8ee4b05d2b
Include box data in the situation where there is no position.
2014-12-05 10:46:58 +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
39494d07ee
Fix dimension count in write_data.
2014-12-05 10:46:45 +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
932bbb05f9
fix value of time in h5md_append
2014-12-05 10:46:41 +01:00
8863ba6933
Fix handling of domain dimension.
2014-12-05 10:46:40 +01:00
ebfb09b17d
correct dims inversion of natoms and dimension
2014-12-05 10:46:39 +01:00
1e82a1905d
correct free into delete
2014-12-05 10:46:38 +01:00
0b262350e0
Add initial version of dump_h5md
2014-12-05 10:46:37 +01:00
aeb7fec23a
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12814 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-12-02 02:15:39 +00:00
70593d92cb
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12812 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-12-02 02:10:17 +00:00
7ea9d856aa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12809 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-12-01 15:19:21 +00:00
362f7ad110
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12808 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-12-01 15:16:00 +00:00
ddb24e6963
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12807 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-12-01 15:15:46 +00:00
0398a7f2c8
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12801 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-26 16:05:52 +00:00
eb8b18913b
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12798 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-26 16:03:06 +00:00
c820756169
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12794 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 23:10:14 +00:00
fe42affff4
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12792 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 22:30:32 +00:00
1f84af1b91
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12788 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 20:57:12 +00:00
6641435368
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12785 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 19:39:20 +00:00
5f9a749582
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12780 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 17:43:21 +00:00
6ee2f9f3e3
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12779 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 17:41:53 +00:00
9f78ad596a
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12776 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 17:26:14 +00:00
11bd1a45ed
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12775 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 17:23:55 +00:00
162e8050ad
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12773 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-24 17:15:05 +00:00
080fe0b70f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12765 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-21 16:34:34 +00:00
3d3a85df2b
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12763 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-20 21:26:10 +00:00
16fbe2f70f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12759 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-20 21:08:48 +00:00
2fecb0f4b8
ATC version 2.0, date: Nov20
...
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12756 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-20 18:58:58 +00:00
50459a7034
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12755 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-20 18:18:55 +00:00
d476b251e9
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12753 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-20 18:16:39 +00:00
7f8f2fd3ed
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12752 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-20 18:02:47 +00:00
973b24564e
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12751 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-20 16:08:33 +00:00
f51b6d103b
Restoring qeq files
...
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12749 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-19 22:43:21 +00:00
72a1dc1552
Fixing bug in qeq
...
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12748 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-19 21:05:07 +00:00
7eca5edcae
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12743 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-11-19 19:51:53 +00:00
