sync latest perl mods and add runlist.pl to run a list of stars from a file (for Nina)

src/perl/scripts2/runlist.pl

+#!/usr/bin/env perl
+use strict; # recommended
+use 5.16.0; # recommended
+use binary_grid2; # required
+use binary_grid::C; # backend : C 
+use rob_misc qw/ncpus/;
+
+############################################################
+#
+# Example script to demonstrate how to use the
+# binary_grid2 module.
+#
+# For full documentation, please see binary_grid2.pdf
+# in the doc/ directory of binary_c
+#
+############################################################
+
+# number of computational threads to launch, usually one 
+# per CPU
+my $nthreads = rob_misc::ncpus();
+
+############################################################
+# Binary_c should output data that we can understand here. 
+# There are two ways to do this:
+#
+# 1) Put output statements, using Printf, in binary_c's
+#    log_every_timestep() function. This requires a rebuild
+#    of libbinary_c.so and a reinstall of the binary_grid module
+#    every time you change the Printf statement.
+#
+#
+# 2) Put a list of hashes in the C_auto_logging grid option
+#
+#  $population->set(
+#    C_auto_logging => {
+#        'MY_STELLAR_DATA' =>
+#            [
+#             'model.time',
+#             'star[0].mass',
+#             'model.probability',
+#             'model.dt'
+#            ]
+#    });
+#
+#  where MY_STELLAR_DATA is the key of the hash {...} and is also 
+#  the header matched in the parse_data function (below). The list [...] 
+#  contains the names of the variables to be output, which are all
+#  assumed to be in stardata.
+#
+#  This option does not require a rebuild of libbinary_c.so or a
+#  reinstall of binary_grid.
+#
+#
+# 3) Put output statements, using Printf, into the C_logging_code
+#    grid option
+#
+#  $population->set( C_logging_code => ' Printf("...\n"); ');
+#
+#    You have access to the stardata variable, so you can
+#    output everything that is available to log_every_timestep();
+#
+#  This option does not require a rebuild of libbinary_c.so or a
+#  reinstall of binary_grid.
+#
+############################################################
+# make a new stellar population
+my $population = binary_grid2->new(
+    # options can be given now ... 
+    metallicity => 0.02, # mass fraction of "metals"
+    max_evolution_time => 15000, # Myr 
+    nthreads=>$nthreads, # number of threads
+    );
+
+# ... or options can be set manually later.
+$population->set(
+    vb=>1, # turn on verbose logging (can be 0,1,2...)
+    return_array_refs=>1, # quicker data parsing mode
+    log_args=>1,
+    sort_args=>1,
+    save_args=>1,
+    log_args_dir=>'/tmp',
+    #log_dt_secs=>1,
+    C_auto_logging => {
+        'MY_STELLAR_DATA' =>
+            [
+             'model.time',
+             'star[0].mass',
+             'model.probability',
+             'model.dt'
+            ]
+    },
+ 
+## or enter more complicated code yourself:
+#       
+#    C_logging_code => '
+#             Printf("MY_STELLAR_DATA %g %g %g %g\n",
+#                    stardata->model.time,
+#                    stardata->star[0].mass,
+#                    stardata->model.probability,
+#                    stardata->model.dt);
+#                       ',
+
+    );
+
+
+############################################################
+# run from a list of stars in a file : you must set the
+# filename to be appropriate
+$population->{_grid_options}->{flexigrid}->{'grid type'} = 'list';
+$population->{_grid_options}->{flexigrid}->{'list filename'} = '/tmp/s3';
+
+
+############################################################
+# scan command line arguments for extra options
+$population->parse_args();     
+
+############################################################
+# link population to custom data parser function
+$population->set(
+    parse_bse_function_pointer => \&main::parse_data
+    );
+
+my %init = $population->initial_abundance_hash('Karakas2002',0.02);
+my %isotope_hash = $population->isotope_hash();
+my @isotope_list = $population->isotope_list();
+my %nuclear_mass_hash = $population->nuclear_mass_hash();
+my @nuclear_mass_list = $population->nuclear_mass_list();
+my @sources = $population->source_list();
+my @ensemble = $population->ensemble_list();
+
+# you can use Data::Dumper to see the contents
+# of the above lists and hashes
+if(0){
+    print Data::Dumper->Dump([
+        #\%init,
+        #\%isotope_hash,
+        #\@isotope_list,
+        #\%nuclear_mass_hash,
+        \@nuclear_mass_list,
+        #\@sources,
+        #\@ensemble
+                         ]);
+}
+
+# uncomment this to show version information
+#print $population->evcode_version_string();
+
+# uncomment this to show the evcode's default args list
+#print join("\n",@{$population->evcode_args_list()});
+
+# evolution the stellar population (this takes some time)
+$population->evolve();
+
+# output the data
+output($population);
+
+# done : exit
+exit;
+
+############################################################
+# subroutines 
+############################################################
+
+sub parse_data
+{
+    my ($population, $results) = @_;
+
+    my $progenitor = $population->progenitor(); 
+     
+    # get initial mass and probability for the initial mass function
+    my $progenitor_initial_mass = 
+        $progenitor->{m1} + $progenitor->{m2};
+    my $progenitor_probability = $population->progenitor()->{prob};
+    
+    # bin initial mass
+    my $binned_initial_mass = $population->rebin($progenitor_initial_mass,1.0);
+
+    # initial mass function
+    $results->{initial_mass_function}->{$binned_initial_mass} += 
+        $progenitor_probability;
+
+    while(1)
+    {
+        # subsequent calls to tbse_line contain
+        # (references to) arrays of data 
+        my $la = $population->tbse_line();
+
+        #print "DATA @$la\n";
+        
+        # first element is the "header" line
+        my $header = shift @$la;
+
+        # break out of the loop if this is 'fin'
+        last if ($header eq 'fin');
+
+        # check if $header matches one of your
+        # expected data lines, if so, act
+        if($header eq 'MY_STELLAR_DATA')
+        {
+            #print "GOT MY_STELLAR_DATA @$la\n";
+            
+            # matched MY_STELLAR_DATA header
+            #
+            # get time, mass, probability etc. as specified above
+            #
+            # (note that $probability is possibly not the same as 
+            #  the progenitor's probability!)
+            my $time = $la->[0];
+            my $mass = $la->[1];
+            my $probability = $la->[2];
+            my $timestep = $la->[3];
+
+            # bin mass to nearest 1.0 Msun
+            $mass = $population->rebin($mass, 1.0);
+
+            # add up the mass distribution
+            $results->{mass_distribution}->{$mass} += $probability * $timestep; 
+        }
+    }
+}
+
+############################################################
+
+sub output
+{
+    my ($population) = @_;
+
+    # $results is a hash reference containing
+    # the results that were added up in parse_data()
+    my $results = $population->results;
+
+    if(0)
+    {
+        # show results hash in full
+        print "############################################################\n";
+        print Data::Dumper::Dumper($results);
+        print "############################################################\n";
+    }
+    
+    # output the initial mass function
+    foreach my $mass (sort {$a<=>$b} keys %{$results->{initial_mass_function}})
+    {
+        printf "IMF %g %g\n",$mass,$results->{initial_mass_function}->{$mass};
+    }
+
+    # output the mass distribution
+    foreach my $mass (sort {$a<=>$b} keys %{$results->{mass_distribution}})
+    {
+        printf "MASS %g %g\n",$mass,$results->{mass_distribution}->{$mass};
+    }
+}

src/perl/scripts2/template.pl

@@ -102,9 +102,6 @@ $population->set(
 
     );
 
-print Data::Dumper::Dumper($population->evcode_args_list());
-exit;
-
 ############################################################
 # scan command line arguments for extra options
 $population->parse_args();