ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 463 by gezelter, Sat Apr 5 03:39:25 2003 UTC vs.
Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC

# Line 1 | Line 1
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
# Line 9 | Line 12 | SimInfo* currentInfo;
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(){
# Line 18 | Line 30 | SimInfo::SimInfo(){
30    n_dipoles = 0;
31    ndf = 0;
32    ndfRaw = 0;
33 +  nZconstraints = 0;
34    the_integrator = NULL;
35    setTemp = 0;
36    thermalTime = 0.0;
37 +  currentTime = 0.0;
38    rCut = 0.0;
39 +  origRcut = -1.0;
40 +  ecr = 0.0;
41 +  origEcr = -1.0;
42 +  est = 0.0;
43 +  oldEcr = 0.0;
44 +  oldRcut = 0.0;
45  
46 +  haveOrigRcut = 0;
47 +  haveOrigEcr = 0;
48 +  boxIsInit = 0;
49 +  
50 +  
51 +
52    usePBC = 0;
53    useLJ = 0;
54    useSticky = 0;
# Line 31 | 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 <  double smallestBox, maxCutoff;
79 <  int status;
80 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
78 >  
79 >  int i, j;
80 >  double tempMat[3][3];
81  
82 <  smallestBox = box_x;
83 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
82 >  for(i=0; i<3; i++)
83 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
84  
85 <  maxCutoff = smallestBox / 2.0;
85 >  tempMat[0][0] = newBox[0];
86 >  tempMat[1][1] = newBox[1];
87 >  tempMat[2][2] = newBox[2];
88  
89 <  if (rList > maxCutoff) {
52 <    sprintf( painCave.errMsg,
53 <             "New Box size is forcing neighborlist radius down to %lf\n",
54 <             maxCutoff );
55 <    painCave.isFatal = 0;
56 <    simError();
89 >  setBoxM( tempMat );
90  
91 <    rList = maxCutoff;
91 > }
92  
93 <    sprintf( painCave.errMsg,
94 <             "New Box size is forcing cutoff radius down to %lf\n",
95 <             maxCutoff - 1.0 );
96 <    painCave.isFatal = 0;
97 <    simError();
93 > void SimInfo::setBoxM( double theBox[3][3] ){
94 >  
95 >  int i, j, status;
96 >  double smallestBoxL, maxCutoff;
97 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
98 >                         // ordering in the array is as follows:
99 >                         // [ 0 3 6 ]
100 >                         // [ 1 4 7 ]
101 >                         // [ 2 5 8 ]
102 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
103  
104 <    rCut = rList - 1.0;
104 >  
105 >  if( !boxIsInit ) boxIsInit = 1;
106  
107 <    // list radius changed so we have to refresh the simulation structure.
108 <    refreshSim();
107 >  for(i=0; i < 3; i++)
108 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
109 >  
110 >  calcBoxL();
111 >  calcHmatInv();
112 >
113 >  for(i=0; i < 3; i++) {
114 >    for (j=0; j < 3; j++) {
115 >      FortranHmat[3*j + i] = Hmat[i][j];
116 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
117 >    }
118    }
119  
120 <  if (rCut > maxCutoff) {
120 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
121 >
122 > }
123 >
124 >
125 > void SimInfo::getBoxM (double theBox[3][3]) {
126 >
127 >  int i, j;
128 >  for(i=0; i<3; i++)
129 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
130 > }
131 >
132 >
133 > void SimInfo::scaleBox(double scale) {
134 >  double theBox[3][3];
135 >  int i, j;
136 >
137 >  // cerr << "Scaling box by " << scale << "\n";
138 >
139 >  for(i=0; i<3; i++)
140 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
141 >
142 >  setBoxM(theBox);
143 >
144 > }
145 >
146 > void SimInfo::calcHmatInv( void ) {
147 >  
148 >  int i,j;
149 >  double smallDiag;
150 >  double tol;
151 >  double sanity[3][3];
152 >
153 >  invertMat3( Hmat, HmatInv );
154 >
155 >  // Check the inverse to make sure it is sane:
156 >
157 >  matMul3( Hmat, HmatInv, sanity );
158 >    
159 >  // check to see if Hmat is orthorhombic
160 >  
161 >  smallDiag = Hmat[0][0];
162 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
163 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
164 >  tol = smallDiag * 1E-6;
165 >
166 >  orthoRhombic = 1;
167 >  
168 >  for (i = 0; i < 3; i++ ) {
169 >    for (j = 0 ; j < 3; j++) {
170 >      if (i != j) {
171 >        if (orthoRhombic) {
172 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
173 >        }        
174 >      }
175 >    }
176 >  }
177 > }
178 >
179 > double SimInfo::matDet3(double a[3][3]) {
180 >  int i, j, k;
181 >  double determinant;
182 >
183 >  determinant = 0.0;
184 >
185 >  for(i = 0; i < 3; i++) {
186 >    j = (i+1)%3;
