1 |
< |
#include <cstdlib> |
2 |
< |
#include <cstring> |
3 |
< |
#include <cmath> |
1 |
> |
#include <stdlib.h> |
2 |
> |
#include <string.h> |
3 |
> |
#include <math.h> |
4 |
|
|
5 |
|
#include <iostream> |
6 |
|
using namespace std; |
20 |
|
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
21 |
|
} |
22 |
|
|
23 |
+ |
inline double min( double a, double b ){ |
24 |
+ |
return (a < b ) ? a : b; |
25 |
+ |
} |
26 |
|
|
27 |
|
SimInfo* currentInfo; |
28 |
|
|
29 |
|
SimInfo::SimInfo(){ |
30 |
|
excludes = NULL; |
31 |
|
n_constraints = 0; |
32 |
+ |
nZconstraints = 0; |
33 |
|
n_oriented = 0; |
34 |
|
n_dipoles = 0; |
35 |
|
ndf = 0; |
36 |
|
ndfRaw = 0; |
37 |
+ |
nZconstraints = 0; |
38 |
|
the_integrator = NULL; |
39 |
|
setTemp = 0; |
40 |
|
thermalTime = 0.0; |
41 |
+ |
currentTime = 0.0; |
42 |
|
rCut = 0.0; |
43 |
|
ecr = 0.0; |
44 |
+ |
est = 0.0; |
45 |
|
|
46 |
+ |
haveRcut = 0; |
47 |
+ |
haveEcr = 0; |
48 |
+ |
boxIsInit = 0; |
49 |
+ |
|
50 |
+ |
resetTime = 1e99; |
51 |
+ |
|
52 |
+ |
orthoTolerance = 1E-6; |
53 |
+ |
useInitXSstate = true; |
54 |
+ |
|
55 |
|
usePBC = 0; |
56 |
|
useLJ = 0; |
57 |
|
useSticky = 0; |
60 |
|
useGB = 0; |
61 |
|
useEAM = 0; |
62 |
|
|
63 |
+ |
myConfiguration = new SimState(); |
64 |
+ |
|
65 |
|
wrapMeSimInfo( this ); |
66 |
|
} |
67 |
|
|
68 |
+ |
|
69 |
+ |
SimInfo::~SimInfo(){ |
70 |
+ |
|
71 |
+ |
delete myConfiguration; |
72 |
+ |
|
73 |
+ |
map<string, GenericData*>::iterator i; |
74 |
+ |
|
75 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
76 |
+ |
delete (*i).second; |
77 |
+ |
|
78 |
+ |
} |
79 |
+ |
|
80 |
|
void SimInfo::setBox(double newBox[3]) { |
81 |
|
|
82 |
|
int i, j; |
95 |
|
|
96 |
|
void SimInfo::setBoxM( double theBox[3][3] ){ |
97 |
|
|
98 |
< |
int i, j, status; |
69 |
< |
double smallestBoxL, maxCutoff; |
98 |
> |
int i, j; |
99 |
|
double FortranHmat[9]; // to preserve compatibility with Fortran the |
100 |
|
// ordering in the array is as follows: |
101 |
|
// [ 0 3 6 ] |
103 |
|
// [ 2 5 8 ] |
104 |
|
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
105 |
|
|
106 |
+ |
if( !boxIsInit ) boxIsInit = 1; |
107 |
|
|
108 |
|
for(i=0; i < 3; i++) |
109 |
|
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
110 |
|
|
81 |
– |
// cerr |
82 |
– |
// << "setting Hmat ->\n" |
83 |
– |
// << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
84 |
– |
// << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
85 |
– |
// << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
86 |
– |
|
111 |
|
calcBoxL(); |
112 |
|
calcHmatInv(); |
113 |
|
|
120 |
|
|
121 |
|
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
122 |
|
|
99 |
– |
smallestBoxL = boxLx; |
100 |
– |
if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
101 |
– |
if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
102 |
– |
|
103 |
– |
maxCutoff = smallestBoxL / 2.0; |
104 |
– |
|
105 |
– |
if (rList > maxCutoff) { |
106 |
– |
sprintf( painCave.errMsg, |
107 |
– |
"New Box size is forcing neighborlist radius down to %lf\n", |
108 |
– |
maxCutoff ); |
109 |
– |
painCave.isFatal = 0; |
110 |
– |
simError(); |
111 |
– |
|
112 |
– |
rList = maxCutoff; |
113 |
– |
|
114 |
– |
sprintf( painCave.errMsg, |
115 |
– |
"New Box size is forcing cutoff radius down to %lf\n", |
116 |
– |
maxCutoff - 1.0 ); |
117 |
– |
painCave.isFatal = 0; |
118 |
– |
simError(); |
119 |
– |
|
120 |
– |
rCut = rList - 1.0; |
121 |
– |
|
122 |
– |
// list radius changed so we have to refresh the simulation structure. |
123 |
– |
refreshSim(); |
124 |
– |
} |
125 |
– |
|
126 |
– |
if( ecr > maxCutoff ){ |
127 |
– |
|
128 |
– |
sprintf( painCave.errMsg, |
129 |
– |
"New Box size is forcing electrostatic cutoff radius " |
130 |
– |
"down to %lf\n", |
131 |
– |
maxCutoff ); |
132 |
– |
painCave.isFatal = 0; |
133 |
– |
simError(); |
134 |
– |
|
135 |
– |
ecr = maxCutoff; |
136 |
– |
est = 0.05 * ecr; |
137 |
– |
|
138 |
– |
refreshSim(); |
139 |
– |
} |
140 |
– |
|
123 |
|
} |
124 |
|
|
125 |
|
|
146 |
|
|
147 |
|
void SimInfo::calcHmatInv( void ) { |
148 |
|
|
149 |
+ |
int oldOrtho; |
150 |
|
int i,j; |
151 |
|
double smallDiag; |
152 |
|
double tol; |
154 |
|
|
155 |
|
invertMat3( Hmat, HmatInv ); |
156 |
|
|
174 |
– |
// Check the inverse to make sure it is sane: |
175 |
– |
|
176 |
– |
matMul3( Hmat, HmatInv, sanity ); |
177 |
– |
|
157 |
|
// check to see if Hmat is orthorhombic |
158 |
|
|
159 |
< |
smallDiag = Hmat[0][0]; |
181 |
< |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
182 |
< |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
183 |
< |
tol = smallDiag * 1E-6; |
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 |
+ |
tol = smallDiag * orthoTolerance; |
165 |
+ |
|
166 |
|
orthoRhombic = 1; |
167 |
|
|
168 |
|
for (i = 0; i < 3; i++ ) { |
169 |
|
for (j = 0 ; j < 3; j++) { |
170 |
|
if (i != j) { |
171 |
|
if (orthoRhombic) { |
172 |
< |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
172 |
> |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
173 |
|
} |
174 |
|
} |
175 |
|
} |
176 |
|
} |
177 |
+ |
|
178 |
+ |
if( oldOrtho != orthoRhombic ){ |
179 |
+ |
|
180 |
+ |
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 orthoBoxTolerance( currently %G ).\n", |
184 |
+ |
orthoTolerance); |
185 |
+ |
simError(); |
186 |
+ |
} |
187 |
+ |
else { |
188 |
+ |
sprintf( painCave.errMsg, |
189 |
+ |
"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
190 |
+ |
" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
191 |
+ |
orthoTolerance); |
192 |
+ |
simError(); |
193 |
+ |
} |
194 |
+ |
} |
195 |
|
} |
196 |
|
|
197 |
|
double SimInfo::matDet3(double a[3][3]) { |
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; |
305 |
– |
int i; |
321 |
|
|
322 |
|
// boxVol = Determinant of Hmat |
323 |
|
|
327 |
|
|
328 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
329 |
|
dsq = dx*dx + dy*dy + dz*dz; |
330 |
< |
boxLx = sqrt( dsq ); |
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 |
< |
boxLy = sqrt( dsq ); |
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 |
< |
boxLz = sqrt( dsq ); |
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, j, k; |
390 |
> |
int i; |
391 |
|
double scaled[3]; |
392 |
|
|
393 |
|
if( !orthoRhombic ){ |
425 |
|
|
426 |
|
|
427 |
|
int SimInfo::getNDF(){ |
428 |
< |
int ndf_local, ndf; |
428 |
> |
int ndf_local; |
429 |
|
|
430 |
|
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
431 |
|
|
435 |
|
ndf = ndf_local; |
436 |
|
#endif |
437 |
|
|
438 |
< |
ndf = ndf - 3; |
438 |
> |
ndf = ndf - 3 - nZconstraints; |
439 |
|
|
440 |
|
return ndf; |
441 |
|
} |
442 |
|
|
443 |
|
int SimInfo::getNDFraw() { |
444 |
< |
int ndfRaw_local, ndfRaw; |
444 |
> |
int ndfRaw_local; |
445 |
|
|
446 |
|
// Raw degrees of freedom that we have to set |
447 |
|
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
454 |
|
|
455 |
|
return ndfRaw; |
456 |
|
} |
457 |
< |
|
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 |
< |
|
409 |
< |
fInfo.rrf = 0.0; |
410 |
< |
fInfo.rt = 0.0; |
480 |
> |
|
481 |
|
fInfo.dielect = 0.0; |
482 |
|
|
413 |
– |
fInfo.rlist = rList; |
414 |
– |
fInfo.rcut = rCut; |
415 |
– |
|
483 |
|
if( useDipole ){ |
417 |
– |
fInfo.rrf = ecr; |
418 |
– |
fInfo.rt = ecr - est; |
484 |
|
if( useReactionField )fInfo.dielect = dielectric; |
485 |
|
} |
486 |
|
|
526 |
|
|
527 |
|
this->ndf = this->getNDF(); |
528 |
|
this->ndfRaw = this->getNDFraw(); |
529 |
+ |
this->ndfTrans = this->getNDFtranslational(); |
530 |
+ |
} |
531 |
|
|
532 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
533 |
+ |
|
534 |
+ |
haveRcut = 1; |
535 |
+ |
rCut = theRcut; |
536 |
+ |
|
537 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
538 |
+ |
|
539 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
540 |
|
} |
541 |
|
|
542 |
+ |
void SimInfo::setDefaultEcr( double theEcr ){ |
543 |
+ |
|
544 |
+ |
haveEcr = 1; |
545 |
+ |
|
546 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
547 |
+ |
|
548 |
+ |
ecr = theEcr; |
549 |
+ |
|
550 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
551 |
+ |
} |
552 |
+ |
|
553 |
+ |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
554 |
+ |
|
555 |
+ |
est = theEst; |
556 |
+ |
setDefaultEcr( theEcr ); |
557 |
+ |
} |
558 |
+ |
|
559 |
+ |
|
560 |
+ |
void SimInfo::checkCutOffs( void ){ |
561 |
+ |
|
562 |
+ |
if( boxIsInit ){ |
563 |
+ |
|
564 |
+ |
//we need to check cutOffs against the box |
565 |
+ |
|
566 |
+ |
if( rCut > maxCutoff ){ |
567 |
+ |
sprintf( painCave.errMsg, |
568 |
+ |
"Box size is too small for the long range cutoff radius, " |
569 |
+ |
"%lf, at time %lf\n", |
570 |
+ |
rCut, currentTime ); |
571 |
+ |
painCave.isFatal = 1; |
572 |
+ |
simError(); |
573 |
+ |
} |
574 |
+ |
|
575 |
+ |
if( haveEcr ){ |
576 |
+ |
if( ecr > maxCutoff ){ |
577 |
+ |
sprintf( painCave.errMsg, |
578 |
+ |
"Box size is too small for the electrostatic cutoff radius, " |
579 |
+ |
"%lf, at time %lf\n", |
580 |
+ |
ecr, currentTime ); |
581 |
+ |
painCave.isFatal = 1; |
582 |
+ |
simError(); |
583 |
+ |
} |
584 |
+ |
} |
585 |
+ |
} else { |
586 |
+ |
// initialize this stuff before using it, OK? |
587 |
+ |
sprintf( painCave.errMsg, |
588 |
+ |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
589 |
+ |
painCave.isFatal = 1; |
590 |
+ |
simError(); |
591 |
+ |
} |
592 |
+ |
|
593 |
+ |
} |
594 |
+ |
|
595 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
596 |
+ |
|
597 |
+ |
map<string, GenericData*>::iterator result; |
598 |
+ |
result = properties.find(prop->getID()); |
599 |
+ |
|
600 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
601 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
602 |
+ |
|
603 |
+ |
if(result != properties.end()){ |
604 |
+ |
|
605 |
+ |
delete (*result).second; |
606 |
+ |
(*result).second = prop; |
607 |
+ |
|
608 |
+ |
} |
609 |
+ |
else{ |
610 |
+ |
|
611 |
+ |
properties[prop->getID()] = prop; |
612 |
+ |
|
613 |
+ |
} |
614 |
+ |
|
615 |
+ |
} |
616 |
+ |
|
617 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
618 |
+ |
|
619 |
+ |
map<string, GenericData*>::iterator result; |
620 |
+ |
|
621 |
+ |
//string lowerCaseName = (); |
622 |
+ |
|
623 |
+ |
result = properties.find(propName); |
624 |
+ |
|
625 |
+ |
if(result != properties.end()) |
626 |
+ |
return (*result).second; |
627 |
+ |
else |
628 |
+ |
return NULL; |
629 |
+ |
} |
630 |
+ |
|
631 |
+ |
vector<GenericData*> SimInfo::getProperties(){ |
632 |
+ |
|
633 |
+ |
vector<GenericData*> result; |
634 |
+ |
map<string, GenericData*>::iterator i; |
635 |
+ |
|
636 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
637 |
+ |
result.push_back((*i).second); |
638 |
+ |
|
639 |
+ |
return result; |
640 |
+ |
} |
641 |
+ |
|
642 |
+ |
double SimInfo::matTrace3(double m[3][3]){ |
643 |
+ |
double trace; |
644 |
+ |
trace = m[0][0] + m[1][1] + m[2][2]; |
645 |
+ |
|
646 |
+ |
return trace; |
647 |
+ |
} |