| 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] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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> |
| 46 |
|
#include <cmath> |
| 47 |
|
#include "nonbonded/Sticky.hpp" |
| 48 |
|
#include "nonbonded/LJ.hpp" |
| 49 |
+ |
#include "types/StickyAdapter.hpp" |
| 50 |
|
#include "utils/simError.h" |
| 51 |
|
|
| 52 |
|
using namespace std; |
| 53 |
|
namespace OpenMD { |
| 52 |
– |
|
| 53 |
– |
bool Sticky::initialized_ = false; |
| 54 |
– |
ForceField* Sticky::forceField_ = NULL; |
| 55 |
– |
map<int, AtomType*> Sticky::StickyMap; |
| 56 |
– |
map<pair<AtomType*, AtomType*>, StickyInteractionData> Sticky::MixingMap; |
| 54 |
|
|
| 55 |
< |
Sticky* Sticky::_instance = NULL; |
| 59 |
< |
|
| 60 |
< |
Sticky* Sticky::Instance() { |
| 61 |
< |
if (!_instance) { |
| 62 |
< |
_instance = new Sticky(); |
| 63 |
< |
} |
| 64 |
< |
return _instance; |
| 65 |
< |
} |
| 66 |
< |
|
| 67 |
< |
StickyParam Sticky::getStickyParam(AtomType* atomType) { |
| 55 |
> |
Sticky::Sticky() : initialized_(false), forceField_(NULL), name_("Sticky") {} |
| 56 |
|
|
| 69 |
– |
// Do sanity checking on the AtomType we were passed before |
| 70 |
– |
// building any data structures: |
| 71 |
– |
if (!atomType->isSticky() && !atomType->isStickyPower()) { |
| 72 |
– |
sprintf( painCave.errMsg, |
| 73 |
– |
"Sticky::getStickyParam was passed an atomType (%s) that does\n" |
| 74 |
– |
"\tnot appear to be a Sticky atom.\n", |
| 75 |
– |
atomType->getName().c_str()); |
| 76 |
– |
painCave.severity = OPENMD_ERROR; |
| 77 |
– |
painCave.isFatal = 1; |
| 78 |
– |
simError(); |
| 79 |
– |
} |
| 80 |
– |
|
| 81 |
– |
DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 82 |
– |
GenericData* data = daType->getPropertyByName("Sticky"); |
| 83 |
– |
if (data == NULL) { |
| 84 |
– |
sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n" |
| 85 |
– |
"\tSticky parameters for atomType %s.\n", |
| 86 |
– |
daType->getName().c_str()); |
| 87 |
– |
painCave.severity = OPENMD_ERROR; |
| 88 |
– |
painCave.isFatal = 1; |
| 89 |
– |
simError(); |
| 90 |
– |
} |
| 91 |
– |
|
| 92 |
– |
StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data); |
| 93 |
– |
if (stickyData == NULL) { |
| 94 |
– |
sprintf( painCave.errMsg, |
| 95 |
– |
"Sticky::getStickyParam could not convert GenericData to\n" |
| 96 |
– |
"\tStickyParamGenericData for atom type %s\n", |
| 97 |
– |
daType->getName().c_str()); |
| 98 |
– |
painCave.severity = OPENMD_ERROR; |
| 99 |
– |
painCave.isFatal = 1; |
| 100 |
– |
simError(); |
| 101 |
– |
} |
| 102 |
– |
|
| 103 |
– |
return stickyData->getData(); |
| 104 |
– |
} |
| 105 |
– |
|
| 57 |
|
void Sticky::initialize() { |
| 58 |
< |
|
| 59 |
< |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 60 |
< |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 61 |
< |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 111 |
< |
AtomType* at; |
| 58 |
> |
Stypes.clear(); |
| 59 |
> |
Stids.clear(); |
| 60 |
> |
MixingMap.clear(); |
| 61 |
> |
nSticky_=0; |
| 62 |
|
|
| 63 |
+ |
Stids.resize( forceField_->getNAtomType(), -1); |
| 64 |
+ |
|
| 65 |
|
// Sticky handles all of the Sticky-Sticky interactions |
| 66 |
|
|
| 67 |
< |
for (at = atomTypes->beginType(i); at != NULL; |
| 68 |
< |
at = atomTypes->nextType(i)) { |
| 69 |
< |
|
| 118 |
< |
if (at->isSticky() || at->isStickyPower()) |
| 119 |
< |
addType(at); |
| 67 |
> |
set<AtomType*>::iterator at; |
| 68 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 69 |
> |
if ((*at)->isSticky()) nSticky_++; |
| 70 |
|
} |
| 71 |
+ |
|
| 72 |
+ |
MixingMap.resize(nSticky_); |
| 73 |
+ |
|
| 74 |
+ |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 75 |
+ |
if ((*at)->isSticky()) addType( *at ); |
| 76 |
+ |
} |
| 77 |
|
|
| 78 |
|
initialized_ = true; |
| 79 |
|
} |
| 80 |
|
|
| 81 |
|
void Sticky::addType(AtomType* atomType){ |
| 82 |
+ |
StickyAdapter sticky1 = StickyAdapter(atomType); |
| 83 |
+ |
|
| 84 |
|
// add it to the map: |
| 127 |
– |
AtomTypeProperties atp = atomType->getATP(); |
| 85 |
|
|
| 86 |
< |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 87 |
< |
ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 86 |
> |
int atid = atomType->getIdent(); |
| 87 |
> |
int stid = Stypes.size(); |
| 88 |
> |
|
| 89 |
> |
pair<set<int>::iterator,bool> ret; |
| 90 |
> |
ret = Stypes.insert( atid ); |
| 91 |
|
if (ret.second == false) { |
| 92 |
|
sprintf( painCave.errMsg, |
| 93 |
|
"Sticky already had a previous entry with ident %d\n", |
| 94 |
< |
atp.ident); |
| 94 |
> |
atid) ; |
| 95 |
|
painCave.severity = OPENMD_INFO; |
| 96 |
|
painCave.isFatal = 0; |
| 97 |
|
simError(); |
| 98 |
|
} |
| 139 |
– |
|
| 140 |
– |
RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi; |
| 141 |
– |
|
| 142 |
– |
StickyParam sticky1 = getStickyParam(atomType); |
| 99 |
|
|
| 100 |
+ |
Stids[atid] = stid; |
| 101 |
+ |
MixingMap[stid].resize( nSticky_ ); |
| 102 |
+ |
|
| 103 |
+ |
|
| 104 |
|
// Now, iterate over all known types and add to the mixing map: |
| 105 |
|
|
| 106 |
< |
map<int, AtomType*>::iterator it; |
| 107 |
< |
for( it = StickyMap.begin(); it != StickyMap.end(); ++it) { |
| 106 |
> |
std::set<int>::iterator it; |
| 107 |
> |
for( it = Stypes.begin(); it != Stypes.end(); ++it) { |
| 108 |
|
|
| 149 |
– |
AtomType* atype2 = (*it).second; |
| 150 |
– |
|
| 151 |
– |
StickyParam sticky2 = getStickyParam(atype2); |
| 109 |
|
|
| 110 |
+ |
int stid2 = Stids[ (*it) ]; |
| 111 |
+ |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 112 |
+ |
StickyAdapter sticky2 = StickyAdapter(atype2); |
| 113 |
+ |
|
| 114 |
|
StickyInteractionData mixer; |
| 115 |
|
|
| 116 |
|
// Mixing two different sticky types is silly, but if you want 2 |
| 118 |
|
// Lorentz- Berthelot mixing rules (which happen to do the right thing |
| 119 |
|
// when atomType and atype2 happen to be the same. |
| 120 |
|
|
| 121 |
< |
mixer.rl = 0.5 * ( sticky1.rl + sticky2.rl ); |
| 122 |
< |
mixer.ru = 0.5 * ( sticky1.ru + sticky2.ru ); |
| 123 |
< |
mixer.rlp = 0.5 * ( sticky1.rlp + sticky2.rlp ); |
| 124 |
< |
mixer.rup = 0.5 * ( sticky1.rup + sticky2.rup ); |
| 121 |
> |
mixer.rl = 0.5 * ( sticky1.getRl() + sticky2.getRl() ); |
| 122 |
> |
mixer.ru = 0.5 * ( sticky1.getRu() + sticky2.getRu() ); |
| 123 |
> |
mixer.rlp = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() ); |
| 124 |
> |
mixer.rup = 0.5 * ( sticky1.getRup() + sticky2.getRup() ); |
| 125 |
|
mixer.rbig = max(mixer.ru, mixer.rup); |
| 126 |
< |
mixer.w0 = sqrt( sticky1.w0 * sticky2.w0 ); |
| 127 |
< |
mixer.v0 = sqrt( sticky1.v0 * sticky2.v0 ); |
| 128 |
< |
mixer.v0p = sqrt( sticky1.v0p * sticky2.v0p ); |
| 129 |
< |
mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower(); |
| 126 |
> |
mixer.w0 = sqrt( sticky1.getW0() * sticky2.getW0() ); |
| 127 |
> |
mixer.v0 = sqrt( sticky1.getV0() * sticky2.getV0() ); |
| 128 |
> |
mixer.v0p = sqrt( sticky1.getV0p() * sticky2.getV0p() ); |
| 129 |
> |
mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower(); |
| 130 |
|
|
| 131 |
|
CubicSpline* s = new CubicSpline(); |
| 132 |
|
s->addPoint(mixer.rl, 1.0); |
| 138 |
|
sp->addPoint(mixer.rup, 0.0); |
| 139 |
|
mixer.sp = sp; |
| 140 |
|
|
| 141 |
< |
|
| 142 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 143 |
< |
key1 = make_pair(atomType, atype2); |
| 144 |
< |
key2 = make_pair(atype2, atomType); |
| 145 |
< |
|
| 185 |
< |
MixingMap[key1] = mixer; |
| 186 |
< |
if (key2 != key1) { |
| 187 |
< |
MixingMap[key2] = mixer; |
| 141 |
> |
MixingMap[stid2].resize( nSticky_ ); |
| 142 |
> |
|
| 143 |
> |
MixingMap[stid][stid2] = mixer; |
| 144 |
> |
if (stid2 != stid) { |
| 145 |
> |
MixingMap[stid2][stid] = mixer; |
| 146 |
|
} |
| 147 |
|
} |
| 148 |
|
} |
| 149 |
|
|
| 150 |
< |
RealType Sticky::getStickyCut(int atid) { |
| 150 |
> |
/** |
| 151 |
> |
* This function does the sticky portion of the SSD potential |
| 152 |
> |
* [Chandra and Ichiye, Journal of Chemical Physics 111, 2701 |
| 153 |
> |
* (1999)]. The Lennard-Jones and dipolar interaction must be |
| 154 |
> |
* handled separately. We assume that the rotation matrices have |
| 155 |
> |
* already been calculated and placed in the A1 & A2 entries in the |
| 156 |
> |
* idat structure. |
| 157 |
> |
*/ |
| 158 |
> |
|
| 159 |
> |
void Sticky::calcForce(InteractionData &idat) { |
| 160 |
> |
|
| 161 |
|
if (!initialized_) initialize(); |
| 194 |
– |
std::map<int, AtomType*> :: const_iterator it; |
| 195 |
– |
it = StickyMap.find(atid); |
| 196 |
– |
if (it == StickyMap.end()) { |
| 197 |
– |
sprintf( painCave.errMsg, |
| 198 |
– |
"Sticky::getStickyCut could not find atid %d in StickyMap\n", |
| 199 |
– |
(atid)); |
| 200 |
– |
painCave.severity = OPENMD_ERROR; |
| 201 |
– |
painCave.isFatal = 1; |
| 202 |
– |
simError(); |
| 203 |
– |
} |
| 204 |
– |
|
| 205 |
– |
AtomType* atype = it->second; |
| 206 |
– |
return MixingMap[make_pair(atype, atype)].rbig; |
| 207 |
– |
} |
| 208 |
– |
|
| 209 |
– |
|
| 210 |
– |
void Sticky::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
| 211 |
– |
RealType rij, RealType r2, RealType sw, |
| 212 |
– |
RealType &vpair, RealType &pot, |
| 213 |
– |
RotMat3x3d A1, RotMat3x3d A2, Vector3d &f1, |
| 214 |
– |
Vector3d &t1, Vector3d &t2) { |
| 215 |
– |
|
| 216 |
– |
// This routine does only the sticky portion of the SSD potential |
| 217 |
– |
// [Chandra and Ichiye, J. Chem. Phys. 111, 2701 (1999)]. |
| 218 |
– |
// The Lennard-Jones and dipolar interaction must be handled separately. |
| 162 |
|
|
| 163 |
< |
// We assume that the rotation matrices have already been calculated |
| 221 |
< |
// and placed in the A array. |
| 163 |
> |
StickyInteractionData &mixer = MixingMap[Stids[idat.atid1]][Stids[idat.atid2]]; |
| 164 |
|
|
| 223 |
– |
if (!initialized_) initialize(); |
| 224 |
– |
|
| 225 |
– |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 226 |
– |
StickyInteractionData mixer = MixingMap[key]; |
| 227 |
– |
|
| 165 |
|
RealType w0 = mixer.w0; |
| 166 |
|
RealType v0 = mixer.v0; |
| 167 |
|
RealType v0p = mixer.v0p; |
| 171 |
|
RealType rup = mixer.rup; |
| 172 |
|
RealType rbig = mixer.rbig; |
| 173 |
|
bool isPower = mixer.isPower; |
| 174 |
< |
|
| 175 |
< |
if (rij <= rbig) { |
| 176 |
< |
|
| 177 |
< |
RealType r3 = r2 * rij; |
| 178 |
< |
RealType r5 = r3 * r2; |
| 179 |
< |
|
| 180 |
< |
RotMat3x3d A1trans = A1.transpose(); |
| 181 |
< |
RotMat3x3d A2trans = A2.transpose(); |
| 182 |
< |
|
| 174 |
> |
|
| 175 |
> |
if ( *(idat.rij) <= rbig) { |
| 176 |
> |
|
| 177 |
> |
RealType r3 = *(idat.r2) * *(idat.rij); |
| 178 |
> |
RealType r5 = r3 * *(idat.r2); |
| 179 |
> |
|
| 180 |
> |
RotMat3x3d A1trans = idat.A1->transpose(); |
| 181 |
> |
RotMat3x3d A2trans = idat.A2->transpose(); |
| 182 |
> |
|
| 183 |
|
// rotate the inter-particle separation into the two different |
| 184 |
|
// body-fixed coordinate systems: |
| 185 |
< |
|
| 186 |
< |
Vector3d ri = A1 * d; |
| 187 |
< |
|
| 185 |
> |
|
| 186 |
> |
Vector3d ri = *(idat.A1) * *(idat.d); |
| 187 |
> |
|
| 188 |
|
// negative sign because this is the vector from j to i: |
| 189 |
< |
|
| 190 |
< |
Vector3d rj = -A2 * d; |
| 191 |
< |
|
| 189 |
> |
|
| 190 |
> |
Vector3d rj = - *(idat.A2) * *(idat.d); |
| 191 |
> |
|
| 192 |
|
RealType xi = ri.x(); |
| 193 |
|
RealType yi = ri.y(); |
| 194 |
|
RealType zi = ri.z(); |
| 195 |
< |
|
| 195 |
> |
|
| 196 |
|
RealType xj = rj.x(); |
| 197 |
|
RealType yj = rj.y(); |
| 198 |
|
RealType zj = rj.z(); |
| 199 |
< |
|
| 199 |
> |
|
| 200 |
|
RealType xi2 = xi * xi; |
| 201 |
|
RealType yi2 = yi * yi; |
| 202 |
|
RealType zi2 = zi * zi; |
| 203 |
< |
|
| 203 |
> |
|
| 204 |
|
RealType xj2 = xj * xj; |
| 205 |
|
RealType yj2 = yj * yj; |
| 206 |
|
RealType zj2 = zj * zj; |
| 207 |
< |
|
| 207 |
> |
|
| 208 |
|
// calculate the switching info. from the splines |
| 209 |
< |
|
| 209 |
> |
|
| 210 |
|
RealType s = 0.0; |
| 211 |
|
RealType dsdr = 0.0; |
| 212 |
|
RealType sp = 0.0; |
| 213 |
|
RealType dspdr = 0.0; |
| 214 |
< |
|
| 215 |
< |
if (rij < ru) { |
| 216 |
< |
if (rij < rl) { |
| 214 |
> |
|
| 215 |
> |
if ( *(idat.rij) < ru) { |
| 216 |
> |
if ( *(idat.rij) < rl) { |
| 217 |
|
s = 1.0; |
| 218 |
|
dsdr = 0.0; |
| 219 |
|
} else { |
| 220 |
< |
// we are in the switching region |
| 221 |
< |
|
| 285 |
< |
pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(rij); |
| 286 |
< |
s = res.first; |
| 287 |
< |
dsdr = res.second; |
| 220 |
> |
// we are in the switching region |
| 221 |
> |
mixer.s->getValueAndDerivativeAt(*(idat.rij), s, dsdr); |
| 222 |
|
} |
| 223 |
|
} |
| 224 |
< |
|
| 225 |
< |
if (rij < rup) { |
| 226 |
< |
if (rij < rlp) { |
| 224 |
> |
|
| 225 |
> |
if (*(idat.rij) < rup) { |
| 226 |
> |
if ( *(idat.rij) < rlp) { |
| 227 |
|
sp = 1.0; |
| 228 |
|
dspdr = 0.0; |
| 229 |
|
} else { |
| 230 |
< |
// we are in the switching region |
| 231 |
< |
|
| 298 |
< |
pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt(rij); |
| 299 |
< |
sp = res.first; |
| 300 |
< |
dspdr = res.second; |
| 230 |
> |
// we are in the switching region |
| 231 |
> |
mixer.sp->getValueAndDerivativeAt( *(idat.rij), sp, dspdr); |
| 232 |
|
} |
| 233 |
|
} |
| 234 |
< |
|
| 234 |
> |
|
| 235 |
> |
|
| 236 |
|
RealType wi = 2.0*(xi2-yi2)*zi / r3; |
| 237 |
|
RealType wj = 2.0*(xj2-yj2)*zj / r3; |
| 238 |
|
RealType w = wi+wj; |
| 239 |
< |
|
| 240 |
