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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 619 by mmeineke, Tue Jul 15 22:22:41 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
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 16 | Line 28 | SimInfo::SimInfo(){
28    n_constraints = 0;
29    n_oriented = 0;
30    n_dipoles = 0;
31 +  ndf = 0;
32 +  ndfRaw = 0;
33    the_integrator = NULL;
34    setTemp = 0;
35    thermalTime = 0.0;
36 +  rCut = 0.0;
37 +  ecr = 0.0;
38 +  est = 0.0;
39  
40    usePBC = 0;
41    useLJ = 0;
# Line 28 | Line 45 | SimInfo::SimInfo(){
45    useGB = 0;
46    useEAM = 0;
47  
48 +  wrapMeSimInfo( this );
49 + }
50  
51 + void SimInfo::setBox(double newBox[3]) {
52 +  
53 +  int i, j;
54 +  double tempMat[3][3];
55  
56 <  wrapMeSimInfo( this );
56 >  for(i=0; i<3; i++)
57 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
58 >
59 >  tempMat[0][0] = newBox[0];
60 >  tempMat[1][1] = newBox[1];
61 >  tempMat[2][2] = newBox[2];
62 >
63 >  setBoxM( tempMat );
64 >
65   }
66  
67 + void SimInfo::setBoxM( double theBox[3][3] ){
68 +  
69 +  int i, j, status;
70 +  double smallestBoxL, maxCutoff;
71 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
72 +                         // ordering in the array is as follows:
73 +                         // [ 0 3 6 ]
74 +                         // [ 1 4 7 ]
75 +                         // [ 2 5 8 ]
76 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
77 +
78 +
79 +  for(i=0; i < 3; i++)
80 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
81 +  
82 +  //  cerr
83 +  // << "setting Hmat ->\n"
84 +  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
85 +  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
86 +  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
87 +
88 +  calcBoxL();
89 +  calcHmatInv();
90 +
91 +  for(i=0; i < 3; i++) {
92 +    for (j=0; j < 3; j++) {
93 +      FortranHmat[3*j + i] = Hmat[i][j];
94 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
95 +    }
96 +  }
97 +
98 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
99 +
100 +  smallestBoxL = boxLx;
101 +  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
102 +  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
103 +
104 +  maxCutoff = smallestBoxL / 2.0;
105 +
106 +  if (rList > maxCutoff) {
107 +    sprintf( painCave.errMsg,
108 +             "New Box size is forcing neighborlist radius down to %lf\n",
109 +             maxCutoff );
110 +    painCave.isFatal = 0;
111 +    simError();
112 +
113 +    rList = maxCutoff;
114 +
115 +    sprintf( painCave.errMsg,
116 +             "New Box size is forcing cutoff radius down to %lf\n",
117 +             maxCutoff - 1.0 );
118 +    painCave.isFatal = 0;
119 +    simError();
120 +
121 +    rCut = rList - 1.0;
122 +
123 +    // list radius changed so we have to refresh the simulation structure.
124 +    refreshSim();
125 +  }
126 +
127 +  if( ecr > maxCutoff ){
128 +
129 +    sprintf( painCave.errMsg,
130 +             "New Box size is forcing electrostatic cutoff radius "
131 +             "down to %lf\n",
132 +             maxCutoff );
133 +    painCave.isFatal = 0;
134 +    simError();
135 +
136 +    ecr = maxCutoff;
137 +    est = 0.05 * ecr;
138 +
139 +    refreshSim();
140 +  }
141 +    
142 + }
143 +
144 +
145 + void SimInfo::getBoxM (double theBox[3][3]) {
146 +
147 +  int i, j;
148 +  for(i=0; i<3; i++)
149 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150 + }
151 +
152 +
153 + void SimInfo::scaleBox(double scale) {
154 +  double theBox[3][3];
155 +  int i, j;
156 +
157 +  // cerr << "Scaling box by " << scale << "\n";
158 +
159 +  for(i=0; i<3; i++)
160 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
161 +
162 +  setBoxM(theBox);
163 +
164 + }
165 +
166 + void SimInfo::calcHmatInv( void ) {
167 +  
168 +  int i,j;
169 +  double smallDiag;
170 +  double tol;
171 +  double sanity[3][3];
172 +
173 +  invertMat3( Hmat, HmatInv );
174 +
175 +  // Check the inverse to make sure it is sane:
176 +
177 +  matMul3( Hmat, HmatInv, sanity );
178 +    
179 +  // check to see if Hmat is orthorhombic
180 +  
181 +  smallDiag = Hmat[0][0];
182 +  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
183 +  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
184 +  tol = smallDiag * 1E-6;
185 +
186 +  orthoRhombic = 1;
187 +  
188 +  for (i = 0; i < 3; i++ ) {
189 +    for (j = 0 ; j < 3; j++) {
190 +      if (i != j) {
191 +        if (orthoRhombic) {
192 +          if (Hmat[i][j] >= tol) orthoRhombic = 0;
193 +        }        
194 +      }
195 +    }
196 +  }
197 + }
198 +
199 + double SimInfo::matDet3(double a[3][3]) {
200 +  int i, j, k;
201 +  double determinant;
202 +
203 +  determinant = 0.0;
204 +
205 +  for(i = 0; i < 3; i++) {
206 +    j = (i+1)%3;
207 +    k = (i+2)%3;
208 +
209 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
210 +  }
211 +
212 +  return determinant;
213 + }
214 +
215 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
216 +  
217 +  int  i, j, k, l, m, n;
218 +  double determinant;
219 +
220 +  determinant = matDet3( a );
221 +
222 +  if (determinant == 0.0) {
223 +    sprintf( painCave.errMsg,
224 +             "Can't invert a matrix with a zero determinant!\n");
225 +    painCave.isFatal = 1;
226 +    simError();
227 +  }
228 +
229 +  for (i=0; i < 3; i++) {
230 +    j = (i+1)%3;
231 +    k = (i+2)%3;
232 +    for(l = 0; l < 3; l++) {
233 +      m = (l+1)%3;
234 +      n = (l+2)%3;
235 +      
236 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
237 +    }
238 +  }
239 + }
240 +
241 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
242 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
243 +
244 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
245 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
246 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
247 +  
248 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
249 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
250 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
251 +  
252 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
253 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
254 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
255 +  
256 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
257 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
258 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
259 + }
260 +
261 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
262 +  double a0, a1, a2;
263 +
264 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
265 +
266 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
267 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
268 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
269 + }
270 +
271 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
272 +  double temp[3][3];
273 +  int i, j;
274 +
275 +  for (i = 0; i < 3; i++) {
276 +    for (j = 0; j < 3; j++) {
277 +      temp[j][i] = in[i][j];
278 +    }
279 +  }
280 +  for (i = 0; i < 3; i++) {
281 +    for (j = 0; j < 3; j++) {
282 +      out[i][j] = temp[i][j];
283 +    }
284 +  }
285 + }
286 +  
287 + void SimInfo::printMat3(double A[3][3] ){
288 +
289 +  std::cerr
290 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
291 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
292 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
293 + }
294 +
295 + void SimInfo::printMat9(double A[9] ){
296 +
297 +  std::cerr
298 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
299 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
300 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
301 + }
302 +
303 + void SimInfo::calcBoxL( void ){
304 +
305 +  double dx, dy, dz, dsq;
306 +  int i;
307 +
308 +  // boxVol = Determinant of Hmat
309 +
310 +  boxVol = matDet3( Hmat );
311 +
312 +  // boxLx
313 +  
314 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
315 +  dsq = dx*dx + dy*dy + dz*dz;
316 +  boxLx = sqrt( dsq );
317 +
318 +  // boxLy
319 +  
320 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
321 +  dsq = dx*dx + dy*dy + dz*dz;
322 +  boxLy = sqrt( dsq );
323 +
324 +  // boxLz
325 +  
326 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
327 +  dsq = dx*dx + dy*dy + dz*dz;
328 +  boxLz = sqrt( dsq );
329 +  
330 + }
331 +
332 +
333 + void SimInfo::wrapVector( double thePos[3] ){
334 +
335 +  int i, j, k;
336 +  double scaled[3];
337 +
338 +  if( !orthoRhombic ){
339 +    // calc the scaled coordinates.
