*
* \author Viveca Lindahl
* \author Berk Hess <hess@kth.se>
+ * \author Magnus Lundborg
*/
/*! \libinternal \file
namespace gmx
{
+template<typename>
+class ArrayRef;
struct AwhHistory;
struct AwhParams;
class Bias;
* 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.
+ * \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.
+ * \param[in] numLambdaStates The number of free energy lambda states.
+ * \param[in] lambdaState The initial free energy lambda state of the system.
+ * \throws InvalidInputError If there is user input (or combinations thereof) that is not allowed.
*/
Awh(FILE* fplog,
const t_inputrec& inputRecord,
const gmx_multisim_t* multiSimRecord,
const AwhParams& awhParams,
const std::string& biasInitFilename,
- pull_t* pull_work);
+ pull_t* pull_work,
+ int numLambdaStates,
+ int lambdaState);
~Awh();
* since AWH needs the current coordinate values (the pull code checks
* for this).
*
- * \param[in] masses Atoms masses.
* \param[in] pbcType Type of periodic boundary conditions.
+ * \param[in] masses Atoms masses.
+ * \param[in] neighborLambdaEnergies An array containing the energy of the system
+ * in neighboring lambdas. The array is of length numLambdas+1, where numLambdas is
+ * the number of free energy lambda states. Element 0 in the array is the energy
+ * of the current state and elements 1..numLambdas contain the energy of the system in the
+ * neighboring lambda states (also including the current state). When there are no free
+ * energy lambda state dimensions this can be empty.
+ * \param[in] neighborLambdaDhdl An array containing the dHdL at the neighboring lambda
+ * points. The array is of length numLambdas+1, where numLambdas is the number of free
+ * energy lambda states. Element 0 in the array is the dHdL
+ * of the current state and elements 1..numLambdas contain the dHdL of the system in the
+ * neighboring lambda states (also including the current state). When there are no free
+ * energy lambda state dimensions this can be empty.
* \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,out] fplog General output file, normally md.log, can be nullptr.
* \returns the potential energy for the bias.
*/
- real applyBiasForcesAndUpdateBias(PbcType pbcType,
- const real* masses,
- const matrix box,
- gmx::ForceWithVirial* forceWithVirial,
- double t,
- int64_t step,
- gmx_wallcycle* wallcycle,
- FILE* fplog);
+ real applyBiasForcesAndUpdateBias(PbcType pbcType,
+ const real* masses,
+ ArrayRef<const double> neighborLambdaEnergies,
+ ArrayRef<const double> neighborLambdaDhdl,
+ 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.
*/
static void registerAwhWithPull(const AwhParams& awhParams, pull_t* pull_work);
+ /*! \brief Get the current free energy lambda state.
+ * \returns The value of lambdaState_.
+ */
+ int fepLambdaState() const { return fepLambdaState_; }
+
+ /*! \brief Returns if foreign energy differences are required during this step.
+ * \param[in] step The current MD step.
+ */
+ bool needForeignEnergyDifferences(int64_t step) const;
+
private:
/*! \brief Returns whether we need to write output at the current step.
*
*/
bool isOutputStep(int64_t step) const;
+ /*! \brief Returns true if AWH has a bias with a free energy lambda state dimension at all.
+ */
+ bool hasFepLambdaDimension() 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 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. */
+ const int numFepLambdaStates_; /**< The number of free energy lambda states of the system. */
+ int fepLambdaState_; /**< The current free energy lambda state. */
};
/*! \brief Makes an Awh and prepares to use it if the user input
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff