1 |
#include <iostream> |
2 |
|
3 |
#include <cstdlib> |
4 |
#include <cstring> |
5 |
#include <cmath> |
6 |
|
7 |
#include "simError.h" |
8 |
#include "SimInfo.hpp" |
9 |
#include "ReadWrite.hpp" |
10 |
|
11 |
#include "MoLocator.hpp" |
12 |
#include "sysBuild.hpp" |
13 |
#include "bilayerSys.hpp" |
14 |
|
15 |
#include "latticeBuilder.hpp" |
16 |
|
17 |
void buildMap( double &x, double &y, double &z, |
18 |
double boxX, double boxY, double boxZ ); |
19 |
|
20 |
int buildRandomBilayer( void ); |
21 |
|
22 |
void getRandomRot( double rot[3][3] ); |
23 |
|
24 |
int buildBilayer( int isRandom ){ |
25 |
|
26 |
if( isRandom ){ |
27 |
return buildRandomBilayer(); |
28 |
} |
29 |
else{ |
30 |
sprintf( painCave.errMsg, |
31 |
"Cannot currently create a non-random bilayer.\n" ); |
32 |
painCave.isFatal = 1; |
33 |
simError(); |
34 |
return 0; |
35 |
} |
36 |
} |
37 |
|
38 |
|
39 |
int buildRandomBilayer( void ){ |
40 |
|
41 |
typedef struct{ |
42 |
double rot[3][3]; |
43 |
double pos[3]; |
44 |
} coord; |
45 |
|
46 |
|
47 |
|
48 |
const double waterRho = 0.0334; // number density per cubic angstrom |
49 |
const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters |
50 |
const double waterCell = 4.929; // fcc unit cell length |
51 |
|
52 |
Lattice myFCC( FCC_LATTICE_TYPE, waterCell ); |
53 |
double *posX, *posY, *posZ; |
54 |
double pos[3], posA[3], posB[3]; |
55 |
|
56 |
const double water_padding = 6.0; |
57 |
const double lipid_spaceing = 8.0; |
58 |
|
59 |
|
60 |
int i,j,k, l, m; |
61 |
int nAtoms, atomIndex, molIndex, molID; |
62 |
int* molSeq; |
63 |
int* molMap; |
64 |
int* molStart; |
65 |
int* cardDeck; |
66 |
int deckSize; |
67 |
int rSite, rCard; |
68 |
double cell; |
69 |
int nCells, nSites, siteIndex; |
70 |
|
71 |
coord testSite; |
72 |
|
73 |
Atom** atoms; |
74 |
SimInfo* simnfo; |
75 |
SimState* theConfig; |
76 |
DumpWriter* writer; |
77 |
|
78 |
MoleculeStamp* lipidStamp; |
79 |
MoleculeStamp* waterStamp; |
80 |
MoLocator *lipidLocate; |
81 |
MoLocator *waterLocate; |
82 |
int foundLipid, foundWater; |
83 |
int nLipids, lipidNatoms, nWaters, waterNatoms; |
84 |
double testBox, maxLength; |
85 |
|
86 |
srand48( RAND_SEED ); |
87 |
|
88 |
|
89 |
// create the simInfo objects |
90 |
|
91 |
simnfo = new SimInfo[3]; |
92 |
|
93 |
|
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// set the the lipidStamp |
95 |
|
96 |
foundLipid = 0; |
97 |
foundWater = 0; |
98 |
for(i=0; i<bsInfo.nComponents; i++){ |
99 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
100 |
|
101 |
foundLipid = 1; |
102 |
lipidStamp = bsInfo.compStamps[i]; |
103 |
nLipids = bsInfo.componentsNmol[i]; |
104 |
} |
105 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
106 |
|
107 |
foundWater = 1; |
108 |
|
109 |
waterStamp = bsInfo.compStamps[i]; |
110 |
nWaters = bsInfo.componentsNmol[i]; |
111 |
} |
112 |
} |
113 |
if( !foundLipid ){ |
114 |
sprintf(painCave.errMsg, |
115 |
"Could not find lipid \"%s\" in the bass file.\n", |
116 |
bsInfo.lipidName ); |
117 |
painCave.isFatal = 1; |
118 |
simError(); |
119 |
} |
120 |
if( !foundWater ){ |
121 |
sprintf(painCave.errMsg, |
122 |
