animationspeed, movementspeed, newatom options.

Check for bom mark
add sphere config option

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

@@ -1079,7 +1079,7 @@ glBindVertexArray(AtomTVAO[0]);
 		eprintf("1 Gl error RenderAtomTrajectoriesUnitCell: %d\n", e);
 //glUseProgram(UnitCellP);
 //glUniformMatrix4fv(m_nUnitCellMatrixLocation, 1, GL_FALSE, matrix);
-glUniform4fv(UnitCellColourLoc, 1, atomtrajectorycoluor);
+glUniform4fv(UnitCellColourLoc, 1, atomtrajectorycolour);
 if ((e = glGetError()) != GL_NO_ERROR)
 	eprintf("Gl error after glUniform4fv 2 RenderAtomTrajectoriesUnitCell: %d\n", e);
 //glEnableVertexAttribArray(0);

NOMADVRLib/ConfigFile.cpp

@@ -57,12 +57,13 @@ bool gazenavigation;
 int transparencyquality;
 float nearclip, farclip;
 
-
 //markers such as hole positions and electron positions
 float ** markers;
 float ** markercolours;
 float cubetrans[3];
 
+float animationspeed;
+float movementspeed;
 
 const char * loadConfigFileErrors[] =
 {
@@ -86,6 +87,7 @@ const char * loadConfigFileErrors[] =
 	"markers with no previous correct timesteps parameter", //-17
 	"markercolours with no previous correct timesteps parameter", //-18
 	"Error reading atomcolour", // -19
+	"Error reading newatom", //-20
 	"Error loading xyz file, add 100 to see the error",//<-100
 	"Error loading cube file, add 200 to see the error",//<-200
 	"Error loading encyclopedia json file, add 300 to see the error",//<-300
@@ -146,7 +148,7 @@ while (*file!='\0') {
 
 void initState()
 {
-		BACKGROUND[0] = 0.95f;
+	BACKGROUND[0] = 0.95f;
 	BACKGROUND[1] = 0.95f;
 	BACKGROUND[2] = 0.95f;
 	SCREENSHOT="C:\\temp\\frame";
@@ -209,6 +211,9 @@ void initState()
 	atomtrajectorycolour[1]=0.0f;
 	atomtrajectorycolour[2]=0.0f;
 	atomtrajectorycolour[3]=1.0f;
+
+	animationspeed=1.0f;
+	movementspeed=1.0f;
 }
 
 int loadConfigFile(const char * f)
@@ -221,7 +226,6 @@ int loadConfigFile(const char * f)
 	initState();
 	char *token=0;
 
-	//
 	FILE *F = fopen(f, "r");
 	if (F == 0)
 	{
@@ -235,6 +239,8 @@ int loadConfigFile(const char * f)
 		r=fscanf(F, "%99s", s);
 		if (r <= 0)
 			continue;
+		if ((unsigned char)s[0]==0xef && (unsigned char)s[1]==0xbb && (unsigned char)s[2]==0xbf) //utf bom
+			strcpy (s, s+3);
 		if (s[0] == '#') {//comment
 			discardline(F);
 			continue;
@@ -452,6 +458,11 @@ int loadConfigFile(const char * f)
 				solid=new Solid(Solid::Type::Octahedron);
 			else if(!strcmp(s, "tetrahedron"))
 				solid=new Solid(Solid::Type::Tetrahedron);
+			else if(!strcmp(s, "sphere")) {
+				int subd;
+				r=fscanf (F, "%d", &subd);
+				solid=new Solid(Solid::Type::Sphere, subd);
+			}
 			else
 				return -15;
 		} else if (!strcmp (s, "token")) {
@@ -481,9 +492,11 @@ int loadConfigFile(const char * f)
 					//for (int s=0;s<3;s++) 
 					//	tmp[s]-=translations[0][s]; //using translation of iso 0
 					//check if coordinates are outside of cell
-					for (int s=0;s<3;s++) {
-						while (tmp[s]<-translations[0][s])
-							tmp[s]+=supercell[2-s];
+					if (translations) {
+						for (int s=0;s<3;s++) {
+							while (tmp[s]<-translations[0][s])
+								tmp[s]+=supercell[2-s];
+						}
 					}
 					for (int s=0;s<3;s++) {
 						markers[i][s]=tmp[2]*abc[0][s]+tmp[1]*abc[1][s]+tmp[0]*abc[2][s]; //hole positions seem to be in zyx
@@ -524,6 +537,34 @@ int loadConfigFile(const char * f)
 			}
 			for (int i=0;i<3;i++)
 				atomColours[a][i]=rgb[i];
+		} else if (!strcmp (s, "newatom")) {
+			char atom [100];
+			float rgb[3];
+			float size;
+			r = fscanf(F, "%s %f %f %f %f", atom, rgb, rgb + 1, rgb + 2, &size);
+			if (r!=5) {
+				eprintf ("Error loading newatom");
+				return -20;
+			}
+			int a=findAtom(atom);
+			if (a!=-1) {
+				if (a<atomsInPeriodicTable) {
+					for (int i=0;i<3;i++)
+						atomColours[a][i]=rgb[i];
+					atomColours[a][3]=size;
+				} else {
+					for (int i=0;i<3;i++)
+						extraAtomData[a-atomsInPeriodicTable][i]=rgb[i];
+					extraAtomData[a-atomsInPeriodicTable][3]=size;
+				}
+			} else { //new
+				extraAtomNames.push_back(strdup(atom));
+				extraAtomData.push_back(new float[4]);
+				float *e=extraAtomData.back();
+				for (int i=0;i<3;i++)
+					e[i]=rgb[i];
+				e[3]=size;
+			}
 		} else if (!strcmp (s, "markerscaling")) {
 			r = fscanf(F, "%f", &markerscaling);
 		} else if (!strcmp (s, "displayunitcell")) {
@@ -544,8 +585,6 @@ int loadConfigFile(const char * f)
 			showcontrollers=true;
 		} else if (!strcmp (s, "gazenavigation")) { 
 			gazenavigation=true;
-		}else if (!strcmp (s, "\x0d")) { //discard windows newline (problem in Sebastian Kokott's phone (?!)
-			continue;
 		} else if (!strcmp (s, "transparencyquality")) {
 			r=fscanf (F, "%d", &transparencyquality);
 			if (r<1)
@@ -570,7 +609,17 @@ int loadConfigFile(const char * f)
 			r=fscanf (F, "%f %f %f", atomtrajectorycolour, atomtrajectorycolour+1, atomtrajectorycolour+2);
 			if (r<3)
 				eprintf ("Error reading atomtrajectorycolour value");
-		}else {
+		} else if (!strcmp (s, "animationspeed")) {
+			r=fscanf (F, "%f", &animationspeed);
+			if (r<1)
+				eprintf ("Error reading animationspeed");
+		} else if (!strcmp (s, "movementspeed")) {
+			r=fscanf (F, "%f", &movementspeed);
+			if (r<1)
+				eprintf ("Error reading movementspeed");
+		} else if (!strcmp (s, "\x0d")) { //discard windows newline (problem in Sebastian Kokott's phone (?!)
+			continue;
+		} else {
 			eprintf( "Unrecognized parameter %s\n", s);
 			for (int i=0;i<strlen(s);i++)
 				eprintf ("<%d>", s[i]);

NOMADVRLib/ConfigFile.h

@@ -54,6 +54,9 @@ extern bool gazenavigation;
 extern int transparencyquality;
 extern float nearclip, farclip;
 
+extern float animationspeed; //how fast to change to next timestep
+extern float movementspeed;  //how fast to move the user
+
 //markers such as hole positions and electron positions
 extern float ** markers;
 extern float ** markercolours;

NOMADVRLib/TessShaders.cpp

@@ -16,6 +16,7 @@ const char * const AtomShaders [] = {
 "#version 300 es\n"
 #endif
 	"uniform sampler2D atomData;\n"
+	"uniform float totalatoms=118.0;\n" //(float)atomsInPeriodicTable
 	"layout(location = 0) in vec3 center;\n"
 	"layout(location = 1) in float atomIn;\n"
 	"out vec4 vcolor;\n" //color , radius
@@ -23,7 +24,7 @@ const char * const AtomShaders [] = {
 	"void main()\n"
 	"{\n"
 	//"gl_Position = matrix * vec4(position+center, 1);\n"
-	"float coord=atomIn/118.0+0.5/118.0;\n"
+	"float coord=atomIn/totalatoms+0.5/totalatoms;\n"
 	"vcolor=vec4(texture(atomData, vec2(coord, 0)));\n"
 	"vcen=center;\n"
 	//"color.a=1;\n"
@@ -96,6 +97,7 @@ const char * const AtomShadersNoTess [] = {
 #endif
 	"uniform sampler2D atomData;\n"
 	"uniform mat4 matrix;\n"
+	"uniform float totalatoms=118.0;\n" //(float)atomsInPeriodicTable
 	"layout(location = 0) in vec3 pos;\n"
 	"layout(location = 1) in vec3 normalIn;\n"
 	"layout(location = 2) in float atomIn;\n"
@@ -106,7 +108,7 @@ const char * const AtomShadersNoTess [] = {
 	"{\n"
 	"gl_Position = matrix * vec4(pos, 1);\n"
 	"normal=normalIn;\n"
-	"float coord=atomIn/118.0+0.5/118.0;\n"
+	"float coord=atomIn/totalatoms+0.5/totalatoms;\n"
 	"color=vec4(texture(atomData, vec2(coord, 0)));\n"
 	"color.a=1.0;\n"
 	"vertex=pos;\n"

NOMADVRLib/atoms.cpp

@@ -28,7 +28,8 @@ const char * TMPDIR;//filled by main
 bool inv_abc_init=false;
 float inv_abc[3][3];
 
-
+std::vector<const char*> extraAtomNames;
+std::vector<float*> extraAtomData;
 
 const char * const atomNames[] =
 
@@ -176,7 +177,10 @@ float atomColours[][4] =
 
 float atomRadius (int i)
 {
-	return atomColours[i][3];
+	if (i<atomsInPeriodicTable)
+		return atomColours[i][3];
+	else
+		return extraAtomData[i-atomsInPeriodicTable][3];
 }
 
 void discardline (FILE *F)
@@ -190,7 +194,19 @@ do {
 int findAtom(const char *const s)
 {
 	//discard number at end
+	//rgh: I have C1A, so better to go from the end to avoid this being confused with C
 	char x[10];
+	strcpy (x, s);
+	char *p=x+strlen(x);
+	p--;
+	while (*p > '0' && *p <= '9') {
+		*p='\0';
+		*p--;
+		if (p==x)
+			break;
+	}
+		
+	/*
 	char *p=x; 
 	const char *q=s;
 	while (*q!=0) {
@@ -199,10 +215,15 @@ int findAtom(const char *const s)
 		*p++=*q++;
 	}
 	*p=0;
+	*/
 	//rgh FIXME, add caching
 	for (unsigned int i=0;i<sizeof(atomNames)/sizeof(const char *);i++)
 		if (!strcmp(x, atomNames[i]))
 			return i;
+	//now check extra atoms, starting at atomsInPeriodicTable
+	for (unsigned int i=0;i<extraAtomNames.size();i++)
+		if (!strcmp(x, extraAtomNames[i]))
+			return i+atomsInPeriodicTable;
 	return -1;
 }
 

NOMADVRLib/atoms.hpp

@@ -11,6 +11,8 @@
 
 extern float atomColours[][4];
 
+const int atomsInPeriodicTable=118;
+
 extern const char * TMPDIR;
 
 int readAtomsXYZ(const char *const file, int **numatoms, int *timesteps, float ***pos);
@@ -44,4 +46,7 @@ void TransformAtoms(std::vector<float>* clonedAtoms, const float abc[3][3]);
 extern bool inv_abc_init;
 extern float inv_abc[3][3];
 
+extern std::vector<const char*> extraAtomNames;
+extern std::vector<float*> extraAtomData;
+
 #endif //__ATOMS_H

NOMADVRLib/atomsGL.cpp

@@ -22,21 +22,28 @@ int getAtomTimesteps()
 GLenum atomTexture(GLuint t)
 {
 	GLenum e;
+	int finalatoms=getTotalAtomsInTexture();
 	//rgh: scale atoms here
 	//in google cardboard, this is called again if the program is running, so leave original or atoms get progresivelly smaller!
-	float *a=new float[118*4];
-	for (int i = 0; i < 118; i++) {
+	float *a=new float[finalatoms*4];
+	for (int i = 0; i < atomsInPeriodicTable; i++) {
 		a[i*4+0]=atomColours[i][0];
 		a[i*4+1]=atomColours[i][1];
 		a[i*4+2]=atomColours[i][2];
 		a[i*4+3]=atomColours[i][3] * atomScaling;
 	}
+	for (int i=0;i<extraAtomNames.size();i++) {
+		a[(i+atomsInPeriodicTable)*4+0]=extraAtomData[i][0];
+		a[(i+atomsInPeriodicTable)*4+1]=extraAtomData[i][1];
+		a[(i+atomsInPeriodicTable)*4+2]=extraAtomData[i][2];
+		a[(i+atomsInPeriodicTable)*4+3]=extraAtomData[i][3]*atomScaling;
+	}
 	glBindTexture(GL_TEXTURE_2D, t); //atom texture
 	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_NEAREST);
 	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_NEAREST);
 	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
 	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
-	glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA32F, 118, 1, 0, GL_RGBA, GL_FLOAT, a);
+	glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA32F, finalatoms, 1, 0, GL_RGBA, GL_FLOAT, a);
 
