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Diffusion lammps 05f4b6013a49

Merge branch 'start_dump_h5md' of github.com:pdebuyl/lammps into start_dump_h5md
05f4b6013a49
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Authored by Pierre de Buyl <pierre.db@itf50.(none)> on Dec 5 2014, 11:47.

Description

Merge branch 'start_dump_h5md' of github.com:pdebuyl/lammps into start_dump_h5md

Details

Committed
Pierre de Buyl <pierre.db@itf50.(none)>Dec 5 2014, 11:47
Pushed
jungeOct 6 2016, 16:49
Parents
rLAMMPSb135f236d66c: Allow optional author name in dump_h5md
rLAMMPS485b411d0f27: Allow optional author name in dump_h5md
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Pierre de Buyl <pierre.db@itf50.(none)> committed rLAMMPS05f4b6013a49: Merge branch 'start_dump_h5md' of github.com:pdebuyl/lammps into start_dump_h5md (authored by Pierre de Buyl <pierre.db@itf50.(none)>).Dec 5 2014, 11:47

Merged Changes

CommitAuthorDetailsCommitted
b135f236d66cPierre de Buyl
Allow optional author name in dump_h5md 
Sep 25 2014
94d539ee4f43Pierre de Buyl
do not write ch5md_SYS{INC,LIB} if HDF5_PATH not set 
Sep 25 2014
9bfef43a7b71Pierre de Buyl
Fix typo '-I' -> '-L' in Makefile 
Sep 24 2014
39e491cc255cPierre de Buyl
create build dir if it does not exist 
Sep 24 2014
ad2f33b61c90Pierre de Buyl
Update Makefile to generate properly Makefile.lammps 
Sep 24 2014
8ef1d7fdd03bPierre de Buyl
close HDF5 data only on root node 
Sep 22 2014
ad7b3caa04b4Pierre de Buyl
add restriction on domain shape 
Sep 22 2014
2b4a5fbfe63ePierre de Buyl
Generate error with triclinic domains 
Sep 22 2014
f4b333487962Pierre de Buyl
Update ch5md and close properly HDF5 identifiers (except file). 
Sep 22 2014
a1f0ecb25613Pierre de Buyl
Change the parsing of 'every' for dump_h5md 
Sep 22 2014
847312aef6fdPierre de Buyl
Make current with respect to txt file. 
Sep 14 2014
f3991236ad9fPierre de Buyl
Update for multiple groups and use of write_dump. 
Sep 10 2014
d13527e24f0dPierre de Buyl
Modify dump_h5md to allow use with write_dump 
Sep 10 2014
76a3871fda55Pierre de Buyl
Allow write_dump to add fixed-in-time elements 
Sep 5 2014
4021256daafaPierre de Buyl
Use LAMMPS_VERSION in dump_h5md 
Sep 5 2014
83e262989087Pierre de Buyl
Update documentation of h5md dump style. 
Aug 22 2014
374243917d34Pierre de Buyl
Include box data in the situation where there is no position. 
Aug 22 2014
c8d1e5f48d0fPierre de Buyl
Add link argument to h5md_create_box. 
Aug 22 2014
6c4c1b00f958Pierre de Buyl
Fix k_species count (dimension is always '1' and not 'dim'). 
Aug 22 2014
11fb0bac4648Pierre de Buyl
Force packing and unpacking of all existing elements at each dump. Else, the… 
Aug 21 2014
1d158c6518c9Pierre de Buyl
Add pack and write for velocity, force and species 
Aug 21 2014
8f9a67a5f97cPierre de Buyl
Refactor pack loop 
Aug 21 2014
2122a1564838Pierre de Buyl
Add variables, argument parsing and h5md elements creation for velocity, force… 
Aug 21 2014
2697d7438d29Pierre de Buyl
Remove 'every' check for image, include in position check 
Aug 20 2014
a3d8392b8571Pierre de Buyl
Make image always match position 
Aug 20 2014
84a7b87b9525Pierre de Buyl
Modularize writing of position and image in dump_h5md. 
Aug 20 2014
fa7ee7d08b50Pierre de Buyl
Change name of coords array to dump_position. 
Aug 20 2014
34a7c1d4bb5ePierre de Buyl
Add image element. 
Aug 20 2014
b640cbaf4c60Pierre de Buyl
Fix library flags. 
Aug 20 2014
597e94483b7bPierre de Buyl
Add contributing author notice. 
Aug 14 2014
8371de1e7eb6Pierre de Buyl
Add a README for USER-H5MD 
Aug 14 2014
ba5ae384e741Pierre de Buyl
add doc for dump_h5md 
Aug 14 2014
e544eb2e9e7dPierre de Buyl
Add README, LICENSE and 'this file is part of ch5md' notice. 
Aug 14 2014
31db652e07f8Pierre de Buyl
Fix dimension count in write_data. 
Aug 14 2014
23c44498e18aPierre de Buyl
use h5cc and add clean target 
Aug 14 2014
b9abb037ef91Pierre de Buyl
Also remove -lhdf5 when no-ing USER-H5MD. 
Aug 14 2014
db5be510c068Pierre de Buyl
Take into account domain boundary. 
Aug 14 2014
3cab25696c7fPierre de Buyl
move ch5md to lib 
Aug 13 2014
108f02fdf6b0Pierre de Buyl
fix value of time in h5md_append 
Aug 12 2014
641f507ba434Pierre de Buyl
Fix handling of domain dimension. 
Aug 12 2014
33333cb0a4d8Pierre de Buyl
correct dims inversion of natoms and dimension 
Aug 12 2014
9b474429feb5Pierre de Buyl
correct free into delete 
Aug 12 2014
3362e44780e7Pierre de Buyl
Add initial version of dump_h5md 
Aug 11 2014

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