ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC vs.
Revision 1113 by tim, Thu Apr 15 16:18:26 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 | SimInfo* currentInfo;
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 <  double smallestBox, maxCutoff;
91 <  int status;
92 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
90 >  
91 >  int i, j;
92 >  double tempMat[3][3];
93  
94 <  smallestBox = box_x;
95 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
94 >  for(i=0; i<3; i++)
95 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
96  
97 <  maxCutoff = smallestBox / 2.0;
97 >  tempMat[0][0] = newBox[0];
98 >  tempMat[1][1] = newBox[1];
99 >  tempMat[2][2] = newBox[2];
100  
101 <  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();
101 >  setBoxM( tempMat );
102  
103 <    rList = maxCutoff;
103 > }
104  
105 <    sprintf( painCave.errMsg,
106 <             "New Box size is forcing cutoff radius down to %lf\n",
107 <             maxCutoff - 1.0 );
108 <    painCave.isFatal = 0;
109 <    simError();
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 <    rCut = rList - 1.0;
115 >  if( !boxIsInit ) boxIsInit = 1;
116  
117 <    // list radius changed so we have to refresh the simulation structure.
118 <    refreshSim();
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 <  if (rCut > maxCutoff) {
131 <    sprintf( painCave.errMsg,
132 <             "New Box size is forcing cutoff radius down to %lf\n",
133 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
130 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
131 >
132 > }
133 >
134  
135 <    status = 0;
136 <    LJ_new_rcut(&rCut, &status);
137 <    if (status != 0) {
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 <               "Error in recomputing LJ shifts based on new rcut\n");
192 <      painCave.isFatal = 1;
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::getBox(double theBox[3]) {
214 <  theBox[0] = box_x;
215 <  theBox[1] = box_y;
216 <  theBox[2] = box_z;
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 < int SimInfo::getNDF(){
251 <  int ndf_local, ndf;
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 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
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 +  ndf_local = 0;
326 +  
327 +  for(int i = 0; i < integrableObjects.size(); i++){
328 +    ndf_local += 3;
329 +    if (integrableObjects[i]->isDirectional())
330 +      ndf_local += 3;
331 +  }
332 +
333 +  // n_constraints is local, so subtract them on each processor:
334 +
335 +  ndf_local -= n_constraints;
336 +
337   #ifdef IS_MPI
338    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
339   #else
340    ndf = ndf_local;
341   #endif
342  
343 <  ndf = ndf - 3;
343 >  // nZconstraints is global, as are the 3 COM translations for the
344 >  // entire system:
345  
346 +  ndf = ndf - 3 - nZconstraints;
347 +
348    return ndf;
349   }
350  
351   int SimInfo::getNDFraw() {
352 <  int ndfRaw_local, ndfRaw;
352 >  int ndfRaw_local;
353  
354    // Raw degrees of freedom that we have to set
355 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
356 <  
355 >  ndfRaw_local = 0;
356 >
357 >  for(int i = 0; i < integrableObjects.size(); i++){
358 >    ndfRaw_local += 3;
359 >    if (integrableObjects[i]->isDirectional())
360 >      ndfRaw_local += 3;
361 >  }
362 >    
363   #ifdef IS_MPI
364    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
365   #else
# Line 123 | Line 368 | int SimInfo::getNDFraw() {
368  
369    return ndfRaw;
370   }
371 <
371 >
372 > int SimInfo::getNDFtranslational() {
373 >  int ndfTrans_local;
374 >
375 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
376 >
377 >
378 > #ifdef IS_MPI
379 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380 > #else
381 >  ndfTrans = ndfTrans_local;
382 > #endif
383 >
384 >  ndfTrans = ndfTrans - 3 - nZconstraints;
385 >
386 >  return ndfTrans;
387 > }
388 >
389 > int SimInfo::getTotIntegrableObjects() {
390 >  int nObjs_local;
391 >  int nObjs;
392 >
393 >  nObjs_local =  integrableObjects.size();
394 >
395 >
396 > #ifdef IS_MPI
397 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
398 > #else
399 >  nObjs = nObjs_local;
400 > #endif
401 >
402 >
403 >  return nObjs;
404 > }
405 >
406   void SimInfo::refreshSim(){
407  
408    simtype fInfo;
409    int isError;
410 +  int n_global;
411    int* excl;
412 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
412 >
413    fInfo.dielect = 0.0;
414  
415 <  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;
415 >  if( useDipoles ){
416      if( useReactionField )fInfo.dielect = dielectric;
417    }
418  
# Line 152 | Line 421 | void SimInfo::refreshSim(){
421    fInfo.SIM_uses_LJ = useLJ;
422    fInfo.SIM_uses_sticky = useSticky;
423    //fInfo.SIM_uses_sticky = 0;
424 <  //fInfo.SIM_uses_dipoles = useDipole;
