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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 463 by gezelter, Sat Apr 5 03:39:25 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 | 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 22 | Line 34 | SimInfo::SimInfo(){
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 35 | Line 49 | void SimInfo::setBox(double newBox[3]) {
49   }
50  
51   void SimInfo::setBox(double newBox[3]) {
52 <  double smallestBox, maxCutoff;
53 <  int status;
54 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
52 >  
53 >  int i, j;
54 >  double tempMat[3][3];
55  
56 <  smallestBox = box_x;
57 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
56 >  for(i=0; i<3; i++)
57 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
58  
59 <  maxCutoff = smallestBox / 2.0;
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",
# Line 69 | Line 124 | void SimInfo::setBox(double newBox[3]) {
124      refreshSim();
125    }
126  
127 <  if (rCut > maxCutoff) {
127 >  if( ecr > maxCutoff ){
128 >
129      sprintf( painCave.errMsg,
130 <             "New Box size is forcing cutoff radius down to %lf\n",
130 >             "New Box size is forcing electrostatic cutoff radius "
131 >             "down to %lf\n",
132               maxCutoff );
133      painCave.isFatal = 0;
134      simError();
135  
136 <    status = 0;
137 <    LJ_new_rcut(&rCut, &status);
138 <    if (status != 0) {
139 <      sprintf( painCave.errMsg,
140 <               "Error in recomputing LJ shifts based on new rcut\n");
141 <      painCave.isFatal = 1;
142 <      simError();
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 < void SimInfo::getBox(double theBox[3]) {
200 <  theBox[0] = box_x;
201 <  theBox[1] = box_y;
202 <  theBox[2] = box_z;
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 <
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    
# Line 128 | Line 404 | 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  
133 –  fInfo.box[0] = box_x;
134 –  fInfo.box[1] = box_y;
135 –  fInfo.box[2] = box_z;
136 –
414    fInfo.rlist = rList;
415    fInfo.rcut = rCut;
139 –  fInfo.rrf = ecr;
140 –  fInfo.rt = ecr - est;
141 –  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;
# Line 154 | Line 434 | void SimInfo::refreshSim(){
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;
162 < //   n_exclude;
163 < //   excludes;
164 < //   nGlobalExcludes;
165 < //   globalExcludes;
166 < //   isError;
445 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
446 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
447 >                  &isError );
448  
168 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
169 –                  &nGlobalExcludes, globalExcludes, &isError );
170 –
449    if( isError ){
450  
451      sprintf( painCave.errMsg,
# Line 182 | Line 460 | void SimInfo::refreshSim(){
460    MPIcheckPoint();
461   #endif // is_mpi
462  
463 <  ndf = this->getNDF();
464 <  ndfRaw = this->getNDFraw();
463 >  this->ndf = this->getNDF();
464 >  this->ndfRaw = this->getNDFraw();
465  
466   }
467  

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