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2014-10-24Fix MingW build.Magnus Lundborg
Corresponds to commit e8cba2b9001c5930ed9d52e0be7ff53a2b00b22c by Roland Schulz in the GROMACS repo. Change-Id: Icb2c5b8ce823ffeed4145a9fd415c4624d15de2e
2014-10-23Fixed bug reading non-particle data.Magnus Lundborg
Change-Id: I981f2c4b0ce0b853f5362566b75ccf53bb0591db
2014-10-23Added tng_util_num_frames_with_data_of_block_id_get()Magnus Lundborg
The function already existed in the tng_io.c, but has now been exposed through the API. Basic code for testing it was added as well. Version bumped to 1.7.0 Change-Id: I369678a69787223b7a979feb749dff4ef0ee4717
2014-10-03More detailed output when some tests fail.Magnus Lundborg
Change-Id: I749db2adcfef0fd79d39beeab700310856f33563
2014-10-03Use @brief in documentation of static functions.Magnus Lundborg
Change-Id: I8f133d330b611a34c38addcd3bcb8c579882440d
2014-09-26Added tng_util_num_frames_with_data_of_block_id_get()Magnus Lundborg
The function already existed in the tng_io.c, but has now been exposed through the API. Basic code for testing it was added as well. Version bumped to 1.7.0 Change-Id: Ia276ce3c7c9225f5d0d07eb6e3cd4cea6b882d24
2014-09-26Combined two data block adding functions.Magnus Lundborg
Combined tng_data_block_add and tng_particle_data_block_add into tng_gen_data_block_add. The original functions were exposed by the API and are therefore still kept without any changes to the outside world. Both are calling the new tng_gen_data_block_add function. Change-Id: I110994715075d63359170f5f860400c56e9816e6
2014-09-25Made a function to append remaining data to md5.Magnus Lundborg
When reading a block append parts that cannot be interpreted (if any) to the MD5 sum. This was done in each block reading function, but has now been moved to a function of its own. Change-Id: I74d076449cfcb66785a3c3d526763cde5485572f
2014-09-24Set the input file len in tng_input_file_initMagnus Lundborg
Change-Id: I25f8d8154f0f6356a08782d260ee8bb335beb645
2014-09-24Added new test (copy trajectory container and molsys)Magnus Lundborg
Also fixed bugs in tng_trajectory_init_from_src. Change-Id: Iaa44e79f388b7add79973165801ab3dba57b3dcf
2014-09-24Improved testing output.Magnus Lundborg
Print the test when it is starting and print success/failure when it is finished. Change-Id: I01b13ec88a9478108155334da1a7d25ece025ca5
2014-09-24Removed some unused (commented out) code.Magnus Lundborg
Change-Id: I2b9a5960f9dad2974ade1c734e2ac0d0987db9ee
2014-09-24Combined data interval retrieval functions.Magnus Lundborg
Combined tng_data_interval_get and tng_particle_data_interval_get into tng_gen_data_interval_get as well as tng_data_vector_interval_get and tng_particle_data_vector_interval_get into tng_gen_data_vector_interval_get. The original functions were exposed by the API and are therefore still kept without any changes to the outside world. They are now calling the new functions. Change-Id: I866bada8cca6e2c80699a2ff4892052da43e5fce
2014-09-24Combined two data vector retrieval functions.Magnus Lundborg
Combined tng_data_vector_get and tng_particle_data_vector_get into tng_gen_data_vector_get. The original functions were exposed by the API and are therefore still kept without any changes to the outside world. Both are calling the new tng_gen_data_vector_get function. Change-Id: I747d89b694021ede6fdd8deaac6d9cd7839c4fde
2014-09-24Only free memory once.Magnus Lundborg
Since there is a problem with tng_particle_data_values_free it is better to free the memory only once. It will not be re-reserved anyhow. Change-Id: Ibef28820bee10e39f00ea0d4f1ee27fafdea6d23
2014-09-24Combined two obsolete data retrieval functions.Magnus Lundborg
Combined tng_data_get and tng_particle_data_get into tng_gen_data_get. The original functions were exposed by the API and are therefore still kept without any changes to the outside world. Both are calling the new tng_gen_data_get function. Change-Id: Ibd07fc7f584560b412b54ba5911ac7c92ad50646
2014-09-24Combined the two frame data writing functions.Magnus Lundborg
Combined tng_frame_data_write and tng_frame_particle_data_write into tng_frame_gen_data_write. The original functions were exposed by the API and are therefore still kept without any changes to the outside world. Both are calling the new tng_frame_gen_data_write function. Change-Id: Icbb1bea2bbd232f24bc80749503696d5483f4dbb
2014-09-24Merged tng_particle_data_block_write and tng_data_block_write.Magnus Lundborg
The above two functions were merged to handle both particle and non-particle data. Change-Id: Id43c72c54e550e5c9b89ab9981ee162adb74e1ce
2014-09-19Merged tng_particle_data_read and tng_data_read.Magnus Lundborg
The above two functions were merged to handle both particle and non-particle data. Change-Id: Ib5f9dd4ec1e1e4710979d613a9b12380cbc6594d
2014-09-19Use only one variable instead of two for tng_data_p.Magnus Lundborg
Where there used to be two separate variables for the different data block structs use only one, where relevant. Change-Id: Ibf8b7235041295e9f1aac349eacda6d3177ed29d
2014-09-19Improved checks to verify that read data is correct.Magnus Lundborg
Change-Id: I9136c2a78bbd4cad380521779139933a936c4af1
2014-09-18Added a dependency flag in the tng_data struct.Magnus Lundborg
Handle frame and particle dependency using the flag in the struct. Change-Id: I020fd5c6cff131da9df3506dde822c74a2113f5b
2014-09-18Merge the two data block structs into one.Magnus Lundborg
Change-Id: If75c9301e02bf7da888fb273bb8e3ba7ec516472
2014-09-17Turned repeated code into functions.Magnus Lundborg
This addresses earlier suggestions to avoid unnecessary repetitions by making functions. New functions for reading and writing strings and numerical data. Also uses size_t for length of strings in many places. Improved documentation of some functions. Bumped version to 1.6.3 Change-Id: Id0c53b87a753c60b03cdbf35fb5bc58cfdd60705
2014-09-11Fixed ICC warningsMagnus Lundborg
Corresponds to the TNG modifications in Roland's commit c6cebcc190cd in the GROMACS repository. Change-Id: I44288fc8a69c4c69c9444e663b57cc773e243516
2014-08-29Improved check if ZLIB is available before using it.Magnus Lundborg
Alos check that there are bonds in a molecule before trying to reserve memory for them. Change-Id: I3b541f32e2945f7b2bbe6a9c10bf47feb0a8094f
2014-08-26Fix tng_util_generic_double_write()Magnus Lundborg
There were unmotivated differences between tng_util_generic_double_write() and tng_util_generic_write(), which were fixed. Also fixed a typo in print statement in tng_data_read(). Change-Id: I86f93e5ae649343ce17bbffae136b8b5d4939377
2014-08-25Initialize tng compressions algorithm completely.Magnus Lundborg
Also fixed a bug where position and velocity compression algorithms were mixed up. Change-Id: Ia52351e0099b2f156ffdc974eef62fb9f548eb4c
2014-08-25Improved testsMagnus Lundborg
Test writing double velocities using utility functions. Change-Id: Ibbf141db75ec502db1d10f4280f0047ccc8367dc
2014-08-22Removed unused variable to fix warning.Magnus Lundborg
Change-Id: Ia76980317ee4d892ac0614ce43053cb6780a7ea2
2014-08-21Moved defines to support large files into tng_io.c.Magnus Lundborg
Change-Id: I63eb5a7205b751228b498851fc4ce0a6b78f7857
2014-08-21Added more sophisticated functions to get n frames with data.Magnus Lundborg
Make it possible to determine how many frames there are containing a data of a specific ID. Change-Id: I0e2d9e0584b74fdad40bcf4849289d9946319bba
2014-08-20Removed compiling of tng_io_gen_versioned_output.cMagnus Lundborg
These lines should not have been committed before. The source files was not committed. Change-Id: I1f27d026018379f76b52817e04071998a12227ec
2014-08-11Check that the data type is float as expected.Magnus Lundborg
Some of the utility functions read data of a certain type. Checks are added to ensure the data type of the block is float if using a function to read float data. Change-Id: I1ae6ced70545388c8d1a38f13f62fd773fd65d22
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
2014-06-30Fixed 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
2014-06-19Use 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
contact: Jan Huwald // Impressum