Added Scripts

This commit is contained in:
caes 2015-10-10 23:14:55 -04:00
parent 95f9f04318
commit e65a755dd9
987 changed files with 4565 additions and 1425 deletions

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#!/bin/bash
# find line number for final emergent line intensities
# Find and display these sets of emission lines.
# wavelengths in Angstroms
Ba_set="6562.85A 4861.36A 4340.49A 4101.76A 3970.09A"
Ly_set="1215.68A 1025.73A 972.543A 949.749A"
Pa_set="1.28181m 1.09381m 1.00494m 9545.99A 9229.03A"
HeII_set="1640.00A 4686.01A"
HeI_set="5875.61A 1.08299m 6678.15A 4471.47A 3888.63A 5015.68A"
C_IV_set="1549.00A 1551.00A 1548.00A"
Mg_II_set="2798.00A"
cloudy_output_file=$1
emergent_lines_start=`grep -n "Emergent line intensities" $cloudy_output_file|tail -n1|sed 's@\([0-9]*\):.*@\1@'`
total_lines=`wc -l $cloudy_output_file|sed 's#^[^0-9]*\([0-9]*\) .*$#\1#'`
echo "Requested Emergent Emission Line Fluxes"
echo "======================================"
echo "Run parameters"
echo "--------------"
HDEN=`grep 'HDEN=' $cloudy_output_file|tail -n1|sed 's#^[^0-9]*\([0-9.]*\) LOG.*$#\1#'`
PHIH=`grep 'phi(h) ' $cloudy_output_file|tail -n1|sed 's#^[^0-9]*\([0-9.]*\) LOG.*$#\1#'`
echo "hden = ${HDEN}"
echo "phi(h) = ${PHIH}"
echo " "
echo "Unit Intensity"
echo "--------------"
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep 1.0000
echo " "
# Extract hydrogen sets
echo -n "Balmer Series"
list_size=`echo $Ba_set|wc -w|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
echo " (seeking ${list_size})"
echo "-------------"
for emission_line in $Ba_set; do
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "H 1 ${emission_line}"
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "Inwd ${emission_line}"
done
echo " "
echo -n "Lyman Series"
list_size=`echo $Ly_set|wc -w|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
echo " (seeking ${list_size})"
echo "------------"
for emission_line in $Ly_set; do
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "H 1 ${emission_line}"
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "Inwd ${emission_line}"
done
echo " "
echo -n "Paschen Series"
list_size=`echo $Pa_set|wc -w|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
echo " (seeking ${list_size})"
echo "------------"
for emission_line in $Pa_set; do
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "H 1 ${emission_line}"
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "Inwd ${emission_line}"
done
echo " "
echo -n "HeII Selected Lines"
list_size=`echo $HeII_set|wc -w|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
echo " (seeking ${list_size})"
echo "-------------------"
for emission_line in $HeII_set; do
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "He 2 ${emission_line}"
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "Inwd ${emission_line}"
done
echo " "
echo -n "HeI Selected Lines"
list_size=`echo $HeI_set|wc -w|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
echo " (seeking ${list_size})"
echo "------------------"
for emission_line in $HeI_set; do
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "He 1 ${emission_line}"
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "Inwd ${emission_line}"
done
echo " "
echo -n "C_IV Selected Lines"
list_size=`echo $C_IV_set|wc -w|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
echo " (seeking ${list_size})"
echo "-------------------"
for emission_line in $C_IV_set; do
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "${emission_line}"
done
echo " "
echo -n "Mg_II Selected Lines"
list_size=`echo $Mg_II_set|wc -w|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
echo " (seeking ${list_size})"
echo "--------------------"
for emission_line in $Mg_II_set; do
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep "${emission_line}"
done
echo " "

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#!/usr/local/bin/bash
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
continuum_file=$1
echo Producing scatter plot for incident continuum from $continuum_file
cut -f1,2 $continuum_file >> tmp.cont.xy

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scripts/analysis/multiplets.sh Executable file
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cloudy_output_file=$1
emergent_lines_start=`grep -n "^\s*Emergent line intensities\s*$" $cloudy_output_file|tail -n1|sed 's@\([0-9]*\):.*@\1@'`
total_lines=`wc -l $cloudy_output_file|sed 's@^\([0-9]*\)[^0-9]*.*$@\1@'`
emission_line_list=`sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file`
echo "Requested Emergent Emission Line Fluxes"
echo "======================================"
echo "Unit Intensity"
echo "--------------"
sed -n $emergent_lines_start,${total_lines}p $cloudy_output_file|grep 1.0000
echo " "
# Possible Multiplets - Rough
echo -n "Possible Multiplets - Rough"
TOTL_lines=`grep -n TOTL $cloudy_output_file|sed 's#\([0-9]\): TOTL.*#\1#'`
list_size=`echo $TOTL_lines|wc -w`
echo " (found ${list_size})"
echo "-------------"
for line_number in $TOTL_lines; do
sed -n $line_number,$((line_number+14))p $cloudy_output_file
echo "==================================================="
done
echo " "

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scripts/cloudy/mpi.in Executable file
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////// CLOUDY 13.03 grid run as hypothetical values for AGN observation
//
title AGN BLR grid hden_vs_phi .25 dex
//
// Arguments varied for this grid:
// log of incident intensity from 17 to 24
// log of hydrogen density from 7 to 14
//
////// Output continua
//
save last incident continuum "incident_continuum"
//
////// Formatting
//
print line column
print line inward
print line iso collapsed
print line faint -3
print last
print short
set line precision 6
//
////// Resolved energy states for atomic models
//
// Defaults: 10, 10, 6
//
atom H-like element hydrogen resolved levels 10
atom H-like element helium resolved levels 10
atom He-like element helium resolved levels 6
//
////// Prevent cloudy from stopping prematurely
//
set nend 5000
//
////// Threshold for emission line inclusion
//
print line faint -3
//
////// Print diffuse continuum information in cloudy output
// and include additional spectral resolution around Lyman, Briggs, Etc.
//
// diffuse_inward can be calculated with (InwT - InwC = InwDiffuse)
//
print continuum
set nFnu diffuse_outward, diffuse_inward, incident_reflected
set nFnu add 910A
set nFnu add 913A
set nFnu add 1650A
set nFnu add 1900A
set nFnu add 3645A
set nFnu add 3648A
set nFnu add 5100A
set nFnu add 6500A
set nFnu add 7000A
set nFnu add 7500A
set nFnu add 8000A
set nFnu add 8204A
set nFnu add 8207A
set nFnu add 8500A
set nFnu add 9000A
set nFnu add 9500A
set nFnu add 10000A
set nFnu add 10500A
set nFnu add 11000A
//
////// Print equivalent widths
//
normalize to 1215 scale to 1215
//
////// Background radiation
//
background z = 0.0172
//
////// Hydrogen density of cloud is varied
//
hden 11 vary
grid range from 7 to 14 with .25 dex
//
////// Central AGN source shape generated by external program
//
interpolate (1.001e-09 1e-36)
continue (0.000734986 -33) (0.000746929 -33.007) (0.000759066 -33.014) (0.000771399 -33.021) (0.000783934 -33.028)
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continue (0.0031353 -15.0571) (0.00318625 -14.8403) (0.00323802 -14.627) (0.00329063 -14.4173) (0.0033441 -14.2109)
continue (0.00339844 -14.008) (0.00345366 -13.8084) (0.00350978 -13.612) (0.0035668 -13.4188) (0.00362476 -13.2288)
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continue (0.544853 -1.32434) (0.553706 -1.33031) (0.562703 -1.33634) (0.571846 -1.34241) (0.581138 -1.34854)
continue (0.590581 -1.35472) (0.600177 -1.36094) (0.609929 -1.36721) (0.61984 -1.37353) (0.629911 -1.3799)
continue (0.640146 -1.38631) (0.650548 -1.39277) (0.661119 -1.39927) (0.671861 -1.40582) (0.682778 -1.41241)
continue (0.693872 -1.41904) (0.705146 -1.42571) (0.716604 -1.43242) (0.728248 -1.43918) (0.740081 -1.44597)
continue (0.752107 -1.45281) (0.764327 -1.45968) (0.776747 -1.46659) (0.789368 -1.47354) (0.802194 -1.48053)
continue (0.815228 -1.48755) (0.828475 -1.49461) (0.841937 -1.50171) (0.855617 -1.50884) (0.86952 -1.51601)
continue (0.883648 -1.52321) (0.898006 -1.53044) (0.912598 -1.53771) (0.927426 -1.54501) (0.942496 -1.55234)
continue (0.95781 -1.5597) (0.973373 -1.5671) (0.989189 -1.57453) (1.00526 -1.58198) (1.0216 -1.58947)
continue (1.0382 -1.59699) (1.05507 -1.60453) (1.07221 -1.61211) (1.08963 -1.61971) (1.10734 -1.62735)
continue (1.12533 -1.63501) (1.14361 -1.6427) (1.1622 -1.65041) (1.18108 -1.65816) (1.20027 -1.66593)
continue (1.21977 -1.67372) (1.23959 -1.68154) (1.25974 -1.68939) (1.2802 -1.69726) (1.30101 -1.70516)
continue (1.32215 -1.71308) (1.34363 -1.72103) (1.36546 -1.729) (1.38765 -1.737) (1.4102 -1.74501)
continue (1.43311 -1.75306) (1.4564 -1.76112) (1.48006 -1.76921) (1.50411 -1.77732) (1.52855 -1.78545)
continue (1.55339 -1.79361) (1.57863 -1.80178) (1.60428 -1.80998) (1.63034 -1.8182) (1.65684 -1.82644)
continue (1.68376 -1.83471) (1.71112 -1.84299) (1.73892 -1.85129) (1.76717 -1.85962) (1.79589 -1.86796)
continue (1.82507 -1.87633) (1.85472 -1.88471) (1.88486 -1.89312) (1.91549 -1.90154) (1.94661 -1.90999)
continue (1.97824 -1.91845) (2.01039 -1.92693) (2.04305 -1.93543) (2.07625 -1.94395) (2.10998 -1.95249)
continue (2.14427 -1.96105) (2.17911 -1.96963) (2.21452 -1.97822) (2.2505 -1.98683) (2.28707 -1.99546)
continue (2.32423 -2.00411) (2.362 -2.01278) (2.40038 -2.02146) (2.43938 -2.03017) (2.47902 -2.03889)
continue (2.5193 -2.04763) (2.56023 -2.05638) (2.60183 -2.06515) (2.64411 -2.07394) (2.68707 -2.08275)
continue (2.73073 -2.09158) (2.7751 -2.10042) (2.8202 -2.10928) (2.86602 -2.11815) (2.91259 -2.12705)
continue (2.95992 -2.13596) (3.00801 -2.14489) (3.05689 -2.15383) (3.10656 -2.16279) (3.15703 -2.17177)
continue (3.20833 -2.18076) (3.26046 -2.18977) (3.31344 -2.1988) (3.36728 -2.20785) (3.42199 -2.21691)
continue (3.4776 -2.22599) (3.5341 -2.23508) (3.59153 -2.24419) (3.64989 -2.25332) (3.70919 -2.26247)
continue (3.76946 -2.27163) (3.83071 -2.28081) (3.89295 -2.29) (3.95621 -2.29922) (4.02049 -2.30845)
continue (4.08582 -2.31769) (4.15221 -2.32695) (4.21968 -2.33623) (4.28824 -2.34553) (4.35792 -2.35484)
continue (4.42873 -2.36417) (4.50069 -2.37352) (4.57382 -2.38288) (4.64814 -2.39227) (4.72367 -2.40166)
continue (4.80042 -2.41108) (4.87842 -2.42051) (4.95769 -2.42996) (5.03825 -2.43943) (5.12011 -2.44892)
continue (5.20331 -2.45842) (5.28785 -2.46794) (5.37377 -2.47747) (5.46109 -2.48703) (5.54983 -2.4966)
continue (5.64 -2.50619) (5.73165 -2.5158) (5.82478 -2.52543) (5.91942 -2.53507) (6.01561 -2.54473)
continue (6.11335 -2.55441) (6.21269 -2.56411) (6.31363 -2.57383) (6.41622 -2.58356) (6.52048 -2.59331)
continue (6.62643 -2.60308) (6.7341 -2.61287) (6.84352 -2.62268) (6.95472 -2.63251) (7.06772 -2.64236)
continue (7.18256 -2.65222) (7.29927 -2.6621) (7.41787 -2.67201) (7.5384 -2.68193) (7.66089 -2.69187)
continue (7.78537 -2.70183) (7.91187 -2.71181) (8.04043 -2.7218) (8.17108 -2.73182) (8.30385 -2.74186)
continue (8.43877 -2.75191) (8.57589 -2.76199) (8.71524 -2.77208) (8.85685 -2.7822) (9.00076 -2.79233)
continue (9.14701 -2.80248) (9.29564 -2.81266) (9.44668 -2.82285) (9.60018 -2.83306) (9.75617 -2.84329)
continue (9.91469 -2.85354) (10.0758 -2.86381) (10.2395 -2.8741) (10.4059 -2.88442) (10.575 -2.89475)
continue (10.7468 -2.90509) (10.9214 -2.91546) (11.0989 -2.92585) (11.2792 -2.93626) (11.4625 -2.94669)
continue (11.6488 -2.95714) (11.838 -2.9676) (12.0304 -2.97809) (12.2259 -2.98859) (12.4245 -2.99911)
continue (12.6264 -3.00966) (12.8316 -3.02022) (13.0401 -3.03079) (13.2519 -3.04139) (13.4673 -3.05201)
continue (13.6861 -3.06264) (13.9085 -3.07329) (14.1345 -3.08396) (14.3641 -3.09464) (14.5975 -3.10535)
continue (14.8347 -3.11606) (15.0758 -3.1268) (15.3207 -3.13755) (15.5697 -3.14832) (15.8227 -3.1591)
continue (16.0798 -3.16989) (16.341 -3.1807) (16.6065 -3.19153) (16.8764 -3.20237) (17.1506 -3.21322)
continue (17.4293 -3.22408) (17.7125 -3.23495) (18.0003 -3.24584) (18.2928 -3.25674) (18.59 -3.26764)
continue (18.8921 -3.27856) (19.199 -3.28948) (19.511 -3.30042) (19.828 -3.31135) (20.1502 -3.3223)
continue (20.4776 -3.33325) (20.8103 -3.34421) (21.1485 -3.35516) (21.4921 -3.36612) (21.8413 -3.37709)
continue (22.1962 -3.38805) (22.5569 -3.39901) (22.9234 -3.40997) (23.2959 -3.42093) (23.6744 -3.43189)
continue (24.0591 -3.44284) (24.45 -3.45378) (24.8473 -3.46472) (25.251 -3.47564) (25.6613 -3.48656)
continue (26.0783 -3.49746) (26.502 -3.50835) (26.9327 -3.51923) (27.3703 -3.53009) (27.815 -3.54093)
continue (28.267 -3.55175) (28.7263 -3.56255) (29.193 -3.57333) (29.6674 -3.58408) (30.1494 -3.59481)
continue (30.6393 -3.60551) (31.1372 -3.61617) (31.6431 -3.62681) (32.1573 -3.63741) (32.6798 -3.64798)
continue (33.2108 -3.65851) (33.7504 -3.669) (34.2988 -3.67945) (34.8561 -3.68985) (35.4225 -3.70021)
continue (35.9981 -3.71053) (36.583 -3.72079) (37.1774 -3.731) (37.7815 -3.74116) (38.3954 -3.75127)
continue (39.0193 -3.76131) (39.6533 -3.7713) (40.2976 -3.78123) (40.9524 -3.79109) (41.6178 -3.80089)
continue (42.2941 -3.81062) (42.9813 -3.82028) (43.6797 -3.82988) (44.3894 -3.8394) (45.1107 -3.84884)
continue (45.8437 -3.85822) (46.5886 -3.86751) (47.3456 -3.87673) (48.1149 -3.88586) (48.8967 -3.89492)
continue (49.6912 -3.90389) (50.4986 -3.91278) (51.3191 -3.92159) (52.153 -3.93031) (53.0004 -3.93894)
continue (53.8616 -3.94749) (54.7368 -3.95595) (55.6262 -3.96431) (56.53 -3.97259) (57.4486 -3.98078)
continue (58.3821 -3.98888) (59.3307 -3.99689) (60.2947 -4.00481) (61.2744 -4.01264) (62.2701 -4.02038)
continue (63.2819 -4.02803) (64.3101 -4.03558) (65.3551 -4.04305) (66.417 -4.05043) (67.4962 -4.05773)
continue (68.5929 -4.06493) (69.7075 -4.07205) (70.8401 -4.07908) (71.9912 -4.08603) (73.161 -4.09289)
continue (74.3497 -4.09968) (75.5578 -4.10638) (76.7855 -4.113) (78.0332 -4.11954) (79.3011 -4.12601)
continue (80.5897 -4.1324) (81.8991 -4.13872) (83.2299 -4.14496) (84.5823 -4.15114) (85.9566 -4.15725)
continue (87.3533 -4.16329) (88.7727 -4.16926) (90.2151 -4.17517) (91.681 -4.18103) (93.1707 -4.18682)
continue (94.6846 -4.19255) (96.2231 -4.19823) (97.7866 -4.20386) (99.3755 -4.20943) (100.99 -4.21496)
continue (102.631 -4.22044) (104.299 -4.22587) (105.994 -4.23125) (107.716 -4.2366) (109.466 -4.2419)
continue (111.245 -4.24717) (113.052 -4.2524) (114.889 -4.25759) (116.756 -4.26275) (118.653 -4.26788)
continue (120.581 -4.27298) (122.54 -4.27805) (124.532 -4.28309) (126.555 -4.28811) (128.611 -4.29311)
continue (130.701 -4.29808) (132.825 -4.30303) (134.983 -4.30795) (137.176 -4.31286) (139.405 -4.31776)
continue (141.67 -4.32263) (143.972 -4.32749) (146.312 -4.33234) (148.689 -4.33717) (151.105 -4.34199)
continue (153.56 -4.3468) (156.056 -4.3516) (158.591 -4.35638) (161.168 -4.36116) (163.787 -4.36593)
continue (166.448 -4.37069) (169.153 -4.37545) (171.901 -4.38019) (174.695 -4.38493) (177.533 -4.38967)
continue (180.418 -4.3944) (183.349 -4.39913) (186.329 -4.40385) (189.356 -4.40857) (192.433 -4.41328)
continue (195.56 -4.418) (198.737 -4.4227) (201.967 -4.42741) (205.248 -4.43212) (208.583 -4.43682)
continue (211.972 -4.44152) (215.417 -4.44622) (218.917 -4.45091) (222.474 -4.45561) (226.089 -4.4603)
continue (229.763 -4.465) (233.496 -4.46969) (237.29 -4.47438) (241.146 -4.47908) (245.064 -4.48377)
continue (249.046 -4.48846) (253.093 -4.49315) (257.205 -4.49784) (261.384 -4.50253) (265.631 -4.50722)
continue (269.948 -4.5119) (274.334 -4.51659) (278.791 -4.52128) (283.321 -4.52597) (287.925 -4.53066)
continue (292.603 -4.53535) (297.358 -4.54004) (302.189 -4.54472) (307.1 -4.54941) (312.09 -4.5541)
continue (317.161 -4.55879) (322.314 -4.56348) (327.551 -4.56816) (332.874 -4.57285) (338.282 -4.57754)
continue (343.779 -4.58223) (349.365 -4.58692) (355.042 -4.5916) (360.811 -4.59629) (366.673 -4.60098)
continue (372.631 -4.60567) (378.686 -4.61036) (384.839 -4.61504) (391.092 -4.61973) (397.447 -4.62442)
continue (403.905 -4.62911) (410.468 -4.6338) (417.138 -4.63849) (423.916 -4.64317) (430.804 -4.64786)
continue (437.804 -4.65255) (444.917 -4.65724) (452.147 -4.66193) (459.493 -4.66662) (466.96 -4.6713)
continue (474.547 -4.67599) (482.258 -4.68068) (490.094 -4.68537) (498.057 -4.69006) (506.15 -4.69475)
continue (514.374 -4.69944) (522.732 -4.70412) (531.226 -4.70881) (539.858 -4.7135) (548.63 -4.71819)
continue (557.544 -4.72288) (566.604 -4.72757) (575.81 -4.73226) (585.166 -4.73695) (594.675 -4.74163)
continue (604.337 -4.74632) (614.157 -4.75101) (624.136 -4.7557) (634.278 -4.76039) (644.584 -4.76508)
continue (655.057 -4.76977) (665.701 -4.77446) (676.518 -4.77915) (687.511 -4.78383) (698.682 -4.78852)
continue (710.034 -4.79321) (721.571 -4.7979) (733.296 -4.80259) (745.211 -4.80728) (757.32 -4.81197)
continue (769.625 -4.81666) (782.131 -4.82135) (794.839 -4.82604) (807.754 -4.83073) (820.879 -4.83541)
continue (834.218 -4.8401) (847.773 -4.84479) (861.548 -4.84948) (875.547 -4.85417) (889.773 -4.85886)
continue (904.231 -4.86355) (918.923 -4.86824) (933.855 -4.87293) (949.029 -4.87762) (964.449 -4.88231)
continue (980.12 -4.887) (996.046 -4.89169) (1012.23 -4.89637) (1028.68 -4.90106) (1045.39 -4.90575)
continue (1062.38 -4.91044) (1079.64 -4.91513) (1097.18 -4.91982) (1115.01 -4.92451) (1133.13 -4.9292)
continue (1151.54 -4.93389) (1170.25 -4.93858) (1189.27 -4.94327) (1208.59 -4.94796) (1228.23 -4.95265)
continue (1248.19 -4.95734) (1268.47 -4.96203) (1289.08 -4.96672) (1310.02 -4.9714) (1331.31 -4.97609)
continue (1352.94 -4.98078) (1374.93 -4.98547) (1397.27 -4.99016) (1419.97 -4.99485) (1443.04 -4.99954)
continue (1466.49 -5.00423) (1490.32 -5.00892) (1514.54 -5.01361) (1539.14 -5.0183) (1564.15 -5.02299)
continue (1589.57 -5.02768) (1615.4 -5.03237) (1641.65 -5.03706) (1668.32 -5.04175) (1695.43 -5.04644)
continue (1722.98 -5.05113) (1750.97 -5.05582) (1779.42 -5.06051) (1808.34 -5.0652) (1837.72 -5.06989)
continue (1867.58 -5.07457) (1897.93 -5.07926) (1928.77 -5.08395) (1960.11 -5.08864) (1991.95 -5.09333)
continue (2024.32 -5.09802) (2057.21 -5.10271) (2090.64 -5.1074) (2124.61 -5.11209) (2159.13 -5.11678)
continue (2194.22 -5.12147) (2229.87 -5.12616) (2266.1 -5.13085) (2302.92 -5.13554) (2340.34 -5.14023)
continue (2378.37 -5.14492) (2417.02 -5.14961) (2456.29 -5.1543) (2496.2 -5.15899) (2536.76 -5.16368)
continue (2577.98 -5.16837) (2619.87 -5.17306) (2662.44 -5.17775) (2705.7 -5.18244) (2749.66 -5.18713)
continue (2794.34 -5.19182) (2839.75 -5.19651) (2885.89 -5.2012) (2932.78 -5.20589) (2980.43 -5.21058)
continue (3028.86 -5.21527) (3078.08 -5.21996) (3128.09 -5.22465) (3178.92 -5.22934) (3230.57 -5.23402)
continue (3283.06 -5.23871) (3336.41 -5.2434) (3390.62 -5.24809) (3445.71 -5.25278) (3501.7 -5.25747)
continue (3558.6 -5.26216) (3616.42 -5.26685) (3675.19 -5.27154) (3734.9 -5.27623) (3795.59 -5.28092)
continue (3857.26 -5.28561) (3919.94 -5.2903) (3983.63 -5.29499) (4048.36 -5.29968) (4114.14 -5.30437)
continue (4180.99 -5.30906) (4248.93 -5.31375) (4317.97 -5.31844) (4388.13 -5.32313) (4459.43 -5.32782)
continue (4531.89 -5.33251) (4605.53 -5.3372) (4680.36 -5.34189) (4756.41 -5.34658) (4833.7 -5.35127)
continue (4912.24 -5.35596) (4992.05 -5.36065) (5073.17 -5.36534) (5155.6 -5.37003) (5239.37 -5.37472)
continue (5324.51 -5.37941) (5411.02 -5.3841) (5498.94 -5.38879) (5588.3 -5.39348) (5679.1 -5.39817)
continue (5771.38 -5.40286) (5865.15 -5.40755) (5960.45 -5.41224) (6057.3 -5.41693) (6155.73 -5.42162)
continue (6255.75 -5.42631) (6357.4 -5.431) (6460.7 -5.43569) (6565.67 -5.44038) (6672.36 -5.44507)
continue (6780.78 -5.44976) (6890.95 -5.45445) (7002.92 -5.45914) (7116.71 -5.46383) (7232.35 -5.46852)
continue (7349.86 -5.47321)(73498.6 -7.47321)(734986 -9.47321)(7.34986e+06 -11.4732)(7.34986e+07 -13.4732)
//
////// Flux is varied
//
phi(h) 23 vary
grid range from 17 to 24 with .25 dex
//
////// Stopping condition and run
//
stop total column density 23
iterate to convergence

View File

@ -0,0 +1,274 @@
////// CLOUDY 13.03 GRID run as hypothetical values for AGN observation
//
title AGN BLR grid phi_vs_hden
//
// Arguments varied for this grid:
// log of incident intensity from 18 to 23
// log of hydrogen density from 8 to 13
//
////// Output information to these files
//
save last continuum "continuum_full"
save last raw continuum "continuum_raw"
save last incident continuum "continuum_incident"
//
////// Formatting
//
print line column
print line inward
print line iso collapsed
set line precision 6
//
////// Resolved energy states for atomic models
//
// Defaults:
atom H-like element hydrogen levels resolved 10
atom H-like element helium levels resolved 10
atom He-like element levels resolved 6
//
//atom H-like element hydrogen levels resolved 18
//atom He-like element helium levels resolved 15
//atom H-like element helium levels resolved 15
//
////// I forget what this does
//
set nend 5000
//
////// Need to find command to decrease threshold for included emission lines
//
//
//
////// Include additional spectral resolution around Lyman, Briggs, Etc.
//
//set nFnu
// Accepted units: : eV, keV, MeV, Hz, kHz, MHz, GHz, Angstrom,
// nm, micron, mm, cm or centimeter, wavenumbers, erg, ryd, K, Kelvin
//set nFnu add 1 ryd
//
////// For equivalent widths
//
//normalize to 1215 scale to 1215
//
////// Background radiation
//
background z = 0.0172
//
////// Central AGN source shape generated by external program
//
interpolate (1.001e-09 1e-36)
continue (0.000734986 -33) (0.000746929 -33.007) (0.000759066 -33.014) (0.000771399 -33.021) (0.000783934 -33.028)
continue (0.000796672 -33.035) (0.000809616 -33.042) (0.000822772 -33.049) (0.000836141 -33.056) (0.000849727 -33.063)
continue (0.000863534 -33.07) (0.000877565 -33.077) (0.000891824 -33.084) (0.000906315 -33.091) (0.000921042 -33.098)
continue (0.000936008 -33.105) (0.000951216 -33.112) (0.000966672 -33.119) (0.00098238 -33.126) (0.000998342 -33.133)
continue (0.00101456 -33.14) (0.00103105 -33.147) (0.0010478 -33.154) (0.00106483 -33.161) (0.00108213 -33.168)
continue (0.00109971 -33.175) (0.00111758 -33.182) (0.00113574 -33.189) (0.0011542 -33.196) (0.00117295 -33.203)
continue (0.00119201 -33.21) (0.00121138 -33.2169) (0.00123106 -33.2236) (0.00125106 -33.2294) (0.00127139 -33.2321)
continue (0.00129205 -33.2245) (0.00131304 -33.1847) (0.00133438 -33.0632) (0.00135606 -32.8038) (0.0013781 -32.4153)
continue (0.00140049 -31.9597) (0.00142324 -31.483) (0.00144637 -31.0045) (0.00146987 -30.5306) (0.00149375 -30.0633)
continue (0.00151803 -29.6033) (0.00154269 -29.1506) (0.00156776 -28.7052) (0.00159323 -28.267) (0.00161912 -27.8359)
continue (0.00164543 -27.4117) (0.00167217 -26.9944) (0.00169934 -26.5838) (0.00172695 -26.1799) (0.00175501 -25.7825)
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continue (94.6846 -4.19255) (96.2231 -4.19823) (97.7866 -4.20386) (99.3755 -4.20943) (100.99 -4.21496)
continue (102.631 -4.22044) (104.299 -4.22587) (105.994 -4.23125) (107.716 -4.2366) (109.466 -4.2419)
continue (111.245 -4.24717) (113.052 -4.2524) (114.889 -4.25759) (116.756 -4.26275) (118.653 -4.26788)
continue (120.581 -4.27298) (122.54 -4.27805) (124.532 -4.28309) (126.555 -4.28811) (128.611 -4.29311)
continue (130.701 -4.29808) (132.825 -4.30303) (134.983 -4.30795) (137.176 -4.31286) (139.405 -4.31776)
continue (141.67 -4.32263) (143.972 -4.32749) (146.312 -4.33234) (148.689 -4.33717) (151.105 -4.34199)
continue (153.56 -4.3468) (156.056 -4.3516) (158.591 -4.35638) (161.168 -4.36116) (163.787 -4.36593)
continue (166.448 -4.37069) (169.153 -4.37545) (171.901 -4.38019) (174.695 -4.38493) (177.533 -4.38967)
continue (180.418 -4.3944) (183.349 -4.39913) (186.329 -4.40385) (189.356 -4.40857) (192.433 -4.41328)
continue (195.56 -4.418) (198.737 -4.4227) (201.967 -4.42741) (205.248 -4.43212) (208.583 -4.43682)
continue (211.972 -4.44152) (215.417 -4.44622) (218.917 -4.45091) (222.474 -4.45561) (226.089 -4.4603)
continue (229.763 -4.465) (233.496 -4.46969) (237.29 -4.47438) (241.146 -4.47908) (245.064 -4.48377)
continue (249.046 -4.48846) (253.093 -4.49315) (257.205 -4.49784) (261.384 -4.50253) (265.631 -4.50722)
continue (269.948 -4.5119) (274.334 -4.51659) (278.791 -4.52128) (283.321 -4.52597) (287.925 -4.53066)
continue (292.603 -4.53535) (297.358 -4.54004) (302.189 -4.54472) (307.1 -4.54941) (312.09 -4.5541)
continue (317.161 -4.55879) (322.314 -4.56348) (327.551 -4.56816) (332.874 -4.57285) (338.282 -4.57754)
continue (343.779 -4.58223) (349.365 -4.58692) (355.042 -4.5916) (360.811 -4.59629) (366.673 -4.60098)
continue (372.631 -4.60567) (378.686 -4.61036) (384.839 -4.61504) (391.092 -4.61973) (397.447 -4.62442)
continue (403.905 -4.62911) (410.468 -4.6338) (417.138 -4.63849) (423.916 -4.64317) (430.804 -4.64786)
continue (437.804 -4.65255) (444.917 -4.65724) (452.147 -4.66193) (459.493 -4.66662) (466.96 -4.6713)
continue (474.547 -4.67599) (482.258 -4.68068) (490.094 -4.68537) (498.057 -4.69006) (506.15 -4.69475)
continue (514.374 -4.69944) (522.732 -4.70412) (531.226 -4.70881) (539.858 -4.7135) (548.63 -4.71819)
continue (557.544 -4.72288) (566.604 -4.72757) (575.81 -4.73226) (585.166 -4.73695) (594.675 -4.74163)
continue (604.337 -4.74632) (614.157 -4.75101) (624.136 -4.7557) (634.278 -4.76039) (644.584 -4.76508)
continue (655.057 -4.76977) (665.701 -4.77446) (676.518 -4.77915) (687.511 -4.78383) (698.682 -4.78852)
continue (710.034 -4.79321) (721.571 -4.7979) (733.296 -4.80259) (745.211 -4.80728) (757.32 -4.81197)
continue (769.625 -4.81666) (782.131 -4.82135) (794.839 -4.82604) (807.754 -4.83073) (820.879 -4.83541)
continue (834.218 -4.8401) (847.773 -4.84479) (861.548 -4.84948) (875.547 -4.85417) (889.773 -4.85886)
continue (904.231 -4.86355) (918.923 -4.86824) (933.855 -4.87293) (949.029 -4.87762) (964.449 -4.88231)
continue (980.12 -4.887) (996.046 -4.89169) (1012.23 -4.89637) (1028.68 -4.90106) (1045.39 -4.90575)
continue (1062.38 -4.91044) (1079.64 -4.91513) (1097.18 -4.91982) (1115.01 -4.92451) (1133.13 -4.9292)
continue (1151.54 -4.93389) (1170.25 -4.93858) (1189.27 -4.94327) (1208.59 -4.94796) (1228.23 -4.95265)
continue (1248.19 -4.95734) (1268.47 -4.96203) (1289.08 -4.96672) (1310.02 -4.9714) (1331.31 -4.97609)
continue (1352.94 -4.98078) (1374.93 -4.98547) (1397.27 -4.99016) (1419.97 -4.99485) (1443.04 -4.99954)
continue (1466.49 -5.00423) (1490.32 -5.00892) (1514.54 -5.01361) (1539.14 -5.0183) (1564.15 -5.02299)
continue (1589.57 -5.02768) (1615.4 -5.03237) (1641.65 -5.03706) (1668.32 -5.04175) (1695.43 -5.04644)
continue (1722.98 -5.05113) (1750.97 -5.05582) (1779.42 -5.06051) (1808.34 -5.0652) (1837.72 -5.06989)
continue (1867.58 -5.07457) (1897.93 -5.07926) (1928.77 -5.08395) (1960.11 -5.08864) (1991.95 -5.09333)
continue (2024.32 -5.09802) (2057.21 -5.10271) (2090.64 -5.1074) (2124.61 -5.11209) (2159.13 -5.11678)
continue (2194.22 -5.12147) (2229.87 -5.12616) (2266.1 -5.13085) (2302.92 -5.13554) (2340.34 -5.14023)
continue (2378.37 -5.14492) (2417.02 -5.14961) (2456.29 -5.1543) (2496.2 -5.15899) (2536.76 -5.16368)
continue (2577.98 -5.16837) (2619.87 -5.17306) (2662.44 -5.17775) (2705.7 -5.18244) (2749.66 -5.18713)
continue (2794.34 -5.19182) (2839.75 -5.19651) (2885.89 -5.2012) (2932.78 -5.20589) (2980.43 -5.21058)
continue (3028.86 -5.21527) (3078.08 -5.21996) (3128.09 -5.22465) (3178.92 -5.22934) (3230.57 -5.23402)
continue (3283.06 -5.23871) (3336.41 -5.2434) (3390.62 -5.24809) (3445.71 -5.25278) (3501.7 -5.25747)
continue (3558.6 -5.26216) (3616.42 -5.26685) (3675.19 -5.27154) (3734.9 -5.27623) (3795.59 -5.28092)
continue (3857.26 -5.28561) (3919.94 -5.2903) (3983.63 -5.29499) (4048.36 -5.29968) (4114.14 -5.30437)
continue (4180.99 -5.30906) (4248.93 -5.31375) (4317.97 -5.31844) (4388.13 -5.32313) (4459.43 -5.32782)
continue (4531.89 -5.33251) (4605.53 -5.3372) (4680.36 -5.34189) (4756.41 -5.34658) (4833.7 -5.35127)
continue (4912.24 -5.35596) (4992.05 -5.36065) (5073.17 -5.36534) (5155.6 -5.37003) (5239.37 -5.37472)
continue (5324.51 -5.37941) (5411.02 -5.3841) (5498.94 -5.38879) (5588.3 -5.39348) (5679.1 -5.39817)
continue (5771.38 -5.40286) (5865.15 -5.40755) (5960.45 -5.41224) (6057.3 -5.41693) (6155.73 -5.42162)
continue (6255.75 -5.42631) (6357.4 -5.431) (6460.7 -5.43569) (6565.67 -5.44038) (6672.36 -5.44507)
continue (6780.78 -5.44976) (6890.95 -5.45445) (7002.92 -5.45914) (7116.71 -5.46383) (7232.35 -5.46852)
continue (7349.86 -5.47321)(73498.6 -7.47321)(734986 -9.47321)(7.34986e+06 -11.4732)(7.34986e+07 -13.4732)
//
////// Flux is varied
//
phi(h) 23 vary
grid range from 18 to 23 with 1 dex
//
////// Hydrogen density of cloud is varied
//
hden 11 vary
grid range from 8 to 13 with 1 dex
//
////// Stopping condition and run
//
stop total column density 24
iterate to convergence

View File

@ -0,0 +1,274 @@
////// CLOUDY 13.03 GRID run as hypothetical values for AGN observation
//
title AGN BLR grid phi_vs_hden
//
// Arguments varied for this grid:
// log of incident intensity from 18 to 23
// log of hydrogen density from 8 to 13
//
////// Output information to these files
//
save continuum "continuum_full"
save raw continuum "continuum_raw"
save incident continuum "continuum_incident"
//
////// Formatting
//
print line column
print line inward
print line iso collapsed
set line precision 6
//
////// Resolved energy states for atomic models
//
// Defaults:
//atom H-like element hydrogen levels 10
//atom H-like element helium levels 10
//atom He-like element levels 6
//
atom H-like element hydrogen levels resolved 18
atom H-like element helium levels resolved 15
atom He-like element helium levels resolved 15
//
////// I forget what this does
//
set nend 5000
//
////// Need to find command to decrease threshold for included emission lines
//
//
//
////// Include additional spectral resolution around Lyman, Briggs, Etc.
//
//set nFnu
// Accepted units: : eV, keV, MeV, Hz, kHz, MHz, GHz, Angstrom,
// nm, micron, mm, cm or centimeter, wavenumbers, erg, ryd, K, Kelvin
//set nFnu add 1 ryd
//
////// For equivalent widths
//
//normalize to 1215 scale to 1215
//
////// Background radiation
//
background z = 0.0172
//
////// Hydrogen density of cloud is varied
//
hden 11 vary
grid range from 8 to 13 with 1 dex
//
////// Central AGN source shape generated by external program
//
interpolate (1.001e-09 1e-36)
continue (0.000734986 -33) (0.000746929 -33.007) (0.000759066 -33.014) (0.000771399 -33.021) (0.000783934 -33.028)
continue (0.000796672 -33.035) (0.000809616 -33.042) (0.000822772 -33.049) (0.000836141 -33.056) (0.000849727 -33.063)
continue (0.000863534 -33.07) (0.000877565 -33.077) (0.000891824 -33.084) (0.000906315 -33.091) (0.000921042 -33.098)
continue (0.000936008 -33.105) (0.000951216 -33.112) (0.000966672 -33.119) (0.00098238 -33.126) (0.000998342 -33.133)
continue (0.00101456 -33.14) (0.00103105 -33.147) (0.0010478 -33.154) (0.00106483 -33.161) (0.00108213 -33.168)
continue (0.00109971 -33.175) (0.00111758 -33.182) (0.00113574 -33.189) (0.0011542 -33.196) (0.00117295 -33.203)
continue (0.00119201 -33.21) (0.00121138 -33.2169) (0.00123106 -33.2236) (0.00125106 -33.2294) (0.00127139 -33.2321)
continue (0.00129205 -33.2245) (0.00131304 -33.1847) (0.00133438 -33.0632) (0.00135606 -32.8038) (0.0013781 -32.4153)
continue (0.00140049 -31.9597) (0.00142324 -31.483) (0.00144637 -31.0045) (0.00146987 -30.5306) (0.00149375 -30.0633)
continue (0.00151803 -29.6033) (0.00154269 -29.1506) (0.00156776 -28.7052) (0.00159323 -28.267) (0.00161912 -27.8359)
continue (0.00164543 -27.4117) (0.00167217 -26.9944) (0.00169934 -26.5838) (0.00172695 -26.1799) (0.00175501 -25.7825)
continue (0.00178353 -25.3915) (0.00181251 -25.0068) (0.00184196 -24.6284) (0.00187189 -24.2561) (0.0019023 -23.8899)
continue (0.00193321 -23.5295) (0.00196462 -23.175) (0.00199655 -22.8263) (0.00202899 -22.4832) (0.00206196 -22.1456)
continue (0.00209546 -21.8135) (0.00212951 -21.4869) (0.00216411 -21.1655) (0.00219927 -20.8493) (0.00223501 -20.5383)
continue (0.00227133 -20.2323) (0.00230823 -19.9312) (0.00234574 -19.6351) (0.00238385 -19.3438) (0.00242259 -19.0572)
continue (0.00246195 -18.7752) (0.00250195 -18.4979) (0.00254261 -18.225) (0.00258392 -17.9566) (0.00262591 -17.6925)
continue (0.00266857 -17.4328) (0.00271194 -17.1773) (0.002756 -16.9259) (0.00280078 -16.6787) (0.00284629 -16.4354)
continue (0.00289254 -16.1961) (0.00293954 -15.9608) (0.0029873 -15.7292) (0.00303584 -15.5015) (0.00308517 -15.2774)
continue (0.0031353 -15.0571) (0.00318625 -14.8403) (0.00323802 -14.627) (0.00329063 -14.4173) (0.0033441 -14.2109)
continue (0.00339844 -14.008) (0.00345366 -13.8084) (0.00350978 -13.612) (0.0035668 -13.4188) (0.00362476 -13.2288)
continue (0.00368366 -13.042) (0.00374351 -12.8581) (0.00380434 -12.6773) (0.00386616 -12.4995) (0.00392898 -12.3246)
continue (0.00399282 -12.1525) (0.00405769 -11.9833) (0.00412363 -11.8169) (0.00419063 -11.6532) (0.00425872 -11.4922)
continue (0.00432792 -11.3338) (0.00439824 -11.1781) (0.00446971 -11.0249) (0.00454234 -10.8742) (0.00461614 -10.726)
continue (0.00469115 -10.5803) (0.00476738 -10.437) (0.00484484 -10.296) (0.00492356 -10.1574) (0.00500356 -10.021)
continue (0.00508486 -9.88693) (0.00516749 -9.75506) (0.00525145 -9.62537) (0.00533678 -9.49783) (0.0054235 -9.37241)
continue (0.00551162 -9.24907) (0.00560118 -9.12777) (0.00569219 -9.00849) (0.00578468 -8.89119) (0.00587867 -8.77584)
continue (0.00597419 -8.66241) (0.00607127 -8.55087) (0.00616992 -8.44118) (0.00627017 -8.33333) (0.00637205 -8.22728)
continue (0.00647559 -8.12299) (0.00658081 -8.02045) (0.00668774 -7.91962) (0.00679641 -7.82048) (0.00690684 -7.723)
continue (0.00701907 -7.62716) (0.00713312 -7.53292) (0.00724902 -7.44026) (0.00736681 -7.34916) (0.00748651 -7.25959)
continue (0.00760815 -7.17153) (0.00773178 -7.08495) (0.00785741 -6.99983) (0.00798508 -6.91614) (0.00811483 -6.83387)
continue (0.00824668 -6.75299) (0.00838068 -6.67348) (0.00851686 -6.59531) (0.00865524 -6.51847) (0.00879588 -6.44293)
continue (0.0089388 -6.36867) (0.00908405 -6.29568) (0.00923165 -6.22392) (0.00938165 -6.15339) (0.00953409 -6.08405)
continue (0.00968901 -6.0159) (0.00984644 -5.94892) (0.0100064 -5.88307) (0.010169 -5.81835) (0.0103343 -5.75474)
continue (0.0105022 -5.69221) (0.0106728 -5.63075) (0.0108462 -5.57034) (0.0110225 -5.51097) (0.0112016 -5.45261)
continue (0.0113836 -5.39524) (0.0115686 -5.33885) (0.0117565 -5.28342) (0.0119476 -5.22894) (0.0121417 -5.17537)
continue (0.012339 -5.12271) (0.0125395 -5.07094) (0.0127432 -5.02003) (0.0129503 -4.96997) (0.0131607 -4.92074)
continue (0.0133746 -4.87231) (0.0135919 -4.82466) (0.0138127 -4.77778) (0.0140372 -4.73164) (0.0142652 -4.68621)
continue (0.014497 -4.64148) (0.0147326 -4.59742) (0.014972 -4.554) (0.0152153 -4.5112) (0.0154625 -4.46899)
continue (0.0157137 -4.42733) (0.0159691 -4.38621) (0.0162285 -4.34558) (0.0164922 -4.30543) (0.0167602 -4.26571)
continue (0.0170325 -4.22639) (0.0173093 -4.18744) (0.0175905 -4.14882) (0.0178764 -4.1105) (0.0181668 -4.07245)
continue (0.018462 -4.03462) (0.018762 -3.99698) (0.0190669 -3.95951) (0.0193767 -3.92216) (0.0196915 -3.8849)
continue (0.0200115 -3.8477) (0.0203366 -3.81053) (0.0206671 -3.77337) (0.0210029 -3.73619) (0.0213442 -3.69898)
continue (0.021691 -3.6617) (0.0220434 -3.62434) (0.0224016 -3.5869) (0.0227656 -3.54937) (0.0231355 -3.51173)
continue (0.0235114 -3.474) (0.0238935 -3.43617) (0.0242817 -3.39824) (0.0246763 -3.36023) (0.0250772 -3.32215)
continue (0.0254847 -3.28402) (0.0258988 -3.24585) (0.0263196 -3.20766) (0.0267473 -3.16948) (0.0271819 -3.13132)
continue (0.0276235 -3.09322) (0.0280724 -3.05519) (0.0285285 -3.01727) (0.0289921 -2.97947) (0.0294632 -2.94183)
continue (0.0299419 -2.90438) (0.0304284 -2.86712) (0.0309228 -2.8301) (0.0314253 -2.79334) (0.0319359 -2.75685)
continue (0.0324548 -2.72065) (0.0329822 -2.68478) (0.0335181 -2.64924) (0.0340627 -2.61406) (0.0346162 -2.57925)
continue (0.0351787 -2.54483) (0.0357503 -2.5108) (0.0363312 -2.47719) (0.0369215 -2.444) (0.0375214 -2.41124)
continue (0.0381311 -2.37893) (0.0387507 -2.34707) (0.0393803 -2.31566) (0.0400202 -2.28472) (0.0406705 -2.25425)
continue (0.0413313 -2.22425) (0.0420029 -2.19472) (0.0426854 -2.16567) (0.043379 -2.1371) (0.0440838 -2.10901)
continue (0.0448001 -2.0814) (0.0455281 -2.05427) (0.0462679 -2.02763) (0.0470196 -2.00146) (0.0477837 -1.97577)
continue (0.0485601 -1.95055) (0.0493491 -1.92581) (0.050151 -1.90154) (0.0509659 -1.87773) (0.051794 -1.85439)
continue (0.0526356 -1.83151) (0.0534908 -1.80909) (0.05436 -1.78713) (0.0552433 -1.76561) (0.0561409 -1.74454)
continue (0.0570531 -1.7239) (0.0579802 -1.70371) (0.0589223 -1.68394) (0.0598797 -1.66461) (0.0608526 -1.6457)
continue (0.0618414 -1.6272) (0.0628462 -1.60912) (0.0638674 -1.59144) (0.0649052 -1.57417) (0.0659598 -1.5573)
continue (0.0670316 -1.54082) (0.0681207 -1.52472) (0.0692276 -1.50902) (0.0703525 -1.49369) (0.0714956 -1.47873)
continue (0.0726573 -1.46414) (0.0738379 -1.44991) (0.0750377 -1.43605) (0.0762569 -1.42253) (0.077496 -1.40937)
continue (0.0787552 -1.39655) (0.0800349 -1.38406) (0.0813354 -1.37192) (0.0826569 -1.3601) (0.084 -1.3486)
continue (0.0853649 -1.33743) (0.086752 -1.32657) (0.0881616 -1.31602) (0.0895941 -1.30578) (0.0910499 -1.29584)
continue (0.0925293 -1.2862) (0.0940328 -1.27685) (0.0955607 -1.26779) (0.0971134 -1.25901) (0.0986914 -1.25052)
continue (0.100295 -1.2423) (0.101925 -1.23435) (0.103581 -1.22667) (0.105264 -1.21925) (0.106974 -1.2121)
continue (0.108712 -1.2052) (0.110479 -1.19855) (0.112274 -1.19215) (0.114098 -1.18599) (0.115952 -1.18008)
continue (0.117836 -1.1744) (0.119751 -1.16895) (0.121697 -1.16373) (0.123674 -1.15874) (0.125684 -1.15398)
continue (0.127726 -1.14943) (0.129801 -1.1451) (0.13191 -1.14098) (0.134054 -1.13707) (0.136232 -1.13336)
continue (0.138446 -1.12986) (0.140695 -1.12656) (0.142981 -1.12346) (0.145305 -1.12054) (0.147666 -1.11782)
continue (0.150065 -1.11529) (0.152503 -1.11294) (0.154981 -1.11077) (0.1575 -1.10879) (0.160059 -1.10697)
continue (0.162659 -1.10534) (0.165302 -1.10387) (0.167988 -1.10257) (0.170718 -1.10143) (0.173492 -1.10046)
continue (0.176311 -1.09965) (0.179176 -1.099) (0.182087 -1.0985) (0.185046 -1.09815) (0.188053 -1.09796)
continue (0.191108 -1.09791) (0.194213 -1.09801) (0.197369 -1.09825) (0.200576 -1.09863) (0.203835 -1.09916)
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continue (1062.38 -4.91044) (1079.64 -4.91513) (1097.18 -4.91982) (1115.01 -4.92451) (1133.13 -4.9292)
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continue (1466.49 -5.00423) (1490.32 -5.00892) (1514.54 -5.01361) (1539.14 -5.0183) (1564.15 -5.02299)
continue (1589.57 -5.02768) (1615.4 -5.03237) (1641.65 -5.03706) (1668.32 -5.04175) (1695.43 -5.04644)
continue (1722.98 -5.05113) (1750.97 -5.05582) (1779.42 -5.06051) (1808.34 -5.0652) (1837.72 -5.06989)
continue (1867.58 -5.07457) (1897.93 -5.07926) (1928.77 -5.08395) (1960.11 -5.08864) (1991.95 -5.09333)
continue (2024.32 -5.09802) (2057.21 -5.10271) (2090.64 -5.1074) (2124.61 -5.11209) (2159.13 -5.11678)
continue (2194.22 -5.12147) (2229.87 -5.12616) (2266.1 -5.13085) (2302.92 -5.13554) (2340.34 -5.14023)
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continue (3028.86 -5.21527) (3078.08 -5.21996) (3128.09 -5.22465) (3178.92 -5.22934) (3230.57 -5.23402)
continue (3283.06 -5.23871) (3336.41 -5.2434) (3390.62 -5.24809) (3445.71 -5.25278) (3501.7 -5.25747)
continue (3558.6 -5.26216) (3616.42 -5.26685) (3675.19 -5.27154) (3734.9 -5.27623) (3795.59 -5.28092)
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continue (4531.89 -5.33251) (4605.53 -5.3372) (4680.36 -5.34189) (4756.41 -5.34658) (4833.7 -5.35127)
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continue (5324.51 -5.37941) (5411.02 -5.3841) (5498.94 -5.38879) (5588.3 -5.39348) (5679.1 -5.39817)
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continue (6255.75 -5.42631) (6357.4 -5.431) (6460.7 -5.43569) (6565.67 -5.44038) (6672.36 -5.44507)
continue (6780.78 -5.44976) (6890.95 -5.45445) (7002.92 -5.45914) (7116.71 -5.46383) (7232.35 -5.46852)
continue (7349.86 -5.47321)(73498.6 -7.47321)(734986 -9.47321)(7.34986e+06 -11.4732)(7.34986e+07 -13.4732)
//
////// Flux is varied
//
phi(h) 23 vary
grid range from 18 to 23 with 1 dex
//
////// Stopping condition and run
//
stop total column density 24
iterate to convergence

