Expand environment variable in egs++ applications

HEN_HOUSE/user_codes/cavity/cavity.cpp

@@ -2822,6 +2822,7 @@ int Cavity_Application::initScoring() {
  if( err3 ) egsFatal(
  "\n\n*** Wrong/missing 'muen file' input for a "
  "HVL calculation\n This is a fatal error\n\n");
+ muen_file = egsExpandPath(muen_file);
  ifstream muen_data(muen_file.c_str());
  if( !muen_data ){
  egsFatal(

HEN_HOUSE/user_codes/egs_cbct/egs_cbct.cpp

@@ -1145,15 +1145,19 @@ int EGS_CBCT::initScoring() {
  if( err3 ) egsFatal(
  "\n\n*** Wrong/missing 'muen file' input for a "
  "kerma calculation\n This is a fatal error\n\n");
+ muen_file = egsExpandPath(muen_file);
  ifstream muen_data(muen_file.c_str());
  if( !muen_data.is_open() ){
  egsFatal(
  "\n\n*** Failed to open muen file %s\n"
  " This is a fatal error\n",muen_file.c_str());
  }
  else{
- egsInformation("\nUsing E*muen file %s for air-kerma calculation\n",
- muen_file.c_str());
+ egsInformation(
+ "\n\n=============== Kerma Scoring ===============\n"
+ "E*muen/rho file: %s\n"
+ "=============================================\n",
+ muen_file.c_str());
  }
  int ndat; muen_data >> ndat;
  if( ndat < 2 || muen_data.fail() ) egsFatal(
@@ -1403,7 +1407,7 @@ void EGS_CBCT::initOutput() {
  scan_type = blank;
  }
  else{
- blank_scan = b_scan;
+ blank_scan = egsExpandPath(b_scan);
  }
  /*
  If no scan file name entry, a warning is issued.
@@ -1417,7 +1421,7 @@ void EGS_CBCT::initOutput() {
  " This is not a proper CBCT calculation.\n\n");
  }
  else{
- real_scan = the_scan;
+ real_scan = egsExpandPath(the_scan);
  }
  /* check what scans are requested by the user
  real => real scan simulation

HEN_HOUSE/user_codes/egs_cbct/example_w5br.egsinp

@@ -31,8 +31,8 @@
 #
 # Projections at other angles can be obtained by modifying input block
 # :cbct setup: below. One can define the projection angle and angular
-# :interval. Negative values of the latter indicate rotation is done
-# :counter-clockwise around the indicated axis.
+# interval. Negative values of the latter indicate rotation is done
+# counter-clockwise around the indicated axis.
 #
 # BEWARE:
 #
@@ -43,8 +43,6 @@
 # - media information in PEGS4 data file 521icru.pegs4dat distributed
 # with EGSnrc.
 #
-# - Replace $EGS_HOME string below with the actual value!!!
-#
 # - If the detector resolution is changed, one must recalculate the blank
 # scan
 #
@@ -183,7 +181,7 @@
  rotation = 0 1.570796326794896619 0
  :stop transformation:
  # Uses file provided in the distribution
- muen file = /home/mainegra/egsnrc_mp/egs_fac/muen_air.data
+ muen file = $HEN_HOUSE/user_codes/egs_fac/examples/muen_air.data
  :stop planar scoring:
 
 :stop scoring options:
@@ -197,13 +195,13 @@
  ###############################################
  # Use the 2 lines below to produce a blank scan
  ###############################################
- #scan file = /home/mainegra/egsnrc_mp/egs_cbct/blank_coll_64.scan
+ #scan file = $EGS_HOME/egs_cbct/blank_coll_64.scan
  #scan type = blank
  ###############################################
  # Use the 3 lines below to produce real scans
  ###############################################
- scan file = /home/mainegra/egsnrc_mp/egs_cbct/scan_w5br_coll_64.scan
- blank scan = /home/mainegra/egsnrc_mp/egs_cbct/blank_coll_64.scan
+ scan file  = $EGS_HOME/egs_cbct/scan_w5br_coll_64.scan
+ blank scan = $EGS_HOME/egs_cbct/blank_coll_64.scan
  scan type = scatter
  ###############################################
  :stop scan output:
@@ -286,18 +284,20 @@
 
 
 ########
-# For fast computation one can use KN for Compton scattering. However,
-# in realistic phantoms this may cause a 3% discrepancy.
+# For fast computation one can assume scattering from free electrons.
+# However, in realistic phantoms this may cause a 3% discrepancy.
 ########
 :start MC transport parameter:
 
  Global ECUT = 1
 
- Photon cross sections = xcom # epdl (or xcom)
+ Photon cross sections  = xcom # epdl (or xcom)
 
  Bound Compton scattering = off
+
+ Rayleigh scattering = off
 
- Rayleigh scattering= on
+ Atomic relaxations = off
 
 :stop MC transport parameter:
 

HEN_HOUSE/user_codes/egs_fac/egs_fac.cpp

@@ -955,9 +955,17 @@ int EGS_FACApplication::initScoring() {
  int err3 = options->getInput("muen file",muen_file);
  if( err3 ) egsFatal("\n\n*** Wrong/missing 'muen file' input\n"
  " This is a fatal error\n\n");
+ muen_file = egsExpandPath(muen_file);
  ifstream muen_data(muen_file.c_str());
  if( !muen_data ) egsFatal("\n\n*** Failed to open muen file %s\n"
  " This is a fatal error\n",muen_file.c_str());
+ else{
+ egsInformation(
+ "\n\n=============== Kerma Scoring ===============\n"
+ "E*muen/rho file: %s\n"
+ "=============================================\n\n",
+ muen_file.c_str());
+ }
  int ndat; muen_data >> ndat;
  if( ndat < 2 || muen_data.fail() ) egsFatal(
  "\n\n*** Failed to read muen dfata file\n");

HEN_HOUSE/user_codes/egs_fac/examples/example_mees_250kV.egsinp

@@ -29,8 +29,7 @@
 #
 # An example input file for egs_fac.
 #
-# NOTE: Substitute every instance of $HEN_HOUSE for its actual value in this
-# file! It is essential to use 'Bound Compton Scattering = norej'. See the MC
+# NOTE: It is essential to use 'Bound Compton Scattering = norej'. See the MC
 # transport parameter input section for more info. See comments accompanying
 # the various inputs for more details.
 #
@@ -803,7 +802,7 @@
  # ignores them (except for the first and last energy, which define the
  # energy interval).
  #
- muen file = $HEN_HOUSE/user_codes/egs_fac/muen_air.data
+ muen file = $HEN_HOUSE/user_codes/egs_fac/examples/muen_air.data
 
 :stop scoring options:
 
@@ -852,4 +851,4 @@
  Bound Compton Scattering = norej
  Photon cross sections = xcom # (could also be epdl or si)
 
-:stop MC transport parameter:
+:stop MC transport parameter:

HEN_HOUSE/user_codes/egs_fac/examples/mxr-320-250kVp_tube.egsinp

@@ -163,9 +163,16 @@ AIRICRU512
 
  :Stop MC Transport Parameter:
  #########################
+ #
+ # User-defined entries
+ #
+ #########################
  :Start user inputs:
 
- # phsp output directory = /home/mainegra/egsnrc_mp/phsp/
+ # Enter here a custom location for phase-space file output
+ # For instance users might want to direct the output to a
+ # device with enough disk space!
+ # phsp output directory = enter_user_defined_location
 
  :Stop user inputs:
  #########################

HEN_HOUSE/user_codes/egs_kerma/egs_kerma.cpp

@@ -1012,12 +1012,22 @@ int EGS_KermaApplication::initScoring() {
  "\n\n*** Wrong/missing 'emuen file' input for a "
  "Kerma calculation\n This is a fatal error\n\n");
  }
+
+ muen_file = egsExpandPath(muen_file);
+
  ifstream muen_data(muen_file.c_str());
  if (!muen_data) {
  egsFatal(
  "\n\n*** Failed to open emuen file %s\n"
  " This is a fatal error\n",muen_file.c_str());
  }
+ else{
+ egsInformation(
+ "\n\n=============== Kerma Scoring ===============\n"
+ "E*muen/rho file: %s\n"
+ "=============================================\n\n",
+ muen_file.c_str());
+ }
  int ndat;
  muen_data >> ndat;
  if (ndat < 2 || muen_data.fail()) egsFatal(

HEN_HOUSE/user_codes/egs_kerma/example_40keV_SDD_1m_FD.egsinp

@@ -211,7 +211,8 @@
  :stop fluence scoring:
 
  ### E*muen file (could also be E*mutr): absolute or relative file path
- emuen file = emuen_icru90_1.5MeV.data
+ ### Use absolute path when submitting parallel jobs!!!
+ emuen file = $EGS_HOME/egs_kerma/emuen_icru90_1.5MeV.data
 
  ### geometry for forced-detection (if omitted, an analog scoring is used)
  cavity geometry = cavity