Initial commit

Added files:
  * mass_profile: developed by Junhua GU, modified by Weitian LI
  * opt_utilities: developed by Junhua GU
  * tools/cosmo_calc: originated from 'calc_distance', modified
  * scripts: scripts used to process Chandra ACIS data
  * files: useful files used in processing
  * HOWTO_chandra_acis_process.txt
  * README.md

1 files changed, 235 insertions, 0 deletions

diff --git a/mod_ly/fit_dbeta_nfw_mass_profile.sh b/mod_ly/fit_dbeta_nfw_mass_profile.sh
new file mode 100755
index 0000000..be0404f
--- /dev/null
+++ b/mod_ly/fit_dbeta_nfw_mass_profile.sh
@@ -0,0 +1,235 @@
+#!/bin/sh
+
+# modified by LIweitaNux, 2012/09/06
+export PATH="/usr/local/bin:/usr/bin:/bin:$PATH"
+
+if [ $# -eq 1 ]; then
+    cfg_file="$1"
+elif [ $# -eq 2 ]; then
+    cfg_file="$1"
+    CENTER_VAL="YES"
+else
+    echo "Usage: $0 <cfg_file> [c]"
+    exit 1
+fi
+
+if ! which xspec > /dev/null; then
+    printf "ERROR: please initialize HEASOFT first\n"
+    exit 2
+fi
+
+if [ -z "${HEADAS}" ]; then
+    printf "ERROR: variable \`HEADAS' not properly set\n"
+    exit 3
+fi
+
+export PGPLOT_FONT="${HEADAS}/lib/grfont.dat"
+printf "## PGPLOT_FONT: \`${PGPLOT_FONT}'\n"
+
+if [ "$0" = `basename $0` ]; then
+    script_path=`which $0`
+    base_path=`dirname ${script_path}`
+else
+    base_path=`dirname $0`
+fi
+printf "## base_path: \`${base_path}'\n"
+printf "## use configuration file: \`${cfg_file}'\n"
+
+#initialize profile type name
+t_profile_type=`grep '^t_profile' $cfg_file | awk '{print $2}'`
+printf "## t_profile_type: \`$t_profile_type'\n"
+#initialize data file name
+t_data_file=`grep '^t_data_file' $cfg_file | awk '{print $2}'`
+t_param_file=`grep '^t_param_file' $cfg_file | awk '{print $2}'`
+#initialize sbp config file
+sbp_cfg=`grep '^sbp_cfg' $cfg_file | awk '{print $2}'`
+#initialize the temperature profile file
+T_file=`grep '^T_file' $sbp_cfg | awk '{print $2}'`
+cfunc_file=`grep '^cfunc_file' ${sbp_cfg} |awk '{print $2}'`
+abund=`grep '^abund' ${cfg_file} |awk '{print $2}'`
+nh=`grep '^nh' ${cfg_file} |awk '{print $2}'`
+## calc `cm_per_pixel' instead {{{
+# cm_per_pixel=`grep '^cm_per_pixel' $sbp_cfg|awk '{print $2}'`
+z=`grep '^z' $sbp_cfg | awk '{ print $2 }'`
+cm_per_pixel=`${base_path}/calc_distance ${z} | grep 'cm_per_pixel' | awk '{ print $2 }'`
+sed -i'' "s/^cm_per_pixel.*$/cm_per_pixel    ${cm_per_pixel}/" ${sbp_cfg}
+printf "## redshift: ${z}, cm_per_pixel: ${cm_per_pixel}\n"
+## cm_per_pixel }}}
+da=`python -c "print($cm_per_pixel/(.492/3600/180*3.1415926))"`
+dl=`python -c "print($da*(1+$z)**2)"`
+printf "da= ${da}\n"
+printf "dl= ${dl}\n"
+## sbp {{{
+sbp_data_file=`grep '^sbp_file' $sbp_cfg | awk '{print $2}'`
+radius_sbp_file=`grep '^radius_sbp_file' ${cfg_file} | awk '{print $2}'`