View File

@ -0,0 +1,274 @@
////// CLOUDY 13.03 grid run as hypothetical values for AGN observation
//
title AGN BLR grid hden_vs_phi .25 dex 10_10_6 levels
//
// Arguments varied for this grid:
// log of incident intensity from 18 to 23
// log of hydrogen density from 8 to 13
//
////// Output information to these files
//
//save continuum "continuum_full"
//save raw continuum "continuum_raw"
save last incident continuum "continuum_incident"
//
////// Formatting
//
print line column
print line inward
print line iso collapsed
set line precision 6
//
////// Resolved energy states for atomic models
//
// Defaults:
atom H-like element hydrogen resolved levels 10
atom H-like element helium resolved levels 10
atom He-like element helium resolved levels 6
//
//atom H-like element hydrogen levels resolved 18
//atom H-like element helium levels resolved 15
//atom He-like element helium levels resolved 15
//
////// Prevent cloudy from stopping prematurely
//
set nend 5000
//
////// Include all emission lines, even those with zero intensity
//
print line faint off
//
////// Include additional spectral resolution around Lyman, Briggs, Etc.
//
//set nFnu
// Accepted units: : eV, keV, MeV, Hz, kHz, MHz, GHz, Angstrom,
// nm, micron, mm, cm or centimeter, wavenumbers, erg, ryd, K, Kelvin
//set nFnu add 1 ryd
//
////// For equivalent widths
//
//normalize to 1215 scale to 1215
//
////// Background radiation
//
background z = 0.0172
//
////// Hydrogen density of cloud is varied
//
hden 11 vary
grid range from 8 to 13 with 1 dex
//
////// Central AGN source shape generated by external program
//
interpolate (1.001e-09 1e-36)
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continue (30.6393 -3.60551) (31.1372 -3.61617) (31.6431 -3.62681) (32.1573 -3.63741) (32.6798 -3.64798)
continue (33.2108 -3.65851) (33.7504 -3.669) (34.2988 -3.67945) (34.8561 -3.68985) (35.4225 -3.70021)
continue (35.9981 -3.71053) (36.583 -3.72079) (37.1774 -3.731) (37.7815 -3.74116) (38.3954 -3.75127)
continue (39.0193 -3.76131) (39.6533 -3.7713) (40.2976 -3.78123) (40.9524 -3.79109) (41.6178 -3.80089)
continue (42.2941 -3.81062) (42.9813 -3.82028) (43.6797 -3.82988) (44.3894 -3.8394) (45.1107 -3.84884)
continue (45.8437 -3.85822) (46.5886 -3.86751) (47.3456 -3.87673) (48.1149 -3.88586) (48.8967 -3.89492)
continue (49.6912 -3.90389) (50.4986 -3.91278) (51.3191 -3.92159) (52.153 -3.93031) (53.0004 -3.93894)
continue (53.8616 -3.94749) (54.7368 -3.95595) (55.6262 -3.96431) (56.53 -3.97259) (57.4486 -3.98078)
continue (58.3821 -3.98888) (59.3307 -3.99689) (60.2947 -4.00481) (61.2744 -4.01264) (62.2701 -4.02038)
continue (63.2819 -4.02803) (64.3101 -4.03558) (65.3551 -4.04305) (66.417 -4.05043) (67.4962 -4.05773)
continue (68.5929 -4.06493) (69.7075 -4.07205) (70.8401 -4.07908) (71.9912 -4.08603) (73.161 -4.09289)
continue (74.3497 -4.09968) (75.5578 -4.10638) (76.7855 -4.113) (78.0332 -4.11954) (79.3011 -4.12601)
continue (80.5897 -4.1324) (81.8991 -4.13872) (83.2299 -4.14496) (84.5823 -4.15114) (85.9566 -4.15725)
continue (87.3533 -4.16329) (88.7727 -4.16926) (90.2151 -4.17517) (91.681 -4.18103) (93.1707 -4.18682)
continue (94.6846 -4.19255) (96.2231 -4.19823) (97.7866 -4.20386) (99.3755 -4.20943) (100.99 -4.21496)
continue (102.631 -4.22044) (104.299 -4.22587) (105.994 -4.23125) (107.716 -4.2366) (109.466 -4.2419)
continue (111.245 -4.24717) (113.052 -4.2524) (114.889 -4.25759) (116.756 -4.26275) (118.653 -4.26788)
continue (120.581 -4.27298) (122.54 -4.27805) (124.532 -4.28309) (126.555 -4.28811) (128.611 -4.29311)
continue (130.701 -4.29808) (132.825 -4.30303) (134.983 -4.30795) (137.176 -4.31286) (139.405 -4.31776)
continue (141.67 -4.32263) (143.972 -4.32749) (146.312 -4.33234) (148.689 -4.33717) (151.105 -4.34199)
continue (153.56 -4.3468) (156.056 -4.3516) (158.591 -4.35638) (161.168 -4.36116) (163.787 -4.36593)
continue (166.448 -4.37069) (169.153 -4.37545) (171.901 -4.38019) (174.695 -4.38493) (177.533 -4.38967)
continue (180.418 -4.3944) (183.349 -4.39913) (186.329 -4.40385) (189.356 -4.40857) (192.433 -4.41328)
continue (195.56 -4.418) (198.737 -4.4227) (201.967 -4.42741) (205.248 -4.43212) (208.583 -4.43682)
continue (211.972 -4.44152) (215.417 -4.44622) (218.917 -4.45091) (222.474 -4.45561) (226.089 -4.4603)
continue (229.763 -4.465) (233.496 -4.46969) (237.29 -4.47438) (241.146 -4.47908) (245.064 -4.48377)
continue (249.046 -4.48846) (253.093 -4.49315) (257.205 -4.49784) (261.384 -4.50253) (265.631 -4.50722)
continue (269.948 -4.5119) (274.334 -4.51659) (278.791 -4.52128) (283.321 -4.52597) (287.925 -4.53066)
continue (292.603 -4.53535) (297.358 -4.54004) (302.189 -4.54472) (307.1 -4.54941) (312.09 -4.5541)
continue (317.161 -4.55879) (322.314 -4.56348) (327.551 -4.56816) (332.874 -4.57285) (338.282 -4.57754)
continue (343.779 -4.58223) (349.365 -4.58692) (355.042 -4.5916) (360.811 -4.59629) (366.673 -4.60098)
continue (372.631 -4.60567) (378.686 -4.61036) (384.839 -4.61504) (391.092 -4.61973) (397.447 -4.62442)
continue (403.905 -4.62911) (410.468 -4.6338) (417.138 -4.63849) (423.916 -4.64317) (430.804 -4.64786)
continue (437.804 -4.65255) (444.917 -4.65724) (452.147 -4.66193) (459.493 -4.66662) (466.96 -4.6713)
continue (474.547 -4.67599) (482.258 -4.68068) (490.094 -4.68537) (498.057 -4.69006) (506.15 -4.69475)
continue (514.374 -4.69944) (522.732 -4.70412) (531.226 -4.70881) (539.858 -4.7135) (548.63 -4.71819)
continue (557.544 -4.72288) (566.604 -4.72757) (575.81 -4.73226) (585.166 -4.73695) (594.675 -4.74163)
continue (604.337 -4.74632) (614.157 -4.75101) (624.136 -4.7557) (634.278 -4.76039) (644.584 -4.76508)
continue (655.057 -4.76977) (665.701 -4.77446) (676.518 -4.77915) (687.511 -4.78383) (698.682 -4.78852)
continue (710.034 -4.79321) (721.571 -4.7979) (733.296 -4.80259) (745.211 -4.80728) (757.32 -4.81197)
continue (769.625 -4.81666) (782.131 -4.82135) (794.839 -4.82604) (807.754 -4.83073) (820.879 -4.83541)
continue (834.218 -4.8401) (847.773 -4.84479) (861.548 -4.84948) (875.547 -4.85417) (889.773 -4.85886)
continue (904.231 -4.86355) (918.923 -4.86824) (933.855 -4.87293) (949.029 -4.87762) (964.449 -4.88231)
continue (980.12 -4.887) (996.046 -4.89169) (1012.23 -4.89637) (1028.68 -4.90106) (1045.39 -4.90575)
continue (1062.38 -4.91044) (1079.64 -4.91513) (1097.18 -4.91982) (1115.01 -4.92451) (1133.13 -4.9292)
continue (1151.54 -4.93389) (1170.25 -4.93858) (1189.27 -4.94327) (1208.59 -4.94796) (1228.23 -4.95265)
continue (1248.19 -4.95734) (1268.47 -4.96203) (1289.08 -4.96672) (1310.02 -4.9714) (1331.31 -4.97609)
continue (1352.94 -4.98078) (1374.93 -4.98547) (1397.27 -4.99016) (1419.97 -4.99485) (1443.04 -4.99954)
continue (1466.49 -5.00423) (1490.32 -5.00892) (1514.54 -5.01361) (1539.14 -5.0183) (1564.15 -5.02299)
continue (1589.57 -5.02768) (1615.4 -5.03237) (1641.65 -5.03706) (1668.32 -5.04175) (1695.43 -5.04644)
continue (1722.98 -5.05113) (1750.97 -5.05582) (1779.42 -5.06051) (1808.34 -5.0652) (1837.72 -5.06989)
continue (1867.58 -5.07457) (1897.93 -5.07926) (1928.77 -5.08395) (1960.11 -5.08864) (1991.95 -5.09333)
continue (2024.32 -5.09802) (2057.21 -5.10271) (2090.64 -5.1074) (2124.61 -5.11209) (2159.13 -5.11678)
continue (2194.22 -5.12147) (2229.87 -5.12616) (2266.1 -5.13085) (2302.92 -5.13554) (2340.34 -5.14023)
continue (2378.37 -5.14492) (2417.02 -5.14961) (2456.29 -5.1543) (2496.2 -5.15899) (2536.76 -5.16368)
continue (2577.98 -5.16837) (2619.87 -5.17306) (2662.44 -5.17775) (2705.7 -5.18244) (2749.66 -5.18713)
continue (2794.34 -5.19182) (2839.75 -5.19651) (2885.89 -5.2012) (2932.78 -5.20589) (2980.43 -5.21058)
continue (3028.86 -5.21527) (3078.08 -5.21996) (3128.09 -5.22465) (3178.92 -5.22934) (3230.57 -5.23402)
continue (3283.06 -5.23871) (3336.41 -5.2434) (3390.62 -5.24809) (3445.71 -5.25278) (3501.7 -5.25747)
continue (3558.6 -5.26216) (3616.42 -5.26685) (3675.19 -5.27154) (3734.9 -5.27623) (3795.59 -5.28092)
continue (3857.26 -5.28561) (3919.94 -5.2903) (3983.63 -5.29499) (4048.36 -5.29968) (4114.14 -5.30437)
continue (4180.99 -5.30906) (4248.93 -5.31375) (4317.97 -5.31844) (4388.13 -5.32313) (4459.43 -5.32782)
continue (4531.89 -5.33251) (4605.53 -5.3372) (4680.36 -5.34189) (4756.41 -5.34658) (4833.7 -5.35127)
continue (4912.24 -5.35596) (4992.05 -5.36065) (5073.17 -5.36534) (5155.6 -5.37003) (5239.37 -5.37472)
continue (5324.51 -5.37941) (5411.02 -5.3841) (5498.94 -5.38879) (5588.3 -5.39348) (5679.1 -5.39817)
continue (5771.38 -5.40286) (5865.15 -5.40755) (5960.45 -5.41224) (6057.3 -5.41693) (6155.73 -5.42162)
continue (6255.75 -5.42631) (6357.4 -5.431) (6460.7 -5.43569) (6565.67 -5.44038) (6672.36 -5.44507)
continue (6780.78 -5.44976) (6890.95 -5.45445) (7002.92 -5.45914) (7116.71 -5.46383) (7232.35 -5.46852)
continue (7349.86 -5.47321)(73498.6 -7.47321)(734986 -9.47321)(7.34986e+06 -11.4732)(7.34986e+07 -13.4732)
//
////// Flux is varied
//
phi(h) 23 vary
grid range from 18 to 23 with 1 dex
//
////// Stopping condition and run
//
stop total column density 23
iterate to convergence

