diff options
32 files changed, 732 insertions, 718 deletions
diff --git a/include/compression/bwlzh.h b/include/compression/bwlzh.h index 70d586a..ce08f69 100644 --- a/include/compression/bwlzh.h +++ b/include/compression/bwlzh.h @@ -17,28 +17,28 @@ allocated to be able to hold worst case. You can obtain this length conveniently by calling comp_get_buflen() */ -void DECLSPECDLLEXPORT bwlzh_compress(unsigned int *vals, int nvals, +void DECLSPECDLLEXPORT bwlzh_compress(unsigned int *vals, const int nvals, unsigned char *output, int *output_len); -void DECLSPECDLLEXPORT bwlzh_compress_no_lz77(unsigned int *vals, int nvals, +void DECLSPECDLLEXPORT bwlzh_compress_no_lz77(unsigned int *vals, const int nvals, unsigned char *output, int *output_len); -int DECLSPECDLLEXPORT bwlzh_get_buflen(int nvals); +int DECLSPECDLLEXPORT bwlzh_get_buflen(const int nvals); -void DECLSPECDLLEXPORT bwlzh_decompress(unsigned char *input, int nvals, +void DECLSPECDLLEXPORT bwlzh_decompress(unsigned char *input, const int nvals, unsigned int *vals); /* The routines below are mostly useful for testing, and for internal use by the library. */ -void DECLSPECDLLEXPORT bwlzh_compress_verbose(unsigned int *vals, int nvals, +void DECLSPECDLLEXPORT bwlzh_compress_verbose(unsigned int *vals, const int nvals, unsigned char *output, int *output_len); -void DECLSPECDLLEXPORT bwlzh_compress_no_lz77_verbose(unsigned int *vals, int nvals, +void DECLSPECDLLEXPORT bwlzh_compress_no_lz77_verbose(unsigned int *vals, const int nvals, unsigned char *output, int *output_len); -void DECLSPECDLLEXPORT bwlzh_decompress_verbose(unsigned char *input, int nvals, +void DECLSPECDLLEXPORT bwlzh_decompress_verbose(unsigned char *input, const int nvals, unsigned int *vals); /* Compress the integers (positive, small integers are preferable) @@ -47,12 +47,12 @@ void DECLSPECDLLEXPORT bwlzh_decompress_verbose(unsigned char *input, int nvals, to be able to hold worst case. You can obtain this length conveniently by calling comp_huff_buflen() */ -void Ptngc_comp_huff_compress(unsigned int *vals, int nvals, +void Ptngc_comp_huff_compress(unsigned int *vals, const int nvals, unsigned char *huffman, int *huffman_len); -int Ptngc_comp_huff_buflen(int nvals); +int Ptngc_comp_huff_buflen(const int nvals); -void Ptngc_comp_huff_decompress(unsigned char *huffman, int huffman_len, +void Ptngc_comp_huff_decompress(unsigned char *huffman, const int huffman_len, unsigned int *vals); @@ -62,11 +62,11 @@ void Ptngc_comp_huff_compress_verbose(unsigned int *vals, int nvals, unsigned char *huffman, int *huffman_len, int *huffdatalen, int *huffman_lengths,int *chosen_algo, - int isvals16); + const int isvals16); #define N_HUFFMAN_ALGO 3 -char *Ptngc_comp_get_huff_algo_name(int algo); -char *Ptngc_comp_get_algo_name(int algo); +char *Ptngc_comp_get_huff_algo_name(const int algo); +char *Ptngc_comp_get_algo_name(const int algo); #endif diff --git a/include/compression/bwt.h b/include/compression/bwt.h index 9f927f8..fedfc3d 100644 --- a/include/compression/bwt.h +++ b/include/compression/bwt.h @@ -12,15 +12,15 @@ #ifndef BWT_H #define BWT_H -void Ptngc_comp_to_bwt(unsigned int *vals, int nvals, +void Ptngc_comp_to_bwt(unsigned int *vals, const int nvals, unsigned int *output, int *index); -void Ptngc_comp_from_bwt(unsigned int *input, int nvals, int index, +void Ptngc_comp_from_bwt(unsigned int *input, const int nvals, int index, unsigned int *vals); -void Ptngc_bwt_merge_sort_inner(int *indices, int nvals,unsigned int *vals, - int start, int end, - unsigned int *nrepeat, - int *workarray); +void Ptngc_bwt_merge_sort_inner(int *indices, const int nvals, unsigned int *vals, + const int start, const int end, + unsigned int *nrepeat, + int *workarray); #endif diff --git a/include/compression/coder.h b/include/compression/coder.h index 34b56c1..d714c82 100644 --- a/include/compression/coder.h +++ b/include/compression/coder.h @@ -29,10 +29,10 @@ struct coder struct coder DECLSPECDLLEXPORT *Ptngc_coder_init(void); void DECLSPECDLLEXPORT Ptngc_coder_deinit(struct coder *coder); -unsigned char DECLSPECDLLEXPORT *Ptngc_pack_array(struct coder *coder,int *input, int *length, int coding, int coding_parameter, int natoms, int speed); -int DECLSPECDLLEXPORT Ptngc_unpack_array(struct coder *coder,unsigned char *packed,int *output, int length, int coding, int coding_parameter, int natoms); +unsigned char DECLSPECDLLEXPORT *Ptngc_pack_array(struct coder *coder,int *input, int *length, const int coding, const int coding_parameter, const int natoms, const int speed); +int DECLSPECDLLEXPORT Ptngc_unpack_array(struct coder *coder,unsigned char *packed,int *output, const int length, const int coding, const int coding_parameter, const int natoms); unsigned char DECLSPECDLLEXPORT *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length); -int DECLSPECDLLEXPORT Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *output, int length); +int DECLSPECDLLEXPORT Ptngc_unpack_array_xtc2(struct coder *coder, unsigned char *packed, int *output, const int length); unsigned char DECLSPECDLLEXPORT *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int speed); int DECLSPECDLLEXPORT Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int natoms); @@ -40,7 +40,7 @@ void DECLSPECDLLEXPORT Ptngc_out8bits(struct coder *coder, unsigned char **outpu void DECLSPECDLLEXPORT Ptngc_pack_flush(struct coder *coder,unsigned char **output); void DECLSPECDLLEXPORT Ptngc_write_pattern(struct coder *coder,unsigned int pattern, int nbits, unsigned char **output); -void DECLSPECDLLEXPORT Ptngc_writebits(struct coder *coder,unsigned int value,int nbits, unsigned char **output_ptr); +void DECLSPECDLLEXPORT Ptngc_writebits(struct coder *coder, unsigned int value, const int nbits, unsigned char **output_ptr); void DECLSPECDLLEXPORT Ptngc_write32bits(struct coder *coder,unsigned int value,int nbits, unsigned char **output_ptr); void DECLSPECDLLEXPORT Ptngc_writemanybits(struct coder *coder,unsigned char *value,int nbits, unsigned char **output_ptr); diff --git a/include/compression/dict.h b/include/compression/dict.h index d66dd23..26eed27 100644 --- a/include/compression/dict.h +++ b/include/compression/dict.h @@ -14,7 +14,7 @@ void Ptngc_comp_canonical_dict(unsigned int *dict, int *ndict); -void Ptngc_comp_make_dict_hist(unsigned int *vals, int nvals, +void Ptngc_comp_make_dict_hist(unsigned int *vals, const int nvals, unsigned int *dict, int *ndict, unsigned int *hist); diff --git a/include/compression/fixpoint.h b/include/compression/fixpoint.h index 6be7482..7b6a667 100644 --- a/include/compression/fixpoint.h +++ b/include/compression/fixpoint.h @@ -17,16 +17,16 @@ typedef unsigned long fix_t; /* Positive double to 32 bit fixed point value */ -fix_t Ptngc_ud_to_fix_t(double d,double max); +fix_t Ptngc_ud_to_fix_t(double d, const double max); /* double to signed 32 bit fixed point value */ -fix_t Ptngc_d_to_fix_t(double d,double max); +fix_t Ptngc_d_to_fix_t(double d, const double max); /* 32 bit fixed point value to positive double */ -double Ptngc_fix_t_to_ud(fix_t f, double max); +double Ptngc_fix_t_to_ud(fix_t f, const double max); /* signed 32 bit fixed point value to double */ -double Ptngc_fix_t_to_d(fix_t f, double max); +double Ptngc_fix_t_to_d(fix_t f, const double max); /* Convert a floating point variable to two 32 bit integers with range -2.1e9 to 2.1e9 and precision to somewhere around 1e-9. */ diff --git a/include/compression/huffman.h b/include/compression/huffman.h index 49347de..f2ce187 100644 --- a/include/compression/huffman.h +++ b/include/compression/huffman.h @@ -12,8 +12,8 @@ #ifndef HUFFMAN_H #define HUFFMAN_H -void Ptngc_comp_conv_to_huffman(unsigned int *vals, int nvals, - unsigned int *dict, int ndict, +void Ptngc_comp_conv_to_huffman(unsigned int *vals, const int nvals, + unsigned int *dict, const int ndict, unsigned int *prob, unsigned char *huffman, int *huffman_len, @@ -23,11 +23,11 @@ void Ptngc_comp_conv_to_huffman(unsigned int *vals, int nvals, int *huffman_dict_unpackedlen); void Ptngc_comp_conv_from_huffman(unsigned char *huffman, - unsigned int *vals, int nvals, - int ndict, + unsigned int *vals, const int nvals, + const int ndict, unsigned char *huffman_dict, - int huffman_dictlen, + const int huffman_dictlen, unsigned int *huffman_dict_unpacked, - int huffman_dict_unpackedlen); + const int huffman_dict_unpackedlen); #endif diff --git a/include/compression/lz77.h b/include/compression/lz77.h index ad37e5b..d4a4beb 100644 --- a/include/compression/lz77.h +++ b/include/compression/lz77.h @@ -12,14 +12,14 @@ #ifndef LZ77_H #define LZ77_H -void Ptngc_comp_to_lz77(unsigned int *vals, int nvals, +void Ptngc_comp_to_lz77(unsigned int *vals, const int nvals, unsigned int *data, int *ndata, unsigned int *len, int *nlens, unsigned int *offsets, int *noffsets); -void Ptngc_comp_from_lz77(unsigned int *data, int ndata, - unsigned int *len, int nlens, - unsigned int *offsets, int noffsets, - unsigned int *vals, int nvals); +void Ptngc_comp_from_lz77(unsigned int *data, const int ndata, + unsigned int *len, const int nlens, + unsigned int *offsets, const int noffsets, + unsigned int *vals, const int nvals); #endif diff --git a/include/compression/merge_sort.h b/include/compression/merge_sort.h index 48ab410..f8aaeb7 100644 --- a/include/compression/merge_sort.h +++ b/include/compression/merge_sort.h @@ -12,7 +12,7 @@ #ifndef MERGE_SORT_H #define MERGE_SORT_H -void Ptngc_merge_sort(void *base, size_t nmemb, size_t size, +void Ptngc_merge_sort(void *base, const size_t nmemb, const size_t size, int (*compar)(const void *v1,const void *v2,const void *private), void *private); diff --git a/include/compression/mtf.h b/include/compression/mtf.h index bc4b2c8..3dc9ace 100644 --- a/include/compression/mtf.h +++ b/include/compression/mtf.h @@ -12,24 +12,24 @@ #ifndef MTF_H #define MTF_H -void Ptngc_comp_conv_to_mtf(unsigned int *vals, int nvals, - unsigned int *dict, int ndict, +void Ptngc_comp_conv_to_mtf(unsigned int *vals, const int nvals, + unsigned int *dict, const int ndict, unsigned int *valsmtf); -void Ptngc_comp_conv_from_mtf(unsigned int *valsmtf, int nvals, - unsigned int *dict, int ndict, +void Ptngc_comp_conv_from_mtf(unsigned int *valsmtf, const int nvals, + unsigned int *dict, const int ndict, unsigned int *vals); -void Ptngc_comp_conv_to_mtf_partial(unsigned int *vals, int nvals, +void Ptngc_comp_conv_to_mtf_partial(unsigned int *vals, const int nvals, unsigned int *valsmtf); -void Ptngc_comp_conv_from_mtf_partial(unsigned int *valsmtf, int nvals, +void Ptngc_comp_conv_from_mtf_partial(unsigned int *valsmtf, const int nvals, unsigned int *vals); -void Ptngc_comp_conv_to_mtf_partial3(unsigned int *vals, int nvals, +void Ptngc_comp_conv_to_mtf_partial3(unsigned int *vals, const int nvals, unsigned char *valsmtf); -void Ptngc_comp_conv_from_mtf_partial3(unsigned char *valsmtf, int nvals, +void Ptngc_comp_conv_from_mtf_partial3(unsigned char *valsmtf, const int nvals, unsigned int *vals); #endif diff --git a/include/compression/rle.h b/include/compression/rle.h index c6d4706..3665dd0 100644 --- a/include/compression/rle.h +++ b/include/compression/rle.h @@ -12,11 +12,11 @@ #ifndef RLE_H #define RLE_H -void Ptngc_comp_conv_to_rle(unsigned int *vals, int nvals, - unsigned int *rle, int *nrle, - int min_rle); +void Ptngc_comp_conv_to_rle(unsigned int *vals, const int nvals, + unsigned int *rle, int *nrle, + const int min_rle); void Ptngc_comp_conv_from_rle(unsigned int *rle, - unsigned int *vals, int nvals); + unsigned int *vals, const int nvals); #endif diff --git a/include/compression/tng_compress.h b/include/compression/tng_compress.h index c8b8db1..0082ba3 100644 --- a/include/compression/tng_compress.h +++ b/include/compression/tng_compress.h @@ -50,18 +50,18 @@ If too large values are input (compared to the precision), NULL is returned. */ -char DECLSPECDLLEXPORT *tng_compress_pos(double *pos, int natoms, int nframes, - double desired_precision, - int speed, int *algo, +char DECLSPECDLLEXPORT *tng_compress_pos(double *pos, const int natoms, const int nframes, + const double desired_precision, + const int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_pos_float(float *pos, int natoms, int nframes, - float desired_precision, - int speed, int *algo, +char DECLSPECDLLEXPORT *tng_compress_pos_float(float *pos, const int natoms, const int nframes, + const float desired_precision, + const int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_pos_int(int *pos, int natoms, int nframes, - unsigned long prec_hi, unsigned long prec_lo, +char DECLSPECDLLEXPORT *tng_compress_pos_int(int *pos, const int natoms, const int nframes, + const unsigned long prec_hi, const unsigned long prec_lo, int speed,int *algo, int *nitems); @@ -90,21 +90,21 @@ char DECLSPECDLLEXPORT *tng_compress_pos_int(int *pos, int natoms, int nframes, by calling tng_compress_nalgo */ -char DECLSPECDLLEXPORT *tng_compress_pos_find_algo(double *pos, int natoms, int nframes, - double desired_precision, - int speed, +char DECLSPECDLLEXPORT *tng_compress_pos_find_algo(double *pos, const int natoms, const int nframes, + const double desired_precision, + const int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_pos_float_find_algo(float *pos, int natoms, int nframes, - float desired_precision, - int speed, +char DECLSPECDLLEXPORT *tng_compress_pos_float_find_algo(float *pos, const int natoms, const int nframes, + const float desired_precision, + const int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_pos_int_find_algo(int *pos, int natoms, int nframes, - unsigned long prec_hi, unsigned long prec_lo, - int speed,int *algo, +char DECLSPECDLLEXPORT *tng_compress_pos_int_find_algo(int *pos, const int natoms, const int nframes, + const unsigned long prec_hi, const unsigned long prec_lo, + const int speed, int *algo, int *nitems); /* This returns the number of integers required for the storage of the algorithm @@ -116,36 +116,36 @@ int DECLSPECDLLEXPORT tng_compress_nalgo(void); selection for velocities is different, so the position and velocities routines should not be mixed. */ -char DECLSPECDLLEXPORT *tng_compress_vel(double *vel, int natoms, int nframes, - double desired_precision, - int speed, int *algo, +char DECLSPECDLLEXPORT *tng_compress_vel(double *vel, const int natoms, const int nframes, + const double desired_precision, + const int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_vel_float(float *vel, int natoms, int nframes, - float desired_precision, - int speed, int *algo, +char DECLSPECDLLEXPORT *tng_compress_vel_float(float *vel, const int natoms, const int nframes, + const float desired_precision, + const int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_vel_int(int *vel, int natoms, int nframes, - unsigned long prec_hi, unsigned long prec_lo, +char DECLSPECDLLEXPORT *tng_compress_vel_int(int *vel, const int natoms, const int nframes, + const unsigned long prec_hi, const unsigned long prec_lo, int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_vel_find_algo(double *vel, int natoms, int nframes, - double desired_precision, - int speed, +char DECLSPECDLLEXPORT *tng_compress_vel_find_algo(double *vel, const int natoms, const int nframes, + const double desired_precision, + const int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_vel_float_find_algo(float *vel, int natoms, int nframes, - float desired_precision, - int speed, +char DECLSPECDLLEXPORT *tng_compress_vel_float_find_algo(float *vel, const int natoms, const int nframes, + const float desired_precision, + const int speed, int *algo, int *nitems); -char DECLSPECDLLEXPORT *tng_compress_vel_int_find_algo(int *vel, int natoms, int nframes, - unsigned long prec_hi, unsigned long prec_lo, - int speed, +char DECLSPECDLLEXPORT *tng_compress_vel_int_find_algo(int *vel, const int natoms, const int nframes, + const unsigned long prec_hi, const unsigned long prec_lo, + const int speed, int *algo, int *nitems); @@ -170,12 +170,12 @@ int DECLSPECDLLEXPORT tng_compress_uncompress_int(char *data,int *posvel, unsign /* This converts a block of integers, as obtained from tng_compress_uncompress_int, to floating point values either double precision or single precision. */ -void DECLSPECDLLEXPORT tng_compress_int_to_double(int *posvel_int,unsigned long prec_hi, unsigned long prec_lo, - int natoms,int nframes, +void DECLSPECDLLEXPORT tng_compress_int_to_double(int *posvel_int, const unsigned long prec_hi, const unsigned long prec_lo, + const int natoms, const int nframes, double *posvel_double); -void DECLSPECDLLEXPORT tng_compress_int_to_float(int *posvel_int,unsigned long prec_hi, unsigned long prec_lo, - int natoms,int nframes, +void DECLSPECDLLEXPORT tng_compress_int_to_float(int *posvel_int, const unsigned long prec_hi, const unsigned long prec_lo, + const int natoms, const int nframes, float *posvel_float); diff --git a/include/compression/vals16.h b/include/compression/vals16.h index 4585755..ba1b8fb 100644 --- a/include/compression/vals16.h +++ b/include/compression/vals16.h @@ -12,10 +12,10 @@ #ifndef VALS16_H #define VALS16_H -void Ptngc_comp_conv_to_vals16(unsigned int *vals,int nvals, - unsigned