340 +  
341 +
342 +    matVecMul3(HmatInv, thePos, scaled);
343 +    
344 +    for(i=0; i<3; i++)
345 +      scaled[i] -= roundMe(scaled[i]);
346 +    
347 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
348 +    
349 +    matVecMul3(Hmat, scaled, thePos);
350 +
351 +  }
352 +  else{
353 +    // calc the scaled coordinates.
354 +    
355 +    for(i=0; i<3; i++)
356 +      scaled[i] = thePos[i]*HmatInv[i][i];
357 +    
358 +    // wrap the scaled coordinates
359 +    
360 +    for(i=0; i<3; i++)
361 +      scaled[i] -= roundMe(scaled[i]);
362 +    
363 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
364 +    
365 +    for(i=0; i<3; i++)
366 +      thePos[i] = scaled[i]*Hmat[i][i];
367 +  }
368 +    
369 + }
370 +
371 +
372 + int SimInfo::getNDF(){
373 +  int ndf_local, ndf;
374 +  
375 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
376 +
377 + #ifdef IS_MPI
378 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
379 + #else
380 +  ndf = ndf_local;
381 + #endif
382 +
383 +  ndf = ndf - 3;
384 +
385 +  return ndf;
386 + }
387 +
388 + int SimInfo::getNDFraw() {
389 +  int ndfRaw_local, ndfRaw;
390 +
391 +  // Raw degrees of freedom that we have to set
392 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
393 +  
394 + #ifdef IS_MPI
395 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396 + #else
397 +  ndfRaw = ndfRaw_local;
398 + #endif
399 +
400 +  return ndfRaw;
401 + }
402 +
403   void SimInfo::refreshSim(){
404  
405    simtype fInfo;
406    int isError;
407 +  int n_global;
408 +  int* excl;
409 +  
410 +  fInfo.rrf = 0.0;
411 +  fInfo.rt = 0.0;
412 +  fInfo.dielect = 0.0;
413  
41 –  fInfo.box[0] = box_x;
42 –  fInfo.box[1] = box_y;
43 –  fInfo.box[2] = box_z;
44 –
414    fInfo.rlist = rList;
415    fInfo.rcut = rCut;
47 –  fInfo.rrf = ecr;
48 –  fInfo.rt = ecr - est;
49 –  fInfo.dielect = dielectric;
416  
417 +  if( useDipole ){
418 +    fInfo.rrf = ecr;
419 +    fInfo.rt = ecr - est;
420 +    if( useReactionField )fInfo.dielect = dielectric;
421 +  }
422 +
423    fInfo.SIM_uses_PBC = usePBC;
424 +  //fInfo.SIM_uses_LJ = 0;
425    fInfo.SIM_uses_LJ = useLJ;
426 <  //fInfo.SIM_uses_sticky = useSticky;
427 <  fInfo.SIM_uses_sticky = 0;
426 >  fInfo.SIM_uses_sticky = useSticky;
427 >  //fInfo.SIM_uses_sticky = 0;
428    fInfo.SIM_uses_dipoles = useDipole;
429 <  fInfo.SIM_uses_RF = useReactionField;
429 >  //fInfo.SIM_uses_dipoles = 0;
430 >  //fInfo.SIM_uses_RF = useReactionField;
431 >  fInfo.SIM_uses_RF = 0;
432    fInfo.SIM_uses_GB = useGB;
433    fInfo.SIM_uses_EAM = useEAM;
434  
435 +  excl = Exclude::getArray();
436  
437 + #ifdef IS_MPI
438 +  n_global = mpiSim->getTotAtoms();
439 + #else
440 +  n_global = n_atoms;
441 + #endif
442 +
443    isError = 0;
444  
445 <  fInfo;
446 <  n_atoms;
447 <  identArray;
66 <  n_exclude;
67 <  excludes;
68 <  nGlobalExcludes;
69 <  globalExcludes;
70 <  isError;
445 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
446 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
447 >                  &isError );
448  
72 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
73 –
449    if( isError ){
450  
451      sprintf( painCave.errMsg,
# Line 84 | Line 459 | void SimInfo::refreshSim(){
459             "succesfully sent the simulation information to fortran.\n");
460    MPIcheckPoint();
461   #endif // is_mpi
462 +
463 +  this->ndf = this->getNDF();
464 +  this->ndfRaw = this->getNDFraw();
465 +
466   }
467  

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