299
scripts/cloudy/mpi_grid.in Executable file
View File

@ -0,0 +1,299 @@
////// CLOUDY 13.03 grid script
//
title AGN BLR grid hden_vs_phi .25 dex
//
// Arguments varied for this grid:
// log of incident intensity from 17 to 24
// log of hydrogen density from 7 to 14
//
////// Output continua
//
save last incident continuum "incident_continuum"
//
////// Formatting and line inclusion
//
print line column
print line inward
print line iso collapsed
print line faint -3
print last
set line precision 6
//
////// Resolved energy states for atomic models
//
// Defaults: 10, 10, 6
//
atom H-like element hydrogen resolved levels 18
atom H-like element helium resolved levels 15
atom He-like element helium resolved levels 15
//
////// Prevent cloudy from stopping prematurely
//
set nend 5000
//
////// Include additional spectral resolution around Lyman, Briggs, Etc.
// for the diffuse continuum
//
set nFnu add 800 angstrom
set nFnu add 840 angstrom
set nFnu add 880 angstrom
set nFnu add 910 angstrom
set nFnu add 913 angstrom
set nFnu add 960 angstrom
set nFnu add 1240 angstrom
set nFnu add 1324 angstrom
set nFnu add 1410 angstrom
set nFnu add 1650 angstrom
set nFnu add 1900 angstrom
set nFnu add 2200 angstrom
set nFnu add 2700 angstrom
set nFnu add 3000 angstrom
set nFnu add 3300 angstrom
set nFnu add 3400 angstrom
set nFnu add 3644 angstrom
set nFnu add 3645 angstrom
set nFnu add 3648 angstrom
set nFnu add 4400 angstrom
set nFnu add 5100 angstrom
set nFnu add 5600 angstrom
set nFnu add 6500 angstrom
set nFnu add 7000 angstrom
set nFnu add 7500 angstrom
set nFnu add 8000 angstrom
set nFnu add 8204 angstrom
set nFnu add 8210 angstrom
set nFnu add 8500 angstrom
set nFnu add 9000 angstrom
set nFnu add 9500 angstrom
set nFnu add 10000 angstrom
set nFnu add 10500 angstrom
set nFnu add 11000 angstrom
set nFnu add 13000 angstrom
//
////// Print equivalent widths
//
normalize to "Inci" 1215.00A scale to 1215.00
//
////// Background radiation
//
background z = 0.0172
//
////// Hydrogen density of cloud is varied
//
hden 11 vary
grid range from 7 to 14 with .25 dex
//
////// Central AGN source shape generated by external program
//
interpolate (1.001e-09 1e-36)
continue (0.000734986 -33) (0.000746929 -33.007) (0.000759066 -33.014) (0.000771399 -33.021) (0.000783934 -33.028)
continue (0.000796672 -33.035) (0.000809616 -33.042) (0.000822772 -33.049) (0.000836141 -33.056) (0.000849727 -33.063)
continue (0.000863534 -33.07) (0.000877565 -33.077) (0.000891824 -33.084) (0.000906315 -33.091) (0.000921042 -33.098)
continue (0.000936008 -33.105) (0.000951216 -33.112) (0.000966672 -33.119) (0.00098238 -33.126) (0.000998342 -33.133)
continue (0.00101456 -33.14) (0.00103105 -33.147) (0.0010478 -33.154) (0.00106483 -33.161) (0.00108213 -33.168)
continue (0.00109971 -33.175) (0.00111758 -33.182) (0.00113574 -33.189) (0.0011542 -33.196) (0.00117295 -33.203)
continue (0.00119201 -33.21) (0.00121138 -33.2169) (0.00123106 -33.2236) (0.00125106 -33.2294) (0.00127139 -33.2321)
continue (0.00129205 -33.2245) (0.00131304 -33.1847) (0.00133438 -33.0632) (0.00135606 -32.8038) (0.0013781 -32.4153)
continue (0.00140049 -31.9597) (0.00142324 -31.483) (0.00144637 -31.0045) (0.00146987 -30.5306) (0.00149375 -30.0633)
continue (0.00151803 -29.6033) (0.00154269 -29.1506) (0.00156776 -28.7052) (0.00159323 -28.267) (0.00161912 -27.8359)
continue (0.00164543 -27.4117) (0.00167217 -26.9944) (0.00169934 -26.5838) (0.00172695 -26.1799) (0.00175501 -25.7825)
continue (0.00178353 -25.3915) (0.00181251 -25.0068) (0.00184196 -24.6284) (0.00187189 -24.2561) (0.0019023 -23.8899)
continue (0.00193321 -23.5295) (0.00196462 -23.175) (0.00199655 -22.8263) (0.00202899 -22.4832) (0.00206196 -22.1456)
continue (0.00209546 -21.8135) (0.00212951 -21.4869) (0.00216411 -21.1655) (0.00219927 -20.8493) (0.00223501 -20.5383)
continue (0.00227133 -20.2323) (0.00230823 -19.9312) (0.00234574 -19.6351) (0.00238385 -19.3438) (0.00242259 -19.0572)
continue (0.00246195 -18.7752) (0.00250195 -18.4979) (0.00254261 -18.225) (0.00258392 -17.9566) (0.00262591 -17.6925)
continue (0.00266857 -17.4328) (0.00271194 -17.1773) (0.002756 -16.9259) (0.00280078 -16.6787) (0.00284629 -16.4354)
continue (0.00289254 -16.1961) (0.00293954 -15.9608) (0.0029873 -15.7292) (0.00303584 -15.5015) (0.00308517 -15.2774)
continue (0.0031353 -15.0571) (0.00318625 -14.8403) (0.00323802 -14.627) (0.00329063 -14.4173) (0.0033441 -14.2109)
continue (0.00339844 -14.008) (0.00345366 -13.8084) (0.00350978 -13.612) (0.0035668 -13.4188) (0.00362476 -13.2288)
continue (0.00368366 -13.042) (0.00374351 -12.8581) (0.00380434 -12.6773) (0.00386616 -12.4995) (0.00392898 -12.3246)
continue (0.00399282 -12.1525) (0.00405769 -11.9833) (0.00412363 -11.8169) (0.00419063 -11.6532) (0.00425872 -11.4922)
continue (0.00432792 -11.3338) (0.00439824 -11.1781) (0.00446971 -11.0249) (0.00454234 -10.8742) (0.00461614 -10.726)
continue (0.00469115 -10.5803) (0.00476738 -10.437) (0.00484484 -10.296) (0.00492356 -10.1574) (0.00500356 -10.021)
continue (0.00508486 -9.88693) (0.00516749 -9.75506) (0.00525145 -9.62537) (0.00533678 -9.49783) (0.0054235 -9.37241)
continue (0.00551162 -9.24907) (0.00560118 -9.12777) (0.00569219 -9.00849) (0.00578468 -8.89119) (0.00587867 -8.77584)
continue (0.00597419 -8.66241) (0.00607127 -8.55087) (0.00616992 -8.44118) (0.00627017 -8.33333) (0.00637205 -8.22728)
continue (0.00647559 -8.12299) (0.00658081 -8.02045) (0.00668774 -7.91962) (0.00679641 -7.82048) (0.00690684 -7.723)
continue (0.00701907 -7.62716) (0.00713312 -7.53292) (0.00724902 -7.44026) (0.00736681 -7.34916) (0.00748651 -7.25959)
continue (0.00760815 -7.17153) (0.00773178 -7.08495) (0.00785741 -6.99983) (0.00798508 -6.91614) (0.00811483 -6.83387)
continue (0.00824668 -6.75299) (0.00838068 -6.67348) (0.00851686 -6.59531) (0.00865524 -6.51847) (0.00879588 -6.44293)
continue (0.0089388 -6.36867) (0.00908405 -6.29568) (0.00923165 -6.22392) (0.00938165 -6.15339) (0.00953409 -6.08405)
continue (0.00968901 -6.0159) (0.00984644 -5.94892) (0.0100064 -5.88307) (0.010169 -5.81835) (0.0103343 -5.75474)
continue (0.0105022 -5.69221) (0.0106728 -5.63075) (0.0108462 -5.57034) (0.0110225 -5.51097) (0.0112016 -5.45261)
continue (0.0113836 -5.39524) (0.0115686 -5.33885) (0.0117565 -5.28342) (0.0119476 -5.22894) (0.0121417 -5.17537)
continue (0.012339 -5.12271) (0.0125395 -5.07094) (0.0127432 -5.02003) (0.0129503 -4.96997) (0.0131607 -4.92074)
continue (0.0133746 -4.87231) (0.0135919 -4.82466) (0.0138127 -4.77778) (0.0140372 -4.73164) (0.0142652 -4.68621)
continue (0.014497 -4.64148) (0.0147326 -4.59742) (0.014972 -4.554) (0.0152153 -4.5112) (0.0154625 -4.46899)
continue (0.0157137 -4.42733) (0.0159691 -4.38621) (0.0162285 -4.34558) (0.0164922 -4.30543) (0.0167602 -4.26571)
continue (0.0170325 -4.22639) (0.0173093 -4.18744) (0.0175905 -4.14882) (0.0178764 -4.1105) (0.0181668 -4.07245)
continue (0.018462 -4.03462) (0.018762 -3.99698) (0.0190669 -3.95951) (0.0193767 -3.92216) (0.0196915 -3.8849)
continue (0.0200115 -3.8477) (0.0203366 -3.81053) (0.0206671 -3.77337) (0.0210029 -3.73619) (0.0213442 -3.69898)
continue (0.021691 -3.6617) (0.0220434 -3.62434) (0.0224016 -3.5869) (0.0227656 -3.54937) (0.0231355 -3.51173)
continue (0.0235114 -3.474) (0.0238935 -3.43617) (0.0242817 -3.39824) (0.0246763 -3.36023) (0.0250772 -3.32215)
continue (0.0254847 -3.28402) (0.0258988 -3.24585) (0.0263196 -3.20766) (0.0267473 -3.16948) (0.0271819 -3.13132)
continue (0.0276235 -3.09322) (0.0280724 -3.05519) (0.0285285 -3.01727) (0.0289921 -2.97947) (0.0294632 -2.94183)
continue (0.0299419 -2.90438) (0.0304284 -2.86712) (0.0309228 -2.8301) (0.0314253 -2.79334) (0.0319359 -2.75685)
continue (0.0324548 -2.72065) (0.0329822 -2.68478) (0.0335181 -2.64924) (0.0340627 -2.61406) (0.0346162 -2.57925)
continue (0.0351787 -2.54483) (0.0357503 -2.5108) (0.0363312 -2.47719) (0.0369215 -2.444) (0.0375214 -2.41124)
continue (0.0381311 -2.37893) (0.0387507 -2.34707) (0.0393803 -2.31566) (0.0400202 -2.28472) (0.0406705 -2.25425)
continue (0.0413313 -2.22425) (0.0420029 -2.19472) (0.0426854 -2.16567) (0.043379 -2.1371) (0.0440838 -2.10901)
continue (0.0448001 -2.0814) (0.0455281 -2.05427) (0.0462679 -2.02763) (0.0470196 -2.00146) (0.0477837 -1.97577)
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continue (3558.6 -5.26216) (3616.42 -5.26685) (3675.19 -5.27154) (3734.9 -5.27623) (3795.59 -5.28092)
continue (3857.26 -5.28561) (3919.94 -5.2903) (3983.63 -5.29499) (4048.36 -5.29968) (4114.14 -5.30437)
continue (4180.99 -5.30906) (4248.93 -5.31375) (4317.97 -5.31844) (4388.13 -5.32313) (4459.43 -5.32782)
continue (4531.89 -5.33251) (4605.53 -5.3372) (4680.36 -5.34189) (4756.41 -5.34658) (4833.7 -5.35127)
continue (4912.24 -5.35596) (4992.05 -5.36065) (5073.17 -5.36534) (5155.6 -5.37003) (5239.37 -5.37472)
continue (5324.51 -5.37941) (5411.02 -5.3841) (5498.94 -5.38879) (5588.3 -5.39348) (5679.1 -5.39817)
continue (5771.38 -5.40286) (5865.15 -5.40755) (5960.45 -5.41224) (6057.3 -5.41693) (6155.73 -5.42162)
continue (6255.75 -5.42631) (6357.4 -5.431) (6460.7 -5.43569) (6565.67 -5.44038) (6672.36 -5.44507)
continue (6780.78 -5.44976) (6890.95 -5.45445) (7002.92 -5.45914) (7116.71 -5.46383) (7232.35 -5.46852)
continue (7349.86 -5.47321)(73498.6 -7.47321)(734986 -9.47321)(7.34986e+06 -11.4732)(7.34986e+07 -13.4732)
//
////// Flux is varied
//
phi(h) 23 vary
grid range from 17 to 24 with .25 dex
//
////// Stopping condition and run
//
stop total column density 23
iterate to convergence max=40

