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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 439 by chuckv, Mon Mar 31 22:09:39 2003 UTC vs.
Revision 590 by mmeineke, Thu Jul 10 22:15:53 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;
# Line 29 | Line 43 | SimInfo::SimInfo(){
43    useGB = 0;
44    useEAM = 0;
45  
46 +  wrapMeSimInfo( this );
47 + }
48  
49 + void SimInfo::setBox(double newBox[3]) {
50 +  
51 +  int i, j;
52 +  double tempMat[3][3];
53  
54 <  wrapMeSimInfo( this );
54 >  for(i=0; i<3; i++)
55 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
56 >
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",
107 >             maxCutoff );
108 >    painCave.isFatal = 0;
109 >    simError();
110 >
111 >    rList = maxCutoff;
112 >
113 >    sprintf( painCave.errMsg,
114 >             "New Box size is forcing cutoff radius down to %lf\n",
115 >             maxCutoff - 1.0 );
116 >    painCave.isFatal = 0;
117 >    simError();
118 >
119 >    rCut = rList - 1.0;
120 >
121 >    // list radius changed so we have to refresh the simulation structure.
122 >    refreshSim();
123 >  }
124 >
125 >  if (rCut > maxCutoff) {
126 >    sprintf( painCave.errMsg,
127 >             "New Box size is forcing cutoff radius down to %lf\n",
128 >             maxCutoff );
129 >    painCave.isFatal = 0;
130 >    simError();
131 >
132 >    status = 0;
133 >    LJ_new_rcut(&rCut, &status);
134 >    if (status != 0) {
135 >      sprintf( painCave.errMsg,
136 >               "Error in recomputing LJ shifts based on new rcut\n");
137 >      painCave.isFatal = 1;
138 >      simError();
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::calcBoxL( void ){
271 +
272 +  double dx, dy, dz, dsq;
273 +  int i;
274 +
275 +  // boxVol = Determinant of Hmat
276 +
277 +  boxVol = matDet3( Hmat );
278 +
279 +  // boxLx
280 +  
281 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
282 +  dsq = dx*dx + dy*dy + dz*dz;
283 +  boxLx = sqrt( dsq );
284 +
285 +  // boxLy
286 +  
287 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
288 +  dsq = dx*dx + dy*dy + dz*dz;
289 +  boxLy = sqrt( dsq );
290 +
291 +  // boxLz
292 +  
293 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
294 +  dsq = dx*dx + dy*dy + dz*dz;
295 +  boxLz = sqrt( dsq );
296 +  
297 + }
298 +
299 +
300 + void SimInfo::wrapVector( double thePos[3] ){
301 +
302 +  int i, j, k;
303 +  double scaled[3];
304 +
305 +  if( !orthoRhombic ){
306 +    // calc the scaled coordinates.
307 +  
308 +
309 +    matVecMul3(HmatInv, thePos, scaled);
310 +    
311 +    for(i=0; i<3; i++)
312 +      scaled[i] -= roundMe(scaled[i]);
313 +    
314 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
315 +    
316 +    matVecMul3(Hmat, scaled, thePos);
317 +
318 +  }
319 +  else{
320 +    // calc the scaled coordinates.
321 +    
322 +    for(i=0; i<3; i++)
323 +      scaled[i] = thePos[i]*HmatInv[i][i];
324 +    
325 +    // wrap the scaled coordinates
326 +    
327 +    for(i=0; i<3; i++)
328 +      scaled[i] -= roundMe(scaled[i]);
329 +    
330 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
331 +    
332 +    for(i=0; i<3; i++)
333 +      thePos[i] = scaled[i]*Hmat[i][i];
334 +  }
335 +    
336 + }
337 +
338 +
339 + int SimInfo::getNDF(){
340 +  int ndf_local, ndf;
341 +  
342 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
343 +
344 + #ifdef IS_MPI
345 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
346 + #else
347 +  ndf = ndf_local;
348 + #endif
349 +
350 +  ndf = ndf - 3;
351 +
352 +  return ndf;
353 + }
354 +
355 + int SimInfo::getNDFraw() {
356 +  int ndfRaw_local, ndfRaw;
357 +
358 +  // Raw degrees of freedom that we have to set
359 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
360 +  
361 + #ifdef IS_MPI
362 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
363 + #else
364 +  ndfRaw = ndfRaw_local;
365 + #endif
366 +
367 +  return ndfRaw;
368 + }
369 +
370   void SimInfo::refreshSim(){
371  
372    simtype fInfo;
373    int isError;
374 +  int n_global;
375    int* excl;
376 +  
377 +  fInfo.rrf = 0.0;
378 +  fInfo.rt = 0.0;
379 +  fInfo.dielect = 0.0;
380  
43 –  fInfo.box[0] = box_x;
44 –  fInfo.box[1] = box_y;
45 –  fInfo.box[2] = box_z;
46 –
381    fInfo.rlist = rList;
382    fInfo.rcut = rCut;
49 –  fInfo.rrf = ecr;
50 –  fInfo.rt = ecr - est;
51 –  fInfo.dielect = dielectric;
383  
384 +  if( useDipole ){
385 +    fInfo.rrf = ecr;
386 +    fInfo.rt = ecr - est;
387 +    if( useReactionField )fInfo.dielect = dielectric;
388 +  }
389 +
390    fInfo.SIM_uses_PBC = usePBC;
391 +  //fInfo.SIM_uses_LJ = 0;
392    fInfo.SIM_uses_LJ = useLJ;
393 <
394 <  //fInfo.SIM_uses_sticky = useSticky;
57 <  fInfo.SIM_uses_sticky = 0;
393 >  fInfo.SIM_uses_sticky = useSticky;
394 >  //fInfo.SIM_uses_sticky = 0;
395    fInfo.SIM_uses_dipoles = useDipole;
396    //fInfo.SIM_uses_dipoles = 0;
397 <  fInfo.SIM_uses_RF = useReactionField;
397 >  //fInfo.SIM_uses_RF = useReactionField;
398 >  fInfo.SIM_uses_RF = 0;
399    fInfo.SIM_uses_GB = useGB;
400    fInfo.SIM_uses_EAM = useEAM;
401  
402    excl = Exclude::getArray();
403  
404 + #ifdef IS_MPI
405 +  n_global = mpiSim->getTotAtoms();
406 + #else
407 +  n_global = n_atoms;
408 + #endif
409 +
410    isError = 0;
411  
412 <  fInfo;
413 <  n_atoms;
414 <  identArray;
71 <  n_exclude;
72 <  excludes;
73 <  nGlobalExcludes;
74 <  globalExcludes;
75 <  isError;
412 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
413 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
414 >                  &isError );
415  
77 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
78 –                  &nGlobalExcludes, globalExcludes, &isError );
79 –
416    if( isError ){
417  
418      sprintf( painCave.errMsg,
# Line 90 | Line 426 | void SimInfo::refreshSim(){
426             "succesfully sent the simulation information to fortran.\n");
427    MPIcheckPoint();
428   #endif // is_mpi
429 +
430 +  this->ndf = this->getNDF();
431 +  this->ndfRaw = this->getNDFraw();
432 +
433   }
434  

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