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2017 runs finished

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caes 2017-06-25 14:29:38 -04:00
parent 75a01cf023
commit 9158437e8d
9 changed files with 76 additions and 28 deletions
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10
notes
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@ -23,15 +23,15 @@ Run grid with new SED, or at least a point, check values: how to find the approp
✓ run models for comparising: 10.5,19.5
□ Why so many Fe 2 lines?
✓ Why so many Fe 2 lines?
□ check if blnds are sums of the expected multiplets
✓ check if blnds are sums of the expected multiplets
✓ add in more levels to the H atom, unresolved, 20, also add some to paschen, maybe others -- check how much time is lost
✓ punch the paschen and balmer lines up to 18
□ Read Intrinsic Lines
✓ Read Intrinsic Lines
□ Smoothing algorithm using n-dimensional smoothing
@ -39,9 +39,9 @@ Run grid with new SED, or at least a point, check values: how to find the approp
✓ Run Grids in c17
□ Email about order of lines
✓ Email about order of lines
□ Find blend correlated names and update
✓ Find blend correlated names and update

2
scripts/cloudy/magdziarz.mpi.in
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@ -52,7 +52,7 @@ set nend 5000
//
// derived quantities added in Otho's program ~2017
// InwD = InwT - InwC = Inward Diffuse
// nFnD = nFnu - InwD = Total Diffuse
// nFnD = nFnu - InwC = Total Diffuse
//
// "print continuum" redundant with set nFnu in c17
//

2
scripts/cloudy/magdziarz.mpi_grid.in
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@ -50,7 +50,7 @@ set nend 5000
//
// derived quantities added in Otho's program ~2017
// InwD = InwT - InwC = Inward Diffuse
// nFnD = nFnu - InwD = Total Diffuse
// nFnD = nFnu - InwC = Total Diffuse
//
// "print continuum" redundant with set nFnu in c17
//

2
scripts/cloudy/mehdipour.mpi.in
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@ -52,7 +52,7 @@ set nend 5000
//
// derived quantities added in Otho's program ~2017
// InwD = InwT - InwC = Inward Diffuse
// nFnD = nFnu - InwD = Total Diffuse
// nFnD = nFnu - InwC = Total Diffuse
//
// "print continuum" redundant with set nFnu in c17
//

2
scripts/cloudy/mehdipour.mpi_grid.in
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@ -50,7 +50,7 @@ set nend 5000
//
// derived quantities added in Otho's program ~2017
// InwD = InwT - InwC = Inward Diffuse
// nFnD = nFnu - InwD = Total Diffuse
// nFnD = nFnu - InwC = Total Diffuse
//
// "print continuum" redundant with set nFnu in c17
//

2
scripts/meta/process_gridoutputs.sh
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@ -7,7 +7,7 @@ script_dir=$(
base_dir=`pwd`
bin_dir="$script_dir/../bin"
for dir in $(echo cldn*)
for dir in $(find . -type 'd' -name 'cldn*')
do
echo "Processing ${dir}."
$script_dir/operations/package_tables.sh $dir

57
scripts/operations/package_tables.sh
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@ -11,8 +11,8 @@ script_dir=$(
base_dir=`pwd`
bin_dir="$script_dir/../bin"
cldndir=$1
cd $cldndir
griddir=$1
cd $griddir
mkdir -p fortfiles
cd fortfiles
# pwd
@ -21,13 +21,14 @@ 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 "Generating inward diffuse tables for $(echo "$inwTfortnums"|wc -l) coordinates."
echo -n "Writing InwD tables to fortfiles:"
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 $inwTfortnums|sort -r)
do
inwCnum=$(($inwTnum + 1))
inwDnum=$(($inwCnum + 1))
allfortnums=$(echo fort.*|sed 's@fort\.\([0-9]\+\)@\1@g')
allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
fortnumstoproc=""
for fortnum in $allfortnums
do
@ -42,14 +43,52 @@ do
newnum=$(( $fortnum + 1 ))
mv fort.$fortnum fort.$newnum
done
echo -n " $inwDnum"
#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."
$script_dir/operations/bulk_interpolation_fix.sh fort.* > interpolation_report
tar cf ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar *
gzip ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar
mv ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar.gz $base_dir
grid_id=$(echo ${griddir}|sed 's@^\.\/\(.*\)@\1@'|sed 's@.grids@@'|sed 's@\/@.@g')
echo "Saving $grid_id grid"
tar cf fortfiles_${grid_id}.tar *
gzip fortfiles_${grid_id}.tar
mv fortfiles_${grid_id}.tar.gz $base_dir
cd $base_dir

18
src/agn.hpp
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@ -335,14 +335,14 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
agn::cloudy_line_data data;
data.index = ++index;
//std::stringstream values;
//data.radiated_energy = atof((*linetext_it).substr(
// radiatedenergystr_pos,
// radiatedenergystr_len).c_str()
//);
//data.eq_width = atof((*linetext_it).substr(
// eqwidthstr_pos,
// eqwidthstr_len).c_str()
//);
data.radiated_energy = atof((*linetext_it).substr(
radiatedenergystr_pos,
radiatedenergystr_len).c_str()
);
data.eq_width = atof((*linetext_it).substr(
eqwidthstr_pos,
eqwidthstr_len).c_str()
);
if(line_debug) {
std::cout
<< std::setprecision(5)
@ -400,7 +400,7 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
getline(inputfile,inputline);
}
if(agn::debug) std::cout
<< "\nAdding point to grid (size "
<< "\nAdding point to grid ("
<< grid.size()
<< " of "
<< coordlist.size()

9
src/create_fort_files.cpp
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@ -37,6 +37,15 @@ int main(int argc, char const *argv[]) {
int num_zeroes=0;
while(table_it != tables.end()) {
if(agn::is_zero(*table_it)) {
std::string linetype = table_it->header[0].substr(0,4);
if (linetype == "nFnu" ||
linetype == "nInu" ||
linetype == "InwT" ||
linetype == "InwC") {
table_it++;
continue;
}
zeroreport << " "
<< table_it->header[0]
<< std::endl;