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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 469 by mmeineke, Mon Apr 7 20:06:31 2003 UTC vs.
Revision 670 by mmeineke, Thu Aug 7 21:47:18 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 21 | Line 33 | SimInfo::SimInfo(){
33    the_integrator = NULL;
34    setTemp = 0;
35    thermalTime = 0.0;
36 +  currentTime = 0.0;
37    rCut = 0.0;
38 +  ecr = 0.0;
39 +  est = 0.0;
40 +  oldEcr = 0.0;
41 +  oldRcut = 0.0;
42  
43 +  haveOrigRcut = 0;
44 +  haveOrigEcr = 0;
45 +  boxIsInit = 0;
46 +  
47 +  
48 +
49    usePBC = 0;
50    useLJ = 0;
51    useSticky = 0;
# Line 31 | Line 54 | SimInfo::SimInfo(){
54    useGB = 0;
55    useEAM = 0;
56  
57 +  myConfiguration = new SimState();
58 +
59    wrapMeSimInfo( this );
60   }
61  
62 +
63 + SimInfo::~SimInfo(){
64 +
65 +  delete myConfiguration;
66 +
67 +  map<string, GenericData*>::iterator i;
68 +  
69 +  for(i = properties.begin(); i != properties.end(); i++)
70 +    delete (*i).second;
71 +    
72 + }
73 +
74   void SimInfo::setBox(double newBox[3]) {
75 <  double smallestBox, maxCutoff;
76 <  int status;
77 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
75 >  
76 >  int i, j;
77 >  double tempMat[3][3];
78  
79 <  smallestBox = box_x;
80 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
79 >  for(i=0; i<3; i++)
80 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
81  
82 <  maxCutoff = smallestBox / 2.0;
82 >  tempMat[0][0] = newBox[0];
83 >  tempMat[1][1] = newBox[1];
84 >  tempMat[2][2] = newBox[2];
85  
86 <  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();
86 >  setBoxM( tempMat );
87  
88 <    rList = maxCutoff;
88 > }
89  
90 <    sprintf( painCave.errMsg,
91 <             "New Box size is forcing cutoff radius down to %lf\n",
92 <             maxCutoff - 1.0 );
93 <    painCave.isFatal = 0;
94 <    simError();
90 > void SimInfo::setBoxM( double theBox[3][3] ){
91 >  
92 >  int i, j, status;
93 >  double smallestBoxL, maxCutoff;
94 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
95 >                         // ordering in the array is as follows:
96 >                         // [ 0 3 6 ]
97 >                         // [ 1 4 7 ]
98 >                         // [ 2 5 8 ]
99 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
100  
101 <    rCut = rList - 1.0;
101 >  
102 >  if( !boxIsInit ) boxIsInit = 1;
103  
104 <    // list radius changed so we have to refresh the simulation structure.
105 <    refreshSim();
104 >  for(i=0; i < 3; i++)
105 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
106 >  
107 >  calcBoxL();
108 >  calcHmatInv();
109 >
110 >  for(i=0; i < 3; i++) {
111 >    for (j=0; j < 3; j++) {
112 >      FortranHmat[3*j + i] = Hmat[i][j];
113 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
114 >    }
115    }
116  
117 <  if (rCut > maxCutoff) {
117 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
118 >
119 > }
120 >
121 >
122 > void SimInfo::getBoxM (double theBox[3][3]) {
123 >
124 >  int i, j;
125 >  for(i=0; i<3; i++)
126 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
127 > }
128 >
129 >
130 > void SimInfo::scaleBox(double scale) {
131 >  double theBox[3][3];
132 >  int i, j;
133 >
134 >  // cerr << "Scaling box by " << scale << "\n";
135 >
136 >  for(i=0; i<3; i++)
137 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
138 >
139 >  setBoxM(theBox);
140 >
141 > }
142 >
143 > void SimInfo::calcHmatInv( void ) {
144 >  
145 >  int i,j;
146 >  double smallDiag;
147 >  double tol;
148 >  double sanity[3][3];
149 >
150 >  invertMat3( Hmat, HmatInv );
151 >
152 >  // Check the inverse to make sure it is sane:
153 >
154 >  matMul3( Hmat, HmatInv, sanity );
155 >    
156 >  // check to see if Hmat is orthorhombic
157 >  
158 >  smallDiag = Hmat[0][0];
159 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
160 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
161 >  tol = smallDiag * 1E-6;
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;
170 >        }        
171 >      }
172 >    }
173 >  }
174 > }
175 >
176 > double SimInfo::matDet3(double a[3][3]) {
177 >  int i, j, k;
178 >  double determinant;
179 >
180 >  determinant = 0.0;
181 >
182 >  for(i = 0; i < 3; i++) {
183 >    j = (i+1)%3;
184 >    k = (i+2)%3;
185 >
186 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
187 >  }
188 >
189 >  return determinant;
190 > }
191 >
192 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
193 >  
194 >  int  i, j, k, l, m, n;
195 >  double determinant;
196 >
197 >  determinant = matDet3( a );
198 >
199 >  if (determinant == 0.0) {
200      sprintf( painCave.errMsg,
201 <             "New Box size is forcing cutoff radius down to %lf\n",
202 <             maxCutoff );
76 <    painCave.isFatal = 0;
201 >             "Can't invert a matrix with a zero determinant!\n");
202 >    painCave.isFatal = 1;
203      simError();
204 +  }
205  
206 <    status = 0;
207 <    LJ_new_rcut(&rCut, &status);
208 <    if (status != 0) {
209 <      sprintf( painCave.errMsg,
210 <               "Error in recomputing LJ shifts based on new rcut\n");
211 <      painCave.isFatal = 1;
212 <      simError();
206 >  for (i=0; i < 3; i++) {
207 >    j = (i+1)%3;
208 >    k = (i+2)%3;
209 >    for(l = 0; l < 3; l++) {
210 >      m = (l+1)%3;
211 >      n = (l+2)%3;
212 >      
213 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
214      }
215    }
216   }
217  
218 < void SimInfo::getBox(double theBox[3]) {
219 <  theBox[0] = box_x;
220 <  theBox[1] = box_y;
221 <  theBox[2] = box_z;
218 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
219 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
220 >
221 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
222 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
223 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
224 >  
225 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
226 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
227 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
228 >  
229 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
230 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
231 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
232 >  
233 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
234 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
235 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
236   }
237 <
237 >
238 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
239 >  double a0, a1, a2;
240 >
241 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
242 >
243 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
244 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
245 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
246 > }
247 >
248 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
249 >  double temp[3][3];
250 >  int i, j;
251 >
252 >  for (i = 0; i < 3; i++) {
253 >    for (j = 0; j < 3; j++) {
254 >      temp[j][i] = in[i][j];
255 >    }
256 >  }
257 >  for (i = 0; i < 3; i++) {
258 >    for (j = 0; j < 3; j++) {
259 >      out[i][j] = temp[i][j];
260 >    }
261 >  }
262 > }
263 >  
264 > void SimInfo::printMat3(double A[3][3] ){
265 >
266 >  std::cerr
267 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
268 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
269 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
270 > }
271 >
272 > void SimInfo::printMat9(double A[9] ){
273 >
274 >  std::cerr
275 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
276 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
277 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
278 > }
279 >
280 > void SimInfo::calcBoxL( void ){
281 >
282 >  double dx, dy, dz, dsq;
283 >  int i;
284 >
285 >  // boxVol = Determinant of Hmat
286 >
287 >  boxVol = matDet3( Hmat );
288 >
289 >  // boxLx
290 >  
291 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
292 >  dsq = dx*dx + dy*dy + dz*dz;
293 >  boxL[0] = sqrt( dsq );
294 >  maxCutoff = 0.5 * boxL[0];
295 >
296 >  // boxLy
297 >  
298 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
299 >  dsq = dx*dx + dy*dy + dz*dz;
300 >  boxL[1] = sqrt( dsq );
301 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
302 >
303 >  // boxLz
304 >  
305 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
306 >  dsq = dx*dx + dy*dy + dz*dz;
307 >  boxL[2] = sqrt( dsq );
308 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
309 >  
310 >  checkCutOffs();
311 >
312 > }
313 >
314 >
315 > void SimInfo::wrapVector( double thePos[3] ){
316 >
317 >  int i, j, k;
318 >  double scaled[3];
319 >
320 >  if( !orthoRhombic ){
321 >    // calc the scaled coordinates.
