Add NOMAD License to various files.

Add InfoCube to Vive.

NOMADVRLib/CompileGLShader.cpp

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
+
 #include <stdio.h>
 #include "MyGL.h"
 #include "eprintf.h"

NOMADVRLib/CompileGLShader.h

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
+
 #include "MyGL.h"
 
 #define SHADERNAME 0

NOMADVRLib/ConfigFile.cpp

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
+
 #include <algorithm>
 #include <errno.h>
 #include <string.h>
@@ -46,6 +63,8 @@ int voxelSize[3];
 float unitcellcolour[4];
 float supercellcolour[4];
 
+float infolinecolour[4];
+
 int repetitions[3];
 Solid *solid;
 
@@ -65,6 +84,8 @@ float cubetrans[3];
 float animationspeed;
 float movementspeed;
 
+std::vector<information> info;
+
 const char * loadConfigFileErrors[] =
 {
 	"All Ok",//0
@@ -214,6 +235,11 @@ void initState()
 
 	animationspeed=1.0f;
 	movementspeed=1.0f;
+
+	infolinecolour[0] = 1.0f;
+	infolinecolour[1] = 1.0f;
+	infolinecolour[2] = 0.0f;
+	infolinecolour[3] = 1.0f;
 }
 
 int loadConfigFile(const char * f)
@@ -609,6 +635,10 @@ 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 if (!strcmp (s, "infolinecolour")) {
+			r=fscanf (F, "%f %f %f", infolinecolour, infolinecolour+1, infolinecolour+2);
+			if (r<3)
+				eprintf ("Error reading atomtrajectorycolour value");
 		} else if (!strcmp (s, "animationspeed")) {
 			r=fscanf (F, "%f", &animationspeed);
 			if (r<1)
@@ -617,6 +647,21 @@ int loadConfigFile(const char * f)
 			r=fscanf (F, "%f", &movementspeed);
 			if (r<1)
 				eprintf ("Error reading movementspeed");
+#ifdef WIN32
+		} else if (!strcmp (s, "info")) {
+			information i;
+			r=fscanf (F, "%f %f %f %f %d", i.pos, i.pos+1, i.pos+2, &(i.size), &(i.atom));
+			if (r<5)
+				eprintf ("Error reading info");
+			r=readString(F, s);
+			if (r!=0)
+				eprintf ("Error reading info");
+			char file[256];
+			sprintf (file, "%s%s", PATH, s);
+			i.filename=strdup(file);
+			//i.tex=LoadPNG(i.filename); //opengl not initialized yet
+			info.push_back(i);
+#endif
 		} else if (!strcmp (s, "\x0d")) { //discard windows newline (problem in Sebastian Kokott's phone (?!)
 			continue;
 		} else {

NOMADVRLib/ConfigFile.h

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
 #ifndef __CONFIGFILE_H
 #define __CONFIGFILE_H
 #include <vector>
+#include "MyGL.h"
 #include "polyhedron.h"
 
 extern const char * PATH;
@@ -40,6 +57,8 @@ extern float markerscaling;
 extern float unitcellcolour[4];
 extern float supercellcolour[4];
 
+extern float infolinecolour[4];
+
 extern int repetitions[3];
 
 extern Solid *solid;
@@ -67,4 +86,14 @@ extern const char * loadConfigFileErrors[];
 
 int loadConfigFile(const char * f);
 
+struct information {
+	float pos[3];
+	float size;
+	int atom; //-1=do not draw line
+	const char* filename;
+	GLuint tex;
+};
+
+extern std::vector<information> info;
+
 #endif //__CONFIGFILE_H

NOMADVRLib/Grid.cpp

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
+
 #include "Grid.h"
 #include "atoms.hpp" //for radius
 #include <math.h>

NOMADVRLib/Grid.h

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
+
 #include <vector>
 
 class grid 

NOMADVRLib/IsoShaders.cpp

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
 #include "IsoShaders.h"
 
 #define GRIDSTR "1"
@@ -55,21 +71,15 @@ const char *const IsoTransparentShaders [] = {"Iso Transparent Renderer",
 	"layout(location = 0) in vec4 position;\n"
 	"layout(location = 1) in vec3 normalsIn;\n"
 	"layout(location = 2) in vec4 colorIn;\n"
-	//		"layout(location = 3) in vec2 uvIn;\n"
 	"out vec4 color;\n"
 	"out vec3 n;\n"
 	"out highp vec4 pos;\n"
-	//		"out vec2 uv;\n"
 	"void main()\n"
 	"{\n"
 	"	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"
+	"	pos = matrix * position;\n"
 	"   gl_Position = pos;\n"
-	//"	gl_Position = matrix * position;\n"
 	"}\n",
 
 		// Fragment Shader
@@ -86,16 +96,13 @@ const char *const IsoTransparentShaders [] = {"Iso Transparent Renderer",
 	"void main()\n"
 	"{\n"
 	"highp vec4 mytex=texture(diffuse, vec2(pos.x/pos.w*0.5+0.5, pos.y/pos.w*0.5+0.5));\n"
-	//http://www.gamedev.net/topic/556521-glsl-manual-shadow-map-biasscale/
-	//"vec2 d=vec2(dFdx(pos.z), dFdy(pos.z));\n"
-	//"highp float m=sqrt(d.x*d.x + d.y*d.y);\n"
-	"if ((pos.z/pos.w+1.0)/2.0 <= mytex.r+0.0001 ) discard;\n"
+
+	"if ((pos.z/pos.w+1.0)/2.0 <= mytex.r+0.00001 ) discard;\n"
 
 	"lowp vec3 nn=normalize(n);"
 	"lowp float a=max(0.0, dot(nn, vec3(0,sqrt(2.0)/2.0,sqrt(2.0)/2.0)));\n"
 	"lowp float b=max(0.0, dot(nn, vec3(0,0,1)));\n"
 	"highp vec4 res=color;\n"
-	//"outputColor = vec4(pos.x/pos.w*0.5+0.5, pos.y/pos.w*0.5+0.5, 0,1);\n"
 	"	outputColor = vec4 ((res.rgb) * (0.2 + 0.2*a + 0.3*b), color.a);\n" 
 
 	"}\n",

NOMADVRLib/IsoShaders.h

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
+
 extern const char * const IsoShaders[];
 extern const char *const IsoTransparentShaders [];
 extern const char *const IsoBlendShaders [];

NOMADVRLib/IsosurfacesGL.cpp

-//#if 0
+/*Uses code from rply which uses the MIT license*/
+/*http://w3.impa.br/~diego/software/rply/*/
+/*This license is compatible with Apache 2.0*/
+
+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
 
 #include <vector>
 #include <math.h>
@@ -153,11 +171,7 @@ int vertex_cb(p_ply_argument argument) {
 
 int face_cb(p_ply_argument argument) {
     long length, value_index;
-//	int v;
     ply_get_argument_property(argument, nullptr, &length, &value_index);
-    //discard the first call with a 3
-	//if (value_index == 0 && 3 != (v = (int)ply_get_argument_value(argument)))
-	//	dprintf("Non-triangular face: %d vertices\n", v);
     if (value_index>=0 && value_index<=2)
         CubeIndices[CurrentIndex++]=(int)(ply_get_argument_value(argument));
 
@@ -350,13 +364,11 @@ if ((e = glGetError()) != GL_NO_ERROR)
 #else
 void CleanDepthTexture (GLuint t, int width, int height)
 {
-//eprintf ("CleanDepthTexture, t %d, w %d, h %d\n", t, width, height);
 GLenum e;
 const std::vector<float> z(width * height * 4, 0.0f);
 glBindTexture(GL_TEXTURE_2D, t);
 if ((e = glGetError()) != GL_NO_ERROR)
 	eprintf("CleanDepthTexture: Gl error after glBindTexture: %d\n", e);
-//rgh FIXME: invalid operation here:
 glTexSubImage2D(GL_TEXTURE_2D, 0, 0, 0, width, height, GL_DEPTH_COMPONENT, GL_FLOAT, z.data());
 if ((e = glGetError()) != GL_NO_ERROR)
 	eprintf("CleanDepthTexture: Gl error after glTexSubImage2D: %d\n", e);
@@ -416,7 +428,7 @@ return glGetError();
 GLenum SetupBlending (GLuint *vao, GLuint *vertex, GLuint *indices)
 {
 	GLenum e;
-	float z = 0.0f; //(m_fNearClip + m_fFarClip) / 2.0f;
+	float z = 0.0f; 
 	const float points[] = {
 		-1, -1, z, 0, 0,
 		-1, 1, z, 0, 1,
@@ -482,4 +494,4 @@ if ((e = glGetError()) != GL_NO_ERROR)
 	eprintf("Gl error BlendTextures glDrawElements: %d\n", e);
 	}
 }
-//#endif
+

NOMADVRLib/IsosurfacesGL.h

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
+
 #ifndef __ISOSURFACESGL_H
 #define __ISOSURFACESGL_H
 

NOMADVRLib/MyGL.h

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
 #ifndef __MYGL_H
 #define __MYGL_H
 

NOMADVRLib/TessShaders.cpp

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
 #include "TessShaders.h"
 
 /*rgh: for now default tesselation control, using 
@@ -16,18 +32,16 @@ const char * const AtomShaders [] = {
 "#version 300 es\n"
 #endif
 	"uniform sampler2D atomData;\n"
-	"uniform float totalatoms;\n" //(float)atomsInPeriodicTable
+    "uniform float totalatoms;\n" //(float)atomsInPeriodicTable
 	"layout(location = 0) in vec3 center;\n"
 	"layout(location = 1) in float atomIn;\n"
 	"out vec4 vcolor;\n" //color , radius
 	"out vec3 vcen;"
 	"void main()\n"
 	"{\n"
-	//"gl_Position = matrix * vec4(position+center, 1);\n"
 	"float coord=atomIn/totalatoms+0.5/totalatoms;\n"
 	"vcolor=vec4(texture(atomData, vec2(coord, 0)));\n"
 	"vcen=center;\n"
-	//"color.a=1;\n"
 	"}\n",
 
 	//fragment shader
@@ -37,20 +51,14 @@ const char * const AtomShaders [] = {
 "#version 300 es\n"
 #endif
 	"in lowp vec4 color;\n"
-//	"in highp vec3 vertex;"
 	"in highp vec3 normal;"
 	"out lowp vec4 outputColor;\n"
 	"void main()\n"
 	"{\n"
-	//"vec3 U = dFdx(vertex);                 "
-	//"vec3 V = dFdy(vertex);                 "
 	"highp vec3 nn = normalize(normal);"
-	//"vec3 nn = normalize(cross(U,V));"
 	"lowp float a=abs(dot(nn, vec3(0,sqrt(2.0)/2.0,sqrt(2.0)/2.0)));\n"
 	"lowp float b=max(0.0, dot(nn, vec3(0,0,1)));\n"
 	"highp vec4 res=color;\n"
-//rgh FIXME: make this depend on the background colour. Otherwise looks almost black with white background
-//version for white background:
 	"	outputColor = vec4 ((res.rgb) * (0.4 + 0.3*a + 0.3*b), color.a);\n"
 	"}\n",
 
@@ -60,18 +68,13 @@ const char * const AtomShaders [] = {
 #else
 "#version 320 es\n"
 #endif
-	//"layout(triangles, equal_spacing, cw) in;\n"
 	"layout(quads, equal_spacing, cw) in;\n"
 	"#define pi 3.1415926535897932384626433832795\n"
 	"uniform mat4 matrix;\n"
-	//"uniform mat4 mv;\n"
 	"in vec4 vcolor[];\n" //color , radius
 	"in vec3 vcen[];"
 	"out vec4 color;\n" //color 
 	"out vec3 normal;\n"
-//	"out vec3 vertex;"
-//	"uniform mat4 Projection;\n"
-//	"uniform mat4 Modelview;\n"
 
 	"void main()\n"
 	"{\n"
@@ -87,8 +90,6 @@ const char * const AtomShaders [] = {
 
 const char * const AtomShadersNoTess [] = {
 	"Atom Renderer No Tess",
-	//No Tess means smooth shading looks very strange. Better use per-face lighting
-		// vertex shader
 //Android 21 gives error: only supports up to '310 es'
 #if defined(WIN32) || defined(CAVE)
 	"#version 410\n"
@@ -97,7 +98,7 @@ const char * const AtomShadersNoTess [] = {