merge from develop

CMakeLists.txt

@@ -75,7 +75,9 @@ if (BUILD_EXAMPLES)
   target_link_libraries(mcplexample_read mcpl)
   add_executable(mcplexample_write "${SRCEX}/rawexample_writemcpl.c")
   target_link_libraries(mcplexample_write mcpl)
-  install(TARGETS mcplexample_read mcplexample_write ${INSTDEST})
+  add_executable(mcplexample_filter "${SRCEX}/rawexample_filtermcpl.c")
+  target_link_libraries(mcplexample_filter mcpl)
+  install(TARGETS mcplexample_read mcplexample_write mcplexample_filter ${INSTDEST})
 endif()
 
 if (BUILD_FAT)

FILES

@@ -24,6 +24,8 @@ src/mcnpssw/        : MCPL hooks for MCNP in C, in the form of a few .h/.c file
                       by MCNP.
 src/mcstas/         : No actual code is here, just a small reminder of how the
                       MCPL plugin shipped with McStas can be used.
+src/mcxtrace/       : No actual code is here, just a small reminder of how the
+                      MCPL plugin shipped with McXtrace can be used.
 src_fat/            : Various "fat" versions of files from the above directories
                       under src/, for convenience. These files are automatically
                       generated and might also contain code under the zlib

LICENSE

@@ -11,10 +11,13 @@ programmes might require additional permissions and licenses, as mandated by the
 third-party programme in question. This is outside the scope of the MCPL
 project, and the authors of MCPL can not be held responsible for any such usage.
 
-If you use MCPL in your scientific work, we would appreciate if you would
-remember to cite the following reference in your writings:
+A substantial effort went into developing MCPL. If you use it for your work, we
+would appreciate it if you would use the following reference in your work:
+
+
+      [ Paper not yet published, please find draft and instructions ]
+      [ for how to cite on https://mctools.github.io/mcpl/          ]
 
-  (submission in progress - please contact [email protected] for details).
 
                           =====================
                          === The CC0 license ===

README

@@ -5,30 +5,32 @@ format with lists of particle state information, for interchanging and
 reshooting events between various Monte Carlo simulation applications.
 
 Hooks for Geant4 (geant4.cern.ch) and MCNP (SSW files) are included in this
-distribution as well. Hooks for McStas (mcstas.org) are already included
-directly upstream in McStas. A few examples of how to use the Geant4 hooks, or
-how to interact with MCPL files from standalone C code, are also provided. Refer
-to the FILES file for more information about included files, and refer to the
-comment at the top of the CMakeLists.txt file for how to build and install with
-CMake.
+distribution as well. Hooks for McStas (mcstas.org) and McXtrace (mcxtrace.org)
+are already included directly upstream in those applications. A few examples of
+how to use the Geant4 hooks, or how to interact with MCPL files from standalone
+C code, are also provided. Refer to the FILES file for more information about
+included files, and refer to the comment at the top of the CMakeLists.txt file
+for how to build and install with CMake.
 
 MCPL and most code distributed here was written 2015-2016 by Thomas Kittelmann
 ([email protected]). The MCNP-SSW converters were written in close
-collaboration with Esben Klinkby ([email protected]), and the McStas converters were
-written by Erik Knudsen ([email protected]) and Peter Willendrup
+collaboration with Esben Klinkby ([email protected]), and the McStas and McXtrace
+converters were written by Erik Knudsen ([email protected]) and Peter Willendrup
 ([email protected]).
 
 See the file LICENSE for usage conditions.
 
+A substantial effort went into developing MCPL. If you use it for your work, we
+would appreciate it if you would use the following reference in your work:
+
+
+      [ Paper not yet published, please find draft and instructions ]
+      [ for how to cite on https://mctools.github.io/mcpl/          ]
+
+
 The latest version of MCPL and further instructions and documentation can be
-found at the websites: http://cern.ch/mcpl and http://mcpl.mccode.org/.
+found at https://mctools.github.io/mcpl/.
 
 Note that instructions for installation and setup of third-party products like
-Geant4, McStas and MCNP are beyond the scope of this file. But for Geant4, a few
-extra tips are given here, to avoid typical issues encountered by new users
-(this was tested with Geant4 10.0.p03):
-
-  1) Refer to the instructions at http://geant4.cern.ch/
-  2) Provide the -DGEANT4_INSTALL_DATA=ON flag to CMake during installation.
-  3) After installation, source <geant4installdir>/bin/geant4.sh to set up
-     a proper runtime environment.
+Geant4, McStas and MCNP are beyond the scope of this file. Please refer to the
+products own instructions for more information.

examples/rawexample_writemcpl.c

@@ -16,6 +16,12 @@
 #include <stdlib.h>
 #include <memory.h>
 
+
+double randuniform(double a, double b)
+{
+  return a + rand() * (b-a) / RAND_MAX;
+}
+
 int main(int argc,char**argv) {
 
   if (argc!=2) {
@@ -32,7 +38,6 @@ int main(int argc,char**argv) {
 
   mcpl_outfile_t f = mcpl_create_outfile(filename);
   mcpl_hdr_set_srcname(f,"my_cool_program_name");
-  mcpl_enable_universal_pdgcode(f,2112);//all particles are neutrons
 
   // By default, floating point numbers will be stored in single precision and
   // neither polarisation nor user-flags will be stored in the file. These
@@ -43,6 +48,10 @@ int main(int argc,char**argv) {
   //    mcpl_enable_polarisation(f);
   //    mcpl_enable_doubleprec(f);
 
+  // If all particles will be of the same type, optimise the file a bit by:
+  //
+  //    mcpl_enable_universal_pdgcode(f,2112);//all particles are neutrons
+
   //We can add comments (strings) to the header. It is always a good idea to add
   //comments explaining things like coordinate system, contents of user-flags
   //(if any), and what the values in the "weight" field means exactly.:
@@ -56,26 +65,31 @@ int main(int argc,char**argv) {
 
   //Allocate the particle structure we will use during the simulation loop
   //to register particle data in the output file:
-  mcpl_particle_t * particle = (mcpl_particle_t*)calloc(sizeof(mcpl_particle_t),1);
+  mcpl_particle_t * particle = mcpl_get_empty_particle(f);
 
   //Simulation loop, modify the particle struct and add to the file as many
   //times as needed (here everything will simply be filled with some stupid
   //random numbers):
   for (int i = 0; i < 1000; ++i) {
+    //particle type:
+    if (rand()%2)
+      particle->pdgcode = 2112;//50% neutrons
+    else
+      particle->pdgcode = 22;//50% gammas
     //position in centimeters:
-    particle->position[0] = rand();
-    particle->position[1] = rand();
-    particle->position[2] = rand();
+    particle->position[0] = randuniform(-100,100);
+    particle->position[1] = randuniform(-100,100);
+    particle->position[2] = randuniform(-100,100);
     //kinetic energy in MeV:
-    particle->ekin = rand();
+    particle->ekin = randuniform(0.001,10);
     //momentum direction (unit vector):
     particle->direction[0] = 0.0;
     particle->direction[1] = 0;
     particle->direction[2] = 1.0;
     //time in milliseconds:
-    particle->time = rand();
+    particle->time = randuniform(0,100);
     //weight in unspecified units:
-    particle->weight = rand();
+    particle->weight = randuniform(0.01,10);
     //modify userflags and polarisation (what units?) as well, if enabled.
 
     //Finally, add the particle to the file:
@@ -84,7 +98,6 @@ int main(int argc,char**argv) {
 
   //At the end, remember to properly close the output file (and cleanup mem if desired):
   mcpl_closeandgzip_outfile(f);
-  free(particle);
 
   //Note: By calling mcpl_closeandgzip_outfile rather than mcpl_close_outfile,
   //the output file will (in most cases) end up being gzipped, resulting in a

src/mcnpssw/sswmcpl.c

@@ -163,7 +163,7 @@ int ssw2mcpl2(const char * sswfile, const char * mcplfile,
       printf("Error: specified configuration file %s does not contain title found in ssw file: \"%s\".\n",inputdeckfile,ssw_title(f));
       return 0;
     }
-    mcpl_hdr_add_data(mcplfh, "mcnp_config_file", (uint32_t)cfgfile_lbuf,(const char *)cfgfile_buf);
+    mcpl_hdr_add_data(mcplfh, "mcnp_input_deck", (uint32_t)cfgfile_lbuf,(const char *)cfgfile_buf);
     free(cfgfile_buf);
   }
 
