# | 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 26 | Line 33 | SimInfo::SimInfo(){ | |
33 | the_integrator = NULL; | |
34 | setTemp = 0; | |
35 | thermalTime = 0.0; | |
36 | + | currentTime = 0.0; |
37 | rCut = 0.0; | |
38 | + | ecr = 0.0; |
39 | + | est = 0.0; |
40 | + | oldEcr = 0.0; |
41 | + | oldRcut = 0.0; |
42 | ||
43 | + | haveOrigRcut = 0; |
44 | + | haveOrigEcr = 0; |
45 | + | boxIsInit = 0; |
46 | + | |
47 | + | |
48 | + | |
49 | usePBC = 0; | |
50 | useLJ = 0; | |
51 | useSticky = 0; | |
# | Line 40 | Line 58 | void SimInfo::setBox(double newBox[3]) { | |
58 | } | |
59 | ||
60 | void SimInfo::setBox(double newBox[3]) { | |
61 | + | |
62 | + | int i, j; |
63 | + | double tempMat[3][3]; |
64 | ||
65 | < | double smallestBoxL, maxCutoff; |
66 | < | int status; |
46 | < | int i; |
65 | > | for(i=0; i<3; i++) |
66 | > | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
67 | ||
68 | < | for(i=0; i<9; i++) Hmat[i] = 0.0;; |
68 | > | tempMat[0][0] = newBox[0]; |
69 | > | tempMat[1][1] = newBox[1]; |
70 | > | tempMat[2][2] = newBox[2]; |
71 | ||
72 | < | Hmat[0] = newBox[0]; |
51 | < | Hmat[4] = newBox[1]; |
52 | < | Hmat[8] = newBox[2]; |
72 | > | setBoxM( tempMat ); |
73 | ||
74 | < | calcHmatI(); |
55 | < | calcBoxL(); |
74 | > | } |
75 | ||
76 | < | setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
76 | > | void SimInfo::setBoxM( double theBox[3][3] ){ |
77 | > | |
78 | > | int i, j, status; |
79 | > | double smallestBoxL, maxCutoff; |
80 | > | double FortranHmat[9]; // to preserve compatibility with Fortran the |
81 | > | // ordering in the array is as follows: |
82 | > | // [ 0 3 6 ] |
83 | > | // [ 1 4 7 ] |
84 | > | // [ 2 5 8 ] |
85 | > | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
86 | ||
87 | < | smallestBoxL = boxLx; |
88 | < | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
61 | < | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
87 | > | |
88 | > | if( !boxIsInit ) boxIsInit = 1; |
89 | ||
90 | < | maxCutoff = smallestBoxL / 2.0; |
90 | > | for(i=0; i < 3; i++) |
91 | > | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
92 | > | |
93 | > | calcBoxL(); |
94 | > | calcHmatInv(); |
95 | ||
96 | < | if (rList > maxCutoff) { |
97 | < | sprintf( painCave.errMsg, |
98 | < | "New Box size is forcing neighborlist radius down to %lf\n", |
99 | < | maxCutoff ); |
100 | < | painCave.isFatal = 0; |
70 | < | simError(); |
71 | < | |
72 | < | rList = maxCutoff; |
73 | < | |
74 | < | sprintf( painCave.errMsg, |
75 | < | "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(); |
96 | > | for(i=0; i < 3; i++) { |
97 | > | for (j=0; j < 3; j++) { |
98 | > | FortranHmat[3*j + i] = Hmat[i][j]; |
99 | > | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
100 | > | } |
101 | } | |
102 | ||
103 | < | if (rCut > maxCutoff) { |
104 | < | sprintf( painCave.errMsg, |
105 | < | "New Box size is forcing cutoff radius down to %lf\n", |
106 | < | maxCutoff ); |
90 | < | painCave.isFatal = 0; |
91 | < | simError(); |
103 | > | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
104 | > | |
105 | > | } |
106 | > | |
107 | ||
108 | < | status = 0; |
109 | < | LJ_new_rcut(&rCut, &status); |
110 | < | if (status != 0) { |
111 | < | sprintf( painCave.errMsg, |
112 | < | "Error in recomputing LJ shifts based on new rcut\n"); |
98 | < | painCave.isFatal = 1; |
99 | < | simError(); |
100 | < | } |
101 | < | } |
108 | > | void SimInfo::getBoxM (double theBox[3][3]) { |
109 | > | |
110 | > | int i, j; |
111 | > | for(i=0; i<3; i++) |
112 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
113 | } | |
114 | ||
104 | – | void SimInfo::setBoxM( double theBox[9] ){ |
105 | – | |
106 | – | int i, status; |
107 | – | double smallestBoxL, maxCutoff; |
115 | ||
116 | < | for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
117 | < | calcHmatI(); |
118 | < | calcBoxL(); |
116 | > | void SimInfo::scaleBox(double scale) { |
117 | > | double theBox[3][3]; |
118 | > | int i, j; |
119 | ||
120 | < | setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
114 | < | |
115 | < | smallestBoxL = boxLx; |
116 | < | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
117 | < | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
120 | > | // cerr << "Scaling box by " << scale << "\n"; |
121 | ||
122 | < | maxCutoff = smallestBoxL / 2.0; |
122 | > | for(i=0; i<3; i++) |
123 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
124 | ||
125 | < | if (rList > maxCutoff) { |
122 | < | sprintf( painCave.errMsg, |
123 | < | "New Box size is forcing neighborlist radius down to %lf\n", |
124 | < | maxCutoff ); |
125 | < | painCave.isFatal = 0; |
126 | < | simError(); |
125 | > | setBoxM(theBox); |
126 | ||
127 | < | rList = maxCutoff; |
127 | > | } |
128 | ||
129 | < | sprintf( painCave.errMsg, |
130 | < | "New Box size is forcing cutoff radius down to %lf\n", |
131 | < | maxCutoff - 1.0 ); |
132 | < | painCave.isFatal = 0; |
133 | < | simError(); |
129 | > | void SimInfo::calcHmatInv( void ) { |
130 | > | |
131 | > | int i,j; |
132 | > | double smallDiag; |
133 | > | double tol; |
134 | > | double sanity[3][3]; |
135 | ||
136 | < | rCut = rList - 1.0; |
136 | > | invertMat3( Hmat, HmatInv ); |
137 | ||
138 | < | // list radius changed so we have to refresh the simulation structure. |
139 | < | refreshSim(); |
140 | < | } |
138 | > | // Check the inverse to make sure it is sane: |
139 | ||
140 | < | if (rCut > maxCutoff) { |
141 | < | sprintf( painCave.errMsg, |
142 | < | "New Box size is forcing cutoff radius down to %lf\n", |
143 | < | maxCutoff ); |
144 | < | painCave.isFatal = 0; |
145 | < | simError(); |
140 | > | matMul3( Hmat, HmatInv, sanity ); |
141 | > | |
142 | > | // check to see if Hmat is orthorhombic |
143 | > | |
144 | > | 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; |
148 | ||
149 | < | status = 0; |
150 | < | LJ_new_rcut(&rCut, &status); |
151 | < | if (status != 0) { |
152 | < | sprintf( painCave.errMsg, |
153 | < | "Error in recomputing LJ shifts based on new rcut\n"); |
154 | < | painCave.isFatal = 1; |
155 | < | simError(); |
149 | > | orthoRhombic = 1; |
150 | > | |
151 | > | for (i = 0; i < 3; i++ ) { |
152 | > | for (j = 0 ; j < 3; j++) { |
153 | > | if (i != j) { |
154 | > | if (orthoRhombic) { |
155 | > | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
156 | > | } |
157 | > | } |
158 | } | |
159 | } | |
160 | } | |
159 | – | |
161 | ||
162 | < | void SimInfo::getBox(double theBox[9]) { |
162 | < | |
163 | < | int i; |
164 | < | for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
165 | < | } |
166 | < | |
167 | < | |
168 | < | void SimInfo::calcHmatI( void ) { |
169 | < | |
170 | < | double C[3][3]; |
171 | < | double detHmat; |
162 | > | double SimInfo::matDet3(double a[3][3]) { |
163 | int i, j, k; | |
164 | < | double smallDiag; |
174 | < | double tol; |
175 | < | double sanity[3][3]; |
164 | > | double determinant; |
165 | ||
166 | < | // calculate the adjunct of Hmat; |
166 | > | determinant = 0.0; |
167 | ||
168 | < | C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
