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#include <cmath> |
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#include "nonbonded/GB.hpp" |
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#include "utils/simError.h" |
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#include "types/LennardJonesAdapter.hpp" |
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#include "types/GayBerneAdapter.hpp" |
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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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/* GB is the Gay-Berne interaction for ellipsoidal particles. The original |
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* paper (for identical uniaxial particles) is: |
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* J. G. Gay and B. J. Berne, J. Chem. Phys., 74, 3316-3319 (1981). |
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* A more-general GB potential for dissimilar uniaxial particles: |
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* D. J. Cleaver, C. M. Care, M. P. Allen and M. P. Neal, Phys. Rev. E, |
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* 54, 559-567 (1996). |
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* Further parameterizations can be found in: |
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* A. P. J. Emerson, G. R. Luckhurst and S. G. Whatling, Mol. Phys., |
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* 82, 113-124 (1994). |
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* And a nice force expression: |
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* G. R. Luckhurst and R. A. Stephens, Liq. Cryst. 8, 451-464 (1990). |
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* Even clearer force and torque expressions: |
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* P. A. Golubkov and P. Y. Ren, J. Chem. Phys., 125, 64103 (2006). |
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* New expressions for cross interactions of strength parameters: |
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* J. Wu, X. Zhen, H. Shen, G. Li, and P. Ren, J. Chem. Phys., |
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* 135, 155104 (2011). |
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* |
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* In this version of the GB interaction, each uniaxial ellipsoidal type |
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* is described using a set of 6 parameters: |
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* d: range parameter for side-by-side (S) and cross (X) configurations |
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* l: range parameter for end-to-end (E) configuration |
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* epsilon_X: well-depth parameter for cross (X) configuration |
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* epsilon_S: well-depth parameter for side-by-side (S) configuration |
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* epsilon_E: well depth parameter for end-to-end (E) configuration |
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* dw: "softness" of the potential |
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* |
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* Additionally, there are two "universal" paramters to govern the overall |
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* importance of the purely orientational (nu) and the mixed |
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* orientational / translational (mu) parts of strength of the interactions. |
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* These parameters have default or "canonical" values, but may be changed |
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* as a force field option: |
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* nu_: purely orientational part : defaults to 1 |
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* mu_: mixed orientational / translational part : defaults to 2 |
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*/ |
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|
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|
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GB::GB() : name_("GB"), initialized_(false), mu_(2.0), nu_(1.0), forceField_(NULL) {} |
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|
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GayBerneParam GB::getGayBerneParam(AtomType* atomType) { |
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// Do sanity checking on the AtomType we were passed before |
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// building any data structures: |
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if (!atomType->isGayBerne()) { |
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sprintf( painCave.errMsg, |
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"GB::getGayBerneParam was passed an atomType (%s) that does\n" |
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"\tnot appear to be a Gay-Berne atom.\n", |
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atomType->getName().c_str()); |
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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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|
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DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
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GenericData* data = daType->getPropertyByName("GayBerne"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "GB::getGayBerneParam could not find\n" |
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"\tGay-Berne parameters for atomType %s.\n", |
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daType->getName().c_str()); |
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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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|
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GayBerneParamGenericData* gbData = dynamic_cast<GayBerneParamGenericData*>(data); |
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if (gbData == NULL) { |
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sprintf( painCave.errMsg, |
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"GB::getGayBerneParam could not convert GenericData to\n" |
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"\tGayBerneParamGenericData for atom type %s\n", |
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daType->getName().c_str()); |
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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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|
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return gbData->getData(); |
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} |
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|
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LJParam GB::getLJParam(AtomType* atomType) { |
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|
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// Do sanity checking on the AtomType we were passed before |
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// building any data structures: |
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if (!atomType->isLennardJones()) { |
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sprintf( painCave.errMsg, |
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"GB::getLJParam was passed an atomType (%s) that does not\n" |
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"\tappear to be a Lennard-Jones atom.\n", |
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atomType->getName().c_str()); |
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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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|
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GenericData* data = atomType->getPropertyByName("LennardJones"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "GB::getLJParam could not find Lennard-Jones\n" |
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"\tparameters for atomType %s.\n", atomType->getName().c_str()); |
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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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|
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LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
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if (ljData == NULL) { |
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sprintf( painCave.errMsg, |
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"GB::getLJParam could not convert GenericData to LJParam for\n" |
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"\tatom type %s\n", atomType->getName().c_str()); |
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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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|
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return ljData->getData(); |
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} |
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|
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RealType GB::getLJEpsilon(AtomType* atomType) { |
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LJParam ljParam = getLJParam(atomType); |
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return ljParam.epsilon; |
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} |
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RealType GB::getLJSigma(AtomType* atomType) { |
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LJParam ljParam = getLJParam(atomType); |
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return ljParam.sigma; |
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} |
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|
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void GB::initialize() { |
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|
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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for (at = atomTypes->beginType(i); at != NULL; |
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at = atomTypes->nextType(i)) { |
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|
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if (at->isGayBerne() || at->isLennardJones()) |
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LennardJonesAdapter lja = LennardJonesAdapter(at); |
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GayBerneAdapter gba = GayBerneAdapter(at); |
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|
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if (gba.isGayBerne() || lja.isLennardJones()) |
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addType(at); |
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} |
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void GB::addType(AtomType* atomType){ |
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// add it to the map: |
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AtomTypeProperties atp = atomType->getATP(); |
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|
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = GBMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
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ret = GBMap.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) ); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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"GB already had a previous entry with ident %d\n", |
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atp.ident); |
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atomType->getIdent() ); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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RealType d1, l1, e1, er1, dw1; |
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|
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if (atomType->isGayBerne()) { |
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GayBerneParam gb1 = getGayBerneParam(atomType); |
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d1 = gb1.GB_d; |
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l1 = gb1.GB_l; |
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e1 = gb1.GB_eps; |
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er1 = gb1.GB_eps_ratio; |
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< |
dw1 = gb1.GB_dw; |
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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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> |
RealType d1, l1, eX1, eS1, eE1, dw1; |
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|
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> |
LennardJonesAdapter lja1 = LennardJonesAdapter(atomType); |
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> |
GayBerneAdapter gba1 = GayBerneAdapter(atomType); |
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if (gba1.isGayBerne()) { |
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d1 = gba1.getD(); |
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> |
l1 = gba1.getL(); |
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> |
eX1 = gba1.getEpsX(); |
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> |
eS1 = gba1.getEpsS(); |
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> |
eE1 = gba1.getEpsE(); |
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> |
dw1 = gba1.getDw(); |
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> |
} else if (lja1.isLennardJones()) { |
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> |
d1 = lja1.getSigma() / sqrt(2.0); |
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l1 = d1; |
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< |
er1 = 1.0; |
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> |
eX1 = lja1.getEpsilon(); |
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> |
eS1 = eX1; |
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> |
eE1 = eX1; |
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dw1 = 1.0; |
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} else { |
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sprintf( painCave.errMsg, |
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for( it = GBMap.begin(); it != GBMap.end(); ++it) { |
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|
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AtomType* atype2 = (*it).second; |
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LennardJonesAdapter lja2 = LennardJonesAdapter(atype2); |
| 168 |
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GayBerneAdapter gba2 = GayBerneAdapter(atype2); |
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RealType d2, l2, eX2, eS2, eE2, dw2; |
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|
| 171 |
< |
RealType d2, l2, e2, er2, dw2; |
| 172 |
< |
|
| 173 |
< |
if (atype2->isGayBerne()) { |
| 174 |
< |
GayBerneParam gb2 = getGayBerneParam(atype2); |
| 175 |
< |
d2 = gb2.GB_d; |
| 176 |
< |
l2 = gb2.GB_l; |
| 177 |
< |
e2 = gb2.GB_eps; |
| 178 |
< |
er2 = gb2.GB_eps_ratio; |
| 179 |
< |
dw2 = gb2.GB_dw; |
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< |
} else if (atype2->isLennardJones()) { |
| 219 |
< |
d2 = getLJSigma(atype2) / sqrt(2.0); |
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< |
e2 = getLJEpsilon(atype2); |
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> |
if (gba2.isGayBerne()) { |
| 172 |
> |
d2 = gba2.getD(); |
| 173 |
> |
l2 = gba2.getL(); |
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> |
eX2 = gba2.getEpsX(); |
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> |
eS2 = gba2.getEpsS(); |
| 176 |
> |
eE2 = gba2.getEpsE(); |
| 177 |
> |
dw2 = gba2.getDw(); |
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> |
} else if (lja2.isLennardJones()) { |
| 179 |
> |
d2 = lja2.getSigma() / sqrt(2.0); |
| 180 |
|
l2 = d2; |
| 181 |
< |
er2 = 1.0; |
| 181 |
> |
eX2 = lja2.getEpsilon(); |
| 182 |
> |
eS2 = eX2; |
| 183 |
> |
eE2 = eX2; |
| 184 |
|
dw2 = 1.0; |
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|
} |
| 186 |
|
|
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|
// assumed LB mixing rules for now: |
| 206 |
|
|
| 207 |
|
mixer1.dw = 0.5 * (dw1 + dw2); |
| 208 |
< |
mixer1.eps0 = sqrt(e1 * e2); |
| 208 |
> |
mixer1.eps0 = sqrt(eX1 * eX2); |
| 209 |
|
|
| 210 |
|
mixer2.dw = mixer1.dw; |
| 211 |
|
mixer2.eps0 = mixer1.eps0; |
| 212 |
+ |
|
| 213 |
+ |
RealType mi = RealType(1.0)/mu_; |
| 214 |
|
|
| 215 |
< |
RealType er = sqrt(er1 * er2); |
| 216 |
< |
RealType ermu = pow(er, (RealType(1.0) / mu_)); |
| 217 |
< |
RealType xp = (1.0 - ermu) / (1.0 + ermu); |
| 218 |
< |
RealType ap2 = 1.0 / (1.0 + ermu); |
| 256 |
< |
|
| 257 |
< |
mixer1.xp2 = xp * xp; |
| 258 |
< |
mixer1.xpap2 = xp * ap2; |
| 259 |
< |
mixer1.xpapi2 = xp / ap2; |
| 215 |
> |
mixer1.xpap2 = (pow(eS1, mi) - pow(eE1, mi)) / (pow(eS1, mi) + pow(eE2, mi)); |
| 216 |
> |
mixer1.xpapi2 = (pow(eS2, mi) - pow(eE2, mi)) / (pow(eS2, mi) + pow(eE1, mi)); |
| 217 |
> |
mixer1.xp2 = (pow(eS1, mi) - pow(eE1, mi)) * (pow(eS2, mi) - pow(eE2, mi)) / |
| 218 |
> |
(pow(eS2, mi) + pow(eE1, mi)) / (pow(eS1, mi) + pow(eE2, mi)) ; |
| 219 |
|
|
| 220 |
+ |
// xpap2 and xpapi2 for j-i pairs are reversed from the same i-j pairing. |
| 221 |
+ |
// Swapping the particles reverses the anisotropy parameters: |
| 222 |
+ |
mixer2.xpap2 = mixer1.xpapi2; |
| 223 |
+ |
mixer2.xpapi2 = mixer1.xpap2; |
| 224 |
|
mixer2.xp2 = mixer1.xp2; |
| 262 |
– |
mixer2.xpap2 = mixer1.xpap2; |
| 263 |
– |
mixer2.xpapi2 = mixer1.xpapi2; |
| 225 |
|
|
| 226 |
|
// only add this pairing if at least one of the atoms is a Gay-Berne atom |
| 227 |
|
|
| 228 |
< |
if (atomType->isGayBerne() || atype2->isGayBerne()) { |
| 228 |
> |
if (gba1.isGayBerne() || gba2.isGayBerne()) { |
| 229 |
|
|
| 230 |
|
pair<AtomType*, AtomType*> key1, key2; |
| 231 |
|
key1 = make_pair(atomType, atype2); |
| 255 |
|
RealType xpap2 = mixer.xpap2; |
| 256 |
|
RealType xpapi2 = mixer.xpapi2; |
| 257 |
|
|
| 258 |
+ |
// cerr << "atypes = " << idat.atypes.first->getName() << " " << idat.atypes.second->getName() << "\n"; |
| 259 |
+ |
// cerr << "sigma0 = " <<mixer.sigma0 <<"\n"; |
| 260 |
+ |
// cerr << "dw = " <<mixer.dw <<"\n"; |
| 261 |
+ |
// cerr << "eps0 = " <<mixer.eps0 <<"\n"; |
| 262 |
+ |
// cerr << "x2 = " <<mixer.x2 <<"\n"; |
| 263 |
+ |
// cerr << "xa2 = " <<mixer.xa2 <<"\n"; |
| 264 |
+ |
// cerr << "xai2 = " <<mixer.xai2 <<"\n"; |
| 265 |
+ |
// cerr << "xp2 = " <<mixer.xp2 <<"\n"; |
| 266 |
+ |
// cerr << "xpap2 = " <<mixer.xpap2 <<"\n"; |
| 267 |
+ |
// cerr << "xpapi2 = " <<mixer.xpapi2 <<"\n"; |
| 268 |
+ |
|
| 269 |
|
Vector3d ul1 = idat.A1->getRow(2); |
| 270 |
|
Vector3d ul2 = idat.A2->getRow(2); |
| 271 |
|
|
| 272 |
+ |
// cerr << "ul1 = " <<ul1<<"\n"; |
| 273 |
+ |
// cerr << "ul2 = " <<ul2<<"\n"; |
| 274 |
+ |
|
| 275 |
|
RealType a, b, g; |
| 276 |
|
|
| 277 |
+ |
// This is not good. We should store this in the mixing map, and not |
| 278 |
+ |
// query atom types in calc force. |
| 279 |
|
bool i_is_LJ = idat.atypes.first->isLennardJones(); |
| 280 |
|
bool j_is_LJ = idat.atypes.second->isLennardJones(); |
| 281 |
|
|
| 304 |
|
RealType au2 = au * au; |
| 305 |
|
RealType bu2 = bu * bu; |
| 306 |
|
RealType g2 = g * g; |
| 307 |
< |
|
| 307 |
> |
|
| 308 |
|
RealType H = (xa2 * au2 + xai2 * bu2 - 2.0*x2*au*bu*g) / (1.0 - x2*g2); |
| 309 |
|
RealType Hp = (xpap2*au2 + xpapi2*bu2 - 2.0*xp2*au*bu*g) / (1.0 - xp2*g2); |
| 310 |
|
|
| 311 |
+ |
// cerr << "au2 = " << au2 << "\n"; |
| 312 |
+ |
// cerr << "bu2 = " << bu2 << "\n"; |
| 313 |
+ |
// cerr << "g2 = " << g2 << "\n"; |
| 314 |
+ |
// cerr << "H = " << H << "\n"; |
| 315 |
+ |
// cerr << "Hp = " << Hp << "\n"; |
| 316 |
+ |
|
| 317 |
|
RealType sigma = sigma0 / sqrt(1.0 - H); |
| 318 |
|
RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
| 319 |
|
RealType e2 = 1.0 - Hp; |
| 331 |
|
RealType s3 = sigma*sigma*sigma; |
| 332 |
|
RealType s03 = sigma0*sigma0*sigma0; |
| 333 |
|
|
| 334 |
+ |
// cerr << "vdwMult = " << *(idat.vdwMult) << "\n"; |
| 335 |
+ |
// cerr << "eps = " << eps <<"\n"; |
| 336 |
+ |
// cerr << "mu = " << mu_ << "\n"; |
| 337 |
+ |
// cerr << "R12 = " << R12 << "\n"; |
| 338 |
+ |
// cerr << "R6 = " << R6 << "\n"; |
| 339 |
+ |
// cerr << "R13 = " << R13 << "\n"; |
| 340 |
+ |
// cerr << "R7 = " << R7 << "\n"; |
| 341 |
+ |
// cerr << "e2 = " << e2 << "\n"; |
| 342 |
+ |
// cerr << "rij = " << *(idat.rij) << "\n"; |
| 343 |
+ |
// cerr << "s3 = " << s3 << "\n"; |
| 344 |
+ |
// cerr << "s03 = " << s03 << "\n"; |
| 345 |
+ |
// cerr << "dw = " << dw << "\n"; |
| 346 |
+ |
|
| 347 |
|
RealType pref1 = - *(idat.vdwMult) * 8.0 * eps * mu_ * (R12 - R6) / |
| 348 |
|
(e2 * *(idat.rij)); |
| 349 |
|
|
| 364 |
|
(1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) * |
| 365 |
|
(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
| 366 |
|
|
| 367 |
+ |
// cerr << "pref = " << pref1 << " " << pref2 << "\n"; |
| 368 |
+ |
// cerr << "dU = " << dUdr << " " << dUda <<" " << dUdb << " " << dUdg << "\n"; |
| 369 |
+ |
|
| 370 |
|
Vector3d rhat = *(idat.d) / *(idat.rij); |
| 371 |
|
Vector3d rxu1 = cross(*(idat.d), ul1); |
| 372 |
|
Vector3d rxu2 = cross(*(idat.d), ul2); |
| 373 |
|
Vector3d uxu = cross(ul1, ul2); |
| 374 |
|
|
| 375 |
|
(*(idat.pot))[VANDERWAALS_FAMILY] += U * *(idat.sw); |
| 376 |
< |
*(idat.f1) += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 377 |
< |
*(idat.t1) += dUda * rxu1 - dUdg * uxu; |
| 378 |
< |
*(idat.t2) += dUdb * rxu2 + dUdg * uxu; |
| 379 |
< |
*(idat.vpair) += U * *(idat.sw); |
| 376 |
> |
*(idat.f1) += (dUdr * rhat + dUda * ul1 + dUdb * ul2) * *(idat.sw); |
| 377 |
> |
*(idat.t1) += (dUda * rxu1 - dUdg * uxu) * *(idat.sw); |
| 378 |
> |
*(idat.t2) += (dUdb * rxu2 + dUdg * uxu) * *(idat.sw); |
| 379 |
> |
*(idat.vpair) += U; |
| 380 |
|
|
| 381 |
+ |
// cerr << "f1 term = " << (dUdr * rhat + dUda * ul1 + dUdb * ul2) * *(idat.sw) << "\n"; |
| 382 |
+ |
// cerr << "t1 term = " << (dUda * rxu1 - dUdg * uxu) * *(idat.sw) << "\n"; |
| 383 |
+ |
// cerr << "t2 term = " << (dUdb * rxu2 + dUdg * uxu) * *(idat.sw) << "\n"; |
| 384 |
+ |
// cerr << "vp term = " << U << "\n"; |
| 385 |
+ |
|
| 386 |
|
return; |
| 387 |
|
|
| 388 |
|
} |
| 392 |
|
|
| 393 |
|
RealType cut = 0.0; |
| 394 |
|
|
| 395 |
< |
if (atypes.first->isGayBerne()) { |
| 396 |
< |
GayBerneParam gb1 = getGayBerneParam(atypes.first); |
| 397 |
< |
RealType d1 = gb1.GB_d; |
| 398 |
< |
RealType l1 = gb1.GB_l; |
| 395 |
> |
LennardJonesAdapter lja1 = LennardJonesAdapter(atypes.first); |
| 396 |
> |
GayBerneAdapter gba1 = GayBerneAdapter(atypes.first); |
| 397 |
> |
LennardJonesAdapter lja2 = LennardJonesAdapter(atypes.second); |
| 398 |
> |
GayBerneAdapter gba2 = GayBerneAdapter(atypes.second); |
| 399 |
> |
|
| 400 |
> |
if (gba1.isGayBerne()) { |
| 401 |
> |
RealType d1 = gba1.getD(); |
| 402 |
> |
RealType l1 = gba1.getL(); |
| 403 |
|
// sigma is actually sqrt(2)*l for prolate ellipsoids |
| 404 |
|
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d1, l1)); |
| 405 |
< |
} else if (atypes.first->isLennardJones()) { |
| 406 |
< |
cut = max(cut, RealType(2.5) * getLJSigma(atypes.first)); |
| 405 |
> |
} else if (lja1.isLennardJones()) { |
| 406 |
> |
cut = max(cut, RealType(2.5) * lja1.getSigma()); |
| 407 |
|
} |
| 408 |
|
|
| 409 |
< |
if (atypes.second->isGayBerne()) { |
| 410 |
< |
GayBerneParam gb2 = getGayBerneParam(atypes.second); |
| 411 |
< |
RealType d2 = gb2.GB_d; |
| 404 |
< |
RealType l2 = gb2.GB_l; |
| 409 |
> |
if (gba2.isGayBerne()) { |
| 410 |
> |
RealType d2 = gba2.getD(); |
| 411 |
> |
RealType l2 = gba2.getL(); |
| 412 |
|
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d2, l2)); |
| 413 |
< |
} else if (atypes.second->isLennardJones()) { |
| 414 |
< |
cut = max(cut, RealType(2.5) * getLJSigma(atypes.second)); |
| 413 |
> |
} else if (lja2.isLennardJones()) { |
| 414 |
> |
cut = max(cut, RealType(2.5) * lja2.getSigma()); |
| 415 |
|
} |
| 416 |
|
|
| 417 |
|
return cut; |
