/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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.
struct gmx_mtop_t;
struct t_inputrec;
struct gmx_tng_trajectory;
-typedef struct gmx_tng_trajectory *gmx_tng_trajectory_t;
+typedef struct gmx_tng_trajectory* gmx_tng_trajectory_t;
struct t_trxframe;
/*! \brief Open a TNG trajectory file
*
* Handles all I/O errors internally via fatal error
*/
-void gmx_tng_open(const char *filename,
- char mode,
- gmx_tng_trajectory_t *tng_data_p);
+void gmx_tng_open(const char* filename, char mode, gmx_tng_trajectory_t* tng_data_p);
/*! \brief Finish writing a TNG trajectory file */
-void gmx_tng_close(gmx_tng_trajectory_t *tng);
+void gmx_tng_close(gmx_tng_trajectory_t* tng);
/*!\brief Add molecular topology information to TNG output (if
* available)
* \param tng Valid handle to a TNG trajectory
* \param mtop Pointer to a topology (can be NULL)
*/
-void gmx_tng_add_mtop(gmx_tng_trajectory_t tng,
- const gmx_mtop_t *mtop);
+void gmx_tng_add_mtop(gmx_tng_trajectory_t tng, const gmx_mtop_t* mtop);
/*! \brief Do all TNG preparation for full-precision whole-system
* trajectory writing during MD simulations.
* \param mtop Global topology
* \param ir Input settings (for writing frequencies)
*/
-void gmx_tng_prepare_md_writing(gmx_tng_trajectory_t tng,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir);
+void gmx_tng_prepare_md_writing(gmx_tng_trajectory_t tng, const gmx_mtop_t* mtop, const t_inputrec* ir);
/*! \brief Set the default compression precision for TNG writing
*
* \param tng Valid handle to a TNG trajectory
* \param prec GROMACS-style precision setting (i.e. 1000 for 3 digits of precision) */
-void gmx_tng_set_compression_precision(gmx_tng_trajectory_t tng,
- real prec);
+void gmx_tng_set_compression_precision(gmx_tng_trajectory_t tng, real prec);
/*! \brief Do all TNG preparation for low-precision selection-based
* trajectory writing during MD simulations.
* \param mtop Global topology
* \param ir Input settings (for writing frequencies)
*/
-void gmx_tng_prepare_low_prec_writing(gmx_tng_trajectory_t tng,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir);
+void gmx_tng_prepare_low_prec_writing(gmx_tng_trajectory_t tng, const gmx_mtop_t* mtop, const t_inputrec* ir);
/*! \brief Write a frame to a TNG file
*
int64_t step,
real elapsedPicoSeconds,
real lambda,
- const rvec *box,
+ const rvec* box,
int nAtoms,
- const rvec *x,
- const rvec *v,
- const rvec *f);
+ const rvec* x,
+ const rvec* v,
+ const rvec* f);
/*! \brief Write the current frame set to disk. Perform compression
* etc.
float gmx_tng_get_time_of_final_frame(gmx_tng_trajectory_t tng);
/*! \brief Prepare to write TNG output from trajectory conversion tools */
-void gmx_prepare_tng_writing(const char *filename,
+void gmx_prepare_tng_writing(const char* filename,
char mode,
- gmx_tng_trajectory_t *in,
- gmx_tng_trajectory_t *out,
+ gmx_tng_trajectory_t* in,
+ gmx_tng_trajectory_t* out,
int nAtoms,
- const struct gmx_mtop_t *mtop,
+ const struct gmx_mtop_t* mtop,
gmx::ArrayRef<const int> index,
- const char *indexGroupName);
+ const char* indexGroupName);
/*! \brief Write a trxframe to a TNG file
*
* parameter natoms supports writing an index-group subset of the
* atoms.
*/
-void gmx_write_tng_from_trxframe(gmx_tng_trajectory_t output,
- const t_trxframe *frame,
- int natoms);
+void gmx_write_tng_from_trxframe(gmx_tng_trajectory_t output, const t_trxframe* frame, int natoms);
/*! \brief Creates a molecule containing only the indexed atoms and sets
* the number of all other molecules to 0. Works similar to a
* selection group. */
-void gmx_tng_setup_atom_subgroup(gmx_tng_trajectory_t tng,
- gmx::ArrayRef<const int> ind,
- const char *name);
+void gmx_tng_setup_atom_subgroup(gmx_tng_trajectory_t tng, gmx::ArrayRef<const int> ind, const char* name);
/*! \brief Read the first/next TNG frame. */
-gmx_bool gmx_read_next_tng_frame(gmx_tng_trajectory_t input,
- struct t_trxframe *fr,
- int64_t *requestedIds,
- int numRequestedIds);
+gmx_bool gmx_read_next_tng_frame(gmx_tng_trajectory_t input,
+ struct t_trxframe* fr,
+ int64_t* requestedIds,
+ int numRequestedIds);
/*! \brief Print the molecule system to stream */
-void gmx_print_tng_molecule_system(gmx_tng_trajectory_t input,
- FILE *stream);
+void gmx_print_tng_molecule_system(gmx_tng_trajectory_t input, FILE* stream);
/*! \brief Get a list of block IDs present in the next frame with data. */
gmx_bool gmx_get_tng_data_block_types_of_next_frame(gmx_tng_trajectory_t input,
int frame,
int nRequestedIds,
- int64_t *requestedIds,
- int64_t *nextFrame,
- int64_t *nBlocks,
- int64_t **blockIds);
+ int64_t* requestedIds,
+ int64_t* nextFrame,
+ int64_t* nBlocks,
+ int64_t** blockIds);
/*! \brief Get data of the next frame with data from the data block
* with the specified block ID. */
gmx_bool gmx_get_tng_data_next_frame_of_block_type(gmx_tng_trajectory_t input,
int64_t blockId,
- real **values,
- int64_t *frameNumber,
- double *frameTime,
- int64_t *nValuesPerFrame,
- int64_t *nAtoms,
- real *prec,
- char *name,
+ real** values,
+ int64_t* frameNumber,
+ double* frameTime,
+ int64_t* nValuesPerFrame,
+ int64_t* nAtoms,
+ real* prec,
+ char* name,
int maxLen,
- gmx_bool *bOK);
+ gmx_bool* bOK);
/*! \brief Get the output interval of box size.
*
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