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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] 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/Electrostatic.hpp" |
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#include "utils/simError.h" |
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#include "types/NonBondedInteractionType.hpp" |
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#include "types/FixedChargeAdapter.hpp" |
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#include "types/FluctuatingChargeAdapter.hpp" |
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#include "types/MultipoleAdapter.hpp" |
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#include "io/Globals.hpp" |
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#include "nonbonded/SlaterIntegrals.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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#include "math/erfc.hpp" |
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#include "math/SquareMatrix.hpp" |
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|
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namespace OpenMD { |
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|
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Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false), |
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forceField_(NULL), info_(NULL), |
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haveCutoffRadius_(false), |
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haveDampingAlpha_(false), |
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haveDielectric_(false), |
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haveElectroSplines_(false) |
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{} |
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|
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void Electrostatic::initialize() { |
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|
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Globals* simParams_ = info_->getSimParams(); |
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|
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summationMap_["HARD"] = esm_HARD; |
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summationMap_["NONE"] = esm_HARD; |
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summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION; |
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summationMap_["SHIFTED_POTENTIAL"] = esm_SHIFTED_POTENTIAL; |
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summationMap_["SHIFTED_FORCE"] = esm_SHIFTED_FORCE; |
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summationMap_["REACTION_FIELD"] = esm_REACTION_FIELD; |
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summationMap_["EWALD_FULL"] = esm_EWALD_FULL; |
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summationMap_["EWALD_PME"] = esm_EWALD_PME; |
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summationMap_["EWALD_SPME"] = esm_EWALD_SPME; |
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screeningMap_["DAMPED"] = DAMPED; |
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screeningMap_["UNDAMPED"] = UNDAMPED; |
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|
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// these prefactors convert the multipole interactions into kcal / mol |
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// all were computed assuming distances are measured in angstroms |
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// Charge-Charge, assuming charges are measured in electrons |
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pre11_ = 332.0637778; |
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// Charge-Dipole, assuming charges are measured in electrons, and |
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// dipoles are measured in debyes |
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pre12_ = 69.13373; |
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// Dipole-Dipole, assuming dipoles are measured in Debye |
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pre22_ = 14.39325; |
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// Charge-Quadrupole, assuming charges are measured in electrons, and |
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// quadrupoles are measured in 10^-26 esu cm^2 |
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// This unit is also known affectionately as an esu centibarn. |
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pre14_ = 69.13373; |
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// Dipole-Quadrupole, assuming dipoles are measured in debyes and |
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// quadrupoles in esu centibarns: |
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pre24_ = 14.39325; |
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// Quadrupole-Quadrupole, assuming esu centibarns: |
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pre44_ = 14.39325; |
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|
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// conversions for the simulation box dipole moment |
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chargeToC_ = 1.60217733e-19; |
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angstromToM_ = 1.0e-10; |
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debyeToCm_ = 3.33564095198e-30; |
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|
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// Default number of points for electrostatic splines |
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np_ = 140; |
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|
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// variables to handle different summation methods for long-range |
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// electrostatics: |
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summationMethod_ = esm_HARD; |
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screeningMethod_ = UNDAMPED; |
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dielectric_ = 1.0; |
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|
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// check the summation method: |
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if (simParams_->haveElectrostaticSummationMethod()) { |
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string myMethod = simParams_->getElectrostaticSummationMethod(); |
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toUpper(myMethod); |
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map<string, ElectrostaticSummationMethod>::iterator i; |
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i = summationMap_.find(myMethod); |
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if ( i != summationMap_.end() ) { |
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summationMethod_ = (*i).second; |
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} else { |
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// throw error |
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sprintf( painCave.errMsg, |
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"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n" |
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"\t(Input file specified %s .)\n" |
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"\telectrostaticSummationMethod must be one of: \"hard\",\n" |
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"\t\"shifted_potential\", \"shifted_force\", or \n" |
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"\t\"reaction_field\".\n", myMethod.c_str() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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// set ElectrostaticSummationMethod to the cutoffMethod: |
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if (simParams_->haveCutoffMethod()){ |
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string myMethod = simParams_->getCutoffMethod(); |
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toUpper(myMethod); |
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map<string, ElectrostaticSummationMethod>::iterator i; |
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i = summationMap_.find(myMethod); |
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if ( i != summationMap_.end() ) { |
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summationMethod_ = (*i).second; |
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} |
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} |
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} |
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|
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if (summationMethod_ == esm_REACTION_FIELD) { |
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if (!simParams_->haveDielectric()) { |
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// throw warning |
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sprintf( painCave.errMsg, |
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"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n" |
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"\tA default value of %f will be used for the dielectric.\n", dielectric_); |
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painCave.isFatal = 0; |
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painCave.severity = OPENMD_INFO; |
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simError(); |
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} else { |
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dielectric_ = simParams_->getDielectric(); |
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} |
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haveDielectric_ = true; |
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} |
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|
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if (simParams_->haveElectrostaticScreeningMethod()) { |
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string myScreen = simParams_->getElectrostaticScreeningMethod(); |
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toUpper(myScreen); |
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map<string, ElectrostaticScreeningMethod>::iterator i; |
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i = screeningMap_.find(myScreen); |
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if ( i != screeningMap_.end()) { |
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screeningMethod_ = (*i).second; |
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} else { |
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sprintf( painCave.errMsg, |
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"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
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"\t(Input file specified %s .)\n" |
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"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
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"or \"damped\".\n", myScreen.c_str() ); |
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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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// check to make sure a cutoff value has been set: |
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if (!haveCutoffRadius_) { |
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sprintf( painCave.errMsg, "Electrostatic::initialize has no Default " |
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"Cutoff value!\n"); |
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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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if (screeningMethod_ == DAMPED) { |
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if (!simParams_->haveDampingAlpha()) { |
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// first set a cutoff dependent alpha value |
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// we assume alpha depends linearly with rcut from 0 to 20.5 ang |
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dampingAlpha_ = 0.425 - cutoffRadius_* 0.02; |
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if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0; |
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|
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// throw warning |
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sprintf( painCave.errMsg, |
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"Electrostatic::initialize: dampingAlpha was not specified in the\n" |
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"\tinput file. A default value of %f (1/ang) will be used for the\n" |
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"\tcutoff of %f (ang).\n", |
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dampingAlpha_, cutoffRadius_); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} else { |
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dampingAlpha_ = simParams_->getDampingAlpha(); |
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} |
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haveDampingAlpha_ = true; |
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} |
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|
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// find all of the Electrostatic 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->isElectrostatic()) |
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addType(at); |
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} |
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|
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if (summationMethod_ == esm_REACTION_FIELD) { |
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preRF_ = (dielectric_ - 1.0) / |
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((2.0 * dielectric_ + 1.0) * pow(cutoffRadius_,3) ); |
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} |
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|
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RealType b0c, b1c, b2c, b3c, b4c, b5c; |
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RealType db0c_1, db0c_2, db0c_3, db0c_4, db0c_5; |
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RealType a2, expTerm, invArootPi; |
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|
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RealType r = cutoffRadius_; |
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RealType r2 = r * r; |
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|
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if (screeningMethod_ == DAMPED) { |
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a2 = dampingAlpha_ * dampingAlpha_; |
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invArootPi = 1.0 / (dampingAlpha_ * sqrt(M_PI)); |
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expTerm = exp(-a2 * r2); |
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// values of Smith's B_l functions at the cutoff radius: |
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b0c = erfc(dampingAlpha_ * r) / r; |
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b1c = ( b0c + 2.0*a2 * expTerm * invArootPi) / r2; |
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b2c = (3.0 * b1c + pow(2.0*a2, 2) * expTerm * invArootPi) / r2; |
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b3c = (5.0 * b2c + pow(2.0*a2, 3) * expTerm * invArootPi) / r2; |
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b4c = (7.0 * b3c + pow(2.0*a2, 4) * expTerm * invArootPi) / r2; |
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b5c = (9.0 * b4c + pow(2.0*a2, 5) * expTerm * invArootPi) / r2; |
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selfMult_ = b0c + a2 * invArootPi; |
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} else { |
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a2 = 0.0; |
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b0c = 1.0 / r; |
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b1c = ( b0c) / r2; |
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b2c = (3.0 * b1c) / r2; |
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b3c = (5.0 * b2c) / r2; |
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b4c = (7.0 * b3c) / r2; |
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b5c = (9.0 * b4c) / r2; |
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selfMult_ = b0c; |
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} |
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|
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// higher derivatives of B_0 at the cutoff radius: |
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db0c_1 = -r * b1c; |
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db0c_2 = -b1c + r2 * b2c; |
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db0c_3 = 3.0*r*b2c - r2*r*b3c; |
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db0c_4 = 3.0*b2c - 6.0*r2*b3c + r2*r2*b4c; |
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db0c_5 = -15.0*r*b3c + 10.0*r2*r*b4c - r2*r2*r*b5c; |
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|
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// working variables for the splines: |
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RealType ri, ri2; |
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RealType b0, b1, b2, b3, b4, b5; |
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RealType db0_1, db0_2, db0_3, db0_4, db0_5; |
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RealType f0; |
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RealType g0, g1, g2, g3, g4; |
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RealType h1, h2, h3, h4; |
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RealType s2, s3, s4; |
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RealType t3, t4; |
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RealType u4; |
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|
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// working variables for Taylor expansion: |
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RealType rmRc, rmRc2, rmRc3, rmRc4; |
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|
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// Approximate using splines using a maximum of 0.1 Angstroms |
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// between points. |
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int nptest = int((cutoffRadius_ + 2.0) / 0.1); |
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np_ = (np_ > nptest) ? np_ : nptest; |
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|
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// Add a 2 angstrom safety window to deal with cutoffGroups that |
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// have charged atoms longer than the cutoffRadius away from each |
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// other. Splining is almost certainly the best choice here. |
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// Direct calls to erfc would be preferrable if it is a very fast |
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// implementation. |
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|
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RealType dx = (cutoffRadius_ + 2.0) / RealType(np_); |
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|
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// Storage vectors for the computed functions |
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vector<RealType> rv; |
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vector<RealType> v01v, v02v; |
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vector<RealType> v11v, v12v, v13v; |
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vector<RealType> v21v, v22v, v23v, v24v; |
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vector<RealType> v31v, v32v, v33v, v34v, v35v; |
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vector<RealType> v41v, v42v, v43v, v44v, v45v, v46v; |
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|
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for (int i = 1; i < np_ + 1; i++) { |
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r = RealType(i) * dx; |
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rv.push_back(r); |
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|
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ri = 1.0 / r; |
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ri2 = ri * ri; |
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|
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r2 = r * r; |
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expTerm = exp(-a2 * r2); |
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|
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// Taylor expansion factors (no need for factorials this way): |
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rmRc = r - cutoffRadius_; |
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rmRc2 = rmRc * rmRc / 2.0; |
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rmRc3 = rmRc2 * rmRc / 3.0; |
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rmRc4 = rmRc3 * rmRc / 4.0; |
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|
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// values of Smith's B_l functions at r: |
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if (screeningMethod_ == DAMPED) { |
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b0 = erfc(dampingAlpha_ * r) * ri; |
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b1 = ( b0 + 2.0*a2 * expTerm * invArootPi) * ri2; |
| 323 |
b2 = (3.0 * b1 + pow(2.0*a2, 2) * expTerm * invArootPi) * ri2; |
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b3 = (5.0 * b2 + pow(2.0*a2, 3) * expTerm * invArootPi) * ri2; |
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b4 = (7.0 * b3 + pow(2.0*a2, 4) * expTerm * invArootPi) * ri2; |
| 326 |
b5 = (9.0 * b4 + pow(2.0*a2, 5) * expTerm * invArootPi) * ri2; |
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} else { |
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b0 = ri; |
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b1 = ( b0) * ri2; |
| 330 |
b2 = (3.0 * b1) * ri2; |
| 331 |
b3 = (5.0 * b2) * ri2; |
| 332 |
b4 = (7.0 * b3) * ri2; |
| 333 |
b5 = (9.0 * b4) * ri2; |
| 334 |
} |
| 335 |
|
| 336 |
// higher derivatives of B_0 at r: |
| 337 |
db0_1 = -r * b1; |
| 338 |
db0_2 = -b1 + r2 * b2; |
| 339 |
db0_3 = 3.0*r*b2 - r2*r*b3; |
| 340 |
db0_4 = 3.0*b2 - 6.0*r2*b3 + r2*r2*b4; |
| 341 |
db0_5 = -15.0*r*b3 + 10.0*r2*r*b4 - r2*r2*r*b5; |
| 342 |
|
| 343 |
|
| 344 |
switch (summationMethod_) { |
| 345 |
case esm_SHIFTED_FORCE: |
| 346 |
f0 = b0 - b0c - rmRc*db0c_1; |
| 347 |
|
| 348 |
g0 = db0_1 - db0c_1; |
| 349 |
g1 = g0 - rmRc *db0c_2; |
| 350 |
g2 = g1 - rmRc2*db0c_3; |
| 351 |
g3 = g2 - rmRc3*db0c_4; |
| 352 |
g4 = g3 - rmRc4*db0c_5; |
| 353 |
|
| 354 |
h1 = db0_2 - db0c_2; |
| 355 |
h2 = h1 - rmRc *db0c_3; |
| 356 |
h3 = h2 - rmRc2*db0c_4; |
| 357 |
h4 = h3 - rmRc3*db0c_5; |
| 358 |
|
| 359 |
s2 = db0_3 - db0c_3; |
| 360 |
s3 = s2 - rmRc *db0c_4; |
| 361 |
s4 = s3 - rmRc2*db0c_5; |
| 362 |
|
| 363 |
t3 = db0_4 - db0c_4; |
| 364 |
t4 = t3 - rmRc *db0c_5; |
| 365 |
|
| 366 |
u4 = db0_5 - db0c_5; |
| 367 |
break; |
| 368 |
|
| 369 |
case esm_SHIFTED_POTENTIAL: |
| 370 |
f0 = b0 - b0c; |
| 371 |
|
| 372 |
g0 = db0_1; |
| 373 |
g1 = db0_1 - db0c_1; |
| 374 |
g2 = g1 - rmRc *db0c_2; |
| 375 |
g3 = g2 - rmRc2*db0c_3; |
| 376 |
g4 = g3 - rmRc3*db0c_4; |
| 377 |
|
| 378 |
h1 = db0_2; |
| 379 |
h2 = db0_2 - db0c_2; |
| 380 |
h3 = h2 - rmRc *db0c_3; |
| 381 |
h4 = h3 - rmRc2*db0c_4; |
| 382 |
|
| 383 |
s2 = db0_3; |
| 384 |
s3 = db0_3 - db0c_3; |
| 385 |
s4 = s3 - rmRc *db0c_4; |
| 386 |
|
| 387 |
t3 = db0_4; |
| 388 |
t4 = db0_4 - db0c_4; |
| 389 |
|
| 390 |
u4 = db0_5; |
| 391 |
break; |
| 392 |
|
| 393 |
case esm_SWITCHING_FUNCTION: |
| 394 |
case esm_HARD: |
| 395 |
f0 = b0; |
| 396 |
|
| 397 |
g0 = db0_1; |
| 398 |
g1 = g0; |
| 399 |
g2 = g1; |
| 400 |
g3 = g2; |
| 401 |
g4 = g3; |
| 402 |
|
| 403 |
h1 = db0_2; |
| 404 |
h2 = h1; |
| 405 |
h3 = h2; |
| 406 |
h4 = h3; |
| 407 |
|
| 408 |
s2 = db0_3; |
| 409 |
s3 = s2; |
| 410 |
s4 = s3; |
| 411 |
|
| 412 |
t3 = db0_4; |
| 413 |
t4 = t3; |
| 414 |
|
| 415 |
u4 = db0_5; |
| 416 |
break; |
| 417 |
|
| 418 |
case esm_REACTION_FIELD: |
| 419 |
|
| 420 |
// following DL_POLY's lead for shifting the image charge potential: |
| 421 |
f0 = b0 + preRF_ * r2 |
| 422 |
- (b0c + preRF_ * cutoffRadius_ * cutoffRadius_); |
| 423 |
|
| 424 |
g0 = db0_1 + preRF_ * 2.0 * r; |
| 425 |
g1 = g0; |
| 426 |
g2 = g1; |
| 427 |
g3 = g2; |
| 428 |
g4 = g3; |
| 429 |
|
| 430 |
h1 = db0_2 + preRF_ * 2.0; |
| 431 |
h2 = h1; |
| 432 |
h3 = h2; |
| 433 |
h4 = h3; |
| 434 |
|
| 435 |
s2 = db0_3; |
| 436 |
s3 = s2; |
| 437 |
s4 = s3; |
| 438 |
|
| 439 |
t3 = db0_4; |
| 440 |
t4 = t3; |
| 441 |
|
| 442 |
u4 = db0_5; |
| 443 |
break; |
| 444 |
|
| 445 |
case esm_EWALD_FULL: |
| 446 |
case esm_EWALD_PME: |
| 447 |
case esm_EWALD_SPME: |
| 448 |
default : |
| 449 |
map<string, ElectrostaticSummationMethod>::iterator i; |
| 450 |
std::string meth; |
| 451 |
for (i = summationMap_.begin(); i != summationMap_.end(); ++i) { |
| 452 |
if ((*i).second == summationMethod_) meth = (*i).first; |
| 453 |
} |
| 454 |
sprintf( painCave.errMsg, |
| 455 |
"Electrostatic::initialize: electrostaticSummationMethod %s \n" |
| 456 |
"\thas not been implemented yet. Please select one of:\n" |
| 457 |
"\t\"hard\", \"shifted_potential\", or \"shifted_force\"\n", |
| 458 |
meth.c_str() ); |
| 459 |
painCave.isFatal = 1; |
| 460 |
simError(); |
| 461 |
break; |
| 462 |
} |
| 463 |
|
| 464 |
v01 = f0; |
| 465 |
v02 = g0; |
| 466 |
|
| 467 |
v11 = g1; |
| 468 |
v12 = g1 * ri; |
| 469 |
v13 = h1 - v12; |
| 470 |
|
| 471 |
v21 = g2 * ri; |
| 472 |
v22 = h2 - v21; |
| 473 |
v23 = v22 * ri; |
| 474 |
v24 = s2 - 3.0*v23; |
| 475 |
|
| 476 |
v31 = (h3 - g3 * ri) * ri; |
| 477 |
v32 = s3 - 3.0*v31; |
| 478 |
v33 = v31 * ri; |
| 479 |
v34 = v32 * ri; |
| 480 |
v35 = t3 - 6.0*v34 - 3.0*v33; |
| 481 |
|
| 482 |
v41 = (h4 - g4 * ri) * ri2; |
| 483 |
v42 = s4 * ri - 3.0*v41; |
| 484 |
v43 = t4 - 6.0*v42 - 3.0*v41; |
| 485 |
v44 = v42 * ri; |
| 486 |
v45 = v43 * ri; |
| 487 |
v46 = u4 - 10.0*v45 - 15.0*v44; |
| 488 |
|
| 489 |
// Add these computed values to the storage vectors for spline creation: |
| 490 |
v01v.push_back(v01); |
| 491 |
v02v.push_back(v02); |
| 492 |
|
| 493 |
v11v.push_back(v11); |
| 494 |
v12v.push_back(v12); |
| 495 |
v13v.push_back(v13); |
| 496 |
|
| 497 |
v21v.push_back(v21); |
| 498 |
v22v.push_back(v22); |
| 499 |
v23v.push_back(v23); |
| 500 |
v24v.push_back(v24); |
| 501 |
|
| 502 |
v31v.push_back(v31); |
| 503 |
v32v.push_back(v32); |
| 504 |
v33v.push_back(v33); |
| 505 |
v34v.push_back(v34); |
| 506 |
v35v.push_back(v35); |
| 507 |
|
| 508 |
v41v.push_back(v41); |
| 509 |
v42v.push_back(v42); |
| 510 |
v43v.push_back(v43); |
| 511 |
v44v.push_back(v44); |
| 512 |
v45v.push_back(v45); |
| 513 |
v46v.push_back(v46); |
| 514 |
} |
| 515 |
|
| 516 |
// construct the spline structures and fill them with the values we've |
| 517 |
// computed: |
| 518 |
|
| 519 |
v01s = new CubicSpline(); |
| 520 |
v01s->addPoints(rv, v01v); |
| 521 |
v02s = new CubicSpline(); |
| 522 |
v02s->addPoints(rv, v02v); |
| 523 |
|
| 524 |
v11s = new CubicSpline(); |
| 525 |
v11s->addPoints(rv, v11v); |
| 526 |
v12s = new CubicSpline(); |
| 527 |
v12s->addPoints(rv, v12v); |
| 528 |
v13s = new CubicSpline(); |
| 529 |
v13s->addPoints(rv, v13v); |
| 530 |
|
| 531 |
v21s = new CubicSpline(); |
| 532 |
v21s->addPoints(rv, v21v); |
| 533 |
v22s = new CubicSpline(); |
| 534 |
v22s->addPoints(rv, v22v); |
| 535 |
v23s = new CubicSpline(); |
| 536 |
v23s->addPoints(rv, v23v); |
| 537 |
v24s = new CubicSpline(); |
| 538 |
v24s->addPoints(rv, v24v); |
| 539 |
|
| 540 |
v31s = new CubicSpline(); |
| 541 |
v31s->addPoints(rv, v31v); |
| 542 |
v32s = new CubicSpline(); |
| 543 |
v32s->addPoints(rv, v32v); |
| 544 |
v33s = new CubicSpline(); |
| 545 |
v33s->addPoints(rv, v33v); |
| 546 |
v34s = new CubicSpline(); |
| 547 |
v34s->addPoints(rv, v34v); |
| 548 |
v35s = new CubicSpline(); |
| 549 |
v35s->addPoints(rv, v35v); |
| 550 |
|
| 551 |
v41s = new CubicSpline(); |
| 552 |
v41s->addPoints(rv, v41v); |
| 553 |
v42s = new CubicSpline(); |
| 554 |
v42s->addPoints(rv, v42v); |
| 555 |
v43s = new CubicSpline(); |
| 556 |
v43s->addPoints(rv, v43v); |
| 557 |
v44s = new CubicSpline(); |
| 558 |
v44s->addPoints(rv, v44v); |
| 559 |
v45s = new CubicSpline(); |
| 560 |
v45s->addPoints(rv, v45v); |
| 561 |
v46s = new CubicSpline(); |
| 562 |
v46s->addPoints(rv, v46v); |
| 563 |
|
| 564 |
haveElectroSplines_ = true; |
| 565 |
|
| 566 |
initialized_ = true; |
| 567 |
} |
| 568 |
|
| 569 |
void Electrostatic::addType(AtomType* atomType){ |
| 570 |
|
| 571 |
ElectrostaticAtomData electrostaticAtomData; |
| 572 |
electrostaticAtomData.is_Charge = false; |
| 573 |
electrostaticAtomData.is_Dipole = false; |
| 574 |
electrostaticAtomData.is_Quadrupole = false; |
| 575 |
electrostaticAtomData.is_Fluctuating = false; |
| 576 |
|
| 577 |
FixedChargeAdapter fca = FixedChargeAdapter(atomType); |
| 578 |
|
| 579 |
if (fca.isFixedCharge()) { |
| 580 |
electrostaticAtomData.is_Charge = true; |
| 581 |
electrostaticAtomData.fixedCharge = fca.getCharge(); |
| 582 |
} |
| 583 |
|
| 584 |
MultipoleAdapter ma = MultipoleAdapter(atomType); |
| 585 |
if (ma.isMultipole()) { |
| 586 |
if (ma.isDipole()) { |
| 587 |
electrostaticAtomData.is_Dipole = true; |
| 588 |
electrostaticAtomData.dipole = ma.getDipole(); |
| 589 |
} |
| 590 |
if (ma.isQuadrupole()) { |
| 591 |
electrostaticAtomData.is_Quadrupole = true; |
| 592 |
electrostaticAtomData.quadrupole = ma.getQuadrupole(); |
| 593 |
} |
| 594 |
} |
| 595 |
|
| 596 |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType); |
| 597 |
|
| 598 |
if (fqa.isFluctuatingCharge()) { |
| 599 |
electrostaticAtomData.is_Fluctuating = true; |
| 600 |
electrostaticAtomData.electronegativity = fqa.getElectronegativity(); |
| 601 |
electrostaticAtomData.hardness = fqa.getHardness(); |
| 602 |
electrostaticAtomData.slaterN = fqa.getSlaterN(); |
| 603 |
electrostaticAtomData.slaterZeta = fqa.getSlaterZeta(); |
| 604 |
} |
| 605 |
|
| 606 |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 607 |
ret = ElectrostaticList.insert( pair<int,AtomType*>(atomType->getIdent(), |
| 608 |
atomType) ); |
| 609 |
if (ret.second == false) { |
| 610 |
sprintf( painCave.errMsg, |
| 611 |
"Electrostatic already had a previous entry with ident %d\n", |
| 612 |
atomType->getIdent() ); |
| 613 |
painCave.severity = OPENMD_INFO; |
| 614 |
painCave.isFatal = 0; |
| 615 |
simError(); |
| 616 |
} |
| 617 |
|
| 618 |
ElectrostaticMap[atomType] = electrostaticAtomData; |
| 619 |
|
| 620 |
// Now, iterate over all known types and add to the mixing map: |
| 621 |
|
| 622 |
map<AtomType*, ElectrostaticAtomData>::iterator it; |
| 623 |
for( it = ElectrostaticMap.begin(); it != ElectrostaticMap.end(); ++it) { |
| 624 |
AtomType* atype2 = (*it).first; |
| 625 |
ElectrostaticAtomData eaData2 = (*it).second; |
| 626 |
if (eaData2.is_Fluctuating && electrostaticAtomData.is_Fluctuating) { |
| 627 |
|
| 628 |
RealType a = electrostaticAtomData.slaterZeta; |
| 629 |
RealType b = eaData2.slaterZeta; |
| 630 |
int m = electrostaticAtomData.slaterN; |
| 631 |
int n = eaData2.slaterN; |
| 632 |
|
| 633 |
// Create the spline of the coulombic integral for s-type |
| 634 |
// Slater orbitals. Add a 2 angstrom safety window to deal |
| 635 |
// with cutoffGroups that have charged atoms longer than the |
| 636 |
// cutoffRadius away from each other. |
| 637 |
|
| 638 |
RealType rval; |
| 639 |
RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1); |
| 640 |
vector<RealType> rvals; |
| 641 |
vector<RealType> Jvals; |
| 642 |
// don't start at i = 0, as rval = 0 is undefined for the |
| 643 |
// slater overlap integrals. |
| 644 |
for (int i = 1; i < np_+1; i++) { |
| 645 |
rval = RealType(i) * dr; |
| 646 |
rvals.push_back(rval); |
| 647 |
Jvals.push_back(sSTOCoulInt( a, b, m, n, rval * |
| 648 |
PhysicalConstants::angstromToBohr ) * |
| 649 |
PhysicalConstants::hartreeToKcal ); |
| 650 |
} |
| 651 |
|
| 652 |
CubicSpline* J = new CubicSpline(); |
| 653 |
J->addPoints(rvals, Jvals); |
| 654 |
|
| 655 |
pair<AtomType*, AtomType*> key1, key2; |
| 656 |
key1 = make_pair(atomType, atype2); |
| 657 |
key2 = make_pair(atype2, atomType); |
| 658 |
|
| 659 |
Jij[key1] = J; |
| 660 |
Jij[key2] = J; |
| 661 |
} |
| 662 |
} |
| 663 |
|
| 664 |
return; |
| 665 |
} |
| 666 |
|
| 667 |
void Electrostatic::setCutoffRadius( RealType rCut ) { |
| 668 |
cutoffRadius_ = rCut; |
| 669 |
haveCutoffRadius_ = true; |
| 670 |
} |
| 671 |
|
| 672 |
void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) { |
| 673 |
summationMethod_ = esm; |
| 674 |
} |
| 675 |
void Electrostatic::setElectrostaticScreeningMethod( ElectrostaticScreeningMethod sm ) { |
| 676 |
screeningMethod_ = sm; |
| 677 |
} |
| 678 |
void Electrostatic::setDampingAlpha( RealType alpha ) { |
| 679 |
dampingAlpha_ = alpha; |
| 680 |
haveDampingAlpha_ = true; |
| 681 |
} |
| 682 |
void Electrostatic::setReactionFieldDielectric( RealType dielectric ){ |
| 683 |
dielectric_ = dielectric; |
| 684 |
haveDielectric_ = true; |
| 685 |
} |
| 686 |
|
| 687 |
void Electrostatic::calcForce(InteractionData &idat) { |
| 688 |
|
| 689 |
RealType C_a, C_b; // Charges |
| 690 |
Vector3d D_a, D_b; // Dipoles (space-fixed) |
| 691 |
Mat3x3d Q_a, Q_b; // Quadrupoles (space-fixed) |
| 692 |
|
| 693 |
RealType ri; // Distance utility scalar |
| 694 |
RealType rdDa, rdDb; // Dipole utility scalars |
| 695 |
Vector3d rxDa, rxDb; // Dipole utility vectors |
| 696 |
RealType rdQar, rdQbr, trQa, trQb; // Quadrupole utility scalars |
| 697 |
Vector3d Qar, Qbr, rQa, rQb, rxQar, rxQbr; // Quadrupole utility vectors |
| 698 |
RealType pref; |
| 699 |
|
| 700 |
RealType DadDb, trQaQb, DadQbr, DbdQar; // Cross-interaction scalars |
| 701 |
RealType rQaQbr; |
| 702 |
Vector3d DaxDb, DadQb, DbdQa, DaxQbr, DbxQar; // Cross-interaction vectors |
| 703 |
Vector3d rQaQb, QaQbr, QaxQb, rQaxQbr; |
| 704 |
Mat3x3d QaQb; // Cross-interaction matrices |
| 705 |
|
| 706 |
RealType U(0.0); // Potential |
| 707 |
Vector3d F(0.0); // Force |
| 708 |
Vector3d Ta(0.0); // Torque on site a |
| 709 |
Vector3d Tb(0.0); // Torque on site b |
| 710 |
Vector3d Ea(0.0); // Electric field at site a |
| 711 |
Vector3d Eb(0.0); // Electric field at site b |
| 712 |
RealType dUdCa(0.0); // fluctuating charge force at site a |
| 713 |
RealType dUdCb(0.0); // fluctuating charge force at site a |
| 714 |
|
| 715 |
// Indirect interactions mediated by the reaction field. |
| 716 |
RealType indirect_Pot(0.0); // Potential |
| 717 |
Vector3d indirect_F(0.0); // Force |
| 718 |
Vector3d indirect_Ta(0.0); // Torque on site a |
| 719 |
Vector3d indirect_Tb(0.0); // Torque on site b |
| 720 |
|
| 721 |
// Excluded potential that is still computed for fluctuating charges |
| 722 |
RealType excluded_Pot(0.0); |
| 723 |
|
| 724 |
RealType rfContrib, coulInt; |
| 725 |
|
| 726 |
// spline for coulomb integral |
| 727 |
CubicSpline* J; |
| 728 |
|
| 729 |
if (!initialized_) initialize(); |
| 730 |
|
| 731 |
ElectrostaticAtomData data1 = ElectrostaticMap[idat.atypes.first]; |
| 732 |
ElectrostaticAtomData data2 = ElectrostaticMap[idat.atypes.second]; |
| 733 |
|
| 734 |
// some variables we'll need independent of electrostatic type: |
| 735 |
|
| 736 |
ri = 1.0 / *(idat.rij); |
| 737 |
Vector3d rhat = *(idat.d) * ri; |
| 738 |
|
| 739 |
// logicals |
| 740 |
|
| 741 |
bool a_is_Charge = data1.is_Charge; |
| 742 |
bool a_is_Dipole = data1.is_Dipole; |
| 743 |
bool a_is_Quadrupole = data1.is_Quadrupole; |
| 744 |
bool a_is_Fluctuating = data1.is_Fluctuating; |
| 745 |
|
| 746 |
bool b_is_Charge = data2.is_Charge; |
| 747 |
bool b_is_Dipole = data2.is_Dipole; |
| 748 |
bool b_is_Quadrupole = data2.is_Quadrupole; |
| 749 |
bool b_is_Fluctuating = data2.is_Fluctuating; |
| 750 |
|
| 751 |
// Obtain all of the required radial function values from the |
| 752 |
// spline structures: |
| 753 |
|
| 754 |
// needed for fields (and forces): |
| 755 |
if (a_is_Charge || b_is_Charge) { |
| 756 |
v02 = v02s->getValueAt( *(idat.rij) ); |
| 757 |
} |
| 758 |
if (a_is_Dipole || b_is_Dipole) { |
| 759 |
v12 = v12s->getValueAt( *(idat.rij) ); |
| 760 |
v13 = v13s->getValueAt( *(idat.rij) ); |
| 761 |
} |
| 762 |
if (a_is_Quadrupole || b_is_Quadrupole) { |
| 763 |
v23 = v23s->getValueAt( *(idat.rij) ); |
| 764 |
v24 = v24s->getValueAt( *(idat.rij) ); |
| 765 |
} |
| 766 |
|
| 767 |
// needed for potentials (and torques): |
| 768 |
if (a_is_Charge && b_is_Charge) { |
| 769 |
v01 = v01s->getValueAt( *(idat.rij) ); |
| 770 |
} |
| 771 |
if ((a_is_Charge && b_is_Dipole) || (b_is_Charge && a_is_Dipole)) { |
| 772 |
v11 = v11s->getValueAt( *(idat.rij) ); |
| 773 |
} |
| 774 |
if ((a_is_Charge && b_is_Quadrupole) || (b_is_Charge && a_is_Quadrupole)) { |
| 775 |
v21 = v21s->getValueAt( *(idat.rij) ); |
| 776 |
v22 = v22s->getValueAt( *(idat.rij) ); |
| 777 |
} else if (a_is_Dipole && b_is_Dipole) { |
| 778 |
v21 = v21s->getValueAt( *(idat.rij) ); |
| 779 |
v22 = v22s->getValueAt( *(idat.rij) ); |
| 780 |
v23 = v23s->getValueAt( *(idat.rij) ); |
| 781 |
v24 = v24s->getValueAt( *(idat.rij) ); |
| 782 |
} |
| 783 |
if ((a_is_Dipole && b_is_Quadrupole) || |
| 784 |
(b_is_Dipole && a_is_Quadrupole)) { |
| 785 |
v31 = v31s->getValueAt( *(idat.rij) ); |
| 786 |
v32 = v32s->getValueAt( *(idat.rij) ); |
| 787 |
v33 = v33s->getValueAt( *(idat.rij) ); |
| 788 |
v34 = v34s->getValueAt( *(idat.rij) ); |
| 789 |
v35 = v35s->getValueAt( *(idat.rij) ); |
| 790 |
} |
| 791 |
if (a_is_Quadrupole && b_is_Quadrupole) { |
| 792 |
v41 = v41s->getValueAt( *(idat.rij) ); |
| 793 |
v42 = v42s->getValueAt( *(idat.rij) ); |
| 794 |
v43 = v43s->getValueAt( *(idat.rij) ); |
| 795 |
v44 = v44s->getValueAt( *(idat.rij) ); |
| 796 |
v45 = v45s->getValueAt( *(idat.rij) ); |
| 797 |
v46 = v46s->getValueAt( *(idat.rij) ); |
| 798 |
} |
| 799 |
|
| 800 |
// calculate the single-site contributions (fields, etc). |
| 801 |
|
| 802 |
if (a_is_Charge) { |
| 803 |
C_a = data1.fixedCharge; |
| 804 |
|
| 805 |
if (a_is_Fluctuating) { |
| 806 |
C_a += *(idat.flucQ1); |
| 807 |
} |
| 808 |
|
| 809 |
if (idat.excluded) { |
| 810 |
*(idat.skippedCharge2) += C_a; |
| 811 |
} |
| 812 |
Eb -= C_a * pre11_ * v02 * rhat; |
| 813 |
} |
| 814 |
|
| 815 |
if (a_is_Dipole) { |
| 816 |
D_a = *(idat.dipole1); |
| 817 |
rdDa = dot(rhat, D_a); |
| 818 |
rxDa = cross(rhat, D_a); |
| 819 |
Eb -= pre12_ * (v13 * rdDa * rhat + v12 * D_a); |
| 820 |
} |
| 821 |
|
| 822 |
if (a_is_Quadrupole) { |
| 823 |
Q_a = *(idat.quadrupole1); |
| 824 |
trQa = Q_a.trace(); |
| 825 |
Qar = Q_a * rhat; |
| 826 |
rQa = rhat * Q_a; |
| 827 |
rdQar = dot(rhat, Qar); |
| 828 |
rxQar = cross(rhat, Qar); |
| 829 |
Eb -= pre14_ * ((trQa * rhat + 2.0 * Qar) * v23 + rdQar * rhat * v24); |
| 830 |
} |
| 831 |
|
| 832 |
if (b_is_Charge) { |
| 833 |
C_b = data2.fixedCharge; |
| 834 |
|
| 835 |
if (b_is_Fluctuating) |
| 836 |
C_b += *(idat.flucQ2); |
| 837 |
|
| 838 |
if (idat.excluded) { |
| 839 |
*(idat.skippedCharge1) += C_b; |
| 840 |
} |
| 841 |
Ea += C_b * pre11_ * v02 * rhat; |
| 842 |
} |
| 843 |
|
| 844 |
if (b_is_Dipole) { |
| 845 |
D_b = *(idat.dipole2); |
| 846 |
rdDb = dot(rhat, D_b); |
| 847 |
rxDb = cross(rhat, D_b); |
| 848 |
Ea += pre12_ * (v13 * rdDb * rhat + v12 * D_b); |
| 849 |
} |
| 850 |
|
| 851 |
if (b_is_Quadrupole) { |
| 852 |
Q_b = *(idat.quadrupole2); |
| 853 |
trQb = Q_b.trace(); |
| 854 |
Qbr = Q_b * rhat; |
| 855 |
rQb = rhat * Q_b; |
| 856 |
rdQbr = dot(rhat, Qbr); |
| 857 |
rxQbr = cross(rhat, Qbr); |
| 858 |
Ea += pre14_ * ((trQb * rhat + 2.0 * Qbr) * v23 + rdQbr * rhat * v24); |
| 859 |
} |
| 860 |
|
| 861 |
if ((a_is_Fluctuating || b_is_Fluctuating) && idat.excluded) { |
| 862 |
J = Jij[idat.atypes]; |
| 863 |
} |
| 864 |
|
| 865 |
if (a_is_Charge) { |
| 866 |
|
| 867 |
if (b_is_Charge) { |
| 868 |
pref = pre11_ * *(idat.electroMult); |
| 869 |
U += C_a * C_b * pref * v01; |
| 870 |
F += C_a * C_b * pref * v02 * rhat; |
| 871 |
|
| 872 |
// If this is an excluded pair, there are still indirect |
| 873 |
// interactions via the reaction field we must worry about: |
| 874 |
|
| 875 |
if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) { |
| 876 |
rfContrib = preRF_ * pref * C_a * C_b * *(idat.r2); |
| 877 |
indirect_Pot += rfContrib; |
| 878 |
indirect_F += rfContrib * 2.0 * ri * rhat; |
| 879 |
} |
| 880 |
|
| 881 |
// Fluctuating charge forces are handled via Coulomb integrals |
| 882 |
// for excluded pairs (i.e. those connected via bonds) and |
| 883 |
// with the standard charge-charge interaction otherwise. |
| 884 |
|
| 885 |
if (idat.excluded) { |
| 886 |
if (a_is_Fluctuating || b_is_Fluctuating) { |
| 887 |
coulInt = J->getValueAt( *(idat.rij) ); |
| 888 |
if (a_is_Fluctuating) dUdCa += coulInt * C_b; |
| 889 |
if (b_is_Fluctuating) dUdCb += coulInt * C_a; |
| 890 |
excluded_Pot += C_a * C_b * coulInt; |
| 891 |
} |
| 892 |
} else { |
| 893 |
if (a_is_Fluctuating) dUdCa += C_b * pref * v01; |
| 894 |
if (a_is_Fluctuating) dUdCb += C_a * pref * v01; |
| 895 |
} |
| 896 |
} |
| 897 |
|
| 898 |
if (b_is_Dipole) { |
| 899 |
pref = pre12_ * *(idat.electroMult); |
| 900 |
U += C_a * pref * v11 * rdDb; |
| 901 |
F += C_a * pref * (v13 * rdDb * rhat + v12 * D_b); |
| 902 |
Tb += C_a * pref * v11 * rxDb; |
| 903 |
|
| 904 |
if (a_is_Fluctuating) dUdCa += pref * v11 * rdDb; |
| 905 |
|
| 906 |
// Even if we excluded this pair from direct interactions, we |
| 907 |
// still have the reaction-field-mediated charge-dipole |
| 908 |
// interaction: |
| 909 |
|
| 910 |
if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) { |
| 911 |
rfContrib = C_a * pref * preRF_ * 2.0 * *(idat.rij); |
| 912 |
indirect_Pot += rfContrib * rdDb; |
| 913 |
indirect_F += rfContrib * D_b / (*idat.rij); |
| 914 |
indirect_Tb += C_a * pref * preRF_ * rxDb; |
| 915 |
} |
| 916 |
} |
| 917 |
|
| 918 |
if (b_is_Quadrupole) { |
| 919 |
pref = pre14_ * *(idat.electroMult); |
| 920 |
U += C_a * pref * (v21 * trQb + v22 * rdQbr); |
| 921 |
F += C_a * pref * (trQb * rhat + 2.0 * Qbr) * v23; |
| 922 |
F += C_a * pref * rdQbr * rhat * v24; |
| 923 |
Tb += C_a * pref * 2.0 * rxQbr * v22; |
| 924 |
|
| 925 |
if (a_is_Fluctuating) dUdCa += pref * (v21 * trQb + v22 * rdQbr); |
| 926 |
} |
| 927 |
} |
| 928 |
|
| 929 |
if (a_is_Dipole) { |
| 930 |
|
| 931 |
if (b_is_Charge) { |
| 932 |
pref = pre12_ * *(idat.electroMult); |
| 933 |
|
| 934 |
U -= C_b * pref * v11 * rdDa; |
| 935 |
F -= C_b * pref * (v13 * rdDa * rhat + v12 * D_a); |
| 936 |
Ta -= C_b * pref * v11 * rxDa; |
| 937 |
|
| 938 |
if (b_is_Fluctuating) dUdCb -= pref * v11 * rdDa; |
| 939 |
|
| 940 |
// Even if we excluded this pair from direct interactions, |
| 941 |
// we still have the reaction-field-mediated charge-dipole |
| 942 |
// interaction: |
| 943 |
if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) { |
| 944 |
rfContrib = C_b * pref * preRF_ * 2.0 * *(idat.rij); |
| 945 |
indirect_Pot -= rfContrib * rdDa; |
| 946 |
indirect_F -= rfContrib * D_a / (*idat.rij); |
| 947 |
indirect_Ta -= C_b * pref * preRF_ * rxDa; |
| 948 |
} |
| 949 |
} |
| 950 |
|
| 951 |
if (b_is_Dipole) { |
| 952 |
pref = pre22_ * *(idat.electroMult); |
| 953 |
DadDb = dot(D_a, D_b); |
| 954 |
DaxDb = cross(D_a, D_b); |
| 955 |
|
| 956 |
U -= pref * (DadDb * v21 + rdDa * rdDb * v22); |
| 957 |
F -= pref * (DadDb * rhat + rdDb * D_a + rdDa * D_b)*v23; |
| 958 |
F -= pref * (rdDa * rdDb) * v24 * rhat; |
| 959 |
Ta += pref * ( v21 * DaxDb - v22 * rdDb * rxDa); |
| 960 |
Tb += pref * (-v21 * DaxDb - v22 * rdDa * rxDb); |
| 961 |
|
| 962 |
// Even if we excluded this pair from direct interactions, we |
| 963 |
// still have the reaction-field-mediated dipole-dipole |
| 964 |
// interaction: |
| 965 |
if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) { |
| 966 |
rfContrib = -pref * preRF_ * 2.0; |
| 967 |
indirect_Pot += rfContrib * DadDb; |
| 968 |
indirect_Ta += rfContrib * DaxDb; |
| 969 |
indirect_Tb -= rfContrib * DaxDb; |
| 970 |
} |
| 971 |
|
| 972 |
} |
| 973 |
|
| 974 |
if (b_is_Quadrupole) { |
| 975 |
pref = pre24_ * *(idat.electroMult); |
| 976 |
DadQb = D_a * Q_b; |
| 977 |
DadQbr = dot(D_a, Qbr); |
| 978 |
DaxQbr = cross(D_a, Qbr); |
| 979 |
|
| 980 |
U -= pref * ((trQb*rdDa + 2.0*DadQbr)*v31 + rdDa*rdQbr*v32); |
| 981 |
F -= pref * (trQb*D_a + 2.0*DadQb) * v33; |
| 982 |
F -= pref * (trQb*rdDa*rhat + 2.0*DadQbr*rhat + D_a*rdQbr |
| 983 |
+ 2.0*rdDa*rQb)*v34; |
| 984 |
F -= pref * (rdDa * rdQbr * rhat * v35); |
| 985 |
Ta += pref * ((-trQb*rxDa + 2.0 * DaxQbr)*v31 - rxDa*rdQbr*v32); |
| 986 |
Tb += pref * ((2.0*cross(DadQb, rhat) - 2.0*DaxQbr)*v31 |
| 987 |
- 2.0*rdDa*rxQbr*v32); |
| 988 |
} |
| 989 |
} |
| 990 |
|
| 991 |
if (a_is_Quadrupole) { |
| 992 |
if (b_is_Charge) { |
| 993 |
pref = pre14_ * *(idat.electroMult); |
| 994 |
U += C_b * pref * (v21 * trQa + v22 * rdQar); |
| 995 |
F += C_b * pref * (trQa * rhat + 2.0 * Qar) * v23; |
| 996 |
F += C_b * pref * rdQar * rhat * v24; |
| 997 |
Ta += C_b * pref * 2.0 * rxQar * v22; |
| 998 |
|
| 999 |
if (b_is_Fluctuating) dUdCb += pref * (v21 * trQa + v22 * rdQar); |
| 1000 |
} |
| 1001 |
if (b_is_Dipole) { |
| 1002 |
pref = pre24_ * *(idat.electroMult); |
| 1003 |
DbdQa = D_b * Q_a; |
| 1004 |
DbdQar = dot(D_b, Qar); |
| 1005 |
DbxQar = cross(D_b, Qar); |
| 1006 |
|
| 1007 |
U += pref * ((trQa*rdDb + 2.0*DbdQar)*v31 + rdDb*rdQar*v32); |
| 1008 |
F += pref * (trQa*D_b + 2.0*DbdQa) * v33; |
| 1009 |
F += pref * (trQa*rdDb*rhat + 2.0*DbdQar*rhat + D_b*rdQar |
| 1010 |
+ 2.0*rdDb*rQa)*v34; |
| 1011 |
F += pref * (rdDb * rdQar * rhat * v35); |
| 1012 |
Ta += pref * ((-2.0*cross(DbdQa, rhat) + 2.0*DbxQar)*v31 |
| 1013 |
+ 2.0*rdDb*rxQar*v32); |
| 1014 |
Tb += pref * ((trQa*rxDb - 2.0 * DbxQar)*v31 + rxDb*rdQar*v32); |
| 1015 |
} |
| 1016 |
if (b_is_Quadrupole) { |
| 1017 |
pref = pre44_ * *(idat.electroMult); // yes |
| 1018 |
QaQb = Q_a * Q_b; |
| 1019 |
trQaQb = QaQb.trace(); |
| 1020 |
rQaQb = rhat * QaQb; |
| 1021 |
QaQbr = QaQb * rhat; |
| 1022 |
QaxQb = cross(Q_a, Q_b); |
| 1023 |
rQaQbr = dot(rQa, Qbr); |
| 1024 |
rQaxQbr = cross(rQa, Qbr); |
| 1025 |
|
| 1026 |
U += pref * (trQa * trQb + 2.0 * trQaQb) * v41; |
| 1027 |
U += pref * (trQa * rdQbr + trQb * rdQar + 4.0 * rQaQbr) * v42; |
| 1028 |
U += pref * (rdQar * rdQbr) * v43; |
| 1029 |
|
| 1030 |
F += pref * rhat * (trQa * trQb + 2.0 * trQaQb)*v44; |
| 1031 |
F += pref * rhat * (trQa * rdQbr + trQb * rdQar + 4.0 * rQaQbr)*v45; |
| 1032 |
F += pref * rhat * (rdQar * rdQbr)*v46; |
| 1033 |
|
| 1034 |
F += pref * 2.0 * (trQb*rQa + trQa*rQb)*v44; |
| 1035 |
F += pref * 4.0 * (rQaQb + QaQbr)*v44; |
| 1036 |
F += pref * 2.0 * (rQa*rdQbr + rdQar*rQb)*v45; |
| 1037 |
|
| 1038 |
Ta += pref * (- 4.0 * QaxQb * v41); |
| 1039 |
Ta += pref * (- 2.0 * trQb * cross(rQa, rhat) |
| 1040 |
+ 4.0 * cross(rhat, QaQbr) |
| 1041 |
- 4.0 * rQaxQbr) * v42; |
| 1042 |
Ta += pref * 2.0 * cross(rhat,Qar) * rdQbr * v43; |
| 1043 |
|
| 1044 |
|
| 1045 |
Tb += pref * (+ 4.0 * QaxQb * v41); |
| 1046 |
Tb += pref * (- 2.0 * trQa * cross(rQb, rhat) |
| 1047 |
- 4.0 * cross(rQaQb, rhat) |
| 1048 |
+ 4.0 * rQaxQbr) * v42; |
| 1049 |
// Possible replacement for line 2 above: |
| 1050 |
// + 4.0 * cross(rhat, QbQar) |
| 1051 |
|
| 1052 |
Tb += pref * 2.0 * cross(rhat,Qbr) * rdQar * v43; |
| 1053 |
|
| 1054 |
// cerr << " tsum = " << Ta + Tb - cross( *(idat.d) , F ) << "\n"; |
| 1055 |
} |
| 1056 |
} |
| 1057 |
|
| 1058 |
if (idat.doElectricField) { |
| 1059 |
*(idat.eField1) += Ea * *(idat.electroMult); |
| 1060 |
*(idat.eField2) += Eb * *(idat.electroMult); |
| 1061 |
} |
| 1062 |
|
| 1063 |
if (a_is_Fluctuating) *(idat.dVdFQ1) += dUdCa * *(idat.sw); |
| 1064 |
if (b_is_Fluctuating) *(idat.dVdFQ2) += dUdCb * *(idat.sw); |
| 1065 |
|
| 1066 |
if (!idat.excluded) { |
| 1067 |
|
| 1068 |
*(idat.vpair) += U; |
| 1069 |
(*(idat.pot))[ELECTROSTATIC_FAMILY] += U * *(idat.sw); |
| 1070 |
*(idat.f1) += F * *(idat.sw); |
| 1071 |
|
| 1072 |
if (a_is_Dipole || a_is_Quadrupole) |
| 1073 |
*(idat.t1) += Ta * *(idat.sw); |
| 1074 |
|
| 1075 |
if (b_is_Dipole || b_is_Quadrupole) |
| 1076 |
*(idat.t2) += Tb * *(idat.sw); |
| 1077 |
|
| 1078 |
} else { |
| 1079 |
|
| 1080 |
// only accumulate the forces and torques resulting from the |
| 1081 |
// indirect reaction field terms. |
| 1082 |
|
| 1083 |
*(idat.vpair) += indirect_Pot; |
| 1084 |
(*(idat.excludedPot))[ELECTROSTATIC_FAMILY] += excluded_Pot; |
| 1085 |
(*(idat.pot))[ELECTROSTATIC_FAMILY] += *(idat.sw) * indirect_Pot; |
| 1086 |
*(idat.f1) += *(idat.sw) * indirect_F; |
| 1087 |
|
| 1088 |
if (a_is_Dipole || a_is_Quadrupole) |
| 1089 |
*(idat.t1) += *(idat.sw) * indirect_Ta; |
| 1090 |
|
| 1091 |
if (b_is_Dipole || b_is_Quadrupole) |
| 1092 |
*(idat.t2) += *(idat.sw) * indirect_Tb; |
| 1093 |
} |
| 1094 |
return; |
| 1095 |
} |
| 1096 |
|
| 1097 |
void Electrostatic::calcSelfCorrection(SelfData &sdat) { |
| 1098 |
|
| 1099 |
if (!initialized_) initialize(); |
| 1100 |
|
| 1101 |
ElectrostaticAtomData data = ElectrostaticMap[sdat.atype]; |
| 1102 |
|
| 1103 |
// logicals |
| 1104 |
bool i_is_Charge = data.is_Charge; |
| 1105 |
bool i_is_Dipole = data.is_Dipole; |
| 1106 |
bool i_is_Fluctuating = data.is_Fluctuating; |
| 1107 |
RealType C_a = data.fixedCharge; |
| 1108 |
RealType self, preVal, DadDa; |
| 1109 |
|
| 1110 |
if (i_is_Fluctuating) { |
| 1111 |
C_a += *(sdat.flucQ); |
| 1112 |
// dVdFQ is really a force, so this is negative the derivative |
| 1113 |
*(sdat.dVdFQ) -= *(sdat.flucQ) * data.hardness + data.electronegativity; |
| 1114 |
(*(sdat.excludedPot))[ELECTROSTATIC_FAMILY] += (*sdat.flucQ) * |
| 1115 |
(*(sdat.flucQ) * data.hardness * 0.5 + data.electronegativity); |
| 1116 |
} |
| 1117 |
|
| 1118 |
switch (summationMethod_) { |
| 1119 |
case esm_REACTION_FIELD: |
| 1120 |
|
| 1121 |
if (i_is_Charge) { |
| 1122 |
// Self potential [see Wang and Hermans, "Reaction Field |
| 1123 |
// Molecular Dynamics Simulation with Friedman’s Image Charge |
| 1124 |
// Method," J. Phys. Chem. 99, 12001-12007 (1995).] |
| 1125 |
preVal = pre11_ * preRF_ * C_a * C_a; |
| 1126 |
(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 * preVal / cutoffRadius_; |
| 1127 |
} |
| 1128 |
|
| 1129 |
if (i_is_Dipole) { |
| 1130 |
DadDa = data.dipole.lengthSquare(); |
| 1131 |
(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= pre22_ * preRF_ * DadDa; |
| 1132 |
} |
| 1133 |
|
| 1134 |
break; |
| 1135 |
|
| 1136 |
case esm_SHIFTED_FORCE: |
| 1137 |
case esm_SHIFTED_POTENTIAL: |
| 1138 |
if (i_is_Charge) { |
| 1139 |
self = - selfMult_ * C_a * (C_a + *(sdat.skippedCharge)) * pre11_; |
| 1140 |
(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self; |
| 1141 |
} |
| 1142 |
break; |
| 1143 |
default: |
| 1144 |
break; |
| 1145 |
} |
| 1146 |
} |
| 1147 |
|
| 1148 |
RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 1149 |
// This seems to work moderately well as a default. There's no |
| 1150 |
// inherent scale for 1/r interactions that we can standardize. |
| 1151 |
// 12 angstroms seems to be a reasonably good guess for most |
| 1152 |
// cases. |
| 1153 |
return 12.0; |
| 1154 |
} |
| 1155 |
} |
