# | Line 2 | Line 2 | |
---|---|---|
2 | #include <cstring> | |
3 | #include <cmath> | |
4 | ||
5 | + | #include <iostream> |
6 | + | using namespace std; |
7 | ||
8 | #include "SimInfo.hpp" | |
9 | #define __C | |
# | Line 14 | Line 16 | |
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 27 | Line 34 | SimInfo::SimInfo(){ | |
34 | setTemp = 0; | |
35 | thermalTime = 0.0; | |
36 | rCut = 0.0; | |
37 | + | ecr = 0.0; |
38 | + | est = 0.0; |
39 | ||
40 | usePBC = 0; | |
41 | useLJ = 0; | |
# | Line 40 | Line 49 | void SimInfo::setBox(double newBox[3]) { | |
49 | } | |
50 | ||
51 | void SimInfo::setBox(double newBox[3]) { | |
52 | + | |
53 | + | int i, j; |
54 | + | double tempMat[3][3]; |
55 | ||
56 | < | double smallestBoxL, maxCutoff; |
57 | < | int status; |
46 | < | int i; |
56 | > | for(i=0; i<3; i++) |
57 | > | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
58 | ||
59 | < | for(i=0; i<9; i++) Hmat[i] = 0.0;; |
59 | > | tempMat[0][0] = newBox[0]; |
60 | > | tempMat[1][1] = newBox[1]; |
61 | > | tempMat[2][2] = newBox[2]; |
62 | ||
63 | < | Hmat[0] = newBox[0]; |
51 | < | Hmat[4] = newBox[1]; |
52 | < | Hmat[8] = newBox[2]; |
63 | > | setBoxM( tempMat ); |
64 | ||
65 | < | calcHmatI(); |
55 | < | calcBoxL(); |
65 | > | } |
66 | ||
67 | < | setFortranBoxSize(Hmat); |
67 | > | void SimInfo::setBoxM( double theBox[3][3] ){ |
68 | > | |
69 | > | int i, j, status; |
70 | > | double smallestBoxL, maxCutoff; |
71 | > | double FortranHmat[9]; // to preserve compatibility with Fortran the |
72 | > | // ordering in the array is as follows: |
73 | > | // [ 0 3 6 ] |
74 | > | // [ 1 4 7 ] |
75 | > | // [ 2 5 8 ] |
76 | > | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
77 | ||
59 | – | smallestBoxL = boxLx; |
60 | – | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
61 | – | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
78 | ||
79 | < | maxCutoff = smallestBoxL / 2.0; |
79 | > | for(i=0; i < 3; i++) |
80 | > | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
81 | > | |
82 | > | // cerr |
83 | > | // << "setting Hmat ->\n" |
84 | > | // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
85 | > | // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
86 | > | // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
87 | ||
88 | < | if (rList > maxCutoff) { |
89 | < | sprintf( painCave.errMsg, |
67 | < | "New Box size is forcing neighborlist radius down to %lf\n", |
68 | < | maxCutoff ); |
69 | < | painCave.isFatal = 0; |
70 | < | simError(); |
88 | > | calcBoxL(); |
89 | > | calcHmatInv(); |
90 | ||
91 | < | rList = maxCutoff; |
92 | < | |
93 | < | sprintf( painCave.errMsg, |
94 | < | "New Box size is forcing cutoff radius down to %lf\n", |
76 | < | maxCutoff - 1.0 ); |
77 | < | painCave.isFatal = 0; |
78 | < | simError(); |
79 | < | |
80 | < | rCut = rList - 1.0; |
81 | < | |
82 | < | // list radius changed so we have to refresh the simulation structure. |
83 | < | refreshSim(); |
84 | < | } |
85 | < | |
86 | < | if (rCut > maxCutoff) { |
87 | < | sprintf( painCave.errMsg, |
88 | < | "New Box size is forcing cutoff radius down to %lf\n", |
89 | < | maxCutoff ); |
90 | < | painCave.isFatal = 0; |
91 | < | simError(); |
92 | < | |
93 | < | status = 0; |
94 | < | LJ_new_rcut(&rCut, &status); |
95 | < | if (status != 0) { |
96 | < | sprintf( painCave.errMsg, |
97 | < | "Error in recomputing LJ shifts based on new rcut\n"); |
98 | < | painCave.isFatal = 1; |
99 | < | simError(); |
91 | > | for(i=0; i < 3; i++) { |
92 | > | for (j=0; j < 3; j++) { |
93 | > | FortranHmat[3*j + i] = Hmat[i][j]; |
94 | > | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
95 | } | |
96 | } | |
102 | – | } |
97 | ||
98 | < | void SimInfo::setBoxM( double theBox[9] ){ |
105 | < | |
106 | < | int i, status; |
107 | < | double smallestBoxL, maxCutoff; |
108 | < | |
109 | < | for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
110 | < | calcHmatI(); |