425 <  fInfo.SIM_uses_dipoles = 0;
426 <  //fInfo.SIM_uses_RF = useReactionField;
427 <  fInfo.SIM_uses_RF = 0;
424 >  fInfo.SIM_uses_charges = useCharges;
425 >  fInfo.SIM_uses_dipoles = useDipoles;
426 >  //fInfo.SIM_uses_dipoles = 0;
427 >  fInfo.SIM_uses_RF = useReactionField;
428 >  //fInfo.SIM_uses_RF = 0;
429    fInfo.SIM_uses_GB = useGB;
430    fInfo.SIM_uses_EAM = useEAM;
431  
432 <  excl = Exclude::getArray();
432 >  n_exclude = excludes->getSize();
433 >  excl = excludes->getFortranArray();
434  
435 + #ifdef IS_MPI
436 +  n_global = mpiSim->getTotAtoms();
437 + #else
438 +  n_global = n_atoms;
439 + #endif
440 +
441    isError = 0;
442  
443 < //   fInfo;
444 < //   n_atoms;
445 < //   identArray;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
443 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
444 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
445 >                  &isError );
446  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
447    if( isError ){
448  
449      sprintf( painCave.errMsg,
# Line 191 | Line 460 | void SimInfo::refreshSim(){
460  
461    this->ndf = this->getNDF();
462    this->ndfRaw = this->getNDFraw();
463 +  this->ndfTrans = this->getNDFtranslational();
464 + }
465  
466 + void SimInfo::setDefaultRcut( double theRcut ){
467 +
468 +  haveRcut = 1;
469 +  rCut = theRcut;
470 +
471 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
472 +
473 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
474   }
475  
476 + void SimInfo::setDefaultEcr( double theEcr ){
477 +
478 +  haveEcr = 1;
479 +  ecr = theEcr;
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, double theEst ){
487 +
488 +  est = theEst;
489 +  setDefaultEcr( theEcr );
490 + }
491 +
492 +
493 + void SimInfo::checkCutOffs( void ){
494 +  
495 +  if( boxIsInit ){
496 +    
497 +    //we need to check cutOffs against the box
498 +    
499 +    if( rCut > maxCutoff ){
500 +      sprintf( painCave.errMsg,
501 +               "LJrcut is too large for the current periodic box.\n"
502 +               "\tCurrent Value of LJrcut = %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, %G"
506 +               "\t[ %G %G %G ]\n"
507 +               "\t[ %G %G %G ]\n"
508 +               "\t[ %G %G %G ]\n",
509 +               rCut, currentTime, maxCutoff,
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 +    if( haveEcr ){
518 +      if( ecr > maxCutoff ){
519 +        sprintf( painCave.errMsg,
520 +                 "electrostaticCutoffRadius is too large for the current\n"
521 +                 "\tperiodic box.\n\n"
522 +                 "\tCurrent Value of ECR = %G at time %G\n "
523 +                 "\tThis is larger than half of at least one of the\n"
524 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
525 +                 "\n"
526 +                 "\t[ %G %G %G ]\n"
527 +                 "\t[ %G %G %G ]\n"
528 +                 "\t[ %G %G %G ]\n",
529 +                 ecr, currentTime,
530 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
531 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
532 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
533 +        painCave.isFatal = 1;
534 +        simError();
535 +      }
536 +    }
537 +  } else {
538 +    // initialize this stuff before using it, OK?
539 +    sprintf( painCave.errMsg,
540 +             "Trying to check cutoffs without a box.\n"
541 +             "\tOOPSE should have better programmers than that.\n" );
542 +    painCave.isFatal = 1;
543 +    simError();      
544 +  }
545 +  
546 + }
547 +
548 + void SimInfo::addProperty(GenericData* prop){
549 +
550 +  map<string, GenericData*>::iterator result;
551 +  result = properties.find(prop->getID());
552 +  
553 +  //we can't simply use  properties[prop->getID()] = prop,
554 +  //it will cause memory leak if we already contain a propery which has the same name of prop
555 +  
556 +  if(result != properties.end()){
557 +    
558 +    delete (*result).second;
559 +    (*result).second = prop;
560 +      
561 +  }
562 +  else{
563 +
564 +    properties[prop->getID()] = prop;
565 +
566 +  }
567 +    
568 + }
569 +
570 + GenericData* SimInfo::getProperty(const string& propName){
571 +
572 +  map<string, GenericData*>::iterator result;
573 +  
574 +  //string lowerCaseName = ();
575 +  
576 +  result = properties.find(propName);
577 +  
578 +  if(result != properties.end())
579 +    return (*result).second;  
580 +  else  
581 +    return NULL;  
582 + }
583 +
584 + vector<GenericData*> SimInfo::getProperties(){
585 +
586 +  vector<GenericData*> result;
587 +  map<string, GenericData*>::iterator i;
588 +  
589 +  for(i = properties.begin(); i != properties.end(); i++)
590 +    result.push_back((*i).second);
591 +    
592 +  return result;
593 + }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines