/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, 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.
*/
class Awh
{
- public:
- /*! \brief Construct an AWH at the start of a simulation.
- *
- * AWH will here also register itself with the pull struct as the
- * potential provider for the pull coordinates given as AWH coordinates
- * in the user input. This allows AWH to later apply the bias force to
- * these coordinate in \ref Awh::applyBiasForcesAndUpdateBias.
- *
- * \param[in,out] fplog General output file, normally md.log, can be nullptr.
- * \param[in] inputRecord General input parameters (as set up by grompp).
- * \param[in] commRecord Struct for communication, can be nullptr.
- * \param[in] multiSimRecord Multi-sim handler
- * \param[in] awhParams AWH input parameters, consistent with the relevant parts of \p inputRecord (as set up by grompp).
- * \param[in] biasInitFilename Name of file to read PMF and target from.
- * \param[in,out] pull_work Pointer to a pull struct which AWH will couple to, has to be initialized, is assumed not to change during the lifetime of the Awh object.
- */
- Awh(FILE *fplog,
- const t_inputrec &inputRecord,
- const t_commrec *commRecord,
- const gmx_multisim_t *multiSimRecord,
- const AwhParams &awhParams,
- const std::string &biasInitFilename,
- pull_t *pull_work);
+public:
+ /*! \brief Construct an AWH at the start of a simulation.
+ *
+ * AWH will here also register itself with the pull struct as the
+ * potential provider for the pull coordinates given as AWH coordinates
+ * in the user input. This allows AWH to later apply the bias force to
+ * these coordinate in \ref Awh::applyBiasForcesAndUpdateBias.
+ *
+ * \param[in,out] fplog General output file, normally md.log, can be nullptr.
+ * \param[in] inputRecord General input parameters (as set up by grompp).
+ * \param[in] commRecord Struct for communication, can be nullptr.
+ * \param[in] multiSimRecord Multi-sim handler
+ * \param[in] awhParams AWH input parameters, consistent with the relevant parts of \p inputRecord (as set up by grompp).
+ * \param[in] biasInitFilename Name of file to read PMF and target from.
+ * \param[in,out] pull_work Pointer to a pull struct which AWH will couple to, has to be initialized, is assumed not to change during the lifetime of the Awh object.
+ */
+ Awh(FILE* fplog,
+ const t_inputrec& inputRecord,
+ const t_commrec* commRecord,
+ const gmx_multisim_t* multiSimRecord,
+ const AwhParams& awhParams,
+ const std::string& biasInitFilename,
+ pull_t* pull_work);
- ~Awh();
+ ~Awh();
- /*! \brief Peform an AWH update, to be called every MD step.
- *
- * An update has two tasks: apply the bias force and improve
- * the bias and the free energy estimate that AWH keeps internally.
- *
- * For the first task, AWH retrieves the pull coordinate values from the pull struct.
- * With these, the bias potential and forces are calculated.
- * The bias force together with the atom forces and virial
- * are passed on to pull which applies the bias force to the atoms.
- * This is done at every step.
- *
- * Secondly, coordinate values are regularly sampled and kept by AWH.
- * Convergence of the bias and free energy estimate is achieved by
- * updating the AWH bias state after a certain number of samples has been collected.
- *
- * \note Requires that pull_potential from pull.h has been called first
- * since AWH needs the current coordinate values (the pull code checks
- * for this).
- *
- * \param[in] mdatoms Atom properties.
- * \param[in] ePBC Type of periodic boundary conditions.
- * \param[in] box Box vectors.
- * \param[in,out] forceWithVirial Force and virial buffers, should cover at least the local atoms.
- * \param[in] t Time.
- * \param[in] step The current MD step.
- * \param[in,out] wallcycle Wallcycle counter, can be nullptr.
- * \param[in,out] fplog General output file, normally md.log, can be nullptr.
- * \returns the potential energy for the bias.
- */
- real applyBiasForcesAndUpdateBias(int ePBC,
- const t_mdatoms &mdatoms,
- const matrix box,
- gmx::ForceWithVirial *forceWithVirial,
- double t,
- int64_t step,
- gmx_wallcycle *wallcycle,
- FILE *fplog);
+ /*! \brief Peform an AWH update, to be called every MD step.
+ *
+ * An update has two tasks: apply the bias force and improve
+ * the bias and the free energy estimate that AWH keeps internally.
