/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2016,2017,2018,2019, 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.
#include "gromacs/utility/path.h"
+#include "testutils/simulationdatabase.h"
#include "testutils/testfilemanager.h"
namespace
TEST_F(TngTest, CanOpenTngFile)
{
gmx_tng_trajectory_t tng;
- gmx_tng_open(gmx::test::TestFileManager::getInputFilePath("spc2-traj.tng").c_str(),
- 'r',
- &tng);
+ gmx_tng_open("spc2-traj.tng", 'r', &tng);
gmx_tng_close(&tng);
}
int
gmx_dyecoupl(int argc, char *argv[]);
-int
-gmx_eneconv(int argc, char *argv[]);
-
int
gmx_enemat(int argc, char *argv[]);
int
gmx_make_edi(int argc, char *argv[]);
-int
-gmx_make_ndx(int argc, char *argv[]);
-
int
gmx_mindist(int argc, char *argv[]);
-int
-gmx_mk_angndx(int argc, char *argv[]);
-
int
gmx_msd(int argc, char *argv[]);
int
gmx_traj(int argc, char *argv[]);
-int
-gmx_trjcat(int argc, char *argv[]);
-
-int
-gmx_trjconv(int argc, char *argv[]);
-
int
gmx_trjorder(int argc, char *argv[]);
-int
-gmx_tune_pme(int argc, char *argv[]);
-
int
gmx_velacc(int argc, char *argv[]);
int
gmx_membed(int argc, char *argv[]);
-int
-gmx_pme_error(int argc, char *argv[]);
-
int
gmx_sans(int argc, char *argv[]);
${exename}
entropy.cpp
gmx_traj.cpp
- gmx_trjconv.cpp
- gmx_make_ndx.cpp
gmx_mindist.cpp
gmx_msd.cpp
)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2016,2017,2018,2019, 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.
#include "gromacs/gmxana/gmx_ana.h"
#include "testutils/cmdlinetest.h"
+#include "testutils/simulationdatabase.h"
#include "testutils/stdiohelper.h"
#include "testutils/textblockmatchers.h"
+++ /dev/null
-
- 6
- 1SOL OW 1 0.569 1.275 1.165 0.569 1.215 1.965
- 1SOL HW1 2 0.476 1.268 1.128 0.669 1.225 1.865
- 1SOL HW2 3 0.580 1.364 1.209 0.769 1.235 1.765
- 2SOL OW 4 1.555 1.511 0.703 0.869 1.245 1.665
- 2SOL HW1 5 1.498 1.495 0.784 0.169 0.275 1.565
- 2SOL HW2 6 1.496 1.521 0.623 0.269 2.275 1.465
- 3.01000 3.01000 3.01000
+++ /dev/null
-[ System ]
- 1 2 3 4 5 6
-[ FirstWaterMolecule ]
- 1 2 3
-[ SecondWaterMolecule ]
- 4 5 6
*/
#include "gmxpre.h"
+#include "eneconv.h"
+
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/listed_forces/disre.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ */
+#ifndef GMX_TOOLS_ENECONV_H
+#define GMX_TOOLS_ENECONV_H
+
+/*! \brief Implements gmx eneconv
+ *
+ * \param[in] argc argc value passed to main().
+ * \param[in] argv argv array passed to main().
+ */
+int gmx_eneconv(int argc, char *argv[]);
+
+#endif
*/
#include "gmxpre.h"
+#include "make_ndx.h"
+
#include <cctype>
#include <cstring>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/index.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ */
+#ifndef GMX_TOOLS_MAKE_NDX_H
+#define GMX_TOOLS_MAKE_NDX_H
+
+/*! \brief Implements gmx make_ndx
+ *
+ * \param[in] argc argc value passed to main().
+ * \param[in] argv argv array passed to main().
+ */
+int gmx_make_ndx(int argc, char *argv[]);
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, 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.
*/
#include "gmxpre.h"
+#include "mk_angndx.h"
+
#include <cmath>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ */
+#ifndef GMX_TOOLS_MK_ANGNDX_H
+#define GMX_TOOLS_MK_ANGNDX_H
+
+/*! \brief Implements gmx mk_angndx
+ *
+ * \param[in] argc argc value passed to main().
+ * \param[in] argv argv array passed to main().
+ */
+int gmx_mk_angndx(int argc, char *argv[]);
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2019, 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.
*/
#include "gmxpre.h"
+#include "pme_error.h"
+
#include "config.h"
#include <cmath>
#include "gromacs/fft/calcgrid.h"
#include "gromacs/fileio/checkpoint.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ */
+#ifndef GMX_TOOLS_PME_ERROR_H
+#define GMX_TOOLS_PME_ERROR_H
+
+/*! \brief Implements gmx pme_error
+ *
+ * \param[in] argc argc value passed to main().
+ * \param[in] argv argv array passed to main().
+ */
+int gmx_pme_error(int argc, char *argv[]);
+
+#endif
gmx_add_unit_test(ToolUnitTests tool-test
dump.cpp
- report_methods.cpp)
+ report_methods.cpp
+ trjconv.cpp)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2016,2017,2018,2019, 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.
*/
#include "gmxpre.h"
-#include "config.h"
+#include "gromacs/tools/trjconv.h"
-#include "gromacs/gmxana/gmx_ana.h"
+#include "config.h"
#include "testutils/cmdlinetest.h"
+#include "testutils/simulationdatabase.h"
#include "testutils/stdiohelper.h"
#include "testutils/textblockmatchers.h"
*/
#include "gmxpre.h"
+#include "trjcat.h"
+
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/xvgr.h"
-#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/index.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ */
+#ifndef GMX_TOOLS_TRJCAT_H
+#define GMX_TOOLS_TRJCAT_H
+
+/*! \brief Implements gmx trjcat
+ *
+ * \param[in] argc argc value passed to main().
+ * \param[in] argv argv array passed to main().
+ */
+int gmx_trjcat(int argc, char *argv[]);
+
+#endif
*/
#include "gmxpre.h"
+#include "trjconv.h"
+
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/xvgr.h"
-#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/do_fit.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ */
+#ifndef GMX_TOOLS_TRJCONV_H
+#define GMX_TOOLS_TRJCONV_H
+
+/*! \brief Implements gmx trjconv
+ *
+ * \param[in] argc argc value passed to main().
+ * \param[in] argv argv array passed to main().
+ */
+int gmx_trjconv(int argc, char *argv[]);
+
+#endif
*/
#include "gmxpre.h"
+#include "tune_pme.h"
+
#include "config.h"
#include <cmath>
#include "gromacs/fft/calcgrid.h"
#include "gromacs/fileio/checkpoint.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/perf_est.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ */
+#ifndef GMX_TOOLS_TUNE_PME_H
+#define GMX_TOOLS_TUNE_PME_H
+
+/*! \brief Implements gmx tune_pme
+ *
+ * \param[in] argc argc value passed to main().
+ * \param[in] argv argv array passed to main().
+ */
+int gmx_tune_pme(int argc, char *argv[]);
+
+#endif
#include "gromacs/tools/check.h"
#include "gromacs/tools/convert_tpr.h"
#include "gromacs/tools/dump.h"
+#include "gromacs/tools/eneconv.h"
+#include "gromacs/tools/make_ndx.h"
+#include "gromacs/tools/mk_angndx.h"
+#include "gromacs/tools/pme_error.h"
#include "gromacs/tools/report_methods.h"
+#include "gromacs/tools/trjcat.h"
+#include "gromacs/tools/trjconv.h"
+#include "gromacs/tools/tune_pme.h"
#include "mdrun/mdrun_main.h"
#include "view/view.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff