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root/group/branches/no-template-branch/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC vs.
Revision 770 by gezelter, Fri Sep 19 14:55:41 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
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(){
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 +  
52 +
53    usePBC = 0;
54    useLJ = 0;
55    useSticky = 0;
# Line 31 | Line 58 | SimInfo::SimInfo(){
58    useGB = 0;
59    useEAM = 0;
60  
61 +  myConfiguration = new SimState();
62 +
63    wrapMeSimInfo( this );
64   }
65  
66 +
67 + SimInfo::~SimInfo(){
68 +
69 +  delete myConfiguration;
70 +
71 +  map<string, GenericData*>::iterator i;
72 +  
73 +  for(i = properties.begin(); i != properties.end(); i++)
74 +    delete (*i).second;
75 +    
76 + }
77 +
78   void SimInfo::setBox(double newBox[3]) {
79 <  double smallestBox, maxCutoff;
80 <  int status;
81 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
79 >  
80 >  int i, j;
81 >  double tempMat[3][3];
82  
83 <  smallestBox = box_x;
84 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
83 >  for(i=0; i<3; i++)
84 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
85  
86 <  maxCutoff = smallestBox / 2.0;
86 >  tempMat[0][0] = newBox[0];
87 >  tempMat[1][1] = newBox[1];
88 >  tempMat[2][2] = newBox[2];
89  
90 <  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();
90 >  setBoxM( tempMat );
91  
92 <    rList = maxCutoff;
92 > }
93  
94 <    sprintf( painCave.errMsg,
95 <             "New Box size is forcing cutoff radius down to %lf\n",
96 <             maxCutoff - 1.0 );
97 <    painCave.isFatal = 0;
98 <    simError();
94 > void SimInfo::setBoxM( double theBox[3][3] ){
95 >  
96 >  int i, j, status;
97 >  double smallestBoxL, maxCutoff;
98 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
99 >                         // ordering in the array is as follows:
100 >                         // [ 0 3 6 ]
101 >                         // [ 1 4 7 ]
102 >                         // [ 2 5 8 ]
103 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
104  
105 <    rCut = rList - 1.0;
105 >  
106 >  if( !boxIsInit ) boxIsInit = 1;
107  
108 <    // list radius changed so we have to refresh the simulation structure.
109 <    refreshSim();
108 >  for(i=0; i < 3; i++)
109 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
110 >  
111 >  calcBoxL();
112 >  calcHmatInv();
113 >
114 >  for(i=0; i < 3; i++) {
115 >    for (j=0; j < 3; j++) {
116 >      FortranHmat[3*j + i] = Hmat[i][j];
117 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
118 >    }
119    }
120  
121 <  if (rCut > maxCutoff) {
121 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
122 >
123 > }
124 >
125 >
126 > void SimInfo::getBoxM (double theBox[3][3]) {
127 >
128 >  int i, j;
129 >  for(i=0; i<3; i++)
130 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
131 > }
132 >
133 >
134 > void SimInfo::scaleBox(double scale) {
135 >  double theBox[3][3];
136 >  int i, j;
137 >
138 >  // cerr << "Scaling box by " << scale << "\n";
139 >
140 >  for(i=0; i<3; i++)
141 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
142 >
143 >  setBoxM(theBox);
144 >
145 > }
146 >
147 > void SimInfo::calcHmatInv( void ) {
148 >  
149 >  int i,j;
150 >  double smallDiag;
151 >  double tol;
152 >  double sanity[3][3];
153 >
154 >  invertMat3( Hmat, HmatInv );
155 >
156 >  // Check the inverse to make sure it is sane:
157 >
158 >  matMul3( Hmat, HmatInv, sanity );
159 >    
160 >  // check to see if Hmat is orthorhombic
161 >  
162 >  smallDiag = Hmat[0][0];
163 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
164 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
165 >  tol = smallDiag * 1E-6;
166 >
167 >  orthoRhombic = 1;
168 >  
169 >  for (i = 0; i < 3; i++ ) {
170 >    for (j = 0 ; j < 3; j++) {
171 >      if (i != j) {
172 >        if (orthoRhombic) {
173 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
174 >        }        
175 >      }
176 >    }
177 >  }
178 > }
179 >
180 > double SimInfo::matDet3(double a[3][3]) {
181 >  int i, j, k;
182 >  double determinant;
183 >
184 >  determinant = 0.0;
185 >
186 >  for(i = 0; i < 3; i++) {
187 >    j = (i+1)%3;
188 >    k = (i+2)%3;
189 >
190 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
191 >  }
192 >
193 >  return determinant;
194 > }
195 >
196 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
197 >  
198 >  int  i, j, k, l, m, n;
