Fix #945, #804: egs_chamber examples don't run by default

Fix the egs_chamber examples so that they now run without needed to
compile any BEAMnrc accelerators or make changes to the input file. Also
fix a typo in the example2 water box size.

HEN_HOUSE/user_codes/egs_chamber/example1_co60_Pfactors.egsinp

@@ -23,19 +23,26 @@
 #
 # Author: Iwan Kawrakow, 2009
 #
-# Contributors:
+# Contributors: Reid Townson
 #
 ###############################################################################
 #
-# An example input file for egs_chamber.
+# An example input file for egs_chamber. This is an advanced example.
 #
 # This file defines an egs_chamber simulation of a farmer type chamber at
 # 5 cm depth in a 30x30x30 cm^3 water phantom irradiated by a Co-60 beam from
-# a BEAMnrc simulation source. The XCSE technique is used combined with
+# a BEAMnrc simulation source. The chamber model is just an example, and does
+# not match any particular specifications.
+#
+# The XCSE variance reduction technique is used combined with
 # correlated sampling for calculation in chamber geometries that do not have
 # a stem, a central electrode, a wall, etc., to compute the various
 # correction factors known as Pstell, Pcell, Pwall, and Prepl.
 #
+# Run this example using 521icru.pegs4dat:
+#
+# egs_chamber -i example1_co60_Pfactors -p 521icru
+#
 ###############################################################################
 
 
@@ -55,48 +62,48 @@
  thickness = 0.0417
  top radii = 0.
  bottom radii = 0.0858
- media = C173521ICRU
+ media = 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 0.1283
  top radii = 0. 0.0858
  bottom radii = 0.3125 0.35
- media = AIR521ICRU C173521ICRU
+ media = AIR521ICRU 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 0.2217
  bottom radii = 0.3125 0.35
- media = AIR521ICRU C173521ICRU
+ media = AIR521ICRU 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 2.05
  top radii = 0.050 0.3125 0.35
  bottom radii = 0.050 0.3125 0.35
- media = AL521ICRU AIR521ICRU C173521ICRU
+ media = AL521ICRU AIR521ICRU 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 0.3
  top radii = 0.050 0.175 0.35 0.4000
  bottom radii = 0.050 0.175 0.35 0.4000
- media = AL521ICRU PTCFE521ICRU C173521ICRU DURAL521ICRU
+ media = AL521ICRU POLYETH521ICRU 170C521ICRU AL521ICRU
  :stop layer:
  :start layer:
  thickness = 1.005
  top radii = 0.050 0.175 0.35 0.4000
  bottom radii = 0.050 0.175 0.35 0.4000
- media = AL521ICRU PTCFE521ICRU C173521ICRU DURAL521ICRU
+ media = AL521ICRU POLYETH521ICRU 170C521ICRU AL521ICRU
  :stop layer:
  :start layer:
  thickness = 0.84
  top radii = 0.050 0.35 0.4000
  bottom radii = 0.050 0.35 0.4000
- media = AL521ICRU PTCFE521ICRU DURAL521ICRU
+ media = AL521ICRU POLYETH521ICRU AL521ICRU
  :stop layer:
  :start layer:
  thickness = 1.655
  top radii = 0.0750 0.3500 0.4000
  bottom radii = 0.0750 0.3500 0.4000
- media = AL521ICRU PTCFE521ICRU DURAL521ICRU
+ media = AL521ICRU POLYETH521ICRU AL521ICRU
  :stop layer:
  :stop geometry:
 
@@ -110,24 +117,24 @@
  thickness = 0.0417
  top radii = 0.
  bottom radii = 0.0858
- media = C173521ICRU
+ media = 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 0.1283
  top radii = 0. 0.0858
  bottom radii = 0.3125 0.35
- media = AIR521ICRU C173521ICRU
+ media = AIR521ICRU 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 0.2217
  bottom radii = 0.3125 0.35
- media = AIR521ICRU C173521ICRU
+ media = AIR521ICRU 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 2.05
  top radii = 0.050 0.3125 0.35
  bottom radii = 0.050 0.3125 0.35
- media = AL521ICRU AIR521ICRU C173521ICRU
+ media = AL521ICRU AIR521ICRU 170C521ICRU
  :stop layer:
  :stop geometry:
 
@@ -143,24 +150,24 @@
  thickness = 0.0417
  top radii = 0.
  bottom radii = 0.0858
- media = C173521ICRU
+ media = 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 0.1283
  top radii = 0. 0.0858
  bottom radii = 0.3125 0.35
- media = AIR521ICRU C173521ICRU
+ media = AIR521ICRU 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 0.2217
  bottom radii = 0.3125 0.35
- media = AIR521ICRU C173521ICRU
+ media = AIR521ICRU 170C521ICRU
  :stop layer:
  :start layer:
  thickness = 2.05
  top radii = 0.050 0.3125 0.35
  bottom radii = 0.050 0.3125 0.35
- media = AIR521ICRU AIR521ICRU C173521ICRU
+ media = AIR521ICRU AIR521ICRU 170C521ICRU
  :stop layer:
  :stop geometry:
 
@@ -350,15 +357,6 @@
  inscribed geometries = chamber
  :stop geometry:
  #
- # Same but for phsp scoring
- #
- :start geometry:
- library = egs_genvelope
- name = chamber_in_water
- base geometry = cse_phantom
- inscribed geometries = chamber
- :stop geometry:
- #
  # Water phantom with chamber without stem
  #
  :start geometry:
@@ -423,18 +421,27 @@
 :stop geometry definition:
 
 ########################################### The source:
-# a full BEAMnrc treatment head
-# simulation
+# A Co-60 collimated spectrum source, for a 10x10cm2 field at the origin.
+# The source is 100cm from the surface of the water.
+# The chamber is at 5cm depth, at z=0.
 :start source definition:
 
  :start source:
- library = egs_beam_source
  name = the_source
- beam code = BEAM_co60
- pegs file = gmora
- input file = 10x10_20000dsb_espl_augrr_delta1.5
- particle type = all
- weight window = 0 1e-4 # This discards fat particles.
+ library = egs_collimated_source
+ charge = 0
+ :start source shape:
+ type = point
+ position = 0 0 -105.000
+ :stop source shape:
+ :start target shape:
+ library = egs_rectangle
+ rectangle = -5 -5 5 5
+ :stop target shape:
+ :start spectrum:
+ type = tabulated spectrum
+ spectrum file = $HEN_HOUSE/spectra/egsnrc/mora_10x10_60co_ssd80.ensrc
+ :stop spectrum:
  :stop source:
 
  simulation source = the_source
@@ -445,7 +452,7 @@
 #
 :start run control:
 
- ncase = 2200000000
+ ncase = 1000000 # Increase this to reduce the uncertainty
 
 :stop run control:
 
@@ -469,17 +476,6 @@
  cavity geometry = inner_phsp_object
  enhance regions = -1 # i.e. enhance everywhere except in region 0
  enhancement = 512
- #
- # Note: the transformation specified below is applied to particle
- # positions before checking if the particle enters the geometry.
- # In the case of a BEAMnrc simulation source, the particle positions
- # are the positions when the particles cross the scoring plane
- # i.e. at (x,y,100) in this case. The top of this geometry is at
- # z=-5 => we must translate the particle positions by -105.
- #
- :start transformation:
- translation = 0 0 -105.0001
- :stop transformation:
  :stop calculation geometry:
 
 # -------------------------------------- the actual calculation geometries