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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 |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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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#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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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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public: |
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RNEMD(SimInfo* info); |
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virtual ~RNEMD(); |
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|
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> |
|
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> |
void doRNEMD(); |
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void doSwap(); |
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void set_RNEMD_swapTime(RealType swapTime) { swapTime_ = swapTime; } |
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void doScale(); |
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void doShiftScale(); |
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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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void set_RNEMD_target_JzKE(RealType targetJzKE) {targetJzKE_ = targetJzKE;} |
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void set_RNEMD_target_jzpx(RealType targetJzpx) {targetJzpx_ = targetJzpx;} |
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void set_RNEMD_target_jzpy(RealType targetJzpy) {targetJzpy_ = targetJzpy;} |
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void set_RNEMD_target_jzpz(RealType targetJzpz) {targetJzpz_ = targetJzpz;} |
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void set_RNEMD_target_jzpz2(RealType targetJzpz2) {targetJzpz2_ = targetJzpz2;} |
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RealType get_RNEMD_exchange_total() { return exchangeSum_; } |
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void set_RNEMD_exchange_total(RealType et) {exchangeSum_ = et;} |
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|
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|
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private: |
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< |
|
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> |
|
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enum RNEMDTypeEnum { |
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rnemdKinetic, |
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> |
rnemdKineticSwap, |
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rnemdKineticScale, |
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> |
rnemdKineticScaleVAM, |
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> |
rnemdKineticScaleAM, |
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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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rnemdShiftScaleV, |
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rnemdShiftScaleVAM, |
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rnemdUnknown |
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}; |
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|
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> |
|
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SimInfo* info_; |
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RandNumGen* randNumGen_; |
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int nBins_; |
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RealType swapTime_; |
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RealType exchangeSum_; |
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> |
map<string, RNEMDTypeEnum> stringToEnumMap_; |
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RNEMDTypeEnum rnemdType_; |
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std::map<std::string, RNEMDTypeEnum> stringToEnumMap_; |
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|
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< |
|
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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 outputTemp_; |
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> |
bool outputVx_; |
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> |
bool outputVy_; |
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> |
bool output3DTemp_; |
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bool outputRotTemp_; |
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// James put this in. |
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bool outputDen_; |
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> |
bool outputVz_; |
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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 targetJzKE_; |
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> |
RealType targetJzpx_; |
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> |
RealType targetJzpy_; |
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> |
RealType targetJzpz_; |
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> |
RealType targetJzpz2_; |
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> |
Vector3d jzp_, njzp_; |
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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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> |
int logFrameCount_; |
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> |
// James added denLog, vzzLog |
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> |
ofstream tempLog_, vxzLog_, vyzLog_, denLog_, vzzLog_, denLog2_; |
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> |
ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_; |
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> |
// keeps track of what's being averaged James added DenHist, pzzHist |
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> |
vector<RealType> tempHist_, pxzHist_, pyzHist_, mHist_, DenHist_, pzzHist_, DenHist2_; |
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> |
vector<RealType> xTempHist_, yTempHist_, zTempHist_, rotTempHist_; |
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> |
// keeps track of the number of degrees of freedom being averaged |
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> |
//vector<int> pxzCount_, pyzCount_; |
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> |
vector<int> tempCount_, xyzTempCount_, rotTempCount_; |
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}; |
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|
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|
} |
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< |
#endif //INTEGRATORS_VELOCITIZER_HPP |
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> |
#endif //INTEGRATORS_RNEMD_HPP |