199 >  double determinant;
200 >
201 >  determinant = matDet3( a );
202 >
203 >  if (determinant == 0.0) {
204      sprintf( painCave.errMsg,
205 <             "New Box size is forcing cutoff radius down to %lf\n",
206 <             maxCutoff );
76 <    painCave.isFatal = 0;
205 >             "Can't invert a matrix with a zero determinant!\n");
206 >    painCave.isFatal = 1;
207      simError();
208 +  }
209  
210 <    status = 0;
211 <    LJ_new_rcut(&rCut, &status);
212 <    if (status != 0) {
213 <      sprintf( painCave.errMsg,
214 <               "Error in recomputing LJ shifts based on new rcut\n");
215 <      painCave.isFatal = 1;
216 <      simError();
210 >  for (i=0; i < 3; i++) {
211 >    j = (i+1)%3;
212 >    k = (i+2)%3;
213 >    for(l = 0; l < 3; l++) {
214 >      m = (l+1)%3;
215 >      n = (l+2)%3;
216 >      
217 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
218      }
219    }
220   }
221  
222 < void SimInfo::getBox(double theBox[3]) {
223 <  theBox[0] = box_x;
224 <  theBox[1] = box_y;
225 <  theBox[2] = box_z;
222 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
223 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
224 >
225 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
226 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
227 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
228 >  
229 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
230 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
231 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
232 >  
233 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
234 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
235 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
236 >  
237 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
238 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
239 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
240   }
241 <
241 >
242 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
243 >  double a0, a1, a2;
244 >
245 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
246 >
247 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
248 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
249 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
250 > }
251 >
252 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
253 >  double temp[3][3];
254 >  int i, j;
255 >
256 >  for (i = 0; i < 3; i++) {
257 >    for (j = 0; j < 3; j++) {
258 >      temp[j][i] = in[i][j];
259 >    }
260 >  }
261 >  for (i = 0; i < 3; i++) {
262 >    for (j = 0; j < 3; j++) {
263 >      out[i][j] = temp[i][j];
264 >    }
265 >  }
266 > }
267 >  
268 > void SimInfo::printMat3(double A[3][3] ){
269 >
270 >  std::cerr
271 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
272 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
273 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
274 > }
275 >
276 > void SimInfo::printMat9(double A[9] ){
277 >
278 >  std::cerr
279 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
280 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
281 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
282 > }
283 >
284 > void SimInfo::calcBoxL( void ){
285 >
286 >  double dx, dy, dz, dsq;
287 >  int i;
288 >
289 >  // boxVol = Determinant of Hmat
290 >
291 >  boxVol = matDet3( Hmat );
292 >
293 >  // boxLx
294 >  
295 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
296 >  dsq = dx*dx + dy*dy + dz*dz;
297 >  boxL[0] = sqrt( dsq );
298 >  maxCutoff = 0.5 * boxL[0];
299 >
300 >  // boxLy
301 >  
302 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
303 >  dsq = dx*dx + dy*dy + dz*dz;
304 >  boxL[1] = sqrt( dsq );
305 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
306 >
307 >  // boxLz
308 >  
309 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
310 >  dsq = dx*dx + dy*dy + dz*dz;
311 >  boxL[2] = sqrt( dsq );
312 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
313 >  
314 >  checkCutOffs();
315 >
316 > }
317 >
318 >
319 > void SimInfo::wrapVector( double thePos[3] ){
320 >
321 >  int i, j, k;
322 >  double scaled[3];
323 >
324 >  if( !orthoRhombic ){
325 >    // calc the scaled coordinates.
326 >  
327 >
328 >    matVecMul3(HmatInv, thePos, scaled);
329 >    
330 >    for(i=0; i<3; i++)
331 >      scaled[i] -= roundMe(scaled[i]);
332 >    
333 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
334 >    
335 >    matVecMul3(Hmat, scaled, thePos);
336 >
337 >  }
338 >  else{
339 >    // calc the scaled coordinates.
