12 |
|
|
13 |
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#include "fortranWrappers.hpp" |
14 |
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|
15 |
+ |
#include "MatVec3.h" |
16 |
+ |
|
17 |
|
#ifdef IS_MPI |
18 |
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#include "mpiSimulation.hpp" |
19 |
|
#endif |
22 |
|
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
23 |
|
} |
24 |
|
|
25 |
+ |
inline double min( double a, double b ){ |
26 |
+ |
return (a < b ) ? a : b; |
27 |
+ |
} |
28 |
|
|
29 |
|
SimInfo* currentInfo; |
30 |
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|
31 |
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SimInfo::SimInfo(){ |
32 |
< |
excludes = NULL; |
32 |
> |
|
33 |
|
n_constraints = 0; |
34 |
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nZconstraints = 0; |
35 |
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n_oriented = 0; |
42 |
|
thermalTime = 0.0; |
43 |
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currentTime = 0.0; |
44 |
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rCut = 0.0; |
40 |
– |
origRcut = -1.0; |
45 |
|
ecr = 0.0; |
42 |
– |
origEcr = -1.0; |
46 |
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est = 0.0; |
44 |
– |
oldEcr = 0.0; |
45 |
– |
oldRcut = 0.0; |
47 |
|
|
48 |
< |
haveOrigRcut = 0; |
49 |
< |
haveOrigEcr = 0; |
48 |
> |
haveRcut = 0; |
49 |
> |
haveEcr = 0; |
50 |
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boxIsInit = 0; |
51 |
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|
52 |
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resetTime = 1e99; |
52 |
– |
|
53 |
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|
54 |
+ |
orthoRhombic = 0; |
55 |
+ |
orthoTolerance = 1E-6; |
56 |
+ |
useInitXSstate = true; |
57 |
+ |
|
58 |
|
usePBC = 0; |
59 |
|
useLJ = 0; |
60 |
|
useSticky = 0; |
61 |
< |
useDipole = 0; |
61 |
> |
useCharges = 0; |
62 |
> |
useDipoles = 0; |
63 |
|
useReactionField = 0; |
64 |
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useGB = 0; |
65 |
|
useEAM = 0; |
66 |
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|
67 |
+ |
excludes = Exclude::Instance(); |
68 |
+ |
|
69 |
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myConfiguration = new SimState(); |
70 |
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|
71 |
+ |
has_minimizer = false; |
72 |
+ |
the_minimizer =NULL; |
73 |
+ |
|
74 |
|
wrapMeSimInfo( this ); |
75 |
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} |
76 |
|
|
112 |
|
// [ 2 5 8 ] |
113 |
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double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
114 |
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|
105 |
– |
|
115 |
|
if( !boxIsInit ) boxIsInit = 1; |
116 |
|
|
117 |
|
for(i=0; i < 3; i++) |
155 |
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|
156 |
|
void SimInfo::calcHmatInv( void ) { |
157 |
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|
158 |
+ |
int oldOrtho; |
159 |
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int i,j; |
160 |
|
double smallDiag; |
161 |
|
double tol; |
163 |
|
|
164 |
|
invertMat3( Hmat, HmatInv ); |
165 |
|
|
156 |
– |
// Check the inverse to make sure it is sane: |
157 |
– |
|
158 |
– |
matMul3( Hmat, HmatInv, sanity ); |
159 |
– |
|
166 |
|
// check to see if Hmat is orthorhombic |
167 |
|
|
168 |
< |
smallDiag = Hmat[0][0]; |
163 |
< |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
164 |
< |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
165 |
< |
tol = smallDiag * 1E-6; |
168 |
> |
oldOrtho = orthoRhombic; |
169 |
|
|
170 |
+ |
smallDiag = fabs(Hmat[0][0]); |
171 |
+ |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
172 |
+ |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
173 |
+ |
tol = smallDiag * orthoTolerance; |
174 |
+ |
|
175 |
|
orthoRhombic = 1; |
176 |
|
|
177 |
|
for (i = 0; i < 3; i++ ) { |
178 |
|
for (j = 0 ; j < 3; j++) { |
179 |
|
if (i != j) { |
180 |
|
if (orthoRhombic) { |
181 |
< |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
181 |
> |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
182 |
|
} |
183 |
|
} |
184 |
|
} |
185 |
|
} |
178 |
– |
} |
186 |
|
|
187 |
< |
double SimInfo::matDet3(double a[3][3]) { |
188 |
< |
int i, j, k; |
189 |
< |
double determinant; |
190 |
< |
|
191 |
< |
determinant = 0.0; |
192 |
< |
|
193 |
< |
for(i = 0; i < 3; i++) { |
194 |
< |
j = (i+1)%3; |
195 |
< |
k = (i+2)%3; |
196 |
< |
|
197 |
< |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
191 |
< |
} |
192 |
< |
|
193 |
< |
return determinant; |
194 |
< |
} |
195 |
< |
|
196 |
< |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
197 |
< |
|
198 |
< |
int i, j, k, l, m, n; |
199 |
< |
double determinant; |
200 |
< |
|
201 |
< |
determinant = matDet3( a ); |
202 |
< |
|
203 |
< |
if (determinant == 0.0) { |
204 |
< |
sprintf( painCave.errMsg, |
205 |
< |
"Can't invert a matrix with a zero determinant!\n"); |
206 |
< |
painCave.isFatal = 1; |
207 |
< |
simError(); |
208 |
< |
} |
209 |
< |
|
210 |
< |
for (i=0; i < 3; i++) { |
211 |
< |
j = (i+1)%3; |
212 |
< |
k = (i+2)%3; |
213 |
< |
for(l = 0; l < 3; l++) { |
214 |
< |
m = (l+1)%3; |
215 |
< |
n = (l+2)%3; |
216 |
< |
|
217 |
< |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
187 |
> |
if( oldOrtho != orthoRhombic ){ |
188 |
> |
|
189 |
> |
if( orthoRhombic ){ |
190 |
> |
sprintf( painCave.errMsg, |
191 |
> |
"OOPSE is switching from the default Non-Orthorhombic\n" |
192 |
> |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
193 |
> |
"\tThis is usually a good thing, but if you wan't the\n" |
194 |
> |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
195 |
> |
"\tvariable ( currently set to %G ) smaller.\n", |
196 |
> |
orthoTolerance); |
197 |
> |
simError(); |
198 |
|
} |
199 |
< |
} |
200 |
< |
} |
201 |
< |
|
202 |
< |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
203 |
< |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
204 |
< |
|
205 |
< |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
206 |
< |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
207 |
< |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
208 |
< |
|
229 |
< |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
230 |
< |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
231 |
< |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
232 |
< |
|
233 |
< |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
234 |
< |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
235 |
< |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
236 |
< |
|
237 |
< |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
238 |
< |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
239 |
< |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
240 |
< |
} |
241 |
< |
|
242 |
< |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
243 |
< |
double a0, a1, a2; |
244 |
< |
|
245 |
< |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
246 |
< |
|
247 |
< |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
248 |
< |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
249 |
< |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
250 |
< |
} |
251 |
< |
|
252 |
< |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
253 |
< |
double temp[3][3]; |
254 |
< |
int i, j; |
255 |
< |
|
256 |
< |
for (i = 0; i < 3; i++) { |
257 |
< |
for (j = 0; j < 3; j++) { |
258 |
< |
temp[j][i] = in[i][j]; |
199 |
> |
else { |
200 |
> |
sprintf( painCave.errMsg, |
201 |
> |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
202 |
