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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 1108 by tim, Wed Apr 14 15:37:41 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 +  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 <  ndf = ndf - 3;
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, ndfRaw;
350 >  int ndfRaw_local;
351  
352    // Raw degrees of freedom that we have to set
353 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
354 <  
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
# Line 123 | Line 365 | int SimInfo::getNDFraw() {
365  
366    return ndfRaw;
367   }
368 <
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 > int SimInfo::getTotIntegrableObjects() {
387 >  int nObjs_local;
388 >  int nObjs;
389 >
390 >  nObjs_local =  integrableObjects.size();
391 >
392 >
393 > #ifdef IS_MPI
394 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395 > #else
396 >  nObjs = nObjs_local;
397 > #endif
398 >
399 >
400 >  return nObjs;
401 > }
402 >
403   void SimInfo::refreshSim(){
404  
405    simtype fInfo;
406    int isError;
407 +  int n_global;
408    int* excl;
409 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
409 >
410    fInfo.dielect = 0.0;
411  
412 <  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;
412 >  if( useDipoles ){
413      if( useReactionField )fInfo.dielect = dielectric;
414    }
415  
# Line 152 | Line 418 | void SimInfo::refreshSim(){
418    fInfo.SIM_uses_LJ = useLJ;
419    fInfo.SIM_uses_sticky = useSticky;
420    //fInfo.SIM_uses_sticky = 0;
421 <  //fInfo.SIM_uses_dipoles = useDipole;
422 <  fInfo.SIM_uses_dipoles = 0;
423 <  //fInfo.SIM_uses_RF = useReactionField;
424 <  fInfo.SIM_uses_RF = 0;
421 >  fInfo.SIM_uses_charges = useCharges;
422 >  fInfo.SIM_uses_dipoles = useDipoles;
423 >  //fInfo.SIM_uses_dipoles = 0;
424 >  fInfo.SIM_uses_RF = useReactionField;
425 >  //fInfo.SIM_uses_RF = 0;
426    fInfo.SIM_uses_GB = useGB;
427    fInfo.SIM_uses_EAM = useEAM;
428  
429 <  excl = Exclude::getArray();
429 >  n_exclude = excludes->getSize();
430 >  excl = excludes->getFortranArray();
431  
432 + #ifdef IS_MPI
433 +  n_global = mpiSim->getTotAtoms();
434 + #else
435 +  n_global = n_atoms;
436 + #endif
437 +
438    isError = 0;
439  
440 < //   fInfo;
441 < //   n_atoms;
442 < //   identArray;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
440 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
441 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
442 >                  &isError );
443  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
444    if( isError ){
445  
446      sprintf( painCave.errMsg,
# Line 189 | Line 455 | void SimInfo::refreshSim(){
455    MPIcheckPoint();
456   #endif // is_mpi
457  
458 <  ndf = this->getNDF();
459 <  ndfRaw = this->getNDFraw();
458 >  this->ndf = this->getNDF();
459 >  this->ndfRaw = this->getNDFraw();
460 >  this->ndfTrans = this->getNDFtranslational();
461 > }
462  
463 + void SimInfo::setDefaultRcut( double theRcut ){
464 +
465 +  haveRcut = 1;
466 +  rCut = theRcut;
467 +
468 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
469 +
470 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
471   }
472  
473 + void SimInfo::setDefaultEcr( double theEcr ){
474 +
475 +  haveEcr = 1;
476 +  ecr = theEcr;
477 +  
478 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
479 +
480 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
481 + }
482 +
483 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
484 +
485 +  est = theEst;
486 +  setDefaultEcr( theEcr );
487 + }
488 +
489 +
490 + void SimInfo::checkCutOffs( void ){
491 +  
492 +  if( boxIsInit ){
493 +    
494 +    //we need to check cutOffs against the box
495 +    
496 +    if( rCut > maxCutoff ){
497 +      sprintf( painCave.errMsg,
498 +               "LJrcut is too large for the current periodic box.\n"
499 +               "\tCurrent Value of LJrcut = %G at time %G\n "
500 +               "\tThis is larger than half of at least one of the\n"
501 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
502 +               "\n, %G"
503 +               "\t[ %G %G %G ]\n"
504 +               "\t[ %G %G %G ]\n"
505 +               "\t[ %G %G %G ]\n",
506 +               rCut, currentTime, maxCutoff,
507 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
508 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
509 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
510 +      painCave.isFatal = 1;
511 +      simError();
512 +    }
513 +    
514 +    if( haveEcr ){
515 +      if( ecr > maxCutoff ){
516 +        sprintf( painCave.errMsg,
517 +                 "electrostaticCutoffRadius is too large for the current\n"
518 +                 "\tperiodic box.\n\n"
519 +                 "\tCurrent Value of ECR = %G at time %G\n "
520 +                 "\tThis is larger than half of at least one of the\n"
521 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
522 +                 "\n"
523 +                 "\t[ %G %G %G ]\n"
524 +                 "\t[ %G %G %G ]\n"
525 +                 "\t[ %G %G %G ]\n",
526 +                 ecr, currentTime,
527 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
528 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
529 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
530 +        painCave.isFatal = 1;
531 +        simError();
532 +      }
533 +    }
534 +  } else {
535 +    // initialize this stuff before using it, OK?
536 +    sprintf( painCave.errMsg,
537 +             "Trying to check cutoffs without a box.\n"
538 +             "\tOOPSE should have better programmers than that.\n" );
539 +    painCave.isFatal = 1;
540 +    simError();      
541 +  }
542 +  
543 + }
544 +
545 + void SimInfo::addProperty(GenericData* prop){
546 +
547 +  map<string, GenericData*>::iterator result;
548 +  result = properties.find(prop->getID());
549 +  
550 +  //we can't simply use  properties[prop->getID()] = prop,
551 +  //it will cause memory leak if we already contain a propery which has the same name of prop
552 +  
553 +  if(result != properties.end()){
554 +    
555 +    delete (*result).second;
556 +    (*result).second = prop;
557 +      
558 +  }
559 +  else{
560 +
561 +    properties[prop->getID()] = prop;
562 +
563 +  }
564 +    
565 + }
566 +
567 + GenericData* SimInfo::getProperty(const string& propName){
568 +
569 +  map<string, GenericData*>::iterator result;
570 +  
571 +  //string lowerCaseName = ();
572 +  
573 +  result = properties.find(propName);
574 +  
575 +  if(result != properties.end())
576 +    return (*result).second;  
577 +  else  
578 +    return NULL;  
579 + }
580 +
581 + vector<GenericData*> SimInfo::getProperties(){
582 +
583 +  vector<GenericData*> result;
584 +  map<string, GenericData*>::iterator i;
585 +  
586 +  for(i = properties.begin(); i != properties.end(); i++)
587 +    result.push_back((*i).second);
588 +    
589 +  return result;
590 + }

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