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@ -1,314 +0,0 @@
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#!/bin/bash
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script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
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basedir=`pwd`
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# Script to prepare input fort files for Dr. Korista's use, starting from
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# an unmodified cloudy grid output file.
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# Separate grid output into individual files.
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$script_dir/operations/split_grid_output_hden_phi.sh $1
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cd gridoutput
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# Create fort tables for these sets of emission lines. Multiplets defined below.
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Inci_lines="1215.00A 4860.00A"
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TOTL_lines="1215.68A"
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HI_lines="1215.68A 1025.73A 972.543A 949.749A 937.809A 6562.85A 4861.36A 4340.49A 4101.76A 3970.09A 3889.07A 1.87511m 1.28181m 1.09381m 1.00494m 9545.99A 9229.03A 2.16553m"
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HeII_lines="1640.00A 1215.23A 1085.03A 1025.35A 992.439A 972.186A 4686.01A 3203.30A 2733.46A 1.01242m 6560.44A 5411.80A 4859.57A 4541.82A 4338.89A 4200.05A 4100.25A 4025.81A 3968.64A"
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HeI_lines="3888.63A 2.05813m 5015.68A 7065.18A 5875.61A 4713.02A 4471.47A 4120.81A 7281.35A 6678.15A 5047.64A 4921.93A 4437.55A 4387.93A"
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metal_lines="C 1 1656.00A
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TOTL 2326.00A
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C 2 2325.00A
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C 2 2324.00A
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C 2 2329.00A
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C 2 2328.00A
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C 2 2327.00A
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C 2 1335.00A
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C 3 977.000A
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TOTL 1909.00A
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C 3 1910.00A
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C 3 1176.00A
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TOTL 1549.00A
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C 4 1551.00A
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C 4 1548.00A
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N 1 1200.00A
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N 2 2141.00A
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N 2 1085.00A
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TOTL 1750.00A
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N 3 1749.00A
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N 3 1747.00A
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N 3 1754.00A
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N 3 1752.00A
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N 3 1751.00A
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N 3 991.000A
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TOTL 1486.00A
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N 4 1486.00A
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N 4 765.000A
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TOTL 1240.00A
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N 5 1243.00A
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N 5 1239.00A
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6lev 8446.00A
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6lev 1304.00A
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TOTL 1665.00A
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O 3 1661.00A
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O 3 1666.00A
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O 3 835.000A
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TOTL 1402.00A
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O 4 1400.00A
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O 4 1397.00A
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O 4 1407.00A
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O 4 1405.00A
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O 4 1401.00A
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O 4 789.000A
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O 5 630.000A
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TOTL 1218.00A
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O 5 1218.00A
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TOTL 1035.00A
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O 6 1031.93A
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O 6 1037.62A
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Ne 5 1141.00A
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TOTL 774.000A
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Ne 8 770.404A
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Ne 8 780.324A
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Na 1 5891.94A
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Mg 1 2853.00A
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TOTL 2798.00A
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Mg 2 2795.53A
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Mg 2 2802.71A
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TOTL 615.000A
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Mg10 609.793A
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Mg10 624.941A
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totl 2665.00A
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Al 2 2670.00A
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TOTL 1860.00A
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Al 3 1855.00A
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Al 3 1863.00A
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TOTL 2335.00A
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Si 2 2334.00A
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Si 2 2329.00A
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Si 2 2350.00A
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Si 2 2344.00A
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Si 2 2336.00A
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Si 2 1813.99A
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Si 2 1531.00A
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Si 2 1307.66A
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Si 2 1263.32A
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Si 3 1207.00A
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TOTL 1888.00A
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Si 3 1892.00A
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PHOT 1895.00A
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TOTL 1397.00A
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Si 4 1403.00A
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Si 4 1394.00A
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S 2 1256.00A
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S 3 1720.00A
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S 3 1197.56A
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TOTL 1406.00A
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S 4 1405.00A
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S 4 1398.00A
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S 4 1424.00A
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S 4 1417.00A
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S 4 1406.00A
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TOTL 1198.00A
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S 5 1198.00A
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S 5 786.473A
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S 6 944.524A
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S 6 933.380A
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Ca2K 3934.00A
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Ca2H 3969.00A
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Ca2X 8498.00A
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Ca2Y 8542.00A
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Ca2Z 8662.00A
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Fe 2 1500.00A
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Fe 2 1.15000m
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Fe 2 2500.00A
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Fe 2 2300.00A
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Fe 2 8900.00A
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Fe 2 1786.00A
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Fe 3 1125.79A
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FeKa 1.78000A"
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continuum_lines="4.11370m 2.32440m 1.64313m 1.48022m 1.43649m 1.11867m 8329.68A 8078.61A 6209.66A 4885.36A 3704.34A 3587.67A 2430.05A 2392.03A 2071.34A 2052.68A 1793.44A 1585.12A 1458.33A 1356.96A 1297.29A 1262.79A 1218.08A 1196.33A 1175.06A 1143.64A 1113.22A 1103.23A 1073.86A 1064.34A 1035.92A 1000.00A 925.144A 897.800A 760.023A 701.514A 608.160A 575.146A 511.948A 496.874A 399.153A 910.000A 913.000A 1650.00A 1900.00A 3644.00A 3648.00A 5100.00A 6500.00A 7000.00A 7500.00A 8000.00A 8204.00A 8207.00A 8500.00A 9000.00A 9500.00A 10000.0A 1.05000m 1.10000m"
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fortfile_number=10
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echo "Aggregating flux (scaled) tables from grid."
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echo " "
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echo "Characteristics"
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echo "---------------"
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for wavelength in $Inci_lines; do
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "Inci ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "Inci ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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done
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for wavelength in $TOTL_lines; do
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "TOTL ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "TOTL ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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done
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echo " "
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echo "H(I) Series"
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echo "-------------"
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for wavelength in $HI_lines; do
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "H 1 ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "H 1 ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "H 1 ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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done
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echo " "
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echo "He(II) Series"
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echo "-----------"
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for wavelength in $HeII_lines; do
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "He 2 ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "He 2 ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "He 2 ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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done
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echo " "
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echo "He(I) Series"
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echo "----------"
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wavelength="1.08299m"
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ref_hden="10.25"
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ref_phi="20.00"
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num_components=`${script_dir}/operations/count_components.sh "TOTL ${wavelength}" $ref_hden $ref_phi`
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component_list=`${script_dir}/operations/find_components.sh "TOTL ${wavelength}" $ref_hden $ref_phi`
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "TOTL ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "TOTL ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "TOTL ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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comp_wavelength=`echo "$component_list"|sed -n 1p|sed 's#^......\(........\).*$#\1#'`
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for component in `seq 1 $num_components`; do
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comp_identifier=`echo "$component_list"|sed -n ${component}p|sed 's#^.\(.............\).*$#\1#'`
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next_wavelength=`echo "$component_list"|sed -n $((component+1))p|sed 's#^......\(........\).*$#\1#'`
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if [[ "$comp_wavelength" == "$next_wavelength" ]]; then
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_previous_total_line_flux.sh "${comp_identifier}" $((component-1)) > tmp.scaledtable.${fortfile_number}
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echo "${comp_identifier} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_previous_inward_line_flux.sh "${comp_identifier}" $((component-1)) > tmp.scaledtable.${fortfile_number}
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echo "Inwd ${comp_wavelength} -> tmp.scaledtable.${fortfile_number}"
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else
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "${comp_identifier}" $((component-1)) > tmp.scaledtable.${fortfile_number}
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echo "${comp_identifier} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "${comp_identifier}" $((component-1)) > tmp.scaledtable.${fortfile_number}
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echo "Inwd ${comp_wavelength} -> tmp.scaledtable.${fortfile_number}"
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fi
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comp_wavelength=${next_wavelength}
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done
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for wavelength in $HeI_lines; do
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "He 1 ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "He 1 ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "He 1 ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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done
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echo " "
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echo "Heavy Elements"
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echo "--------------"
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num_lines=`echo "$metal_lines"|wc -l|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
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for line_index in `seq 1 $num_lines`; do
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line_id=`echo "${metal_lines}"|sed -n ${line_index}p`
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wavelength=`echo "$line_id"|sed 's#.....\(........\).*#\1#'`
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "${line_id}" > tmp.scaledtable.${fortfile_number}
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echo "${line_id} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "${line_id}" > tmp.scaledtable.${fortfile_number}
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echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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done
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echo " "
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echo "Continua"
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echo "--------"
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for wavelength in $continuum_lines; do
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "nFnu ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "nFnu ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "nInu ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "nInu ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "InwT ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "InwT ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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(( fortfile_number++ ))
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${script_dir}/operations/aggregate_table_for_total_line_flux.sh "InwC ${wavelength}" > tmp.scaledtable.${fortfile_number}
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echo "InwC ${wavelength} -> tmp.scaledtable.${fortfile_number}"
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#(( fortfile_number++ ))
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#${script_dir}/operations/aggregate_table_for_total_line_flux.sh "InwT ${wavelength}" > tmp.totreflcont.${fortfile_number}
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#echo -n "InwT ${wavelength} -> tmp.totreflcont.${fortfile_number}, "
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#${script_dir}/operations/aggregate_table_for_total_line_flux.sh "InwC ${wavelength}" > tmp.increflcont.${fortfile_number}
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#echo "InwC ${wavelength} -> tmp.increflcont.${fortfile_number}"
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#${script_dir}/../bin/output_difference_table tmp.totreflcont.${fortfile_number} tmp.increflcont.${fortfile_number} > tmp.scaledtable.${fortfile_number}
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#echo "tmp.totreflcont.${fortfile_number} - tmp.increflcont.${fortfile_number} -> tmp.scaledtable.${fortfile_number}"
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done
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num=10
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echo " "
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echo "Computing relative intensity tables for all scaled tables."
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for scaledtable in `echo tmp.scaledtable.*`; do
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num=`echo "$scaledtable"|sed 's#^tmp\.scaledtable\.\(.*\)$#\1#'`
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#(( num++ ))
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newtable=fort.$num
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${script_dir}/../bin/sort_and_normalize_table $scaledtable > $newtable
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echo "$scaledtable -> $newtable"
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done
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echo " "
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echo "Filing and cleaning."
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mkdir -p ${basedir}/fortfiles
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mv fort.* ${basedir}/fortfiles
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cd ${basedir}/fortfiles
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tar zcf ${basedir}/fortfiles.tar.gz *
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cd ${basedir}
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# ${script_dir}/util/cleantmp.sh
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echo "Archive generated. Done."
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exit 0
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@ -1,12 +0,0 @@
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#!/bin/bash
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# This script not generalized. Use with caution.
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mkdir fortfiles
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cd fortfiles
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../../../../../bin/create_fort_files ../mpi_grid.out ../../../../../reference/linelist
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../../../../../scripts/meta/bulk_interpolation_fix.sh fort.* >> interpolation_report
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tar cf ../fortfiles_4thdex_ngc5548_mehdipour_cldn24.tar fort.*
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cd ..
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gzip fortfiles_4thdex_ngc5548_mehdipour_cldn24.tar
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echo done
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