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path: root/src/lib/tng_io.c
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2014-06-19When adding a bond do not automatically check if it exists.Magnus Lundborg
Leave that responsibility to the caller to speed things up. Change-Id: Ide4741d0ad7461bf600766cbc49ad3b5e781fd9e
2014-06-18Bug fix. Did not look through all chains.Magnus Lundborg
Always set the residues in the chain when adding residues. Change-Id: I785b829ab3ae68fa5ac39ba2accf02ce22a03fab
2014-06-18Fixed another eternal loop.Magnus Lundborg
Change-Id: I242b6a38ed20d3340f66e4208fc3e4f7ca1b71f1
2014-06-18Fixed loop going on forever.Magnus Lundborg
Change-Id: I4248f3ba571754a8fe620b9cc239d2d241c341a8
2014-06-17Fixed some compilation warnings.Magnus Lundborg
Change-Id: Ibce6352de35b0b258f547816cf295d0089e2c284
2014-06-17Some checks to handle unreadable block headers.Magnus Lundborg
If blocks are migrated there will be empty space in the file. This is handled by this commit. Change-Id: I15733e56d5ba937a87f28fd181871088e282b673
2014-06-17Fixed a compilation warning when !USE_ZLIB.Magnus Lundborg
Change-Id: Ie6ecf260acf0bd80674ab825bcd51fddb54626ab
2014-06-16Migrating data blocks.Magnus Lundborg
Now it should be possible to modify e.g. the general info block and move frame sets to make room for more data. Change-Id: I28875a9c6891a396f80f7bb1490c3d6db58dc7a4
2014-06-16Fixed compilation warnings.Magnus Lundborg
Also updated copyright dates in tng_io.h. Change-Id: I59b93d3d73d34be7a9af2efafeb2ec4ee97cfb62
2014-06-16Migrating data blocks [WIP].Magnus Lundborg
Also includes some simple tests to verify that it is working. Change-Id: I6d465000a6fd202d53af033d7e839bfecdccc068
2014-06-16Added project and API versions to CMakeLists.txt.Rossen Apostolov
TNG_VERSION was renamed to TNG_API_VERSION which is configured through API_VERSION in CMakeLists.txt. Updated the header to 2014. Change-Id: I6a37825cd1d236927ac0e21a797abc4e98f7ce59
2014-06-11Check to ensure not reading past end of file.Magnus Lundborg
Also do not check what data blocks are present if that has already been done. Change-Id: Idda85c94c0fbaa1ae08cb358cf5d062aa125c391
2014-05-28Reread frame set after getting stride length.Magnus Lundborg
After determining the stride length reread the current frame set so that no data is skipped when reading a file. Change-Id: I99c36b0cefe918ea39f22a559553d65b9a72a48f
2014-05-28Handle one frame frame sets when reading data.Magnus Lundborg
Do not use the stride length if the frame set only contains one frame. Change-Id: I2fc98f6f405385dcf12c1da8a946cf0ad99a6ff7
2014-05-28More work with migrating data blocks. WIP.Magnus Lundborg
Change-Id: I0ac8bce978e28b77b7795a0747b66bb72ea7f1de
2014-05-05Check if number of written frames should be updated.Magnus Lundborg
When reading a frame set the number of written frames in the frame set should only be updated if the output file and the input files are the same. This fixes a bug in one of the tests in tng_testing. Change-Id: Ia21d501b9723f756dfccf75e5d5bbac606cdc582
2014-04-15Improved adding to, and finding in, molecule systemMagnus Lundborg
When adding molecules, chains, residues atoms set the ID to the last ID+1. When searching in the molecule system do a reverse search since it is often the last added item that is searched for. Change-Id: I293d95284405e517e05a33ad529c05359d953a7d
2014-04-14Functions for migrating data blocks. "Unreversed" for loops.Magnus Lundborg
The functions for migrating data blocks are still not in use - WIP. Reversed for loops were "unreversed" for improved readability. The speed difference should not be noticable anyhow. Change-Id: I084871a62bb279e648ef790218c52ea19faa72a3
2014-02-19Fixed some warnings about uninitialized variables.Magnus Lundborg
Change-Id: I6fa7b9ea5d4be21112d4ec3f01417128c1a87a72
2014-02-11Fixed some clang warnings.Magnus Lundborg
Change-Id: I7463cab38975107cfff102434c525233ed996563
2014-02-11Open files in binary mode to fix bug on Windows.Magnus Lundborg
On e.g. Linux it does not make a difference if a file is opened in binary mode or not, but apparently it does in Windows. This fixes the crashes noticed before. Warnings from MSVC fixed as well. Change-Id: I23dc209211b5462e6989ee550e78e36d7bb181ab
2014-01-21Bump version number. Added changes to change log.Magnus Lundborg
2014-01-14More improvements to reading next frame.Magnus Lundborg
2014-01-14Improved reading next frame.Magnus Lundborg
2014-01-14Use relative paths for includes.Magnus Lundborg
2014-01-13Fixed some warnings. Still needs to fix tng_particle_data_values_free() and ↵Magnus Lundborg
tng_data_values_free()
2014-01-13Some fixes in tng_trajectory_init_from_src()Magnus Lundborg
2014-01-13Reset current frame set file pos after counting frame sets.Magnus Lundborg
2014-01-13Fix to last commit.Magnus Lundborg
2014-01-13Reset the current frame set after counting the number of frame sets.Magnus Lundborg
2014-01-13New static function for reading data block meta data.Magnus Lundborg
2014-01-10Fixed bug in name comparisons.Magnus Lundborg
Added function to get residue of atom.
2014-01-10Do not automatically clear particle mappings when adding new frame set.Magnus Lundborg
Make tng_frame_set_particle_mappings_free() public.
2014-01-08Further improvements on implicit particles.Magnus Lundborg
2014-01-08Improved molecule handling (set num particles and num impl particles).Magnus Lundborg
2014-01-08Do forward declarations in separate header file.Magnus Lundborg
Also fixed some cmake warnings.
2013-12-17Fixes to determine if writing first frame of data in frame set.Magnus Lundborg
2013-12-17Remove error message when not finding data block.Magnus Lundborg
2013-12-13Direct output to stderr.Magnus Lundborg
2013-12-13Fixed bug when reading next frame.Magnus Lundborg
2013-12-06Just added a TODO and updated a comment.Magnus Lundborg
2013-12-05Added function tng_util_prepare_append_after_frame()Magnus Lundborg
2013-12-05New function for reading frame set, including particle mapping and data blocks.Magnus Lundborg
2013-12-05Fixed some bugs.Magnus Lundborg
2013-12-05Write headers first in file. Seek to end when appending to file.Magnus Lundborg
2013-12-05Fix bug reading last program name.Magnus Lundborg
2013-12-05Set number of written frames when reading a frame set.Magnus Lundborg
2013-12-05Get the number of frame sets when opening a file for reading.Magnus Lundborg
2013-12-05Further improved reading data from next frame.Magnus Lundborg
2013-12-05Improved reading data from next frame.Magnus Lundborg
contact: Jan Huwald // Impressum