169 | < | C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
170 | < | C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
168 | > | for(i = 0; i < 3; i++) { |
169 | > | j = (i+1)%3; |
170 | > | k = (i+2)%3; |
171 | ||
172 | < | C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
173 | < | C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
185 | < | C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
172 | > | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
173 | > | } |
174 | ||
175 | < | C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
176 | < | C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
189 | < | C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
175 | > | return determinant; |
176 | > | } |
177 | ||
178 | < | // calcutlate the determinant of Hmat |
178 | > | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
179 | ||
180 | < | detHmat = 0.0; |
181 | < | for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
180 | > | int i, j, k, l, m, n; |
181 | > | double determinant; |
182 | ||
183 | < | |
197 | < | // H^-1 = C^T / det(H) |
198 | < | |
199 | < | i=0; |
200 | < | for(j=0; j<3; j++){ |
201 | < | for(k=0; k<3; k++){ |
183 | > | determinant = matDet3( a ); |
184 | ||
185 | < | HmatI[i] = C[j][k] / detHmat; |
186 | < | i++; |
187 | < | } |
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 | < | // sanity check |
193 | < | |
194 | < | for(i=0; i<3; i++){ |
195 | < | for(j=0; j<3; j++){ |
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 | < | sanity[i][j] = 0.0; |
214 | < | for(k=0; k<3; k++){ |
215 | < | sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
216 | < | } |
199 | > | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
200 | } | |
201 | } | |
202 | + | } |
203 | ||
204 | < | cerr << "sanity => \n" |
205 | < | << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
222 | < | << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
223 | < | << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
224 | < | << "\n"; |
225 | < | |
204 | > | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
205 | > | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
206 | ||
207 | < | // check to see if Hmat is orthorhombic |
207 | > | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
208 | > | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
209 | > | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
210 | ||
211 | < | smallDiag = Hmat[0]; |
212 | < | if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
213 | < | if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
214 | < | tol = smallDiag * 1E-6; |
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 | < | orthoRhombic = 1; |
225 | < | for(i=0; (i<9) && orthoRhombic; i++){ |
226 | < | |
227 | < | if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
228 | < | orthoRhombic = (Hmat[i] <= tol); |
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]; |
241 | } | |
242 | } | |
243 | < | |
243 | > | for (i = 0; i < 3; i++) { |
244 | > | for (j = 0; j < 3; j++) { |
245 | > | out[i][j] = temp[i][j]; |
246 | > | } |
247 | > | } |
248 | } | |
249 | + | |
250 | + | void SimInfo::printMat3(double A[3][3] ){ |
251 | ||
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 | + | |
266 | void SimInfo::calcBoxL( void ){ | |
267 | ||
268 | double dx, dy, dz, dsq; | |
269 | int i; | |
270 | ||
271 | < | // boxVol = h1 (dot) h2 (cross) h3 |
271 | > | // boxVol = Determinant of Hmat |
272 | ||
273 | < | boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
252 | < | + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
253 | < | + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
273 | > | boxVol = matDet3( Hmat ); |
274 | ||
255 | – | |
275 | // boxLx | |
276 | ||
277 | < | dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
277 | > | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
278 | dsq = dx*dx + dy*dy + dz*dz; | |
279 | < | boxLx = sqrt( dsq ); |
279 | > | boxL[0] = sqrt( dsq ); |
280 | > | maxCutoff = 0.5 * boxL[0]; |
281 | ||
282 | // boxLy | |
283 | ||
284 | < | dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
284 | > | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
285 | dsq = dx*dx + dy*dy + dz*dz; | |
286 | < | boxLy = sqrt( dsq ); |
286 | > | boxL[1] = sqrt( dsq ); |
287 | > | if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
288 | ||
289 | // boxLz | |
290 | ||
291 | < | dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
291 | > | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
292 | dsq = dx*dx + dy*dy + dz*dz; | |
293 | < | boxLz = sqrt( dsq ); |
294 | < | |
293 | > | boxL[2] = sqrt( dsq ); |
294 | > | if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
295 | > | |
296 | } | |
297 | ||
298 | ||
# | Line 281 | Line 303 | void SimInfo::wrapVector( double thePos[3] ){ | |
303 | ||
304 | if( !orthoRhombic ){ | |
305 | // calc the scaled coordinates. | |
306 | + | |
307 | + | |
308 | + | matVecMul3(HmatInv, thePos, scaled); |
309 | ||
310 | for(i=0; i<3; i++) | |
311 | < | scaled[i] = |
287 | < | thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
311 | > | scaled[i] -= roundMe(scaled[i]); |
312 | ||
289 | – | // wrap the scaled coordinates |
290 | – | |
291 | – | for(i=0; i<3; i++) |
292 | – | scaled[i] -= round(scaled[i]); |
293 | – | |
313 | // calc the wrapped real coordinates from the wrapped scaled coordinates | |
314 | ||
315 | < | for(i=0; i<3; i++) |
316 | < | thePos[i] = |
298 | < | scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[3]*Hmat[i+6]; |
315 | > | matVecMul3(Hmat, scaled, thePos); |
316 | > | |
317 | } | |
318 | else{ | |
319 | // calc the scaled coordinates. | |
320 | ||
321 | for(i=0; i<3; i++) | |
322 | < | scaled[i] = thePos[i]*HmatI[i*4]; |
322 | > | scaled[i] = thePos[i]*HmatInv[i][i]; |
323 | ||
324 | // wrap the scaled coordinates | |
325 | ||
326 | for(i=0; i<3; i++) | |
327 | < | scaled[i] -= round(scaled[i]); |
327 | > | scaled[i] -= roundMe(scaled[i]); |
328 | ||
329 | // calc the wrapped real coordinates from the wrapped scaled coordinates | |
330 | ||
331 | for(i=0; i<3; i++) | |
332 | < | thePos[i] = scaled[i]*Hmat[i*4]; |
332 | > | thePos[i] = scaled[i]*Hmat[i][i]; |
333 | } | |
334 | ||
317 | – | |
335 | } | |
336 | ||
337 | ||
# | Line 355 | Line 372 | void SimInfo::refreshSim(){ | |
372 | int isError; | |
373 | int n_global; | |
374 | int* excl; | |
375 | < | |
359 | < | fInfo.rrf = 0.0; |
360 | < | fInfo.rt = 0.0; |
375 | > | |
376 | fInfo.dielect = 0.0; | |
377 | ||
363 | – | fInfo.box[0] = box_x; |
364 | – | fInfo.box[1] = box_y; |
365 | – | fInfo.box[2] = box_z; |
366 | – | |
367 | – | fInfo.rlist = rList; |
368 | – | fInfo.rcut = rCut; |
369 | – | |
378 | if( useDipole ){ | |
371 | – | fInfo.rrf = ecr; |
372 | – | fInfo.rt = ecr - est; |
379 | if( useReactionField )fInfo.dielect = dielectric; | |
380 | } | |
381 | ||
# | Line 418 | Line 424 | void SimInfo::refreshSim(){ | |
424 | ||
425 | } | |
426 | ||
427 | + | |
428 | + | void SimInfo::setRcut( double theRcut ){ |
429 | + | |
430 | + | if( !haveOrigRcut ){ |
431 | + | haveOrigRcut = 1; |
432 | + | origRcut = theRcut; |
