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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 |
| 11 |
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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 |
| 13 |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
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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 |
| 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 |
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* 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. |
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* |
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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). |
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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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#ifndef APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP |
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#define APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP |
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#include "selection/SelectionManager.hpp" |
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#include "applications/staticProps/StaticAnalyser.hpp" |
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#include "utils/Tuple.hpp" |
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namespace oopse { |
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class SCDElem { |
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public: |
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SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3); |
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> |
namespace OpenMD { |
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> |
class SCDElem { |
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> |
public: |
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> |
SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3); |
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|
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std::string getSelection1() const {return sele1_;} |
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std::string getSelection2() const {return sele2_;} |
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std::string getSelection3() const {return sele3_;} |
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double calcSCD(Snapshot* snapshot); |
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> |
std::string getSelection1() const {return sele1_;} |
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> |
std::string getSelection2() const {return sele2_;} |
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> |
std::string getSelection3() const {return sele3_;} |
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> |
RealType calcSCD(Snapshot* snapshot); |
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|
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private: |
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> |
private: |
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|
|
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std::string sele1_; |
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< |
std::string sele2_; |
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< |
std::string sele3_; |
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< |
|
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typedef tuple3<StuntDouble*, StuntDouble*, StuntDouble*> SDTuple3; |
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> |
std::string sele1_; |
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> |
std::string sele2_; |
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> |
std::string sele3_; |
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> |
bool usePeriodicBoundaryConditions_; |
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> |
|
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> |
typedef tuple3<StuntDouble*, StuntDouble*, StuntDouble*> SDTuple3; |
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|
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std::vector<SDTuple3> tuples_; |
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< |
}; |
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> |
std::vector<SDTuple3> tuples_; |
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> |
}; |
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|
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|
|
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< |
class SCDOrderParameter : public StaticAnalyser{ |
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public: |
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< |
SCDOrderParameter(SimInfo* info, const std::string& filename, |
| 74 |
< |
const std::string& sele1, const std::string& sele2, const std::string& sele3); |
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> |
class SCDOrderParameter : public StaticAnalyser{ |
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> |
public: |
| 73 |
> |
SCDOrderParameter(SimInfo* info, const std::string& filename, |
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> |
const std::string& sele1, const std::string& sele2, const std::string& sele3); |
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|
|
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< |
SCDOrderParameter(SimInfo* info, const std::string& filename, |
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const std::string& molname, int beginIndex, int endIndex); |
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virtual void process(); |
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> |
SCDOrderParameter(SimInfo* info, const std::string& filename, |
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> |
const std::string& molname, int beginIndex, int endIndex); |
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> |
virtual void process(); |
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|
|
| 80 |
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private: |
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< |
void writeSCD(); |
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> |
private: |
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> |
void writeSCD(); |
| 82 |
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|
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< |
std::vector<SCDElem> scdElems_; |
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< |
std::vector<double> scdParam_; |
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> |
std::vector<SCDElem> scdElems_; |
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> |
std::vector<RealType> scdParam_; |
| 85 |
|
|
| 86 |
< |
Snapshot* currentSnapshot_; |
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> |
Snapshot* currentSnapshot_; |
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|
|
| 88 |
|
|
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< |
}; |
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> |
}; |
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} |
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|
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#endif |