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#!/bin/bash
# This script converts a cloudy incident continuum's photon
# energy unit from Rydberg to eV. Best if continuum is
# parsed to a raw table, first. Photon energy needs to be
# in the first column. The bash program bc is required.
continuum_file_orig=$1
continuum_file_new=hnuineV.$continuum_file_orig
while read photon_energy_in_ryd everything_else; do
# 1 Ryd = 13.60569253 eV
photon_energy_in_eV=`bc <<< "$photon_energy_in_ryd * 13.60569253"`
done <$continuum_file_orig

314
scripts/meta/create_fort_files.sh Executable file
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#!/bin/bash
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
basedir=`pwd`
# Script to prepare input fort files for Dr. Korista's use, starting from
# an unmodified cloudy grid output file.
# Separate grid output into individual files.
$script_dir/operations/split_grid_output_hden_phi.sh $1
cd gridoutput
# Create fort tables for these sets of emission lines. Multiplets defined below.
Inci_lines="1215.00A 4860.00A"
TOTL_lines="1215.68A"
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"
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"
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"
metal_lines="C 1 1656.00A
TOTL 2326.00A
C 2 2325.00A
C 2 2324.00A
C 2 2329.00A
C 2 2328.00A
C 2 2327.00A
C 2 1335.00A
C 3 977.000A
TOTL 1909.00A
C 3 1910.00A
C 3 1176.00A
TOTL 1549.00A
C 4 1551.00A
C 4 1548.00A
N 1 1200.00A
N 2 2141.00A
N 2 1085.00A
TOTL 1750.00A
N 3 1749.00A
N 3 1747.00A
N 3 1754.00A
N 3 1752.00A
N 3 1751.00A
N 3 991.000A
TOTL 1486.00A
N 4 1486.00A
N 4 765.000A
TOTL 1240.00A
N 5 1243.00A
N 5 1239.00A
6lev 8446.00A
6lev 1304.00A
TOTL 1665.00A
O 3 1661.00A
O 3 1666.00A
O 3 835.000A
TOTL 1402.00A
O 4 1400.00A
O 4 1397.00A
O 4 1407.00A
O 4 1405.00A
O 4 1401.00A
O 4 789.000A
O 5 630.000A
TOTL 1218.00A
O 5 1218.00A
TOTL 1035.00A
O 6 1031.93A
O 6 1037.62A
Ne 5 1141.00A
TOTL 774.000A
Ne 8 770.404A
Ne 8 780.324A
Na 1 5891.94A
Mg 1 2853.00A
TOTL 2798.00A
Mg 2 2795.53A
Mg 2 2802.71A
TOTL 615.000A
Mg10 609.793A
Mg10 624.941A
totl 2665.00A
Al 2 2670.00A
TOTL 1860.00A
Al 3 1855.00A
Al 3 1863.00A
TOTL 2335.00A
Si 2 2334.00A
Si 2 2329.00A
Si 2 2350.00A
Si 2 2344.00A
Si 2 2336.00A
Si 2 1813.99A
Si 2 1531.00A
Si 2 1307.66A
Si 2 1263.32A
Si 3 1207.00A
TOTL 1888.00A
Si 3 1892.00A
PHOT 1895.00A
TOTL 1397.00A
Si 4 1403.00A
Si 4 1394.00A
S 2 1256.00A
S 3 1720.00A
S 3 1197.56A
TOTL 1406.00A
S 4 1405.00A
S 4 1398.00A
S 4 1424.00A
S 4 1417.00A
S 4 1406.00A
TOTL 1198.00A
S 5 1198.00A
S 5 786.473A
S 6 944.524A
S 6 933.380A
Ca2K 3934.00A
Ca2H 3969.00A
Ca2X 8498.00A
Ca2Y 8542.00A
Ca2Z 8662.00A
Fe 2 1500.00A
Fe 2 1.15000m
Fe 2 2500.00A
Fe 2 2300.00A
Fe 2 8900.00A
Fe 2 1786.00A
Fe 3 1125.79A
FeKa 1.78000A"
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"
fortfile_number=10
echo "Aggregating flux (scaled) tables from grid."
echo " "
echo "Characteristics"
echo "---------------"
for wavelength in $Inci_lines; do
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "Inci ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "Inci ${wavelength} -> tmp.scaledtable.${fortfile_number}"
done
for wavelength in $TOTL_lines; do
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "TOTL ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "TOTL ${wavelength} -> tmp.scaledtable.${fortfile_number}"
done
echo " "
echo "H(I) Series"
echo "-------------"
for wavelength in $HI_lines; do
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "H 1 ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "H 1 ${wavelength} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "H 1 ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
done
echo " "
echo "He(II) Series"
echo "-----------"
for wavelength in $HeII_lines; do
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "He 2 ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "He 2 ${wavelength} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "He 2 ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
done
echo " "
echo "He(I) Series"
echo "----------"
wavelength="1.08299m"
ref_hden="10.25"
ref_phi="20.00"
num_components=`${script_dir}/operations/count_components.sh "TOTL ${wavelength}" $ref_hden $ref_phi`
component_list=`${script_dir}/operations/find_components.sh "TOTL ${wavelength}" $ref_hden $ref_phi`
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "TOTL ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "TOTL ${wavelength} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "TOTL ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
comp_wavelength=`echo "$component_list"|sed -n 1p|sed 's#^......\(........\).*$#\1#'`
for component in `seq 1 $num_components`; do
comp_identifier=`echo "$component_list"|sed -n ${component}p|sed 's#^.\(.............\).*$#\1#'`
next_wavelength=`echo "$component_list"|sed -n $((component+1))p|sed 's#^......\(........\).*$#\1#'`
if [[ "$comp_wavelength" == "$next_wavelength" ]]; then
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_previous_total_line_flux.sh "${comp_identifier}" $((component-1)) > tmp.scaledtable.${fortfile_number}
echo "${comp_identifier} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_previous_inward_line_flux.sh "${comp_identifier}" $((component-1)) > tmp.scaledtable.${fortfile_number}
echo "Inwd ${comp_wavelength} -> tmp.scaledtable.${fortfile_number}"
else
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "${comp_identifier}" $((component-1)) > tmp.scaledtable.${fortfile_number}
echo "${comp_identifier} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "${comp_identifier}" $((component-1)) > tmp.scaledtable.${fortfile_number}
echo "Inwd ${comp_wavelength} -> tmp.scaledtable.${fortfile_number}"
fi
comp_wavelength=${next_wavelength}
done
for wavelength in $HeI_lines; do
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "He 1 ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "He 1 ${wavelength} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "He 1 ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
done
echo " "
echo "Heavy Elements"
echo "--------------"
num_lines=`echo "$metal_lines"|wc -l|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
for line_index in `seq 1 $num_lines`; do
line_id=`echo "${metal_lines}"|sed -n ${line_index}p`
wavelength=`echo "$line_id"|sed 's#.....\(........\).*#\1#'`
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "${line_id}" > tmp.scaledtable.${fortfile_number}
echo "${line_id} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_inward_line_flux.sh "${line_id}" > tmp.scaledtable.${fortfile_number}
echo "Inwd ${wavelength} -> tmp.scaledtable.${fortfile_number}"
done
echo " "
echo "Continua"
echo "--------"
for wavelength in $continuum_lines; do
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "nFnu ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "nFnu ${wavelength} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "nInu ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "nInu ${wavelength} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "InwT ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "InwT ${wavelength} -> tmp.scaledtable.${fortfile_number}"
(( fortfile_number++ ))
${script_dir}/operations/aggregate_table_for_total_line_flux.sh "InwC ${wavelength}" > tmp.scaledtable.${fortfile_number}
echo "InwC ${wavelength} -> tmp.scaledtable.${fortfile_number}"
#(( fortfile_number++ ))
#${script_dir}/operations/aggregate_table_for_total_line_flux.sh "InwT ${wavelength}" > tmp.totreflcont.${fortfile_number}
#echo -n "InwT ${wavelength} -> tmp.totreflcont.${fortfile_number}, "
#${script_dir}/operations/aggregate_table_for_total_line_flux.sh "InwC ${wavelength}" > tmp.increflcont.${fortfile_number}
#echo "InwC ${wavelength} -> tmp.increflcont.${fortfile_number}"
#${script_dir}/../bin/output_difference_table tmp.totreflcont.${fortfile_number} tmp.increflcont.${fortfile_number} > tmp.scaledtable.${fortfile_number}
#echo "tmp.totreflcont.${fortfile_number} - tmp.increflcont.${fortfile_number} -> tmp.scaledtable.${fortfile_number}"
done
num=10
echo " "
echo "Computing relative intensity tables for all scaled tables."
for scaledtable in `echo tmp.scaledtable.*`; do
num=`echo "$scaledtable"|sed 's#^tmp\.scaledtable\.\(.*\)$#\1#'`
#(( num++ ))
newtable=fort.$num
${script_dir}/../bin/sort_and_normalize_table $scaledtable > $newtable
echo "$scaledtable -> $newtable"
done
echo " "
echo "Filing and cleaning."
mkdir -p ${basedir}/fortfiles
mv fort.* ${basedir}/fortfiles
cd ${basedir}/fortfiles
tar zcf ${basedir}/fortfiles.tar.gz *
cd ${basedir}
# ${script_dir}/util/cleantmp.sh
echo "Archive generated. Done."
exit 0

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date;qstat|grep xaw;echo "`grep 'stopped' ../grid_25dex_18_15_15_cldn23/*.out|wc -l`/841 complete"
num=0; for file in `grep -l '40 of 40' [0-9]*_[0-9]*|cut -d: -f1`; do echo $(( ++num )) - $file; grep "40 of 40" $file|tail -n1|cut -d'.' -f4; grep "HDEN=" $file|head -n1|sed 's#\*##g'|sed 's#^\s*# #'; grep "phi(h)" $file|head -n1|sed s#\*##g|sed 's#^\s*# #';egrep "C-" $file; echo; done > max_iterations_report.txt; less max_iterations_report.txt
ls -l grid*|grep "Jun 9 21"
tail -n3 *540*.out|grep iter|less
Make joke about this:
#He I Lines:
TOTL 1.08299m
He 1 1.08291m
Inwd 1.08291m
He 1 1.08303m
Inwd 1.08303m
He 1 1.08303m
Inwd 1.08303m
num=0; for file in `grep -l '40 of 40' gridoutput/[0-9]*_[0-9]*|cut -d: -f1`; do echo $(( ++num )) - $file; grep "40 of 40" $file|tail -n1|cut -d'.' -f4; grep "HDEN=" $file|head -n1|sed 's#\*##g'|sed 's#^\s*# #'; grep "phi(h)" $file|head -n1|sed s#\*##g|sed 's#^\s*# #';egrep "C-" $file; echo; done > max_iterations_report.txt; less max_iterations_report.txt
num=0; for file in `grep -l '50 of 50' gridoutput/[0-9]*_[0-9]*|cut -d: -f1`; do echo $(( ++num )) - $file; grep "50 of 50" $file|tail -n1|cut -d'.' -f4; grep "HDEN=" $file|head -n1|sed 's#\*##g'|sed 's#^\s*# #'; grep "phi(h)" $file|head -n1|sed s#\*##g|sed 's#^\s*# #';egrep "C-" $file; echo; done > max_iterations_report.txt; less max_iterations_report.txt
num=0; for file in `grep -l '10 of 10' gridoutput/[0-9]*_[0-9]*|cut -d: -f1`; do echo $(( ++num )) - $file; grep "10 of 10" $file|tail -n1|cut -d'.' -f4; grep "HDEN=" $file|head -n1|sed 's#\*##g'|sed 's#^\s*# #'; grep "phi(h)" $file|head -n1|sed s#\*##g|sed 's#^\s*# #';egrep "C-" $file; echo; done > max_iterations_report.txt; less max_iterations_report.txt

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#!/bin/bash
line_id=$1
wavelength=`echo "$line_id"|sed 's#^.....\(........\).*$#\1#'`
gridfiles=`echo [0-9]*_[0-9]*`
if [[ $2 ]]; then
echo "Inwd ${wavelength} j=$2 relative to Inci 1215.00A scaled to 1215.00"
else
echo "Inwd ${wavelength} relative to Inci 1215.00A scaled to 1215.00"
fi
echo "Hden Phi(H) ScaInten"
for file in $gridfiles; do
hden=`echo $file|cut -d_ -f1|sed 's#^\(.....\).*$#\1#'`
phi=`echo $file|cut -d_ -f2|sed 's#^\(......\).*$#\1#'`
line_number=`grep -n "$1" $file|tail -n1|sed 's@\([0-9]*\):.*@\1@'`
value=`sed -n $((line_number+1))p $file|grep "Inwd"|sed 's#^......................\(.........\).*$#\1#'|tail -n1`
if [[ $value == "" ]]; then
value=0.0000;
fi
echo "$hden $phi $value"
done