187 >    k = (i+2)%3;
188 >
189 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
190 >  }
191 >
192 >  return determinant;
193 > }
194 >
195 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
196 >  
197 >  int  i, j, k, l, m, n;
198 >  double determinant;
199 >
200 >  determinant = matDet3( a );
201 >
202 >  if (determinant == 0.0) {
203      sprintf( painCave.errMsg,
204 <             "New Box size is forcing cutoff radius down to %lf\n",
205 <             maxCutoff );
76 <    painCave.isFatal = 0;
204 >             "Can't invert a matrix with a zero determinant!\n");
205 >    painCave.isFatal = 1;
206      simError();
207 +  }
208  
209 <    status = 0;
210 <    LJ_new_rcut(&rCut, &status);
211 <    if (status != 0) {
212 <      sprintf( painCave.errMsg,
213 <               "Error in recomputing LJ shifts based on new rcut\n");
214 <      painCave.isFatal = 1;
215 <      simError();
209 >  for (i=0; i < 3; i++) {
210 >    j = (i+1)%3;
211 >    k = (i+2)%3;
212 >    for(l = 0; l < 3; l++) {
213 >      m = (l+1)%3;
214 >      n = (l+2)%3;
215 >      
216 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
217      }
218    }
219   }
220  
221 < void SimInfo::getBox(double theBox[3]) {
222 <  theBox[0] = box_x;
223 <  theBox[1] = box_y;
224 <  theBox[2] = box_z;
221 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
222 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
223 >
224 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
225 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
226 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
227 >  
228 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
229 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
230 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
231 >  
232 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
233 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
234 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
235 >  
236 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
237 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
238 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
239   }
240 <
240 >
241 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
242 >  double a0, a1, a2;
243 >
244 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
245 >
246 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
247 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
248 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
249 > }
250 >
251 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
252 >  double temp[3][3];
253 >  int i, j;
254 >
255 >  for (i = 0; i < 3; i++) {
256 >    for (j = 0; j < 3; j++) {
257 >      temp[j][i] = in[i][j];
258 >    }
259 >  }
260 >  for (i = 0; i < 3; i++) {
261 >    for (j = 0; j < 3; j++) {
262 >      out[i][j] = temp[i][j];
263 >    }
264 >  }
265 > }
266 >  
267 > void SimInfo::printMat3(double A[3][3] ){
268 >
269 >  std::cerr
270 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
271 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
272 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
273 > }
274 >
275 > void SimInfo::printMat9(double A[9] ){
276 >
277 >  std::cerr
278 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
279 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
280 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
281 > }
282 >
283 > void SimInfo::calcBoxL( void ){
284 >
285 >  double dx, dy, dz, dsq;
286 >  int i;
287 >
288 >  // boxVol = Determinant of Hmat
289 >
290 >  boxVol = matDet3( Hmat );
291 >
292 >  // boxLx
293 >  
294 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
295 >  dsq = dx*dx + dy*dy + dz*dz;
296 >  boxL[0] = sqrt( dsq );
297 >  maxCutoff = 0.5 * boxL[0];
298 >
299 >  // boxLy
300 >  
301 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
302 >  dsq = dx*dx + dy*dy + dz*dz;
303 >  boxL[1] = sqrt( dsq );
304 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
305 >
306 >  // boxLz
307 >  
308 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
309 >  dsq = dx*dx + dy*dy + dz*dz;
310 >  boxL[2] = sqrt( dsq );
311 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
312 >  
313 >  checkCutOffs();
314 >
315 > }
316 >
317 >
318 > void SimInfo::wrapVector( double thePos[3] ){
319 >
320 >  int i, j, k;
321 >  double scaled[3];
322 >
323 >  if( !orthoRhombic ){
324 >    // calc the scaled coordinates.
325 >  
326 >
327 >    matVecMul3(HmatInv, thePos, scaled);
328 >    
329 >    for(i=0; i<3; i++)
330 >      scaled[i] -= roundMe(scaled[i]);
331 >    
332 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
333 >    
334 >    matVecMul3(Hmat, scaled, thePos);
335 >
336 >  }
337 >  else{
338 >    // calc the scaled coordinates.
339 >    
340 >    for(i=0; i<3; i++)
341 >      scaled[i] = thePos[i]*HmatInv[i][i];
342 >    
343 >    // wrap the scaled coordinates
344 >    
345 >    for(i=0; i<3; i++)
346 >      scaled[i] -= roundMe(scaled[i]);
347 >    
348 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
349 >    
350 >    for(i=0; i<3; i++)
351 >      thePos[i] = scaled[i]*Hmat[i][i];
352 >  }
353 >    
354 > }
355 >
356 >
357   int SimInfo::getNDF(){
358    int ndf_local, ndf;
359    
# Line 104 | Line 365 | int SimInfo::getNDF(){
365    ndf = ndf_local;
366   #endif
367  
368 <  ndf = ndf - 3;
368 >  ndf = ndf - 3 - nZconstraints;
369  
370    return ndf;
371   }
# Line 128 | Line 389 | void SimInfo::refreshSim(){
389  
390    simtype fInfo;
391    int isError;
392 +  int n_global;
393    int* excl;
394  
395 <  fInfo.box[0] = box_x;
134 <  fInfo.box[1] = box_y;
135 <  fInfo.box[2] = box_z;
395 >  fInfo.dielect = 0.0;
396  
397 <  fInfo.rlist = rList;
398 <  fInfo.rcut = rCut;
399 <  fInfo.rrf = ecr;
140 <  fInfo.rt = ecr - est;
141 <  fInfo.dielect = dielectric;
397 >  if( useDipole ){
398 >    if( useReactionField )fInfo.dielect = dielectric;
399 >  }
400  
401    fInfo.SIM_uses_PBC = usePBC;
402    //fInfo.SIM_uses_LJ = 0;
# Line 154 | Line 412 | void SimInfo::refreshSim(){
412  
413    excl = Exclude::getArray();
414  
415 + #ifdef IS_MPI
416 +  n_global = mpiSim->getTotAtoms();
417 + #else
418 +  n_global = n_atoms;
419 + #endif
420 +
421    isError = 0;
422  
423 < //   fInfo;
424 < //   n_atoms;
425 < //   identArray;
162 < //   n_exclude;
163 < //   excludes;
164 < //   nGlobalExcludes;
165 < //   globalExcludes;
166 < //   isError;
423 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
424 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
425 >                  &isError );
426  
168 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
169 –                  &nGlobalExcludes, globalExcludes, &isError );
170 –
427    if( isError ){
428  
429      sprintf( painCave.errMsg,
# Line 182 | Line 438 | void SimInfo::refreshSim(){
438    MPIcheckPoint();
439   #endif // is_mpi
440  
441 <  ndf = this->getNDF();
442 <  ndfRaw = this->getNDFraw();
441 >  this->ndf = this->getNDF();
442 >  this->ndfRaw = this->getNDFraw();
443  
444   }
445  
446 +
447 + void SimInfo::setRcut( double theRcut ){
448 +
449 +  if( !haveOrigRcut ){
450 +    haveOrigRcut = 1;
451 +    origRcut = theRcut;
452 +  }
453 +
454 +  rCut = theRcut;
455 +  checkCutOffs();
456 + }
457 +
458 + void SimInfo::setEcr( double theEcr ){
459 +
460 +  if( !haveOrigEcr ){
461 +    haveOrigEcr = 1;
462 +    origEcr = theEcr;
463 +  }
464 +
465 +  ecr = theEcr;
466 +  checkCutOffs();
467 + }
468 +
469 + void SimInfo::setEcr( double theEcr, double theEst ){
470 +
471 +  est = theEst;
472 +  setEcr( theEcr );
473 + }
474 +
475 +
476 + void SimInfo::checkCutOffs( void ){
477 +
478 +  int cutChanged = 0;
479 +
480 +
481 +
