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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 458 by gezelter, Fri Apr 4 19:47:19 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
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 + #include "MatVec3.h"
16 +
17 + #include "ConstraintManager.hpp"
18 +
19 + #ifdef IS_MPI
20 + #include "mpiSimulation.hpp"
21 + #endif
22 +
23 + inline double roundMe( double x ){
24 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
25 + }
26 +          
27 + inline double min( double a, double b ){
28 +  return (a < b ) ? a : b;
29 + }
30 +
31   SimInfo* currentInfo;
32  
33   SimInfo::SimInfo(){
34 <  excludes = NULL;
34 >
35    n_constraints = 0;
36 +  nZconstraints = 0;
37    n_oriented = 0;
38    n_dipoles = 0;
39    ndf = 0;
40    ndfRaw = 0;
41 +  nZconstraints = 0;
42    the_integrator = NULL;
43    setTemp = 0;
44    thermalTime = 0.0;
45 +  currentTime = 0.0;
46    rCut = 0.0;
47 +  rSw = 0.0;
48  
49 +  haveRcut = 0;
50 +  haveRsw = 0;
51 +  boxIsInit = 0;
52 +  
53 +  resetTime = 1e99;
54 +
55 +  orthoRhombic = 0;
56 +  orthoTolerance = 1E-6;
57 +  useInitXSstate = true;
58 +
59    usePBC = 0;
60    useLJ = 0;
61    useSticky = 0;
62 <  useDipole = 0;
62 >  useCharges = 0;
63 >  useDipoles = 0;
64    useReactionField = 0;
65    useGB = 0;
66    useEAM = 0;
67 +  useSolidThermInt = 0;
68 +  useLiquidThermInt = 0;
69  
70 +  haveCutoffGroups = false;
71 +
72 +  excludes = Exclude::Instance();
73 +
74 +  myConfiguration = new SimState();
75 +
76 +  has_minimizer = false;
77 +  the_minimizer =NULL;
78 +
79 +  ngroup = 0;
80 +
81 +  consMan = NULL;
82 +  
83    wrapMeSimInfo( this );
84   }
85  
86 +
87 + SimInfo::~SimInfo(){
88 +
89 +  delete myConfiguration;
90 +
91 +  map<string, GenericData*>::iterator i;
92 +  
93 +  for(i = properties.begin(); i != properties.end(); i++)
94 +    delete (*i).second;
95 +
96 +  if (!consMan)
97 +    delete consMan;  
98 + }
99 +
100   void SimInfo::setBox(double newBox[3]) {
101 <  box_x = newBox[0];
102 <  box_y = newBox[1];
103 <  box_z = newBox[2];
104 <  setFortranBoxSize(newBox);
101 >  
102 >  int i, j;
103 >  double tempMat[3][3];
104 >
105 >  for(i=0; i<3; i++)
106 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
107 >
108 >  tempMat[0][0] = newBox[0];
109 >  tempMat[1][1] = newBox[1];
110 >  tempMat[2][2] = newBox[2];
111 >
112 >  setBoxM( tempMat );
113 >
114   }
115  
116 < void SimInfo::getBox(double theBox[3]) {
117 <  theBox[0] = box_x;
118 <  theBox[1] = box_y;
119 <  theBox[2] = box_z;
116 > void SimInfo::setBoxM( double theBox[3][3] ){
117 >  
118 >  int i, j;
119 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
120 >                         // ordering in the array is as follows:
121 >                         // [ 0 3 6 ]
122 >                         // [ 1 4 7 ]
123 >                         // [ 2 5 8 ]
124 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
125 >
126 >  if( !boxIsInit ) boxIsInit = 1;
127 >
128 >  for(i=0; i < 3; i++)
129 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
130 >  
131 >  calcBoxL();
132 >  calcHmatInv();
133 >
134 >  for(i=0; i < 3; i++) {
135 >    for (j=0; j < 3; j++) {
136 >      FortranHmat[3*j + i] = Hmat[i][j];
137 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
138 >    }
139 >  }
140 >
141 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
142 >
143   }
144  
145 < int SimInfo::getNDF(){
146 <  int ndf_local, ndf;
145 >
146 > void SimInfo::getBoxM (double theBox[3][3]) {
147 >
148 >  int i, j;
149 >  for(i=0; i<3; i++)
150 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
151 > }
152 >
153 >
154 > void SimInfo::scaleBox(double scale) {
155 >  double theBox[3][3];
156 >  int i, j;
157 >
158 >  // cerr << "Scaling box by " << scale << "\n";
159 >
160 >  for(i=0; i<3; i++)
161 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
162 >
163 >  setBoxM(theBox);
164 >
165 > }
166 >
