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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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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. 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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* 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 |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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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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* 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 |
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* work. Good starting points are: |
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* |
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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). |
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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 $Id$ |
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* |
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*/ |
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|
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/* Calculates the undulation spectrum of the lipid membrance. */ |
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|
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#include <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/Hxy.hpp" |
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#include "utils/simError.h" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include<stdio.h> |
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#include<string.h> |
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#include<stdlib.h> |
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#include<math.h> |
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|
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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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|
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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|
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gridsample_.resize(nBinsX_*nBinsY_); |
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gridZ_.resize(nBinsX_*nBinsY_); |
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mag.resize(nBinsX_*nBinsY_); |
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newmag.resize(nBinsX_*nBinsY_); |
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|
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sum_bin.resize(nbins_); |
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avg_bin.resize(nbins_); |
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errbin_sum.resize(nbins_); |
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errbin.resize(nbins_); |
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sum_bin_sq.resize(nbins_); |
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avg_bin_sq.resize(nbins_); |
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errbin_sum_sq.resize(nbins_); |
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errbin_sq.resize(nbins_); |
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|
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bin.resize(nbins_); |
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samples.resize(nbins_); |
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|
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setOutputName(getPrefix(filename) + ".Hxy"); |
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} |
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|
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Hxy::~Hxy(){ |
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gridsample_.clear(); |
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gridZ_.clear(); |
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sum_bin.clear(); |
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avg_bin.clear(); |
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errbin_sum.clear(); |
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errbin.clear(); |
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sum_bin_sq.clear(); |
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avg_bin_sq.clear(); |
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errbin_sum_sq.clear(); |
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errbin_sq.clear(); |
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|
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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(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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newmag.clear(); |
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} |
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|
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void Hxy::process() { |
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#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames/step_; |
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|
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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(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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RealType interpsum, value; |
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int ninterp, px, py, newp; |
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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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|
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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); |
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std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0); |
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|
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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(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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|
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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|
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#ifdef HAVE_FFTW3_H |
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fftw_plan p; |
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#else |
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fftwnd_plan p; |
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#endif |
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fftw_complex *in, *out; |
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|
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in = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * (nBinsX_*nBinsY_)); |
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out = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) *(nBinsX_*nBinsY_)); |
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|
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#ifdef HAVE_FFTW3_H |
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p = fftw_plan_dft_2d(nBinsX_, nBinsY_, in, out, |
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FFTW_FORWARD, FFTW_ESTIMATE); |
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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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|
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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(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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int i, j; |
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|
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StuntDouble* sd; |
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|
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lenX_ = hmat(0,0); |
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lenY_ = hmat(1,1); |
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|
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gridX_ = lenX_ /(nBinsX_); |
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gridY_ = lenY_ /(nBinsY_); |
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|
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halfBoxX_ = lenX_ / 2.0; |
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halfBoxY_ = lenY_ / 2.0; |
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|
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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|
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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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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(pos); |
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sd->setPos(pos); |
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} |
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|
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//determine which atom belongs to which grid |
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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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//int binNo = (pos.z() /deltaR_) - 1; |
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int binNoX = (int) ((pos.x() + halfBoxX_) / gridX_); |
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int binNoY = (int) ((pos.y() + halfBoxY_) / gridY_); |
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//std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = " << deltaR_ << " binNo = " << binNo << "\n"; |
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gridZ_[binNoX*nBinsY_+binNoY] += pos.z(); |
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gridsample_[binNoX*nBinsY_+binNoY]++; |
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} |
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|
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// FFT stuff depends on nx and ny, so delay allocation until we have |
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// that information |
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|
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for(i = 0; i < nBinsX_; i++){ |
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for(j = 0; j < nBinsY_; j++){ |
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newindex = i * nBinsY_ + j; |
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if(gridsample_[newindex] > 0){ |
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gridZ_[newindex] = gridZ_[newindex] / (RealType)gridsample_[newindex]; |
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} |
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} |
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} |
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|
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for (i=0; i< nBinsX_; i++) { |
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for(j=0; j< nBinsY_; j++) { |
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newindex = i*nBinsY_ + j; |
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if (gridsample_[newindex] == 0) { |
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// interpolate from surrounding points: |
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|
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interpsum = 0.0; |
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ninterp = 0; |
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|
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//point1 = bottom; |
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|
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px = i; |
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py = j - 1; |
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newp = px*nBinsY_ + py; |
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if ((py >= 0) && (gridsample_[newp] > 0)) { |
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interpsum += gridZ_[newp]; |
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ninterp++; |
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} |
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|
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//point2 = top; |
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|
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px = i; |
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py = j + 1; |
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newp = px*nBinsY_ + py; |
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if ((py < nBinsY_) && (gridsample_[newp] > 0)) { |
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interpsum += gridZ_[newp]; |
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ninterp++; |
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} |
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|
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//point3 = left; |
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|
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px = i - 1; |
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py = j; |
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newp = px*nBinsY_ + py; |
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if ((px >= 0) && (gridsample_[newp] > 0)) { |
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interpsum += gridZ_[newp]; |
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ninterp++; |
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} |
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|
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//point4 = right; |
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|
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px = i + 1; |
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py = j; |
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newp = px*nBinsY_ + py; |
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if ( (px < nBinsX_ ) && ( gridsample_[newp] > 0 )) { |
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interpsum += gridZ_[newp]; |
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ninterp++; |
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} |
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|
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value = interpsum / (RealType)ninterp; |
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|
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gridZ_[newindex] = value; |
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} |
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} |
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} |
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|
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for (i=0; i < nBinsX_; i++) { |
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for (j=0; j < nBinsY_; j++) { |
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newindex = i*nBinsY_ + j; |
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|
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c_re(in[newindex]) = gridZ_[newindex]; |
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c_im(in[newindex]) = 0.0; |
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} |
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} |
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|
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#ifdef HAVE_FFTW3_H |
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fftw_execute(p); |
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#else |
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fftwnd_one(p, in, out); |
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#endif |
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|
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for (i=0; i< nBinsX_; i++) { |
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for(j=0; j< nBinsY_; j++) { |
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newindex = i*nBinsY_ + j; |
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mag[newindex] = pow(c_re(out[newindex]),2) + pow(c_im(out[newindex]),2); |
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} |
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} |
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|
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#ifdef HAVE_FFTW3_H |
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fftw_destroy_plan(p); |
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#else |
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fftwnd_destroy_plan(p); |
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#endif |
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fftw_free(out); |
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fftw_free(in); |
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|
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for (i=0; i< (nBinsX_/2); i++) { |
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for(j=0; j< (nBinsY_/2); j++) { |
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index = i*nBinsY_ + j; |
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new_i = i + (nBinsX_/2); |
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new_j = j + (nBinsY_/2); |
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new_index = new_i*nBinsY_ + new_j; |
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newmag[new_index] = mag[index]; |
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} |
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} |
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|
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for (i=(nBinsX_/2); i< nBinsX_; i++) { |
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for(j=0; j< (nBinsY_/2); j++) { |
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index = i*nBinsY_ + j; |
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new_i = i - (nBinsX_/2); |
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new_j = j + (nBinsY_/2); |
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new_index = new_i*nBinsY_ + new_j; |
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newmag[new_index] = mag[index]; |
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} |
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} |
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|
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for (i=0; i< (nBinsX_/2); i++) { |
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for(j=(nBinsY_/2); j< nBinsY_; j++) { |
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index = i*nBinsY_ + j; |
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new_i = i + (nBinsX_/2); |
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new_j = j - (nBinsY_/2); |
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new_index = new_i*nBinsY_ + new_j; |
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newmag[new_index] = mag[index]; |
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} |
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} |
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|
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for (i=(nBinsX_/2); i< nBinsX_; i++) { |
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for(j=(nBinsY_/2); j< nBinsY_; j++) { |
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index = i*nBinsY_ + j; |
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new_i = i - (nBinsX_/2); |
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new_j = j - (nBinsY_/2); |
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new_index = new_i*nBinsY_ + new_j; |
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newmag[new_index] = mag[index]; |
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} |
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} |
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|
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maxfreqx = 1.0 / gridX_; |
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maxfreqy = 1.0 / gridY_; |
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|
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// printf("%lf\t%lf\t%lf\t%lf\n", dx, dy, maxfreqx, maxfreqy); |
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|
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maxfreq = sqrt(maxfreqx*maxfreqx + maxfreqy*maxfreqy); |
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dfreq = maxfreq/(RealType)(nbins_-1); |
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|
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//printf("%lf\n", dfreq); |
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|
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zero_freq_x = nBinsX_/2; |
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zero_freq_y = nBinsY_/2; |
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|
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for (i=0; i< nBinsX_; i++) { |
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for(j=0; j< nBinsY_; j++) { |
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|
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freq_x = (RealType)(i - zero_freq_x)*maxfreqx*2 / nBinsX_; |
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freq_y = (RealType)(j - zero_freq_y)*maxfreqy*2 / nBinsY_; |
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|
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freq = sqrt(freq_x*freq_x + freq_y*freq_y); |
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|
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whichbin = (int) (freq / dfreq); |
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newindex = i*nBinsY_ + j; |
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// printf("%d %d %lf %lf\n", whichbin, newindex, freq, dfreq); |
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bin[whichbin][istep] += newmag[newindex]; |
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samples[whichbin][istep]++; |
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} |
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} |
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|
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for ( i = 0; i < nbins_; i++) { |
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if ( samples[i][istep] > 0) { |
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bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_; |
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} |
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} |
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} |
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|
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for (int i = 0; i < nbins_; i++) { |
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for (int j = 0; j < nFrames; j++) { |
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sum_bin[i] += bin[i][j]; |
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sum_bin_sq[i] += bin[i][j] * bin[i][j]; |
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} |
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avg_bin[i] = sum_bin[i] / (RealType)nFrames; |
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avg_bin_sq[i] = sum_bin_sq[i] / (RealType)nFrames; |
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for (int j = 0; j < nFrames; j++) { |
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errbin_sum[i] += pow((bin[i][j] - avg_bin[i]), 2); |
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errbin_sum_sq[i] += pow((bin[i][j] * bin[i][j] - avg_bin_sq[i]), 2); |
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} |
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errbin[i] = sqrt( errbin_sum[i] / (RealType)nFrames ); |
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errbin_sq[i] = sqrt( errbin_sum_sq[i] / (RealType)nFrames ); |
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} |
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|
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printSpectrum(); |
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|
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#else |
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sprintf(painCave.errMsg, "Hxy: FFTW support was not compiled in!\n"); |
| 410 |
painCave.isFatal = 1; |
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simError(); |
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|
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#endif |
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} |
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|
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void Hxy::printSpectrum() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
| 418 |
if (rdfStream.is_open()) { |
| 419 |
|
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for (int i = 0; i < nbins_; ++i) { |
| 421 |
if ( avg_bin[i] > 0 ){ |
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rdfStream << (RealType)i * dfreq << "\t" |
| 423 |
<<pow(avg_bin[i], 2)<<"\t" |
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<<errbin_sq[i]<<"\t" |
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<<avg_bin[i]<<"\t" |
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<<errbin[i]<<"\n"; |
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} |
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} |
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} else { |
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|
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sprintf(painCave.errMsg, "Hxy: unable to open %s\n", outputFilename_.c_str()); |
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painCave.isFatal = 1; |
| 433 |
simError(); |
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} |
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|
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rdfStream.close(); |
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|
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} |
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|
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} |