"Could not find solvent \"%s\" in the bass file.\n", |
123 |
bsInfo.waterName ); |
124 |
painCave.isFatal = 1; |
125 |
simError(); |
126 |
} |
127 |
|
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//create the temp Molocator and atom Arrays |
129 |
|
130 |
lipidLocate = new MoLocator( lipidStamp ); |
131 |
lipidNatoms = lipidStamp->getNAtoms(); |
132 |
maxLength = lipidLocate->getMaxLength(); |
133 |
|
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waterLocate = new MoLocator( waterStamp ); |
135 |
waterNatoms = waterStamp->getNAtoms(); |
136 |
|
137 |
nAtoms = lipidNatoms; |
138 |
|
139 |
simnfo[0].n_atoms = nAtoms; |
140 |
simnfo[0].atoms=new Atom*[nAtoms]; |
141 |
|
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theConfig = simnfo[0].getConfiguration(); |
143 |
theConfig->createArrays( simnfo[0].n_atoms ); |
144 |
|
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atoms=simnfo[0].atoms; |
146 |
|
147 |
|
148 |
// create the test box for initial water displacement |
149 |
|
150 |
testBox = maxLength + waterCell * 4.0; // pad with 4 cells |
151 |
nCells = (int)( testBox / waterCell + 1.0 ); |
152 |
int testWaters = 4 * nCells * nCells * nCells; |
153 |
|
154 |
double* waterX = new double[testWaters]; |
155 |
double* waterY = new double[testWaters]; |
156 |
double* waterZ = new double[testWaters]; |
157 |
|
158 |
double x0 = 0.0 - ( testBox * 0.5 ); |
159 |
double y0 = 0.0 - ( testBox * 0.5 ); |
160 |
double z0 = 0.0 - ( testBox * 0.5 ); |
161 |
|
162 |
|
163 |
// create an fcc lattice in the water box. |
164 |
|
165 |
int ndx = 0; |
166 |
for( i=0; i < nCells; i++ ){ |
167 |
for( j=0; j < nCells; j++ ){ |
168 |
for( k=0; k < nCells; k++ ){ |
169 |
|
170 |
myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k); |
171 |
for(l=0; l<4; l++){ |
172 |
waterX[ndx]=posX[l]; |
173 |
waterY[ndx]=posY[l]; |
174 |
waterZ[ndx]=posZ[l]; |
175 |
ndx++; |
176 |
} |
177 |
} |
178 |
} |
179 |
} |
180 |
|
181 |
// calculate the number of water's displaced by our lipid. |
182 |
|
183 |
testSite.rot[0][0] = 1.0; |
184 |
testSite.rot[0][1] = 0.0; |
185 |
testSite.rot[0][2] = 0.0; |
186 |
|
187 |
testSite.rot[1][0] = 0.0; |
188 |
testSite.rot[1][1] = 1.0; |
189 |
testSite.rot[1][2] = 0.0; |
190 |
|
191 |
testSite.rot[2][0] = 0.0; |
192 |
testSite.rot[2][1] = 0.0; |
193 |
testSite.rot[2][2] = 1.0; |
194 |
|
195 |
testSite.pos[0] = 0.0; |
196 |
testSite.pos[1] = 0.0; |
197 |
testSite.pos[2] = 0.0; |
198 |
|
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lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig ); |
200 |
|
201 |
int *isActive = new int[testWaters]; |
202 |
for(i=0; i<testWaters; i++) isActive[i] = 1; |
203 |
|
204 |
int n_deleted = 0; |
205 |
double dx, dy, dz; |
206 |
double dx2, dy2, dz2, dSqr; |
207 |
double rCutSqr = water_padding * water_padding; |
208 |
|
209 |
for(i=0; ( (i<testWaters) && isActive[i] ); i++){ |
210 |
for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){ |
211 |
|
212 |
atoms[j]->getPos( pos ); |
213 |
|
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dx = waterX[i] - pos[0]; |
215 |
dy = waterY[i] - pos[1]; |
216 |