167 > void SimInfo::calcHmatInv( void ) {
168    
169 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
169 >  int oldOrtho;
170 >  int i,j;
171 >  double smallDiag;
172 >  double tol;
173 >  double sanity[3][3];
174  
175 +  invertMat3( Hmat, HmatInv );
176 +
177 +  // check to see if Hmat is orthorhombic
178 +  
179 +  oldOrtho = orthoRhombic;
180 +
181 +  smallDiag = fabs(Hmat[0][0]);
182 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
183 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
184 +  tol = smallDiag * orthoTolerance;
185 +
186 +  orthoRhombic = 1;
187 +  
188 +  for (i = 0; i < 3; i++ ) {
189 +    for (j = 0 ; j < 3; j++) {
190 +      if (i != j) {
191 +        if (orthoRhombic) {
192 +          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
193 +        }        
194 +      }
195 +    }
196 +  }
197 +
198 +  if( oldOrtho != orthoRhombic ){
199 +    
200 +    if( orthoRhombic ) {
201 +      sprintf( painCave.errMsg,
202 +               "OOPSE is switching from the default Non-Orthorhombic\n"
203 +               "\tto the faster Orthorhombic periodic boundary computations.\n"
204 +               "\tThis is usually a good thing, but if you wan't the\n"
205 +               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
206 +               "\tvariable ( currently set to %G ) smaller.\n",
207 +               orthoTolerance);
208 +      painCave.severity = OOPSE_INFO;
209 +      simError();
210 +    }
211 +    else {
212 +      sprintf( painCave.errMsg,
213 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
214 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
215 +               "\tThis is usually because the box has deformed under\n"
216 +               "\tNPTf integration. If you wan't to live on the edge with\n"
217 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
218 +               "\tvariable ( currently set to %G ) larger.\n",
219 +               orthoTolerance);
220 +      painCave.severity = OOPSE_WARNING;
221 +      simError();
222 +    }
223 +  }
224 + }
225 +
226 + void SimInfo::calcBoxL( void ){
227 +
228 +  double dx, dy, dz, dsq;
229 +
230 +  // boxVol = Determinant of Hmat
231 +
232 +  boxVol = matDet3( Hmat );
233 +
234 +  // boxLx
235 +  
236 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
237 +  dsq = dx*dx + dy*dy + dz*dz;
238 +  boxL[0] = sqrt( dsq );
239 +  //maxCutoff = 0.5 * boxL[0];
240 +
241 +  // boxLy
242 +  
243 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
244 +  dsq = dx*dx + dy*dy + dz*dz;
245 +  boxL[1] = sqrt( dsq );
246 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
247 +
248 +
249 +  // boxLz
250 +  
251 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
252 +  dsq = dx*dx + dy*dy + dz*dz;
253 +  boxL[2] = sqrt( dsq );
254 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
255 +
256 +  //calculate the max cutoff
257 +  maxCutoff =  calcMaxCutOff();
258 +  
259 +  checkCutOffs();
260 +
261 + }
262 +
263 +
264 + double SimInfo::calcMaxCutOff(){
265 +
266 +  double ri[3], rj[3], rk[3];
267 +  double rij[3], rjk[3], rki[3];
268 +  double minDist;
269 +
270 +  ri[0] = Hmat[0][0];
271 +  ri[1] = Hmat[1][0];
272 +  ri[2] = Hmat[2][0];
273 +
274 +  rj[0] = Hmat[0][1];
275 +  rj[1] = Hmat[1][1];
276 +  rj[2] = Hmat[2][1];
277 +
278 +  rk[0] = Hmat[0][2];
279 +  rk[1] = Hmat[1][2];
280 +  rk[2] = Hmat[2][2];
281 +    
282 +  crossProduct3(ri, rj, rij);
283 +  distXY = dotProduct3(rk,rij) / norm3(rij);
284 +
285 +  crossProduct3(rj,rk, rjk);
286 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
287 +
288 +  crossProduct3(rk,ri, rki);
289 +  distZX = dotProduct3(rj,rki) / norm3(rki);
290 +
291 +  minDist = min(min(distXY, distYZ), distZX);
292 +  return minDist/2;
293 +  
294 + }
295 +
296 + void SimInfo::wrapVector( double thePos[3] ){
297 +
298 +  int i;
299 +  double scaled[3];
300 +
301 +  if( !orthoRhombic ){
302 +    // calc the scaled coordinates.
