1 |
|
#include <cstdlib> |
2 |
|
#include <cstring> |
3 |
+ |
#include <cmath> |
4 |
|
|
5 |
+ |
#include <iostream> |
6 |
+ |
using namespace std; |
7 |
|
|
8 |
|
#include "SimInfo.hpp" |
9 |
|
#define __C |
12 |
|
|
13 |
|
#include "fortranWrappers.hpp" |
14 |
|
|
15 |
+ |
#ifdef IS_MPI |
16 |
+ |
#include "mpiSimulation.hpp" |
17 |
+ |
#endif |
18 |
+ |
|
19 |
+ |
inline double roundMe( double x ){ |
20 |
+ |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
21 |
+ |
} |
22 |
+ |
|
23 |
+ |
|
24 |
|
SimInfo* currentInfo; |
25 |
|
|
26 |
|
SimInfo::SimInfo(){ |
27 |
|
excludes = NULL; |
28 |
|
n_constraints = 0; |
29 |
+ |
nZconstraints = 0; |
30 |
|
n_oriented = 0; |
31 |
|
n_dipoles = 0; |
32 |
|
ndf = 0; |
33 |
|
ndfRaw = 0; |
34 |
+ |
nZconstraints = 0; |
35 |
|
the_integrator = NULL; |
36 |
|
setTemp = 0; |
37 |
|
thermalTime = 0.0; |
38 |
+ |
currentTime = 0.0; |
39 |
|
rCut = 0.0; |
40 |
+ |
origRcut = -1.0; |
41 |
+ |
ecr = 0.0; |
42 |
+ |
origEcr = -1.0; |
43 |
+ |
est = 0.0; |
44 |
+ |
oldEcr = 0.0; |
45 |
+ |
oldRcut = 0.0; |
46 |
|
|
47 |
+ |
haveOrigRcut = 0; |
48 |
+ |
haveOrigEcr = 0; |
49 |
+ |
boxIsInit = 0; |
50 |
+ |
|
51 |
+ |
resetTime = 1e99; |
52 |
+ |
|
53 |
+ |
|
54 |
|
usePBC = 0; |
55 |
|
useLJ = 0; |
56 |
|
useSticky = 0; |
59 |
|
useGB = 0; |
60 |
|
useEAM = 0; |
61 |
|
|
62 |
+ |
myConfiguration = new SimState(); |
63 |
+ |
|
64 |
|
wrapMeSimInfo( this ); |
65 |
|
} |
66 |
|
|
67 |
+ |
|
68 |
+ |
SimInfo::~SimInfo(){ |
69 |
+ |
|
70 |
+ |
delete myConfiguration; |
71 |
+ |
|
72 |
+ |
map<string, GenericData*>::iterator i; |
73 |
+ |
|
74 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
75 |
+ |
delete (*i).second; |
76 |
+ |
|
77 |
+ |
} |
78 |
+ |
|
79 |
|
void SimInfo::setBox(double newBox[3]) { |
80 |
< |
double smallestBox, maxCutoff; |
81 |
< |
int status; |
82 |
< |
box_x = newBox[0]; |
41 |
< |
box_y = newBox[1]; |
42 |
< |
box_z = newBox[2]; |
43 |
< |
setFortranBoxSize(newBox); |
80 |
> |
|
81 |
> |
int i, j; |
82 |
> |
double tempMat[3][3]; |
83 |
|
|
84 |
< |
smallestBox = box_x; |
85 |
< |
if (box_y < smallestBox) smallestBox = box_y; |
47 |
< |
if (box_z < smallestBox) smallestBox = box_z; |
84 |
> |
for(i=0; i<3; i++) |
85 |
> |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
86 |
|
|
87 |
< |
maxCutoff = smallestBox / 2.0; |
87 |
> |
tempMat[0][0] = newBox[0]; |
88 |
> |
tempMat[1][1] = newBox[1]; |
89 |
> |
tempMat[2][2] = newBox[2]; |
90 |
|
|
91 |
< |
if (rList > maxCutoff) { |
52 |
< |
sprintf( painCave.errMsg, |
53 |
< |
"New Box size is forcing neighborlist radius down to %lf\n", |
54 |
< |
maxCutoff ); |
55 |
< |
painCave.isFatal = 0; |
56 |
< |
simError(); |
91 |
> |
setBoxM( tempMat ); |
92 |
|
|
93 |
< |
rList = maxCutoff; |
93 |
> |
} |
94 |
|
|
95 |
< |
sprintf( painCave.errMsg, |
96 |
< |
"New Box size is forcing cutoff radius down to %lf\n", |
97 |
< |
maxCutoff - 1.0 ); |
98 |
< |
painCave.isFatal = 0; |
99 |
< |
simError(); |
95 |
> |
void SimInfo::setBoxM( double theBox[3][3] ){ |
