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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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/** |
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* @file RNEMD.hpp |
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* @author gezelter |
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* @date 03/13/2009 |
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* @time 15:56pm |
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* @version 1.0 |
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*/ |
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|
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#ifndef INTEGRATORS_RNEMD_HPP |
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#define INTEGRATORS_RNEMD_HPP |
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#include "brains/SimInfo.hpp" |
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#include "math/RandNumGen.hpp" |
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#include "selection/SelectionEvaluator.hpp" |
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#include "selection/SelectionManager.hpp" |
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#include <iostream> |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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/** |
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* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp" |
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* @todo document |
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*/ |
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class RNEMD { |
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public: |
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RNEMD(SimInfo* info); |
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virtual ~RNEMD(); |
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|
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void doRNEMD(); |
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void doSwap(); |
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void doScale(); |
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void collectData(); |
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void getStarted(); |
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void getStatus(); |
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void set_RNEMD_exchange_time(RealType exchangeTime) { |
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exchangeTime_ = exchangeTime; |
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} |
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void set_RNEMD_nBins(int nbins) { nBins_ = nbins; } |
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void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; } |
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void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; } |
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void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;} |
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RealType get_RNEMD_exchange_total() { return exchangeSum_; } |
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|
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private: |
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|
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enum RNEMDTypeEnum { |
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rnemdKineticSwap, |
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rnemdKineticScale, |
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rnemdPxScale, |
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rnemdPyScale, |
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rnemdPzScale, |
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rnemdPx, |
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rnemdPy, |
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rnemdPz, |
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rnemdUnknown |
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}; |
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|
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SimInfo* info_; |
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RandNumGen* randNumGen_; |
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map<string, RNEMDTypeEnum> stringToEnumMap_; |
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RNEMDTypeEnum rnemdType_; |
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string rnemdObjectSelection_; |
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SelectionEvaluator evaluator_; |
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SelectionManager seleMan_; |
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bool usePeriodicBoundaryConditions_; |
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bool output3DTemp_; |
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int nBins_; /**< The number of bins to divide the simulation box into. */ |
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/*! |
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The middle bin for the RNEMD method. midBin_ = nBins_/2; |
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Depending on the setting of the flux, this box should contain the minimum energy (temperature) |
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within the simulation. |
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*/ |
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int midBin_; |
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int rnemdLogWidth_; /**< Number of elements to print out in logs */ |
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RealType zShift_; |
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RealType exchangeTime_; |
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RealType targetFlux_; |
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RealType exchangeSum_; |
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int failTrialCount_; |
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int failRootCount_; |
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ofstream rnemdLog_; |
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// keeps track of what's being averaged |
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vector<RealType> valueHist_; |
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vector<int> valueCount_, xyzTempCount_; |
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// keeps track of the number of degrees of freedom being averaged |
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vector<RealType> xTempHist_, yTempHist_, zTempHist_; |
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ofstream xTempLog_, yTempLog_, zTempLog_; |
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}; |
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|
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} |
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#endif //INTEGRATORS_RNEMD_HPP |
