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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 469 by mmeineke, Mon Apr 7 20:06:31 2003 UTC vs.
Revision 1118 by tim, Mon Apr 19 03:52:27 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 +      if (integrableObjects[i]->isLinear())
331 +        ndf_local += 2;
332 +      else
333 +        ndf_local += 3;
334 +    }
335 +  }
336 +
337 +  // n_constraints is local, so subtract them on each processor:
338 +
339 +  ndf_local -= n_constraints;
340 +
341   #ifdef IS_MPI
342    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343   #else
344    ndf = ndf_local;
345   #endif
346  
347 <  ndf = ndf - 3;
347 >  // nZconstraints is global, as are the 3 COM translations for the
348 >  // entire system:
349  
350 +  ndf = ndf - 3 - nZconstraints;
351 +
352    return ndf;
353   }
354  
355   int SimInfo::getNDFraw() {
356 <  int ndfRaw_local, ndfRaw;
356 >  int ndfRaw_local;
357  
358    // Raw degrees of freedom that we have to set
359 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
360 <  
359 >  ndfRaw_local = 0;
360 >
361 >  for(int i = 0; i < integrableObjects.size(); i++){
362 >    ndfRaw_local += 3;
363 >    if (integrableObjects[i]->isDirectional()) {
364 >       if (integrableObjects[i]->isLinear())
365 >        ndfRaw_local += 2;
366 >      else
367 >        ndfRaw_local += 3;
368 >    }
369 >  }
370 >    
371   #ifdef IS_MPI
372    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
373   #else
# Line 123 | Line 376 | int SimInfo::getNDFraw() {
376  
377    return ndfRaw;
378   }
379 <
379 >
380 > int SimInfo::getNDFtranslational() {
381 >  int ndfTrans_local;
382 >
383 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
384 >
385 >
386 > #ifdef IS_MPI
387 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
388 > #else
389 >  ndfTrans = ndfTrans_local;
390 > #endif
391 >
392 >  ndfTrans = ndfTrans - 3 - nZconstraints;
393 >
394 >  return ndfTrans;
395 > }
396 >
397 > int SimInfo::getTotIntegrableObjects() {
398 >  int nObjs_local;
399 >  int nObjs;
400 >
401 >  nObjs_local =  integrableObjects.size();
402 >
403 >
404 > #ifdef IS_MPI
405 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
406 > #else
407 >  nObjs = nObjs_local;
408 > #endif
409 >
410 >
411 >  return nObjs;
412 > }
413 >
414   void SimInfo::refreshSim(){
415  
416    simtype fInfo;
417    int isError;
418 +  int n_global;
419    int* excl;
420 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
420 >
421    fInfo.dielect = 0.0;
422  
423 <  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;
423 >  if( useDipoles ){
424      if( useReactionField )fInfo.dielect = dielectric;
425    }
426  
# Line 152 | Line 429 | void SimInfo::refreshSim(){
429    fInfo.SIM_uses_LJ = useLJ;
430    fInfo.SIM_uses_sticky = useSticky;
431    //fInfo.SIM_uses_sticky = 0;
432 <  //fInfo.SIM_uses_dipoles = useDipole;
433 <  fInfo.SIM_uses_dipoles = 0;
434 <  //fInfo.SIM_uses_RF = useReactionField;
435 <  fInfo.SIM_uses_RF = 0;
432 >  fInfo.SIM_uses_charges = useCharges;
433 >  fInfo.SIM_uses_dipoles = useDipoles;
434 >  //fInfo.SIM_uses_dipoles = 0;
435 >  fInfo.SIM_uses_RF = useReactionField;
436 >  //fInfo.SIM_uses_RF = 0;
437    fInfo.SIM_uses_GB = useGB;
438    fInfo.SIM_uses_EAM = useEAM;
439  
440 <  excl = Exclude::getArray();
440 >  n_exclude = excludes->getSize();
441 >  excl = excludes->getFortranArray();
442  
443 + #ifdef IS_MPI
444 +  n_global = mpiSim->getTotAtoms();
445 + #else
446 +  n_global = n_atoms;
447 + #endif
448 +
449    isError = 0;
450  
451 < //   fInfo;
452 < //   n_atoms;
453 < //   identArray;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
451 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
452 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
453 >                  &isError );
454  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
455    if( isError ){
456  
457      sprintf( painCave.errMsg,
# Line 189 | Line 466 | void SimInfo::refreshSim(){
466    MPIcheckPoint();