96 |
> |
|
97 |
> |
int i, j, status; |
98 |
> |
double smallestBoxL, maxCutoff; |
99 |
> |
double FortranHmat[9]; // to preserve compatibility with Fortran the |
100 |
> |
// ordering in the array is as follows: |
101 |
> |
// [ 0 3 6 ] |
102 |
> |
// [ 1 4 7 ] |
103 |
> |
// [ 2 5 8 ] |
104 |
> |
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
105 |
|
|
106 |
< |
rCut = rList - 1.0; |
106 |
> |
|
107 |
> |
if( !boxIsInit ) boxIsInit = 1; |
108 |
|
|
109 |
< |
// list radius changed so we have to refresh the simulation structure. |
110 |
< |
refreshSim(); |
109 |
> |
for(i=0; i < 3; i++) |
110 |
> |
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
111 |
> |
|
112 |
> |
calcBoxL(); |
113 |
> |
calcHmatInv(); |
114 |
> |
|
115 |
> |
for(i=0; i < 3; i++) { |
116 |
> |
for (j=0; j < 3; j++) { |
117 |
> |
FortranHmat[3*j + i] = Hmat[i][j]; |
118 |
> |
FortranHmatInv[3*j + i] = HmatInv[i][j]; |
119 |
> |
} |
120 |
|
} |
121 |
|
|
122 |
< |
if (rCut > maxCutoff) { |
122 |
> |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
123 |
> |
|
124 |
> |
} |
125 |
> |
|
126 |
> |
|
127 |
> |
void SimInfo::getBoxM (double theBox[3][3]) { |
128 |
> |
|
129 |
> |
int i, j; |
130 |
> |
for(i=0; i<3; i++) |
131 |
> |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
132 |
> |
} |
133 |
> |
|
134 |
> |
|
135 |
> |
void SimInfo::scaleBox(double scale) { |
136 |
> |
double theBox[3][3]; |
137 |
> |
int i, j; |
138 |
> |
|
139 |
> |
// cerr << "Scaling box by " << scale << "\n"; |
140 |
> |
|
141 |
> |
for(i=0; i<3; i++) |
142 |
> |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
143 |
> |
|
144 |
> |
setBoxM(theBox); |
145 |
> |
|
146 |
> |
} |
147 |
> |
|
148 |
> |
void SimInfo::calcHmatInv( void ) { |
149 |
> |
|
150 |
> |
int i,j; |
151 |
> |
double smallDiag; |
152 |
> |
double tol; |
153 |
> |
double sanity[3][3]; |
154 |
> |
|
155 |
> |
invertMat3( Hmat, HmatInv ); |
156 |
> |
|
157 |
> |
// Check the inverse to make sure it is sane: |
158 |
> |
|
159 |
> |
matMul3( Hmat, HmatInv, sanity ); |
160 |
> |
|
161 |
> |
// check to see if Hmat is orthorhombic |
162 |
> |
|
163 |
> |
smallDiag = Hmat[0][0]; |
164 |
> |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
165 |
> |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
166 |
> |
tol = smallDiag * 1E-6; |
167 |
> |
|
168 |
> |
orthoRhombic = 1; |
169 |
> |
|
170 |
> |
for (i = 0; i < 3; i++ ) { |
171 |
> |
for (j = 0 ; j < 3; j++) { |
172 |
> |
if (i != j) { |
173 |
> |
if (orthoRhombic) { |
174 |
> |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
175 |
> |
} |
176 |
> |
} |
177 |
> |
} |
178 |
> |
} |
179 |
> |
} |
180 |
> |
|
181 |
> |
double SimInfo::matDet3(double a[3][3]) { |
182 |
> |
int i, j, k; |
183 |
> |
double determinant; |
184 |
> |
|
185 |
> |
determinant = 0.0; |
186 |
> |
|
187 |
> |
for(i = 0; i < 3; i++) { |
188 |
> |
j = (i+1)%3; |
189 |
> |
k = (i+2)%3; |
190 |
> |
|
191 |
> |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
192 |
> |
} |
193 |
> |
|
194 |
> |
return determinant; |
195 |
> |
} |
196 |
> |
|
197 |
> |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
198 |
> |
|
199 |
> |
int i, j, k, l, m, n; |
200 |
> |
double determinant; |
201 |
> |
|
202 |
> |
determinant = matDet3( a ); |
203 |
> |
|
204 |
> |
if (determinant == 0.0) { |
205 |
|
sprintf( painCave.errMsg, |
206 |
< |
"New Box size is forcing cutoff radius down to %lf\n", |
207 |
< |
maxCutoff ); |
76 |
< |
painCave.isFatal = 0; |
206 |
> |
"Can't invert a matrix with a zero determinant!\n"); |
207 |
> |
painCave.isFatal = 1; |
208 |
|
simError(); |
209 |
+ |
} |
210 |
|
|
211 |
< |
status = 0; |
212 |
< |
LJ_new_rcut(&rCut, &status); |
213 |
< |
if (status != 0) { |
214 |
< |
sprintf( painCave.errMsg, |
215 |
< |
"Error in recomputing LJ shifts based on new rcut\n"); |
216 |
< |
painCave.isFatal = 1; |
217 |
< |
simError(); |
211 |
> |
for (i=0; i < 3; i++) { |
212 |
> |
j = (i+1)%3; |
213 |
> |
k = (i+2)%3; |
214 |
> |
for(l = 0; l < 3; l++) { |
215 |
> |
m = (l+1)%3; |
216 |
> |
n = (l+2)%3; |
217 |
> |
|
218 |
> |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
219 |
|
} |
220 |
|
} |
221 |
|
} |
222 |
|
|
223 |
< |
void SimInfo::getBox(double theBox[3]) { |
224 |
< |
theBox[0] = box_x; |
225 |
< |
theBox[1] = box_y; |
226 |
< |
theBox[2] = box_z; |
223 |
> |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
224 |
> |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
225 |
> |
|
226 |
> |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
227 |
> |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
228 |
> |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
229 |
> |
|
230 |
> |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
231 |
> |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
232 |
> |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
233 |
> |
|
234 |
> |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
235 |
> |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
236 |
> |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
237 |
> |
|
238 |
> |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
239 |
> |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
240 |
> |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
241 |
|
} |
242 |
< |
|
242 |
> |
|
243 |
> |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
244 |
> |
double a0, a1, a2; |
245 |
> |
|
246 |
> |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
247 |
> |
|
248 |
> |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
249 |
> |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
250 |
> |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
251 |
> |
} |
252 |
> |
|
253 |
> |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
254 |
> |
double temp[3][3]; |
255 |
> |
int i, j; |
256 |
> |
|
257 |
> |
for (i = 0; i < 3; i++) { |
258 |
> |
for (j = 0; j < 3; j++) { |
259 |
> |
temp[j][i] = in[i][j]; |
260 |
> |
} |
261 |
> |
} |
262 |
> |
for (i = 0; i < 3; i++) { |
263 |
> |
for (j = 0; j < 3; j++) { |
