Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / trajectoryanalysis / runnercommon.cpp

diff --git a/src/gromacs/trajectoryanalysis/runnercommon.cpp b/src/gromacs/trajectoryanalysis/runnercommon.cpp
index 889df25daa4f9b755bea55be54380ff3f457d5bd..4d9513ed28d6268e8245c7eebea9125b1f535e7f 100644 (file)
--- a/src/gromacs/trajectoryanalysis/runnercommon.cpp
+++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp
@@ -1,10 +1,10 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
  *
  * GROMACS is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -39,30 +39,31 @@
  * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_trajectoryanalysis
  */
-#include "runnercommon.h"
+#include "gmxpre.h"
 
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
+#include "runnercommon.h"
 
 #include <string.h>
 
+#include "gromacs/fileio/timecontrol.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/rmpbc.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/statutil.h"
-#include "gromacs/legacyheaders/tpxio.h"
-#include "gromacs/legacyheaders/vec.h"
-
+#include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"
 #include "gromacs/options/options.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/selectioncollection.h"
 #include "gromacs/selection/selectionfileoption.h"
+#include "gromacs/topology/topology.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "analysissettings-impl.h"
@@ -185,7 +186,6 @@ TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
                            .store(&impl_->ndxfile_)
                            .defaultBasename("index")
                            .description("Extra index groups"));
-    options->addOption(SelectionFileOption("sf"));
 
     // Add options for trajectory time control.
     options->addOption(DoubleOption("b").store(&impl_->startTime_).timeValue()
@@ -212,6 +212,8 @@ TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
                                .description("Use periodic boundary conditions for distance calculation"));
     }
+
+    options->addOption(SelectionFileOption("sf"));
 }
 
 
@@ -249,18 +251,22 @@ TrajectoryAnalysisRunnerCommon::optionsFinished(Options *options)
 
 
 void
-TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections)
+TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections,
+                                                bool                 bUseDefaults)
 {
     if (impl_->ndxfile_.empty())
     {
-        // TODO: Initialize default selections
-        selections->setIndexGroups(NULL);
-    }
-    else
-    {
-        gmx_ana_indexgrps_init(&impl_->grps_, NULL, impl_->ndxfile_.c_str());
-        selections->setIndexGroups(impl_->grps_);
+        if (!bUseDefaults)
+        {
+            selections->setIndexGroups(NULL);
+            return;
+        }
+        initTopology(selections);
     }
+    const char *const ndxfile
+        = (!impl_->ndxfile_.empty() ? impl_->ndxfile_.c_str() : NULL);
+    gmx_ana_indexgrps_init(&impl_->grps_, impl_->topInfo_.topology(), ndxfile);
+    selections->setIndexGroups(impl_->grps_);
 }
 
 
@@ -279,8 +285,14 @@ TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
 void
 TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
 {
+    // Return immediately if the topology has already been loaded.
+    if (impl_->topInfo_.hasTopology())
+    {
+        return;
+    }
+
     const TrajectoryAnalysisSettings &settings = impl_->settings_;
-    bool bRequireTop
+    const bool bRequireTop
         = settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
             || selections->requiresTopology();
     if (bRequireTop && impl_->topfile_.empty())
@@ -335,7 +347,7 @@ TrajectoryAnalysisRunnerCommon::initFirstFrame()
     }
     time_unit_t time_unit
         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
-    output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
+    output_env_init(&impl_->oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
 
     int frflags = impl_->settings_.frflags();
     frflags |= TRX_NEED_X;
@@ -358,17 +370,6 @@ TrajectoryAnalysisRunnerCommon::initFirstFrame()
                                                      "Trajectory (%d atoms) does not match topology (%d atoms)",
                                                      impl_->fr->natoms, top.topology()->atoms.nr)));
         }
-        // TODO: Check index groups if they have been initialized based on the topology.
-        /*
-           if (top)
-           {
-            for (int i = 0; i < impl_->sel->nr(); ++i)
-            {
-                gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
-                                    impl_->fr->natoms);
-            }
-           }
-         */
     }
     else
     {