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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 1139 by gezelter, Wed Apr 28 22:06:29 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 +  useMolecularCutoffs = 0;
67  
68 +  excludes = Exclude::Instance();
69 +
70 +  myConfiguration = new SimState();
71 +
72 +  has_minimizer = false;
73 +  the_minimizer =NULL;
74 +
75    wrapMeSimInfo( this );
76   }
77  
78 +
79 + SimInfo::~SimInfo(){
80 +
81 +  delete myConfiguration;
82 +
83 +  map<string, GenericData*>::iterator i;
84 +  
85 +  for(i = properties.begin(); i != properties.end(); i++)
86 +    delete (*i).second;
87 +    
88 + }
89 +
90   void SimInfo::setBox(double newBox[3]) {
91 <  double smallestBox, maxCutoff;
92 <  int status;
93 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
91 >  
92 >  int i, j;
93 >  double tempMat[3][3];
94  
95 <  smallestBox = box_x;
96 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
95 >  for(i=0; i<3; i++)
96 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
97  
98 <  maxCutoff = smallestBox / 2.0;
98 >  tempMat[0][0] = newBox[0];
99 >  tempMat[1][1] = newBox[1];
100 >  tempMat[2][2] = newBox[2];
101  
102 <  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();
102 >  setBoxM( tempMat );
103  
104 <    rList = maxCutoff;
104 > }
105  
106 <    sprintf( painCave.errMsg,
107 <             "New Box size is forcing cutoff radius down to %lf\n",
108 <             maxCutoff - 1.0 );
109 <    painCave.isFatal = 0;
110 <    simError();
106 > void SimInfo::setBoxM( double theBox[3][3] ){
107 >  
108 >  int i, j;
109 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
110 >                         // ordering in the array is as follows:
111 >                         // [ 0 3 6 ]
112 >                         // [ 1 4 7 ]
113 >                         // [ 2 5 8 ]
114 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
115  
116 <    rCut = rList - 1.0;
116 >  if( !boxIsInit ) boxIsInit = 1;
117  
118 <    // list radius changed so we have to refresh the simulation structure.
119 <    refreshSim();
118 >  for(i=0; i < 3; i++)
119 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
120 >  
121 >  calcBoxL();
122 >  calcHmatInv();
123 >
124 >  for(i=0; i < 3; i++) {
125 >    for (j=0; j < 3; j++) {
126 >      FortranHmat[3*j + i] = Hmat[i][j];
127 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
128 >    }
129    }
130  
131 <  if (rCut > maxCutoff) {
132 <    sprintf( painCave.errMsg,
133 <             "New Box size is forcing cutoff radius down to %lf\n",
134 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
131 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
132 >
133 > }
134 >
135  
136 <    status = 0;
137 <    LJ_new_rcut(&rCut, &status);
138 <    if (status != 0) {
136 > void SimInfo::getBoxM (double theBox[3][3]) {
137 >
138 >  int i, j;
139 >  for(i=0; i<3; i++)
140 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
141 > }
142 >
143 >
144 > void SimInfo::scaleBox(double scale) {
145 >  double theBox[3][3];
146 >  int i, j;
147 >
148 >  // cerr << "Scaling box by " << scale << "\n";
149 >
150 >  for(i=0; i<3; i++)
151 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
152 >
153 >  setBoxM(theBox);
154 >
155 > }
156 >
157 > void SimInfo::calcHmatInv( void ) {
158 >  
159 >  int oldOrtho;
160 >  int i,j;
161 >  double smallDiag;
162 >  double tol;
163 >  double sanity[3][3];
164 >
165 >  invertMat3( Hmat, HmatInv );
166 >
167 >  // check to see if Hmat is orthorhombic
168 >  
169 >  oldOrtho = orthoRhombic;
170 >
171 >  smallDiag = fabs(Hmat[0][0]);
172 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
173 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
174 >  tol = smallDiag * orthoTolerance;
175 >
176 >  orthoRhombic = 1;
177 >  
178 >  for (i = 0; i < 3; i++ ) {
179 >    for (j = 0 ; j < 3; j++) {
180 >      if (i != j) {
181 >        if (orthoRhombic) {
182 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
183 >        }        
184 >      }
185 >    }
186 >  }
187 >
188 >  if( oldOrtho != orthoRhombic ){
189 >    
190 >    if( orthoRhombic ){
191        sprintf( painCave.errMsg,
192 <               "Error in recomputing LJ shifts based on new rcut\n");
193 <      painCave.isFatal = 1;
192 >               "OOPSE is switching from the default Non-Orthorhombic\n"
193 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
194 >               "\tThis is usually a good thing, but if you wan't the\n"
195 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
196 >               "\tvariable ( currently set to %G ) smaller.\n",
197 >               orthoTolerance);
198        simError();
199      }
200 +    else {
201 +      sprintf( painCave.errMsg,
202 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
203 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
204 +               "\tThis is usually because the box has deformed under\n"
205 +               "\tNPTf integration. If you wan't to live on the edge with\n"
206 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
207 +               "\tvariable ( currently set to %G ) larger.\n",
208 +               orthoTolerance);
209 +      simError();
210 +    }
211    }
212   }
213  
214 < void SimInfo::getBox(double theBox[3]) {
215 <  theBox[0] = box_x;
216 <  theBox[1] = box_y;
217 <  theBox[2] = box_z;
214 > void SimInfo::calcBoxL( void ){
215 >
216 >  double dx, dy, dz, dsq;
217 >
218 >  // boxVol = Determinant of Hmat
219 >
220 >  boxVol = matDet3( Hmat );
221 >
222 >  // boxLx
223 >  
224 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
225 >  dsq = dx*dx + dy*dy + dz*dz;
226 >  boxL[0] = sqrt( dsq );
227 >  //maxCutoff = 0.5 * boxL[0];
228 >
229 >  // boxLy
230 >  
231 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
232 >  dsq = dx*dx + dy*dy + dz*dz;
233 >  boxL[1] = sqrt( dsq );
234 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
235 >
236 >
237 >  // boxLz
238 >  
239 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
240 >  dsq = dx*dx + dy*dy + dz*dz;
241 >  boxL[2] = sqrt( dsq );
242 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
243 >
244 >  //calculate the max cutoff
245 >  maxCutoff =  calcMaxCutOff();
246 >  
247 >  checkCutOffs();
248 >
249   }
250 <
251 < int SimInfo::getNDF(){
252 <  int ndf_local, ndf;
250 >
251 >
252 > double SimInfo::calcMaxCutOff(){
253 >
254 >  double ri[3], rj[3], rk[3];
255 >  double rij[3], rjk[3], rki[3];
256 >  double minDist;
257 >
258 >  ri[0] = Hmat[0][0];
259 >  ri[1] = Hmat[1][0];
260 >  ri[2] = Hmat[2][0];
261 >
262 >  rj[0] = Hmat[0][1];
263 >  rj[1] = Hmat[1][1];
264 >  rj[2] = Hmat[2][1];
265 >
266 >  rk[0] = Hmat[0][2];
267 >  rk[1] = Hmat[1][2];
268 >  rk[2] = Hmat[2][2];
269 >    
270 >  crossProduct3(ri, rj, rij);
271 >  distXY = dotProduct3(rk,rij) / norm3(rij);
272 >
273 >  crossProduct3(rj,rk, rjk);
274 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
275 >
276 >  crossProduct3(rk,ri, rki);
277 >  distZX = dotProduct3(rj,rki) / norm3(rki);
278 >
279 >  minDist = min(min(distXY, distYZ), distZX);
280 >  return minDist/2;
281    
282 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
282 > }
283  
284 + void SimInfo::wrapVector( double thePos[3] ){
285 +
286 +  int i;
287 +  double scaled[3];
288 +
289 +  if( !orthoRhombic ){
290 +    // calc the scaled coordinates.
291 +  
292 +
293 +    matVecMul3(HmatInv, thePos, scaled);
294 +    
295 +    for(i=0; i<3; i++)
296 +      scaled[i] -= roundMe(scaled[i]);
297 +    
298 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
299 +    
300 +    matVecMul3(Hmat, scaled, thePos);
301 +
302 +  }
303 +  else{
304 +    // calc the scaled coordinates.
