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* 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 |
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* 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 41 |
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* |
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– |
* Hxy.cpp |
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– |
* OOPSE-2.0 |
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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 1.5 2006-05-22 15:30:42 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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RealType gridX_, gridY_; |
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RealType halfBoxX_, halfBoxY_; |
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|
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int binNoX, binNoY; |
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RealType interpsum, value; |
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int ninterp, px, py, newp; |
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int newx, newy, newindex, index; |
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> |
int newindex, index; |
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int new_i, new_j, new_index; |
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|
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RealType freq_x, freq_y, zero_freq_x, zero_freq_y, freq; |
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RealType maxfreqx, maxfreqy, maxfreq; |
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|
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int whichbin; |
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< |
int nMolecules; |
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< |
|
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> |
|
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> |
std::fill(sum_bin.begin(), sum_bin.end(), 0.0); |
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> |
std::fill(avg_bin.begin(), avg_bin.end(), 0.0); |
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> |
std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0); |
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> |
std::fill(errbin.begin(), errbin.end(), 0.0); |
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> |
std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0); |
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> |
std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0); |
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> |
std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0); |
| 144 |
> |
std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0); |
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> |
|
| 146 |
> |
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(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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|
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reader.readFrame(istep); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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– |
nMolecules = info_->getNGlobalMolecules(); |
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|
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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|
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|
#else |
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p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE); |
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#endif |
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< |
|
| 167 |
< |
int i, j; |
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< |
|
| 175 |
> |
|
| 176 |
|
std::fill(gridsample_.begin(), gridsample_.end(), 0); |
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|
std::fill(gridZ_.begin(), gridZ_.end(), 0.0); |
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– |
std::fill(sum_bin.begin(), sum_bin.end(), 0.0); |
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– |
std::fill(avg_bin.begin(), avg_bin.end(), 0.0); |
| 173 |
– |
std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0); |
| 174 |
– |
std::fill(errbin.begin(), errbin.end(), 0.0); |
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std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0); |
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std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0); |
| 177 |
– |
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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std::fill(mag.begin(), mag.end(), 0.0); |
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std::fill(newmag.begin(), newmag.end(), 0.0); |
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|
|
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< |
for(i=0; i < bin.size(); i++) |
| 183 |
< |
std::fill(bin[i].begin(), bin[i].end(), 0.0); |
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< |
|
| 185 |
< |
for(i=0; i < samples.size(); i++) |
| 186 |
< |
std::fill(samples[i].begin(), samples[i].end(), 0); |
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> |
int i, j; |
| 182 |
|
|
| 183 |
|
StuntDouble* sd; |
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|
|
| 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 |
|
|
| 383 |
|
|
| 384 |
|
for ( i = 0; i < nbins_; i++) { |
| 385 |
|
if ( samples[i][istep] > 0) { |
| 386 |
< |
bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nMolecules; |
| 386 |
> |
bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_; |
| 387 |
|
} |
| 388 |
|
} |
| 389 |
|
} |
