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using namespace std; |
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namespace OpenMD { |
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< |
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< |
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> |
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SHAPES::SHAPES() { |
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initialized_ = false; |
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lMax_ = 64; |
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for (at = atomTypes->beginType(i); at != NULL; |
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at = atomTypes->nextType(i)) { |
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if (at->isShape() || at->isLennardJones()) |
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addType(at); |
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if (at->isShape()) |
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addShape(dynamic_cast<ShapeAtomType*>(at)); |
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if (at->isLennardJones()) |
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addLJ(at); |
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} |
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initialized_ = true; |
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} |
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void SHAPES::addType(AtomType* atomType){ |
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void SHAPES::addShape(ShapeAtomType* atomType){ |
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// add it to the map: |
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AtomTypeProperties atp = atomType->getATP(); |
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = ShapesMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
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pair<map<int,ShapeAtomType*>::iterator, bool> ret; |
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ret = shapesMap.insert( pair<int, ShapeAtomType*>(atp.ident, atomType)); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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sprintf( painCave.errmsg, |
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"SHAPES already had a previous entry with ident %d\n", |
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atp.ident); |
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painCave.severity = OPENMD_INFO; |
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simError(); |
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} |
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if (atomType->isShape()) { |
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ShapeAtomType* sAtomType = dynamic_cast<ShapeAtomType*>(atomType); |
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if (sAtomType == NULL) { |
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sprintf(painCave.errMsg, |
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"SHAPES:: Can't cast to ShapeAtomType"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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ShapesMap.insert( pair<int, ShapeAtomType*>(atp.ident, sAtomType) ); |
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} else if (atomType->isLennardJones()) { |
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ShapesMap.insert( pair<int, ShapeAtomType*>(atp.ident, sAtomType) ); |
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} else if (atomType->isLennardJones()) { |
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d1 = getLJSigma(atomType) / sqrt(2.0); |
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e1 = getLJEpsilon(atomType); |
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} else { |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// Now, iterate over all known types and add to the mixing map: |
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map<int, AtomType*>::iterator it; |
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for( it = ShapesMap.begin(); it != SHAPESMap.end(); ++it) { |
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AtomType* atype2 = (*it).second; |
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RealType d2, l2, e2, er2, dw2; |
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if (atype2->isGayBerne()) { |
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GayBerneParam gb2 = getGayBerneParam(atype2); |
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d2 = gb2.SHAPES_d; |
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l2 = gb2.SHAPES_l; |
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e2 = gb2.SHAPES_eps; |
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er2 = gb2.SHAPES_eps_ratio; |
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dw2 = gb2.SHAPES_dw; |
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} else if (atype2->isLennardJones()) { |
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d2 = getLJSigma(atype2) / sqrt(2.0); |
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e2 = getLJEpsilon(atype2); |
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l2 = d2; |
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er2 = 1.0; |
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dw2 = 1.0; |
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} |
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SHAPESInteractionData mixer; |
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// Cleaver paper uses sqrt of squares to get sigma0 for |
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// mixed interactions. |
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mixer.sigma0 = sqrt(d1*d1 + d2*d2); |
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mixer.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); |
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mixer.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); |
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mixer.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / |
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((l2*l2 + d1*d1) * (l1*l1 + d2*d2)); |
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// assumed LB mixing rules for now: |
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mixer.dw = 0.5 * (dw1 + dw2); |
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mixer.eps0 = sqrt(e1 * e2); |
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RealType er = sqrt(er1 * er2); |
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RealType ermu = pow(er,(1.0 / mu_)); |
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RealType xp = (1.0 - ermu) / (1.0 + ermu); |
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RealType ap2 = 1.0 / (1.0 + ermu); |
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mixer.xp2 = xp * xp; |
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mixer.xpap2 = xp * ap2; |
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mixer.xpapi2 = xp / ap2; |
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// only add this pairing if at least one of the atoms is a Gay-Berne atom |
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if (atomType->isGayBerne() || atype2->isGayBerne()) { |
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pair<AtomType*, AtomType*> key1, key2; |
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key1 = make_pair(atomType, atype2); |
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key2 = make_pair(atype2, atomType); |
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MixingMap[key1] = mixer; |
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if (key2 != key1) { |
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MixingMap[key2] = mixer; |
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} |
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} |
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} |
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} |
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} |
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