations of mesh vertices in the z direction. e_bounds : list of floats The minimum and maximum bounds for energy bins mesh : An PyMOAB core instance tagged with all results and relative errors tag_names : iterable Four strs that specify the tag names for the results, relative errors, total results, and relative errors of the total results. Notes ----- All Mesh/StatMesh attributes are also present via a super() call to StatMesh.__init__(). """ def __init__(self, f, tally_number, tag_names=None, mesh_has_mats=False): """Create MeshTally object from a filestream open to the second line of a mesh tally header (the neutron/photon line). MeshTally objects should be instantiated only through the Meshtal class. Parameters ---------- f : filestream Open to the neutron/photon line. tally_number : int The MCNP fmesh4 tally number (e.g. 4, 14, 24). tag_names : iterable, optional Four strs that specify the tag names for the results, relative errors, total results and relative errors of the total results. This should come from the Meshtal.tags attribute dict. mesh_has_mats : bool If false, Meshtally objects will be created without PyNE material objects. """ if not HAVE_PYMOAB: raise RuntimeError("PyMOAB is not available, " "unable to create Meshtally Mesh.") self.tally_number = tally_number self._read_meshtally_head(f) self._read_column_order(f) if tag_names is None: self.tag_names = ("{0}_result".format(self.particle), "{0}_result_rel_error".format(self.particle), "{0}_result_total".format(self.particle), "{0}_result_total_rel_error".format(self.particle)) else: self.tag_names = tag_names self._create_mesh(f, mesh_has_mats) def _read_meshtally_head(self, f): """Get the particle type, spacial and energy bounds, and whether or not flux-to-dose conversion factors are being used. """ line = f.readline() if ('neutron' in line): self.particle = 'neutron' elif ('photon' in line): self.particle = 'photon' # determine if meshtally flux-to-dose conversion factors are being used. line = f.readline() dr_str = 'This mesh tally is modified by a dose response function.' if line.strip() == dr_str: self.dose_response = True else: self.dose_response = False # advance the file to the line where x, y, z, bounds start while line.strip() != 'Tally bin boundaries:': line = f.readline() self.x_bounds = [float(x) for x in f.readline().split()[2:]] self.y_bounds = [float(x) for x in f.readline().split()[2:]] self.z_bounds = [float(x) for x in f.readline().split()[2:]] # "Energy bin boundaries" contain one more word than "X boundaries" self.e_bounds = [float(x) for x in f.readline().split()[3:]] self.dims = [0, 0, 0] + [len(self.x_bounds) - 1, len(self.y_bounds) - 1, len(self.z_bounds) - 1] # skip blank line between enery bin boundaries and table headings f.readline() def _read_column_order(self, f): """Create dictionary with table headings as keys and their column location as values. Dictionary is the private attribute _column_idx. """ line = f.readline() column_names = line.replace('Rel ', 'Rel_').replace( 'Rslt * ', 'Rslt_*_').strip().split() self._column_idx = dict(zip(column_names, range(0, len(column_names)))) def _create_mesh(self, f, mesh_has_mats): """Instantiate a Mesh object and tag the PyMOAB core instance with results and relative errors. """ mats = () if mesh_has_mats is True else None super(MeshTally, self).__init__(structured_coords=[self.x_bounds, self.y_bounds, self.z_bounds], structured=True, mats=mats) num_vol_elements = (len(self.x_bounds)-1) * (len(self.y_bounds)-1)\ * (len(self.z_bounds)-1) num_e_groups = len(self.e_bounds)-1 # get result and relative error data from file result = np.empty(shape=(num_e_groups, num_vol_elements)) rel_error = np.empty(shape=(num_e_groups, num_vol_elements)) for i in range(0, num_e_groups): result_row = [] rel_error_row = [] for j in range(0, num_vol_elements): line = f.readline().split() result_row.append(float(line[self._column_idx["Result"]])) rel_error_row.append( float(line[self._column_idx["Rel_Error"]])) result[i] = result_row rel_error[i] = rel_error_row # Tag results and error vector to mesh self.tag(self.tag_names[0], tagtype='nat_mesh', size=num_e_groups, dtype=float) res_tag = self.get_tag(self.tag_names[0]) self.tag(self.tag_names[1], tagtype='nat_mesh', size=num_e_groups, dtype=float) rel_err_tag = self.get_tag(self.tag_names[1]) if num_e_groups == 1: res_tag[:] = result[0] rel_err_tag[:] = rel_error[0] else: res_tag[:] = result.transpose() rel_err_tag[:] = rel_error.transpose() # If "total" data exists (i.e. if there is more than # 1 energy group) get it and tag it onto the mesh. if num_e_groups > 1: result = [] rel_error = [] for i in range(0, num_vol_elements): line = f.readline().split() result.append(float(line[self._column_idx["Result"]])) rel_error.append( float(line[self._column_idx["Rel_Error"]])) self.tag(self.tag_names[2], size=1, dtype=float, tagtype='nat_mesh') res_tot_tag = self.get_tag(self.tag_names[2]) self.tag(self.tag_names[3], size=1, dtype=float, tagtype='nat_mesh') rel_err_tot_tag = self.get_tag(self.tag_names[3]) res_tot_tag[:] = result rel_err_tot_tag[:] = rel_error
[docs]def mesh_to_geom(mesh, frac_type='mass', title_card="Generated from PyNE Mesh"): """This function reads a structured Mesh object and returns the geometry portion of an MCNP input file (cells, surfaces, materials), prepended by a title card. The mesh must be axis aligned. Surfaces and cells are written in xyz iteration order (z changing fastest). Parameters ---------- mesh : PyNE Mesh object A structured Mesh object with materials and valid densities. frac_type : str, optional Either 'mass' or 'atom'. The type of fraction to use for the material definition. title_card : str, optional The MCNP title card to appear at the top of the input file. Returns ------- geom : str The title, cell, surface, and material cards of an MCNP input file in the proper order. """ mesh._structured_check() divs = (mesh.structured_get_divisions('x'), mesh.structured_get_divisions('y'), mesh.structured_get_divisions('z')) cell_cards = _mesh_to_cell_cards(mesh, divs) surf_cards = _mesh_to_surf_cards(mesh, divs) mat_cards = _mesh_to_mat_cards(mesh, divs, frac_type) return "{0}\n{1}\n{2}\n{3}".format(title_card, cell_cards, surf_cards, mat_cards)
def _mesh_to_cell_cards(mesh, divs): """Prepares the cell cards for mesh_to_geom.""" cell_cards = "" count = 1 idx = mesh.iter_structured_idx('xyz') # Establish min and max idx values for each dimension. x_min = 1 x_max = len(divs[0]) y_min = x_max + 1 y_max = x_max + len(divs[1]) z_min = y_max + 1 z_max = y_max + len(divs[2]) for i in range(1, len(divs[0])): for j in range(1, len(divs[1])): for k in range(1, len(divs[2])): # Cell number, mat number, density cell_cards += "{0} {1} {2} ".format(count, count, mesh.density[]) # x, y, and z surfaces cell_cards += "{0} -{1} {2} -{3} {4} -{5}\n".format( i, i + 1, j + x_max, j + x_max + 1, k + y_max, k + y_max + 1) count += 1 # Append graveyard. cell_cards += "{0} 0 -{1}:{2}:-{3}:{4}:-{5}:{6}\n".format( count, x_min, x_max, y_min, y_max, z_min, z_max) return cell_cards def _mesh_to_surf_cards(mesh, divs): """Prepares the surface cards for mesh_to_geom.""" surf_cards = "" count = 1 for i, dim in enumerate("xyz"): for div in divs[i]: surf_cards += "{0} p{1} {2}\n".format(count, dim, div) count += 1 return surf_cards def _mesh_to_mat_cards(mesh, divs, frac_type): """Prepares the material cards for mesh_to_geom.""" mat_cards = "" idx = mesh.iter_structured_idx('xyz') for i in idx: mesh.mats[i].metadata['mat_number'] = i + 1 mat_cards += mesh.mats[i].mcnp(frac_type=frac_type) return mat_cards