| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
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* 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
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|
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#include <algorithm> |
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|
#include "RadialDistrFunc.hpp" |
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#include "io/DumpReader.hpp" |
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|
#include "primitives/Molecule.hpp" |
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
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< |
RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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< |
: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), |
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> |
RadialDistrFunc::RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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> |
: StaticAnalyser(info, filename), |
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|
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
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|
seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){ |
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|
| 131 |
|
//stage 3 are completely overlapping |
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|
|
| 133 |
|
if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
| 134 |
– |
|
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|
common_ = seleMan1_ & seleMan2_; |
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|
sele1_minus_common_ = seleMan1_ - common_; |
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|
sele2_minus_common_ = seleMan2_ - common_; |
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|
int nSelected2 = seleMan2_.getSelectionCount(); |
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|
int nIntersect = common_.getSelectionCount(); |
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|
|
| 141 |
< |
nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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> |
nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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|
} |
| 144 |
– |
|
| 143 |
|
processNonOverlapping(sele1_minus_common_, seleMan2_); |
| 144 |
|
processNonOverlapping(common_, sele2_minus_common_); |
| 145 |
|
processOverlapping(common_); |
| 146 |
< |
|
| 149 |
< |
|
| 146 |
> |
|
| 147 |
|
processHistogram(); |
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|
|
| 149 |
|
} |
