| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* 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). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 52 |
|
#define INTEGRATORS_RNEMD_HPP |
| 53 |
|
#include "brains/SimInfo.hpp" |
| 54 |
|
#include "math/RandNumGen.hpp" |
| 55 |
+ |
#include "selection/SelectionEvaluator.hpp" |
| 56 |
+ |
#include "selection/SelectionManager.hpp" |
| 57 |
+ |
#include <iostream> |
| 58 |
|
|
| 59 |
< |
namespace oopse { |
| 59 |
> |
using namespace std; |
| 60 |
> |
namespace OpenMD { |
| 61 |
|
|
| 62 |
|
/** |
| 63 |
|
* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp" |
| 67 |
|
public: |
| 68 |
|
RNEMD(SimInfo* info); |
| 69 |
|
virtual ~RNEMD(); |
| 70 |
< |
|
| 70 |
> |
|
| 71 |
> |
void doRNEMD(); |
| 72 |
|
void doSwap(); |
| 73 |
< |
void set_RNEMD_swapTime(RealType swapTime) { swapTime_ = swapTime; } |
| 73 |
> |
void doScale(); |
| 74 |
> |
void doShiftScale(); |
| 75 |
> |
void collectData(); |
| 76 |
> |
void getStarted(); |
| 77 |
> |
void getStatus(); |
| 78 |
> |
void set_RNEMD_exchange_time(RealType exchangeTime) { |
| 79 |
> |
exchangeTime_ = exchangeTime; |
| 80 |
> |
} |
| 81 |
|
void set_RNEMD_nBins(int nbins) { nBins_ = nbins; } |
| 82 |
+ |
void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; } |
| 83 |
+ |
void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; } |
| 84 |
+ |
void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;} |
| 85 |
+ |
void set_RNEMD_target_JzKE(RealType targetJzKE) {targetJzKE_ = targetJzKE;} |
| 86 |
+ |
void set_RNEMD_target_jzpx(RealType targetJzpx) {targetJzpx_ = targetJzpx;} |
| 87 |
+ |
void set_RNEMD_target_jzpy(RealType targetJzpy) {targetJzpy_ = targetJzpy;} |
| 88 |
+ |
void set_RNEMD_target_jzpz(RealType targetJzpz) {targetJzpz_ = targetJzpz;} |
| 89 |
+ |
void set_RNEMD_target_jzpz2(RealType targetJzpz2) {targetJzpz2_ = targetJzpz2;} |
| 90 |
|
RealType get_RNEMD_exchange_total() { return exchangeSum_; } |
| 91 |
< |
void set_RNEMD_exchange_total(RealType et) {exchangeSum_ = et;} |
| 71 |
< |
|
| 91 |
> |
|
| 92 |
|
private: |
| 93 |
< |
|
| 93 |
> |
|
| 94 |
|
enum RNEMDTypeEnum { |
| 95 |
< |
rnemdKinetic, |
| 95 |
> |
rnemdKineticSwap, |
| 96 |
> |
rnemdKineticScale, |
| 97 |
> |
rnemdKineticScaleVAM, |
| 98 |
> |
rnemdKineticScaleAM, |
| 99 |
> |
rnemdPxScale, |
| 100 |
> |
rnemdPyScale, |
| 101 |
> |
rnemdPzScale, |
| 102 |
|
rnemdPx, |
| 103 |
|
rnemdPy, |
| 104 |
|
rnemdPz, |
| 105 |
+ |
rnemdShiftScaleV, |
| 106 |
+ |
rnemdShiftScaleVAM, |
| 107 |
|
rnemdUnknown |
| 108 |
|
}; |
| 109 |
< |
|
| 109 |
> |
|
| 110 |
|
SimInfo* info_; |
| 111 |
|
RandNumGen* randNumGen_; |
| 112 |
< |
int nBins_; |
| 85 |
< |
RealType swapTime_; |
| 86 |
< |
RealType exchangeSum_; |
| 112 |
> |
map<string, RNEMDTypeEnum> stringToEnumMap_; |
| 113 |
|
RNEMDTypeEnum rnemdType_; |
| 114 |
< |
std::map<std::string, RNEMDTypeEnum> stringToEnumMap_; |
| 115 |
< |
|
| 116 |
< |
|
| 114 |
> |
string rnemdObjectSelection_; |
| 115 |
> |
SelectionEvaluator evaluator_; |
| 116 |
> |
SelectionManager seleMan_; |
| 117 |
> |
bool usePeriodicBoundaryConditions_; |
| 118 |
> |
bool outputTemp_; |
| 119 |
> |
bool outputVx_; |
| 120 |
> |
bool outputVy_; |
| 121 |
> |
bool output3DTemp_; |
| 122 |
> |
bool outputRotTemp_; |
| 123 |
> |
// James put this in. |
| 124 |
> |
bool outputDen_; |
| 125 |
> |
bool outputVz_; |
| 126 |
> |
int nBins_; /**< The number of bins to divide the simulation box into. */ |
| 127 |
> |
/*! |
| 128 |
> |
The middle bin for the RNEMD method. midBin_ = nBins_/2; |
| 129 |
> |
Depending on the setting of the flux, this box should contain the minimum energy (temperature) |
| 130 |
> |
within the simulation. |
| 131 |
> |
*/ |
| 132 |
> |
int midBin_; |
| 133 |
> |
int rnemdLogWidth_; /**< Number of elements to print out in logs */ |
| 134 |
> |
RealType zShift_; |
| 135 |
> |
RealType exchangeTime_; |
| 136 |
> |
RealType targetFlux_; |
| 137 |
> |
RealType targetJzKE_; |
| 138 |
> |
RealType targetJzpx_; |
| 139 |
> |
RealType targetJzpy_; |
| 140 |
> |
RealType targetJzpz_; |
| 141 |
> |
RealType targetJzpz2_; |
| 142 |
> |
Vector3d jzp_, njzp_; |
| 143 |
> |
RealType exchangeSum_; |
| 144 |
> |
int failTrialCount_; |
| 145 |
> |
int failRootCount_; |
| 146 |
> |
ofstream rnemdLog_; |
| 147 |
> |
int logFrameCount_; |
| 148 |
> |
// James added denLog, vzzLog |
| 149 |
> |
ofstream tempLog_, vxzLog_, vyzLog_, denLog_, vzzLog_, denLog2_; |
| 150 |
> |
ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_, AhLog_; |
| 151 |
> |
// keeps track of what's being averaged James added DenHist, pzzHist |
| 152 |
> |
vector<RealType> tempHist_, pxzHist_, pyzHist_, mHist_, DenHist_, pzzHist_, DenHist2_; |
| 153 |
> |
vector<RealType> xTempHist_, yTempHist_, zTempHist_, rotTempHist_; |
| 154 |
> |
// keeps track of the number of degrees of freedom being averaged |
| 155 |
> |
//vector<int> pxzCount_, pyzCount_; |
| 156 |
> |
vector<int> tempCount_, xyzTempCount_, rotTempCount_; |
| 157 |
> |
RealType Asum_, Jsum_, AhCount_, runTime_, statusTime_; |
| 158 |
> |
int Numcount_; |
| 159 |
> |
bool outputAh_; |
| 160 |
|
}; |
| 161 |
|
|
| 162 |
|
} |
| 163 |
< |
#endif //INTEGRATORS_VELOCITIZER_HPP |
| 163 |
> |
#endif //INTEGRATORS_RNEMD_HPP |