303 +  
304 +
305 +    matVecMul3(HmatInv, thePos, scaled);
306 +    
307 +    for(i=0; i<3; i++)
308 +      scaled[i] -= roundMe(scaled[i]);
309 +    
310 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
311 +    
312 +    matVecMul3(Hmat, scaled, thePos);
313 +
314 +  }
315 +  else{
316 +    // calc the scaled coordinates.
317 +    
318 +    for(i=0; i<3; i++)
319 +      scaled[i] = thePos[i]*HmatInv[i][i];
320 +    
321 +    // wrap the scaled coordinates
322 +    
323 +    for(i=0; i<3; i++)
324 +      scaled[i] -= roundMe(scaled[i]);
325 +    
326 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
327 +    
328 +    for(i=0; i<3; i++)
329 +      thePos[i] = scaled[i]*Hmat[i][i];
330 +  }
331 +    
332 + }
333 +
334 +
335 + int SimInfo::getNDF(){
336 +  int ndf_local;
337 +
338 +  ndf_local = 0;
339 +  
340 +  for(int i = 0; i < integrableObjects.size(); i++){
341 +    ndf_local += 3;
342 +    if (integrableObjects[i]->isDirectional()) {
343 +      if (integrableObjects[i]->isLinear())
344 +        ndf_local += 2;
345 +      else
346 +        ndf_local += 3;
347 +    }
348 +  }
349 +
350 +  // n_constraints is local, so subtract them on each processor:
351 +
352 +  ndf_local -= n_constraints;
353 +
354   #ifdef IS_MPI
355    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356   #else
357    ndf = ndf_local;
358   #endif
359  
360 <  ndf = ndf - 3;
360 >  // nZconstraints is global, as are the 3 COM translations for the
361 >  // entire system:
362  
363 +  ndf = ndf - 3 - nZconstraints;
364 +
365    return ndf;
366   }
367  
368   int SimInfo::getNDFraw() {
369 <  int ndfRaw_local, ndfRaw;
369 >  int ndfRaw_local;
370  
371    // Raw degrees of freedom that we have to set
372 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
373 <  
372 >  ndfRaw_local = 0;
373 >
374 >  for(int i = 0; i < integrableObjects.size(); i++){
375 >    ndfRaw_local += 3;
376 >    if (integrableObjects[i]->isDirectional()) {
377 >       if (integrableObjects[i]->isLinear())
378 >        ndfRaw_local += 2;
379 >      else
380 >        ndfRaw_local += 3;
381 >    }
382 >  }
383 >    
384   #ifdef IS_MPI
385    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
386   #else
# Line 77 | Line 389 | int SimInfo::getNDFraw() {
389  
390    return ndfRaw;
391   }
392 <
392 >
393 > int SimInfo::getNDFtranslational() {
394 >  int ndfTrans_local;
395 >
396 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
397 >
398 >
399 > #ifdef IS_MPI
400 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
401 > #else
402 >  ndfTrans = ndfTrans_local;
403 > #endif
404 >
405 >  ndfTrans = ndfTrans - 3 - nZconstraints;
406 >
407 >  return ndfTrans;
408 > }
409 >
410 > int SimInfo::getTotIntegrableObjects() {
411 >  int nObjs_local;
412 >  int nObjs;
413 >
414 >  nObjs_local =  integrableObjects.size();
415 >
416 >
417 > #ifdef IS_MPI
418 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
419 > #else
420 >  nObjs = nObjs_local;
421 > #endif
422 >
423 >
424 >  return nObjs;
425 > }
426 >
427   void SimInfo::refreshSim(){
428  
429    simtype fInfo;
430    int isError;
431 +  int n_global;
432    int* excl;
433  
434 <  fInfo.box[0] = box_x;
88 <  fInfo.box[1] = box_y;
89 <  fInfo.box[2] = box_z;
434 >  fInfo.dielect = 0.0;
435  
436 <  fInfo.rlist = rList;
437 <  fInfo.rcut = rCut;
438 <  fInfo.rrf = ecr;
94 <  fInfo.rt = ecr - est;
95 <  fInfo.dielect = dielectric;
436 >  if( useDipoles ){
437 >    if( useReactionField )fInfo.dielect = dielectric;
438 >  }
439  
440    fInfo.SIM_uses_PBC = usePBC;
441    //fInfo.SIM_uses_LJ = 0;
442    fInfo.SIM_uses_LJ = useLJ;
443    fInfo.SIM_uses_sticky = useSticky;
444    //fInfo.SIM_uses_sticky = 0;
