--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, 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.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for gmx msd.
+ *
+ * \author Kevin Boyd <kevin.boyd@uconn.edu>
+ */
+
+#include "gmxpre.h"
+
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/textreader.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/refdata.h"
+#include "testutils/testfilemanager.h"
+#include "testutils/textblockmatchers.h"
+#include "testutils/xvgtest.h"
+
+namespace
+{
+
+using gmx::test::CommandLine;
+using gmx::test::XvgMatch;
+
+class MsdTest : public gmx::test::CommandLineTestBase
+{
+ public:
+ MsdTest()
+ {
+ setOutputFile("-o", "msd.xvg", XvgMatch());
+ setInputFile("-f", "msd_traj.xtc");
+ setInputFile("-s", "msd_coords.gro");
+ setInputFile("-n", "msd.ndx");
+ }
+
+ void runTest(const CommandLine &args)
+ {
+ CommandLine &cmdline = commandLine();
+ cmdline.merge(args);
+ ASSERT_EQ(0, gmx_msd(cmdline.argc(), cmdline.argv()));
+ checkOutputFiles();
+ }
+};
+
+/* msd_traj.xtc contains a 10 frame (1 ps per frame) simulation
+ * containing 3 atoms, with different starting positions but identical
+ * displacements. The displacements are calculated to yield the following
+ * diffusion coefficients when lag is calculated ONLY FROM TIME 0
+ * D_x = 8 * 10 ^ -5 cm^2 /s, D_y = 4 * 10^ -5 cm^2 /s , D_z = 0
+ *
+ * To test for these results, -trestart is set to a larger value than the
+ * total simulation length, so that only lag 0 is calculated
+ */
+
+// for 3D, (8 + 4 + 0) / 3 should yield 4 cm^2 / s
+TEST_F(MsdTest, threeDimensionalDiffusion)
+{
+ const char *const cmdline[] = {
+ "msd", "-mw", "no", "-trestart", "200",
+ };
+ runTest(CommandLine(cmdline));
+}
+
+// for lateral z, (8 + 4) / 2 should yield 6 cm^2 /s
+TEST_F(MsdTest, twoDimensionalDiffusion)
+{
+ const char *const cmdline[] = {
+ "msd", "-mw", "no", "-trestart", "200", "-lateral", "z"
+ };
+ runTest(CommandLine(cmdline));
+}
+
+// for type x, should yield 8 cm^2 / s
+TEST_F(MsdTest, oneDimensionalDiffusion)
+{
+ const char *const cmdline[] = {
+ "msd", "-mw", "no", "-trestart", "200", "-type", "x"
+ };
+ runTest(CommandLine(cmdline));
+}
+} //namespace
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff