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; |
44 |
|
rCut = 0.0; |
45 |
|
ecr = 0.0; |
46 |
|
est = 0.0; |
40 |
– |
oldEcr = 0.0; |
41 |
– |
oldRcut = 0.0; |
47 |
|
|
48 |
< |
haveOrigRcut = 0; |
49 |
< |
haveOrigEcr = 0; |
48 |
> |
haveRcut = 0; |
49 |
> |
haveEcr = 0; |
50 |
|
boxIsInit = 0; |
51 |
|
|
52 |
< |
|
52 |
> |
resetTime = 1e99; |
53 |
|
|
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 |
|
useGB = 0; |
65 |
|
useEAM = 0; |
66 |
|
|
67 |
+ |
excludes = Exclude::Instance(); |
68 |
+ |
|
69 |
+ |
myConfiguration = new SimState(); |
70 |
+ |
|
71 |
+ |
has_minimizer = false; |
72 |
+ |
the_minimizer =NULL; |
73 |
+ |
|
74 |
|
wrapMeSimInfo( this ); |
75 |
|
} |
76 |
|
|
77 |
+ |
|
78 |
+ |
SimInfo::~SimInfo(){ |
79 |
+ |
|
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 |
+ |
|
87 |
+ |
} |
88 |
+ |
|
89 |
|
void SimInfo::setBox(double newBox[3]) { |
90 |
|
|
91 |
|
int i, j; |
104 |
|
|
105 |
|
void SimInfo::setBoxM( double theBox[3][3] ){ |
106 |
|
|
107 |
< |
int i, j, status; |
79 |
< |
double smallestBoxL, maxCutoff; |
107 |
> |
int i, j; |
108 |
|
double FortranHmat[9]; // to preserve compatibility with Fortran the |
109 |
|
// ordering in the array is as follows: |
110 |
|
// [ 0 3 6 ] |
112 |
|
// [ 2 5 8 ] |
113 |
|
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
114 |
|
|
87 |
– |
|
115 |
|
if( !boxIsInit ) boxIsInit = 1; |
116 |
|
|
117 |
|
for(i=0; i < 3; i++) |
155 |
|
|
156 |
|
void SimInfo::calcHmatInv( void ) { |
157 |
|
|
158 |
+ |
int oldOrtho; |
159 |
|
int i,j; |
160 |
|
double smallDiag; |
161 |
|
double tol; |
163 |
|
|
164 |
|
invertMat3( Hmat, HmatInv ); |
165 |
|
|
138 |
– |
// Check the inverse to make sure it is sane: |
139 |
– |
|
140 |
– |
matMul3( Hmat, HmatInv, sanity ); |
141 |
– |
|
166 |
|
// check to see if Hmat is orthorhombic |
167 |
|
|
168 |
< |
smallDiag = Hmat[0][0]; |
145 |
< |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
146 |
< |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
147 |
< |
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 |
|
} |
160 |
– |
} |
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]); |
173 |
< |
} |
174 |
< |
|
175 |
< |
return determinant; |
176 |
< |
} |
177 |
< |
|
178 |
< |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
179 |
< |
|
180 |
< |
int i, j, k, l, m, n; |
181 |
< |
double determinant; |
182 |
< |
|
183 |
< |
determinant = matDet3( a ); |
184 |
< |
|
185 |
< |
if (determinant == 0.0) { |
186 |
< |
sprintf( painCave.errMsg, |
187 |
< |
"Can't invert a matrix with a zero determinant!\n"); |
188 |
< |
painCave.isFatal = 1; |
189 |
< |
simError(); |
190 |
< |
} |
191 |
< |
|
192 |
< |
for (i=0; i < 3; i++) { |
193 |
< |
j = (i+1)%3; |
194 |
< |
k = (i+2)%3; |
195 |
< |
for(l = 0; l < 3; l++) { |
196 |
< |
m = (l+1)%3; |
197 |
< |
n = (l+2)%3; |
198 |
< |
|
199 |
< |
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 |
< |
|
211 |
< |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
212 |
< |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
213 |
< |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
214 |
< |
|
215 |
< |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
216 |
< |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
217 |
< |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
218 |
< |
|
219 |
< |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
220 |
< |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
221 |
< |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
222 |
< |
} |
223 |
< |
|
224 |
< |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
225 |
< |
double a0, a1, a2; |
226 |
< |
|
227 |
< |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
228 |
< |
|
229 |
< |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
230 |
< |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
231 |
< |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
232 |
< |
} |
233 |
< |
|
234 |
< |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
235 |
< |
double temp[3][3]; |
236 |
< |
int i, j; |
237 |
< |
|
238 |
< |
for (i = 0; i < 3; i++) { |
239 |
< |
for (j = 0; j < 3; j++) { |
240 |
< |
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 |
|
} |
243 |
– |
for (i = 0; i < 3; i++) { |
244 |
– |
for (j = 0; j < 3; j++) { |
245 |
– |
out[i][j] = temp[i][j]; |
246 |
– |
} |
247 |
– |
} |
211 |
|
} |
249 |
– |
|
250 |
– |
void SimInfo::printMat3(double A[3][3] ){ |
212 |
|
|
252 |
– |
std::cerr |
253 |
– |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
254 |
– |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
255 |
– |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
256 |
– |
} |
257 |
– |
|
258 |
– |
void SimInfo::printMat9(double A[9] ){ |
259 |
– |
|
260 |
– |
std::cerr |
261 |
– |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
262 |
– |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
263 |
– |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
264 |
– |
} |
265 |
– |
|
213 |
|
void SimInfo::calcBoxL( void ){ |
214 |
|
|
215 |
|
double dx, dy, dz, dsq; |
269 |
– |
int i; |
216 |
|
|
217 |
|
// boxVol = Determinant of Hmat |
218 |
|
|
223 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
224 |
|
dsq = dx*dx + dy*dy + dz*dz; |
225 |
|
boxL[0] = sqrt( dsq ); |
226 |
< |
maxCutoff = 0.5 * boxL[0]; |
226 |
> |
//maxCutoff = 0.5 * boxL[0]; |
227 |
|
|
228 |
|
// boxLy |
229 |
|
|
230 |
|
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
231 |
|
dsq = dx*dx + dy*dy + dz*dz; |
232 |
|
boxL[1] = sqrt( dsq ); |
233 |
< |
if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
233 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
234 |
|
|
235 |
+ |
|
236 |
|
// boxLz |
237 |
|
|
238 |
|
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]; |
241 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
242 |
|
|
243 |
+ |
//calculate the max cutoff |
244 |
+ |
maxCutoff = calcMaxCutOff(); |
245 |
+ |
|
246 |
+ |
checkCutOffs(); |
247 |
+ |
|
248 |
|
} |
249 |
|
|
250 |
|
|
251 |
+ |
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, j, k; |
285 |
> |
int i; |
286 |
|
double scaled[3]; |
287 |
|
|
288 |
|
if( !orthoRhombic ){ |
320 |
|
|
321 |
|
|
322 |
|
int SimInfo::getNDF(){ |
323 |
< |
int ndf_local, ndf; |
323 |
> |
int ndf_local; |
324 |
> |
|
325 |
> |
ndf_local = 0; |
326 |
|
|
327 |
< |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
327 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
328 |
> |
ndf_local += 3; |
329 |
> |
if (integrableObjects[i]->isDirectional()) |
330 |
> |
ndf_local += 3; |
331 |
> |
} |
332 |
|
|
333 |
+ |
// n_constraints is local, so subtract them on each processor: |
334 |
+ |
|
335 |
+ |
ndf_local -= n_constraints; |
336 |
+ |
|
337 |
|
#ifdef IS_MPI |
338 |
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
339 |
|
#else |
340 |
|
ndf = ndf_local; |
341 |
|
#endif |
342 |
|
|
343 |
< |
ndf = ndf - 3; |
343 |
> |
// nZconstraints is global, as are the 3 COM translations for the |
344 |
> |
// entire system: |
345 |
|
|
346 |
+ |
ndf = ndf - 3 - nZconstraints; |
347 |
+ |
|
348 |
|
return ndf; |
349 |
|
} |
350 |
|
|
351 |
|
int SimInfo::getNDFraw() { |
352 |
< |
int ndfRaw_local, ndfRaw; |
352 |
> |
int ndfRaw_local; |
353 |
|
|
354 |
|
// Raw degrees of freedom that we have to set |
355 |
< |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
356 |
< |
|
355 |
> |
ndfRaw_local = 0; |
356 |
> |
|
357 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
358 |
> |
ndfRaw_local += 3; |
359 |
> |
if (integrableObjects[i]->isDirectional()) |
360 |
> |
ndfRaw_local += 3; |
361 |
> |
} |
362 |
> |
|
363 |
|
#ifdef IS_MPI |
364 |
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
365 |
|
#else |
368 |
|
|
369 |
|
return ndfRaw; |
370 |
|
} |
371 |
< |
|
371 |
> |
|
372 |
> |
int SimInfo::getNDFtranslational() { |
373 |
> |
int ndfTrans_local; |
374 |
> |
|
375 |
> |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
376 |
> |
|
377 |
> |
|
378 |
> |
#ifdef IS_MPI |
379 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
380 |
> |
#else |
381 |
> |
ndfTrans = ndfTrans_local; |
382 |
> |
#endif |
383 |
> |
|
384 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
385 |
> |
|
386 |
> |
return ndfTrans; |
387 |
> |
} |
388 |
> |
|
389 |
> |
int SimInfo::getTotIntegrableObjects() { |
390 |
> |
int nObjs_local; |
391 |
> |
int nObjs; |
392 |
> |
|
393 |
> |
nObjs_local = integrableObjects.size(); |
394 |
> |
|
395 |
> |
|
396 |
> |
#ifdef IS_MPI |
397 |
> |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
398 |
> |
#else |
399 |
> |
nObjs = nObjs_local; |
400 |
> |
#endif |
401 |
> |
|
402 |
> |
|
403 |
> |
return nObjs; |
404 |
> |
} |
405 |
> |
|
406 |
|
void SimInfo::refreshSim(){ |
407 |
|
|
408 |
|
simtype fInfo; |
412 |
|
|
413 |
|
fInfo.dielect = 0.0; |
414 |
|
|
415 |
< |
if( useDipole ){ |
415 |
> |
if( useDipoles ){ |
416 |
|
if( useReactionField )fInfo.dielect = dielectric; |
417 |
|
} |
418 |
|
|
421 |
|
fInfo.SIM_uses_LJ = useLJ; |
422 |
|
fInfo.SIM_uses_sticky = useSticky; |
423 |
|
//fInfo.SIM_uses_sticky = 0; |
424 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
424 |
> |
fInfo.SIM_uses_charges = useCharges; |
425 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
426 |
|
//fInfo.SIM_uses_dipoles = 0; |
427 |
< |
//fInfo.SIM_uses_RF = useReactionField; |
428 |
< |
fInfo.SIM_uses_RF = 0; |
427 |
> |
fInfo.SIM_uses_RF = useReactionField; |
428 |
> |
//fInfo.SIM_uses_RF = 0; |
429 |
|
fInfo.SIM_uses_GB = useGB; |
430 |
|
fInfo.SIM_uses_EAM = useEAM; |
431 |
|
|
432 |
< |
excl = Exclude::getArray(); |
432 |
> |
n_exclude = excludes->getSize(); |
433 |
> |
excl = excludes->getFortranArray(); |
434 |
|
|
435 |
|
#ifdef IS_MPI |
436 |
|
n_global = mpiSim->getTotAtoms(); |
460 |
|
|
461 |
|
this->ndf = this->getNDF(); |
462 |
|
this->ndfRaw = this->getNDFraw(); |
463 |
< |
|
463 |
> |
this->ndfTrans = this->getNDFtranslational(); |
464 |
|
} |
465 |
|
|
466 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
467 |
|
|
468 |
< |
void SimInfo::setRcut( double theRcut ){ |
468 |
> |
haveRcut = 1; |
469 |
> |
rCut = theRcut; |
470 |
|
|
471 |
< |
if( !haveOrigRcut ){ |
431 |
< |
haveOrigRcut = 1; |
432 |
< |
origRcut = theRcut; |
433 |
< |
} |
471 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
472 |
|
|
473 |
< |
rCut = theRcut; |
436 |
< |
checkCutOffs(); |
473 |
> |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
474 |
|
} |
475 |
|
|
476 |
< |
void SimInfo::setEcr( double theEcr ){ |
476 |
> |
void SimInfo::setDefaultEcr( double theEcr ){ |
477 |
|
|
478 |
< |
if( !haveOrigEcr ){ |
442 |
< |
haveOrigEcr = 1; |
443 |
< |
origEcr = theEcr; |
444 |
< |
} |
445 |
< |
|
478 |
> |
haveEcr = 1; |
479 |
|
ecr = theEcr; |
480 |
< |
checkCutOffs(); |
480 |
> |
|
481 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
482 |
> |
|
483 |
> |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
484 |
|
} |
485 |
|
|
486 |
< |
void SimInfo::setEcr( double theEcr, double theEst ){ |
486 |
> |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
487 |
|
|
488 |
|
est = theEst; |
489 |
< |
setEcr( theEcr ); |
489 |
> |
setDefaultEcr( theEcr ); |
490 |
|
} |
491 |
|
|
492 |
|
|
493 |
|
void SimInfo::checkCutOffs( void ){ |
494 |
< |
|
459 |
< |
int cutChanged = 0; |
460 |
< |
|
494 |
> |
|
495 |
|
if( boxIsInit ){ |
496 |
|
|
497 |
|
//we need to check cutOffs against the box |
498 |
|
|
499 |
< |
if( maxCutoff > rCut ){ |
500 |
< |
if( rCut < origRcut ){ |
501 |
< |
rCut = origRcut; |
502 |
< |
if (rCut > maxCutoff) rCut = maxCutoff; |
503 |
< |
|
504 |
< |
sprintf( painCave.errMsg, |
505 |
< |
"New Box size is setting the long range cutoff radius " |
506 |
< |
"to %lf\n", |
507 |
< |
rCut ); |
508 |
< |
painCave.isFatal = 0; |
509 |
< |
simError(); |
510 |
< |
} |
499 |
> |
if( rCut > maxCutoff ){ |
500 |
> |
sprintf( painCave.errMsg, |
501 |
> |
"LJrcut is too large for the current periodic box.\n" |
502 |
> |
"\tCurrent Value of LJrcut = %G at time %G\n " |
503 |
> |
"\tThis is larger than half of at least one of the\n" |
504 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
505 |
> |
"\n, %G" |
506 |
> |
"\t[ %G %G %G ]\n" |
507 |
> |
"\t[ %G %G %G ]\n" |
508 |
> |
"\t[ %G %G %G ]\n", |
509 |
> |
rCut, currentTime, maxCutoff, |
510 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
511 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
512 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
513 |
> |
painCave.isFatal = 1; |
514 |
> |
simError(); |
515 |
|
} |
516 |
< |
|
517 |
< |
if( maxCutoff > ecr ){ |
518 |
< |
if( ecr < origEcr ){ |
481 |
< |
rCut = origEcr; |
482 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
483 |
< |
|
516 |
> |
|
517 |
> |
if( haveEcr ){ |
518 |
> |
if( ecr > maxCutoff ){ |
519 |
|
sprintf( painCave.errMsg, |
520 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
521 |
< |
"to %lf\n", |
522 |
< |
ecr ); |
523 |
< |
painCave.isFatal = 0; |
520 |
> |
"electrostaticCutoffRadius is too large for the current\n" |
521 |
> |
"\tperiodic box.\n\n" |
522 |
> |
"\tCurrent Value of ECR = %G at time %G\n " |
523 |
> |
"\tThis is larger than half of at least one of the\n" |
524 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
525 |
> |
"\n" |
526 |
> |
"\t[ %G %G %G ]\n" |
527 |
> |
"\t[ %G %G %G ]\n" |
528 |
> |
"\t[ %G %G %G ]\n", |
529 |
> |
ecr, currentTime, |
530 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
531 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
532 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
533 |
> |
painCave.isFatal = 1; |
534 |
|
simError(); |
535 |
|
} |
536 |
|
} |
537 |
< |
|
538 |
< |
|
539 |
< |
if (rCut > maxCutoff) { |
540 |
< |
sprintf( painCave.errMsg, |
541 |
< |
"New Box size is setting the long range cutoff radius " |
542 |
< |
"to %lf\n", |
543 |
< |
maxCutoff ); |
499 |
< |
painCave.isFatal = 0; |
500 |
< |
simError(); |
501 |
< |
rCut = maxCutoff; |
502 |
< |
} |
503 |
< |
|
504 |
< |
if( ecr > maxCutoff){ |
505 |
< |
sprintf( painCave.errMsg, |
506 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
507 |
< |
"to %lf\n", |
508 |
< |
maxCutoff ); |
509 |
< |
painCave.isFatal = 0; |
510 |
< |
simError(); |
511 |
< |
ecr = maxCutoff; |
512 |
< |
} |
513 |
< |
|
514 |
< |
|
537 |
> |
} else { |
538 |
> |
// initialize this stuff before using it, OK? |
539 |
> |
sprintf( painCave.errMsg, |
540 |
> |
"Trying to check cutoffs without a box.\n" |
541 |
> |
"\tOOPSE should have better programmers than that.\n" ); |
542 |
> |
painCave.isFatal = 1; |
543 |
> |
simError(); |
544 |
|
} |
516 |
– |
|
517 |
– |
|
518 |
– |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
519 |
– |
|
520 |
– |
// rlist is the 1.0 plus max( rcut, ecr ) |
545 |
|
|
522 |
– |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
523 |
– |
|
524 |
– |
if( cutChanged ){ |
525 |
– |
|
526 |
– |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
527 |
– |
} |
528 |
– |
|
529 |
– |
oldEcr = ecr; |
530 |
– |
oldRcut = rCut; |
546 |
|
} |
547 |
|
|
548 |
|
void SimInfo::addProperty(GenericData* prop){ |
591 |
|
|
592 |
|
return result; |
593 |
|
} |
579 |
– |
|
580 |
– |
|