| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* 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. |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
|
* |
| 32 |
< |
* BondAngleDistribution.cpp |
| 33 |
< |
* OOPSE-4 |
| 34 |
< |
* |
| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 41 |
|
* Created by J. Daniel Gezelter on 07/27/07. |
| 42 |
|
* @author J. Daniel Gezelter |
| 43 |
< |
* @version $Id: BondAngleDistribution.cpp,v 1.1 2007-09-17 20:05:51 chuckv Exp $ |
| 43 |
> |
* @version $Id$ |
| 44 |
|
* |
| 45 |
|
*/ |
| 46 |
|
|
| 50 |
|
#include "primitives/Molecule.hpp" |
| 51 |
|
#include "utils/NumericConstant.hpp" |
| 52 |
|
|
| 53 |
< |
namespace oopse { |
| 53 |
> |
namespace OpenMD { |
| 54 |
|
|
| 55 |
|
BondAngleDistribution::BondAngleDistribution(SimInfo* info, |
| 56 |
|
const std::string& filename, |
| 81 |
|
histogram_.clear(); |
| 82 |
|
} |
| 83 |
|
|
| 84 |
< |
void BondAngleDistribution::initalizeHistogram() { |
| 84 |
> |
void BondAngleDistribution::initializeHistogram() { |
| 85 |
|
for (int bin = 0; bin < nBins_; bin++) { |
| 86 |
|
histogram_[bin] = 0; |
| 87 |
|
} |
| 99 |
|
Vector3d vec; |
| 100 |
|
std::vector<Vector3d> bondvec; |
| 101 |
|
std::vector<RealType> bonddist; |
| 102 |
< |
RealType costheta; |
| 103 |
< |
RealType r; |
| 104 |
< |
RealType dist; |
| 102 |
> |
RealType r; |
| 103 |
> |
int nBonds; |
| 104 |
> |
int i; |
| 105 |
|
|
| 109 |
– |
int nBonds; |
| 110 |
– |
|
| 111 |
– |
int i, j; |
| 112 |
– |
|
| 106 |
|
DumpReader reader(info_, dumpFilename_); |
| 107 |
|
int nFrames = reader.getNFrames(); |
| 108 |
|
frameCounter_ = 0; |
| 181 |
|
if (theta > 180.0){ |
| 182 |
|
theta = 360.0 - theta; |
| 183 |
|
} |
| 184 |
< |
int whichBin = theta/deltaTheta_; |
| 184 |
> |
int whichBin = int(theta/deltaTheta_); |
| 185 |
|
|
| 186 |
|
histogram_[whichBin] += 2; |
| 187 |
|
} |
