share/template/template.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 #include <string>
  36 #include <vector>
  37
  38 #include <gromacs/trajectoryanalysis.h>
  39
  40 using namespace gmx;
  41
  42 /*! \brief
  43  * Template class to serve as a basis for user analysis tools.
  44  */
  45 class AnalysisTemplate : public TrajectoryAnalysisModule
  46 {
  47     public:
  48         AnalysisTemplate();
  49
  50         virtual void initOptions(Options                    *options,
  51                                  TrajectoryAnalysisSettings *settings);
  52         virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
  53                                   const TopologyInformation        &top);
  54
  55         virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
  56                                   TrajectoryAnalysisModuleData *pdata);
  57
  58         virtual void finishAnalysis(int nframes);
  59         virtual void writeOutput();
  60
  61     private:
  62         class ModuleData;
  63
  64         std::string                      fnDist_;
  65         double                           cutoff_;
  66         Selection                        refsel_;
  67         SelectionList                    sel_;
  68
  69         AnalysisNeighborhood             nb_;
  70
  71         AnalysisData                     data_;
  72         AnalysisDataAverageModulePointer avem_;
  73 };
  74
  75
  76 AnalysisTemplate::AnalysisTemplate()
  77     : TrajectoryAnalysisModule("template", "Template analysis tool"),
  78       cutoff_(0.0)
  79 {
  80     registerAnalysisDataset(&data_, "avedist");
  81 }
  82
  83
  84 void
  85 AnalysisTemplate::initOptions(Options                    *options,
  86                               TrajectoryAnalysisSettings *settings)
  87 {
  88     static const char *const desc[] = {
  89         "This is a template for writing your own analysis tools for",
  90         "GROMACS. The advantage of using GROMACS for this is that you",
  91         "have access to all information in the topology, and your",
  92         "program will be able to handle all types of coordinates and",
  93         "trajectory files supported by GROMACS. In addition,",
  94         "you get a lot of functionality for free from the trajectory",
  95         "analysis library, including support for flexible dynamic",
  96         "selections. Go ahead an try it![PAR]",
  97         "To get started with implementing your own analysis program,",
  98         "follow the instructions in the README file provided.",
  99         "This template implements a simple analysis programs that calculates",
 100         "average distances from a reference group to one or more",
 101         "analysis groups."
 102     };
 103
 104     options->setDescription(desc);
 105
 106     options->addOption(FileNameOption("o")
 107                            .filetype(eftPlot).outputFile()
 108                            .store(&fnDist_).defaultBasename("avedist")
 109                            .description("Average distances from reference group"));
 110
 111     options->addOption(SelectionOption("reference")
 112                            .store(&refsel_).required()
 113                            .description("Reference group to calculate distances from"));
 114     options->addOption(SelectionOption("select")
 115                            .storeVector(&sel_).required().multiValue()
 116                            .description("Groups to calculate distances to"));
 117
 118     options->addOption(DoubleOption("cutoff").store(&cutoff_)
 119                            .description("Cutoff for distance calculation (0 = no cutoff)"));
 120
 121     settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
 122 }
 123
 124
 125 void
 126 AnalysisTemplate::initAnalysis(const TrajectoryAnalysisSettings &settings,
 127                                const TopologyInformation         & /*top*/)
 128 {
 129     nb_.setCutoff(cutoff_);
 130
 131     data_.setColumnCount(0, sel_.size());
 132
 133     avem_.reset(new AnalysisDataAverageModule());
 134     data_.addModule(avem_);
 135
 136     if (!fnDist_.empty())
 137     {
 138         AnalysisDataPlotModulePointer plotm(
 139                 new AnalysisDataPlotModule(settings.plotSettings()));
 140         plotm->setFileName(fnDist_);
 141         plotm->setTitle("Average distance");
 142         plotm->setXAxisIsTime();
 143         plotm->setYLabel("Distance (nm)");
 144         data_.addModule(plotm);
 145     }
 146 }
 147
 148
 149 void
 150 AnalysisTemplate::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
 151                                TrajectoryAnalysisModuleData *pdata)
 152 {
 153     AnalysisDataHandle         dh     = pdata->dataHandle(data_);
 154     const Selection           &refsel = pdata->parallelSelection(refsel_);
 155
 156     AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, refsel);
 157     dh.startFrame(frnr, fr.time);
 158     for (size_t g = 0; g < sel_.size(); ++g)
 159     {
 160         const Selection &sel   = pdata->parallelSelection(sel_[g]);
 161         int              nr    = sel.posCount();
 162         real             frave = 0.0;
 163         for (int i = 0; i < nr; ++i)
 164         {
 165             SelectionPosition p = sel.position(i);
 166             frave += nbsearch.minimumDistance(p.x());
 167         }
 168         frave /= nr;
 169         dh.setPoint(g, frave);
 170     }
 171     dh.finishFrame();
 172 }
 173
 174
 175 void
 176 AnalysisTemplate::finishAnalysis(int /*nframes*/)
 177 {
 178 }
 179
 180
 181 void
 182 AnalysisTemplate::writeOutput()
 183 {
 184     // We print out the average of the mean distances for each group.
 185     for (size_t g = 0; g < sel_.size(); ++g)
 186     {
 187         fprintf(stderr, "Average mean distance for '%s': %.3f nm\n",
 188                 sel_[g].name(), avem_->average(0, g));
 189     }
 190 }
 191
 192 /*! \brief
 193  * The main function for the analysis template.
 194  */
 195 int
 196 main(int argc, char *argv[])
 197 {
 198     return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<AnalysisTemplate>(argc, argv);
 199 }