305 +    
306 +    for(i=0; i<3; i++)
307 +      scaled[i] = thePos[i]*HmatInv[i][i];
308 +    
309 +    // wrap the scaled coordinates
310 +    
311 +    for(i=0; i<3; i++)
312 +      scaled[i] -= roundMe(scaled[i]);
313 +    
314 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
315 +    
316 +    for(i=0; i<3; i++)
317 +      thePos[i] = scaled[i]*Hmat[i][i];
318 +  }
319 +    
320 + }
321 +
322 +
323 + int SimInfo::getNDF(){
324 +  int ndf_local;
325 +
326 +  ndf_local = 0;
327 +  
328 +  for(int i = 0; i < integrableObjects.size(); i++){
329 +    ndf_local += 3;
330 +    if (integrableObjects[i]->isDirectional()) {
331 +      if (integrableObjects[i]->isLinear())
332 +        ndf_local += 2;
333 +      else
334 +        ndf_local += 3;
335 +    }
336 +  }
337 +
338 +  // n_constraints is local, so subtract them on each processor:
339 +
340 +  ndf_local -= n_constraints;
341 +
342   #ifdef IS_MPI
343    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344   #else
345    ndf = ndf_local;
346   #endif
347  
348 <  ndf = ndf - 3;
348 >  // nZconstraints is global, as are the 3 COM translations for the
349 >  // entire system:
350  
351 +  ndf = ndf - 3 - nZconstraints;
352 +
353    return ndf;
354   }
355  
356   int SimInfo::getNDFraw() {
357 <  int ndfRaw_local, ndfRaw;
357 >  int ndfRaw_local;
358  
359    // Raw degrees of freedom that we have to set
360 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
361 <  
360 >  ndfRaw_local = 0;
361 >
362 >  for(int i = 0; i < integrableObjects.size(); i++){
363 >    ndfRaw_local += 3;
364 >    if (integrableObjects[i]->isDirectional()) {
365 >       if (integrableObjects[i]->isLinear())
366 >        ndfRaw_local += 2;
367 >      else
368 >        ndfRaw_local += 3;
369 >    }
370 >  }
371 >    
372   #ifdef IS_MPI
373    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374   #else
# Line 123 | Line 377 | int SimInfo::getNDFraw() {
377  
378    return ndfRaw;
379   }
380 <
380 >
381 > int SimInfo::getNDFtranslational() {
382 >  int ndfTrans_local;
383 >
384 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
385 >
386 >
387 > #ifdef IS_MPI
388 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
389 > #else
390 >  ndfTrans = ndfTrans_local;
391 > #endif
392 >
393 >  ndfTrans = ndfTrans - 3 - nZconstraints;
394 >
395 >  return ndfTrans;
396 > }
397 >
398 > int SimInfo::getTotIntegrableObjects() {
399 >  int nObjs_local;
400 >  int nObjs;
401 >
402 >  nObjs_local =  integrableObjects.size();
403 >
404 >
405 > #ifdef IS_MPI
406 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
407 > #else
408 >  nObjs = nObjs_local;
409 > #endif
410 >
411 >
412 >  return nObjs;
413 > }
414 >
415   void SimInfo::refreshSim(){
416  
417    simtype fInfo;
418    int isError;
419 +  int n_global;
420    int* excl;
421 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
421 >
422    fInfo.dielect = 0.0;
423  
424 <  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 <
144 <  if( useDipole ){
145 <    fInfo.rrf = ecr;
146 <    fInfo.rt = ecr - est;
424 >  if( useDipoles ){
425      if( useReactionField )fInfo.dielect = dielectric;
426    }
427  
# Line 152 | Line 430 | void SimInfo::refreshSim(){
430    fInfo.SIM_uses_LJ = useLJ;
431    fInfo.SIM_uses_sticky = useSticky;
432    //fInfo.SIM_uses_sticky = 0;
433 <  fInfo.SIM_uses_dipoles = useDipole;
433 >  fInfo.SIM_uses_charges = useCharges;
434 >  fInfo.SIM_uses_dipoles = useDipoles;
435    //fInfo.SIM_uses_dipoles = 0;
436 <  //fInfo.SIM_uses_RF = useReactionField;
437 <  fInfo.SIM_uses_RF = 0;
436 >  fInfo.SIM_uses_RF = useReactionField;
437 >  //fInfo.SIM_uses_RF = 0;
438    fInfo.SIM_uses_GB = useGB;
439    fInfo.SIM_uses_EAM = useEAM;
440 +  fInfo.SIM_uses_molecular_cutoffs = useMolecularCutoffs;
441  
442 <  excl = Exclude::getArray();
442 >  n_exclude = excludes->getSize();
443 >  excl = excludes->getFortranArray();
444  
445 + #ifdef IS_MPI
446 +  n_global = mpiSim->getTotAtoms();
447 + #else
448 +  n_global = n_atoms;
449 + #endif
450 +
451    isError = 0;
452  
453 <  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
453 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
454                    &nGlobalExcludes, globalExcludes, molMembershipArray,
455                    &isError );
456  
# Line 183 | Line 470 | void SimInfo::refreshSim(){
470  
471    this->ndf = this->getNDF();
472    this->ndfRaw = this->getNDFraw();
473 +  this->ndfTrans = this->getNDFtranslational();
474 + }
475  
476 + void SimInfo::setDefaultRcut( double theRcut ){
477 +
478 +  haveRcut = 1;
479 +  rCut = theRcut;
480 +
481 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
482 +
483 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
484   }
485  
486 + void SimInfo::setDefaultEcr( double theEcr ){
487 +
488 +  haveEcr = 1;
489 +  ecr = theEcr;
490 +  
491 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
492 +
493 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
494 + }
495 +
496 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
497 +
498 +  est = theEst;
499 +  setDefaultEcr( theEcr );
500 + }
501 +
502 +
503 + void SimInfo::checkCutOffs( void ){
504 +  
505 +  if( boxIsInit ){
506 +    
507 +    //we need to check cutOffs against the box
508 +    
509 +    if( rCut > maxCutoff ){
510 +      sprintf( painCave.errMsg,
511 +               "LJrcut is too large for the current periodic box.\n"
512 +               "\tCurrent Value of LJrcut = %G at time %G\n "
513 +               "\tThis is larger than half of at least one of the\n"
514 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
515 +               "\n"
516 +               "\t[ %G %G %G ]\n"
517 +               "\t[ %G %G %G ]\n"
518 +               "\t[ %G %G %G ]\n",
519 +               rCut, currentTime,
520 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
521 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
522 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523 +      painCave.isFatal = 1;
524 +      simError();
525 +    }
526 +    
527 +    if( haveEcr ){
528 +      if( ecr > maxCutoff ){
529 +        sprintf( painCave.errMsg,
530 +                 "electrostaticCutoffRadius is too large for the current\n"
531 +                 "\tperiodic box.\n\n"
532 +                 "\tCurrent Value of ECR = %G at time %G\n "
533 +                 "\tThis is larger than half of at least one of the\n"
534 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
535 +                 "\n"
536 +                 "\t[ %G %G %G ]\n"
537 +                 "\t[ %G %G %G ]\n"
538 +                 "\t[ %G %G %G ]\n",
539 +                 ecr, currentTime,
540 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
541 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
542 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
543 +        painCave.isFatal = 1;
544 +        simError();
545 +      }
546 +    }
547 +  } else {
548 +    // initialize this stuff before using it, OK?
549 +    sprintf( painCave.errMsg,
550 +             "Trying to check cutoffs without a box.\n"
551 +             "\tOOPSE should have better programmers than that.\n" );
552 +    painCave.isFatal = 1;
553 +    simError();      
554 +  }
555 +  
556 + }
557 +
558 + void SimInfo::addProperty(GenericData* prop){
559 +
560 +  map<string, GenericData*>::iterator result;
561 +  result = properties.find(prop->getID());
562 +  
563 +  //we can't simply use  properties[prop->getID()] = prop,
564 +  //it will cause memory leak if we already contain a propery which has the same name of prop
565 +  
566 +  if(result != properties.end()){
567 +    
568 +    delete (*result).second;
569 +    (*result).second = prop;
570 +      
571 +  }
572 +  else{
573 +
574 +    properties[prop->getID()] = prop;
575 +
576 +  }
577 +    
578 + }
579 +
580 + GenericData* SimInfo::getProperty(const string& propName){
581 +
582 +  map<string, GenericData*>::iterator result;
583 +  
584 +  //string lowerCaseName = ();
585 +  
586 +  result = properties.find(propName);
587 +  
588 +  if(result != properties.end())
589 +    return (*result).second;  
590 +  else  
591 +    return NULL;  
592 + }
593 +

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