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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 1031 by tim, Fri Feb 6 18:58:06 2004 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 12 | Line 12 | using namespace std;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17   #ifdef IS_MPI
18   #include "mpiSimulation.hpp"
19   #endif
# Line 27 | Line 29 | SimInfo::SimInfo(){
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34    nZconstraints = 0;
35    n_oriented = 0;
# Line 49 | Line 51 | SimInfo::SimInfo(){
51    
52    resetTime = 1e99;
53  
54 +  orthoRhombic = 0;
55    orthoTolerance = 1E-6;
56    useInitXSstate = true;
57  
# Line 61 | Line 64 | SimInfo::SimInfo(){
64    useGB = 0;
65    useEAM = 0;
66  
67 +  excludes = Exclude::Instance();
68 +
69    myConfiguration = new SimState();
70  
71    has_minimizer = false;
# Line 183 | Line 188 | void SimInfo::calcHmatInv( void ) {
188      
189      if( orthoRhombic ){
190        sprintf( painCave.errMsg,
191 <               "Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n"
192 <               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
193 <               "\tvariable ( currently set to %G ).\n",
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 <               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
202 <               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
203 <               "\tvariable ( currently set to %G ).\n",
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  
203 – double SimInfo::matDet3(double a[3][3]) {
204 –  int i, j, k;
205 –  double determinant;
206 –
207 –  determinant = 0.0;
208 –
209 –  for(i = 0; i < 3; i++) {
210 –    j = (i+1)%3;
211 –    k = (i+2)%3;
212 –
213 –    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
214 –  }
215 –
216 –  return determinant;
217 – }
218 –
219 – void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
220 –  
221 –  int  i, j, k, l, m, n;
222 –  double determinant;
223 –
224 –  determinant = matDet3( a );
225 –
226 –  if (determinant == 0.0) {
227 –    sprintf( painCave.errMsg,
228 –             "Can't invert a matrix with a zero determinant!\n");
229 –    painCave.isFatal = 1;
230 –    simError();
231 –  }
232 –
233 –  for (i=0; i < 3; i++) {
234 –    j = (i+1)%3;
235 –    k = (i+2)%3;
236 –    for(l = 0; l < 3; l++) {
237 –      m = (l+1)%3;
238 –      n = (l+2)%3;
239 –      
240 –      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
241 –    }
242 –  }
243 – }
244 –
245 – void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
246 –  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
247 –
248 –  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
249 –  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
250 –  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
251 –  
252 –  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
253 –  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
254 –  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
255 –  
256 –  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
257 –  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
258 –  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
259 –  
260 –  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
261 –  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
262 –  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
263 – }
264 –
265 – void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
266 –  double a0, a1, a2;
267 –
268 –  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
269 –
270 –  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
271 –  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
272 –  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
273 – }
274 –
275 – void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
276 –  double temp[3][3];
277 –  int i, j;
278 –
279 –  for (i = 0; i < 3; i++) {
280 –    for (j = 0; j < 3; j++) {
281 –      temp[j][i] = in[i][j];
282 –    }
283 –  }
284 –  for (i = 0; i < 3; i++) {
285 –    for (j = 0; j < 3; j++) {
286 –      out[i][j] = temp[i][j];
287 –    }
288 –  }
289 – }
290 –  
291 – void SimInfo::printMat3(double A[3][3] ){
292 –
293 –  std::cerr
294 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
295 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
296 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
297 – }
298 –
299 – void SimInfo::printMat9(double A[9] ){
300 –
301 –  std::cerr
302 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
303 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
304 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
