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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 482 by chuckv, Tue Apr 8 22:38:43 2003 UTC vs.
Revision 642 by mmeineke, Mon Jul 21 16:23:57 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 21 | Line 33 | SimInfo::SimInfo(){
33    the_integrator = NULL;
34    setTemp = 0;
35    thermalTime = 0.0;
36 +  currentTime = 0.0;
37    rCut = 0.0;
38 +  ecr = 0.0;
39 +  est = 0.0;
40 +  oldEcr = 0.0;
41 +  oldRcut = 0.0;
42  
43 +  haveOrigRcut = 0;
44 +  haveOrigEcr = 0;
45 +  boxIsInit = 0;
46 +  
47 +  
48 +
49    usePBC = 0;
50    useLJ = 0;
51    useSticky = 0;
# Line 35 | Line 58 | void SimInfo::setBox(double newBox[3]) {
58   }
59  
60   void SimInfo::setBox(double newBox[3]) {
61 <  double smallestBox, maxCutoff;
62 <  int status;
63 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
61 >  
62 >  int i, j;
63 >  double tempMat[3][3];
64  
65 <  smallestBox = box_x;
66 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
65 >  for(i=0; i<3; i++)
66 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
67  
68 <  maxCutoff = smallestBox / 2.0;
68 >  tempMat[0][0] = newBox[0];
69 >  tempMat[1][1] = newBox[1];
70 >  tempMat[2][2] = newBox[2];
71  
72 <  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();
72 >  setBoxM( tempMat );
73  
74 <    rList = maxCutoff;
74 > }
75  
76 <    sprintf( painCave.errMsg,
77 <             "New Box size is forcing cutoff radius down to %lf\n",
78 <             maxCutoff - 1.0 );
79 <    painCave.isFatal = 0;
80 <    simError();
76 > void SimInfo::setBoxM( double theBox[3][3] ){
77 >  
78 >  int i, j, status;
79 >  double smallestBoxL, maxCutoff;
80 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
81 >                         // ordering in the array is as follows:
82 >                         // [ 0 3 6 ]
83 >                         // [ 1 4 7 ]
84 >                         // [ 2 5 8 ]
85 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
86  
87 <    rCut = rList - 1.0;
87 >  
88 >  if( !boxIsInit ) boxIsInit = 1;
89  
90 <    // list radius changed so we have to refresh the simulation structure.
91 <    refreshSim();
90 >  for(i=0; i < 3; i++)
91 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
92 >  
93 >  calcBoxL();
94 >  calcHmatInv();
95 >
96 >  for(i=0; i < 3; i++) {
97 >    for (j=0; j < 3; j++) {
98 >      FortranHmat[3*j + i] = Hmat[i][j];
99 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
100 >    }
101    }
102  
103 <  if (rCut > maxCutoff) {
103 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
104 >
105 > }
106 >
107 >
108 > void SimInfo::getBoxM (double theBox[3][3]) {
109 >
110 >  int i, j;
111 >  for(i=0; i<3; i++)
112 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
113 > }
114 >
115 >
116 > void SimInfo::scaleBox(double scale) {
117 >  double theBox[3][3];
118 >  int i, j;
119 >
120 >  // cerr << "Scaling box by " << scale << "\n";
121 >
122 >  for(i=0; i<3; i++)
123 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
124 >
125 >  setBoxM(theBox);
126 >
127 > }
128 >
129 > void SimInfo::calcHmatInv( void ) {
130 >  
131 >  int i,j;
132 >  double smallDiag;
133 >  double tol;
134 >  double sanity[3][3];
135 >
136 >  invertMat3( Hmat, HmatInv );
137 >
138 >  // Check the inverse to make sure it is sane:
139 >
140 >  matMul3( Hmat, HmatInv, sanity );
141 >    
142 >  // check to see if Hmat is orthorhombic
143 >  
144 >  smallDiag = Hmat[0][0];
145 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
146 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
147 >  tol = smallDiag * 1E-6;
148 >
149 >  orthoRhombic = 1;
150 >  
151 >  for (i = 0; i < 3; i++ ) {
152 >    for (j = 0 ; j < 3; j++) {
153 >      if (i != j) {
154 >        if (orthoRhombic) {
155 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
156 >        }        
157 >      }
158 >    }
159 >  }
160 > }
161 >
162 > double SimInfo::matDet3(double a[3][3]) {
163 >  int i, j, k;
164 >  double determinant;
165 >
166 >  determinant = 0.0;
167 >
168 >  for(i = 0; i < 3; i++) {
169 >    j = (i+1)%3;
170 >    k = (i+2)%3;
171 >
172 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
173 >  }
174 >
175 >  return determinant;
176 > }
177 >
178 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
179 >  
180 >  int  i, j, k, l, m, n;
181 >  double determinant;
182 >
183 >  determinant = matDet3( a );
184 >
185 >  if (determinant == 0.0) {
186      sprintf( painCave.errMsg,
187 <             "New Box size is forcing cutoff radius down to %lf\n",
188 <             maxCutoff );
76 <    painCave.isFatal = 0;
187 >             "Can't invert a matrix with a zero determinant!\n");
188 >    painCave.isFatal = 1;
189      simError();
190 +  }
191  
192 <    status = 0;
193 <    LJ_new_rcut(&rCut, &status);
194 <    if (status != 0) {
195 <      sprintf( painCave.errMsg,
196 <               "Error in recomputing LJ shifts based on new rcut\n");
197 <      painCave.isFatal = 1;
198 <      simError();
192 >  for (i=0; i < 3; i++) {
193 >    j = (i+1)%3;
194 >    k = (i+2)%3;
195 >    for(l = 0; l < 3; l++) {
196 >      m = (l+1)%3;
197 >      n = (l+2)%3;
198 >      
199 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
200      }
201    }
202   }
203  
204 < void SimInfo::getBox(double theBox[3]) {
205 <  theBox[0] = box_x;
206 <  theBox[1] = box_y;
207 <  theBox[2] = box_z;
204 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
205 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
206 >
207 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
208 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
209 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
210 >  
211 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
212 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
213 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
214 >  
215 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
216 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
217 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
218 >  
219 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
220 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
221 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
222   }
223 <
223 >
224 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
225 >  double a0, a1, a2;
226 >
227 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
228 >
229 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
230 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
231 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
232 > }
233 >
234 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
235 >  double temp[3][3];
236 >  int i, j;
237 >
238 >  for (i = 0; i < 3; i++) {
239 >    for (j = 0; j < 3; j++) {
240 >      temp[j][i] = in[i][j];
241 >    }
242 >  }
243 >  for (i = 0; i < 3; i++) {
244 >    for (j = 0; j < 3; j++) {
245 >      out[i][j] = temp[i][j];
246 >    }
247 >  }
248 > }
249 >  
250 > void SimInfo::printMat3(double A[3][3] ){
251 >
252 >  std::cerr
253 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
254 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
255 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
256 > }
257 >
258 > void SimInfo::printMat9(double A[9] ){
259 >
260 >  std::cerr
261 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
262 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
263 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
264 > }
265 >
266 > void SimInfo::calcBoxL( void ){
267 >
268 >  double dx, dy, dz, dsq;
269 >  int i;
270 >
271 >  // boxVol = Determinant of Hmat
272 >
273 >  boxVol = matDet3( Hmat );
274 >
275 >  // boxLx
276 >  
277 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
278 >  dsq = dx*dx + dy*dy + dz*dz;
279 >  boxL[0] = sqrt( dsq );
280 >  maxCutoff = 0.5 * boxL[0];
281 >
282 >  // boxLy
283 >  
284 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
285 >  dsq = dx*dx + dy*dy + dz*dz;
286 >  boxL[1] = sqrt( dsq );
287 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
288 >
289 >  // boxLz
290 >  
291 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
292 >  dsq = dx*dx + dy*dy + dz*dz;
293 >  boxL[2] = sqrt( dsq );
294 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
295 >
296 > }
297 >
298 >
299 > void SimInfo::wrapVector( double thePos[3] ){
300 >
301 >  int i, j, k;
302 >  double scaled[3];
303 >
304 >  if( !orthoRhombic ){
305 >    // calc the scaled coordinates.
306 >  
307 >
308 >    matVecMul3(HmatInv, thePos, scaled);
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 >    matVecMul3(Hmat, scaled, thePos);
316 >
317 >  }
318 >  else{
319 >    // calc the scaled coordinates.
320 >    
321 >    for(i=0; i<3; i++)
322 >      scaled[i] = thePos[i]*HmatInv[i][i];
323 >    
324 >    // wrap the scaled coordinates
325 >    
326 >    for(i=0; i<3; i++)
327 >      scaled[i] -= roundMe(scaled[i]);
328 >    
329 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
330 >    
331 >    for(i=0; i<3; i++)
332 >      thePos[i] = scaled[i]*Hmat[i][i];
333 >  }
334 >    
335 > }
336 >
337 >
338   int SimInfo::getNDF(){
339    int ndf_local, ndf;
340    
# Line 128 | Line 370 | void SimInfo::refreshSim(){
370  
371    simtype fInfo;
372    int isError;
373 +  int n_global;
374    int* excl;
375 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
375 >
376    fInfo.dielect = 0.0;
377  
137 –  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 –
378    if( useDipole ){
145 –    fInfo.rrf = ecr;
146 –    fInfo.rt = ecr - est;
379      if( useReactionField )fInfo.dielect = dielectric;
380    }
381  
# Line 161 | Line 393 | void SimInfo::refreshSim(){
393  
394    excl = Exclude::getArray();
395  
396 + #ifdef IS_MPI
397 +  n_global = mpiSim->getTotAtoms();
398 + #else
399 +  n_global = n_atoms;
400 + #endif
401 +
402    isError = 0;
403  
404 < //   fInfo;
405 < //   n_atoms;
406 < //   identArray;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
404 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
405 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
406 >                  &isError );
407  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
408    if( isError ){
409  
410      sprintf( painCave.errMsg,
# Line 194 | Line 424 | void SimInfo::refreshSim(){
424  
425   }
426  
427 +
428 + void SimInfo::setRcut( double theRcut ){
429 +
430 +  if( !haveOrigRcut ){
431 +    haveOrigRcut = 1;
432 +    origRcut = theRcut;
433 +  }
434 +
435 +  rCut = theRcut;
436 +  checkCutOffs();
437 + }
438 +
439 + void SimInfo::setEcr( double theEcr ){
440 +
441 +  if( !haveOrigEcr ){
442 +    haveOrigEcr = 1;
443 +    origEcr = theEcr;
444 +  }
445 +
446 +  ecr = theEcr;
447 +  checkCutOffs();
448 + }
449 +
450 + void SimInfo::setEcr( double theEcr, double theEst ){
451 +
452 +  est = theEst;
453 +  setEcr( theEcr );
454 + }
455 +
456 +
457 + void SimInfo::checkCutOffs( void ){
458 +
459 +  int cutChanged = 0;
460 +
461 +  if( boxIsInit ){
462 +    
463 +    //we need to check cutOffs against the box
464 +    
465 +    if( maxCutoff > rCut ){
466 +      if( rCut < origRcut ){
467 +        rCut = origRcut;
468 +        if (rCut > maxCutoff) rCut = maxCutoff;
469 +        
470 +        sprintf( painCave.errMsg,
471 +                 "New Box size is setting the long range cutoff radius "
472 +                 "to %lf\n",
473 +                 rCut );
474 +        painCave.isFatal = 0;
475 +        simError();
476 +      }
477 +    }
478 +
479 +    if( maxCutoff > ecr ){
480 +      if( ecr < origEcr ){
481 +        rCut = origEcr;
482 +        if (ecr > maxCutoff) ecr = maxCutoff;
483 +        
484 +        sprintf( painCave.errMsg,
485 +                 "New Box size is setting the electrostaticCutoffRadius "
486 +                 "to %lf\n",
487 +                 ecr );
488 +        painCave.isFatal = 0;
489 +        simError();
490 +      }
491 +    }
492 +
493 +
494 +    if (rCut > maxCutoff) {
495 +      sprintf( painCave.errMsg,
496 +               "New Box size is setting the long range cutoff radius "
497 +               "to %lf\n",
498 +               maxCutoff );
499 +      painCave.isFatal = 0;
500 +      simError();
501 +      rCut = maxCutoff;
502 +    }
503 +
504 +    if( ecr > maxCutoff){
505 +      sprintf( painCave.errMsg,
506 +               "New Box size is setting the electrostaticCutoffRadius "
507 +               "to %lf\n",
508 +               maxCutoff  );
509 +      painCave.isFatal = 0;
510 +      simError();      
511 +      ecr = maxCutoff;
512 +    }
513 +
514 +    
515 +  }
516 +  
517 +
518 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
519 +
520 +  // rlist is the 1.0 plus max( rcut, ecr )
521 +  
522 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
523 +
524 +  if( cutChanged ){
525 +    
526 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
527 +  }
528 +
529 +  oldEcr = ecr;
530 +  oldRcut = rCut;
531 + }

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