/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009-2016, The GROMACS development team.
+ * Copyright (c) 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.
* Without the flag, center-of-geometry positions are calculated.
* Does not have any effect if the calculation type is \ref POS_ATOM.
*/
-#define POS_MASS 1
+#define POS_MASS 1
/*! \brief
* Calculate positions for the same atoms in residues/molecules.
*
* Has no effect unless \ref POS_DYNAMIC is set or if the calculation type
* is not \ref POS_RES of \ref POS_MOL.
*/
-#define POS_COMPLMAX 2
+#define POS_COMPLMAX 2
/*! \brief
* Calculate positions for whole residues/molecules.
*
*
* Has no effect unless the calculation type is \ref POS_RES or \ref POS_MOL.
*/
-#define POS_COMPLWHOLE 4
+#define POS_COMPLWHOLE 4
/*! \brief
* Enable handling of changing calculation groups.
*
* Can be used for static calculations as well, but implies a small
* performance penalty.
*/
-#define POS_DYNAMIC 16
+#define POS_DYNAMIC 16
/*! \brief
* Update \c gmx_ana_pos_t::m dynamically for an otherwise static
* calculation.
*
* Has effect only if \ref POS_DYNAMIC is not set.
*/
-#define POS_MASKONLY 32
+#define POS_MASKONLY 32
/*! \brief
* Calculate velocities of the positions.
*/
-#define POS_VELOCITIES 64
+#define POS_VELOCITIES 64
/*! \brief
* Calculate forces on the positions.
*/
-#define POS_FORCES 128
+#define POS_FORCES 128
/*@}*/
/** Specifies the type of positions to be calculated. */
typedef enum
{
- POS_ATOM, /**< Copy atomic coordinates. */
- POS_RES, /**< Calculate center for each residue. */
- POS_MOL, /**< Calculate center for each molecule. */
- POS_ALL, /**< Calculate center for the whole group. */
- POS_ALL_PBC /**< Calculate center for the whole group with PBC. */
+ POS_ATOM, /**< Copy atomic coordinates. */
+ POS_RES, /**< Calculate center for each residue. */
+ POS_MOL, /**< Calculate center for each molecule. */
+ POS_ALL, /**< Calculate center for the whole group. */
+ POS_ALL_PBC /**< Calculate center for the whole group with PBC. */
} e_poscalc_t;
/** Data structure for position calculation. */
*/
class PositionCalculationCollection
{
- public:
- //! Describes what topology information is needed for position calculation.
- enum class RequiredTopologyInfo
- {
- None, //!< No topology is needed.
- Topology, //!< Topology is needed (residue/molecule info).
- TopologyAndMasses //!< Masses are needed.
- };
+public:
+ //! Describes what topology information is needed for position calculation.
+ enum class RequiredTopologyInfo
+ {
+ None, //!< No topology is needed.
+ Topology, //!< Topology is needed (residue/molecule info).
+ TopologyAndMasses //!< Masses are needed.
+ };
- /*! \brief
- * Array of strings acceptable for position calculation type enum.
- *
- * This array contains the acceptable values for typeFromEnum() and
- * createCalculationFromEnum().
- * The array contains a NULL pointer after the last item to indicate
- * the end of the list.
- */
- static const char * const typeEnumValues[];
+ /*! \brief
+ * Array of strings acceptable for position calculation type enum.
+ *
+ * This array contains the acceptable values for typeFromEnum() and
+ * createCalculationFromEnum().
+ * The array contains a NULL pointer after the last item to indicate
+ * the end of the list.
+ */
+ static const char* const typeEnumValues[];
- /*! \brief
- * Converts a string to parameters for createCalculationFromEnum().
- *
- * \param[in] post String (typically an enum argument).
- * Allowed values: 'atom', 'res_com', 'res_cog', 'mol_com', 'mol_cog',
- * or one of the last four prepended by 'whole_', 'part_', or 'dyn_'.
- * \param[out] type \c e_poscalc_t corresponding to \p post.
- * \param[in,out] flags Flags corresponding to \p post.
- * On input, the flags should contain the default flags.
- * On exit, the flags \ref POS_MASS, \ref POS_COMPLMAX and
- * \ref POS_COMPLWHOLE have been set according to \p post
- * (the completion flags are left at the default values if no
- * completion prefix is given).
- * \throws InternalError if post is not recognized.
- *
- * \attention
- * Checking is not complete, and other values than those listed above
- * may be accepted for \p post, but the results are undefined.
- *
- * \see typeEnumValues
- */
- static void typeFromEnum(const char *post, e_poscalc_t *type, int *flags);
- /*! \brief
- * Returns what information is needed for position evaluation.
- *
- * \param[in] post Position type (see typeFromEnum()).
- * \param[in] forces Whether forces are needed.
- * \returns What topology information is required for initializing
- * and/or evaluating the positions.
- */
- static RequiredTopologyInfo requiredTopologyInfoForType(const char *post, bool forces);
+ /*! \brief
+ * Converts a string to parameters for createCalculationFromEnum().
+ *
+ * \param[in] post String (typically an enum argument).
+ * Allowed values: 'atom', 'res_com', 'res_cog', 'mol_com', 'mol_cog',
+ * or one of the last four prepended by 'whole_', 'part_', or 'dyn_'.
+ * \param[out] type \c e_poscalc_t corresponding to \p post.
+ * \param[in,out] flags Flags corresponding to \p post.
+ * On input, the flags should contain the default flags.
+ * On exit, the flags \ref POS_MASS, \ref POS_COMPLMAX and
+ * \ref POS_COMPLWHOLE have been set according to \p post
+ * (the completion flags are left at the default values if no
+ * completion prefix is given).
+ * \throws InternalError if post is not recognized.
+ *
+ * \attention
+ * Checking is not complete, and other values than those listed above
+ * may be accepted for \p post, but the results are undefined.
+ *
+ * \see typeEnumValues
+ */
+ static void typeFromEnum(const char* post, e_poscalc_t* type, int* flags);
+ /*! \brief
+ * Returns what information is needed for position evaluation.
+ *
+ * \param[in] post Position type (see typeFromEnum()).
+ * \param[in] forces Whether forces are needed.
+ * \returns What topology information is required for initializing
+ * and/or evaluating the positions.
+ */
+ static RequiredTopologyInfo requiredTopologyInfoForType(const char* post, bool forces);
- /*! \brief
- * Creates a new position calculation collection object.
- *
- * \throws std::bad_alloc if out of memory.
- */
- PositionCalculationCollection();
- /*! \brief
- * Destroys a position calculation collection and its calculations.
- *
- * Any calculations in the collection are also freed, even if
- * references to them are left.
- */
- ~PositionCalculationCollection();
+ /*! \brief
+ * Creates a new position calculation collection object.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ PositionCalculationCollection();
+ /*! \brief
+ * Destroys a position calculation collection and its calculations.
+ *
+ * Any calculations in the collection are also freed, even if
+ * references to them are left.
+ */
+ ~PositionCalculationCollection();
- /*! \brief
- * Sets the topology used for the calculations.
- *
- * \param[in] top Topology data structure.
- *
- * This function should be called to set the topology before using
- * gmx_ana_poscalc_set_maxindex() for any calculation that requires
- * topology information.
- *
- * Does not throw.
- */
- void setTopology(const gmx_mtop_t *top);
- /*! \brief
- * Prints information about calculations.
- *
- * \param[in] fp File handle to receive the output.
- *
- * The output is very technical, making this function mainly useful for
- * debugging purposes.
- *
- * Does not throw.
- */
- void printTree(FILE *fp) const;
+ /*! \brief
+ * Sets the topology used for the calculations.
+ *
+ * \param[in] top Topology data structure.
+ *
+ * This function should be called to set the topology before using
+ * gmx_ana_poscalc_set_maxindex() for any calculation that requires
+ * topology information.
+ *
+ * Does not throw.
+ */
+ void setTopology(const gmx_mtop_t* top);
+ /*! \brief
+ * Prints information about calculations.
+ *
+ * \param[in] fp File handle to receive the output.
+ *
+ * The output is very technical, making this function mainly useful for
+ * debugging purposes.
+ *
+ * Does not throw.
+ */
+ void printTree(FILE* fp) const;
- /*! \brief
- * Creates a new position calculation.
- *
- * \param[in] type Type of calculation.
- * \param[in] flags Flags for setting calculation options
- * (see \ref poscalc_flags "documentation of the flags").
- *
- * Does not throw currently, but may throw std::bad_alloc in the
- * future.
- */
- gmx_ana_poscalc_t *createCalculation(e_poscalc_t type, int flags);
- /*! \brief
- * Creates a new position calculation based on an enum value.
- *
- * \param[in] post One of the strings acceptable for
- * typeFromEnum().
- * \param[in] flags Flags for setting calculation options
- * (see \ref poscalc_flags "documentation of the flags").
- * \throws InternalError if post is not recognized.
- *
- * This is a convenience wrapper for createCalculation().
- * \p flags sets the default calculation options if not overridden by
- * \p post; see typeFromEnum().
- *
- * May also throw std::bad_alloc in the future.
- *
- * \see createCalculation(), typeFromEnum()
- */
- gmx_ana_poscalc_t *createCalculationFromEnum(const char *post, int flags);
+ /*! \brief
+ * Creates a new position calculation.
+ *
+ * \param[in] type Type of calculation.
+ * \param[in] flags Flags for setting calculation options
+ * (see \ref poscalc_flags "documentation of the flags").
+ *
+ * Does not throw currently, but may throw std::bad_alloc in the
+ * future.
+ */
+ gmx_ana_poscalc_t* createCalculation(e_poscalc_t type, int flags);
+ /*! \brief
+ * Creates a new position calculation based on an enum value.
+ *
+ * \param[in] post One of the strings acceptable for
+ * typeFromEnum().
+ * \param[in] flags Flags for setting calculation options
+ * (see \ref poscalc_flags "documentation of the flags").
+ * \throws InternalError if post is not recognized.
+ *
+ * This is a convenience wrapper for createCalculation().
+ * \p flags sets the default calculation options if not overridden by
+ * \p post; see typeFromEnum().
+ *
+ * May also throw std::bad_alloc in the future.
+ *
+ * \see createCalculation(), typeFromEnum()
+ */
+ gmx_ana_poscalc_t* createCalculationFromEnum(const char* post, int flags);
- /*! \brief
- * Computes the atoms required to evaluate this collection.
- *
- * \param[out] out Maximal group of atoms required to evaluate the
- * positions.
- *
- * Does not throw.
- */
- void getRequiredAtoms(gmx_ana_index_t *out) const;
+ /*! \brief
+ * Computes the atoms required to evaluate this collection.
+ *
+ * \param[out] out Maximal group of atoms required to evaluate the
+ * positions.
+ *
+ * Does not throw.
+ */
+ void getRequiredAtoms(gmx_ana_index_t* out) const;
- /*! \brief
- * Initializes evaluation for a position calculation collection.
- *
- * This function does some final initialization of the data structures
- * in the collection to prepare them for evaluation.
- * After this function has been called, it is no longer possible to add
- * new calculations to the collection.
- *
- * Multiple calls to the function are ignored.
- *
- * Does not throw currently, but may throw std::bad_alloc in the
- * future.
- */
- void initEvaluation();
- /*! \brief
- * Initializes a position calculation collection for a new frame.
- *
- * \param[in] fr Frame to initialize evaluation for.
- *
- * Should be called for each frame before calling
- * gmx_ana_poscalc_update().
- *
- * This function calls initEvaluation() automatically if it has not
- * been called earlier.
- *
- * Does not currently throw, but may throw std::bad_alloc in the
- * future.
- */
- void initFrame(const t_trxframe *fr);
+ /*! \brief
+ * Initializes evaluation for a position calculation collection.
+ *
+ * This function does some final initialization of the data structures
+ * in the collection to prepare them for evaluation.
+ * After this function has been called, it is no longer possible to add
+ * new calculations to the collection.
+ *
+ * Multiple calls to the function are ignored.
+ *
+ * Does not throw currently, but may throw std::bad_alloc in the
+ * future.
+ */
+ void initEvaluation();
+ /*! \brief
+ * Initializes a position calculation collection for a new frame.
+ *
+ * \param[in] fr Frame to initialize evaluation for.
+ *
+ * Should be called for each frame before calling
+ * gmx_ana_poscalc_update().
+ *
+ * This function calls initEvaluation() automatically if it has not
+ * been called earlier.
+ *
+ * Does not currently throw, but may throw std::bad_alloc in the
+ * future.
+ */
+ void initFrame(const t_trxframe* fr);
- private:
- class Impl;
+private:
+ class Impl;
- PrivateImplPointer<Impl> impl_;
+ PrivateImplPointer<Impl> impl_;
- /*! \brief
- * Needed to access the implementation class from the C code.
- */
- friend struct ::gmx_ana_poscalc_t;
+ /*! \brief
+ * Needed to access the implementation class from the C code.
+ */
+ friend struct ::gmx_ana_poscalc_t;
};
} // namespace gmx
/** Sets the flags for position calculation. */
-void
-gmx_ana_poscalc_set_flags(gmx_ana_poscalc_t *pc, int flags);
+void gmx_ana_poscalc_set_flags(gmx_ana_poscalc_t* pc, int flags);
/** Sets the maximum possible input index group for position calculation. */
-void
-gmx_ana_poscalc_set_maxindex(gmx_ana_poscalc_t *pc, gmx_ana_index_t *g);
+void gmx_ana_poscalc_set_maxindex(gmx_ana_poscalc_t* pc, gmx_ana_index_t* g);
/** Initializes positions for position calculation output. */
-void
-gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p);
+void gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t* pc, gmx_ana_pos_t* p);
/** Frees the memory allocated for position calculation. */
-void
-gmx_ana_poscalc_free(gmx_ana_poscalc_t *pc);
+void gmx_ana_poscalc_free(gmx_ana_poscalc_t* pc);
/*! \brief
* Returns true if the position calculation requires topology information.
*
* and/or evaluation.
*/
gmx::PositionCalculationCollection::RequiredTopologyInfo
-gmx_ana_poscalc_required_topology_info(gmx_ana_poscalc_t *pc);
+gmx_ana_poscalc_required_topology_info(gmx_ana_poscalc_t* pc);
/** Updates a single COM/COG structure for a frame. */
-void
-gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc,
- gmx_ana_pos_t *p, gmx_ana_index_t *g,
- t_trxframe *fr, const t_pbc *pbc);
+void gmx_ana_poscalc_update(gmx_ana_poscalc_t* pc,
+ gmx_ana_pos_t* p,
+ gmx_ana_index_t* g,
+ t_trxframe* fr,
+ const t_pbc* pbc);
#endif
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