atomsGL.cpp 27.9 KB
Newer Older
1
/*
2
# Copyright 2016-2018 Ruben Jesus Garcia Hernandez
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
 #
 # 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.
*/


18 19 20 21 22
#include <math.h>

#include "eprintf.h"
#include "TessShaders.h"
#include "UnitCellShaders.h"
23
#include "markerShaders.h"
24 25 26 27 28
#include "atomsGL.h"
#include "atoms.hpp"
#include "ConfigFile.h"
#include "CompileGLShader.h"
#include "polyhedron.h"
29
#include "Grid.h"
30 31 32 33

GLenum atomTexture(GLuint t)
{
	GLenum e;
34
	int finalatoms=getTotalAtomsInTexture();
35
	//rgh: scale atoms here
36
	//in google cardboard, this is called again if the program is running, so leave original or atoms get progresivelly smaller!
37 38
	float *a=new float[finalatoms*4];
	for (int i = 0; i < atomsInPeriodicTable; i++) {
39 40 41 42 43
		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;
	}
44 45 46 47 48 49
	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;
	}
50
	glBindTexture(GL_TEXTURE_2D, t); //atom texture
51 52 53
	if ((e = glGetError()) != GL_NO_ERROR) {
		eprintf("opengl error %d, atomTexture bind\n", e);
	}
54 55 56 57
	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);
58 59 60
	if ((e = glGetError()) != GL_NO_ERROR) {
		eprintf("opengl error %d, atomTexture parameter\n", e);
	}
61
    glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA32F, finalatoms, 1, 0, GL_RGBA, GL_FLOAT, a);
62 63 64
	if ((e = glGetError()) != GL_NO_ERROR) {
		eprintf("opengl error %d, atomTexture glTexImage2D\n", e);
	}
65 66
	glBindTexture( GL_TEXTURE_2D, 0 );
	if ((e = glGetError()) != GL_NO_ERROR) {
67
		eprintf("opengl error %d, atomTexture\n", e);
68
	}
69
	delete [] a;
70 71 72 73 74 75
	return e;
}

//WARNING: This should be called after SetupAtoms
//This means that numAtoms now has the cummulative distribution!
//This should be called after the atom texture is prepared, and therefore has the atomscaling pre-multiplied
76
GLenum SetupAtomsNoTess (GLuint **AtomVAO /*[4]*/, GLuint **AtomVertBuffer/*[3]*/, GLuint **AtomIndexBuffer/*[2]*/)
77 78
	//atoms, cloned atoms
	//rgh: FIXME: add AtomVAO[2] for atom trajectories
79 80 81 82
{
if (!numAtoms)
		return 0;

83 84 85 86 87
if (!solid) {
	eprintf ("SetupAtomsNoTess, error: no solid defined");
	return 0;
}

88
	//http://prideout.net/blog/?p=48 //public domain code
89
	//xyz nxnynz u=atom type ; 7 floats; u only used for colour
90 91
	int e;

92
	int totalatoms=numAtoms[getAtomTimesteps() -1];
93
	
94
	*AtomVAO = new GLuint[4]; //atoms, cloned atoms, unused (bonds use Tess atom positions), trajectories
95
	*AtomIndexBuffer= new GLuint[3];//atoms, cloned atoms, bonds
96
	*AtomVertBuffer = new GLuint[3];//atoms, cloned atoms, trajectories
97

98
	glGenVertexArrays(4, *AtomVAO);
99
	glGenBuffers(2, *AtomIndexBuffer);
100
	glGenBuffers(3, *AtomVertBuffer);
101 102 103 104 105 106 107
	glBindVertexArray((*AtomVAO)[0]);
	glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, (*AtomIndexBuffer)[0]);
	glBindBuffer(GL_ARRAY_BUFFER, (*AtomVertBuffer)[0]);
	glEnableVertexAttribArray(0);
	glEnableVertexAttribArray(1);
	glEnableVertexAttribArray(2);
	glDisableVertexAttribArray(3);
108
	float *tmp = new float[solid->nVerts * 7 * totalatoms];
109
#ifdef INDICESGL32		
110
	int *tmpi = new int[solid->nFaces*3 * totalatoms];
111 112
	int *currenti=tmpi;
#else
113
	unsigned short *tmpi = new unsigned short[solid->nFaces*3 * totalatoms];
114 115 116 117 118
	unsigned short *currenti=tmpi;
#endif

