| 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 |
| 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(){ |
| 47 |
|
} |
| 48 |
|
|
| 49 |
|
void SimInfo::setBox(double newBox[3]) { |
| 50 |
< |
double smallestBox, maxCutoff; |
| 51 |
< |
int status; |
| 52 |
< |
box_x = newBox[0]; |
| 45 |
< |
box_y = newBox[1]; |
| 46 |
< |
box_z = newBox[2]; |
| 47 |
< |
setFortranBoxSize(newBox); |
| 50 |
> |
|
| 51 |
> |
int i; |
| 52 |
> |
double tempMat[9]; |
| 53 |
|
|
| 54 |
< |
smallestBox = box_x; |
| 50 |
< |
if (box_y < smallestBox) smallestBox = box_y; |
| 51 |
< |
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", |
| 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 |
|
|
| 341 |
|
fInfo.rt = 0.0; |
| 342 |
|
fInfo.dielect = 0.0; |
| 343 |
|
|
| 142 |
– |
fInfo.box[0] = box_x; |
| 143 |
– |
fInfo.box[1] = box_y; |
| 144 |
– |
fInfo.box[2] = box_z; |
| 145 |
– |
|
| 344 |
|
fInfo.rlist = rList; |
| 345 |
|
fInfo.rcut = rCut; |
| 346 |
|
|