433 | + | } |
434 | + | |
435 | + | rCut = theRcut; |
436 | + | checkCutOffs(); |
437 | + | } |
438 | + | |
439 | + | void SimInfo::setEcr( double theEcr ){ |
440 | + | |
441 | + | if( !haveOrigEcr ){ |
442 | + | haveOrigEcr = 1; |
443 | + | origEcr = theEcr; |
444 | + | } |
445 | + | |
446 | + | ecr = theEcr; |
447 | + | checkCutOffs(); |
448 | + | } |
449 | + | |
450 | + | void SimInfo::setEcr( double theEcr, double theEst ){ |
451 | + | |
452 | + | est = theEst; |
453 | + | setEcr( theEcr ); |
454 | + | } |
455 | + | |
456 | + | |
457 | + | void SimInfo::checkCutOffs( void ){ |
458 | + | |
459 | + | int cutChanged = 0; |
460 | + | |
461 | + | if( boxIsInit ){ |
462 | + | |
463 | + | //we need to check cutOffs against the box |
464 | + | |
465 | + | if( maxCutoff > rCut ){ |
466 | + | if( rCut < origRcut ){ |
467 | + | rCut = origRcut; |
468 | + | if (rCut > maxCutoff) rCut = maxCutoff; |
469 | + | |
470 | + | sprintf( painCave.errMsg, |
471 | + | "New Box size is setting the long range cutoff radius " |
472 | + | "to %lf\n", |
473 | + | rCut ); |
474 | + | painCave.isFatal = 0; |
475 | + | simError(); |
476 | + | } |
477 | + | } |
478 | + | |
479 | + | if( maxCutoff > ecr ){ |
480 | + | if( ecr < origEcr ){ |
481 | + | rCut = origEcr; |
482 | + | if (ecr > maxCutoff) ecr = maxCutoff; |
483 | + | |
484 | + | sprintf( painCave.errMsg, |
485 | + | "New Box size is setting the electrostaticCutoffRadius " |
486 | + | "to %lf\n", |
487 | + | ecr ); |
488 | + | painCave.isFatal = 0; |
489 | + | simError(); |
490 | + | } |
491 | + | } |
492 | + | |
493 | + | |
494 | + | if (rCut > maxCutoff) { |
495 | + | sprintf( painCave.errMsg, |
496 | + | "New Box size is setting the long range cutoff radius " |
497 | + | "to %lf\n", |
498 | + | 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 | + | |
515 | + | } |
516 | + | |
517 | + | |
518 | + | if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
519 | + | |
520 | + | // rlist is the 1.0 plus max( rcut, ecr ) |
521 | + | |
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; |
531 | + | } |
532 | + | |
533 | + | void SimInfo::addProperty(GenericData* prop){ |
534 | + | |
535 | + | map<string, GenericData*>::iterator result; |
536 | + | result = properties.find(prop->getID()); |
537 | + | |
538 | + | //we can't simply use properties[prop->getID()] = prop, |
539 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
540 | + | |
541 | + | if(result != properties.end()){ |
542 | + | |
543 | + | delete (*result).second; |
544 | + | (*result).second = prop; |
545 | + | |
546 | + | } |
547 | + | else{ |
548 | + | |
549 | + | properties[prop->getID()] = prop; |
550 | + | |
551 | + | } |
552 | + | |
553 | + | } |
554 | + | |
555 | + | GenericData* SimInfo::getProperty(const string& propName){ |
556 | + | |
557 | + | map<string, GenericData*>::iterator result; |
558 | + | |
559 | + | //string lowerCaseName = (); |
560 | + | |
561 | + | result = properties.find(propName); |
562 | + | |
563 | + | if(result != properties.end()) |
564 | + | return (*result).second; |
565 | + | else |
566 | + | return NULL; |
567 | + | } |
568 | + | |
569 | + | vector<GenericData*> SimInfo::getProperties(){ |
570 | + | |
571 | + | vector<GenericData*> result; |
572 | + | map<string, GenericData*>::iterator i; |
573 | + | |
574 | + | for(i = properties.begin(); i != properties.end(); i++) |
575 | + | result.push_back((*i).second); |
576 | + | |
577 | + | return result; |
578 | + | } |
579 | + | |
580 | + |
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