482 +  if( boxIsInit ){
483 +    
484 +    //we need to check cutOffs against the box
485 +  
486 +    if(( maxCutoff > rCut )&&(usePBC)){
487 +      if( rCut < origRcut ){
488 +        rCut = origRcut;
489 +        if (rCut > maxCutoff) rCut = maxCutoff;
490 +        
491 +        sprintf( painCave.errMsg,
492 +                 "New Box size is setting the long range cutoff radius "
493 +                 "to %lf\n",
494 +                 rCut );
495 +        painCave.isFatal = 0;
496 +        simError();
497 +      }
498 +    }
499 +
500 +    if( maxCutoff > ecr ){
501 +      if( ecr < origEcr ){
502 +        rCut = origEcr;
503 +        if (ecr > maxCutoff) ecr = maxCutoff;
504 +        
505 +        sprintf( painCave.errMsg,
506 +                 "New Box size is setting the electrostaticCutoffRadius "
507 +                 "to %lf\n",
508 +                 ecr );
509 +        painCave.isFatal = 0;
510 +        simError();
511 +      }
512 +    }
513 +
514 +
515 +    if ((rCut > maxCutoff)&&(usePBC)) {
516 +      sprintf( painCave.errMsg,
517 +               "New Box size is setting the long range cutoff radius "
518 +               "to %lf\n",
519 +               maxCutoff );
520 +      painCave.isFatal = 0;
521 +      simError();
522 +      rCut = maxCutoff;
523 +    }
524 +
525 +    if( ecr > maxCutoff){
526 +      sprintf( painCave.errMsg,
527 +               "New Box size is setting the electrostaticCutoffRadius "
528 +               "to %lf\n",
529 +               maxCutoff  );
530 +      painCave.isFatal = 0;
531 +      simError();      
532 +      ecr = maxCutoff;
533 +    }
534 +
535 +    
536 +  }
537 +  
538 +
539 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
540 +
541 +  // rlist is the 1.0 plus max( rcut, ecr )
542 +  
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  if( cutChanged ){
546 +    
547 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 +  }
549 +
550 +  oldEcr = ecr;
551 +  oldRcut = rCut;
552 + }
553 +
554 + void SimInfo::addProperty(GenericData* prop){
555 +
556 +  map<string, GenericData*>::iterator result;
557 +  result = properties.find(prop->getID());
558 +  
559 +  //we can't simply use  properties[prop->getID()] = prop,
560 +  //it will cause memory leak if we already contain a propery which has the same name of prop
561 +  
562 +  if(result != properties.end()){
563 +    
564 +    delete (*result).second;
565 +    (*result).second = prop;
566 +      
567 +  }
568 +  else{
569 +
570 +    properties[prop->getID()] = prop;
571 +
572 +  }
573 +    
574 + }
575 +
576 + GenericData* SimInfo::getProperty(const string& propName){
577 +
578 +  map<string, GenericData*>::iterator result;
579 +  
580 +  //string lowerCaseName = ();
581 +  
582 +  result = properties.find(propName);
583 +  
584 +  if(result != properties.end())
585 +    return (*result).second;  
586 +  else  
587 +    return NULL;  
588 + }
589 +
590 + vector<GenericData*> SimInfo::getProperties(){
591 +
592 +  vector<GenericData*> result;
593 +  map<string, GenericData*>::iterator i;
594 +  
595 +  for(i = properties.begin(); i != properties.end(); i++)
596 +    result.push_back((*i).second);
597 +    
598 +  return result;
599 + }
600 +
601 +

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines