--- trunk/src/applications/staticProps/Hxy.cpp 2006/05/22 15:30:42 967 +++ trunk/src/applications/staticProps/Hxy.cpp 2012/09/10 18:38:44 1796 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -38,13 +29,19 @@ * University of Notre Dame has been advised of the possibility of * such damages. * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * * - * Hxy.cpp - * OOPSE-2.0 - * * Created by Xiuquan Sun on 05/09/06. * @author Xiuquan Sun - * @version $Id: Hxy.cpp,v 1.5 2006-05-22 15:30:42 xsun Exp $ + * @version $Id$ * */ @@ -61,7 +58,7 @@ #include #include -namespace oopse { +namespace OpenMD { Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){ @@ -103,9 +100,9 @@ namespace oopse { errbin_sum_sq.clear(); errbin_sq.clear(); - for(int i=0; i < bin.size(); i++) + for(unsigned int i=0; i < bin.size(); i++) bin[i].clear(); - for(int i=0; i < samples.size(); i++) + for(unsigned int i=0; i < samples.size(); i++) samples[i].clear(); mag.clear(); @@ -118,32 +115,44 @@ namespace oopse { int nFrames = reader.getNFrames(); nProcessed_ = nFrames/step_; - for(int k=0; k < bin.size(); k++) + for(unsigned int k=0; k < bin.size(); k++) bin[k].resize(nFrames); - for(int k=0; k < samples.size(); k++) + for(unsigned int k=0; k < samples.size(); k++) samples[k].resize(nFrames); RealType lenX_, lenY_; RealType gridX_, gridY_; RealType halfBoxX_, halfBoxY_; - int binNoX, binNoY; RealType interpsum, value; int ninterp, px, py, newp; - int newx, newy, newindex, index; + int newindex, index; int new_i, new_j, new_index; RealType freq_x, freq_y, zero_freq_x, zero_freq_y, freq; RealType maxfreqx, maxfreqy, maxfreq; int whichbin; - int nMolecules; - + + std::fill(sum_bin.begin(), sum_bin.end(), 0.0); + std::fill(avg_bin.begin(), avg_bin.end(), 0.0); + std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0); + std::fill(errbin.begin(), errbin.end(), 0.0); + std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0); + std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0); + std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0); + std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0); + + for(unsigned int i=0; i < bin.size(); i++) + std::fill(bin[i].begin(), bin[i].end(), 0.0); + + for(unsigned int i=0; i < samples.size(); i++) + std::fill(samples[i].begin(), samples[i].end(), 0); + for (int istep = 0; istep < nFrames; istep += step_) { reader.readFrame(istep); currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); - nMolecules = info_->getNGlobalMolecules(); Mat3x3d hmat = currentSnapshot_->getHmat(); @@ -163,27 +172,13 @@ namespace oopse { #else p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE); #endif - - int i, j; - + std::fill(gridsample_.begin(), gridsample_.end(), 0); std::fill(gridZ_.begin(), gridZ_.end(), 0.0); - std::fill(sum_bin.begin(), sum_bin.end(), 0.0); - std::fill(avg_bin.begin(), avg_bin.end(), 0.0); - std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0); - std::fill(errbin.begin(), errbin.end(), 0.0); - std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0); - std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0); - std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0); - std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0); std::fill(mag.begin(), mag.end(), 0.0); std::fill(newmag.begin(), newmag.end(), 0.0); - for(i=0; i < bin.size(); i++) - std::fill(bin[i].begin(), bin[i].end(), 0.0); - - for(i=0; i < samples.size(); i++) - std::fill(samples[i].begin(), samples[i].end(), 0); + int i, j; StuntDouble* sd; @@ -203,7 +198,8 @@ namespace oopse { //wrap the stuntdoubles into a cell for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { Vector3d pos = sd->getPos(); - currentSnapshot_->wrapVector(pos); + if (usePeriodicBoundaryConditions_) + currentSnapshot_->wrapVector(pos); sd->setPos(pos); } @@ -387,7 +383,7 @@ namespace oopse { for ( i = 0; i < nbins_; i++) { if ( samples[i][istep] > 0) { - bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nMolecules; + bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_; } } }