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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 483 by gezelter, Wed Apr 9 04:06:43 2003 UTC vs.
Revision 674 by mmeineke, Mon Aug 11 18:29:46 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 +  ecr = 0.0;
40 +  est = 0.0;
41 +  oldEcr = 0.0;
42 +  oldRcut = 0.0;
43  
44 +  haveOrigRcut = 0;
45 +  haveOrigEcr = 0;
46 +  boxIsInit = 0;
47 +  
48 +  
49 +
50    usePBC = 0;
51    useLJ = 0;
52    useSticky = 0;
# Line 31 | Line 55 | SimInfo::SimInfo(){
55    useGB = 0;
56    useEAM = 0;
57  
58 +  myConfiguration = new SimState();
59 +
60    wrapMeSimInfo( this );
61   }
62  
63 +
64 + SimInfo::~SimInfo(){
65 +
66 +  delete myConfiguration;
67 +
68 +  map<string, GenericData*>::iterator i;
69 +  
70 +  for(i = properties.begin(); i != properties.end(); i++)
71 +    delete (*i).second;
72 +    
73 + }
74 +
75   void SimInfo::setBox(double newBox[3]) {
76 <  double smallestBox, maxCutoff;
77 <  int status;
78 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
76 >  
77 >  int i, j;
78 >  double tempMat[3][3];
79  
80 <  smallestBox = box_x;
81 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
80 >  for(i=0; i<3; i++)
81 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
82  
83 <  maxCutoff = smallestBox / 2.0;
83 >  tempMat[0][0] = newBox[0];
84 >  tempMat[1][1] = newBox[1];
85 >  tempMat[2][2] = newBox[2];
86  
87 <  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();
87 >  setBoxM( tempMat );
88  
89 <    rList = maxCutoff;
89 > }
90  
91 <    sprintf( painCave.errMsg,
92 <             "New Box size is forcing cutoff radius down to %lf\n",
93 <             maxCutoff - 1.0 );
94 <    painCave.isFatal = 0;
95 <    simError();
91 > void SimInfo::setBoxM( double theBox[3][3] ){
92 >  
93 >  int i, j, status;
94 >  double smallestBoxL, maxCutoff;
95 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
96 >                         // ordering in the array is as follows:
97 >                         // [ 0 3 6 ]
98 >                         // [ 1 4 7 ]
99 >                         // [ 2 5 8 ]
100 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
101  
102 <    rCut = rList - 1.0;
102 >  
103 >  if( !boxIsInit ) boxIsInit = 1;
104  
105 <    // list radius changed so we have to refresh the simulation structure.
106 <    refreshSim();
105 >  for(i=0; i < 3; i++)
106 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107 >  
108 >  calcBoxL();
109 >  calcHmatInv();
110 >
111 >  for(i=0; i < 3; i++) {
112 >    for (j=0; j < 3; j++) {
113 >      FortranHmat[3*j + i] = Hmat[i][j];
114 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
115 >    }
116    }
117  
118 <  if (rCut > maxCutoff) {
118 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119 >
120 > }
121 >
122 >
123 > void SimInfo::getBoxM (double theBox[3][3]) {
124 >
125 >  int i, j;
126 >  for(i=0; i<3; i++)
127 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
128 > }
129 >
130 >
131 > void SimInfo::scaleBox(double scale) {
132 >  double theBox[3][3];
133 >  int i, j;
134 >
135 >  // cerr << "Scaling box by " << scale << "\n";
136 >
137 >  for(i=0; i<3; i++)
138 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
139 >
140 >  setBoxM(theBox);
141 >
142 > }
143 >
144 > void SimInfo::calcHmatInv( void ) {
145 >  
146 >  int i,j;
147 >  double smallDiag;
148 >  double tol;
149 >  double sanity[3][3];
150 >
151 >  invertMat3( Hmat, HmatInv );
152 >
153 >  // Check the inverse to make sure it is sane:
154 >
155 >  matMul3( Hmat, HmatInv, sanity );
156 >    
157 >  // check to see if Hmat is orthorhombic
158 >  
159 >  smallDiag = Hmat[0][0];
160 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
161 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
162 >  tol = smallDiag * 1E-6;
163 >
164 >  orthoRhombic = 1;
165 >  
166 >  for (i = 0; i < 3; i++ ) {
167 >    for (j = 0 ; j < 3; j++) {
168 >      if (i != j) {
169 >        if (orthoRhombic) {
170 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
171 >        }        
172 >      }
173 >    }
174 >  }
175 > }
176 >
177 > double SimInfo::matDet3(double a[3][3]) {
178 >  int i, j, k;
179 >  double determinant;
180 >
181 >  determinant = 0.0;
182 >
183 >  for(i = 0; i < 3; i++) {
184 >    j = (i+1)%3;
185 >    k = (i+2)%3;
186 >
187 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
188 >  }
189 >
190 >  return determinant;
191 > }
192 >
193 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
194 >  
195 >  int  i, j, k, l, m, n;
196 >  double determinant;
197 >
198 >  determinant = matDet3( a );
199 >
200 >  if (determinant == 0.0) {
201      sprintf( painCave.errMsg,
202 <             "New Box size is forcing cutoff radius down to %lf\n",
203 <             maxCutoff );
76 <    painCave.isFatal = 0;
202 >             "Can't invert a matrix with a zero determinant!\n");
203 >    painCave.isFatal = 1;
204      simError();
205 +  }
206  
207 <    status = 0;
208 <    LJ_new_rcut(&rCut, &status);
209 <    if (status != 0) {
210 <      sprintf( painCave.errMsg,
211 <               "Error in recomputing LJ shifts based on new rcut\n");
212 <      painCave.isFatal = 1;
213 <      simError();
207 >  for (i=0; i < 3; i++) {
208 >    j = (i+1)%3;
209 >    k = (i+2)%3;
210 >    for(l = 0; l < 3; l++) {
211 >      m = (l+1)%3;
212 >      n = (l+2)%3;
213 >      
214 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
215      }
216    }
217   }
218  
219 < void SimInfo::getBox(double theBox[3]) {
220 <  theBox[0] = box_x;
221 <  theBox[1] = box_y;
222 <  theBox[2] = box_z;
219 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
220 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
221 >
222 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
223 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
224 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
225 >  
226 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
227 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
228 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
229 >  
230 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
231 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
232 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
233 >  
234 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
235 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
236 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
237   }
238 <
238 >
239 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
240 >  double a0, a1, a2;
241 >
242 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
243 >
244 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
245 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
246 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
247 > }
248 >
249 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
250 >  double temp[3][3];
251 >  int i, j;
252 >
253 >  for (i = 0; i < 3; i++) {
254 >    for (j = 0; j < 3; j++) {
255 >      temp[j][i] = in[i][j];
256 >    }
257 >  }
258 >  for (i = 0; i < 3; i++) {
259 >    for (j = 0; j < 3; j++) {
260 >      out[i][j] = temp[i][j];
261 >    }
262 >  }
263 > }
264 >  
265 > void SimInfo::printMat3(double A[3][3] ){
266 >
267 >  std::cerr
268 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
269 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
270 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
271 > }
272 >
273 > void SimInfo::printMat9(double A[9] ){
274 >
275 >  std::cerr
276 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
277 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
278 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
279 > }
280 >
281 > void SimInfo::calcBoxL( void ){
282 >
283 >  double dx, dy, dz, dsq;
284 >  int i;
285 >
286 >  // boxVol = Determinant of Hmat
287 >
288 >  boxVol = matDet3( Hmat );
289 >
290 >  // boxLx
291 >  
292 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
293 >  dsq = dx*dx + dy*dy + dz*dz;
294 >  boxL[0] = sqrt( dsq );
295 >  maxCutoff = 0.5 * boxL[0];
296 >
297 >  // boxLy
298 >  
299 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
300 >  dsq = dx*dx + dy*dy + dz*dz;
301 >  boxL[1] = sqrt( dsq );
302 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
303 >
304 >  // boxLz
305 >  
306 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
307 >  dsq = dx*dx + dy*dy + dz*dz;
308 >  boxL[2] = sqrt( dsq );
309 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
310 >  
311 >  checkCutOffs();
312 >
313 > }
314 >
315 >
316 > void SimInfo::wrapVector( double thePos[3] ){
317 >
318 >  int i, j, k;
319 >  double scaled[3];
320 >
321 >  if( !orthoRhombic ){
322 >    // calc the scaled coordinates.
