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; |
12 |
|
|
13 |
|
#include "fortranWrappers.hpp" |
14 |
|
|
15 |
+ |
#include "MatVec3.h" |
16 |
+ |
|
17 |
|
#ifdef IS_MPI |
18 |
|
#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 |
|
|
31 |
|
SimInfo::SimInfo(){ |
32 |
< |
excludes = NULL; |
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; |
39 |
< |
est = 0.0; |
40 |
< |
oldEcr = 0.0; |
41 |
< |
oldRcut = 0.0; |
45 |
> |
rSw = 0.0; |
46 |
|
|
47 |
< |
haveOrigRcut = 0; |
48 |
< |
haveOrigEcr = 0; |
47 |
> |
haveRcut = 0; |
48 |
> |
haveRsw = 0; |
49 |
|
boxIsInit = 0; |
50 |
|
|
51 |
< |
|
51 |
> |
resetTime = 1e99; |
52 |
|
|
53 |
+ |
orthoRhombic = 0; |
54 |
+ |
orthoTolerance = 1E-6; |
55 |
+ |
useInitXSstate = true; |
56 |
+ |
|
57 |
|
usePBC = 0; |
58 |
|
useLJ = 0; |
59 |
|
useSticky = 0; |
60 |
< |
useDipole = 0; |
60 |
> |
useCharges = 0; |
61 |
> |
useDipoles = 0; |
62 |
|
useReactionField = 0; |
63 |
|
useGB = 0; |
64 |
|
useEAM = 0; |
65 |
+ |
|
66 |
+ |
haveCutoffGroups = false; |
67 |
|
|
68 |
+ |
excludes = Exclude::Instance(); |
69 |
+ |
|
70 |
+ |
myConfiguration = new SimState(); |
71 |
+ |
|
72 |
+ |
has_minimizer = false; |
73 |
+ |
the_minimizer =NULL; |
74 |
+ |
|
75 |
+ |
ngroup = 0; |
76 |
+ |
|
77 |
|
wrapMeSimInfo( this ); |
78 |
|
} |
79 |
|
|
80 |
+ |
|
81 |
|
SimInfo::~SimInfo(){ |
82 |
|
|
83 |
+ |
delete myConfiguration; |
84 |
+ |
|
85 |
|
map<string, GenericData*>::iterator i; |
86 |
|
|
87 |
|
for(i = properties.begin(); i != properties.end(); i++) |
88 |
|
delete (*i).second; |
66 |
– |
|
89 |
|
|
90 |
|
} |
91 |
|
|
107 |
|
|
108 |
|
void SimInfo::setBoxM( double theBox[3][3] ){ |
109 |
|
|
110 |
< |
int i, j, status; |
89 |
< |
double smallestBoxL, maxCutoff; |
110 |
> |
int i, j; |
111 |
|
double FortranHmat[9]; // to preserve compatibility with Fortran the |
112 |
|
// ordering in the array is as follows: |
113 |
|
// [ 0 3 6 ] |
115 |
|
// [ 2 5 8 ] |
116 |
|
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
117 |
|
|
97 |
– |
|
118 |
|
if( !boxIsInit ) boxIsInit = 1; |
119 |
|
|
120 |
|
for(i=0; i < 3; i++) |
158 |
|
|
159 |
|
void SimInfo::calcHmatInv( void ) { |
160 |
|
|
161 |
+ |
int oldOrtho; |
162 |
|
int i,j; |
163 |
|
double smallDiag; |
164 |
|
double tol; |
166 |
|
|
167 |
|
invertMat3( Hmat, HmatInv ); |
168 |
|
|
148 |
– |
// Check the inverse to make sure it is sane: |
149 |
– |
|
150 |
– |
matMul3( Hmat, HmatInv, sanity ); |
151 |
– |
|
169 |
|
// check to see if Hmat is orthorhombic |
170 |
|
|
171 |
< |
smallDiag = Hmat[0][0]; |
155 |
< |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
156 |
< |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
157 |
< |
tol = smallDiag * 1E-6; |
171 |
> |
oldOrtho = orthoRhombic; |
172 |
|
|
173 |
+ |
smallDiag = fabs(Hmat[0][0]); |
174 |
+ |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
175 |
+ |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
176 |
+ |
tol = smallDiag * orthoTolerance; |
177 |
+ |
|
178 |
|
orthoRhombic = 1; |
179 |
|
|
180 |
|
for (i = 0; i < 3; i++ ) { |
181 |
|
for (j = 0 ; j < 3; j++) { |
182 |
|
if (i != j) { |
183 |
|
if (orthoRhombic) { |
184 |
< |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
184 |
> |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
185 |
|
} |
186 |
|
} |
187 |
|
} |
188 |
|
} |
170 |
– |
} |
189 |
|
|
190 |
< |
double SimInfo::matDet3(double a[3][3]) { |
191 |
< |
int i, j, k; |
192 |
< |
double determinant; |
193 |
< |
|
194 |
< |
determinant = 0.0; |
195 |
< |
|
196 |
< |
for(i = 0; i < 3; i++) { |
197 |
< |
j = (i+1)%3; |
198 |
< |
k = (i+2)%3; |
199 |
< |
|
200 |
< |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
183 |
< |
} |
184 |
< |
|
185 |
< |
return determinant; |
186 |
< |
} |
187 |
< |
|
188 |
< |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
189 |
< |
|
190 |
< |
int i, j, k, l, m, n; |
191 |
< |
double determinant; |
192 |
< |
|
193 |
< |
determinant = matDet3( a ); |
194 |
< |
|
195 |
< |
if (determinant == 0.0) { |
196 |
< |
sprintf( painCave.errMsg, |
197 |
< |
"Can't invert a matrix with a zero determinant!\n"); |
198 |
< |
painCave.isFatal = 1; |
199 |
< |
simError(); |
200 |
< |
} |
201 |
< |
|
202 |
< |
for (i=0; i < 3; i++) { |
203 |
< |
j = (i+1)%3; |
204 |
< |
k = (i+2)%3; |
205 |
< |
for(l = 0; l < 3; l++) { |
206 |
< |
m = (l+1)%3; |
207 |
< |
n = (l+2)%3; |
208 |
< |
|
209 |
< |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
190 |
> |
if( oldOrtho != orthoRhombic ){ |
191 |
> |
|
192 |
> |
if( orthoRhombic ){ |
193 |
> |
sprintf( painCave.errMsg, |
194 |
> |
"OOPSE is switching from the default Non-Orthorhombic\n" |
195 |
> |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
196 |
> |
"\tThis is usually a good thing, but if you wan't the\n" |
197 |
> |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
198 |
> |
"\tvariable ( currently set to %G ) smaller.\n", |
199 |
> |
orthoTolerance); |
200 |
> |
simError(); |
201 |
|
} |
202 |
< |
} |
203 |
< |
} |
204 |
< |
|
205 |
< |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
206 |
< |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
207 |
< |
|
208 |
< |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
209 |
< |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
210 |
< |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
211 |
< |
|
221 |
< |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
222 |
< |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
223 |
< |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
224 |
< |
|
225 |
< |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
226 |
< |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
227 |
< |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
228 |
< |
|
229 |
< |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
230 |
< |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
231 |
< |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
232 |
< |
} |
233 |
< |
|
234 |
< |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
235 |
< |
double a0, a1, a2; |
236 |
< |
|
237 |
< |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
238 |
< |
|
239 |
< |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
240 |
< |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
241 |
< |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
242 |
< |
} |
243 |
< |
|
244 |
< |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
245 |
< |
double temp[3][3]; |
246 |
< |
int i, j; |
247 |
< |
|
248 |
< |
for (i = 0; i < 3; i++) { |
249 |
< |
for (j = 0; j < 3; j++) { |
250 |
< |
temp[j][i] = in[i][j]; |
202 |
> |
else { |
203 |
> |
sprintf( painCave.errMsg, |
204 |
> |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
205 |
> |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
206 |
> |
"\tThis is usually because the box has deformed under\n" |
207 |
> |
"\tNPTf integration. If you wan't to live on the edge with\n" |
208 |
> |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
209 |
> |
"\tvariable ( currently set to %G ) larger.\n", |
210 |
> |
orthoTolerance); |
211 |
> |
simError(); |
212 |
|
} |
213 |
|
} |
253 |
– |
for (i = 0; i < 3; i++) { |
254 |
– |
for (j = 0; j < 3; j++) { |
255 |
– |
out[i][j] = temp[i][j]; |
256 |
– |
} |
257 |
– |
} |
214 |
|
} |
259 |
– |
|
260 |
– |
void SimInfo::printMat3(double A[3][3] ){ |
215 |
|
|
262 |
– |
std::cerr |
263 |
– |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
264 |
– |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
265 |
– |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
266 |
– |
} |
267 |
– |
|
268 |
– |
void SimInfo::printMat9(double A[9] ){ |
269 |
– |
|
270 |
– |
std::cerr |
271 |
– |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
272 |
– |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
273 |
– |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
274 |
– |
} |
275 |
– |
|
216 |
|
void SimInfo::calcBoxL( void ){ |
217 |
|
|
218 |
|
double dx, dy, dz, dsq; |
279 |
– |
int i; |
219 |
|
|
220 |
|
// boxVol = Determinant of Hmat |
221 |
|
|
226 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
227 |
|
dsq = dx*dx + dy*dy + dz*dz; |
228 |
|
boxL[0] = sqrt( dsq ); |
229 |
< |
maxCutoff = 0.5 * boxL[0]; |
229 |
> |
//maxCutoff = 0.5 * boxL[0]; |
230 |
|
|
231 |
|
// boxLy |
232 |
|
|
233 |
|
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
234 |
|
dsq = dx*dx + dy*dy + dz*dz; |
235 |
|
boxL[1] = sqrt( dsq ); |
236 |
< |
if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
236 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
237 |
|
|
238 |
+ |
|
239 |
|
// boxLz |
240 |
|
|
241 |
|
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
242 |
|
dsq = dx*dx + dy*dy + dz*dz; |
243 |
|
boxL[2] = sqrt( dsq ); |
244 |
< |
if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
244 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
245 |
> |
|
246 |
> |
//calculate the max cutoff |
247 |
> |
maxCutoff = calcMaxCutOff(); |
248 |
|
|
249 |
|
checkCutOffs(); |
250 |
|
|
251 |
|
} |
252 |
|
|
253 |
|
|
254 |
+ |
double SimInfo::calcMaxCutOff(){ |
255 |
+ |
|
256 |
+ |
double ri[3], rj[3], rk[3]; |
257 |
+ |
double rij[3], rjk[3], rki[3]; |
258 |
+ |
double minDist; |
259 |
+ |
|
260 |
+ |
ri[0] = Hmat[0][0]; |
261 |
+ |
ri[1] = Hmat[1][0]; |
262 |
+ |
ri[2] = Hmat[2][0]; |
263 |
+ |
|
264 |
+ |
rj[0] = Hmat[0][1]; |
265 |
+ |
rj[1] = Hmat[1][1]; |
266 |
+ |
rj[2] = Hmat[2][1]; |
267 |
+ |
|
268 |
+ |
rk[0] = Hmat[0][2]; |
269 |
+ |
rk[1] = Hmat[1][2]; |
270 |
+ |
rk[2] = Hmat[2][2]; |
271 |
+ |
|
272 |
+ |
crossProduct3(ri, rj, rij); |
273 |
+ |
distXY = dotProduct3(rk,rij) / norm3(rij); |
274 |
+ |
|
275 |
+ |
crossProduct3(rj,rk, rjk); |
276 |
+ |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
277 |
+ |
|
278 |
+ |
crossProduct3(rk,ri, rki); |
279 |
+ |
distZX = dotProduct3(rj,rki) / norm3(rki); |
280 |
+ |
|
281 |
+ |
minDist = min(min(distXY, distYZ), distZX); |
282 |
+ |
return minDist/2; |
283 |
+ |
|
284 |
+ |
} |
285 |
+ |
|
286 |
|
void SimInfo::wrapVector( double thePos[3] ){ |
287 |
|
|
288 |
< |
int i, j, k; |
288 |
> |
int i; |
289 |
|
double scaled[3]; |
290 |
|
|
291 |
|
if( !orthoRhombic ){ |
323 |
|
|
324 |
|
|
325 |
|
int SimInfo::getNDF(){ |
326 |
< |
int ndf_local, ndf; |
326 |
> |
int ndf_local; |
327 |
> |
|
328 |
> |
ndf_local = 0; |
329 |
|
|
330 |
< |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
330 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
331 |
> |
ndf_local += 3; |
332 |
> |
if (integrableObjects[i]->isDirectional()) { |
333 |
> |
if (integrableObjects[i]->isLinear()) |
334 |
> |
ndf_local += 2; |
335 |
> |
else |
336 |
> |
ndf_local += 3; |
337 |
> |
} |
338 |
> |
} |
339 |
|
|
340 |
+ |
// n_constraints is local, so subtract them on each processor: |
341 |
+ |
|
342 |
+ |
ndf_local -= n_constraints; |
343 |
+ |
|
344 |
|
#ifdef IS_MPI |
345 |
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
346 |
|
#else |
347 |
|
ndf = ndf_local; |
348 |
|
#endif |
349 |
|
|
350 |
< |
ndf = ndf - 3; |
350 |
> |
// nZconstraints is global, as are the 3 COM translations for the |
351 |
> |
// entire system: |
352 |
|
|
353 |
+ |
ndf = ndf - 3 - nZconstraints; |
354 |
+ |
|
355 |
|
return ndf; |
356 |
|
} |
357 |
|
|
358 |
|
int SimInfo::getNDFraw() { |
359 |
< |
int ndfRaw_local, ndfRaw; |
359 |
> |
int ndfRaw_local; |
360 |
|
|
361 |
|
// Raw degrees of freedom that we have to set |
362 |
< |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
363 |
< |
|
362 |
> |
ndfRaw_local = 0; |
363 |
> |
|
364 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
365 |
> |
ndfRaw_local += 3; |
366 |
> |
if (integrableObjects[i]->isDirectional()) { |
367 |
> |
if (integrableObjects[i]->isLinear()) |
368 |
> |
ndfRaw_local += 2; |
369 |
> |
else |
370 |
> |
ndfRaw_local += 3; |
371 |
> |
} |
372 |
> |
} |
373 |
> |
|
374 |
|
#ifdef IS_MPI |
375 |
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
376 |
|
#else |
379 |
|
|
380 |
|
return ndfRaw; |
381 |
|
} |
382 |
< |
|
382 |
> |
|
383 |
> |
int SimInfo::getNDFtranslational() { |
384 |
> |
int ndfTrans_local; |
385 |
> |
|
386 |
> |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
387 |
> |
|
388 |
> |
|
389 |
> |
#ifdef IS_MPI |
390 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
391 |
> |
#else |
392 |
> |
ndfTrans = ndfTrans_local; |
393 |
> |
#endif |
394 |
> |
|
395 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
396 |
> |
|
397 |
> |
return ndfTrans; |
398 |
> |
} |
399 |
> |
|
400 |
> |
int SimInfo::getTotIntegrableObjects() { |
401 |
> |
int nObjs_local; |
402 |
> |
int nObjs; |
403 |
> |
|
404 |
> |
nObjs_local = integrableObjects.size(); |
405 |
> |
|
406 |
> |
|
407 |
> |
#ifdef IS_MPI |
408 |
> |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
409 |
> |
#else |
410 |
> |
nObjs = nObjs_local; |
411 |
> |
#endif |
412 |
> |
|
413 |
> |
|
414 |
> |
return nObjs; |
415 |
> |
} |
416 |
> |
|
417 |
|
void SimInfo::refreshSim(){ |
418 |
|
|
419 |
|
simtype fInfo; |
423 |
|
|
424 |
|
fInfo.dielect = 0.0; |
425 |
|
|
426 |
< |
if( useDipole ){ |
426 |
> |
if( useDipoles ){ |
427 |
|
if( useReactionField )fInfo.dielect = dielectric; |
428 |
|
} |
429 |
|
|
432 |
|
fInfo.SIM_uses_LJ = useLJ; |
433 |
|
fInfo.SIM_uses_sticky = useSticky; |
434 |
|
//fInfo.SIM_uses_sticky = 0; |
435 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
435 |
> |
fInfo.SIM_uses_charges = useCharges; |
436 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
437 |
|
//fInfo.SIM_uses_dipoles = 0; |
438 |
< |
//fInfo.SIM_uses_RF = useReactionField; |
439 |
< |
fInfo.SIM_uses_RF = 0; |
438 |
> |
fInfo.SIM_uses_RF = useReactionField; |
439 |
> |
//fInfo.SIM_uses_RF = 0; |
440 |
|
fInfo.SIM_uses_GB = useGB; |
441 |
|
fInfo.SIM_uses_EAM = useEAM; |
442 |
|
|
443 |
< |
excl = Exclude::getArray(); |
444 |
< |
|
443 |
> |
n_exclude = excludes->getSize(); |
444 |
> |
excl = excludes->getFortranArray(); |
445 |
> |
|
446 |
|
#ifdef IS_MPI |
447 |
|
n_global = mpiSim->getTotAtoms(); |
448 |
|
#else |
449 |
|
n_global = n_atoms; |
450 |
|
#endif |
451 |
< |
|
451 |
> |
|
452 |
|
isError = 0; |
453 |
< |
|
453 |
> |
|
454 |
> |
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
455 |
> |
//it may not be a good idea to pass the address of first element in vector |
456 |
> |
//since c++ standard does not require vector to be stored continously in meomory |
457 |
> |
//Most of the compilers will organize the memory of vector continously |
458 |
|
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
459 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
460 |
< |
&isError ); |
461 |
< |
|
459 |
> |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
460 |
> |
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
461 |
> |
|
462 |
|
if( isError ){ |
463 |
< |
|
463 |
> |
|
464 |
|
sprintf( painCave.errMsg, |
465 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
465 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
466 |
|
painCave.isFatal = 1; |
467 |
|
simError(); |
468 |
|
} |
469 |
< |
|
469 |
> |
|
470 |
|
#ifdef IS_MPI |
471 |
|
sprintf( checkPointMsg, |
472 |
|
"succesfully sent the simulation information to fortran.\n"); |
473 |
|
MPIcheckPoint(); |
474 |
|
#endif // is_mpi |
475 |
< |
|
475 |
> |
|
476 |
|
this->ndf = this->getNDF(); |
477 |
|
this->ndfRaw = this->getNDFraw(); |
478 |
< |
|
478 |
> |
this->ndfTrans = this->getNDFtranslational(); |
479 |
|
} |
480 |
|
|
481 |
< |
|
482 |
< |
void SimInfo::setRcut( double theRcut ){ |
483 |
< |
|
442 |
< |
if( !haveOrigRcut ){ |
443 |
< |
haveOrigRcut = 1; |
444 |
< |
origRcut = theRcut; |
445 |
< |
} |
446 |
< |
|
481 |
> |
void SimInfo::setDefaultRcut( double theRcut ){ |
482 |
> |
|
483 |
> |
haveRcut = 1; |
484 |
|
rCut = theRcut; |
485 |
< |
checkCutOffs(); |
485 |
> |
rList = rCut + 1.0; |
486 |
> |
|
487 |
> |
notifyFortranCutOffs( &rCut, &rSw, &rList ); |
488 |
|
} |
489 |
|
|
490 |
< |
void SimInfo::setEcr( double theEcr ){ |
490 |
> |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
491 |
|
|
492 |
< |
if( !haveOrigEcr ){ |
493 |
< |
haveOrigEcr = 1; |
455 |
< |
origEcr = theEcr; |
456 |
< |
} |
457 |
< |
|
458 |
< |
ecr = theEcr; |
459 |
< |
checkCutOffs(); |
492 |
> |
rSw = theRsw; |
493 |
> |
setDefaultRcut( theRcut ); |
494 |
|
} |
495 |
|
|
462 |
– |
void SimInfo::setEcr( double theEcr, double theEst ){ |
496 |
|
|
464 |
– |
est = theEst; |
465 |
– |
setEcr( theEcr ); |
466 |
– |
} |
467 |
– |
|
468 |
– |
|
497 |
|
void SimInfo::checkCutOffs( void ){ |
498 |
< |
|
471 |
< |
int cutChanged = 0; |
472 |
< |
|
473 |
< |
|
474 |
< |
|
498 |
> |
|
499 |
|
if( boxIsInit ){ |
500 |
|
|
501 |
|
//we need to check cutOffs against the box |
502 |
< |
|
503 |
< |
if(( maxCutoff > rCut )&&(usePBC)){ |
480 |
< |
if( rCut < origRcut ){ |
481 |
< |
rCut = origRcut; |
482 |
< |
if (rCut > maxCutoff) rCut = maxCutoff; |
483 |
< |
|
484 |
< |
sprintf( painCave.errMsg, |
485 |
< |
"New Box size is setting the long range cutoff radius " |
486 |
< |
"to %lf\n", |
487 |
< |
rCut ); |
488 |
< |
painCave.isFatal = 0; |
489 |
< |
simError(); |
490 |
< |
} |
491 |
< |
} |
492 |
< |
|
493 |
< |
if( maxCutoff > ecr ){ |
494 |
< |
if( ecr < origEcr ){ |
495 |
< |
rCut = origEcr; |
496 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
497 |
< |
|
498 |
< |
sprintf( painCave.errMsg, |
499 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
500 |
< |
"to %lf\n", |
501 |
< |
ecr ); |
502 |
< |
painCave.isFatal = 0; |
503 |
< |
simError(); |
504 |
< |
} |
505 |
< |
} |
506 |
< |
|
507 |
< |
|
508 |
< |
if ((rCut > maxCutoff)&&(usePBC)) { |
502 |
> |
|
503 |
> |
if( rCut > maxCutoff ){ |
504 |
|
sprintf( painCave.errMsg, |
505 |
< |
"New Box size is setting the long range cutoff radius " |
506 |
< |
"to %lf\n", |
507 |
< |
maxCutoff ); |
508 |
< |
painCave.isFatal = 0; |
505 |
> |
"cutoffRadius is too large for the current periodic box.\n" |
506 |
> |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
507 |
> |
"\tThis is larger than half of at least one of the\n" |
508 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
509 |
> |
"\n" |
510 |
> |
"\t[ %G %G %G ]\n" |
511 |
> |
"\t[ %G %G %G ]\n" |
512 |
> |
"\t[ %G %G %G ]\n", |
513 |
> |
rCut, currentTime, |
514 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
515 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
516 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
517 |
> |
painCave.isFatal = 1; |
518 |
|
simError(); |
519 |
< |
rCut = maxCutoff; |
520 |
< |
} |
521 |
< |
|
522 |
< |
if( ecr > maxCutoff){ |
523 |
< |
sprintf( painCave.errMsg, |
524 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
525 |
< |
"to %lf\n", |
526 |
< |
maxCutoff ); |
523 |
< |
painCave.isFatal = 0; |
524 |
< |
simError(); |
525 |
< |
ecr = maxCutoff; |
526 |
< |
} |
527 |
< |
|
528 |
< |
|
519 |
> |
} |
520 |
> |
} else { |
521 |
> |
// initialize this stuff before using it, OK? |
522 |
> |
sprintf( painCave.errMsg, |
523 |
> |
"Trying to check cutoffs without a box.\n" |
524 |
> |
"\tOOPSE should have better programmers than that.\n" ); |
525 |
> |
painCave.isFatal = 1; |
526 |
> |
simError(); |
527 |
|
} |
530 |
– |
|
531 |
– |
|
532 |
– |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
533 |
– |
|
534 |
– |
// rlist is the 1.0 plus max( rcut, ecr ) |
528 |
|
|
536 |
– |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
537 |
– |
|
538 |
– |
if( cutChanged ){ |
539 |
– |
|
540 |
– |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
541 |
– |
} |
542 |
– |
|
543 |
– |
oldEcr = ecr; |
544 |
– |
oldRcut = rCut; |
529 |
|
} |
530 |
|
|
531 |
|
void SimInfo::addProperty(GenericData* prop){ |
564 |
|
return NULL; |
565 |
|
} |
566 |
|
|
583 |
– |
vector<GenericData*> SimInfo::getProperties(){ |
567 |
|
|
568 |
< |
vector<GenericData*> result; |
569 |
< |
map<string, GenericData*>::iterator i; |
568 |
> |
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
569 |
> |
vector<int>& groupList, vector<int>& groupStart){ |
570 |
> |
Molecule* myMols; |
571 |
> |
Atom** myAtoms; |
572 |
> |
int numAtom; |
573 |
> |
int curIndex; |
574 |
> |
double mtot; |
575 |
> |
int numMol; |
576 |
> |
int numCutoffGroups; |
577 |
> |
CutoffGroup* myCutoffGroup; |
578 |
> |
vector<CutoffGroup*>::iterator iterCutoff; |
579 |
> |
Atom* cutoffAtom; |
580 |
> |
vector<Atom*>::iterator iterAtom; |
581 |
> |
int atomIndex; |
582 |
|
|
583 |
< |
for(i = properties.begin(); i != properties.end(); i++) |
584 |
< |
result.push_back((*i).second); |
583 |
> |
mfact.clear(); |
584 |
> |
groupList.clear(); |
585 |
> |
groupStart.clear(); |
586 |
> |
|
587 |
> |
//Be careful, fortran array begin at 1 |
588 |
> |
curIndex = 1; |
589 |
> |
|
590 |
> |
myMols = info->molecules; |
591 |
> |
numMol = info->n_mol; |
592 |
> |
for(int i = 0; i < numMol; i++){ |
593 |
> |
numAtom = myMols[i].getNAtoms(); |
594 |
> |
myAtoms = myMols[i].getMyAtoms(); |
595 |
> |
|
596 |
|
|
597 |
< |
return result; |
592 |
< |
} |
597 |
> |
for(int j = 0; j < numAtom; j++){ |
598 |
|
|
599 |
+ |
|
600 |
+ |
#ifdef IS_MPI |
601 |
+ |
atomIndex = myAtoms[j]->getGlobalIndex(); |
602 |
+ |
#else |
603 |
+ |
atomIndex = myAtoms[j]->getIndex(); |
604 |
+ |
#endif |
605 |
|
|
606 |
+ |
if(myMols[i].belongToCutoffGroup(atomIndex)) |
607 |
+ |
continue; |
608 |
+ |
else{ |
609 |
+ |
mfact.push_back(myAtoms[j]->getMass()); |
610 |
+ |
groupList.push_back(myAtoms[j]->getIndex() + 1); |
611 |
+ |
groupStart.push_back(curIndex++); |
612 |
+ |
} |
613 |
+ |
} |
614 |
+ |
|
615 |
+ |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
616 |
+ |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
617 |
+ |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
618 |
+ |
|
619 |
+ |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
620 |
+ |
cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){ |
621 |
+ |
groupList.push_back(cutoffAtom->getIndex() + 1); |
622 |
+ |
} |
623 |
+ |
|
624 |
+ |
groupStart.push_back(curIndex); |
625 |
+ |
curIndex += myCutoffGroup->getNumAtom(); |
626 |
+ |
} |
627 |
+ |
|
628 |
+ |
} |
629 |
+ |
|
630 |
+ |
ngroup = groupStart.size(); |
631 |
+ |
} |