264 |
> |
out[i][j] = temp[i][j]; |
265 |
> |
} |
266 |
> |
} |
267 |
> |
} |
268 |
> |
|
269 |
> |
void SimInfo::printMat3(double A[3][3] ){ |
270 |
> |
|
271 |
> |
std::cerr |
272 |
> |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
273 |
> |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
274 |
> |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
275 |
> |
} |
276 |
> |
|
277 |
> |
void SimInfo::printMat9(double A[9] ){ |
278 |
> |
|
279 |
> |
std::cerr |
280 |
> |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
281 |
> |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
282 |
> |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
283 |
> |
} |
284 |
> |
|
285 |
> |
|
286 |
> |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
287 |
> |
|
288 |
> |
out[0] = a[1] * b[2] - a[2] * b[1]; |
289 |
> |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
290 |
> |
out[2] = a[0] * b[1] - a[1] * b[0]; |
291 |
> |
|
292 |
> |
} |
293 |
> |
|
294 |
> |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
295 |
> |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
296 |
> |
} |
297 |
> |
|
298 |
> |
double SimInfo::length3(double a[3]){ |
299 |
> |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
300 |
> |
} |
301 |
> |
|
302 |
> |
void SimInfo::calcBoxL( void ){ |
303 |
> |
|
304 |
> |
double dx, dy, dz, dsq; |
305 |
> |
int i; |
306 |
> |
|
307 |
> |
// boxVol = Determinant of Hmat |
308 |
> |
|
309 |
> |
boxVol = matDet3( Hmat ); |
310 |
> |
|
311 |
> |
// boxLx |
312 |
> |
|
313 |
> |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
314 |
> |
dsq = dx*dx + dy*dy + dz*dz; |
315 |
> |
boxL[0] = sqrt( dsq ); |
316 |
> |
//maxCutoff = 0.5 * boxL[0]; |
317 |
> |
|
318 |
> |
// boxLy |
319 |
> |
|
320 |
> |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
321 |
> |
dsq = dx*dx + dy*dy + dz*dz; |
322 |
> |
boxL[1] = sqrt( dsq ); |
323 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
324 |
> |
|
325 |
> |
|
326 |
> |
// boxLz |
327 |
> |
|
328 |
> |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
329 |
> |
dsq = dx*dx + dy*dy + dz*dz; |
330 |
> |
boxL[2] = sqrt( dsq ); |
331 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
332 |
> |
|
333 |
> |
//calculate the max cutoff |
334 |
> |
maxCutoff = calcMaxCutOff(); |
335 |
> |
|
336 |
> |
checkCutOffs(); |
337 |
> |
|
338 |
> |
} |
339 |
> |
|
340 |
> |
|
341 |
> |
double SimInfo::calcMaxCutOff(){ |
342 |
> |
|
343 |
> |
double ri[3], rj[3], rk[3]; |
344 |
> |
double rij[3], rjk[3], rki[3]; |
345 |
> |
double minDist; |
346 |
> |
|
347 |
> |
ri[0] = Hmat[0][0]; |
348 |
> |
ri[1] = Hmat[1][0]; |
349 |
> |
ri[2] = Hmat[2][0]; |
350 |
> |
|
351 |
> |
rj[0] = Hmat[0][1]; |
352 |
> |
rj[1] = Hmat[1][1]; |
353 |
> |
rj[2] = Hmat[2][1]; |
354 |
> |
|
355 |
> |
rk[0] = Hmat[0][2]; |
356 |
> |
rk[1] = Hmat[1][2]; |
357 |
> |
rk[2] = Hmat[2][2]; |
358 |
> |
|
359 |
> |
crossProduct3(ri,rj, rij); |
360 |
> |
distXY = dotProduct3(rk,rij) / length3(rij); |
361 |
> |
|
362 |
> |
