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 bc97d3acc423358f257e5bcc05f78d2e3d64147c..4d9513ed28d6268e8245c7eebea9125b1f535e7f 100644 (file)
--- a/src/gromacs/trajectoryanalysis/runnercommon.cpp
+++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp
@@ -39,19 +39,17 @@
  * \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/legacyheaders/oenv.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/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"
@@ -60,6 +58,7 @@
 #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"
@@ -348,7 +347,7 @@ TrajectoryAnalysisRunnerCommon::initFirstFrame()
     }
     time_unit_t time_unit
         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
-    output_env_init(&impl_->oenv_, getProgramContext(), 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;
@@ -371,17 +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
     {