+ *
+ * For the first task, AWH retrieves the pull coordinate values from the pull struct.
+ * With these, the bias potential and forces are calculated.
+ * The bias force together with the atom forces and virial
+ * are passed on to pull which applies the bias force to the atoms.
+ * This is done at every step.
+ *
+ * Secondly, coordinate values are regularly sampled and kept by AWH.
+ * Convergence of the bias and free energy estimate is achieved by
+ * updating the AWH bias state after a certain number of samples has been collected.
+ *
+ * \note Requires that pull_potential from pull.h has been called first
+ * since AWH needs the current coordinate values (the pull code checks
+ * for this).
+ *
+ * \param[in] mdatoms Atom properties.
+ * \param[in] ePBC Type of periodic boundary conditions.
+ * \param[in] box Box vectors.
+ * \param[in,out] forceWithVirial Force and virial buffers, should cover at least the local atoms.
+ * \param[in] t Time.
+ * \param[in] step The current MD step.
+ * \param[in,out] wallcycle Wallcycle counter, can be nullptr.
+ * \param[in,out] fplog General output file, normally md.log, can be nullptr.
+ * \returns the potential energy for the bias.
+ */
+ real applyBiasForcesAndUpdateBias(int ePBC,
+ const t_mdatoms& mdatoms,
+ const matrix box,
+ gmx::ForceWithVirial* forceWithVirial,
+ double t,
+ int64_t step,
+ gmx_wallcycle* wallcycle,
+ FILE* fplog);
- /*! \brief
- * Update the AWH history in preparation for writing to checkpoint file.
- *
- * Should be called at least on the master rank at checkpoint steps.
- *
- * Should be called with a valid \p awhHistory (is checked).
- *
- * \param[in,out] awhHistory AWH history to set.
- */
- void updateHistory(AwhHistory *awhHistory) const;
+ /*! \brief
+ * Update the AWH history in preparation for writing to checkpoint file.
+ *
+ * Should be called at least on the master rank at checkpoint steps.
+ *
+ * Should be called with a valid \p awhHistory (is checked).
+ *
+ * \param[in,out] awhHistory AWH history to set.
+ */
+ void updateHistory(AwhHistory* awhHistory) const;
- /*! \brief
- * Allocate and initialize an AWH history with the given AWH state.
- *
- * This function should be called at the start of a new simulation
- * at least on the master rank.
- * Note that only constant data will be initialized here.
- * History data is set by \ref Awh::updateHistory.
- *
- * \returns a shared pointer to the AWH history on the rank that does I/O, nullptr otherwise.
- */
-
std::shared_ptr<AwhHistory> initHistoryFromState() const;
+ /*! \brief
+ * Allocate and initialize an AWH history with the given AWH state.
+ *
+ * This function should be called at the start of a new simulation
+ * at least on the master rank.
+ * Note that only constant data will be initialized here.
+ * History data is set by \ref Awh::updateHistory.
+ *
+ * \returns a shared pointer to the AWH history on the rank that does I/O, nullptr otherwise.
+ */
+ std::shared_ptr<AwhHistory> initHistoryFromState() const;
- /*! \brief Restore the AWH state from the given history.
- *
- * Should be called on all ranks (for internal MPI broadcast).
- * Should pass a point to an AwhHistory on the master rank that
- * is compatible with the AWH setup in this simulation. Will throw
- * an exception if it is not compatible.
- *
- * \param[in] awhHistory AWH history to restore from.
- */
- void restoreStateFromHistory(const AwhHistory *awhHistory);
+ /*! \brief Restore the AWH state from the given history.
+ *
+ * Should be called on all ranks (for internal MPI broadcast).
+ * Should pass a point to an AwhHistory on the master rank that
+ * is compatible with the AWH setup in this simulation. Will throw
+ * an exception if it is not compatible.
+ *
+ * \param[in] awhHistory AWH history to restore from.
+ */
+ void restoreStateFromHistory(const AwhHistory* awhHistory);
- /*! \brief Fills the AWH data block of an energy frame with data at certain steps.
- *
- * \param[in] step The current MD step.
- * \param[in,out] fr Energy data frame.
- */
- void writeToEnergyFrame(int64_t step,
- t_enxframe *fr) const;
+ /*! \brief Fills the AWH data block of an energy frame with data at certain steps.
+ *
+ * \param[in] step The current MD step.
+ * \param[in,out] fr Energy data frame.
+ */
+ void writeToEnergyFrame(int64_t step, t_enxframe* fr) const;
- /*! \brief Returns string "AWH" for registering AWH as an external potential provider with the pull module.
- */
- static const char *externalPotentialString();
+ /*! \brief Returns string "AWH" for registering AWH as an external potential provider with the pull module.
+ */
+ static const char* externalPotentialString();
- /*! \brief Register the AWH biased coordinates with pull.
- *
- * This function is public because it needs to be called by grompp
- * (and is otherwise only called by Awh()).
- * Pull requires all external potentials to register themselves
- * before the end of pre-processing and before the first MD step.
- * If this has not happened, pull with throw an error.
- *
- * \param[in] awhParams The AWH parameters.
- * \param[in,out] pull_work Pull struct which AWH will register the bias into.
- */
- static void registerAwhWithPull(const AwhParams &awhParams,
- pull_t *pull_work);
+ /*! \brief Register the AWH biased coordinates with pull.
+ *
+ * This function is public because it needs to be called by grompp
+ * (and is otherwise only called by Awh()).
+ * Pull requires all external potentials to register themselves
+ * before the end of pre-processing and before the first MD step.
+ * If this has not happened, pull with throw an error.
+ *
+ * \param[in] awhParams The AWH parameters.
+ * \param[in,out] pull_work Pull struct which AWH will register the bias into.
+ */
+ static void registerAwhWithPull(const AwhParams& awhParams, pull_t* pull_work);
- private:
- /*! \brief Returns whether we need to write output at the current step.
- *
- * \param[in] step The current MD step.
- */
- bool isOutputStep(int64_t step) const;
+private:
+ /*! \brief Returns whether we need to write output at the current step.
+ *
+ * \param[in] step The current MD step.
+ */
+ bool isOutputStep(int64_t step) const;
- private:
- std::vector<BiasCoupledToSystem> biasCoupledToSystem_; /**< AWH biases and definitions of their coupling to the system. */
- const int64_t seed_; /**< Random seed for MC jumping with umbrella type bias potential. */
- const int nstout_; /**< Interval in steps for writing to energy file. */
- const t_commrec *commRecord_; /**< Pointer to the communication record. */
- const gmx_multisim_t *multiSimRecord_; /**< Handler for multi-simulations. */
- pull_t *pull_; /**< Pointer to the pull working data. */
- double potentialOffset_; /**< The offset of the bias potential which changes due to bias updates. */
+private:
+ std::vector<BiasCoupledToSystem> biasCoupledToSystem_; /**< AWH biases and definitions of their coupling to the system. */
+ const int64_t seed_; /**< Random seed for MC jumping with umbrella type bias potential. */
+ const int nstout_; /**< Interval in steps for writing to energy file. */
+ const t_commrec* commRecord_; /**< Pointer to the communication record. */
+ const gmx_multisim_t* multiSimRecord_; /**< Handler for multi-simulations. */
+ pull_t* pull_; /**< Pointer to the pull working data. */
+ double potentialOffset_; /**< The offset of the bias potential which changes due to bias updates. */
};
/*! \brief Makes an Awh and prepares to use it if the user input
* \returns An initialized Awh module, or nullptr if none was requested.
* \throws InvalidInputError If another active module is not supported.
*/
-std::unique_ptr<Awh>
-prepareAwhModule(FILE *fplog,
- const t_inputrec &inputRecord,
- t_state *stateGlobal,
- const t_commrec *commRecord,
- const gmx_multisim_t *multiSimRecord,
- bool startingFromCheckpoint,
- bool usingShellParticles,
- const std::string &biasInitFilename,
- pull_t *pull_work);
+std::unique_ptr<Awh> prepareAwhModule(FILE* fplog,
+ const t_inputrec& inputRecord,
+ t_state* stateGlobal,
+ const t_commrec* commRecord,
+ const gmx_multisim_t* multiSimRecord,
+ bool startingFromCheckpoint,
+ bool usingShellParticles,
+ const std::string& biasInitFilename,
+ pull_t* pull_work);
-} // namespace gmx
+} // namespace gmx
#endif /* GMX_AWH_H */
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