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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 |
| 12 |
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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. |
| 11 |
|
* |
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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 |
| 14 |
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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 |
| 33 |
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* research, please cite the appropriate papers when you publish your |
| 34 |
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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, 234107 (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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#ifndef CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP |
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#include "brains/ForceManager.hpp" |
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#include "constraints/ZconsStruct.hpp" |
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#include "io/ZConsWriter.hpp" |
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namespace oopse { |
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> |
namespace OpenMD { |
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|
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class ZconstraintForceManager : public ForceManager { |
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public: |
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ZconstraintForceManager(SimInfo* info); |
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~ZconstraintForceManager(); |
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|
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virtual void calcForces(bool needPotential, bool needStress); |
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> |
virtual void calcForces(); |
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|
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double getZConsTime() { return zconsTime_; } |
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> |
RealType getZConsTime() { return zconsTime_; } |
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std::string getZConsOutput() { return zconsOutput_; } |
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|
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void update(); |
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void calcTotalMassMovingZMols(); |
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bool haveMovingZMols(); |
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bool haveFixedZMols(); |
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double getZTargetPos(int index); |
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double getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce) ; |
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double getZFOfMovingMols(Molecule* mol, double totalForce) ; |
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double getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce); |
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double getHFOfUnconsMols(Molecule* mol, double totalForce); |
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> |
RealType getZTargetPos(int index); |
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> |
RealType getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce) ; |
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> |
RealType getZFOfMovingMols(Molecule* mol, RealType totalForce) ; |
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> |
RealType getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce); |
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> |
RealType getHFOfUnconsMols(Molecule* mol, RealType totalForce); |
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|
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std::list<ZconstraintMol> movingZMols_; /**< moving zconstraint molecules*/ |
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std::list<ZconstraintMol> fixedZMols_; /**< fixed zconstraint molecules*/ |
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std::vector<Molecule*> unzconsMols_; /**< free molecules*/ |
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|
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< |
double zconsTime_; |
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> |
RealType zconsTime_; |
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std::string zconsOutput_; |
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< |
double zconsTol_; |
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> |
RealType zconsTol_; |
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bool usingSMD_; |
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< |
double zconsFixingTime_; |
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< |
double zconsGap_; |
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> |
RealType zconsFixingTime_; |
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> |
RealType zconsGap_; |
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bool usingZconsGap_; |
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< |
double dt_; |
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> |
RealType dt_; |
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|
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const static int whichDirection = 2; |
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|
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std::map<int, ZconstraintParam> allZMolIndices_; |
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|
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Snapshot* currSnapshot_; |
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double currZconsTime_; |
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> |
RealType currZconsTime_; |
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|
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< |
double totMassMovingZMols_; |
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< |
double totMassUnconsMols_; /**< mass of unconstraint molecules in the whole system (never change) */ |
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> |
RealType totMassMovingZMols_; |
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> |
RealType totMassUnconsMols_; /**< mass of unconstraint molecules in the whole system (never change) */ |
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|
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ZConsWriter* fzOut; |
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const double infiniteTime; |
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> |
const RealType infiniteTime; |
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}; |
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|
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} |