int *vals16, int *nvals16); +void Ptngc_comp_conv_to_vals16(unsigned int *vals, const int nvals, + unsigned int *vals16, int *nvals16); -void Ptngc_comp_conv_from_vals16(unsigned int *vals16,int nvals16, - unsigned int *vals, int *nvals); +void Ptngc_comp_conv_from_vals16(unsigned int *vals16, const int nvals16, + unsigned int *vals, int *nvals); #endif diff --git a/include/compression/warnmalloc.h b/include/compression/warnmalloc.h index 4444271..aa63111 100644 --- a/include/compression/warnmalloc.h +++ b/include/compression/warnmalloc.h @@ -14,11 +14,11 @@ #include "../compression/tng_compress.h" -void DECLSPECDLLEXPORT *Ptngc_warnmalloc_x(size_t size, char *file, int line); +void DECLSPECDLLEXPORT *Ptngc_warnmalloc_x(const size_t size, char *file, const int line); #define warnmalloc(size) Ptngc_warnmalloc_x(size,__FILE__,__LINE__) -void DECLSPECDLLEXPORT *Ptngc_warnrealloc_x(void *old, size_t size, char *file, int line); +void DECLSPECDLLEXPORT *Ptngc_warnrealloc_x(void *old, const size_t size, char *file, const int line); #define warnrealloc(old,size) Ptngc_warnrealloc_x(old,size,__FILE__,__LINE__) diff --git a/include/tng/tng_io.h b/include/tng/tng_io.h index a80af58..668acbe 100644 --- a/include/tng/tng_io.h +++ b/include/tng/tng_io.h @@ -640,7 +640,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src - (tng_trajectory_t src, tng_trajectory_t *dest_p); + (const tng_trajectory_t src, tng_trajectory_t *dest_p); /** * @brief Get the name of the input file. @@ -672,7 +672,7 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_input_file_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *file_name); /** @@ -705,7 +705,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_output_file_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *file_name); /** @@ -721,7 +721,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_set * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_output_append_file_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *file_name); /** @@ -752,7 +752,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_get * could not be set. */ tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const tng_file_endianness endianness); /** @@ -785,7 +785,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name); /** @@ -818,7 +818,7 @@ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name); /** @@ -851,7 +851,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name); /** @@ -884,7 +884,7 @@ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name); /** @@ -917,7 +917,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name); /** @@ -950,7 +950,7 @@ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name); /** @@ -983,7 +983,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_signature_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_first_signature_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *signature); /** @@ -1016,7 +1016,7 @@ tng_function_status DECLSPECDLLEXPORT tng_last_signature_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_last_signature_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *signature); /** @@ -1049,7 +1049,7 @@ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name); /** @@ -1075,7 +1075,7 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get * has occurred. */ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t len); /** @@ -1101,7 +1101,7 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get * has occurred. */ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t len); /** @@ -1128,7 +1128,7 @@ tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_get * has occurred. */ tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const double time); /** @@ -1187,7 +1187,7 @@ tng_function_status DECLSPECDLLEXPORT tng_compression_precision_get * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_compression_precision_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const double precision); /** @@ -1202,7 +1202,7 @@ tng_function_status DECLSPECDLLEXPORT tng_compression_precision_set * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t n); /** @@ -1378,7 +1378,7 @@ tng_function_status DECLSPECDLLEXPORT tng_current_frame_set_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t nr); /** @@ -1394,7 +1394,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_of_frame_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame); /** @@ -1480,7 +1480,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_free(const tng_trajectory_t t */ tng_function_status DECLSPECDLLEXPORT tng_molecule_init (const tng_trajectory_t tng_data, - tng_molecule_t molecule); + const tng_molecule_t molecule); /** * @brief Clean up a molecule container. @@ -1493,7 +1493,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_init */ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy (const tng_trajectory_t tng_data, - tng_molecule_t molecule); + const tng_molecule_t molecule); /** * @brief Add a molecule to the trajectory. @@ -1508,7 +1508,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *name, tng_molecule_t *molecule); @@ -1526,7 +1526,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *name, const int64_t id, tng_molecule_t *molecule); @@ -1542,7 +1542,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_existing_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, tng_molecule_t *molecule); /** @@ -1578,8 +1578,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *new_name); /** @@ -1610,8 +1610,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const int64_t cnt); /** @@ -1632,9 +1632,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set * be found. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *name, - int64_t id, + const int64_t id, tng_molecule_t *molecule); /** @@ -1649,8 +1649,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_find * molecule is not found. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_of_index_get - (tng_trajectory_t tng_data, - int64_t index, + (const tng_trajectory_t tng_data, + const int64_t index, tng_molecule_t *molecule); /** @@ -1667,8 +1667,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_of_index_get * @return TNG_SUCCESS(0) if the copying is successful, TNG_FAILURE if a minor * error has occured or TNG_CRITICAL(2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t tng_data_src, - tng_trajectory_t tng_data_dest); +tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(const tng_trajectory_t tng_data_src, + const tng_trajectory_t tng_data_dest); /** * @brief Get the number of chains in a molecule. @@ -1697,9 +1697,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_num_chains_get * chain is not found. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_of_index_get - (tng_trajectory_t tng_data, - tng_molecule_t molecule, - int64_t index, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, + const int64_t index, tng_chain_t *chain); /** @@ -1785,10 +1785,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_of_index_get * be found. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *name, - int64_t id, + const int64_t id, tng_chain_t *chain); /** @@ -1805,8 +1805,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *name, tng_chain_t *chain); @@ -1825,8 +1825,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *name, const int64_t id, tng_chain_t *chain); @@ -1845,7 +1845,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add */ tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add (const tng_trajectory_t tng_data, - tng_molecule_t molecule, + const tng_molecule_t molecule, const int64_t from_atom_id, const int64_t to_atom_id, tng_bond_t *bond); @@ -1867,10 +1867,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add * be found. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_find - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *name, - int64_t id, + const int64_t id, tng_atom_t *atom); /** @@ -1904,8 +1904,8 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_chain_name_set - (tng_trajectory_t tng_data, - tng_chain_t chain, + (const tng_trajectory_t tng_data, + const tng_chain_t chain, const char *new_name); /** @@ -1957,10 +1957,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_of_index_get * be found. */ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find - (tng_trajectory_t tng_data, - tng_chain_t chain, + (const tng_trajectory_t tng_data, + const tng_chain_t chain, const char *name, - int64_t id, + const int64_t id, tng_residue_t *residue); /** @@ -1977,8 +1977,8 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add - (tng_trajectory_t tng_data, - tng_chain_t chain, + (const tng_trajectory_t tng_data, + const tng_chain_t chain, const char *name, tng_residue_t *residue); @@ -1997,8 +1997,8 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add - (tng_trajectory_t tng_data, - tng_chain_t chain, + (const tng_trajectory_t tng_data, + const tng_chain_t chain, const char *name, const int64_t id, tng_residue_t *residue); @@ -2036,8 +2036,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set - (tng_trajectory_t tng_data, - tng_residue_t residue, + (const tng_trajectory_t tng_data, + const tng_residue_t residue, const char *new_name); /** @@ -2089,8 +2089,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_of_index_get * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add - (tng_trajectory_t tng_data, - tng_residue_t residue, + (const tng_trajectory_t tng_data, + const tng_residue_t residue, const char *atom_name, const char *atom_type, tng_atom_t *atom); @@ -2113,8 +2113,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add - (tng_trajectory_t tng_data, - tng_residue_t residue, + (const tng_trajectory_t tng_data, + const tng_residue_t residue, const char *atom_name, const char *atom_type, const int64_t id, @@ -2165,8 +2165,8 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_atom_name_set - (tng_trajectory_t tng_data, - tng_atom_t atom, + (const tng_trajectory_t tng_data, + const tng_atom_t atom, const char *new_name); /** @@ -2202,8 +2202,8 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_type_get * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_atom_type_set - (tng_trajectory_t tng_data, - tng_atom_t atom, + (const tng_trajectory_t tng_data, + const tng_atom_t atom, const char *new_type); /** @@ -2224,7 +2224,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, - int max_len); + const int max_len); /** * @brief Get the molecule id of real particle number (number in mol system). @@ -2290,7 +2290,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, - int max_len); + const int max_len); /** * @brief Get the residue name of real particle number (number in mol system). @@ -2310,7 +2310,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, - int max_len); + const int max_len); /** * @brief Get the residue id (local to molecule) of real particle number @@ -2364,7 +2364,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, - int max_len); + const int max_len); /** * @brief Get the atom type of real particle number (number in mol system). @@ -2384,7 +2384,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_type_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *type, - int max_len); + const int max_len); /** * @brief Add a particle mapping table. @@ -2408,7 +2408,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_type_of_particle_nr_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t num_first_particle, const int64_t n_particles, const int64_t *mapping_table); @@ -2424,7 +2424,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free - (tng_trajectory_t tng_data); + (const tng_trajectory_t tng_data); /** * @brief Read the header blocks from the input_file of tng_data. @@ -2443,7 +2443,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_file_headers_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode); /** @@ -2462,7 +2462,7 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_read * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_file_headers_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode); /** @@ -2486,8 +2486,8 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_write * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_block_read_next - (tng_trajectory_t tng_data, - tng_gen_block_t block_data, + (const tng_trajectory_t tng_data, + const tng_gen_block_t block_data, const char hash_mode); /** @@ -2503,7 +2503,7 @@ tng_function_status DECLSPECDLLEXPORT tng_block_read_next * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode); /** @@ -2523,7 +2523,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_current_only_data_from_block_id - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode, const int64_t block_id); @@ -2543,7 +2543,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_current_only_data_from_ * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode); /** @@ -2563,7 +2563,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next_only_data_from_block_id - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode, const int64_t block_id); @@ -2582,7 +2582,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next_only_data_from_blo * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode); /** @@ -2603,7 +2603,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_write * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_premature_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode); /** @@ -2622,7 +2622,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_premature_write * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames); @@ -2644,7 +2644,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames, const double first_frame_time); @@ -2661,7 +2661,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const double first_frame_time); /** @@ -2710,7 +2710,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_frame_nr_of_next_frame_set_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_data_block_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, @@ -2755,7 +2755,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, @@ -2783,10 +2783,10 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add * TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_data_block_name_get - (tng_trajectory_t tng_data, - int64_t block_id, + (const tng_trajectory_t tng_data, + const int64_t block_id, char *name, - int max_len); + const int max_len); /** @brief Get the dependency of a data block of a specific ID. * @param tng_data is the trajectory data container. @@ -2805,7 +2805,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_name_get */ tng_function_status DECLSPECDLLEXPORT tng_data_block_dependency_get (const tng_trajectory_t tng_data, - int64_t block_id, + const int64_t block_id, int *block_dependency); /** @brief Get the number of values per frame of a data block of a specific ID. @@ -2822,7 +2822,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_dependency_get */ tng_function_status DECLSPECDLLEXPORT tng_data_block_num_values_per_frame_get (const tng_trajectory_t tng_data, - int64_t block_id, + const int64_t block_id, int64_t *n_values_per_frame); /** @@ -2846,7 +2846,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_num_values_per_frame_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_data_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const int64_t block_id, const void *values, @@ -2880,7 +2880,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_data_write * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const int64_t block_id, const int64_t val_first_particle, @@ -2957,7 +2957,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_data, +tng_function_status DECLSPECDLLEXPORT tng_data_get(const tng_trajectory_t tng_data, const int64_t block_id, union data_values ***values, int64_t *n_frames, @@ -2995,7 +2995,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_data_vector_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, void **values, int64_t *n_frames, @@ -3036,7 +3036,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const int64_t start_frame_nr, const int64_t end_frame_nr, @@ -3081,7 +3081,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const int64_t start_frame_nr, const int64_t end_frame_nr, @@ -3128,7 +3128,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, union data_values ****values, int64_t *n_frames, @@ -3173,7 +3173,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, void **values, int64_t *n_frames, @@ -3224,7 +3224,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const int64_t start_frame_nr, const int64_t end_frame_nr, @@ -3278,7 +3278,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const int64_t start_frame_nr, const int64_t end_frame_nr, @@ -3374,7 +3374,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close * minor error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, double *time); @@ -3392,7 +3392,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get * @return TNG_SUCCESS (0) if successful. */ /*tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t *n_mols, int64_t **molecule_cnt_list, tng_molecule_t *mols); @@ -3410,14 +3410,14 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get * has occured or TNG_CRITICAL (2) if a major error has occured. */ /*tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *name, const int64_t cnt, tng_molecule_t *mol); */ /* // tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get -// (tng_trajectory_t tng_data, +// (const tng_trajectory_t tng_data, // const tng_molecule_t mol, // int64_t *n_particles, // char ***names, @@ -3428,7 +3428,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get // int64_t **chain_ids); // // tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_set -// (tng_trajectory_t tng_data, +// (const tng_trajectory_t tng_data, // tng_molecule_t mol, // const int64_t n_particles, // const char **names, @@ -3459,7 +3459,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, float **positions, int64_t *stride_length); @@ -3484,7 +3484,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, float **velocities, int64_t *stride_length); @@ -3509,7 +3509,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, float **forces, int64_t *stride_length); @@ -3537,7 +3537,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, float **box_shape, int64_t *stride_length); @@ -3572,7 +3572,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, void **values, char *data_type, @@ -3608,7 +3608,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, void **values, char *data_type, @@ -3640,7 +3640,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t last_frame, float **positions, @@ -3671,7 +3671,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t last_frame, float **velocities, @@ -3702,7 +3702,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t last_frame, float **forces, @@ -3739,7 +3739,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t last_frame, float **box_shape, @@ -3774,7 +3774,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i, const int64_t n_values_per_frame, const int64_t block_id, @@ -3812,7 +3812,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i, const int64_t n_values_per_frame, const int64_t block_id, @@ -3849,7 +3849,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_double_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i, const int64_t n_values_per_frame, const int64_t block_id, @@ -3873,7 +3873,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -3892,7 +3892,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -3913,7 +3913,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_double_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -3932,7 +3932,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequency_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -3951,7 +3951,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -3969,7 +3969,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_double_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -3988,7 +3988,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequency_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -4007,7 +4007,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -4025,7 +4025,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_double_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -4044,7 +4044,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequency_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -4063,7 +4063,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -4081,7 +4081,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_double_s * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i); /** @@ -4120,7 +4120,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_frequency_set * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *values, const int64_t n_values_per_frame, @@ -4166,7 +4166,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *values, const int64_t n_values_per_frame, @@ -4197,7 +4197,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *positions); @@ -4224,7 +4224,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *positions); @@ -4250,7 +4250,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *velocities); @@ -4277,7 +4277,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *velocities); @@ -4303,7 +4303,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *forces); @@ -4330,7 +4330,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *forces); @@ -4355,7 +4355,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *box_shape); @@ -4381,7 +4381,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *box_shape); @@ -4425,7 +4425,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *values, @@ -4475,7 +4475,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *values, @@ -4511,7 +4511,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *positions); @@ -4542,7 +4542,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *positions); @@ -4573,7 +4573,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *velocities); @@ -4604,7 +4604,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *velocities); @@ -4635,7 +4635,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *forces); @@ -4666,7 +4666,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *forces); @@ -4696,7 +4696,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *box_shape); @@ -4726,7 +4726,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *box_shape); @@ -4753,7 +4753,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_frame_current_compression_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, int64_t *codec_id, double *factor); @@ -4792,7 +4792,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_frame_current_compression_get * has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_next_frame_present_data_blocks_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t current_frame, const int64_t n_requested_data_block_ids, const int64_t *requested_data_block_ids, @@ -4858,7 +4858,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_next_frame_present_dat */ /* tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_all_data_block_types_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t *n_data_blocks, int64_t **data_block_ids, char ***data_block_names, @@ -4881,7 +4881,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_all_data_block_types_g * if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_prepare_append_after_frame - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t prev_frame); @@ -4894,7 +4894,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_prepare_append_after_frame * error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_util_num_frames_with_data_of_block_id_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, int64_t *n_frames); /** @} */ /* end of group2 */ diff --git a/src/compression/bwlzh.c b/src/compression/bwlzh.c index de009d9..f4c0c28 100644 --- a/src/compression/bwlzh.c +++ b/src/compression/bwlzh.c @@ -40,13 +40,13 @@ #define PARTIAL_MTF #endif -int bwlzh_get_buflen(int nvals) +int bwlzh_get_buflen(const int nvals) { return 132000+nvals*8+12*((nvals+MAX_VALS_PER_BLOCK)/MAX_VALS_PER_BLOCK); } #ifdef SHOWIT -static void printvals(char *name, unsigned int *vals, int nvals) +static void printvals(const char *name, unsigned int *vals, const int nvals) { int i; int nvalsmax=nvals; @@ -69,10 +69,10 @@ static void printvals(char *name, unsigned int *vals, int nvals) #endif -static void bwlzh_compress_gen(unsigned int *vals, int nvals, +static void bwlzh_compress_gen(unsigned int *vals, const int nvals, unsigned char *output, int *output_len, - int enable_lz77, - int verbose) + const int enable_lz77, + const int verbose) { unsigned int *vals16; int nvals16; @@ -460,35 +460,35 @@ static void bwlzh_compress_gen(unsigned int *vals, int nvals, } -void DECLSPECDLLEXPORT bwlzh_compress(unsigned int *vals, int nvals, +void DECLSPECDLLEXPORT bwlzh_compress(unsigned int *vals, const int nvals, unsigned char *output, int *output_len) { bwlzh_compress_gen(vals,nvals,output,output_len,1,0); } -void DECLSPECDLLEXPORT bwlzh_compress_verbose(unsigned int *vals, int nvals, +void DECLSPECDLLEXPORT bwlzh_compress_verbose(unsigned int *vals, const int nvals, unsigned char *output, int *output_len) { bwlzh_compress_gen(vals,nvals,output,output_len,1,1); } -void DECLSPECDLLEXPORT bwlzh_compress_no_lz77(unsigned int *vals, int nvals, +void DECLSPECDLLEXPORT bwlzh_compress_no_lz77(unsigned int *vals, const int nvals, unsigned char *output, int *output_len) { bwlzh_compress_gen(vals,nvals,output,output_len,0,0); } -void DECLSPECDLLEXPORT bwlzh_compress_no_lz77_verbose(unsigned int *vals, int nvals, +void DECLSPECDLLEXPORT bwlzh_compress_no_lz77_verbose(unsigned int *vals, const int nvals, unsigned char *output, int *output_len) { bwlzh_compress_gen(vals,nvals,output,output_len,0,1); } -static void bwlzh_decompress_gen(unsigned char *input, int nvals, +static void bwlzh_decompress_gen(unsigned char *input, const int nvals, unsigned int *vals, - int verbose) + const int verbose) { unsigned int *vals16; int nvals16; @@ -785,13 +785,13 @@ static void bwlzh_decompress_gen(unsigned char *input, int nvals, } -void DECLSPECDLLEXPORT bwlzh_decompress(unsigned char *input, int nvals, +void DECLSPECDLLEXPORT bwlzh_decompress(unsigned char *input, const int nvals, unsigned int *vals) { bwlzh_decompress_gen(input,nvals,vals,0); } -void DECLSPECDLLEXPORT bwlzh_decompress_verbose(unsigned char *input, int nvals, +void DECLSPECDLLEXPORT bwlzh_decompress_verbose(unsigned char *input, const int nvals, unsigned int *vals) { bwlzh_decompress_gen(input,nvals,vals,1); diff --git a/src/compression/bwt.c b/src/compression/bwt.c index 681d66b..c5c46df 100644 --- a/src/compression/bwt.c +++ b/src/compression/bwt.c @@ -22,7 +22,7 @@ #define SHOWIT2 #endif -static int compare_index(int i1,int i2,int nvals,unsigned int *vals,unsigned int *nrepeat) +static int compare_index(int i1,int i2, const int nvals, unsigned int *vals, unsigned int *nrepeat) { int i,j; for (i=0; i<nvals; i++) @@ -75,10 +75,10 @@ static int compare_index(int i1,int i2,int nvals,unsigned int *vals,unsigned int return 0; } -void Ptngc_bwt_merge_sort_inner(int *indices, int nvals,unsigned int *vals, - int start, int end, - unsigned int *nrepeat, - int *workarray) +void Ptngc_bwt_merge_sort_inner(int *indices, const int nvals,unsigned int *vals, + const int start, const int end, + unsigned int *nrepeat, + int *workarray) { int middle; if ((end-start)>1) @@ -140,8 +140,8 @@ void Ptngc_bwt_merge_sort_inner(int *indices, int nvals,unsigned int *vals, } /* Burrows-Wheeler transform. */ -void Ptngc_comp_to_bwt(unsigned int *vals, int nvals, - unsigned int *output, int *index) +void Ptngc_comp_to_bwt(unsigned int *vals, const int nvals, + unsigned int *output, int *index) { int i; int *indices=warnmalloc(2*nvals*sizeof *indices); @@ -305,8 +305,8 @@ void Ptngc_comp_to_bwt(unsigned int *vals, int nvals, } /* Burrows-Wheeler inverse transform. */ -void Ptngc_comp_from_bwt(unsigned int *input, int nvals, int index, - unsigned int *vals) +void Ptngc_comp_from_bwt(unsigned int *input, const int nvals, int index, + unsigned int *vals) { /* Straightforward from the Burrows-Wheeler paper (page 13). */ int i; diff --git a/src/compression/coder.c b/src/compression/coder.c index d51e8cd..d0a0d99 100644 --- a/src/compression/coder.c +++ b/src/compression/coder.c @@ -78,7 +78,7 @@ void DECLSPECDLLEXPORT Ptngc_write_pattern(struct coder *coder_inst, unsigned in /* Write up to 24 bits */ TNG_INLINE void DECLSPECDLLEXPORT Ptngc_writebits(struct coder *coder_inst, - unsigned int value, int nbits, + unsigned int value, const int nbits, unsigned char **output_ptr) { /* Make room for the bits. */ @@ -89,7 +89,7 @@ TNG_INLINE void DECLSPECDLLEXPORT Ptngc_writebits(struct coder *coder_inst, } /* Write up to 32 bits */ -void DECLSPECDLLEXPORT Ptngc_write32bits(struct coder *coder_inst,unsigned int value, +void DECLSPECDLLEXPORT Ptngc_write32bits(struct coder *coder_inst, unsigned int value, int nbits, unsigned char **output_ptr) { unsigned int mask; @@ -165,8 +165,8 @@ static int write_stop_bit_code(struct coder *coder_inst, unsigned int s, return 0; } -static int pack_stopbits_item(struct coder *coder_inst,int item, - unsigned char **output, int coding_parameter) +static int pack_stopbits_item(struct coder *coder_inst, const int item, + unsigned char **output, const int coding_parameter) { /* Find this symbol in table. */ int s=0; @@ -178,8 +178,8 @@ static int pack_stopbits_item(struct coder *coder_inst,int item, } static int pack_triplet(struct coder *coder_inst, unsigned int *s, - unsigned char **output, int coding_parameter, - unsigned int max_base, int maxbits) + unsigned char **output, const int coding_parameter, + const unsigned int max_base, const int maxbits) { /* Determine base for this triplet. */ unsigned int min_base=1U<<coding_parameter; @@ -211,7 +211,7 @@ static int pack_triplet(struct coder *coder_inst, unsigned int *s, return 0; } -void DECLSPECDLLEXPORT Ptngc_pack_flush(struct coder *coder_inst,unsigned char **output) +void DECLSPECDLLEXPORT Ptngc_pack_flush(struct coder *coder_inst, unsigned char **output) { /* Zero-fill just enough. */ if (coder_inst->pack_temporary_bits>0) @@ -219,8 +219,8 @@ void DECLSPECDLLEXPORT Ptngc_pack_flush(struct coder *coder_inst,unsigned char * } unsigned char DECLSPECDLLEXPORT *Ptngc_pack_array(struct coder *coder_inst, - int *input, int *length, int coding, - int coding_parameter, int natoms, int speed) + int *input, int *length, const int coding, + const int coding_parameter, const int natoms, const int speed) { if ((coding==TNG_COMPRESS_ALGO_BWLZH1) || (coding==TNG_COMPRESS_ALGO_BWLZH2)) { @@ -337,7 +337,7 @@ unsigned char DECLSPECDLLEXPORT *Ptngc_pack_array(struct coder *coder_inst, static int unpack_array_stop_bits(struct coder *coder_inst, unsigned char *packed,int *output, - int length, int coding_parameter) + const int length, const int coding_parameter) { int i,j; unsigned int extract_mask=0x80; @@ -392,7 +392,7 @@ static int unpack_array_stop_bits(struct coder *coder_inst, static int unpack_array_triplet(struct coder *coder_inst, unsigned char *packed, int *output, - int length, int coding_parameter) + int length, const int coding_parameter) { int i,j; unsigned int extract_mask=0x80; @@ -466,7 +466,7 @@ static int unpack_array_triplet(struct coder *coder_inst, static int unpack_array_bwlzh(struct coder *coder_inst, unsigned char *packed, int *output, - int length, int natoms) + const int length, const int natoms) { int i,j,k,n=length; unsigned int *pval=warnmalloc(n*sizeof *pval); @@ -491,8 +491,8 @@ static int unpack_array_bwlzh(struct coder *coder_inst, int DECLSPECDLLEXPORT Ptngc_unpack_array(struct coder *coder_inst, unsigned char *packed, int *output, - int length, int coding, int coding_parameter, - int natoms) + const int length, const int coding, const int coding_parameter, + const int natoms) { if ((coding==TNG_COMPRESS_ALGO_STOPBIT) || (coding==TNG_COMPRESS_ALGO_VEL_STOPBIT_INTER)) diff --git a/src/compression/dict.c b/src/compression/dict.c index fdfe7a0..7c32d74 100644 --- a/src/compression/dict.c +++ b/src/compression/dict.c @@ -21,7 +21,7 @@ void Ptngc_comp_canonical_dict(unsigned int *dict, int *ndict) *ndict=0x20004; } -void Ptngc_comp_make_dict_hist(unsigned int *vals, int nvals, +void Ptngc_comp_make_dict_hist(unsigned int *vals, const int nvals, unsigned int *dict, int *ndict, unsigned int *hist) { diff --git a/src/compression/fixpoint.c b/src/compression/fixpoint.c index 17fe6e8..f769a43 100644 --- a/src/compression/fixpoint.c +++ b/src/compression/fixpoint.c @@ -19,7 +19,7 @@ /* Conversion routines from / to double precision */ /* Positive double to 32 bit fixed point value */ -fix_t Ptngc_ud_to_fix_t(double d,double max) +fix_t Ptngc_ud_to_fix_t(double d, const double max) { fix_t val; if (d<0.) @@ -33,7 +33,7 @@ fix_t Ptngc_ud_to_fix_t(double d,double max) } /* double to signed 32 bit fixed point value */ -fix_t Ptngc_d_to_fix_t(double d,double max) +fix_t Ptngc_d_to_fix_t(double d, const double max) { fix_t val; int sign=0; @@ -54,13 +54,13 @@ fix_t Ptngc_d_to_fix_t(double d,double max) /* 32 bit fixed point value to positive double */ -double Ptngc_fix_t_to_ud(fix_t f, double max) +double Ptngc_fix_t_to_ud(fix_t f, const double max) { return (double)f*(max/MAX32BIT); } /* signed 32 bit fixed point value to double */ -double Ptngc_fix_t_to_d(fix_t f, double max) +double Ptngc_fix_t_to_d(fix_t f, const double max) { int sign=0; double d; diff --git a/src/compression/huffman.c b/src/compression/huffman.c index 2abcbcf..f2a2933 100644 --- a/src/compression/huffman.c +++ b/src/compression/huffman.c @@ -70,7 +70,7 @@ static void assign_codes(union htree_nodeleaf *htree, struct codelength *codelength, unsigned int code, int length, - int top) + const int top) { #if 0 printf("Assign codes called with code %d length %d\n",code,length); @@ -131,7 +131,7 @@ static void flush_8bits(unsigned int *combine, unsigned char **output, int *bitp } } -static void writebits(unsigned int value,int length, unsigned char **output, int *bitptr) +static void writebits(unsigned int value, int length, unsigned char **output, int *bitptr) { unsigned int mask; unsigned int combine=(unsigned int)**output; @@ -216,8 +216,8 @@ static int comp_codes_value(const void *codeptr1, const void *codeptr2, const vo /* The huffman_dict array should be 131077 (0x20005) long. The huffman_dict_unpacked array should be 131077 long (note five longer than 0x20000) */ -void Ptngc_comp_conv_to_huffman(unsigned int *vals, int nvals, - unsigned int *dict, int ndict, +void Ptngc_comp_conv_to_huffman(unsigned int *vals, const int nvals, + unsigned int *dict, const int ndict, unsigned int *prob, unsigned char *huffman, int *huffman_len, @@ -463,12 +463,12 @@ void Ptngc_comp_conv_to_huffman(unsigned int *vals, int nvals, } void Ptngc_comp_conv_from_huffman(unsigned char *huffman, - unsigned int *vals, int nvals, - int ndict, + unsigned int *vals, const int nvals, + const int ndict, unsigned char *huffman_dict, - int huffman_dictlen, + const int huffman_dictlen, unsigned int *huffman_dict_unpacked, - int huffman_dict_unpackedlen) + const int huffman_dict_unpackedlen) { struct codelength *codelength=warnmalloc(ndict*sizeof *codelength); int i,j; diff --git a/src/compression/huffmem.c b/src/compression/huffmem.c index 183eff1..3898115 100644 --- a/src/compression/huffmem.c +++ b/src/compression/huffmem.c @@ -19,7 +19,7 @@ #include "../../include/compression/rle.h" #include "../../include/compression/vals16.h" -int Ptngc_comp_huff_buflen(int nvals) +int Ptngc_comp_huff_buflen(const int nvals) { return 132000+nvals*8; } @@ -29,7 +29,7 @@ void Ptngc_comp_huff_compress_verbose(unsigned int *vals, int nvals, unsigned char *huffman, int *huffman_len, int *huffdatalen, int *huffman_lengths,int *chosen_algo, - int isvals16) + const int isvals16) { unsigned int *dict=warnmalloc(0x20005*sizeof *dict); unsigned int *hist=warnmalloc(0x20005*sizeof *hist); @@ -227,7 +227,7 @@ void Ptngc_comp_huff_compress_verbose(unsigned int *vals, int nvals, free(dict); } -void Ptngc_comp_huff_compress(unsigned int *vals, int nvals, +void Ptngc_comp_huff_compress(unsigned int *vals, const int nvals, unsigned char *huffman, int *huffman_len) { int huffman_lengths[N_HUFFMAN_ALGO]; @@ -237,7 +237,7 @@ void Ptngc_comp_huff_compress(unsigned int *vals, int nvals, huffman_lengths,&algo,0); } -void Ptngc_comp_huff_decompress(unsigned char *huffman, int huffman_len, +void Ptngc_comp_huff_decompress(unsigned char *huffman, const int huffman_len, unsigned int *vals) { int isvals16=(int)huffman[0]; @@ -346,7 +346,7 @@ static char *huff_algo_names[N_HUFFMAN_ALGO]= "Huffman (dict=RLE+Huffman)" }; -char *Ptngc_comp_get_huff_algo_name(int algo) +char *Ptngc_comp_get_huff_algo_name(const int algo) { if (algo<0) return NULL; diff --git a/src/compression/lz77.c b/src/compression/lz77.c index 17b147c..d8bfecb 100644 --- a/src/compression/lz77.c +++ b/src/compression/lz77.c @@ -147,7 +147,7 @@ static void sort_strings(unsigned int *vals, int nvals, #define MAX_OFFSET 0xFFFF #define MAX_STRING_SEARCH 8 -static void add_circular(int *previous,int v, int i) +static void add_circular(int *previous, const int v, const int i) { if (previous[(NUM_PREVIOUS+3)*v+2]!=i-1) { @@ -162,7 +162,7 @@ static void add_circular(int *previous,int v, int i) previous[(NUM_PREVIOUS+3)*v+2]=i; } -void Ptngc_comp_to_lz77(unsigned int *vals, int nvals, +void Ptngc_comp_to_lz77(unsigned int *vals, const int nvals, unsigned int *data, int *ndata, unsigned int *len, int *nlens, unsigned int *offsets, int *noffsets) @@ -306,10 +306,10 @@ void Ptngc_comp_to_lz77(unsigned int *vals, int nvals, free(previous); } -void Ptngc_comp_from_lz77(unsigned int *data, int ndata, - unsigned int *len, int nlens, - unsigned int *offsets, int noffsets, - unsigned int *vals, int nvals) +void Ptngc_comp_from_lz77(unsigned int *data, const int ndata, + unsigned int *len, const int nlens, + unsigned int *offsets, const int noffsets, + unsigned int *vals, const int nvals) { int i=0; int joff=0; diff --git a/src/compression/merge_sort.c b/src/compression/merge_sort.c index 7cb9837..63622cc 100644 --- a/src/compression/merge_sort.c +++ b/src/compression/merge_sort.c @@ -15,8 +15,8 @@ #include "../../include/compression/warnmalloc.h" #include "../../include/compression/merge_sort.h" -static void ms_inner(void *base, size_t size, - size_t start, size_t end, +static void ms_inner(void *base, const size_t size, + const size_t start, const size_t end, int (*compar)(const void *v1,const void *v2,const void *private), const void *private, char *workarray) @@ -80,7 +80,7 @@ static void ms_inner(void *base, size_t size, } -void Ptngc_merge_sort(void *base, size_t nmemb, size_t size, +void Ptngc_merge_sort(void *base, const size_t nmemb, const size_t size, int (*compar)(const void *v1,const void *v2,const void *private), void *private) { diff --git a/src/compression/mtf.c b/src/compression/mtf.c index bfb0e19..5219413 100644 --- a/src/compression/mtf.c +++ b/src/compression/mtf.c @@ -17,7 +17,7 @@ /* "Partial" MTF. Byte based. */ /* Move to front coding. Acceptable inputs are max 8 bits (0-0xFF) */ -static void comp_conv_to_mtf_byte(unsigned char *vals, int nvals, +static void comp_conv_to_mtf_byte(unsigned char *vals, const int nvals, unsigned char *valsmtf) { int i; @@ -59,7 +59,7 @@ static void comp_conv_to_mtf_byte(unsigned char *vals, int nvals, } } -void Ptngc_comp_conv_to_mtf_partial(unsigned int *vals, int nvals, +void Ptngc_comp_conv_to_mtf_partial(unsigned int *vals, const int nvals, unsigned int *valsmtf) { unsigned char *tmp=warnmalloc(nvals*2); @@ -78,7 +78,7 @@ void Ptngc_comp_conv_to_mtf_partial(unsigned int *vals, int nvals, free(tmp); } -void Ptngc_comp_conv_to_mtf_partial3(unsigned int *vals, int nvals, +void Ptngc_comp_conv_to_mtf_partial3(unsigned int *vals, const int nvals, unsigned char *valsmtf) { unsigned char *tmp=warnmalloc(nvals); @@ -93,7 +93,7 @@ void Ptngc_comp_conv_to_mtf_partial3(unsigned int *vals, int nvals, } /* Move to front decoding */ -static void comp_conv_from_mtf_byte(unsigned char *valsmtf, int nvals, +static void comp_conv_from_mtf_byte(unsigned char *valsmtf, const int nvals, unsigned char *vals) { int i; @@ -135,7 +135,7 @@ static void comp_conv_from_mtf_byte(unsigned char *valsmtf, int nvals, } } -void Ptngc_comp_conv_from_mtf_partial(unsigned int *valsmtf, int nvals, +void Ptngc_comp_conv_from_mtf_partial(unsigned int *valsmtf, const int nvals, unsigned int *vals) { unsigned char *tmp=warnmalloc(nvals*2); @@ -154,7 +154,7 @@ void Ptngc_comp_conv_from_mtf_partial(unsigned int *valsmtf, int nvals, free(tmp); } -void Ptngc_comp_conv_from_mtf_partial3(unsigned char *valsmtf, int nvals, +void Ptngc_comp_conv_from_mtf_partial3(unsigned char *valsmtf, const int nvals, unsigned int *vals) { unsigned char *tmp=warnmalloc(nvals); @@ -173,8 +173,8 @@ void Ptngc_comp_conv_from_mtf_partial3(unsigned char *valsmtf, int nvals, /* Move to front coding. Acceptable inputs are max 24 bits (0-0xFFFFFF) */ -void Ptngc_comp_conv_to_mtf(unsigned int *vals, int nvals, - unsigned int *dict, int ndict, +void Ptngc_comp_conv_to_mtf(unsigned int *vals, const int nvals, + unsigned int *dict, const int ndict, unsigned int *valsmtf) { int i; @@ -215,8 +215,8 @@ void Ptngc_comp_conv_to_mtf(unsigned int *vals, int nvals, } /* Move to front decoding */ -void Ptngc_comp_conv_from_mtf(unsigned int *valsmtf, int nvals, - unsigned int *dict, int ndict, +void Ptngc_comp_conv_from_mtf(unsigned int *valsmtf, const int nvals, + unsigned int *dict, const int ndict, unsigned int *vals) { int i; diff --git a/src/compression/rle.c b/src/compression/rle.c index adaee65..1273dd8 100644 --- a/src/compression/rle.c +++ b/src/compression/rle.c @@ -12,8 +12,8 @@ #include "../../include/compression/rle.h" static void add_rle(unsigned int *rle, - int v,int nsim, - int *j,int min_rle) + const int v, int nsim, + int *j, const int min_rle) { if (nsim>min_rle) { @@ -36,9 +36,9 @@ static void add_rle(unsigned int *rle, /* Run length encoding. Acceptable inputs are about 16 bits (0-0xFFFF) If input is 0-N output will be be values of 0-(N+2) */ -void Ptngc_comp_conv_to_rle(unsigned int *vals, int nvals, - unsigned int *rle, int *nrle, - int min_rle) +void Ptngc_comp_conv_to_rle(unsigned int *vals, const int nvals, + unsigned int *rle, int *nrle, + const int min_rle) { int i; int j=0; @@ -69,7 +69,7 @@ void Ptngc_comp_conv_to_rle(unsigned int *vals, int nvals, } void Ptngc_comp_conv_from_rle(unsigned int *rle, - unsigned int *vals, int nvals) + unsigned int *vals, const int nvals) { int i=0; int j=0; diff --git a/src/compression/tng_compress.c b/src/compression/tng_compress.c index b39d722..d6497d5 100644 --- a/src/compression/tng_compress.c +++ b/src/compression/tng_compress.c @@ -28,7 +28,7 @@ #define MAX_FVAL 2147483647. -static int verify_input_data(double *x, int natoms, int nframes, double precision) +static int verify_input_data(double *x, const int natoms, const int nframes, const double precision) { int iframe, i, j; for (iframe=0; iframe<nframes; iframe++) @@ -48,7 +48,7 @@ static int verify_input_data(double *x, int natoms, int nframes, double precisio return 1; } -static int verify_input_data_float(float *x, int natoms, int nframes, float precision) +static int verify_input_data_float(float *x, const int natoms, const int nframes, const float precision) { int iframe, i, j; for (iframe=0; iframe<nframes; iframe++) @@ -68,9 +68,9 @@ static int verify_input_data_float(float *x, int natoms, int nframes, float prec return 1; } -static int quantize(double *x, int natoms, int nframes, - double precision, - int *quant) +static int quantize(double *x, const int natoms, const int nframes, + const double precision, + int *quant) { int iframe, i, j; for (iframe=0; iframe<nframes; iframe++) @@ -80,9 +80,9 @@ static int quantize(double *x, int natoms, int nframes, return verify_input_data(x,natoms,nframes,precision); } -static int quantize_float(float *x, int natoms, int nframes, - float precision, - int *quant) +static int quantize_float(float *x, int natoms, const int nframes, + const float precision, + int *quant) { int iframe, i, j; for (iframe=0; iframe<nframes; iframe++) @@ -92,7 +92,7 @@ static int quantize_float(float *x, int natoms, int nframes, return verify_input_data_float(x,natoms,nframes,precision); } -static void quant_inter_differences(int *quant, int natoms, int nframes, +static void quant_inter_differences(int *quant, const int natoms, const int nframes, int *quant_inter) { int iframe, i, j; @@ -107,7 +107,7 @@ static void quant_inter_differences(int *quant, int natoms, int nframes, quant_inter[iframe*natoms*3+i*3+j]=quant[iframe*natoms*3+i*3+j]-quant[(iframe-1)*natoms*3+i*3+j]; } -static void quant_intra_differences(int *quant, int natoms, int nframes, +static void quant_intra_differences(int *quant, const int natoms, const int nframes, int *quant_intra) { int iframe, i, j; @@ -123,8 +123,8 @@ static void quant_intra_differences(int *quant, int natoms, int nframes, } } -static void unquantize(double *x, int natoms, int nframes, - double precision, +static void unquantize(double *x, int natoms, const int nframes, + const double precision, int *quant) { int iframe, i, j; @@ -134,8 +134,8 @@ static void unquantize(double *x, int natoms, int nframes, x[iframe*natoms*3+i*3+j]=(double)quant[iframe*natoms*3+i*3+j]*precision; } -static void unquantize_float(float *x, int natoms, int nframes, - float precision, +static void unquantize_float(float *x, const int natoms, const int nframes, + const float precision, int *quant) { int iframe, i, j; @@ -145,8 +145,8 @@ static void unquantize_float(float *x, int natoms, int nframes, x[iframe*natoms*3+i*3+j]=(float)quant[iframe*natoms*3+i*3+j]*precision; } -static void unquantize_inter_differences(double *x, int natoms, int nframes, - double precision, +static void unquantize_inter_differences(double *x, int natoms, const int nframes, + const double precision, int *quant) { int iframe, i, j; @@ -163,8 +163,8 @@ static void unquantize_inter_differences(double *x, int natoms, int nframes, } } -static void unquantize_inter_differences_float(float *x, int natoms, int nframes, - float precision, +static void unquantize_inter_differences_float(float *x, const int natoms, const int nframes, + const float precision, int *quant) { int iframe, i, j; @@ -181,7 +181,7 @@ static void unquantize_inter_differences_float(float *x, int natoms, int nframes } } -static void unquantize_inter_differences_int(int *x, int natoms, int nframes, +static void unquantize_inter_differences_int(int *x, const int natoms, const int nframes, int *quant) { int iframe, i, j; @@ -200,7 +200,7 @@ static void unquantize_inter_differences_int(int *x, int natoms, int nframes, /* In frame update required for the initial frame if intra-frame compression was used. */ -static void unquant_intra_differences_first_frame(int *quant, int natoms) +static void unquant_intra_differences_first_frame(int *quant, const int natoms) { int i,j; for (j=0; j<3; j++) @@ -221,8 +221,8 @@ static void unquant_intra_differences_first_frame(int *quant, int natoms) #endif } -static void unquantize_intra_differences(double *x, int natoms, int nframes, - double precision, +static void unquantize_intra_differences(double *x, const int natoms, const int nframes, + const double precision, int *quant) { int iframe, i, j; @@ -242,8 +242,8 @@ static void unquantize_intra_differences(double *x, int natoms, int nframes, } } -static void unquantize_intra_differences_float(float *x, int natoms, int nframes, - float precision, +static void unquantize_intra_differences_float(float *x, const int natoms, const int nframes, + const float precision, int *quant) { int iframe, i, j; @@ -260,7 +260,7 @@ static void unquantize_intra_differences_float(float *x, int natoms, int nframes } } -static void unquantize_intra_differences_int(int *x, int natoms, int nframes, +static void unquantize_intra_differences_int(int *x, const int natoms, const int nframes, int *quant) { int iframe, i, j; @@ -308,11 +308,11 @@ static fix_t readbufferfix(unsigned char *buf, int num) /* Perform position compression from the quantized data. */ static void compress_quantized_pos(int *quant, int *quant_inter, int *quant_intra, - int natoms, int nframes, - int speed, - int initial_coding, int initial_coding_parameter, - int coding, int coding_parameter, - fix_t prec_hi, fix_t prec_lo, + const int natoms, const int nframes, + const int speed, + const int initial_coding, const int initial_coding_parameter, + const int coding, const int coding_parameter, + const fix_t prec_hi, const fix_t prec_lo, int *nitems, char *data) { @@ -436,11 +436,11 @@ static void compress_quantized_pos(int *quant, int *quant_inter, int *quant_intr /* Perform velocity compression from vel into the data block */ static void compress_quantized_vel(int *quant, int *quant_inter, - int natoms, int nframes, - int speed, - int initial_coding, int initial_coding_parameter, - int coding, int coding_parameter, - fix_t prec_hi, fix_t prec_lo, + const int natoms, const int nframes, + const int speed, + const int initial_coding, const int initial_coding_parameter, + const int coding, const int coding_parameter, + const fix_t prec_hi, const fix_t prec_lo, int *nitems, char *data) { @@ -544,7 +544,7 @@ static void compress_quantized_vel(int *quant, int *quant_inter, } static int determine_best_coding_stop_bits(struct coder *coder,int *input, int *length, - int *coding_parameter, int natoms) + int *coding_parameter, const int natoms) { int bits; unsigned char *packed; @@ -575,7 +575,7 @@ static int determine_best_coding_stop_bits(struct coder *coder,int *input, int * } static int determine_best_coding_triple(struct coder *coder,int *input, int *length, - int *coding_parameter, int natoms) + int *coding_parameter, const int natoms) { int bits; unsigned char *packed; @@ -605,8 +605,8 @@ static int determine_best_coding_triple(struct coder *coder,int *input, int *len return 0; } -static void determine_best_pos_initial_coding(int *quant, int *quant_intra, int natoms, int speed, - fix_t prec_hi, fix_t prec_lo, +static void determine_best_pos_initial_coding(int *quant, int *quant_intra, const int natoms, const int speed, + const fix_t prec_hi, const fix_t prec_lo, int *initial_coding, int *initial_coding_parameter) { if (*initial_coding==-1) @@ -718,8 +718,8 @@ static void determine_best_pos_initial_coding(int *quant, int *quant_intra, int } } -static void determine_best_pos_coding(int *quant, int *quant_inter, int *quant_intra, int natoms, int nframes, int speed, - fix_t prec_hi, fix_t prec_lo, +static void determine_best_pos_coding(int *quant, int *quant_inter, int *quant_intra, const int natoms, const int nframes, const int speed, + const fix_t prec_hi, const fix_t prec_lo, int *coding, int *coding_parameter) { if (*coding==-1) @@ -896,8 +896,8 @@ static void determine_best_pos_coding(int *quant, int *quant_inter, int *quant_i } } -static void determine_best_vel_initial_coding(int *quant, int natoms, int speed, - fix_t prec_hi, fix_t prec_lo, +static void determine_best_vel_initial_coding(int *quant, const int natoms, const int speed, + const fix_t prec_hi, const fix_t prec_lo, int *initial_coding, int *initial_coding_parameter) { if (*initial_coding==-1) @@ -979,8 +979,8 @@ static void determine_best_vel_initial_coding(int *quant, int natoms, int speed, } } -static void determine_best_vel_coding(int *quant, int *quant_inter, int natoms, int nframes, int speed, - fix_t prec_hi, fix_t prec_lo, +static void determine_best_vel_coding(int *quant, int *quant_inter, const int natoms, const int nframes, const int speed, + const fix_t prec_hi, const fix_t prec_lo, int *coding, int *coding_parameter) { if (*coding==-1) @@ -1137,8 +1137,8 @@ static void determine_best_vel_coding(int *quant, int *quant_inter, int natoms, } } -char DECLSPECDLLEXPORT *tng_compress_pos_int(int *pos, int natoms, int nframes, - unsigned long prec_hi, unsigned long prec_lo, +char DECLSPECDLLEXPORT *tng_compress_pos_int(int *pos, const int natoms, const int nframes, + const unsigned long prec_hi, const unsigned long prec_lo, int speed,int *algo, int *nitems) { @@ -1217,9 +1217,9 @@ char DECLSPECDLLEXPORT *tng_compress_pos_int(int *pos, int natoms, int nframes, return data; } -char DECLSPECDLLEXPORT *tng_compress_pos(double *pos, int natoms, int nframes, - double desired_precision, - int speed,int *algo, +char DECLSPECDLLEXPORT *tng_compress_pos(double *pos, const int natoms, const int nframes, + const double desired_precision, + const int speed,int *algo, int *nitems) { int *quant=malloc(natoms*nframes*3*sizeof *quant); @@ -1235,9 +1235,9 @@ char DECLSPECDLLEXPORT *tng_compress_pos(double *pos, int natoms, int nframes, return data; } -char DECLSPECDLLEXPORT *tng_compress_pos_float(float *pos, int natoms, int nframes, - float desired_precision, - int speed,int *algo, +char DECLSPECDLLEXPORT *tng_compress_pos_float(float *pos, const int natoms, const int nframes, + const float desired_precision, + const int speed, int *algo, int *nitems) { int *quant=malloc(natoms*nframes*3*sizeof *quant); @@ -1253,9 +1253,9 @@ char DECLSPECDLLEXPORT *tng_compress_pos_float(float *pos, int natoms, int nfram return data; } -char DECLSPECDLLEXPORT *tng_compress_pos_find_algo(double *pos, int natoms, int nframes, - double desired_precision, - int speed, +char DECLSPECDLLEXPORT *tng_compress_pos_find_algo(double *pos, const int natoms, const int nframes, + const double desired_precision, + const int speed, int *algo, int *nitems) { @@ -1266,9 +1266,9 @@ char DECLSPECDLLEXPORT *tng_compress_pos_find_algo(double *pos, int natoms, int return tng_compress_pos(pos,natoms,nframes,desired_precision,speed,algo,nitems); } -char DECLSPECDLLEXPORT *tng_compress_pos_float_find_algo(float *pos, int natoms, int nframes, - float desired_precision, - int speed, +char DECLSPECDLLEXPORT *tng_compress_pos_float_find_algo(float *pos, const int natoms, const int nframes, + const float desired_precision, + const int speed, int *algo, int *nitems) { @@ -1279,9 +1279,9 @@ char DECLSPECDLLEXPORT *tng_compress_pos_float_find_algo(float *pos, int natoms, return tng_compress_pos_float(pos,natoms,nframes,desired_precision,speed,algo,nitems); } -char DECLSPECDLLEXPORT *tng_compress_pos_int_find_algo(int *pos, int natoms, int nframes, - unsigned long prec_hi, unsigned long prec_lo, - int speed,int *algo, +char DECLSPECDLLEXPORT *tng_compress_pos_int_find_algo(int *pos, const int natoms, const int nframes, + const unsigned long prec_hi, const unsigned long prec_lo, + const int speed, int *algo, int *nitems) { algo[0]=-1; @@ -1303,8 +1303,8 @@ int DECLSPECDLLEXPORT tng_compress_nalgo(void) 4) One parameter to the algorithm for the remaining frames (the coding parameter). */ } -char DECLSPECDLLEXPORT *tng_compress_vel_int(int *vel, int natoms, int nframes, - unsigned long prec_hi, unsigned long prec_lo, +char DECLSPECDLLEXPORT *tng_compress_vel_int(int *vel, const int natoms, const int nframes, + const unsigned long prec_hi, const unsigned long prec_lo, int speed, int *algo, int *nitems) { @@ -1380,9 +1380,9 @@ char DECLSPECDLLEXPORT *tng_compress_vel_int(int *vel, int natoms, int nframes, return data; } -char DECLSPECDLLEXPORT *tng_compress_vel(double *vel, int natoms, int nframes, - double desired_precision, - int speed, int *algo, +char DECLSPECDLLEXPORT *tng_compress_vel(double *vel, const int natoms, const int nframes, + const double desired_precision, + const int speed, int *algo, int *nitems) { int *quant=malloc(natoms*nframes*3*sizeof *quant); @@ -1397,9 +1397,9 @@ char DECLSPECDLLEXPORT *tng_compress_vel(double *vel, int natoms, int nframes, return data; } -char DECLSPECDLLEXPORT *tng_compress_vel_float(float *vel, int natoms, int nframes, - float desired_precision, - int speed, int *algo, +char DECLSPECDLLEXPORT *tng_compress_vel_float(float *vel, const int natoms, const int nframes, + const float desired_precision, + const int speed, int *algo, int *nitems) { int *quant=malloc(natoms*nframes*3*sizeof *quant); @@ -1414,9 +1414,9 @@ char DECLSPECDLLEXPORT *tng_compress_vel_float(float *vel, int natoms, int nfram return data; } -char DECLSPECDLLEXPORT *tng_compress_vel_find_algo(double *vel, int natoms, int nframes, - double desired_precision, - int speed, +char DECLSPECDLLEXPORT *tng_compress_vel_find_algo(double *vel, const int natoms, const int nframes, + const double desired_precision, + const int speed, int *algo, int *nitems) { @@ -1427,9 +1427,9 @@ char DECLSPECDLLEXPORT *tng_compress_vel_find_algo(double *vel, int natoms, int return tng_compress_vel(vel,natoms,nframes,desired_precision,speed,algo,nitems); } -char DECLSPECDLLEXPORT *tng_compress_vel_float_find_algo(float *vel, int natoms, int nframes, - float desired_precision, - int speed, +char DECLSPECDLLEXPORT *tng_compress_vel_float_find_algo(float *vel, const int natoms, const int nframes, + const float desired_precision, + const int speed, int *algo, int *nitems) { @@ -1440,9 +1440,9 @@ char DECLSPECDLLEXPORT *tng_compress_vel_float_find_algo(float *vel, int natoms, return tng_compress_vel_float(vel,natoms,nframes,desired_precision,speed,algo,nitems); } -char DECLSPECDLLEXPORT *tng_compress_vel_int_find_algo(int *vel, int natoms, int nframes, - unsigned long prec_hi, unsigned long prec_lo, - int speed, +char DECLSPECDLLEXPORT *tng_compress_vel_int_find_algo(int *vel, const int natoms, const int nframes, + const unsigned long prec_hi, const unsigned long prec_lo, + const int speed, int *algo, int *nitems) { @@ -1811,15 +1811,15 @@ int DECLSPECDLLEXPORT tng_compress_uncompress_int(char *data,int *posvel, unsign return 1; } -void DECLSPECDLLEXPORT tng_compress_int_to_double(int *posvel_int,unsigned long prec_hi, unsigned long prec_lo, - int natoms,int nframes, +void DECLSPECDLLEXPORT tng_compress_int_to_double(int *posvel_int, const unsigned long prec_hi, const unsigned long prec_lo, + const int natoms, const int nframes, double *posvel_double) { unquantize(posvel_double,natoms,nframes,PRECISION(prec_hi,prec_lo),posvel_int); } -void DECLSPECDLLEXPORT tng_compress_int_to_float(int *posvel_int,unsigned long prec_hi, unsigned long prec_lo, - int natoms,int nframes, +void DECLSPECDLLEXPORT tng_compress_int_to_float(int *posvel_int, const unsigned long prec_hi, const unsigned long prec_lo, + const int natoms, const int nframes, float *posvel_float) { unquantize_float(posvel_float,natoms,nframes,(float)PRECISION(prec_hi,prec_lo),posvel_int); diff --git a/src/compression/vals16.c b/src/compression/vals16.c index c4ed635..48186f6 100644 --- a/src/compression/vals16.c +++ b/src/compression/vals16.c @@ -13,8 +13,8 @@ /* Coding 32 bit ints in sequences of 16 bit ints. Worst case the output is 3*nvals long. */ -void Ptngc_comp_conv_to_vals16(unsigned int *vals,int nvals, - unsigned int *vals16, int *nvals16) +void Ptngc_comp_conv_to_vals16(unsigned int *vals, const int nvals, + unsigned int *vals16, int *nvals16) { int i; int j=0; @@ -45,8 +45,8 @@ void Ptngc_comp_conv_to_vals16(unsigned int *vals,int nvals, *nvals16=j; } -void Ptngc_comp_conv_from_vals16(unsigned int *vals16,int nvals16, - unsigned int *vals, int *nvals) +void Ptngc_comp_conv_from_vals16(unsigned int *vals16, const int nvals16, + unsigned int *vals, int *nvals) { int i=0; int j=0; diff --git a/src/compression/warnmalloc.c b/src/compression/warnmalloc.c index 36f0d9f..55bdaf7 100644 --- a/src/compression/warnmalloc.c +++ b/src/compression/warnmalloc.c @@ -14,7 +14,7 @@ #include "../../include/compression/tng_compress.h" #include "../../include/compression/warnmalloc.h" -void DECLSPECDLLEXPORT *Ptngc_warnmalloc_x(size_t size, char *file, int line) +void DECLSPECDLLEXPORT *Ptngc_warnmalloc_x(const size_t size, char *file, const int line) { void *mem=malloc(size); if (!mem) @@ -25,7 +25,7 @@ void DECLSPECDLLEXPORT *Ptngc_warnmalloc_x(size_t size, char *file, int line) return mem; } -void DECLSPECDLLEXPORT *Ptngc_warnrealloc_x(void *old, size_t size, char *file, int line) +void DECLSPECDLLEXPORT *Ptngc_warnrealloc_x(void *old, const size_t size, char *file, const int line) { void *mem=realloc(old,size); if (!mem) diff --git a/src/compression/widemuldiv.c b/src/compression/widemuldiv.c index 46cb039..c469238 100644 --- a/src/compression/widemuldiv.c +++ b/src/compression/widemuldiv.c @@ -106,7 +106,7 @@ static TNG_INLINE void Ptngc_widemul(unsigned int i1, unsigned int i2, unsigned /* Divide a 64 bit unsigned value in hi:lo with the 32 bit value i and return the result in result and the remainder in remainder */ -static TNG_INLINE void Ptngc_widediv(unsigned int hi, unsigned int lo, unsigned int i, unsigned int *result, unsigned int *remainder) +static TNG_INLINE void Ptngc_widediv(unsigned int hi, unsigned int lo, const unsigned int i, unsigned int *result, unsigned int *remainder) { #if defined(TRAJNG_X86_GCC_INLINE_MULDIV) __asm__ __volatile__ ("divl %%ecx\n\t" diff --git a/src/compression/xtc2.c b/src/compression/xtc2.c index 888ff8d..7332f5f 100644 --- a/src/compression/xtc2.c +++ b/src/compression/xtc2.c @@ -171,7 +171,7 @@ static const double iflipgaincheck=0.89089871814033927; /* 1./(2**(1./6)) */ #define TNG_INLINE inline #endif -int Ptngc_magic(unsigned int i) +int Ptngc_magic(const unsigned int i) { return magic[i]; } @@ -262,7 +262,7 @@ static const int seq_instr[MAXINSTR][2]= more efficiently coded with two large instructions. */ }; -static void write_instruction(struct coder *coder,int instr,unsigned char **output_ptr) +static void write_instruction(struct coder *coder, const int instr, unsigned char **output_ptr) { Ptngc_writebits(coder,seq_instr[instr][0],seq_instr[instr][1],output_ptr); #ifdef SHOWIT @@ -388,7 +388,7 @@ static void swap_is_better(int *input, int *minint, int *sum_normal, int *sum_sw *sum_swapped=swapped_max; } -static void swapdecide(struct coder *coder, int *input,int *swapatoms, int *large_index, int *minint, unsigned char **output_ptr) +static void swapdecide(struct coder *coder, int *input, int *swapatoms, int *large_index, int *minint, unsigned char **output_ptr) { int didswap=0; int normal,swapped; @@ -1299,7 +1299,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length } -int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *output, int length) +int Ptngc_unpack_array_xtc2(struct coder *coder, unsigned char *packed, int *output, const int length) { unsigned char *ptr=packed; int bitptr=0; diff --git a/src/compression/xtc3.c b/src/compression/xtc3.c index 7b493ab..5cdebdf 100644 --- a/src/compression/xtc3.c +++ b/src/compression/xtc3.c @@ -70,7 +70,7 @@ static const double iflipgaincheck=0.89089871814033927; /* 1./(2**(1./6)) */ int Ptngc_magic(unsigned int i); int Ptngc_find_magic_index(const unsigned int maxval); -static TNG_INLINE unsigned int positive_int(int item) +static TNG_INLINE unsigned int positive_int(const int item) { int s=0; if (item>0) @@ -80,7 +80,7 @@ static TNG_INLINE unsigned int positive_int(int item) return s; } -static TNG_INLINE int unpositive_int(int val) +static TNG_INLINE int unpositive_int(const int val) { int s=(val+1)/2; if ((val%2)==0) @@ -159,14 +159,14 @@ static void free_xtc3_context(struct xtc3_context *xtc3_context) } /* Modifies three integer values for better compression of water */ -static void swap_ints(int *in, int *out) +static void swap_ints(const int *in, int *out) { out[0]=in[0]+in[1]; out[1]=-in[1]; out[2]=in[1]+in[2]; } -static void swap_is_better(int *input, int *minint, int *sum_normal, int *sum_swapped) +static void swap_is_better(const int *input, const int *minint, int *sum_normal, int *sum_swapped) { int normal_max=0; int swapped_max=0; @@ -206,7 +206,7 @@ static void allocate_enough_memory(unsigned int **ptr, int *nele, int *nele_allo } static void insert_value_in_array(unsigned int **ptr, int *nele, int *nele_alloc, - unsigned int value, + const unsigned int value, char *arrayname) { #ifndef SHOWIT @@ -272,7 +272,7 @@ static void swapdecide(struct xtc3_context *xtc3_context, int *input,int *swapat /* It is "large" if we have to increase the small index quite a bit. Not so much to be rejected by the not very large check later. */ -static int is_quite_large(int *input, int small_index, int max_large_index) +static int is_quite_large(const int *input, const int small_index, const int max_large_index) { int is=0; int i; @@ -295,7 +295,7 @@ int nbits_sum; int nvalues_sum; #endif -static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord, int *encode_ints, int startenc, int *nenc) +static void insert_batch(const int *input_ptr, const int ntriplets_left, const int *prevcoord, int *encode_ints, const int startenc, int *nenc) { int nencode=startenc*3; int tmp_prevcoord[3]; @@ -353,7 +353,7 @@ static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord, int *nenc=nencode; } -static void large_instruction_change(struct xtc3_context *xtc3_context, int i) +static void large_instruction_change(struct xtc3_context *xtc3_context, const int i) { /* If the first large is of a different kind than the currently used we must emit an "instruction" to change the large type. */ @@ -375,7 +375,7 @@ static void large_instruction_change(struct xtc3_context *xtc3_context, int i) } static void write_three_large(struct xtc3_context *xtc3_context, - int i) + const int i) { int m; if (xtc3_context->current_large_type==0) @@ -405,7 +405,7 @@ static void write_three_large(struct xtc3_context *xtc3_context, } static void flush_large(struct xtc3_context *xtc3_context, - int n) /* How many to flush. */ + const int n) /* How many to flush. */ { int i; i=0; @@ -470,8 +470,8 @@ static double compute_intlen(unsigned int *ints) return (double)m; } -static void buffer_large(struct xtc3_context *xtc3_context, int *input, int inpdata, - int natoms, int intradelta_ok) +static void buffer_large(struct xtc3_context *xtc3_context, int *input, const int inpdata, + const int natoms, const int intradelta_ok) { unsigned int direct[3], intradelta[3]={0,}, interdelta[3]={0,}; double minlen; @@ -542,7 +542,7 @@ static void buffer_large(struct xtc3_context *xtc3_context, int *input, int inpd xtc3_context->has_large++; } -static void output_int(unsigned char *output,int *outdata, unsigned int n) +static void output_int(unsigned char *output,int *outdata, const unsigned int n) { output[(*outdata)++]=((unsigned int)n)&0xFFU; output[(*outdata)++]=(((unsigned int)n)>>8)&0xFFU; @@ -574,7 +574,7 @@ static void printarray(unsigned int *a, int n, char *name) #define BASEINTERVAL 8 /* How many bytes are needed to store n values in base base */ -static int base_bytes(unsigned int base, int n) +static int base_bytes(const unsigned int base, const int n) { int i,j; unsigned int largeint[MAXMAXBASEVALS+1]; @@ -600,7 +600,7 @@ static int base_bytes(unsigned int base, int n) return numbytes; } -static void base_compress(unsigned int *data, int len, unsigned char *output, int *outlen) +static void base_compress(unsigned int *data, const int len, unsigned char *output, int *outlen) { unsigned int largeint[MAXBASEVALS+1]; unsigned int largeint_tmp[MAXBASEVALS+1]; @@ -707,7 +707,7 @@ static void base_compress(unsigned int *data, int len, unsigned char *output, in *outlen=nwrittenout; } -static void base_decompress(unsigned char *input, int len, unsigned int *output) +static void base_decompress(unsigned char *input, const int len, unsigned int *output) { unsigned int largeint[MAXMAXBASEVALS+1]; unsigned int largeint_tmp[MAXMAXBASEVALS+1]; @@ -795,7 +795,7 @@ static void base_decompress(unsigned char *input, int len, unsigned int *output) } /* If a large proportion of the integers are large (More than 10\% are >14 bits) we return 0, otherwise 1 */ -static int heuristic_bwlzh(unsigned int *ints, int nints) +static int heuristic_bwlzh(unsigned int *ints, const int nints) { int i,num; num=0; @@ -814,7 +814,7 @@ static int heuristic_bwlzh(unsigned int *ints, int nints) Speed 5 enables the LZ77 component of BWLZH. Speed 6 always tests if BWLZH is better and if it is uses it. This can be very slow. */ -unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int speed) +unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, const int natoms, int speed) { unsigned char *output=NULL; int i,ienc,j; @@ -1669,7 +1669,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp } static void decompress_bwlzh_block(unsigned char **ptr, - int nvals, + const int nvals, unsigned int **vals) { int bwlzh_buf_len=(int)(((unsigned int)(*ptr)[0]) | @@ -1683,7 +1683,7 @@ static void decompress_bwlzh_block(unsigned char **ptr, } static void decompress_base_block(unsigned