859cf367ce
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12826 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:48 +01:00
0ccfbc2373
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12824 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:47 +01:00
9e9ee8f949
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12823 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:47 +01:00
22230ee743
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12822 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:46 +01:00
06955cfb20
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12821 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:46 +01:00
10aba3855b
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12820 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:45 +01:00
5eefdbb659
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12819 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:44 +01:00
087b9e3e59
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12818 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:44 +01:00
9b16b44f95
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12817 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:43 +01:00
a3c57b9ae5
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12816 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-11 15:24:42 +01:00
ef82ec9d7c
add Makefile.lammps as a dependency for target all
2015-01-19 12:46:30 +01:00
05f4b6013a
Merge branch 'start_dump_h5md' of github.com:pdebuyl/lammps into start_dump_h5md
2014-12-05 11:47:27 +01:00
485b411d0f
Allow optional author name in dump_h5md
2014-12-05 10:47:12 +01:00
1b649866ae
do not write ch5md_SYS{INC,LIB} if HDF5_PATH not set
2014-12-05 10:47:11 +01:00
32a0d17b69
Fix typo '-I' -> '-L' in Makefile
2014-12-05 10:47:10 +01:00
a5b70d2304
create build dir if it does not exist
2014-12-05 10:47:09 +01:00
5185449867
Update Makefile to generate properly Makefile.lammps
2014-12-05 10:47:09 +01:00
1252fb3e62
close HDF5 data only on root node
2014-12-05 10:47:08 +01:00
012da252f8
add restriction on domain shape
2014-12-05 10:47:07 +01:00
1fa74d14d5
Generate error with triclinic domains
2014-12-05 10:47:06 +01:00
5e63424f30
Update ch5md and close properly HDF5 identifiers (except file).
2014-12-05 10:47:05 +01:00
e8de865a30
Change the parsing of 'every' for dump_h5md
...
The sub-intervals are now specified by appending the 'every N_element' option
to a given data element and is optional.
2014-12-05 10:47:04 +01:00
41ca640667
Make current with respect to txt file.
2014-12-05 10:47:03 +01:00
6a78fab84c
Update for multiple groups and use of write_dump.
2014-12-05 10:47:02 +01:00
1fddfe7853
Modify dump_h5md to allow use with write_dump
...
The arguments modifying the behavior of the dump are now box and
create_group, both accepting "yes" or "no".
2014-12-05 10:47:01 +01:00
f2900c0a52
Allow write_dump to add fixed-in-time elements
...
write_dump uses every_dump=0, it is possible to detect its use.
The addition of arguments "file_from" and "nobox" was needed.
2014-12-05 10:47:00 +01:00
679d74c908
Use LAMMPS_VERSION in dump_h5md
2014-12-05 10:47:00 +01:00
e5c8e4acdc
Update documentation of h5md dump style.
2014-12-05 10:46:59 +01:00
8ee4b05d2b
Include box data in the situation where there is no position.
2014-12-05 10:46:58 +01:00
ec7fd1327d
Add link argument to h5md_create_box.
2014-12-05 10:46:57 +01:00
cc4adb535a
Fix k_species count (dimension is always '1' and not 'dim').
2014-12-05 10:46:57 +01:00
5509eeef95
Force packing and unpacking of all existing elements at each dump.
...
Else, the buffer has a varying size depending on the timestep and this
breaks the data collection.
TODO: make this more efficient, if possible. General dump code might prevent that, however.
TODO: a bug appeared when running in parallel.
2014-12-05 10:46:56 +01:00
2443bce1c4
Add pack and write for velocity, force and species
2014-12-05 10:46:55 +01:00
e3d12cbafe
Refactor pack loop
2014-12-05 10:46:54 +01:00
9717e09833
Add variables, argument parsing and h5md elements creation for velocity, force and species
2014-12-05 10:46:53 +01:00
b516393fc6
Remove 'every' check for image, include in position check
2014-12-05 10:46:53 +01:00
ae115b3fd3
Make image always match position
2014-12-05 10:46:52 +01:00
692b14eb74
Modularize writing of position and image in dump_h5md.
2014-12-05 10:46:51 +01:00
4d6ef607b7
Change name of coords array to dump_position.
2014-12-05 10:46:50 +01:00
d124cf1bae
Add image element.
2014-12-05 10:46:49 +01:00
dee5c2f8e6
Fix library flags.
2014-12-05 10:46:49 +01:00
86a050c200
Add contributing author notice.
2014-12-05 10:46:48 +01:00
dc8d5a8ba3
Add a README for USER-H5MD
2014-12-05 10:46:47 +01:00
f2a34ec70e
add doc for dump_h5md
2014-12-05 10:46:46 +01:00
f269e7f505
Add README, LICENSE and 'this file is part of ch5md' notice.
2014-12-05 10:46:46 +01:00
39494d07ee
Fix dimension count in write_data.
2014-12-05 10:46:45 +01:00
6ae24fe41f
use h5cc and add clean target
2014-12-05 10:46:44 +01:00
97ca47a424
Also remove -lhdf5 when no-ing USER-H5MD.
2014-12-05 10:46:44 +01:00
329f226707
Take into account domain boundary.
2014-12-05 10:46:43 +01:00
095e00995b
move ch5md to lib
2014-12-05 10:46:42 +01:00
