From 29e2816249cc7902ef7ffc5c5d87eb1206ef9b49 Mon Sep 17 00:00:00 2001
From: Qianqian Fang <fangqq@gmail.com>
Date: Mon, 19 Oct 2015 16:49:30 -0400
Subject: [PATCH] fix voidtime flag, fix mesh entry and exit with retessellated
 meshes

---
 mmc/trunk/mmclab/example/demo_compare_mmc_mcx.m |  3 ++-
 mmc/trunk/mmclab/mmclab.m                       |  5 ++++-
 mmc/trunk/src/mmclab.cpp                        |  2 ++
 mmc/trunk/src/tettracing.c                      | 16 +++++++++-------
 4 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/mmc/trunk/mmclab/example/demo_compare_mmc_mcx.m b/mmc/trunk/mmclab/example/demo_compare_mmc_mcx.m
index f21031b8..8dc6442e 100644
--- a/mmc/trunk/mmclab/example/demo_compare_mmc_mcx.m
+++ b/mmc/trunk/mmclab/example/demo_compare_mmc_mcx.m
@@ -57,7 +57,7 @@
 
 if(planarsrc)   % when planar src is used, re-tessellate the mesh
     cfg.srctype='planar';
-    cfg.srcpos=[10 10 -1];
+    cfg.srcpos=[10 10 -10];
     cfg.srcparam1=[40 0 0 0];
     cfg.srcparam2=[0 40 0 0];
 
@@ -73,6 +73,7 @@
     cfg.elemprop=cfg.elem(:,5);
     cfg.elem=cfg.elem(:,1:4);
 end
+cfg=mmclab(cfg,'prep');
 
 %%-----------------------------------------------------------------
 %% run mmclab
diff --git a/mmc/trunk/mmclab/mmclab.m b/mmc/trunk/mmclab/mmclab.m
index 1fcbc46e..681a1376 100644
--- a/mmc/trunk/mmclab/mmclab.m
+++ b/mmc/trunk/mmclab/mmclab.m
@@ -164,7 +164,10 @@
     if(~isfield(cfg(i),'elemprop') ||isempty(cfg(i).elemprop) && size(cfg(i).elem,2)>4)
         cfg(i).elemprop=cfg(i).elem(:,5);
     end
-    cfg(i).elem=meshreorient(cfg(i).node,cfg(i).elem(:,1:4));
+    if(~isfield(cfg(i),'isreoriented') || cfg(i).isreoriented==0)
+        cfg(i).elem=meshreorient(cfg(i).node,cfg(i).elem(:,1:4));
+        cfg(i).isreoriented=1;
+    end
     if(~isfield(cfg(i),'facenb') || isempty(cfg(i).facenb))
         cfg(i).facenb=faceneighbors(cfg(i).elem);
     end
diff --git a/mmc/trunk/src/mmclab.cpp b/mmc/trunk/src/mmclab.cpp
index e93096d9..786d06a7 100644
--- a/mmc/trunk/src/mmclab.cpp
+++ b/mmc/trunk/src/mmclab.cpp
@@ -483,6 +483,8 @@ void mmc_set_field(const mxArray *root,const mxArray *item,int idx, mcconfig *cf
             cfg->nphoton=arraydim[1];
             printf("mmc.nphoton=%d;\n",cfg->nphoton);
         }
+    }else if(strcmp(name,"isreoriented")==0){
+        /*internal flag, don't need to do anything*/
     }else{
         printf("WARNING: redundant field '%s'\n",name);
     }
diff --git a/mmc/trunk/src/tettracing.c b/mmc/trunk/src/tettracing.c
index bab1b584..bc4f4ea7 100644
--- a/mmc/trunk/src/tettracing.c
+++ b/mmc/trunk/src/tettracing.c
@@ -779,16 +779,18 @@ float onephoton(unsigned int id,raytracer *tracer,tetmesh *mesh,mcconfig *cfg,
 		    }
 	    	    if(r.eid==0) break;
 		    /*when a photon enters the domain from the background*/
-		    if((cfg->debuglevel&dlExit) && mesh->med[mesh->type[oldeid-1]].n == cfg->nout && mesh->med[mesh->type[r.eid-1]].n != cfg->nout ){
+		    if(mesh->type[oldeid-1]==0 && mesh->type[r.eid-1]){
+                        if(cfg->debuglevel&dlExit)
 			    fprintf(cfg->flog,"e %f %f %f %f %f %f %f %d\n",r.p0.x,r.p0.y,r.p0.z,
 			    	r.vec.x,r.vec.y,r.vec.z,r.weight,r.eid);
-                            if(!cfg->voidtime)
-                                r.photontimer=0.f;
-                     }
+                        if(!cfg->voidtime)
+                            r.photontimer=0.f;
+                    }
 		    /*when a photon exits the domain into the background*/
-		    if((cfg->debuglevel&dlExit) && mesh->med[mesh->type[oldeid-1]].n != cfg->nout && mesh->med[mesh->type[r.eid-1]].n == cfg->nout ){
-		        fprintf(cfg->flog,"x %f %f %f %f %f %f %f %d\n",r.p0.x,r.p0.y,r.p0.z,
-			    r.vec.x,r.vec.y,r.vec.z,r.weight,r.eid);
+		    if(mesh->type[oldeid-1] && mesh->type[r.eid-1]==0){
+                        if(cfg->debuglevel&dlExit)
+		            fprintf(cfg->flog,"x %f %f %f %f %f %f %f %d\n",r.p0.x,r.p0.y,r.p0.z,
+			        r.vec.x,r.vec.y,r.vec.z,r.weight,r.eid);
 			if(!cfg->isextdet){
                             r.eid=0;
         		    break;