# | Line 1 | Line 1 | |
---|---|---|
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 | |
# | Line 9 | Line 12 | |
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(){ | |
# | Line 35 | Line 47 | void SimInfo::setBox(double newBox[3]) { | |
47 | } | |
48 | ||
49 | void SimInfo::setBox(double newBox[3]) { | |
50 | < | double smallestBox, maxCutoff; |
51 | < | int status; |
52 | < | box_x = newBox[0]; |
41 | < | box_y = newBox[1]; |
42 | < | box_z = newBox[2]; |
43 | < | setFortranBoxSize(newBox); |
50 | > | |
51 | > | int i; |
52 | > | double tempMat[9]; |
53 | ||
54 | < | smallestBox = box_x; |
46 | < | if (box_y < smallestBox) smallestBox = box_y; |
47 | < | if (box_z < smallestBox) smallestBox = box_z; |
54 | > | for(i=0; i<9; i++) tempMat[i] = 0.0;; |
55 | ||
56 | < | maxCutoff = smallestBox / 2.0; |
56 | > | tempMat[0] = newBox[0]; |
57 | > | tempMat[4] = newBox[1]; |
58 | > | tempMat[8] = newBox[2]; |
59 | ||
60 | + | setBoxM( tempMat ); |
61 | + | |
62 | + | } |
63 | + | |
64 | + | void SimInfo::setBoxM( double theBox[9] ){ |
65 | + | |
66 | + | int i, status; |
67 | + | double smallestBoxL, maxCutoff; |
68 | + | |
69 | + | for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
70 | + | |
71 | + | cerr |
72 | + | << "setting Hmat ->\n" |
73 | + | << "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n" |
74 | + | << "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n" |
75 | + | << "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n"; |
76 | + | |
77 | + | calcHmatI(); |
78 | + | calcBoxL(); |
79 | + | |
80 | + | |
81 | + | |
82 | + | setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
83 | + | |
84 | + | smallestBoxL = boxLx; |
85 | + | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
86 | + | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
87 | + | |
88 | + | maxCutoff = smallestBoxL / 2.0; |
89 | + | |
90 | if (rList > maxCutoff) { | |
91 | sprintf( painCave.errMsg, | |
92 | "New Box size is forcing neighborlist radius down to %lf\n", | |
# | Line 86 | Line 125 | void SimInfo::setBox(double newBox[3]) { | |
125 | } | |
126 | } | |
127 | } | |
128 | + | |
129 | ||
130 | < | void SimInfo::getBox(double theBox[3]) { |
131 | < | theBox[0] = box_x; |
132 | < | theBox[1] = box_y; |
133 | < | theBox[2] = box_z; |
130 | > | void SimInfo::getBoxM (double theBox[9]) { |
131 | > | |
132 | > | int i; |
133 | > | for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
134 | } | |
135 | < | |
135 | > | |
136 | > | |
137 | > | void SimInfo::scaleBox(double scale) { |
138 | > | double theBox[9]; |
139 | > | int i; |
140 | > | |
141 | > | cerr << "Scaling box by " << scale << "\n"; |
142 | > | |
143 | > | for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale; |
144 | > | |
145 | > | setBoxM(theBox); |
146 | > | |
147 | > | } |
148 | > | |
149 | > | void SimInfo::calcHmatI( void ) { |
150 | > | |
151 | > | double C[3][3]; |
152 | > | double detHmat; |
153 | > | int i, j, k; |
154 | > | double smallDiag; |
155 | > | double tol; |
156 | > | double sanity[3][3]; |
157 | > | |
158 | > | // calculate the adjunct of Hmat; |
159 | > | |
160 | > | C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
161 | > | C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
162 | > | C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
163 | > | |
164 | > | C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
165 | > | C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
166 | > | C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
167 | > | |
168 | > | C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
169 | > | C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
170 | > | C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
171 | > | |
172 | > | // calcutlate the determinant of Hmat |
173 | > | |
174 | > | detHmat = 0.0; |
175 | > | for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
176 | > | |
177 | > | |
178 | > | // H^-1 = C^T / det(H) |
179 | > | |
180 | > | i=0; |
181 | > | for(j=0; j<3; j++){ |
182 | > | for(k=0; k<3; k++){ |
183 | > | |
184 | > | HmatI[i] = C[j][k] / detHmat; |
185 | > | i++; |
186 | > | } |
187 | > | } |
188 | > | |
189 | > | // sanity check |
190 | > | |
191 | > | for(i=0; i<3; i++){ |
192 | > | for(j=0; j<3; j++){ |
193 | > | |
194 | > | sanity[i][j] = 0.0; |
195 | > | for(k=0; k<3; k++){ |
196 | > | sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
197 | > | } |
198 | > | } |
199 | > | } |
200 | > | |
201 | > | cerr << "sanity => \n" |
202 | > | << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
203 | > | << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
204 | > | << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
205 | > | << "\n"; |
206 | > | |
207 | > | |
208 | > | // check to see if Hmat is orthorhombic |
209 | > | |
210 | > | smallDiag = Hmat[0]; |
211 | > | if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
212 | > | if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
213 | > | tol = smallDiag * 1E-6; |
214 | > | |
215 | > | orthoRhombic = 1; |
216 | > | for(i=0; (i<9) && orthoRhombic; i++){ |
217 | > | |
218 | > | if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
219 | > | orthoRhombic = (Hmat[i] <= tol); |
220 | > | } |
221 | > | } |
222 | > | |
223 | > | } |
224 | > | |
225 | > | void SimInfo::calcBoxL( void ){ |
226 | > | |
227 | > | double dx, dy, dz, dsq; |
228 | > | int i; |
229 | > | |
230 | > | // boxVol = h1 (dot) h2 (cross) h3 |
231 | > | |
232 | > | boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
233 | > | + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
234 | > | + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
235 | > | |
236 | > | |
237 | > | // boxLx |
238 | > | |
239 | > | dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
240 | > | dsq = dx*dx + dy*dy + dz*dz; |
241 | > | boxLx = sqrt( dsq ); |
242 | > | |
243 | > | // boxLy |
244 | > | |
245 | > | dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
246 | > | dsq = dx*dx + dy*dy + dz*dz; |
247 | > | boxLy = sqrt( dsq ); |
248 | > | |
249 | > | // boxLz |
250 | > | |
251 | > | dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
252 | > | dsq = dx*dx + dy*dy + dz*dz; |
253 | > | boxLz = sqrt( dsq ); |
254 | > | |
255 | > | } |
256 | > | |
257 | > | |
258 | > | void SimInfo::wrapVector( double thePos[3] ){ |
259 | > | |
260 | > | int i, j, k; |
261 | > | double scaled[3]; |
262 | > | |
263 | > | if( !orthoRhombic ){ |
264 | > | // calc the scaled coordinates. |
265 | > | |
266 | > | for(i=0; i<3; i++) |
267 | > | scaled[i] = |
268 | > | thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
269 | > | |
270 | > | // wrap the scaled coordinates |
271 | > | |
272 | > | for(i=0; i<3; i++) |
273 | > | scaled[i] -= roundMe(scaled[i]); |
274 | > | |
275 | > | // calc the wrapped real coordinates from the wrapped scaled coordinates |
276 | > | |
277 | > | for(i=0; i<3; i++) |
278 | > | thePos[i] = |
279 | > | scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
280 | > | } |
281 | > | else{ |
282 | > | // calc the scaled coordinates. |
283 | > | |
284 | > | for(i=0; i<3; i++) |
285 | > | scaled[i] = thePos[i]*HmatI[i*4]; |
286 | > | |
287 | > | // wrap the scaled coordinates |
288 | > | |
289 | > | for(i=0; i<3; i++) |
290 | > | scaled[i] -= roundMe(scaled[i]); |
291 | > | |
292 | > | // calc the wrapped real coordinates from the wrapped scaled coordinates |
293 | > | |
294 | > | for(i=0; i<3; i++) |
295 | > | thePos[i] = scaled[i]*Hmat[i*4]; |
296 | > | } |
297 | > | |
298 | > | |
299 | > | } |
300 | > | |
301 | > | |
302 | int SimInfo::getNDF(){ | |
303 | int ndf_local, ndf; | |
304 | ||
# | Line 128 | Line 334 | void SimInfo::refreshSim(){ | |
334 | ||
335 | simtype fInfo; | |
336 | int isError; | |
337 | + | int n_global; |
338 | int* excl; | |
339 | ||
340 | fInfo.rrf = 0.0; | |
341 | fInfo.rt = 0.0; | |
342 | fInfo.dielect = 0.0; | |
343 | ||
137 | – | fInfo.box[0] = box_x; |
138 | – | fInfo.box[1] = box_y; |
139 | – | fInfo.box[2] = box_z; |
140 | – | |
344 | fInfo.rlist = rList; | |
345 | fInfo.rcut = rCut; | |
346 | ||
# | Line 161 | Line 364 | void SimInfo::refreshSim(){ | |
364 | ||
365 | excl = Exclude::getArray(); | |
366 | ||
367 | + | #ifdef IS_MPI |
368 | + | n_global = mpiSim->getTotAtoms(); |
369 | + | #else |
370 | + | n_global = n_atoms; |
371 | + | #endif |
372 | + | |
373 | isError = 0; | |
374 | ||
375 | < | // fInfo; |
376 | < | // n_atoms; |
377 | < | // identArray; |
169 | < | // n_exclude; |
170 | < | // excludes; |
171 | < | // nGlobalExcludes; |
172 | < | // globalExcludes; |
173 | < | // isError; |
375 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
376 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
377 | > | &isError ); |
378 | ||
175 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
176 | – | &nGlobalExcludes, globalExcludes, &isError ); |
177 | – | |
379 | if( isError ){ | |
380 | ||
381 | sprintf( painCave.errMsg, |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |