| 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). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
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|
| 43 |
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#include <stdio.h> |
| 46 |
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#include <cmath> |
| 47 |
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#include "nonbonded/Sticky.hpp" |
| 48 |
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#include "nonbonded/LJ.hpp" |
| 49 |
+ |
#include "types/StickyAdapter.hpp" |
| 50 |
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#include "utils/simError.h" |
| 51 |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {} |
| 54 |
– |
|
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– |
StickyParam Sticky::getStickyParam(AtomType* atomType) { |
| 56 |
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|
| 57 |
– |
// Do sanity checking on the AtomType we were passed before |
| 58 |
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// building any data structures: |
| 59 |
– |
if (!atomType->isSticky() && !atomType->isStickyPower()) { |
| 60 |
– |
sprintf( painCave.errMsg, |
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"Sticky::getStickyParam was passed an atomType (%s) that does\n" |
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"\tnot appear to be a Sticky atom.\n", |
| 63 |
– |
atomType->getName().c_str()); |
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– |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
| 66 |
– |
simError(); |
| 67 |
– |
} |
| 68 |
– |
|
| 69 |
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DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 70 |
– |
GenericData* data = daType->getPropertyByName("Sticky"); |
| 71 |
– |
if (data == NULL) { |
| 72 |
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sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n" |
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– |
"\tSticky parameters for atomType %s.\n", |
| 74 |
– |
daType->getName().c_str()); |
| 75 |
– |
painCave.severity = OPENMD_ERROR; |
| 76 |
– |
painCave.isFatal = 1; |
| 77 |
– |
simError(); |
| 78 |
– |
} |
| 79 |
– |
|
| 80 |
– |
StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data); |
| 81 |
– |
if (stickyData == NULL) { |
| 82 |
– |
sprintf( painCave.errMsg, |
| 83 |
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"Sticky::getStickyParam could not convert GenericData to\n" |
| 84 |
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"\tStickyParamGenericData for atom type %s\n", |
| 85 |
– |
daType->getName().c_str()); |
| 86 |
– |
painCave.severity = OPENMD_ERROR; |
| 87 |
– |
painCave.isFatal = 1; |
| 88 |
– |
simError(); |
| 89 |
– |
} |
| 90 |
– |
|
| 91 |
– |
return stickyData->getData(); |
| 92 |
– |
} |
| 93 |
– |
|
| 57 |
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void Sticky::initialize() { |
| 58 |
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|
| 59 |
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 66 |
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for (at = atomTypes->beginType(i); at != NULL; |
| 67 |
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at = atomTypes->nextType(i)) { |
| 68 |
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|
| 69 |
< |
if (at->isSticky() || at->isStickyPower()) |
| 70 |
< |
addType(at); |
| 69 |
> |
StickyAdapter sa = StickyAdapter(at); |
| 70 |
> |
if (sa.isSticky()) addType(at); |
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} |
| 72 |
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|
| 73 |
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initialized_ = true; |
| 75 |
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| 76 |
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void Sticky::addType(AtomType* atomType){ |
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// add it to the map: |
| 115 |
– |
AtomTypeProperties atp = atomType->getATP(); |
| 78 |
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|
| 79 |
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pair<map<int,AtomType*>::iterator,bool> ret; |
| 80 |
< |
ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 80 |
> |
ret = StickyMap.insert( pair<int, AtomType*>(atomType->getIdent(), |
| 81 |
> |
atomType) ); |
| 82 |
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if (ret.second == false) { |
| 83 |
|
sprintf( painCave.errMsg, |
| 84 |
|
"Sticky already had a previous entry with ident %d\n", |
| 85 |
< |
atp.ident); |
| 85 |
> |
atomType->getIdent() ); |
| 86 |
|
painCave.severity = OPENMD_INFO; |
| 87 |
|
painCave.isFatal = 0; |
| 88 |
|
simError(); |
| 90 |
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|
| 91 |
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RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi; |
| 92 |
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|
| 93 |
< |
StickyParam sticky1 = getStickyParam(atomType); |
| 93 |
> |
StickyAdapter sticky1 = StickyAdapter(atomType); |
| 94 |
|
|
| 95 |
|
// Now, iterate over all known types and add to the mixing map: |
| 96 |
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|
| 98 |
|
for( it = StickyMap.begin(); it != StickyMap.end(); ++it) { |
| 99 |
|
|
| 100 |
|
AtomType* atype2 = (*it).second; |
| 101 |
< |
|
| 102 |
< |
StickyParam sticky2 = getStickyParam(atype2); |
| 101 |
> |
|
| 102 |
> |
StickyAdapter sticky2 = StickyAdapter(atype2); |
| 103 |
|
|
| 104 |
|
StickyInteractionData mixer; |
| 105 |
|
|
| 108 |
|
// Lorentz- Berthelot mixing rules (which happen to do the right thing |
| 109 |
|
// when atomType and atype2 happen to be the same. |
| 110 |
|
|
| 111 |
< |
mixer.rl = 0.5 * ( sticky1.rl + sticky2.rl ); |
| 112 |
< |
mixer.ru = 0.5 * ( sticky1.ru + sticky2.ru ); |
| 113 |
< |
mixer.rlp = 0.5 * ( sticky1.rlp + sticky2.rlp ); |
| 114 |
< |
mixer.rup = 0.5 * ( sticky1.rup + sticky2.rup ); |
| 111 |
> |
mixer.rl = 0.5 * ( sticky1.getRl() + sticky2.getRl() ); |
| 112 |
> |
mixer.ru = 0.5 * ( sticky1.getRu() + sticky2.getRu() ); |
| 113 |
> |
mixer.rlp = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() ); |
| 114 |
> |
mixer.rup = 0.5 * ( sticky1.getRup() + sticky2.getRup() ); |
| 115 |
|
mixer.rbig = max(mixer.ru, mixer.rup); |
| 116 |
< |
mixer.w0 = sqrt( sticky1.w0 * sticky2.w0 ); |
| 117 |
< |
mixer.v0 = sqrt( sticky1.v0 * sticky2.v0 ); |
| 118 |
< |
mixer.v0p = sqrt( sticky1.v0p * sticky2.v0p ); |
| 119 |
< |
mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower(); |
| 116 |
> |
mixer.w0 = sqrt( sticky1.getW0() * sticky2.getW0() ); |
| 117 |
> |
mixer.v0 = sqrt( sticky1.getW0() * sticky2.getV0() ); |
| 118 |
> |
mixer.v0p = sqrt( sticky1.getV0p() * sticky2.getV0p() ); |
| 119 |
> |
mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower(); |
| 120 |
|
|
| 121 |
|
CubicSpline* s = new CubicSpline(); |
| 122 |
|
s->addPoint(mixer.rl, 1.0); |
| 154 |
|
if (!initialized_) initialize(); |
| 155 |
|
|
| 156 |
|
map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it; |
| 157 |
< |
it = MixingMap.find(*(idat.atypes)); |
| 157 |
> |
it = MixingMap.find(idat.atypes); |
| 158 |
|
if (it != MixingMap.end()) { |
| 159 |
|
|
| 160 |
|
StickyInteractionData mixer = (*it).second; |
| 293 |
|
// sticky power has no w' function: |
| 294 |
|
w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p; |
| 295 |
|
wp = 0.0; |
| 296 |
< |
dwi = frac1*3.0*wi2*dwi + frac2*dwi; |
| 297 |
< |
dwj = frac1*3.0*wj2*dwi + frac2*dwi; |
| 296 |
> |
dwi = frac1*RealType(3.0)*wi2*dwi + frac2*dwi; |
| 297 |
> |
dwj = frac1*RealType(3.0)*wj2*dwi + frac2*dwi; |
| 298 |
|
dwip = V3Zero; |
| 299 |
|
dwjp = V3Zero; |
| 300 |
< |
dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu; |
| 301 |
< |
dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu; |
| 300 |
> |
dwidu = frac1*RealType(3.0)*wi2*dwidu + frac2*dwidu; |
| 301 |
> |
dwidu = frac1*RealType(3.0)*wj2*dwjdu + frac2*dwjdu; |
| 302 |
|
dwipdu = V3Zero; |
| 303 |
|
dwjpdu = V3Zero; |
| 304 |
|
sp = 0.0; |
| 305 |
|
dspdr = 0.0; |
| 306 |
|
} |
| 307 |
|
|
| 308 |
< |
*(idat.vpair) += 0.5*(v0*s*w + v0p*sp*wp); |
| 309 |
< |
idat.pot[HYDROGENBONDING_FAMILY] += 0.5*(v0*s*w + v0p*sp*wp)* *(idat.sw) ; |
| 308 |
> |
*(idat.vpair) += RealType(0.5)*(v0*s*w + v0p*sp*wp); |
| 309 |
> |
(*(idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)*(v0*s*w + v0p*sp*wp)* *(idat.sw) ; |
| 310 |
|
|
| 311 |
|
// do the torques first since they are easy: |
| 312 |
|
// remember that these are still in the body-fixed axes |
| 313 |
|
|
| 314 |
< |
Vector3d ti = 0.5* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu); |
| 315 |
< |
Vector3d tj = 0.5* *(idat.sw) *(v0*s*dwjdu + v0p*sp*dwjpdu); |
| 314 |
> |
Vector3d ti = RealType(0.5)* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu); |
| 315 |
> |
Vector3d tj = RealType(0.5)* *(idat.sw) *(v0*s*dwjdu + v0p*sp*dwjpdu); |
| 316 |
|
|
| 317 |
|
// go back to lab frame using transpose of rotation matrix: |
| 318 |
|
|
| 331 |
|
|
| 332 |
|
// now assemble these with the radial-only terms: |
| 333 |
|
|
| 334 |
< |
*(idat.f1) += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) / |
| 335 |
< |
*(idat.rij) + fii - fjj); |
| 334 |
> |
*(idat.f1) += RealType(0.5) * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) / |
| 335 |
> |
*(idat.rij) + fii - fjj); |
| 336 |
|
|
| 337 |
|
} |
| 338 |
|
} |
