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root/group/branches/new-templateless/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.
branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 852 by mmeineke, Thu Nov 6 18:20:47 2003 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
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(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32 +  ndf = 0;
33 +  ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38 +  currentTime = 0.0;
39    rCut = 0.0;
40 +  origRcut = -1.0;
41 +  ecr = 0.0;
42 +  origEcr = -1.0;
43 +  est = 0.0;
44 +  oldEcr = 0.0;
45 +  oldRcut = 0.0;
46  
47 +  haveOrigRcut = 0;
48 +  haveOrigEcr = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +  
53 +
54    usePBC = 0;
55    useLJ = 0;
56    useSticky = 0;
# Line 29 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63  
64 +  properties = new GenericData();
65  
66    wrapMeSimInfo( this );
67   }
68  
69 +
70 + SimInfo::~SimInfo(){
71 +
72 +  delete myConfiguration;
73 +  delete properties;    
74 + }
75 +
76 + void SimInfo::setBox(double newBox[3]) {
77 +  
78 +  int i, j;
79 +  double tempMat[3][3];
80 +
81 +  for(i=0; i<3; i++)
82 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
83 +
84 +  tempMat[0][0] = newBox[0];
85 +  tempMat[1][1] = newBox[1];
86 +  tempMat[2][2] = newBox[2];
87 +
88 +  setBoxM( tempMat );
89 +
90 + }
91 +
92 + void SimInfo::setBoxM( double theBox[3][3] ){
93 +  
94 +  int i, j;
95 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
96 +                         // ordering in the array is as follows:
97 +                         // [ 0 3 6 ]
98 +                         // [ 1 4 7 ]
99 +                         // [ 2 5 8 ]
100 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
101 +
102 +  
103 +  if( !boxIsInit ) boxIsInit = 1;
104 +
105 +  for(i=0; i < 3; i++)
106 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107 +  
108 +  calcBoxL();
109 +  calcHmatInv();
110 +
111 +  for(i=0; i < 3; i++) {
112 +    for (j=0; j < 3; j++) {
113 +      FortranHmat[3*j + i] = Hmat[i][j];
114 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
115 +    }
116 +  }
117 +
118 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119 +
120 + }
121 +
122 +
123 + void SimInfo::getBoxM (double theBox[3][3]) {
124 +
125 +  int i, j;
126 +  for(i=0; i<3; i++)
127 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
128 + }
129 +
130 +
131 + void SimInfo::scaleBox(double scale) {
132 +  double theBox[3][3];
133 +  int i, j;
134 +
135 +  // cerr << "Scaling box by " << scale << "\n";
136 +
137 +  for(i=0; i<3; i++)
138 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
139 +
140 +  setBoxM(theBox);
141 +
142 + }
143 +
144 + void SimInfo::calcHmatInv( void ) {
145 +
146 +  int oldOrtho;
147 +  int i,j;
148 +  double smallDiag;
149 +  double tol;
150 +  double sanity[3][3];
151 +
152 +  invertMat3( Hmat, HmatInv );
153 +
154 +  // Check the inverse to make sure it is sane:
155 +
156 +  // matMul3( Hmat, HmatInv, sanity );
157 +    
158 +  // check to see if Hmat is orthorhombic
159 +
160 +  
161 +  oldOrtho = orthoRhombic;
162 +
163 +  smallDiag = fabs(Hmat[0][0]);
164 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
165 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
166 +  tol = smallDiag * 1E-6;
167 +
168 +  orthoRhombic = 1;
169 +  
170 +  for (i = 0; i < 3; i++ ) {
171 +    for (j = 0 ; j < 3; j++) {
172 +      if (i != j) {
173 +        if (orthoRhombic) {
174 +          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
175 +        }        
176 +      }
177 +    }
178 +  }
179 +  
180 +  if( oldOrtho != orthoRhombic ){
181 +    
182 +    if( orthoRhombic ){
183 +      sprintf( painCave.errMsg,
184 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
185 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
186 +      simError();
187 +    }
188 +    else {
189 +      sprintf( painCave.errMsg,
190 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
192 +      simError();
193 +    }
194 +  }
195 + }
196 +
197 + double SimInfo::matDet3(double a[3][3]) {
198 +  int i, j, k;
199 +  double determinant;
200 +
201 +  determinant = 0.0;
202 +
203 +  for(i = 0; i < 3; i++) {
204 +    j = (i+1)%3;
205 +    k = (i+2)%3;
206 +
207 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
208 +  }
209 +
210 +  return determinant;
211 + }
212 +
213 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
214 +  
215 +  int  i, j, k, l, m, n;
216 +  double determinant;
217 +
218 +  determinant = matDet3( a );
219 +
220 +  if (determinant == 0.0) {
221 +    sprintf( painCave.errMsg,
222 +             "Can't invert a matrix with a zero determinant!\n");
223 +    painCave.isFatal = 1;