crossProduct3(rj,rk, rjk); |
363 |
> |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
364 |
> |
|
365 |
> |
crossProduct3(rk,ri, rki); |
366 |
> |
distZX = dotProduct3(rj,rki) / length3(rki); |
367 |
> |
|
368 |
> |
minDist = min(min(distXY, distYZ), distZX); |
369 |
> |
return minDist/2; |
370 |
> |
|
371 |
> |
} |
372 |
> |
|
373 |
> |
void SimInfo::wrapVector( double thePos[3] ){ |
374 |
> |
|
375 |
> |
int i, j, k; |
376 |
> |
double scaled[3]; |
377 |
> |
|
378 |
> |
if( !orthoRhombic ){ |
379 |
> |
// calc the scaled coordinates. |
380 |
> |
|
381 |
> |
|
382 |
> |
matVecMul3(HmatInv, thePos, scaled); |
383 |
> |
|
384 |
> |
for(i=0; i<3; i++) |
385 |
> |
scaled[i] -= roundMe(scaled[i]); |
386 |
> |
|
387 |
> |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
388 |
> |
|
389 |
> |
matVecMul3(Hmat, scaled, thePos); |
390 |
> |
|
391 |
> |
} |
392 |
> |
else{ |
393 |
> |
// calc the scaled coordinates. |
394 |
> |
|
395 |
> |
for(i=0; i<3; i++) |
396 |
> |
scaled[i] = thePos[i]*HmatInv[i][i]; |
397 |
> |
|
398 |
> |
// wrap the scaled coordinates |
399 |
> |
|
400 |
> |
for(i=0; i<3; i++) |
401 |
> |
scaled[i] -= roundMe(scaled[i]); |
402 |
> |
|
403 |
> |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
404 |
> |
|
405 |
> |
for(i=0; i<3; i++) |
406 |
> |
thePos[i] = scaled[i]*Hmat[i][i]; |
407 |
> |
} |
408 |
> |
|
409 |
> |
} |
410 |
> |
|
411 |
> |
|
412 |
|
int SimInfo::getNDF(){ |
413 |
|
int ndf_local, ndf; |
414 |
|
|
420 |
|
ndf = ndf_local; |
421 |
|
#endif |
422 |
|
|
423 |
< |
ndf = ndf - 3; |
423 |
> |
ndf = ndf - 3 - nZconstraints; |
424 |
|
|
425 |
|
return ndf; |
426 |
|
} |
439 |
|
|
440 |
|
return ndfRaw; |
441 |
|
} |
442 |
< |
|
442 |
> |
|
443 |
> |
int SimInfo::getNDFtranslational() { |
444 |
> |
int ndfTrans_local, ndfTrans; |
445 |
> |
|
446 |
> |
ndfTrans_local = 3 * n_atoms - n_constraints; |
447 |
> |
|
448 |
> |
#ifdef IS_MPI |
449 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
450 |
> |
#else |
451 |
> |
ndfTrans = ndfTrans_local; |
452 |
> |
#endif |
453 |
> |
|
454 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
455 |
> |
|
456 |
> |
return ndfTrans; |
457 |
> |
} |
458 |
> |
|
459 |
|
void SimInfo::refreshSim(){ |
460 |
|
|
461 |
|
simtype fInfo; |
462 |
|
int isError; |
463 |
+ |
int n_global; |
464 |
|
int* excl; |
465 |
< |
|
133 |
< |
fInfo.rrf = 0.0; |
134 |
< |
fInfo.rt = 0.0; |
465 |
> |
|
466 |
|
fInfo.dielect = 0.0; |
467 |
|
|
137 |
– |
fInfo.box[0] = box_x; |
138 |
– |
fInfo.box[1] = box_y; |
139 |
– |
fInfo.box[2] = box_z; |
140 |
– |
|
141 |
– |
fInfo.rlist = rList; |
142 |
– |
fInfo.rcut = rCut; |
143 |
– |
|
468 |
|
if( useDipole ){ |
145 |
– |
fInfo.rrf = ecr; |
146 |
– |
fInfo.rt = ecr - est; |
469 |
|
if( useReactionField )fInfo.dielect = dielectric; |
470 |
|
} |
471 |
|
|
474 |
|
fInfo.SIM_uses_LJ = useLJ; |
475 |
|
fInfo.SIM_uses_sticky = useSticky; |
476 |
|
//fInfo.SIM_uses_sticky = 0; |
477 |
< |
//fInfo.SIM_uses_dipoles = useDipole; |
478 |
< |
fInfo.SIM_uses_dipoles = 0; |
