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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; | |
# | Line 12 | Line 12 | using namespace std; | |
12 | ||
13 | #include "fortranWrappers.hpp" | |
14 | ||
15 | + | #include "MatVec3.h" |
16 | + | |
17 | #ifdef IS_MPI | |
18 | #include "mpiSimulation.hpp" | |
19 | #endif | |
# | Line 20 | Line 22 | inline double roundMe( double x ){ | |
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; | |
43 | + | currentTime = 0.0; |
44 | rCut = 0.0; | |
45 | + | rSw = 0.0; |
46 | ||
47 | + | haveRcut = 0; |
48 | + | haveRsw = 0; |
49 | + | boxIsInit = 0; |
50 | + | |
51 | + | resetTime = 1e99; |
52 | + | |
53 | + | orthoRhombic = 0; |
54 | + | orthoTolerance = 1E-6; |
55 | + | useInitXSstate = true; |
56 | + | |
57 | usePBC = 0; | |
58 | useLJ = 0; | |
59 | useSticky = 0; | |
60 | < | useDipole = 0; |
60 | > | useCharges = 0; |
61 | > | useDipoles = 0; |
62 | useReactionField = 0; | |
63 | useGB = 0; | |
64 | useEAM = 0; | |
65 | + | useThermInt = 0; |
66 | ||
67 | < | wrapMeSimInfo( this ); |
47 | < | } |
67 | > | haveCutoffGroups = false; |
68 | ||
69 | < | void SimInfo::setBox(double newBox[3]) { |
69 | > | excludes = Exclude::Instance(); |
70 | ||
71 | < | double smallestBoxL, maxCutoff; |
52 | < | int status; |
53 | < | int i; |
71 | > | myConfiguration = new SimState(); |
72 | ||
73 | < | for(i=0; i<9; i++) Hmat[i] = 0.0;; |
73 | > | has_minimizer = false; |
74 | > | the_minimizer =NULL; |
75 | ||
76 | < | Hmat[0] = newBox[0]; |
58 | < | Hmat[4] = newBox[1]; |
59 | < | Hmat[8] = newBox[2]; |
76 | > | ngroup = 0; |
77 | ||
78 | < | calcHmatI(); |
79 | < | calcBoxL(); |
78 | > | wrapMeSimInfo( this ); |
79 | > | } |
80 | ||
64 | – | setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
81 | ||
82 | < | smallestBoxL = boxLx; |
67 | < | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
68 | < | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
82 | > | SimInfo::~SimInfo(){ |
83 | ||
84 | < | maxCutoff = smallestBoxL / 2.0; |
84 | > | delete myConfiguration; |
85 | ||
86 | < | if (rList > maxCutoff) { |
87 | < | sprintf( painCave.errMsg, |
88 | < | "New Box size is forcing neighborlist radius down to %lf\n", |
89 | < | maxCutoff ); |
90 | < | painCave.isFatal = 0; |
91 | < | simError(); |
86 | > | map<string, GenericData*>::iterator i; |
87 | > | |
88 | > | for(i = properties.begin(); i != properties.end(); i++) |
89 | > | delete (*i).second; |
90 | > | |
91 | > | } |
92 | ||
93 | < | rList = maxCutoff; |
93 | > | void SimInfo::setBox(double newBox[3]) { |
94 | > | |
95 | > | int i, j; |
96 | > | double tempMat[3][3]; |
97 | ||
98 | < | sprintf( painCave.errMsg, |
99 | < | "New Box size is forcing cutoff radius down to %lf\n", |
83 | < | maxCutoff - 1.0 ); |
84 | < | painCave.isFatal = 0; |
85 | < | simError(); |
98 | > | for(i=0; i<3; i++) |
99 | > | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
100 | ||
101 | < | rCut = rList - 1.0; |
101 | > | tempMat[0][0] = newBox[0]; |
102 | > | tempMat[1][1] = newBox[1]; |
103 | > | tempMat[2][2] = newBox[2]; |
104 | ||
105 | < | // list radius changed so we have to refresh the simulation structure. |
90 | < | refreshSim(); |
91 | < | } |
105 | > | setBoxM( tempMat ); |
106 | ||
93 | – | if (rCut > maxCutoff) { |
94 | – | sprintf( painCave.errMsg, |
95 | – | "New Box size is forcing cutoff radius down to %lf\n", |
96 | – | maxCutoff ); |
97 | – | painCave.isFatal = 0; |
98 | – | simError(); |
99 | – | |
100 | – | status = 0; |
101 | – | LJ_new_rcut(&rCut, &status); |
102 | – | if (status != 0) { |
103 | – | sprintf( painCave.errMsg, |
104 | – | "Error in recomputing LJ shifts based on new rcut\n"); |
105 | – | painCave.isFatal = 1; |
106 | – | simError(); |
107 | – | } |
108 | – | } |
107 | } | |
108 | ||
109 | < | void SimInfo::setBoxM( double theBox[9] ){ |
109 | > | void SimInfo::setBoxM( double theBox[3][3] ){ |
110 | ||
111 | < | int i, status; |
112 | < | double smallestBoxL, maxCutoff; |
111 | > | int i, j; |
112 | > | double FortranHmat[9]; // to preserve compatibility with Fortran the |
113 | > | // ordering in the array is as follows: |
114 | > | // [ 0 3 6 ] |
115 | > | // [ 1 4 7 ] |
116 | > | // [ 2 5 8 ] |
117 | > | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
118 | ||
119 | < | for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
120 | < | calcHmatI(); |
119 | > | if( !boxIsInit ) boxIsInit = 1; |
120 | > | |
121 | > | for(i=0; i < 3; i++) |
122 | > | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
123 | > | |
124 | calcBoxL(); | |
125 | + | calcHmatInv(); |
126 | ||
127 | < | setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
127 | > | for(i=0; i < 3; i++) { |
128 | > | for (j=0; j < 3; j++) { |
129 | > | FortranHmat[3*j + i] = Hmat[i][j]; |
130 | > | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
131 | > | } |
132 | > | } |
133 | > | |
134 | > | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
135 | ||
136 | < | smallestBoxL = boxLx; |
137 | < | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
124 | < | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
136 | > | } |
137 | > | |
138 | ||
139 | < | maxCutoff = smallestBoxL / 2.0; |
139 | > | void SimInfo::getBoxM (double theBox[3][3]) { |
140 | ||
141 | < | if (rList > maxCutoff) { |
142 | < | sprintf( painCave.errMsg, |
143 | < | "New Box size is forcing neighborlist radius down to %lf\n", |
144 | < | maxCutoff ); |
132 | < | painCave.isFatal = 0; |
133 | < | simError(); |
141 | > | int i, j; |
142 | > | for(i=0; i<3; i++) |
143 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
144 | > | } |
145 | ||
135 | – | rList = maxCutoff; |
146 | ||
147 | < | sprintf( painCave.errMsg, |
148 | < | "New Box size is forcing cutoff radius down to %lf\n", |
149 | < | maxCutoff - 1.0 ); |
140 | < | painCave.isFatal = 0; |
141 | < | simError(); |
147 | > | void SimInfo::scaleBox(double scale) { |
148 | > | double theBox[3][3]; |
149 | > | int i, j; |
150 | ||
151 | < | rCut = rList - 1.0; |
151 | > | // cerr << "Scaling box by " << scale << "\n"; |
152 | ||
153 | < | // list radius changed so we have to refresh the simulation structure. |
154 | < | refreshSim(); |
147 | < | } |
153 | > | for(i=0; i<3; i++) |
154 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
155 | ||
156 | < | if (rCut > maxCutoff) { |
150 | < | sprintf( painCave.errMsg, |
151 | < | "New Box size is forcing cutoff radius down to %lf\n", |
152 | < | maxCutoff ); |
153 | < | painCave.isFatal = 0; |
154 | < | simError(); |
156 | > | setBoxM(theBox); |
157 | ||
158 | < | status = 0; |
157 | < | LJ_new_rcut(&rCut, &status); |
158 | < | if (status != 0) { |
159 | < | sprintf( painCave.errMsg, |
160 | < | "Error in recomputing LJ shifts based on new rcut\n"); |
161 | < | painCave.isFatal = 1; |
162 | < | simError(); |
163 | < | } |
164 | < | } |
165 | < | } |
166 | < | |
158 | > | } |
159 | ||
160 | < | void SimInfo::getBoxM (double theBox[9]) { |
161 | < | |
162 | < | int i; |
163 | < | for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
172 | < | } |
173 | < | |
174 | < | |
175 | < | void SimInfo::calcHmatI( void ) { |
176 | < | |
177 | < | double C[3][3]; |
178 | < | double detHmat; |
179 | < | int i, j, k; |
160 | > | void SimInfo::calcHmatInv( void ) { |
161 | > | |
162 | > | int oldOrtho; |
163 | > | int i,j; |
164 | double smallDiag; | |
165 | double tol; | |
166 | double sanity[3][3]; | |
167 | ||
168 | < | // calculate the adjunct of Hmat; |
168 | > | invertMat3( Hmat, HmatInv ); |
169 | ||
170 | < | C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
187 | < | C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
188 | < | C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
189 | < | |
190 | < | C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
191 | < | C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
192 | < | C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
193 | < | |
194 | < | C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
195 | < | C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
196 | < | C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
197 | < | |
198 | < | // calcutlate the determinant of Hmat |
170 | > | // check to see if Hmat is orthorhombic |
171 | ||
172 | < | detHmat = 0.0; |
201 | < | for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
172 | > | oldOrtho = orthoRhombic; |
173 | ||
174 | < | |
175 | < | // H^-1 = C^T / det(H) |
176 | < | |
177 | < | i=0; |
207 | < | for(j=0; j<3; j++){ |
208 | < | for(k=0; k<3; k++){ |
174 | > | smallDiag = fabs(Hmat[0][0]); |
175 | > | if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
176 | > | if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
177 | > | tol = smallDiag * orthoTolerance; |
178 | ||
179 | < | HmatI[i] = C[j][k] / detHmat; |
180 | < | i++; |
181 | < | } |
182 | < | } |
183 | < | |
184 | < | // sanity check |
185 | < | |
186 | < | for(i=0; i<3; i++){ |
218 | < | for(j=0; j<3; j++){ |
219 | < | |
220 | < | sanity[i][j] = 0.0; |
221 | < | for(k=0; k<3; k++){ |
222 | < | sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
179 | > | orthoRhombic = 1; |
180 | > | |
181 | > | for (i = 0; i < 3; i++ ) { |
182 | > | for (j = 0 ; j < 3; j++) { |
183 | > | if (i != j) { |
184 | > | if (orthoRhombic) { |
185 | > | if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
186 | > | } |
187 | } | |
188 | } | |
189 | } | |
190 | ||
191 | < | cerr << "sanity => \n" |
228 | < | << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
229 | < | << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
230 | < | << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
231 | < | << "\n"; |
191 | > | if( oldOrtho != orthoRhombic ){ |
192 | ||
193 | < | |
194 | < | // check to see if Hmat is orthorhombic |
195 | < | |
196 | < | smallDiag = Hmat[0]; |
197 | < | if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
198 | < | if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
199 | < | tol = smallDiag * 1E-6; |
200 | < | |
201 | < | orthoRhombic = 1; |
242 | < | for(i=0; (i<9) && orthoRhombic; i++){ |
243 | < | |
244 | < | if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
245 | < | orthoRhombic = (Hmat[i] <= tol); |
193 | > | if( orthoRhombic ){ |
194 | > | sprintf( painCave.errMsg, |
195 | > | "OOPSE is switching from the default Non-Orthorhombic\n" |
196 | > | "\tto the faster Orthorhombic periodic boundary computations.\n" |
197 | > | "\tThis is usually a good thing, but if you wan't the\n" |
198 | > | "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
199 | > | "\tvariable ( currently set to %G ) smaller.\n", |
200 | > | orthoTolerance); |
201 | > | simError(); |
202 | } | |
203 | + | else { |
204 | + | sprintf( painCave.errMsg, |
205 | + | "OOPSE is switching from the faster Orthorhombic to the more\n" |
206 | + | "\tflexible Non-Orthorhombic periodic boundary computations.\n" |
207 | + | "\tThis is usually because the box has deformed under\n" |
208 | + | "\tNPTf integration. If you wan't to live on the edge with\n" |
209 | + | "\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
210 | + | "\tvariable ( currently set to %G ) larger.\n", |
211 | + | orthoTolerance); |
212 | + | simError(); |
213 | + | } |
214 | } | |
248 | – | |
215 | } | |
216 | ||
217 | void SimInfo::calcBoxL( void ){ | |
218 | ||
219 | double dx, dy, dz, dsq; | |
254 | – | int i; |
220 | ||
221 | < | // boxVol = h1 (dot) h2 (cross) h3 |
221 | > | // boxVol = Determinant of Hmat |
222 | ||
223 | < | boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
259 | < | + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
260 | < | + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
223 | > | boxVol = matDet3( Hmat ); |
224 | ||
262 | – | |
225 | // boxLx | |
226 | ||
227 | < | dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
227 | > | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
228 | dsq = dx*dx + dy*dy + dz*dz; | |
229 | < | boxLx = sqrt( dsq ); |
229 | > | boxL[0] = sqrt( dsq ); |
230 | > | //maxCutoff = 0.5 * boxL[0]; |
231 | ||
232 | // boxLy | |
233 | ||
234 | < | dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
234 | > | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
235 | dsq = dx*dx + dy*dy + dz*dz; | |
236 | < | boxLy = sqrt( dsq ); |
236 | > | boxL[1] = sqrt( dsq ); |
237 | > | //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
238 | ||
239 | + | |
240 | // boxLz | |
241 | ||
242 | < | dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
242 | > | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
243 | dsq = dx*dx + dy*dy + dz*dz; | |
244 | < | boxLz = sqrt( dsq ); |
244 | > | boxL[2] = sqrt( dsq ); |
245 | > | //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
246 | > | |
247 | > | //calculate the max cutoff |
248 | > | maxCutoff = calcMaxCutOff(); |
249 | ||
250 | + | checkCutOffs(); |
251 | + | |
252 | } | |
253 | ||
254 | ||
255 | + | double SimInfo::calcMaxCutOff(){ |
256 | + | |
257 | + | double ri[3], rj[3], rk[3]; |
258 | + | double rij[3], rjk[3], rki[3]; |
259 | + | double minDist; |
260 | + | |
261 | + | ri[0] = Hmat[0][0]; |
262 | + | ri[1] = Hmat[1][0]; |
263 | + | ri[2] = Hmat[2][0]; |
264 | + | |
265 | + | rj[0] = Hmat[0][1]; |
266 | + | rj[1] = Hmat[1][1]; |
267 | + | rj[2] = Hmat[2][1]; |
268 | + | |
269 | + | rk[0] = Hmat[0][2]; |
270 | + | rk[1] = Hmat[1][2]; |
271 | + | rk[2] = Hmat[2][2]; |
272 | + | |
273 | + | crossProduct3(ri, rj, rij); |
274 | + | distXY = dotProduct3(rk,rij) / norm3(rij); |
275 | + | |
276 | + | crossProduct3(rj,rk, rjk); |
277 | + | distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
278 | + | |
279 | + | crossProduct3(rk,ri, rki); |
280 | + | distZX = dotProduct3(rj,rki) / norm3(rki); |
281 | + | |
282 | + | minDist = min(min(distXY, distYZ), distZX); |
283 | + | return minDist/2; |
284 | + | |
285 | + | } |
286 | + | |
287 | void SimInfo::wrapVector( double thePos[3] ){ | |
288 | ||
289 | < | int i, j, k; |
289 | > | int i; |
290 | double scaled[3]; | |
291 | ||
292 | if( !orthoRhombic ){ | |
293 | // calc the scaled coordinates. | |
294 | + | |
295 | + | |
296 | + | matVecMul3(HmatInv, thePos, scaled); |
297 | ||
298 | for(i=0; i<3; i++) | |
293 | – | scaled[i] = |
294 | – | thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
295 | – | |
296 | – | // wrap the scaled coordinates |
297 | – | |
298 | – | for(i=0; i<3; i++) |
299 | scaled[i] -= roundMe(scaled[i]); | |
300 | ||
301 | // calc the wrapped real coordinates from the wrapped scaled coordinates | |
302 | ||
303 | < | for(i=0; i<3; i++) |
304 | < | thePos[i] = |
305 | < | scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
303 | > | matVecMul3(Hmat, scaled, thePos); |
304 | > | |
305 | } | |
306 | else{ | |
307 | // calc the scaled coordinates. | |
308 | ||
309 | for(i=0; i<3; i++) | |
310 | < | scaled[i] = thePos[i]*HmatI[i*4]; |
310 | > | scaled[i] = thePos[i]*HmatInv[i][i]; |
311 | ||
312 | // wrap the scaled coordinates | |
313 | ||
# | Line 318 | Line 317 | void SimInfo::wrapVector( double thePos[3] ){ | |
317 | // calc the wrapped real coordinates from the wrapped scaled coordinates | |
318 | ||
319 | for(i=0; i<3; i++) | |
320 | < | thePos[i] = scaled[i]*Hmat[i*4]; |
320 | > | thePos[i] = scaled[i]*Hmat[i][i]; |
321 | } | |
322 | ||
324 | – | |
323 | } | |
324 | ||
325 | ||
326 | int SimInfo::getNDF(){ | |
327 | < | int ndf_local, ndf; |
327 | > | int ndf_local; |
328 | > | |
329 | > | ndf_local = 0; |
330 | ||
331 | < | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
331 | > | for(int i = 0; i < integrableObjects.size(); i++){ |
332 | > | ndf_local += 3; |
333 | > | if (integrableObjects[i]->isDirectional()) { |
334 | > | if (integrableObjects[i]->isLinear()) |
335 | > | ndf_local += 2; |
336 | > | else |
337 | > | ndf_local += 3; |
338 | > | } |
339 | > | } |
340 | ||
341 | + | // n_constraints is local, so subtract them on each processor: |
342 | + | |
343 | + | ndf_local -= n_constraints; |
344 | + | |
345 | #ifdef IS_MPI | |
346 | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
347 | #else | |
348 | ndf = ndf_local; | |
349 | #endif | |
350 | ||
351 | < | ndf = ndf - 3; |
351 | > | // nZconstraints is global, as are the 3 COM translations for the |
352 | > | // entire system: |
353 | ||
354 | + | ndf = ndf - 3 - nZconstraints; |
355 | + | |
356 | return ndf; | |
357 | } | |
358 | ||
359 | int SimInfo::getNDFraw() { | |
360 | < | int ndfRaw_local, ndfRaw; |
360 | > | int ndfRaw_local; |
361 | ||
362 | // Raw degrees of freedom that we have to set | |
363 | < | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
364 | < | |
363 | > | ndfRaw_local = 0; |
364 | > | |
365 | > | for(int i = 0; i < integrableObjects.size(); i++){ |
366 | > | ndfRaw_local += 3; |
367 | > | if (integrableObjects[i]->isDirectional()) { |
368 | > | if (integrableObjects[i]->isLinear()) |
369 | > | ndfRaw_local += 2; |
370 | > | else |
371 | > | ndfRaw_local += 3; |
372 | > | } |
373 | > | } |
374 | > | |
375 | #ifdef IS_MPI | |
376 | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
377 | #else | |
# | Line 355 | Line 380 | int SimInfo::getNDFraw() { | |
380 | ||
381 | return ndfRaw; | |
382 | } | |
383 | < | |
383 | > | |
384 | > | int SimInfo::getNDFtranslational() { |
385 | > | int ndfTrans_local; |
386 | > | |
387 | > | ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
388 | > | |
389 | > | |
390 | > | #ifdef IS_MPI |
391 | > | MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
392 | > | #else |
393 | > | ndfTrans = ndfTrans_local; |
394 | > | #endif |
395 | > | |
396 | > | ndfTrans = ndfTrans - 3 - nZconstraints; |
397 | > | |
398 | > | return ndfTrans; |
399 | > | } |
400 | > | |
401 | > | int SimInfo::getTotIntegrableObjects() { |
402 | > | int nObjs_local; |
403 | > | int nObjs; |
404 | > | |
405 | > | nObjs_local = integrableObjects.size(); |
406 | > | |
407 | > | |
408 | > | #ifdef IS_MPI |
409 | > | MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
410 | > | #else |
411 | > | nObjs = nObjs_local; |
412 | > | #endif |
413 | > | |
414 | > | |
415 | > | return nObjs; |
416 | > | } |
417 | > | |
418 | void SimInfo::refreshSim(){ | |
419 | ||
420 | simtype fInfo; | |
421 | int isError; | |
422 | int n_global; | |
423 | int* excl; | |
424 | < | |
366 | < | fInfo.rrf = 0.0; |
367 | < | fInfo.rt = 0.0; |
424 | > | |
425 | fInfo.dielect = 0.0; | |
426 | ||
427 | < | fInfo.rlist = rList; |
371 | < | fInfo.rcut = rCut; |
372 | < | |
373 | < | if( useDipole ){ |
374 | < | fInfo.rrf = ecr; |
375 | < | fInfo.rt = ecr - est; |
427 | > | if( useDipoles ){ |
428 | if( useReactionField )fInfo.dielect = dielectric; | |
429 | } | |
430 | ||
# | Line 381 | Line 433 | void SimInfo::refreshSim(){ | |
433 | fInfo.SIM_uses_LJ = useLJ; | |
434 | fInfo.SIM_uses_sticky = useSticky; | |
435 | //fInfo.SIM_uses_sticky = 0; | |
436 | < | fInfo.SIM_uses_dipoles = useDipole; |
436 | > | fInfo.SIM_uses_charges = useCharges; |
437 | > | fInfo.SIM_uses_dipoles = useDipoles; |
438 | //fInfo.SIM_uses_dipoles = 0; | |
439 | < | //fInfo.SIM_uses_RF = useReactionField; |
440 | < | fInfo.SIM_uses_RF = 0; |
439 | > | fInfo.SIM_uses_RF = useReactionField; |
440 | > | //fInfo.SIM_uses_RF = 0; |
441 | fInfo.SIM_uses_GB = useGB; | |
442 | fInfo.SIM_uses_EAM = useEAM; | |
443 | ||
444 | < | excl = Exclude::getArray(); |
445 | < | |
444 | > | n_exclude = excludes->getSize(); |
445 | > | excl = excludes->getFortranArray(); |
446 | > | |
447 | #ifdef IS_MPI | |
448 | n_global = mpiSim->getTotAtoms(); | |
449 | #else | |
450 | n_global = n_atoms; | |
451 | #endif | |
452 | < | |
452 | > | |
453 | isError = 0; | |
454 | < | |
454 | > | |
455 | > | getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
456 | > | //it may not be a good idea to pass the address of first element in vector |
457 | > | //since c++ standard does not require vector to be stored continuously in meomory |
458 | > | //Most of the compilers will organize the memory of vector continuously |
459 | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, | |
460 | < | &nGlobalExcludes, globalExcludes, molMembershipArray, |
461 | < | &isError ); |
462 | < | |
460 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
461 | > | &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
462 | > | |
463 | if( isError ){ | |
464 | < | |
464 | > | |
465 | sprintf( painCave.errMsg, | |
466 | < | "There was an error setting the simulation information in fortran.\n" ); |
466 | > | "There was an error setting the simulation information in fortran.\n" ); |
467 | painCave.isFatal = 1; | |
468 | simError(); | |
469 | } | |
470 | < | |
470 | > | |
471 | #ifdef IS_MPI | |
472 | sprintf( checkPointMsg, | |
473 | "succesfully sent the simulation information to fortran.\n"); | |
474 | MPIcheckPoint(); | |
475 | #endif // is_mpi | |
476 | < | |
476 | > | |
477 | this->ndf = this->getNDF(); | |
478 | this->ndfRaw = this->getNDFraw(); | |
479 | + | this->ndfTrans = this->getNDFtranslational(); |
480 | + | } |
481 | ||
482 | + | void SimInfo::setDefaultRcut( double theRcut ){ |
483 | + | |
484 | + | haveRcut = 1; |
485 | + | rCut = theRcut; |
486 | + | rList = rCut + 1.0; |
487 | + | |
488 | + | notifyFortranCutOffs( &rCut, &rSw, &rList ); |
489 | } | |
490 | ||
491 | + | void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
492 | + | |
493 | + | rSw = theRsw; |
494 | + | setDefaultRcut( theRcut ); |
495 | + | } |
496 | + | |
497 | + | |
498 | + | void SimInfo::checkCutOffs( void ){ |
499 | + | |
500 | + | if( boxIsInit ){ |
501 | + | |
502 | + | //we need to check cutOffs against the box |
503 | + | |
504 | + | if( rCut > maxCutoff ){ |
505 | + | sprintf( painCave.errMsg, |
506 | + | "cutoffRadius is too large for the current periodic box.\n" |
507 | + | "\tCurrent Value of cutoffRadius = %G at time %G\n " |
508 | + | "\tThis is larger than half of at least one of the\n" |
509 | + | "\tperiodic box vectors. Right now, the Box matrix is:\n" |
510 | + | "\n" |
511 | + | "\t[ %G %G %G ]\n" |
512 | + | "\t[ %G %G %G ]\n" |
513 | + | "\t[ %G %G %G ]\n", |
514 | + | rCut, currentTime, |
515 | + | Hmat[0][0], Hmat[0][1], Hmat[0][2], |
516 | + | Hmat[1][0], Hmat[1][1], Hmat[1][2], |
517 | + | Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
518 | + | painCave.isFatal = 1; |
519 | + | simError(); |
520 | + | } |
521 | + | } else { |
522 | + | // initialize this stuff before using it, OK? |
523 | + | sprintf( painCave.errMsg, |
524 | + | "Trying to check cutoffs without a box.\n" |
525 | + | "\tOOPSE should have better programmers than that.\n" ); |
526 | + | painCave.isFatal = 1; |
527 | + | simError(); |
528 | + | } |
529 | + | |
530 | + | } |
531 | + | |
532 | + | void SimInfo::addProperty(GenericData* prop){ |
533 | + | |
534 | + | map<string, GenericData*>::iterator result; |
535 | + | result = properties.find(prop->getID()); |
536 | + | |
537 | + | //we can't simply use properties[prop->getID()] = prop, |
538 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
539 | + | |
540 | + | if(result != properties.end()){ |
541 | + | |
542 | + | delete (*result).second; |
543 | + | (*result).second = prop; |
544 | + | |
545 | + | } |
546 | + | else{ |
547 | + | |
548 | + | properties[prop->getID()] = prop; |
549 | + | |
550 | + | } |
551 | + | |
552 | + | } |
553 | + | |
554 | + | GenericData* SimInfo::getProperty(const string& propName){ |
555 | + | |
556 | + | map<string, GenericData*>::iterator result; |
557 | + | |
558 | + | //string lowerCaseName = (); |
559 | + | |
560 | + | result = properties.find(propName); |
561 | + | |
562 | + | if(result != properties.end()) |
563 | + | return (*result).second; |
564 | + | else |
565 | + | return NULL; |
566 | + | } |
567 | + | |
568 | + | |
569 | + | void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
570 | + | vector<int>& groupList, vector<int>& groupStart){ |
571 | + | Molecule* myMols; |
572 | + | Atom** myAtoms; |
573 | + | int numAtom; |
574 | + | int curIndex; |
575 | + | double mtot; |
576 | + | int numMol; |
577 | + | int numCutoffGroups; |
578 | + | CutoffGroup* myCutoffGroup; |
579 | + | vector<CutoffGroup*>::iterator iterCutoff; |
580 | + | Atom* cutoffAtom; |
581 | + | vector<Atom*>::iterator iterAtom; |
582 | + | int atomIndex; |
583 | + | double totalMass; |
584 | + | |
585 | + | mfact.clear(); |
586 | + | groupList.clear(); |
587 | + | groupStart.clear(); |
588 | + | |
589 | + | //Be careful, fortran array begin at 1 |
590 | + | curIndex = 1; |
591 | + | |
592 | + | myMols = info->molecules; |
593 | + | numMol = info->n_mol; |
594 | + | for(int i = 0; i < numMol; i++){ |
595 | + | numCutoffGroups = myMols[i].getNCutoffGroups(); |
596 | + | for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
597 | + | myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
598 | + | |
599 | + | totalMass = myCutoffGroup->getMass(); |
600 | + | |
601 | + | for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
602 | + | cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
603 | + | mfact.push_back(cutoffAtom->getMass()/totalMass); |
604 | + | groupList.push_back(cutoffAtom->getIndex() + 1); |
605 | + | } |
606 | + | |
607 | + | groupStart.push_back(curIndex); |
608 | + | curIndex += myCutoffGroup->getNumAtom(); |
609 | + | |
610 | + | }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) |
611 | + | |
612 | + | }//end for(int i = 0; i < numMol; i++) |
613 | + | |
614 | + | |
615 | + | //The last cutoff group need more element to indicate the end of the cutoff |
616 | + | groupStart.push_back(curIndex); |
617 | + | ngroup = groupStart.size() - 1; |
618 | + | } |
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