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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <stdio.h> |
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#include <string.h> |
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|
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#include <cmath> |
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#include <numeric> |
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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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#include "primitives/Molecule.hpp" |
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|
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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_["TAYLOR_SHIFTED"] = esm_TAYLOR_SHIFTED; |
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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_ = 100; |
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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\",\n" |
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"\t\"taylor_shifted\", or \"reaction_field\".\n", |
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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 || summationMethod_ == esm_EWALD_FULL) { |
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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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// 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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|
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Etypes.clear(); |
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Etids.clear(); |
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FQtypes.clear(); |
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FQtids.clear(); |
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ElectrostaticMap.clear(); |
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Jij.clear(); |
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nElectro_ = 0; |
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nFlucq_ = 0; |
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|
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Etids.resize( forceField_->getNAtomType(), -1); |
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FQtids.resize( forceField_->getNAtomType(), -1); |
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|
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set<AtomType*>::iterator at; |
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for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
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if ((*at)->isElectrostatic()) nElectro_++; |
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if ((*at)->isFluctuatingCharge()) nFlucq_++; |
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} |
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|
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Jij.resize(nFlucq_); |
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|
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for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
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if ((*at)->isElectrostatic()) 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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RealType ric = 1.0 / r; |
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RealType ric2 = ric * ric; |
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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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// Half the Smith self piece: |
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selfMult1_ = - a2 * invArootPi; |
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selfMult2_ = - 2.0 * a2 * a2 * invArootPi / 3.0; |
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selfMult4_ = - 4.0 * a2 * a2 * a2 * invArootPi / 5.0; |
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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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selfMult1_ = 0.0; |
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selfMult2_ = 0.0; |
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selfMult4_ = 0.0; |
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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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if (summationMethod_ != esm_EWALD_FULL) { |
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selfMult1_ -= b0c; |
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selfMult2_ += (db0c_2 + 2.0*db0c_1*ric) / 3.0; |
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selfMult4_ -= (db0c_4 + 4.0*db0c_3*ric) / 15.0; |
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} |
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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 f, fc, f0; |
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RealType g, gc, g0, g1, g2, g3, g4; |
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RealType h, hc, h1, h2, h3, h4; |
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RealType s, sc, s2, s3, s4; |
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RealType t, tc, t3, t4; |
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RealType u, uc, 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; |
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vector<RealType> v11v; |
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vector<RealType> v21v, v22v; |
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vector<RealType> v31v, v32v; |
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vector<RealType> v41v, v42v, v43v; |
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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); |
| 336 |
|
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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): |
| 344 |
rmRc = r - cutoffRadius_; |
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rmRc2 = rmRc * rmRc / 2.0; |
| 346 |
rmRc3 = rmRc2 * rmRc / 3.0; |
| 347 |
rmRc4 = rmRc3 * rmRc / 4.0; |
| 348 |
|
| 349 |
// values of Smith's B_l functions at r: |
| 350 |
if (screeningMethod_ == DAMPED) { |
| 351 |
b0 = erfc(dampingAlpha_ * r) * ri; |
| 352 |
b1 = ( b0 + 2.0*a2 * expTerm * invArootPi) * ri2; |
| 353 |
b2 = (3.0 * b1 + pow(2.0*a2, 2) * expTerm * invArootPi) * ri2; |
| 354 |
b3 = (5.0 * b2 + pow(2.0*a2, 3) * expTerm * invArootPi) * ri2; |
| 355 |
b4 = (7.0 * b3 + pow(2.0*a2, 4) * expTerm * invArootPi) * ri2; |
| 356 |
b5 = (9.0 * b4 + pow(2.0*a2, 5) * expTerm * invArootPi) * ri2; |
| 357 |
} else { |
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b0 = ri; |
| 359 |
b1 = ( b0) * ri2; |
| 360 |
b2 = (3.0 * b1) * ri2; |
| 361 |
b3 = (5.0 * b2) * ri2; |
| 362 |
b4 = (7.0 * b3) * ri2; |
| 363 |
b5 = (9.0 * b4) * ri2; |
| 364 |
} |
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|
| 366 |
// higher derivatives of B_0 at r: |
| 367 |
db0_1 = -r * b1; |
| 368 |
db0_2 = -b1 + r2 * b2; |
| 369 |
db0_3 = 3.0*r*b2 - r2*r*b3; |
| 370 |
db0_4 = 3.0*b2 - 6.0*r2*b3 + r2*r2*b4; |
| 371 |
db0_5 = -15.0*r*b3 + 10.0*r2*r*b4 - r2*r2*r*b5; |
| 372 |
|
| 373 |
f = b0; |
| 374 |
fc = b0c; |
| 375 |
f0 = f - fc - rmRc*db0c_1; |
| 376 |
|
| 377 |
g = db0_1; |
| 378 |
gc = db0c_1; |
| 379 |
g0 = g - gc; |
| 380 |
g1 = g0 - rmRc *db0c_2; |
| 381 |
g2 = g1 - rmRc2*db0c_3; |
| 382 |
g3 = g2 - rmRc3*db0c_4; |
| 383 |
g4 = g3 - rmRc4*db0c_5; |
| 384 |
|
| 385 |
h = db0_2; |
| 386 |
hc = db0c_2; |
| 387 |
h1 = h - hc; |
| 388 |
h2 = h1 - rmRc *db0c_3; |
| 389 |
h3 = h2 - rmRc2*db0c_4; |
| 390 |
h4 = h3 - rmRc3*db0c_5; |
| 391 |
|
| 392 |
s = db0_3; |
| 393 |
sc = db0c_3; |
| 394 |
s2 = s - sc; |
| 395 |
s3 = s2 - rmRc *db0c_4; |
| 396 |
s4 = s3 - rmRc2*db0c_5; |
| 397 |
|
| 398 |
t = db0_4; |
| 399 |
tc = db0c_4; |
| 400 |
t3 = t - tc; |
| 401 |
t4 = t3 - rmRc *db0c_5; |
| 402 |
|
| 403 |
u = db0_5; |
| 404 |
uc = db0c_5; |
| 405 |
u4 = u - uc; |
| 406 |
|
| 407 |
// in what follows below, the various v functions are used for |
| 408 |
// potentials and torques, while the w functions show up in the |
| 409 |
// forces. |
| 410 |
|
| 411 |
switch (summationMethod_) { |
| 412 |
case esm_SHIFTED_FORCE: |
| 413 |
|
| 414 |
v01 = f - fc - rmRc*gc; |
| 415 |
v11 = g - gc - rmRc*hc; |
| 416 |
v21 = g*ri - gc*ric - rmRc*(hc - gc*ric)*ric; |
| 417 |
v22 = h - g*ri - (hc - gc*ric) - rmRc*(sc - (hc - gc*ric)*ric); |
| 418 |
v31 = (h-g*ri)*ri - (hc-gc*ric)*ric - rmRc*(sc-2.0*(hc-gc*ric)*ric)*ric; |
| 419 |
v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric) |
| 420 |
- rmRc*(tc - 3.0*(sc-2.0*(hc-gc*ric)*ric)*ric); |
| 421 |
v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2 |
| 422 |
- rmRc*(sc - 3.0*(hc-gc*ric)*ric)*ric2; |
| 423 |
v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric |
| 424 |
- rmRc*(tc - (4.0*sc - 9.0*(hc - gc*ric)*ric)*ric)*ric; |
| 425 |
|
| 426 |
v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri) |
| 427 |
- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric) |
| 428 |
- rmRc*(uc-3.0*(2.0*tc - (7.0*sc - 15.0*(hc - gc*ric)*ric)*ric)*ric); |
| 429 |
|
| 430 |
dv01 = g - gc; |
| 431 |
dv11 = h - hc; |
| 432 |
dv21 = (h - g*ri)*ri - (hc - gc*ric)*ric; |
| 433 |
dv22 = (s - (h - g*ri)*ri) - (sc - (hc - gc*ric)*ric); |
| 434 |
dv31 = (s - 2.0*(h-g*ri)*ri)*ri - (sc - 2.0*(hc-gc*ric)*ric)*ric; |
| 435 |
dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri) |
| 436 |
- (tc - 3.0*(sc-2.0*(hc-gc*ric)*ric)*ric); |
| 437 |
dv41 = (s - 3.0*(h - g*ri)*ri)*ri2 - (sc - 3.0*(hc - gc*ric)*ric)*ric2; |
| 438 |
dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri |
| 439 |
- (tc - (4.0*sc - 9.0*(hc-gc*ric)*ric)*ric)*ric; |
| 440 |
dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri) |
| 441 |
- (uc - 3.0*(2.0*tc - (7.0*sc - 15.0*(hc - gc*ric)*ric)*ric)*ric); |
| 442 |
|
| 443 |
break; |
| 444 |
|
| 445 |
case esm_TAYLOR_SHIFTED: |
| 446 |
|
| 447 |
v01 = f0; |
| 448 |
v11 = g1; |
| 449 |
v21 = g2 * ri; |
| 450 |
v22 = h2 - v21; |
| 451 |
v31 = (h3 - g3 * ri) * ri; |
| 452 |
v32 = s3 - 3.0*v31; |
| 453 |
v41 = (h4 - g4 * ri) * ri2; |
| 454 |
v42 = s4 * ri - 3.0*v41; |
| 455 |
v43 = t4 - 6.0*v42 - 3.0*v41; |
| 456 |
|
| 457 |
dv01 = g0; |
| 458 |
dv11 = h1; |
| 459 |
dv21 = (h2 - g2*ri)*ri; |
| 460 |
dv22 = (s2 - (h2 - g2*ri)*ri); |
| 461 |
dv31 = (s3 - 2.0*(h3-g3*ri)*ri)*ri; |
| 462 |
dv32 = (t3 - 3.0*(s3-2.0*(h3-g3*ri)*ri)*ri); |
| 463 |
dv41 = (s4 - 3.0*(h4 - g4*ri)*ri)*ri2; |
| 464 |
dv42 = (t4 - (4.0*s4 - 9.0*(h4-g4*ri)*ri)*ri)*ri; |
| 465 |
dv43 = (u4 - 3.0*(2.0*t4 - (7.0*s4 - 15.0*(h4 - g4*ri)*ri)*ri)*ri); |
| 466 |
|
| 467 |
break; |
| 468 |
|
| 469 |
case esm_SHIFTED_POTENTIAL: |
| 470 |
|
| 471 |
v01 = f - fc; |
| 472 |
v11 = g - gc; |
| 473 |
v21 = g*ri - gc*ric; |
| 474 |
v22 = h - g*ri - (hc - gc*ric); |
| 475 |
v31 = (h-g*ri)*ri - (hc-gc*ric)*ric; |
| 476 |
v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric); |
| 477 |
v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2; |
| 478 |
v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric; |
| 479 |
v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri) |
| 480 |
- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric); |
| 481 |
|
| 482 |
dv01 = g; |
| 483 |
dv11 = h; |
| 484 |
dv21 = (h - g*ri)*ri; |
| 485 |
dv22 = (s - (h - g*ri)*ri); |
| 486 |
dv31 = (s - 2.0*(h-g*ri)*ri)*ri; |
| 487 |
dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri); |
| 488 |
dv41 = (s - 3.0*(h - g*ri)*ri)*ri2; |
| 489 |
dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri; |
| 490 |
dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri); |
| 491 |
|
| 492 |
break; |
| 493 |
|
| 494 |
case esm_SWITCHING_FUNCTION: |
| 495 |
case esm_HARD: |
| 496 |
case esm_EWALD_FULL: |
| 497 |
|
| 498 |
v01 = f; |
| 499 |
v11 = g; |
| 500 |
v21 = g*ri; |
| 501 |
v22 = h - g*ri; |
| 502 |
v31 = (h-g*ri)*ri; |
| 503 |
v32 = (s - 3.0*(h-g*ri)*ri); |
| 504 |
v41 = (h - g*ri)*ri2; |
| 505 |
v42 = (s-3.0*(h-g*ri)*ri)*ri; |
| 506 |
v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri); |
| 507 |
|
| 508 |
dv01 = g; |
| 509 |
dv11 = h; |
| 510 |
dv21 = (h - g*ri)*ri; |
| 511 |
dv22 = (s - (h - g*ri)*ri); |
| 512 |
dv31 = (s - 2.0*(h-g*ri)*ri)*ri; |
| 513 |
dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri); |
| 514 |
dv41 = (s - 3.0*(h - g*ri)*ri)*ri2; |
| 515 |
dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri; |
| 516 |
dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri); |
| 517 |
|
| 518 |
break; |
| 519 |
|
| 520 |
case esm_REACTION_FIELD: |
| 521 |
|
| 522 |
// following DL_POLY's lead for shifting the image charge potential: |
| 523 |
f = b0 + preRF_ * r2; |
| 524 |
fc = b0c + preRF_ * cutoffRadius_ * cutoffRadius_; |
| 525 |
|
| 526 |
g = db0_1 + preRF_ * 2.0 * r; |
| 527 |
gc = db0c_1 + preRF_ * 2.0 * cutoffRadius_; |
| 528 |
|
| 529 |
h = db0_2 + preRF_ * 2.0; |
| 530 |
hc = db0c_2 + preRF_ * 2.0; |
| 531 |
|
| 532 |
v01 = f - fc; |
| 533 |
v11 = g - gc; |
| 534 |
v21 = g*ri - gc*ric; |
| 535 |
v22 = h - g*ri - (hc - gc*ric); |
| 536 |
v31 = (h-g*ri)*ri - (hc-gc*ric)*ric; |
| 537 |
v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric); |
| 538 |
v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2; |
| 539 |
v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric; |
| 540 |
v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri) |
| 541 |
- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric); |
| 542 |
|
| 543 |
dv01 = g; |
| 544 |
dv11 = h; |
| 545 |
dv21 = (h - g*ri)*ri; |
| 546 |
dv22 = (s - (h - g*ri)*ri); |
| 547 |
dv31 = (s - 2.0*(h-g*ri)*ri)*ri; |
| 548 |
dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri); |
| 549 |
dv41 = (s - 3.0*(h - g*ri)*ri)*ri2; |
| 550 |
dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri; |
| 551 |
dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri); |
| 552 |
|
| 553 |
break; |
| 554 |
|
| 555 |
case esm_EWALD_PME: |
| 556 |
case esm_EWALD_SPME: |
| 557 |
default : |
| 558 |
map<string, ElectrostaticSummationMethod>::iterator i; |
| 559 |
std::string meth; |
| 560 |
for (i = summationMap_.begin(); i != summationMap_.end(); ++i) { |
| 561 |
if ((*i).second == summationMethod_) meth = (*i).first; |
| 562 |
} |
| 563 |
sprintf( painCave.errMsg, |
| 564 |
"Electrostatic::initialize: electrostaticSummationMethod %s \n" |
| 565 |
"\thas not been implemented yet. Please select one of:\n" |
| 566 |
"\t\"hard\", \"shifted_potential\", or \"shifted_force\"\n", |
| 567 |
meth.c_str() ); |
| 568 |
painCave.isFatal = 1; |
| 569 |
simError(); |
| 570 |
break; |
| 571 |
} |
| 572 |
|
| 573 |
// Add these computed values to the storage vectors for spline creation: |
| 574 |
v01v.push_back(v01); |
| 575 |
v11v.push_back(v11); |
| 576 |
v21v.push_back(v21); |
| 577 |
v22v.push_back(v22); |
| 578 |
v31v.push_back(v31); |
| 579 |
v32v.push_back(v32); |
| 580 |
v41v.push_back(v41); |
| 581 |
v42v.push_back(v42); |
| 582 |
v43v.push_back(v43); |
| 583 |
} |
| 584 |
|
| 585 |
// construct the spline structures and fill them with the values we've |
| 586 |
// computed: |
| 587 |
|
| 588 |
v01s = new CubicSpline(); |
| 589 |
v01s->addPoints(rv, v01v); |
| 590 |
v11s = new CubicSpline(); |
| 591 |
v11s->addPoints(rv, v11v); |
| 592 |
v21s = new CubicSpline(); |
| 593 |
v21s->addPoints(rv, v21v); |
| 594 |
v22s = new CubicSpline(); |
| 595 |
v22s->addPoints(rv, v22v); |
| 596 |
v31s = new CubicSpline(); |
| 597 |
v31s->addPoints(rv, v31v); |
| 598 |
v32s = new CubicSpline(); |
| 599 |
v32s->addPoints(rv, v32v); |
| 600 |
v41s = new CubicSpline(); |
| 601 |
v41s->addPoints(rv, v41v); |
| 602 |
v42s = new CubicSpline(); |
| 603 |
v42s->addPoints(rv, v42v); |
| 604 |
v43s = new CubicSpline(); |
| 605 |
v43s->addPoints(rv, v43v); |
| 606 |
|
| 607 |
haveElectroSplines_ = true; |
| 608 |
|
| 609 |
initialized_ = true; |
| 610 |
} |
| 611 |
|
| 612 |
void Electrostatic::addType(AtomType* atomType){ |
| 613 |
|
| 614 |
ElectrostaticAtomData electrostaticAtomData; |
| 615 |
electrostaticAtomData.is_Charge = false; |
| 616 |
electrostaticAtomData.is_Dipole = false; |
| 617 |
electrostaticAtomData.is_Quadrupole = false; |
| 618 |
electrostaticAtomData.is_Fluctuating = false; |
| 619 |
|
| 620 |
FixedChargeAdapter fca = FixedChargeAdapter(atomType); |
| 621 |
|
| 622 |
if (fca.isFixedCharge()) { |
| 623 |
electrostaticAtomData.is_Charge = true; |
| 624 |
electrostaticAtomData.fixedCharge = fca.getCharge(); |
| 625 |
} |
| 626 |
|
| 627 |
MultipoleAdapter ma = MultipoleAdapter(atomType); |
| 628 |
if (ma.isMultipole()) { |
| 629 |
if (ma.isDipole()) { |
| 630 |
electrostaticAtomData.is_Dipole = true; |
| 631 |
electrostaticAtomData.dipole = ma.getDipole(); |
| 632 |
} |
| 633 |
if (ma.isQuadrupole()) { |
| 634 |
electrostaticAtomData.is_Quadrupole = true; |
| 635 |
electrostaticAtomData.quadrupole = ma.getQuadrupole(); |
| 636 |
} |
| 637 |
} |
| 638 |
|
| 639 |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType); |
| 640 |
|
| 641 |
if (fqa.isFluctuatingCharge()) { |
| 642 |
electrostaticAtomData.is_Fluctuating = true; |
| 643 |
electrostaticAtomData.electronegativity = fqa.getElectronegativity(); |
| 644 |
electrostaticAtomData.hardness = fqa.getHardness(); |
| 645 |
electrostaticAtomData.slaterN = fqa.getSlaterN(); |
| 646 |
electrostaticAtomData.slaterZeta = fqa.getSlaterZeta(); |
| 647 |
} |
| 648 |
|
| 649 |
int atid = atomType->getIdent(); |
| 650 |
int etid = Etypes.size(); |
| 651 |
int fqtid = FQtypes.size(); |
| 652 |
|
| 653 |
pair<set<int>::iterator,bool> ret; |
| 654 |
ret = Etypes.insert( atid ); |
| 655 |
if (ret.second == false) { |
| 656 |
sprintf( painCave.errMsg, |
| 657 |
"Electrostatic already had a previous entry with ident %d\n", |
| 658 |
atid); |
| 659 |
painCave.severity = OPENMD_INFO; |
| 660 |
painCave.isFatal = 0; |
| 661 |
simError(); |
| 662 |
} |
| 663 |
|
| 664 |
Etids[ atid ] = etid; |
| 665 |
ElectrostaticMap.push_back(electrostaticAtomData); |
| 666 |
|
| 667 |
if (electrostaticAtomData.is_Fluctuating) { |
| 668 |
ret = FQtypes.insert( atid ); |
| 669 |
if (ret.second == false) { |
| 670 |
sprintf( painCave.errMsg, |
| 671 |
"Electrostatic already had a previous fluctuating charge entry with ident %d\n", |
| 672 |
atid ); |
| 673 |
painCave.severity = OPENMD_INFO; |
| 674 |
painCave.isFatal = 0; |
| 675 |
simError(); |
| 676 |
} |
| 677 |
FQtids[atid] = fqtid; |
| 678 |
Jij[fqtid].resize(nFlucq_); |
| 679 |
|
| 680 |
// Now, iterate over all known fluctuating and add to the |
| 681 |
// coulomb integral map: |
| 682 |
|
| 683 |
std::set<int>::iterator it; |
| 684 |
for( it = FQtypes.begin(); it != FQtypes.end(); ++it) { |
| 685 |
int etid2 = Etids[ (*it) ]; |
| 686 |
int fqtid2 = FQtids[ (*it) ]; |
| 687 |
ElectrostaticAtomData eaData2 = ElectrostaticMap[ etid2 ]; |
| 688 |
RealType a = electrostaticAtomData.slaterZeta; |
| 689 |
RealType b = eaData2.slaterZeta; |
| 690 |
int m = electrostaticAtomData.slaterN; |
| 691 |
int n = eaData2.slaterN; |
| 692 |
|
| 693 |
// Create the spline of the coulombic integral for s-type |
| 694 |
// Slater orbitals. Add a 2 angstrom safety window to deal |
| 695 |
// with cutoffGroups that have charged atoms longer than the |
| 696 |
// cutoffRadius away from each other. |
| 697 |
|
| 698 |
RealType rval; |
| 699 |
RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1); |
| 700 |
vector<RealType> rvals; |
| 701 |
vector<RealType> Jvals; |
| 702 |
// don't start at i = 0, as rval = 0 is undefined for the |
| 703 |
// slater overlap integrals. |
| 704 |
for (int i = 1; i < np_+1; i++) { |
| 705 |
rval = RealType(i) * dr; |
| 706 |
rvals.push_back(rval); |
| 707 |
Jvals.push_back(sSTOCoulInt( a, b, m, n, rval * |
| 708 |
PhysicalConstants::angstromToBohr ) * |
| 709 |
PhysicalConstants::hartreeToKcal ); |
| 710 |
} |
| 711 |
|
| 712 |
CubicSpline* J = new CubicSpline(); |
| 713 |
J->addPoints(rvals, Jvals); |
| 714 |
Jij[fqtid][fqtid2] = J; |
| 715 |
Jij[fqtid2].resize( nFlucq_ ); |
| 716 |
Jij[fqtid2][fqtid] = J; |
| 717 |
} |
| 718 |
} |
| 719 |
return; |
| 720 |
} |
| 721 |
|
| 722 |
void Electrostatic::setCutoffRadius( RealType rCut ) { |
| 723 |
cutoffRadius_ = rCut; |
| 724 |
haveCutoffRadius_ = true; |
| 725 |
} |
| 726 |
|
| 727 |
void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) { |
| 728 |
summationMethod_ = esm; |
| 729 |
} |
| 730 |
void Electrostatic::setElectrostaticScreeningMethod( ElectrostaticScreeningMethod sm ) { |
| 731 |
screeningMethod_ = sm; |
| 732 |
} |
| 733 |
void Electrostatic::setDampingAlpha( RealType alpha ) { |
| 734 |
dampingAlpha_ = alpha; |
| 735 |
haveDampingAlpha_ = true; |
| 736 |
} |
| 737 |
void Electrostatic::setReactionFieldDielectric( RealType dielectric ){ |
| 738 |
dielectric_ = dielectric; |
| 739 |
haveDielectric_ = true; |
| 740 |
} |
| 741 |
|
| 742 |
void Electrostatic::calcForce(InteractionData &idat) { |
| 743 |
|
| 744 |
if (!initialized_) initialize(); |
| 745 |
|
| 746 |
data1 = ElectrostaticMap[Etids[idat.atid1]]; |
| 747 |
data2 = ElectrostaticMap[Etids[idat.atid2]]; |
| 748 |
|
| 749 |
U = 0.0; // Potential |
| 750 |
F.zero(); // Force |
| 751 |
Ta.zero(); // Torque on site a |
| 752 |
Tb.zero(); // Torque on site b |
| 753 |
Ea.zero(); // Electric field at site a |
| 754 |
Eb.zero(); // Electric field at site b |
| 755 |
dUdCa = 0.0; // fluctuating charge force at site a |
| 756 |
dUdCb = 0.0; // fluctuating charge force at site a |
| 757 |
|
| 758 |
// Indirect interactions mediated by the reaction field. |
| 759 |
indirect_Pot = 0.0; // Potential |
| 760 |
indirect_F.zero(); // Force |
| 761 |
indirect_Ta.zero(); // Torque on site a |
| 762 |
indirect_Tb.zero(); // Torque on site b |
| 763 |
|
| 764 |
// Excluded potential that is still computed for fluctuating charges |
| 765 |
excluded_Pot= 0.0; |
| 766 |
|
| 767 |
|
| 768 |
// some variables we'll need independent of electrostatic type: |
| 769 |
|
| 770 |
ri = 1.0 / *(idat.rij); |
| 771 |
rhat = *(idat.d) * ri; |
| 772 |
|
| 773 |
// logicals |
| 774 |
|
| 775 |
a_is_Charge = data1.is_Charge; |
| 776 |
a_is_Dipole = data1.is_Dipole; |
| 777 |
a_is_Quadrupole = data1.is_Quadrupole; |
| 778 |
a_is_Fluctuating = data1.is_Fluctuating; |
| 779 |
|
| 780 |
b_is_Charge = data2.is_Charge; |
| 781 |
b_is_Dipole = data2.is_Dipole; |
| 782 |
b_is_Quadrupole = data2.is_Quadrupole; |
| 783 |
b_is_Fluctuating = data2.is_Fluctuating; |
| 784 |
|
| 785 |
// Obtain all of the required radial function values from the |
| 786 |
// spline structures: |
| 787 |
|
| 788 |
// needed for fields (and forces): |
| 789 |
if (a_is_Charge || b_is_Charge) { |
| 790 |
v01s->getValueAndDerivativeAt( *(idat.rij), v01, dv01); |
| 791 |
} |
| 792 |
if (a_is_Dipole || b_is_Dipole) { |
| 793 |
v11s->getValueAndDerivativeAt( *(idat.rij), v11, dv11); |
| 794 |
v11or = ri * v11; |
| 795 |
} |
| 796 |
if (a_is_Quadrupole || b_is_Quadrupole || (a_is_Dipole && b_is_Dipole)) { |
| 797 |
v21s->getValueAndDerivativeAt( *(idat.rij), v21, dv21); |
| 798 |
v22s->getValueAndDerivativeAt( *(idat.rij), v22, dv22); |
| 799 |
v22or = ri * v22; |
| 800 |
} |
| 801 |
|
| 802 |
// needed for potentials (and forces and torques): |
| 803 |
if ((a_is_Dipole && b_is_Quadrupole) || |
| 804 |
(b_is_Dipole && a_is_Quadrupole)) { |
| 805 |
v31s->getValueAndDerivativeAt( *(idat.rij), v31, dv31); |
| 806 |
v32s->getValueAndDerivativeAt( *(idat.rij), v32, dv32); |
| 807 |
v31or = v31 * ri; |
| 808 |
v32or = v32 * ri; |
| 809 |
} |
| 810 |
if (a_is_Quadrupole && b_is_Quadrupole) { |
| 811 |
v41s->getValueAndDerivativeAt( *(idat.rij), v41, dv41); |
| 812 |
v42s->getValueAndDerivativeAt( *(idat.rij), v42, dv42); |
| 813 |
v43s->getValueAndDerivativeAt( *(idat.rij), v43, dv43); |
| 814 |
v42or = v42 * ri; |
| 815 |
v43or = v43 * ri; |
| 816 |
} |
| 817 |
|
| 818 |
// calculate the single-site contributions (fields, etc). |
| 819 |
|
| 820 |
if (a_is_Charge) { |
| 821 |
C_a = data1.fixedCharge; |
| 822 |
|
| 823 |
if (a_is_Fluctuating) { |
| 824 |
C_a += *(idat.flucQ1); |
| 825 |
} |
| 826 |
|
| 827 |
if (idat.excluded) { |
| 828 |
*(idat.skippedCharge2) += C_a; |
| 829 |
} else { |
| 830 |
// only do the field if we're not excluded: |
| 831 |
Eb -= C_a * pre11_ * dv01 * rhat; |
| 832 |
} |
| 833 |
} |
| 834 |
|
| 835 |
if (a_is_Dipole) { |
| 836 |
D_a = *(idat.dipole1); |
| 837 |
rdDa = dot(rhat, D_a); |
| 838 |
rxDa = cross(rhat, D_a); |
| 839 |
if (!idat.excluded) |
| 840 |
Eb -= pre12_ * ((dv11-v11or) * rdDa * rhat + v11or * D_a); |
| 841 |
} |
| 842 |
|
| 843 |
if (a_is_Quadrupole) { |
| 844 |
Q_a = *(idat.quadrupole1); |
| 845 |
trQa = Q_a.trace(); |
| 846 |
Qar = Q_a * rhat; |
| 847 |
rQa = rhat * Q_a; |
| 848 |
rdQar = dot(rhat, Qar); |
| 849 |
rxQar = cross(rhat, Qar); |
| 850 |
if (!idat.excluded) |
| 851 |
Eb -= pre14_ * (trQa * rhat * dv21 + 2.0 * Qar * v22or |
| 852 |
+ rdQar * rhat * (dv22 - 2.0*v22or)); |
| 853 |
} |
| 854 |
|
| 855 |
if (b_is_Charge) { |
| 856 |
C_b = data2.fixedCharge; |
| 857 |
|
| 858 |
if (b_is_Fluctuating) |
| 859 |
C_b += *(idat.flucQ2); |
| 860 |
|
| 861 |
if (idat.excluded) { |
| 862 |
*(idat.skippedCharge1) += C_b; |
| 863 |
} else { |
| 864 |
// only do the field if we're not excluded: |
| 865 |
Ea += C_b * pre11_ * dv01 * rhat; |
| 866 |
} |
| 867 |
} |
| 868 |
|
| 869 |
if (b_is_Dipole) { |
| 870 |
D_b = *(idat.dipole2); |
| 871 |
rdDb = dot(rhat, D_b); |
| 872 |
rxDb = cross(rhat, D_b); |
| 873 |
if (!idat.excluded) |
| 874 |
Ea += pre12_ * ((dv11-v11or) * rdDb * rhat + v11or * D_b); |
| 875 |
} |
| 876 |
|
| 877 |
if (b_is_Quadrupole) { |
| 878 |
Q_b = *(idat.quadrupole2); |
| 879 |
trQb = Q_b.trace(); |
| 880 |
Qbr = Q_b * rhat; |
| 881 |
rQb = rhat * Q_b; |
| 882 |
rdQbr = dot(rhat, Qbr); |
| 883 |
rxQbr = cross(rhat, Qbr); |
| 884 |
if (!idat.excluded) |
| 885 |
Ea += pre14_ * (trQb * rhat * dv21 + 2.0 * Qbr * v22or |
| 886 |
+ rdQbr * rhat * (dv22 - 2.0*v22or)); |
| 887 |
} |
| 888 |
|
| 889 |
if ((a_is_Fluctuating || b_is_Fluctuating) && idat.excluded) { |
| 890 |
J = Jij[FQtids[idat.atid1]][FQtids[idat.atid2]]; |
| 891 |
} |
| 892 |
|
| 893 |
if (a_is_Charge) { |
| 894 |
|
| 895 |
if (b_is_Charge) { |
| 896 |
pref = pre11_ * *(idat.electroMult); |
| 897 |
U += C_a * C_b * pref * v01; |
| 898 |
F += C_a * C_b * pref * dv01 * rhat; |
| 899 |
|
| 900 |
// If this is an excluded pair, there are still indirect |
| 901 |
// interactions via the reaction field we must worry about: |
| 902 |
|
| 903 |
if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) { |
| 904 |
rfContrib = preRF_ * pref * C_a * C_b * *(idat.r2); |
| 905 |
indirect_Pot += rfContrib; |
| 906 |
indirect_F += rfContrib * 2.0 * ri * rhat; |
| 907 |
} |
| 908 |
|
| 909 |
// Fluctuating charge forces are handled via Coulomb integrals |
| 910 |
// for excluded pairs (i.e. those connected via bonds) and |
| 911 |
// with the standard charge-charge interaction otherwise. |
| 912 |
|
| 913 |
if (idat.excluded) { |
| 914 |
if (a_is_Fluctuating || b_is_Fluctuating) { |
| 915 |
coulInt = J->getValueAt( *(idat.rij) ); |
| 916 |
if (a_is_Fluctuating) dUdCa += coulInt * C_b; |
| 917 |
if (b_is_Fluctuating) dUdCb += coulInt * C_a; |
| 918 |
excluded_Pot += C_a * C_b * coulInt; |
| 919 |
} |
| 920 |
} else { |
| 921 |
if (a_is_Fluctuating) dUdCa += C_b * pref * v01; |
| 922 |
if (a_is_Fluctuating) dUdCb += C_a * pref * v01; |
| 923 |
} |
| 924 |
} |
| 925 |
|
| 926 |
if (b_is_Dipole) { |
| 927 |
pref = pre12_ * *(idat.electroMult); |
| 928 |
U += C_a * pref * v11 * rdDb; |
| 929 |
F += C_a * pref * ((dv11 - v11or) * rdDb * rhat + v11or * D_b); |
| 930 |
Tb += C_a * pref * v11 * rxDb; |
| 931 |
|
| 932 |
if (a_is_Fluctuating) dUdCa += pref * v11 * rdDb; |
| 933 |
|
| 934 |
// Even if we excluded this pair from direct interactions, we |
| 935 |
// still have the reaction-field-mediated charge-dipole |
| 936 |
// interaction: |
| 937 |
|
| 938 |
if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) { |
| 939 |
rfContrib = C_a * pref * preRF_ * 2.0 * *(idat.rij); |
| 940 |
indirect_Pot += rfContrib * rdDb; |
| 941 |
indirect_F += rfContrib * D_b / (*idat.rij); |
| 942 |
indirect_Tb += C_a * pref * preRF_ * rxDb; |
| 943 |
} |
| 944 |
} |
| 945 |
|
| 946 |
if (b_is_Quadrupole) { |
| 947 |
pref = pre14_ * *(idat.electroMult); |
| 948 |
U += C_a * pref * (v21 * trQb + v22 * rdQbr); |
| 949 |
F += C_a * pref * (trQb * dv21 * rhat + 2.0 * Qbr * v22or); |
| 950 |
F += C_a * pref * rdQbr * rhat * (dv22 - 2.0*v22or); |
| 951 |
Tb += C_a * pref * 2.0 * rxQbr * v22; |
| 952 |
|
| 953 |
if (a_is_Fluctuating) dUdCa += pref * (v21 * trQb + v22 * rdQbr); |
| 954 |
} |
| 955 |
} |
| 956 |
|
| 957 |
if (a_is_Dipole) { |
| 958 |
|
| 959 |
if (b_is_Charge) { |
| 960 |
pref = pre12_ * *(idat.electroMult); |
| 961 |
|
| 962 |
U -= C_b * pref * v11 * rdDa; |
| 963 |
F -= C_b * pref * ((dv11-v11or) * rdDa * rhat + v11or * D_a); |
| 964 |
Ta -= C_b * pref * v11 * rxDa; |
| 965 |
|
| 966 |
if (b_is_Fluctuating) dUdCb -= pref * v11 * rdDa; |
| 967 |
|
| 968 |
// Even if we excluded this pair from direct interactions, |
| 969 |
// we still have the reaction-field-mediated charge-dipole |
| 970 |
// interaction: |
| 971 |
if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) { |
| 972 |
rfContrib = C_b * pref * preRF_ * 2.0 * *(idat.rij); |
| 973 |
indirect_Pot -= rfContrib * rdDa; |
| 974 |
indirect_F -= rfContrib * D_a / (*idat.rij); |
| 975 |
indirect_Ta -= C_b * pref * preRF_ * rxDa; |
| 976 |
} |
| 977 |
} |
| 978 |
|
| 979 |
if (b_is_Dipole) { |
| 980 |
pref = pre22_ * *(idat.electroMult); |
| 981 |
DadDb = dot(D_a, D_b); |
| 982 |
DaxDb = cross(D_a, D_b); |
| 983 |
|
| 984 |
U -= pref * (DadDb * v21 + rdDa * rdDb * v22); |
| 985 |
F -= pref * (dv21 * DadDb * rhat + v22or * (rdDb * D_a + rdDa * D_b)); |
| 986 |
F -= pref * (rdDa * rdDb) * (dv22 - 2.0*v22or) * rhat; |
| 987 |
Ta += pref * ( v21 * DaxDb - v22 * rdDb * rxDa); |
| 988 |
Tb += pref * (-v21 * DaxDb - v22 * rdDa * rxDb); |
| 989 |
|
| 990 |
// Even if we excluded this pair from direct interactions, we |
| 991 |
// still have the reaction-field-mediated dipole-dipole |
| 992 |
// interaction: |
| 993 |
if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) { |
| 994 |
rfContrib = -pref * preRF_ * 2.0; |
| 995 |
indirect_Pot += rfContrib * DadDb; |
| 996 |
indirect_Ta += rfContrib * DaxDb; |
| 997 |
indirect_Tb -= rfContrib * DaxDb; |
| 998 |
} |
| 999 |
} |
| 1000 |
|
| 1001 |
if (b_is_Quadrupole) { |
| 1002 |
pref = pre24_ * *(idat.electroMult); |
| 1003 |
DadQb = D_a * Q_b; |
| 1004 |
DadQbr = dot(D_a, Qbr); |
| 1005 |
DaxQbr = cross(D_a, Qbr); |
| 1006 |
|
| 1007 |
U -= pref * ((trQb*rdDa + 2.0*DadQbr)*v31 + rdDa*rdQbr*v32); |
| 1008 |
F -= pref * (trQb*D_a + 2.0*DadQb) * v31or; |
| 1009 |
F -= pref * (trQb*rdDa + 2.0*DadQbr) * (dv31-v31or) * rhat; |
| 1010 |
F -= pref * (D_a*rdQbr + 2.0*rdDa*rQb) * v32or; |
| 1011 |
F -= pref * (rdDa * rdQbr * rhat * (dv32-3.0*v32or)); |
| 1012 |
Ta += pref * ((-trQb*rxDa + 2.0 * DaxQbr)*v31 - rxDa*rdQbr*v32); |
| 1013 |
Tb += pref * ((2.0*cross(DadQb, rhat) - 2.0*DaxQbr)*v31 |
| 1014 |
- 2.0*rdDa*rxQbr*v32); |
| 1015 |
} |
| 1016 |
} |
| 1017 |
|
| 1018 |
if (a_is_Quadrupole) { |
| 1019 |
if (b_is_Charge) { |
| 1020 |
pref = pre14_ * *(idat.electroMult); |
| 1021 |
U += C_b * pref * (v21 * trQa + v22 * rdQar); |
| 1022 |
F += C_b * pref * (trQa * rhat * dv21 + 2.0 * Qar * v22or); |
| 1023 |
F += C_b * pref * rdQar * rhat * (dv22 - 2.0*v22or); |
| 1024 |
Ta += C_b * pref * 2.0 * rxQar * v22; |
| 1025 |
|
| 1026 |
if (b_is_Fluctuating) dUdCb += pref * (v21 * trQa + v22 * rdQar); |
| 1027 |
} |
| 1028 |
if (b_is_Dipole) { |
| 1029 |
pref = pre24_ * *(idat.electroMult); |
| 1030 |
DbdQa = D_b * Q_a; |
| 1031 |
DbdQar = dot(D_b, Qar); |
| 1032 |
DbxQar = cross(D_b, Qar); |
| 1033 |
|
| 1034 |
U += pref * ((trQa*rdDb + 2.0*DbdQar)*v31 + rdDb*rdQar*v32); |
| 1035 |
F += pref * (trQa*D_b + 2.0*DbdQa) * v31or; |
| 1036 |
F += pref * (trQa*rdDb + 2.0*DbdQar) * (dv31-v31or) * rhat; |
| 1037 |
F += pref * (D_b*rdQar + 2.0*rdDb*rQa) * v32or; |
| 1038 |
F += pref * (rdDb * rdQar * rhat * (dv32-3.0*v32or)); |
| 1039 |
Ta += pref * ((-2.0*cross(DbdQa, rhat) + 2.0*DbxQar)*v31 |
| 1040 |
+ 2.0*rdDb*rxQar*v32); |
| 1041 |
Tb += pref * ((trQa*rxDb - 2.0 * DbxQar)*v31 + rxDb*rdQar*v32); |
| 1042 |
} |
| 1043 |
if (b_is_Quadrupole) { |
| 1044 |
pref = pre44_ * *(idat.electroMult); // yes |
| 1045 |
QaQb = Q_a * Q_b; |
| 1046 |
trQaQb = QaQb.trace(); |
| 1047 |
rQaQb = rhat * QaQb; |
| 1048 |
QaQbr = QaQb * rhat; |
| 1049 |
QaxQb = cross(Q_a, Q_b); |
| 1050 |
rQaQbr = dot(rQa, Qbr); |
| 1051 |
rQaxQbr = cross(rQa, Qbr); |
| 1052 |
|
| 1053 |
U += pref * (trQa * trQb + 2.0 * trQaQb) * v41; |
| 1054 |
U += pref * (trQa * rdQbr + trQb * rdQar + 4.0 * rQaQbr) * v42; |
| 1055 |
U += pref * (rdQar * rdQbr) * v43; |
| 1056 |
|
| 1057 |
F += pref * rhat * (trQa * trQb + 2.0 * trQaQb)*dv41; |
| 1058 |
F += pref*rhat*(trQa*rdQbr + trQb*rdQar + 4.0*rQaQbr)*(dv42-2.0*v42or); |
| 1059 |
F += pref * rhat * (rdQar * rdQbr)*(dv43 - 4.0*v43or); |
| 1060 |
|
| 1061 |
F += pref * 2.0 * (trQb*rQa + trQa*rQb) * v42or; |
| 1062 |
F += pref * 4.0 * (rQaQb + QaQbr) * v42or; |
| 1063 |
F += pref * 2.0 * (rQa*rdQbr + rdQar*rQb) * v43or; |
| 1064 |
|
| 1065 |
Ta += pref * (- 4.0 * QaxQb * v41); |
| 1066 |
Ta += pref * (- 2.0 * trQb * cross(rQa, rhat) |
| 1067 |
+ 4.0 * cross(rhat, QaQbr) |
| 1068 |
- 4.0 * rQaxQbr) * v42; |
| 1069 |
Ta += pref * 2.0 * cross(rhat,Qar) * rdQbr * v43; |
| 1070 |
|
| 1071 |
|
| 1072 |
Tb += pref * (+ 4.0 * QaxQb * v41); |
| 1073 |
Tb += pref * (- 2.0 * trQa * cross(rQb, rhat) |
| 1074 |
- 4.0 * cross(rQaQb, rhat) |
| 1075 |
+ 4.0 * rQaxQbr) * v42; |
| 1076 |
// Possible replacement for line 2 above: |
| 1077 |
// + 4.0 * cross(rhat, QbQar) |
| 1078 |
|
| 1079 |
Tb += pref * 2.0 * cross(rhat,Qbr) * rdQar * v43; |
| 1080 |
|
| 1081 |
} |
| 1082 |
} |
| 1083 |
|
| 1084 |
if (idat.doElectricField) { |
| 1085 |
*(idat.eField1) += Ea * *(idat.electroMult); |
| 1086 |
*(idat.eField2) += Eb * *(idat.electroMult); |
| 1087 |
} |
| 1088 |
|
| 1089 |
if (a_is_Fluctuating) *(idat.dVdFQ1) += dUdCa * *(idat.sw); |
| 1090 |
if (b_is_Fluctuating) *(idat.dVdFQ2) += dUdCb * *(idat.sw); |
| 1091 |
|
| 1092 |
if (!idat.excluded) { |
| 1093 |
|
| 1094 |
*(idat.vpair) += U; |
| 1095 |
(*(idat.pot))[ELECTROSTATIC_FAMILY] += U * *(idat.sw); |
| 1096 |
*(idat.f1) += F * *(idat.sw); |
| 1097 |
|
| 1098 |
if (a_is_Dipole || a_is_Quadrupole) |
| 1099 |
*(idat.t1) += Ta * *(idat.sw); |
| 1100 |
|
| 1101 |
if (b_is_Dipole || b_is_Quadrupole) |
| 1102 |
*(idat.t2) += Tb * *(idat.sw); |
| 1103 |
|
| 1104 |
} else { |
| 1105 |
|
| 1106 |
// only accumulate the forces and torques resulting from the |
| 1107 |
// indirect reaction field terms. |
| 1108 |
|
| 1109 |
*(idat.vpair) += indirect_Pot; |
| 1110 |
(*(idat.excludedPot))[ELECTROSTATIC_FAMILY] += excluded_Pot; |
| 1111 |
(*(idat.pot))[ELECTROSTATIC_FAMILY] += *(idat.sw) * indirect_Pot; |
| 1112 |
*(idat.f1) += *(idat.sw) * indirect_F; |
| 1113 |
|
| 1114 |
if (a_is_Dipole || a_is_Quadrupole) |
| 1115 |
*(idat.t1) += *(idat.sw) * indirect_Ta; |
| 1116 |
|
| 1117 |
if (b_is_Dipole || b_is_Quadrupole) |
| 1118 |
*(idat.t2) += *(idat.sw) * indirect_Tb; |
| 1119 |
} |
| 1120 |
return; |
| 1121 |
} |
| 1122 |
|
| 1123 |
void Electrostatic::calcSelfCorrection(SelfData &sdat) { |
| 1124 |
|
| 1125 |
if (!initialized_) initialize(); |
| 1126 |
|
| 1127 |
ElectrostaticAtomData data = ElectrostaticMap[Etids[sdat.atid]]; |
| 1128 |
|
| 1129 |
// logicals |
| 1130 |
bool i_is_Charge = data.is_Charge; |
| 1131 |
bool i_is_Dipole = data.is_Dipole; |
| 1132 |
bool i_is_Quadrupole = data.is_Quadrupole; |
| 1133 |
bool i_is_Fluctuating = data.is_Fluctuating; |
| 1134 |
RealType C_a = data.fixedCharge; |
| 1135 |
RealType self(0.0), preVal, DdD, trQ, trQQ; |
| 1136 |
|
| 1137 |
if (i_is_Dipole) { |
| 1138 |
DdD = data.dipole.lengthSquare(); |
| 1139 |
} |
| 1140 |
|
| 1141 |
if (i_is_Fluctuating) { |
| 1142 |
C_a += *(sdat.flucQ); |
| 1143 |
// dVdFQ is really a force, so this is negative the derivative |
| 1144 |
*(sdat.dVdFQ) -= *(sdat.flucQ) * data.hardness + data.electronegativity; |
| 1145 |
(*(sdat.excludedPot))[ELECTROSTATIC_FAMILY] += (*sdat.flucQ) * |
| 1146 |
(*(sdat.flucQ) * data.hardness * 0.5 + data.electronegativity); |
| 1147 |
} |
| 1148 |
|
| 1149 |
switch (summationMethod_) { |
| 1150 |
case esm_REACTION_FIELD: |
| 1151 |
|
| 1152 |
if (i_is_Charge) { |
| 1153 |
// Self potential [see Wang and Hermans, "Reaction Field |
| 1154 |
// Molecular Dynamics Simulation with Friedman’s Image Charge |
| 1155 |
// Method," J. Phys. Chem. 99, 12001-12007 (1995).] |
| 1156 |
preVal = pre11_ * preRF_ * C_a * C_a; |
| 1157 |
(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 * preVal / cutoffRadius_; |
| 1158 |
} |
| 1159 |
|
| 1160 |
if (i_is_Dipole) { |
| 1161 |
(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= pre22_ * preRF_ * DdD; |
| 1162 |
} |
| 1163 |
|
| 1164 |
break; |
| 1165 |
|
| 1166 |
case esm_SHIFTED_FORCE: |
| 1167 |
case esm_SHIFTED_POTENTIAL: |
| 1168 |
case esm_TAYLOR_SHIFTED: |
| 1169 |
case esm_EWALD_FULL: |
| 1170 |
if (i_is_Charge) |
| 1171 |
self += selfMult1_ * pre11_ * C_a * (C_a + *(sdat.skippedCharge)); |
| 1172 |
if (i_is_Dipole) |
| 1173 |
self += selfMult2_ * pre22_ * DdD; |
| 1174 |
if (i_is_Quadrupole) { |
| 1175 |
trQ = data.quadrupole.trace(); |
| 1176 |
trQQ = (data.quadrupole * data.quadrupole).trace(); |
| 1177 |
self += selfMult4_ * pre44_ * (2.0*trQQ + trQ*trQ); |
| 1178 |
if (i_is_Charge) |
| 1179 |
self -= selfMult2_ * pre14_ * 2.0 * C_a * trQ; |
| 1180 |
} |
| 1181 |
(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self; |
| 1182 |
break; |
| 1183 |
default: |
| 1184 |
break; |
| 1185 |
} |
| 1186 |
} |
| 1187 |
|
| 1188 |
RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 1189 |
// This seems to work moderately well as a default. There's no |
| 1190 |
// inherent scale for 1/r interactions that we can standardize. |
| 1191 |
// 12 angstroms seems to be a reasonably good guess for most |
| 1192 |
// cases. |
| 1193 |
return 12.0; |
| 1194 |
} |
| 1195 |
|
| 1196 |
|
| 1197 |
void Electrostatic::ReciprocalSpaceSum(potVec& pot) { |
| 1198 |
|
| 1199 |
RealType kPot = 0.0; |
| 1200 |
RealType kVir = 0.0; |
| 1201 |
|
| 1202 |
const RealType mPoleConverter = 0.20819434; // converts from the |
| 1203 |
// internal units of |
| 1204 |
// Debye (for dipoles) |
| 1205 |
// or Debye-angstroms |
| 1206 |
// (for quadrupoles) to |
| 1207 |
// electron angstroms or |
| 1208 |
// electron-angstroms^2 |
| 1209 |
|
| 1210 |
const RealType eConverter = 332.0637778; // convert the |
| 1211 |
// Charge-Charge |
| 1212 |
// electrostatic |
| 1213 |
// interactions into kcal / |
| 1214 |
// mol assuming distances |
| 1215 |
// are measured in |
| 1216 |
// angstroms. |
| 1217 |
|
| 1218 |
Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
| 1219 |
Vector3d box = hmat.diagonals(); |
| 1220 |
RealType boxMax = box.max(); |
| 1221 |
|
| 1222 |
//int kMax = int(2.0 * M_PI / (pow(dampingAlpha_,2)*cutoffRadius_ * boxMax) ); |
| 1223 |
int kMax = 7; |
| 1224 |
int kSqMax = kMax*kMax + 2; |
| 1225 |
|
| 1226 |
int kLimit = kMax+1; |
| 1227 |
int kLim2 = 2*kMax+1; |
| 1228 |
int kSqLim = kSqMax; |
| 1229 |
|
| 1230 |
vector<RealType> AK(kSqLim+1, 0.0); |
| 1231 |
RealType xcl = 2.0 * M_PI / box.x(); |
| 1232 |
RealType ycl = 2.0 * M_PI / box.y(); |
| 1233 |
RealType zcl = 2.0 * M_PI / box.z(); |
| 1234 |
RealType rcl = 2.0 * M_PI / boxMax; |
| 1235 |
RealType rvol = 2.0 * M_PI /(box.x() * box.y() * box.z()); |
| 1236 |
|
| 1237 |
if(dampingAlpha_ < 1.0e-12) return; |
| 1238 |
|
| 1239 |
RealType ralph = -0.25/pow(dampingAlpha_,2); |
| 1240 |
|
| 1241 |
// Calculate and store exponential factors |
| 1242 |
|
| 1243 |
vector<vector<Vector3d> > eCos; |
| 1244 |
vector<vector<Vector3d> > eSin; |
| 1245 |
|
| 1246 |
int nMax = info_->getNAtoms(); |
| 1247 |
|
| 1248 |
eCos.resize(kLimit+1); |
| 1249 |
eSin.resize(kLimit+1); |
| 1250 |
for (int j = 0; j < kLimit+1; j++) { |
| 1251 |
eCos[j].resize(nMax); |
| 1252 |
eSin[j].resize(nMax); |
| 1253 |
} |
| 1254 |
|
| 1255 |
Vector3d t( 2.0 * M_PI ); |
| 1256 |
t.Vdiv(t, box); |
| 1257 |
|
| 1258 |
|
| 1259 |
SimInfo::MoleculeIterator mi; |
| 1260 |
Molecule::AtomIterator ai; |
| 1261 |
int i; |
| 1262 |
Vector3d r; |
| 1263 |
Vector3d tt; |
| 1264 |
Vector3d w; |
| 1265 |
Vector3d u; |
| 1266 |
Vector3d a; |
| 1267 |
Vector3d b; |
| 1268 |
|
| 1269 |
for (Molecule* mol = info_->beginMolecule(mi); mol != NULL; |
| 1270 |
mol = info_->nextMolecule(mi)) { |
| 1271 |
for(Atom* atom = mol->beginAtom(ai); atom != NULL; |
| 1272 |
atom = mol->nextAtom(ai)) { |
| 1273 |
|
| 1274 |
i = atom->getLocalIndex(); |
| 1275 |
r = atom->getPos(); |
| 1276 |
info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(r); |
| 1277 |
|
| 1278 |
tt.Vmul(t, r); |
| 1279 |
|
| 1280 |
|
| 1281 |
eCos[1][i] = Vector3d(1.0, 1.0, 1.0); |
| 1282 |
eSin[1][i] = Vector3d(0.0, 0.0, 0.0); |
| 1283 |
eCos[2][i] = Vector3d(cos(tt.x()), cos(tt.y()), cos(tt.z())); |
| 1284 |
eSin[2][i] = Vector3d(sin(tt.x()), sin(tt.y()), sin(tt.z())); |
| 1285 |
|
| 1286 |
u = eCos[2][i]; |
| 1287 |
w = eSin[2][i]; |
| 1288 |
|
| 1289 |
for(int l = 3; l <= kLimit; l++) { |
| 1290 |
eCos[l][i].x() = eCos[l-1][i].x()*eCos[2][i].x() - eSin[l-1][i].x()*eSin[2][i].x(); |
| 1291 |
eCos[l][i].y() = eCos[l-1][i].y()*eCos[2][i].y() - eSin[l-1][i].y()*eSin[2][i].y(); |
| 1292 |
eCos[l][i].z() = eCos[l-1][i].z()*eCos[2][i].z() - eSin[l-1][i].z()*eSin[2][i].z(); |
| 1293 |
|
| 1294 |
eSin[l][i].x() = eSin[l-1][i].x()*eCos[2][i].x() + eCos[l-1][i].x()*eSin[2][i].x(); |
| 1295 |
eSin[l][i].y() = eSin[l-1][i].y()*eCos[2][i].y() + eCos[l-1][i].y()*eSin[2][i].z(); |
| 1296 |
eSin[l][i].z() = eSin[l-1][i].z()*eCos[2][i].z() + eCos[l-1][i].z()*eSin[2][i].y(); |
| 1297 |
|
| 1298 |
|
| 1299 |
// a.Vmul(eCos[l-1][i], u); |
| 1300 |
// b.Vmul(eSin[l-1][i], w); |
| 1301 |
// eCos[l][i] = a - b; |
| 1302 |
// a.Vmul(eSin[l-1][i], u); |
| 1303 |
// b.Vmul(eCos[l-1][i], w); |
| 1304 |
// eSin[l][i] = a + b; |
| 1305 |
|
| 1306 |
} |
| 1307 |
} |
| 1308 |
} |
| 1309 |
|
| 1310 |
// Calculate and store AK coefficients: |
| 1311 |
|
| 1312 |
RealType eksq = 1.0; |
| 1313 |
RealType expf = 0.0; |
| 1314 |
if (ralph < 0.0) expf = exp(ralph*rcl*rcl); |
| 1315 |
for (i = 1; i <= kSqLim; i++) { |
| 1316 |
RealType rksq = float(i)*rcl*rcl; |
| 1317 |
eksq = expf*eksq; |
| 1318 |
AK[i] = eConverter * eksq/rksq; |
| 1319 |
} |
| 1320 |
|
| 1321 |
/* |
| 1322 |
* Loop over all k vectors k = 2 pi (ll/Lx, mm/Ly, nn/Lz) |
| 1323 |
* the values of ll, mm and nn are selected so that the symmetry of |
| 1324 |
* reciprocal lattice is taken into account i.e. the following |
| 1325 |
* rules apply. |
| 1326 |
* |
| 1327 |
* ll ranges over the values 0 to kMax only. |
| 1328 |
* |
| 1329 |
* mm ranges over 0 to kMax when ll=0 and over |
| 1330 |
* -kMax to kMax otherwise. |
| 1331 |
* nn ranges over 1 to kMax when ll=mm=0 and over |
| 1332 |
* -kMax to kMax otherwise. |
| 1333 |
* |
| 1334 |
* Hence the result of the summation must be doubled at the end. |
| 1335 |
*/ |
| 1336 |
|
| 1337 |
std::vector<RealType> clm(nMax, 0.0); |
| 1338 |
std::vector<RealType> slm(nMax, 0.0); |
| 1339 |
std::vector<RealType> ckr(nMax, 0.0); |
| 1340 |
std::vector<RealType> skr(nMax, 0.0); |
| 1341 |
std::vector<RealType> ckc(nMax, 0.0); |
| 1342 |
std::vector<RealType> cks(nMax, 0.0); |
| 1343 |
std::vector<RealType> dkc(nMax, 0.0); |
| 1344 |
std::vector<RealType> dks(nMax, 0.0); |
| 1345 |
std::vector<RealType> qkc(nMax, 0.0); |
| 1346 |
std::vector<RealType> qks(nMax, 0.0); |
| 1347 |
std::vector<Vector3d> dxk(nMax, V3Zero); |
| 1348 |
std::vector<Vector3d> qxk(nMax, V3Zero); |
| 1349 |
|
| 1350 |
int mMin = kLimit; |
| 1351 |
int nMin = kLimit + 1; |
| 1352 |
for (int l = 1; l <= kLimit; l++) { |
| 1353 |
int ll = l - 1; |
| 1354 |
RealType rl = xcl * float(ll); |
| 1355 |
for (int mmm = mMin; mmm <= kLim2; mmm++) { |
| 1356 |
int mm = mmm - kLimit; |
| 1357 |
int m = abs(mm) + 1; |
| 1358 |
RealType rm = ycl * float(mm); |
| 1359 |
// Set temporary products of exponential terms |
| 1360 |
for (Molecule* mol = info_->beginMolecule(mi); mol != NULL; |
| 1361 |
mol = info_->nextMolecule(mi)) { |
| 1362 |
for(Atom* atom = mol->beginAtom(ai); atom != NULL; |
| 1363 |
atom = mol->nextAtom(ai)) { |
| 1364 |
|
| 1365 |
i = atom->getLocalIndex(); |
| 1366 |
if(mm < 0) { |
| 1367 |
clm[i] = eCos[l][i].x()*eCos[m][i].y() |
| 1368 |
+ eSin[l][i].x()*eSin[m][i].y(); |
| 1369 |
slm[i] = eSin[l][i].x()*eCos[m][i].y() |
| 1370 |
- eSin[m][i].y()*eCos[l][i].x(); |
| 1371 |
} else { |
| 1372 |
clm[i] = eCos[l][i].x()*eCos[m][i].y() |
| 1373 |
- eSin[l][i].x()*eSin[m][i].y(); |
| 1374 |
slm[i] = eSin[l][i].x()*eCos[m][i].y() |
| 1375 |
+ eSin[m][i].y()*eCos[l][i].x(); |
| 1376 |
} |
| 1377 |
} |
| 1378 |
} |
| 1379 |
for (int nnn = nMin; nnn <= kLim2; nnn++) { |
| 1380 |
int nn = nnn - kLimit; |
| 1381 |
int n = abs(nn) + 1; |
| 1382 |
RealType rn = zcl * float(nn); |
| 1383 |
// Test on magnitude of k vector: |
| 1384 |
int kk=ll*ll + mm*mm + nn*nn; |
| 1385 |
if(kk <= kSqLim) { |
| 1386 |
Vector3d kVec = Vector3d(rl, rm, rn); |
| 1387 |
Mat3x3d k2 = outProduct(kVec, kVec); |
| 1388 |
// Calculate exp(ikr) terms |
| 1389 |
for (Molecule* mol = info_->beginMolecule(mi); mol != NULL; |
| 1390 |
mol = info_->nextMolecule(mi)) { |
| 1391 |
for(Atom* atom = mol->beginAtom(ai); atom != NULL; |
| 1392 |
atom = mol->nextAtom(ai)) { |
| 1393 |
i = atom->getLocalIndex(); |
| 1394 |
|
| 1395 |
if (nn < 0) { |
| 1396 |
ckr[i]=clm[i]*eCos[n][i].z()+slm[i]*eSin[n][i].z(); |
| 1397 |
skr[i]=slm[i]*eCos[n][i].z()-clm[i]*eSin[n][i].z(); |
| 1398 |
} else { |
| 1399 |
ckr[i]=clm[i]*eCos[n][i].z()-slm[i]*eSin[n][i].z(); |
| 1400 |
skr[i]=slm[i]*eCos[n][i].z()+clm[i]*eSin[n][i].z(); |
| 1401 |
} |
| 1402 |
} |
| 1403 |
} |
| 1404 |
|
| 1405 |
// Calculate scalar and vector products for each site: |
| 1406 |
|
| 1407 |
for (Molecule* mol = info_->beginMolecule(mi); mol != NULL; |
| 1408 |
mol = info_->nextMolecule(mi)) { |
| 1409 |
for(Atom* atom = mol->beginAtom(ai); atom != NULL; |
| 1410 |
atom = mol->nextAtom(ai)) { |
| 1411 |
i = atom->getLocalIndex(); |
| 1412 |
int atid = atom->getAtomType()->getIdent(); |
| 1413 |
ElectrostaticAtomData data = ElectrostaticMap[Etids[atid]]; |
| 1414 |
|
| 1415 |
if (data.is_Charge) { |
| 1416 |
RealType C = data.fixedCharge; |
| 1417 |
if (atom->isFluctuatingCharge()) C += atom->getFlucQPos(); |
| 1418 |
ckc[i] = C * ckr[i]; |
| 1419 |
cks[i] = C * skr[i]; |
| 1420 |
} |
| 1421 |
|
| 1422 |
if (data.is_Dipole) { |
| 1423 |
Vector3d D = atom->getDipole() * mPoleConverter; |
| 1424 |
RealType dk = dot(kVec, D); |
| 1425 |
dxk[i] = cross(kVec, D); |
| 1426 |
dkc[i] = dk * ckr[i]; |
| 1427 |
dks[i] = dk * skr[i]; |
| 1428 |
} |
| 1429 |
if (data.is_Quadrupole) { |
| 1430 |
Mat3x3d Q = atom->getQuadrupole(); |
| 1431 |
Q *= mPoleConverter; |
| 1432 |
RealType qk = -( Q * k2 ).trace(); |
| 1433 |
qxk[i] = -2.0 * cross(k2, Q); |
| 1434 |
qkc[i] = qk * ckr[i]; |
| 1435 |
qks[i] = qk * skr[i]; |
| 1436 |
} |
| 1437 |
} |
| 1438 |
} |
| 1439 |
|
| 1440 |
// calculate vector sums |
| 1441 |
|
| 1442 |
RealType ckcs = std::accumulate(ckc.begin(),ckc.end(),0.0); |
| 1443 |
RealType ckss = std::accumulate(cks.begin(),cks.end(),0.0); |
| 1444 |
RealType dkcs = std::accumulate(dkc.begin(),dkc.end(),0.0); |
| 1445 |
RealType dkss = std::accumulate(dks.begin(),dks.end(),0.0); |
| 1446 |
RealType qkcs = std::accumulate(qkc.begin(),qkc.end(),0.0); |
| 1447 |
RealType qkss = std::accumulate(qks.begin(),qks.end(),0.0); |
| 1448 |
|
| 1449 |
|
| 1450 |
#ifdef IS_MPI |
| 1451 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckcs, 1, MPI::REALTYPE, |
| 1452 |
MPI::SUM); |
| 1453 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckss, 1, MPI::REALTYPE, |
| 1454 |
MPI::SUM); |
| 1455 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkcs, 1, MPI::REALTYPE, |
| 1456 |
MPI::SUM); |
| 1457 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkss, 1, MPI::REALTYPE, |
| 1458 |
MPI::SUM); |
| 1459 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkcs, 1, MPI::REALTYPE, |
| 1460 |
MPI::SUM); |
| 1461 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkss, 1, MPI::REALTYPE, |
| 1462 |
MPI::SUM); |
| 1463 |
#endif |
| 1464 |
|
| 1465 |
// Accumulate potential energy and virial contribution: |
| 1466 |
|
| 1467 |
kPot += 2.0 * rvol * AK[kk]*((ckss+dkcs-qkss)*(ckss+dkcs-qkss) |
| 1468 |
+ (ckcs-dkss-qkcs)*(ckcs-dkss-qkss)); |
| 1469 |
|
| 1470 |
kVir -= 2.0 * rvol * AK[kk]*(ckcs*ckcs+ckss*ckss |
| 1471 |
+4.0*(ckss*dkcs-ckcs*dkss) |
| 1472 |
+3.0*(dkcs*dkcs+dkss*dkss) |
| 1473 |
-6.0*(ckss*qkss+ckcs*qkcs) |
| 1474 |
+8.0*(dkss*qkcs-dkcs*qkss) |
| 1475 |
+5.0*(qkss*qkss+qkcs*qkcs)); |
| 1476 |
|
| 1477 |
// Calculate force and torque for each site: |
| 1478 |
|
| 1479 |
for (Molecule* mol = info_->beginMolecule(mi); mol != NULL; |
| 1480 |
mol = info_->nextMolecule(mi)) { |
| 1481 |
for(Atom* atom = mol->beginAtom(ai); atom != NULL; |
| 1482 |
atom = mol->nextAtom(ai)) { |
| 1483 |
|
| 1484 |
i = atom->getLocalIndex(); |
| 1485 |
int atid = atom->getAtomType()->getIdent(); |
| 1486 |
ElectrostaticAtomData data = ElectrostaticMap[Etids[atid]]; |
| 1487 |
|
| 1488 |
RealType qfrc = AK[kk]*((cks[i]+dkc[i]-qks[i])*(ckcs-dkss-qkcs) |
| 1489 |
- (ckc[i]-dks[i]-qkc[i])*(ckss+dkcs-qkss)); |
| 1490 |
RealType qtrq1 = AK[kk]*(skr[i]*(ckcs-dkss-qkcs) |
| 1491 |
-ckr[i]*(ckss+dkcs-qkss)); |
| 1492 |
RealType qtrq2 = 2.0*AK[kk]*(ckr[i]*(ckcs-dkss-qkcs)+ |
| 1493 |
skr[i]*(ckss+dkcs-qkss)); |
| 1494 |
|
| 1495 |
atom->addFrc( 4.0 * rvol * qfrc * kVec ); |
| 1496 |
|
| 1497 |
if (data.is_Dipole) { |
| 1498 |
atom->addTrq( 4.0 * rvol * qtrq1 * dxk[i] ); |
| 1499 |
} |
| 1500 |
if (data.is_Quadrupole) { |
| 1501 |
atom->addTrq( 4.0 * rvol * qtrq2 * qxk[i] ); |
| 1502 |
} |
| 1503 |
} |
| 1504 |
} |
| 1505 |
} |
| 1506 |
} |
| 1507 |
nMin = 1; |
| 1508 |
} |
| 1509 |
mMin = 1; |
| 1510 |
} |
| 1511 |
cerr << "kPot = " << kPot << "\n"; |
| 1512 |
pot[ELECTROSTATIC_FAMILY] += kPot; |
| 1513 |
} |
| 1514 |
} |
