Make it build with Gromacs 2016 rc1

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 63b6d4fbc23a98d66b3c572e12c418c9b183b817..09e340d9a415ad58733a558ee3571cc60ad71030 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -11,4 +11,7 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
 find_package(GROMACS 2016)
 
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+include_directories(${CMAKE_SOURCE_DIR}/stub_headers)
+
 add_subdirectory(src)

diff --git a/src/sip/trajectoryanalysis/TrajectoryAnalysis.sip b/src/sip/trajectoryanalysis/TrajectoryAnalysis.sip
index 338d07ebcdbd7761bc52c3f1005b8a8c2da89df8..6ff73d6d4b78ccf35d2383ffb4647718876ad82c 100644 (file)
--- a/src/sip/trajectoryanalysis/TrajectoryAnalysis.sip
+++ b/src/sip/trajectoryanalysis/TrajectoryAnalysis.sip
@@ -46,7 +46,6 @@
 %Include analysissettings.sip
 %Include analysismodule.sip
 %Include runnercommon.sip
-%Include modules.sip
 %Include analysisdata.sip
 %Include cmdlinerunner.sip
 

diff --git a/src/sip/trajectoryanalysis/modules.sip b/src/sip/trajectoryanalysis/modules.sip
deleted file mode 100644 (file)
index 4e11af3..0000000
--- a/src/sip/trajectoryanalysis/modules.sip
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015, 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
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-%ModuleHeaderCode
-#include <gromacs/trajectoryanalysis/modules.h>
-using gmx::createModuleByName;
-using gmx::registerTrajectoryAnalysisModules;
-%End
-
-std::unique_ptr<TrajectoryAnalysisModule> createModuleByName(const char *name) /Factory/;
-
-%PostInitialisationCode
-    registerTrajectoryAnalysisModules(nullptr);
-%End

diff --git a/src/sip/trajectoryanalysis/runnercommon.sip b/src/sip/trajectoryanalysis/runnercommon.sip
index a1be44bb37793f57194dc2c7e8b1049860ac5fb4..3fef87d1475c72d1b5d64fa03e39073f9589afd4 100644 (file)
--- a/src/sip/trajectoryanalysis/runnercommon.sip
+++ b/src/sip/trajectoryanalysis/runnercommon.sip
@@ -82,5 +82,4 @@ public:
     bool hasTrajectory() const;
     const TopologyInformation &topologyInformation() const;
     t_trxframe                &frame() const;
-    t_pbc                     *pbc() const;
 };

diff --git a/stub_headers/gromacs/analysisdata/paralleloptions.h b/stub_headers/gromacs/analysisdata/paralleloptions.h
new file mode 100644 (file)
index 0000000..ce51098
--- /dev/null
+++ b/stub_headers/gromacs/analysisdata/paralleloptions.h
@@ -0,0 +1,11 @@
+#ifndef PARALLELOPTIONS_H
+#define PARALLELOPTIONS_H
+
+namespace gmx {
+class AnalysisDataParallelOptions {
+    public:
+        AnalysisDataParallelOptions();
+};
+}
+
+#endif

diff --git a/stub_headers/gromacs/trajectoryanalysis/runnercommon.h b/stub_headers/gromacs/trajectoryanalysis/runnercommon.h
new file mode 100644 (file)
index 0000000..28e1304
--- /dev/null
+++ b/stub_headers/gromacs/trajectoryanalysis/runnercommon.h
@@ -0,0 +1,27 @@
+#ifndef RUNNERCOMMON_H
+#define RUNNERCOMMON_h
+
+namespace gmx {
+class ITopologyProvider;
+class TrajectoryAnalysisRunnerCommon {
+    public:
+    explicit TrajectoryAnalysisRunnerCommon(TrajectoryAnalysisSettings*);
+    ~TrajectoryAnalysisRunnerCommon();
+
+    ITopologyProvider *topologyProvider();
+
+    void initOptions(IOptionsContainer*, TimeUnitBehavior*);
+    void optionsFinished();
+    void initTopology();
+    void initFirstFrame();
+    void initFrameIndexGroup();
+    bool readNextFrame();
+    void initFrame();
+
+    bool hasTrajectory() const;
+    const TopologyInformation &topologyInformation() const;
+    t_trxframe &frame() const;
+};
+}
+
+#endif