224 +    simError();
225 +  }
226 +
227 +  for (i=0; i < 3; i++) {
228 +    j = (i+1)%3;
229 +    k = (i+2)%3;
230 +    for(l = 0; l < 3; l++) {
231 +      m = (l+1)%3;
232 +      n = (l+2)%3;
233 +      
234 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
235 +    }
236 +  }
237 + }
238 +
239 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
240 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
241 +
242 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
243 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
244 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
245 +  
246 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
247 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
248 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
249 +  
250 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
251 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
252 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
253 +  
254 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
255 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
256 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
257 + }
258 +
259 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
260 +  double a0, a1, a2;
261 +
262 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
263 +
264 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
265 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
266 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
267 + }
268 +
269 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
270 +  double temp[3][3];
271 +  int i, j;
272 +
273 +  for (i = 0; i < 3; i++) {
274 +    for (j = 0; j < 3; j++) {
275 +      temp[j][i] = in[i][j];
276 +    }
277 +  }
278 +  for (i = 0; i < 3; i++) {
279 +    for (j = 0; j < 3; j++) {
280 +      out[i][j] = temp[i][j];
281 +    }
282 +  }
283 + }
284 +  
285 + void SimInfo::printMat3(double A[3][3] ){
286 +
287 +  std::cerr
288 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
289 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
290 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
291 + }
292 +
293 + void SimInfo::printMat9(double A[9] ){
294 +
295 +  std::cerr
296 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
297 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
298 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
299 + }
300 +
301 +
302 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
303 +
304 +      out[0] = a[1] * b[2] - a[2] * b[1];
305 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
306 +      out[2] = a[0] * b[1] - a[1] * b[0];
307 +      
308 + }
309 +
310 + double SimInfo::dotProduct3(double a[3], double b[3]){
311 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
312 + }
313 +
314 + double SimInfo::length3(double a[3]){
315 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
316 + }
317 +
318 + void SimInfo::calcBoxL( void ){
319 +
320 +  double dx, dy, dz, dsq;
321 +
322 +  // boxVol = Determinant of Hmat
323 +
324 +  boxVol = matDet3( Hmat );
325 +
326 +  // boxLx
327 +  
328 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
329 +  dsq = dx*dx + dy*dy + dz*dz;
330 +  boxL[0] = sqrt( dsq );
331 +  //maxCutoff = 0.5 * boxL[0];
332 +
333 +  // boxLy
334 +  
335 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
336 +  dsq = dx*dx + dy*dy + dz*dz;
337 +  boxL[1] = sqrt( dsq );
338 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
339 +
340 +
341 +  // boxLz
342 +  
343 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
344 +  dsq = dx*dx + dy*dy + dz*dz;
345 +  boxL[2] = sqrt( dsq );
346 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
347 +
348 +  //calculate the max cutoff
349 +  maxCutoff =  calcMaxCutOff();
350 +  
351 +  checkCutOffs();
352 +
353 + }
354 +
355 +
356 + double SimInfo::calcMaxCutOff(){
357 +
358 +  double ri[3], rj[3], rk[3];
359 +  double rij[3], rjk[3], rki[3];
360 +  double minDist;
361 +
362 +  ri[0] = Hmat[0][0];
363 +  ri[1] = Hmat[1][0];
364 +  ri[2] = Hmat[2][0];
365 +
366 +  rj[0] = Hmat[0][1];
367 +  rj[1] = Hmat[1][1];
368 +  rj[2] = Hmat[2][1];
369 +
370 +  rk[0] = Hmat[0][2];
371 +  rk[1] = Hmat[1][2];
372 +  rk[2] = Hmat[2][2];
373 +  
374 +  crossProduct3(ri,rj, rij);
375 +  distXY = dotProduct3(rk,rij) / length3(rij);
376 +
377 +  crossProduct3(rj,rk, rjk);
378 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
379 +
380 +  crossProduct3(rk,ri, rki);
381 +  distZX = dotProduct3(rj,rki) / length3(rki);
382 +
383 +  minDist = min(min(distXY, distYZ), distZX);
384 +  return minDist/2;
385 +  
386 + }
387 +
388 + void SimInfo::wrapVector( double thePos[3] ){
389 +
390 +  int i;
391 +  double scaled[3];
392 +
393 +  if( !orthoRhombic ){
394 +    // calc the scaled coordinates.
395 +  
396 +
397 +    matVecMul3(HmatInv, thePos, scaled);
398 +    
399 +    for(i=0; i<3; i++)
400 +      scaled[i] -= roundMe(scaled[i]);
401 +    
402 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
403 +    
404 +    matVecMul3(Hmat, scaled, thePos);
405 +
406 +  }
407 +  else{
408 +    // calc the scaled coordinates.
409 +    
410 +    for(i=0; i<3; i++)
411 +      scaled[i] = thePos[i]*HmatInv[i][i];
412 +    
413 +    // wrap the scaled coordinates
414 +    
415 +    for(i=0; i<3; i++)
416 +      scaled[i] -= roundMe(scaled[i]);
417 +    
418 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
419 +    
420 +    for(i=0; i<3; i++)
421 +      thePos[i] = scaled[i]*Hmat[i][i];
422 +  }
423 +    
424 + }
425 +
426 +
427 + int SimInfo::getNDF(){
428 +  int ndf_local;
429 +  
430 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
431 +
432 + #ifdef IS_MPI
433 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
434 + #else
435 +  ndf = ndf_local;
436 + #endif
437 +
438 +  ndf = ndf - 3 - nZconstraints;
439 +
440 +  return ndf;
441 + }
442 +
443 + int SimInfo::getNDFraw() {
444 +  int ndfRaw_local;
445 +
446 +  // Raw degrees of freedom that we have to set
447 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
448 +  
449 + #ifdef IS_MPI
450 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
451 + #else
452 +  ndfRaw = ndfRaw_local;
453 + #endif
454 +
455 +  return ndfRaw;
456 + }
457 +
458 + int SimInfo::getNDFtranslational() {
459 +  int ndfTrans_local;
460 +
461 +  ndfTrans_local = 3 * n_atoms - n_constraints;
462 +
463 + #ifdef IS_MPI
464 +  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
465 + #else
466 +  ndfTrans = ndfTrans_local;
467 + #endif
468 +
469 +  ndfTrans = ndfTrans - 3 - nZconstraints;
470 +
471 +  return ndfTrans;
472 + }
473 +
474   void SimInfo::refreshSim(){
475  
476    simtype fInfo;
477    int isError;
478 +  int n_global;
479    int* excl;
480  
481 <  fInfo.box[0] = box_x;
44 <  fInfo.box[1] = box_y;
45 <  fInfo.box[2] = box_z;
481 >  fInfo.dielect = 0.0;
482  
483 <  fInfo.rlist = rList;
484 <  fInfo.rcut = rCut;
485 <  fInfo.rrf = ecr;
50 <  fInfo.rt = ecr - est;
51 <  fInfo.dielect = dielectric;
483 >  if( useDipole ){
484 >    if( useReactionField )fInfo.dielect = dielectric;
485 >  }
486  
487    fInfo.SIM_uses_PBC = usePBC;
488 +  //fInfo.SIM_uses_LJ = 0;
489    fInfo.SIM_uses_LJ = useLJ;
490 <
491 <  //fInfo.SIM_uses_sticky = useSticky;
57 <  fInfo.SIM_uses_sticky = 0;
490 >  fInfo.SIM_uses_sticky = useSticky;
491 >  //fInfo.SIM_uses_sticky = 0;
492    fInfo.SIM_uses_dipoles = useDipole;
493    //fInfo.SIM_uses_dipoles = 0;
494 <  fInfo.SIM_uses_RF = useReactionField;
494 >  //fInfo.SIM_uses_RF = useReactionField;
495 >  fInfo.SIM_uses_RF = 0;
496    fInfo.SIM_uses_GB = useGB;
497    fInfo.SIM_uses_EAM = useEAM;
498  
499    excl = Exclude::getArray();
500  
501 + #ifdef IS_MPI
502 +  n_global = mpiSim->getTotAtoms();
503 + #else
504 +  n_global = n_atoms;
505 + #endif
506 +
507    isError = 0;
508  
509 <  fInfo;
510 <  n_atoms;
511 <  identArray;
71 <  n_exclude;
72 <  excludes;
73 <  nGlobalExcludes;
74 <  globalExcludes;
75 <  isError;
509 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
510 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
511 >                  &isError );
512  
77 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
78 –                  &nGlobalExcludes, globalExcludes, &isError );
79 –
513    if( isError ){
514  
515      sprintf( painCave.errMsg,
# Line 90 | Line 523 | void SimInfo::refreshSim(){
523             "succesfully sent the simulation information to fortran.\n");
524    MPIcheckPoint();
525   #endif // is_mpi
526 +
527 +  this->ndf = this->getNDF();
528 +  this->ndfRaw = this->getNDFraw();
529 +  this->ndfTrans = this->getNDFtranslational();
530   }
531  
532 +
533 + void SimInfo::setRcut( double theRcut ){
534 +
535 +  rCut = theRcut;
536 +  checkCutOffs();
537 + }
538 +
539 + void SimInfo::setDefaultRcut( double theRcut ){
540 +
541 +  haveOrigRcut = 1;
542 +  origRcut = theRcut;
543 +  rCut = theRcut;
544 +
545 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
546 +
547 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 + }
549 +
550 + void SimInfo::setEcr( double theEcr ){
551 +
552 +  ecr = theEcr;
553 +  checkCutOffs();
554 + }
555 +
556 + void SimInfo::setDefaultEcr( double theEcr ){
557 +
558 +  haveOrigEcr = 1;
559 +  origEcr = theEcr;
560 +  
561 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
562 +
563 +  ecr = theEcr;
564 +
565 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
566 + }
567 +
568 + void SimInfo::setEcr( double theEcr, double theEst ){
569 +
570 +  est = theEst;
571 +  setEcr( theEcr );
572 + }
573 +
574 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
575 +
576 +  est = theEst;
577 +  setDefaultEcr( theEcr );
578 + }
579 +
580 +
581 + void SimInfo::checkCutOffs( void ){
582 +
583 +  int cutChanged = 0;
584 +  
585 +  if( boxIsInit ){
586 +    
587 +    //we need to check cutOffs against the box
588 +
589 +    //detect the change of rCut
590 +    if(( maxCutoff > rCut )&&(usePBC)){
591 +      if( rCut < origRcut ){
592 +        rCut = origRcut;
593 +        
594 +        if (rCut > maxCutoff)
595 +          rCut = maxCutoff;
596 +  
597 +          sprintf( painCave.errMsg,
598 +                    "New Box size is setting the long range cutoff radius "
599 +                    "to %lf at time %lf\n",
600 +                    rCut, currentTime );
601 +          painCave.isFatal = 0;
602 +          simError();
603 +      }
604 +    }
605 +    else if ((rCut > maxCutoff)&&(usePBC)) {
606 +      sprintf( painCave.errMsg,
607 +               "New Box size is setting the long range cutoff radius "
608 +               "to %lf at time %lf\n",
609 +               maxCutoff, currentTime );
610 +      painCave.isFatal = 0;
611 +      simError();
612 +      rCut = maxCutoff;
613 +    }
614 +
615 +
616 +    //detect the change of ecr
617 +    if( maxCutoff > ecr ){
618 +      if( ecr < origEcr ){
619 +        ecr = origEcr;
620 +        if (ecr > maxCutoff) ecr = maxCutoff;
621 +  
622 +          sprintf( painCave.errMsg,
623 +                    "New Box size is setting the electrostaticCutoffRadius "
624 +                    "to %lf at time %lf\n",
625 +                    ecr, currentTime );
626 +            painCave.isFatal = 0;
627 +            simError();
628 +      }
629 +    }
630 +    else if( ecr > maxCutoff){
631 +      sprintf( painCave.errMsg,
632 +               "New Box size is setting the electrostaticCutoffRadius "
633 +               "to %lf at time %lf\n",
634 +               maxCutoff, currentTime  );
635 +      painCave.isFatal = 0;
636 +      simError();      
637 +      ecr = maxCutoff;
638 +    }
639 +
640 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
641 +    
642 +    // rlist is the 1.0 plus max( rcut, ecr )
643 +    
644 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
645 +    
646 +    if( cutChanged ){
647 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
648 +    }
649 +    
650 +    oldEcr = ecr;
651 +    oldRcut = rCut;
652 +    
653 +  } else {
654 +    // initialize this stuff before using it, OK?
655 +    sprintf( painCave.errMsg,
656 +             "Trying to check cutoffs without a box. Be smarter.\n" );
657 +    painCave.isFatal = 1;
658 +    simError();      
659 +  }
660 +  
661 + }
662 +
663 + GenericData* SimInfo::getProperty(char* propName){
664 +
665 +  return properties->find( propName );
666 + }
667 +
668 + double SimInfo::matTrace3(double m[3][3]){
669 +  double trace;
670 +  trace = m[0][0] + m[1][1] + m[2][2];
671 +
672 +  return trace;
673 + }

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