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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 439 by chuckv, Mon Mar 31 22:09:39 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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 + #ifdef IS_MPI
18 + #include "mpiSimulation.hpp"
19 + #endif
20 +
21 + inline double roundMe( double x ){
22 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
23 + }
24 +          
25 + inline double min( double a, double b ){
26 +  return (a < b ) ? a : b;
27 + }
28 +
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34 +  nZconstraints = 0;
35    n_oriented = 0;
36    n_dipoles = 0;
37 +  ndf = 0;
38 +  ndfRaw = 0;
39 +  nZconstraints = 0;
40    the_integrator = NULL;
41    setTemp = 0;
42    thermalTime = 0.0;
43 +  currentTime = 0.0;
44    rCut = 0.0;
45 +  ecr = 0.0;
46 +  est = 0.0;
47  
48 +  haveRcut = 0;
49 +  haveEcr = 0;
50 +  boxIsInit = 0;
51 +  
52 +  resetTime = 1e99;
53 +
54 +  orthoRhombic = 0;
55 +  orthoTolerance = 1E-6;
56 +  useInitXSstate = true;
57 +
58    usePBC = 0;
59    useLJ = 0;
60    useSticky = 0;
61 <  useDipole = 0;
61 >  useCharges = 0;
62 >  useDipoles = 0;
63    useReactionField = 0;
64    useGB = 0;
65    useEAM = 0;
66  
67 +  excludes = Exclude::Instance();
68  
69 +  myConfiguration = new SimState();
70  
71 +  has_minimizer = false;
72 +  the_minimizer =NULL;
73 +
74    wrapMeSimInfo( this );
75   }
76  
77 +
78 + SimInfo::~SimInfo(){
79 +
80 +  delete myConfiguration;
81 +
82 +  map<string, GenericData*>::iterator i;
83 +  
84 +  for(i = properties.begin(); i != properties.end(); i++)
85 +    delete (*i).second;
86 +    
87 + }
88 +
89 + void SimInfo::setBox(double newBox[3]) {
90 +  
91 +  int i, j;
92 +  double tempMat[3][3];
93 +
94 +  for(i=0; i<3; i++)
95 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
96 +
97 +  tempMat[0][0] = newBox[0];
98 +  tempMat[1][1] = newBox[1];
99 +  tempMat[2][2] = newBox[2];
100 +
101 +  setBoxM( tempMat );
102 +
103 + }
104 +
105 + void SimInfo::setBoxM( double theBox[3][3] ){
106 +  
107 +  int i, j;
108 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
109 +                         // ordering in the array is as follows:
110 +                         // [ 0 3 6 ]
111 +                         // [ 1 4 7 ]
112 +                         // [ 2 5 8 ]
113 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
114 +
115 +  if( !boxIsInit ) boxIsInit = 1;
116 +
117 +  for(i=0; i < 3; i++)
118 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
119 +  
120 +  calcBoxL();
121 +  calcHmatInv();
122 +
123 +  for(i=0; i < 3; i++) {
124 +    for (j=0; j < 3; j++) {
125 +      FortranHmat[3*j + i] = Hmat[i][j];
126 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
127 +    }
128 +  }
129 +
130 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
131 +
132 + }
133 +
134 +
135 + void SimInfo::getBoxM (double theBox[3][3]) {
136 +
137 +  int i, j;
138 +  for(i=0; i<3; i++)
139 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
140 + }
141 +
142 +
143 + void SimInfo::scaleBox(double scale) {
144 +  double theBox[3][3];
145 +  int i, j;
146 +
147 +  // cerr << "Scaling box by " << scale << "\n";
148 +
149 +  for(i=0; i<3; i++)
150 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
151 +
152 +  setBoxM(theBox);
153 +
154 + }
155 +
156 + void SimInfo::calcHmatInv( void ) {
157 +  
158 +  int oldOrtho;
159 +  int i,j;
160 +  double smallDiag;
161 +  double tol;
162 +  double sanity[3][3];
163 +
164 +  invertMat3( Hmat, HmatInv );
165 +
166 +  // check to see if Hmat is orthorhombic
167 +  
168 +  oldOrtho = orthoRhombic;
169 +
170 +  smallDiag = fabs(Hmat[0][0]);
171 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
172 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
173 +  tol = smallDiag * orthoTolerance;
174 +
175 +  orthoRhombic = 1;
176 +  
177 +  for (i = 0; i < 3; i++ ) {
178 +    for (j = 0 ; j < 3; j++) {
179 +      if (i != j) {
180 +        if (orthoRhombic) {
181 +          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
182 +        }        
183 +      }
184 +    }
185 +  }
186 +
187 +  if( oldOrtho != orthoRhombic ){
188 +    
189 +    if( orthoRhombic ){
190 +      sprintf( painCave.errMsg,
191 +               "OOPSE is switching from the default Non-Orthorhombic\n"
192 +               "\tto the faster Orthorhombic periodic boundary computations.\n"
193 +               "\tThis is usually a good thing, but if you wan't the\n"
194 +               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
195 +               "\tvariable ( currently set to %G ) smaller.\n",
196 +               orthoTolerance);
197 +      simError();
198 +    }
199 +    else {
200 +      sprintf( painCave.errMsg,
201 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
202 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
203 +               "\tThis is usually because the box has deformed under\n"
204 +               "\tNPTf integration. If you wan't to live on the edge with\n"
205 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
206 +               "\tvariable ( currently set to %G ) larger.\n",
207 +               orthoTolerance);
208 +      simError();
209 +    }
210 +  }
211 + }
212 +
213 + void SimInfo::calcBoxL( void ){
214 +
215 +  double dx, dy, dz, dsq;
216 +
217 +  // boxVol = Determinant of Hmat
218 +
219 +  boxVol = matDet3( Hmat );
220 +
221 +  // boxLx
222 +  
223 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
224 +  dsq = dx*dx + dy*dy + dz*dz;
225 +  boxL[0] = sqrt( dsq );
226 +  //maxCutoff = 0.5 * boxL[0];
227 +
228 +  // boxLy
229 +  
230 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
231 +  dsq = dx*dx + dy*dy + dz*dz;
232 +  boxL[1] = sqrt( dsq );
233 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
234 +
235 +
236 +  // boxLz
237 +  
238 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
239 +  dsq = dx*dx + dy*dy + dz*dz;
240 +  boxL[2] = sqrt( dsq );
241 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
242 +
243 +  //calculate the max cutoff
244 +  maxCutoff =  calcMaxCutOff();
245 +  
246 +  checkCutOffs();
247 +
248 + }
249 +
250 +
251 + double SimInfo::calcMaxCutOff(){
252 +
253 +  double ri[3], rj[3], rk[3];
254 +  double rij[3], rjk[3], rki[3];
255 +  double minDist;
256 +
257 +  ri[0] = Hmat[0][0];
258 +  ri[1] = Hmat[1][0];
259 +  ri[2] = Hmat[2][0];
260 +
261 +  rj[0] = Hmat[0][1];
262 +  rj[1] = Hmat[1][1];
263 +  rj[2] = Hmat[2][1];
264 +
265 +  rk[0] = Hmat[0][2];
266 +  rk[1] = Hmat[1][2];
267 +  rk[2] = Hmat[2][2];
268 +    
269 +  crossProduct3(ri, rj, rij);
270 +  distXY = dotProduct3(rk,rij) / norm3(rij);
271 +
272 +  crossProduct3(rj,rk, rjk);
273 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
274 +
275 +  crossProduct3(rk,ri, rki);
276 +  distZX = dotProduct3(rj,rki) / norm3(rki);
277 +
278 +  minDist = min(min(distXY, distYZ), distZX);
279 +  return minDist/2;
280 +  
281 + }
282 +
283 + void SimInfo::wrapVector( double thePos[3] ){
284 +
285 +  int i;
286 +  double scaled[3];
287 +
288 +  if( !orthoRhombic ){
289 +    // calc the scaled coordinates.
290 +  
291 +
292 +    matVecMul3(HmatInv, thePos, scaled);
293 +    
294 +    for(i=0; i<3; i++)
295 +      scaled[i] -= roundMe(scaled[i]);
296 +    
297 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
298 +    
299 +    matVecMul3(Hmat, scaled, thePos);
300 +
301 +  }
302 +  else{
303 +    // calc the scaled coordinates.
