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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <stdio.h> |
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#include <string.h> |
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|
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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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void GB::initialize() { |
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|
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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mu_ = fopts.getGayBerneMu(); |
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nu_ = fopts.getGayBerneNu(); |
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ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
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ForceField::AtomTypeContainer::MapTypeIterator i; |
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AtomType* at; |
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|
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// GB handles all of the GB-GB interactions as well as GB-LJ cross |
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// interactions: |
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|
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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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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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|
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initialized_ = true; |
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} |
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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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|
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pair<map<int,AtomType*>::iterator,bool> ret; |
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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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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, 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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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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"GB::addType was passed an atomType (%s) that does not\n" |
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"\tappear to be a Gay-Berne or 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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|
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// Now, iterate over all known types and add to the mixing map: |
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|
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map<int, AtomType*>::iterator it; |
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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); |
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GayBerneAdapter gba2 = GayBerneAdapter(atype2); |
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RealType d2, l2, eX2, eS2, eE2, dw2; |
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|
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if (gba2.isGayBerne()) { |
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d2 = gba2.getD(); |
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l2 = gba2.getL(); |
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eX2 = gba2.getEpsX(); |
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eS2 = gba2.getEpsS(); |
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eE2 = gba2.getEpsE(); |
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dw2 = gba2.getDw(); |
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} else if (lja2.isLennardJones()) { |
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d2 = lja2.getSigma() / sqrt(2.0); |
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l2 = d2; |
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eX2 = lja2.getEpsilon(); |
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eS2 = eX2; |
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eE2 = eX2; |
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dw2 = 1.0; |
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} else { |
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sprintf( painCave.errMsg, |
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"GB::addType found an atomType (%s) that does not\n" |
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"\tappear to be a Gay-Berne or Lennard-Jones atom.\n", |
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atype2->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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|
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GBInteractionData mixer1, mixer2; |
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|
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// Cleaver paper uses sqrt of squares to get sigma0 for |
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// mixed interactions. |
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|
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mixer1.sigma0 = sqrt(d1*d1 + d2*d2); |
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mixer1.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); |
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mixer1.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); |
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mixer1.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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|
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mixer2.sigma0 = mixer1.sigma0; |
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// xa2 and xai2 for j-i pairs are reversed from the same i-j pairing. |
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// Swapping the particles reverses the anisotropy parameters: |
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mixer2.xa2 = mixer1.xai2; |
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mixer2.xai2 = mixer1.xa2; |
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mixer2.x2 = mixer1.x2; |
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|
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// assumed LB mixing rules for now: |
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|
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mixer1.dw = 0.5 * (dw1 + dw2); |
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mixer1.eps0 = sqrt(eX1 * eX2); |
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|
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mixer2.dw = mixer1.dw; |
