src/programs/mdrun/tests/swapcoords.cpp

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  35
  36 /*! \internal \file
  37  * \brief
  38  * Tests utilities for "Computational Electrophysiology" setups.
  39  *
  40  * \author Carsten Kutzner <ckutzne@gwdg.de>
  41  * \ingroup module_mdrun_integration_tests
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "moduletest.h"
  46
  47 namespace gmx
  48 {
  49 namespace test
  50 {
  51
  52 class SwapTestFixture : public MdrunTestFixture
  53 {
  54     protected:
  55         SwapTestFixture();
  56         ~SwapTestFixture() override;
  57 };
  58
  59
  60 SwapTestFixture::SwapTestFixture()
  61 {
  62 }
  63
  64 SwapTestFixture::~SwapTestFixture()
  65 {
  66 }
  67
  68
  69
  70 //! Test fixture for mdrun with "Computational Electrophysiology" settings,
  71 // i.e. double membrane sandwich with ion/water exchange protocol
  72 typedef gmx::test::SwapTestFixture CompelTest;
  73
  74 /* This test ensures that the compel protocol can be run, that all of
  75  * the swapcoords parameters from the .mdp file are understood, and that
  76  * the swap state variables can be written to and read from checkpoint. */
  77 TEST_F(CompelTest, SwapCanRun)
  78 {
  79     runner_.useTopGroAndNdxFromDatabase("OctaneSandwich");
  80     const std::string mdpContents = R"(
  81         dt                       = 0.005
  82         nsteps                   = 2
  83         tcoupl                   = Berendsen
  84         tc-grps                  = System
  85         tau-t                    = 0.5
  86         ref-t                    = 300
  87         constraints              = all-bonds
  88         cutoff-scheme            = Verlet
  89         swapcoords               = Z
  90         swap_frequency           = 1
  91         split_group0             = Ch0
  92         split_group1             = Ch1
  93         massw_split0             = yes
  94         massw_split1             = no
  95         solvent_group            = SOL
  96         cyl0_r                   = 1
  97         cyl0_up                  = 0.5
  98         cyl0_down                = 0.5
  99         cyl1_r                   = 1
 100         cyl1_up                  = 0.5
 101         cyl1_down                = 0.5
 102         coupl_steps              = 5
 103         iontypes                 = 2
 104         iontype0-name            = NA+
 105         iontype0-in-A            = 8
 106         iontype0-in-B            = 11
 107         iontype1-name            = CL-
 108         iontype1-in-A            = -1
 109         iontype1-in-B            = -1
 110         threshold                = 1
 111      )";
 112
 113     runner_.useStringAsMdpFile(mdpContents);
 114
 115     EXPECT_EQ(0, runner_.callGrompp());
 116
 117     runner_.cptFileName_       = fileManager_.getTemporaryFilePath(".cpt");
 118     runner_.groOutputFileName_ = fileManager_.getTemporaryFilePath(".gro");
 119     runner_.swapFileName_      = fileManager_.getTemporaryFilePath("swap.xvg");
 120
 121     ::gmx::test::CommandLine swapCaller;
 122     swapCaller.addOption("-c", runner_.groOutputFileName_);
 123     swapCaller.addOption("-swap", runner_.swapFileName_);
 124
 125     // Do an initial mdrun that writes a checkpoint file
 126     ::gmx::test::CommandLine firstCaller(swapCaller);
 127     firstCaller.addOption("-cpo", runner_.cptFileName_);
 128     ASSERT_EQ(0, runner_.callMdrun(firstCaller));
 129     // Continue mdrun from that checkpoint file
 130     ::gmx::test::CommandLine secondCaller(swapCaller);
 131     secondCaller.addOption("-cpi", runner_.cptFileName_);
 132     runner_.nsteps_ = 2;
 133     ASSERT_EQ(0, runner_.callMdrun(secondCaller));
 134 }
 135
 136
 137
 138 /*! \todo Add other tests for the compel module, e.g.
 139  *
 140  *  - a test that checks that actually ion/water swaps have been done, by
 141  *    calling gmxcheck on the swap output file and a reference file
 142  */
 143
 144
 145 } // namespace test
 146 } // namespace gmx