src/programs/mdrun/tests/swapcoords.cpp

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  36
  37 /*! \internal \file
  38  * \brief
  39  * Tests utilities for "Computational Electrophysiology" setups.
  40  *
  41  * \author Carsten Kutzner <ckutzne@gwdg.de>
  42  * \ingroup module_mdrun_integration_tests
  43  */
  44 #include "gmxpre.h"
  45
  46 #include "moduletest.h"
  47
  48 namespace gmx
  49 {
  50 namespace test
  51 {
  52
  53 class SwapTestFixture : public MdrunTestFixture
  54 {
  55 protected:
  56     SwapTestFixture();
  57     ~SwapTestFixture() override;
  58 };
  59
  60
  61 SwapTestFixture::SwapTestFixture() {}
  62
  63 SwapTestFixture::~SwapTestFixture() {}
  64
  65
  66 //! Test fixture for mdrun with "Computational Electrophysiology" settings,
  67 // i.e. double membrane sandwich with ion/water exchange protocol
  68 typedef gmx::test::SwapTestFixture CompelTest;
  69
  70 /* This test ensures that the compel protocol can be run, that all of
  71  * the swapcoords parameters from the .mdp file are understood, and that
  72  * the swap state variables can be written to and read from checkpoint. */
  73 TEST_F(CompelTest, SwapCanRun)
  74 {
  75     runner_.useTopGroAndNdxFromDatabase("OctaneSandwich");
  76     const std::string mdpContents = R"(
  77         dt                       = 0.005
  78         nsteps                   = 2
  79         tcoupl                   = Berendsen
  80         tc-grps                  = System
  81         tau-t                    = 0.5
  82         ref-t                    = 300
  83         constraints              = all-bonds
  84         cutoff-scheme            = Verlet
  85         swapcoords               = Z
  86         swap_frequency           = 1
  87         split_group0             = Ch0
  88         split_group1             = Ch1
  89         massw_split0             = yes
  90         massw_split1             = no
  91         solvent_group            = SOL
  92         cyl0_r                   = 1
  93         cyl0_up                  = 0.5
  94         cyl0_down                = 0.5
  95         cyl1_r                   = 1
  96         cyl1_up                  = 0.5
  97         cyl1_down                = 0.5
  98         coupl_steps              = 5
  99         iontypes                 = 2
 100         iontype0-name            = NA+
 101         iontype0-in-A            = 8
 102         iontype0-in-B            = 11
 103         iontype1-name            = CL-
 104         iontype1-in-A            = -1
 105         iontype1-in-B            = -1
 106         threshold                = 1
 107      )";
 108
 109     runner_.useStringAsMdpFile(mdpContents);
 110
 111     EXPECT_EQ(0, runner_.callGrompp());
 112
 113     runner_.cptFileName_       = fileManager_.getTemporaryFilePath(".cpt");
 114     runner_.groOutputFileName_ = fileManager_.getTemporaryFilePath(".gro");
 115     runner_.swapFileName_      = fileManager_.getTemporaryFilePath("swap.xvg");
 116
 117     ::gmx::test::CommandLine swapCaller;
 118     swapCaller.addOption("-c", runner_.groOutputFileName_);
 119     swapCaller.addOption("-swap", runner_.swapFileName_);
 120
 121     // Do an initial mdrun that writes a checkpoint file
 122     ::gmx::test::CommandLine firstCaller(swapCaller);
 123     firstCaller.addOption("-cpo", runner_.cptFileName_);
 124     ASSERT_EQ(0, runner_.callMdrun(firstCaller));
 125     // Continue mdrun from that checkpoint file
 126     ::gmx::test::CommandLine secondCaller(swapCaller);
 127     secondCaller.addOption("-cpi", runner_.cptFileName_);
 128     runner_.nsteps_ = 2;
 129     ASSERT_EQ(0, runner_.callMdrun(secondCaller));
 130 }
 131
 132
 133 /*! \todo Add other tests for the compel module, e.g.
 134  *
 135  *  - a test that checks that actually ion/water swaps have been done, by
 136  *    calling gmxcheck on the swap output file and a reference file
 137  */
 138
 139
 140 } // namespace test
 141 } // namespace gmx