322 >  
323 >
324 >    matVecMul3(HmatInv, thePos, scaled);
325 >    
326 >    for(i=0; i<3; i++)
327 >      scaled[i] -= roundMe(scaled[i]);
328 >    
329 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
330 >    
331 >    matVecMul3(Hmat, scaled, thePos);
332 >
333 >  }
334 >  else{
335 >    // calc the scaled coordinates.
336 >    
337 >    for(i=0; i<3; i++)
338 >      scaled[i] = thePos[i]*HmatInv[i][i];
339 >    
340 >    // wrap the scaled coordinates
341 >    
342 >    for(i=0; i<3; i++)
343 >      scaled[i] -= roundMe(scaled[i]);
344 >    
345 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
346 >    
347 >    for(i=0; i<3; i++)
348 >      thePos[i] = scaled[i]*Hmat[i][i];
349 >  }
350 >    
351 > }
352 >
353 >
354   int SimInfo::getNDF(){
355    int ndf_local, ndf;
356    
# Line 128 | Line 386 | void SimInfo::refreshSim(){
386  
387    simtype fInfo;
388    int isError;
389 +  int n_global;
390    int* excl;
391 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
391 >
392    fInfo.dielect = 0.0;
393  
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 –
394    if( useDipole ){
145 –    fInfo.rrf = ecr;
146 –    fInfo.rt = ecr - est;
395      if( useReactionField )fInfo.dielect = dielectric;
396    }
397  
# Line 152 | Line 400 | void SimInfo::refreshSim(){
400    fInfo.SIM_uses_LJ = useLJ;
401    fInfo.SIM_uses_sticky = useSticky;
402    //fInfo.SIM_uses_sticky = 0;
403 <  //fInfo.SIM_uses_dipoles = useDipole;
404 <  fInfo.SIM_uses_dipoles = 0;
403 >  fInfo.SIM_uses_dipoles = useDipole;
404 >  //fInfo.SIM_uses_dipoles = 0;
405    //fInfo.SIM_uses_RF = useReactionField;
406    fInfo.SIM_uses_RF = 0;
407    fInfo.SIM_uses_GB = useGB;
# Line 161 | Line 409 | void SimInfo::refreshSim(){
409  
410    excl = Exclude::getArray();
411  
412 + #ifdef IS_MPI
413 +  n_global = mpiSim->getTotAtoms();
414 + #else
415 +  n_global = n_atoms;
416 + #endif
417 +
418    isError = 0;
419  
420 < //   fInfo;
421 < //   n_atoms;
422 < //   identArray;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
420 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
421 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
422 >                  &isError );
423  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
424    if( isError ){
425  
426      sprintf( painCave.errMsg,
# Line 189 | Line 435 | void SimInfo::refreshSim(){
435    MPIcheckPoint();
436   #endif // is_mpi
437  
438 <  ndf = this->getNDF();
439 <  ndfRaw = this->getNDFraw();
438 >  this->ndf = this->getNDF();
439 >  this->ndfRaw = this->getNDFraw();
440  
441   }
442  
443 +
444 + void SimInfo::setRcut( double theRcut ){
445 +
446 +  if( !haveOrigRcut ){
447 +    haveOrigRcut = 1;
448 +    origRcut = theRcut;
449 +  }
450 +
451 +  rCut = theRcut;
452 +  checkCutOffs();
453 + }
454 +
455 + void SimInfo::setEcr( double theEcr ){
456 +
457 +  if( !haveOrigEcr ){
458 +    haveOrigEcr = 1;
459 +    origEcr = theEcr;
460 +  }
461 +
462 +  ecr = theEcr;
463 +  checkCutOffs();
464 + }
465 +
466 + void SimInfo::setEcr( double theEcr, double theEst ){
467 +
468 +  est = theEst;
469 +  setEcr( theEcr );
470 + }
471 +
472 +
473 + void SimInfo::checkCutOffs( void ){
474 +
475 +  int cutChanged = 0;
476 +
477 +
478 +
479 +  if( boxIsInit ){
