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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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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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/SHAPES.hpp" |
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#include "nonbonded/LJ.hpp" |
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#include "utils/simError.h" |
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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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|
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SHAPES::SHAPES() { |
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initialized_ = false; |
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lMax_ = 64; |
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mMax_ = 64; |
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forceField_ = NULL; |
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} |
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|
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void SHAPES::initialize() { |
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|
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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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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// SHAPES handles all of the SHAPES-SHAPES interactions as well as |
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// SHAPES-LJ cross 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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if (at->isShape() || at->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 SHAPES::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 = ShapesMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
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if (ret.second == false) { |
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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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painCave.isFatal = 0; |
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simError(); |
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} |
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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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|
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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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sprintf( painCave.errMsg, |
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"SHAPES::addType was passed an atomType (%s) that does not\n" |
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"\tappear to be a SHAPES 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 = ShapesMap.begin(); it != SHAPESMap.end(); ++it) { |
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|
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AtomType* atype2 = (*it).second; |
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|
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RealType d2, l2, e2, er2, dw2; |
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|
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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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|
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SHAPESInteractionData mixer; |
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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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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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|
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// assumed LB mixing rules for now: |
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|
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mixer.dw = 0.5 * (dw1 + dw2); |
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mixer.eps0 = sqrt(e1 * e2); |
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|
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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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|
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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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|
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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 (atomType->isGayBerne() || atype2->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] = 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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|
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LJParam SHAPES::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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"SHAPES::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, "SHAPES::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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"SHAPES::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 SHAPES::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 SHAPES::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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RealType SHAPES::getGayBerneCut(int atid) { |
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if (!initialized_) initialize(); |
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std::map<int, AtomType*> :: const_iterator it; |
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it = SHAPESMap.find(atid); |
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if (it == SHAPESMap.end()) { |
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sprintf( painCave.errMsg, |
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"SHAPES::getGayBerneCut could not find atid %d in SHAPESMap\n", |
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(atid)); |
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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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AtomType* atype = it->second; |
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|
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RealType gbCut; |
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|
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if (atype->isGayBerne()) { |
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GayBerneParam gb = getGayBerneParam(atype); |
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|
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// sigma is actually sqrt(2) * l for prolate ellipsoids |
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gbCut = 2.5 * sqrt(2.0) * max(gb.SHAPES_l, gb.SHAPES_d); |
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|
