Science/cloudy-agn
1
0
Fork 0
mirror of https://asciireactor.com/otho/cloudy-agn.git synced 2024-12-05 01:55:08 +00:00
Code Issues Packages Projects Releases Wiki Activity

fixed multi-line stuff?

Browse Source
This commit is contained in:
caes 2017-06-30 05:21:50 -04:00
parent c7aab2929f
commit 26f18dcd5d
4 changed files with 114 additions and 77 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

24
notes
View File

@ -5,6 +5,30 @@ look at paper from kirk's student and find the value of that parameter
copy grids from thor
this shows only the transition between 1s and 2p... where are the rest of the contributions?
if indeed cloudy is meaning to print these out individually?
this may not be true for hydrogen-like iron, but for H-alpha the three transitions should be included
is this just sloppy notation in output file, or is this really accurate and then where is all the rest of it?
save species line "species_lines" all
save species labels "species_labels" all
OR
save species labels "species_labels"
H[:]
end
2017 grids needed

120
scripts/operations/package_tables.sh
View File

@ -29,66 +29,66 @@ cd fortfiles
echo "Directory ready. Calling fort file creation."
$bin_dir/create_fort_files ../mpi_grid.out $script_dir/../reference/linelist.c17
inwTfortnums=$(grep 'InwT' fort.*|sed 's@^fort\.\([0-9]\+\):InwT.*@\1@'|sort -nr)
echo "Computing inward diffuse tables for $(echo "$inwTfortnums"|wc -l) coordinates."
echo -n "Writing InwD tables to fortfiles and shifting files:"
count=0
for inwTnum in $(echo $inwTfortnums|sort -r)
do
inwCnum=$(($inwTnum + 1))
inwDnum=$(($inwCnum + 1))
allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
fortnumstoproc=""
for fortnum in $allfortnums
do
if (( $fortnum > $inwCnum ))
then
fortnumstoproc="$fortnum $fortnumstoproc"
fi
done
# echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
for fortnum in $fortnumstoproc
do
newnum=$(( $fortnum + 1 ))
mv fort.$fortnum fort.$newnum
done
#echo -n " $inwDnum"
$bin_dir/subtract_fortfiles fort.$inwTnum fort.$inwCnum InwD > fort.$inwDnum
echo -ne "\033[2K" ; printf "\r"
echo -n "Writing InwD tables to fortfiles and shifting files: $(( ++count ))"
done
echo ""
inwCfortnums=$(grep 'InwC' fort.*|sed 's@^fort\.\([0-9]\+\):InwC.*@\1@'|sort -nr)
echo "Computing total diffuse tables for $(echo "$inwCfortnums"|wc -l) coordinates."
echo -n "Writing nFnD tables to fortfiles and shifting files: 0"
count=0
for inwCnum in $(echo $inwCfortnums|sort -r)
do
nFnunum=$(($inwCnum - 3))
nFnDnum=$(($inwCnum + 2))
allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
fortnumstoproc=""
for fortnum in $allfortnums
do
if (( $fortnum >= $nFnDnum ))
then
fortnumstoproc="$fortnum $fortnumstoproc"
fi
done
# echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
for fortnum in $fortnumstoproc
do
newnum=$(( $fortnum + 1 ))
mv fort.$fortnum fort.$newnum
done
#echo -n " $nFnDnum"
$bin_dir/subtract_fortfiles fort.$nFnunum fort.$inwCnum nFnD > fort.$nFnDnum
echo -ne "\033[2K" ; printf "\r"
echo -n "Writing nFnD tables to fortfiles and shifting files: $(( ++count ))"
done
echo ""
# inwTfortnums=$(grep 'InwT' fort.*|sed 's@^fort\.\([0-9]\+\):InwT.*@\1@'|sort -nr)
# echo "Computing inward diffuse tables for $(echo "$inwTfortnums"|wc -l) coordinates."
# echo -n "Writing InwD tables to fortfiles and shifting files:"
# count=0
# for inwTnum in $(echo $inwTfortnums|sort -r)
# do
# inwCnum=$(($inwTnum + 1))
# inwDnum=$(($inwCnum + 1))
# allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
# fortnumstoproc=""
# for fortnum in $allfortnums
# do
# if (( $fortnum > $inwCnum ))
# then
# fortnumstoproc="$fortnum $fortnumstoproc"
# fi
# done
# # echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
# for fortnum in $fortnumstoproc
# do
# newnum=$(( $fortnum + 1 ))
# mv fort.$fortnum fort.$newnum
# done
# #echo -n " $inwDnum"
# $bin_dir/subtract_fortfiles fort.$inwTnum fort.$inwCnum InwD > fort.$inwDnum
# echo -ne "\033[2K" ; printf "\r"
# echo -n "Writing InwD tables to fortfiles and shifting files: $(( ++count ))"
# done
# echo ""
#
# inwCfortnums=$(grep 'InwC' fort.*|sed 's@^fort\.\([0-9]\+\):InwC.*@\1@'|sort -nr)
# echo "Computing total diffuse tables for $(echo "$inwCfortnums"|wc -l) coordinates."
# echo -n "Writing nFnD tables to fortfiles and shifting files: 0"
# count=0
# for inwCnum in $(echo $inwCfortnums|sort -r)
# do
# nFnunum=$(($inwCnum - 3))
# nFnDnum=$(($inwCnum + 2))
# allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
# fortnumstoproc=""
# for fortnum in $allfortnums
# do
# if (( $fortnum >= $nFnDnum ))
# then
# fortnumstoproc="$fortnum $fortnumstoproc"
# fi
# done
# # echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
# for fortnum in $fortnumstoproc
# do
# newnum=$(( $fortnum + 1 ))
# mv fort.$fortnum fort.$newnum
# done
#
# #echo -n " $nFnDnum"
# $bin_dir/subtract_fortfiles fort.$nFnunum fort.$inwCnum nFnD > fort.$nFnDnum
# echo -ne "\033[2K" ; printf "\r"
# echo -n "Writing nFnD tables to fortfiles and shifting files: $(( ++count ))"
# done
# echo ""
echo "Applying interpolative smoothing."
$script_dir/operations/bulk_interpolation_fix.sh fort.* > interpolation_report

