| 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 |
+ |
* 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 |
+ |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 41 |
|
* |
| 42 |
– |
* Hxy.cpp |
| 43 |
– |
* OOPSE-2.0 |
| 44 |
– |
* |
| 42 |
|
* Created by Xiuquan Sun on 05/09/06. |
| 43 |
|
* @author Xiuquan Sun |
| 44 |
< |
* @version $Id: Hxy.cpp,v 1.6 2006-05-23 21:12:45 xsun Exp $ |
| 44 |
> |
* @version $Id$ |
| 45 |
|
* |
| 46 |
|
*/ |
| 47 |
|
|
| 58 |
|
#include<stdlib.h> |
| 59 |
|
#include<math.h> |
| 60 |
|
|
| 61 |
< |
namespace oopse { |
| 61 |
> |
namespace OpenMD { |
| 62 |
|
|
| 63 |
|
Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins) |
| 64 |
|
: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){ |
| 100 |
|
errbin_sum_sq.clear(); |
| 101 |
|
errbin_sq.clear(); |
| 102 |
|
|
| 103 |
< |
for(int i=0; i < bin.size(); i++) |
| 103 |
> |
for(unsigned int i=0; i < bin.size(); i++) |
| 104 |
|
bin[i].clear(); |
| 105 |
< |
for(int i=0; i < samples.size(); i++) |
| 105 |
> |
for(unsigned int i=0; i < samples.size(); i++) |
| 106 |
|
samples[i].clear(); |
| 107 |
|
|
| 108 |
|
mag.clear(); |
| 115 |
|
int nFrames = reader.getNFrames(); |
| 116 |
|
nProcessed_ = nFrames/step_; |
| 117 |
|
|
| 118 |
< |
for(int k=0; k < bin.size(); k++) |
| 118 |
> |
for(unsigned int k=0; k < bin.size(); k++) |
| 119 |
|
bin[k].resize(nFrames); |
| 120 |
< |
for(int k=0; k < samples.size(); k++) |
| 120 |
> |
for(unsigned int k=0; k < samples.size(); k++) |
| 121 |
|
samples[k].resize(nFrames); |
| 122 |
|
|
| 123 |
|
RealType lenX_, lenY_; |
| 124 |
|
RealType gridX_, gridY_; |
| 125 |
|
RealType halfBoxX_, halfBoxY_; |
| 126 |
|
|
| 130 |
– |
int binNoX, binNoY; |
| 127 |
|
RealType interpsum, value; |
| 128 |
|
int ninterp, px, py, newp; |
| 129 |
< |
int newx, newy, newindex, index; |
| 129 |
> |
int newindex, index; |
| 130 |
|
int new_i, new_j, new_index; |
| 131 |
|
|
| 132 |
|
RealType freq_x, freq_y, zero_freq_x, zero_freq_y, freq; |
| 133 |
|
RealType maxfreqx, maxfreqy, maxfreq; |
| 134 |
|
|
| 135 |
|
int whichbin; |
| 140 |
– |
int nMolecules; |
| 136 |
|
|
| 137 |
|
std::fill(sum_bin.begin(), sum_bin.end(), 0.0); |
| 138 |
|
std::fill(avg_bin.begin(), avg_bin.end(), 0.0); |
| 143 |
|
std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0); |
| 144 |
|
std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0); |
| 145 |
|
|
| 146 |
< |
for(int i=0; i < bin.size(); i++) |
| 146 |
> |
for(unsigned int i=0; i < bin.size(); i++) |
| 147 |
|
std::fill(bin[i].begin(), bin[i].end(), 0.0); |
| 148 |
|
|
| 149 |
< |
for(int i=0; i < samples.size(); i++) |
| 149 |
> |
for(unsigned int i=0; i < samples.size(); i++) |
| 150 |
|
std::fill(samples[i].begin(), samples[i].end(), 0); |
| 151 |
|
|
| 152 |
|
for (int istep = 0; istep < nFrames; istep += step_) { |
| 153 |
|
|
| 154 |
|
reader.readFrame(istep); |
| 155 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 161 |
– |
nMolecules = info_->getNGlobalMolecules(); |
| 156 |
|
|
| 157 |
|
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 158 |
|
|
| 198 |
|
//wrap the stuntdoubles into a cell |
| 199 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
| 200 |
|
Vector3d pos = sd->getPos(); |
| 201 |
< |
currentSnapshot_->wrapVector(pos); |
| 201 |
> |
if (usePeriodicBoundaryConditions_) |
| 202 |
> |
currentSnapshot_->wrapVector(pos); |
| 203 |
|
sd->setPos(pos); |
| 204 |
|
} |
| 205 |
|
|