323 >  
324 >
325 >    matVecMul3(HmatInv, thePos, scaled);
326 >    
327 >    for(i=0; i<3; i++)
328 >      scaled[i] -= roundMe(scaled[i]);
329 >    
330 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
331 >    
332 >    matVecMul3(Hmat, scaled, thePos);
333 >
334 >  }
335 >  else{
336 >    // calc the scaled coordinates.
337 >    
338 >    for(i=0; i<3; i++)
339 >      scaled[i] = thePos[i]*HmatInv[i][i];
340 >    
341 >    // wrap the scaled coordinates
342 >    
343 >    for(i=0; i<3; i++)
344 >      scaled[i] -= roundMe(scaled[i]);
345 >    
346 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
347 >    
348 >    for(i=0; i<3; i++)
349 >      thePos[i] = scaled[i]*Hmat[i][i];
350 >  }
351 >    
352 > }
353 >
354 >
355   int SimInfo::getNDF(){
356    int ndf_local, ndf;
357    
# Line 104 | Line 363 | int SimInfo::getNDF(){
363    ndf = ndf_local;
364   #endif
365  
366 <  ndf = ndf - 3;
366 >  ndf = ndf - 3 - nZconstraints;
367  
368    return ndf;
369   }
# Line 128 | Line 387 | void SimInfo::refreshSim(){
387  
388    simtype fInfo;
389    int isError;
390 +  int n_global;
391    int* excl;
392 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
392 >
393    fInfo.dielect = 0.0;
394  
137 –  fInfo.box[0] = box_x;
138 –  fInfo.box[1] = box_y;
139 –  fInfo.box[2] = box_z;
140 –
141 –  fInfo.rlist = rList;
142 –  fInfo.rcut = rCut;
143 –
395    if( useDipole ){
145 –    fInfo.rrf = ecr;
146 –    fInfo.rt = ecr - est;
396      if( useReactionField )fInfo.dielect = dielectric;
397    }
398  
# Line 161 | Line 410 | void SimInfo::refreshSim(){
410  
411    excl = Exclude::getArray();
412  
413 + #ifdef IS_MPI
414 +  n_global = mpiSim->getTotAtoms();
415 + #else
416 +  n_global = n_atoms;
417 + #endif
418 +
419    isError = 0;
420  
421 <  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
421 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
422                    &nGlobalExcludes, globalExcludes, molMembershipArray,
423                    &isError );
424  
# Line 186 | Line 441 | void SimInfo::refreshSim(){
441  
442   }
443  
444 +
445 + void SimInfo::setRcut( double theRcut ){
446 +
447 +  if( !haveOrigRcut ){
448 +    haveOrigRcut = 1;
449 +    origRcut = theRcut;
450 +  }
451 +
452 +  rCut = theRcut;
453 +  checkCutOffs();
454 + }
455 +
456 + void SimInfo::setEcr( double theEcr ){
457 +
458 +  if( !haveOrigEcr ){
459 +    haveOrigEcr = 1;
460 +    origEcr = theEcr;
461 +  }
462 +
463 +  ecr = theEcr;
464 +  checkCutOffs();
465 + }
466 +
467 + void SimInfo::setEcr( double theEcr, double theEst ){
468 +
469 +  est = theEst;
470 +  setEcr( theEcr );
471 + }
472 +
473 +
474 + void SimInfo::checkCutOffs( void ){
475 +
476 +  int cutChanged = 0;
477 +
478 +
479 +
480 +  if( boxIsInit ){
481 +    
482 +    //we need to check cutOffs against the box
483 +  
484 +    if(( maxCutoff > rCut )&&(usePBC)){
485 +      if( rCut < origRcut ){
486 +        rCut = origRcut;
487 +        if (rCut > maxCutoff) rCut = maxCutoff;
488 +        
489 +        sprintf( painCave.errMsg,
490 +                 "New Box size is setting the long range cutoff radius "
491 +                 "to %lf\n",
492 +                 rCut );
493 +        painCave.isFatal = 0;
494 +        simError();
495 +      }
496 +    }
497 +
498 +    if( maxCutoff > ecr ){
499 +      if( ecr < origEcr ){
500 +        rCut = origEcr;
501 +        if (ecr > maxCutoff) ecr = maxCutoff;
502 +        
503 +        sprintf( painCave.errMsg,
504 +                 "New Box size is setting the electrostaticCutoffRadius "
505 +                 "to %lf\n",
506 +                 ecr );
507 +        painCave.isFatal = 0;
508 +        simError();
509 +      }
510 +    }
511 +
512 +
513 +    if ((rCut > maxCutoff)&&(usePBC)) {
514 +      sprintf( painCave.errMsg,
515 +               "New Box size is setting the long range cutoff radius "
516 +               "to %lf\n",
517 +               maxCutoff );
518 +      painCave.isFatal = 0;
519 +      simError();
520 +      rCut = maxCutoff;
521 +    }
522 +
523 +    if( ecr > maxCutoff){
524 +      sprintf( painCave.errMsg,
525 +               "New Box size is setting the electrostaticCutoffRadius "
526 +               "to %lf\n",
527 +               maxCutoff  );
528 +      painCave.isFatal = 0;
529 +      simError();      
530 +      ecr = maxCutoff;
531 +    }
532 +
533 +    
534 +  }
535 +  
536 +
537 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
538 +
539 +  // rlist is the 1.0 plus max( rcut, ecr )
540 +  
541 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542 +
543 +  if( cutChanged ){
544 +    
545 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 +  }
547 +
548 +  oldEcr = ecr;
549 +  oldRcut = rCut;
550 + }
551 +
552 + void SimInfo::addProperty(GenericData* prop){
553 +
554 +  map<string, GenericData*>::iterator result;
555 +  result = properties.find(prop->getID());
556 +  
557 +  //we can't simply use  properties[prop->getID()] = prop,
558 +  //it will cause memory leak if we already contain a propery which has the same name of prop
559 +  
560 +  if(result != properties.end()){
561 +    
562 +    delete (*result).second;
563 +    (*result).second = prop;
564 +      
565 +  }
566 +  else{
567 +
568 +    properties[prop->getID()] = prop;
569 +
570 +  }
571 +    
572 + }
573 +
574 + GenericData* SimInfo::getProperty(const string& propName){
575 +
576 +  map<string, GenericData*>::iterator result;
577 +  
578 +  //string lowerCaseName = ();
579 +  
580 +  result = properties.find(propName);
581 +  
582 +  if(result != properties.end())
583 +    return (*result).second;  
584 +  else  
585 +    return NULL;  
586 + }
587 +
588 + vector<GenericData*> SimInfo::getProperties(){
589 +
590 +  vector<GenericData*> result;
591 +  map<string, GenericData*>::iterator i;
592 +  
593 +  for(i = properties.begin(); i != properties.end(); i++)
594 +    result.push_back((*i).second);
595 +    
596 +  return result;
597 + }
598 +
599 +

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