305 – }
306 –
307 –
308 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
309 –
310 –      out[0] = a[1] * b[2] - a[2] * b[1];
311 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
312 –      out[2] = a[0] * b[1] - a[1] * b[0];
313 –      
314 – }
315 –
316 – double SimInfo::dotProduct3(double a[3], double b[3]){
317 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
318 – }
319 –
320 – double SimInfo::length3(double a[3]){
321 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
322 – }
323 –
213   void SimInfo::calcBoxL( void ){
214  
215    double dx, dy, dz, dsq;
# Line 376 | Line 265 | double SimInfo::calcMaxCutOff(){
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) / length3(rij);
268 >    
269 >  crossProduct3(ri, rj, rij);
270 >  distXY = dotProduct3(rk,rij) / norm3(rij);
271  
272    crossProduct3(rj,rk, rjk);
273 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
273 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
274  
275    crossProduct3(rk,ri, rki);
276 <  distZX = dotProduct3(rj,rki) / length3(rki);
276 >  distZX = dotProduct3(rj,rki) / norm3(rki);
277  
278    minDist = min(min(distXY, distYZ), distZX);
279    return minDist/2;
# Line 432 | Line 321 | int SimInfo::getNDF(){
321  
322   int SimInfo::getNDF(){
323    int ndf_local;
435 –  
436 –  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
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 +  // nZconstraints is global, as are the 3 COM translations for the
342 +  // entire system:
343 +
344    ndf = ndf - 3 - nZconstraints;
345  
346    return ndf;
# Line 450 | Line 350 | int SimInfo::getNDFraw() {
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 464 | Line 369 | int SimInfo::getNDFtranslational() {
369   int SimInfo::getNDFtranslational() {
370    int ndfTrans_local;
371  
372 <  ndfTrans_local = 3 * n_atoms - n_constraints;
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
# Line 503 | Line 409 | void SimInfo::refreshSim(){
409    fInfo.SIM_uses_GB = useGB;
410    fInfo.SIM_uses_EAM = useEAM;
411  
412 <  excl = Exclude::getArray();
412 >  n_exclude = excludes->getSize();
413 >  excl = excludes->getFortranArray();
414  
415   #ifdef IS_MPI
416    n_global = mpiSim->getTotAtoms();
# Line 571 | Line 478 | void SimInfo::checkCutOffs( void ){
478      
479      if( rCut > maxCutoff ){
480        sprintf( painCave.errMsg,
481 <               "Box size is too small for the long range cutoff radius, "
482 <               "%G, at time %G\n"
481 >               "LJrcut is too large for the current periodic box.\n"
482 >               "\tCurrent Value of LJrcut = %G at time %G\n "
483 >               "\tThis is larger than half of at least one of the\n"
484 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
485 >               "\n, %G"
486                 "\t[ %G %G %G ]\n"
487                 "\t[ %G %G %G ]\n"
488                 "\t[ %G %G %G ]\n",
489 <               rCut, currentTime,
489 >               rCut, currentTime, maxCutoff,
490                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
491                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
492                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
# Line 587 | Line 497 | void SimInfo::checkCutOffs( void ){
497      if( haveEcr ){
498        if( ecr > maxCutoff ){
499          sprintf( painCave.errMsg,
500 <                 "Box size is too small for the electrostatic cutoff radius, "
501 <                 "%G, at time %G\n"
502 <                 "\t[ %G %G %G ]\n"
503 <                 "\t[ %G %G %G ]\n"
504 <                 "\t[ %G %G %G ]\n",
500 >                 "electrostaticCutoffRadius is too large for the current\n"
501 >                 "\tperiodic box.\n\n"
502 >                 "\tCurrent Value of ECR = %G at time %G\n "
503 >                 "\tThis is larger than half of at least one of the\n"
504 >                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
505 >                 "\n"
506 >                 "\t[ %G %G %G ]\n"
507 >                 "\t[ %G %G %G ]\n"
508 >                 "\t[ %G %G %G ]\n",
509                   ecr, currentTime,
510                   Hmat[0][0], Hmat[0][1], Hmat[0][2],
511                   Hmat[1][0], Hmat[1][1], Hmat[1][2],
# Line 657 | Line 571 | vector<GenericData*> SimInfo::getProperties(){
571      
572    return result;
573   }
660 –
661 – double SimInfo::matTrace3(double m[3][3]){
662 –  double trace;
663 –  trace = m[0][0] + m[1][1] + m[2][2];
664 –
665 –  return trace;
666 – }

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