> |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
203 |
> |
"\tThis is usually because the box has deformed under\n" |
204 |
> |
"\tNPTf integration. If you wan't to live on the edge with\n" |
205 |
> |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
206 |
> |
"\tvariable ( currently set to %G ) larger.\n", |
207 |
> |
orthoTolerance); |
208 |
> |
simError(); |
209 |
|
} |
210 |
|
} |
261 |
– |
for (i = 0; i < 3; i++) { |
262 |
– |
for (j = 0; j < 3; j++) { |
263 |
– |
out[i][j] = temp[i][j]; |
264 |
– |
} |
265 |
– |
} |
211 |
|
} |
267 |
– |
|
268 |
– |
void SimInfo::printMat3(double A[3][3] ){ |
212 |
|
|
270 |
– |
std::cerr |
271 |
– |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
272 |
– |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
273 |
– |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
274 |
– |
} |
275 |
– |
|
276 |
– |
void SimInfo::printMat9(double A[9] ){ |
277 |
– |
|
278 |
– |
std::cerr |
279 |
– |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
280 |
– |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
281 |
– |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
282 |
– |
} |
283 |
– |
|
284 |
– |
|
285 |
– |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
286 |
– |
|
287 |
– |
out[0] = a[1] * b[2] - a[2] * b[1]; |
288 |
– |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
289 |
– |
out[2] = a[0] * b[1] - a[1] * b[0]; |
290 |
– |
|
291 |
– |
} |
292 |
– |
|
293 |
– |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
294 |
– |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
295 |
– |
} |
296 |
– |
|
297 |
– |
double SimInfo::length3(double a[3]){ |
298 |
– |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
299 |
– |
} |
300 |
– |
|
213 |
|
void SimInfo::calcBoxL( void ){ |
214 |
|
|
215 |
|
double dx, dy, dz, dsq; |
265 |
|
rk[0] = Hmat[0][2]; |
266 |
|
rk[1] = Hmat[1][2]; |
267 |
|
rk[2] = Hmat[2][2]; |
268 |
< |
|
269 |
< |
crossProduct3(ri,rj, rij); |
270 |
< |
distXY = dotProduct3(rk,rij) / length3(rij); |
268 |
> |
|
269 |
> |
crossProduct3(ri, rj, rij); |
270 |
> |
distXY = dotProduct3(rk,rij) / norm3(rij); |
271 |
|
|
272 |
|
crossProduct3(rj,rk, rjk); |
273 |
< |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
273 |
> |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
274 |
|
|
275 |
|
crossProduct3(rk,ri, rki); |
276 |
< |
distZX = dotProduct3(rj,rki) / length3(rki); |
276 |
> |
distZX = dotProduct3(rj,rki) / norm3(rki); |
277 |
|
|
278 |
|
minDist = min(min(distXY, distYZ), distZX); |
279 |
|
return minDist/2; |
321 |
|
|
322 |
|
int SimInfo::getNDF(){ |
323 |
|
int ndf_local; |
324 |
< |
|
325 |
< |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
324 |
> |
|
325 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
326 |
> |
ndf_local += 3; |
327 |
> |
if (integrableObjects[i]->isDirectional()) |
328 |
> |
ndf_local += 3; |
329 |
> |
} |
330 |
|
|
331 |
+ |
// n_constraints is local, so subtract them on each processor: |
332 |
+ |
|
333 |
+ |
ndf_local -= n_constraints; |
334 |
+ |
|
335 |
|
#ifdef IS_MPI |
336 |
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
337 |
|
#else |
338 |
|
ndf = ndf_local; |
339 |
|
#endif |
340 |
|
|
341 |
+ |
// nZconstraints is global, as are the 3 COM translations for the |
342 |
+ |
// entire system: |
343 |
+ |
|
344 |
|
ndf = ndf - 3 - nZconstraints; |
345 |
|
|
346 |
|
return ndf; |
350 |
|
int ndfRaw_local; |
351 |
|
|
352 |
|
// Raw degrees of freedom that we have to set |
353 |
< |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
354 |
< |
|
353 |
> |
|
354 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
355 |
> |
ndfRaw_local += 3; |
356 |
> |
if (integrableObjects[i]->isDirectional()) |
357 |
> |
ndfRaw_local += 3; |
358 |
> |
} |
359 |
> |
|
360 |
|
#ifdef IS_MPI |
361 |
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
362 |
|
#else |
369 |
|
int SimInfo::getNDFtranslational() { |
370 |
|
int ndfTrans_local; |
371 |
|
|
372 |
< |
ndfTrans_local = 3 * n_atoms - n_constraints; |
372 |
> |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
373 |
|
|
374 |
+ |
|
375 |
|
#ifdef IS_MPI |
376 |
|
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
377 |
|
#else |
383 |
|
return ndfTrans; |
384 |
|
} |
385 |
|
|
386 |
+ |
int SimInfo::getTotIntegrableObjects() { |
387 |
+ |
int nObjs_local; |
388 |
+ |
int nObjs; |
389 |
+ |
|
390 |
+ |
nObjs_local = integrableObjects.size(); |
391 |
+ |
|
392 |
+ |
|
393 |
+ |
#ifdef IS_MPI |
394 |
+ |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
395 |
+ |
#else |
396 |
+ |
nObjs = nObjs_local; |
397 |
+ |
#endif |
398 |
+ |
|
399 |
+ |
|
400 |
+ |
return nObjs; |
401 |
+ |
} |
402 |
+ |
|
403 |
|
void SimInfo::refreshSim(){ |
404 |
|
|
405 |
|
simtype fInfo; |
409 |
|
|
410 |
|
fInfo.dielect = 0.0; |
411 |
|
|
412 |
< |
if( useDipole ){ |
412 |
> |
if( useDipoles ){ |
413 |
|
if( useReactionField )fInfo.dielect = dielectric; |
414 |
|
} |
415 |
|
|
418 |
|
fInfo.SIM_uses_LJ = useLJ; |
419 |
|
fInfo.SIM_uses_sticky = useSticky; |
420 |
|
//fInfo.SIM_uses_sticky = 0; |
421 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
421 |
> |
fInfo.SIM_uses_charges = useCharges; |
422 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
423 |
|
//fInfo.SIM_uses_dipoles = 0; |
424 |
< |
//fInfo.SIM_uses_RF = useReactionField; |
425 |
< |
fInfo.SIM_uses_RF = 0; |
424 |
> |
fInfo.SIM_uses_RF = useReactionField; |
425 |
> |
//fInfo.SIM_uses_RF = 0; |
426 |
|
fInfo.SIM_uses_GB = useGB; |
427 |
|
fInfo.SIM_uses_EAM = useEAM; |
428 |
|
|
429 |
< |
excl = Exclude::getArray(); |
429 |
> |
n_exclude = excludes->getSize(); |
430 |
> |
excl = excludes->getFortranArray(); |
431 |
|
|
432 |
|
#ifdef IS_MPI |
433 |
|
n_global = mpiSim->getTotAtoms(); |
460 |
|
this->ndfTrans = this->getNDFtranslational(); |
461 |
|
} |
462 |
|
|
515 |
– |
|
516 |
– |
void SimInfo::setRcut( double theRcut ){ |
517 |
– |
|
518 |
– |
rCut = theRcut; |
519 |
– |
checkCutOffs(); |
520 |
– |
} |
521 |
– |
|
463 |
|
void SimInfo::setDefaultRcut( double theRcut ){ |
464 |
|
|
465 |
< |
haveOrigRcut = 1; |
525 |
< |
origRcut = theRcut; |
465 |
> |
haveRcut = 1; |
466 |
|
rCut = theRcut; |
467 |
|
|
468 |
|
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
470 |
|
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
471 |
|
} |
472 |
|
|
533 |
– |
void SimInfo::setEcr( double theEcr ){ |
534 |
– |
|
535 |
– |
ecr = theEcr; |
536 |
– |
checkCutOffs(); |
537 |
– |
} |
538 |
– |
|
473 |
|
void SimInfo::setDefaultEcr( double theEcr ){ |
474 |
|
|
475 |
< |
haveOrigEcr = 1; |
476 |
< |
origEcr = theEcr; |
475 |
> |
haveEcr = 1; |
476 |
> |
ecr = theEcr; |
477 |
|
|
478 |
|
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
479 |
|
|
546 |
– |
ecr = theEcr; |
547 |
– |
|
480 |
|
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
481 |
|
} |
482 |
|
|
551 |
– |
void SimInfo::setEcr( double theEcr, double theEst ){ |
552 |
– |
|
553 |
– |
est = theEst; |
554 |
– |
setEcr( theEcr ); |
555 |
– |
} |
556 |
– |
|
483 |
|
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
484 |
|
|
485 |
|
est = theEst; |
488 |
|
|
489 |
|
|
490 |
|
void SimInfo::checkCutOffs( void ){ |
565 |
– |
|
566 |
– |
int cutChanged = 0; |
491 |
|
|
492 |
|
if( boxIsInit ){ |
493 |
|
|
494 |
|
//we need to check cutOffs against the box |
495 |
< |
|
496 |
< |
//detect the change of rCut |
573 |
< |
if(( maxCutoff > rCut )&&(usePBC)){ |
574 |
< |
if( rCut < origRcut ){ |
575 |
< |
rCut = origRcut; |
576 |
< |
|
577 |
< |
if (rCut > maxCutoff) |
578 |
< |
rCut = maxCutoff; |
579 |
< |
|
580 |
< |
sprintf( painCave.errMsg, |
581 |
< |
"New Box size is setting the long range cutoff radius " |
582 |
< |
"to %lf at time %lf\n", |
583 |
< |
rCut, currentTime ); |
584 |
< |
painCave.isFatal = 0; |
585 |
< |
simError(); |
586 |
< |
} |
587 |
< |
} |
588 |
< |
else if ((rCut > maxCutoff)&&(usePBC)) { |
495 |
> |
|
496 |
> |
if( rCut > maxCutoff ){ |
497 |
|
sprintf( painCave.errMsg, |
498 |
< |
"New Box size is setting the long range cutoff radius " |
499 |
< |
"to %lf at time %lf\n", |
500 |
< |
maxCutoff, currentTime ); |
501 |
< |
painCave.isFatal = 0; |
498 |
> |
"LJrcut is too large for the current periodic box.\n" |
499 |
> |
"\tCurrent Value of LJrcut = %G at time %G\n " |
500 |
> |
"\tThis is larger than half of at least one of the\n" |
501 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
502 |
> |
"\n, %G" |
503 |
> |
"\t[ %G %G %G ]\n" |
504 |
> |
"\t[ %G %G %G ]\n" |
505 |
> |
"\t[ %G %G %G ]\n", |
506 |
> |
rCut, currentTime, maxCutoff, |
507 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
508 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
509 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
510 |
> |
painCave.isFatal = 1; |
511 |
|
simError(); |
595 |
– |
rCut = maxCutoff; |
512 |
|
} |
513 |
< |
|
514 |
< |
|
515 |
< |
//detect the change of ecr |
516 |
< |
if( maxCutoff > ecr ){ |
517 |
< |
if( ecr < origEcr ){ |
518 |
< |
ecr = origEcr; |
519 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
520 |
< |
|
521 |
< |
sprintf( painCave.errMsg, |
522 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
523 |
< |
"to %lf at time %lf\n", |
524 |
< |
ecr, currentTime ); |
525 |
< |
painCave.isFatal = 0; |
526 |
< |
simError(); |
513 |
> |
|
514 |
> |
if( haveEcr ){ |
515 |
> |
if( ecr > maxCutoff ){ |
516 |
> |
sprintf( painCave.errMsg, |
517 |
> |
"electrostaticCutoffRadius is too large for the current\n" |
518 |
> |
"\tperiodic box.\n\n" |
519 |
> |
"\tCurrent Value of ECR = %G at time %G\n " |
520 |
> |
"\tThis is larger than half of at least one of the\n" |
521 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
522 |
> |
"\n" |
523 |
> |
"\t[ %G %G %G ]\n" |
524 |
> |
"\t[ %G %G %G ]\n" |
525 |
> |
"\t[ %G %G %G ]\n", |
526 |
> |
ecr, currentTime, |
527 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
528 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
529 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
530 |
> |
painCave.isFatal = 1; |
531 |
> |
simError(); |
532 |
|
} |
533 |
|
} |
613 |
– |
else if( ecr > maxCutoff){ |
614 |
– |
sprintf( painCave.errMsg, |
615 |
– |
"New Box size is setting the electrostaticCutoffRadius " |
616 |
– |
"to %lf at time %lf\n", |
617 |
– |
maxCutoff, currentTime ); |
618 |
– |
painCave.isFatal = 0; |
619 |
– |
simError(); |
620 |
– |
ecr = maxCutoff; |
621 |
– |
} |
622 |
– |
|
623 |
– |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
624 |
– |
|
625 |
– |
// rlist is the 1.0 plus max( rcut, ecr ) |
626 |
– |
|
627 |
– |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
628 |
– |
|
629 |
– |
if( cutChanged ){ |
630 |
– |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
631 |
– |
} |
632 |
– |
|
633 |
– |
oldEcr = ecr; |
634 |
– |
oldRcut = rCut; |
635 |
– |
|
534 |
|
} else { |
535 |
|
// initialize this stuff before using it, OK? |
536 |
|
sprintf( painCave.errMsg, |
537 |
< |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
537 |
> |
"Trying to check cutoffs without a box.\n" |
538 |
> |
"\tOOPSE should have better programmers than that.\n" ); |
539 |
|
painCave.isFatal = 1; |
540 |
|
simError(); |
541 |
|
} |
588 |
|
|
589 |
|
return result; |
590 |
|
} |
692 |
– |
|
693 |
– |
double SimInfo::matTrace3(double m[3][3]){ |
694 |
– |
double trace; |
695 |
– |
trace = m[0][0] + m[1][1] + m[2][2]; |
696 |
– |
|
697 |
– |
return trace; |
698 |
– |
} |