# | 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 | + | origRcut = -1.0; |
41 | + | ecr = 0.0; |
42 | + | origEcr = -1.0; |
43 | + | est = 0.0; |
44 | + | oldEcr = 0.0; |
45 | + | oldRcut = 0.0; |
46 | ||
47 | + | haveOrigRcut = 0; |
48 | + | haveOrigEcr = 0; |
49 | + | boxIsInit = 0; |
50 | + | |
51 | + | resetTime = 1e99; |
52 | + | |
53 | + | orthoTolerance = 1E-6; |
54 | + | useInitXSstate = true; |
55 | + | |
56 | usePBC = 0; | |
57 | useLJ = 0; | |
58 | useSticky = 0; | |
# | Line 43 | Line 61 | SimInfo::SimInfo(){ | |
61 | useGB = 0; | |
62 | useEAM = 0; | |
63 | ||
64 | + | myConfiguration = new SimState(); |
65 | + | |
66 | wrapMeSimInfo( this ); | |
67 | } | |
68 | ||
69 | + | |
70 | + | SimInfo::~SimInfo(){ |
71 | + | |
72 | + | delete myConfiguration; |
73 | + | |
74 | + | map<string, GenericData*>::iterator i; |
75 | + | |
76 | + | for(i = properties.begin(); i != properties.end(); i++) |
77 | + | delete (*i).second; |
78 | + | |
79 | + | } |
80 | + | |
81 | void SimInfo::setBox(double newBox[3]) { | |
82 | ||
83 | int i, j; | |
# | Line 64 | Line 96 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
96 | ||
97 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
98 | ||
99 | < | int i, j, status; |
68 | < | double smallestBoxL, maxCutoff; |
99 | > | int i, j; |
100 | double FortranHmat[9]; // to preserve compatibility with Fortran the | |
101 | // ordering in the array is as follows: | |
102 | // [ 0 3 6 ] | |
# | Line 73 | Line 104 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
104 | // [ 2 5 8 ] | |
105 | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); | |
106 | ||
107 | + | |
108 | + | if( !boxIsInit ) boxIsInit = 1; |
109 | ||
110 | for(i=0; i < 3; i++) | |
111 | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; | |
112 | ||
80 | – | // cerr |
81 | – | // << "setting Hmat ->\n" |
82 | – | // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
83 | – | // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
84 | – | // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
85 | – | |
113 | calcBoxL(); | |
114 | calcHmatInv(); | |
115 | ||
# | Line 95 | Line 122 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
122 | ||
123 | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); | |
124 | ||
98 | – | smallestBoxL = boxLx; |
99 | – | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
100 | – | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
101 | – | |
102 | – | maxCutoff = smallestBoxL / 2.0; |
103 | – | |
104 | – | if (rList > maxCutoff) { |
105 | – | sprintf( painCave.errMsg, |
106 | – | "New Box size is forcing neighborlist radius down to %lf\n", |
107 | – | maxCutoff ); |
108 | – | painCave.isFatal = 0; |
109 | – | simError(); |
110 | – | |
111 | – | rList = maxCutoff; |
112 | – | |
113 | – | sprintf( painCave.errMsg, |
114 | – | "New Box size is forcing cutoff radius down to %lf\n", |
115 | – | maxCutoff - 1.0 ); |
116 | – | painCave.isFatal = 0; |
117 | – | simError(); |
118 | – | |
119 | – | rCut = rList - 1.0; |
120 | – | |
121 | – | // list radius changed so we have to refresh the simulation structure. |
122 | – | refreshSim(); |
123 | – | } |
124 | – | |
125 | – | if (rCut > maxCutoff) { |
126 | – | sprintf( painCave.errMsg, |
127 | – | "New Box size is forcing cutoff radius down to %lf\n", |
128 | – | maxCutoff ); |
129 | – | painCave.isFatal = 0; |
130 | – | simError(); |
131 | – | |
132 | – | status = 0; |
133 | – | LJ_new_rcut(&rCut, &status); |
134 | – | if (status != 0) { |
135 | – | sprintf( painCave.errMsg, |
136 | – | "Error in recomputing LJ shifts based on new rcut\n"); |
137 | – | painCave.isFatal = 1; |
138 | – | simError(); |
139 | – | } |
140 | – | } |
125 | } | |
126 | ||
127 | ||
# | Line 164 | Line 148 | void SimInfo::calcHmatInv( void ) { | |
148 | ||
149 | void SimInfo::calcHmatInv( void ) { | |
150 | ||
151 | + | int oldOrtho; |
152 | int i,j; | |
153 | double smallDiag; | |
154 | double tol; | |
# | Line 171 | Line 156 | void SimInfo::calcHmatInv( void ) { | |
156 | ||
157 | invertMat3( Hmat, HmatInv ); | |
158 | ||
174 | – | // Check the inverse to make sure it is sane: |
175 | – | |
176 | – | matMul3( Hmat, HmatInv, sanity ); |
177 | – | |
159 | // check to see if Hmat is orthorhombic | |
160 | ||
161 | < | smallDiag = Hmat[0][0]; |
181 | < | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
182 | < | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
183 | < | tol = smallDiag * 1E-6; |
161 | > | oldOrtho = orthoRhombic; |
162 | ||
163 | + | smallDiag = fabs(Hmat[0][0]); |
164 | + | if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
165 | + | if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
166 | + | tol = smallDiag * orthoTolerance; |
167 | + | |
168 | orthoRhombic = 1; | |
169 | ||
170 | for (i = 0; i < 3; i++ ) { | |
171 | for (j = 0 ; j < 3; j++) { | |
172 | if (i != j) { | |
173 | if (orthoRhombic) { | |
174 | < | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
174 | > | if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
175 | } | |
176 | } | |
177 | } | |
178 | } | |
179 | + | |
180 | + | if( oldOrtho != orthoRhombic ){ |
181 | + | |
182 | + | if( orthoRhombic ){ |
183 | + | sprintf( painCave.errMsg, |
184 | + | "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
185 | + | " If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
186 | + | orthoTolerance); |
187 | + | simError(); |
188 | + | } |
189 | + | else { |
190 | + | sprintf( painCave.errMsg, |
191 | + | "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
192 | + | " If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
193 | + | orthoTolerance); |
194 | + | simError(); |
195 | + | } |
196 | + | } |
197 | } | |
198 | ||
199 | double SimInfo::matDet3(double a[3][3]) { | |
# | Line 299 | Line 300 | void SimInfo::printMat9(double A[9] ){ | |
300 | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; | |
301 | } | |
302 | ||
303 | + | |
304 | + | void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
305 | + | |
306 | + | out[0] = a[1] * b[2] - a[2] * b[1]; |
307 | + | out[1] = a[2] * b[0] - a[0] * b[2] ; |
308 | + | out[2] = a[0] * b[1] - a[1] * b[0]; |
309 | + | |
310 | + | } |
311 | + | |
312 | + | double SimInfo::dotProduct3(double a[3], double b[3]){ |
313 | + | return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
314 | + | } |
315 | + | |
316 | + | double SimInfo::length3(double a[3]){ |
317 | + | return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
318 | + | } |
319 | + | |
320 | void SimInfo::calcBoxL( void ){ | |
321 | ||
322 | double dx, dy, dz, dsq; | |
305 | – | int i; |
323 | ||
324 | // boxVol = Determinant of Hmat | |
325 | ||
# | Line 312 | Line 329 | void SimInfo::calcBoxL( void ){ | |
329 | ||
330 | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; | |
331 | dsq = dx*dx + dy*dy + dz*dz; | |
332 | < | boxLx = sqrt( dsq ); |
332 | > | boxL[0] = sqrt( dsq ); |
333 | > | //maxCutoff = 0.5 * boxL[0]; |
334 | ||
335 | // boxLy | |
336 | ||
337 | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; | |
338 | dsq = dx*dx + dy*dy + dz*dz; | |
339 | < | boxLy = sqrt( dsq ); |
339 | > | boxL[1] = sqrt( dsq ); |
340 | > | //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
341 | ||
342 | + | |
343 | // boxLz | |
344 | ||
345 | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; | |
346 | dsq = dx*dx + dy*dy + dz*dz; | |
347 | < | boxLz = sqrt( dsq ); |
347 | > | boxL[2] = sqrt( dsq ); |
348 | > | //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
349 | > | |
350 | > | //calculate the max cutoff |
351 | > | maxCutoff = calcMaxCutOff(); |
352 | ||
353 | + | checkCutOffs(); |
354 | + | |
355 | } | |
356 | ||
357 | ||
358 | + | double SimInfo::calcMaxCutOff(){ |
359 | + | |
360 | + | double ri[3], rj[3], rk[3]; |
361 | + | double rij[3], rjk[3], rki[3]; |
362 | + | double minDist; |
363 | + | |
364 | + | ri[0] = Hmat[0][0]; |
365 | + | ri[1] = Hmat[1][0]; |
366 | + | ri[2] = Hmat[2][0]; |
367 | + | |
368 | + | rj[0] = Hmat[0][1]; |
369 | + | rj[1] = Hmat[1][1]; |
370 | + | rj[2] = Hmat[2][1]; |
371 | + | |
372 | + | rk[0] = Hmat[0][2]; |
373 | + | rk[1] = Hmat[1][2]; |
374 | + | rk[2] = Hmat[2][2]; |
375 | + | |
376 | + | crossProduct3(ri,rj, rij); |
377 | + | distXY = dotProduct3(rk,rij) / length3(rij); |
378 | + | |
379 | + | crossProduct3(rj,rk, rjk); |
380 | + | distYZ = dotProduct3(ri,rjk) / length3(rjk); |
381 | + | |
382 | + | crossProduct3(rk,ri, rki); |
383 | + | distZX = dotProduct3(rj,rki) / length3(rki); |
384 | + | |
385 | + | minDist = min(min(distXY, distYZ), distZX); |
386 | + | return minDist/2; |
387 | + | |
388 | + | } |
389 | + | |
390 | void SimInfo::wrapVector( double thePos[3] ){ | |
391 | ||
392 | < | int i, j, k; |
392 | > | int i; |
393 | double scaled[3]; | |
394 | ||
395 | if( !orthoRhombic ){ | |
# | Line 369 | Line 427 | int SimInfo::getNDF(){ | |
427 | ||
428 | ||
429 | int SimInfo::getNDF(){ | |
430 | < | int ndf_local, ndf; |
430 | > | int ndf_local; |
431 | ||
432 | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; | |
433 | ||
# | Line 379 | Line 437 | int SimInfo::getNDF(){ | |
437 | ndf = ndf_local; | |
438 | #endif | |
439 | ||
440 | < | ndf = ndf - 3; |
440 | > | ndf = ndf - 3 - nZconstraints; |
441 | ||
442 | return ndf; | |
443 | } | |
444 | ||
445 | int SimInfo::getNDFraw() { | |
446 | < | int ndfRaw_local, ndfRaw; |
446 | > | int ndfRaw_local; |
447 | ||
448 | // Raw degrees of freedom that we have to set | |
449 | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; | |
# | Line 398 | Line 456 | int SimInfo::getNDFraw() { | |
456 | ||
457 | return ndfRaw; | |
458 | } | |
459 | < | |
459 | > | |
460 | > | int SimInfo::getNDFtranslational() { |
461 | > | int ndfTrans_local; |
462 | > | |
463 | > | ndfTrans_local = 3 * n_atoms - n_constraints; |
464 | > | |
465 | > | #ifdef IS_MPI |
466 | > | MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
467 | > | #else |
468 | > | ndfTrans = ndfTrans_local; |
469 | > | #endif |
470 | > | |
471 | > | ndfTrans = ndfTrans - 3 - nZconstraints; |
472 | > | |
473 | > | return ndfTrans; |
474 | > | } |
475 | > | |
476 | void SimInfo::refreshSim(){ | |
477 | ||
478 | simtype fInfo; | |
479 | int isError; | |
480 | int n_global; | |
481 | int* excl; | |
482 | < | |
409 | < | fInfo.rrf = 0.0; |
410 | < | fInfo.rt = 0.0; |
482 | > | |
483 | fInfo.dielect = 0.0; | |
484 | ||
413 | – | fInfo.rlist = rList; |
414 | – | fInfo.rcut = rCut; |
415 | – | |
485 | if( useDipole ){ | |
417 | – | fInfo.rrf = ecr; |
418 | – | fInfo.rt = ecr - est; |
486 | if( useReactionField )fInfo.dielect = dielectric; | |
487 | } | |
488 | ||
# | Line 461 | Line 528 | void SimInfo::refreshSim(){ | |
528 | ||
529 | this->ndf = this->getNDF(); | |
530 | this->ndfRaw = this->getNDFraw(); | |
531 | + | this->ndfTrans = this->getNDFtranslational(); |
532 | + | } |
533 | ||
534 | + | |
535 | + | void SimInfo::setRcut( double theRcut ){ |
536 | + | |
537 | + | rCut = theRcut; |
538 | + | checkCutOffs(); |
539 | } | |
540 | ||
541 | + | void SimInfo::setDefaultRcut( double theRcut ){ |
542 | + | |
543 | + | haveOrigRcut = 1; |
544 | + | origRcut = theRcut; |
545 | + | rCut = theRcut; |
546 | + | |
547 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
548 | + | |
549 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
550 | + | } |
551 | + | |
552 | + | void SimInfo::setEcr( double theEcr ){ |
553 | + | |
554 | + | ecr = theEcr; |
555 | + | checkCutOffs(); |
556 | + | } |
557 | + | |
558 | + | void SimInfo::setDefaultEcr( double theEcr ){ |
559 | + | |
560 | + | haveOrigEcr = 1; |
561 | + | origEcr = theEcr; |
562 | + | |
563 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
564 | + | |
565 | + | ecr = theEcr; |
566 | + | |
567 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
568 | + | } |
569 | + | |
570 | + | void SimInfo::setEcr( double theEcr, double theEst ){ |
571 | + | |
572 | + | est = theEst; |
573 | + | setEcr( theEcr ); |
574 | + | } |
575 | + | |
576 | + | void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
577 | + | |
578 | + | est = theEst; |
579 | + | setDefaultEcr( theEcr ); |
580 | + | } |
581 | + | |
582 | + | |
583 | + | void SimInfo::checkCutOffs( void ){ |
584 | + | |
585 | + | int cutChanged = 0; |
586 | + | |
587 | + | if( boxIsInit ){ |
588 | + | |
589 | + | //we need to check cutOffs against the box |
590 | + | |
591 | + | //detect the change of rCut |
592 | + | if(( maxCutoff > rCut )&&(usePBC)){ |
593 | + | if( rCut < origRcut ){ |
594 | + | rCut = origRcut; |
595 | + | |
596 | + | if (rCut > maxCutoff) |
597 | + | rCut = maxCutoff; |
598 | + | |
599 | + | sprintf( painCave.errMsg, |
600 | + | "New Box size is setting the long range cutoff radius " |
601 | + | "to %lf at time %lf\n", |
602 | + | rCut, currentTime ); |
603 | + | painCave.isFatal = 0; |
604 | + | simError(); |
605 | + | } |
606 | + | } |
607 | + | else if ((rCut > maxCutoff)&&(usePBC)) { |
608 | + | sprintf( painCave.errMsg, |
609 | + | "New Box size is setting the long range cutoff radius " |
610 | + | "to %lf at time %lf\n", |
611 | + | maxCutoff, currentTime ); |
612 | + | painCave.isFatal = 0; |
613 | + | simError(); |
614 | + | rCut = maxCutoff; |
615 | + | } |
616 | + | |
617 | + | |
618 | + | //detect the change of ecr |
619 | + | if( maxCutoff > ecr ){ |
620 | + | if( ecr < origEcr ){ |
621 | + | ecr = origEcr; |
622 | + | if (ecr > maxCutoff) ecr = maxCutoff; |
623 | + | |
624 | + | sprintf( painCave.errMsg, |
625 | + | "New Box size is setting the electrostaticCutoffRadius " |
626 | + | "to %lf at time %lf\n", |
627 | + | ecr, currentTime ); |
628 | + | painCave.isFatal = 0; |
629 | + | simError(); |
630 | + | } |
631 | + | } |
632 | + | else if( ecr > maxCutoff){ |
633 | + | sprintf( painCave.errMsg, |
634 | + | "New Box size is setting the electrostaticCutoffRadius " |
635 | + | "to %lf at time %lf\n", |
636 | + | maxCutoff, currentTime ); |
637 | + | painCave.isFatal = 0; |
638 | + | simError(); |
639 | + | ecr = maxCutoff; |
640 | + | } |
641 | + | |
642 | + | if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
643 | + | |
644 | + | // rlist is the 1.0 plus max( rcut, ecr ) |
645 | + | |
646 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
647 | + | |
648 | + | if( cutChanged ){ |
649 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
650 | + | } |
651 | + | |
652 | + | oldEcr = ecr; |
653 | + | oldRcut = rCut; |
654 | + | |
655 | + | } else { |
656 | + | // initialize this stuff before using it, OK? |
657 | + | sprintf( painCave.errMsg, |
658 | + | "Trying to check cutoffs without a box. Be smarter.\n" ); |
659 | + | painCave.isFatal = 1; |
660 | + | simError(); |
661 | + | } |
662 | + | |
663 | + | } |
664 | + | |
665 | + | void SimInfo::addProperty(GenericData* prop){ |
666 | + | |
667 | + | map<string, GenericData*>::iterator result; |
668 | + | result = properties.find(prop->getID()); |
669 | + | |
670 | + | //we can't simply use properties[prop->getID()] = prop, |
671 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
672 | + | |
673 | + | if(result != properties.end()){ |
674 | + | |
675 | + | delete (*result).second; |
676 | + | (*result).second = prop; |
677 | + | |
678 | + | } |
679 | + | else{ |
680 | + | |
681 | + | properties[prop->getID()] = prop; |
682 | + | |
683 | + | } |
684 | + | |
685 | + | } |
686 | + | |
687 | + | GenericData* SimInfo::getProperty(const string& propName){ |
688 | + | |
689 | + | map<string, GenericData*>::iterator result; |
690 | + | |
691 | + | //string lowerCaseName = (); |
692 | + | |
693 | + | result = properties.find(propName); |
694 | + | |
695 | + | if(result != properties.end()) |
696 | + | return (*result).second; |
697 | + | else |
698 | + | return NULL; |
699 | + | } |
700 | + | |
701 | + | vector<GenericData*> SimInfo::getProperties(){ |
702 | + | |
703 | + | vector<GenericData*> result; |
704 | + | map<string, GenericData*>::iterator i; |
705 | + | |
706 | + | for(i = properties.begin(); i != properties.end(); i++) |
707 | + | result.push_back((*i).second); |
708 | + | |
709 | + | return result; |
710 | + | } |
711 | + | |
712 | + | double SimInfo::matTrace3(double m[3][3]){ |
713 | + | double trace; |
714 | + | trace = m[0][0] + m[1][1] + m[2][2]; |
715 | + | |
716 | + | return trace; |
717 | + | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |