1 |
< |
#include <cstdlib> |
2 |
< |
#include <cstring> |
3 |
< |
#include <cmath> |
1 |
> |
#include <stdlib.h> |
2 |
> |
#include <string.h> |
3 |
> |
#include <math.h> |
4 |
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|
5 |
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#include <iostream> |
6 |
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using namespace std; |
26 |
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SimInfo::SimInfo(){ |
27 |
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excludes = NULL; |
28 |
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n_constraints = 0; |
29 |
+ |
nZconstraints = 0; |
30 |
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n_oriented = 0; |
31 |
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n_dipoles = 0; |
32 |
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ndf = 0; |
33 |
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ndfRaw = 0; |
34 |
+ |
nZconstraints = 0; |
35 |
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the_integrator = NULL; |
36 |
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setTemp = 0; |
37 |
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thermalTime = 0.0; |
38 |
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currentTime = 0.0; |
39 |
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rCut = 0.0; |
40 |
+ |
origRcut = -1.0; |
41 |
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ecr = 0.0; |
42 |
+ |
origEcr = -1.0; |
43 |
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est = 0.0; |
44 |
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oldEcr = 0.0; |
45 |
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oldRcut = 0.0; |
48 |
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haveOrigEcr = 0; |
49 |
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boxIsInit = 0; |
50 |
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|
51 |
+ |
resetTime = 1e99; |
52 |
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|
53 |
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|
54 |
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usePBC = 0; |
59 |
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useGB = 0; |
60 |
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useEAM = 0; |
61 |
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|
62 |
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myConfiguration = new SimState(); |
63 |
+ |
|
64 |
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wrapMeSimInfo( this ); |
65 |
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} |
66 |
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|
67 |
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|
68 |
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SimInfo::~SimInfo(){ |
69 |
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|
70 |
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delete myConfiguration; |
71 |
+ |
|
72 |
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map<string, GenericData*>::iterator i; |
73 |
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|
74 |
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for(i = properties.begin(); i != properties.end(); i++) |
75 |
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delete (*i).second; |
76 |
< |
|
67 |
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|
76 |
> |
|
77 |
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} |
78 |
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|
79 |
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void SimInfo::setBox(double newBox[3]) { |
94 |
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|
95 |
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void SimInfo::setBoxM( double theBox[3][3] ){ |
96 |
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|
97 |
< |
int i, j, status; |
89 |
< |
double smallestBoxL, maxCutoff; |
97 |
> |
int i, j; |
98 |
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double FortranHmat[9]; // to preserve compatibility with Fortran the |
99 |
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// ordering in the array is as follows: |
100 |
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// [ 0 3 6 ] |
146 |
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|
147 |
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void SimInfo::calcHmatInv( void ) { |
148 |
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|
149 |
+ |
int oldOrtho; |
150 |
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int i,j; |
151 |
