1 |
#include <stdlib.h> |
2 |
#include <string.h> |
3 |
#include <math.h> |
4 |
|
5 |
#include <iostream> |
6 |
using namespace std; |
7 |
|
8 |
#include "brains/SimInfo.hpp" |
9 |
#define __C |
10 |
#include "brains/fSimulation.h" |
11 |
#include "utils/simError.h" |
12 |
#include "UseTheForce/DarkSide/simulation_interface.h" |
13 |
#include "UseTheForce/notifyCutoffs_interface.h" |
14 |
|
15 |
//#include "UseTheForce/fortranWrappers.hpp" |
16 |
|
17 |
#include "math/MatVec3.h" |
18 |
|
19 |
#ifdef IS_MPI |
20 |
#include "brains/mpiSimulation.hpp" |
21 |
#endif |
22 |
|
23 |
inline double roundMe( double x ){ |
24 |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
25 |
} |
26 |
|
27 |
inline double min( double a, double b ){ |
28 |
return (a < b ) ? a : b; |
29 |
} |
30 |
|
31 |
SimInfo* currentInfo; |
32 |
|
33 |
SimInfo::SimInfo(){ |
34 |
|
35 |
n_constraints = 0; |
36 |
nZconstraints = 0; |
37 |
n_oriented = 0; |
38 |
n_dipoles = 0; |
39 |
ndf = 0; |
40 |
ndfRaw = 0; |
41 |
nZconstraints = 0; |
42 |
the_integrator = NULL; |
43 |
setTemp = 0; |
44 |
thermalTime = 0.0; |
45 |
currentTime = 0.0; |
46 |
rCut = 0.0; |
47 |
rSw = 0.0; |
48 |
|
49 |
haveRcut = 0; |
50 |
haveRsw = 0; |
51 |
boxIsInit = 0; |
52 |
|
53 |
resetTime = 1e99; |
54 |
|
55 |
orthoRhombic = 0; |
56 |
orthoTolerance = 1E-6; |
57 |
useInitXSstate = true; |
58 |
|
59 |
usePBC = 0; |
60 |
useDirectionalAtoms = 0; |
61 |
useLennardJones = 0; |
62 |
useElectrostatics = 0; |
63 |
useCharges = 0; |
64 |
useDipoles = 0; |
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useSticky = 0; |
66 |
useGayBerne = 0; |
67 |
useEAM = 0; |
68 |
useShapes = 0; |
69 |
useFLARB = 0; |
70 |
|
71 |
useSolidThermInt = 0; |
72 |
useLiquidThermInt = 0; |
73 |
|
74 |
haveCutoffGroups = false; |
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|
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excludes = Exclude::Instance(); |
77 |
|
78 |
myConfiguration = new SimState(); |
79 |
|
80 |
has_minimizer = false; |
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the_minimizer =NULL; |
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|
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ngroup = 0; |
84 |
|
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} |
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|
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|
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SimInfo::~SimInfo(){ |
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|
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delete myConfiguration; |
91 |
|
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map<string, GenericData*>::iterator i; |
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|
94 |
for(i = properties.begin(); i != properties.end(); i++) |
95 |
delete (*i).second; |
96 |
|
97 |
} |
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|
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void SimInfo::setBox(double newBox[3]) { |
100 |
|
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int i, j; |
102 |
double tempMat[3][3]; |
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|
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for(i=0; i<3; i++) |
105 |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
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|
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tempMat[0][0] = newBox[0]; |
108 |
tempMat[1][1] = newBox[1]; |
109 |
tempMat[2][2] = newBox[2]; |
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|
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setBoxM( tempMat ); |
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|
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} |
114 |
|
115 |
void SimInfo::setBoxM( double theBox[3][3] ){ |
116 |
|
117 |
int i, j; |
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double FortranHmat[9]; // to preserve compatibility with Fortran the |
119 |
// ordering in the array is as follows: |
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// [ 0 3 6 ] |
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// [ 1 4 7 ] |
122 |
// [ 2 5 8 ] |
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double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
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|
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if( !boxIsInit ) boxIsInit = 1; |
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|
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for(i=0; i < 3; i++) |
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for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
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|
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calcBoxL(); |
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calcHmatInv(); |
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|
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for(i=0; i < 3; i++) { |
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for (j=0; j < 3; j++) { |
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FortranHmat[3*j + i] = Hmat[i][j]; |
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FortranHmatInv[3*j + i] = HmatInv[i][j]; |
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} |
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} |
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|
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setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic); |
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|
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} |
143 |
|
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|
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void SimInfo::getBoxM (double theBox[3][3]) { |
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|
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int i, j; |
148 |
for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
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} |
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|
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|
153 |
void SimInfo::scaleBox(double scale) { |
154 |
double theBox[3][3]; |
155 |
int i, j; |
156 |
|
157 |
// cerr << "Scaling box by " << scale << "\n"; |
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|
159 |
for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
161 |
|
162 |
setBoxM(theBox); |
163 |
|
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} |
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|
166 |
void SimInfo::calcHmatInv( void ) { |
167 |
|
168 |
int oldOrtho; |
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int i,j; |
170 |
double smallDiag; |
171 |
double tol; |
172 |
double sanity[3][3]; |
173 |
|
174 |
invertMat3( Hmat, HmatInv ); |
175 |
|
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// check to see if Hmat is orthorhombic |
177 |
|
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oldOrtho = orthoRhombic; |
179 |
|
180 |
smallDiag = fabs(Hmat[0][0]); |
181 |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
182 |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
183 |
tol = smallDiag * orthoTolerance; |
184 |
|
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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 ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
192 |
} |
193 |
} |
194 |
} |
195 |
} |
196 |
|
197 |
if( oldOrtho != orthoRhombic ){ |
198 |
|
199 |
if( orthoRhombic ) { |
200 |
sprintf( painCave.errMsg, |
201 |
"OOPSE is switching from the default Non-Orthorhombic\n" |
202 |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
203 |
"\tThis is usually a good thing, but if you wan't the\n" |
204 |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
205 |
"\tvariable ( currently set to %G ) smaller.\n", |
206 |
orthoTolerance); |
207 |
painCave.severity = OOPSE_INFO; |
208 |
simError(); |
209 |
} |
