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root/group/branches/no-template-branch/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 441 by chuckv, Tue Apr 1 16:50:14 2003 UTC vs.
Revision 618 by mmeineke, Tue Jul 15 21:34:56 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
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  
39    usePBC = 0;
40    useLJ = 0;
# Line 29 | Line 44 | SimInfo::SimInfo(){
44    useGB = 0;
45    useEAM = 0;
46  
47 +  wrapMeSimInfo( this );
48 + }
49  
50 + void SimInfo::setBox(double newBox[3]) {
51 +  
52 +  int i, j;
53 +  double tempMat[3][3];
54  
55 <  wrapMeSimInfo( this );
55 >  for(i=0; i<3; i++)
56 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
57 >
58 >  tempMat[0][0] = newBox[0];
59 >  tempMat[1][1] = newBox[1];
60 >  tempMat[2][2] = newBox[2];
61 >
62 >  setBoxM( tempMat );
63 >
64 > }
65 >
66 > void SimInfo::setBoxM( double theBox[3][3] ){
67 >  
68 >  int i, j, status;
69 >  double smallestBoxL, maxCutoff;
70 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
71 >                         // ordering in the array is as follows:
72 >                         // [ 0 3 6 ]
73 >                         // [ 1 4 7 ]
74 >                         // [ 2 5 8 ]
75 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
76 >
77 >
78 >  for(i=0; i < 3; i++)
79 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
80 >  
81 >  //  cerr
82 >  // << "setting Hmat ->\n"
83 >  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
84 >  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
85 >  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
86 >
87 >  calcBoxL();
88 >  calcHmatInv();
89 >
90 >  for(i=0; i < 3; i++) {
91 >    for (j=0; j < 3; j++) {
92 >      FortranHmat[3*j + i] = Hmat[i][j];
93 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
94 >    }
95 >  }
96 >
97 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
98 >
99 >  smallestBoxL = boxLx;
100 >  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
101 >  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
102 >
103 >  maxCutoff = smallestBoxL / 2.0;
104 >
105 >  if (rList > maxCutoff) {
106 >    sprintf( painCave.errMsg,
107 >             "New Box size is forcing neighborlist radius down to %lf\n",
108 >             maxCutoff );
109 >    painCave.isFatal = 0;
110 >    simError();
111 >
112 >    rList = maxCutoff;
113 >
114 >    sprintf( painCave.errMsg,
115 >             "New Box size is forcing cutoff radius down to %lf\n",
116 >             maxCutoff - 1.0 );
117 >    painCave.isFatal = 0;
118 >    simError();
119 >
120 >    rCut = rList - 1.0;
121 >
122 >    // list radius changed so we have to refresh the simulation structure.
123 >    refreshSim();
124 >  }
125 >
126 >  if( ecr > maxCutoff ){
127 >
128 >    sprintf( painCave.errMsg,
129 >             "New Box size is forcing electrostatic cutoff radius "
130 >             "down to %lf\n",
131 >             maxCutoff );
132 >    painCave.isFatal = 0;
133 >    simError();
134 >
135 >    ecr = maxCutoff;
136 >    est = 0.05 * ecr;
137 >
138 >    refreshSim();
139 >  }
140 >    
141 > }
142 >
143 >
144 > void SimInfo::getBoxM (double theBox[3][3]) {
145 >
146 >  int i, j;
147 >  for(i=0; i<3; i++)
148 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
149 > }
150 >
151 >
152 > void SimInfo::scaleBox(double scale) {
153 >  double theBox[3][3];
154 >  int i, j;
155 >
156 >  // cerr << "Scaling box by " << scale << "\n";
157 >
158 >  for(i=0; i<3; i++)
159 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
160 >
161 >  setBoxM(theBox);
162 >
163 > }
164 >
165 > void SimInfo::calcHmatInv( void ) {
166 >  
167 >  int i,j;
168 >  double smallDiag;
169 >  double tol;
170 >  double sanity[3][3];
171 >
172 >  invertMat3( Hmat, HmatInv );
173 >
174 >  // Check the inverse to make sure it is sane:
175 >
176 >  matMul3( Hmat, HmatInv, sanity );
177 >    
178 >  // check to see if Hmat is orthorhombic
179 >  
180 >  smallDiag = Hmat[0][0];
181 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
182 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
183 >  tol = smallDiag * 1E-6;
184 >
185 >  orthoRhombic = 1;
186 >  
187 >  for (i = 0; i < 3; i++ ) {
188 >    for (j = 0 ; j < 3; j++) {
189 >      if (i != j) {
190 >        if (orthoRhombic) {
191 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
192 >        }        
193 >      }
194 >    }
195 >  }
196 > }
197 >
198 > double SimInfo::matDet3(double a[3][3]) {
199 >  int i, j, k;
200 >  double determinant;
201 >
202 >  determinant = 0.0;
203 >
204 >  for(i = 0; i < 3; i++) {
205 >    j = (i+1)%3;
206 >    k = (i+2)%3;
207 >
208 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
209 >  }
210 >
211 >  return determinant;
212 > }
213 >
214 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
215 >  
216 >  int  i, j, k, l, m, n;
217 >  double determinant;
218 >
219 >  determinant = matDet3( a );
220 >
221 >  if (determinant == 0.0) {
222 >    sprintf( painCave.errMsg,
223 >             "Can't invert a matrix with a zero determinant!\n");
224 >    painCave.isFatal = 1;
225 >    simError();
226 >  }
227 >
228 >  for (i=0; i < 3; i++) {
229 >    j = (i+1)%3;
230 >    k = (i+2)%3;
231 >    for(l = 0; l < 3; l++) {
232 >      m = (l+1)%3;
233 >      n = (l+2)%3;
234 >      
235 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
236 >    }
237 >  }
238 > }
239 >
240 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
241 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
242 >
243 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
244 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
245 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
246 >  
247 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
248 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
249 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
250 >  
251 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
252 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
253 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
254 >  
255 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
256 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
257 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
258   }
259  
260 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
261 +  double a0, a1, a2;
262 +
263 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
264 +
265 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
266 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
267 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
268 + }
269 +
270 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
271 +  double temp[3][3];
272 +  int i, j;
273 +
274 +  for (i = 0; i < 3; i++) {
275 +    for (j = 0; j < 3; j++) {
276 +      temp[j][i] = in[i][j];
277 +    }
278 +  }
279 +  for (i = 0; i < 3; i++) {
280 +    for (j = 0; j < 3; j++) {
281 +      out[i][j] = temp[i][j];
282 +    }
283 +  }
284 + }
285 +  
286 + void SimInfo::printMat3(double A[3][3] ){
287 +
288 +  std::cerr
289 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
290 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
291 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
292 + }
293 +
294 + void SimInfo::printMat9(double A[9] ){
295 +
296 +  std::cerr
297 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
298 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
299 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300 + }
301 +
302 + void SimInfo::calcBoxL( void ){
303 +
304 +  double dx, dy, dz, dsq;
305 +  int i;
306 +
307 +  // boxVol = Determinant of Hmat
308 +
309 +  boxVol = matDet3( Hmat );
310 +
311 +  // boxLx
312 +  
313 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314 +  dsq = dx*dx + dy*dy + dz*dz;
315 +  boxLx = sqrt( dsq );
316 +
317 +  // boxLy
318 +  
319 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
320 +  dsq = dx*dx + dy*dy + dz*dz;
321 +  boxLy = sqrt( dsq );
322 +
323 +  // boxLz
324 +  
325 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
326 +  dsq = dx*dx + dy*dy + dz*dz;
327 +  boxLz = sqrt( dsq );
328 +  
329 + }
330 +
331 +
332 + void SimInfo::wrapVector( double thePos[3] ){
333 +
334 +  int i, j, k;
335 +  double scaled[3];
336 +
337 +  if( !orthoRhombic ){
338 +    // calc the scaled coordinates.
339 +  
340 +
341 +    matVecMul3(HmatInv, thePos, scaled);
342 +    
343 +    for(i=0; i<3; i++)
344 +      scaled[i] -= roundMe(scaled[i]);
345 +    
346 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
347 +    
348 +    matVecMul3(Hmat, scaled, thePos);
349 +
350 +  }
351 +  else{
352 +    // calc the scaled coordinates.