< |
|
| 241 |
< |
RealType zif = zi/rij - 0.6; |
| 242 |
< |
RealType zis = zi/rij + 0.8; |
| 243 |
< |
|
| 244 |
< |
RealType zjf = zj/rij - 0.6; |
| 245 |
< |
RealType zjs = zj/rij + 0.8; |
| 246 |
< |
|
| 239 |
> |
|
| 240 |
> |
|
| 241 |
> |
RealType zif = zi/ *(idat.rij) - 0.6; |
| 242 |
> |
RealType zis = zi/ *(idat.rij) + 0.8; |
| 243 |
> |
|
| 244 |
> |
RealType zjf = zj/ *(idat.rij) - 0.6; |
| 245 |
> |
RealType zjs = zj/ *(idat.rij) + 0.8; |
| 246 |
> |
|
| 247 |
|
RealType wip = zif*zif*zis*zis - w0; |
| 248 |
|
RealType wjp = zjf*zjf*zjs*zjs - w0; |
| 249 |
|
RealType wp = wip + wjp; |
| 250 |
< |
|
| 250 |
> |
|
| 251 |
|
Vector3d dwi(4.0*xi*zi/r3 - 6.0*xi*zi*(xi2-yi2)/r5, |
| 252 |
|
- 4.0*yi*zi/r3 - 6.0*yi*zi*(xi2-yi2)/r5, |
| 253 |
|
2.0*(xi2-yi2)/r3 - 6.0*zi2*(xi2-yi2)/r5); |
| 255 |
|
Vector3d dwj(4.0*xj*zj/r3 - 6.0*xj*zj*(xj2-yj2)/r5, |
| 256 |
|
- 4.0*yj*zj/r3 - 6.0*yj*zj*(xj2-yj2)/r5, |
| 257 |
|
2.0*(xj2-yj2)/r3 - 6.0*zj2*(xj2-yj2)/r5); |
| 258 |
< |
|
| 258 |
> |
|
| 259 |
|
RealType uglyi = zif*zif*zis + zif*zis*zis; |
| 260 |
|
RealType uglyj = zjf*zjf*zjs + zjf*zjs*zjs; |
| 261 |
< |
|
| 261 |
> |
|
| 262 |
|
Vector3d dwip(-2.0*xi*zi*uglyi/r3, |
| 263 |
|
-2.0*yi*zi*uglyi/r3, |
| 264 |
< |
2.0*(1.0/rij - zi2/r3)*uglyi); |
| 265 |
< |
|
| 264 |
> |
2.0*(1.0/ *(idat.rij) - zi2/r3)*uglyi); |
| 265 |
> |
|
| 266 |
|
Vector3d dwjp(-2.0*xj*zj*uglyj/r3, |
| 267 |
|
-2.0*yj*zj*uglyj/r3, |
| 268 |
< |
2.0*(1.0/rij - zj2/r3)*uglyj); |
| 269 |
< |
|
| 268 |
> |
2.0*(1.0/ *(idat.rij) - zj2/r3)*uglyj); |
| 269 |
> |
|
| 270 |
|
Vector3d dwidu(4.0*(yi*zi2 + 0.5*yi*(xi2-yi2))/r3, |
| 271 |
|
4.0*(xi*zi2 - 0.5*xi*(xi2-yi2))/r3, |
| 272 |
|
- 8.0*xi*yi*zi/r3); |
| 273 |
< |
|
| 273 |
> |
|
| 274 |
|
Vector3d dwjdu(4.0*(yj*zj2 + 0.5*yj*(xj2-yj2))/r3, |
| 275 |
|
4.0*(xj*zj2 - 0.5*xj*(xj2-yj2))/r3, |
| 276 |
|
- 8.0*xj*yj*zj/r3); |
| 277 |
|
|
| 278 |
< |
Vector3d dwipdu(2.0*yi*uglyi/rij, |
| 279 |
< |
-2.0*xi*uglyi/rij, |
| 278 |
> |
Vector3d dwipdu(2.0*yi*uglyi/ *(idat.rij) , |
| 279 |
> |
-2.0*xi*uglyi/ *(idat.rij) , |
| 280 |
|
0.0); |
| 281 |
< |
|
| 282 |
< |
Vector3d dwjpdu(2.0*yj*uglyj/rij, |
| 283 |
< |
-2.0*xj*uglyj/rij, |
| 281 |
> |
|
| 282 |
> |
Vector3d dwjpdu(2.0*yj*uglyj/ *(idat.rij) , |
| 283 |
> |
-2.0*xj*uglyj/ *(idat.rij) , |
| 284 |
|
0.0); |
| 285 |
< |
|
| 285 |
> |
|
| 286 |
|
if (isPower) { |
| 287 |
+ |
cerr << "This is probably an error!\n"; |
| 288 |
|
RealType frac1 = 0.25; |
| 289 |
|
RealType frac2 = 0.75; |
| 290 |
|
RealType wi2 = wi*wi; |
| 292 |
|
// sticky power has no w' function: |
| 293 |
|
w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p; |
| 294 |
|
wp = 0.0; |
| 295 |
