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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 463 by gezelter, Sat Apr 5 03:39:25 2003 UTC vs.
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC

# Line 1 | Line 1
1   #include <cstdlib>
2   #include <cstring>
3 + #include <cmath>
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 + #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(){
# Line 22 | Line 34 | SimInfo::SimInfo(){
34    setTemp = 0;
35    thermalTime = 0.0;
36    rCut = 0.0;
37 +  ecr = 0.0;
38 +  est = 0.0;
39 +  oldEcr = 0.0;
40 +  oldRcut = 0.0;
41  
42 +  haveOrigRcut = 0;
43 +  haveOrigEcr = 0;
44 +  boxIsInit = 0;
45 +  
46 +  
47 +
48    usePBC = 0;
49    useLJ = 0;
50    useSticky = 0;
# Line 35 | Line 57 | void SimInfo::setBox(double newBox[3]) {
57   }
58  
59   void SimInfo::setBox(double newBox[3]) {
60 <  double smallestBox, maxCutoff;
61 <  int status;
62 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
60 >  
61 >  int i, j;
62 >  double tempMat[3][3];
63  
64 <  smallestBox = box_x;
65 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
64 >  for(i=0; i<3; i++)
65 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
66  
67 <  maxCutoff = smallestBox / 2.0;
67 >  tempMat[0][0] = newBox[0];
68 >  tempMat[1][1] = newBox[1];
69 >  tempMat[2][2] = newBox[2];
70  
71 <  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();
71 >  setBoxM( tempMat );
72  
73 <    rList = maxCutoff;
73 > }
74  
75 <    sprintf( painCave.errMsg,
76 <             "New Box size is forcing cutoff radius down to %lf\n",
77 <             maxCutoff - 1.0 );
78 <    painCave.isFatal = 0;
79 <    simError();
75 > void SimInfo::setBoxM( double theBox[3][3] ){
76 >  
77 >  int i, j, status;
78 >  double smallestBoxL, maxCutoff;
79 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
80 >                         // ordering in the array is as follows:
81 >                         // [ 0 3 6 ]
82 >                         // [ 1 4 7 ]
83 >                         // [ 2 5 8 ]
84 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
85  
86 <    rCut = rList - 1.0;
86 >  
87 >  if( !boxIsInit ) boxIsInit = 1;
88  
89 <    // list radius changed so we have to refresh the simulation structure.
90 <    refreshSim();
89 >  for(i=0; i < 3; i++)
90 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
91 >  
92 >  calcBoxL();
93 >  calcHmatInv();
94 >
95 >  for(i=0; i < 3; i++) {
96 >    for (j=0; j < 3; j++) {
97 >      FortranHmat[3*j + i] = Hmat[i][j];
98 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
99 >    }
100    }
101  
102 <  if (rCut > maxCutoff) {
102 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
103 >
104 > }
105 >
106 >
107 > void SimInfo::getBoxM (double theBox[3][3]) {
108 >
109 >  int i, j;
110 >  for(i=0; i<3; i++)
111 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
112 > }
113 >
114 >
115 > void SimInfo::scaleBox(double scale) {
116 >  double theBox[3][3];
117 >  int i, j;
118 >
119 >  // cerr << "Scaling box by " << scale << "\n";
120 >
121 >  for(i=0; i<3; i++)
122 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
123 >
124 >  setBoxM(theBox);
125 >
126 > }
127 >
128 > void SimInfo::calcHmatInv( void ) {
129 >  
130 >  int i,j;
131 >  double smallDiag;
132 >  double tol;
133 >  double sanity[3][3];
134 >
135 >  invertMat3( Hmat, HmatInv );
136 >
137 >  // Check the inverse to make sure it is sane:
138 >
139 >  matMul3( Hmat, HmatInv, sanity );
140 >    
141 >  // check to see if Hmat is orthorhombic
142 >  
143 >  smallDiag = Hmat[0][0];
144 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
145 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
146 >  tol = smallDiag * 1E-6;
147 >
148 >  orthoRhombic = 1;
149 >  
150 >  for (i = 0; i < 3; i++ ) {
151 >    for (j = 0 ; j < 3; j++) {
152 >      if (i != j) {
153 >        if (orthoRhombic) {
154 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
155 >        }        
156 >      }
157 >    }
158 >  }
159 > }
160 >
161 > double SimInfo::matDet3(double a[3][3]) {
162 >  int i, j, k;
163 >  double determinant;
164 >
165 >  determinant = 0.0;
166 >
167 >  for(i = 0; i < 3; i++) {
168 >    j = (i+1)%3;
169 >    k = (i+2)%3;
170 >
171 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
172 >  }
173 >
174 >  return determinant;
175 > }
176 >
177 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
178 >  
179 >  int  i, j, k, l, m, n;
180 >  double determinant;
181 >
182 >  determinant = matDet3( a );
183 >
184 >  if (determinant == 0.0) {
185      sprintf( painCave.errMsg,
186 <             "New Box size is forcing cutoff radius down to %lf\n",
187 <             maxCutoff );
76 <    painCave.isFatal = 0;
186 >             "Can't invert a matrix with a zero determinant!\n");
187 >    painCave.isFatal = 1;
188      simError();
189 +  }
190  
191 <    status = 0;
192 <    LJ_new_rcut(&rCut, &status);
193 <    if (status != 0) {
194 <      sprintf( painCave.errMsg,
195 <               "Error in recomputing LJ shifts based on new rcut\n");
196 <      painCave.isFatal = 1;
197 <      simError();
191 >  for (i=0; i < 3; i++) {
192 >    j = (i+1)%3;
193 >    k = (i+2)%3;
194 >    for(l = 0; l < 3; l++) {
195 >      m = (l+1)%3;
196 >      n = (l+2)%3;
197 >      
198 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
199      }
200    }
201   }
202  
203 < void SimInfo::getBox(double theBox[3]) {
204 <  theBox[0] = box_x;
205 <  theBox[1] = box_y;
206 <  theBox[2] = box_z;
203 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
204 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
205 >
206 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
207 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
208 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
209 >  
210 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
211 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
212 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
213 >  
214 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
215 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
216 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
217 >  
218 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
219 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
220 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
221   }
222 <
222 >
223 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
224 >  double a0, a1, a2;
225 >
226 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
227 >
228 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
229 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
230 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
231 > }
232 >
233 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
234 >  double temp[3][3];
235 >  int i, j;
236 >
237 >  for (i = 0; i < 3; i++) {
238 >    for (j = 0; j < 3; j++) {
239 >      temp[j][i] = in[i][j];
240 >    }
241 >  }
242 >  for (i = 0; i < 3; i++) {
243 >    for (j = 0; j < 3; j++) {
244 >      out[i][j] = temp[i][j];
245 >    }
246 >  }
247 > }
248 >  
249 > void SimInfo::printMat3(double A[3][3] ){
250 >
251 >  std::cerr
252 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
253 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
254 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
255 > }
256 >
257 > void SimInfo::printMat9(double A[9] ){
258 >
259 >  std::cerr
260 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
261 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
262 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
263 > }
264 >
265 > void SimInfo::calcBoxL( void ){
266 >
267 >  double dx, dy, dz, dsq;
268 >  int i;
269 >
270 >  // boxVol = Determinant of Hmat
271 >
272 >  boxVol = matDet3( Hmat );
273 >
274 >  // boxLx
275 >  
276 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
277 >  dsq = dx*dx + dy*dy + dz*dz;
278 >  boxL[0] = sqrt( dsq );
279 >  maxCutoff = 0.5 * boxL[0];
280 >
281 >  // boxLy
282 >  
283 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
284 >  dsq = dx*dx + dy*dy + dz*dz;
285 >  boxL[1] = sqrt( dsq );
286 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
287 >
288 >  // boxLz
289 >  
290 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
291 >  dsq = dx*dx + dy*dy + dz*dz;
292 >  boxL[2] = sqrt( dsq );
293 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
294 >
295 > }
296 >
297 >
298 > void SimInfo::wrapVector( double thePos[3] ){
299 >
300 >  int i, j, k;
301 >  double scaled[3];
302 >
303 >  if( !orthoRhombic ){
304 >    // calc the scaled coordinates.
305 >  
306 >
307 >    matVecMul3(HmatInv, thePos, scaled);
308 >    
309 >    for(i=0; i<3; i++)
310 >      scaled[i] -= roundMe(scaled[i]);
311 >    
312 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
313 >    
314 >    matVecMul3(Hmat, scaled, thePos);
315 >
316 >  }
317 >  else{
318 >    // calc the scaled coordinates.
319 >    
320 >    for(i=0; i<3; i++)
321 >      scaled[i] = thePos[i]*HmatInv[i][i];
322 >    
323 >    // wrap the scaled coordinates
324 >    
325 >    for(i=0; i<3; i++)
326 >      scaled[i] -= roundMe(scaled[i]);
327 >    
328 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
329 >    
330 >    for(i=0; i<3; i++)
331 >      thePos[i] = scaled[i]*Hmat[i][i];
332 >  }
333 >    
334 > }
335 >
336 >
337   int SimInfo::getNDF(){
338    int ndf_local, ndf;
339    
# Line 128 | Line 369 | void SimInfo::refreshSim(){
369  
370    simtype fInfo;
371    int isError;
372 +  int n_global;
373    int* excl;
374  
375 <  fInfo.box[0] = box_x;
134 <  fInfo.box[1] = box_y;
135 <  fInfo.box[2] = box_z;
375 >  fInfo.dielect = 0.0;
376  
377 <  fInfo.rlist = rList;
378 <  fInfo.rcut = rCut;
379 <  fInfo.rrf = ecr;
140 <  fInfo.rt = ecr - est;
141 <  fInfo.dielect = dielectric;
377 >  if( useDipole ){
378 >    if( useReactionField )fInfo.dielect = dielectric;
379 >  }
380  
381    fInfo.SIM_uses_PBC = usePBC;
382    //fInfo.SIM_uses_LJ = 0;
# Line 154 | Line 392 | void SimInfo::refreshSim(){
392  
393    excl = Exclude::getArray();
394  
395 + #ifdef IS_MPI
396 +  n_global = mpiSim->getTotAtoms();
397 + #else
398 +  n_global = n_atoms;
399 + #endif
400 +
401    isError = 0;
402  
403 < //   fInfo;
404 < //   n_atoms;
405 < //   identArray;
162 < //   n_exclude;
163 < //   excludes;
164 < //   nGlobalExcludes;
165 < //   globalExcludes;
166 < //   isError;
403 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
404 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
405 >                  &isError );
406  
168 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
169 –                  &nGlobalExcludes, globalExcludes, &isError );
170 –
407    if( isError ){
408  
409      sprintf( painCave.errMsg,
# Line 182 | Line 418 | void SimInfo::refreshSim(){
418    MPIcheckPoint();
419   #endif // is_mpi
420  
421 <  ndf = this->getNDF();
422 <  ndfRaw = this->getNDFraw();
421 >  this->ndf = this->getNDF();
422 >  this->ndfRaw = this->getNDFraw();
423  
424   }
425  
426 +
427 + void SimInfo::setRcut( double theRcut ){
428 +
429 +  if( !haveOrigRcut ){
430 +    haveOrigRcut = 1;
431 +    origRcut = theRcut;
432 +  }
433 +
434 +  rCut = theRcut;
435 +  checkCutOffs();
436 + }
437 +
438 + void SimInfo::setEcr( double theEcr ){
439 +
440 +  if( !haveOrigEcr ){
441 +    haveOrigEcr = 1;
442 +    origEcr = theEcr;
443 +  }
444 +
445 +  ecr = theEcr;
446 +  checkCutOffs();
447 + }
448 +
449 + void SimInfo::setEcr( double theEcr, double theEst ){
450 +
451 +  est = theEst;
452 +  setEcr( theEcr );
453 + }
454 +
455 +
456 + void SimInfo::checkCutOffs( void ){
457 +
458 +  int cutChanged = 0;
459 +
460 +  if( boxIsInit ){
461 +    
462 +    //we need to check cutOffs against the box
463 +    
464 +    if( maxCutoff > rCut ){
465 +      if( rCut < origRcut ){
466 +        rCut = origRcut;
467 +        if (rCut > maxCutoff) rCut = maxCutoff;
468 +        
469 +        sprintf( painCave.errMsg,
470 +                 "New Box size is setting the long range cutoff radius "
471 +                 "to %lf\n",
472 +                 rCut );
473 +        painCave.isFatal = 0;
474 +        simError();
475 +      }
476 +    }
477 +
478 +    if( maxCutoff > ecr ){
479 +      if( ecr < origEcr ){
480 +        rCut = origEcr;
481 +        if (ecr > maxCutoff) ecr = maxCutoff;
482 +        
483 +        sprintf( painCave.errMsg,
484 +                 "New Box size is setting the electrostaticCutoffRadius "
485 +                 "to %lf\n",
486 +                 ecr );
487 +        painCave.isFatal = 0;
488 +        simError();
489 +      }
490 +    }
491 +
492 +
493 +    if (rCut > maxCutoff) {
494 +      sprintf( painCave.errMsg,
495 +               "New Box size is setting the long range cutoff radius "
496 +               "to %lf\n",
497 +               maxCutoff );
498 +      painCave.isFatal = 0;
499 +      simError();
500 +      rCut = maxCutoff;
501 +    }
502 +
503 +    if( ecr > maxCutoff){
504 +      sprintf( painCave.errMsg,
505 +               "New Box size is setting the electrostaticCutoffRadius "
506 +               "to %lf\n",
507 +               maxCutoff  );
508 +      painCave.isFatal = 0;
509 +      simError();      
510 +      ecr = maxCutoff;
511 +    }
512 +
513 +    
514 +  }
515 +  
516 +
517 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
518 +
519 +  // rlist is the 1.0 plus max( rcut, ecr )
520 +  
521 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
522 +
523 +  if( cutChanged ){
524 +    
525 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
526 +  }
527 +
528 +  oldEcr = ecr;
529 +  oldRcut = rCut;
530 + }

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