summaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
2014-07-23Improved TNG compression speed.Magnus Lundborg
Change-Id: I71c66c6b534cb402048dcd75e008d3db4bd3fb71
2014-07-21Improved testing of TNG functions.Magnus Lundborg
The coverage of the testing suite is improved. Better checks to verify that the data is what is expected. Change-Id: I294779456fee2da2e3617de985d23d2f42f09f56
2014-07-17Rewrite of file i/o.Magnus Lundborg
Do not read and write data blocks in whole chunks. Read and write value by value and do the md5 summing in steps. This hopefully avoids memory alignment problems reported on ARM architectures. Fixed a bug freeing trajectory mapping memory. Change-Id: I3438b3d3faf5349dcd477a31cfb4bacf236ed582
2014-07-01Fix bug causing reading next frame not to stop.Magnus Lundborg
Change-Id: I132d22f4e7e7dbdea14351e2e813a391590d58b9
2014-07-01Adjust include directory for some corner casesMagnus Lundborg
This corresponds to the changes in BuildTNG.cmake in commit e43be47fad70e in the GROMACS repository. Change-Id: I0f2fdd4356dd8132a9d7947ccbcb8f46547648eb
2014-06-30Fixed tng_num_frame_sets_get()Magnus Lundborg
tng_num_frame_sets_get() should not fail if there are no frame sets. Change-Id: Ie01a6b3230af7413a51ba144bd03c5fe00c25519
2014-06-26Version 1.6 of the TNG library.Magnus Lundborg
Added functions to get the version of the header and the library. Improved version control of the library using CMake config and version files. Changed tng_util_frame_current_compression_get() return type to double before the API is widely circulated (no release has been made since that function was added). Compiling compression functions into the tng_io library. Uses BuildTNG.cmake instead of including add_subdirectories. Change-Id: I5e4818736fb2632c06ca7df8e84ce9544bf2acaf
2014-06-19Raised minimum cmake version to 2.8.8.Magnus Lundborg
Change-Id: I0f377b32c8fa6ed1267ee8a6581d29dc45b51fc3
2014-06-19Use CMAKE_INSTALL_LIBDIR as location for installation.Magnus Lundborg
Change-Id: If2b6ffad5cec9dd687afcbe1ce4c11bbc62c88fc
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
2014-06-16Enhancements to CMake usageMark Abraham
These changes mostly address being able to use fully-constructed source-file targets in GROMACS, e.g. to construct an object library. Thus compilation properties are moved onto the source files, rather than the library into which they are linked. Removed unnecessary library properties Made it easier to handle lists of source files in non-repetitious ways. Change-Id: I01a4a56ba8a8d45ba02d95d08c948b9ca5015013
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
2014-06-16Install TNG documentation.Rossen Apostolov
Change-Id: Ie0b0edaa1527c4f2a6e74485a055e7a771d1d50b
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
2014-03-11Install tng_io_fwd.h as well when installing.Magnus Lundborg
Change-Id: I851e6b1ac6a1f5bd70ff3aa7c1575f8198dc0177
2014-03-04Updated path to tng header files.Magnus Lundborg
Change-Id: I8793ad7c3da4cc40c919167dbf3ce5a9ac3ce27e
2014-03-01Modify the option to specify if ZLIB should be used.Magnus Lundborg
In GROMACS there is an extra check to see that ZLIB can actually be linked against. This change uses those options properly. Change-Id: I910be0cf81a47c9feea2d3494925cc4a3c82dc4b
2014-02-19Fixed some warnings about uninitialized variables.Magnus Lundborg
Change-Id: I6fa7b9ea5d4be21112d4ec3f01417128c1a87a72
2014-02-13Improved compiler checks for setting warning flags.Magnus Lundborg
Change-Id: I567e237357b5292378e892d64a25af312492713f
2014-02-12Remove OpenMP option.Magnus Lundborg
It was only used for building some of the examples. Now, those example are only built if OpenMP is found. Change-Id: I816a52595fb00bb729adce83477f8e2f35dd6761
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
2014-02-04Revert "Test gerrit."Rossen Apostolov
This reverts commit 06fdeeb20bbe66e23fe618af5ef50627e5d0ba71.
2014-02-04Test gerrit.Rossen Apostolov
Change-Id: I9aca165530e9e0631fde5872282d0d3a09af89db
2014-02-04Cleaned up unused and non-portable /tmp invocations.Rossen Apostolov
2014-01-21Updated change log.Magnus Lundborg
2014-01-21Bump version number. Added changes to change log.Magnus Lundborg
2014-01-21Make finding zlib fail quietly.Magnus Lundborg
2014-01-14More improvements to reading next frame.Magnus Lundborg
2014-01-14Improved reading next frame.Magnus Lundborg
2014-01-14One more include path fixed.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
contact: Jan Huwald // Impressum