 	glBindTexture( GL_TEXTURE_2D, 0 );
 	if ((e = glGetError()) != GL_NO_ERROR) {
@@ -301,7 +308,7 @@ GLenum SetupAtoms(GLuint **AtomVAO /*[4]*/, GLuint **AtomVertBuffer /*[3]*/, GLu
 						M[k]=atoms[p][4*a+k];
 				}
 			}
-			grid g(m, M, pow(numAtoms[p], 1.0/3), bondscaling);
+			grid g(m, M, pow(numAtoms[p], 1.0f/3.0f), bondscaling);
 			for (int a = 1; a < numAtoms[p]; a++) 
 				g.add(atoms[p]+4*a);
 			for (int a = 0; a < numAtoms[p]; a++) {
@@ -546,8 +553,8 @@ GLenum SetupUnitCell(GLuint *UnitCellVAO, GLuint *UnitCellVertBuffer, GLuint *Un
 
 bool PrepareUnitCellAtomShader (GLuint *AtomP, GLuint *cellP, GLuint *MarkerP, 
 								GLint *AtomMatrixLocation, GLint *UnitCellMatrixLocation,  GLint *UnitCellColourLocation,
-								GLint *MarkerMatrixLocation){
-	if (!PrepareAtomShader(AtomP, AtomMatrixLocation))
+								GLint *MarkerMatrixLocation, GLint *totalatomsLocation){
+	if (!PrepareAtomShader(AtomP, AtomMatrixLocation, totalatomsLocation))
 		return false;
 
 	if (!PrepareUnitCellShader(cellP, UnitCellMatrixLocation, UnitCellColourLocation))
@@ -559,7 +566,7 @@ bool PrepareUnitCellAtomShader (GLuint *AtomP, GLuint *cellP, GLuint *MarkerP,
 	return true;
 }
 
-bool PrepareAtomShader (GLuint *AtomP, GLint *AtomMatrixLocation){
+bool PrepareAtomShader (GLuint *AtomP, GLint *AtomMatrixLocation, GLint *totalatomsLocation){
 		//https://www.gamedev.net/topic/591110-geometry-shader-point-sprites-to-spheres/
 	//no rotation, only translations means we can do directional lighting in the shader.
 	//FIXME
@@ -576,6 +583,13 @@ bool PrepareAtomShader (GLuint *AtomP, GLint *AtomMatrixLocation){
 		eprintf( "Unable to find matrix uniform in atom shader\n" );
 		return false;
 	}
+	*totalatomsLocation=glGetUniformLocation(*AtomP, "totalatoms");
+	if( *totalatomsLocation == -1 )
+	{
+		eprintf( "Unable to find matrix uniform in atom shader\n" );
+		return false;
+	}
+
 	return true;
 }
 
@@ -599,7 +613,7 @@ bool PrepareMarkerShader (GLuint *MP, GLint *MMatrixLocation){
 	return true;
 }
 
-bool PrepareAtomShaderNoTess (GLuint *AtomP, GLint *AtomMatrixLocation){
+bool PrepareAtomShaderNoTess (GLuint *AtomP, GLint *AtomMatrixLocation, GLint *totalatomsLocation){
 		//https://www.gamedev.net/topic/591110-geometry-shader-point-sprites-to-spheres/
 	//no rotation, only translations means we can do directional lighting in the shader.
 	//FIXME
@@ -616,6 +630,12 @@ bool PrepareAtomShaderNoTess (GLuint *AtomP, GLint *AtomMatrixLocation){
 		eprintf( "Unable to find matrix uniform in atom shader no tess\n" );
 		return false;
 	}
+	*totalatomsLocation=glGetUniformLocation(*AtomP, "totalatoms");
+	if( *totalatomsLocation == -1 )
+	{
+		eprintf( "Unable to find matrix uniform in atom shader\n" );
+		return false;
+	}
 	return true;
 }
 

NOMADVRLib/atomsGL.h

@@ -2,6 +2,7 @@
 #define __ATOMSGL_H
 
 #include "MyGL.h"
+#include "atoms.hpp"
 
 GLenum atomTexture(GLuint t);
 GLenum SetupAtoms(GLuint **AtomVAO, GLuint **AtomVertBuffer, GLuint *BondIndices);
@@ -11,14 +12,18 @@ GLenum SetupMarker(GLuint *MarkerVAO, GLuint *MarkerVertBuffer);
 
 bool PrepareUnitCellAtomShader (GLuint *AtomP, GLuint *cellP, GLuint *MarkerP, 
 								GLint *AtomMatrixLocation, GLint *UnitCellMatrixLocation,  GLint *UnitCellColourLocation,
-								GLint *MarkerMatrixLocation);
-bool PrepareAtomShader (GLuint *AtomP, GLint *AtomMatrixLocation);
-bool PrepareAtomShaderNoTess (GLuint *AtomP, GLint *AtomMatrixLocation);
+								GLint *MarkerMatrixLocation, GLint *totalatomsLocation);
+bool PrepareAtomShader (GLuint *AtomP, GLint *AtomMatrixLocation, GLint *totalatomsLocation);
+bool PrepareAtomShaderNoTess (GLuint *AtomP, GLint *AtomMatrixLocation, GLint *totalatomsLocation);
 bool PrepareUnitCellShader (GLuint *cellP, GLint *UnitCellMatrixLocation,  GLint *UnitCellColourLocation);
 bool PrepareMarkerShader (GLuint *MP, GLint *MMatrixLocation);
 
 void GetDisplacement(int p[3], float f[3]);
 
 int getAtomTimesteps();
+inline int getTotalAtomsInTexture()
+{
+	return atomsInPeriodicTable+extraAtomNames.size();
+}
 #endif //__ATOMSGL_H
 

NOMADVRLib/polyhedron.h

@@ -63,8 +63,8 @@ public:
 			for (int i=0;i<SphereFacets;i++)
 				for (int j=0;j<SphereFacets;j++) {
 					float t, f;
-					t=i*2*M_PI/(float)(SphereFacets-1);
-					f=j*M_PI/(float)(SphereFacets-1);
+					t=i*2.0f*(float)M_PI/(float)(SphereFacets-1);
+					f=j*(float)M_PI/(float)(SphereFacets-1);
 					
 					tVerts[i*SphereFacets*3 + j*3]=sin(f)*sin(t);
 					tVerts[i*SphereFacets*3 + j*3+1]=sin(f)*cos(t);

OpenVR/TimestepData/hellovr_opengl_main.cpp

@@ -287,6 +287,7 @@ private: // OpenGL bookkeeping
 	GLint m_nAtomMVLocation;
 	GLint m_nUnitCellMatrixLocation, m_nUnitCellColourLocation;
 	GLint m_nMarkerMatrixLocation;
+	GLint m_nTotalatomsLocation;
 
 	struct FramebufferDesc
 	{
@@ -869,7 +870,7 @@ bool CMainApplication::HandleInput()
 	SDL_Event sdlEvent;
 	bool bRet = false;
 
-	float speed = 0.02f;
+	float speed = 0.02f*movementspeed;
 
 	while (SDL_PollEvent(&sdlEvent) != 0)
 	{
@@ -1002,8 +1003,8 @@ bool CMainApplication::HandleInput()
 					}
 				}
 				else {
-					float newtime = videospeed*float(SDL_GetTicks());;
-					if (newtime-elapsedtime > 1) {
+					float newtime = videospeed*float(SDL_GetTicks());
+					if (newtime-elapsedtime > 1.0f/animationspeed) {
 						elapsedtime = newtime;
 						currentset++;
 						if (currentset >= TIMESTEPS)
@@ -1300,7 +1301,7 @@ bool CMainApplication::CreateAllShaders()
 	}
 
 	if (!PrepareUnitCellAtomShader (&m_unAtomsProgramID, &m_unUnitCellProgramID, &m_unMarkerProgramID,
-		&m_nAtomMatrixLocation, &m_nUnitCellMatrixLocation,  &m_nUnitCellColourLocation, &m_nMarkerMatrixLocation))
+		&m_nAtomMatrixLocation, &m_nUnitCellMatrixLocation,  &m_nUnitCellColourLocation, &m_nMarkerMatrixLocation, &m_nTotalatomsLocation))
 		return false;
 
 
@@ -2196,6 +2197,7 @@ float delta[3];
 ::GetDisplacement(p, delta);
 Vector3 iPos(delta[0], delta[1], delta[2]);
 glUseProgram(m_unAtomsProgramID);
+glUniform1f(m_nTotalatomsLocation, (float)getTotalAtomsInTexture());
 
 float levelso[4] = { TESSSUB, TESSSUB, TESSSUB, TESSSUB };
 float levelsi[2] = { TESSSUB, TESSSUB};