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double smallDiag; |
152 |
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double tol; |
154 |
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|
155 |
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invertMat3( Hmat, HmatInv ); |
156 |
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|
148 |
– |
// Check the inverse to make sure it is sane: |
149 |
– |
|
150 |
– |
matMul3( Hmat, HmatInv, sanity ); |
151 |
– |
|
157 |
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// check to see if Hmat is orthorhombic |
158 |
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|
159 |
< |
smallDiag = Hmat[0][0]; |
160 |
< |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
161 |
< |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
159 |
> |
oldOrtho = orthoRhombic; |
160 |
> |
|
161 |
> |
smallDiag = fabs(Hmat[0][0]); |
162 |
> |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
163 |
> |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
164 |
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tol = smallDiag * 1E-6; |
165 |
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|
166 |
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orthoRhombic = 1; |
169 |
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for (j = 0 ; j < 3; j++) { |
170 |
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if (i != j) { |
171 |
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if (orthoRhombic) { |
172 |
< |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
172 |
> |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
173 |
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} |
174 |
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} |
175 |
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} |
176 |
+ |
} |
177 |
+ |
|
178 |
+ |
if( oldOrtho != orthoRhombic ){ |
179 |
+ |
|
180 |
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if( orthoRhombic ){ |
181 |
+ |
sprintf( painCave.errMsg, |
182 |
+ |
"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
183 |
+ |
" If this is a bad thing change the ortho tolerance in SimInfo.\n" ); |
184 |
+ |
simError(); |
185 |
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} |
186 |
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else { |
187 |
+ |
sprintf( painCave.errMsg, |
188 |
+ |
"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
189 |
+ |
" If this is a bad thing change the ortho tolerance in SimInfo.\n" ); |
190 |
+ |
simError(); |
191 |
+ |
} |
192 |
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} |
193 |
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} |
194 |
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|
296 |
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<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
297 |
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} |
298 |
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|
299 |
+ |
|
300 |
+ |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
301 |
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|
302 |
+ |
out[0] = a[1] * b[2] - a[2] * b[1]; |
303 |
+ |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
304 |
+ |
out[2] = a[0] * b[1] - a[1] * b[0]; |
305 |
+ |
|
306 |
+ |
} |
307 |
+ |
|
308 |
+ |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
309 |
+ |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
310 |
+ |
} |
311 |
+ |
|
312 |
+ |
double SimInfo::length3(double a[3]){ |
313 |
+ |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
314 |
+ |
} |
315 |
+ |
|
316 |
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void SimInfo::calcBoxL( void ){ |
317 |
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|
318 |
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double dx, dy, dz, dsq; |
279 |
– |
int i; |
319 |
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|
320 |
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// boxVol = Determinant of Hmat |
321 |
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|
326 |
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dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
327 |
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dsq = dx*dx + dy*dy + dz*dz; |
328 |
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boxL[0] = sqrt( dsq ); |
329 |
< |
maxCutoff = 0.5 * boxL[0]; |
329 |
> |
//maxCutoff = 0.5 * boxL[0]; |
330 |
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|
331 |
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// boxLy |
332 |
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|
333 |
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dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
334 |
|
dsq = dx*dx + dy*dy + dz*dz; |
335 |
|
boxL[1] = sqrt( dsq ); |
336 |
< |
if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
336 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
337 |
|
|
338 |
+ |
|
339 |
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// boxLz |
340 |
|
|
341 |
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dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
342 |
|
dsq = dx*dx + dy*dy + dz*dz; |
343 |
|
boxL[2] = sqrt( dsq ); |
344 |
< |
if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
344 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
345 |
|
|
346 |
+ |
//calculate the max cutoff |
347 |
+ |
maxCutoff = calcMaxCutOff(); |
348 |
+ |
|
349 |
+ |
checkCutOffs(); |
350 |
+ |
|
351 |
|
} |
352 |
|
|
353 |
|
|
354 |
+ |
double SimInfo::calcMaxCutOff(){ |
355 |
+ |
|
356 |
+ |
double ri[3], rj[3], rk[3]; |
357 |
+ |
double rij[3], rjk[3], rki[3]; |
358 |
+ |
double minDist; |
359 |
+ |
|
360 |
+ |
ri[0] = Hmat[0][0]; |
361 |
+ |
ri[1] = Hmat[1][0]; |
362 |
+ |
ri[2] = Hmat[2][0]; |
363 |
+ |
|
364 |
+ |
rj[0] = Hmat[0][1]; |
365 |
+ |
rj[1] = Hmat[1][1]; |
366 |
+ |
rj[2] = Hmat[2][1]; |
367 |
+ |
|
368 |
+ |
rk[0] = Hmat[0][2]; |
369 |
+ |
rk[1] = Hmat[1][2]; |
370 |
+ |
rk[2] = Hmat[2][2]; |
371 |
+ |
|
372 |
+ |
crossProduct3(ri,rj, rij); |
373 |
+ |
distXY = dotProduct3(rk,rij) / length3(rij); |
374 |
+ |
|
375 |
+ |
crossProduct3(rj,rk, rjk); |
376 |
+ |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
377 |
+ |
|
378 |
+ |
crossProduct3(rk,ri, rki); |
379 |
+ |
distZX = dotProduct3(rj,rki) / length3(rki); |
380 |
+ |
|
381 |
+ |
minDist = min(min(distXY, distYZ), distZX); |
382 |
+ |
return minDist/2; |
383 |
+ |
|
384 |
+ |
} |
385 |
+ |
|
386 |
|
void SimInfo::wrapVector( double thePos[3] ){ |
387 |
|
|
388 |
< |
int i, j, k; |
388 |
> |
int i; |
389 |
|
double scaled[3]; |
390 |
|
|
391 |
|
if( !orthoRhombic ){ |
423 |
|
|
424 |
|
|
425 |
|
int SimInfo::getNDF(){ |
426 |
< |
int ndf_local, ndf; |
426 |
> |
int ndf_local; |
427 |
|
|
428 |
|
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
429 |
|
|
433 |
|
ndf = ndf_local; |
434 |
|
#endif |
435 |
|
|
436 |
< |
ndf = ndf - 3; |
436 |
> |
ndf = ndf - 3 - nZconstraints; |
437 |
|
|
438 |
|
return ndf; |
439 |
|
} |
440 |
|
|
441 |
|
int SimInfo::getNDFraw() { |
442 |
< |
int ndfRaw_local, ndfRaw; |
442 |
> |
int ndfRaw_local; |
443 |
|
|
444 |
|
// Raw degrees of freedom that we have to set |
445 |
|
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
452 |
|
|
453 |
|
return ndfRaw; |
454 |
|
} |
455 |
< |
|
455 |
> |
|
456 |
> |
int SimInfo::getNDFtranslational() { |
457 |
> |
int ndfTrans_local; |
458 |
> |
|
459 |
> |
ndfTrans_local = 3 * n_atoms - n_constraints; |
460 |
> |
|
461 |
> |
#ifdef IS_MPI |
462 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
463 |
> |
#else |
464 |
> |
ndfTrans = ndfTrans_local; |
465 |
> |
#endif |
466 |
> |
|
467 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
468 |
> |
|
469 |
> |
return ndfTrans; |
470 |
> |
} |
471 |
> |
|
472 |
|
void SimInfo::refreshSim(){ |
473 |
|
|
474 |
|
simtype fInfo; |
524 |
|
|
525 |
|
this->ndf = this->getNDF(); |
526 |
|
this->ndfRaw = this->getNDFraw(); |
527 |
< |
|
527 |
> |
this->ndfTrans = this->getNDFtranslational(); |
528 |
|
} |
529 |
|
|
530 |
|
|
531 |
|
void SimInfo::setRcut( double theRcut ){ |
532 |
|
|
440 |
– |
if( !haveOrigRcut ){ |
441 |
– |
haveOrigRcut = 1; |
442 |
– |
origRcut = theRcut; |
443 |
– |
} |
444 |
– |
|
533 |
|
rCut = theRcut; |
534 |
|
checkCutOffs(); |
535 |
|
} |
536 |
|
|
537 |
< |
void SimInfo::setEcr( double theEcr ){ |
537 |
> |
void SimInfo::setDefaultRcut( double theRcut ){ |
538 |
> |
|
539 |
> |
haveOrigRcut = 1; |
540 |
> |
origRcut = theRcut; |
541 |
> |
rCut = theRcut; |
542 |
|
|
543 |
< |
if( !haveOrigEcr ){ |
452 |
< |
haveOrigEcr = 1; |
453 |
< |
origEcr = theEcr; |
454 |
< |
} |
543 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
544 |
|
|
545 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
546 |
+ |
} |
547 |
+ |
|
548 |
+ |
void SimInfo::setEcr( double theEcr ){ |
549 |
+ |
|
550 |
|
ecr = theEcr; |
551 |
|
checkCutOffs(); |
552 |
|
} |
553 |
|
|
554 |
+ |
void SimInfo::setDefaultEcr( double theEcr ){ |
555 |
+ |
|
556 |
+ |
haveOrigEcr = 1; |
557 |
+ |
origEcr = theEcr; |
558 |
+ |
|
559 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
560 |
+ |
|
561 |
+ |
ecr = theEcr; |
562 |
+ |
|
563 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
564 |
+ |
} |
565 |
+ |
|
566 |
|
void SimInfo::setEcr( double theEcr, double theEst ){ |
567 |
|
|
568 |
|
est = theEst; |
569 |
|
setEcr( theEcr ); |
570 |
|
} |
571 |
|
|
572 |
+ |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
573 |
|
|
574 |
+ |
est = theEst; |
575 |
+ |
setDefaultEcr( theEcr ); |
576 |
+ |
} |
577 |
+ |
|
578 |
+ |
|
579 |
|
void SimInfo::checkCutOffs( void ){ |
580 |
|
|
581 |
|
int cutChanged = 0; |
582 |
< |
|
582 |
> |
|
583 |
|
if( boxIsInit ){ |
584 |
|
|
585 |
|
//we need to check cutOffs against the box |
586 |
< |
|
587 |
< |
if( maxCutoff > rCut ){ |
586 |
> |
|
587 |
> |
//detect the change of rCut |
588 |
> |
if(( maxCutoff > rCut )&&(usePBC)){ |
589 |
|
if( rCut < origRcut ){ |
590 |
< |
rCut = origRcut; |
591 |
< |
if (rCut > maxCutoff) rCut = maxCutoff; |
592 |
< |
|
593 |
< |
sprintf( painCave.errMsg, |
594 |
< |
"New Box size is setting the long range cutoff radius " |
595 |
< |
"to %lf\n", |
596 |
< |
rCut ); |
597 |
< |
painCave.isFatal = 0; |
598 |
< |
simError(); |
590 |
> |
rCut = origRcut; |
591 |
> |
|
592 |
> |
if (rCut > maxCutoff) |
593 |
> |
rCut = maxCutoff; |
594 |
> |
|
595 |
> |
sprintf( painCave.errMsg, |
596 |
> |
"New Box size is setting the long range cutoff radius " |
597 |
> |
"to %lf at time %lf\n", |
598 |
> |
rCut, currentTime ); |
599 |
> |
painCave.isFatal = 0; |
600 |
> |
simError(); |
601 |
|
} |
602 |
|
} |
603 |
< |
|
489 |
< |
if( maxCutoff > ecr ){ |
490 |
< |
if( ecr < origEcr ){ |
491 |
< |
rCut = origEcr; |
492 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
493 |
< |
|
494 |
< |
sprintf( painCave.errMsg, |
495 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
496 |
< |
"to %lf\n", |
497 |
< |
ecr ); |
498 |
< |
painCave.isFatal = 0; |
499 |
< |
simError(); |
500 |
< |
} |
501 |
< |
} |
502 |
< |
|
503 |
< |
|
504 |
< |
if (rCut > maxCutoff) { |
603 |
> |
else if ((rCut > maxCutoff)&&(usePBC)) { |
604 |
|
sprintf( painCave.errMsg, |
605 |
|
"New Box size is setting the long range cutoff radius " |
606 |
< |
"to %lf\n", |
607 |
< |
maxCutoff ); |
606 |
> |
"to %lf at time %lf\n", |
607 |
> |
maxCutoff, currentTime ); |
608 |
|
painCave.isFatal = 0; |
609 |
|
simError(); |
610 |
|
rCut = maxCutoff; |
611 |
|
} |
612 |
|
|
613 |
< |
if( ecr > maxCutoff){ |
613 |
> |
|
614 |
> |
//detect the change of ecr |
615 |
> |
if( maxCutoff > ecr ){ |
616 |
> |
if( ecr < origEcr ){ |
617 |
> |
ecr = origEcr; |
618 |
> |
if (ecr > maxCutoff) ecr = maxCutoff; |
619 |
> |
|
620 |
> |
sprintf( painCave.errMsg, |
621 |
> |
"New Box size is setting the electrostaticCutoffRadius " |
622 |
> |
"to %lf at time %lf\n", |
623 |
> |
ecr, currentTime ); |
624 |
> |
painCave.isFatal = 0; |
625 |
> |
simError(); |
626 |
> |
} |
627 |
> |
} |
628 |
> |
else if( ecr > maxCutoff){ |
629 |
|
sprintf( painCave.errMsg, |
630 |
|
"New Box size is setting the electrostaticCutoffRadius " |
631 |
< |
"to %lf\n", |
632 |
< |
maxCutoff ); |
631 |
> |
"to %lf at time %lf\n", |
632 |
> |
maxCutoff, currentTime ); |
633 |
|
painCave.isFatal = 0; |
634 |
|
simError(); |
635 |
|
ecr = maxCutoff; |
636 |
|
} |
637 |
|
|
638 |
+ |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
639 |
|
|
640 |
< |
} |
526 |
< |
|
527 |
< |
|
528 |
< |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
529 |
< |
|
530 |
< |
// rlist is the 1.0 plus max( rcut, ecr ) |
531 |
< |
|
532 |
< |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
533 |
< |
|
534 |
< |
if( cutChanged ){ |
640 |
> |
// rlist is the 1.0 plus max( rcut, ecr ) |
641 |
|
|
642 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
642 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
643 |
> |
|
644 |
> |
if( cutChanged ){ |
645 |
> |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
646 |
> |
} |
647 |
> |
|
648 |
> |
oldEcr = ecr; |
649 |
> |
oldRcut = rCut; |
650 |
> |
|
651 |
> |
} else { |
652 |
> |
// initialize this stuff before using it, OK? |
653 |
> |
sprintf( painCave.errMsg, |
654 |
> |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
655 |
> |
painCave.isFatal = 1; |
656 |
> |
simError(); |
657 |
|
} |
658 |
< |
|
539 |
< |
oldEcr = ecr; |
540 |
< |
oldRcut = rCut; |
658 |
> |
|
659 |
|
} |
660 |
|
|
661 |
|
void SimInfo::addProperty(GenericData* prop){ |
705 |
|
return result; |
706 |
|
} |
707 |
|
|
708 |
+ |
double SimInfo::matTrace3(double m[3][3]){ |
709 |
+ |
double trace; |
710 |
+ |
trace = m[0][0] + m[1][1] + m[2][2]; |
711 |
|
|
712 |
+ |
return trace; |
713 |
+ |
} |