| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
#include <stdio.h> |
| 44 |
#include <string.h> |
| 45 |
|
| 46 |
#include <cmath> |
| 47 |
#include "nonbonded/Sticky.hpp" |
| 48 |
#include "nonbonded/LJ.hpp" |
| 49 |
#include "utils/simError.h" |
| 50 |
|
| 51 |
using namespace std; |
| 52 |
namespace OpenMD { |
| 53 |
|
| 54 |
Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {} |
| 55 |
|
| 56 |
StickyParam Sticky::getStickyParam(AtomType* atomType) { |
| 57 |
|
| 58 |
// Do sanity checking on the AtomType we were passed before |
| 59 |
// building any data structures: |
| 60 |
if (!atomType->isSticky() && !atomType->isStickyPower()) { |
| 61 |
sprintf( painCave.errMsg, |
| 62 |
"Sticky::getStickyParam was passed an atomType (%s) that does\n" |
| 63 |
"\tnot appear to be a Sticky atom.\n", |
| 64 |
atomType->getName().c_str()); |
| 65 |
painCave.severity = OPENMD_ERROR; |
| 66 |
painCave.isFatal = 1; |
| 67 |
simError(); |
| 68 |
} |
| 69 |
|
| 70 |
DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 71 |
GenericData* data = daType->getPropertyByName("Sticky"); |
| 72 |
if (data == NULL) { |
| 73 |
sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n" |
| 74 |
"\tSticky parameters for atomType %s.\n", |
| 75 |
daType->getName().c_str()); |
| 76 |
painCave.severity = OPENMD_ERROR; |
| 77 |
painCave.isFatal = 1; |
| 78 |
simError(); |
| 79 |
} |
| 80 |
|
| 81 |
StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data); |
| 82 |
if (stickyData == NULL) { |
| 83 |
sprintf( painCave.errMsg, |
| 84 |
"Sticky::getStickyParam could not convert GenericData to\n" |
| 85 |
"\tStickyParamGenericData for atom type %s\n", |
| 86 |
daType->getName().c_str()); |
| 87 |
painCave.severity = OPENMD_ERROR; |
| 88 |
painCave.isFatal = 1; |
| 89 |
simError(); |
| 90 |
} |
| 91 |
|
| 92 |
return stickyData->getData(); |
| 93 |
} |
| 94 |
|
| 95 |
void Sticky::initialize() { |
| 96 |
|
| 97 |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 98 |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 99 |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 100 |
AtomType* at; |
| 101 |
|
| 102 |
// Sticky handles all of the Sticky-Sticky interactions |
| 103 |
|
| 104 |
for (at = atomTypes->beginType(i); at != NULL; |
| 105 |
at = atomTypes->nextType(i)) { |
| 106 |
|
| 107 |
if (at->isSticky() || at->isStickyPower()) |
| 108 |
addType(at); |
| 109 |
} |
| 110 |
|
| 111 |
initialized_ = true; |
| 112 |
} |
| 113 |
|
| 114 |
void Sticky::addType(AtomType* atomType){ |
| 115 |
// add it to the map: |
| 116 |
AtomTypeProperties atp = atomType->getATP(); |
| 117 |
|
| 118 |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 119 |
ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 120 |
if (ret.second == false) { |
| 121 |
sprintf( painCave.errMsg, |
| 122 |
"Sticky already had a previous entry with ident %d\n", |
| 123 |
atp.ident); |
| 124 |
painCave.severity = OPENMD_INFO; |
| 125 |
painCave.isFatal = 0; |
| 126 |
simError(); |
| 127 |
} |
| 128 |
|
| 129 |
RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi; |
| 130 |
|
| 131 |
StickyParam sticky1 = getStickyParam(atomType); |
| 132 |
|
| 133 |
// Now, iterate over all known types and add to the mixing map: |
| 134 |
|
| 135 |
map<int, AtomType*>::iterator it; |
| 136 |
for( it = StickyMap.begin(); it != StickyMap.end(); ++it) { |
| 137 |
|
| 138 |
AtomType* atype2 = (*it).second; |
| 139 |
|
| 140 |
StickyParam sticky2 = getStickyParam(atype2); |
| 141 |
|
| 142 |
StickyInteractionData mixer; |
| 143 |
|
| 144 |
// Mixing two different sticky types is silly, but if you want 2 |
| 145 |
// sticky types in your simulation, we'll let you do it with the |
| 146 |
// Lorentz- Berthelot mixing rules (which happen to do the right thing |
| 147 |
// when atomType and atype2 happen to be the same. |
| 148 |
|
| 149 |
mixer.rl = 0.5 * ( sticky1.rl + sticky2.rl ); |
| 150 |
mixer.ru = 0.5 * ( sticky1.ru + sticky2.ru ); |
| 151 |
mixer.rlp = 0.5 * ( sticky1.rlp + sticky2.rlp ); |
| 152 |
mixer.rup = 0.5 * ( sticky1.rup + sticky2.rup ); |
| 153 |
mixer.rbig = max(mixer.ru, mixer.rup); |
| 154 |
mixer.w0 = sqrt( sticky1.w0 * sticky2.w0 ); |
| 155 |
mixer.v0 = sqrt( sticky1.v0 * sticky2.v0 ); |
| 156 |
mixer.v0p = sqrt( sticky1.v0p * sticky2.v0p ); |
| 157 |
mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower(); |
| 158 |
|
| 159 |
CubicSpline* s = new CubicSpline(); |
| 160 |
s->addPoint(mixer.rl, 1.0); |
| 161 |
s->addPoint(mixer.ru, 0.0); |
| 162 |
mixer.s = s; |
| 163 |
|
| 164 |
CubicSpline* sp = new CubicSpline(); |
| 165 |
sp->addPoint(mixer.rlp, 1.0); |
| 166 |
sp->addPoint(mixer.rup, 0.0); |
| 167 |
mixer.sp = sp; |
| 168 |
|
| 169 |
|
| 170 |
pair<AtomType*, AtomType*> key1, key2; |
| 171 |
key1 = make_pair(atomType, atype2); |
| 172 |
key2 = make_pair(atype2, atomType); |
| 173 |
|
| 174 |
MixingMap[key1] = mixer; |
| 175 |
if (key2 != key1) { |
| 176 |
MixingMap[key2] = mixer; |
| 177 |
} |
| 178 |
} |
| 179 |
} |
| 180 |
|
| 181 |
/** |
| 182 |
* This function does the sticky portion of the SSD potential |
| 183 |
* [Chandra and Ichiye, Journal of Chemical Physics 111, 2701 |
| 184 |
* (1999)]. The Lennard-Jones and dipolar interaction must be |
| 185 |
* handled separately. We assume that the rotation matrices have |
| 186 |
* already been calculated and placed in the A1 & A2 entries in the |
| 187 |
* idat structure. |
| 188 |
*/ |
| 189 |
|
| 190 |
void Sticky::calcForce(InteractionData &idat) { |
| 191 |
|
| 192 |
if (!initialized_) initialize(); |
| 193 |
|
| 194 |
map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it; |
| 195 |
it = MixingMap.find(idat.atypes); |
| 196 |
if (it != MixingMap.end()) { |
| 197 |
|
| 198 |
StickyInteractionData mixer = (*it).second; |
| 199 |
|
| 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 |
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 |
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*RealType(3.0)*wi2*dwi + frac2*dwi; |
| 335 |
dwj = frac1*RealType(3.0)*wj2*dwi + frac2*dwi; |
| 336 |
dwip = V3Zero; |
| 337 |
dwjp = V3Zero; |
| 338 |
dwidu = frac1*RealType(3.0)*wi2*dwidu + frac2*dwidu; |
| 339 |
dwidu = frac1*RealType(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) += RealType(0.5)*(v0*s*w + v0p*sp*wp); |
| 347 |
(*(idat.pot))[HYDROGENBONDING_FAMILY] += RealType(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 = RealType(0.5)* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu); |
| 353 |
Vector3d tj = RealType(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) += RealType(0.5) * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) / |
| 373 |
*(idat.rij) + fii - fjj); |
| 374 |
|
| 375 |
} |
| 376 |
} |
| 377 |
|
| 378 |
return; |
| 379 |
} |
| 380 |
|
| 381 |
RealType Sticky::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 382 |
if (!initialized_) initialize(); |
| 383 |
map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it; |
| 384 |
it = MixingMap.find(atypes); |
| 385 |
if (it == MixingMap.end()) |
| 386 |
return 0.0; |
| 387 |
else { |
| 388 |
StickyInteractionData mixer = (*it).second; |
| 389 |
return mixer.rbig; |
| 390 |
} |
| 391 |
} |
| 392 |
} |
