src/gromacs/trajectoryanalysis/analysissettings.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, 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 /*! \internal \file
  36  * \brief
  37  * Implements classes in analysissettings.h.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "analysissettings.h"
  45
  46 #include "gromacs/commandline/cmdlineoptionsmodule.h"
  47 #include "gromacs/fileio/trxio.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/topology/mtop_util.h"
  50 #include "gromacs/topology/topology.h"
  51 #include "gromacs/utility/arrayref.h"
  52 #include "gromacs/utility/exceptions.h"
  53 #include "gromacs/utility/gmxassert.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 #include "analysissettings-impl.h"
  57
  58 namespace gmx
  59 {
  60
  61
  62 /********************************************************************
  63  * TrajectoryAnalysisSettings
  64  */
  65
  66 TrajectoryAnalysisSettings::TrajectoryAnalysisSettings()
  67     : impl_(new Impl)
  68 {
  69     impl_->frflags |= TRX_NEED_X;
  70 }
  71
  72
  73 TrajectoryAnalysisSettings::~TrajectoryAnalysisSettings()
  74 {
  75 }
  76
  77
  78 void TrajectoryAnalysisSettings::setOptionsModuleSettings(
  79         ICommandLineOptionsModuleSettings *settings)
  80 {
  81     impl_->optionsModuleSettings_ = settings;
  82 }
  83
  84
  85 TimeUnit
  86 TrajectoryAnalysisSettings::timeUnit() const
  87 {
  88     return impl_->timeUnit;
  89 }
  90
  91
  92 const AnalysisDataPlotSettings &
  93 TrajectoryAnalysisSettings::plotSettings() const
  94 {
  95     return impl_->plotSettings;
  96 }
  97
  98
  99 unsigned long
 100 TrajectoryAnalysisSettings::flags() const
 101 {
 102     return impl_->flags;
 103 }
 104
 105
 106 bool
 107 TrajectoryAnalysisSettings::hasFlag(unsigned long flag) const
 108 {
 109     return impl_->flags & flag;
 110 }
 111
 112
 113 bool
 114 TrajectoryAnalysisSettings::hasPBC() const
 115 {
 116     return impl_->bPBC;
 117 }
 118
 119
 120 bool
 121 TrajectoryAnalysisSettings::hasRmPBC() const
 122 {
 123     return impl_->bRmPBC;
 124 }
 125
 126
 127 int
 128 TrajectoryAnalysisSettings::frflags() const
 129 {
 130     return impl_->frflags;
 131 }
 132
 133
 134 void
 135 TrajectoryAnalysisSettings::setFlags(unsigned long flags)
 136 {
 137     impl_->flags = flags;
 138 }
 139
 140
 141 void
 142 TrajectoryAnalysisSettings::setFlag(unsigned long flag, bool bSet)
 143 {
 144     if (bSet)
 145     {
 146         impl_->flags |= flag;
 147     }
 148     else
 149     {
 150         impl_->flags &= ~flag;
 151     }
 152 }
 153
 154
 155 void
 156 TrajectoryAnalysisSettings::setPBC(bool bPBC)
 157 {
 158     impl_->bPBC = bPBC;
 159 }
 160
 161
 162 void
 163 TrajectoryAnalysisSettings::setRmPBC(bool bRmPBC)
 164 {
 165     impl_->bRmPBC = bRmPBC;
 166 }
 167
 168
 169 void
 170 TrajectoryAnalysisSettings::setFrameFlags(int frflags)
 171 {
 172     impl_->frflags = frflags;
 173 }
 174
 175 void
 176 TrajectoryAnalysisSettings::setHelpText(const ConstArrayRef<const char *> &help)
 177 {
 178     GMX_RELEASE_ASSERT(impl_->optionsModuleSettings_ != nullptr,
 179                        "setHelpText() called in invalid context");
 180     impl_->optionsModuleSettings_->setHelpText(help);
 181 }
 182
 183
 184 /********************************************************************
 185  * TopologyInformation
 186  */
 187
 188 TopologyInformation::TopologyInformation()
 189     : mtop_(NULL), top_(NULL), bTop_(false), xtop_(NULL), ePBC_(-1)
 190 {
 191     clear_mat(boxtop_);
 192 }
 193
 194
 195 TopologyInformation::~TopologyInformation()
 196 {
 197     done_top_mtop(top_, mtop_);
 198     sfree(mtop_);
 199     sfree(top_);
 200     sfree(xtop_);
 201 }
 202
 203
 204 t_topology *TopologyInformation::topology() const
 205 {
 206     if (top_ == nullptr && mtop_ != nullptr)
 207     {
 208         snew(top_, 1);
 209         *top_ = gmx_mtop_t_to_t_topology(mtop_, false);
 210     }
 211     return top_;
 212 }
 213
 214
 215 void
 216 TopologyInformation::getTopologyConf(rvec **x, matrix box) const
 217 {
 218     if (box)
 219     {
 220         copy_mat(const_cast<rvec *>(boxtop_), box);
 221     }
 222     if (x)
 223     {
 224         if (!xtop_)
 225         {
 226             *x = NULL;
 227             GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));
 228         }
 229         *x = xtop_;
 230     }
 231 }
 232
 233 } // namespace gmx