+
+if [ "x$radius_sbp_file" = "x" ]; then
+    echo "ERROR, must have radius_sbp_file assigned, this file should be a 4-column file, which contains the radius, radius err, sbp, and sbp err"
+    exit 200
+fi
+
+TMP_RSBP="_tmp_rsbp.txt"
+[ -e "${TMP_RSBP}" ] && rm -f ${TMP_RSBP}
+cat ${radius_sbp_file} | sed 's/#.*$//' | grep -Ev '^\s*$' > ${TMP_RSBP}
+# mv -f _tmp_rsbp.txt ${radius_sbp_file}
+radius_sbp_file="${TMP_RSBP}"
+## sbp }}}
+
+# determine which temperature profile to be used, and fit the T profile {{{
+if [ "$t_profile_type" = "zyy" ]; then
+    $base_path/fit_zyy_model $t_data_file $t_param_file $cm_per_pixel
+    # mv -f zyy_dump.qdp ${T_file}
+    mv -f zyy_dump.qdp zyy_dump_center.qdp
+elif [ "$t_profile_type" = "m0603246" ]; then
+    $base_path/fit_m0603246 $t_data_file $cm_per_pixel
+    # mv -f m0603246_dump.qdp ${T_file}
+    mv -f m0603246_dump.qdp m0603246_dump_center.qdp
+elif [ "$t_profile_type" = "wang2012" ]; then
+    $base_path/fit_wang2012_model $t_data_file $t_param_file $cm_per_pixel 2> /dev/null | tee wang2012_center_param.txt
+    # mv -f wang2012_dump.qdp ${T_file}
+    cp -fv wang2012_dump.qdp ${T_file}
+    T_file_center="wang2012_dump_center.qdp"
+    mv -fv wang2012_dump.qdp ${T_file_center}
+    mv -fv fit_result.qdp wang2012_fit_center.qdp
+elif [ "$t_profile_type" = "allen" ]; then
+    $base_path/fit_allen_model $t_data_file $cm_per_pixel
+    # mv -f allen_dump.qdp ${T_file}
+    mv -f allen_dump.qdp allen_dump_center.qdp
+elif [ "$t_profile_type" = "zzl" ]; then
+    $base_path/fit_zzl_model $t_data_file $t_param_file
+    # mv -f zzl_dump.qdp ${T_file}
+    mv -f zzl_dump.qdp zzl_dump_center.qdp
+else
+    printf "ERROR: temperature profile name \`${t_profile_type}' invalid!\n"
+    exit 10
+fi
+# temp profile }}}
+
+$base_path/coolfunc_calc_bolo.sh ${T_file_center} $abund $nh $z cfunc_bolo.dat
+$base_path/coolfunc_calc.sh ${T_file_center} $abund $nh $z $cfunc_file
+mv -fv flux_cnt_ratio.txt flux_cnt_ratio_center.txt
+# fit sbp (double-beta)
+$base_path/fit_dbeta_sbp $sbp_cfg 2> /dev/null
+mv -fv dbeta_param.txt dbeta_param_center.txt
+cat dbeta_param_center.txt
+mv -fv sbp_fit.qdp sbp_fit_center.qdp
+mv -fv rho_fit.qdp rho_fit_center.qdp
+mv -fv rho_fit.dat rho_fit_center.dat
+$base_path/fit_nfw_mass mass_int.dat $z 2> /dev/null
+mv -fv nfw_param.txt nfw_param_center.txt
+mv -fv nfw_fit_result.qdp nfw_fit_center.qdp
+mv -fv nfw_dump.qdp mass_int_center.qdp
+mv -fv overdensity.qdp overdensity_center.qdp
+mv -fv gas_mass_int.qdp gas_mass_int_center.qdp
+
+#exit 233
+
+## cooling time
+$base_path/cooling_time rho_fit_center.dat ${T_file_center} cfunc_bolo.dat $dl $cm_per_pixel > cooling_time.dat
+## radius to calculate tcool, not the cooling time!
