Atom bonds in Google Cardboard

bondthickness parameter

GoogleCardboardAndroid/NOMADgvrT/src/main/jni/treasure_hunt_renderer.cc

@@ -1089,6 +1089,25 @@ void TreasureHuntRenderer::RenderAtoms(const float *m) //m[16]
 			if ((e = glGetError()) != GL_NO_ERROR)
 				eprintf("Gl error after Render cloned Atom timestep =%d: %d\n", currentSet, e);
 		} // painting cloned atoms
+		//now bonds
+		if (numBonds && displaybonds /*&& showAtoms*/) {
+			glLineWidth(bondThickness);
+			glBindVertexArray(AtomTVAO[2]);
+			glUseProgram(UnitCellP);
+			glUniformMatrix4fv(UnitCellMatrixLoc, 1, GL_FALSE, m);
+			glUniform4fv(UnitCellColourLoc, 1, bondscolours);
+			if ((e = glGetError()) != GL_NO_ERROR)
+				eprintf("Gl error after Render Atom bonds uniform timestep =%d: %d\n", currentSet, e);
+			if (currentSet==0||fixedAtoms)
+				glDrawElements(GL_LINES, numBonds[0],  GL_UNSIGNED_INT, (void*)0);
+			else
+				glDrawElements(GL_LINES, numBonds[currentSet]-numBonds[currentSet-1], GL_UNSIGNED_INT, 
+					(void*)(sizeof(int)*numBonds[currentSet-1]) );
+			glLineWidth(1.0f);
+			if ((e = glGetError()) != GL_NO_ERROR)
+				eprintf("Gl error after Render Atom bonds timestep =%d: %d\n", currentSet, e);
+			glBindVertexArray(0);
+		}
 	} // no tess
 }
 

GoogleCardboardAndroid/NOMADgvrT/src/main/jni/treasure_hunt_renderer.h

@@ -130,8 +130,6 @@ void loadConfigFile(void);
 
 //gles 2 does not have vao, porting demo to gles3
 
-int currentset;
-
   gvr::Mat4f head_view_;
   gvr::Mat4f model_cube_;
   gvr::Mat4f camera_;

NOMADVRLib/ConfigFile.cpp

@@ -240,6 +240,7 @@ void initState()
 	menubutton = Record;
 
 	bondscaling = 0.7f;
+	bondThickness = 1.0f;
 }
 
 int loadConfigFile(const char * f)
@@ -649,12 +650,17 @@ int loadConfigFile(const char * f)
 			if (r < 1)
 				eprintf("Error reading animationspeed");
 		}
-		else if (!strcmp(s, "")) {
+		else if (!strcmp(s, "bondscaling")) {
 			r = fscanf(F, "%f", &bondscaling);
 			if (r<1)
 				eprintf("Error reading bondscaling");
 			bondscaling = sqrt(bondscaling);
-		} else if (!strcmp(s, "menubutton")) {
+		} else if (!strcmp(s, "bondthickness")) {
+			r = fscanf(F, "%f", &bondThickness);
+			if (r<1)
+				eprintf("Error reading bondthickness");
+		}
+		else if (!strcmp(s, "menubutton")) {
 			r = fscanf(F, "%s", s);
 			if (!strcmp(s, "Record"))
 				menubutton = Record;

NOMADVRLib/ConfigFileAtoms.cpp

@@ -14,6 +14,8 @@
  # limitations under the License.
 */
 
+#include "ConfigFileAtoms.h"
+
 float abc[3][3]; //basis vectors
 bool has_abc = false;
 
@@ -26,4 +28,5 @@ float cubetrans[3];
 float supercell[3];
 int voxelSize[3];
 
-float bondscaling;
+float bondscaling;
\ No newline at end of file
+float bondThickness;

NOMADVRLib/ConfigFileAtoms.h

@@ -30,5 +30,6 @@ extern int voxelSize[3];
 extern float supercell[3];
 
 extern float bondscaling;
+extern float bondThickness;
 
 #endif //CONFIGFILEATOMS_H

NOMADVRLib/atomsGL.cpp

@@ -546,7 +546,7 @@ GLenum SetupMarkerNoTess(GLuint *MarkerVAO, GLuint *MarkerVertBuffer, GLuint *Ma
 			for (int j = 0; j < MARKERSOLID::nVerts; j++) {
 				for (int k = 0; k < 3; k++) { //pos
 					float s = getMarkerLobeScaling(l, k);
-					*current++ = s*MARKERSOLID::Verts[j * 3 + k] * markerscaling * atomScaling/* * atomRadius(0)*/ +
+					*current++ = s*MARKERSOLID::Verts[j * 3 + k] * markerscaling * atomScaling * atomRadius(0) +
 						markers[i][k];
 				}
 				float length=0;