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2016-01-11Changes to TNG to include the HRTC format.HEADmasterJan Huwald
Almost all of this code has been created by Stephan Richter <s.richter@keawe.de>. Only minor changes and this squashed commit have been prepared by Jan Huwald <jh@sotun.de>.
2014-12-12Reverted a change in last commit.Magnus Lundborg
Change-Id: I0b49d2651851dc29d4dd8781e115f7648cfc95c2
2014-12-11Fixed bug reading last frame and time of last frame.Magnus Lundborg
Change-Id: I983333cc30b2d3add0b5a35e29b5d67736927cd4
2014-12-08Bumped version to 1.7.1, to be used in GROMACS 5.1Magnus Lundborg
Change-Id: Id262c7c623be18b84230694b4058bd0ab274ff0e
2014-12-08Made function arguments const where relevant.Magnus Lundborg
Change-Id: I5b196b57976c8c718b079336a805188ccb03ef4b
2014-12-03Fixed compiler warnings.Magnus Lundborg
Change-Id: I548a5f0a5d0e79777d96474b46a29c4caf5c416e
2014-12-02Update the number of frames in the current frame set.Magnus Lundborg
When setting the overall expected number of frames per frame set also update the current frame set if there is one. It is OK to have frame sets with different numbers of frames, so previous frame sets are unaffected. Change-Id: I2051243dfb589810b4073e251281261797c8aa74
2014-12-02Replace all 'WIN32 AND NOT CYGWIN' with 'WIN32'.Magnus Lundborg
Cmake 2.8.4 WIN32 doesn't include CYGWIN. This corresponds to commit 065e529e40, by Roland Schulz, in the GROMACS repository. Change-Id: I5daefdebb9e9e839cf509c36eed6046a1c2a4761
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
2014-10-03Added change log for v 1.7Magnus Lundborg
Change-Id: Ifb48de3dd90335945eb459bbaca6461cd52d1959
2014-10-03Fix input file for generating documentation.Magnus Lundborg
The include path was not correct - no documentation was generated. Do not set the version number specifically in doxyfile.in - use the variables that have already been set. Change-Id: Ie5035c39e68c6df2cff17e9427cb8081396bc6a9
2014-10-03Use @brief in documentation of static functions.Magnus Lundborg
Change-Id: I8f133d330b611a34c38addcd3bcb8c579882440d
2014-10-03Version bumped to 1.7.0Magnus Lundborg
Change-Id: Ia276ce3c7c9225f5d0d07eb6e3cd4cea6b882d24
2014-10-03Added change log for v 1.7Magnus Lundborg
Change-Id: Ifb48de3dd90335945eb459bbaca6461cd52d1959
2014-10-03Fix input file for generating documentation.Magnus Lundborg
The include path was not correct - no documentation was generated. Do not set the version number specifically in doxyfile.in - use the variables that have already been set. Change-Id: Ie5035c39e68c6df2cff17e9427cb8081396bc6a9
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
2014-09-24Added notification that two functions are obsolete.Magnus Lundborg
Change-Id: I050687ad061e03fe43904e549d5f7968d04893e7
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
2014-08-22Fix ZLIB usage.Magnus Lundborg
Using zlib for TNG requires also that the the #include file can be found, and this can be in a non-standard path. (Committed by Mark Abraham in the GROMACS repository.) Change-Id: I607105b9702b8f75f416fec584888b05897f32fa
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
contact: Jan Huwald // Impressum