+rcool=`$base_path/analyze_mass_profile.py 500 c | grep '^r500' | awk -F "=" '{print .048*$2}'`
+printf "rcool= ${rcool}\n"
+
+## center value {{{
+if [ "${CENTER_VAL}" = "YES" ]; then
+    $base_path/analyze_mass_profile.py 200 c
+    $base_path/analyze_mass_profile.py 500 c
+    $base_path/extract_tcool.py $rcool | tee cooling_time_result.txt
+    exit 0
+fi
+## center value }}}
+
+# clean previous files
+rm -f summary_shuffle_mass_profile.qdp
+rm -f summary_overdensity.qdp
+rm -f summary_mass_profile.qdp
+rm -f summary_gas_mass_profile.qdp
+
+## count
+COUNT=1
+
+#100 times of Monte-carlo simulation to determine error
+#just repeat above steps
+printf "\n+++++++++++++++++++ Monte Carlo +++++++++++++++++++++\n"
+for i in `seq 1 100`; do
+    # echo $t_data_file
+    $base_path/shuffle_T.py $t_data_file temp_shuffled_t.dat
+    $base_path/shuffle_sbp.py $sbp_data_file temp_shuffled_sbp.dat
+    # t_data_file=temp_shuffled_t.dat
+#exit
+
+    if [ "$t_profile_type" = "zyy" ]; then
+	$base_path/fit_zyy_model temp_shuffled_t.dat $t_param_file $cm_per_pixel
+	mv -f zyy_dump.qdp ${T_file}
+    elif [ "$t_profile_type" = "m0603246" ]; then
+	$base_path/fit_m0603246 temp_shuffled_t.dat $cm_per_pixel
+	mv -f m0603246_dump.qdp ${T_file}
+    elif [ "$t_profile_type" = "wang2012" ]; then
+	$base_path/fit_wang2012_model temp_shuffled_t.dat $t_param_file $cm_per_pixel 2> /dev/null
+        mv -f wang2012_dump.qdp ${T_file}
+    elif [ "$t_profile_type" = "allen" ]; then
+	$base_path/fit_allen_model temp_shuffled_t.dat $cm_per_pixel
+	mv -f allen_dump.qdp ${T_file}
+    elif [ "$t_profile_type" = "zzl" ]; then
+        $base_path/fit_zzl_model temp_shuffled_t.dat $t_param_file
+        mv -f zzl_dump.qdp ${T_file}
+    else
+        printf "ERROR: temperature profile name \`${t_profile_type}' invalid!\n"
+        exit 10
+    fi
+
+#exit
+    : > temp_sbp.cfg
+    
+    cat $sbp_cfg | while read l; do
+        if echo $l | grep -q 'sbp_file'; then
+            echo "sbp_file temp_shuffled_sbp.dat" >> temp_sbp.cfg
+        elif echo $l | grep -q 'T_file'; then
+            echo "T_file ${T_file}" >> temp_sbp.cfg
+        else
+            echo $l >> temp_sbp.cfg
+        fi
+    done
+
+    ## count
+    printf "## ${COUNT} ##\n"
+    COUNT=`expr ${COUNT} + 1`
+    printf "## `pwd` ##\n"
+    $base_path/coolfunc_calc.sh ${T_file} ${abund} ${nh} ${z} ${cfunc_file}
+
+    # double-beta model
+    $base_path/fit_dbeta_sbp temp_sbp.cfg 2> /dev/null
+    [ -r "dbeta_param.txt" ] && cat dbeta_param.txt
+    $base_path/fit_nfw_mass mass_int.dat $z 2> /dev/null
+    cat nfw_dump.qdp >> summary_mass_profile.qdp
+    echo "no no no" >> summary_mass_profile.qdp
+
+    cat overdensity.qdp >> summary_overdensity.qdp
+    echo "no no no" >> summary_overdensity.qdp
+
+    cat gas_mass_int.qdp >> summary_gas_mass_profile.qdp
+    echo "no no no" >> summary_gas_mass_profile.qdp
+
+done        # end `while'
+printf "\n+++++++++++++++++++ Monte Carlo +++++++++++++++++++++\n"
+
+#analys the errors
+printf "\n+++++++++++++++ RESULTS (double-beta) +++++++++++++++\n"
+RESULT="results_dbeta_mrl.txt"
+[ -e "${RESULT}" ] && mv -fv ${RESULT} ${RESULT}_bak
+
+$base_path/analyze_mass_profile.py 200 | tee -a ${RESULT}
+$base_path/analyze_mass_profile.py 500 | tee -a ${RESULT}
+$base_path/analyze_mass_profile.py 1500 | tee -a ${RESULT}
+$base_path/analyze_mass_profile.py 2500 | tee -a ${RESULT}
+
+R200_VAL=`grep '^r200' ${RESULT} | awk '{ print $2 }'`
+R500_VAL=`grep '^r500' ${RESULT} | awk '{ print $2 }'`
+printf "\n## R200: ${R200_VAL}, R500: ${R500_VAL}\n"
+L200=`$base_path/calc_lx $radius_sbp_file flux_cnt_ratio_center.txt $z ${R200_VAL} $t_data_file | grep '^Lx' | awk '{ print $2,$3,$4 }'`
+L500=`$base_path/calc_lx $radius_sbp_file flux_cnt_ratio_center.txt $z ${R500_VAL} $t_data_file | grep '^Lx' | awk '{ print $2,$3,$4 }'`
+printf "L200= ${L200} erg/s\n" | tee -a ${RESULT}
+printf "L500= ${L500} erg/s\n" | tee -a ${RESULT}
+$base_path/extract_tcool.py $rcool | tee cooling_time_result.txt
+printf "\n+++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+