NOMAD Cardboard changes:

-Allow android api level 23
-Add icon
-Add file picker on init
-Display transparent isos using additive blending
-Make shaders gles 3.0 compatible
-Update to latest NOMAD VR Lib

GoogleCardboardAndroid/NOMADgvrT/build.gradle

@@ -8,7 +8,7 @@ model {
         defaultConfig.with {
             applicationId = "com.google.vr.ndk.samples.treasurehunt"
             minSdkVersion.apiLevel = 19
-            targetSdkVersion.apiLevel = 24
+            targetSdkVersion.apiLevel = 23
             versionCode = 1
             versionName = "1.0"
         }

GoogleCardboardAndroid/NOMADgvrT/src/main/AndroidManifest.xml

@@ -27,6 +27,7 @@
 
   <application
       android:allowBackup="true"
+	android:icon="@drawable/ic_launcher"
       android:label="NOMADgvrT"
       android:theme="@style/VrActivityTheme">
     <activity

GoogleCardboardAndroid/NOMADgvrT/src/main/java/com/google/vr/ndk/samples/treasurehunt/MainActivity.java

@@ -79,23 +79,63 @@ public static void verifyStoragePermissions(Activity activity) {
     }
 }
 
+    @Override
+    protected void onActivityResult(int requestCode, int resultCode, android.content.Intent data) {
+        super.onActivityResult(requestCode, resultCode, data);
+        if(requestCode==123 && resultCode==RESULT_OK) {
+		String s=data.getDataString();
+		android.util.Log.d("NOMADgvrT","OnActivityResult, s="+s);
+		String uriString="";
+     		if (s.startsWith("file://")) {
+			uriString=s.substring(7);
+		} else if (s.startsWith("content://com.asus.filemanager.OpenFileProvider/file")) {
+			uriString=s.substring(52);
+		} else {
+			uriString=s;
+		}
+		android.util.Log.d("NOMADgvrT","OnActivityResult, uri="+uriString);
+		nativeSetConfigFile(uriString, android.os.Environment.getExternalStorageDirectory().getPath() + "/");   
+		nativeLoadConfigFile(nativeTreasureHuntRenderer);    
+        }
+    }
+
   @Override
   protected void onCreate(Bundle savedInstanceState) {
     super.onCreate(savedInstanceState);
 
 	verifyStoragePermissions(this);
+
+//http://stackoverflow.com/questions/36557879/how-to-use-native-android-file-open-dialog
+/////////
+        //setContentView(R.layout.activity_main);
+
+ 
+///////////
+
+
+
 	String externalsd=android.os.Environment.getExternalStorageDirectory().getPath() + "/";
 	//intents
 	android.content.Intent intent = getIntent();
 	
 	String s=intent.getDataString();
 	String uriString=externalsd+"material.ncfg";
-	if (s==null)
-			android.util.Log.d("NOMADgvrT","String intent is null");
+	if (s==null) {
+		android.util.Log.d("NOMADgvrT","String intent is null");
+	       android.content.Intent intentSent = new android.content.Intent()
+		.setType("*/*")
+		.setAction(android.content.Intent.ACTION_GET_CONTENT);
+
+		startActivityForResult(android.content.Intent.createChooser(intentSent, "Select NOMAD VR config file (.ncfg)"), 123);		
+		s=intentSent.getDataString();
+	}
 	else
 		android.util.Log.d("NOMADgvrT","String intent is <"+ s+">");
+
+	android.util.Log.d("NOMADgvrT","String intent finally is <"+s+">");	
 	if (s!=null) {
-		if (s.startsWith("content://")) {
+		if (s.startsWith("content://")) {//this only works with ncfg with no associated data
+			android.util.Log.d("NOMADgvrT","String intent is <"+s+">");
 			try {
 				java.io.InputStream input = getContentResolver().openInputStream(intent.getData());
 				byte[] buffer = new byte[8 * 1024];
@@ -289,4 +329,26 @@ public static void verifyStoragePermissions(Activity activity) {
   private native void nativeOnResume(long nativeTreasureHuntRenderer);
 
