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38 * API for structured and optimized calculation of positions.
40 * This header declares an API for calculating positions in an automated way,
41 * for internal use by the selection engine. This is useful in particular with
42 * dynamic selections, because the same COM/COG positions may be needed in
43 * several contexts. The API makes it possible to optimize the evaluation such
44 * that any heavy calculation is only done once, and the results just copied if
45 * needed more than once. The functions also provide a convenient interface
46 * for keeping the whole \c gmx_ana_pos_t structure up-to-date.
48 * The API is documented in more detail in gmx::PositionCalculationCollection.
50 * \author Teemu Murtola <teemu.murtola@gmail.com>
51 * \ingroup module_selection
53 #ifndef GMX_SELECTION_POSCALC_H
54 #define GMX_SELECTION_POSCALC_H
58 #include "gromacs/utility/classhelpers.h"
60 /*! \name Flags for position calculation.
61 * \anchor poscalc_flags
67 * If this flag is set, the positions will be calculated using mass weighting,
68 * i.e., one gets center-of-mass positions.
69 * Without the flag, center-of-geometry positions are calculated.
70 * Does not have any effect if the calculation type is \ref POS_ATOM.
74 * Calculate positions for the same atoms in residues/molecules.
76 * If this flag is set, the positions are always calculated using the same
77 * atoms for each residue/molecule, even if the evaluation group contains only
78 * some of the atoms for some frames.
79 * The group passed to gmx_ana_poscalc_set_maxindex() is used to determine
80 * the atoms to use for the calculation.
82 * Has no effect unless \ref POS_DYNAMIC is set or if the calculation type
83 * is not \ref POS_RES of \ref POS_MOL.
85 #define POS_COMPLMAX 2
87 * Calculate positions for whole residues/molecules.
89 * If this flag is set, the positions will be calculated for whole
90 * residues/molecules, even if the group contains only some of the atoms in
91 * the residue/molecule.
93 * Has no effect unless the calculation type is \ref POS_RES or \ref POS_MOL.
95 #define POS_COMPLWHOLE 4
97 * Enable handling of changing calculation groups.
99 * Can be used for static calculations as well, but implies a small
100 * performance penalty.
102 #define POS_DYNAMIC 16
104 * Update \c gmx_ana_pos_t::m dynamically for an otherwise static
107 * Has effect only if \ref POS_DYNAMIC is not set.
109 #define POS_MASKONLY 32
111 * Calculate velocities of the positions.
113 #define POS_VELOCITIES 64
115 * Calculate forces on the positions.
117 #define POS_FORCES 128
120 /** Specifies the type of positions to be calculated. */
123 POS_ATOM, /**< Copy atomic coordinates. */
124 POS_RES, /**< Calculate center for each residue. */
125 POS_MOL, /**< Calculate center for each molecule. */
126 POS_ALL, /**< Calculate center for the whole group. */
127 POS_ALL_PBC /**< Calculate center for the whole group with PBC. */
130 /** Data structure for position calculation. */
131 struct gmx_ana_poscalc_t;
133 struct gmx_ana_index_t;
134 struct gmx_ana_pos_t;
144 * Collection of \c gmx_ana_poscalc_t structures for the same topology.
146 * Calculations within one collection share the same topology, and they are
147 * optimized. Calculations in different collections do not interact.
148 * The topology for a collection can be set with setTopology().
149 * This needs to be done before calling gmx_ana_poscalc_set_maxindex() for
150 * any calculation in the collection, unless that calculation does not
151 * require topology information.
153 * A new calculation is created with createCalculation().
154 * If flags need to be adjusted later, gmx_ana_poscalc_set_flags() can be
156 * After the flags are final, the largest possible index group for which the
157 * positions are needed has to be set with gmx_ana_poscalc_set_maxindex().
158 * setTopology() should have been called before this function is called.
159 * After the above calls, gmx_ana_poscalc_init_pos() can be used to initialize
160 * output to a \c gmx_ana_pos_t structure. Several different structures can be
161 * initialized for the same calculation; the only requirement is that the
162 * structure passed later to gmx_ana_poscalc_update() has been initialized
164 * The memory allocated for a calculation can be freed with
165 * gmx_ana_poscalc_free().
167 * The position evaluation is simple: initFrame() should be
168 * called once for each frame, and gmx_ana_poscalc_update() can then be called
169 * for each calculation that is needed for that frame.
171 * It is also possible to initialize the calculations based on a type provided
173 * The possible strings are listed in \ref typeEnumValues, and the string can
174 * be converted to the parameters for createCalculation() using typeFromEnum().
175 * createCalculationFromEnum() is also provided for convenience.
177 * \ingroup module_selection
179 class PositionCalculationCollection
182 //! Describes what topology information is needed for position calculation.
183 enum class RequiredTopologyInfo
185 None, //!< No topology is needed.
186 Topology, //!< Topology is needed (residue/molecule info).
187 TopologyAndMasses //!< Masses are needed.
191 * Array of strings acceptable for position calculation type enum.
193 * This array contains the acceptable values for typeFromEnum() and
194 * createCalculationFromEnum().
195 * The array contains a NULL pointer after the last item to indicate
196 * the end of the list.