480 +    
481 +    //we need to check cutOffs against the box
482 +  
483 +    if(( maxCutoff > rCut )&&(usePBC)){
484 +      if( rCut < origRcut ){
485 +        rCut = origRcut;
486 +        if (rCut > maxCutoff) rCut = maxCutoff;
487 +        
488 +        sprintf( painCave.errMsg,
489 +                 "New Box size is setting the long range cutoff radius "
490 +                 "to %lf\n",
491 +                 rCut );
492 +        painCave.isFatal = 0;
493 +        simError();
494 +      }
495 +    }
496 +
497 +    if( maxCutoff > ecr ){
498 +      if( ecr < origEcr ){
499 +        rCut = origEcr;
500 +        if (ecr > maxCutoff) ecr = maxCutoff;
501 +        
502 +        sprintf( painCave.errMsg,
503 +                 "New Box size is setting the electrostaticCutoffRadius "
504 +                 "to %lf\n",
505 +                 ecr );
506 +        painCave.isFatal = 0;
507 +        simError();
508 +      }
509 +    }
510 +
511 +
512 +    if ((rCut > maxCutoff)&&(usePBC)) {
513 +      sprintf( painCave.errMsg,
514 +               "New Box size is setting the long range cutoff radius "
515 +               "to %lf\n",
516 +               maxCutoff );
517 +      painCave.isFatal = 0;
518 +      simError();
519 +      rCut = maxCutoff;
520 +    }
521 +
522 +    if( ecr > maxCutoff){
523 +      sprintf( painCave.errMsg,
524 +               "New Box size is setting the electrostaticCutoffRadius "
525 +               "to %lf\n",
526 +               maxCutoff  );
527 +      painCave.isFatal = 0;
528 +      simError();      
529 +      ecr = maxCutoff;
530 +    }
531 +
532 +    
533 +  }
534 +  
535 +
536 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
537 +
538 +  // rlist is the 1.0 plus max( rcut, ecr )
539 +  
540 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
541 +
542 +  if( cutChanged ){
543 +    
544 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
545 +  }
546 +
547 +  oldEcr = ecr;
548 +  oldRcut = rCut;
549 + }
550 +
551 + void SimInfo::addProperty(GenericData* prop){
552 +
553 +  map<string, GenericData*>::iterator result;
554 +  result = properties.find(prop->getID());
555 +  
556 +  //we can't simply use  properties[prop->getID()] = prop,
557 +  //it will cause memory leak if we already contain a propery which has the same name of prop
558 +  
559 +  if(result != properties.end()){
560 +    
561 +    delete (*result).second;
562 +    (*result).second = prop;
563 +      
564 +  }
565 +  else{
566 +
567 +    properties[prop->getID()] = prop;
568 +
569 +  }
570 +    
571 + }
572 +
573 + GenericData* SimInfo::getProperty(const string& propName){
574 +
575 +  map<string, GenericData*>::iterator result;
576 +  
577 +  //string lowerCaseName = ();
578 +  
579 +  result = properties.find(propName);
580 +  
581 +  if(result != properties.end())
582 +    return (*result).second;  
583 +  else  
584 +    return NULL;  
585 + }
586 +
587 + vector<GenericData*> SimInfo::getProperties(){
588 +
589 +  vector<GenericData*> result;
590 +  map<string, GenericData*>::iterator i;
591 +  
592 +  for(i = properties.begin(); i != properties.end(); i++)
593 +    result.push_back((*i).second);
594 +    
595 +  return result;
596 + }
597 +
598 +

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