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} else if (atype->isLennardJones()) { |
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gbCut = 2.5 * LJ::Instance()->getSigma(atype); |
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} |
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|
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return gbCut; |
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} |
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|
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|
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void SHAPES::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
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RealType r, RealType r2, RealType sw, |
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RealType &vpair, RealType &pot, |
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RotMat3x3d A1, RotMat3x3d A2, Vector3d &f1, |
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Vector3d &t1, Vector3d &t2) { |
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|
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if (!initialized_) initialize(); |
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|
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pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
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SHAPESInteractionData mixer = MixingMap[key]; |
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|
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RealType r3 = r2 * r; |
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RealType r5 = r3 * r2; |
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|
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Vector3d drdi = -d / r; |
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Vector3d drdui = V3Zero; |
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Vector3d drdj = d / r; |
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Vector3d drduj = V3Zero; |
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|
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bool i_is_LJ = at1->isLennardJones(); |
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bool j_is_LJ = at2->isLennardJones(); |
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|
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RealType sigma_i; |
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RealType s_i; |
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RealType eps_i; |
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Vector3d dsigmaidr; |
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Vector3d disgmaidu; |
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Vector3d dsidr; |
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Vector3d dsidu; |
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Vector3d depsidr; |
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Vector3d depsidu; |
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|
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if (i_is_LJ) { |
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sigma_i = LJ::Instance()->getSigma(at1); |
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s_i = sigma_i; |
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epsilon_i = LJ::Instance()->getEpsilon(at1); |
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dsigmaidr = V3Zero; |
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dsigmaidu = V3Zero; |
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dsidr = V3Zero; |
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dsidu = V3Zero; |
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depsidr = V3Zero; |
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depsidu = V3Zero; |
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} else { |
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|
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// rotate the inter-particle separation into the two different |
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// body-fixed coordinate systems: |
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|
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Vector3d ri = A1 * d; |
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|
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RealType xi = ri.x() / r; |
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RealType yi = ri.y() / r; |
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RealType zi = ri.z() / r; |
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RealType xi2 = xi * xi; |
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RealType yi2 = yi * yi; |
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RealType zi2 = zi * zi; |
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RealType cti = zi / r; |
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|
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if (cti > 1.0) cti = 1.0; |
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if (cti < -1.0_dp) cti = -1.0; |
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|
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Vector3d dctidr(-zi * xi / r3, |
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-zi * yi / r3, |
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1.0 / r - zi2 / r3); |
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|
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Vector3d dctidu(yi / r, |
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-zi / r, |
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0.0); |
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|
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// this is an attempt to try to truncate the singularity when |
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// sin(theta) is near 0.0: |
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|
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RealType sti2 = 1.0 - cti*cti; |
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if (fabs(sti2) < 1.0e-12) { |
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RealType proji = sqrt(r * 1.0e-12); |
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Vector3d dcpidx(1.0 / proji, |
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0.0, |
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|
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dcpidx = 1.0_dp / proji |
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dcpidy = 0.0_dp |
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dcpidux = xi / proji |
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dcpiduy = 0.0_dp |
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dspidx = 0.0_dp |
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dspidy = 1.0_dp / proji |
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dspidux = 0.0_dp |
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dspiduy = yi / proji |
