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37 * API for structured and optimized calculation of positions.
39 * This header declares an API for calculating positions in an automated way,
40 * for internal use by the selection engine. This is useful in particular with
41 * dynamic selections, because the same COM/COG positions may be needed in
42 * several contexts. The API makes it possible to optimize the evaluation such
43 * that any heavy calculation is only done once, and the results just copied if
44 * needed more than once. The functions also provide a convenient interface
45 * for keeping the whole \c gmx_ana_pos_t structure up-to-date.
47 * The API is documented in more detail in gmx::PositionCalculationCollection.
49 * \author Teemu Murtola <teemu.murtola@gmail.com>
50 * \ingroup module_selection
52 #ifndef GMX_SELECTION_POSCALC_H
53 #define GMX_SELECTION_POSCALC_H
57 #include "../utility/common.h"
59 /*! \name Flags for position calculation.
60 * \anchor poscalc_flags
66 * If this flag is set, the positions will be calculated using mass weighting,
67 * i.e., one gets center-of-mass positions.
68 * Without the flag, center-of-geometry positions are calculated.
69 * Does not have any effect if the calculation type is \ref POS_ATOM.
73 * Calculate positions for the same atoms in residues/molecules.
75 * If this flag is set, the positions are always calculated using the same
76 * atoms for each residue/molecule, even if the evaluation group contains only
77 * some of the atoms for some frames.
78 * The group passed to gmx_ana_poscalc_set_maxindex() is used to determine
79 * the atoms to use for the calculation.
81 * Has no effect unless \ref POS_DYNAMIC is set or if the calculation type
82 * is not \ref POS_RES of \ref POS_MOL.
84 #define POS_COMPLMAX 2
86 * Calculate positions for whole residues/molecules.
88 * If this flag is set, the positions will be calculated for whole
89 * residues/molecules, even if the group contains only some of the atoms in
90 * the residue/molecule.
92 * Has no effect unless the calculation type is \ref POS_RES or \ref POS_MOL.
94 #define POS_COMPLWHOLE 4
96 * Enable handling of changing calculation groups.
98 * Can be used for static calculations as well, but implies a small
99 * performance penalty.
101 #define POS_DYNAMIC 16
103 * Update \c gmx_ana_pos_t::m dynamically for an otherwise static
106 * Has effect only if \ref POS_DYNAMIC is not set.
108 #define POS_MASKONLY 32
110 * Calculate velocities of the positions.
112 #define POS_VELOCITIES 64
114 * Calculate forces on the positions.
116 #define POS_FORCES 128
119 /** Specifies the type of positions to be calculated. */
122 POS_ATOM, /**< Copy atomic coordinates. */
123 POS_RES, /**< Calculate center for each residue. */
124 POS_MOL, /**< Calculate center for each molecule. */
125 POS_ALL, /**< Calculate center for the whole group. */
126 POS_ALL_PBC /**< Calculate center for the whole group with PBC. */
129 /** Data structure for position calculation. */
130 struct gmx_ana_poscalc_t;
132 struct gmx_ana_index_t;
133 struct gmx_ana_pos_t;
143 * Collection of \c gmx_ana_poscalc_t structures for the same topology.
145 * Calculations within one collection share the same topology, and they are
146 * optimized. Calculations in different collections do not interact.
147 * The topology for a collection can be set with setTopology().
148 * This needs to be done before calling gmx_ana_poscalc_set_maxindex() for
149 * any calculation in the collection, unless that calculation does not
150 * require topology information.
152 * A new calculation is created with createCalculation().
153 * If flags need to be adjusted later, gmx_ana_poscalc_set_flags() can be
155 * After the flags are final, the largest possible index group for which the
156 * positions are needed has to be set with gmx_ana_poscalc_set_maxindex().
157 * setTopology() should have been called before this function is called.
158 * After the above calls, gmx_ana_poscalc_init_pos() can be used to initialize
159 * output to a \c gmx_ana_pos_t structure. Several different structures can be
160 * initialized for the same calculation; the only requirement is that the
161 * structure passed later to gmx_ana_poscalc_update() has been initialized
163 * The memory allocated for a calculation can be freed with
164 * gmx_ana_poscalc_free().
166 * The position evaluation is simple: initFrame() should be
167 * called once for each frame, and gmx_ana_poscalc_update() can then be called
168 * for each calculation that is needed for that frame.
170 * It is also possible to initialize the calculations based on a type provided
172 * The possible strings are listed in \ref typeEnumValues, and the string can
173 * be converted to the parameters for createCalculation() using typeFromEnum().
174 * createCalculationFromEnum() is also provided for convenience.
176 * \ingroup module_selection
178 class PositionCalculationCollection
182 * Array of strings acceptable for position calculation type enum.
184 * This array contains the acceptable values for typeFromEnum() and
185 * createCalculationFromEnum().
186 * The array contains a NULL pointer after the last item to indicate
187 * the end of the list.
189 static const char * const typeEnumValues[];
192 * Converts a string to parameters for createCalculationFromEnum().
194 * \param[in] post String (typically an enum argument).
195 * Allowed values: 'atom', 'res_com', 'res_cog', 'mol_com', 'mol_cog',
196 * or one of the last four prepended by 'whole_', 'part_', or 'dyn_'.
197 * \param[out] type \c e_poscalc_t corresponding to \p post.
198 * \param[in,out] flags Flags corresponding to \p post.
199 * On input, the flags should contain the default flags.
200 * On exit, the flags \ref POS_MASS, \ref POS_COMPLMAX and
201 * \ref POS_COMPLWHOLE have been set according to \p post
202 * (the completion flags are left at the default values if no
203 * completion prefix is given).
204 * \throws InternalError if post is not recognized.
207 * Checking is not complete, and other values than those listed above
208 * may be accepted for \p post, but the results are undefined.
210 * \see typeEnumValues
212 static void typeFromEnum(const char *post, e_poscalc_t *type, int *flags);
215 * Creates a new position calculation collection object.
217 * \throws std::bad_alloc if out of memory.
219 PositionCalculationCollection();
221 * Destroys a position calculation collection and its calculations.
223 * Any calculations in the collection are also freed, even if
224 * references to them are left.
226 ~PositionCalculationCollection();
229 * Sets the topology used for the calculations.
231 * \param[in] top Topology data structure.
233 * This function should be called to set the topology before using
234 * gmx_ana_poscalc_set_maxindex() for any calculation that requires
235 * topology information.
239 void setTopology(t_topology *top);
241 * Prints information about calculations.
243 * \param[in] fp File handle to receive the output.
245 * The output is very technical, making this function mainly useful for
246 * debugging purposes.
250 void printTree(FILE *fp) const;
253 * Creates a new position calculation.
255 * \param[in] type Type of calculation.
256 * \param[in] flags Flags for setting calculation options
257 * (see \ref poscalc_flags "documentation of the flags").
259 * Does not throw currently, but may throw std::bad_alloc in the
262 gmx_ana_poscalc_t *createCalculation(e_poscalc_t type, int flags);
264 * Creates a new position calculation based on an enum value.
266 * \param[in] post One of the strings acceptable for
268 * \param[in] flags Flags for setting calculation options
269 * (see \ref poscalc_flags "documentation of the flags").
270 * \throws InternalError if post is not recognized.
272 * This is a convenience wrapper for createCalculation().
273 * \p flags sets the default calculation options if not overridden by
274 * \p post; see typeFromEnum().
276 * May also throw std::bad_alloc in the future.
278 * \see createCalculation(), typeFromEnum()
280 gmx_ana_poscalc_t *createCalculationFromEnum(const char *post, int flags);
283 * Computes the highest atom index required to evaluate this collection.
287 int getHighestRequiredAtomIndex() const;
290 * Initializes evaluation for a position calculation collection.
292 * This function does some final initialization of the data structures
293 * in the collection to prepare them for evaluation.
294 * After this function has been called, it is no longer possible to add
295 * new calculations to the collection.
297 * Multiple calls to the function are ignored.
299 * Does not throw currently, but may throw std::bad_alloc in the
302 void initEvaluation();
304 * Initializes a position calculation collection for a new frame.
306 * Clears the evaluation flag for all calculations.
307 * Should be called for each frame before calling
308 * gmx_ana_poscalc_update().
310 * This function calls initEvaluation() automatically if it has not
311 * been called earlier.
313 * Does not throw, but may throw if initEvaluation() is changed to
321 PrivateImplPointer<Impl> impl_;
324 * Needed to access the implementation class from the C code.
326 friend struct ::gmx_ana_poscalc_t;
331 /** Sets the flags for position calculation. */
333 gmx_ana_poscalc_set_flags(gmx_ana_poscalc_t *pc, int flags);
334 /** Sets the maximum possible input index group for position calculation. */
336 gmx_ana_poscalc_set_maxindex(gmx_ana_poscalc_t *pc, gmx_ana_index_t *g);
337 /** Initializes positions for position calculation output. */
339 gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p);
340 /** Frees the memory allocated for position calculation. */
342 gmx_ana_poscalc_free(gmx_ana_poscalc_t *pc);
343 /** Returns true if the position calculation requires topology information. */
345 gmx_ana_poscalc_requires_top(gmx_ana_poscalc_t *pc);
347 /** Updates a single COM/COG structure for a frame. */
349 gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc,
350 gmx_ana_pos_t *p, gmx_ana_index_t *g,
351 t_trxframe *fr, t_pbc *pbc);