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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC vs.
Revision 617 by gezelter, Tue Jul 15 19:56:08 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 35 | Line 47 | void SimInfo::setBox(double newBox[3]) {
47   }
48  
49   void SimInfo::setBox(double newBox[3]) {
50 <  double smallestBox, maxCutoff;
51 <  int status;
52 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
50 >  
51 >  int i, j;
52 >  double tempMat[3][3];
53  
54 <  smallestBox = box_x;
55 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
54 >  for(i=0; i<3; i++)
55 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
56  
57 <  maxCutoff = smallestBox / 2.0;
57 >  tempMat[0][0] = newBox[0];
58 >  tempMat[1][1] = newBox[1];
59 >  tempMat[2][2] = newBox[2];
60  
61 +  setBoxM( tempMat );
62 +
63 + }
64 +
65 + void SimInfo::setBoxM( double theBox[3][3] ){
66 +  
67 +  int i, j, status;
68 +  double smallestBoxL, maxCutoff;
69 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
70 +                         // ordering in the array is as follows:
71 +                         // [ 0 3 6 ]
72 +                         // [ 1 4 7 ]
73 +                         // [ 2 5 8 ]
74 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
75 +
76 +
77 +  for(i=0; i < 3; i++)
78 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
79 +  
80 +  //  cerr
81 +  // << "setting Hmat ->\n"
82 +  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
83 +  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
84 +  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
85 +
86 +  calcBoxL();
87 +  calcHmatInv();
88 +
89 +  for(i=0; i < 3; i++) {
90 +    for (j=0; j < 3; j++) {
91 +      FortranHmat[3*j + i] = Hmat[i][j];
92 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
93 +    }
94 +  }
95 +
96 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
97 +
98 +  smallestBoxL = boxLx;
99 +  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
100 +  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
101 +
102 +  maxCutoff = smallestBoxL / 2.0;
103 +
104    if (rList > maxCutoff) {
105      sprintf( painCave.errMsg,
106               "New Box size is forcing neighborlist radius down to %lf\n",
# Line 86 | Line 139 | void SimInfo::setBox(double newBox[3]) {
139      }
140    }
141   }
142 +
143  
144 < void SimInfo::getBox(double theBox[3]) {
145 <  theBox[0] = box_x;
146 <  theBox[1] = box_y;
147 <  theBox[2] = box_z;
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 <
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    
# Line 128 | Line 403 | 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  
137 –  fInfo.box[0] = box_x;
138 –  fInfo.box[1] = box_y;
139 –  fInfo.box[2] = box_z;
140 –
413    fInfo.rlist = rList;
414    fInfo.rcut = rCut;
415  
# Line 152 | Line 424 | void SimInfo::refreshSim(){
424    fInfo.SIM_uses_LJ = useLJ;
425    fInfo.SIM_uses_sticky = useSticky;
426    //fInfo.SIM_uses_sticky = 0;
427 <  //fInfo.SIM_uses_dipoles = useDipole;
428 <  fInfo.SIM_uses_dipoles = 0;
427 >  fInfo.SIM_uses_dipoles = useDipole;
428 >  //fInfo.SIM_uses_dipoles = 0;
429    //fInfo.SIM_uses_RF = useReactionField;
430    fInfo.SIM_uses_RF = 0;
431    fInfo.SIM_uses_GB = useGB;
# Line 161 | Line 433 | void SimInfo::refreshSim(){
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;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
444 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
445 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
446 >                  &isError );
447  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
448    if( isError ){
449  
450      sprintf( painCave.errMsg,

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