	float *current=tmp;
	//eprintf ("Before For 1");
119
	for (int p=0;p<getAtomTimesteps() ;p++) {
120 121
		for (int a = 0; a < numAtoms[p]-(p==0?0:numAtoms[p-1]); a++) {
			const int atomNumber = static_cast<int>(atoms[p][4 * a + 3]);
122
			const float radius = atomRadius(atomNumber)*atomScaling;
123
			for (int i = 0; i < solid->nVerts; i++) { //verts
124
				for (int k = 0; k < 3; k++) {
125
					*current++ = solid->Verts[3 * i + k]* radius +atoms[p][4 * a + k]; //pos
126 127
				}
				for (int k = 0; k < 3; k++) {
128
					*current++ = solid->Verts[3 * i + k]; //normal
129
				}
130
				*current++ = static_cast<float>(atomNumber);
131
			} //i
132 133
			for (int i = 0; i < solid->nFaces * 3; i++)
				*currenti++ = solid->Faces[i] + (a+(p==0?0:numAtoms[p-1]))*solid->nVerts;
134 135
		} //a
	} //p
136
		glBufferData(GL_ARRAY_BUFFER, sizeof(float) *totalatoms* 7 * solid->nVerts, tmp,
137 138 139 140 141 142 143 144 145 146
			GL_STATIC_DRAW);
		if ((e = glGetError()) != GL_NO_ERROR)
			eprintf("opengl error %d, glBufferData, l %d\n", e, __LINE__);

		glBufferData(GL_ELEMENT_ARRAY_BUFFER, 
#ifdef INDICESGL32		
	sizeof(int)
#else
	sizeof(unsigned int)
#endif
147
		* totalatoms * 3 * solid->nFaces, tmpi, GL_STATIC_DRAW);
148 149 150 151 152 153 154 155 156 157 158 159 160 161 162


	glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 7*sizeof(float), (const void *)0);
	glVertexAttribPointer(1, 3, GL_FLOAT, GL_FALSE, 7 * sizeof(float), (const void *)(3*sizeof(float)));
	glVertexAttribPointer(2, 1, GL_FLOAT, GL_FALSE, 7 * sizeof(float), (const void *)(6 * sizeof(float)));

	if (glGetError() != GL_NO_ERROR)
		eprintf("opengl error attrib pointer 0\n");

	delete[] tmp;
	delete[] tmpi;
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf("opengl error %d, end of SetupAtoms, l %d\n", e, __LINE__);

	//FIXME TODO: cloned atoms
163
	tmp = new float[solid->nVerts * 7 * numClonedAtoms];
164 165
	current=tmp;
#ifdef INDICESGL32		
166
	tmpi = new int[solid->nFaces*3 * numClonedAtoms];
167 168
	currenti=tmpi;
#else
169
	tmpi = new unsigned short[solid->nFaces*3 * numClonedAtoms];
170 171 172 173 174
	currenti=tmpi;
#endif

	for (int a = 0; a < numClonedAtoms; a++) {
		const int atomNumber = static_cast<int>(clonedAtoms[0][4 * a + 3]);
175
		const float radius = atomRadius(atomNumber)*atomScaling;
176
		for (int i = 0; i < solid->nVerts; i++) { //verts
177
				for (int k = 0; k < 3; k++) {
178
					*current++ = solid->Verts[3 * i + k]* radius +clonedAtoms[0][4 * a + k]; //pos
179 180
				}
				for (int k = 0; k < 3; k++) {
181
					*current++ = solid->Verts[3 * i + k]; //normal
182
				}
183
				*current++ =  static_cast<float>(atomNumber);
184
		} //i
185 186
		for (int i = 0; i < solid->nFaces * 3; i++)
			*currenti++ = solid->Faces[i] + a*solid->nVerts;
187 188 189 190 191 192 193 194 195 196 197
	} //a
	
	glBindVertexArray((*AtomVAO)[1]);
	glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, (*AtomIndexBuffer)[1]);
	glBindBuffer(GL_ARRAY_BUFFER, (*AtomVertBuffer)[1]);

	glEnableVertexAttribArray(0);
	glEnableVertexAttribArray(1);
	glEnableVertexAttribArray(2);
	glDisableVertexAttribArray(3);

198
	glBufferData(GL_ARRAY_BUFFER, sizeof(float) *numClonedAtoms* 7 * solid->nVerts, tmp,
199 200 201 202 203 204 205 206 207 208
			GL_STATIC_DRAW);
		if ((e = glGetError()) != GL_NO_ERROR)
			eprintf("opengl error %d, glBufferData, l %d\n", e, __LINE__);
	//eprintf ("After bufferdata, array buffer");
		glBufferData(GL_ELEMENT_ARRAY_BUFFER, 
#ifdef INDICESGL32		
	sizeof(int)
#else
	sizeof(unsigned int)
#endif
209
		* numClonedAtoms * 3 * solid->nFaces, tmpi, GL_STATIC_DRAW);
210 211 212 213 214 215 216 217 218 219
	//eprintf ("After bufferdata, element array buffer");
	glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 7*sizeof(float), (const void *)0);
	glVertexAttribPointer(1, 3, GL_FLOAT, GL_FALSE, 7 * sizeof(float), (const void *)(3*sizeof(float)));
	glVertexAttribPointer(2, 1, GL_FLOAT, GL_FALSE, 7 * sizeof(float), (const void *)(6 * sizeof(float)));

