1 |
#include <cstdlib> |
2 |
#include <cstring> |
3 |
#include <cmath> |
4 |
|
5 |
#include <iostream> |
6 |
using namespace std; |
7 |
|
8 |
#include "SimInfo.hpp" |
9 |
#define __C |
10 |
#include "fSimulation.h" |
11 |
#include "simError.h" |
12 |
|
13 |
#include "fortranWrappers.hpp" |
14 |
|
15 |
#ifdef IS_MPI |
16 |
#include "mpiSimulation.hpp" |
17 |
#endif |
18 |
|
19 |
inline double roundMe( double x ){ |
20 |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
21 |
} |
22 |
|
23 |
|
24 |
SimInfo* currentInfo; |
25 |
|
26 |
SimInfo::SimInfo(){ |
27 |
excludes = NULL; |
28 |
n_constraints = 0; |
29 |
n_oriented = 0; |
30 |
n_dipoles = 0; |
31 |
ndf = 0; |
32 |
ndfRaw = 0; |
33 |
the_integrator = NULL; |
34 |
setTemp = 0; |
35 |
thermalTime = 0.0; |
36 |
rCut = 0.0; |
37 |
ecr = 0.0; |
38 |
est = 0.0; |
39 |
oldEcr = 0.0; |
40 |
oldRcut = 0.0; |
41 |
|
42 |
haveOrigRcut = 0; |
43 |
haveOrigEcr = 0; |
44 |
boxIsInit = 0; |
45 |
|
46 |
|
47 |
|
48 |
usePBC = 0; |
49 |
useLJ = 0; |
50 |
useSticky = 0; |
51 |
useDipole = 0; |
52 |
useReactionField = 0; |
53 |
useGB = 0; |
54 |
useEAM = 0; |
55 |
|
56 |
wrapMeSimInfo( this ); |
57 |
} |
58 |
|
59 |
void SimInfo::setBox(double newBox[3]) { |
60 |
|
61 |
int i, j; |
62 |
double tempMat[3][3]; |
63 |
|
64 |
for(i=0; i<3; i++) |
65 |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
66 |
|
67 |
tempMat[0][0] = newBox[0]; |
68 |
tempMat[1][1] = newBox[1]; |
69 |
tempMat[2][2] = newBox[2]; |
70 |
|
71 |
setBoxM( tempMat ); |
72 |
|
73 |
} |
74 |
|
75 |
void SimInfo::setBoxM( double theBox[3][3] ){ |
76 |
|
77 |
int i, j, status; |
78 |
double smallestBoxL, maxCutoff; |
79 |
double FortranHmat[9]; // to preserve compatibility with Fortran the |
80 |
// ordering in the array is as follows: |
81 |
// [ 0 3 6 ] |
82 |
// [ 1 4 7 ] |
83 |
// [ 2 5 8 ] |
84 |
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
85 |
|
86 |
|
87 |
if( !boxIsInit ) boxIsInit = 1; |
88 |
|
89 |
for(i=0; i < 3; i++) |
90 |
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
91 |
|
92 |
calcBoxL(); |
93 |
calcHmatInv(); |
94 |
|
95 |
for(i=0; i < 3; i++) { |
96 |
for (j=0; j < 3; j++) { |
97 |
FortranHmat[3*j + i] = Hmat[i][j]; |
98 |
FortranHmatInv[3*j + i] = HmatInv[i][j]; |
99 |
} |
100 |
} |
101 |
|
102 |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
103 |
|
104 |
} |
105 |
|
106 |
|
107 |
void SimInfo::getBoxM (double theBox[3][3]) { |
108 |
|
109 |
int i, j; |
110 |
for(i=0; i<3; i++) |
111 |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
112 |
} |
113 |
|
114 |
|
115 |
void SimInfo::scaleBox(double scale) { |
116 |
double theBox[3][3]; |
117 |
int i, j; |
118 |
|
119 |
// cerr << "Scaling box by " << scale << "\n"; |
120 |
|
121 |
for(i=0; i<3; i++) |
122 |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
123 |
|
124 |
setBoxM(theBox); |
125 |
|
126 |
} |
127 |
|
128 |
void SimInfo::calcHmatInv( void ) { |
129 |
|
130 |
int i,j; |
131 |
double smallDiag; |
132 |
double tol; |
133 |
double sanity[3][3]; |
134 |
|
135 |
invertMat3( Hmat, HmatInv ); |
136 |
|
137 |
// Check the inverse to make sure it is sane: |
138 |
|
139 |
matMul3( Hmat, HmatInv, sanity ); |
140 |
|
141 |
// check to see if Hmat is orthorhombic |
142 |
|
143 |
smallDiag = Hmat[0][0]; |
144 |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
145 |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
146 |
tol = smallDiag * 1E-6; |
147 |
|
148 |
orthoRhombic = 1; |
149 |
|
150 |
for (i = 0; i < 3; i++ ) { |
151 |
for (j = 0 ; j < 3; j++) { |
152 |
if (i != j) { |
153 |
if (orthoRhombic) { |
154 |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
155 |
} |
156 |
} |
157 |
} |
158 |
} |
159 |
} |
160 |
|
161 |
double SimInfo::matDet3(double a[3][3]) { |
162 |
int i, j, k; |
163 |
double determinant; |
164 |
|
165 |
determinant = 0.0; |
166 |
|
167 |
for(i = 0; i < 3; i++) { |
168 |
j = (i+1)%3; |
169 |
k = (i+2)%3; |
170 |
|
171 |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
172 |
} |
173 |
|
174 |
return determinant; |
175 |
} |
176 |
|
177 |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
178 |
|
179 |
int i, j, k, l, m, n; |
180 |
double determinant; |
181 |
|
182 |
determinant = matDet3( a ); |
183 |
|
184 |
if (determinant == 0.0) { |
185 |
sprintf( painCave.errMsg, |
186 |
"Can't invert a matrix with a zero determinant!\n"); |
187 |
painCave.isFatal = 1; |
188 |
simError(); |
189 |
} |
190 |
|
191 |
for (i=0; i < 3; i++) { |
192 |
j = (i+1)%3; |
193 |
k = (i+2)%3; |
194 |
for(l = 0; l < 3; l++) { |
195 |
m = (l+1)%3; |
196 |
n = (l+2)%3; |
197 |
|
198 |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
199 |
} |
200 |
} |
201 |
} |
202 |
|
203 |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
204 |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
205 |
|
206 |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
207 |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
208 |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
209 |
|
210 |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
211 |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
212 |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
213 |
|
214 |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
215 |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
216 |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
217 |
|
218 |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
219 |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
220 |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
221 |
} |
222 |
|
223 |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
224 |
double a0, a1, a2; |
225 |
|
226 |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
227 |
|
228 |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
229 |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
230 |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
231 |
} |
232 |
|
233 |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
234 |
double temp[3][3]; |
235 |
int i, j; |
236 |
|
237 |
for (i = 0; i < 3; i++) { |
238 |
for (j = 0; j < 3; j++) { |
239 |
temp[j][i] = in[i][j]; |
240 |
} |
241 |
} |
242 |
for (i = 0; i < 3; i++) { |
243 |
for (j = 0; j < 3; j++) { |
244 |
out[i][j] = temp[i][j]; |
245 |
} |
246 |
} |
247 |
} |
248 |
|
249 |
void SimInfo::printMat3(double A[3][3] ){ |
250 |
|
251 |
std::cerr |
252 |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
253 |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
254 |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
255 |
} |
256 |
|
257 |
void SimInfo::printMat9(double A[9] ){ |
258 |
|
259 |
std::cerr |
260 |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
261 |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
262 |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
263 |
} |
264 |
|
265 |
void SimInfo::calcBoxL( void ){ |
266 |
|
267 |
double dx, dy, dz, dsq; |
268 |
int i; |
269 |
|
270 |
// boxVol = Determinant of Hmat |
271 |
|
272 |
boxVol = matDet3( Hmat ); |
273 |
|
274 |
// boxLx |
275 |
|
276 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
277 |
dsq = dx*dx + dy*dy + dz*dz; |
278 |
boxL[0] = sqrt( dsq ); |
279 |
maxCutoff = 0.5 * boxL[0]; |
280 |
|
281 |
// boxLy |
282 |
|
283 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
284 |
dsq = dx*dx + dy*dy + dz*dz; |
285 |
boxL[1] = sqrt( dsq ); |
286 |
if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
287 |
|
288 |
// boxLz |
289 |
|
290 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
291 |
dsq = dx*dx + dy*dy + dz*dz; |
292 |
boxL[2] = sqrt( dsq ); |
293 |
if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
294 |
|
295 |
} |
296 |
|
297 |
|
298 |
void SimInfo::wrapVector( double thePos[3] ){ |
299 |
|
300 |
int i, j, k; |
301 |
double scaled[3]; |
302 |
|
303 |
if( !orthoRhombic ){ |
304 |
// calc the scaled coordinates. |
305 |
|
306 |
|
307 |
matVecMul3(HmatInv, thePos, scaled); |
308 |
|
309 |
for(i=0; i<3; i++) |
310 |
scaled[i] -= roundMe(scaled[i]); |
311 |
|
312 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
313 |
|
314 |
matVecMul3(Hmat, scaled, thePos); |
315 |
|
316 |
} |
317 |
else{ |
318 |
// calc the scaled coordinates. |
319 |
|
320 |
for(i=0; i<3; i++) |
321 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
322 |
|
323 |
// wrap the scaled coordinates |
324 |
|
325 |
for(i=0; i<3; i++) |
326 |
scaled[i] -= roundMe(scaled[i]); |
327 |
|
328 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
329 |
|
330 |
for(i=0; i<3; i++) |
331 |
thePos[i] = scaled[i]*Hmat[i][i]; |
332 |
} |
333 |
|
334 |
} |
335 |
|
336 |
|
337 |
int SimInfo::getNDF(){ |
338 |
int ndf_local, ndf; |
339 |
|
340 |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
341 |
|
342 |
#ifdef IS_MPI |
343 |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
#else |
345 |
ndf = ndf_local; |
346 |
#endif |
347 |
|
348 |
ndf = ndf - 3; |
349 |
|
350 |
return ndf; |
351 |
} |
352 |
|
353 |
int SimInfo::getNDFraw() { |
354 |
int ndfRaw_local, ndfRaw; |
355 |
|
356 |
// Raw degrees of freedom that we have to set |
357 |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
358 |
|
359 |
#ifdef IS_MPI |
360 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
361 |
#else |
362 |
ndfRaw = ndfRaw_local; |
363 |
#endif |
364 |
|
365 |
return ndfRaw; |
366 |
} |
367 |
|
368 |
void SimInfo::refreshSim(){ |
369 |
|
370 |
simtype fInfo; |
371 |
int isError; |
372 |
int n_global; |
373 |
int* excl; |
374 |
|
375 |
fInfo.dielect = 0.0; |
376 |
|
377 |
if( useDipole ){ |
378 |
if( useReactionField )fInfo.dielect = dielectric; |
379 |
} |
380 |
|
381 |
fInfo.SIM_uses_PBC = usePBC; |
382 |
//fInfo.SIM_uses_LJ = 0; |
383 |
fInfo.SIM_uses_LJ = useLJ; |
384 |
fInfo.SIM_uses_sticky = useSticky; |
385 |
//fInfo.SIM_uses_sticky = 0; |
386 |
fInfo.SIM_uses_dipoles = useDipole; |
387 |
//fInfo.SIM_uses_dipoles = 0; |
388 |
//fInfo.SIM_uses_RF = useReactionField; |
389 |
fInfo.SIM_uses_RF = 0; |
390 |
fInfo.SIM_uses_GB = useGB; |
391 |
fInfo.SIM_uses_EAM = useEAM; |
392 |
|
393 |
excl = Exclude::getArray(); |
394 |
|
395 |
#ifdef IS_MPI |
396 |
n_global = mpiSim->getTotAtoms(); |
397 |
#else |
398 |
n_global = n_atoms; |
399 |
#endif |
400 |
|
401 |
isError = 0; |
402 |
|
403 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
404 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
405 |
&isError ); |
406 |
|
407 |
if( isError ){ |
408 |
|
409 |
sprintf( painCave.errMsg, |
410 |
"There was an error setting the simulation information in fortran.\n" ); |
411 |
painCave.isFatal = 1; |
412 |
simError(); |
413 |
} |
414 |
|
415 |
#ifdef IS_MPI |
416 |
sprintf( checkPointMsg, |
417 |
"succesfully sent the simulation information to fortran.\n"); |
418 |
MPIcheckPoint(); |
419 |
#endif // is_mpi |
420 |
|
421 |
this->ndf = this->getNDF(); |
422 |
this->ndfRaw = this->getNDFraw(); |
423 |
|
424 |
} |
425 |
|
426 |
|
427 |
void SimInfo::setRcut( double theRcut ){ |
428 |
|
429 |
if( !haveOrigRcut ){ |
430 |
haveOrigRcut = 1; |
431 |
origRcut = theRcut; |
432 |
} |
433 |
|
434 |
rCut = theRcut; |
435 |
checkCutOffs(); |
436 |
} |
437 |
|
438 |
void SimInfo::setEcr( double theEcr ){ |
439 |
|
440 |
if( !haveOrigEcr ){ |
441 |
haveOrigEcr = 1; |
442 |
origEcr = theEcr; |
443 |
} |
444 |
|
445 |
ecr = theEcr; |
446 |
checkCutOffs(); |
447 |
} |
448 |
|
449 |
void SimInfo::setEcr( double theEcr, double theEst ){ |
450 |
|
451 |
est = theEst; |
452 |
setEcr( theEcr ); |
453 |
} |
454 |
|
455 |
|
456 |
void SimInfo::checkCutOffs( void ){ |
457 |
|
458 |
int cutChanged = 0; |
459 |
|
460 |
if( boxIsInit ){ |
461 |
|
462 |
//we need to check cutOffs against the box |
463 |
|
464 |
if( maxCutoff > rCut ){ |
465 |
if( rCut < origRcut ){ |
466 |
rCut = origRcut; |
467 |
if (rCut > maxCutoff) rCut = maxCutoff; |
468 |
|
469 |
sprintf( painCave.errMsg, |
470 |
"New Box size is setting the long range cutoff radius " |
471 |
"to %lf\n", |
472 |
rCut ); |
473 |
painCave.isFatal = 0; |
474 |
simError(); |
475 |
} |
476 |
} |
477 |
|
478 |
if( maxCutoff > ecr ){ |
479 |
if( ecr < origEcr ){ |
480 |
rCut = origEcr; |
481 |
if (ecr > maxCutoff) ecr = maxCutoff; |
482 |
|
483 |
sprintf( painCave.errMsg, |
484 |
"New Box size is setting the electrostaticCutoffRadius " |
485 |
"to %lf\n", |
486 |
ecr ); |
487 |
painCave.isFatal = 0; |
488 |
simError(); |
489 |
} |
490 |
} |
491 |
|
492 |
|
493 |
if (rCut > maxCutoff) { |
494 |
sprintf( painCave.errMsg, |
495 |
"New Box size is setting the long range cutoff radius " |
496 |
"to %lf\n", |
497 |
maxCutoff ); |
498 |
painCave.isFatal = 0; |
499 |
simError(); |
500 |
rCut = maxCutoff; |
501 |
} |
502 |
|
503 |
if( ecr > maxCutoff){ |
504 |
sprintf( painCave.errMsg, |
505 |
"New Box size is setting the electrostaticCutoffRadius " |
506 |
"to %lf\n", |
507 |
maxCutoff ); |
508 |
painCave.isFatal = 0; |
509 |
simError(); |
510 |
ecr = maxCutoff; |
511 |
} |
512 |
|
513 |
|
514 |
} |
515 |
|
516 |
|
517 |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
518 |
|
519 |
// rlist is the 1.0 plus max( rcut, ecr ) |
520 |
|
521 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
522 |
|
523 |
if( cutChanged ){ |
524 |
|
525 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
526 |
} |
527 |
|
528 |
oldEcr = ecr; |
529 |
oldRcut = rCut; |
530 |
} |