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mixer2.eps0 = mixer1.eps0; |
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|
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RealType mi = RealType(1.0)/mu_; |
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|
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mixer1.xpap2 = (pow(eS1, mi) - pow(eE1, mi)) / (pow(eS1, mi) + pow(eE2, mi)); |
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mixer1.xpapi2 = (pow(eS2, mi) - pow(eE2, mi)) / (pow(eS2, mi) + pow(eE1, mi)); |
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mixer1.xp2 = (pow(eS1, mi) - pow(eE1, mi)) * (pow(eS2, mi) - pow(eE2, mi)) / |
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(pow(eS2, mi) + pow(eE1, mi)) / (pow(eS1, mi) + pow(eE2, mi)) ; |
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|
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// xpap2 and xpapi2 for j-i pairs are reversed from the same i-j pairing. |
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// Swapping the particles reverses the anisotropy parameters: |
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mixer2.xpap2 = mixer1.xpapi2; |
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mixer2.xpapi2 = mixer1.xpap2; |
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mixer2.xp2 = mixer1.xp2; |
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|
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// only add this pairing if at least one of the atoms is a Gay-Berne atom |
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|
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if (gba1.isGayBerne() || gba2.isGayBerne()) { |
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|
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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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|
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MixingMap[key1] = mixer1; |
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if (key2 != key1) { |
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MixingMap[key2] = mixer2; |
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} |
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} |
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} |
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} |
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|
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void GB::calcForce(InteractionData &idat) { |
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|
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if (!initialized_) initialize(); |
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|
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GBInteractionData mixer = MixingMap[idat.atypes]; |
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|
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RealType sigma0 = mixer.sigma0; |
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RealType dw = mixer.dw; |
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RealType eps0 = mixer.eps0; |
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RealType x2 = mixer.x2; |
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RealType xa2 = mixer.xa2; |
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RealType xai2 = mixer.xai2; |
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RealType xp2 = mixer.xp2; |
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RealType xpap2 = mixer.xpap2; |
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RealType xpapi2 = mixer.xpapi2; |
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|
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// cerr << "atypes = " << idat.atypes.first->getName() << " " << idat.atypes.second->getName() << "\n"; |
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// cerr << "sigma0 = " <<mixer.sigma0 <<"\n"; |
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// cerr << "dw = " <<mixer.dw <<"\n"; |
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// cerr << "eps0 = " <<mixer.eps0 <<"\n"; |
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// cerr << "x2 = " <<mixer.x2 <<"\n"; |
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// cerr << "xa2 = " <<mixer.xa2 <<"\n"; |
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// cerr << "xai2 = " <<mixer.xai2 <<"\n"; |
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// cerr << "xp2 = " <<mixer.xp2 <<"\n"; |
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// cerr << "xpap2 = " <<mixer.xpap2 <<"\n"; |
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// cerr << "xpapi2 = " <<mixer.xpapi2 <<"\n"; |
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|
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Vector3d ul1 = idat.A1->getRow(2); |
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Vector3d ul2 = idat.A2->getRow(2); |
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|
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// cerr << "ul1 = " <<ul1<<"\n"; |
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// cerr << "ul2 = " <<ul2<<"\n"; |
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|
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RealType a, b, g; |
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|
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// This is not good. We should store this in the mixing map, and not |
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// query atom types in calc force. |
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bool i_is_LJ = idat.atypes.first->isLennardJones(); |
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bool j_is_LJ = idat.atypes.second->isLennardJones(); |
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|
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if (i_is_LJ) { |
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a = 0.0; |
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ul1 = V3Zero; |
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} else { |
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a = dot(*(idat.d), ul1); |
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} |
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|
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if (j_is_LJ) { |
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b = 0.0; |
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ul2 = V3Zero; |
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} else { |
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b = dot(*(idat.d), ul2); |
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} |
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|
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if (i_is_LJ || j_is_LJ) |
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g = 0.0; |
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else |
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g = dot(ul1, ul2); |
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|
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RealType au = a / *(idat.rij); |
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RealType bu = b / *(idat.rij); |
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|
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RealType au2 = au * au; |
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RealType bu2 = bu * bu; |
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RealType g2 = g * g; |
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|
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RealType H = (xa2 * au2 + xai2 * bu2 - 2.0*x2*au*bu*g) / (1.0 - x2*g2); |
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RealType Hp = (xpap2*au2 + xpapi2*bu2 - 2.0*xp2*au*bu*g) / (1.0 - xp2*g2); |
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|
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// cerr << "au2 = " << au2 << "\n"; |
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// cerr << "bu2 = " << bu2 << "\n"; |
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// cerr << "g2 = " << g2 << "\n"; |
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// cerr << "H = " << H << "\n"; |
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// cerr << "Hp = " << Hp << "\n"; |
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|
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RealType sigma = sigma0 / sqrt(1.0 - H); |
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RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
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RealType e2 = 1.0 - Hp; |
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RealType eps = eps0 * pow(e1,nu_) * pow(e2,mu_); |
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RealType BigR = dw*sigma0 / (*(idat.rij) - sigma + dw*sigma0); |
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|
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RealType R3 = BigR*BigR*BigR; |
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RealType R6 = R3*R3; |
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RealType R7 = R6 * BigR; |
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RealType R12 = R6*R6; |
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RealType R13 = R6*R7; |
| 337 |
|
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RealType U = *(idat.vdwMult) * 4.0 * eps * (R12 - R6); |
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|
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RealType s3 = sigma*sigma*sigma; |
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RealType s03 = sigma0*sigma0*sigma0; |
| 342 |
|
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// cerr << "vdwMult = " << *(idat.vdwMult) << "\n"; |
| 344 |
// cerr << "eps = " << eps <<"\n"; |
| 345 |
// cerr << "mu = " << mu_ << "\n"; |
| 346 |
// cerr << "R12 = " << R12 << "\n"; |
| 347 |
// cerr << "R6 = " << R6 << "\n"; |
| 348 |
// cerr << "R13 = " << R13 << "\n"; |
| 349 |
// cerr << "R7 = " << R7 << "\n"; |
| 350 |
// cerr << "e2 = " << e2 << "\n"; |
| 351 |
// cerr << "rij = " << *(idat.rij) << "\n"; |
| 352 |
// cerr << "s3 = " << s3 << "\n"; |
| 353 |
// cerr << "s03 = " << s03 << "\n"; |
| 354 |
// cerr << "dw = " << dw << "\n"; |
| 355 |
|
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RealType pref1 = - *(idat.vdwMult) * 8.0 * eps * mu_ * (R12 - R6) / |
| 357 |
(e2 * *(idat.rij)); |
| 358 |
|
| 359 |
RealType pref2 = *(idat.vdwMult) * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) / |
| 360 |
(dw* *(idat.rij) * s03); |
| 361 |
|
| 362 |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0 * sigma0 * |
| 363 |
*(idat.rij) / s3 + H)); |
| 364 |
|
| 365 |
RealType dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0 - xp2 * g2) |
| 366 |
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0 - x2 * g2); |
| 367 |
|
| 368 |
RealType dUdb = pref1 * (xpapi2*bu - xp2*au*g) / (1.0 - xp2 * g2) |
| 369 |
+ pref2 * (xai2 * bu - x2 *au*g) / (1.0 - x2 * g2); |
| 370 |
|
| 371 |
RealType dUdg = 4.0 * eps * nu_ * (R12 - R6) * x2 * g / (1.0 - x2*g2) |
| 372 |
+ 8.0 * eps * mu_ * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / |
| 373 |
(1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) * |
| 374 |
(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
| 375 |
|
| 376 |
// cerr << "pref = " << pref1 << " " << pref2 << "\n"; |
| 377 |
// cerr << "dU = " << dUdr << " " << dUda <<" " << dUdb << " " << dUdg << "\n"; |
| 378 |
|
| 379 |
Vector3d rhat = *(idat.d) / *(idat.rij); |
| 380 |
Vector3d rxu1 = cross(*(idat.d), ul1); |
| 381 |
Vector3d rxu2 = cross(*(idat.d), ul2); |
| 382 |
Vector3d uxu = cross(ul1, ul2); |
| 383 |
|
| 384 |
(*(idat.pot))[VANDERWAALS_FAMILY] += U * *(idat.sw); |
| 385 |
*(idat.f1) += (dUdr * rhat + dUda * ul1 + dUdb * ul2) * *(idat.sw); |
| 386 |
*(idat.t1) += (dUda * rxu1 - dUdg * uxu) * *(idat.sw); |
| 387 |
*(idat.t2) += (dUdb * rxu2 + dUdg * uxu) * *(idat.sw); |
| 388 |
*(idat.vpair) += U; |
| 389 |
|
| 390 |
// cerr << "f1 term = " << (dUdr * rhat + dUda * ul1 + dUdb * ul2) * *(idat.sw) << "\n"; |
| 391 |
// cerr << "t1 term = " << (dUda * rxu1 - dUdg * uxu) * *(idat.sw) << "\n"; |
| 392 |
// cerr << "t2 term = " << (dUdb * rxu2 + dUdg * uxu) * *(idat.sw) << "\n"; |
| 393 |
// cerr << "vp term = " << U << "\n"; |
| 394 |
|
| 395 |
return; |
| 396 |
|
| 397 |
} |
| 398 |
|
| 399 |
RealType GB::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 400 |
if (!initialized_) initialize(); |
| 401 |
|
| 402 |
RealType cut = 0.0; |
| 403 |
|
| 404 |
LennardJonesAdapter lja1 = LennardJonesAdapter(atypes.first); |
| 405 |
GayBerneAdapter gba1 = GayBerneAdapter(atypes.first); |
| 406 |
LennardJonesAdapter lja2 = LennardJonesAdapter(atypes.second); |
| 407 |
GayBerneAdapter gba2 = GayBerneAdapter(atypes.second); |
| 408 |
|
| 409 |
if (gba1.isGayBerne()) { |
| 410 |
RealType d1 = gba1.getD(); |
| 411 |
RealType l1 = gba1.getL(); |
| 412 |
// sigma is actually sqrt(2)*l for prolate ellipsoids |
| 413 |
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d1, l1)); |
| 414 |
} else if (lja1.isLennardJones()) { |
| 415 |
cut = max(cut, RealType(2.5) * lja1.getSigma()); |
| 416 |
} |
| 417 |
|
| 418 |
if (gba2.isGayBerne()) { |
| 419 |
RealType d2 = gba2.getD(); |
| 420 |
RealType l2 = gba2.getL(); |
| 421 |
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d2, l2)); |
| 422 |
} else if (lja2.isLennardJones()) { |
| 423 |
cut = max(cut, RealType(2.5) * lja2.getSigma()); |
| 424 |
} |
| 425 |
|
| 426 |
return cut; |
| 427 |
} |
| 428 |
} |
| 429 |
|
