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 |
10 |
#include "fSimulation.h" |
11 |
#include "simError.h" |
12 |
|
13 |
#include "fortranWrappers.hpp" |
14 |
|
15 |
#include "MatVec3.h" |
16 |
|
17 |
#ifdef IS_MPI |
18 |
#include "mpiSimulation.hpp" |
19 |
#endif |
20 |
|
21 |
inline double roundMe( double x ){ |
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 |
|
31 |
SimInfo::SimInfo(){ |
32 |
|
33 |
n_constraints = 0; |
34 |
nZconstraints = 0; |
35 |
n_oriented = 0; |
36 |
n_dipoles = 0; |
37 |
ndf = 0; |
38 |
ndfRaw = 0; |
39 |
nZconstraints = 0; |
40 |
the_integrator = NULL; |
41 |
setTemp = 0; |
42 |
thermalTime = 0.0; |
43 |
currentTime = 0.0; |
44 |
rCut = 0.0; |
45 |
ecr = 0.0; |
46 |
est = 0.0; |
47 |
|
48 |
haveRcut = 0; |
49 |
haveEcr = 0; |
50 |
boxIsInit = 0; |
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|
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resetTime = 1e99; |
53 |
|
54 |
orthoRhombic = 0; |
55 |
orthoTolerance = 1E-6; |
56 |
useInitXSstate = true; |
57 |
|
58 |
usePBC = 0; |
59 |
useLJ = 0; |
60 |
useSticky = 0; |
61 |
useCharges = 0; |
62 |
useDipoles = 0; |
63 |
useReactionField = 0; |
64 |
useGB = 0; |
65 |
useEAM = 0; |
66 |
|
67 |
excludes = Exclude::Instance(); |
68 |
|
69 |
myConfiguration = new SimState(); |
70 |
|
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has_minimizer = false; |
72 |
the_minimizer =NULL; |
73 |
|
74 |
wrapMeSimInfo( this ); |
75 |
} |
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|
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|
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SimInfo::~SimInfo(){ |
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|
80 |
delete myConfiguration; |
81 |
|
82 |
map<string, GenericData*>::iterator i; |
83 |
|
84 |
for(i = properties.begin(); i != properties.end(); i++) |
85 |
delete (*i).second; |
86 |
|
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} |
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|
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void SimInfo::setBox(double newBox[3]) { |
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|
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int i, j; |
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double tempMat[3][3]; |
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|
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for(i=0; i<3; i++) |
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for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
96 |
|
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tempMat[0][0] = newBox[0]; |
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tempMat[1][1] = newBox[1]; |
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tempMat[2][2] = newBox[2]; |
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|
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setBoxM( tempMat ); |
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|
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} |
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|
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void SimInfo::setBoxM( double theBox[3][3] ){ |
106 |
|
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int i, j; |
108 |
double FortranHmat[9]; // to preserve compatibility with Fortran the |
109 |
// ordering in the array is as follows: |
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// [ 0 3 6 ] |
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// [ 1 4 7 ] |
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// [ 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; |
116 |
|
117 |
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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|
120 |
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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setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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|
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} |
133 |
|
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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; |
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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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|
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void SimInfo::scaleBox(double scale) { |
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double theBox[3][3]; |
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int i, j; |
146 |
|
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// cerr << "Scaling box by " << scale << "\n"; |
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|
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for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
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|
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setBoxM(theBox); |
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|
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} |
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|
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void SimInfo::calcHmatInv( void ) { |
157 |
|
158 |
int oldOrtho; |
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int i,j; |
160 |
double smallDiag; |
161 |
double tol; |
162 |
double sanity[3][3]; |
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|
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invertMat3( Hmat, HmatInv ); |
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|
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// check to see if Hmat is orthorhombic |
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|
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oldOrtho = orthoRhombic; |
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|
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smallDiag = fabs(Hmat[0][0]); |
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if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
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if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
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tol = smallDiag * orthoTolerance; |
174 |
|
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orthoRhombic = 1; |
176 |
|
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for (i = 0; i < 3; i++ ) { |
178 |
for (j = 0 ; j < 3; j++) { |
179 |
if (i != j) { |
180 |
if (orthoRhombic) { |
181 |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
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} |
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} |
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} |
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} |
186 |
|
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if( oldOrtho != orthoRhombic ){ |
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|
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(); |
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} |
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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", |
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orthoTolerance); |
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simError(); |
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} |
210 |
} |
211 |
} |
212 |
|
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void SimInfo::calcBoxL( void ){ |
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|
215 |
double dx, dy, dz, dsq; |
216 |
|
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// boxVol = Determinant of Hmat |
218 |
|
219 |
boxVol = matDet3( Hmat ); |
220 |
|
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// boxLx |
222 |
|
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dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxL[0] = sqrt( dsq ); |
226 |
//maxCutoff = 0.5 * boxL[0]; |
227 |
|
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// boxLy |
229 |
|
230 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
231 |
dsq = dx*dx + dy*dy + dz*dz; |
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boxL[1] = sqrt( dsq ); |
233 |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
234 |
|
235 |
|
236 |
// boxLz |
237 |
|
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dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
239 |
dsq = dx*dx + dy*dy + dz*dz; |
240 |
boxL[2] = sqrt( dsq ); |
241 |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
242 |
|
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//calculate the max cutoff |
244 |
maxCutoff = calcMaxCutOff(); |
245 |
|
246 |
checkCutOffs(); |
247 |
|
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} |
249 |
|
250 |
|
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double SimInfo::calcMaxCutOff(){ |
252 |
|
253 |
double ri[3], rj[3], rk[3]; |
254 |
double rij[3], rjk[3], rki[3]; |
255 |
double minDist; |
256 |
|
257 |
ri[0] = Hmat[0][0]; |
258 |
ri[1] = Hmat[1][0]; |
259 |
ri[2] = Hmat[2][0]; |
260 |
|
261 |
rj[0] = Hmat[0][1]; |
262 |
rj[1] = Hmat[1][1]; |
263 |
rj[2] = Hmat[2][1]; |
264 |
|
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) / norm3(rij); |
271 |
|
272 |
crossProduct3(rj,rk, rjk); |
273 |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
274 |
|
275 |
crossProduct3(rk,ri, rki); |
276 |
distZX = dotProduct3(rj,rki) / norm3(rki); |
277 |
|
278 |
minDist = min(min(distXY, distYZ), distZX); |
279 |
return minDist/2; |
280 |
|
281 |
} |
282 |
|
283 |
void SimInfo::wrapVector( double thePos[3] ){ |
284 |
|
285 |
int i; |
286 |
double scaled[3]; |
287 |
|
288 |
if( !orthoRhombic ){ |
289 |
// calc the scaled coordinates. |
290 |
|
291 |
|
292 |
matVecMul3(HmatInv, thePos, scaled); |
293 |
|
294 |
for(i=0; i<3; i++) |
295 |
scaled[i] -= roundMe(scaled[i]); |
296 |
|
297 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
298 |
|
299 |
matVecMul3(Hmat, scaled, thePos); |
300 |
|
301 |
} |
302 |
else{ |
303 |
// calc the scaled coordinates. |
304 |
|
305 |
for(i=0; i<3; i++) |
306 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
307 |
|
308 |
// wrap the scaled coordinates |
309 |
|
310 |
for(i=0; i<3; i++) |
311 |
scaled[i] -= roundMe(scaled[i]); |
312 |
|
313 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
314 |
|
315 |
for(i=0; i<3; i++) |
316 |
thePos[i] = scaled[i]*Hmat[i][i]; |
317 |
} |
318 |
|
319 |
} |
320 |
|
321 |
|
322 |
int SimInfo::getNDF(){ |
323 |
int ndf_local; |
324 |
|
325 |
ndf_local = 0; |
326 |
|
327 |
for(int i = 0; i < integrableObjects.size(); i++){ |
328 |
ndf_local += 3; |
329 |
if (integrableObjects[i]->isDirectional()) { |
330 |
if (integrableObjects[i]->isLinear()) |
331 |
ndf_local += 2; |
332 |
else |
333 |
ndf_local += 3; |
334 |
} |
335 |
} |
336 |
|
337 |
// n_constraints is local, so subtract them on each processor: |
338 |
|
339 |
ndf_local -= n_constraints; |
340 |
|
341 |
#ifdef IS_MPI |
342 |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
343 |
#else |
344 |
ndf = ndf_local; |
345 |
#endif |
346 |
|
347 |
// nZconstraints is global, as are the 3 COM translations for the |
348 |
// entire system: |
349 |
|
350 |
ndf = ndf - 3 - nZconstraints; |
351 |
|
352 |
return ndf; |
353 |
} |
354 |
|
355 |
int SimInfo::getNDFraw() { |
356 |
int ndfRaw_local; |
357 |
|
358 |
// Raw degrees of freedom that we have to set |
359 |
ndfRaw_local = 0; |
360 |
|
361 |
for(int i = 0; i < integrableObjects.size(); i++){ |
362 |
ndfRaw_local += 3; |
363 |
if (integrableObjects[i]->isDirectional()) { |
364 |
if (integrableObjects[i]->isLinear()) |
365 |
ndfRaw_local += 2; |
366 |
else |
367 |
ndfRaw_local += 3; |
368 |
} |
369 |
} |
370 |
|
371 |
#ifdef IS_MPI |
372 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
373 |
#else |
374 |
ndfRaw = ndfRaw_local; |
375 |
#endif |
376 |
|
377 |
return ndfRaw; |
378 |
} |
379 |
|
380 |
int SimInfo::getNDFtranslational() { |
381 |
int ndfTrans_local; |
382 |
|
383 |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
384 |
|
385 |
|
386 |
#ifdef IS_MPI |
387 |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
388 |
#else |
389 |
ndfTrans = ndfTrans_local; |
390 |
#endif |
391 |
|
392 |
ndfTrans = ndfTrans - 3 - nZconstraints; |
393 |
|
394 |
return ndfTrans; |
395 |
} |
396 |
|
397 |
int SimInfo::getTotIntegrableObjects() { |
398 |
int nObjs_local; |
399 |
int nObjs; |
400 |
|
401 |
nObjs_local = integrableObjects.size(); |
402 |
|
403 |
|
404 |
#ifdef IS_MPI |
405 |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
406 |
#else |
407 |
nObjs = nObjs_local; |
408 |
#endif |
409 |
|
410 |
|
411 |
return nObjs; |
412 |
} |
413 |
|
414 |
void SimInfo::refreshSim(){ |
415 |
|
416 |
simtype fInfo; |
417 |
int isError; |
418 |
int n_global; |
419 |
int* excl; |
420 |
|
421 |
fInfo.dielect = 0.0; |
422 |
|
423 |
if( useDipoles ){ |
424 |
if( useReactionField )fInfo.dielect = dielectric; |
425 |
} |
426 |
|
427 |
fInfo.SIM_uses_PBC = usePBC; |
428 |
//fInfo.SIM_uses_LJ = 0; |
429 |
fInfo.SIM_uses_LJ = useLJ; |
430 |
fInfo.SIM_uses_sticky = useSticky; |
431 |
//fInfo.SIM_uses_sticky = 0; |
432 |
fInfo.SIM_uses_charges = useCharges; |
433 |
fInfo.SIM_uses_dipoles = useDipoles; |
434 |
//fInfo.SIM_uses_dipoles = 0; |
435 |
fInfo.SIM_uses_RF = useReactionField; |
436 |
//fInfo.SIM_uses_RF = 0; |
437 |
fInfo.SIM_uses_GB = useGB; |
438 |
fInfo.SIM_uses_EAM = useEAM; |
439 |
|
440 |
n_exclude = excludes->getSize(); |
441 |
excl = excludes->getFortranArray(); |
442 |
|
443 |
#ifdef IS_MPI |
444 |
n_global = mpiSim->getTotAtoms(); |
445 |
#else |
446 |
n_global = n_atoms; |
447 |
#endif |
448 |
|
449 |
isError = 0; |
450 |
|
451 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
452 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
453 |
&isError ); |
454 |
|
455 |
if( isError ){ |
456 |
|
457 |
sprintf( painCave.errMsg, |
458 |
"There was an error setting the simulation information in fortran.\n" ); |
459 |
painCave.isFatal = 1; |
460 |
simError(); |
461 |
} |
462 |
|
463 |
#ifdef IS_MPI |
464 |
sprintf( checkPointMsg, |
465 |
"succesfully sent the simulation information to fortran.\n"); |
466 |
MPIcheckPoint(); |
467 |
#endif // is_mpi |
468 |
|
469 |
this->ndf = this->getNDF(); |
470 |
this->ndfRaw = this->getNDFraw(); |
471 |
this->ndfTrans = this->getNDFtranslational(); |
472 |
} |
473 |
|
474 |
void SimInfo::setDefaultRcut( double theRcut ){ |
475 |
|
476 |
haveRcut = 1; |
477 |
rCut = theRcut; |
478 |
|
479 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
480 |
|
481 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
482 |
} |
483 |
|
484 |
void SimInfo::setDefaultEcr( double theEcr ){ |
485 |
|
486 |
haveEcr = 1; |
487 |
ecr = theEcr; |
488 |
|
489 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
490 |
|
491 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
492 |
} |
493 |
|
494 |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
495 |
|
496 |
est = theEst; |
497 |
setDefaultEcr( theEcr ); |
498 |
} |
499 |
|
500 |
|
501 |
void SimInfo::checkCutOffs( void ){ |
502 |
|
503 |
if( boxIsInit ){ |
504 |
|
505 |
//we need to check cutOffs against the box |
506 |
|
507 |
if( rCut > maxCutoff ){ |
508 |
sprintf( painCave.errMsg, |
509 |
"LJrcut is too large for the current periodic box.\n" |
510 |
"\tCurrent Value of LJrcut = %G at time %G\n " |
511 |
"\tThis is larger than half of at least one of the\n" |
512 |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
513 |
"\n" |
514 |
"\t[ %G %G %G ]\n" |
515 |
"\t[ %G %G %G ]\n" |
516 |
"\t[ %G %G %G ]\n", |
517 |
rCut, currentTime, |
518 |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
519 |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
520 |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
521 |
painCave.isFatal = 1; |
522 |
simError(); |
523 |
} |
524 |
|
525 |
if( haveEcr ){ |
526 |
if( ecr > maxCutoff ){ |
527 |
sprintf( painCave.errMsg, |
528 |
"electrostaticCutoffRadius is too large for the current\n" |
529 |
"\tperiodic box.\n\n" |
530 |
"\tCurrent Value of ECR = %G at time %G\n " |
531 |
"\tThis is larger than half of at least one of the\n" |
532 |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
533 |
"\n" |
534 |
"\t[ %G %G %G ]\n" |
535 |
"\t[ %G %G %G ]\n" |
536 |
"\t[ %G %G %G ]\n", |
537 |
ecr, currentTime, |
538 |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
539 |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
540 |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
541 |
painCave.isFatal = 1; |
542 |
simError(); |
543 |
} |
544 |
} |
545 |
} else { |
546 |
// initialize this stuff before using it, OK? |
547 |
sprintf( painCave.errMsg, |
548 |
"Trying to check cutoffs without a box.\n" |
549 |
"\tOOPSE should have better programmers than that.\n" ); |
550 |
painCave.isFatal = 1; |
551 |
simError(); |
552 |
} |
553 |
|
554 |
} |
555 |
|
556 |
void SimInfo::addProperty(GenericData* prop){ |
557 |
|
558 |
map<string, GenericData*>::iterator result; |
559 |
result = properties.find(prop->getID()); |
560 |
|
561 |
//we can't simply use properties[prop->getID()] = prop, |
562 |
//it will cause memory leak if we already contain a propery which has the same name of prop |
563 |
|
564 |
if(result != properties.end()){ |
565 |
|
566 |
delete (*result).second; |
567 |
(*result).second = prop; |
568 |
|
569 |
} |
570 |
else{ |
571 |
|
572 |
properties[prop->getID()] = prop; |
573 |
|
574 |
} |
575 |
|
576 |
} |
577 |
|
578 |
GenericData* SimInfo::getProperty(const string& propName){ |
579 |
|
580 |
map<string, GenericData*>::iterator result; |
581 |
|
582 |
//string lowerCaseName = (); |
583 |
|
584 |
result = properties.find(propName); |
585 |
|
586 |
if(result != properties.end()) |
587 |
return (*result).second; |
588 |
else |
589 |
return NULL; |
590 |
} |
591 |
|