@@ -199,13 +199,14 @@ int ssw2mcpl2(const char * sswfile, const char * mcplfile,
   actual_filename[0]='\0';
   strcat(actual_filename,tmp);
 
+  int did_gzip = 0;
   if (opt_gzip)
-    mcpl_closeandgzip_outfile(mcplfh);
+    did_gzip = mcpl_closeandgzip_outfile_rc(mcplfh);
   else
     mcpl_close_outfile(mcplfh);
   ssw_close_file(f);
 
-  printf("Created %s%s\n",actual_filename,(opt_gzip?".gz":""));
+  printf("Created %s%s\n",actual_filename,(did_gzip?".gz":""));
   free(actual_filename);
   return 1;
 }
@@ -227,18 +228,18 @@ void ssw2mcpl_parse_args(int argc,char **argv, const char** infile,
       progname = progname ? progname + 1 : argv[0];
       printf("Usage:\n\n");
       printf("  %s [options] input.ssw [output.mcpl]\n\n",progname);
-      printf("Converts the Monte Carlo particles in the input.ssw file (MCNP Surface \n"
+      printf("Converts the Monte Carlo particles in the input.ssw file (MCNP Surface\n"
              "Source Write format) to MCPL format and stores in the designated output\n"
              "file (defaults to \"output.mcpl\").\n"
              "\n"
              "Options:\n"
              "\n"
              "  -h, --help   : Show this usage information.\n"
              "  -d, --double : Enable double-precision storage of floating point values.\n"
-             "  -s, --surf   : Store SSW surface id information in the MCPL userflags.\n"
+             "  -s, --surf   : Store SSW surface IDs in the MCPL userflags.\n"
              "  -n, --nogzip : Do not attempt to gzip output file.\n"
-             "  -c FILE      : Embed entire configuration FILE used to produce input.sww\n"
-             "                 in the MCPL header.\n"
+             "  -c FILE      : Embed entire configuration FILE (the input deck)\n"
+             "                 used to produce input.ssw in the MCPL header.\n"
              );
       exit(0);
     }
@@ -475,8 +476,6 @@ int mcpl2ssw(const char * inmcplfile, const char * outsswfile, const char * refs
       rawtype = conv_mcnp6_pdg2ssw(mcpl_p->pdgcode);
     else
       rawtype = conv_mcnpx_pdg2ssw(mcpl_p->pdgcode);
-    if (rawtype==2)
-      rawtype=0;
     if (!rawtype) {
       ++skipped_nosswtype;
       if (skipped_nosswtype<=100) {
@@ -555,30 +554,31 @@ int mcpl2ssw_app_usage( const char** argv, const char * errmsg ) {
   progname =  progname ? progname + 1 : argv[0];
   printf("Usage:\n\n");
   printf("  %s [options] <input.mcpl> <reference.ssw> [output.ssw]\n\n",progname);
-  printf("Converts the Monte Carlo particles in the input MCPL file to SSW format (MCNP\n"
-         "Surface Source Write) and stores the result in the designated output file (defaults\n"
-         "to \"output.ssw\").\n"
+  printf("Converts the Monte Carlo particles in the input MCPL file to SSW format\n"
+         "(MCNP Surface Source Write) and stores the result in the designated output\n"
+         "file (defaults to \"output.ssw\").\n"
          "\n"
-         "In order to do so and get the details of the SSW format correct, the user must also\n"
-         "provide a reference SSW file from the same approximate setup (MCNP version, input\n"
-         "deck...) where the new SSW file is to be used. The reference SSW file can of course\n"
-         "be very small, as only the file header is important (the new file essentially gets\n"
-         "a copy of the header found in the reference file, except for certain fields related\n"
-         "to number of particles whose values are changed).\n"
+         "In order to do so and get the details of the SSW format correct, the user\n"
+         "must also provide a reference SSW file from the same approximate setup\n"
+         "(MCNP version, input deck...) where the new SSW file is to be used. The\n"
+         "reference SSW file can of course be very small, as only the file header is\n"
+         "important (the new file essentially gets a copy of the header found in the\n"
+         "reference file, except for certain fields related to number of particles\n"
+         "whose values are changed).\n"
          "\n"
-         "Finally, one must pay attention to the Surface ID assigned to the particles in the\n"
-         "resulting SSW file: Either the user specifies a global one with -s<ID>, or it is assumed\n"
-         "that the MCPL userflags field in the input file is actually intended to become the\n"
-         "Surface ID. Note that not all MCPL files have userflag fields and that valid Surface\n"
-         "IDs are integers in the range 1-999999.\n"
+         "Finally, one must pay attention to the Surface ID assigned to the\n"
+         "particles in the resulting SSW file: Either the user specifies a global\n"
+         "one with -s<ID>, or it is assumed that the MCPL userflags field in the\n"
+         "input file is actually intended to become the Surface ID. Note that not\n"
+         "all MCPL files have userflag fields and that valid Surface IDs are\n"
+         "integers in the range 1-999999.\n"
          "\n"
          "Options:\n"
          "\n"
          "  -h, --help   : Show this usage information.\n"
-         "  -d, --double : Enable double-precision storage of floating point values.\n"
-         "  -s<ID>       : All particles in the resulting SSW file will have this surface ID.\n"
-         "  -l<LIMIT>    : Limit the maximum number of particles to put in the SSW file (note\n"
-         "                 that SSW files only supports up to 2147483647 particles).\n"
+         "  -s<ID>       : All particles in the SSW file will get this surface ID.\n"
+         "  -l<LIMIT>    : Limit the number of particles transferred to the SSW file\n"
+         "                 (defaults to 2147483647, the maximal SSW capacity).\n"
          );
   return 0;
 }
@@ -624,6 +624,10 @@ int mcpl2ssw_parse_args(int argc,const char **argv, const char** inmcplfile,
             return mcpl2ssw_app_usage(argv,"Bad option: missing number");
         }
       }
+
+    } else if (n==6 && strcmp(a,"--help")==0) {
+      mcpl2ssw_app_usage(argv,0);
+      return -1;
     } else if (n>=1&&a[0]!='-') {
       if (*outsswfile)
         return mcpl2ssw_app_usage(argv,"Too many arguments.");

