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Updates uwuwmatlib.py for new uw2 material naming convention and adds… #531

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Updates uwuwmatlib.py for new uw2 material naming convention and adds… #531

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24 changes: 19 additions & 5 deletions tools/uwuw_matlib.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,9 @@
#!/usr/bin/env python
#
# add option to make more compatible with uwuw_prepoc
# -use default nucpath,datapath
# -use material names like 11 instead of m11
#
################################################################################
# This script read an MCNP5 input file and creates a material library for use
# with the UWUW workflow. The naming scheme in the material library is
Expand All @@ -13,31 +18,40 @@
from pyne.material import Material, MultiMaterial, MaterialLibrary
from pyne.mcnp import mats_from_inp

def uwuw_matlib(inp, out):
def uwuw_matlib(inp, out, enhanced_uwuw):
mats = mats_from_inp(inp)
uwuw_mats = {}
for mat in mats.values():
if isinstance(mat, MultiMaterial):
m = mat._mats.keys()[0]
else:
m = mat
mat_name = "m{0}".format(m.metadata["mat_number"])
if enhanced_uwuw:
print "Using enhanced uwuw_preproc compatibility mat_name...(no leading m)"
mat_name = str(m.metadata["mat_number"])
else:
mat_name = "m{0}".format(m.metadata["mat_number"]) # adds "m" to mat_name
m.metadata["name"] = mat_name
uwuw_mats[mat_name] = m

ml = MaterialLibrary(uwuw_mats)
ml.write_hdf5(out, datapath='/material_library/materials',
ml = MaterialLibrary(uwuw_mats)
if enhanced_uwuw:
print "\n Setting enhanced uwuw_preproc compatibility for writing material library..."
ml.write_hdf5(out) # don't set datapath,nucpath...will be pyne default values
else:
ml.write_hdf5(out, datapath='/material_library/materials',
nucpath='/material_library/nucid')

def main():
description = ("This program read MCNP5 input files and creates UWUW material libraries"
" with naming schemes that match mcnp2cad with the -U flag.")
parser = argparse.ArgumentParser(description=description)
parser.add_argument("-u","--uwuw_preproc", help="produce library more compatible with uwuw_preproc",action="store_true")
parser.add_argument("inp", action='store', help="Name of the MCNP input file.")
parser.add_argument("-o", "--output", action='store', dest='out',
default="matlib.h5m", help="The name of the .h5m file to produce.")
args = parser.parse_args()
uwuw_matlib(args.inp, args.out)
uwuw_matlib(args.inp, args.out, args.uwuw_preproc)

if __name__ == '__main__':
main()
24 changes: 20 additions & 4 deletions uwuw/uwuw_preproc.cpp
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Original file line number Diff line number Diff line change
@@ -1,7 +1,18 @@
#include "uwuw_preprocessor.hpp"
#include "moab/ProgOptions.hpp"
#include <stdlib.h>
#include <fstream>

int main(int argc, char* argv[]) {
// useful functions
bool file_exists(std::string filename)
{
//this function returns true if a file can be opened
std::ifstream ifile(filename.c_str());
return (bool)ifile; // casts file object to a boolean
};

int main(int argc, char* argv[])
{

ProgOptions po("uwuw_preproc: a tool for preprocessing DAGMC files to incorporate UWUW workflow information");

Expand All @@ -17,16 +28,21 @@ int main(int argc, char* argv[]) {
po.addOpt<void>("fatal,f", "Fatal errors cause exit", &fatal_errors);
po.addOpt<void>("simulate,s", "Fatal errors cause exit", &simulate);

po.addRequiredArg<std::string>("dag_file", "Path to DAGMC file to proccess", &dag_file);
po.addOpt<std::string>("lib_file,l", "Path to PyNE Material Library file to proccess", &lib_file);
po.addRequiredArg<std::string>("dag_file", "Path to DAGMC file to process", &dag_file);
po.addOpt<std::string>("lib_file,l", "File name (with path) for PyNE Material Library file to process", &lib_file);
po.addOpt<std::string>("output,o", "Specify the output filename (default "")", &out_file);

po.addOptionHelpHeading("Options for loading files");

po.parseCommandLine(argc, argv);

if (lib_file == "") {
std::cout << "need to set the library" << std::endl;
std::cout << "You need to set the PyNE material library filename" << std::endl;
exit(1);
} else if (file_exists(lib_file)) {
std::cout <<"Will read materials from file: "<< lib_file << std::endl;
} else {
std::cout << "Cannot open the material library filename:" << lib_file << std::endl;
exit(1);
}

Expand Down
90 changes: 60 additions & 30 deletions uwuw/uwuw_preprocessor.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,8 @@

// constructor
uwuw_preprocessor::uwuw_preprocessor(std::string material_library_filename, std::string dagmc_filename,
std::string output_file, bool verbosity, bool fatal_errors) {
std::string output_file, bool verbosity, bool fatal_errors)
{
// make new name concatenator class
ncr = new name_concatenator();

Expand Down Expand Up @@ -32,11 +33,13 @@ uwuw_preprocessor::uwuw_preprocessor(std::string material_library_filename, std:
}

// destructor
uwuw_preprocessor::~uwuw_preprocessor() {
uwuw_preprocessor::~uwuw_preprocessor()
{
}

// write the new material library
void uwuw_preprocessor::write_uwuw_materials() {
void uwuw_preprocessor::write_uwuw_materials()
{
std::map<std::string, pyne::Material> :: iterator it;

// loop over the processed material library and write each one to the file
Expand All @@ -45,9 +48,9 @@ void uwuw_preprocessor::write_uwuw_materials() {
pyne::Material mat = it->second;
// write the material to the file
if (verbose) {
std::cout << "writing material, " << mat.metadata["name"].asString();
std::cout << "writing material, " << mat.metadata["fluka_name"].asString();
std::cout << " to file " << output_filename << std::endl;
std::cout << "writing material," << mat.metadata["name"].asString();
std::cout << " writing material," << mat.metadata["fluka_name"].asString();
std::cout << " to file: " << output_filename << std::endl;
}
// write the uwuw materials to the geometry
mat.write_hdf5(output_filename, "/materials");
Expand All @@ -57,7 +60,8 @@ void uwuw_preprocessor::write_uwuw_materials() {
}

// write the new material library
void uwuw_preprocessor::write_uwuw_tallies() {
void uwuw_preprocessor::write_uwuw_tallies()
{
std::list<pyne::Tally> :: iterator it;

std::string tally_destination = "/tally"; // to avoid compiler warning
Expand All @@ -80,7 +84,8 @@ void uwuw_preprocessor::write_uwuw_tallies() {


// creates a new material using the Material material as a basis
pyne::Material uwuw_preprocessor::create_new_material(pyne::Material material, std::string density) {
pyne::Material uwuw_preprocessor::create_new_material(pyne::Material material, std::string density)
{
pyne::Material new_mat; // to return
pyne::comp_map comp = material.comp;

Expand Down Expand Up @@ -112,7 +117,8 @@ pyne::Material uwuw_preprocessor::create_new_material(pyne::Material material, s
}

// process the group names into unique material objects
void uwuw_preprocessor::process_materials() {
void uwuw_preprocessor::process_materials()
{
std::set<std::string> material_names;

// vol prop iterator
Expand All @@ -123,7 +129,7 @@ void uwuw_preprocessor::process_materials() {
for (it = volume_property_map.begin() ; it != volume_property_map.end() ; ++it) {
std::string group_name = it->second;
if (verbose) {
std::cout << "Making materiral group name ";
std::cout << "Making material group name=";
std::cout << group_name << std::endl;
}
material_names.insert(group_name);
Expand All @@ -133,7 +139,10 @@ void uwuw_preprocessor::process_materials() {
std::set<std::string> :: iterator s_it;

if (verbose) {
std::cout << "Materials Present, :" << std::endl;
std::cout << std::endl;
int numinmatllib=material_library.size();
std::cout << "Number of materials in material library=" << numinmatllib << std::endl;
std::cout << "Materials present in the material library:" << std::endl;
std::map<std::string, pyne::Material> :: iterator m_it;
for (m_it = material_library.begin() ; m_it != material_library.end() ; ++m_it) {
pyne::Material mat = m_it->second;
Expand All @@ -144,34 +153,44 @@ void uwuw_preprocessor::process_materials() {

// loop over the unique material/density combinations
for (s_it = material_names.begin() ; s_it != material_names.end() ; ++s_it) {
// material namesa are in the form mat:Name/rho:density
// if we find / then we have a density token
// material names are in the form mat:Name/rho:density
// if we find a / then we have a density token



std::string mat_name = dmd->return_property(*s_it, "mat");
std::string density = dmd->return_property(*s_it, "rho");

// print some info while looping
if (verbose) {
std::cout << " material_names iterator=" << *s_it << std::endl;
std::cout << " mat_name=" << mat_name << std::endl;
}

// find grave or vacuum
std::size_t found_grave = mat_name.find("Graveyard");
std::size_t found_vacuum = mat_name.find("Vacuum");

// check for missing materials
if (found_grave == std::string::npos && found_vacuum == std::string::npos) {
if (material_library.count(mat_name) == 0) {
std::cout << "material " << mat_name << " was not found in the material library" << std::endl;

std::cout << "material with name=" << mat_name << " was not found in the material library." << " Its density was=" << density << std::endl;
exit(EXIT_FAILURE);
}

// make a new material object with the appropriate density & name
pyne::Material new_material = create_new_material(material_library[mat_name],
density);
density);
uwuw_material_library[*s_it] = new_material;
}
}
return;
}

// process and create all the tally objects
void uwuw_preprocessor::process_tallies() {
void uwuw_preprocessor::process_tallies()
{
std::vector<std::string>::iterator it;

// first volumes
Expand Down Expand Up @@ -225,7 +244,8 @@ void uwuw_preprocessor::process_tallies() {
}

void uwuw_preprocessor::check_material_props(std::vector<std::string> material_props,
std::vector<std::string> density_props, int cellid) {
std::vector<std::string> density_props, int cellid)
{

if (material_props.size() == 0) {
if (verbose || fatal) {
Expand Down Expand Up @@ -279,7 +299,8 @@ void uwuw_preprocessor::check_material_props(std::vector<std::string> material_p
}
}

void uwuw_preprocessor::print_summary() {
void uwuw_preprocessor::print_summary()
{
std::cout << "+----------------------------------------------------" << std::endl;
std::cout << "| UWUW Summary " << std::endl;
std::cout << "+----------------------------------------------------" << std::endl;
Expand All @@ -300,7 +321,8 @@ void uwuw_preprocessor::print_summary() {
}

// used for printing & debugging only
void uwuw_preprocessor::property_vector(std::vector<int> props) {
void uwuw_preprocessor::property_vector(std::vector<int> props)
{
if (props.size() == 0)
return;
for (int i = 0 ; i < props.size() ; i++) {
Expand All @@ -319,8 +341,9 @@ void uwuw_preprocessor::property_vector(std::vector<int> props) {


tally_info uwuw_preprocessor::make_tally_groupname(std::string tally_props,
int dimension,
moab::EntityHandle entity) {
int dimension,
moab::EntityHandle entity)
{
// tally props should be of the form Neutron and Flux or, Photon and Current etc

// split tally_props into the particle and tally type
Expand Down Expand Up @@ -398,9 +421,10 @@ tally_info uwuw_preprocessor::make_tally_groupname(std::string tally_props,
}

void uwuw_preprocessor::check_tally_props(std::string particle_name,
std::string tally_type,
int dimension,
int entityid) {
std::string tally_type,
int dimension,
int entityid)
{

// check to make sure the particle is allowed
std::cout << "particle_name " << particle_name << std::endl;
Expand Down Expand Up @@ -434,15 +458,18 @@ void uwuw_preprocessor::check_tally_props(std::string particle_name,


// constructor
name_concatenator::name_concatenator() {
name_concatenator::name_concatenator()
{
}

// destructor
name_concatenator::~name_concatenator() {
name_concatenator::~name_concatenator()
{
}

// make the fluka name from the string
std::string name_concatenator::make_name_8bytes(std::string name) {
std::string name_concatenator::make_name_8bytes(std::string name)
{
// fluka name needs to be 8 chars long uppercase and unique
std::string b8_name = name;
std::transform(b8_name.begin(), b8_name.end(), b8_name.begin(), toupper);
Expand All @@ -467,7 +494,8 @@ std::string name_concatenator::make_name_8bytes(std::string name) {
}

// function to extract only the letters [A-Z] and numbers [0-9]
std::string name_concatenator::extract_alpha_num(std::string name) {
std::string name_concatenator::extract_alpha_num(std::string name)
{
// loop over the string accepting only ascii
std::string :: iterator it;
std::string str;
Expand All @@ -485,7 +513,8 @@ std::string name_concatenator::extract_alpha_num(std::string name) {

// Generates a new name but incremented by 1 relative to the last time
// the function was called.
std::string name_concatenator::shift_and_increment(std::string name) {
std::string name_concatenator::shift_and_increment(std::string name)
{
int count = 0;
// the following statements in braces are intended to turn the 8 char long string
// version of the name into a unique 8 character ID string, mainly for fluka
Expand Down Expand Up @@ -533,7 +562,8 @@ std::string name_concatenator::shift_and_increment(std::string name) {
return name;
}

void name_concatenator::int_to_string(int convert, std::string& string) {
void name_concatenator::int_to_string(int convert, std::string& string)
{
std::stringstream ss;
ss << convert;
string = ss.str();
Expand Down