467   #endif // is_mpi
468  
469 <  ndf = this->getNDF();
470 <  ndfRaw = this->getNDFraw();
469 >  this->ndf = this->getNDF();
470 >  this->ndfRaw = this->getNDFraw();
471 >  this->ndfTrans = this->getNDFtranslational();
472 > }
473  
474 + void SimInfo::setDefaultRcut( double theRcut ){
475 +
476 +  haveRcut = 1;
477 +  rCut = theRcut;
478 +
479 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
480 +
481 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
482   }
483  
484 + void SimInfo::setDefaultEcr( double theEcr ){
485 +
486 +  haveEcr = 1;
487 +  ecr = theEcr;
488 +  
489 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
490 +
491 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
492 + }
493 +
494 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
495 +
496 +  est = theEst;
497 +  setDefaultEcr( theEcr );
498 + }
499 +
500 +
501 + void SimInfo::checkCutOffs( void ){
502 +  
503 +  if( boxIsInit ){
504 +    
505 +    //we need to check cutOffs against the box
506 +    
507 +    if( rCut > maxCutoff ){
508 +      sprintf( painCave.errMsg,
509 +               "LJrcut is too large for the current periodic box.\n"
510 +               "\tCurrent Value of LJrcut = %G at time %G\n "
511 +               "\tThis is larger than half of at least one of the\n"
512 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
513 +               "\n, %G"
514 +               "\t[ %G %G %G ]\n"
515 +               "\t[ %G %G %G ]\n"
516 +               "\t[ %G %G %G ]\n",
517 +               rCut, currentTime, maxCutoff,
518 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
519 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
520 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
521 +      painCave.isFatal = 1;
522 +      simError();
523 +    }
524 +    
525 +    if( haveEcr ){
526 +      if( ecr > maxCutoff ){
527 +        sprintf( painCave.errMsg,
528 +                 "electrostaticCutoffRadius is too large for the current\n"
529 +                 "\tperiodic box.\n\n"
530 +                 "\tCurrent Value of ECR = %G at time %G\n "
531 +                 "\tThis is larger than half of at least one of the\n"
532 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
533 +                 "\n"
534 +                 "\t[ %G %G %G ]\n"
535 +                 "\t[ %G %G %G ]\n"
536 +                 "\t[ %G %G %G ]\n",
537 +                 ecr, currentTime,
538 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
539 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
540 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
541 +        painCave.isFatal = 1;
542 +        simError();
543 +      }
544 +    }
545 +  } else {
546 +    // initialize this stuff before using it, OK?
547 +    sprintf( painCave.errMsg,
548 +             "Trying to check cutoffs without a box.\n"
549 +             "\tOOPSE should have better programmers than that.\n" );
550 +    painCave.isFatal = 1;
551 +    simError();      
552 +  }
553 +  
554 + }
555 +
556 + void SimInfo::addProperty(GenericData* prop){
557 +
558 +  map<string, GenericData*>::iterator result;
559 +  result = properties.find(prop->getID());
560 +  
561 +  //we can't simply use  properties[prop->getID()] = prop,
562 +  //it will cause memory leak if we already contain a propery which has the same name of prop
563 +  
564 +  if(result != properties.end()){
565 +    
566 +    delete (*result).second;
567 +    (*result).second = prop;
568 +      
569 +  }
570 +  else{
571 +
572 +    properties[prop->getID()] = prop;
573 +
574 +  }
575 +    
576 + }
577 +
578 + GenericData* SimInfo::getProperty(const string& propName){
579 +
580 +  map<string, GenericData*>::iterator result;
581 +  
582 +  //string lowerCaseName = ();
583 +  
584 +  result = properties.find(propName);
585 +  
586 +  if(result != properties.end())
587 +    return (*result).second;  
588 +  else  
589 +    return NULL;  
590 + }
591 +

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