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39 * \author Kevin Boyd <kevin.boyd@uconn.edu>
44 #include "gromacs/gmxana/gmx_ana.h"
45 #include "gromacs/utility/futil.h"
46 #include "gromacs/utility/textreader.h"
48 #include "testutils/cmdlinetest.h"
49 #include "testutils/refdata.h"
50 #include "testutils/testfilemanager.h"
51 #include "testutils/textblockmatchers.h"
52 #include "testutils/xvgtest.h"
57 using gmx::test::CommandLine;
58 using gmx::test::XvgMatch;
60 class MsdTest : public gmx::test::CommandLineTestBase
65 setOutputFile("-o", "msd.xvg", XvgMatch());
66 setInputFile("-f", "msd_traj.xtc");
67 setInputFile("-s", "msd_coords.gro");
68 setInputFile("-n", "msd.ndx");
71 void runTest(const CommandLine &args)
73 CommandLine &cmdline = commandLine();
75 ASSERT_EQ(0, gmx_msd(cmdline.argc(), cmdline.argv()));
80 /* msd_traj.xtc contains a 10 frame (1 ps per frame) simulation
81 * containing 3 atoms, with different starting positions but identical
82 * displacements. The displacements are calculated to yield the following
83 * diffusion coefficients when lag is calculated ONLY FROM TIME 0
84 * D_x = 8 * 10 ^ -5 cm^2 /s, D_y = 4 * 10^ -5 cm^2 /s , D_z = 0
86 * To test for these results, -trestart is set to a larger value than the
87 * total simulation length, so that only lag 0 is calculated
90 // for 3D, (8 + 4 + 0) / 3 should yield 4 cm^2 / s
91 TEST_F(MsdTest, threeDimensionalDiffusion)
93 const char *const cmdline[] = {
94 "msd", "-mw", "no", "-trestart", "200",
96 runTest(CommandLine(cmdline));
99 // for lateral z, (8 + 4) / 2 should yield 6 cm^2 /s
100 TEST_F(MsdTest, twoDimensionalDiffusion)
102 const char *const cmdline[] = {
103 "msd", "-mw", "no", "-trestart", "200", "-lateral", "z"
105 runTest(CommandLine(cmdline));
108 // for type x, should yield 8 cm^2 / s
109 TEST_F(MsdTest, oneDimensionalDiffusion)
111 const char *const cmdline[] = {
112 "msd", "-mw", "no", "-trestart", "200", "-type", "x"
114 runTest(CommandLine(cmdline));