# | Line 1 | Line 1 | |
---|---|---|
1 | < | #include <cstdlib> |
2 | < | #include <cstring> |
3 | < | #include <cmath> |
1 | > | #include <stdlib.h> |
2 | > | #include <string.h> |
3 | > | #include <math.h> |
4 | ||
5 | #include <iostream> | |
6 | using namespace std; | |
# | Line 26 | Line 26 | SimInfo::SimInfo(){ | |
26 | SimInfo::SimInfo(){ | |
27 | excludes = NULL; | |
28 | n_constraints = 0; | |
29 | + | nZconstraints = 0; |
30 | n_oriented = 0; | |
31 | n_dipoles = 0; | |
32 | ndf = 0; | |
33 | ndfRaw = 0; | |
34 | + | nZconstraints = 0; |
35 | the_integrator = NULL; | |
36 | setTemp = 0; | |
37 | thermalTime = 0.0; | |
38 | + | currentTime = 0.0; |
39 | rCut = 0.0; | |
40 | ecr = 0.0; | |
41 | est = 0.0; | |
42 | ||
43 | + | haveRcut = 0; |
44 | + | haveEcr = 0; |
45 | + | boxIsInit = 0; |
46 | + | |
47 | + | resetTime = 1e99; |
48 | + | |
49 | + | orthoTolerance = 1E-6; |
50 | + | useInitXSstate = true; |
51 | + | |
52 | usePBC = 0; | |
53 | useLJ = 0; | |
54 | useSticky = 0; | |
# | Line 45 | Line 57 | SimInfo::SimInfo(){ | |
57 | useGB = 0; | |
58 | useEAM = 0; | |
59 | ||
60 | + | myConfiguration = new SimState(); |
61 | + | |
62 | wrapMeSimInfo( this ); | |
63 | } | |
64 | ||
65 | + | |
66 | + | SimInfo::~SimInfo(){ |
67 | + | |
68 | + | delete myConfiguration; |
69 | + | |
70 | + | map<string, GenericData*>::iterator i; |
71 | + | |
72 | + | for(i = properties.begin(); i != properties.end(); i++) |
73 | + | delete (*i).second; |
74 | + | |
75 | + | } |
76 | + | |
77 | void SimInfo::setBox(double newBox[3]) { | |
78 | ||
79 | int i, j; | |
# | Line 66 | Line 92 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
92 | ||
93 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
94 | ||
95 | < | int i, j, status; |
70 | < | double smallestBoxL, maxCutoff; |
95 | > | int i, j; |
96 | double FortranHmat[9]; // to preserve compatibility with Fortran the | |
97 | // ordering in the array is as follows: | |
98 | // [ 0 3 6 ] | |
# | Line 75 | Line 100 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
100 | // [ 2 5 8 ] | |
101 | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); | |
102 | ||
103 | + | if( !boxIsInit ) boxIsInit = 1; |
104 | ||
105 | for(i=0; i < 3; i++) | |
106 | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; | |
107 | ||
82 | – | // cerr |
83 | – | // << "setting Hmat ->\n" |
84 | – | // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
85 | – | // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
86 | – | // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
87 | – | |
108 | calcBoxL(); | |
109 | calcHmatInv(); | |
110 | ||
# | Line 97 | Line 117 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
117 | ||
118 | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); | |
119 | ||
100 | – | smallestBoxL = boxL[0]; |
101 | – | if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1]; |
102 | – | if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2]; |
103 | – | |
104 | – | maxCutoff = smallestBoxL / 2.0; |
105 | – | |
106 | – | if (rList > maxCutoff) { |
107 | – | sprintf( painCave.errMsg, |
108 | – | "New Box size is forcing neighborlist radius down to %lf\n", |
109 | – | maxCutoff ); |
110 | – | painCave.isFatal = 0; |
111 | – | simError(); |
112 | – | rList = maxCutoff; |
113 | – | |
114 | – | if (rCut > (rList - 1.0)) { |
115 | – | sprintf( painCave.errMsg, |
116 | – | "New Box size is forcing LJ cutoff radius down to %lf\n", |
117 | – | rList - 1.0 ); |
118 | – | painCave.isFatal = 0; |
119 | – | simError(); |
120 | – | rCut = rList - 1.0; |
121 | – | } |
122 | – | |
123 | – | if( ecr > (rList - 1.0) ){ |
124 | – | sprintf( painCave.errMsg, |
125 | – | "New Box size is forcing electrostaticCutoffRadius " |
126 | – | "down to %lf\n" |
127 | – | "electrostaticSkinThickness is now %lf\n", |
128 | – | rList - 1.0, 0.05*(rList-1.0) ); |
129 | – | painCave.isFatal = 0; |
130 | – | simError(); |
131 | – | ecr = maxCutoff; |
132 | – | est = 0.05 * ecr; |
133 | – | } |
134 | – | |
135 | – | // At least one of the radii changed, so we need a refresh: |
136 | – | refreshSim(); |
137 | – | } |
120 | } | |
121 | ||
122 | ||
# | Line 161 | Line 143 | void SimInfo::calcHmatInv( void ) { | |
143 | ||
144 | void SimInfo::calcHmatInv( void ) { | |
145 | ||
146 | + | int oldOrtho; |
147 | int i,j; | |
148 | double smallDiag; | |
149 | double tol; | |
# | Line 168 | Line 151 | void SimInfo::calcHmatInv( void ) { | |
151 | ||
152 | invertMat3( Hmat, HmatInv ); | |
153 | ||
171 | – | // Check the inverse to make sure it is sane: |
172 | – | |
173 | – | matMul3( Hmat, HmatInv, sanity ); |
174 | – | |
154 | // check to see if Hmat is orthorhombic | |
155 | ||
156 | < | smallDiag = Hmat[0][0]; |
178 | < | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
179 | < | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
180 | < | tol = smallDiag * 1E-6; |
156 | > | oldOrtho = orthoRhombic; |
157 | ||
158 | + | smallDiag = fabs(Hmat[0][0]); |
159 | + | if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
160 | + | if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
161 | + | tol = smallDiag * orthoTolerance; |
162 | + | |
163 | orthoRhombic = 1; | |
164 | ||
165 | for (i = 0; i < 3; i++ ) { | |
166 | for (j = 0 ; j < 3; j++) { | |
167 | if (i != j) { | |
168 | if (orthoRhombic) { | |
169 | < | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
169 | > | if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
170 | } | |
171 | } | |
172 | } | |
173 | } | |
174 | + | |
175 | + | if( oldOrtho != orthoRhombic ){ |
176 | + | |
177 | + | if( orthoRhombic ){ |
178 | + | sprintf( painCave.errMsg, |
179 | + | "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
180 | + | " If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
181 | + | orthoTolerance); |
182 | + | simError(); |
183 | + | } |
184 | + | else { |
185 | + | sprintf( painCave.errMsg, |
186 | + | "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
187 | + | " If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
188 | + | orthoTolerance); |
189 | + | simError(); |
190 | + | } |
191 | + | } |
192 | } | |
193 | ||
194 | double SimInfo::matDet3(double a[3][3]) { | |
# | Line 296 | Line 295 | void SimInfo::printMat9(double A[9] ){ | |
295 | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; | |
296 | } | |
297 | ||
298 | + | |
299 | + | void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
300 | + | |
301 | + | out[0] = a[1] * b[2] - a[2] * b[1]; |
302 | + | out[1] = a[2] * b[0] - a[0] * b[2] ; |
303 | + | out[2] = a[0] * b[1] - a[1] * b[0]; |
304 | + | |
305 | + | } |
306 | + | |
307 | + | double SimInfo::dotProduct3(double a[3], double b[3]){ |
308 | + | return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
309 | + | } |
310 | + | |
311 | + | double SimInfo::length3(double a[3]){ |
312 | + | return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
313 | + | } |
314 | + | |
315 | void SimInfo::calcBoxL( void ){ | |
316 | ||
317 | double dx, dy, dz, dsq; | |
302 | – | int i; |
318 | ||
319 | // boxVol = Determinant of Hmat | |
320 | ||
# | Line 310 | Line 325 | void SimInfo::calcBoxL( void ){ | |
325 | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; | |
326 | dsq = dx*dx + dy*dy + dz*dz; | |
327 | boxL[0] = sqrt( dsq ); | |
328 | + | //maxCutoff = 0.5 * boxL[0]; |
329 | ||
330 | // boxLy | |
331 | ||
332 | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; | |
333 | dsq = dx*dx + dy*dy + dz*dz; | |
334 | boxL[1] = sqrt( dsq ); | |
335 | + | //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
336 | ||
337 | + | |
338 | // boxLz | |
339 | ||
340 | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; | |
341 | dsq = dx*dx + dy*dy + dz*dz; | |
342 | boxL[2] = sqrt( dsq ); | |
343 | + | //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
344 | + | |
345 | + | //calculate the max cutoff |
346 | + | maxCutoff = calcMaxCutOff(); |
347 | ||
348 | + | checkCutOffs(); |
349 | + | |
350 | } | |
351 | ||
352 | ||
353 | + | double SimInfo::calcMaxCutOff(){ |
354 | + | |
355 | + | double ri[3], rj[3], rk[3]; |
356 | + | double rij[3], rjk[3], rki[3]; |
357 | + | double minDist; |
358 | + | |
359 | + | ri[0] = Hmat[0][0]; |
360 | + | ri[1] = Hmat[1][0]; |
361 | + | ri[2] = Hmat[2][0]; |
362 | + | |
363 | + | rj[0] = Hmat[0][1]; |
364 | + | rj[1] = Hmat[1][1]; |
365 | + | rj[2] = Hmat[2][1]; |
366 | + | |
367 | + | rk[0] = Hmat[0][2]; |
368 | + | rk[1] = Hmat[1][2]; |
369 | + | rk[2] = Hmat[2][2]; |
370 | + | |
371 | + | crossProduct3(ri,rj, rij); |
372 | + | distXY = dotProduct3(rk,rij) / length3(rij); |
373 | + | |
374 | + | crossProduct3(rj,rk, rjk); |
375 | + | distYZ = dotProduct3(ri,rjk) / length3(rjk); |
376 | + | |
377 | + | crossProduct3(rk,ri, rki); |
378 | + | distZX = dotProduct3(rj,rki) / length3(rki); |
379 | + | |
380 | + | minDist = min(min(distXY, distYZ), distZX); |
381 | + | return minDist/2; |
382 | + | |
383 | + | } |
384 | + | |
385 | void SimInfo::wrapVector( double thePos[3] ){ | |
386 | ||
387 | < | int i, j, k; |
387 | > | int i; |
388 | double scaled[3]; | |
389 | ||
390 | if( !orthoRhombic ){ | |
# | Line 366 | Line 422 | int SimInfo::getNDF(){ | |
422 | ||
423 | ||
424 | int SimInfo::getNDF(){ | |
425 | < | int ndf_local, ndf; |
425 | > | int ndf_local; |
426 | ||
427 | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; | |
428 | ||
# | Line 376 | Line 432 | int SimInfo::getNDF(){ | |
432 | ndf = ndf_local; | |
433 | #endif | |
434 | ||
435 | < | ndf = ndf - 3; |
435 | > | ndf = ndf - 3 - nZconstraints; |
436 | ||
437 | return ndf; | |
438 | } | |
439 | ||
440 | int SimInfo::getNDFraw() { | |
441 | < | int ndfRaw_local, ndfRaw; |
441 | > | int ndfRaw_local; |
442 | ||
443 | // Raw degrees of freedom that we have to set | |
444 | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; | |
# | Line 395 | Line 451 | int SimInfo::getNDFraw() { | |
451 | ||
452 | return ndfRaw; | |
453 | } | |
454 | < | |
454 | > | |
455 | > | int SimInfo::getNDFtranslational() { |
456 | > | int ndfTrans_local; |
457 | > | |
458 | > | ndfTrans_local = 3 * n_atoms - n_constraints; |
459 | > | |
460 | > | #ifdef IS_MPI |
461 | > | MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
462 | > | #else |
463 | > | ndfTrans = ndfTrans_local; |
464 | > | #endif |
465 | > | |
466 | > | ndfTrans = ndfTrans - 3 - nZconstraints; |
467 | > | |
468 | > | return ndfTrans; |
469 | > | } |
470 | > | |
471 | void SimInfo::refreshSim(){ | |
472 | ||
473 | simtype fInfo; | |
474 | int isError; | |
475 | int n_global; | |
476 | int* excl; | |
477 | < | |
406 | < | fInfo.rrf = 0.0; |
407 | < | fInfo.rt = 0.0; |
477 | > | |
478 | fInfo.dielect = 0.0; | |
479 | ||
410 | – | fInfo.rlist = rList; |
411 | – | fInfo.rcut = rCut; |
412 | – | |
480 | if( useDipole ){ | |
414 | – | fInfo.rrf = ecr; |
415 | – | fInfo.rt = ecr - est; |
481 | if( useReactionField )fInfo.dielect = dielectric; | |
482 | } | |
483 | ||
# | Line 458 | Line 523 | void SimInfo::refreshSim(){ | |
523 | ||
524 | this->ndf = this->getNDF(); | |
525 | this->ndfRaw = this->getNDFraw(); | |
526 | + | this->ndfTrans = this->getNDFtranslational(); |
527 | + | } |
528 | ||
529 | + | void SimInfo::setDefaultRcut( double theRcut ){ |
530 | + | |
531 | + | haveRcut = 1; |
532 | + | rCut = theRcut; |
533 | + | |
534 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
535 | + | |
536 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
537 | } | |
538 | ||
539 | + | void SimInfo::setDefaultEcr( double theEcr ){ |
540 | + | |
541 | + | haveEcr = 1; |
542 | + | |
543 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
544 | + | |
545 | + | ecr = theEcr; |
546 | + | |
547 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
548 | + | } |
549 | + | |
550 | + | void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
551 | + | |
552 | + | est = theEst; |
553 | + | setDefaultEcr( theEcr ); |
554 | + | } |
555 | + | |
556 | + | |
557 | + | void SimInfo::checkCutOffs( void ){ |
558 | + | |
559 | + | if( boxIsInit ){ |
560 | + | |
561 | + | //we need to check cutOffs against the box |
562 | + | |
563 | + | if( rCut > maxCutoff ){ |
564 | + | sprintf( painCave.errMsg, |
565 | + | "Box size is too small for the long range cutoff radius, " |
566 | + | "%lf, at time %lf\n", |
567 | + | rCut, currentTime ); |
568 | + | painCave.isFatal = 1; |
569 | + | simError(); |
570 | + | } |
571 | + | |
572 | + | if( haveEcr ){ |
573 | + | if( ecr > maxCutoff ){ |
574 | + | sprintf( painCave.errMsg, |
575 | + | "Box size is too small for the electrostatic cutoff radius, " |
576 | + | "%lf, at time %lf\n", |
577 | + | ecr, currentTime ); |
578 | + | painCave.isFatal = 1; |
579 | + | simError(); |
580 | + | } |
581 | + | } |
582 | + | } else { |
583 | + | // initialize this stuff before using it, OK? |
584 | + | sprintf( painCave.errMsg, |
585 | + | "Trying to check cutoffs without a box. Be smarter.\n" ); |
586 | + | painCave.isFatal = 1; |
587 | + | simError(); |
588 | + | } |
589 | + | |
590 | + | } |
591 | + | |
592 | + | void SimInfo::addProperty(GenericData* prop){ |
593 | + | |
594 | + | map<string, GenericData*>::iterator result; |
595 | + | result = properties.find(prop->getID()); |
596 | + | |
597 | + | //we can't simply use properties[prop->getID()] = prop, |
598 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
599 | + | |
600 | + | if(result != properties.end()){ |
601 | + | |
602 | + | delete (*result).second; |
603 | + | (*result).second = prop; |
604 | + | |
605 | + | } |
606 | + | else{ |
607 | + | |
608 | + | properties[prop->getID()] = prop; |
609 | + | |
610 | + | } |
611 | + | |
612 | + | } |
613 | + | |
614 | + | GenericData* SimInfo::getProperty(const string& propName){ |
615 | + | |
616 | + | map<string, GenericData*>::iterator result; |
617 | + | |
618 | + | //string lowerCaseName = (); |
619 | + | |
620 | + | result = properties.find(propName); |
621 | + | |
622 | + | if(result != properties.end()) |
623 | + | return (*result).second; |
624 | + | else |
625 | + | return NULL; |
626 | + | } |
627 | + | |
628 | + | vector<GenericData*> SimInfo::getProperties(){ |
629 | + | |
630 | + | vector<GenericData*> result; |
631 | + | map<string, GenericData*>::iterator i; |
632 | + | |
633 | + | for(i = properties.begin(); i != properties.end(); i++) |
634 | + | result.push_back((*i).second); |
635 | + | |
636 | + | return result; |
637 | + | } |
638 | + | |
639 | + | double SimInfo::matTrace3(double m[3][3]){ |
640 | + | double trace; |
641 | + | trace = m[0][0] + m[1][1] + m[2][2]; |
642 | + | |
643 | + | return trace; |
644 | + | } |
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