   private native void nativeSetConfigFile(String s, String e);
+  private native void nativeLoadConfigFile(long nativeTreasureHuntRenderer);
+
+  public void DisplayMessage (final String s)
+  {
+//http://stackoverflow.com/questions/3875184/cant-create-handler-inside-thread-that-has-not-called-looper-prepare
+//rgh: this hangs, need to investigate
+	new Thread()
+	{
+	    public void run()
+	    {
+		MainActivity.this.runOnUiThread(new Runnable()
+		{
+		    public void run()
+		    {
+			android.widget.Toast toast = android.widget.Toast.makeText(MainActivity.this.getApplicationContext(), s,
+				android.widget.Toast.LENGTH_LONG);		        
+		    }
+		});
+	    }
+	}.start();
+
+  }
 }

GoogleCardboardAndroid/NOMADgvrT/src/main/java/com/google/vr/ndk/samples/treasurehunt/NOMAD.java

+//http://stackoverflow.com/questions/4875114/android-save-image-from-url-onto-sd-card
+
+class NOMAD {
+public static boolean i=false;
+public static void Init () 
+//we are going to block anyway until we have the datasets
+{
+if (android.os.Build.VERSION.SDK_INT > 9) {
+    android.os.StrictMode.ThreadPolicy policy = new android.os.StrictMode.ThreadPolicy.Builder().permitAll().build();
+    android.os.StrictMode.setThreadPolicy(policy);
+}
+i=true;
+}
+
+public static void GetUrl (String url, String path) 
+{
+if (!i)
+	Init();
+ 
+android.util.Log.d("NOMAD", "Java NOMAD.GetUrlThread(\""+url+"\",\""+path+"\") called");
+
+try {
+  java.net.URL u = new java.net.URL(url);
+  java.net.HttpURLConnection urlConnection = (java.net.HttpURLConnection) u.openConnection();
+  urlConnection.setRequestMethod("GET");
+  urlConnection.setDoOutput(true);   
+  java.io.File file = new java.io.File(path);
+  java.io.FileOutputStream fileOutput = new java.io.FileOutputStream(file);
+  int status = urlConnection.getResponseCode();
+
+  if (status != java.net.HttpURLConnection.HTTP_OK) {
+	return; //http error or redirect, we probably want to exit here as NOMAD encyclopedia should not do that
+  }
+  java.io.InputStream inputStream = urlConnection.getInputStream();
+  int totalSize = urlConnection.getContentLength();
+  int downloadedSize = 0;   
+  byte[] buffer = new byte[1024];
+  int bufferLength = 0;
+  while ( (bufferLength = inputStream.read(buffer)) > 0 ) 
+  {                 
+    fileOutput.write(buffer, 0, bufferLength);                  
+    downloadedSize += bufferLength;                 
+  }             
+  fileOutput.close();
+
+} //try
+catch (Exception e) {
+ e.printStackTrace();
+}
+
+} //GetUrl
+
+} //class NOMAD

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

@@ -23,10 +23,16 @@
 #include "vr/gvr/capi/include/gvr_audio.h"
 #include "NOMADVRLib/atoms.hpp" //for TMPDIR
 
+#include "treasure_hunt_jni.h"
+
 #define JNI_METHOD(return_type, method_name) \
   JNIEXPORT return_type JNICALL              \
       Java_com_google_vr_ndk_samples_treasurehunt_MainActivity_##method_name
 
+//http://stackoverflow.com/questions/12900695/how-to-obtain-jni-interface-pointer-jnienv-for-asynchronous-calls
+    JavaVM* javaVM = nullptr;
+    jobject jo;
+
 namespace {
 
 inline jlong jptr(TreasureHuntRenderer *native_treasure_hunt) {
@@ -38,6 +44,28 @@ inline TreasureHuntRenderer *native(jlong ptr) {
 }
 }  // anonymous namespace
 