111 | < | calcBoxL(); |
112 | < | |
113 | < | setFortranBoxSize(Hmat); |
98 | > | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
99 | ||
100 | < | smallestBoxL = boxLx; |
101 | < | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
102 | < | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
100 | > | smallestBoxL = boxL[0]; |
101 | > | if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1]; |
102 | > | if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2]; |
103 | ||
104 | maxCutoff = smallestBoxL / 2.0; | |
105 | ||
# | Line 124 | Line 109 | void SimInfo::setBoxM( double theBox[9] ){ | |
109 | maxCutoff ); | |
110 | painCave.isFatal = 0; | |
111 | simError(); | |
127 | – | |
112 | rList = maxCutoff; | |
113 | ||
114 | < | sprintf( painCave.errMsg, |
131 | < | "New Box size is forcing cutoff radius down to %lf\n", |
132 | < | maxCutoff - 1.0 ); |
133 | < | painCave.isFatal = 0; |
134 | < | simError(); |
135 | < | |
136 | < | rCut = rList - 1.0; |
137 | < | |
138 | < | // list radius changed so we have to refresh the simulation structure. |
139 | < | refreshSim(); |
140 | < | } |
141 | < | |
142 | < | if (rCut > maxCutoff) { |
143 | < | sprintf( painCave.errMsg, |
144 | < | "New Box size is forcing cutoff radius down to %lf\n", |
145 | < | maxCutoff ); |
146 | < | painCave.isFatal = 0; |
147 | < | simError(); |
148 | < | |
149 | < | status = 0; |
150 | < | LJ_new_rcut(&rCut, &status); |
151 | < | if (status != 0) { |
114 | > | if (rCut > (rList - 1.0)) { |
115 | sprintf( painCave.errMsg, | |
116 | < | "Error in recomputing LJ shifts based on new rcut\n"); |
117 | < | painCave.isFatal = 1; |
116 | > | "New Box size is forcing LJ cutoff radius down to %lf\n", |
117 | > | rList - 1.0 ); |
118 | > | painCave.isFatal = 0; |
119 | simError(); | |
120 | + | rCut = rList - 1.0; |
121 | } | |
122 | < | } |
122 | > | |
123 | > | if( ecr > (rList - 1.0) ){ |
124 | > | sprintf( painCave.errMsg, |
125 | > | "New Box size is forcing electrostaticCutoffRadius " |
126 | > | "down to %lf\n" |
127 | > | "electrostaticSkinThickness is now %lf\n", |
128 | > | rList - 1.0, 0.05*(rList-1.0) ); |
129 | > | painCave.isFatal = 0; |
130 | > | simError(); |
131 | > | ecr = maxCutoff; |
132 | > | est = 0.05 * ecr; |
133 | > | } |
134 | > | |
135 | > | // At least one of the radii changed, so we need a refresh: |
136 | > | refreshSim(); |
137 | > | } |
138 | } | |
139 | ||
140 | ||
141 | < | void SimInfo::getBox(double theBox[9]) { |
141 | > | void SimInfo::getBoxM (double theBox[3][3]) { |
142 | ||
143 | < | int i; |
144 | < | for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
143 | > | int i, j; |
144 | > | for(i=0; i<3; i++) |
145 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
146 | } | |
166 | – | |
147 | ||
168 | – | void SimInfo::calcHmatI( void ) { |
148 | ||
149 | < | double C[3][3]; |
150 | < | double detHmat; |
151 | < | int i, j, k; |
149 | > | void SimInfo::scaleBox(double scale) { |
150 | > | double theBox[3][3]; |
151 | > | int i, j; |
152 | ||
153 | < | // calculate the adjunct of Hmat; |
153 | > | // cerr << "Scaling box by " << scale << "\n"; |
154 | ||
155 | < | C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
156 | < | C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
178 | < | C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
155 | > | for(i=0; i<3; i++) |
156 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
157 | ||
158 | < | C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
181 | < | C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
182 | < | C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
158 | > | setBoxM(theBox); |
159 | ||
160 | < | C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
185 | < | C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
186 | < | C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
160 | > | } |
161 | ||
162 | < | // calcutlate the determinant of Hmat |
162 | > | void SimInfo::calcHmatInv( void ) { |
163 | ||
164 | < | detHmat = 0.0; |
165 | < | for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
164 | > | int i,j; |
165 | > | double smallDiag; |
166 | > | double tol; |
167 | > | double sanity[3][3]; |
168 | ||
169 | < | |
194 | < | // H^-1 = C^T / det(H) |
195 | < | |
196 | < | i=0; |
197 | < | for(j=0; j<3; j++){ |
198 | < | for(k=0; k<3; k++){ |
169 | > | invertMat3( Hmat, HmatInv ); |
170 | ||
171 | < | HmatI[i] = C[j][k] / detHmat; |
172 | < | i++; |
171 | > | // Check the inverse to make sure it is sane: |
172 | > | |
173 | > | matMul3( Hmat, HmatInv, sanity ); |
174 | > | |
175 | > | // check to see if Hmat is orthorhombic |
176 | > | |
177 | > | smallDiag = Hmat[0][0]; |
178 | > | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
179 | > | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
180 | > | tol = smallDiag * 1E-6; |
181 | > | |
182 | > | orthoRhombic = 1; |
183 | > | |
184 | > | for (i = 0; i < 3; i++ ) { |
185 | > | for (j = 0 ; j < 3; j++) { |
186 | > | if (i != j) { |
187 | > | if (orthoRhombic) { |
188 | > | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
189 | > | } |
190 | > | } |
191 | } | |
192 | } | |
193 | } | |
194 | ||
195 | + | double SimInfo::matDet3(double a[3][3]) { |
196 | + | int i, j, k; |
197 | + | double determinant; |
198 | + | |
199 | + | determinant = 0.0; |
200 | + | |
201 | + | for(i = 0; i < 3; i++) { |
202 | + | j = (i+1)%3; |
203 | + | k = (i+2)%3; |
204 | + | |
205 | + | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
206 | + | } |
207 | + | |
208 | + | return determinant; |
209 | + | } |
210 | + | |
211 | + | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
212 | + | |
213 | + | int i, j, k, l, m, n; |
214 | + | double determinant; |
215 | + | |
216 | + | determinant = matDet3( a ); |
217 | + | |
218 | + | if (determinant == 0.0) { |
219 | + | sprintf( painCave.errMsg, |
220 | + | "Can't invert a matrix with a zero determinant!\n"); |
221 | + | painCave.isFatal = 1; |
222 | + | simError(); |
223 | + | } |
224 | + | |
225 | + | for (i=0; i < 3; i++) { |
226 | + | j = (i+1)%3; |
227 | + | k = (i+2)%3; |
228 | + | for(l = 0; l < 3; l++) { |
229 | + | m = (l+1)%3; |
230 | + | n = (l+2)%3; |
231 | + | |
232 | + | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
233 | + | } |
234 | + | } |
235 | + | } |
236 | + | |
237 | + | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
238 | + | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
239 | + | |
240 | + | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
241 | + | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
242 | + | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
243 | + | |
244 | + | r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
245 | + | r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
246 | + | r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
247 | + | |
248 | + | r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
249 | + | r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
250 | + | r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
251 | + | |
252 | + | c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
253 | + | c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
254 | + | c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
255 | + | } |
256 | + | |
257 | + | void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
258 | + | double a0, a1, a2; |
259 | + | |
260 | + | a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
261 | + | |
262 | + | outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
263 | + | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
264 | + | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
265 | + | } |
266 | + | |
267 | + | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
268 | + | double temp[3][3]; |
269 | + | int i, j; |
270 | + | |
271 | + | for (i = 0; i < 3; i++) { |
272 | + | for (j = 0; j < 3; j++) { |
273 | + | temp[j][i] = in[i][j]; |
274 | + | } |
275 | + | } |
276 | + | for (i = 0; i < 3; i++) { |
277 | + | for (j = 0; j < 3; j++) { |
278 | + | out[i][j] = temp[i][j]; |
279 | + | } |
280 | + | } |
281 | + | } |
282 | + | |
283 | + | void SimInfo::printMat3(double A[3][3] ){ |
284 | + | |
285 | + | std::cerr |
286 | + | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
287 | + | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
288 | + | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
289 | + | } |
290 | + | |
291 | + | void SimInfo::printMat9(double A[9] ){ |
292 | + | |
293 | + | std::cerr |
294 | + | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
295 | + | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
296 | + | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
297 | + | } |
298 | + | |
299 | void SimInfo::calcBoxL( void ){ | |
300 | ||
301 | double dx, dy, dz, dsq; | |
302 | int i; | |
303 | ||
304 | < | // boxVol = h1 (dot) h2 (cross) h3 |
304 | > | // boxVol = Determinant of Hmat |
305 | ||
306 | < | boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
214 | < | + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
215 | < | + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
306 | > | boxVol = matDet3( Hmat ); |
307 | ||
217 | – | |
308 | // boxLx | |
309 | ||
310 | < | dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
310 | > | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
311 | dsq = dx*dx + dy*dy + dz*dz; | |
312 | < | boxLx = sqrt( dsq ); |
312 | > | boxL[0] = sqrt( dsq ); |
313 | ||
314 | // boxLy | |
315 | ||
316 | < | dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
316 | > | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
317 | dsq = dx*dx + dy*dy + dz*dz; | |
318 | < | boxLy = sqrt( dsq ); |
318 | > | boxL[1] = sqrt( dsq ); |
319 | ||
320 | // boxLz | |
321 | ||
322 | < | dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
322 | > | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
323 | dsq = dx*dx + dy*dy + dz*dz; | |
324 | < | boxLz = sqrt( dsq ); |
324 | > | boxL[2] = sqrt( dsq ); |
325 | ||
326 | } | |
327 | ||
# | Line 241 | Line 331 | void SimInfo::wrapVector( double thePos[3] ){ | |
331 | int i, j, k; | |
332 | double scaled[3]; | |
333 | ||
334 | < | // calc the scaled coordinates. |
334 | > | if( !orthoRhombic ){ |
335 | > | // calc the scaled coordinates. |
336 | ||
246 | – | for(i=0; i<3; i++) |
247 | – | scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6]; |
337 | ||
338 | < | // wrap the scaled coordinates |
338 | > | matVecMul3(HmatInv, thePos, scaled); |
339 | > | |
340 | > | for(i=0; i<3; i++) |
341 | > | scaled[i] -= roundMe(scaled[i]); |
342 | > | |
343 | > | // calc the wrapped real coordinates from the wrapped scaled coordinates |
344 | > | |
345 | > | matVecMul3(Hmat, scaled, thePos); |
346 | ||
347 | < | for(i=0; i<3; i++) |
348 | < | scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5)); |
349 | < | |
350 | < | |
347 | > | } |
348 | > | else{ |
349 | > | // calc the scaled coordinates. |
350 | > | |
351 | > | for(i=0; i<3; i++) |
352 | > | scaled[i] = thePos[i]*HmatInv[i][i]; |
353 | > | |
354 | > | // wrap the scaled coordinates |
355 | > | |
356 | > | for(i=0; i<3; i++) |
357 | > | scaled[i] -= roundMe(scaled[i]); |
358 | > | |
359 | > | // calc the wrapped real coordinates from the wrapped scaled coordinates |
360 | > | |
361 | > | for(i=0; i<3; i++) |
362 | > | thePos[i] = scaled[i]*Hmat[i][i]; |
363 | > | } |
364 | > | |
365 | } | |
366 | ||
367 | ||
# | Line 297 | Line 407 | void SimInfo::refreshSim(){ | |
407 | fInfo.rt = 0.0; | |
408 | fInfo.dielect = 0.0; | |
409 | ||
300 | – | fInfo.box[0] = box_x; |
301 | – | fInfo.box[1] = box_y; |
302 | – | fInfo.box[2] = box_z; |
303 | – | |
410 | fInfo.rlist = rList; | |
411 | fInfo.rcut = rCut; | |
412 |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |