Fix crashes caused by unneccesary updateParticleList call prior to RB attached...

Fix crashes caused by unneccesary updateParticleList call prior to RB attached particle update and improper initialization of atomic indicies for RB attached particles

src/GrandBrownTown.cu

@@ -566,19 +566,20 @@ void GrandBrownTown::run()
     wkf_timer_start(timer0);
     wkf_timer_start(timerS);
 
-    if (fullLongRange == 0)
-    {
-        // cudaSetDevice(0);
-        internal->decompose();
-        gpuErrchk(cudaDeviceSynchronize());
-        #ifdef _OPENMP
-        omp_set_num_threads(4);
-        #endif
-        #pragma omp parallel for
-        for(int i = 0; i < numReplicas; ++i)
-            RBC[i]->updateParticleLists( (internal->getPos_d()[0])+i*(num+conf.num_rb_attached_particles), sys_d);
-        gpuErrchk(cudaDeviceSynchronize());
-    }
+    //// Happens at step 1 later anyway!
+    // if (fullLongRange == 0)
+    // {
+    //     // cudaSetDevice(0);
+    //     internal->decompose();
+    //     gpuErrchk(cudaDeviceSynchronize());
+    //     #ifdef _OPENMP
+    //     omp_set_num_threads(4);
+    //     #endif
+    //     #pragma omp parallel for
+    //     for(int i = 0; i < numReplicas; ++i)
+    //         RBC[i]->updateParticleLists( (internal->getPos_d()[0])+i*(num+conf.num_rb_attached_particles), sys_d);
+    //     gpuErrchk(cudaDeviceSynchronize());
+    // }
 
     float t; // simulation time
 
@@ -643,7 +644,6 @@ void GrandBrownTown::run()
                     switch (fullLongRange)
                     {
                         case 0: // [ N*log(N) ] interactions, + cutoff | decomposition
-                            if (s % decompPeriod == 0)
                             {
                                 // cudaSetDevice(0);
                                  internal -> decompose();

src/RigidBodyType.cu

@@ -217,7 +217,7 @@ void RigidBodyType::initializeParticleLists() {
 			// Build temporary id array of type j particles
 			int tmp[conf->numPartsOfType[j]];
 			int currId = 0;
-			for (int aid = 0; aid < conf->num; ++aid) {
+			for (int aid = 0; aid < conf->num + conf->num_rb_attached_particles ; ++aid) {
 			    if (conf->type[aid] == j)
 				tmp[currId++] = aid;
 			}