304 +    
305 +    for(i=0; i<3; i++)
306 +      scaled[i] = thePos[i]*HmatInv[i][i];
307 +    
308 +    // wrap the scaled coordinates
309 +    
310 +    for(i=0; i<3; i++)
311 +      scaled[i] -= roundMe(scaled[i]);
312 +    
313 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
314 +    
315 +    for(i=0; i<3; i++)
316 +      thePos[i] = scaled[i]*Hmat[i][i];
317 +  }
318 +    
319 + }
320 +
321 +
322 + int SimInfo::getNDF(){
323 +  int ndf_local;
324 +
325 +  for(int i = 0; i < integrableObjects.size(); i++){
326 +    ndf_local += 3;
327 +    if (integrableObjects[i]->isDirectional())
328 +      ndf_local += 3;
329 +  }
330 +
331 +  // n_constraints is local, so subtract them on each processor:
332 +
333 +  ndf_local -= n_constraints;
334 +
335 + #ifdef IS_MPI
336 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
337 + #else
338 +  ndf = ndf_local;
339 + #endif
340 +
341 +  // nZconstraints is global, as are the 3 COM translations for the
342 +  // entire system:
343 +
344 +  ndf = ndf - 3 - nZconstraints;
345 +
346 +  return ndf;
347 + }
348 +
349 + int SimInfo::getNDFraw() {
350 +  int ndfRaw_local;
351 +
352 +  // Raw degrees of freedom that we have to set
353 +
354 +  for(int i = 0; i < integrableObjects.size(); i++){
355 +    ndfRaw_local += 3;
356 +    if (integrableObjects[i]->isDirectional())
357 +      ndfRaw_local += 3;
358 +  }
359 +    
360 + #ifdef IS_MPI
361 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
362 + #else
363 +  ndfRaw = ndfRaw_local;
364 + #endif
365 +
366 +  return ndfRaw;
367 + }
368 +
369 + int SimInfo::getNDFtranslational() {
370 +  int ndfTrans_local;
371 +
372 +  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
373 +
374 +
375 + #ifdef IS_MPI
376 +  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
377 + #else
378 +  ndfTrans = ndfTrans_local;
379 + #endif
380 +
381 +  ndfTrans = ndfTrans - 3 - nZconstraints;
382 +
383 +  return ndfTrans;
384 + }
385 +
386   void SimInfo::refreshSim(){
387  
388    simtype fInfo;
389    int isError;
390 +  int n_global;
391    int* excl;
392  
393 <  fInfo.box[0] = box_x;
44 <  fInfo.box[1] = box_y;
45 <  fInfo.box[2] = box_z;
393 >  fInfo.dielect = 0.0;
394  
395 <  fInfo.rlist = rList;
396 <  fInfo.rcut = rCut;
397 <  fInfo.rrf = ecr;
50 <  fInfo.rt = ecr - est;
51 <  fInfo.dielect = dielectric;
395 >  if( useDipoles ){
396 >    if( useReactionField )fInfo.dielect = dielectric;
397 >  }
398  
399    fInfo.SIM_uses_PBC = usePBC;
400 +  //fInfo.SIM_uses_LJ = 0;
401    fInfo.SIM_uses_LJ = useLJ;
402 <
403 <  //fInfo.SIM_uses_sticky = useSticky;
404 <  fInfo.SIM_uses_sticky = 0;
405 <  fInfo.SIM_uses_dipoles = useDipole;
402 >  fInfo.SIM_uses_sticky = useSticky;
403 >  //fInfo.SIM_uses_sticky = 0;
404 >  fInfo.SIM_uses_charges = useCharges;
405 >  fInfo.SIM_uses_dipoles = useDipoles;
406    //fInfo.SIM_uses_dipoles = 0;
407    fInfo.SIM_uses_RF = useReactionField;
408 +  //fInfo.SIM_uses_RF = 0;
409    fInfo.SIM_uses_GB = useGB;
410    fInfo.SIM_uses_EAM = useEAM;
411  
412 <  excl = Exclude::getArray();
412 >  n_exclude = excludes->getSize();
413 >  excl = excludes->getFortranArray();
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;
71 <  n_exclude;
72 <  excludes;
73 <  nGlobalExcludes;
74 <  globalExcludes;
75 <  isError;
423 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
424 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
425 >                  &isError );
426  
77 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
78 –                  &nGlobalExcludes, globalExcludes, &isError );
79 –
427    if( isError ){
428  
429      sprintf( painCave.errMsg,
# Line 90 | Line 437 | void SimInfo::refreshSim(){
437             "succesfully sent the simulation information to fortran.\n");
438    MPIcheckPoint();
439   #endif // is_mpi
440 +
441 +  this->ndf = this->getNDF();
442 +  this->ndfRaw = this->getNDFraw();
443 +  this->ndfTrans = this->getNDFtranslational();
444   }
445  
446 + void SimInfo::setDefaultRcut( double theRcut ){
447 +
448 +  haveRcut = 1;
449 +  rCut = theRcut;
450 +
451 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
452 +
453 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
454 + }
455 +
456 + void SimInfo::setDefaultEcr( double theEcr ){
457 +
458 +  haveEcr = 1;
459 +  ecr = theEcr;
460 +  
461 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
462 +
463 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
464 + }
465 +
466 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
467 +
468 +  est = theEst;
469 +  setDefaultEcr( theEcr );
470 + }
471 +
472 +
473 + void SimInfo::checkCutOffs( void ){
474 +  
475 +  if( boxIsInit ){
476 +    
477 +    //we need to check cutOffs against the box
478 +    
479 +    if( rCut > maxCutoff ){
480 +      sprintf( painCave.errMsg,
481 +               "LJrcut is too large for the current periodic box.\n"
482 +               "\tCurrent Value of LJrcut = %G at time %G\n "
483 +               "\tThis is larger than half of at least one of the\n"
484 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
485 +               "\n, %G"
486 +               "\t[ %G %G %G ]\n"
487 +               "\t[ %G %G %G ]\n"
488 +               "\t[ %G %G %G ]\n",
489 +               rCut, currentTime, maxCutoff,
490 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
491 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
492 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
493 +      painCave.isFatal = 1;
494 +      simError();
495 +    }
496 +    
497 +    if( haveEcr ){
498 +      if( ecr > maxCutoff ){
499 +        sprintf( painCave.errMsg,
500 +                 "electrostaticCutoffRadius is too large for the current\n"
501 +                 "\tperiodic box.\n\n"
502 +                 "\tCurrent Value of ECR = %G at time %G\n "
503 +                 "\tThis is larger than half of at least one of the\n"
504 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
505 +                 "\n"
506 +                 "\t[ %G %G %G ]\n"
507 +                 "\t[ %G %G %G ]\n"
508 +                 "\t[ %G %G %G ]\n",
509 +                 ecr, currentTime,
510 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
511 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
512 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
513 +        painCave.isFatal = 1;
514 +        simError();
515 +      }
516 +    }
517 +  } else {
518 +    // initialize this stuff before using it, OK?
519 +    sprintf( painCave.errMsg,
520 +             "Trying to check cutoffs without a box.\n"
521 +             "\tOOPSE should have better programmers than that.\n" );
522 +    painCave.isFatal = 1;
523 +    simError();      
524 +  }
525 +  
526 + }
527 +
528 + void SimInfo::addProperty(GenericData* prop){
529 +
530 +  map<string, GenericData*>::iterator result;
531 +  result = properties.find(prop->getID());
532 +  
533 +  //we can't simply use  properties[prop->getID()] = prop,
534 +  //it will cause memory leak if we already contain a propery which has the same name of prop
535 +  
536 +  if(result != properties.end()){
537 +    
538 +    delete (*result).second;
539 +    (*result).second = prop;
540 +      
541 +  }
542 +  else{
543 +
544 +    properties[prop->getID()] = prop;
545 +
546 +  }
547 +    
548 + }
549 +
550 + GenericData* SimInfo::getProperty(const string& propName){
551 +
552 +  map<string, GenericData*>::iterator result;
553 +  
554 +  //string lowerCaseName = ();
555 +  
556 +  result = properties.find(propName);
557 +  
558 +  if(result != properties.end())
559 +    return (*result).second;  
560 +  else  
561 +    return NULL;  
562 + }
563 +
564 + vector<GenericData*> SimInfo::getProperties(){
565 +
566 +  vector<GenericData*> result;
567 +  map<string, GenericData*>::iterator i;
568 +  
569 +  for(i = properties.begin(); i != properties.end(); i++)
570 +    result.push_back((*i).second);
571 +    
572 +  return result;
573 + }

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