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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/EAM.hpp" |
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#include "utils/simError.h" |
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#include "types/NonBondedInteractionType.hpp" |
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|
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|
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namespace OpenMD { |
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|
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EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL), |
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mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {} |
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|
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EAMParam EAM::getEAMParam(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->isEAM()) { |
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sprintf( painCave.errMsg, |
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"EAM::getEAMParam was passed an atomType (%s) that does not\n" |
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"\tappear to be an embedded atom method (EAM) 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("EAM"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n" |
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"\tparameters for atomType %s.\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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EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
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if (eamData == NULL) { |
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sprintf( painCave.errMsg, |
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"EAM::getEAMParam could not convert GenericData to EAMParam 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 eamData->getData(); |
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} |
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|
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CubicSpline* EAM::getZ(AtomType* atomType) { |
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EAMParam eamParam = getEAMParam(atomType); |
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int nr = eamParam.nr; |
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RealType dr = eamParam.dr; |
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vector<RealType> rvals; |
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|
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for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); |
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|
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CubicSpline* cs = new CubicSpline(); |
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cs->addPoints(rvals, eamParam.Z); |
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return cs; |
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} |
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|
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RealType EAM::getRcut(AtomType* atomType) { |
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EAMParam eamParam = getEAMParam(atomType); |
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return eamParam.rcut; |
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} |
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|
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CubicSpline* EAM::getRho(AtomType* atomType) { |
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EAMParam eamParam = getEAMParam(atomType); |
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int nr = eamParam.nr; |
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RealType dr = eamParam.dr; |
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vector<RealType> rvals; |
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|
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for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); |
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|
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CubicSpline* cs = new CubicSpline(); |
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cs->addPoints(rvals, eamParam.rho); |
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return cs; |
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} |
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|
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CubicSpline* EAM::getF(AtomType* atomType) { |
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EAMParam eamParam = getEAMParam(atomType); |
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int nrho = eamParam.nrho; |
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RealType drho = eamParam.drho; |
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vector<RealType> rhovals; |
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vector<RealType> scaledF; |
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|
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for (int i = 0; i < nrho; i++) { |
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rhovals.push_back(RealType(i) * drho); |
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scaledF.push_back( eamParam.F[i] * 23.06054 ); |
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} |
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|
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CubicSpline* cs = new CubicSpline(); |
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cs->addPoints(rhovals, scaledF); |
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return cs; |
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} |
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|
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CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) { |
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EAMParam eamParam1 = getEAMParam(atomType1); |
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EAMParam eamParam2 = getEAMParam(atomType2); |
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CubicSpline* z1 = getZ(atomType1); |
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CubicSpline* z2 = getZ(atomType2); |
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|
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// make the r grid: |
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|
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|
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// we need phi out to the largest value we'll encounter in the radial space; |
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|
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RealType rmax = 0.0; |
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rmax = max(rmax, eamParam1.rcut); |
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rmax = max(rmax, eamParam1.nr * eamParam1.dr); |
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|
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rmax = max(rmax, eamParam2.rcut); |
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rmax = max(rmax, eamParam2.nr * eamParam2.dr); |
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|
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// use the smallest dr (finest grid) to build our grid: |
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|
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RealType dr = min(eamParam1.dr, eamParam2.dr); |
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|
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int nr = int(rmax/dr + 0.5); |
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|
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vector<RealType> rvals; |
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for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr)); |
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|
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// construct the pair potential: |
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|
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vector<RealType> phivals; |
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RealType phi; |
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RealType r; |
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RealType zi, zj; |
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|
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phivals.push_back(0.0); |
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|
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for (int i = 1; i < rvals.size(); i++ ) { |
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r = rvals[i]; |
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|
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// only use z(r) if we're inside this atom's cutoff radius, |
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// otherwise, we'll use zero for the charge. This effectively |
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// means that our phi grid goes out beyond the cutoff of the |
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// pair potential |
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|
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zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0; |
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zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0; |
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|
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phi = 331.999296 * (zi * zj) / r; |
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|
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phivals.push_back(phi); |
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} |
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|
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CubicSpline* cs = new CubicSpline(); |
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cs->addPoints(rvals, phivals); |
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return cs; |
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} |
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|
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void EAM::setCutoffRadius( RealType rCut ) { |
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eamRcut_ = rCut; |
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haveCutoffRadius_ = true; |
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} |
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|
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void EAM::initialize() { |
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|
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// set up the mixing method: |
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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string EAMMixMeth = fopts.getEAMMixingMethod(); |
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toUpper(EAMMixMeth); |
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|
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if (EAMMixMeth == "JOHNSON") |
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mixMeth_ = eamJohnson; |
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else if (EAMMixMeth == "DAW") |
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mixMeth_ = eamDaw; |
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else |
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mixMeth_ = eamUnknown; |
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|
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// find all of the EAM atom Types: |
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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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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->isEAM()) |
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addType(at); |
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} |
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|
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// find all of the explicit EAM interactions (setfl): |
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ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
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ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
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NonBondedInteractionType* nbt; |
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|
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for (nbt = nbiTypes->beginType(j); nbt != NULL; |
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nbt = nbiTypes->nextType(j)) { |
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|
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if (nbt->isEAM()) { |
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|
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pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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|
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GenericData* data = nbt->getPropertyByName("EAM"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n" |
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"\tEAM parameters for %s - %s interaction.\n", |
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atypes.first->getName().c_str(), |
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atypes.second->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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EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data); |
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if (eamData == NULL) { |
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sprintf( painCave.errMsg, |
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"EAM::rebuildMixingMap could not convert GenericData to\n" |
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"\tEAMMixingData for %s - %s interaction.\n", |
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atypes.first->getName().c_str(), |
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atypes.second->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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EAMMixingParam eamParam = eamData->getData(); |
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|
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vector<RealType> phiAB = eamParam.phi; |
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RealType dr = eamParam.dr; |
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int nr = eamParam.nr; |
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|
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addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB); |
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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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|
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|
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void EAM::addType(AtomType* atomType){ |
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|
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EAMAtomData eamAtomData; |
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|
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eamAtomData.rho = getRho(atomType); |
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eamAtomData.F = getF(atomType); |
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eamAtomData.Z = getZ(atomType); |
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eamAtomData.rcut = getRcut(atomType); |
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|
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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 = EAMlist.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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"EAM 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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EAMMap[atomType] = eamAtomData; |
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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<AtomType*, EAMAtomData>::iterator it; |
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for( it = EAMMap.begin(); it != EAMMap.end(); ++it) { |
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|
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AtomType* atype2 = (*it).first; |
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|
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EAMInteractionData mixer; |
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mixer.phi = getPhi(atomType, atype2); |
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mixer.explicitlySet = false; |
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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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return; |
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} |
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|
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void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2, |
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RealType dr, int nr, |
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vector<RealType> phiVals) { |
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|
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// in case these weren't already in the map |
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addType(atype1); |
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addType(atype2); |
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|
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EAMInteractionData mixer; |
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CubicSpline* cs = new CubicSpline(); |
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vector<RealType> rVals; |
| 337 |
|
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for (int i = 0; i < nr; i++) rVals.push_back(i * dr); |
| 339 |
|
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cs->addPoints(rVals, phiVals); |
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mixer.phi = cs; |
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mixer.explicitlySet = true; |
| 343 |
|
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pair<AtomType*, AtomType*> key1, key2; |
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key1 = make_pair(atype1, atype2); |
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key2 = make_pair(atype2, atype1); |
| 347 |
|
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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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return; |
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} |
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|
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void EAM::calcDensity(InteractionData &idat) { |
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|
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if (!initialized_) initialize(); |
| 358 |
|
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EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 360 |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 361 |
|
| 362 |
if (haveCutoffRadius_) |
| 363 |
if ( *(idat.rij) > eamRcut_) return; |
| 364 |
|
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if ( *(idat.rij) < data1.rcut) { |
| 366 |
*(idat.rho1) += data1.rho->getValueAt( *(idat.rij)); |
| 367 |
|
| 368 |
|
| 369 |
if ( *(idat.rij) < data2.rcut) |
| 370 |
*(idat.rho2) += data2.rho->getValueAt( *(idat.rij)); |
| 371 |
|
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return; |
| 373 |
} |
| 374 |
} |
| 375 |
|
| 376 |
void EAM::calcFunctional(SelfData &sdat) { |
| 377 |
|
| 378 |
if (!initialized_) initialize(); |
| 379 |
|
| 380 |
EAMAtomData data1 = EAMMap[ sdat.atype ]; |
| 381 |
|
| 382 |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) ); |
| 383 |
|
| 384 |
*(sdat.frho) = result.first; |
| 385 |
*(sdat.dfrhodrho) = result.second; |
| 386 |
|
| 387 |
(*(sdat.pot))[METALLIC_FAMILY] += result.first; |
| 388 |
*(sdat.particlePot) += result.first; |
| 389 |
|
| 390 |
return; |
| 391 |
} |
| 392 |
|
| 393 |
|
| 394 |
void EAM::calcForce(InteractionData &idat) { |
| 395 |
|
| 396 |
if (!initialized_) initialize(); |
| 397 |
|
| 398 |
|
| 399 |
|
| 400 |
if (haveCutoffRadius_) |
| 401 |
if ( *(idat.rij) > eamRcut_) return; |
| 402 |
|
| 403 |
pair<RealType, RealType> res; |
| 404 |
|
| 405 |
|
| 406 |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 407 |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 408 |
|
| 409 |
// get type-specific cutoff radii |
| 410 |
|
| 411 |
RealType rci = data1.rcut; |
| 412 |
RealType rcj = data2.rcut; |
| 413 |
|
| 414 |
RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0); |
| 415 |
RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0); |
| 416 |
RealType phab(0.0), dvpdr(0.0); |
| 417 |
RealType drhoidr, drhojdr, dudr; |
| 418 |
|
| 419 |
if ( *(idat.rij) < rci) { |
| 420 |
res = data1.rho->getValueAndDerivativeAt( *(idat.rij)); |
| 421 |
rha = res.first; |
| 422 |
drha = res.second; |
| 423 |
|
| 424 |
res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 425 |
pha = res.first; |
| 426 |
dpha = res.second; |
| 427 |
} |
| 428 |
|
| 429 |
if ( *(idat.rij) < rcj) { |
| 430 |
res = data2.rho->getValueAndDerivativeAt( *(idat.rij) ); |
| 431 |
rhb = res.first; |
| 432 |
drhb = res.second; |
| 433 |
|
| 434 |
res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 435 |
phb = res.first; |
| 436 |
dphb = res.second; |
| 437 |
} |
| 438 |
|
| 439 |
switch(mixMeth_) { |
| 440 |
case eamJohnson: |
| 441 |
|
| 442 |
if ( *(idat.rij) < rci) { |
| 443 |
phab = phab + 0.5 * (rhb / rha) * pha; |
| 444 |
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 445 |
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 446 |
} |
| 447 |
|
| 448 |
|
| 449 |
|
| 450 |
if ( *(idat.rij) < rcj) { |
| 451 |
phab = phab + 0.5 * (rha / rhb) * phb; |
| 452 |
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 453 |
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 454 |
} |
| 455 |
|
| 456 |
break; |
| 457 |
|
| 458 |
case eamDaw: |
| 459 |
res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij)); |
| 460 |
phab = res.first; |
| 461 |
dvpdr = res.second; |
| 462 |
|
| 463 |
break; |
| 464 |
case eamUnknown: |
| 465 |
default: |
| 466 |
|
| 467 |
sprintf(painCave.errMsg, |
| 468 |
"EAM::calcForce hit a mixing method it doesn't know about!\n" |
| 469 |
); |
| 470 |
painCave.severity = OPENMD_ERROR; |
| 471 |
painCave.isFatal = 1; |
| 472 |
simError(); |
| 473 |
|
| 474 |
} |
| 475 |
|
| 476 |
drhoidr = drha; |
| 477 |
drhojdr = drhb; |
| 478 |
|
| 479 |
dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; |
| 480 |
|
| 481 |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 482 |
|
| 483 |
// particlePot is the difference between the full potential and |
| 484 |
// the full potential without the presence of a particular |
| 485 |
// particle (atom1). |
| 486 |
// |
| 487 |
// This reduces the density at other particle locations, so we |
| 488 |
// need to recompute the density at atom2 assuming atom1 didn't |
| 489 |
// contribute. This then requires recomputing the density |
| 490 |
// functional for atom2 as well. |
| 491 |
|
| 492 |
*(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) |
| 493 |
- *(idat.frho2); |
| 494 |
|
| 495 |
*(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb) |
| 496 |
- *(idat.frho1); |
| 497 |
|
| 498 |
(*(idat.pot))[METALLIC_FAMILY] += phab; |
| 499 |
|
| 500 |
*(idat.vpair) += phab; |
| 501 |
|
| 502 |
return; |
| 503 |
|
| 504 |
} |
| 505 |
|
| 506 |
RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 507 |
if (!initialized_) initialize(); |
| 508 |
|
| 509 |
RealType cut = 0.0; |
| 510 |
|
| 511 |
map<AtomType*, EAMAtomData>::iterator it; |
| 512 |
|
| 513 |
it = EAMMap.find(atypes.first); |
| 514 |
if (it != EAMMap.end()) { |
| 515 |
EAMAtomData data1 = (*it).second; |
| 516 |
cut = data1.rcut; |
| 517 |
} |
| 518 |
|
| 519 |
it = EAMMap.find(atypes.second); |
| 520 |
if (it != EAMMap.end()) { |
| 521 |
EAMAtomData data2 = (*it).second; |
| 522 |
if (data2.rcut > cut) |
| 523 |
cut = data2.rcut; |
| 524 |
} |
| 525 |
|
| 526 |
return cut; |
| 527 |
} |
| 528 |
} |
| 529 |
|
