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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 |
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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 |
< |
* 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 |
|
* |
| 12 |
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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 |
| 13 |
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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. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
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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_GOFANGLE2_HPP |
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#define APPLICATIONS_STATICPROPS_GOFANGLE2_HPP |
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|
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#include "applications/staticProps/RadialDistrFunc.hpp" |
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namespace oopse { |
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> |
namespace OpenMD { |
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|
|
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class GofAngle2 : public RadialDistrFunc { |
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> |
class GofAngle2 : public RadialDistrFunc { |
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|
|
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public: |
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< |
GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2); |
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> |
public: |
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> |
GofAngle2(SimInfo* info, const std::string& filename, |
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> |
const std::string& sele1, const std::string& sele2, |
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> |
int nangleBins); |
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> |
GofAngle2(SimInfo* info, const std::string& filename, |
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> |
const std::string& sele1, const std::string& sele2, |
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> |
const std::string& sele3, int nangleBins); |
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|
|
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< |
void setNAngleBins(int nbins) { |
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< |
assert(nbins >0); |
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< |
nAngleBins_ = nbins; |
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< |
deltaCosAngle_ = 2.0 / nAngleBins_; |
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< |
for (int i = 0 ; i < nAngleBins_; ++i) { |
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< |
histogram_[i].resize(nAngleBins_); |
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< |
avgGofr_[i].resize(nAngleBins_); |
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< |
} |
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< |
} |
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> |
int getNAngleBins() {return nAngleBins_;} |
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|
|
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< |
int getNAngleBins() {return nAngleBins_;} |
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< |
|
| 64 |
< |
private: |
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> |
private: |
| 61 |
|
|
| 62 |
< |
virtual void preProcess(); |
| 63 |
< |
virtual void initalizeHistogram(); |
| 64 |
< |
virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2); |
| 65 |
< |
virtual void processHistogram(); |
| 62 |
> |
virtual void preProcess(); |
| 63 |
> |
virtual void processNonOverlapping( SelectionManager& sman1, |
| 64 |
> |
SelectionManager& sman2); |
| 65 |
> |
virtual void processOverlapping( SelectionManager& sman ); |
| 66 |
> |
virtual void initializeHistogram(); |
| 67 |
> |
virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2); |
| 68 |
> |
virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2, |
| 69 |
> |
StuntDouble* sd3); |
| 70 |
> |
virtual void processHistogram(); |
| 71 |
|
|
| 72 |
< |
virtual void writeRdf(); |
| 72 |
> |
virtual void writeRdf(); |
| 73 |
|
|
| 74 |
< |
double deltaCosAngle_; |
| 75 |
< |
int nAngleBins_; |
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> |
|
| 75 |
> |
RealType deltaCosAngle_; |
| 76 |
> |
int nAngleBins_; |
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> |
bool doSele3_; |
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> |
|
| 79 |
> |
SelectionManager seleMan3_; |
| 80 |
> |
SelectionEvaluator evaluator3_; |
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> |
std::string selectionScript3_; |
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|
|
| 83 |
< |
std::vector<std::vector<int> > histogram_; |
| 84 |
< |
std::vector<std::vector<int> > avgGofr_; |
| 85 |
< |
int npairs_; |
| 86 |
< |
}; |
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> |
std::vector<std::vector<int> > histogram_; |
| 84 |
> |
std::vector<std::vector<int> > avgGofr_; |
| 85 |
> |
int npairs_; |
| 86 |
> |
}; |
| 87 |
|
|
| 88 |
|
} |
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|
#endif |