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#!/bin/bash
line_id=$1
wavelength=`echo "$line_id"|sed 's#^.....\(........\).*$#\1#'`
gridfiles=`echo [0-9]*_[0-9]*`
if [[ $2 ]]; then
echo "Inwd ${wavelength} j=$2 relative to Inci 1215.00A scaled to 1215.00"
else
echo "Inwd ${wavelength} relative to Inci 1215.00A scaled to 1215.00"
fi
echo "Hden Phi(H) ScaInten"
for file in $gridfiles; do
hden=`echo $file|cut -d_ -f1|sed 's#^\(.....\).*$#\1#'`
phi=`echo $file|cut -d_ -f2|sed 's#^\(......\).*$#\1#'`
line_number=`grep -n "$1" $file|tail -n1|sed 's@\([0-9]*\):.*@\1@'`
if [[ $line_number == "" ]]; then
value=0.0000;
else
value=`sed -n $((line_number-1))p $file|grep "Inwd ${wavelength}"|sed 's#^......................\(.........\).*$#\1#'|tail -n1`
fi
if [[ $value == "" ]]; then
value=0.0000;
fi
echo "$hden $phi $value"
done

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#!/bin/bash
line_id=$1
gridfiles=`echo [0-9]*_[0-9]*`
if [[ $2 ]]; then
echo "$1 j=$2 relative to Inci 1215.00A scaled to 1215.00"
else
echo "$1 relative to Inci 1215.00A scaled to 1215.00"
fi
echo "Hden Phi(H) ScaInten"
for file in $gridfiles; do
hden=`echo $file|cut -d_ -f1|sed 's#^\(.....\).*$#\1#'`
phi=`echo $file|cut -d_ -f2|sed 's#^\(......\).*$#\1#'`
line_number=`grep -n "$1" $file|tail -n1|sed 's@\([0-9]*\):.*@\1@'`
if [[ $line_number == "" ]]; then
value=0.0000;
else
value=`sed -n $(( line_number - 2 )),$(( line_number - 1 ))p $file|grep "$1"|sed 's#^......................\(.........\).*$#\1#'|head -n1`
fi
if [[ $value == "" ]]; then
value=0.0000;
fi
echo "$hden $phi $value"
done

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#!/bin/bash
line_id=$1
gridfiles=`echo [0-9]*_[0-9]*`
if [[ $2 ]]; then
echo "$1 j=$2 relative to Inci 1215.00A scaled to 1215.00"
else
echo "$1 relative to Inci 1215.00A scaled to 1215.00"
fi
echo "Hden Phi(H) ScaInten"
for file in $gridfiles; do
hden=`echo $file|cut -d_ -f1|sed 's#^\(.....\).*$#\1#'`
phi=`echo $file|cut -d_ -f2|sed 's#^\(......\).*$#\1#'`
value=`grep "$1" $file|tail -n1|sed 's#^......................\(.........\).*$#\1#'`
if [[ $value == "" ]]; then
value=0.0000;
fi
echo "$hden $phi $value"
done

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#!/bin/bash
reference_file=`echo ${2}[0-9]*_${3}[0-9]*`
line_number=`grep -n "$1" ${reference_file}|tail -n1|sed 's#\([0-9]\): TOTL.*#\1#'`
avg_wavelength=`sed -n ${line_number}p ${reference_file}|sed 's#......\(.......\).*#\1#'`
components_found=0
num_potential_components=14
for line_num in `seq $num_potential_components`; do
line=`sed -n $((line_number + $line_num))p ${reference_file}`
# echo "$line"
if [[ `echo $line|grep Inwd` != "" ]]; then continue; fi
if [[ `echo $line|grep TOTL` != "" ]]; then break; fi
element_in_line=`echo "$line"|sed 's#^.\(....\).*$#\1#'`
if [[ ${element} == "" ]]; then element=${element_in_line}; fi
if [[ ${element} != ${element_in_line} ]]; then continue; fi
component_wavelength=`echo "$line"|sed 's#......\(.......\).*#\1#'`
# echo $avg_wavelength $component_wavelength
if [[ `bc <<< "scale=5; sqrt( ( ( ${avg_wavelength} - ${component_wavelength} ) / ${avg_wavelength} )^2 ) < .015"` == 1 ]]; then
(( components_found++ ))
else
break
fi
done
echo $components_found
exit 0

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#!/bin/bash
reference_file=`echo ${2}[0-9]*_${3}[0-9]*`
line_number=`grep -n "$1" ${reference_file}|tail -n1|sed 's#\([0-9]\): .*#\1#'`
avg_wavelength=`sed -n ${line_number}p ${reference_file}|sed 's#^......\(.......\).*$#\1#'`
num_potential_components=14
element=""
for line_num in `seq $num_potential_components`; do
line=`sed -n $((line_number + $line_num))p ${reference_file}`
# echo "$line"
if [[ `echo $line|grep Inwd` != "" ]]; then continue; fi
if [[ `echo $line|grep TOTL` != "" ]]; then break; fi
element_in_line=`echo "$line"|sed 's#^.\(....\).*$#\1#'`
if [[ ${element} == "" ]]; then element=${element_in_line}; fi
if [[ ${element} != ${element_in_line} ]]; then continue; fi
component_wavelength=`echo "$line"|sed 's#^......\(.......\).*$#\1#'`
# echo $avg_wavelength $component_wavelength
if [[ `bc <<< "scale=5; sqrt( ( ( ${avg_wavelength} - ${component_wavelength} ) / ${avg_wavelength} )^2 ) < .0162"` == 1 ]]; then
echo "$line"
else
break
fi
done
exit 0

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#!/bin/bash
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
continuum_file=$1
grid_delimits=`grep -n 'GRID_DELIMIT' $continuum_file|sed 's#^\([0-9]*\):.*$#\1 #'`
echo Parse Grid Continuum
echo ====================
echo Scanning file $continuum_file.
echo `echo $grid_delimits|wc -w` grids found.
#echo Grid delimits: $grid_delimits
grid_index=0
# Skips extra line at beginning of first grid component
interval_origin=1
# Parse the continua for each grid component into a separate file
echo Parsing continua into separate grid components.
for line_number in $grid_delimits; do
(( interval_origin++ ))
tmpfile=tmp.cont.$grid_index
#echo lines $interval_origin to $line_number to file $tmpfile
sed -n ${interval_origin},${line_number}p $continuum_file > $tmpfile
interval_origin=$line_number
(( grid_index++ ))
done
# Parse the final continuum for each grid component and save
grid_component=0
echo "Parsing continua for final iteration of $grid_index grid components."
while [[ $grid_component -lt $grid_index ]]; do
cont_tmp_file=tmp.cont.$grid_component
permanent_file=${continuum_file}.$((grid_component++))
iteration_delimits=`grep -n '###########################' $cont_tmp_file|sed 's#^\([0-9]*\):.*$#\1 #'`
iterations=`echo $iteration_delimits|wc -w`
sed -n $((`echo $iteration_delimits|cut -d' ' -f$(( iterations - 1 ))` + 1 )),`echo $iteration_delimits|cut -d' ' -f$(( iterations ))`p $cont_tmp_file > $permanent_file
done
$script_dir/util/cleantmp.sh
echo Done.

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#!/bin/bash
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
basedir=`pwd`
echo "Separating grid by hden and phi(H)."
outputdir="gridoutput"
mkdir -p $outputdir; cd $outputdir
cloudy_output="../$1"
echo scanning cloudy output file $1
grid_delimits=`grep -n 'GRID_DELIMIT' $cloudy_output|sed 's#^\([0-9]*\):.*$#\1 #'`
echo $( echo $grid_delimits|wc -w|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#' ) grid delimiters found.
metafile=tmp.out.meta
hdenfile=tmp.out.hden_list
phifile=tmp.out.phi_list
grid_number=0
interval_origin=0
echo "Separating grids."
for line_number in $grid_delimits; do
if [[ $interval_origin == 0 ]]; then
sed -n 1,${line_number}p $cloudy_output > $metafile
interval_origin=$line_number
echo Metafile collected.
continue
fi
tmpfile=tmp.out.$grid_number
touch $tmpfile
sed -n ${interval_origin},${line_number}p $cloudy_output > $tmpfile
interval_origin=$line_number
(( grid_number++ ))
done
echo "Output organized by linear index."
params_start=`grep -n "MPI grid mode " $metafile|cut -d':' -f1`
endline=`wc -l $metafile|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
echo Reading parameters from lines $params_start to $endline
sed -n ${params_start},${endline}p $metafile|grep "HDEN="|sed 's#^[^0-9]*\([0-9.]*\) LOG.*$#\1#' > ${hdenfile}
sed -n ${params_start},${endline}p $metafile|grep "phi(h) "|sed 's#^[^0-9]*\([0-9.]*\) LOG.*$#\1#' > ${phifile}
num_params=`wc -l ${hdenfile}|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
# Note that this program assumes for each hden, phi was varied
# over its domain. Come to think of it, however, the program should
# remain consistent, either way.
files_processed=0
for tmpfile in `echo tmp.out.[0-9]*`; do
linear_index=`echo $tmpfile|sed 's#^[^0-9]*\([0-9]*\)[^0-9]*$#\1#'`
(( linear_index++ ))
hden=`sed -n ${linear_index}p ${hdenfile}`
phi=`sed -n ${linear_index}p ${phifile}`
cp $tmpfile ${hden}_${phi}
(( files_processed++ ))
done
echo Output organized by grid parameters.
echo $files_processed grid events were processed. This should be 29 x 29.
${script_dir}/util/cleantmp.sh
cd ${basedir}

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#!/bin/bash
cloudy_output=$1
grid_delimits=`grep -n 'GRID_DELIMIT' $cloudy_output|sed 's#^\([0-9]*\):.*$#\1 #'`
echo Information Captured
echo ====================
echo scanning cloudy output file $cloudy_output
echo grid_delimits: $grid_delimits
grid_number=0
interval_origin=0
for line_number in $grid_delimits; do
if [[ $interval_origin == 0 ]]; then
interval_origin=$line_number
continue
fi
tmpfile=tmp.out.$grid_number
touch $tmpfile
echo lines $interval_origin to $line_number to file $tmpfile
sed -n ${interval_origin},${line_number}p $cloudy_output >> $tmpfile
interval_origin=$line_number
(( grid_number++ ))
done

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#!/bin/sh -login
#PBS -l mem=128GB
#PBS -l nodes=4:ppn=16:research
#PBS -l walltime=150:00:00
#PBS -N cldy_4_181515_23
#PBS -j oe
RUN_FILE="mpi_grid"
RUN_DIR="cloudy/runs/4thdex_181515models_23cldn"
num_proc=$(cat ${PBS_NODEFILE} | wc -l)
module load openmpi/gnu/1.7.3
# replace ~/cloudy/cloudy_mpi with path to cloudy MPI executable file
cd ~/${RUN_DIR}
time mpirun -machinefile ${PBS_NODEFILE} -np ${num_proc} ~/cloudy/cloudy_mpi -r ${RUN_FILE}

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@ -0,0 +1,18 @@
#!/bin/sh -login
#PBS -l mem=128GB
#PBS -l nodes=4:ppn=16:research
#PBS -l walltime=150:00:00
#PBS -N .25_181515_cldn23
#PBS -j oe
RUN_FILE="mpi_grid"
RUN_DIR="cloudy/runs/4thdex_181515models_23cldn"
num_proc=$(cat ${PBS_NODEFILE} | wc -l)
module load openmpi/gnu/1.7.3
# replace ~/cloudy/cloudy_mpi with path to cloudy MPI executable file
cd ~/${RUN_DIR}
time mpirun -machinefile ${PBS_NODEFILE} -np ${num_proc} ~/cloudy/cloudy_mpi -r ${RUN_FILE}

5
scripts/util/cleantmp.sh Executable file
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@ -0,0 +1,5 @@
#!/usr/local/bin/bash
echo Cleaning temporary files.
rm ./*tmp*

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@ -0,0 +1,10 @@
#!/bin/bash
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
date > $script_dir/refresh_date
scp -ro port=17940 caes@fulgeo.shadydealings.net:/usr/local/sfs/store/science/agn/scripts/* $script_dir/
chmod -R 700 $script_dir/*

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@ -0,0 +1,10 @@
#!/usr/local/bin/bash
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
runs_dir=$script_dir/../syracuse_runs
date > $runs_dir/refresh_date
rsync -avv --exclude 'reports' --exclude 'mnt' --exclude 'inc' --exclude 'devel' --exclude 'papers' --exclude 'proc' caes@192.168.1.11:/mnt/science/agn/cloudy/runs/ $runs_dir

10
scripts/util/sync_thor_runs.sh Executable file
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@ -0,0 +1,10 @@
#!/usr/local/bin/bash
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
runs_dir=$script_dir/../thor_runs
date > $runs_dir/refresh_date
rsync -avv xaw5719@thor.cs.wmich.edu:/home/research/xaw5719/cloudy/runs/good/ $runs_dir

304
scripts/xmgrace/fullview.par Executable file
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@ -0,0 +1,304 @@
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xaxis type zero false
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xaxis bar linewidth 1.0
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325
scripts/xmgrace/fullview_ELe.par Executable file
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@ -0,0 +1,325 @@
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#
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map font 46 to "URWPalladioL-BoldItalic", "URWPalladioL-BoldItalic"
map font 47 to "URWPalladioL-Italic", "URWPalladioL-Italic"
map font 48 to "URWPalladioL-Roman", "URWPalladioL-Roman"
map font 13 to "ZapfDingbats", "ZapfDingbats"
map color 0 to (255, 255, 255), "white"
map color 1 to (0, 0, 0), "black"
map color 2 to (255, 0, 0), "red"
map color 3 to (0, 255, 0), "green"
map color 4 to (0, 0, 255), "blue"
map color 5 to (255, 255, 0), "yellow"
map color 6 to (188, 143, 143), "brown"
map color 7 to (220, 220, 220), "grey"
map color 8 to (148, 0, 211), "violet"
map color 9 to (0, 255, 255), "cyan"
map color 10 to (255, 0, 255), "magenta"
map color 11 to (255, 165, 0), "orange"
map color 12 to (114, 33, 188), "indigo"
map color 13 to (103, 7, 72), "maroon"
map color 14 to (64, 224, 208), "turquoise"
map color 15 to (0, 139, 0), "green4"
reference date 0
date wrap off
date wrap year 1950
default linewidth 1.0
default linestyle 1
default color 1
default pattern 1
default font 0
default char size 1.000000
default symbol size 1.000000
default sformat "%.8g"
background color 0
page background fill on
timestamp off
timestamp 0.03, 0.03
timestamp color 1
timestamp rot 0
timestamp font 0
timestamp char size 1.000000
timestamp def "Fri May 22 03:01:52 2015"
r0 off
link r0 to g0
r0 type above
r0 linestyle 1
r0 linewidth 1.0
r0 color 1
r0 line 0, 0, 0, 0
r1 off
link r1 to g0
r1 type above
r1 linestyle 1
r1 linewidth 1.0
r1 color 1
r1 line 0, 0, 0, 0
r2 off
link r2 to g0
r2 type above
r2 linestyle 1
r2 linewidth 1.0
r2 color 1
r2 line 0, 0, 0, 0
r3 off
link r3 to g0
r3 type above
r3 linestyle 1
r3 linewidth 1.0
r3 color 1
r3 line 0, 0, 0, 0
r4 off
link r4 to g0
r4 type above
r4 linestyle 1
r4 linewidth 1.0
r4 color 1
r4 line 0, 0, 0, 0
g0 on
g0 hidden false
g0 type XY
g0 stacked false
g0 bar hgap 0.000000
g0 fixedpoint off
g0 fixedpoint type 0
g0 fixedpoint xy 0.000000, 0.000000
g0 fixedpoint format general general
g0 fixedpoint prec 6, 6
with g0
world 0.1, 1e+42, 100000, 1e+45
stack world 0, 0, 0, 0
znorm 1
view 0.150000, 0.150000, 1.150000, 0.850000
title ""
title font 0
title size 1.500000
title color 1
subtitle ""
subtitle font 0
subtitle size 1.000000
subtitle color 1
xaxes scale Logarithmic
yaxes scale Logarithmic
xaxes invert off
yaxes invert off
xaxis on
xaxis type zero false
xaxis offset 0.000000 , 0.000000
xaxis bar on
xaxis bar color 1
xaxis bar linestyle 1
xaxis bar linewidth 1.0
xaxis label "Photon Energy ( eV )"
xaxis label layout para
xaxis label place auto
xaxis label char size 1.000000
xaxis label font 0
xaxis label color 1
xaxis label place normal
xaxis tick on
xaxis tick major 10
xaxis tick minor ticks 8
xaxis tick default 6
xaxis tick place rounded true
xaxis tick in
xaxis tick major size 1.040000
xaxis tick major color 1
xaxis tick major linewidth 1.0
xaxis tick major linestyle 1
xaxis tick major grid off
xaxis tick minor color 1
xaxis tick minor linewidth 1.0
xaxis tick minor linestyle 1
xaxis tick minor grid off
xaxis tick minor size 0.500000
xaxis ticklabel on
xaxis ticklabel format general
xaxis ticklabel prec 5
xaxis ticklabel formula ""
xaxis ticklabel append ""
xaxis ticklabel prepend ""
xaxis ticklabel angle 0
xaxis ticklabel skip 0
xaxis ticklabel stagger 0
xaxis ticklabel place normal
xaxis ticklabel offset auto
xaxis ticklabel offset 0.000000 , 0.010000
xaxis ticklabel start type auto
xaxis ticklabel start 0.000000
xaxis ticklabel stop type auto
xaxis ticklabel stop 0.000000
xaxis ticklabel char size 1.000000
xaxis ticklabel font 0
xaxis ticklabel color 1
xaxis tick place both
xaxis tick spec type none
yaxis on
yaxis type zero false
yaxis offset 0.000000 , 0.000000
yaxis bar on
yaxis bar color 1
yaxis bar linestyle 1
yaxis bar linewidth 1.0
yaxis label "EL[e] (relative)"
yaxis label layout para
yaxis label place auto
yaxis label char size 1.000000
yaxis label font 0
yaxis label color 1
yaxis label place normal
yaxis tick on
yaxis tick major 10
yaxis tick minor ticks 8
yaxis tick default 6
yaxis tick place rounded true
yaxis tick in
yaxis tick major size 1.000000
yaxis tick major color 1
yaxis tick major linewidth 1.0
yaxis tick major linestyle 1
yaxis tick major grid off
yaxis tick minor color 1
yaxis tick minor linewidth 1.0
yaxis tick minor linestyle 1
yaxis tick minor grid off
yaxis tick minor size 0.500000
yaxis ticklabel on
yaxis ticklabel format general
yaxis ticklabel prec 5
yaxis ticklabel formula ""
yaxis ticklabel append ""
yaxis ticklabel prepend ""
yaxis ticklabel angle 0
yaxis ticklabel skip 0
yaxis ticklabel stagger 0
yaxis ticklabel place normal
yaxis ticklabel offset auto
yaxis ticklabel offset 0.000000 , 0.010000
yaxis ticklabel start type auto
yaxis ticklabel start 0.000000
yaxis ticklabel stop type auto
yaxis ticklabel stop 0.000000
yaxis ticklabel char size 1.000000
yaxis ticklabel font 0
yaxis ticklabel color 1
yaxis tick place both
yaxis tick spec type none
altxaxis off
altyaxis off
legend on
legend loctype view
legend 0.85, 0.8
legend box color 1
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legend box linestyle 1
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legend box fill pattern 1
legend font 0
legend char size 1.000000
legend color 1
legend length 4
legend vgap 1
legend hgap 1
legend invert false
frame type 0
frame linestyle 1
frame linewidth 1.0
frame color 1
frame pattern 1
frame background color 0
frame background pattern 0
s0 hidden false
s0 type xy
s0 symbol 0
s0 symbol size 1.000000
s0 symbol color 1
s0 symbol pattern 1
s0 symbol fill color 1
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s0 symbol linestyle 1
s0 symbol char 65
s0 symbol char font 0
s0 symbol skip 0
s0 line type 1
s0 line linestyle 1
s0 line linewidth 1.0
s0 line color 1
s0 line pattern 1
s0 baseline type 0
s0 baseline off
s0 dropline off
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s0 fill color 1
s0 fill pattern 1
s0 avalue off
s0 avalue type 2
s0 avalue char size 1.000000
s0 avalue font 0
s0 avalue color 1
s0 avalue rot 0
s0 avalue format general
s0 avalue prec 3
s0 avalue prepend ""
s0 avalue append ""
s0 avalue offset 0.000000 , 0.000000
s0 errorbar on
s0 errorbar place both
s0 errorbar color 1
s0 errorbar pattern 1
s0 errorbar size 1.000000
s0 errorbar linewidth 1.0
s0 errorbar linestyle 1
s0 errorbar riser linewidth 1.0
s0 errorbar riser linestyle 1
s0 errorbar riser clip off
s0 errorbar riser clip length 0.100000
s0 comment "/sfs/store/science/agn/trans/grid_cont_test_2/continuum_incident.1.ineV"
s0 legend ""

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@ -1,82 +0,0 @@
#
# Copyright (C) 2007,2008 Alex Shulgin
#
# This file is part of png++ the C++ wrapper for libpng. PNG++ is free
# software; the exact copying conditions are as follows:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
#
# 3. The name of the author may not be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
# NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
ifndef PREFIX
PREFIX := /usr/local
endif
ifndef PNGPP
PNGPP := ..
endif
make_cflags := -Wall $(CFLAGS) -I$(PREFIX)/include -I$(PNGPP)
make_ldflags := $(LDFLAGS) -L$(PREFIX)/lib
ifndef NDEBUG
make_cflags := $(make_cflags) -g
make_ldflags := $(make_ldflags) -g
endif
ifndef LIBPNG_CONFIG
LIBPNG_CONFIG := libpng-config
endif
sources := pixel_generator.cpp
deps := $(sources:.cpp=.dep)
objects := $(sources:.cpp=.o)
targets := $(sources:.cpp=$(bin_suffix))
all: $(deps) $(targets)
dist-copy-files:
mkdir $(dist_dir)/example
cp $(sources) Makefile $(dist_dir)/example
clean: clean-deps
rm -f $(targets) $(objects)
.PHONY: all dist-copy-files clean clean-deps
%$(bin_suffix): %.o
g++ -o $@ $< $(make_ldflags) `$(LIBPNG_CONFIG) --ldflags`
%.o: %.cpp
g++ -c -o $@ $< $(make_cflags) `$(LIBPNG_CONFIG) --cflags`
%.dep: %.cpp
g++ -M $(CPPFLAGS) $(make_cflags) $< -o- | \
sed 's/\($*\)\.o[ :]*/\1.o $@ : /g' > $@
clean-deps:
rm -f $(deps)
include $(deps)

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@ -1,82 +0,0 @@
/*
* Copyright (C) 2007,2008 Alex Shulgin
*
* This file is part of png++ the C++ wrapper for libpng. PNG++ is free
* software; the exact copying conditions are as follows:
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
*
* 3. The name of the author may not be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
* NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
* TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cstdlib>
#include <iostream>
#include <ostream>
#include <png.hpp>
class pixel_generator
: public png::generator< png::gray_pixel_1, pixel_generator >
{
public:
pixel_generator(size_t width, size_t height)
: png::generator< png::gray_pixel_1, pixel_generator >(width, height),
m_row(width)
{
for (size_t i = 0; i < m_row.size(); ++i)
{
m_row[i] = i > m_row.size() / 2 ? 1 : 0;
}
}
png::byte* get_next_row(size_t /*pos*/)
{
size_t i = std::rand() % m_row.size();
size_t j = std::rand() % m_row.size();
png::gray_pixel_1 t = m_row[i];
m_row[i] = m_row[j];
m_row[j] = t;
return reinterpret_cast< png::byte* >(row_traits::get_data(m_row));
}
private:
typedef png::packed_pixel_row< png::gray_pixel_1 > row;
typedef png::row_traits< row > row_traits;
row m_row;
};
int
main()
try
{
size_t const width = 32;
size_t const height = 512;
std::ofstream file("generated.png", std::ios::binary);
pixel_generator generator(width, height);
generator.write(file);
}
catch (std::exception const& error)
{
std::cerr << "pixel_generator: " << error.what() << std::endl;
return EXIT_FAILURE;
}

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@ -1,100 +0,0 @@
#
# Copyright (C) 2007,2008 Alex Shulgin
#
# This file is part of png++ the C++ wrapper for libpng. PNG++ is free
# software; the exact copying conditions are as follows:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
#
# 3. The name of the author may not be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
# NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
ifndef PREFIX
PREFIX := /usr/local
endif
ifndef PNGPP
PNGPP := ..
endif
make_cflags := -Wall $(CFLAGS) -I$(PREFIX)/include -I$(PNGPP)
make_ldflags := $(LDFLAGS) -L$(PREFIX)/lib
ifndef NDEBUG
make_cflags := $(make_cflags) -g
make_ldflags := $(make_ldflags) -g
endif
ifndef LIBPNG_CONFIG
LIBPNG_CONFIG := libpng-config
endif
sources := convert_color_space.cpp \
generate_gray_packed.cpp \
read_write_gray_packed.cpp \
generate_palette.cpp \
write_gray_16.cpp \
read_write_param.cpp \
dump.cpp
deps := $(sources:.cpp=.dep)
objects := $(sources:.cpp=.o)
targets := $(sources:.cpp=$(bin_suffix))
all: $(deps) $(targets)
dist-copy-files:
mkdir $(dist_dir)/test
cp -r $(sources) Makefile test.sh README cmp $(dist_dir)/test
tar cf - pngsuite --exclude=\*.out | tar xf - -C $(dist_dir)/test
clean: clean-targets clean-tests-output clean-deps
clean-targets:
rm -f $(targets) $(objects)
test: all
./test.sh
clean-tests-output:
rm -f *.out pngsuite/*.out
.PHONY: all dist-copy-files \
clean clean-targets \
test test-convert_color_space \
clean-tests-output \
clean-deps
%$(bin_suffix): %.o
g++ -o $@ $< $(make_ldflags) `$(LIBPNG_CONFIG) --ldflags`
%.o: %.cpp
g++ -c -o $@ $< $(make_cflags) `$(LIBPNG_CONFIG) --cflags`
%.dep: %.cpp
g++ -M $(CPPFLAGS) $(make_cflags) $< -o- | \
sed 's/\($*\)\.o[ :]*/\1.o $@ : /g' > $@
clean-deps:
rm -f $(deps)
include $(deps)

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@ -1,85 +0,0 @@
pngsuite
--------
(c) Willem van Schaik, 1999
Permission to use, copy, and distribute these images for any purpose and
without fee is hereby granted.
These 15 images are part of the much larger PngSuite test-set of
images, available for developers of PNG supporting software. The
complete set, available at http:/www.schaik.com/pngsuite/, contains
a variety of images to test interlacing, gamma settings, ancillary
chunks, etc.
The images in this directory represent the basic PNG color-types:
grayscale (1-16 bit deep), full color (8 or 16 bit), paletted
(1-8 bit) and grayscale or color images with alpha channel. You
can use them to test the proper functioning of PNG software.
filename depth type
------------ ------ --------------
basn0g01.png 1-bit grayscale
basn0g02.png 2-bit grayscale
basn0g04.png 4-bit grayscale
basn0g08.png 8-bit grayscale
basn0g16.png 16-bit grayscale
basn2c08.png 8-bit truecolor
basn2c16.png 16-bit truecolor
basn3p01.png 1-bit paletted
basn3p02.png 2-bit paletted
basn3p04.png 4-bit paletted
basn3p08.png 8-bit paletted
basn4a08.png 8-bit gray with alpha
basn4a16.png 16-bit gray with alpha
basn6a08.png 8-bit RGBA
basn6a16.png 16-bit RGBA
Here is the correct result of typing "pngtest -m *.png" in
this directory:
Testing basn0g01.png: PASS (524 zero samples)
Filter 0 was used 32 times
Testing basn0g02.png: PASS (448 zero samples)
Filter 0 was used 32 times
Testing basn0g04.png: PASS (520 zero samples)
Filter 0 was used 32 times
Testing basn0g08.png: PASS (3 zero samples)
Filter 1 was used 9 times
Filter 4 was used 23 times
Testing basn0g16.png: PASS (1 zero samples)
Filter 1 was used 1 times
Filter 2 was used 31 times
Testing basn2c08.png: PASS (6 zero samples)
Filter 1 was used 5 times
Filter 4 was used 27 times
Testing basn2c16.png: PASS (592 zero samples)
Filter 1 was used 1 times
Filter 4 was used 31 times
Testing basn3p01.png: PASS (512 zero samples)
Filter 0 was used 32 times
Testing basn3p02.png: PASS (448 zero samples)
Filter 0 was used 32 times
Testing basn3p04.png: PASS (544 zero samples)
Filter 0 was used 32 times
Testing basn3p08.png: PASS (4 zero samples)
Filter 0 was used 32 times
Testing basn4a08.png: PASS (32 zero samples)
Filter 1 was used 1 times
Filter 4 was used 31 times
Testing basn4a16.png: PASS (64 zero samples)
Filter 0 was used 1 times
Filter 1 was used 2 times
Filter 2 was used 1 times
Filter 4 was used 28 times
Testing basn6a08.png: PASS (160 zero samples)
Filter 1 was used 1 times
Filter 4 was used 31 times
Testing basn6a16.png: PASS (1072 zero samples)
Filter 1 was used 4 times
Filter 4 was used 28 times
libpng passes test
Willem van Schaik
<willem@schaik.com>
October 1999

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