33
src/agn.hpp
View File

@ -17,7 +17,7 @@
namespace agn {
const bool debug = false;
const bool debug = true;
const bool line_debug = false;
// General constants
@ -159,8 +159,8 @@ std::ostream& agn::operator<< (std::ostream& outstream, cloudy_result output) {
<< std::setprecision(0)
<< output.colden
<< "): "
<< output.emergent_line_intensity.size()
<< " emission lines, "
<< output.intrinsic_line_intensity.size()
<< " intrinsic emission lines, "
<< output.cautions.size()
<< " cautions present.";
return outstream;
@ -363,33 +363,44 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
eqwidthstr_len).c_str()
<< "\n";
}
if(point.emergent_line_intensity.count(label) == 0) {
if(point.intrinsic_line_intensity.count(label) == 0) {
data.has_duplicates = false;
point.emergent_line_intensity[label] = data;
point.intrinsic_line_intensity[label] = data;
}
else {
duplicate_labels.push_back(label);
data.has_duplicates = true;
point.emergent_line_intensity[label].has_duplicates = true;
std::stringstream zerolabel(label);
zerolabel << " j=0";
point.intrinsic_line_intensity[zerolabel.str()]
= point.intrinsic_line_intensity[label];
point.intrinsic_line_intensity[zerolabel.str()].has_duplicates = true;
point.intrinsic_line_intensity.erase(label);
int j=1;
data.has_duplicates = true;
while(true) {
std::stringstream newlabel;
newlabel << label;
newlabel << " j=" << j;
if(point.emergent_line_intensity.count(newlabel.str()) != 0) {
if(point.intrinsic_line_intensity.count(newlabel.str()) != 0) {
j++;
continue;
}
else {
point.emergent_line_intensity[newlabel.str()] = data;
point.intrinsic_line_intensity[newlabel.str()] = data;
break;
}
}
}
linetext_it++;
}
if(agn::debug) std::cout
<< " Grabbing footer.";
if(agn::debug) {
std::cout << " Duplicates found: ";
std::list<std::string>::iterator dup_it = duplicate_labels.begin();
while (dup_it != duplicate_labels.end() ) {
std::cout << *dup_it << " ";
}
std::cout << " Grabbing footer.";
}
while (inputline == "")
getline(inputfile,inputline);
std::string footer="";

14
src/spectral_lines.hpp
View File

@ -157,8 +157,9 @@ std::string agn::format_eqwidth_table_slice(agn::eqwidth_table table,agn::iterat
std::ostream& agn::operator<< (std::ostream& outstream, agn::eqwidth_table table) {
std::string header0_trimmed = table.header[0]; // need to setup a trim function for this
outstream
<< table.header[0]
<< header0_trimmed
<< std::endl
<< table.header[1]
<< std::endl;
@ -222,6 +223,7 @@ agn::line_list agn::read_line_list(std::ifstream& inputfile) {
std::list<agn::eqwidth_table> agn::compile_eqwidth_tables(agn::cloudy_grid grid,agn::line_list line_labels,double scale_factor) {
std::list<eqwidth_table> table_list_eq_width,table_list_radiated_energy;
agn::line_list::iterator line_label_it = line_labels.begin();
// Iterate over labels, creating table for each:
while (line_label_it != line_labels.end()) {
double x,y;
agn::cloudy_line_data data;
@ -233,9 +235,8 @@ std::list<agn::eqwidth_table> agn::compile_eqwidth_tables(agn::cloudy_grid grid,
std::stringstream header0;
header0
<< *line_label_it
<< " relative to Inci 1215.00A scaled to "
<< scale_factor
<< "A.";
<< " relative to Inci 1215.00A scaled to "
<< scale_factor;
new_table.header[0] = header0.str();
new_table.header[1] = "Hden Phi(H) Eq_Width (A)";
agn::cloudy_grid::iterator result_it = grid.begin();
@ -243,12 +244,13 @@ std::list<agn::eqwidth_table> agn::compile_eqwidth_tables(agn::cloudy_grid grid,
x = result_it->first.first;
y = result_it->first.second;
std::string label = *line_label_it;
if ( result_it->second.emergent_line_intensity.count(label) == 0 ) {
// if no data exist under this label, initialize some:
if ( result_it->second.intrinsic_line_intensity.count(label) == 0 ) {
data.radiated_energy=-35.0;
data.eq_width=0.0;
}
else {
data = result_it->second.emergent_line_intensity[label];
data = result_it->second.intrinsic_line_intensity[label];
data.eq_width /= scale_factor;
if(agn::line_debug) std::cout
<< "Added "