char **ptr, - int nvals, + const int nvals, unsigned int **vals) { int base_buf_len=(int)(((unsigned int)(*ptr)[0]) | @@ -1700,8 +1700,8 @@ static void unpack_one_large(struct xtc3_context *xtc3_context, int *ilargedir, int *ilargeintra, int *ilargeinter, int *prevcoord, int *minint, int *output, - int outdata, int didswap, - int natoms, int current_large_type) + const int outdata, const int didswap, + const int natoms, const int current_large_type) { int large_ints[3]={0,0,0}; if (current_large_type==0 && xtc3_context->large_direct) @@ -1738,7 +1738,7 @@ static void unpack_one_large(struct xtc3_context *xtc3_context, } -int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int natoms) +int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, const int length, const int natoms) { int i; int minint[3]; diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index cf870fa..6b467a8 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -376,17 +376,17 @@ struct tng_trajectory { #define TNG_SNPRINTF snprintf #endif -static TNG_INLINE size_t tng_min_size(size_t a, size_t b) +static TNG_INLINE size_t tng_min_size(const size_t a, const size_t b) { return (a < b ? a : b); } -static TNG_INLINE int64_t tng_min_i64(int64_t a, int64_t b) +static TNG_INLINE int64_t tng_min_i64(const int64_t a, const int64_t b) { return (a < b ? a : b); } -static TNG_INLINE int64_t tng_max_i64(int64_t a, int64_t b) +static TNG_INLINE int64_t tng_max_i64(const int64_t a, const int64_t b) { return (a > b ? a : b); } @@ -593,7 +593,7 @@ static tng_function_status tng_swap_byte_order_little_endian_64 * @param line_nr is the line number where this function was called, to be * able to give more useful error messages. */ -static tng_function_status tng_freadstr(tng_trajectory_t tng_data, +static tng_function_status tng_freadstr(const tng_trajectory_t tng_data, char **str, const char hash_mode, md5_state_t *md5_state, @@ -688,7 +688,7 @@ static TNG_INLINE tng_function_status tng_fwritestr(tng_trajectory_t tng_data, * able to give more useful error messages. */ static TNG_INLINE tng_function_status tng_file_input_numerical - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, void *dest, const size_t len, const char hash_mode, @@ -743,8 +743,8 @@ static TNG_INLINE tng_function_status tng_file_input_numerical * able to give more useful error messages. */ static TNG_INLINE tng_function_status tng_file_output_numerical - (tng_trajectory_t tng_data, - void *src, + (const tng_trajectory_t tng_data, + const void *src, const size_t len, const char hash_mode, md5_state_t *md5_state, @@ -813,7 +813,7 @@ static TNG_INLINE tng_function_status tng_file_output_numerical * @param block is a general block container. * @return TNG_SUCCESS (0) if successful. */ -static tng_function_status tng_block_md5_hash_generate(tng_gen_block_t block) +static tng_function_status tng_block_md5_hash_generate(const tng_gen_block_t block) { md5_state_t md5_state; @@ -835,7 +835,7 @@ static tng_function_status tng_block_md5_hash_generate(tng_gen_block_t block) * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -static tng_function_status tng_md5_remaining_append(tng_trajectory_t tng_data, +static tng_function_status tng_md5_remaining_append(const tng_trajectory_t tng_data, const tng_gen_block_t block, const int64_t start_pos, md5_state_t *md5_state) @@ -874,7 +874,7 @@ static tng_function_status tng_md5_remaining_append(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -static tng_function_status tng_input_file_init(tng_trajectory_t tng_data) +static tng_function_status tng_input_file_init(const tng_trajectory_t tng_data) { int64_t file_pos; @@ -912,7 +912,7 @@ static tng_function_status tng_input_file_init(tng_trajectory_t tng_data) * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -static tng_function_status tng_output_file_init(tng_trajectory_t tng_data) +static tng_function_status tng_output_file_init(const tng_trajectory_t tng_data) { if(!tng_data->output_file) { @@ -1017,7 +1017,7 @@ static tng_function_status tng_block_destroy(struct tng_gen_block **block_p) * the block) or TNG_CRITICAL (2) if a major error has occured. */ static tng_function_status tng_block_header_read - (tng_trajectory_t tng_data, tng_gen_block_t block) + (const tng_trajectory_t tng_data, const tng_gen_block_t block) { int64_t start_pos; @@ -1194,8 +1194,8 @@ static tng_function_status tng_block_header_read * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -static tng_function_status tng_md5_hash_update(tng_trajectory_t tng_data, - tng_gen_block_t block, +static tng_function_status tng_md5_hash_update(const tng_trajectory_t tng_data, + const tng_gen_block_t block, const int64_t header_start_pos, const int64_t contents_start_pos) { @@ -1239,7 +1239,7 @@ static tng_function_status tng_md5_hash_update(tng_trajectory_t tng_data, * error has occured. */ static tng_function_status tng_header_pointers_update - (tng_trajectory_t tng_data, const char hash_mode) + (const tng_trajectory_t tng_data, const char hash_mode) { tng_gen_block_t block; FILE *temp = tng_data->input_file; @@ -1337,7 +1337,7 @@ static tng_function_status tng_header_pointers_update * error has occured. */ static tng_function_status tng_frame_set_pointers_update - (tng_trajectory_t tng_data, const char hash_mode) + (const tng_trajectory_t tng_data, const char hash_mode) { tng_gen_block_t block; tng_trajectory_frame_set_t frame_set; @@ -1646,7 +1646,7 @@ static tng_function_status tng_frame_set_pointers_update } static tng_function_status tng_reread_frame_set_at_file_pos - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t pos) { tng_gen_block_t block; @@ -1680,7 +1680,7 @@ static tng_function_status tng_reread_frame_set_at_file_pos } static tng_function_status tng_file_pos_of_subsequent_trajectory_block_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t *pos) { int64_t orig_pos, curr_frame_set_pos; @@ -1769,10 +1769,10 @@ static tng_function_status tng_file_pos_of_subsequent_trajectory_block_get * @param hash_mode is an option to decide whether to generate/update the relevant md5 hashes. */ static tng_function_status tng_frame_set_complete_migrate - (tng_trajectory_t tng_data, - int64_t block_start_pos, - int64_t block_len, - int64_t new_pos, + (const tng_trajectory_t tng_data, + const int64_t block_start_pos, + const int64_t block_len, + const int64_t new_pos, const char hash_mode) { tng_bool updated = TNG_FALSE; @@ -1844,7 +1844,7 @@ static tng_function_status tng_frame_set_complete_migrate } static tng_function_status tng_length_of_current_frame_set_contents_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t *len) { int64_t orig_pos, pos, curr_frame_set_pos; @@ -1910,9 +1910,9 @@ static tng_function_status tng_length_of_current_frame_set_contents_get * data. */ static tng_function_status tng_migrate_data_in_file - (tng_trajectory_t tng_data, - int64_t start_pos, - int64_t offset, + (const tng_trajectory_t tng_data, + const int64_t start_pos, + const int64_t offset, const char hash_mode) { int64_t traj_start_pos, empty_space, orig_file_pos, frame_set_length; @@ -1991,7 +1991,7 @@ static tng_function_status tng_migrate_data_in_file static tng_function_status tng_block_header_len_calculate (const tng_trajectory_t tng_data, - tng_gen_block_t block, + const tng_gen_block_t block, int64_t *len) { int name_len; @@ -2034,8 +2034,8 @@ static tng_function_status tng_block_header_len_calculate * error has occured. */ static tng_function_status tng_block_header_write - (tng_trajectory_t tng_data, - tng_gen_block_t block) + (const tng_trajectory_t tng_data, + const tng_gen_block_t block) { TNG_ASSERT(block != 0, "TNG library: Trying to write uninitialized block (NULL pointer)."); @@ -2097,7 +2097,7 @@ static tng_function_status tng_block_header_write } static tng_function_status tng_general_info_block_len_calculate - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t *len) { size_t first_program_name_len, first_user_name_len; @@ -2260,7 +2260,8 @@ static tng_function_status tng_general_info_block_len_calculate * error has occured. */ static tng_function_status tng_general_info_block_read - (tng_trajectory_t tng_data, tng_gen_block_t block, + (const tng_trajectory_t tng_data, + const tng_gen_block_t block, const char hash_mode) { int64_t start_pos; @@ -2400,7 +2401,7 @@ static tng_function_status tng_general_info_block_read * error has occured. */ static tng_function_status tng_general_info_block_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode) { int64_t header_file_pos, curr_file_pos; @@ -2593,8 +2594,8 @@ static tng_function_status tng_general_info_block_write * if hash_mode == TNG_USE_HASH. * @return TNG_SUCCESS(0) is successful. */ -static tng_function_status tng_chain_data_read(tng_trajectory_t tng_data, - tng_chain_t chain, +static tng_function_status tng_chain_data_read(const tng_trajectory_t tng_data, + const tng_chain_t chain, const char hash_mode, md5_state_t *md5_state) { @@ -2626,8 +2627,8 @@ static tng_function_status tng_chain_data_read(tng_trajectory_t tng_data, * if hash_mode == TNG_USE_HASH. * @return TNG_SUCCESS(0) is successful. */ -static tng_function_status tng_chain_data_write(tng_trajectory_t tng_data, - tng_chain_t chain, +static tng_function_status tng_chain_data_write(const tng_trajectory_t tng_data, + const tng_chain_t chain, const char hash_mode, md5_state_t *md5_state) { @@ -2663,8 +2664,8 @@ static tng_function_status tng_chain_data_write(tng_trajectory_t tng_data, * if hash_mode == TNG_USE_HASH. * @return TNG_SUCCESS(0) is successful. */ -static tng_function_status tng_residue_data_read(tng_trajectory_t tng_data, - tng_residue_t residue, +static tng_function_status tng_residue_data_read(const tng_trajectory_t tng_data, + const tng_residue_t residue, const char hash_mode, md5_state_t *md5_state) { @@ -2696,8 +2697,8 @@ static tng_function_status tng_residue_data_read(tng_trajectory_t tng_data, * if hash_mode == TNG_USE_HASH. * @return TNG_SUCCESS(0) is successful. */ -static tng_function_status tng_residue_data_write(tng_trajectory_t tng_data, - tng_residue_t residue, +static tng_function_status tng_residue_data_write(const tng_trajectory_t tng_data, + const tng_residue_t residue, const char hash_mode, md5_state_t *md5_state) { @@ -2733,8 +2734,8 @@ static tng_function_status tng_residue_data_write(tng_trajectory_t tng_data, * if hash_mode == TNG_USE_HASH. * @return TNG_SUCCESS(0) is successful. */ -static tng_function_status tng_atom_data_read(tng_trajectory_t tng_data, - tng_atom_t atom, +static tng_function_status tng_atom_data_read(const tng_trajectory_t tng_data, + const tng_atom_t atom, const char hash_mode, md5_state_t *md5_state) { @@ -2761,8 +2762,8 @@ static tng_function_status tng_atom_data_read(tng_trajectory_t tng_data, * if hash_mode == TNG_USE_HASH. * @return TNG_SUCCESS(0) is successful. */ -static tng_function_status tng_atom_data_write(tng_trajectory_t tng_data, - tng_atom_t atom, +static tng_function_status tng_atom_data_write(const tng_trajectory_t tng_data, + const tng_atom_t atom, const char hash_mode, md5_state_t *md5_state) { @@ -2929,8 +2930,8 @@ static tng_function_status tng_molecules_block_len_calculate * error has occured. */ static tng_function_status tng_molecules_block_read - (tng_trajectory_t tng_data, - tng_gen_block_t block, + (const tng_trajectory_t tng_data, + const tng_gen_block_t block, const char hash_mode) { int64_t start_pos, i, j, k, l; @@ -3317,7 +3318,7 @@ static tng_function_status tng_molecules_block_read * error has occured. */ static tng_function_status tng_molecules_block_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode) { int name_len; @@ -3752,8 +3753,8 @@ static tng_function_status tng_frame_set_block_read * error has occured. */ static tng_function_status tng_frame_set_block_write - (tng_trajectory_t tng_data, - tng_gen_block_t block, + (const tng_trajectory_t tng_data, + const tng_gen_block_t block, const char hash_mode) { char *temp_name; @@ -3930,8 +3931,8 @@ static tng_function_status tng_trajectory_mapping_block_len_calculate * error has occured. */ static tng_function_status tng_trajectory_mapping_block_read - (tng_trajectory_t tng_data, - tng_gen_block_t block, + (const tng_trajectory_t tng_data, + const tng_gen_block_t block, const char hash_mode) { int64_t start_pos, i; @@ -4060,9 +4061,9 @@ static tng_function_status tng_trajectory_mapping_block_read * has occurred or TNG_CRITICAL (2) if a major error has occured. */ static tng_function_status tng_trajectory_mapping_block_write - (tng_trajectory_t tng_data, - tng_gen_block_t block, - int mapping_block_nr, + (const tng_trajectory_t tng_data, + const tng_gen_block_t block, + const int mapping_block_nr, const char hash_mode) { int64_t header_file_pos, curr_file_pos; @@ -4196,7 +4197,7 @@ static tng_function_status tng_trajectory_mapping_block_write * error has occured. */ static tng_function_status tng_particle_data_block_create - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char block_type_flag) { tng_trajectory_frame_set_t frame_set = @@ -4244,8 +4245,8 @@ static tng_function_status tng_particle_data_block_create return(TNG_SUCCESS); } -static tng_function_status tng_compress(tng_trajectory_t tng_data, - tng_gen_block_t block, +static tng_function_status tng_compress(const tng_trajectory_t tng_data, + const tng_gen_block_t block, const int64_t n_frames, const int64_t n_particles, const char type, @@ -4586,8 +4587,8 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -static tng_function_status tng_uncompress(tng_trajectory_t tng_data, - tng_gen_block_t block, +static tng_function_status tng_uncompress(const tng_trajectory_t tng_data, + const tng_gen_block_t block, const char type, char **data, const int64_t uncompressed_len) @@ -4653,7 +4654,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data, } #ifdef USE_ZLIB -static tng_function_status tng_gzip_compress(tng_trajectory_t tng_data, +static tng_function_status tng_gzip_compress(const tng_trajectory_t tng_data, char **data, const int64_t len, int64_t *new_len) { @@ -4695,7 +4696,7 @@ static tng_function_status tng_gzip_compress(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -static tng_function_status tng_gzip_uncompress(tng_trajectory_t tng_data, +static tng_function_status tng_gzip_uncompress(const tng_trajectory_t tng_data, char **data, const int64_t compressed_len, const int64_t uncompressed_len) @@ -4758,10 +4759,10 @@ static tng_function_status tng_gzip_uncompress(tng_trajectory_t tng_data, * error has occured. */ static tng_function_status tng_allocate_particle_data_mem - (tng_trajectory_t tng_data, - tng_data_t data, + (const tng_trajectory_t tng_data, + const tng_data_t data, int64_t n_frames, - int64_t stride_length, + const int64_t stride_length, const int64_t n_particles, const int64_t n_values_per_frame) { @@ -4865,7 +4866,7 @@ static tng_function_status tng_allocate_particle_data_mem } static tng_function_status tng_particle_data_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t id, tng_data_t *data) { @@ -4917,7 +4918,7 @@ static tng_function_status tng_particle_data_find } static tng_function_status tng_data_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t id, tng_data_t *data) { @@ -5091,7 +5092,7 @@ static tng_function_status tng_data_block_len_calculate * error has occured. */ static tng_function_status tng_data_block_create - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char block_type_flag) { tng_trajectory_frame_set_t frame_set = @@ -5148,10 +5149,10 @@ static tng_function_status tng_data_block_create * error has occured. */ static tng_function_status tng_allocate_data_mem - (tng_trajectory_t tng_data, - tng_data_t data, + (const tng_trajectory_t tng_data, + const tng_data_t data, int64_t n_frames, - int64_t stride_length, + const int64_t stride_length, const int64_t n_values_per_frame) { void **values; @@ -5247,6 +5248,7 @@ static tng_function_status tng_allocate_data_mem * @param tng_data is a trajectory data container. * @param block is the block to store the data (should already contain * the block headers and the block contents). + * @param block_data_len is the length of the data contents of the block. * @param datatype is the type of data of the data block (char, int, float or * double). * @param num_first_particle is the number of the first particle in the data @@ -5270,9 +5272,9 @@ static tng_function_status tng_allocate_data_mem * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -static tng_function_status tng_data_read(tng_trajectory_t tng_data, - tng_gen_block_t block, - int64_t block_data_len, +static tng_function_status tng_data_read(const tng_trajectory_t tng_data, + const tng_gen_block_t block, + const int64_t block_data_len, const char datatype, const int64_t num_first_particle, const int64_t n_particles, @@ -5677,8 +5679,8 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, - tng_gen_block_t block, +static tng_function_status tng_data_block_write(const tng_trajectory_t tng_data, + const tng_gen_block_t block, const int64_t block_index, const tng_bool is_particle_data, const tng_particle_mapping_t mapping, @@ -6265,7 +6267,7 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, * error has occured. */ static tng_function_status tng_data_block_meta_information_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, char *datatype, char *dependency, char *sparse_data, @@ -6405,8 +6407,8 @@ static tng_function_status tng_data_block_meta_information_read * error has occured. */ static tng_function_status tng_data_block_contents_read - (tng_trajectory_t tng_data, - tng_gen_block_t block, + (const tng_trajectory_t tng_data, + const tng_gen_block_t block, const char hash_mode) { int64_t start_pos, n_values, codec_id, n_frames, first_frame_with_data; @@ -6578,7 +6580,8 @@ static tng_function_status tng_data_block_contents_read * error has occured. */ static tng_function_status tng_frame_set_finalize - (tng_trajectory_t tng_data, const char hash_mode) + (const tng_trajectory_t tng_data, + const char hash_mode) { tng_gen_block_t block; tng_trajectory_frame_set_t frame_set; @@ -6717,8 +6720,8 @@ tng_function_status tng_atom_name_get(const tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_atom_name_set(tng_trajectory_t tng_data, - tng_atom_t atom, +tng_function_status tng_atom_name_set(const tng_trajectory_t tng_data, + const tng_atom_t atom, const char *new_name) { unsigned int len; @@ -6771,8 +6774,8 @@ tng_function_status tng_atom_type_get(const tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_atom_type_set(tng_trajectory_t tng_data, - tng_atom_t atom, +tng_function_status tng_atom_type_set(const tng_trajectory_t tng_data, + const tng_atom_t atom, const char *new_type) { unsigned int len; @@ -6811,7 +6814,7 @@ tng_function_status tng_atom_type_set(tng_trajectory_t tng_data, * @param atom is the atom to initialise. * @return TNG_SUCCESS (0) if successful. */ -static tng_function_status tng_atom_init(tng_atom_t atom) +static tng_function_status tng_atom_init(const tng_atom_t atom) { atom->name = 0; atom->atom_type = 0; @@ -6824,7 +6827,7 @@ static tng_function_status tng_atom_init(tng_atom_t atom) * @param atom is the atom to destroy. * @return TNG_SUCCESS (0) if successful. */ -static tng_function_status tng_atom_destroy(tng_atom_t atom) +static tng_function_status tng_atom_destroy(const tng_atom_t atom) { if(atom->name) { @@ -6887,7 +6890,7 @@ tng_function_status DECLSPECDLLEXPORT tng_version } tng_function_status DECLSPECDLLEXPORT tng_molecule_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *name, tng_molecule_t *molecule) { @@ -6910,7 +6913,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add } tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *name, const int64_t id, tng_molecule_t *molecule) @@ -6970,7 +6973,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add } tng_function_status DECLSPECDLLEXPORT tng_molecule_existing_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, tng_molecule_t *molecule_p) { int64_t *new_molecule_cnt_list, id; @@ -7059,8 +7062,8 @@ tng_function_status tng_molecule_name_get(const tng_trajectory_t tng_data, } tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *new_name) { unsigned int len; @@ -7122,8 +7125,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get } tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const int64_t cnt) { int64_t i, old_cnt, index = -1; @@ -7165,9 +7168,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set } tng_function_status DECLSPECDLLEXPORT tng_molecule_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *name, - int64_t nr, + const int64_t nr, tng_molecule_t *molecule) { int64_t i, n_molecules; @@ -7196,8 +7199,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_find } tng_function_status DECLSPECDLLEXPORT tng_molecule_of_index_get - (tng_trajectory_t tng_data, - int64_t index, + (const tng_trajectory_t tng_data, + const int64_t index, tng_molecule_t *molecule) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -7212,8 +7215,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_of_index_get return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t tng_data_src, - tng_trajectory_t tng_data_dest) +tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(const tng_trajectory_t tng_data_src, + const tng_trajectory_t tng_data_dest) { tng_molecule_t molecule, molecule_temp; tng_chain_t chain, chain_temp; @@ -7360,9 +7363,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_num_chains_get } tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_of_index_get - (tng_trajectory_t tng_data, - tng_molecule_t molecule, - int64_t index, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, + const int64_t index, tng_chain_t *chain) { (void) tng_data; @@ -7445,10 +7448,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_of_index_get } tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *name, - int64_t nr, + const int64_t nr, tng_chain_t *chain) { int64_t i, n_chains; @@ -7477,8 +7480,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find } tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *name, tng_chain_t *chain) { @@ -7502,8 +7505,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add } tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *name, const int64_t id, tng_chain_t *chain) @@ -7547,7 +7550,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add (const tng_trajectory_t tng_data, - tng_molecule_t molecule, + const tng_molecule_t molecule, const int64_t from_atom_id, const int64_t to_atom_id, tng_bond_t *bond) @@ -7583,10 +7586,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add } tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_find - (tng_trajectory_t tng_data, - tng_molecule_t molecule, + (const tng_trajectory_t tng_data, + const tng_molecule_t molecule, const char *name, - int64_t id, + const int64_t id, tng_atom_t *atom) { int64_t i, n_atoms; @@ -7633,8 +7636,8 @@ tng_function_status tng_chain_name_get(const tng_trajectory_t tng_data, } tng_function_status DECLSPECDLLEXPORT tng_chain_name_set - (tng_trajectory_t tng_data, - tng_chain_t chain, + (const tng_trajectory_t tng_data, + const tng_chain_t chain, const char *new_name) { unsigned int len; @@ -7701,10 +7704,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_of_index_get } tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find - (tng_trajectory_t tng_data, - tng_chain_t chain, + (const tng_trajectory_t tng_data, + const tng_chain_t chain, const char *name, - int64_t id, + const int64_t id, tng_residue_t *residue) { int64_t i, n_residues; @@ -7732,8 +7735,8 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find } tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add - (tng_trajectory_t tng_data, - tng_chain_t chain, + (const tng_trajectory_t tng_data, + const tng_chain_t chain, const char *name, tng_residue_t *residue) { @@ -7757,8 +7760,8 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add } tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add - (tng_trajectory_t tng_data, - tng_chain_t chain, + (const tng_trajectory_t tng_data, + const tng_chain_t chain, const char *name, const int64_t id, tng_residue_t *residue) @@ -7864,8 +7867,8 @@ tng_function_status tng_residue_name_get(const tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(tng_trajectory_t tng_data, - tng_residue_t residue, +tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(const tng_trajectory_t tng_data, + const tng_residue_t residue, const char *new_name) { unsigned int len; @@ -7945,8 +7948,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_of_index_get } tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add - (tng_trajectory_t tng_data, - tng_residue_t residue, + (const tng_trajectory_t tng_data, + const tng_residue_t residue, const char *atom_name, const char *atom_type, tng_atom_t *atom) @@ -7972,8 +7975,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add } tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add - (tng_trajectory_t tng_data, - tng_residue_t residue, + (const tng_trajectory_t tng_data, + const tng_residue_t residue, const char *atom_name, const char *atom_type, const int64_t id, @@ -8057,7 +8060,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_free(const tng_trajectory_t t } tng_function_status DECLSPECDLLEXPORT tng_molecule_init(const tng_trajectory_t tng_data, - tng_molecule_t molecule) + const tng_molecule_t molecule) { (void)tng_data; molecule->quaternary_str = 1; @@ -8075,7 +8078,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_init(const tng_trajectory_t t } tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_t tng_data, - tng_molecule_t molecule) + const tng_molecule_t molecule) { int64_t i; (void)tng_data; @@ -8141,7 +8144,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, - int max_len) + const int max_len) { int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; @@ -8302,7 +8305,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, - int max_len) + const int max_len) { int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; @@ -8354,7 +8357,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, - int max_len) + const int max_len) { int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; @@ -8501,7 +8504,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, - int max_len) + const int max_len) { int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; @@ -8549,7 +8552,7 @@ tng_function_status tng_atom_type_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *type, - int max_len) + const int max_len) { int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; @@ -8594,7 +8597,7 @@ tng_function_status tng_atom_type_of_particle_nr_get } tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t num_first_particle, const int64_t n_particles, const int64_t *mapping_table) @@ -8679,7 +8682,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free(tng_trajectory_t tng_data) +tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free(const tng_trajectory_t tng_data) { tng_trajectory_frame_set_t frame_set; tng_particle_mapping_t mapping; @@ -9229,8 +9232,9 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajectory_t src, - tng_trajectory_t *dest_p) +tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src + (const tng_trajectory_t src, + tng_trajectory_t *dest_p) { tng_trajectory_frame_set_t frame_set; tng_trajectory_t dest; @@ -9365,8 +9369,10 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajector return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_input_file_get(const tng_trajectory_t tng_data, - char *file_name, const int max_len) +tng_function_status DECLSPECDLLEXPORT tng_input_file_get + (const tng_trajectory_t tng_data, + char *file_name, + const int max_len) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(file_name, "TNG library: file_name must not be a NULL pointer"); @@ -9381,8 +9387,9 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_get(const tng_trajectory_t return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_input_file_set(tng_trajectory_t tng_data, - const char *file_name) +tng_function_status DECLSPECDLLEXPORT tng_input_file_set + (const tng_trajectory_t tng_data, + const char *file_name) { unsigned int len; char *temp; @@ -9419,8 +9426,10 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_set(tng_trajectory_t tng_da return(tng_input_file_init(tng_data)); } -tng_function_status tng_output_file_get(const tng_trajectory_t tng_data, - char *file_name, const int max_len) +tng_function_status tng_output_file_get + (const tng_trajectory_t tng_data, + char *file_name, + const int max_len) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(file_name, "TNG library: file_name must not be a NULL pointer"); @@ -9435,8 +9444,9 @@ tng_function_status tng_output_file_get(const tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_output_file_set(tng_trajectory_t tng_data, - const char *file_name) +tng_function_status DECLSPECDLLEXPORT tng_output_file_set + (const tng_trajectory_t tng_data, + const char *file_name) { int len; char *temp; @@ -9473,7 +9483,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_set(tng_trajectory_t tng_d } tng_function_status DECLSPECDLLEXPORT tng_output_append_file_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *file_name) { int len; @@ -9597,7 +9607,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_get } tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const tng_file_endianness endianness) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -9661,7 +9671,8 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_set tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get (const tng_trajectory_t tng_data, - char *name, const int max_len) + char *name, + const int max_len) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(name, "TNG library: name must not be a NULL pointer"); @@ -9676,8 +9687,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set(tng_trajectory_t tng_data, - const char *new_name) +tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set + (const tng_trajectory_t tng_data, + const char *new_name) { unsigned int len; @@ -9725,7 +9737,7 @@ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get } tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name) { unsigned int len; @@ -9774,7 +9786,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get } tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name) { unsigned int len; @@ -9825,7 +9837,7 @@ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get } tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name) { unsigned int len; @@ -9876,7 +9888,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get } tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name) { unsigned int len; @@ -9927,7 +9939,7 @@ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get } tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name) { unsigned int len; @@ -9979,7 +9991,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_signature_get } tng_function_status DECLSPECDLLEXPORT tng_first_signature_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *signature) { unsigned int len; @@ -10031,7 +10043,7 @@ tng_function_status DECLSPECDLLEXPORT tng_last_signature_get } tng_function_status DECLSPECDLLEXPORT tng_last_signature_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *signature) { unsigned int len; @@ -10083,7 +10095,7 @@ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get } tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *new_name) { unsigned int len; @@ -10129,7 +10141,7 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get } tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t len) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -10156,7 +10168,7 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get } tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t len) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -10183,7 +10195,7 @@ tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_get } tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const double time) { tng_trajectory_frame_set_t frame_set; @@ -10290,7 +10302,7 @@ tng_function_status DECLSPECDLLEXPORT tng_compression_precision_get } tng_function_status DECLSPECDLLEXPORT tng_compression_precision_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const double precision) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -10301,7 +10313,7 @@ tng_function_status DECLSPECDLLEXPORT tng_compression_precision_set } tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t n) { tng_molecule_t mol; @@ -10711,7 +10723,7 @@ tng_function_status DECLSPECDLLEXPORT tng_current_frame_set_get } tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t nr) { int64_t long_stride_length, medium_stride_length; @@ -11035,7 +11047,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find } tng_function_status DECLSPECDLLEXPORT tng_frame_set_of_frame_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame) { int64_t first_frame, last_frame, n_frames_per_frame_set; @@ -11551,7 +11563,7 @@ static TNG_INLINE tng_function_status tng_particle_mapping_get_real_particle */ static tng_function_status tng_file_headers_len_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t *len) { int64_t orig_pos; @@ -11590,7 +11602,7 @@ static tng_function_status tng_file_headers_len_get } tng_function_status DECLSPECDLLEXPORT tng_file_headers_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode) { int64_t prev_pos = 0; @@ -11631,7 +11643,7 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_read } tng_function_status DECLSPECDLLEXPORT tng_file_headers_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode) { int i; @@ -11751,9 +11763,10 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_write return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_block_read_next(tng_trajectory_t tng_data, - tng_gen_block_t block, - const char hash_mode) +tng_function_status DECLSPECDLLEXPORT tng_block_read_next + (const tng_trajectory_t tng_data, + const tng_gen_block_t block, + const char hash_mode) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(block, "TNG library: block must be initialised and must not be a NULL pointer."); @@ -11783,7 +11796,7 @@ tng_function_status DECLSPECDLLEXPORT tng_block_read_next(tng_trajectory_t tng_d } tng_function_status DECLSPECDLLEXPORT tng_frame_set_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode) { int64_t file_pos; @@ -11858,7 +11871,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_current_only_data_from_block_id - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode, const int64_t block_id) { @@ -11985,7 +11998,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_current_only_data_from_ } tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode) { int64_t file_pos; @@ -12019,7 +12032,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next } tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next_only_data_from_block_id - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode, const int64_t block_id) { @@ -12077,8 +12090,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next_only_data_from_blo return(stat); } -tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, - const char hash_mode) +tng_function_status tng_frame_set_write + (const tng_trajectory_t tng_data, + const char hash_mode) { int i, j; tng_gen_block_t block; @@ -12172,7 +12186,7 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, } tng_function_status DECLSPECDLLEXPORT tng_frame_set_premature_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char hash_mode) { tng_trajectory_frame_set_t frame_set; @@ -12191,7 +12205,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_premature_write } tng_function_status DECLSPECDLLEXPORT tng_frame_set_new - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames) { @@ -12376,7 +12390,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new } tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames, const double first_frame_time) @@ -12400,7 +12414,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new } tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const double first_frame_time) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -12470,7 +12484,7 @@ tng_function_status DECLSPECDLLEXPORT tng_first_frame_nr_of_next_frame_set_get } static tng_function_status tng_gen_data_block_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t id, const tng_bool is_particle_data, const char *block_name, @@ -12732,7 +12746,7 @@ static tng_function_status tng_gen_data_block_add } tng_function_status DECLSPECDLLEXPORT tng_data_block_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, @@ -12753,7 +12767,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add } tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, @@ -12779,10 +12793,10 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add } tng_function_status DECLSPECDLLEXPORT tng_data_block_name_get - (tng_trajectory_t tng_data, - int64_t block_id, + (const tng_trajectory_t tng_data, + const int64_t block_id, char *name, - int max_len) + const int max_len) { int64_t i; tng_trajectory_frame_set_t frame_set; @@ -12882,7 +12896,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_name_get tng_function_status DECLSPECDLLEXPORT tng_data_block_dependency_get (const tng_trajectory_t tng_data, - int64_t block_id, + const int64_t block_id, int *block_dependency) { int64_t i; @@ -12955,7 +12969,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_dependency_get tng_function_status DECLSPECDLLEXPORT tng_data_block_num_values_per_frame_get (const tng_trajectory_t tng_data, - int64_t block_id, + const int64_t block_id, int64_t *n_values_per_frame) { int64_t i; @@ -13027,7 +13041,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_num_values_per_frame_get } tng_function_status DECLSPECDLLEXPORT tng_frame_set_n_frames_of_data_block_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, int64_t *n_frames) { @@ -13108,7 +13122,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_n_frames_of_data_block_get } static tng_function_status tng_frame_gen_data_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const int64_t block_id, const tng_bool is_particle_data, @@ -13594,7 +13608,7 @@ static tng_function_status tng_frame_gen_data_write } tng_function_status DECLSPECDLLEXPORT tng_frame_data_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const int64_t block_id, const void *values, @@ -13612,7 +13626,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_data_write } tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const int64_t block_id, const int64_t val_first_particle, @@ -13844,9 +13858,9 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free } static tng_function_status tng_gen_data_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, - tng_bool is_particle_data, + const tng_bool is_particle_data, union data_values ****values, int64_t *n_frames, int64_t *n_particles, @@ -14118,7 +14132,7 @@ static tng_function_status tng_gen_data_get } tng_function_status DECLSPECDLLEXPORT tng_data_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, union data_values ***values, int64_t *n_frames, @@ -14135,7 +14149,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get } static tng_function_status tng_gen_data_vector_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const tng_bool is_particle_data, void **values, @@ -14308,7 +14322,7 @@ static tng_function_status tng_gen_data_vector_get } tng_function_status DECLSPECDLLEXPORT tng_data_vector_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, void **values, int64_t *n_frames, @@ -14328,9 +14342,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_get } static tng_function_status tng_gen_data_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, - tng_bool is_particle_data, + const tng_bool is_particle_data, const int64_t start_frame_nr, const int64_t end_frame_nr, const char hash_mode, @@ -14651,7 +14665,7 @@ static tng_function_status tng_gen_data_interval_get } tng_function_status DECLSPECDLLEXPORT tng_data_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const int64_t start_frame_nr, const int64_t end_frame_nr, @@ -14671,9 +14685,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get } static tng_function_status tng_gen_data_vector_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, - tng_bool is_particle_data, + const tng_bool is_particle_data, const int64_t start_frame_nr, const int64_t end_frame_nr, const char hash_mode, @@ -14937,7 +14951,7 @@ static tng_function_status tng_gen_data_vector_interval_get tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const int64_t start_frame_nr, const int64_t end_frame_nr, @@ -14960,7 +14974,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get } tng_function_status DECLSPECDLLEXPORT tng_particle_data_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, union data_values ****values, int64_t *n_frames, @@ -14979,7 +14993,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get } tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, void **values, int64_t *n_frames, @@ -15000,7 +15014,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get } tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const int64_t start_frame_nr, const int64_t end_frame_nr, @@ -15022,7 +15036,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get } tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, const int64_t start_frame_nr, const int64_t end_frame_nr, @@ -15270,7 +15284,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close } tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, double *time) { @@ -15304,7 +15318,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get /* tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t *n_mols, int64_t **molecule_cnt_list, tng_molecule_t *mols) @@ -15333,7 +15347,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get */ /* tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const char *name, const int64_t cnt, tng_molecule_t *mol) @@ -15354,7 +15368,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add } */ tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const tng_molecule_t mol, int64_t *n_particles, char ***names, @@ -15400,8 +15414,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get } tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_set - (tng_trajectory_t tng_data, - tng_molecule_t mol, + (const tng_trajectory_t tng_data, + const tng_molecule_t mol, const int64_t n_particles, const char **names, const char **types, @@ -15456,7 +15470,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_set } tng_function_status DECLSPECDLLEXPORT tng_util_pos_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, float **positions, int64_t *stride_length) { int64_t n_frames, n_particles, n_values_per_frame; @@ -15485,7 +15499,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read } tng_function_status DECLSPECDLLEXPORT tng_util_vel_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, float **velocities, int64_t *stride_length) { int64_t n_frames, n_particles, n_values_per_frame; @@ -15514,7 +15528,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read } tng_function_status DECLSPECDLLEXPORT tng_util_force_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, float **forces, int64_t *stride_length) { int64_t n_frames, n_particles, n_values_per_frame; @@ -15543,7 +15557,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, float **box_shape, int64_t *stride_length) { @@ -15572,7 +15586,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read } tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, void **values, char *data_type, @@ -15736,7 +15750,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read } tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, void **values, char *data_type, @@ -15895,7 +15909,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read } tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t last_frame, float **positions, @@ -15928,7 +15942,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range } tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t last_frame, float **velocities, @@ -15961,7 +15975,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range } tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t last_frame, float **forces, @@ -15994,7 +16008,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t first_frame, const int64_t last_frame, float **box_shape, @@ -16026,7 +16040,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range } tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i, const int64_t n_values_per_frame, const int64_t block_id, @@ -16167,7 +16181,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set } tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i, const int64_t n_values_per_frame, const int64_t block_id, @@ -16286,7 +16300,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_double_set } tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i, const int64_t n_values_per_frame, const int64_t block_id, @@ -16302,7 +16316,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set compression)); } tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -16316,7 +16330,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_set } tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -16330,7 +16344,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_double_set } tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { fprintf(stderr, "TNG library: Using obsolete function tng_util_pos_write_frequency_set(). " @@ -16339,7 +16353,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequency_set } tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -16353,7 +16367,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_set } tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -16367,7 +16381,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_double_set } tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { fprintf(stderr, "TNG library: Using obsolete function tng_util_vel_write_frequency_set(). " @@ -16376,7 +16390,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequency_set } tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -16390,7 +16404,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_set } tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -16404,7 +16418,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_double_set } tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { fprintf(stderr, "TNG library: Using obsolete function tng_util_force_write_frequency_set(). " @@ -16413,7 +16427,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequency_set } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -16427,7 +16441,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_set } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_double_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -16441,7 +16455,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_double_s } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_frequency_set - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t i) { fprintf(stderr, "TNG library: Using obsolete function tng_util_box_shape_write_frequency_set(). " @@ -16450,7 +16464,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_frequency_set } tng_function_status DECLSPECDLLEXPORT tng_util_generic_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *values, const int64_t n_values_per_frame, @@ -16662,7 +16676,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write } tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *values, const int64_t n_values_per_frame, @@ -16875,7 +16889,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_pos_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *positions) { @@ -16889,7 +16903,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write } tng_function_status DECLSPECDLLEXPORT tng_util_pos_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *positions) { @@ -16903,7 +16917,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_vel_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *velocities) { @@ -16917,7 +16931,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write } tng_function_status DECLSPECDLLEXPORT tng_util_vel_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *velocities) { @@ -16931,7 +16945,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_force_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *forces) { @@ -16945,7 +16959,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write } tng_function_status DECLSPECDLLEXPORT tng_util_force_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *forces) { @@ -16959,7 +16973,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const float *box_shape) { @@ -16973,7 +16987,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double *box_shape) { @@ -16987,7 +17001,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *values, @@ -17037,7 +17051,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_write } tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *values, @@ -17087,7 +17101,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *positions) @@ -17104,7 +17118,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_write } tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *positions) @@ -17123,7 +17137,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *velocities) @@ -17142,7 +17156,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_write } tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *velocities) @@ -17161,7 +17175,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *forces) @@ -17178,7 +17192,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_write } tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *forces) @@ -17196,7 +17210,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const float *box_shape) @@ -17213,7 +17227,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_write } tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t frame_nr, const double time, const double *box_shape) @@ -17232,7 +17246,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write } tng_function_status DECLSPECDLLEXPORT tng_util_frame_current_compression_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, int64_t *codec_id, double *factor) @@ -17342,7 +17356,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_frame_current_compression_get } tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_next_frame_present_data_blocks_find - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t current_frame, const int64_t n_requested_data_block_ids, const int64_t *requested_data_block_ids, @@ -17630,7 +17644,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_next_frame_present_dat /* tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_all_data_block_types_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, int64_t *n_data_blocks, int64_t **data_block_ids, char ***data_block_names, @@ -17680,7 +17694,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_all_data_block_types_g } */ tng_function_status DECLSPECDLLEXPORT tng_util_prepare_append_after_frame - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t prev_frame) { tng_function_status stat; @@ -17706,7 +17720,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_prepare_append_after_frame } tng_function_status DECLSPECDLLEXPORT tng_util_num_frames_with_data_of_block_id_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, const int64_t block_id, int64_t *n_frames) { |