| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
* publication of scientific results based in part on use of the |
| 11 |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
* the article in which the program was described (Matthew |
| 13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
* |
| 18 |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
/** |
| 43 |
* @file RNEMD.hpp |
| 44 |
* @author gezelter |
| 45 |
* @date 03/13/2009 |
| 46 |
* @time 15:56pm |
| 47 |
* @version 1.0 |
| 48 |
*/ |
| 49 |
|
| 50 |
#ifndef INTEGRATORS_RNEMD_HPP |
| 51 |
#define INTEGRATORS_RNEMD_HPP |
| 52 |
#include "brains/SimInfo.hpp" |
| 53 |
#include "math/RandNumGen.hpp" |
| 54 |
#include "selection/SelectionEvaluator.hpp" |
| 55 |
#include "selection/SelectionManager.hpp" |
| 56 |
#include <iostream> |
| 57 |
|
| 58 |
namespace oopse { |
| 59 |
|
| 60 |
/** |
| 61 |
* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp" |
| 62 |
* @todo document |
| 63 |
*/ |
| 64 |
class RNEMD { |
| 65 |
public: |
| 66 |
RNEMD(SimInfo* info); |
| 67 |
virtual ~RNEMD(); |
| 68 |
|
| 69 |
void doRNEMD(); |
| 70 |
void doSwap(); |
| 71 |
void doScale(); |
| 72 |
void collectData(); |
| 73 |
void getStarted(); |
| 74 |
void getStatus(); |
| 75 |
void set_RNEMD_exchange_time(RealType exchangeTime) { |
| 76 |
exchangeTime_ = exchangeTime; |
| 77 |
} |
| 78 |
void set_RNEMD_nBins(int nbins) { nBins_ = nbins; } |
| 79 |
RealType get_RNEMD_exchange_total() { return exchangeSum_; } |
| 80 |
void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; } |
| 81 |
void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;} |
| 82 |
|
| 83 |
private: |
| 84 |
|
| 85 |
enum RNEMDTypeEnum { |
| 86 |
rnemdKineticSwap, |
| 87 |
rnemdKineticScale, |
| 88 |
rnemdPxScale, |
| 89 |
rnemdPyScale, |
| 90 |
rnemdPzScale, |
| 91 |
rnemdPx, |
| 92 |
rnemdPy, |
| 93 |
rnemdPz, |
| 94 |
rnemdUnknown |
| 95 |
}; |
| 96 |
|
| 97 |
SimInfo* info_; |
| 98 |
RandNumGen* randNumGen_; |
| 99 |
std::map<std::string, RNEMDTypeEnum> stringToEnumMap_; |
| 100 |
RNEMDTypeEnum rnemdType_; |
| 101 |
std::string rnemdObjectSelection_; |
| 102 |
SelectionEvaluator evaluator_; |
| 103 |
SelectionManager seleMan_; |
| 104 |
bool usePeriodicBoundaryConditions_; |
| 105 |
int nBins_; |
| 106 |
int midBin_; |
| 107 |
int rnemdLogWidth_; |
| 108 |
RealType exchangeTime_; |
| 109 |
RealType targetFlux_; |
| 110 |
RealType exchangeSum_; |
| 111 |
int failTrialCount_; |
| 112 |
int failRootCount_; |
| 113 |
std::ofstream rnemdLog_; |
| 114 |
// keeps track of what's being averaged |
| 115 |
std::vector<RealType> valueHist_; |
| 116 |
std::vector<int> valueCount_; |
| 117 |
// keeps track of the number of degrees of freedom being averaged |
| 118 |
std::vector<RealType> xTempHist_, yTempHist_, zTempHist_; |
| 119 |
std::ofstream xTempLog_, yTempLog_, zTempLog_; |
| 120 |
}; |
| 121 |
|
| 122 |
} |
| 123 |
#endif //INTEGRATORS_RNEMD_HPP |
