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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 458 by gezelter, Fri Apr 4 19:47:19 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 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 + #ifdef IS_MPI
16 + #include "mpiSimulation.hpp"
17 + #endif
18 +
19 + inline double roundMe( double x ){
20 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21 + }
22 +          
23 +
24   SimInfo* currentInfo;
25  
26   SimInfo::SimInfo(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32    ndf = 0;
33    ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38 +  currentTime = 0.0;
39    rCut = 0.0;
40 +  ecr = 0.0;
41 +  est = 0.0;
42  
43 +  haveRcut = 0;
44 +  haveEcr = 0;
45 +  boxIsInit = 0;
46 +  
47 +  resetTime = 1e99;
48 +
49 +  orthoTolerance = 1E-6;
50 +  useInitXSstate = true;
51 +
52    usePBC = 0;
53    useLJ = 0;
54    useSticky = 0;
# Line 31 | Line 57 | SimInfo::SimInfo(){
57    useGB = 0;
58    useEAM = 0;
59  
60 +  myConfiguration = new SimState();
61 +
62    wrapMeSimInfo( this );
63   }
64  
65 +
66 + SimInfo::~SimInfo(){
67 +
68 +  delete myConfiguration;
69 +
70 +  map<string, GenericData*>::iterator i;
71 +  
72 +  for(i = properties.begin(); i != properties.end(); i++)
73 +    delete (*i).second;
74 +    
75 + }
76 +
77   void SimInfo::setBox(double newBox[3]) {
78 <  box_x = newBox[0];
79 <  box_y = newBox[1];
80 <  box_z = newBox[2];
81 <  setFortranBoxSize(newBox);
78 >  
79 >  int i, j;
80 >  double tempMat[3][3];
81 >
82 >  for(i=0; i<3; i++)
83 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
84 >
85 >  tempMat[0][0] = newBox[0];
86 >  tempMat[1][1] = newBox[1];
87 >  tempMat[2][2] = newBox[2];
88 >
89 >  setBoxM( tempMat );
90 >
91   }
92  
93 < void SimInfo::getBox(double theBox[3]) {
94 <  theBox[0] = box_x;
95 <  theBox[1] = box_y;
96 <  theBox[2] = box_z;
93 > void SimInfo::setBoxM( double theBox[3][3] ){
94 >  
95 >  int i, j;
96 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
97 >                         // ordering in the array is as follows:
98 >                         // [ 0 3 6 ]
99 >                         // [ 1 4 7 ]
100 >                         // [ 2 5 8 ]
101 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102 >
103 >  if( !boxIsInit ) boxIsInit = 1;
104 >
105 >  for(i=0; i < 3; i++)
106 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107 >  
108 >  calcBoxL();
109 >  calcHmatInv();
110 >
111 >  for(i=0; i < 3; i++) {
112 >    for (j=0; j < 3; j++) {
113 >      FortranHmat[3*j + i] = Hmat[i][j];
114 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
115 >    }
116 >  }
117 >
118 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119 >
120   }
121  
122 +
123 + void SimInfo::getBoxM (double theBox[3][3]) {
124 +
125 +  int i, j;
126 +  for(i=0; i<3; i++)
127 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
128 + }
129 +
130 +
131 + void SimInfo::scaleBox(double scale) {
132 +  double theBox[3][3];
133 +  int i, j;
134 +
135 +  // cerr << "Scaling box by " << scale << "\n";
136 +
137 +  for(i=0; i<3; i++)
138 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
139 +
140 +  setBoxM(theBox);
141 +
142 + }
143 +
144 + void SimInfo::calcHmatInv( void ) {
145 +  
146 +  int oldOrtho;
147 +  int i,j;
148 +  double smallDiag;
149 +  double tol;
150 +  double sanity[3][3];
151 +
152 +  invertMat3( Hmat, HmatInv );
153 +
154 +  // check to see if Hmat is orthorhombic
155 +  
156 +  oldOrtho = orthoRhombic;
157 +
158 +  smallDiag = fabs(Hmat[0][0]);
159 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
160 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
161 +  tol = smallDiag * orthoTolerance;
162 +
163 +  orthoRhombic = 1;
164 +  
165 +  for (i = 0; i < 3; i++ ) {
166 +    for (j = 0 ; j < 3; j++) {
167 +      if (i != j) {
168 +        if (orthoRhombic) {
169 +          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
170 +        }        
171 +      }
172 +    }
173 +  }
174 +
175 +  if( oldOrtho != orthoRhombic ){
176 +    
177 +    if( orthoRhombic ){
178 +      sprintf( painCave.errMsg,
179 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
180 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
181 +               orthoTolerance);
182 +      simError();
183 +    }
184 +    else {
185 +      sprintf( painCave.errMsg,
186 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
187 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
188 +               orthoTolerance);
189 +      simError();
190 +    }
191 +  }
192 + }
193 +
194 + double SimInfo::matDet3(double a[3][3]) {
195 +  int i, j, k;
196 +  double determinant;
197 +
198 +  determinant = 0.0;
199 +
200 +  for(i = 0; i < 3; i++) {
201 +    j = (i+1)%3;
202 +    k = (i+2)%3;
203 +
204 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
205 +  }
206 +
207 +  return determinant;
208 + }
209 +
210 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
211 +  
212 +  int  i, j, k, l, m, n;
213 +  double determinant;
214 +
215 +  determinant = matDet3( a );
216 +
217 +  if (determinant == 0.0) {
218 +    sprintf( painCave.errMsg,
219 +             "Can't invert a matrix with a zero determinant!\n");
220 +    painCave.isFatal = 1;
221 +    simError();
222 +  }
223 +
224 +  for (i=0; i < 3; i++) {
225 +    j = (i+1)%3;
226 +    k = (i+2)%3;
227 +    for(l = 0; l < 3; l++) {
228 +      m = (l+1)%3;
229 +      n = (l+2)%3;
230 +      
231 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
232 +    }
233 +  }
234 + }
235 +
236 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
237 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
238 +
239 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
240 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
241 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
242 +  
243 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
244 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
245 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
246 +  
247 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
248 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
249 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
250 +  
251 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
252 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
253 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
254 + }
255 +
256 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
257 +  double a0, a1, a2;
258 +
259 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
260 +
261 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
262 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
263 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
264 + }
265 +
266 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
267 +  double temp[3][3];
268 +  int i, j;
269 +
270 +  for (i = 0; i < 3; i++) {
271 +    for (j = 0; j < 3; j++) {
272 +      temp[j][i] = in[i][j];
273 +    }
274 +  }
275 +  for (i = 0; i < 3; i++) {
276 +    for (j = 0; j < 3; j++) {
277 +      out[i][j] = temp[i][j];
278 +    }
279 +  }
280 + }
281 +  
282 + void SimInfo::printMat3(double A[3][3] ){
283 +
284 +  std::cerr
285 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
286 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
287 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
288 + }
289 +
290 + void SimInfo::printMat9(double A[9] ){
291 +
292 +  std::cerr
293 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
294 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
295 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
296 + }
297 +
298 +
299 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
300 +
301 +      out[0] = a[1] * b[2] - a[2] * b[1];
302 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
303 +      out[2] = a[0] * b[1] - a[1] * b[0];
304 +      
305 + }
306 +
307 + double SimInfo::dotProduct3(double a[3], double b[3]){
308 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
309 + }
310 +
311 + double SimInfo::length3(double a[3]){
312 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
313 + }
314 +
315 + void SimInfo::calcBoxL( void ){
316 +
317 +  double dx, dy, dz, dsq;
318 +
319 +  // boxVol = Determinant of Hmat
320 +
321 +  boxVol = matDet3( Hmat );
322 +
323 +  // boxLx
324 +  
325 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
326 +  dsq = dx*dx + dy*dy + dz*dz;
327 +  boxL[0] = sqrt( dsq );
328 +  //maxCutoff = 0.5 * boxL[0];
329 +
330 +  // boxLy
331 +  
332 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
333 +  dsq = dx*dx + dy*dy + dz*dz;
334 +  boxL[1] = sqrt( dsq );
335 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
336 +
337 +
338 +  // boxLz
339 +  
340 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
341 +  dsq = dx*dx + dy*dy + dz*dz;
342 +  boxL[2] = sqrt( dsq );
343 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
344 +
345 +  //calculate the max cutoff
346 +  maxCutoff =  calcMaxCutOff();
347 +  
348 +  checkCutOffs();
349 +
350 + }
351 +
352 +
353 + double SimInfo::calcMaxCutOff(){
354 +
355 +  double ri[3], rj[3], rk[3];
356 +  double rij[3], rjk[3], rki[3];
357 +  double minDist;
358 +
359 +  ri[0] = Hmat[0][0];
360 +  ri[1] = Hmat[1][0];
361 +  ri[2] = Hmat[2][0];
362 +
363 +  rj[0] = Hmat[0][1];
364 +  rj[1] = Hmat[1][1];
365 +  rj[2] = Hmat[2][1];
366 +
367 +  rk[0] = Hmat[0][2];
368 +  rk[1] = Hmat[1][2];
369 +  rk[2] = Hmat[2][2];
370 +  
371 +  crossProduct3(ri,rj, rij);
372 +  distXY = dotProduct3(rk,rij) / length3(rij);
373 +
374 +  crossProduct3(rj,rk, rjk);
375 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
376 +
377 +  crossProduct3(rk,ri, rki);
378 +  distZX = dotProduct3(rj,rki) / length3(rki);
379 +
380 +  minDist = min(min(distXY, distYZ), distZX);
381 +  return minDist/2;
382 +  
383 + }
384 +
385 + void SimInfo::wrapVector( double thePos[3] ){
386 +
387 +  int i;
388 +  double scaled[3];
389 +
390 +  if( !orthoRhombic ){
391 +    // calc the scaled coordinates.
392 +  
393 +
394 +    matVecMul3(HmatInv, thePos, scaled);
395 +    
396 +    for(i=0; i<3; i++)
397 +      scaled[i] -= roundMe(scaled[i]);
398 +    
399 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
400 +    
401 +    matVecMul3(Hmat, scaled, thePos);
402 +
403 +  }
404 +  else{
405 +    // calc the scaled coordinates.
406 +    
407 +    for(i=0; i<3; i++)
408 +      scaled[i] = thePos[i]*HmatInv[i][i];
409 +    
410 +    // wrap the scaled coordinates
411 +    
412 +    for(i=0; i<3; i++)
413 +      scaled[i] -= roundMe(scaled[i]);
414 +    
415 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
416 +    
417 +    for(i=0; i<3; i++)
418 +      thePos[i] = scaled[i]*Hmat[i][i];
419 +  }
420 +    
421 + }
422 +
423 +
424   int SimInfo::getNDF(){
425 <  int ndf_local, ndf;
425 >  int ndf_local;
426    
427    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
428  
# Line 58 | Line 432 | int SimInfo::getNDF(){
432    ndf = ndf_local;
433   #endif
434  
435 <  ndf = ndf - 3;
435 >  ndf = ndf - 3 - nZconstraints;
436  
437    return ndf;
438   }
439  
440   int SimInfo::getNDFraw() {
441 <  int ndfRaw_local, ndfRaw;
441 >  int ndfRaw_local;
442  
443    // Raw degrees of freedom that we have to set
444    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 77 | Line 451 | int SimInfo::getNDFraw() {
451  
452    return ndfRaw;
453   }
454 <
454 >
455 > int SimInfo::getNDFtranslational() {
456 >  int ndfTrans_local;
457 >
458 >  ndfTrans_local = 3 * n_atoms - n_constraints;
459 >
460 > #ifdef IS_MPI
461 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
462 > #else
463 >  ndfTrans = ndfTrans_local;
464 > #endif
465 >
466 >  ndfTrans = ndfTrans - 3 - nZconstraints;
467 >
468 >  return ndfTrans;
469 > }
470 >
471   void SimInfo::refreshSim(){
472  
473    simtype fInfo;
474    int isError;
475 +  int n_global;
476    int* excl;
477  
478 <  fInfo.box[0] = box_x;
88 <  fInfo.box[1] = box_y;
89 <  fInfo.box[2] = box_z;
478 >  fInfo.dielect = 0.0;
479  
480 <  fInfo.rlist = rList;
481 <  fInfo.rcut = rCut;
482 <  fInfo.rrf = ecr;
94 <  fInfo.rt = ecr - est;
95 <  fInfo.dielect = dielectric;
480 >  if( useDipole ){
481 >    if( useReactionField )fInfo.dielect = dielectric;
482 >  }
483  
484    fInfo.SIM_uses_PBC = usePBC;
485    //fInfo.SIM_uses_LJ = 0;
# Line 108 | Line 495 | void SimInfo::refreshSim(){
495  
496    excl = Exclude::getArray();
497  
498 + #ifdef IS_MPI
499 +  n_global = mpiSim->getTotAtoms();
500 + #else
501 +  n_global = n_atoms;
502 + #endif
503 +
504    isError = 0;
505  
506 < //   fInfo;
507 < //   n_atoms;
508 < //   identArray;
116 < //   n_exclude;
117 < //   excludes;
118 < //   nGlobalExcludes;
119 < //   globalExcludes;
120 < //   isError;
506 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
507 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
508 >                  &isError );
509  
122 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
123 –                  &nGlobalExcludes, globalExcludes, &isError );
124 –
510    if( isError ){
511  
512      sprintf( painCave.errMsg,
# Line 136 | Line 521 | void SimInfo::refreshSim(){
521    MPIcheckPoint();
522   #endif // is_mpi
523  
524 <  ndf = this->getNDF();
525 <  ndfRaw = this->getNDFraw();
524 >  this->ndf = this->getNDF();
525 >  this->ndfRaw = this->getNDFraw();
526 >  this->ndfTrans = this->getNDFtranslational();
527 > }
528  
529 + void SimInfo::setDefaultRcut( double theRcut ){
530 +
531 +  haveRcut = 1;
532 +  rCut = theRcut;
533 +
534 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535 +
536 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537   }
538  
539 + void SimInfo::setDefaultEcr( double theEcr ){
540 +
541 +  haveEcr = 1;
542 +  
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  ecr = theEcr;
546 +
547 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 + }
549 +
550 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
551 +
552 +  est = theEst;
553 +  setDefaultEcr( theEcr );
554 + }
555 +
556 +
557 + void SimInfo::checkCutOffs( void ){
558 +  
559 +  if( boxIsInit ){
560 +    
561 +    //we need to check cutOffs against the box
562 +    
563 +    if( rCut > maxCutoff ){
564 +      sprintf( painCave.errMsg,
565 +               "Box size is too small for the long range cutoff radius, "
566 +               "%lf, at time %lf\n",
567 +               rCut, currentTime );
568 +      painCave.isFatal = 1;
569 +      simError();
570 +    }
571 +    
572 +    if( haveEcr ){
573 +      if( ecr > maxCutoff ){
574 +        sprintf( painCave.errMsg,
575 +                 "Box size is too small for the electrostatic cutoff radius, "
576 +                 "%lf, at time %lf\n",
577 +                 ecr, currentTime );
578 +        painCave.isFatal = 1;
579 +        simError();
580 +      }
581 +    }
582 +  } else {
583 +    // initialize this stuff before using it, OK?
584 +    sprintf( painCave.errMsg,
585 +             "Trying to check cutoffs without a box. Be smarter.\n" );
586 +    painCave.isFatal = 1;
587 +    simError();      
588 +  }
589 +  
590 + }
591 +
592 + void SimInfo::addProperty(GenericData* prop){
593 +
594 +  map<string, GenericData*>::iterator result;
595 +  result = properties.find(prop->getID());
596 +  
597 +  //we can't simply use  properties[prop->getID()] = prop,
598 +  //it will cause memory leak if we already contain a propery which has the same name of prop
599 +  
600 +  if(result != properties.end()){
601 +    
602 +    delete (*result).second;
603 +    (*result).second = prop;
604 +      
605 +  }
606 +  else{
607 +
608 +    properties[prop->getID()] = prop;
609 +
610 +  }
611 +    
612 + }
613 +
614 + GenericData* SimInfo::getProperty(const string& propName){
615 +
616 +  map<string, GenericData*>::iterator result;
617 +  
618 +  //string lowerCaseName = ();
619 +  
620 +  result = properties.find(propName);
621 +  
622 +  if(result != properties.end())
623 +    return (*result).second;  
624 +  else  
625 +    return NULL;  
626 + }
627 +
628 + vector<GenericData*> SimInfo::getProperties(){
629 +
630 +  vector<GenericData*> result;
631 +  map<string, GenericData*>::iterator i;
632 +  
633 +  for(i = properties.begin(); i != properties.end(); i++)
634 +    result.push_back((*i).second);
635 +    
636 +  return result;
637 + }
638 +
639 + double SimInfo::matTrace3(double m[3][3]){
640 +  double trace;
641 +  trace = m[0][0] + m[1][1] + m[2][2];
642 +
643 +  return trace;
644 + }

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