Update #38

BvB93 · 2019-06-03T15:41:23Z

Added

Potential energy surfaces, over the course of last ARMC super-iteration, are now stored in .hdf5 format.
Added increased control over the non-bonded inter-atomic potential.

Changed

Molecular dynamics (MD) jobs are now preceded by a geometry optimization.
MD simulations can now be skipped if the geometry optimization RMSD is too large.
Docstrings changed to NumPy style.
Cleaned up the AMRC code.
Comments in .xyz files are now parsed.

…evel

…rameters

… rejected as intended

…evel

This reverts commit d41e2cb.

…es can be now imported and exported

…evel

Bas van Beek and others added 30 commits May 3, 2019 17:10

Added a module for reading .pdb files

596997a

Moved io related modules from FOX.functions to FOX.io

ceec375

Update README.rst

562f57b

Merge branch 'master' into devel

34d398f

Merge branch 'devel' of https://github.com/nlesc-nano/auto-FOX into d…

fae6333

…evel

Merge branch 'master' into devel

44b97a0

added the __str__ & __repr__ methods

8648caf

Update monte_carlo.py

3cf6de2

Added comments

0ea50f6

Improved the speed of the _mol_to_file method

4afa346

Added an argument for controling the logfile

0664911

bug fix: Fixed a typo

a348f0f

Added a precaution against crashing jobs

c981689

Bug fix

ce6226a

Added the missing io directory

1b9d91c

Merge branch 'devel' of https://github.com/nlesc-nano/auto-FOX into d…

7a05291

…evel

Temporary fix for a charge-constrain related bug

95c747e

Units can now be specified for the Lennard-Jones sigma and epsilon pa…

b22369c

…rameters

Reverted a recent commit

1ca939e

Code style improvements

0bd4f1f

Changed parameters to closer match doi: 10.1021/acs.jctc.6b01089

3722cfe

Update charge_utils.py

c737eb0

Units can now be specified for Lennard-Jones parameters

320d0e4

Update cp2k_md_v2.py

d73a5e6

Bug fix: raising the auxiliary error now causes a parameter set to be…

7965ff9

… rejected as intended

Update utils.py

2503517

Merge branch 'devel' of https://github.com/nlesc-nano/auto-FOX into d…

c629c66

…evel

Renamed formate.* to ligand.*

9495e03

Parenthesis are now displayed when printing type objects

4c76108

Removed redundant keywords

89ca50b

Bas van Beek and others added 24 commits May 26, 2019 16:54

Added missing argument

11ecd8b

Update armc.py

d41e2cb

Revert "Update armc.py"

d278f90

This reverts commit d41e2cb.

Wrapped up the implementation of NumPy-styled docstrings

74f3264

Paramater update

1d84802

WiP: ARMC restarts

126eaf1

Docstring updates

ced46bb

Changed reference to "**self**" into "this instance"; xyz comment lin…

593b05d

…es can be now imported and exported

Cleaned up sanitization and __str__

80bd24f

Update

a634936

Update .travis.yml

a77977f

Changed dirname from 'test' to 'tests'

0c0ed4c

Merge branch 'devel' of https://github.com/nlesc-nano/auto-FOX into d…

7270d86

…evel

Update requirements.txt

cd7415e

Removed nbsphinx

051c3fa

Removed nbsphinx

1ce8d7a

Update hdf5_utils.py

87a4dd7

Updated tests

fd1b839

Update CHANGELOG.rst

d409957

More test updates

2982e43

Merge branch 'devel' of https://github.com/nlesc-nano/auto-FOX into d…

5b0cf7b

…evel

Update setup.py

a5d4a10

Documentation update

e5ad2ff

Merge branch 'devel' of https://github.com/nlesc-nano/auto-FOX into d…

ef72ce5

…evel

BvB93 added the enhancement New feature or request label Jun 3, 2019

BvB93 self-assigned this Jun 3, 2019

BvB93 added 2 commits June 3, 2019 18:02

Update .travis.yml

71a2aac

Update test_example.py

9163295

BvB93 merged commit 407b7de into master Jun 3, 2019

BvB93 mentioned this pull request Jun 11, 2019

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Update #38

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