Fix various small issues ahead of release

HEN_HOUSE/doc/src/pirs898-egs++/egs_cbct.doxy

@@ -160,7 +160,7 @@ By default sources are placed at the origin and directed along the positive z-ax
 If the source should be somewhere else, an affine transformation must be applied.
 Transformations are not implemented in most sources, hence one must use a transformed
 source. The example below rotates the collimated source from the previous slide
-\f$90^{o}\f$ around the y-axis, placing it on the negative x-axis:
+\f$90^{o}\f$ around the y-axis, placing it on the positive x-axis:
 
 \verbatim
 :start source:

HEN_HOUSE/doc/src/pirs898-egs++/main.doxy

@@ -55,7 +55,7 @@
  </tr>
  <tr>
  <td>
- <a href="https://github.com/nrc-cnrc/EGSnrc/wiki/FAQ#how-do-i-cite-the-egsnrc-software">How to cite EGSnrc</a>
+ <a href="https://github.com/nrc-cnrc/EGSnrc/wiki/Citing-EGSnrc">Citing EGSnrc</a>
  </td>
  </tr>
  <tr>

HEN_HOUSE/egs++/egs_advanced_application.cpp

@@ -407,19 +407,19 @@ EGS_AdvancedApplication::~EGS_AdvancedApplication() {
  delete [] rng_buffer;
  }
  if (nmed > 0) {
- delete [] i_ededx;
- delete [] i_pdedx;
- delete [] i_esig;
- delete [] i_psig;
- delete [] i_ebr1;
- delete [] i_pbr1;
- delete [] i_pbr2;
- delete [] i_gmfp;
- delete [] i_gbr1;
- delete [] i_gbr2;
- delete [] i_cohe;
- delete [] i_photonuc;
- }
+  delete [] i_ededx;
+  delete [] i_pdedx;
+  delete [] i_esig;
+  delete [] i_psig;
+  delete [] i_ebr1;
+  delete [] i_pbr1;
+  delete [] i_pbr2;
+  delete [] i_gmfp;
+  delete [] i_gbr1;
+  delete [] i_gbr2;
+  delete [] i_cohe;
+  delete [] i_photonuc;
+  }
 }
 
 void EGS_AdvancedApplication::describeSimulation() {

HEN_HOUSE/egs++/egs_application.cpp

@@ -1007,7 +1007,7 @@ void EGS_Application::addAusgabObject(EGS_AusgabObject *o) {
  for (int j=0; j<a_objects_list.size(); ++j) {
  if (a_objects_list[j]->getObjectType() == "EGS_TrackScoring") {
  egsFatal("error: only one ausgab object of type "
- "'EGS_TrackScoring' is allowed\n");
+  "'EGS_TrackScoring' is allowed\n");
  }
  }
  }

HEN_HOUSE/egs++/egs_spectra.cpp

@@ -726,7 +726,7 @@ class EGS_EXPORT EGS_RadionuclideBetaSpectrum {
  for (int k=1; k<=4; k++) {
 
  gk = sqrt(k*k-az*az);
- x1 = pow((pow(p,k-1)/dfac[k-1]) ,2);
+ x1 = pow((pow(p,k-1)/dfac[k-1]), 2);
 
  aa = clgamma(complex<double>(gk,y));
  double aa_real = real(aa);

HEN_HOUSE/egs++/geometry/egs_vhp_geometry/egs_vhp_geometry.cpp

@@ -655,7 +655,7 @@ EGS_TestMicro::EGS_TestMicro(EGS_Float Dx, EGS_Float Dy, EGS_Float Dz,
  nreg = nr*micro->mx*micro->my*micro->mz;
 }
 
-void EGS_TestMicro::setMedia(EGS_Input *, int , const int *) {
+void EGS_TestMicro::setMedia(EGS_Input *, int, const int *) {
  egsFatal("EGS_TestMicro::setMedia(EGS_Input*,int,const int *):\n"
  " Don't use this method. Media are only set via the micro matrix"
  " data\n");

HEN_HOUSE/scripts/configure

@@ -125,7 +125,7 @@ read response
 
 printf $format "Checking system type ... " >&2
 canonical_system=$($my_dir/config.guess)
-system_name=$(uname -s | sed ":/:_:g" | tr '[:upper:]' '[:lower:]')
+system_name=$(uname -s | sed "s|/|_|g" | tr '[:upper:]' '[:lower:]')
 if test "x$system_name" = xdarwin; then
  system_name="osx"
 fi

HEN_HOUSE/src/egsnrc.macros

@@ -1429,10 +1429,6 @@ DO J=1,$MXREG [
 ]
 ;}
 
-REPLACE {$KERMA-INSERT;} WITH {;}
- "USED IN KERMA CALCULATIONS---DEFAULT IS NULL"
-; "---------- BUFFER FLUSH SEMICOLON ----------"
-
 "MACRO FOR CONTROLLING NEGATIVE USTEP"
 REPLACE {$USER-CONTROLS-NEGATIVE-USTEP;} WITH {
 " ============================"

HEN_HOUSE/src/egsnrc.mortran

@@ -6703,30 +6703,9 @@ IF (IQI = 2) ["PI-ZERO OPTION"
  CALL UPHI(3,2);
 ]"end of pi-zero option"
 
-"The following convoluted logic is difficult to follow"
-"when one modifies the outcome of certain interactions"
-"using nbr_split, Russian Roulette, or one of the "
-"particle selection macros. I'm simplifying it "
-"so that ircode becomes irrelevant. IK, August 2002 "
-":TOPSTACK:"
-"LOOP["
-" $KERMA-INSERT;"
-" IF(IQ(NP) = 0) GO TO :PHOTON:;"
-" LOOP ["
-" :ELECTRON:"
-" CALL ELECTR(IRCODE);"
-" IF(IRCODE.EQ.2) EXIT; "
-" :PHOTON:"
-" CALL PHOTON(IRCODE);"
-" IF(IRCODE.EQ.2) EXIT;"
-" ]REPEAT"
-" IF(NP <= 0) EXIT;"
-"]REPEAT "
-
 LOOP [
  ;
  IF( np <= 0 ) EXIT;
- $KERMA-INSERT; " DEFAULT FOR $KERMA-INSERT; IS ; (NULL)"
  IF( iq(np) = 0 ) [ call photon(ircode); ]
  ELSE [ call electr(ircode); ]
 

HEN_HOUSE/user_codes/tutor7pp/tutor7pp.cpp

@@ -163,14 +163,14 @@ class APP_EXPORT Tutor7_Application : public EGS_AdvancedApplication {
  bool deflect_brems;
 
  EGS_Float *ph_de; // bin widths if the pulse height distributions.
- int *ph_regions; // region indeces of the ph-dsitributions
+ int *ph_regions; // region indices of the ph-distributions
  static string revision; // the CVS revision number
 
 public:
 
  /*! Constructor
  The command line arguments are passed to the EGS_AdvancedApplication
- contructor, which determines the input file, the pegs file, if the
+ constructor, which determines the input file, the pegs file, if the
  simulation is a parallel run, etc.
  */
  Tutor7_Application(int argc, char **argv) :
@@ -312,7 +312,7 @@ void Tutor7_Application::describeUserCode() const {
 }
 
 int Tutor7_Application::initScoring() {
- // Get the numner of regions in the geometry.
+ // Get the number of regions in the geometry.
  nreg = geometry->regions();
  score = new EGS_ScoringArray(nreg+2);
  //i.e. we always score energy fractions