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else |
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proji = sqrt(xi2 + yi2) |
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proji3 = proji*proji*proji |
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dcpidx = 1.0_dp / proji - xi2 / proji3 |
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dcpidy = - xi * yi / proji3 |
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dcpidux = xi / proji - (xi2 * xi) / proji3 |
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dcpiduy = - (xi * yi2) / proji3 |
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dspidx = - xi * yi / proji3 |
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dspidy = 1.0_dp / proji - yi2 / proji3 |
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dspidux = - (yi * xi2) / proji3 |
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dspiduy = yi / proji - (yi2 * yi) / proji3 |
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endif |
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|
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cpi = xi / proji |
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dcpidz = 0.0_dp |
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dcpiduz = 0.0_dp |
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|
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spi = yi / proji |
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dspidz = 0.0_dp |
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dspiduz = 0.0_dp |
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|
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|
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|
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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; |
| 381 |
|
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Vector3d ul1 = A1.getRow(2); |
| 383 |
Vector3d ul2 = A2.getRow(2); |
| 384 |
|
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RealType a, b, g; |
| 386 |
|
| 387 |
|
| 388 |
if (i_is_LJ) { |
| 389 |
a = 0.0; |
| 390 |
ul1 = V3Zero; |
| 391 |
} else { |
| 392 |
a = dot(d, ul1); |
| 393 |
} |
| 394 |
|
| 395 |
if (j_is_LJ) { |
| 396 |
b = 0.0; |
| 397 |
ul2 = V3Zero; |
| 398 |
} else { |
| 399 |
b = dot(d, ul2); |
| 400 |
} |
| 401 |
|
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if (i_is_LJ || j_is_LJ) |
| 403 |
g = 0.0; |
| 404 |
else |
| 405 |
g = dot(ul1, ul2); |
| 406 |
|
| 407 |
RealType au = a / r; |
| 408 |
RealType bu = b / r; |
| 409 |
|
| 410 |
RealType au2 = au * au; |
| 411 |
RealType bu2 = bu * bu; |
| 412 |
RealType g2 = g * g; |
| 413 |
|
| 414 |
RealType H = (xa2 * au2 + xai2 * bu2 - 2.0*x2*au*bu*g) / (1.0 - x2*g2); |
| 415 |
RealType Hp = (xpap2*au2 + xpapi2*bu2 - 2.0*xp2*au*bu*g) / (1.0 - xp2*g2); |
| 416 |
|
| 417 |
RealType sigma = sigma0 / sqrt(1.0 - H); |
| 418 |
RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
| 419 |
RealType e2 = 1.0 - Hp; |
| 420 |
RealType eps = eps0 * pow(e1,nu_) * pow(e2,mu_); |
| 421 |
RealType BigR = dw*sigma0 / (r - sigma + dw*sigma0); |
| 422 |
|
| 423 |
RealType R3 = BigR*BigR*BigR; |
| 424 |
RealType R6 = R3*R3; |
| 425 |
RealType R7 = R6 * BigR; |
| 426 |
RealType R12 = R6*R6; |
| 427 |
RealType R13 = R6*R7; |
| 428 |
|
| 429 |
RealType U = vdwMult * 4.0 * eps * (R12 - R6); |
| 430 |
|
| 431 |
RealType s3 = sigma*sigma*sigma; |
| 432 |
RealType s03 = sigma0*sigma0*sigma0; |
| 433 |
|
| 434 |
RealType pref1 = - vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * r); |
| 435 |
|
| 436 |
RealType pref2 = vdwMult * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /(dw*r*s03); |
| 437 |
|
| 438 |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*r/s3 + H)); |
| 439 |
|
| 440 |
RealType dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0 - xp2 * g2) |
| 441 |
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0 - x2 * g2); |
| 442 |
|
| 443 |
RealType dUdb = pref1 * (xpapi2*bu - xp2*au*g) / (1.0 - xp2 * g2) |
| 444 |
+ pref2 * (xai2 * bu - x2 *au*g) / (1.0 - x2 * g2); |
| 445 |
|
| 446 |
RealType dUdg = 4.0 * eps * nu_ * (R12 - R6) * x2 * g / (1.0 - x2*g2) |
| 447 |
+ 8.0 * eps * mu_ * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / |
| 448 |
(1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) * |
| 449 |
(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
| 450 |
|
| 451 |
|
| 452 |
Vector3d rhat = d / r; |
| 453 |
Vector3d rxu1 = cross(d, ul1); |
| 454 |
Vector3d rxu2 = cross(d, ul2); |
| 455 |
Vector3d uxu = cross(ul1, ul2); |
| 456 |
|
| 457 |
pot += U*sw; |
| 458 |
f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 459 |
t1 += dUda * rxu1 - dUdg * uxu; |
| 460 |
t2 += dUdb * rxu2 - dUdg * uxu; |
| 461 |
vpair += U*sw; |
| 462 |
|
| 463 |
return; |
| 464 |
|
| 465 |
} |
| 466 |
|
| 467 |
void SHAPES::do_gb_pair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 468 |
RealType *r2, RealType *sw, RealType *vdwMult, |
| 469 |
RealType *vpair, RealType *pot, RealType *A1, |
| 470 |
RealType *A2, RealType *f1, RealType *t1, RealType *t2) { |
| 471 |
|
| 472 |
if (!initialized_) initialize(); |
| 473 |
|
| 474 |
AtomType* atype1 = SHAPESMap[*atid1]; |
| 475 |
AtomType* atype2 = SHAPESMap[*atid2]; |
| 476 |
|
| 477 |
Vector3d disp(d); |
| 478 |
Vector3d frc(f1); |
| 479 |
Vector3d trq1(t1); |
| 480 |
Vector3d trq2(t2); |
| 481 |
RotMat3x3d Ai(A1); |
| 482 |
RotMat3x3d Aj(A2); |
| 483 |
|
| 484 |
// Fortran has the opposite matrix ordering from c++, so we'll use |
| 485 |
// transpose here. When we finish the conversion to C++, this wrapper |
| 486 |
// will disappear, as will the transpose below: |
| 487 |
|
| 488 |
calcForce(atype1, atype2, disp, *r, *r2, *sw, *vdwMult, *vpair, *pot, |
| 489 |
Ai, Aj, frc, trq1, trq1); |
| 490 |
|
| 491 |
f1[0] = frc.x(); |
| 492 |
f1[1] = frc.y(); |
| 493 |
f1[2] = frc.z(); |
| 494 |
|
| 495 |
t1[0] = trq1.x(); |
| 496 |
t1[1] = trq1.y(); |
| 497 |
t1[2] = trq1.z(); |
| 498 |
|
| 499 |
t2[0] = trq2.x(); |
| 500 |
t2[1] = trq2.y(); |
| 501 |
t2[2] = trq2.z(); |
| 502 |
|
| 503 |
return; |
| 504 |
} |
| 505 |
} |
| 506 |
|
| 507 |
extern "C" { |
| 508 |
|
| 509 |
#define fortranGetGayBerneCut FC_FUNC(getgaybernecut, GETGAYBERNECUT) |
| 510 |
#define fortranDoSHAPESPair FC_FUNC(do_gb_pair, DO_SHAPES_PAIR) |
| 511 |
|
| 512 |
RealType fortranGetGayBerneCut(int* atid) { |
| 513 |
return OpenMD::SHAPES::Instance()->getGayBerneCut(*atid); |
| 514 |
} |
| 515 |
|
| 516 |
void fortranDoSHAPESPair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 517 |
RealType *r2, RealType *sw, RealType *vdwMult, |
| 518 |
RealType *vpair, RealType *pot, RealType *A1, |
| 519 |
RealType *A2, RealType *f1, RealType *t1, RealType *t2){ |
| 520 |
|
| 521 |
return OpenMD::SHAPES::Instance()->do_gb_pair(atid1, atid2, d, r, r2, sw, |
| 522 |
vdwMult, vpair, pot, A1, A2, f1, |
| 523 |
t1, t2); |
| 524 |
} |
| 525 |
} |
