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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 443 by mmeineke, Wed Apr 2 22:19:03 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 29 | 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  
43 –  fInfo.box[0] = box_x;
44 –  fInfo.box[1] = box_y;
45 –  fInfo.box[2] = box_z;
46 –
410    fInfo.rlist = rList;
411    fInfo.rcut = rCut;
49 –  fInfo.rrf = ecr;
50 –  fInfo.rt = ecr - est;
51 –  fInfo.dielect = dielectric;
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;
# Line 64 | Line 430 | void SimInfo::refreshSim(){
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;
72 < //   n_exclude;
73 < //   excludes;
74 < //   nGlobalExcludes;
75 < //   globalExcludes;
76 < //   isError;
441 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
442 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
443 >                  &isError );
444  
78 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
79 –                  &nGlobalExcludes, globalExcludes, &isError );
80 –
445    if( isError ){
446  
447      sprintf( painCave.errMsg,
# Line 91 | 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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