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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. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
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< |
* 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 |
< |
* |
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< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 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 |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
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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 |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [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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#include "selection/SelectionManager.hpp" |
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#include <iostream> |
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|
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< |
namespace oopse { |
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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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exchangeTime_ = exchangeTime; |
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} |
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void set_RNEMD_nBins(int nbins) { nBins_ = nbins; } |
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< |
RealType get_RNEMD_exchange_total() { return exchangeSum_; } |
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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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|
|
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SimInfo* info_; |
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RandNumGen* randNumGen_; |
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< |
std::map<std::string, RNEMDTypeEnum> stringToEnumMap_; |
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> |
map<string, RNEMDTypeEnum> stringToEnumMap_; |
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RNEMDTypeEnum rnemdType_; |
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< |
std::string rnemdObjectSelection_; |
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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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< |
int nBins_; |
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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_; |
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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_; |
| 123 |
< |
std::ofstream rnemdLog_; |
| 123 |
> |
ofstream rnemdLog_; |
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|
// keeps track of what's being averaged |
| 125 |
< |
std::vector<RealType> valueHist_; |
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< |
std::vector<int> valueCount_; |
| 125 |
> |
vector<RealType> valueHist_; |
| 126 |
> |
vector<int> valueCount_, xyzTempCount_; |
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|
// keeps track of the number of degrees of freedom being averaged |
| 128 |
< |
std::vector<RealType> xTempHist_, yTempHist_, zTempHist_; |
| 129 |
< |
std::ofstream xTempLog_, yTempLog_, zTempLog_; |
| 128 |
> |
vector<RealType> xTempHist_, yTempHist_, zTempHist_; |
| 129 |
> |
ofstream xTempLog_, yTempLog_, zTempLog_; |
| 130 |
|
}; |
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|
|
| 132 |
|
} |