353 +    
354 +    for(i=0; i<3; i++)
355 +      scaled[i] = thePos[i]*HmatInv[i][i];
356 +    
357 +    // wrap the scaled coordinates
358 +    
359 +    for(i=0; i<3; i++)
360 +      scaled[i] -= roundMe(scaled[i]);
361 +    
362 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
363 +    
364 +    for(i=0; i<3; i++)
365 +      thePos[i] = scaled[i]*Hmat[i][i];
366 +  }
367 +    
368 + }
369 +
370 +
371 + int SimInfo::getNDF(){
372 +  int ndf_local, ndf;
373 +  
374 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
375 +
376 + #ifdef IS_MPI
377 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
378 + #else
379 +  ndf = ndf_local;
380 + #endif
381 +
382 +  ndf = ndf - 3;
383 +
384 +  return ndf;
385 + }
386 +
387 + int SimInfo::getNDFraw() {
388 +  int ndfRaw_local, ndfRaw;
389 +
390 +  // Raw degrees of freedom that we have to set
391 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
392 +  
393 + #ifdef IS_MPI
394 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395 + #else
396 +  ndfRaw = ndfRaw_local;
397 + #endif
398 +
399 +  return ndfRaw;
400 + }
401 +
402   void SimInfo::refreshSim(){
403  
404    simtype fInfo;
405    int isError;
406 +  int n_global;
407    int* excl;
408 +  
409 +  fInfo.rrf = 0.0;
410 +  fInfo.rt = 0.0;
411 +  fInfo.dielect = 0.0;
412  
43 –  fInfo.box[0] = box_x;
44 –  fInfo.box[1] = box_y;
45 –  fInfo.box[2] = box_z;
46 –
413    fInfo.rlist = rList;
414    fInfo.rcut = rCut;
49 –  fInfo.rrf = ecr;
50 –  fInfo.rt = ecr - est;
51 –  fInfo.dielect = dielectric;
415  
416 +  if( useDipole ){
417 +    fInfo.rrf = ecr;
418 +    fInfo.rt = ecr - est;
419 +    if( useReactionField )fInfo.dielect = dielectric;
420 +  }
421 +
422    fInfo.SIM_uses_PBC = usePBC;
423 +  //fInfo.SIM_uses_LJ = 0;
424    fInfo.SIM_uses_LJ = useLJ;
425 <
426 <  //fInfo.SIM_uses_sticky = useSticky;
57 <  fInfo.SIM_uses_sticky = 0;
425 >  fInfo.SIM_uses_sticky = useSticky;
426 >  //fInfo.SIM_uses_sticky = 0;
427    fInfo.SIM_uses_dipoles = useDipole;
428    //fInfo.SIM_uses_dipoles = 0;
429 <  fInfo.SIM_uses_RF = useReactionField;
429 >  //fInfo.SIM_uses_RF = useReactionField;
430 >  fInfo.SIM_uses_RF = 0;
431    fInfo.SIM_uses_GB = useGB;
432    fInfo.SIM_uses_EAM = useEAM;
433  
434    excl = Exclude::getArray();
435  
436 + #ifdef IS_MPI
437 +  n_global = mpiSim->getTotAtoms();
438 + #else
439 +  n_global = n_atoms;
440 + #endif
441 +
442    isError = 0;
443  
444 < //   fInfo;
445 < //   n_atoms;
446 < //   identArray;
71 < //   n_exclude;
72 < //   excludes;
73 < //   nGlobalExcludes;
74 < //   globalExcludes;
75 < //   isError;
444 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
445 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
446 >                  &isError );
447  
77 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
78 –                  &nGlobalExcludes, globalExcludes, &isError );
79 –
448    if( isError ){
449  
450      sprintf( painCave.errMsg,
# Line 90 | Line 458 | void SimInfo::refreshSim(){
458             "succesfully sent the simulation information to fortran.\n");
459    MPIcheckPoint();
460   #endif // is_mpi
461 +
462 +  this->ndf = this->getNDF();
463 +  this->ndfRaw = this->getNDFraw();
464 +
465   }
466  

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