< |
dwi = frac1*3.0*wi2*dwi + frac2*dwi; |
| 296 |
< |
dwj = frac1*3.0*wj2*dwi + frac2*dwi; |
| 295 |
> |
dwi = frac1*RealType(3.0)*wi2*dwi + frac2*dwi; |
| 296 |
> |
dwj = frac1*RealType(3.0)*wj2*dwi + frac2*dwi; |
| 297 |
|
dwip = V3Zero; |
| 298 |
|
dwjp = V3Zero; |
| 299 |
< |
dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu; |
| 300 |
< |
dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu; |
| 299 |
> |
dwidu = frac1*RealType(3.0)*wi2*dwidu + frac2*dwidu; |
| 300 |
> |
dwidu = frac1*RealType(3.0)*wj2*dwjdu + frac2*dwjdu; |
| 301 |
|
dwipdu = V3Zero; |
| 302 |
|
dwjpdu = V3Zero; |
| 303 |
|
sp = 0.0; |
| 304 |
|
dspdr = 0.0; |
| 305 |
|
} |
| 306 |
< |
|
| 307 |
< |
vpair += 0.5*(v0*s*w + v0p*sp*wp); |
| 308 |
< |
pot += 0.5*(v0*s*w + v0p*sp*wp)*sw; |
| 309 |
< |
|
| 306 |
> |
|
| 307 |
> |
|
| 308 |
> |
|
| 309 |
> |
*(idat.vpair) += RealType(0.5)*(v0*s*w + v0p*sp*wp); |
| 310 |
> |
(*(idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)*(v0*s*w + v0p*sp*wp)* *(idat.sw) ; |
| 311 |
> |
|
| 312 |
|
// do the torques first since they are easy: |
| 313 |
|
// remember that these are still in the body-fixed axes |
| 314 |
< |
|
| 315 |
< |
Vector3d ti = 0.5*sw*(v0*s*dwidu + v0p*sp*dwipdu); |
| 316 |
< |
Vector3d tj = 0.5*sw*(v0*s*dwjdu + v0p*sp*dwjpdu); |
| 317 |
< |
|
| 314 |
> |
|
| 315 |
> |
Vector3d ti = RealType(0.5)* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu); |
| 316 |
> |
Vector3d tj = RealType(0.5)* *(idat.sw) *(v0*s*dwjdu + v0p*sp*dwjpdu); |
| 317 |
> |
|
| 318 |
|
// go back to lab frame using transpose of rotation matrix: |
| 319 |
< |
|
| 320 |
< |
t1 += A1trans * ti; |
| 321 |
< |
t2 += A2trans * tj; |
| 322 |
< |
|
| 319 |
> |
|
| 320 |
> |
*(idat.t1) += A1trans * ti; |
| 321 |
> |
*(idat.t2) += A2trans * tj; |
| 322 |
> |
|
| 323 |
|
// Now, on to the forces: |
| 324 |
< |
|
| 324 |
> |
|
| 325 |
|
// first rotate the i terms back into the lab frame: |
| 326 |
< |
|
| 327 |
< |
Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * sw; |
| 328 |
< |
Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * sw; |
| 329 |
< |
|
| 326 |
> |
|
| 327 |
> |
Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * *(idat.sw); |
| 328 |
> |
Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * *(idat.sw); |
| 329 |
> |
|
| 330 |
|
Vector3d fii = A1trans * radcomi; |
| 331 |
|
Vector3d fjj = A2trans * radcomj; |
| 332 |
|
|
| 333 |
|
// now assemble these with the radial-only terms: |
| 334 |
|
|
| 335 |
< |
f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * d / rij + fii - fjj); |
| 336 |
< |
|
| 402 |
< |
} |
| 335 |
> |
*(idat.f1) += RealType(0.5) * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) / |
| 336 |
> |
*(idat.rij) + fii - fjj); |
| 337 |
|
|
| 338 |
< |
return; |
| 338 |
> |
} |
| 339 |
|
|
| 340 |
+ |
return; |
| 341 |
|
} |
| 407 |
– |
|
| 408 |
– |
void Sticky::do_sticky_pair(int *atid1, int *atid2, RealType *d, |
| 409 |
– |
RealType *r, RealType *r2, RealType *sw, |
| 410 |
– |
RealType *vpair, RealType *pot, RealType *A1, |
| 411 |
– |
RealType *A2, RealType *f1, |
| 412 |
– |
RealType *t1, RealType *t2) { |
| 413 |
– |
|
| 414 |
– |
if (!initialized_) initialize(); |
| 415 |
– |
|
| 416 |
– |
AtomType* atype1 = StickyMap[*atid1]; |
| 417 |
– |
AtomType* atype2 = StickyMap[*atid2]; |
| 418 |
– |
|
| 419 |
– |
Vector3d disp(d); |
| 420 |
– |
Vector3d frc(f1); |
| 421 |
– |
Vector3d trq1(t1); |
| 422 |
– |
Vector3d trq2(t2); |
| 423 |
– |
RotMat3x3d Ai(A1); |
| 424 |
– |
RotMat3x3d Aj(A2); |
| 425 |
– |
|
| 426 |
– |
calcForce(atype1, atype2, disp, *r, *r2, *sw, *vpair, *pot, |
| 427 |
– |
Ai, Aj, frc, trq1, trq2); |
| 428 |
– |
|
| 429 |
– |
f1[0] = frc.x(); |
| 430 |
– |
f1[1] = frc.y(); |
| 431 |
– |
f1[2] = frc.z(); |
| 432 |
– |
|
| 433 |
– |
t1[0] = trq1.x(); |
| 434 |
– |
t1[1] = trq1.y(); |
| 435 |
– |
t1[2] = trq1.z(); |
| 436 |
– |
|
| 437 |
– |
t2[0] = trq2.x(); |
| 438 |
– |
t2[1] = trq2.y(); |
| 439 |
– |
t2[2] = trq2.z(); |
| 440 |
– |
|
| 441 |
– |
return; |
| 442 |
– |
} |
| 443 |
– |
} |
| 444 |
– |
|
| 445 |
– |
extern "C" { |
| 342 |
|
|
| 343 |
< |
#define fortranGetStickyCut FC_FUNC(getstickycut, GETSTICKYCUT) |
| 344 |
< |
#define fortranDoStickyPair FC_FUNC(do_sticky_pair, DO_STICKY_PAIR) |
| 345 |
< |
|
| 346 |
< |
RealType fortranGetStickyCut(int* atid) { |
| 347 |
< |
return OpenMD::Sticky::Instance()->getStickyCut(*atid); |
| 348 |
< |
} |
| 453 |
< |
|
| 454 |
< |
void fortranDoStickyPair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 455 |
< |
RealType *r2, RealType *sw, RealType *vpair, RealType *pot, |
| 456 |
< |
RealType *A1, RealType *A2, RealType *f1, |
| 457 |
< |
RealType *t1, RealType *t2){ |
| 343 |
> |
RealType Sticky::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 344 |
> |
if (!initialized_) initialize(); |
| 345 |
> |
int atid1 = atypes.first->getIdent(); |
| 346 |
> |
int atid2 = atypes.second->getIdent(); |
| 347 |
> |
int stid1 = Stids[atid1]; |
| 348 |
> |
int stid2 = Stids[atid2]; |
| 349 |
|
|
| 350 |
< |
return OpenMD::Sticky::Instance()->do_sticky_pair(atid1, atid2, d, r, r2, |
| 351 |
< |
sw, vpair, pot, A1, A2, |
| 352 |
< |
f1, t1, t2); |
| 350 |
> |
if (stid1 == -1 || stid2 == -1) return 0.0; |
| 351 |
> |
else { |
| 352 |
> |
return MixingMap[stid1][stid2].rbig; |
| 353 |
> |
} |
| 354 |
|
} |
| 355 |
|
} |
