diff options
Diffstat (limited to 'include/compression')
| -rw-r--r-- | include/compression/bwlzh.h | 74 | ||||
| -rw-r--r-- | include/compression/bwt.h | 28 | ||||
| -rw-r--r-- | include/compression/coder.h | 42 | ||||
| -rw-r--r-- | include/compression/dict.h | 23 | ||||
| -rw-r--r-- | include/compression/fixpoint.h | 45 | ||||
| -rw-r--r-- | include/compression/huffman.h | 35 | ||||
| -rw-r--r-- | include/compression/lz77.h | 27 | ||||
| -rw-r--r-- | include/compression/merge_sort.h | 22 | ||||
| -rw-r--r-- | include/compression/mtf.h | 37 | ||||
| -rw-r--r-- | include/compression/my64bit.h | 67 | ||||
| -rw-r--r-- | include/compression/rle.h | 24 | ||||
| -rw-r--r-- | include/compression/tng_compress.h | 165 | ||||
| -rw-r--r-- | include/compression/vals16.h | 23 | ||||
| -rw-r--r-- | include/compression/warnmalloc.h | 32 | ||||
| -rw-r--r-- | include/compression/widemuldiv.h | 33 |
15 files changed, 677 insertions, 0 deletions
diff --git a/include/compression/bwlzh.h b/include/compression/bwlzh.h new file mode 100644 index 0000000..3e58d2d --- /dev/null +++ b/include/compression/bwlzh.h @@ -0,0 +1,74 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef BWLZH_H +#define BWLZH_H + +/* Compress the integers (positive, small integers are preferable) + using bwlzh compression. The unsigned char *output should be + 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, + unsigned char *output, int *output_len); + +void DECLSPECDLLEXPORT bwlzh_compress_no_lz77(unsigned int *vals, int nvals, + unsigned char *output, int *output_len); + +int DECLSPECDLLEXPORT bwlzh_get_buflen(int nvals); + +void DECLSPECDLLEXPORT bwlzh_decompress(unsigned char *input, 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, + unsigned char *output, int *output_len); + +void DECLSPECDLLEXPORT bwlzh_compress_no_lz77_verbose(unsigned int *vals, int nvals, + unsigned char *output, int *output_len); + +void DECLSPECDLLEXPORT bwlzh_decompress_verbose(unsigned char *input, int nvals, + unsigned int *vals); + +/* Compress the integers (positive, small integers are preferable) + using huffman coding, with automatic selection of how to handle the + huffman dictionary. The unsigned char *huffman should be allocated + 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, + unsigned char *huffman, int *huffman_len); + +int Ptngc_comp_huff_buflen(int nvals); + +void Ptngc_comp_huff_decompress(unsigned char *huffman, int huffman_len, + unsigned int *vals); + + +/* the value pointed to by chosen_algo should be + sent as -1 for autodetect. */ +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); + +#define N_HUFFMAN_ALGO 3 +char *Ptngc_comp_get_huff_algo_name(int algo); +char *Ptngc_comp_get_algo_name(int algo); + + +#endif diff --git a/include/compression/bwt.h b/include/compression/bwt.h new file mode 100644 index 0000000..e95f7ee --- /dev/null +++ b/include/compression/bwt.h @@ -0,0 +1,28 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef BWT_H +#define BWT_H + +void Ptngc_comp_to_bwt(unsigned int *vals, int nvals, + unsigned int *output, int *index); + +void Ptngc_comp_from_bwt(unsigned int *input, 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); + +#endif diff --git a/include/compression/coder.h b/include/compression/coder.h new file mode 100644 index 0000000..5cef38a --- /dev/null +++ b/include/compression/coder.h @@ -0,0 +1,42 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + +#ifndef CODER_H +#define CODER_H + +struct coder +{ + unsigned int pack_temporary; + int pack_temporary_bits; + int stat_overflow; + int stat_numval; +}; + +struct coder *Ptngc_coder_init(void); +void Ptngc_coder_deinit(struct coder *coder); +unsigned char *Ptngc_pack_array(struct coder *coder,int *input, int *length, int coding, int coding_parameter, int natoms, int speed); +int Ptngc_unpack_array(struct coder *coder,unsigned char *packed,int *output, int length, int coding, int coding_parameter, int natoms); +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); +unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int speed); +int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int natoms); + +void Ptngc_out8bits(struct coder *coder, unsigned char **output); +void Ptngc_pack_flush(struct coder *coder,unsigned char **output); +void Ptngc_write_pattern(struct coder *coder,unsigned int pattern, int nbits, unsigned char **output); + +void Ptngc_writebits(struct coder *coder,unsigned int value,int nbits, unsigned char **output_ptr); +void Ptngc_write32bits(struct coder *coder,unsigned int value,int nbits, unsigned char **output_ptr); +void Ptngc_writemanybits(struct coder *coder,unsigned char *value,int nbits, unsigned char **output_ptr); + + +#endif diff --git a/include/compression/dict.h b/include/compression/dict.h new file mode 100644 index 0000000..e29b17f --- /dev/null +++ b/include/compression/dict.h @@ -0,0 +1,23 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef DICT_H +#define DICT_H + +void Ptngc_comp_canonical_dict(unsigned int *dict, int *ndict); + +void Ptngc_comp_make_dict_hist(unsigned int *vals, int nvals, + unsigned int *dict, int *ndict, + unsigned int *hist); + +#endif diff --git a/include/compression/fixpoint.h b/include/compression/fixpoint.h new file mode 100644 index 0000000..d20d5e1 --- /dev/null +++ b/include/compression/fixpoint.h @@ -0,0 +1,45 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + +#ifndef FIXPOINT_H +#define FIXPOINT_H + +#if HAVE_CONFIG_H +#include <config.h> +#endif + +#include "my64bit.h" + +/* There are at least 32 bits available in a long. */ +typedef unsigned long fix_t; + +/* Positive double to 32 bit fixed point value */ +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); + +/* 32 bit fixed point value to positive double */ +double Ptngc_fix_t_to_ud(fix_t f, double max); + +/* signed 32 bit fixed point value to double */ +double Ptngc_fix_t_to_d(fix_t f, 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. */ +void Ptngc_d_to_i32x2(double d, fix_t *hi, fix_t *lo); + +/* Convert two 32 bit integers to a floating point variable + -2.1e9 to 2.1e9 and precision to somewhere around 1e-9. */ +double Ptngc_i32x2_to_d(fix_t hi, fix_t lo); + +#endif diff --git a/include/compression/huffman.h b/include/compression/huffman.h new file mode 100644 index 0000000..c36e94d --- /dev/null +++ b/include/compression/huffman.h @@ -0,0 +1,35 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef HUFFMAN_H +#define HUFFMAN_H + +void Ptngc_comp_conv_to_huffman(unsigned int *vals, int nvals, + unsigned int *dict, int ndict, + unsigned int *prob, + unsigned char *huffman, + int *huffman_len, + unsigned char *huffman_dict, + int *huffman_dictlen, + unsigned int *huffman_dict_unpacked, + int *huffman_dict_unpackedlen); + +void Ptngc_comp_conv_from_huffman(unsigned char *huffman, + unsigned int *vals, int nvals, + int ndict, + unsigned char *huffman_dict, + int huffman_dictlen, + unsigned int *huffman_dict_unpacked, + int huffman_dict_unpackedlen); + +#endif diff --git a/include/compression/lz77.h b/include/compression/lz77.h new file mode 100644 index 0000000..e811256 --- /dev/null +++ b/include/compression/lz77.h @@ -0,0 +1,27 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef LZ77_H +#define LZ77_H + +void Ptngc_comp_to_lz77(unsigned int *vals, 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); + +#endif diff --git a/include/compression/merge_sort.h b/include/compression/merge_sort.h new file mode 100644 index 0000000..970d5ee --- /dev/null +++ b/include/compression/merge_sort.h @@ -0,0 +1,22 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef MERGE_SORT_H +#define MERGE_SORT_H + +void Ptngc_merge_sort(void *base, size_t nmemb, size_t size, + int (*compar)(const void *v1,const void *v2,const void *private), + void *private); + + +#endif diff --git a/include/compression/mtf.h b/include/compression/mtf.h new file mode 100644 index 0000000..9c5e175 --- /dev/null +++ b/include/compression/mtf.h @@ -0,0 +1,37 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef MTF_H +#define MTF_H + +void Ptngc_comp_conv_to_mtf(unsigned int *vals, int nvals, + unsigned int *dict, int ndict, + unsigned int *valsmtf); + +void Ptngc_comp_conv_from_mtf(unsigned int *valsmtf, int nvals, + unsigned int *dict, int ndict, + unsigned int *vals); + +void Ptngc_comp_conv_to_mtf_partial(unsigned int *vals, int nvals, + unsigned int *valsmtf); + +void Ptngc_comp_conv_from_mtf_partial(unsigned int *valsmtf, int nvals, + unsigned int *vals); + +void Ptngc_comp_conv_to_mtf_partial3(unsigned int *vals, int nvals, + unsigned char *valsmtf); + +void Ptngc_comp_conv_from_mtf_partial3(unsigned char *valsmtf, int nvals, + unsigned int *vals); + +#endif diff --git a/include/compression/my64bit.h b/include/compression/my64bit.h new file mode 100644 index 0000000..fb2d5d0 --- /dev/null +++ b/include/compression/my64bit.h @@ -0,0 +1,67 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +/* Here presence of 64 bit integers are checked for. If on windows + define USE_WINDOWS if it does not get defined automatically. + If on UNIX, define the sizes of SIZEOF_INT, SIZEOF_LONG, SIZEOF_LONG_LONG + If none of these symbols are defined, stdint.h is included (if on C99 + or USE_STDINT is defined) and 64 bit integers are assumed to be + present. If none of this is fulfilled, 64 bit integers are not + available. */ + +#ifndef MY64BIT_H +#define MY64BIT_H + +#if HAVE_CONFIG_H +#include <config.h> +#endif + +#if HAVE_STDINT_H +#include <stdint.h> +#endif + +/* The USE_WINDOWS symbol should be automatically defined in tng_compress.h */ +#include "tng_compress.h" + +#ifdef USE_WINDOWS +typedef __int64 my_int64_t; +typedef unsigned __int64 my_uint64_t; +#define HAVE64BIT +#else /* USE_WINDOWS */ +/* UNIX. Use config.h */ +#if SIZEOF_INT >= 8 +typedef int my_int64_t; +typedef unsigned int my_uint64_t; +#define HAVE64BIT +#else /* SIZEOF_INT */ +#if SIZEOF_LONG >= 8 +typedef long my_int64_t; +typedef unsigned long my_uint64_t; +#define HAVE64BIT +#else /* SIZEOF_LONG */ +#if SIZEOF_LONG_LONG >= 8 +typedef long long my_int64_t; +typedef unsigned long long my_uint64_t; +#define HAVE64BIT +#else /* SIZEOF_LONG_LONG */ +#if HAVE_STDINT_H +typedef int64_t my_int64_t; +typedef uint64_t my_uint64_t; +#define HAVE64BIT +#endif /* STDINT_H */ +#endif /* SIZEOF_LONG_LONG */ +#endif /* SIZEOF_LONG */ +#endif /* SIZEOF_INT */ +#endif /* USE_WINDOWS */ + +#endif diff --git a/include/compression/rle.h b/include/compression/rle.h new file mode 100644 index 0000000..3adf8dc --- /dev/null +++ b/include/compression/rle.h @@ -0,0 +1,24 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#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_from_rle(unsigned int *rle, + unsigned int *vals, int nvals); + +#endif diff --git a/include/compression/tng_compress.h b/include/compression/tng_compress.h new file mode 100644 index 0000000..eefcfaa --- /dev/null +++ b/include/compression/tng_compress.h @@ -0,0 +1,165 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + +#ifndef TNG_COMPRESS_H +#define TNG_COMPRESS_H + +#ifndef USE_WINDOWS +#if defined(WIN32) || defined(_WIN32) || defined(WIN64) || defined(_WIN64) +#define USE_WINDOWS +#endif /* win32... */ +#endif /* not defined USE_WINDOWS */ + +#ifdef USE_WINDOWS +#define DECLSPECDLLEXPORT __declspec(dllexport) +#else +#define DECLSPECDLLEXPORT +#endif + +#ifdef __cplusplus + extern "C" { +#endif + +/* tng_compress_pos expects positions to have the order: + first xyz, then sorted in atom order + then all the frames repeated, i.e.: + nframes * [ + natoms* [ + x, y, z + ] + ] + desired_precision what to round the numbers to, i.e. integers will be created as: + round(pos[]/desired_precision). + + algo should first be determined by calling + tng_compress_pos_find_algo + + The compressed data is returned in a malloced pointer (so free can + be called to free the memory), the number of chars in the compressed + data is put into *nitems. +*/ + +char DECLSPECDLLEXPORT *tng_compress_pos(double *pos, int natoms, int nframes, + double desired_precision, + int speed, int *algo, + int *nitems); + + +/* The tng_compress_pos_find_algo works the same as tng_compress_pos, but + it performs benchmarking to find the algorithms with the best + compression ratio. + The search is controlled by giving speed: + speed=1: Fast algorithms only. This excludes all BWLZH algorithms and + the XTC3 algorithm. + speed=2: Same as 1 and also includes the XTC3 algorithm using base compression + only. + speed=3: Same as 2 and also includes the XTC3 algorithm which will use BWLZH + compression when it seems likely to give better + compression. Also includes the interframe BWLZH algorithm for + coordinates and velocities. + speed=4: Enable the inter frame BWLZH algorithm for the coordinates. + The one-to-one BWLZH algorithm is enabled for velocities. + speed=5: Enable the LZ77 part of the BWLZH algorithm. + speed=6: Enable the intra frame BWLZH algorithm for the coordinates. Always try + the BWLZH compression in the XTC3 algorithm. + + Set speed=0 to allow tng_compression to set the default speed (which is currently 2). + For very good compression it makes sense to choose speed=4 or speed=5 + + The number of items required in the algorithm array can be found + by calling tng_compress_nalgo +*/ + +char DECLSPECDLLEXPORT *tng_compress_pos_find_algo(double *pos, int natoms, int nframes, + double desired_precision, + int speed, + int *algo, + int *nitems); + +/* This returns the number of integers required for the storage of the algorithm + with the best compression ratio. */ +int DECLSPECDLLEXPORT tng_compress_nalgo(void); + +/* The following two routines does the same as the compression of the + positions, but compresses velocities instead. The algorithm + 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, + int *nitems); + +char DECLSPECDLLEXPORT *tng_compress_vel_find_algo(double *vel, int natoms, int nframes, + double desired_precision, + int speed, + int *algo, + int *nitems); + +/* From a compressed block, obtain information about + whether it is a position or velocity block: + *vel=1 means velocity block, *vel=0 means position block. + It also gives info about the number of atoms, + frames, and the precision used to compress the block, and the algorithms used to + compress the block. The return value=0 if the block looks like a tng compressed block, + and 1 otherwise. If the return value is 1 no information is returned. */ +int DECLSPECDLLEXPORT tng_compress_inquire(char *data,int *vel, int *natoms, + int *nframes, double *precision, + int *algo); + +/* Uncompresses any tng compress block, positions or velocities. It determines whether it is positions or velocities from the data buffer. The return value is 0 if ok, and 1 if not. +*/ +int DECLSPECDLLEXPORT tng_compress_uncompress(char *data,double *posvel); + + + /* Compression algorithms (matching the original trajng + assignments) The compression backends require that some of the + algorithms must have the same value. */ + +#define TNG_COMPRESS_ALGO_STOPBIT 1 +#define TNG_COMPRESS_ALGO_TRIPLET 2 +#define TNG_COMPRESS_ALGO_BWLZH1 8 +#define TNG_COMPRESS_ALGO_BWLZH2 9 + +#define TNG_COMPRESS_ALGO_POS_STOPBIT_INTER TNG_COMPRESS_ALGO_STOPBIT +#define TNG_COMPRESS_ALGO_POS_TRIPLET_INTER TNG_COMPRESS_ALGO_TRIPLET +#define TNG_COMPRESS_ALGO_POS_TRIPLET_INTRA 3 +#define TNG_COMPRESS_ALGO_POS_XTC2 5 +#define TNG_COMPRESS_ALGO_POS_TRIPLET_ONETOONE 7 +#define TNG_COMPRESS_ALGO_POS_BWLZH_INTER TNG_COMPRESS_ALGO_BWLZH1 +#define TNG_COMPRESS_ALGO_POS_BWLZH_INTRA TNG_COMPRESS_ALGO_BWLZH2 +#define TNG_COMPRESS_ALGO_POS_XTC3 10 +#define TNG_COMPRESS_ALGO_VEL_STOPBIT_ONETOONE TNG_COMPRESS_ALGO_STOPBIT +#define TNG_COMPRESS_ALGO_VEL_TRIPLET_INTER TNG_COMPRESS_ALGO_TRIPLET +#define TNG_COMPRESS_ALGO_VEL_TRIPLET_ONETOONE 3 +#define TNG_COMPRESS_ALGO_VEL_STOPBIT_INTER 6 +#define TNG_COMPRESS_ALGO_VEL_BWLZH_INTER TNG_COMPRESS_ALGO_BWLZH1 +#define TNG_COMPRESS_ALGO_VEL_BWLZH_ONETOONE TNG_COMPRESS_ALGO_BWLZH2 +#define TNG_COMPRESS_ALGO_MAX 11 + + + +/* Obtain strings describing the actual algorithms. These point to static memory, so should + not be freed. */ +char DECLSPECDLLEXPORT *tng_compress_initial_pos_algo(int *algo); +char DECLSPECDLLEXPORT *tng_compress_pos_algo(int *algo); +char DECLSPECDLLEXPORT *tng_compress_initial_vel_algo(int *algo); +char DECLSPECDLLEXPORT *tng_compress_vel_algo(int *algo); + + + +#ifdef __cplusplus + } +#endif + + +#endif diff --git a/include/compression/vals16.h b/include/compression/vals16.h new file mode 100644 index 0000000..a8acdf4 --- /dev/null +++ b/include/compression/vals16.h @@ -0,0 +1,23 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#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_from_vals16(unsigned int *vals16,int nvals16, + unsigned int *vals, int *nvals); + +#endif diff --git a/include/compression/warnmalloc.h b/include/compression/warnmalloc.h new file mode 100644 index 0000000..c2eb28d --- /dev/null +++ b/include/compression/warnmalloc.h @@ -0,0 +1,32 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef WARNMALLOC_H +#define WARNMALLOC_H + +#if HAVE_CONFIG_H +#include <config.h> +#endif + +#include "tng_compress.h" + +void DECLSPECDLLEXPORT *Ptngc_warnmalloc_x(size_t size, char *file, 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); + +#define warnrealloc(old,size) Ptngc_warnrealloc_x(old,size,__FILE__,__LINE__) + + +#endif diff --git a/include/compression/widemuldiv.h b/include/compression/widemuldiv.h new file mode 100644 index 0000000..b7574fa --- /dev/null +++ b/include/compression/widemuldiv.h @@ -0,0 +1,33 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + + +#ifndef WIDEMULDIV_H +#define WIDEMULDIV_H + +/* Multiply two 32 bit unsigned integers returning a 64 bit unsigned value (in two integers) */ +void Ptngc_widemul(unsigned int i1, unsigned int i2, unsigned int *ohi, unsigned int *olo); + +/* 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 */ +void Ptngc_widediv(unsigned int hi, unsigned int lo, unsigned int i, unsigned int *result, unsigned int *remainder); + +/* Add a unsigned int to a largeint. */ +void Ptngc_largeint_add(unsigned int v1, unsigned int *largeint, int n); + +/* Multiply v1 with largeint_in and return result in largeint_out */ +void Ptngc_largeint_mul(unsigned int v1, unsigned int *largeint_in, unsigned int *largeint_out, int n); + +/* Return the remainder from dividing largeint_in with v1. Result of the division is returned in largeint_out */ +unsigned int Ptngc_largeint_div(unsigned int v1, unsigned int *largeint_in, unsigned int *largeint_out, int n); + +#endif |