| 191 |
|
if (!initialized_) initialize(); |
| 192 |
|
|
| 193 |
|
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
| 194 |
< |
StickyInteractionData mixer = MixingMap[key]; |
| 195 |
< |
|
| 196 |
< |
RealType w0 = mixer.w0; |
| 197 |
< |
RealType v0 = mixer.v0; |
| 198 |
< |
RealType v0p = mixer.v0p; |
| 199 |
< |
RealType rl = mixer.rl; |
| 200 |
< |
RealType ru = mixer.ru; |
| 201 |
< |
RealType rlp = mixer.rlp; |
| 202 |
< |
RealType rup = mixer.rup; |
| 203 |
< |
RealType rbig = mixer.rbig; |
| 204 |
< |
bool isPower = mixer.isPower; |
| 205 |
< |
|
| 206 |
< |
if (idat.rij <= rbig) { |
| 207 |
< |
|
| 208 |
< |
RealType r3 = idat.r2 * idat.rij; |
| 209 |
< |
RealType r5 = r3 * idat.r2; |
| 210 |
< |
|
| 211 |
< |
RotMat3x3d A1trans = idat.A1.transpose(); |
| 212 |
< |
RotMat3x3d A2trans = idat.A2.transpose(); |
| 213 |
< |
|
| 214 |
< |
// rotate the inter-particle separation into the two different |
| 215 |
< |
// body-fixed coordinate systems: |
| 216 |
< |
|
| 217 |
< |
Vector3d ri = idat.A1 * idat.d; |
| 218 |
< |
|
| 219 |
< |
// negative sign because this is the vector from j to i: |
| 220 |
< |
|
| 221 |
< |
Vector3d rj = - idat.A2 * idat.d; |
| 222 |
< |
|
| 223 |
< |
RealType xi = ri.x(); |
| 224 |
< |
RealType yi = ri.y(); |
| 225 |
< |
RealType zi = ri.z(); |
| 226 |
< |
|
| 227 |
< |
RealType xj = rj.x(); |
| 228 |
< |
RealType yj = rj.y(); |
| 229 |
< |
RealType zj = rj.z(); |
| 230 |
< |
|
| 231 |
< |
RealType xi2 = xi * xi; |
| 232 |
< |
RealType yi2 = yi * yi; |
| 233 |
< |
RealType zi2 = zi * zi; |
| 234 |
< |
|
| 235 |
< |
RealType xj2 = xj * xj; |
| 236 |
< |
RealType yj2 = yj * yj; |
| 237 |
< |
RealType zj2 = zj * zj; |
| 238 |
< |
|
| 239 |
< |
// calculate the switching info. from the splines |
| 240 |
< |
|
| 241 |
< |
RealType s = 0.0; |
| 242 |
< |
RealType dsdr = 0.0; |
| 243 |
< |
RealType sp = 0.0; |
| 244 |
< |
RealType dspdr = 0.0; |
| 245 |
< |
|
| 246 |
< |
if (idat.rij < ru) { |
| 247 |
< |
if (idat.rij < rl) { |
| 248 |
< |
s = 1.0; |
| 249 |
< |
dsdr = 0.0; |
| 250 |
< |
} else { |
| 251 |
< |
// we are in the switching region |
| 252 |
< |
|
| 253 |
< |
pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(idat.rij); |
| 254 |
< |
s = res.first; |
| 255 |
< |
dsdr = res.second; |
| 256 |
< |
} |
| 257 |
< |
} |
| 258 |
< |
|
| 259 |
< |
if (idat.rij < rup) { |
| 260 |
< |
if (idat.rij < rlp) { |
| 261 |
< |
sp = 1.0; |
| 262 |
< |
dspdr = 0.0; |
| 263 |
< |
} else { |
| 264 |
< |
// we are in the switching region |
| 265 |
< |
|
| 266 |
< |
pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt(idat.rij); |
| 267 |
< |
sp = res.first; |
| 268 |
< |
dspdr = res.second; |
| 269 |
< |
} |
| 270 |
< |
} |
| 271 |
< |
|
| 272 |
< |
RealType wi = 2.0*(xi2-yi2)*zi / r3; |
| 273 |
< |
RealType wj = 2.0*(xj2-yj2)*zj / r3; |
| 274 |
< |
RealType w = wi+wj; |
| 275 |
< |
|
| 276 |
< |
|
| 277 |
< |
RealType zif = zi/idat.rij - 0.6; |
| 278 |
< |
RealType zis = zi/idat.rij + 0.8; |
| 279 |
< |
|
| 280 |
< |
RealType zjf = zj/idat.rij - 0.6; |
| 281 |
< |
RealType zjs = zj/idat.rij + 0.8; |
| 282 |
< |
|
| 283 |
< |
RealType wip = zif*zif*zis*zis - w0; |
| 284 |
< |
RealType wjp = zjf*zjf*zjs*zjs - w0; |
| 285 |
< |
RealType wp = wip + wjp; |
| 194 |
> |
map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it; |
| 195 |
> |
it = MixingMap.find(key); |
| 196 |
> |
if (it != MixingMap.end()) { |
| 197 |
|
|
| 198 |
< |
Vector3d dwi(4.0*xi*zi/r3 - 6.0*xi*zi*(xi2-yi2)/r5, |
| 288 |
< |
- 4.0*yi*zi/r3 - 6.0*yi*zi*(xi2-yi2)/r5, |
| 289 |
< |
2.0*(xi2-yi2)/r3 - 6.0*zi2*(xi2-yi2)/r5); |
| 198 |
> |
StickyInteractionData mixer = (*it).second; |
| 199 |
|
|
| 200 |
< |
Vector3d dwj(4.0*xj*zj/r3 - 6.0*xj*zj*(xj2-yj2)/r5, |
| 201 |
< |
- 4.0*yj*zj/r3 - 6.0*yj*zj*(xj2-yj2)/r5, |
| 202 |
< |
2.0*(xj2-yj2)/r3 - 6.0*zj2*(xj2-yj2)/r5); |
| 203 |
< |
|
| 204 |
< |
RealType uglyi = zif*zif*zis + zif*zis*zis; |
| 205 |
< |
RealType uglyj = zjf*zjf*zjs + zjf*zjs*zjs; |
| 206 |
< |
|
| 207 |
< |
Vector3d dwip(-2.0*xi*zi*uglyi/r3, |
| 208 |
< |
-2.0*yi*zi*uglyi/r3, |
| 300 |
< |
2.0*(1.0/idat.rij - zi2/r3)*uglyi); |
| 301 |
< |
|
| 302 |
< |
Vector3d dwjp(-2.0*xj*zj*uglyj/r3, |
| 303 |
< |
-2.0*yj*zj*uglyj/r3, |
| 304 |
< |
2.0*(1.0/idat.rij - zj2/r3)*uglyj); |
| 305 |
< |
|
| 306 |
< |
Vector3d dwidu(4.0*(yi*zi2 + 0.5*yi*(xi2-yi2))/r3, |
| 307 |
< |
4.0*(xi*zi2 - 0.5*xi*(xi2-yi2))/r3, |
| 308 |
< |
- 8.0*xi*yi*zi/r3); |
| 309 |
< |
|
| 310 |
< |
Vector3d dwjdu(4.0*(yj*zj2 + 0.5*yj*(xj2-yj2))/r3, |
| 311 |
< |
4.0*(xj*zj2 - 0.5*xj*(xj2-yj2))/r3, |
| 312 |
< |
- 8.0*xj*yj*zj/r3); |
| 200 |
> |
RealType w0 = mixer.w0; |
| 201 |
> |
RealType v0 = mixer.v0; |
| 202 |
> |
RealType v0p = mixer.v0p; |
| 203 |
> |
RealType rl = mixer.rl; |
| 204 |
> |
RealType ru = mixer.ru; |
| 205 |
> |
RealType rlp = mixer.rlp; |
| 206 |
> |
RealType rup = mixer.rup; |
| 207 |
> |
RealType rbig = mixer.rbig; |
| 208 |
> |
bool isPower = mixer.isPower; |
| 209 |
|
|
| 210 |
< |
Vector3d dwipdu(2.0*yi*uglyi/idat.rij, |
| 211 |
< |
-2.0*xi*uglyi/idat.rij, |
| 212 |
< |
0.0); |
| 213 |
< |
|
| 214 |
< |
Vector3d dwjpdu(2.0*yj*uglyj/idat.rij, |
| 215 |
< |
-2.0*xj*uglyj/idat.rij, |
| 216 |
< |
0.0); |
| 210 |
> |
if (idat.rij <= rbig) { |
| 211 |
> |
|
| 212 |
> |
RealType r3 = idat.r2 * idat.rij; |
| 213 |
> |
RealType r5 = r3 * idat.r2; |
| 214 |
> |
|
| 215 |
> |
RotMat3x3d A1trans = idat.A1.transpose(); |
| 216 |
> |
RotMat3x3d A2trans = idat.A2.transpose(); |
| 217 |
> |
|
| 218 |
> |
// rotate the inter-particle separation into the two different |
| 219 |
> |
// body-fixed coordinate systems: |
| 220 |
> |
|
| 221 |
> |
Vector3d ri = idat.A1 * idat.d; |
| 222 |
> |
|
| 223 |
> |
// negative sign because this is the vector from j to i: |
| 224 |
> |
|
| 225 |
> |
Vector3d rj = - idat.A2 * idat.d; |
| 226 |
> |
|
| 227 |
> |
RealType xi = ri.x(); |
| 228 |
> |
RealType yi = ri.y(); |
| 229 |
> |
RealType zi = ri.z(); |
| 230 |
> |
|
| 231 |
> |
RealType xj = rj.x(); |
| 232 |
> |
RealType yj = rj.y(); |
| 233 |
> |
RealType zj = rj.z(); |
| 234 |
> |
|
| 235 |
> |
RealType xi2 = xi * xi; |
| 236 |
> |
RealType yi2 = yi * yi; |
| 237 |
> |
RealType zi2 = zi * zi; |
| 238 |
> |
|
| 239 |
> |
RealType xj2 = xj * xj; |
| 240 |
> |
RealType yj2 = yj * yj; |
| 241 |
> |
RealType zj2 = zj * zj; |
| 242 |
> |
|
| 243 |
> |
// calculate the switching info. from the splines |
| 244 |
> |
|
| 245 |
> |
RealType s = 0.0; |
| 246 |
> |
RealType dsdr = 0.0; |
| 247 |
> |
RealType sp = 0.0; |
| 248 |
> |
RealType dspdr = 0.0; |
| 249 |
> |
|
| 250 |
> |
if (idat.rij < ru) { |
| 251 |
> |
if (idat.rij < rl) { |
| 252 |
> |
s = 1.0; |
| 253 |
> |
dsdr = 0.0; |
| 254 |
> |
} else { |
| 255 |
> |
// we are in the switching region |
| 256 |
> |
|
| 257 |
> |
pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(idat.rij); |
| 258 |
> |
s = res.first; |
| 259 |
> |
dsdr = res.second; |
| 260 |
> |
} |
| 261 |
> |
} |
| 262 |
> |
|
| 263 |
> |
if (idat.rij < rup) { |
| 264 |
> |
if (idat.rij < rlp) { |
| 265 |
> |
sp = 1.0; |
| 266 |
> |
dspdr = 0.0; |
| 267 |
> |
} else { |
| 268 |
> |
// we are in the switching region |
| 269 |
> |
|
| 270 |
> |
pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt(idat.rij); |
| 271 |
> |
sp = res.first; |
| 272 |
> |
dspdr = res.second; |
| 273 |
> |
} |
| 274 |
> |
} |
| 275 |
> |
|
| 276 |
> |
RealType wi = 2.0*(xi2-yi2)*zi / r3; |
| 277 |
> |
RealType wj = 2.0*(xj2-yj2)*zj / r3; |
| 278 |
> |
RealType w = wi+wj; |
| 279 |
> |
|
| 280 |
> |
|
| 281 |
> |
RealType zif = zi/idat.rij - 0.6; |
| 282 |
> |
RealType zis = zi/idat.rij + 0.8; |
| 283 |
> |
|
| 284 |
> |
RealType zjf = zj/idat.rij - 0.6; |
| 285 |
> |
RealType zjs = zj/idat.rij + 0.8; |
| 286 |
> |
|
| 287 |
> |
RealType wip = zif*zif*zis*zis - w0; |
| 288 |
> |
RealType wjp = zjf*zjf*zjs*zjs - w0; |
| 289 |
> |
RealType wp = wip + wjp; |
| 290 |
> |
|
| 291 |
> |
Vector3d dwi(4.0*xi*zi/r3 - 6.0*xi*zi*(xi2-yi2)/r5, |
| 292 |
> |
- 4.0*yi*zi/r3 - 6.0*yi*zi*(xi2-yi2)/r5, |
| 293 |
> |
2.0*(xi2-yi2)/r3 - 6.0*zi2*(xi2-yi2)/r5); |
| 294 |
> |
|
| 295 |
> |
Vector3d dwj(4.0*xj*zj/r3 - 6.0*xj*zj*(xj2-yj2)/r5, |
| 296 |
> |
- 4.0*yj*zj/r3 - 6.0*yj*zj*(xj2-yj2)/r5, |
| 297 |
> |
2.0*(xj2-yj2)/r3 - 6.0*zj2*(xj2-yj2)/r5); |
| 298 |
> |
|
| 299 |
> |
RealType uglyi = zif*zif*zis + zif*zis*zis; |
| 300 |
> |
RealType uglyj = zjf*zjf*zjs + zjf*zjs*zjs; |
| 301 |
|
|
| 302 |
< |
if (isPower) { |
| 303 |
< |
RealType frac1 = 0.25; |
| 304 |
< |
RealType frac2 = 0.75; |
| 305 |
< |
RealType wi2 = wi*wi; |
| 306 |
< |
RealType wj2 = wj*wj; |
| 307 |
< |
// sticky power has no w' function: |
| 308 |
< |
w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p; |
| 309 |
< |
wp = 0.0; |
| 310 |
< |
dwi = frac1*3.0*wi2*dwi + frac2*dwi; |
| 311 |
< |
dwj = frac1*3.0*wj2*dwi + frac2*dwi; |
| 312 |
< |
dwip = V3Zero; |
| 313 |
< |
dwjp = V3Zero; |
| 314 |
< |
dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu; |
| 315 |
< |
dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu; |
| 316 |
< |
dwipdu = V3Zero; |
| 317 |
< |
dwjpdu = V3Zero; |
| 318 |
< |
sp = 0.0; |
| 319 |
< |
dspdr = 0.0; |
| 302 |
> |
Vector3d dwip(-2.0*xi*zi*uglyi/r3, |
| 303 |
> |
-2.0*yi*zi*uglyi/r3, |
| 304 |
> |
2.0*(1.0/idat.rij - zi2/r3)*uglyi); |
| 305 |
> |
|
| 306 |
> |
Vector3d dwjp(-2.0*xj*zj*uglyj/r3, |
| 307 |
> |
-2.0*yj*zj*uglyj/r3, |
| 308 |
> |
2.0*(1.0/idat.rij - zj2/r3)*uglyj); |
| 309 |
> |
|
| 310 |
> |
Vector3d dwidu(4.0*(yi*zi2 + 0.5*yi*(xi2-yi2))/r3, |
| 311 |
> |
4.0*(xi*zi2 - 0.5*xi*(xi2-yi2))/r3, |
| 312 |
> |
- 8.0*xi*yi*zi/r3); |
| 313 |
> |
|
| 314 |
> |
Vector3d dwjdu(4.0*(yj*zj2 + 0.5*yj*(xj2-yj2))/r3, |
| 315 |
> |
4.0*(xj*zj2 - 0.5*xj*(xj2-yj2))/r3, |
| 316 |
> |
- 8.0*xj*yj*zj/r3); |
| 317 |
> |
|
| 318 |
> |
Vector3d dwipdu(2.0*yi*uglyi/idat.rij, |
| 319 |
> |
-2.0*xi*uglyi/idat.rij, |
| 320 |
> |
0.0); |
| 321 |
> |
|
| 322 |
> |
Vector3d dwjpdu(2.0*yj*uglyj/idat.rij, |
| 323 |
> |
-2.0*xj*uglyj/idat.rij, |
| 324 |
> |
0.0); |
| 325 |
> |
|
| 326 |
> |
if (isPower) { |
| 327 |
> |
RealType frac1 = 0.25; |
| 328 |
> |
RealType frac2 = 0.75; |
| 329 |
> |
RealType wi2 = wi*wi; |
| 330 |
> |
RealType wj2 = wj*wj; |
| 331 |
> |
// sticky power has no w' function: |
| 332 |
> |
w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p; |
| 333 |
> |
wp = 0.0; |
| 334 |
> |
dwi = frac1*3.0*wi2*dwi + frac2*dwi; |
| 335 |
> |
dwj = frac1*3.0*wj2*dwi + frac2*dwi; |
| 336 |
> |
dwip = V3Zero; |
| 337 |
> |
dwjp = V3Zero; |
| 338 |
> |
dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu; |
| 339 |
> |
dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu; |
| 340 |
> |
dwipdu = V3Zero; |
| 341 |
> |
dwjpdu = V3Zero; |
| 342 |
> |
sp = 0.0; |
| 343 |
> |
dspdr = 0.0; |
| 344 |
> |
} |
| 345 |
> |
|
| 346 |
> |
idat.vpair += 0.5*(v0*s*w + v0p*sp*wp); |
| 347 |
> |
idat.pot += 0.5*(v0*s*w + v0p*sp*wp)*idat.sw; |
| 348 |
> |
|
| 349 |
> |
// do the torques first since they are easy: |
| 350 |
> |
// remember that these are still in the body-fixed axes |
| 351 |
> |
|
| 352 |
> |
Vector3d ti = 0.5*idat.sw*(v0*s*dwidu + v0p*sp*dwipdu); |
| 353 |
> |
Vector3d tj = 0.5*idat.sw*(v0*s*dwjdu + v0p*sp*dwjpdu); |
| 354 |
> |
|
| 355 |
> |
// go back to lab frame using transpose of rotation matrix: |
| 356 |
> |
|
| 357 |
> |
idat.t1 += A1trans * ti; |
| 358 |
> |
idat.t2 += A2trans * tj; |
| 359 |
> |
|
| 360 |
> |
// Now, on to the forces: |
| 361 |
> |
|
| 362 |
> |
// first rotate the i terms back into the lab frame: |
| 363 |
> |
|
| 364 |
> |
Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * idat.sw; |
| 365 |
> |
Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * idat.sw; |
| 366 |
> |
|
| 367 |
> |
Vector3d fii = A1trans * radcomi; |
| 368 |
> |
Vector3d fjj = A2trans * radcomj; |
| 369 |
> |
|
| 370 |
> |
// now assemble these with the radial-only terms: |
| 371 |
> |
|
| 372 |
> |
idat.f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * idat.d / |
| 373 |
> |
idat.rij + fii - fjj); |
| 374 |
> |
|
| 375 |
|
} |
| 341 |
– |
|
| 342 |
– |
idat.vpair += 0.5*(v0*s*w + v0p*sp*wp); |
| 343 |
– |
idat.pot += 0.5*(v0*s*w + v0p*sp*wp)*idat.sw; |
| 344 |
– |
|
| 345 |
– |
// do the torques first since they are easy: |
| 346 |
– |
// remember that these are still in the body-fixed axes |
| 347 |
– |
|
| 348 |
– |
Vector3d ti = 0.5*idat.sw*(v0*s*dwidu + v0p*sp*dwipdu); |
| 349 |
– |
Vector3d tj = 0.5*idat.sw*(v0*s*dwjdu + v0p*sp*dwjpdu); |
| 350 |
– |
|
| 351 |
– |
// go back to lab frame using transpose of rotation matrix: |
| 352 |
– |
|
| 353 |
– |
idat.t1 += A1trans * ti; |
| 354 |
– |
idat.t2 += A2trans * tj; |
| 355 |
– |
|
| 356 |
– |
// Now, on to the forces: |
| 357 |
– |
|
| 358 |
– |
// first rotate the i terms back into the lab frame: |
| 359 |
– |
|
| 360 |
– |
Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * idat.sw; |
| 361 |
– |
Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * idat.sw; |
| 362 |
– |
|
| 363 |
– |
Vector3d fii = A1trans * radcomi; |
| 364 |
– |
Vector3d fjj = A2trans * radcomj; |
| 365 |
– |
|
| 366 |
– |
// now assemble these with the radial-only terms: |
| 367 |
– |
|
| 368 |
– |
idat.f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * idat.d / |
| 369 |
– |
idat.rij + fii - fjj); |
| 370 |
– |
|
| 376 |
|
} |
| 372 |
– |
|
| 373 |
– |
return; |
| 377 |
|
|
| 378 |
+ |
return; |
| 379 |
|
} |
| 380 |
+ |
|
| 381 |
+ |
RealType Sticky::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 382 |
+ |
if (!initialized_) initialize(); |
| 383 |
+ |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 384 |
+ |
map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it; |
| 385 |
+ |
it = MixingMap.find(key); |
| 386 |
+ |
if (it == MixingMap.end()) |
| 387 |
+ |
return 0.0; |
| 388 |
+ |
else { |
| 389 |
+ |
StickyInteractionData mixer = (*it).second; |
| 390 |
+ |
return mixer.rbig; |
| 391 |
+ |
} |
| 392 |
+ |
} |
| 393 |
|
} |