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else { |
211 |
sprintf( painCave.errMsg, |
212 |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
213 |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
214 |
"\tThis is usually because the box has deformed under\n" |
215 |
"\tNPTf integration. If you wan't to live on the edge with\n" |
216 |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
217 |
"\tvariable ( currently set to %G ) larger.\n", |
218 |
orthoTolerance); |
219 |
painCave.severity = OOPSE_WARNING; |
220 |
simError(); |
221 |
} |
222 |
} |
223 |
} |
224 |
|
225 |
void SimInfo::calcBoxL( void ){ |
226 |
|
227 |
double dx, dy, dz, dsq; |
228 |
|
229 |
// boxVol = Determinant of Hmat |
230 |
|
231 |
boxVol = matDet3( Hmat ); |
232 |
|
233 |
// boxLx |
234 |
|
235 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
236 |
dsq = dx*dx + dy*dy + dz*dz; |
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boxL[0] = sqrt( dsq ); |
238 |
//maxCutoff = 0.5 * boxL[0]; |
239 |
|
240 |
// boxLy |
241 |
|
242 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
243 |
dsq = dx*dx + dy*dy + dz*dz; |
244 |
boxL[1] = sqrt( dsq ); |
245 |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
246 |
|
247 |
|
248 |
// boxLz |
249 |
|
250 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
251 |
dsq = dx*dx + dy*dy + dz*dz; |
252 |
boxL[2] = sqrt( dsq ); |
253 |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
254 |
|
255 |
//calculate the max cutoff |
256 |
maxCutoff = calcMaxCutOff(); |
257 |
|
258 |
checkCutOffs(); |
259 |
|
260 |
} |
261 |
|
262 |
|
263 |
double SimInfo::calcMaxCutOff(){ |
264 |
|
265 |
double ri[3], rj[3], rk[3]; |
266 |
double rij[3], rjk[3], rki[3]; |
267 |
double minDist; |
268 |
|
269 |
ri[0] = Hmat[0][0]; |
270 |
ri[1] = Hmat[1][0]; |
271 |
ri[2] = Hmat[2][0]; |
272 |
|
273 |
rj[0] = Hmat[0][1]; |
274 |
rj[1] = Hmat[1][1]; |
275 |
rj[2] = Hmat[2][1]; |
276 |
|
277 |
rk[0] = Hmat[0][2]; |
278 |
rk[1] = Hmat[1][2]; |
279 |
rk[2] = Hmat[2][2]; |
280 |
|
281 |
crossProduct3(ri, rj, rij); |
282 |
distXY = dotProduct3(rk,rij) / norm3(rij); |
283 |
|
284 |
crossProduct3(rj,rk, rjk); |
285 |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
286 |
|
287 |
crossProduct3(rk,ri, rki); |
288 |
distZX = dotProduct3(rj,rki) / norm3(rki); |
289 |
|
290 |
minDist = min(min(distXY, distYZ), distZX); |
291 |
return minDist/2; |
292 |
|
293 |
} |
294 |
|
295 |
void SimInfo::wrapVector( double thePos[3] ){ |
296 |
|
297 |
int i; |
298 |
double scaled[3]; |
299 |
|
300 |
if( !orthoRhombic ){ |
301 |
// calc the scaled coordinates. |
302 |
|
303 |
|
304 |
matVecMul3(HmatInv, thePos, scaled); |
305 |
|
306 |
for(i=0; i<3; i++) |
307 |
scaled[i] -= roundMe(scaled[i]); |
308 |
|
309 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
310 |
|
311 |
matVecMul3(Hmat, scaled, thePos); |
312 |
|
313 |
} |
314 |
else{ |
315 |
// calc the scaled coordinates. |
316 |
|
317 |
for(i=0; i<3; i++) |
318 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
319 |
|
320 |
// wrap the scaled coordinates |
321 |
|
322 |
for(i=0; i<3; i++) |
323 |
scaled[i] -= roundMe(scaled[i]); |
324 |
|
325 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
326 |
|
327 |
for(i=0; i<3; i++) |
328 |
thePos[i] = scaled[i]*Hmat[i][i]; |
329 |
} |
330 |
|
331 |
} |
332 |
|
333 |
|
334 |
int SimInfo::getNDF(){ |
335 |
int ndf_local; |
336 |
|
337 |
ndf_local = 0; |
338 |
|
339 |
for(int i = 0; i < integrableObjects.size(); i++){ |
340 |
ndf_local += 3; |
341 |
if (integrableObjects[i]->isDirectional()) { |
342 |
if (integrableObjects[i]->isLinear()) |
343 |
ndf_local += 2; |
344 |
else |
345 |
ndf_local += 3; |
346 |
} |
347 |
} |
348 |
|
349 |
// n_constraints is local, so subtract them on each processor: |
350 |
|
351 |
ndf_local -= n_constraints; |
352 |
|
353 |
#ifdef IS_MPI |
354 |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
355 |
#else |
356 |
ndf = ndf_local; |
357 |
#endif |
358 |
|
359 |
// nZconstraints is global, as are the 3 COM translations for the |
360 |
// entire system: |
361 |
|
362 |
ndf = ndf - 3 - nZconstraints; |
363 |
|
364 |
return ndf; |
365 |
} |
366 |
|
367 |
int SimInfo::getNDFraw() { |
368 |
int ndfRaw_local; |
369 |
|
370 |
// Raw degrees of freedom that we have to set |
371 |
ndfRaw_local = 0; |
372 |
|
373 |
for(int i = 0; i < integrableObjects.size(); i++){ |
374 |
ndfRaw_local += 3; |
375 |
if (integrableObjects[i]->isDirectional()) { |
376 |
if (integrableObjects[i]->isLinear()) |
377 |
ndfRaw_local += 2; |
378 |
else |
379 |
ndfRaw_local += 3; |
380 |
} |
381 |
} |
382 |
|
383 |
#ifdef IS_MPI |
384 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
385 |
#else |
386 |
ndfRaw = ndfRaw_local; |
387 |
#endif |
388 |
|
389 |
return ndfRaw; |
390 |
} |
391 |
|
392 |
int SimInfo::getNDFtranslational() { |
393 |
int ndfTrans_local; |
394 |
|
395 |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
396 |
|
397 |
|
398 |
#ifdef IS_MPI |
399 |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
400 |
#else |
401 |
ndfTrans = ndfTrans_local; |
402 |
#endif |
403 |
|
404 |
ndfTrans = ndfTrans - 3 - nZconstraints; |
405 |
|
406 |
return ndfTrans; |
407 |
} |
408 |
|
409 |
int SimInfo::getTotIntegrableObjects() { |
410 |
int nObjs_local; |
411 |
int nObjs; |
412 |
|
413 |
nObjs_local = integrableObjects.size(); |
414 |
|
415 |
|
416 |
#ifdef IS_MPI |
417 |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
418 |
#else |
419 |
nObjs = nObjs_local; |
420 |
#endif |
421 |
|
422 |
|
423 |
return nObjs; |
424 |
} |
425 |
|
426 |
void SimInfo::refreshSim(){ |
427 |
|
428 |
simtype fInfo; |
429 |
int isError; |
430 |
int n_global; |
431 |
int* excl; |
432 |
|
433 |
fInfo.dielect = 0.0; |
434 |
|
435 |
if( useDipoles ){ |
436 |
if( useReactionField )fInfo.dielect = dielectric; |
437 |
} |
438 |
|
439 |
fInfo.SIM_uses_PBC = usePBC; |
440 |
|
441 |
if (useSticky || useDipoles || useGayBerne || useShapes) { |
442 |
useDirectionalAtoms = 1; |
443 |
fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms; |
444 |
} |
445 |
|
446 |
fInfo.SIM_uses_LennardJones = useLennardJones; |
447 |
|
448 |
if (useCharges || useDipoles) { |
449 |
useElectrostatics = 1; |
450 |
fInfo.SIM_uses_Electrostatics = useElectrostatics; |
451 |
} |
452 |
|
453 |
fInfo.SIM_uses_Charges = useCharges; |
454 |
fInfo.SIM_uses_Dipoles = useDipoles; |
455 |
fInfo.SIM_uses_Sticky = useSticky; |
456 |
fInfo.SIM_uses_GayBerne = useGayBerne; |
457 |
fInfo.SIM_uses_EAM = useEAM; |
458 |
fInfo.SIM_uses_Shapes = useShapes; |
459 |
fInfo.SIM_uses_FLARB = useFLARB; |
460 |
fInfo.SIM_uses_RF = useReactionField; |
461 |
|
462 |
n_exclude = excludes->getSize(); |
463 |
excl = excludes->getFortranArray(); |
464 |
|
465 |
#ifdef IS_MPI |
466 |
n_global = mpiSim->getNAtomsGlobal(); |
467 |
#else |
468 |
n_global = n_atoms; |
469 |
#endif |
470 |
|
471 |
isError = 0; |
472 |
|
473 |
getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
474 |
//it may not be a good idea to pass the address of first element in vector |
475 |
//since c++ standard does not require vector to be stored continuously in meomory |
476 |
//Most of the compilers will organize the memory of vector continuously |
477 |
setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
478 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
479 |
&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
480 |
|
481 |
if( isError ){ |
482 |
|
483 |
sprintf( painCave.errMsg, |
484 |
"There was an error setting the simulation information in fortran.\n" ); |
485 |
painCave.isFatal = 1; |
486 |
painCave.severity = OOPSE_ERROR; |
487 |
simError(); |
488 |
} |
489 |
|
490 |
#ifdef IS_MPI |
491 |
sprintf( checkPointMsg, |
492 |
"succesfully sent the simulation information to fortran.\n"); |
493 |
MPIcheckPoint(); |
494 |
#endif // is_mpi |
495 |
|
496 |
this->ndf = this->getNDF(); |
497 |
this->ndfRaw = this->getNDFraw(); |
498 |
this->ndfTrans = this->getNDFtranslational(); |
499 |
} |
500 |
|
501 |
void SimInfo::setDefaultRcut( double theRcut ){ |
502 |
|
503 |
haveRcut = 1; |
504 |
rCut = theRcut; |
505 |
rList = rCut + 1.0; |
506 |
|
507 |
notifyFortranCutoffs( &rCut, &rSw, &rList ); |
508 |
} |
509 |
|
510 |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
511 |
|
512 |
rSw = theRsw; |
513 |
setDefaultRcut( theRcut ); |
514 |
} |
515 |
|
516 |
|
517 |
void SimInfo::checkCutOffs( void ){ |
518 |
|
519 |
if( boxIsInit ){ |
520 |
|
521 |
//we need to check cutOffs against the box |
522 |
|
523 |
if( rCut > maxCutoff ){ |
524 |
sprintf( painCave.errMsg, |
525 |
"cutoffRadius is too large for the current periodic box.\n" |
526 |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
527 |
"\tThis is larger than half of at least one of the\n" |
528 |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
529 |
"\n" |
530 |
"\t[ %G %G %G ]\n" |
531 |
"\t[ %G %G %G ]\n" |
532 |
"\t[ %G %G %G ]\n", |
533 |
rCut, currentTime, |
534 |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
535 |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
536 |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
537 |
painCave.severity = OOPSE_ERROR; |
538 |
painCave.isFatal = 1; |
539 |
simError(); |
540 |
} |
541 |
} else { |
542 |
// initialize this stuff before using it, OK? |
543 |
sprintf( painCave.errMsg, |
544 |
"Trying to check cutoffs without a box.\n" |
545 |
"\tOOPSE should have better programmers than that.\n" ); |
546 |
painCave.severity = OOPSE_ERROR; |
547 |
painCave.isFatal = 1; |
548 |
simError(); |
549 |
} |
550 |
|
551 |
} |
552 |
|
553 |
void SimInfo::addProperty(GenericData* prop){ |
554 |
|
555 |
map<string, GenericData*>::iterator result; |
556 |
result = properties.find(prop->getID()); |
557 |
|
558 |
//we can't simply use properties[prop->getID()] = prop, |
559 |
//it will cause memory leak if we already contain a propery which has the same name of prop |
560 |
|
561 |
if(result != properties.end()){ |
562 |
|
563 |
delete (*result).second; |
564 |
(*result).second = prop; |
565 |
|
566 |
} |
567 |
else{ |
568 |
|
569 |
properties[prop->getID()] = prop; |
570 |
|
571 |
} |
572 |
|
573 |
} |
574 |
|
575 |
GenericData* SimInfo::getPropertyByName(const string& propName){ |
576 |
|
577 |
map<string, GenericData*>::iterator result; |
578 |
|
579 |
//string lowerCaseName = (); |
580 |
|
581 |
result = properties.find(propName); |
582 |
|
583 |
if(result != properties.end()) |
584 |
return (*result).second; |
585 |
else |
586 |
return NULL; |
587 |
} |
588 |
|
589 |
|
590 |
void SimInfo::getFortranGroupArrays(SimInfo* info, |
591 |
vector<int>& FglobalGroupMembership, |
592 |
vector<double>& mfact){ |
593 |
|
594 |
Molecule* myMols; |
595 |
Atom** myAtoms; |
596 |
int numAtom; |
597 |
double mtot; |
598 |
int numMol; |
599 |
int numCutoffGroups; |
600 |
CutoffGroup* myCutoffGroup; |
601 |
vector<CutoffGroup*>::iterator iterCutoff; |
602 |
Atom* cutoffAtom; |
603 |
vector<Atom*>::iterator iterAtom; |
604 |
int atomIndex; |
605 |
double totalMass; |
606 |
|
607 |
mfact.clear(); |
608 |
FglobalGroupMembership.clear(); |
609 |
|
610 |
|
611 |
// Fix the silly fortran indexing problem |
612 |
#ifdef IS_MPI |
613 |
numAtom = mpiSim->getNAtomsGlobal(); |
614 |
#else |
615 |
numAtom = n_atoms; |
616 |
#endif |
617 |
for (int i = 0; i < numAtom; i++) |
618 |
FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
619 |
|
620 |
|
621 |
myMols = info->molecules; |
622 |
numMol = info->n_mol; |
623 |
for(int i = 0; i < numMol; i++){ |
624 |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
625 |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
626 |
myCutoffGroup != NULL; |
627 |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
628 |
|
629 |
totalMass = myCutoffGroup->getMass(); |
630 |
|
631 |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
632 |
cutoffAtom != NULL; |
633 |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
634 |
mfact.push_back(cutoffAtom->getMass()/totalMass); |
635 |
} |
636 |
} |
637 |
} |
638 |
|
639 |
} |