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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 393 by mmeineke, Mon Mar 24 18:33:51 2003 UTC vs.
Revision 621 by gezelter, Wed Jul 16 02:11:02 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 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 = boxL[0];
101 +  if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1];
102 +  if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2];
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 +    rList = maxCutoff;
113 +
114 +    if (rCut > (rList - 1.0)) {
115 +      sprintf( painCave.errMsg,
116 +               "New Box size is forcing LJ cutoff radius down to %lf\n",
117 +               rList - 1.0 );
118 +      painCave.isFatal = 0;
119 +      simError();
120 +      rCut = rList - 1.0;
121 +    }
122 +
123 +    if( ecr > (rList - 1.0) ){
124 +      sprintf( painCave.errMsg,
125 +               "New Box size is forcing electrostaticCutoffRadius "
126 +               "down to %lf\n"
127 +               "electrostaticSkinThickness is now %lf\n",
128 +               rList - 1.0, 0.05*(rList-1.0) );
129 +      painCave.isFatal = 0;
130 +      simError();      
131 +      ecr = maxCutoff;
132 +      est = 0.05 * ecr;
133 +    }
134 +
135 +    // At least one of the radii changed, so we need a refresh:
136 +    refreshSim();
137 +  }    
138 + }
139 +
140 +
141 + void SimInfo::getBoxM (double theBox[3][3]) {
142 +
143 +  int i, j;
144 +  for(i=0; i<3; i++)
145 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146 + }
147 +
148 +
149 + void SimInfo::scaleBox(double scale) {
150 +  double theBox[3][3];
151 +  int i, j;
152 +
153 +  // cerr << "Scaling box by " << scale << "\n";
154 +
155 +  for(i=0; i<3; i++)
156 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
157 +
158 +  setBoxM(theBox);
159 +
160 + }
161 +
162 + void SimInfo::calcHmatInv( void ) {
163 +  
164 +  int i,j;
165 +  double smallDiag;
166 +  double tol;
167 +  double sanity[3][3];
168 +
169 +  invertMat3( Hmat, HmatInv );
170 +
171 +  // Check the inverse to make sure it is sane:
172 +
173 +  matMul3( Hmat, HmatInv, sanity );
174 +    
175 +  // check to see if Hmat is orthorhombic
176 +  
177 +  smallDiag = Hmat[0][0];
178 +  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
179 +  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
180 +  tol = smallDiag * 1E-6;
181 +
182 +  orthoRhombic = 1;
183 +  
184 +  for (i = 0; i < 3; i++ ) {
185 +    for (j = 0 ; j < 3; j++) {
186 +      if (i != j) {
187 +        if (orthoRhombic) {
188 +          if (Hmat[i][j] >= tol) orthoRhombic = 0;
189 +        }        
190 +      }
191 +    }
192 +  }
193 + }
194 +
195 + double SimInfo::matDet3(double a[3][3]) {
196 +  int i, j, k;
197 +  double determinant;
198 +
199 +  determinant = 0.0;
200 +
201 +  for(i = 0; i < 3; i++) {
202 +    j = (i+1)%3;
203 +    k = (i+2)%3;
204 +
205 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
206 +  }
207 +
208 +  return determinant;
209 + }
210 +
211 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
212 +  
213 +  int  i, j, k, l, m, n;
214 +  double determinant;
215 +
216 +  determinant = matDet3( a );
217 +
218 +  if (determinant == 0.0) {
219 +    sprintf( painCave.errMsg,
220 +             "Can't invert a matrix with a zero determinant!\n");
221 +    painCave.isFatal = 1;
222 +    simError();
223 +  }
224 +
225 +  for (i=0; i < 3; i++) {
226 +    j = (i+1)%3;
227 +    k = (i+2)%3;
228 +    for(l = 0; l < 3; l++) {
229 +      m = (l+1)%3;
230 +      n = (l+2)%3;
231 +      
232 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
233 +    }
234 +  }
235 + }
236 +
237 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
238 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
239 +
240 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
241 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
242 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
243 +  
244 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
245 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
246 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
247 +  
248 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
249 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
250 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
251 +  
252 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
253 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
254 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
255 + }
256 +
257 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
258 +  double a0, a1, a2;
259 +
260 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
261 +
262 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
263 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
264 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
265 + }
266 +
267 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268 +  double temp[3][3];
269 +  int i, j;
270 +
271 +  for (i = 0; i < 3; i++) {
272 +    for (j = 0; j < 3; j++) {
273 +      temp[j][i] = in[i][j];
274 +    }
275 +  }
276 +  for (i = 0; i < 3; i++) {
277 +    for (j = 0; j < 3; j++) {
278 +      out[i][j] = temp[i][j];
279 +    }
280 +  }
281 + }
282 +  
283 + void SimInfo::printMat3(double A[3][3] ){
284 +
285 +  std::cerr
286 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289 + }
290 +
291 + void SimInfo::printMat9(double A[9] ){
292 +
293 +  std::cerr
294 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297 + }
298 +
299 + void SimInfo::calcBoxL( void ){
300 +
301 +  double dx, dy, dz, dsq;
302 +  int i;
303 +
304 +  // boxVol = Determinant of Hmat
305 +
306 +  boxVol = matDet3( Hmat );
307 +
308 +  // boxLx
309 +  
310 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
311 +  dsq = dx*dx + dy*dy + dz*dz;
312 +  boxL[0] = sqrt( dsq );
313 +
314 +  // boxLy
315 +  
316 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
317 +  dsq = dx*dx + dy*dy + dz*dz;
318 +  boxL[1] = sqrt( dsq );
319 +
320 +  // boxLz
321 +  
322 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
323 +  dsq = dx*dx + dy*dy + dz*dz;
324 +  boxL[2] = sqrt( dsq );
325 +  
326 + }
327 +
328 +
329 + void SimInfo::wrapVector( double thePos[3] ){
330 +
331 +  int i, j, k;
332 +  double scaled[3];
333 +
334 +  if( !orthoRhombic ){
335 +    // calc the scaled coordinates.
336 +  
337 +
338 +    matVecMul3(HmatInv, thePos, scaled);
339 +    
340 +    for(i=0; i<3; i++)
341 +      scaled[i] -= roundMe(scaled[i]);
342 +    
343 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
344 +    
345 +    matVecMul3(Hmat, scaled, thePos);
346 +
347 +  }
348 +  else{
349 +    // calc the scaled coordinates.
350 +    
351 +    for(i=0; i<3; i++)
352 +      scaled[i] = thePos[i]*HmatInv[i][i];
353 +    
354 +    // wrap the scaled coordinates
355 +    
356 +    for(i=0; i<3; i++)
357 +      scaled[i] -= roundMe(scaled[i]);
358 +    
359 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
360 +    
361 +    for(i=0; i<3; i++)
362 +      thePos[i] = scaled[i]*Hmat[i][i];
363 +  }
364 +    
365 + }
366 +
367 +
368 + int SimInfo::getNDF(){
369 +  int ndf_local, ndf;
370 +  
371 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
372 +
373 + #ifdef IS_MPI
374 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
375 + #else
376 +  ndf = ndf_local;
377 + #endif
378 +
379 +  ndf = ndf - 3;
380 +
381 +  return ndf;
382 + }
383 +
384 + int SimInfo::getNDFraw() {
385 +  int ndfRaw_local, ndfRaw;
386 +
387 +  // Raw degrees of freedom that we have to set
388 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
389 +  
390 + #ifdef IS_MPI
391 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
392 + #else
393 +  ndfRaw = ndfRaw_local;
394 + #endif
395 +
396 +  return ndfRaw;
397 + }
398 +
399   void SimInfo::refreshSim(){
400  
401    simtype fInfo;
402    int isError;
403 +  int n_global;
404 +  int* excl;
405 +  
406 +  fInfo.rrf = 0.0;
407 +  fInfo.rt = 0.0;
408 +  fInfo.dielect = 0.0;
409  
41 –  fInfo.box[0] = box_x;
42 –  fInfo.box[1] = box_y;
43 –  fInfo.box[2] = box_z;
44 –
410    fInfo.rlist = rList;
411    fInfo.rcut = rCut;
47 –  fInfo.rrf = rRF;
48 –  fInfo.rt = 0.95 * rRF;
49 –  fInfo.dielect = dielectric;
50 –
412  
413 +  if( useDipole ){
414 +    fInfo.rrf = ecr;
415 +    fInfo.rt = ecr - est;
416 +    if( useReactionField )fInfo.dielect = dielectric;
417 +  }
418 +
419    fInfo.SIM_uses_PBC = usePBC;
420 +  //fInfo.SIM_uses_LJ = 0;
421    fInfo.SIM_uses_LJ = useLJ;
422    fInfo.SIM_uses_sticky = useSticky;
423 <  fInfo.SIM_uses_dipoles = 0;
424 <  //  fInfo.SIM_uses_dipoles = useDipole;
423 >  //fInfo.SIM_uses_sticky = 0;
424 >  fInfo.SIM_uses_dipoles = useDipole;
425 >  //fInfo.SIM_uses_dipoles = 0;
426 >  //fInfo.SIM_uses_RF = useReactionField;
427    fInfo.SIM_uses_RF = 0;
58 –  //  fInfo.SIM_uses_RF = useReactionField;
428    fInfo.SIM_uses_GB = useGB;
429    fInfo.SIM_uses_EAM = useEAM;
430  
431 +  excl = Exclude::getArray();
432  
433 + #ifdef IS_MPI
434 +  n_global = mpiSim->getTotAtoms();
435 + #else
436 +  n_global = n_atoms;
437 + #endif
438 +
439    isError = 0;
440  
441 <  fInfo;
442 <  n_atoms;
443 <  identArray;
68 <  n_exclude;
69 <  excludes;
70 <  nGlobalExcludes;
71 <  globalExcludes;
72 <  isError;
441 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
442 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
443 >                  &isError );
444  
74 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
75 –
445    if( isError ){
446  
447      sprintf( painCave.errMsg,
# Line 86 | Line 455 | void SimInfo::refreshSim(){
455             "succesfully sent the simulation information to fortran.\n");
456    MPIcheckPoint();
457   #endif // is_mpi
458 +
459 +  this->ndf = this->getNDF();
460 +  this->ndfRaw = this->getNDFraw();
461 +
462   }
463  

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