dz = waterZ[i] - pos[2]; |
217 |
|
218 |
buildMap( dx, dy, dz, testBox, testBox, testBox ); |
219 |
|
220 |
dx2 = dx * dx; |
221 |
dy2 = dy * dy; |
222 |
dz2 = dz * dz; |
223 |
|
224 |
dSqr = dx2 + dy2 + dz2; |
225 |
if( dSqr < rCutSqr ){ |
226 |
isActive[i] = 0; |
227 |
n_deleted++; |
228 |
} |
229 |
} |
230 |
} |
231 |
|
232 |
int targetWaters = nWaters + n_deleted * nLipids; |
233 |
|
234 |
targetWaters = (int) ( targetWaters * 1.2 ); |
235 |
|
236 |
// find the best box size for the sim |
237 |
|
238 |
int testTot; |
239 |
int done = 0; |
240 |
ndx = 0; |
241 |
while( !done ){ |
242 |
|
243 |
ndx++; |
244 |
testTot = 4 * ndx * ndx * ndx; |
245 |
|
246 |
if( testTot >= targetWaters ) done = 1; |
247 |
} |
248 |
|
249 |
nCells = ndx; |
250 |
|
251 |
|
252 |
// create the new water box to the new specifications |
253 |
|
254 |
int newWaters = nCells * nCells * nCells * 4; |
255 |
|
256 |
delete[] waterX; |
257 |
delete[] waterY; |
258 |
delete[] waterZ; |
259 |
|
260 |
coord* waterSites = new coord[newWaters]; |
261 |
|
262 |
double box_x = waterCell * nCells; |
263 |
double box_y = waterCell * nCells; |
264 |
double box_z = waterCell * nCells; |
265 |
|
266 |
// create an fcc lattice in the water box. |
267 |
|
268 |
ndx = 0; |
269 |
for( i=0; i < nCells; i++ ){ |
270 |
for( j=0; j < nCells; j++ ){ |
271 |
for( k=0; k < nCells; k++ ){ |
272 |
|
273 |
myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k); |
274 |
for(l=0; l<4; l++){ |
275 |
waterSites[ndx].pos[0] = posX[l]; |
276 |
waterSites[ndx].pos[1] = posY[l]; |
277 |
waterSites[ndx].pos[2] = posZ[l]; |
278 |
ndx++; |
279 |
} |
280 |
} |
281 |
} |
282 |
} |
283 |
|
284 |
coord* lipidSites = new coord[nLipids]; |
285 |
|
286 |
// start a 3D RSA for the for the lipid placements |
287 |
|
288 |
|
289 |
int reject; |
290 |
int testDX, acceptedDX; |
291 |
|
292 |
nAtoms = nLipids * lipidNatoms; |
293 |
|
294 |
simnfo[1].n_atoms = nAtoms; |
295 |
simnfo[1].atoms=new Atom*[nAtoms]; |
296 |
|
297 |
theConfig = simnfo[1].getConfiguration(); |
298 |
theConfig->createArrays( simnfo[1].n_atoms ); |
299 |
|
300 |
atoms=simnfo[1].atoms; |
301 |
|
302 |
rCutSqr = lipid_spaceing * lipid_spaceing; |
303 |
|
304 |
for(i=0; i<nLipids; i++ ){ |
305 |
done = 0; |
306 |
while( !done ){ |
307 |
|
308 |
lipidSites[i].pos[0] = drand48() * box_x; |
309 |
lipidSites[i].pos[1] = drand48() * box_y; |
310 |
lipidSites[i].pos[2] = drand48() * box_z; |
311 |
|
312 |
getRandomRot( lipidSites[i].rot ); |
313 |
|
314 |
ndx = i * lipidNatoms; |
315 |
|
316 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
317 |
ndx, theConfig ); |
318 |
|
319 |
reject = 0; |
320 |
for( j=0; !reject && j<i; j++){ |
321 |
for(k=0; !reject && k<lipidNatoms; k++){ |
322 |
|
323 |
acceptedDX = j*lipidNatoms + k; |
324 |
for(l=0; !reject && l<lipidNatoms; l++){ |
325 |
|
326 |
testDX = ndx + l; |
327 |
|
328 |
atoms[testDX]->getPos( posA ); |
329 |
atoms[acceptedDX]->getPos( posB ); |
330 |
|
331 |
dx = posA[0] - posB[0]; |
332 |
dy = posA[1] - posB[1]; |
333 |
dz = posA[2] - posB[2]; |
334 |
|
335 |
buildMap( dx, dy, dz, box_x, box_y, box_z ); |
336 |
|
337 |
dx2 = dx * dx; |
338 |
dy2 = dy * dy; |
339 |
dz2 = dz * dz; |
340 |
|
341 |
dSqr = dx2 + dy2 + dz2; |
342 |
if( dSqr < rCutSqr ) reject = 1; |
343 |
} |
344 |
} |
345 |
} |
346 |
|
347 |
if( reject ){ |
348 |
|
349 |
for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j]; |
350 |
} |
351 |
else{ |
352 |
done = 1; |
353 |
std::cout << (i+1) << " has been accepted\n"; |
354 |
} |
355 |
} |
356 |
} |
357 |
|
358 |
// cut out the waters that overlap with the lipids. |
359 |
|
360 |
|
361 |
delete[] isActive; |
362 |
isActive = new int[newWaters]; |
363 |
for(i=0; i<newWaters; i++) isActive[i] = 1; |
364 |
int n_active = newWaters; |
365 |
rCutSqr = water_padding * water_padding; |
366 |
|
367 |
for(i=0; ( (i<newWaters) && isActive[i] ); i++){ |
368 |
for(j=0; ( (j<nAtoms) && isActive[i] ); j++){ |
369 |
|
370 |
atoms[j]->getPos( pos ); |
371 |
|
372 |
dx = waterSites[i].pos[0] - pos[0]; |
373 |
dy = waterSites[i].pos[1] - pos[1]; |
374 |
dz = waterSites[i].pos[2] - pos[2]; |
375 |
|
376 |
buildMap( dx, dy, dz, box_x, box_y, box_z ); |
377 |
|
378 |
dx2 = dx * dx; |
379 |
dy2 = dy * dy; |
380 |
dz2 = dz * dz; |
381 |
|
382 |
dSqr = dx2 + dy2 + dz2; |
383 |
if( dSqr < rCutSqr ){ |
384 |
isActive[i] = 0; |
385 |
n_active--; |
386 |
|
387 |
|
388 |
} |
389 |
} |
390 |
} |
391 |
|
392 |
|
393 |
|
394 |
|
395 |
if( n_active < nWaters ){ |
396 |
|
397 |
sprintf( painCave.errMsg, |
398 |
"Too many waters were removed, edit code and try again.\n" ); |
399 |
|
400 |
painCave.isFatal = 1; |
401 |
simError(); |
402 |
} |
403 |
|
404 |
int quickKill; |
405 |
while( n_active > nWaters ){ |
406 |
|
407 |
quickKill = (int)(drand48()*newWaters); |
408 |
|
409 |
if( isActive[quickKill] ){ |
410 |
isActive[quickKill] = 0; |
411 |
n_active--; |
412 |
|
413 |
} |
414 |
} |
415 |
|
416 |
if( n_active != nWaters ){ |
417 |
|
418 |
sprintf( painCave.errMsg, |
419 |
"QuickKill didn't work right. n_active = %d, and nWaters = %d\n", |
420 |
n_active, nWaters ); |
421 |
painCave.isFatal = 1; |
422 |
simError(); |
423 |
} |
424 |
|
425 |
// clean up our messes before building the final system. |
426 |
|
427 |
simnfo[0].getConfiguration()->destroyArrays(); |
428 |
simnfo[1].getConfiguration()->destroyArrays(); |
429 |
|
430 |
// create the real Atom arrays |
431 |
|
432 |
nAtoms = 0; |
433 |
molIndex = 0; |
434 |
molStart = new int[nLipids + nWaters]; |
435 |
|
436 |
for(j=0; j<nLipids; j++){ |
437 |
molStart[molIndex] = nAtoms; |
438 |
molIndex++; |
439 |
nAtoms += lipidNatoms; |
440 |
} |
441 |
|
442 |
for(j=0; j<nWaters; j++){ |
443 |
molStart[molIndex] = nAtoms; |
444 |
molIndex++; |
445 |
nAtoms += waterNatoms; |
446 |
} |
447 |
|
448 |
theConfig = simnfo[2].getConfiguration(); |
449 |
theConfig->createArrays( nAtoms ); |
450 |
simnfo[2].atoms = new Atom*[nAtoms]; |
451 |
atoms = simnfo[2].atoms; |
452 |
simnfo[2].n_atoms = nAtoms; |
453 |
|
454 |
// initialize lipid positions |
455 |
|
456 |
molIndex = 0; |
457 |
for(i=0; i<nLipids; i++ ){ |
458 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
459 |
molStart[molIndex], theConfig ); |
460 |
molIndex++; |
461 |
} |
462 |
|
463 |
// initialize the water positions |
464 |
|
465 |
for(i=0; i<newWaters; i++){ |
466 |
|
467 |
if( isActive[i] ){ |
468 |
|
469 |
getRandomRot( waterSites[i].rot ); |
470 |
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
471 |
molStart[molIndex], theConfig ); |
472 |
molIndex++; |
473 |
} |
474 |
} |
475 |
|
476 |
// set up the SimInfo object |
477 |
|
478 |
double Hmat[3][3]; |
479 |
|
480 |
Hmat[0][0] = box_x; |
481 |
Hmat[0][1] = 0.0; |
482 |
Hmat[0][2] = 0.0; |
483 |
|
484 |
Hmat[1][0] = 0.0; |
485 |
Hmat[1][1] = box_y; |
486 |
Hmat[1][2] = 0.0; |
487 |
|
488 |
Hmat[2][0] = 0.0; |
489 |
Hmat[2][1] = 0.0; |
490 |
Hmat[2][2] = box_z; |
491 |
|
492 |
|
493 |
bsInfo.boxX = box_x; |
494 |
bsInfo.boxY = box_y; |
495 |
bsInfo.boxZ = box_z; |
496 |
|
497 |
simnfo[2].setBoxM( Hmat ); |
498 |
|
499 |
sprintf( simnfo[2].sampleName, "%s.dump", bsInfo.outPrefix ); |
500 |
sprintf( simnfo[2].finalName, "%s.init", bsInfo.outPrefix ); |
501 |
|
502 |
// set up the writer and write out |
503 |
|
504 |
writer = new DumpWriter( &simnfo[2] ); |
505 |
writer->writeFinal( 0.0 ); |
506 |
|
507 |
// clean up the memory |
508 |
|
509 |
// if( molMap != NULL ) delete[] molMap; |
510 |
// if( cardDeck != NULL ) delete[] cardDeck; |
511 |
// if( locate != NULL ){ |
512 |
// for(i=0; i<bsInfo.nComponents; i++){ |
513 |
// delete locate[i]; |
514 |
// } |
515 |
// delete[] locate; |
516 |
// } |
517 |
// if( atoms != NULL ){ |
518 |
// for(i=0; i<nAtoms; i++){ |
519 |
// delete atoms[i]; |
520 |
// } |
521 |
// Atom::destroyArrays(); |
522 |
// delete[] atoms; |
523 |
// } |
524 |
// if( molSeq != NULL ) delete[] molSeq; |
525 |
// if( simnfo != NULL ) delete simnfo; |
526 |
// if( writer != NULL ) delete writer; |
527 |
|
528 |
return 1; |
529 |
} |
530 |
|
531 |
void getRandomRot( double rot[3][3] ){ |
532 |
|
533 |
double theta, phi, psi; |
534 |
double cosTheta; |
535 |
|
536 |
// select random phi, psi, and cosTheta |
537 |
|
538 |
phi = 2.0 * M_PI * drand48(); |
539 |
psi = 2.0 * M_PI * drand48(); |
540 |
cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
541 |
|
542 |
theta = acos( cosTheta ); |
543 |
|
544 |
rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
545 |
rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
546 |
rot[0][2] = sin(theta) * sin(psi); |
547 |
|
548 |
rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
549 |
rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
550 |
rot[1][2] = sin(theta) * cos(psi); |
551 |
|
552 |
rot[2][0] = sin(phi) * sin(theta); |
553 |
rot[2][1] = -cos(phi) * sin(theta); |
554 |
rot[2][2] = cos(theta); |
555 |
} |
556 |
|
557 |
|
558 |
|
559 |
void buildMap( double &x, double &y, double &z, |
560 |
double boxX, double boxY, double boxZ ){ |
561 |
|
562 |
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
563 |
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
564 |
|
565 |
if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) ); |
566 |
else y -= boxY * (double)( (int)( (y / boxY ) + 0.5)); |
567 |
|
568 |
if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) ); |
569 |
else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5)); |
570 |
} |