src/mcnpssw/sswread.c

@@ -315,8 +315,8 @@ ssw_file_t ssw_open_file(const char * filename)
   /* printf("ssw_open_file: Found aids  = '%s'\n",f->aids); */
 
   if ( f->is_mcnp6 ) {
-    if ( strcmp(f->vers,"6")!=0 ) {
-      printf("ssw_open_file error: Unsupported MCNP6 source version :\"%s\" (must be \"6\")\n",f->vers);
+    if ( strcmp(f->vers,"6")!=0 && strcmp(f->vers,"6.mpi")!=0 ) {
+      printf("ssw_open_file error: Unsupported MCNP6 source version :\"%s\" (must be \"6\" or \"6.mpi\")\n",f->vers);
       return ssw_openerror(f,"ssw_open_file error: Unsupported MCNP6 source version");
     }
   } else {
@@ -536,7 +536,7 @@ int32_t conv_mcnpx_ssw2pdg(int32_t c)
   if (c<=34)
     return conv_mcnpx_to_pdg_0to34[c];
   if (c>=401&&c<=434)
-    return - conv_mcnpx_to_pdg_0to34[c%100];
+    return c==402 ? 22 : - conv_mcnpx_to_pdg_0to34[c%100];
   int32_t sign = 1;
   if (c%1000==435) {
     sign = -1;
@@ -554,6 +554,10 @@ int32_t conv_mcnpx_ssw2pdg(int32_t c)
     long ZM1 = c%1000;
     return sign * (1000000000 + (ZM1+1)*10000 + A*10);
   }
+  //Retry without non-type related parts:
+  int j = (c%1000)/100;
+  if (j==2||j==6)
+    return conv_mcnpx_ssw2pdg(c-200);
   return 0;
 }
 
@@ -568,7 +572,7 @@ int32_t conv_mcnp6_ssw2pdg(int32_t c)
     //Note that A (see below) has been observed in SSW files to have non-zero
     //values for ptype<37 as well, so don't require A, Z or S to be 0 here.
     int32_t p = conv_mcnp6_to_pdg_0to36[ptype];
-    return antibit ? -p : p;
+    return (antibit&&p!=22) ? -p : p;
   }
   if (ptype==37) {
     int A = c%512;  c /=  512;