477 |
> |
fInfo.SIM_uses_dipoles = useDipole; |
478 |
> |
//fInfo.SIM_uses_dipoles = 0; |
479 |
|
//fInfo.SIM_uses_RF = useReactionField; |
480 |
|
fInfo.SIM_uses_RF = 0; |
481 |
|
fInfo.SIM_uses_GB = useGB; |
483 |
|
|
484 |
|
excl = Exclude::getArray(); |
485 |
|
|
486 |
+ |
#ifdef IS_MPI |
487 |
+ |
n_global = mpiSim->getTotAtoms(); |
488 |
+ |
#else |
489 |
+ |
n_global = n_atoms; |
490 |
+ |
#endif |
491 |
+ |
|
492 |
|
isError = 0; |
493 |
|
|
494 |
< |
// fInfo; |
495 |
< |
// n_atoms; |
496 |
< |
// identArray; |
169 |
< |
// n_exclude; |
170 |
< |
// excludes; |
171 |
< |
// nGlobalExcludes; |
172 |
< |
// globalExcludes; |
173 |
< |
// isError; |
494 |
> |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
495 |
> |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
496 |
> |
&isError ); |
497 |
|
|
175 |
– |
setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
176 |
– |
&nGlobalExcludes, globalExcludes, &isError ); |
177 |
– |
|
498 |
|
if( isError ){ |
499 |
|
|
500 |
|
sprintf( painCave.errMsg, |
511 |
|
|
512 |
|
this->ndf = this->getNDF(); |
513 |
|
this->ndfRaw = this->getNDFraw(); |
514 |
+ |
this->ndfTrans = this->getNDFtranslational(); |
515 |
+ |
} |
516 |
|
|
517 |
+ |
|
518 |
+ |
void SimInfo::setRcut( double theRcut ){ |
519 |
+ |
|
520 |
+ |
if( !haveOrigRcut ){ |
521 |
+ |
haveOrigRcut = 1; |
522 |
+ |
origRcut = theRcut; |
523 |
+ |
} |
524 |
+ |
|
525 |
+ |
rCut = theRcut; |
526 |
+ |
checkCutOffs(); |
527 |
|
} |
528 |
|
|
529 |
+ |
void SimInfo::setEcr( double theEcr ){ |
530 |
+ |
|
531 |
+ |
if( !haveOrigEcr ){ |
532 |
+ |
haveOrigEcr = 1; |
533 |
+ |
origEcr = theEcr; |
534 |
+ |
} |
535 |
+ |
|
536 |
+ |
ecr = theEcr; |
537 |
+ |
checkCutOffs(); |
538 |
+ |
} |
539 |
+ |
|
540 |
+ |
void SimInfo::setEcr( double theEcr, double theEst ){ |
541 |
+ |
|
542 |
+ |
est = theEst; |
543 |
+ |
setEcr( theEcr ); |
544 |
+ |
} |
545 |
+ |
|
546 |
+ |
|
547 |
+ |
void SimInfo::checkCutOffs( void ){ |
548 |
+ |
|
549 |
+ |
int cutChanged = 0; |
550 |
+ |
|
551 |
+ |
if( boxIsInit ){ |
552 |
+ |
|
553 |
+ |
//we need to check cutOffs against the box |
554 |
+ |
|
555 |
+ |
//detect the change of rCut |
556 |
+ |
if(( maxCutoff > rCut )&&(usePBC)){ |
557 |
+ |
if( rCut < origRcut ){ |
558 |
+ |
rCut = origRcut; |
559 |
+ |
|
560 |
+ |
if (rCut > maxCutoff) |
561 |
+ |
rCut = maxCutoff; |
562 |
+ |
|
563 |
+ |
sprintf( painCave.errMsg, |
564 |
+ |
"New Box size is setting the long range cutoff radius " |
565 |
+ |
"to %lf at time %lf\n", |
566 |
+ |
rCut, currentTime ); |
567 |
+ |
painCave.isFatal = 0; |
568 |
+ |
simError(); |
569 |
+ |
} |
570 |
+ |
} |
571 |
+ |
else if ((rCut > maxCutoff)&&(usePBC)) { |
572 |
+ |
sprintf( painCave.errMsg, |
573 |
+ |
"New Box size is setting the long range cutoff radius " |
574 |
+ |
"to %lf at time %lf\n", |
575 |
+ |
maxCutoff, currentTime ); |
576 |
+ |
painCave.isFatal = 0; |
577 |
+ |
simError(); |
578 |
+ |
rCut = maxCutoff; |
579 |
+ |
} |
580 |
+ |
|
581 |
+ |
|
582 |
+ |
//detect the change of ecr |
583 |
+ |
if( maxCutoff > ecr ){ |
584 |
+ |
if( ecr < origEcr ){ |
585 |
+ |
ecr = origEcr; |
586 |
+ |
if (ecr > maxCutoff) ecr = maxCutoff; |
587 |
+ |
|
588 |
+ |
sprintf( painCave.errMsg, |
589 |
+ |
"New Box size is setting the electrostaticCutoffRadius " |
590 |
+ |
"to %lf at time %lf\n", |
591 |
+ |
ecr, currentTime ); |
592 |
+ |
painCave.isFatal = 0; |
593 |
+ |
simError(); |
594 |
+ |
} |
595 |
+ |
} |
596 |
+ |
else if( ecr > maxCutoff){ |
597 |
+ |
sprintf( painCave.errMsg, |
598 |
+ |
"New Box size is setting the electrostaticCutoffRadius " |
599 |
+ |
"to %lf at time %lf\n", |
600 |
+ |
maxCutoff, currentTime ); |
601 |
+ |
painCave.isFatal = 0; |
602 |
+ |
simError(); |
603 |
+ |
ecr = maxCutoff; |
604 |
+ |
} |
605 |
+ |
|
606 |
+ |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
607 |
+ |
|
608 |
+ |
// rlist is the 1.0 plus max( rcut, ecr ) |
609 |
+ |
|
610 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
611 |
+ |
|
612 |
+ |
if( cutChanged ){ |
613 |
+ |
|
614 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
615 |
+ |
} |
616 |
+ |
|
617 |
+ |
oldEcr = ecr; |
618 |
+ |
oldRcut = rCut; |
619 |
+ |
|
620 |
+ |
} else { |
621 |
+ |
// initialize this stuff before using it, OK? |
622 |
+ |
sprintf( painCave.errMsg, |
623 |
+ |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
624 |
+ |
painCave.isFatal = 1; |
625 |
+ |
simError(); |
626 |
+ |
} |
627 |
+ |
|
628 |
+ |
} |
629 |
+ |
|
630 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
631 |
+ |
|
632 |
+ |
map<string, GenericData*>::iterator result; |
633 |
+ |
result = properties.find(prop->getID()); |
634 |
+ |
|
635 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
636 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
637 |
+ |
|
638 |
+ |
if(result != properties.end()){ |
639 |
+ |
|
640 |
+ |
delete (*result).second; |
641 |
+ |
(*result).second = prop; |
642 |
+ |
|
643 |
+ |
} |
644 |
+ |
else{ |
645 |
+ |
|
646 |
+ |
properties[prop->getID()] = prop; |
647 |
+ |
|
648 |
+ |
} |
649 |
+ |
|
650 |
+ |
} |
651 |
+ |
|
652 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
653 |
+ |
|
654 |
+ |
map<string, GenericData*>::iterator result; |
655 |
+ |
|
656 |
+ |
//string lowerCaseName = (); |
657 |
+ |
|
658 |
+ |
result = properties.find(propName); |
659 |
+ |
|
660 |
+ |
if(result != properties.end()) |
661 |
+ |
return (*result).second; |
662 |
+ |
else |
663 |
+ |
return NULL; |
664 |
+ |
} |
665 |
+ |
|
666 |
+ |
vector<GenericData*> SimInfo::getProperties(){ |
667 |
+ |
|
668 |
+ |
vector<GenericData*> result; |
669 |
+ |
map<string, GenericData*>::iterator i; |
670 |
+ |
|
671 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
672 |
+ |
result.push_back((*i).second); |
673 |
+ |
|
674 |
+ |
return result; |
675 |
+ |
} |
676 |
+ |
|
677 |
+ |
double SimInfo::matTrace3(double m[3][3]){ |
678 |
+ |
double trace; |
679 |
+ |
trace = m[0][0] + m[1][1] + m[2][2]; |
680 |
+ |
|
681 |
+ |
return trace; |
682 |
+ |
} |