445 <  fInfo.SIM_uses_dipoles = useDipole;
445 >  fInfo.SIM_uses_charges = useCharges;
446 >  fInfo.SIM_uses_dipoles = useDipoles;
447    //fInfo.SIM_uses_dipoles = 0;
448 <  //fInfo.SIM_uses_RF = useReactionField;
449 <  fInfo.SIM_uses_RF = 0;
448 >  fInfo.SIM_uses_RF = useReactionField;
449 >  //fInfo.SIM_uses_RF = 0;
450    fInfo.SIM_uses_GB = useGB;
451    fInfo.SIM_uses_EAM = useEAM;
452  
453 <  excl = Exclude::getArray();
454 <
453 >  n_exclude = excludes->getSize();
454 >  excl = excludes->getFortranArray();
455 >  
456 > #ifdef IS_MPI
457 >  n_global = mpiSim->getNAtomsGlobal();
458 > #else
459 >  n_global = n_atoms;
460 > #endif
461 >  
462    isError = 0;
463 +  
464 +  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
465 +  //it may not be a good idea to pass the address of first element in vector
466 +  //since c++ standard does not require vector to be stored continuously in meomory
467 +  //Most of the compilers will organize the memory of vector continuously
468 +  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
469 +                  &nGlobalExcludes, globalExcludes, molMembershipArray,
470 +                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
471  
113 – //   fInfo;
114 – //   n_atoms;
115 – //   identArray;
116 – //   n_exclude;
117 – //   excludes;
118 – //   nGlobalExcludes;
119 – //   globalExcludes;
120 – //   isError;
121 –
122 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
123 –                  &nGlobalExcludes, globalExcludes, &isError );
124 –
472    if( isError ){
473 <
473 >    
474      sprintf( painCave.errMsg,
475 <             "There was an error setting the simulation information in fortran.\n" );
475 >             "There was an error setting the simulation information in fortran.\n" );
476      painCave.isFatal = 1;
477 +    painCave.severity = OOPSE_ERROR;
478      simError();
479    }
480 <
480 >  
481   #ifdef IS_MPI
482    sprintf( checkPointMsg,
483             "succesfully sent the simulation information to fortran.\n");
484    MPIcheckPoint();
485   #endif // is_mpi
486 +  
487 +  this->ndf = this->getNDF();
488 +  this->ndfRaw = this->getNDFraw();
489 +  this->ndfTrans = this->getNDFtranslational();
490 + }
491  
492 <  ndf = this->getNDF();
493 <  ndfRaw = this->getNDFraw();
492 > void SimInfo::setDefaultRcut( double theRcut ){
493 >  
494 >  haveRcut = 1;
495 >  rCut = theRcut;
496 >  rList = rCut + 1.0;
497 >  
498 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
499 > }
500  
501 + void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
502 +
503 +  rSw = theRsw;
504 +  setDefaultRcut( theRcut );
505   }
506  
507 +
508 + void SimInfo::checkCutOffs( void ){
509 +  
510 +  if( boxIsInit ){
511 +    
512 +    //we need to check cutOffs against the box
513 +    
514 +    if( rCut > maxCutoff ){
515 +      sprintf( painCave.errMsg,
516 +               "cutoffRadius is too large for the current periodic box.\n"
517 +               "\tCurrent Value of cutoffRadius = %G at time %G\n "
518 +               "\tThis is larger than half of at least one of the\n"
519 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
520 +               "\n"
521 +               "\t[ %G %G %G ]\n"
522 +               "\t[ %G %G %G ]\n"
523 +               "\t[ %G %G %G ]\n",
524 +               rCut, currentTime,
525 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
526 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
527 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
528 +      painCave.severity = OOPSE_ERROR;
529 +      painCave.isFatal = 1;
530 +      simError();
531 +    }    
532 +  } else {
533 +    // initialize this stuff before using it, OK?
534 +    sprintf( painCave.errMsg,
535 +             "Trying to check cutoffs without a box.\n"
536 +             "\tOOPSE should have better programmers than that.\n" );
537 +    painCave.severity = OOPSE_ERROR;
538 +    painCave.isFatal = 1;
539 +    simError();      
540 +  }
541 +  
542 + }
543 +
544 + void SimInfo::addProperty(GenericData* prop){
545 +
546 +  map<string, GenericData*>::iterator result;
547 +  result = properties.find(prop->getID());
548 +  
549 +  //we can't simply use  properties[prop->getID()] = prop,
550 +  //it will cause memory leak if we already contain a propery which has the same name of prop
551 +  
552 +  if(result != properties.end()){
553 +    
554 +    delete (*result).second;
555 +    (*result).second = prop;
556 +      
557 +  }
558 +  else{
559 +
560 +    properties[prop->getID()] = prop;
561 +
562 +  }
563 +    
564 + }
565 +
566 + GenericData* SimInfo::getProperty(const string& propName){
567 +
568 +  map<string, GenericData*>::iterator result;
569 +  
570 +  //string lowerCaseName = ();
571 +  
572 +  result = properties.find(propName);
573 +  
574 +  if(result != properties.end())
575 +    return (*result).second;  
576 +  else  
577 +    return NULL;  
578 + }
579 +
580 +
581 + void SimInfo::getFortranGroupArrays(SimInfo* info,
582 +                                    vector<int>& FglobalGroupMembership,
583 +                                    vector<double>& mfact){
584 +  
585 +  Molecule* myMols;
586 +  Atom** myAtoms;
587 +  int numAtom;
588 +  double mtot;
589 +  int numMol;
590 +  int numCutoffGroups;
591 +  CutoffGroup* myCutoffGroup;
592 +  vector<CutoffGroup*>::iterator iterCutoff;
593 +  Atom* cutoffAtom;
594 +  vector<Atom*>::iterator iterAtom;
595 +  int atomIndex;
596 +  double totalMass;
597 +  
598 +  mfact.clear();
599 +  FglobalGroupMembership.clear();
600 +  
601 +
602 +  // Fix the silly fortran indexing problem
603 + #ifdef IS_MPI
604 +  numAtom = mpiSim->getNAtomsGlobal();
605 + #else
606 +  numAtom = n_atoms;
607 + #endif
608 +  for (int i = 0; i < numAtom; i++)
609 +    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
610 +  
611 +
612 +  myMols = info->molecules;
613 +  numMol = info->n_mol;
614 +  for(int i  = 0; i < numMol; i++){
615 +    numCutoffGroups = myMols[i].getNCutoffGroups();
616 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
617 +        myCutoffGroup != NULL;
618 +        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
619 +
620 +      totalMass = myCutoffGroup->getMass();
621 +      
622 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
623 +          cutoffAtom != NULL;
624 +          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
625 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
626 +      }  
627 +    }
628 +  }
629 +
630 + }

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