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arriving into the present with the public branch #140

Merged
merged 167 commits into from
Aug 1, 2019
Merged

arriving into the present with the public branch #140

merged 167 commits into from
Aug 1, 2019

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stenczelt
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After a long time of very sparse work, the python 3 version of quippy is here and ready to break everyone's old python 2 code!!!

stenczelt and others added 30 commits January 7, 2019 17:55
@stenczelt
eng of day0: first attempt, unsuccessful
0f7cdd7
@stenczelt
attempt_2 Makefile updatess: VPATH in main one, tabs and // in quippy…
8b9ca22 
…/...
@stenczelt
managed to compile one module
5a03577
@stenczelt
managed to compile Atoms.f95 with skipping three subroutines: [atoms_…
4d6c376 
…finalise atoms_shallowcopy atoms_initialise_ptr]
@stenczelt
unsuccessful attempt to compile Potential.f95, BUT error.inc copied t…
5ea6b9b 
…o src/Potential from src/libAtoms because that fortran code also needs it
@stenczelt
compiled Potential.f95 and added debug-quippy option to makefile
2947709
@stenczelt
addition (typo fix) to previous commit
f29009c
@stenczelt
compiled Atoms.f95 with atoms_finalise in it, only omitting the atoms…
d8cba33 
…_finalise_multi to make it work
@stenczelt
compiling potential too, still has errors
8c6d499
@stenczelt
removing old quippy files to start from scratch
37dbbf5
@stenczelt
initial atoms.py
2c9323f
@stenczelt
empty init.py and updates on atoms object
fd62115
@stenczelt
wrapping Table.f95 (f90wrap updates in py3 branch are needed for this)
6563fed
@stenczelt
wrapping System.f95 and adding some to init.py
67b97ee
@stenczelt
wrapping Dictionary.f95 and adding some reformat of code by PyCharm
45e073b
@stenczelt
conversion between fortran and ase atoms, untested
5484d18
@stenczelt
simple calculator, untested
70a329d
@stenczelt
imports of packages for __init__.py
4c71414
@stenczelt
potential works for the simple things we did by hand earlier
c0921e4
@stenczelt
changing names to be consistent, using quip everywhere
ea0f991
@stenczelt
remove a few unneeded old files
7eb031f
@stenczelt
a few notebooks used for testing
9615806
@stenczelt
try wrapping descriptors -- fail, log in root dir
71e36e0
@stenczelt
use 4-space indentation, reformat code by PyCharm
d690f4f
@jameskermode
rename dictionary_get_array -> dictionary__array__
ecec154
@jameskermode
hard-code numpy dtype codes for dictionary__array__
b15ae6a
@stenczelt
Merge branch 'py3' of github.com:libAtoms/QUIP into py3
bd76543
@stenczelt
utils to retrieve arrays from quip dictionary
d6ba994
@stenczelt
all parameters calculated by potential object, tested in notebook
f353156
@stenczelt
stress calculation with potential object
0ca1130
stenczelt added 27 commits July 30, 2019 18:21
@stenczelt
'build in travis using the deploy key'
8e95fe3
@stenczelt
converter updated to handle velocities too, needed for DynamicalSystems
c83a29f
@stenczelt
wrap DynamicalSystems.f95
bc004f2
@stenczelt
'the old works around the dynamical systems'
4705d01
@stenczelt
change the imports and the source of units
34a1367
@stenczelt
remove old runner, will need to write new
5228a14
@stenczelt
use hidden quip atoms object
f6b235c
@stenczelt
inherit from ase.optimize.optimize.Dynamics instead of object
281039e
@stenczelt
reformat the file by PyCharm
33b32d7
@stenczelt
accelerations added
b3001b7
@stenczelt
use two converters between velocities and ONLY those from now on
146f817
@stenczelt
update self.atoms to self.ase_atoms for clarity
2779890
@stenczelt
update __init__(), very unfinished now
2c7d55b
@stenczelt
update the step logic, update py2 syntax, raise NotImplenemtedError i…
1f540a4 
…n cases with no work yet
@stenczelt
'take the old dynamical systems tester'
807524a
@stenczelt
'reformat file with PyCharm'
078d0cf
@stenczelt
unfinished test
2e717bb
@stenczelt
'adding an f90wrap plugin for docstring generation'
63667dd
@stenczelt
inferring type of the arguments in the documentation table making and…
3e57a57 
… using the headers as the descriptors documentation does now
@stenczelt
update the plugin
d820560
@stenczelt
merging convert and utils, cleaning up init, updating docstrings
7fa1a79
@stenczelt
update the plugin and use in makefile
6e845d6
@stenczelt
remove obsolete files
3838d17
@stenczelt
'f90wrap updated to newly released master'
0e60ae0
@stenczelt
descriptor gradient output reshaped to the same shape as earlier in py2
b9d4c26
@stenczelt
updated headers of quippy files and added myself to the readme
c9f7fb4
@stenczelt
update .travis.yml to only do documentation on archived_py2
f78825a
@stenczelt stenczelt requested a review from gabor1 August 1, 2019 19:28
@jameskermode
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I’m happy to go ahead and merge this now. Any objections, @gabor1?

@stenczelt stenczelt merged commit f78825a into public Aug 1, 2019
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@gabor1 gabor1 Awaiting requested review from gabor1

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3 participants
@stenczelt @jameskermode @albapa