340 >    
341 >    for(i=0; i<3; i++)
342 >      scaled[i] = thePos[i]*HmatInv[i][i];
343 >    
344 >    // wrap the scaled coordinates
345 >    
346 >    for(i=0; i<3; i++)
347 >      scaled[i] -= roundMe(scaled[i]);
348 >    
349 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
350 >    
351 >    for(i=0; i<3; i++)
352 >      thePos[i] = scaled[i]*Hmat[i][i];
353 >  }
354 >    
355 > }
356 >
357 >
358   int SimInfo::getNDF(){
359    int ndf_local, ndf;
360    
# Line 104 | Line 366 | int SimInfo::getNDF(){
366    ndf = ndf_local;
367   #endif
368  
369 <  ndf = ndf - 3;
369 >  ndf = ndf - 3 - nZconstraints;
370  
371    return ndf;
372   }
# Line 123 | Line 385 | int SimInfo::getNDFraw() {
385  
386    return ndfRaw;
387   }
388 <
388 >
389 > int SimInfo::getNDFtranslational() {
390 >  int ndfTrans_local, ndfTrans;
391 >
392 >  ndfTrans_local = 3 * n_atoms - n_constraints;
393 >
394 > #ifdef IS_MPI
395 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396 > #else
397 >  ndfTrans = ndfTrans_local;
398 > #endif
399 >
400 >  ndfTrans = ndfTrans - 3 - nZconstraints;
401 >
402 >  return ndfTrans;
403 > }
404 >
405   void SimInfo::refreshSim(){
406  
407    simtype fInfo;
408    int isError;
409 +  int n_global;
410    int* excl;
411 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
411 >
412    fInfo.dielect = 0.0;
413  
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 –
414    if( useDipole ){
145 –    fInfo.rrf = ecr;
146 –    fInfo.rt = ecr - est;
415      if( useReactionField )fInfo.dielect = dielectric;
416    }
417  
# Line 152 | Line 420 | void SimInfo::refreshSim(){
420    fInfo.SIM_uses_LJ = useLJ;
421    fInfo.SIM_uses_sticky = useSticky;
422    //fInfo.SIM_uses_sticky = 0;
423 <  //fInfo.SIM_uses_dipoles = useDipole;
424 <  fInfo.SIM_uses_dipoles = 0;
423 >  fInfo.SIM_uses_dipoles = useDipole;
424 >  //fInfo.SIM_uses_dipoles = 0;
425    //fInfo.SIM_uses_RF = useReactionField;
426    fInfo.SIM_uses_RF = 0;
427    fInfo.SIM_uses_GB = useGB;
# Line 161 | Line 429 | void SimInfo::refreshSim(){
429  
430    excl = Exclude::getArray();
431  
432 + #ifdef IS_MPI
433 +  n_global = mpiSim->getTotAtoms();
434 + #else
435 +  n_global = n_atoms;
436 + #endif
437 +
438    isError = 0;
439  
440 < //   fInfo;
441 < //   n_atoms;
442 < //   identArray;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
440 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
441 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
442 >                  &isError );
443  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
444    if( isError ){
445  
446      sprintf( painCave.errMsg,
# Line 191 | Line 457 | void SimInfo::refreshSim(){
457  
458    this->ndf = this->getNDF();
459    this->ndfRaw = this->getNDFraw();
460 +  this->ndfTrans = this->getNDFtranslational();
461 + }
462  
463 +
464 + void SimInfo::setRcut( double theRcut ){
465 +
466 +  if( !haveOrigRcut ){
467 +    haveOrigRcut = 1;
468 +    origRcut = theRcut;
469 +  }
470 +
471 +  rCut = theRcut;
472 +  checkCutOffs();
473   }
474  
475 + void SimInfo::setEcr( double theEcr ){
476 +
477 +  if( !haveOrigEcr ){
478 +    haveOrigEcr = 1;
479 +    origEcr = theEcr;
480 +  }
481 +
482 +  ecr = theEcr;
483 +  checkCutOffs();
484 + }
485 +
486 + void SimInfo::setEcr( double theEcr, double theEst ){
487 +
488 +  est = theEst;
489 +  setEcr( theEcr );
490 + }
491 +
492 +
493 + void SimInfo::checkCutOffs( void ){
494 +
495 +  int cutChanged = 0;
496 +  
497 +  if( boxIsInit ){
498 +    
499 +    //we need to check cutOffs against the box
500 +    
501 +    if(( maxCutoff > rCut )&&(usePBC)){
502 +      if( rCut < origRcut ){
503 +        rCut = origRcut;
504 +        if (rCut > maxCutoff) rCut = maxCutoff;
505 +        
506 +        sprintf( painCave.errMsg,
507 +                 "New Box size is setting the long range cutoff radius "
508 +                 "to %lf at time %lf\n",
509 +                 rCut, currentTime );
510 +        painCave.isFatal = 0;
511 +        simError();
512 +      }
513 +    }
514 +    
515 +    if( maxCutoff > ecr ){
516 +      if( ecr < origEcr ){
517 +        ecr = origEcr;
518 +        if (ecr > maxCutoff) ecr = maxCutoff;
519 +        
520 +        sprintf( painCave.errMsg,
521 +                 "New Box size is setting the electrostaticCutoffRadius "
522 +                 "to %lf at time %lf\n",
523 +                 ecr, currentTime );
524 +        painCave.isFatal = 0;
525 +        simError();
526 +      }
527 +    }
528 +    
529 +    
530 +    if ((rCut > maxCutoff)&&(usePBC)) {
531 +      sprintf( painCave.errMsg,
532 +               "New Box size is setting the long range cutoff radius "
533 +               "to %lf at time %lf\n",
534 +               maxCutoff, currentTime );
535 +      painCave.isFatal = 0;
536 +      simError();
537 +      rCut = maxCutoff;
538 +    }
539 +    
540 +    if( ecr > maxCutoff){
541 +      sprintf( painCave.errMsg,
542 +               "New Box size is setting the electrostaticCutoffRadius "
543 +               "to %lf at time %lf\n",
544 +               maxCutoff, currentTime  );
545 +      painCave.isFatal = 0;
546 +      simError();      
547 +      ecr = maxCutoff;
548 +    }
549 +
550 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
551 +    
552 +    // rlist is the 1.0 plus max( rcut, ecr )
553 +    
554 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
555 +    
556 +    if( cutChanged ){
557 +      
558 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
559 +    }
560 +    
561 +    oldEcr = ecr;
562 +    oldRcut = rCut;
563 +    
564 +  } else {
565 +    // initialize this stuff before using it, OK?
566 +    sprintf( painCave.errMsg,
567 +             "Trying to check cutoffs without a box. Be smarter.\n" );
568 +    painCave.isFatal = 1;
569 +    simError();      
570 +  }
571 +  
572 + }
573 +
574 + void SimInfo::addProperty(GenericData* prop){
575 +
576 +  map<string, GenericData*>::iterator result;
577 +  result = properties.find(prop->getID());
578 +  
579 +  //we can't simply use  properties[prop->getID()] = prop,
580 +  //it will cause memory leak if we already contain a propery which has the same name of prop
581 +  
582 +  if(result != properties.end()){
583 +    
584 +    delete (*result).second;
585 +    (*result).second = prop;
586 +      
587 +  }
588 +  else{
589 +
590 +    properties[prop->getID()] = prop;
591 +
592 +  }
593 +    
594 + }
595 +
596 + GenericData* SimInfo::getProperty(const string& propName){
597 +
598 +  map<string, GenericData*>::iterator result;
599 +  
600 +  //string lowerCaseName = ();
601 +  
602 +  result = properties.find(propName);
603 +  
604 +  if(result != properties.end())
605 +    return (*result).second;  
606 +  else  
607 +    return NULL;  
608 + }
609 +
610 + vector<GenericData*> SimInfo::getProperties(){
611 +
612 +  vector<GenericData*> result;
613 +  map<string, GenericData*>::iterator i;
614 +  
615 +  for(i = properties.begin(); i != properties.end(); i++)
616 +    result.push_back((*i).second);
617 +    
618 +  return result;
619 + }
620 +
621 + double SimInfo::matTrace3(double m[3][3]){
622 +  double trace;
623 +  trace = m[0][0] + m[1][1] + m[2][2];
624 +
625 +  return trace;
626 + }

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