diff options
Diffstat (limited to 'include')
| -rw-r--r-- | include/compression/bwlzh.h | 6 | ||||
| -rw-r--r-- | include/compression/bwt.h | 4 | ||||
| -rw-r--r-- | include/compression/coder.h | 4 | ||||
| -rw-r--r-- | include/compression/dict.h | 4 | ||||
| -rw-r--r-- | include/compression/fixpoint.h | 4 | ||||
| -rw-r--r-- | include/compression/huffman.h | 4 | ||||
| -rw-r--r-- | include/compression/lz77.h | 4 | ||||
| -rw-r--r-- | include/compression/merge_sort.h | 4 | ||||
| -rw-r--r-- | include/compression/mtf.h | 4 | ||||
| -rw-r--r-- | include/compression/my64bit.h | 4 | ||||
| -rw-r--r-- | include/compression/rle.h | 6 | ||||
| -rw-r--r-- | include/compression/tng_compress.h | 30 | ||||
| -rw-r--r-- | include/compression/vals16.h | 4 | ||||
| -rw-r--r-- | include/compression/warnmalloc.h | 4 | ||||
| -rw-r--r-- | include/compression/widemuldiv.h | 4 | ||||
| -rw-r--r-- | include/md5.h | 2 | ||||
| -rw-r--r-- | include/tng_io.h | 13 | ||||
| -rw-r--r-- | include/tng_io.hpp | 39 |
18 files changed, 62 insertions, 82 deletions
diff --git a/include/compression/bwlzh.h b/include/compression/bwlzh.h index 3e58d2d..70d586a 100644 --- a/include/compression/bwlzh.h +++ b/include/compression/bwlzh.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ @@ -32,7 +30,7 @@ void DECLSPECDLLEXPORT bwlzh_decompress(unsigned char *input, int nvals, /* The routines below are mostly useful for testing, and for internal - use by the library. */ + use by the library. */ void DECLSPECDLLEXPORT bwlzh_compress_verbose(unsigned int *vals, int nvals, unsigned char *output, int *output_len); diff --git a/include/compression/bwt.h b/include/compression/bwt.h index e95f7ee..9f927f8 100644 --- a/include/compression/bwt.h +++ b/include/compression/bwt.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/compression/coder.h b/include/compression/coder.h index 570bc6d..34b56c1 100644 --- a/include/compression/coder.h +++ b/include/compression/coder.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ #ifndef CODER_H diff --git a/include/compression/dict.h b/include/compression/dict.h index e29b17f..d66dd23 100644 --- a/include/compression/dict.h +++ b/include/compression/dict.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/compression/fixpoint.h b/include/compression/fixpoint.h index b1e7130..f448dbf 100644 --- a/include/compression/fixpoint.h +++ b/include/compression/fixpoint.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ #ifndef FIXPOINT_H diff --git a/include/compression/huffman.h b/include/compression/huffman.h index c36e94d..49347de 100644 --- a/include/compression/huffman.h +++ b/include/compression/huffman.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/compression/lz77.h b/include/compression/lz77.h index e811256..ad37e5b 100644 --- a/include/compression/lz77.h +++ b/include/compression/lz77.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/compression/merge_sort.h b/include/compression/merge_sort.h index 970d5ee..48ab410 100644 --- a/include/compression/merge_sort.h +++ b/include/compression/merge_sort.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/compression/mtf.h b/include/compression/mtf.h index 9c5e175..bc4b2c8 100644 --- a/include/compression/mtf.h +++ b/include/compression/mtf.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/compression/my64bit.h b/include/compression/my64bit.h index f88c797..2959a8d 100644 --- a/include/compression/my64bit.h +++ b/include/compression/my64bit.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ #ifndef MY64BIT_H diff --git a/include/compression/rle.h b/include/compression/rle.h index 3adf8dc..c6d4706 100644 --- a/include/compression/rle.h +++ b/include/compression/rle.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ @@ -18,7 +16,7 @@ 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, +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 index 51597be..c8b8db1 100644 --- a/include/compression/tng_compress.h +++ b/include/compression/tng_compress.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ #ifndef TNG_COMPRESS_H @@ -41,27 +39,27 @@ ] 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. 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, + double desired_precision, int speed, int *algo, int *nitems); char DECLSPECDLLEXPORT *tng_compress_pos_float(float *pos, int natoms, int nframes, - float desired_precision, + float desired_precision, 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, int speed,int *algo, @@ -78,13 +76,13 @@ char DECLSPECDLLEXPORT *tng_compress_pos_int(int *pos, int natoms, int nframes, 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. + 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 @@ -108,7 +106,7 @@ char DECLSPECDLLEXPORT *tng_compress_pos_int_find_algo(int *pos, int natoms, int unsigned long prec_hi, unsigned long prec_lo, 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); @@ -132,7 +130,7 @@ char DECLSPECDLLEXPORT *tng_compress_vel_int(int *vel, int natoms, int nframes, unsigned long prec_hi, 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, @@ -152,9 +150,9 @@ char DECLSPECDLLEXPORT *tng_compress_vel_int_find_algo(int *vel, int natoms, int int *nitems); /* From a compressed block, obtain information about - whether it is a position or velocity block: + 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, + 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. */ @@ -184,7 +182,7 @@ void DECLSPECDLLEXPORT tng_compress_int_to_float(int *posvel_int,unsigned long p /* 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 diff --git a/include/compression/vals16.h b/include/compression/vals16.h index a8acdf4..4585755 100644 --- a/include/compression/vals16.h +++ b/include/compression/vals16.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/compression/warnmalloc.h b/include/compression/warnmalloc.h index 945afbe..46e7d52 100644 --- a/include/compression/warnmalloc.h +++ b/include/compression/warnmalloc.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/compression/widemuldiv.h b/include/compression/widemuldiv.h index b7574fa..8ca24ee 100644 --- a/include/compression/widemuldiv.h +++ b/include/compression/widemuldiv.h @@ -5,9 +5,7 @@ * * * 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. + * modify it under the terms of the Revised BSD License. */ diff --git a/include/md5.h b/include/md5.h index 5776af8..80fbf6c 100644 --- a/include/md5.h +++ b/include/md5.h @@ -54,8 +54,6 @@ # define md5_INCLUDED -/* The comment below does not apply to the version included in the TNG - * library. */ /* * This package supports both compile-time and run-time determination of CPU * byte order. If ARCH_IS_BIG_ENDIAN is defined as 0, the code will be diff --git a/include/tng_io.h b/include/tng_io.h index 08eb0cb..f13563b 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -3,14 +3,12 @@ * VERSION 1.4 * * Written by Magnus Lundborg - * Copyright (c) 2012, The GROMACS development team. + * Copyright (c) 2012-2013, The GROMACS development team. * Check out http://www.gromacs.org for more information. * * * 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. + * modify it under the terms of the Revised BSD License. */ /** @file tng_io.h @@ -51,8 +49,8 @@ * Copyright (c) 2012, The GROMACS development team. * check out http://www.gromacs.org for more information. * - * The TNG API is released under LGPL 2.1 and is free to redistribute according - * to that license (or a later version of the LGPL license). + * The TNG API is released under the Revised BSD License and is free to + * redistribute according to that license. * * A license file (named COPYING) should be included with each copy of the API. * @@ -76,7 +74,8 @@ * * Revisions * - * v. 1.4 - More flexible support for digital signatures in header. + * v. 1.4 - Changed from LGPL to the Revised BSD License. + * - More flexible support for digital signatures in header. * - Block ID numbers changed. * * v. 1.3 - Second stable release of the API. diff --git a/include/tng_io.hpp b/include/tng_io.hpp index a4247d5..202f9db 100644 --- a/include/tng_io.hpp +++ b/include/tng_io.hpp @@ -1,3 +1,16 @@ +/* This code is part of the tng binary trajectory format. + * + * VERSION 1.4 + * + * Written by Anders Gärdenäs + * Copyright (c) 2012-2013, The GROMACS development team. + * Check out http://www.gromacs.org for more information. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the Revised BSD License. + */ + #ifndef TNG_IO_HPP #define TNG_IO_HPP @@ -102,7 +115,7 @@ public: { return status = tng_output_file_set(traj, file_name); } - + /** * @brief Get the endianness of the output file. * current output file. @@ -429,8 +442,8 @@ public: { return status = tng_time_per_frame_get(traj, time); } - - + + /** * @brief Set the time per frame of the trajectory. * @param len is the new time per frame. @@ -442,7 +455,7 @@ public: return status = tng_time_per_frame_set(traj, time); } - + /** * @brief Get the length of the input file. * @param len is pointing to a value set to the file length. @@ -834,7 +847,7 @@ public: return status = tng_frame_set_new(traj, first_frame, n_frames); } - + /** * @brief Create and initialise a frame set with the time of the first frame * specified. @@ -864,7 +877,7 @@ public: tng_function_status setTimeOfFirstFrameOfFrameSet (const double first_frame_time) { - return status = tng_frame_set_first_frame_time_set(traj, + return status = tng_frame_set_first_frame_time_set(traj, first_frame_time); } @@ -1121,7 +1134,7 @@ public: n_values_per_frame, type); } - + /** * @brief Read and retrieve a vector (1D array) of non-particle data, * in a specific interval. @@ -1233,7 +1246,7 @@ public: return status = tng_particle_data_vector_get(traj, block_id, values, n_frames, stride_length, - n_particles, + n_particles, n_values_per_frame, type); } @@ -1277,7 +1290,7 @@ public: type)); } - + /** * @brief Read and retrieve a vector (1D array) particle data, in a * specific interval. @@ -1442,7 +1455,7 @@ tng_function_status Trajectory::findMolecule int64_t id, Molecule_t molecule) { - return status = tng_molecule_find(traj, name, id, + return status = tng_molecule_find(traj, name, id, &molecule->mol); } @@ -1545,7 +1558,7 @@ public: atom_type, &atom->atom); } - + /** * @brief Add an atom with a specific ID to a residue. * @param atom_name is a string containing the name of the atom. @@ -1636,7 +1649,7 @@ public: return status = tng_chain_residue_add(traj->traj, chain, name, &residue->residue); } - + /** * @brief Add a residue with a specific ID to a chain. * @param name is a string containing the name of the residue. @@ -1684,7 +1697,7 @@ tng_function_status Molecule::findChain int64_t id, Chain *chain) { - return status = tng_molecule_chain_find(traj->traj, mol, name, id, + return status = tng_molecule_chain_find(traj->traj, mol, name, id, &chain->chain); } |