198 static const char* const typeEnumValues[];
201 * Converts a string to parameters for createCalculationFromEnum().
203 * \param[in] post String (typically an enum argument).
204 * Allowed values: 'atom', 'res_com', 'res_cog', 'mol_com', 'mol_cog',
205 * or one of the last four prepended by 'whole_', 'part_', or 'dyn_'.
206 * \param[out] type \c e_poscalc_t corresponding to \p post.
207 * \param[in,out] flags Flags corresponding to \p post.
208 * On input, the flags should contain the default flags.
209 * On exit, the flags \ref POS_MASS, \ref POS_COMPLMAX and
210 * \ref POS_COMPLWHOLE have been set according to \p post
211 * (the completion flags are left at the default values if no
212 * completion prefix is given).
213 * \throws InternalError if post is not recognized.
216 * Checking is not complete, and other values than those listed above
217 * may be accepted for \p post, but the results are undefined.
219 * \see typeEnumValues
221 static void typeFromEnum(const char* post, e_poscalc_t* type, int* flags);
223 * Returns what information is needed for position evaluation.
225 * \param[in] post Position type (see typeFromEnum()).
226 * \param[in] forces Whether forces are needed.
227 * \returns What topology information is required for initializing
228 * and/or evaluating the positions.
230 static RequiredTopologyInfo requiredTopologyInfoForType(const char* post, bool forces);
233 * Creates a new position calculation collection object.
235 * \throws std::bad_alloc if out of memory.
237 PositionCalculationCollection();
239 * Destroys a position calculation collection and its calculations.
241 * Any calculations in the collection are also freed, even if
242 * references to them are left.
244 ~PositionCalculationCollection();
247 * Sets the topology used for the calculations.
249 * \param[in] top Topology data structure.
251 * This function should be called to set the topology before using
252 * gmx_ana_poscalc_set_maxindex() for any calculation that requires
253 * topology information.
257 void setTopology(const gmx_mtop_t* top);
259 * Prints information about calculations.
261 * \param[in] fp File handle to receive the output.
263 * The output is very technical, making this function mainly useful for
264 * debugging purposes.
268 void printTree(FILE* fp) const;
271 * Creates a new position calculation.
273 * \param[in] type Type of calculation.
274 * \param[in] flags Flags for setting calculation options
275 * (see \ref poscalc_flags "documentation of the flags").
277 * Does not throw currently, but may throw std::bad_alloc in the
280 gmx_ana_poscalc_t* createCalculation(e_poscalc_t type, int flags);
282 * Creates a new position calculation based on an enum value.
284 * \param[in] post One of the strings acceptable for
286 * \param[in] flags Flags for setting calculation options
287 * (see \ref poscalc_flags "documentation of the flags").
288 * \throws InternalError if post is not recognized.
290 * This is a convenience wrapper for createCalculation().
291 * \p flags sets the default calculation options if not overridden by
292 * \p post; see typeFromEnum().
294 * May also throw std::bad_alloc in the future.
296 * \see createCalculation(), typeFromEnum()
298 gmx_ana_poscalc_t* createCalculationFromEnum(const char* post, int flags);
301 * Computes the atoms required to evaluate this collection.
303 * \param[out] out Maximal group of atoms required to evaluate the
308 void getRequiredAtoms(gmx_ana_index_t* out) const;
311 * Initializes evaluation for a position calculation collection.
313 * This function does some final initialization of the data structures
314 * in the collection to prepare them for evaluation.
315 * After this function has been called, it is no longer possible to add
316 * new calculations to the collection.
318 * Multiple calls to the function are ignored.
320 * Does not throw currently, but may throw std::bad_alloc in the
323 void initEvaluation();
325 * Initializes a position calculation collection for a new frame.
327 * \param[in] fr Frame to initialize evaluation for.
329 * Should be called for each frame before calling
330 * gmx_ana_poscalc_update().
332 * This function calls initEvaluation() automatically if it has not
333 * been called earlier.
335 * Does not currently throw, but may throw std::bad_alloc in the
338 void initFrame(const t_trxframe* fr);
343 PrivateImplPointer<Impl> impl_;
346 * Needed to access the implementation class from the C code.
348 friend struct ::gmx_ana_poscalc_t;
353 /** Sets the flags for position calculation. */
354 void gmx_ana_poscalc_set_flags(gmx_ana_poscalc_t* pc, int flags);
355 /** Sets the maximum possible input index group for position calculation. */
356 void gmx_ana_poscalc_set_maxindex(gmx_ana_poscalc_t* pc, gmx_ana_index_t* g);
357 /** Initializes positions for position calculation output. */
358 void gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t* pc, gmx_ana_pos_t* p);
359 /** Frees the memory allocated for position calculation. */
360 void gmx_ana_poscalc_free(gmx_ana_poscalc_t* pc);
362 * Returns true if the position calculation requires topology information.
364 * \param[in] pc Position calculation data to query.
365 * \returns Which topology information \p pc requires for initialization
368 gmx::PositionCalculationCollection::RequiredTopologyInfo
369 gmx_ana_poscalc_required_topology_info(gmx_ana_poscalc_t* pc);
371 /** Updates a single COM/COG structure for a frame. */
372 void gmx_ana_poscalc_update(gmx_ana_poscalc_t* pc,