	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf("opengl error %d, glVertexAttribPointer, l %d\n", e, __LINE__);

	delete[] tmp;
	delete[] tmpi;
220

221
	glBindVertexArray(0);
222 223 224
	return e;
} //SetupAtomsNoTess

225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244
void CleanAtoms (GLuint **AtomVAO /*[4]*/, GLuint **AtomVertBuffer /*[3]*/, GLuint *BondIndices)
{
	if (!numAtoms)
		return;

	glDeleteVertexArrays(4, *AtomVAO);
	glDeleteBuffers(3, *AtomVertBuffer);
	glDeleteBuffers(1, BondIndices);

	delete[] (*AtomVAO);
	delete[] (*AtomVertBuffer);
	*AtomVAO=nullptr;
	*AtomVertBuffer=nullptr;


	if (numBonds)
		delete[] numBonds;
	numBonds=nullptr;
	bonds.clear();
}
245

246
GLenum SetupAtoms(GLuint **AtomVAO /*[4]*/, GLuint **AtomVertBuffer /*[3]*/, GLuint *BondIndices)
247 248
{
	if (!numAtoms)
249
		return glGetError();
250 251 252 253 254 255 256
	//rgh FIXME: put this all in the same vao
	
	//http://prideout.net/blog/?p=48 //public domain code
	//xyz u=atom type ; 4 floats
	int e;

	int totalatoms=0;
257
	for (int i=0;i<getAtomTimesteps() ;i++) {
258 259
		totalatoms += numAtoms[i];
	}
260
	//eprintf("SetupAtoms: totalatoms=%d", totalatoms);
261

262 263
	*AtomVAO = new GLuint[4]; //atoms, cloned atoms, bonds, trajectories
	*AtomVertBuffer = new GLuint[3]; //atoms, cloned atoms, trajectories
264

265 266
	glGenVertexArrays(4, *AtomVAO);
	glGenBuffers(3, *AtomVertBuffer);
267
	glGenBuffers(1, BondIndices);
268 269 270 271 272 273 274 275

	glBindVertexArray((*AtomVAO)[0]);
	glBindBuffer(GL_ARRAY_BUFFER, (*AtomVertBuffer)[0]);

	glEnableVertexAttribArray(0);
	glEnableVertexAttribArray(1);
	glDisableVertexAttribArray(2);
	glDisableVertexAttribArray(3);
276 277 278 279

	e=glGetError();
	if (e!=GL_NO_ERROR)
		eprintf ("gl error %d, %s %d", e, __FILE__, __LINE__);
280 281
	float *tmp = new float[4 * totalatoms];
	float *current=tmp;
282 283 284
	
	const int atomlimit=30;

285
	for (int p=0;p<getAtomTimesteps() ;p++) {
286 287 288 289 290 291
		for (int a = 0; a < numAtoms[p]; a++) {
			for (int k = 0; k < 4; k++) {
				*current++ = atoms[p][4 * a + k];
			}
		} //a
	}
292

293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317
	if (!displaybonds) {
		numBonds=nullptr;
		for (int p=1; p<getAtomTimesteps() ;p++) 
				numAtoms[p]+=numAtoms[p-1];
	} else {
		numBonds=new int[getAtomTimesteps() ];
		//can be slow, add loading screen here if Vive
		for (int p=0;p<getAtomTimesteps() ;p++) {
 
		if (numAtoms[p]<atomlimit) {
			//eprintf ("searching bonds basic");
			//bonds FIXME quadractic complexity	
					for (int a1=0; a1 < numAtoms[p]; a1++) {
						for (int a2=a1+1; a2 < numAtoms[p]; a2++){
							float d=0, r;
							for (int k=0;k<3;k++) {
								float dif=atoms[p][4 * a1 + k]-atoms[p][4 * a2 + k];
								d+=dif*dif;
							}
							r=atomRadius(static_cast<int>(atoms[p][4 * a1 + 3]))+
								atomRadius(static_cast<int>(atoms[p][4 * a2 + 3]));
							if (d*bondscaling<r*r) {// bond
								bonds.push_back(a1+(p==0?0:numAtoms[p-1]));
								bonds.push_back(a2+(p==0?0:numAtoms[p-1]));
							}
318 319
						}
					}
320 321
			} else { //more than 30 atoms, try grid optimization
			//eprintf ("searching bonds grid");
322

323 324
				float m[3];
				float M[3];
325
				for (int k=0; k<3;k++) {
326
					m[k]=M[k]=atoms[p][k];
327
				}
328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346
				for (int a = 1; a < numAtoms[p]; a++) {
					for (int k=0; k<3;k++) {
						if (m[k]>atoms[p][4*a+k])
							m[k]=atoms[p][4*a+k];
						if (M[k]<atoms[p][4*a+k])
							M[k]=atoms[p][4*a+k];
					}
				}
				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++) {
					std::vector<float*> found=g.find(atoms[p]+4*a);
					for (int b=0;b<found.size();b++) {
						//if (found[b] < tmp+4*a) // already got this bound
						//	continue;
						bonds.push_back(a+(p==0?0:numAtoms[p-1]));
						bonds.push_back(((found[b]-atoms[p])/4)+(p==0?0:numAtoms[p-1]));
					}
347 348
				}
			}
349 350 351 352 353
			numBonds[p]=bonds.size();
			if (p!=0)
				numAtoms[p]+=numAtoms[p-1];
		} //p
	} // showbonds
354 355 356
	glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 4 * sizeof(float), (const void *)(0));
	glVertexAttribPointer(1, 1, GL_FLOAT, GL_FALSE, 4 * sizeof(float), (const void *)(3 * sizeof(float)));
	glBufferData(GL_ARRAY_BUFFER, sizeof(float) * totalatoms * 4 , tmp,
357 358 359
		GL_STATIC_DRAW);
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf( "opengl error %d, glBufferData, l %d\n", e, __LINE__);
360

361
	glBindVertexArray(0);
362 363 364

	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf( "opengl error %d, end of SetupAtoms, l %d\n", e, __LINE__);
365
	
366 367 368 369 370 371 372 373 374 375 376 377 378 379
	if (showTrajectories) {
			//fill the restart buffer
		//use abc for measuring
		float max=0;
		if (has_abc) {
			for (int i=0;i<3;i++)
				for (int j=0;j<3;j++)
				max+=abc[i][j];
			max /=9*2;
		}

		for (unsigned int t=0;t<atomtrajectories.size();t++) {
			atomtrajectoryrestarts.push_back(std::vector<int>());
			atomtrajectoryrestarts[t].push_back(0);
380
			for (int p=1;p<getAtomTimesteps() ;p++) {
381
				int a=atomtrajectories[t];
382 383 384 385 386
				if (has_abc)
					if (fabs(atoms[p][a*4+0]-atoms[p-1][a*4+0])+
						fabs(atoms[p][a*4+1]-atoms[p-1][a*4+1])+
						fabs(atoms[p][a*4+2]-atoms[p-1][a*4+2])>max)
							atomtrajectoryrestarts[t].push_back(p);
387
			}
388
			atomtrajectoryrestarts[t].push_back(getAtomTimesteps() );
389
		}
390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412
	//need to setup a specific buffer because of GL_MAX_VERTEX_ATTRIB_STRIDE
	//only need xyz, not atom size
	//rgh FIXME: If we use index buffer instead, GPU storage is 1/3 of this
		float *traj = new float[atomtrajectories.size()*TIMESTEPS*3];
		for (unsigned int t = 0; t < atomtrajectories.size(); t++) {
			for (int i=0;i<TIMESTEPS;i++)
				for (int j = 0; j < 3; j++) {
					traj[t*TIMESTEPS * 3 + i * 3 + j] = tmp[i*numAtoms[0]*4+
																+atomtrajectories[t]*4
																+j];
				}
		}
		glBindVertexArray((*AtomVAO)[3]);
		glBindBuffer(GL_ARRAY_BUFFER, (*AtomVertBuffer)[2]);
		glBufferData(GL_ARRAY_BUFFER, sizeof(float) *atomtrajectories.size()*TIMESTEPS * 3, traj,
			GL_STATIC_DRAW);
		glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 3 * sizeof(float), (const void *)(0));
		glEnableVertexAttribArray(0);
		e = glGetError();
		if ((e = glGetError()) != GL_NO_ERROR)
			eprintf("opengl error %d, creating atom trajectories, l %d\n", e, __LINE__);

		delete[] traj;
413 414
	}
	delete[] tmp;
415
	//bonds
416 417 418 419 420 421 422 423 424 425 426
	if (displaybonds) {
		glBindVertexArray((*AtomVAO)[2]);
		glBindBuffer(GL_ARRAY_BUFFER, (*AtomVertBuffer)[0]);
		glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, *BondIndices);
		glBufferData(GL_ELEMENT_ARRAY_BUFFER, sizeof(int)*bonds.size(), bonds.data(), GL_STATIC_DRAW);
		glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 4 * sizeof(float), (const void *)(0));
		glEnableVertexAttribArray(0);
		glBindVertexArray(0);
	
		e=glGetError();
		if ((e = glGetError()) != GL_NO_ERROR)
427
			eprintf("opengl error %d, creating chemical bonds, l %d\n", e, __LINE__);
428
	}
429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447
	//now clones
	if (basisvectorreps ||!clonedAtoms) //do not replicate
		return e;


	glBindVertexArray((*AtomVAO)[1]); //rgh FIXME, only works for TIMESTEPS=1
	glBindBuffer(GL_ARRAY_BUFFER, (*AtomVertBuffer)[1]);
	glBufferData(GL_ARRAY_BUFFER, sizeof(float) * clonedAtoms[0].size(), clonedAtoms[0].data(),
			GL_STATIC_DRAW);
	glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 4 * sizeof(float), (const void *)(0));
	glVertexAttribPointer(1, 1, GL_FLOAT, GL_FALSE, 4 * sizeof(float), (const void *)(3 * sizeof(float)));
	glEnableVertexAttribArray(0);
	glEnableVertexAttribArray(1);
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf( "opengl error %d, end of Setup cloned Atoms, l %d\n", e, __LINE__);

	//rgh: we will need these again if we don't have tesselation
	//delete[] clonedAtoms;
	//clonedAtoms=0;
448
	glBindVertexArray(0);
449 450 451
	return e;
}

452 453 454 455 456 457 458
void CleanInfoCube  (GLuint *VAO, GLuint *VertBuffer, GLuint *IndexBuffer)
{
	glDeleteVertexArrays(1, VAO);
	glDeleteBuffers(1, VertBuffer);
	glDeleteBuffers(1, IndexBuffer);
}

459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531
GLenum SetupInfoCube (GLuint *VAO, GLuint *VertBuffer, GLuint *IndexBuffer)
{
	glGenVertexArrays(1, VAO);
	glGenBuffers(1, VertBuffer);
	glGenBuffers(1, IndexBuffer);

	glBindVertexArray(*VAO);
	glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, *IndexBuffer);
	glBindBuffer(GL_ARRAY_BUFFER, *VertBuffer);

	glEnableVertexAttribArray(0);
	glEnableVertexAttribArray(1);
	glEnableVertexAttribArray(2);
	glDisableVertexAttribArray(3);
	//vec4 pos, vec3 normal, vec2 uv
	const int Nvert=9*26;
	const GLfloat vert[]={
		-1, +1, -1, 0,		0, 0, -1,	0, 1, //-z
		-1, -1, -1,	0,		0, 0, -1,	0, 0,
		+1, +1, -1,	0,		0, 0, -1,	1, 1,
		+1, -1, -1,	0,		0, 0, -1,	1, 0,
		-1, +1, +1, 0,		0, 0, 1,	0, 0,//+z
		-1, -1, +1,	0,		0, 0, 1,	0, 1,
		+1, +1, +1,	0,		0, 0, 1,	1, 0,
		+1, -1, +1,	0,		0, 0, 1,	1, 1,

		+1, -1, -1, 0,		+1, 0, 0,	0, 1,//+x
		+1, -1, +1, 0,		+1, 0, 0,	0, 0,//+x
		+1, +1, -1, 0,		+1, 0, 0,	1, 1,//+x
		+1, +1, +1, 0,		+1, 0, 0,	1, 0,//+x
		-1, -1, -1, 0,		-1, 0, 0,	0, 0,//-x
		-1, -1, +1, 0,		-1, 0, 0,	0, 1,//-x
		-1, +1, -1, 0,		-1, 0, 0,	1, 0,//-x
		-1, +1, +1, 0,		-1, 0, 0,	1, 1,//-x

		-1, 1, +1, 0,		0, -1, 0,	0, 1, //+y
		-1, 1, -1, 0,		0, -1, 0,	0, 0,
		+1, 1, +1, 0,		0, -1, 0,	1, 1,
		+1, 1, -1, 0,		0, -1, 0,	1, 0,
		-1, -1, +1, 0,		0, +1, 0,	0, 0,//-y
		-1, -1, -1, 0,		0, +1, 0,	0, 1,
		+1, -1, +1, 0,		0, +1, 0,	1, 0,
		+1, -1, -1, 0,		0, +1, 0,	1, 1,
		0, 0, 0, 1,			0,0,0,		0,0, //for the line between the cube and the atom
		0, 0, 1, 1,			0, 0, 0,	0, 0, //for the line between the cube and the atom

	};
	const short int ind[]={
		0, 1, 2, //z
		1, 3, 2,
		4, 5, 6,
		5, 7, 6,
		8, 9, 10,//x
		9, 11, 10,
		12, 13, 14,
		13, 15, 14,
		16, 17, 18,//y
		17, 19, 18,
		20, 21, 22,
		21, 23, 22,
	};

	glBufferData(GL_ARRAY_BUFFER, sizeof(float) * Nvert , vert,
			GL_STATIC_DRAW);
	glBufferData(GL_ELEMENT_ARRAY_BUFFER, sizeof(ind), ind, GL_STATIC_DRAW);
	glVertexAttribPointer(0, 4, GL_FLOAT, GL_FALSE, 9 * sizeof(float), (const void *)(0));
	glVertexAttribPointer(1, 3, GL_FLOAT, GL_FALSE, 9 * sizeof(float), (const void *)(4*sizeof(float)));
	glVertexAttribPointer(2, 2, GL_FLOAT, GL_FALSE, 9 * sizeof(float), (const void *)(7*sizeof(float)));
	glBindVertexArray(0);

	return glGetError();
}

532
float getMarkerLobeScaling(int l, int k)
533
{
534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571
	if (l == k)
		return 2.0f;
	return 0.5f;
}

GLenum SetupMarkerNoTess(GLuint *MarkerVAO, GLuint *MarkerVertBuffer, GLuint *MarkerIndexBuffer)
{
	if (!markers)
		return glGetError();

	GLenum e;
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf("opengl error %d, begin of SetupMarkerNoTess\n", e, __LINE__);

	glGenVertexArrays(1, MarkerVAO);
	glGenBuffers(1, MarkerVertBuffer);
	glGenBuffers(1, MarkerIndexBuffer);

	glBindVertexArray(*MarkerVAO);
	glBindBuffer(GL_ARRAY_BUFFER, *MarkerVertBuffer);
	glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, *MarkerIndexBuffer);

	glEnableVertexAttribArray(0);
	glEnableVertexAttribArray(1);
	glEnableVertexAttribArray(2);
	glDisableVertexAttribArray(3);

	glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 10 * sizeof(float), (const void *)0);
	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)));

	float *tmp = new float[10 * MARKERSOLID::nVerts*3* TIMESTEPS]; //xyz, nxnynz, rgba; compatible with IsoShaders
	float *current = tmp;
	for (int i = 0; i < TIMESTEPS; i++) {
		for (int l = 0; l < 3; l++) {//3 ellipsoids
			for (int j = 0; j < MARKERSOLID::nVerts; j++) {
				for (int k = 0; k < 3; k++) { //pos
					float s = getMarkerLobeScaling(l, k);
572
					*current++ = s*MARKERSOLID::Verts[j * 3 + k] * markerscaling * atomScaling * atomRadius(0) +
573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627
						markers[i][k];
				}
				float length=0;
				for (int k = 0; k < 3; k++) { //normal; normalized in IsoShader
					float s = getMarkerLobeScaling(l, k);
					*current = MARKERSOLID::Verts[j * 3 + k]*s;
					length += (*current)*(*current);
					current++;
				}
				length=1.0f / sqrtf(length);
				for (int k=0;k<3;k++) {
					*(current-1-k)*=length;
				}
				for (int k = 0; k < 4; k++) { //colour
					*current++ = markercolours[i][k];
				}
			}
		}
	}
	glBufferData(GL_ARRAY_BUFFER, sizeof(float) * 10 * MARKERSOLID::nVerts * 3 * TIMESTEPS, tmp,
		GL_STATIC_DRAW);

	delete[] tmp;
#ifdef INDICESGL32		
	int *tmpi=new int[TIMESTEPS * 3 * Icosahedron::nFaces * 3];
	int * currenti;
#else
	short *tmpi = new short[TIMESTEPS * 3 * Icosahedron::nFaces * 3];
	short *currenti;
#endif

	currenti = tmpi;
	for (int i = 0; i < TIMESTEPS; i++) {
		for (int l = 0; l < 3; l++) {//ellipsoids
			for (int j = 0; j < MARKERSOLID::nFaces; j++) {
				for (int k = 0; k < 3; k++) {
					*currenti++ = MARKERSOLID::Faces[j * 3 + k] + 
						MARKERSOLID::nVerts * (l+3*i);
				}
			}
		}
	}

	glBufferData(GL_ELEMENT_ARRAY_BUFFER,
#ifdef INDICESGL32		
		sizeof(int)*MARKERSOLID::nFaces * 3 * TIMESTEPS * 3
#else
		sizeof(unsigned int)*MARKERSOLID::nFaces * 3 * TIMESTEPS * 3
#endif
		, tmpi, GL_STATIC_DRAW);
	delete[] tmpi;
	glBindVertexArray(0);
	return e;
}

628 629 630 631 632 633
void CleanMarker (GLuint *MarkerVAO, GLuint *MarkerVertBuffer)
{
	glDeleteVertexArrays(1, MarkerVAO);
	glDeleteBuffers(1, MarkerVertBuffer);
}

634 635
GLenum SetupMarker(GLuint *MarkerVAO, GLuint *MarkerVertBuffer)
{//requires tesselation
636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674
	if (!markers)
		return glGetError();
	GLenum e;
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf( "opengl error %d, begin of SetupMarker\n", e, __LINE__);

	glGenVertexArrays(1, MarkerVAO);
	glGenBuffers(1, MarkerVertBuffer);
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf( "opengl error %d, glGenBuffers, l %d\n", e, __LINE__);

	glBindVertexArray(*MarkerVAO);
	glBindBuffer(GL_ARRAY_BUFFER, *MarkerVertBuffer);

	glEnableVertexAttribArray(0);
	glEnableVertexAttribArray(1);
	glDisableVertexAttribArray(2);
	glDisableVertexAttribArray(3);

	const float size=atomRadius(0)*atomScaling*markerscaling;
	float *tmp = new float [8*TIMESTEPS];
	for (int i=0;i<TIMESTEPS;i++) {
		for (int j=0;j<3;j++) { //center [3]
			tmp[i*8+j]=markers[i][j];
		}
		tmp[i*8+3]=0.8*size; //size [1]
		for (int j=0;j<4;j++) {//colour[4]
			tmp[i*8+4+j]=markercolours[i][j];
		}
	}
	
	glBufferData(GL_ARRAY_BUFFER, sizeof(float) * TIMESTEPS*8 , tmp,
			GL_STATIC_DRAW);
	glVertexAttribPointer(0, 4, GL_FLOAT, GL_FALSE, 8 * sizeof(float), (const void *)(0));
	glVertexAttribPointer(1, 4, GL_FLOAT, GL_FALSE, 8 * sizeof(float), (const void *)(4*sizeof(float)));
	glBindVertexArray(0);
	return glGetError();
}

675 676 677 678 679 680 681
void CleanUnitCell (GLuint *UnitCellVAO, GLuint *UnitCellVertBuffer, GLuint *UnitCellIndexBuffer)
{
	glDeleteVertexArrays(1, UnitCellVAO);
	glDeleteBuffers(1, UnitCellVertBuffer);
	glDeleteBuffers(1, UnitCellIndexBuffer);
}

682 683
GLenum SetupUnitCell(GLuint *UnitCellVAO, GLuint *UnitCellVertBuffer, GLuint *UnitCellIndexBuffer)
{
684
	//add here both unit cell and supercell
685
	GLenum e;
686 687 688 689
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf( "opengl error %d, begin of SetupUnitCell\n", e, __LINE__);
	if (!has_abc)
		return e;
690 691 692 693 694 695 696 697 698 699 700 701 702 703 704
	glGenVertexArrays(1, UnitCellVAO);
	glGenBuffers(1, UnitCellVertBuffer);
	glGenBuffers(1, UnitCellIndexBuffer);
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf( "opengl error %d, glGenBuffers, l %d\n", e, __LINE__);

	glBindVertexArray(*UnitCellVAO);
	glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, *UnitCellIndexBuffer);
	glBindBuffer(GL_ARRAY_BUFFER, *UnitCellVertBuffer);

	glEnableVertexAttribArray(0);
	glDisableVertexAttribArray(1);
	glDisableVertexAttribArray(2);
	glDisableVertexAttribArray(3);

705
	float *tmp = new float[3*8*2];
706
	//0, a, b, c, a+b+c, b+c, a+c, a+b
707
	for (int i=0;i<3;i++) { //unit cell
708 709 710 711 712 713 714 715
		tmp[0+i]=0;
		for (int j=0;j<3;j++)
			tmp[3*(j+1)+i]=abc[j][i];
		tmp[3*4+i]=abc[0][i]+abc[1][i]+abc[2][i];
		tmp[3*5+i]=			abc[1][i]+abc[2][i];
		tmp[3*6+i]=abc[0][i]+		abc[2][i];
		tmp[3*7+i]=abc[0][i]+abc[1][i];
	}
716 717 718 719 720 721 722 723 724 725 726 727 728 729 730
	float displ[3]={0,0,0};
	if (translations && ISOS) 
		for (int j=0;j<3;j++)
			for (int i=0;i<3;i++)
				displ[i]+=-translations[0][i]*abc[j][i];
	for (int i=0;i<3;i++) { //rgh fixme, add displacement here as well
		tmp[3*8+i]=displ[i];
		for (int j=0;j<3;j++)
			tmp[3*(j+8+1)+i]=abc[j][i]*supercell[j]+displ[i];
		tmp[3*12+i]=abc[0][i]*supercell[0]+abc[1][i]*supercell[1]+abc[2][i]*supercell[2]+displ[i];
		tmp[3*13+i]=			abc[1][i]*supercell[1]+abc[2][i]*supercell[2]+displ[i];
		tmp[3*14+i]=abc[0][i]*supercell[0]+		abc[2][i]*supercell[2]+displ[i];
		tmp[3*15+i]=abc[0][i]*supercell[0]+abc[1][i]*supercell[1]+displ[i];
	}
	int tmpi[12*2*2]={ //lines, unit cell, 
731 732 733 734 735 736 737 738 739 740 741
		0,1, 
		1,6,
		6,3,
		3,0,
		2,7,
		7,4,
		4,5,
		5,2,
		0,2,
		1,7,
		6,4,
742 743 744 745 746 747 748 749 750 751 752 753 754
		3,5, // supercell
		0+8,1+8, 
		1+8,6+8,
		6+8,3+8,
		3+8,0+8,
		2+8,7+8,
		7+8,4+8,
		4+8,5+8,
		5+8,2+8,
		0+8,2+8,
		1+8,7+8,
		6+8,4+8,
		3+8,5+8
755
	};
756
	glBufferData(GL_ARRAY_BUFFER, sizeof(float) * 3*8*2 , tmp,
757 758
			GL_STATIC_DRAW);
	if ((e = glGetError()) != GL_NO_ERROR)
759
		eprintf( "opengl error %d, glBufferData vertex, l %d\n", e, __LINE__);
760 761
	glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 3 * sizeof(float), (const void *)(0));
	glBufferData(GL_ELEMENT_ARRAY_BUFFER, sizeof(tmpi), tmpi, GL_STATIC_DRAW);
762 763
	if ((e = glGetError()) != GL_NO_ERROR)
		eprintf( "opengl error %d, glBufferData index, l %d\n", e, __LINE__);
764
	glBindVertexArray(0);
765 766 767 768
	return e;
}


769 770
bool PrepareUnitCellAtomShader (GLuint *AtomP, GLuint *cellP, GLuint *MarkerP, 
								GLint *AtomMatrixLocation, GLint *UnitCellMatrixLocation,  GLint *UnitCellColourLocation,
771 772
								GLint *MarkerMatrixLocation, GLint *totalatomsLocation, GLint *selectedAtomLocation){
	if (!PrepareAtomShader(AtomP, AtomMatrixLocation, totalatomsLocation, selectedAtomLocation))
773 774 775 776 777
		return false;

	if (!PrepareUnitCellShader(cellP, UnitCellMatrixLocation, UnitCellColourLocation))
		return false;

778 779 780
	if (!PrepareMarkerShader(MarkerP, MarkerMatrixLocation))
		return false;

781 782 783
	return true;
}

784
bool PrepareAtomShader (GLuint *AtomP, GLint *AtomMatrixLocation, GLint *totalatomsLocation, GLint *selectedAtomLocation){
785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800
		//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
	//http://stackoverflow.com/questions/40101023/flat-shading-in-webgl
	*AtomP = CompileGLShader(
		AtomShaders[SHADERNAME],
		AtomShaders[SHADERVERTEX],
		AtomShaders[SHADERFRAGMENT],
		AtomShaders[SHADERTESSEVAL]
		);
	*AtomMatrixLocation=glGetUniformLocation(*AtomP, "matrix");
	if( *AtomMatrixLocation == -1 )
	{
		eprintf( "Unable to find matrix uniform in atom shader\n" );
		return false;
	}
801 802 803 804 805 806
	*totalatomsLocation=glGetUniformLocation(*AtomP, "totalatoms");
	if( *totalatomsLocation == -1 )
	{
		eprintf( "Unable to find matrix uniform in atom shader\n" );
		return false;
	}
807 808 809 810 811 812
	*selectedAtomLocation=glGetUniformLocation(*AtomP, "selectedAtom");
	if( *totalatomsLocation == -1 )
	{
		eprintf( "Unable to find selectedAtom uniform in atom shader\n" );
		return false;
	}
813 814 815
	return true;
}

816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835
bool PrepareMarkerShader (GLuint *MP, GLint *MMatrixLocation){
		//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
	//http://stackoverflow.com/questions/40101023/flat-shading-in-webgl
	*MP = CompileGLShader(
		MarkerShaders[SHADERNAME],
		MarkerShaders[SHADERVERTEX],
		MarkerShaders[SHADERFRAGMENT],
		MarkerShaders[SHADERTESSEVAL]
		);
	*MMatrixLocation=glGetUniformLocation(*MP, "matrix");
	if( *MMatrixLocation == -1 )
	{
		eprintf( "Unable to find matrix uniform in atom shader\n" );
		return false;
	}
	return true;
}

836
bool PrepareAtomShaderNoTess (GLuint *AtomP, GLint *AtomMatrixLocation, GLint *totalatomsLocation){
837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852
		//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
	//http://stackoverflow.com/questions/40101023/flat-shading-in-webgl
	*AtomP = CompileGLShader(
		AtomShadersNoTess[SHADERNAME],
		AtomShadersNoTess[SHADERVERTEX],
		AtomShadersNoTess[SHADERFRAGMENT],
		AtomShadersNoTess[SHADERTESSEVAL]
		);
	*AtomMatrixLocation=glGetUniformLocation(*AtomP, "matrix");
	if( *AtomMatrixLocation == -1 )
	{
		eprintf( "Unable to find matrix uniform in atom shader no tess\n" );
		return false;
	}
853 854 855 856 857 858
	*totalatomsLocation=glGetUniformLocation(*AtomP, "totalatoms");
	if( *totalatomsLocation == -1 )
	{
		eprintf( "Unable to find matrix uniform in atom shader\n" );
		return false;
	}
859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899
	return true;
}


bool PrepareUnitCellShader (GLuint *cellP, GLint *UnitCellMatrixLocation,  GLint *UnitCellColourLocation){
	*cellP= CompileGLShader(
		UnitCellShaders[SHADERNAME],
		UnitCellShaders[SHADERVERTEX],
		UnitCellShaders[SHADERFRAGMENT],
		UnitCellShaders[SHADERTESSEVAL]
		);
	*UnitCellMatrixLocation=glGetUniformLocation(*cellP, "matrix");
	if( *UnitCellMatrixLocation == -1 )
	{
		eprintf( "Unable to find matrix uniform in UnitCell shader\n" );
		return false;
	}
	*UnitCellColourLocation=glGetUniformLocation(*cellP, "color");
	if( *UnitCellColourLocation == -1 )
	{
		eprintf( "Unable to find color uniform in UnitCell shader\n" );
		return false;
	}
	return true;
}


/**p: input, f: output*/
void GetDisplacement(int p[3], float f[3])
{
float delta[3][3];
for (int ss=0;ss<3;ss++)
	for (int i=0;i<3;i++)
		delta[ss][i]=static_cast<float>(p[ss])*abc[ss][i];

for (int i=0;i<3;i++)
	f[i]=0;

for (int ss=0;ss<3;ss++)
	for (int i=0;i<3;i++)
		f[i]+=delta[ss][i];
900
}