+//http://stackoverflow.com/questions/28622036/android-ndk-calling-java-functions-from-c
+/*void GetUrl (const char *url, const char *path) 
+{
+    jstring jurl = genv->NewStringUTF(url);
+    jstring jpath = genv->NewStringUTF(path);
+
+    jclass jc = genv->FindClass("NOMAD");
+    jmethodID mid = genv->GetStaticMethodID(jc, "GetUrl", "(Ljava/lang/String;Ljava/lang/String;)V");
+
+    genv->CallStaticVoidMethod(jc, mid, jurl, jpath);	
+}*/
+
+void DisplayMessage (const char *s)
+{
+	JNIEnv *env;
+    	javaVM->AttachCurrentThread(&env, nullptr);
+	jstring js = env->NewStringUTF(s);
+	jclass cls = env->GetObjectClass(jo);
+	jmethodID mid = env->GetMethodID(cls, "DisplayMessage", "(Ljava/lang/String;)V");
+	env->CallVoidMethod(jo, mid, js);
+} 
+
 extern "C" {
 
 JNI_METHOD(jlong, nativeCreateRenderer)
@@ -82,11 +110,20 @@ JNI_METHOD(void, nativeOnResume)
   native(native_treasure_hunt)->OnResume();
 }
 
+//https://library.vuforia.com/articles/Solution/How-To-Communicate-Between-Java-and-C-using-the-JNI
 JNI_METHOD(void, nativeSetConfigFile)
 (JNIEnv *env, jobject obj, jstring s, jstring e) {
+	env->GetJavaVM(&javaVM);
+	jo=env->NewGlobalRef(obj);
 	configPath = env->GetStringUTFChars(s , NULL ) ;
 	TMPDIR=env->GetStringUTFChars(e , NULL ) ;
 
 }
 
+JNI_METHOD(void, nativeLoadConfigFile)
+(JNIEnv *env, jobject obj, jlong native_treasure_hunt) {
+  native(native_treasure_hunt)->loadConfigFile();
+}
+
+
 }  // extern "C"

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

+//void GetUrl (const char *url, const char *path);
+void DisplayMessage (const char *s);

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

@@ -16,6 +16,7 @@
 #include <unistd.h>
 
 #include "treasure_hunt_renderer.h"  // NOLINT
+#include "treasure_hunt_jni.h"
 
 #include <android/log.h>
 #include <assert.h>
@@ -33,7 +34,7 @@
 #include "NOMADVRLib/polyhedron.h"
 #include "NOMADVRLib/IsosurfacesGL.h"
 
-#define LOG_TAG "TreasureHuntCPP"
+#define LOG_TAG "NOMADgvrT"
 #define LOGW(...) __android_log_print(ANDROID_LOG_WARN, LOG_TAG, __VA_ARGS__)
 #define LOGD(...) __android_log_print(ANDROID_LOG_DEBUG, LOG_TAG, __VA_ARGS__)
 #define LOGE(...) __android_log_print(ANDROID_LOG_ERROR, LOG_TAG, __VA_ARGS__)
@@ -59,6 +60,8 @@ void eprintf( const char *fmt, ... )
 	if (*fmt=='\0')
 		LOGD("Empty format");
 	LOGD("<%s>", buffer);
+	//rgh: does not work yet
+	//DisplayMessage(buffer);
 }
 
 
@@ -305,13 +308,8 @@ static float VectorInnerProduct(const std::array<float, 4>& vect1,
 }
 }  // anonymous namespace
 
-TreasureHuntRenderer::TreasureHuntRenderer(
-    gvr_context* gvr_context, std::unique_ptr<gvr::AudioApi> gvr_audio_api)
-    : gvr_api_(gvr::GvrApi::WrapNonOwned(gvr_context)),
-      scratch_viewport_(gvr_api_->CreateBufferViewport()),
-      gvr_controller_api_(nullptr),
-      gvr_viewer_type_(gvr_api_->GetViewerType()) {
-
+void TreasureHuntRenderer::loadConfigFile(void)
+{
 	if (configPath!=nullptr)
 		eprintf ("configPath=<%s>", configPath);
 	else
@@ -326,7 +324,7 @@ TreasureHuntRenderer::TreasureHuntRenderer(
 	chdir(s.substr(0, s.find_last_of("\\/")).c_str());
 	
 
-	if ((error=loadConfigFile(configPath))<0) {
+	if ((error=::loadConfigFile(configPath))<0) {
 		if (-100<error) {
 			eprintf(loadConfigFileErrors[-error]);
 			eprintf("Config file reading error");
@@ -345,7 +343,17 @@ TreasureHuntRenderer::TreasureHuntRenderer(
 		LOGD("No atom glyph specified, using Icosahedron");
 		solid=new Solid(Solid::Type::Icosahedron);
 	}
-	eprintf("after config load, timesteps=%d", TIMESTEPS);
+}
+
+TreasureHuntRenderer::TreasureHuntRenderer(
+    gvr_context* gvr_context, std::unique_ptr<gvr::AudioApi> gvr_audio_api)
+    : gvr_api_(gvr::GvrApi::WrapNonOwned(gvr_context)),
+      scratch_viewport_(gvr_api_->CreateBufferViewport()),
+      gvr_controller_api_(nullptr),
+      gvr_viewer_type_(gvr_api_->GetViewerType()) {
+
+	loadConfigFile();
+	//eprintf("after config load, timesteps=%d", TIMESTEPS);
 	
   ResumeControllerApiAsNeeded();
   if (gvr_viewer_type_ == GVR_VIEWER_TYPE_CARDBOARD) {
@@ -374,6 +382,7 @@ void TreasureHuntRenderer::InitializeGl() {
   gvr_api_->InitializeGl();
 
 glGenTextures(2, textures);
+glGenTextures(2+ZLAYERS, textDepthPeeling);
     //white
     unsigned char data2[4]={255,255,255,255}; //white texture for non-textured meshes
     glBindTexture(GL_TEXTURE_2D, textures[0]);
@@ -409,7 +418,7 @@ glGenTextures(2, textures);
 		error=-403;
 	}
 
-	e=SetupAtoms(&AtomTVAO, &AtomTBuffer);
+	e=SetupAtoms(&AtomTVAO, &AtomTBuffer, &BondIndices);
 	if (e!=GL_NO_ERROR) {
 		eprintf ("SetupAtoms error %d", e);
 		error=-404;
@@ -428,8 +437,50 @@ glGenTextures(2, textures);
 		error=-406;
 	}
 
+  // Because we are using 2X MSAA, we can render to half as many pixels and
+  // achieve similar quality.
+  render_size_ =
+      HalfPixelCount(gvr_api_->GetMaximumEffectiveRenderTargetSize());
+  std::vector<gvr::BufferSpec> specs;
+
+  specs.push_back(gvr_api_->CreateBufferSpec());
+  specs[0].SetColorFormat(GVR_COLOR_FORMAT_RGBA_8888);
+  specs[0].SetDepthStencilFormat(GVR_DEPTH_STENCIL_FORMAT_DEPTH_16);
+  specs[0].SetSize(render_size_);
+  specs[0].SetSamples(2);
+
+  swapchain_.reset(new gvr::SwapChain(gvr_api_->CreateSwapChain(specs)));
+
+  viewport_list_.reset(
+      new gvr::BufferViewportList(gvr_api_->CreateEmptyBufferViewportList()));
+
 //isosurfaces
 	if (ISOS) {
+		//rgh: FIXME Additive blending for android; do not need most of these textures
+		//additive blending means white background makes everything white
+		float m=BACKGROUND[0];
+		m=std::max(m, BACKGROUND[1]);
+		m=std::max(m, BACKGROUND[2]);
+		if (m>0.2f) { //make background darker, preserving colour, so additive blending works
+			for (int i=0;i<3;i++)
+				BACKGROUND[i]*=0.2f / m;
+		}
+
+		e=SetupDepthPeeling(render_size_.width, render_size_.height, ZLAYERS, 
+			textDepthPeeling, &peelingFramebuffer);
+		if (!e) {
+			eprintf("Error setting up DepthPeeling\n");
+			error=-407;
+		}
+
+
+		if (GL_NO_ERROR!=(e=PrepareISOTransShader (&TransP, 
+			&TransMatrixLoc, &BlendP)))
+		{
+			eprintf( "Error Preparing Transparency shader, %d\n", e );
+			error=-408;
+		}
+		SetupBlending(&BlendVAO, &BlendBuffer, &BlendIndices);
 		PrepareISOShader(&ISOP, &ISOMatrixLoc);
 
 		std::vector<float> vertices;
@@ -501,28 +552,13 @@ glGenTextures(2, textures);
 			indices.clear();
 
 			if (p % ISOS == ISOS - 1) {
-				eprintf ("timestep %d", timestep);
+				//eprintf ("timestep %d", timestep);
 				timestep++;
 			}
 		}
 	}
 
-  // Because we are using 2X MSAA, we can render to half as many pixels and
-  // achieve similar quality.
-  render_size_ =
-      HalfPixelCount(gvr_api_->GetMaximumEffectiveRenderTargetSize());
-  std::vector<gvr::BufferSpec> specs;
 
-  specs.push_back(gvr_api_->CreateBufferSpec());
-  specs[0].SetColorFormat(GVR_COLOR_FORMAT_RGBA_8888);
-  specs[0].SetDepthStencilFormat(GVR_DEPTH_STENCIL_FORMAT_DEPTH_16);
-  specs[0].SetSize(render_size_);
-  specs[0].SetSamples(2);
-
-  swapchain_.reset(new gvr::SwapChain(gvr_api_->CreateSwapChain(specs)));
-
-  viewport_list_.reset(
-      new gvr::BufferViewportList(gvr_api_->CreateEmptyBufferViewportList()));
 
 }
 
@@ -621,6 +657,7 @@ if (animateTimesteps) {
   // Draw the world.
   frame.BindBuffer(0);
   if (error<0) {
+	//rgh: FIXME, add textures with messages here
 		if (-100<error) {
 			glClearColor(1.f, 0.f, 0.f, 1.f); 
 		} else if (-200<error){
@@ -633,7 +670,7 @@ if (animateTimesteps) {
 			glClearColor(1.f, 0.f, 1.f, 1.f); 
 		}
   } else {
-	glClearColor(BACKGROUND[0], BACKGROUND[1], BACKGROUND[2], 0.5f);
+	glClearColor(BACKGROUND[0], BACKGROUND[1], BACKGROUND[2], 1.f);
   }
 
     // Dark background so text shows up.
@@ -764,10 +801,10 @@ for (int i=0;i<4;i++)
 		t[j*4+i]=transform.m[i][j];
 
 glUseProgram(ISOP);
-	if ((e = glGetError()) != GL_NO_ERROR)
+if ((e = glGetError()) != GL_NO_ERROR)
 		eprintf("1 Gl error RenderIsos timestep =%d: %d\n", currentSet, e);
 glUniformMatrix4fv(ISOMatrixLoc, 1, GL_FALSE, t);
-	if ((e = glGetError()) != GL_NO_ERROR)
+if ((e = glGetError()) != GL_NO_ERROR)
 		eprintf("2 Gl error RenderIsos timestep =%d: %d\n", currentSet, e);
 
 if (curDataPos!=ISOS) {
@@ -779,31 +816,58 @@ if (curDataPos!=ISOS) {
 	if ((e = glGetError()) != GL_NO_ERROR)
 		eprintf("4 Gl error RenderIsos timestep =%d: %d\n", currentSet, e);
 } else {
+//transparency; FIXME disabled as I get 1fps, with screen in 4 columns and z-check is incorrect
+/*
+	glDisable(GL_BLEND);
+	glDepthMask(GL_TRUE);
+	//do depth peeling
+	CleanDepthTexture(textDepthPeeling[0], render_size_.width, render_size_.height);
+	GLint dfb;
+	glGetIntegerv(GL_DRAW_FRAMEBUFFER_BINDING, &dfb);
+if ((e = glGetError()) != GL_NO_ERROR)
+	eprintf("Gl error RenderIsos, before zl loop: %d\n", e);
+	for (int zl = 0; zl < ZLAYERS; zl++) {
+		EnableDepthFB(zl, TransP, 
+			peelingFramebuffer, textDepthPeeling);
+		glUniformMatrix4fv(TransMatrixLoc, 1, GL_FALSE, t);
+		for (int i=0;i<ISOS;i++) {
+			glBindVertexArray(ISOVAO[currentSet*ISOS+i]);
+			glDrawElements(GL_TRIANGLES,numISOIndices[currentSet*ISOS+i] , GL_UNSIGNED_INT, 0);	
+		}
+	}
+	glUseProgram(BlendP);
+	glBindFramebuffer(GL_FRAMEBUFFER, dfb);
+	glBindVertexArray(BlendVAO);
+if ((e = glGetError()) != GL_NO_ERROR)
+	eprintf("Gl error RenderIsos, after glBindVertexArray: %d\n", e);
+	BlendTextures(textDepthPeeling, ZLAYERS);
+	glBindVertexArray(0);
+if ((e = glGetError()) != GL_NO_ERROR)
+	eprintf("Gl error RenderIsos, after BlendTextures: %d\n", e);*/
+/* no transparency*/
+	glEnable(GL_BLEND);
+	glBlendFunc(GL_SRC_ALPHA, GL_ONE);
+	glDepthMask(GL_FALSE);
 	for (int i=0;i<ISOS;i++) {
 		glBindVertexArray(ISOVAO[currentSet*ISOS+i]);
-		glBindBuffer(GL_ARRAY_BUFFER, ISOBuffer[currentSet*ISOS+i]);
-		glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, ISOIndices[currentSet*ISOS+i]);
-		glEnableVertexAttribArray(0);
-		glEnableVertexAttribArray(1);
-		glEnableVertexAttribArray(2);
-		glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 10*sizeof(float), (const void *)(0*sizeof(float)));
-		glVertexAttribPointer(1, 3, GL_FLOAT, GL_FALSE, 10*sizeof(float), (const void *)(3*sizeof(float)));
-		glVertexAttribPointer(2, 4, GL_FLOAT, GL_FALSE, 10*sizeof(float), (const void *)(6*sizeof(float)));
 	if ((e = glGetError()) != GL_NO_ERROR)
 		eprintf("5 Gl error RenderIsos timestep =%d: %d\n", currentSet, e);
 		eprintf ("Drawing %d vertices, isos", numISOIndices[currentSet*ISOS+i]);
-		glDrawElements(GL_TRIANGLES,numISOIndices[currentSet*ISOS+i] , GL_UNSIGNED_INT, 0);		
+		glDrawElements(GL_TRIANGLES,numISOIndices[currentSet*ISOS+i] , GL_UNSIGNED_INT, 0);	
 	if ((e = glGetError()) != GL_NO_ERROR)
 		eprintf("6 Gl error RenderIsos timestep =%d: %d\n", currentSet, e);
 	}
-}
+	glDisable(GL_BLEND);
+} //if (curDataPos!=ISOS) 
+//eprintf ("end of RenderIsos");
+glBindVertexArray(0);
 }
 
 void TreasureHuntRenderer::RenderAtoms(const float *m) //m[16]
 {
 	//return;
-	eprintf ("RenderAtoms start numatoms %d, timestep %d", numAtoms[currentSet], currentSet);
-	eprintf ("solid nfaces %d", solid->nFaces);
+	//eprintf ("RenderAtoms start numatoms %d, timestep %d", numAtoms[currentSet], currentSet);
+	//eprintf ("solid nfaces %d", solid->nFaces);
 	int e;
 	if (numAtoms==0)
 		return;
@@ -977,7 +1041,7 @@ void TreasureHuntRenderer::RenderUnitCell(const gvr::Mat4f eyeViewProjection)
 	//for (int i=0;i<4;i++)
 	//	for (int j=0;j<4;j++)
 	//		eprintf ("%d %d = %f", i, j, eyeViewProjection.m[i][j]);
-	eprintf ("RenderUnitCell, has_abc=%d", has_abc);
+	//eprintf ("RenderUnitCell, has_abc=%d", has_abc);
 	if (!has_abc)
 		return;
 	if (UnitCellVAO==0)

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

@@ -30,6 +30,8 @@
 #include "vr/gvr/capi/include/gvr_controller.h"
 #include "vr/gvr/capi/include/gvr_types.h"
 
+#define ZLAYERS 2
+
 extern const char * configPath;
 
 class TreasureHuntRenderer {
@@ -69,6 +71,7 @@ class TreasureHuntRenderer {
    */
   void OnResume();
 void OnTriggerEvent();
+void loadConfigFile(void);
  private:
   int CreateTexture(int width, int height, int textureFormat, int textureType);
 
@@ -150,17 +153,23 @@ int currentset;
   gvr::ViewerType gvr_viewer_type_;
 
 GLuint textures[2]; // white, atoms
+GLuint textDepthPeeling[ZLAYERS+2]; 
+GLuint peelingFramebuffer;
 	//if no tesselation is available, we still need the tess atoms for the trajectories!
 	GLuint *AtomTVAO=nullptr, *AtomTBuffer=nullptr, *AtomVAO=nullptr, *AtomBuffer=nullptr, *AtomIndices=nullptr,//[2], atoms, extraatoms
+		BondIndices,
 		UnitCellVAO, UnitCellBuffer, UnitCellIndexBuffer;
 GLuint			AtomsP, UnitCellP; // framework does not provide support for tesselation and provides many things we don't need.
 	GLint		AtomMatrixLoc, UnitCellMatrixLoc, UnitCellColourLoc;
+GLuint	TransP=0, BlendP=0;
+GLint	TransMatrixLoc=-1;
 bool hasTess=true;
 
 GLuint *ISOVAO=nullptr/*[ISOS*TIMESTEPS]*/, *ISOBuffer=nullptr/*[ISOS*TIMESTEPS]*/,
 	*ISOIndices=nullptr/*[ISOS*TIMESTEPS]*/;
 GLuint ISOP;
 GLint ISOMatrixLoc;
+GLuint BlendVAO=0, BlendBuffer=0, BlendIndices=0;
 int *numISOIndices=nullptr/*[ISOS*TIMESTEPS]*/;
 
 int currentSet=0;

NOMADVRLib/IsoShaders.cpp

@@ -65,9 +65,9 @@ const char *const IsoTransparentShaders [] = {"Iso Transparent Renderer",
 	"	color = vec4(colorIn.rgba);\n"
 	"   n=normalize(normalsIn);\n"
 	//		"   uv=uvIn;\n"
-	"int i=gl_InstanceID / " GRIDSTR ";\n"
-	"int j=gl_InstanceID % " GRIDSTR ";\n"
-	"	pos = matrix * (position + vec4 (float(i)*0.15*101.0, 0, float(j)*0.15*101.0, 0));\n"
+//	"int i=gl_InstanceID / " GRIDSTR ";\n"
+//	"int j=gl_InstanceID % " GRIDSTR ";\n"
+	"	pos = matrix * (position /*+ vec4 (float(i)*0.15*101.0, 0, float(j)*0.15*101.0, 0)*/);\n"
 	"   gl_Position = pos;\n"
 	//"	gl_Position = matrix * position;\n"
 	"}\n",
@@ -79,17 +79,17 @@ const char *const IsoTransparentShaders [] = {"Iso Transparent Renderer",
 	"#version 300 es\n"
 #endif
 	"uniform sampler2D diffuse;\n" //now extra depth texture for peeling
-	"in vec4 color;\n"
-	"in vec3 n;\n"
+	"in lowp vec4 color;\n"
+	"in lowp vec3 n;\n"
 	"in highp vec4 pos;\n"
-	"out vec4 outputColor;\n"
+	"out lowp vec4 outputColor;\n"
 	"void main()\n"
 	"{\n"
-	"vec4 mytex=texture(diffuse, vec2(pos.x/pos.w*0.5+0.5, pos.y/pos.w*0.5+0.5));\n"
+	"highp vec4 mytex=texture(diffuse, vec2(pos.x/pos.w*0.5+0.5, pos.y/pos.w*0.5+0.5));\n"