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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 |
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* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* 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)) |
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< |
* |
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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 |
| 10 |
|
* 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). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [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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/* Calculates Rho(R) for nanoparticle with radius R*/ |
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#include "utils/NumericConstant.hpp" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "math.h" |
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> |
#include "brains/Thermo.hpp" |
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> |
#include <math.h> |
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|
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namespace oopse { |
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> |
namespace OpenMD { |
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|
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|
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RhoR::RhoR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins, RealType particleR) |
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|
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|
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void RhoR::process() { |
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|
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< |
|
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|
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> |
|
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> |
Thermo thermo(info_); |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames/step_; |
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StuntDouble* sd; |
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reader.readFrame(istep); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Vector3d CenterOfMass = info_->getCom(); |
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> |
Vector3d CenterOfMass = thermo.getCom(); |
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|
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– |
|
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– |
|
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– |
|
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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RealType distance = r12.length(); |
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|
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if (distance < len_) { |
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< |
int whichBin = distance / deltaR_; |
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> |
int whichBin = int(distance / deltaR_); |
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histogram_[whichBin] += 1; |
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} |
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|
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RealType particleDensity = 3.0 * info_->getNGlobalMolecules() / (4.0 * NumericConstant::PI * pow(particleR_,3)); |
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RealType pairConstant = ( 4.0 * NumericConstant::PI * particleDensity ) / 3.0; |
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|
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< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
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> |
for(unsigned int i = 0 ; i < histogram_.size(); ++i){ |
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|
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RealType rLower = i * deltaR_; |
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RealType rUpper = rLower + deltaR_; |
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if (rdfStream.is_open()) { |
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rdfStream << "#radial density function rho(r)\n"; |
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rdfStream << "#r\tcorrValue\n"; |
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< |
for (int i = 0; i < avgRhoR_.size(); ++i) { |
| 144 |
> |
for (unsigned int i = 0; i < avgRhoR_.size(); ++i) { |
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RealType r = deltaR_ * (i + 0.5); |
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rdfStream << r << "\t" << avgRhoR_[i]/nProcessed_ << "\n"; |
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} |
