const std::string &biasInitFilename,
pull_t *pull_work);
- /*! \brief Destructor. */
~Awh();
/*! \brief Peform an AWH update, to be called every MD step.
//! The awh Bias
std::unique_ptr<Bias> bias_;
- //! Constructor
BiasTest() :
coordinates_(std::begin(g_coords), std::end(g_coords))
{
public:
std::unique_ptr<BiasState> biasState_; //!< The bias state
- //! Constructor
BiasStateTest()
{
AwhTestParameters params = getAwhTestParameters();
/*! \brief The number of reals in gmx_ddzone_t */
constexpr int c_ddzoneNumReals = 7;
-/*! \brief Forward declaration */
template<typename T> class DDBufferAccess;
/*! \brief Temporary storage container that minimizes (re)allocation and clearing
buffer = ddBuffer_.acquire(numElements);
}
- /*! \brief Destructor */
~DDBufferAccess()
{
ddBuffer_.release();
class PmeBSplineModuliTest : public ::testing::TestWithParam<BSplineModuliInputParameters>
{
public:
- //! Default constructor
PmeBSplineModuliTest() = default;
//! The whole logic being tested is contained here
void runTest()
static InputDataByAtomCount s_inputAtomDataSets_;
public:
- //! Default constructor
PmeGatherTest() = default;
//! Sets the input atom data references once
static void SetUpTestCase()
class PmeSolveTest : public ::testing::TestWithParam<SolveInputParameters>
{
public:
- //! Default constructor
PmeSolveTest() = default;
//! The test
class PmeSplineAndSpreadTest : public ::testing::TestWithParam<SplineAndSpreadInputParameters>
{
public:
- //! Default constructor
PmeSplineAndSpreadTest() = default;
//! The test
void runTest()
//! Information about GPUs that are present.
gmx_gpu_info_t *gpuInfo_;
- //! Constructor
GpuTest();
- //! Destructor
~GpuTest() override;
//! Getter for convenience in testing
bool haveValidGpus() const;
* constructor. */
struct CreationHelper;
- //! Destructor.
~Constraints();
/*! \brief Returns the total number of flexible constraints in the system. */
HostVector<real> chargeA_;
public:
// TODO make this private
- //! Constructor.
MDAtoms();
- //! Destructor.
~MDAtoms();
//! Getter.
t_mdatoms *mdatoms()
void mde_delta_h_coll_init(t_mde_delta_h_coll *dhc,
const t_inputrec *ir);
-//! Destructor
void done_mde_delta_h_coll(t_mde_delta_h_coll *dhc);
/* add a bunch of samples to the delta_h collection
//! \internal \brief Options for writing checkpoint files
struct CheckpointOptions
{
- //! \brief Constructor
CheckpointOptions() :
keepAndNumberCheckpointFiles(FALSE),
period(15)
//! \internal \brief Options for IMD
struct ImdOptions
{
- //! Constructor
ImdOptions() :
port(8888),
wait(FALSE),
/* Thread-local work struct, contains part of nbnxn_grid_t */
struct nbnxn_search_work_t
{
- /* Constructor */
nbnxn_search_work_t();
- /* Destructor */
~nbnxn_search_work_t();
gmx_cache_protect_t cp0; /* Buffer to avoid cache polution */
//! PBC option to test
t_pbc pbcXYZ_;
- //! Constructor
SettleTest() :
updatedPositions_(std::begin(g_positions), std::end(g_positions)),
velocities_(updatedPositions_.size(), 0)
class SignalTest : public ::testing::Test
{
public:
- //! Constructor
SignalTest() : signals_ {}
{
signals_[0].sig = 1;
/* Data for handling vsites, needed with OpenMP threading or with charge-groups and PBC */
struct gmx_vsite_t
{
- /* Constructor */
gmx_vsite_t();
- /* Destructor */
~gmx_vsite_t();
gmx_bool bHaveChargeGroups; /* Do we have charge groups? */
//! Whether the lambda value is set. Here for backward-compatibility.
gmx_bool start_lambda_set;
- //! Constructor
delta_h_history_t() :
start_time(0),
start_lambda(0),
//! History for energy difference for foreign lambdas (useful for BAR)
std::unique_ptr<delta_h_history_t> deltaHForeignLambdas;
- //! Constructor
energyhistory_t() : nsteps(0),
nsum(0),
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, 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.
//! Ion/water position swapping history
std::unique_ptr<swaphistory_t> swapHistory;
- //! Default constructor
ObservablesHistory();
- //! Default destructor
~ObservablesHistory();
};
class history_t
{
public:
- //! Constructor
history_t();
real disre_initf; //!< The scaling factor for initializing the time av.
class t_state
{
public:
- //! Constructor
t_state();
// All things public
//! \cond libapi
//! Initializes option properties with the given name.
explicit AbstractOptionSection(const char *name) : name_(name) {}
- //! Destructor
virtual ~AbstractOptionSection() {}
/*! \brief
* Creates a storage object corresponding to this section.
class SingleRankChecker
{
public:
- //! Constructor
SingleRankChecker() : value_(false) {}
/*! \brief Call this function for each possible condition
under which a single rank is required, along with a string
/*! \brief Molecules type data: atoms, interactions and exclusions */
struct gmx_moltype_t
{
- /*! \brief Constructor */
gmx_moltype_t();
- /*! \brief Destructor */
~gmx_moltype_t();
/*! \brief Deleted copy assignment operator to avoid (not) freeing pointers */
*/
struct gmx_mtop_t //NOLINT(clang-analyzer-optin.performance.Padding)
{
- /* Constructor */
gmx_mtop_t();
- /* Destructor */
~gmx_mtop_t();
char **name; /* Name of the topology */
class ISerializer
{
public:
- //! Destructor.
virtual ~ISerializer() {}
/*! \brief Returns whether the serializer is reading or
* writing, because details like memory management vary
class DifferentTasksTest : public ::testing::TestWithParam<TaskType>
{
public:
- //! Constructor
DifferentTasksTest()
{
g_sharedValue = 0;
return keys;
}
-//! Forward declaration
class EnergyFrameReader;
//! Convenience smart pointer typedef
typedef std::unique_ptr<EnergyFrameReader> EnergyFrameReaderPtr;
public ::testing::WithParamInterface<const char *>
{
public:
- //! Constructor
MultiSimTest();
/*! \brief Organize the .mdp file for this rank
namespace gmx
{
-//! Forward declaration
class TrajectoryFrame;
namespace test
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