Science/cloudy-agn
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setup to run c17 release grids

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caes 2017-06-02 03:24:59 -04:00
parent 29a3f3743a
commit 1acd016d89
5 changed files with 12 additions and 5 deletions
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0
scripts/cloudy/mpi.in → scripts/cloudy/c13/mpi.in
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0
scripts/cloudy/mpi_grid.in → scripts/cloudy/c13/mpi_grid.in
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2
scripts/thor/cloudy_grid.pbs
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@ -15,4 +15,4 @@ module load openmpi/gnu/1.7.3
# replace ~/cloudy-agn/bin/cloudy_mpi with path to cloudy MPI executable file # replace ~/cloudy-agn/bin/cloudy_mpi with path to cloudy MPI executable file
cd ~/${RUN_DIR} cd ~/${RUN_DIR}
time mpirun -machinefile ${PBS_NODEFILE} -np ${num_proc} ~/cloudy-agn/bin/cloudy_mpi -r ${RUN_FILE} time mpirun -machinefile ${PBS_NODEFILE} -np ${num_proc} ~/cloudy/bin/cloudy_mpi -r ${RUN_FILE}

9
src/agn.hpp
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@ -38,6 +38,10 @@ typedef table2d::iterator iterator2d;
typedef std::pair<double,double> coord2d; typedef std::pair<double,double> coord2d;
typedef std::list<coord2d> gridcoordlist; typedef std::list<coord2d> gridcoordlist;
// Seeks an instream to the line after the first occurrence of seek_string.
void seek_to(std::string,std::istream&);
struct cloudy_line_data { struct cloudy_line_data {
double radiated_energy,eq_width; double radiated_energy,eq_width;
int index; int index;
@ -68,12 +72,13 @@ struct cloudy_result {
}; };
typedef std::map<coord2d,cloudy_result> cloudy_grid; typedef std::map<coord2d,cloudy_result> cloudy_grid;
// Easiest to read the entire grid from the file at once. // Easiest to read the entire grid from the file at once.
cloudy_grid read_cloudy_grid(std::ifstream&); cloudy_grid read_cloudy_grid(std::ifstream&);
// Operator<< prints general info about the run result. // Operator<< prints general info about the run result.
std::ostream& operator<< (std::ostream&, cloudy_result); std::ostream& operator<< (std::ostream&, cloudy_result);
// Seeks an instream to the line after the first occurrence of seek_string.
void seek_to(std::string,std::istream&);
} // end namespace agn } // end namespace agn

6
src/create_fort_files.cpp
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@ -23,7 +23,8 @@ int main(int argc, char const *argv[]) {
<< "Compiling table2ds for " << "Compiling table2ds for "
<< lines_to_print.size() << lines_to_print.size()
<< " emission lines.\n"; << " emission lines.\n";
std::list<agn::eqwidth_table> tables = agn::compile_eqwidth_tables(grid,lines_to_print,1215.00); std::list<agn::eqwidth_table> tables =
agn::compile_eqwidth_tables(grid,lines_to_print,1215.00);
// Remove any tables that are zero. // Remove any tables that are zero.
@ -91,7 +92,8 @@ int main(int argc, char const *argv[]) {
<< std::endl << std::endl
<< "───────────────────────────" << "───────────────────────────"
<< std::endl; << std::endl;
std::list<std::string>::iterator caution_it = result_it->second.cautions.begin(); std::list<std::string>::iterator caution_it =
result_it->second.cautions.begin();
while(caution_it != result_it->second.cautions.end()) { while(caution_it != result_it->second.cautions.end()) {
cautionreportfile cautionreportfile
<< *caution_it << *caution_it