[feat] use self-contained json input including mesh data

examples/validation/cube2.json

@@ -0,0 +1,61 @@
+{
+    "Domain": {
+        "MeshNode": [
+            [ 0, 0, 0],
+            [60, 0, 0],
+            [ 0,60, 0],
+            [60,60, 0],
+            [ 0, 0,60],
+            [60, 0,60],
+            [ 0,60,60],
+            [60,60,60]
+         ],
+        "MeshElem": [
+	    [1, 2, 8, 4, 1],
+	    [1, 3, 4, 8, 1],
+	    [1, 2, 6, 8, 1],
+	    [1, 5, 8, 6, 1],
+	    [1, 3, 8, 7, 1],
+	    [1, 5, 7, 8, 1]
+         ],
+	 "InitElem": 2,
+         "Media": [
+             {"mua": 0.00, "mus": 0.0, "g": 1.00, "n": 1.0},
+             {"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.37}
+         ]
+    },
+    "Session": {
+	"Photons":  30000000,
+	"RNGSeed":  27182818,
+	"ID":       "cube"
+    },
+    "Forward": {
+	"T0": 0.0e+00,
+	"T1": 5.0e-09,
+	"Dt": 1.0e-10
+    },
+    "Optode": {
+	"Source": {
+	    "Pos": [30.1, 30.2, 0.0],
+	    "Dir": [0.0, 0.0, 1.0]
+	},
+	"Detector": [
+	    {
+		"Pos": [30.0, 20.0, 0.0],
+		"R": 1.0
+	    },
+            {
+                "Pos": [30.0, 40.0, 0.0],
+                "R": 1.0
+            },
+            {
+                "Pos": [20.0, 30.0, 0.0],
+                "R": 1.0
+            },
+            {
+                "Pos": [40.0, 30.0, 0.0],
+                "R": 1.0
+            }
+	]
+    }
+}

src/mmc_highorder.cpp

@@ -31,8 +31,11 @@
 
 #include <set>
 #include <list>
+#include <vector>
+#include <map>
 #include <algorithm>
 #include <string.h>
+
 #include "mmc_mesh.h"
 #include "mmc_highorder.h"
 #include "mmc_utils.h"
@@ -41,6 +44,8 @@
 
 const int edgepair[TETEDGE][2] = {{0, 1}, {0, 2}, {0, 3}, {1, 2}, {1, 3}, {2, 3}};
 
+const int facelist[4][3] = {{0, 1, 2}, {0, 1, 3}, {0, 2, 3}, {1, 2, 3}};
+
 #ifdef __cplusplus
     extern "C"
 #endif
@@ -99,3 +104,52 @@ void mesh_10nodetet(tetmesh* mesh, mcconfig* cfg) {
         pos++;
     }
 }
+
+std::string face_to_string(int a, int b, int c) {
+    int ar[3];
+    ar[0] = MIN(MIN(a, b), c);
+    ar[2] = MAX(MAX(a, b), c);
+    ar[1] = - ar[0] - ar[2] + a + b + c;
+
+    return std::to_string(ar[0]) + "," + std::to_string(ar[1]) + "," + std::to_string(ar[2]);
+}
+
+#ifdef __cplusplus
+    extern "C"
+#endif
+void mesh_getfacenb(tetmesh* mesh, mcconfig* cfg) {
+    std::vector<std::string> faces;
+    std::map<std::string, std::pair<unsigned int, unsigned int>> facenb;
+
+    faces.reserve(mesh->ne << 2);
+
+    for (int i = 0; i < mesh->ne; i++) {
+        int* ee = mesh->elem + i * mesh->elemlen;
+
+        for (int j = 0; j < 4; j++) {
+            faces.push_back(face_to_string(ee[facelist[j][0]], ee[facelist[j][1]], ee[facelist[j][2]]));
+        }
+    }
+
+    for (unsigned int i = 0; i < faces.size(); i++) {
+        if (facenb.count(faces[i])) {
+            facenb[faces[i]].second = (i >> 2) + 1;
+        } else {
+            facenb[faces[i]] = std::make_pair((i >> 2) + 1, 0);
+        }
+    }
+
+    if (mesh->facenb) {
+        free(mesh->facenb);
+    }
+
+    mesh->facenb = (int*)calloc(sizeof(int) * mesh->elemlen, mesh->ne);
+
+    for (unsigned int i = 0; i < faces.size(); i++) {
+        std::pair<unsigned int, unsigned int> item = facenb[faces[i]];
+
+        if (item.second != 0) {
+            mesh->facenb[i] = ((i >> 2) + 1 == item.first ? item.second : item.first);
+        }
+    }
+}

src/mmc_highorder.h

@@ -33,8 +33,13 @@
 #define _MCEXTREME_LOGISTIC_RAND_H
 
 #ifdef __cplusplus
-    extern "C"
+extern "C" {
 #endif
 void mesh_10nodetet(tetmesh* mesh, mcconfig* cfg);
+void mesh_getfacenb(tetmesh* mesh, mcconfig* cfg);
+
+#ifdef __cplusplus
+}
+#endif
 
 #endif

src/mmc_host.c

@@ -120,7 +120,7 @@ int mmc_reset(mcconfig* cfg, tetmesh* mesh, raytracer* tracer) {
 
 int mmc_cleanup(mcconfig* cfg, tetmesh* mesh, raytracer* tracer) {
     tracer_clear(tracer);
-    mesh_clear(mesh);
+    mesh_clear(mesh, cfg);
     mcx_clearcfg(cfg);
     return 0;
 }