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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 |
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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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
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* |
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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 |
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* distribution. |
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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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* |
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* Hxy.cpp |
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* OOPSE-2.0 |
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> |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
| 34 |
> |
* work. Good starting points are: |
| 35 |
> |
* |
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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, 24107 (2008). |
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> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* |
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* Created by Xiuquan Sun on 05/09/06. |
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* @author Xiuquan Sun |
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* @version $Id: Hxy.cpp,v 1.6 2006-05-23 21:12:45 xsun Exp $ |
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* @version $Id$ |
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* |
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*/ |
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|
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#include<stdlib.h> |
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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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Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){ |
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errbin_sum_sq.clear(); |
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errbin_sq.clear(); |
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|
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for(int i=0; i < bin.size(); i++) |
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for(unsigned int i=0; i < bin.size(); i++) |
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bin[i].clear(); |
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for(int i=0; i < samples.size(); i++) |
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for(unsigned int i=0; i < samples.size(); i++) |
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samples[i].clear(); |
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|
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mag.clear(); |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames/step_; |
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|
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for(int k=0; k < bin.size(); k++) |
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for(unsigned int k=0; k < bin.size(); k++) |
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bin[k].resize(nFrames); |
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for(int k=0; k < samples.size(); k++) |
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for(unsigned int k=0; k < samples.size(); k++) |
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samples[k].resize(nFrames); |
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|
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RealType lenX_, lenY_; |
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std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0); |
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std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0); |
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|
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for(int i=0; i < bin.size(); i++) |
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> |
for(unsigned int i=0; i < bin.size(); i++) |
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std::fill(bin[i].begin(), bin[i].end(), 0.0); |
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|
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for(int i=0; i < samples.size(); i++) |
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> |
for(unsigned int i=0; i < samples.size(); i++) |
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std::fill(samples[i].begin(), samples[i].end(), 0); |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
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//wrap the stuntdoubles into a cell |
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for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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Vector3d pos = sd->getPos(); |
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currentSnapshot_->wrapVector(pos); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(pos); |
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sd->setPos(pos); |
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} |
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|
