ase merge requestshttps://staging.gitlab.com/ase/ase/-/merge_requests2017-07-27T15:14:54Zhttps://staging.gitlab.com/ase/ase/-/merge_requests/574ase gui render2017-07-27T15:14:54Zusername-removed-71312asklarsen@gmail.comase gui renderRe-enable the ase gui rendering functionality, at least partially.Re-enable the ase gui rendering functionality, at least partially.https://staging.gitlab.com/ase/ase/-/merge_requests/573Slice Atoms without modifying original constraints2017-07-12T00:35:08Zusername-removed-256065Slice Atoms without modifying original constraints[sort_atoms.py](/uploads/6b4b2e55b6cdc01b6879398da89c9bb1/sort_atoms.py)
The attached file courtesy of @AlTy shows that constraints on the original Atoms object will be changed when slicing.
Here the copy.deepcopy of the constraints is...[sort_atoms.py](/uploads/6b4b2e55b6cdc01b6879398da89c9bb1/sort_atoms.py)
The attached file courtesy of @AlTy shows that constraints on the original Atoms object will be changed when slicing.
Here the copy.deepcopy of the constraints is performed before changing them.https://staging.gitlab.com/ase/ase/-/merge_requests/572BUG: Only call subprocess on master node2017-07-11T14:50:12Zusername-removed-473205BUG: Only call subprocess on master nodeFix suggested in issue #145Fix suggested in issue #145https://staging.gitlab.com/ase/ase/-/merge_requests/570Update ase-gui.desktop2017-07-08T15:46:30Zusername-removed-910973Update ase-gui.desktopExec 'ase gui' instead of 'ase-gui', name the application 'ASE GUI' to be consistent with documentationExec 'ase gui' instead of 'ase-gui', name the application 'ASE GUI' to be consistent with documentationhttps://staging.gitlab.com/ase/ase/-/merge_requests/568QMMM+TIP4P fix2017-07-07T08:04:20Zusername-removed-71423QMMM+TIP4P fixhttps://staging.gitlab.com/ase/ase/-/merge_requests/567fixed PrepareDB in GA2017-07-05T14:07:51Zusername-removed-256065fixed PrepareDB in GAThe function to add relaxed candidates during the initialization of the db in the genetic algorithm was faulty. (Did not test for raw_score for example).
This is now fixed.The function to add relaxed candidates during the initialization of the db in the genetic algorithm was faulty. (Did not test for raw_score for example).
This is now fixed.username-removed-256065username-removed-256065https://staging.gitlab.com/ase/ase/-/merge_requests/566Fixed dipole moment error in vasp_xml.py test.2017-07-03T14:13:49Zusername-removed-256065Fixed dipole moment error in vasp_xml.py test.Also comparing arrays is now performed with numpy.allclose instead of
home-made solution.Also comparing arrays is now performed with numpy.allclose instead of
home-made solution.username-removed-256065username-removed-256065https://staging.gitlab.com/ase/ase/-/merge_requests/564raise an error if images have same calculator2017-07-08T18:15:28Zusername-removed-71312asklarsen@gmail.comraise an error if images have same calculatorFixes: #141Fixes: #141https://staging.gitlab.com/ase/ase/-/merge_requests/563StrainFilter now calls the Filter constructor. This will fix some issues like…2017-06-30T16:05:28Zusername-removed-71312asklarsen@gmail.comStrainFilter now calls the Filter constructor. This will fix some issues like…StrainFilter now calls the Filter constructor. This will fix some issues like having an atoms_for_saving attribute (so one can save StrainFilters to trajectories). Also self.n was calculated incorrectly, but that variable appears unuse...StrainFilter now calls the Filter constructor. This will fix some issues like having an atoms_for_saving attribute (so one can save StrainFilters to trajectories). Also self.n was calculated incorrectly, but that variable appears unused anyway.https://staging.gitlab.com/ase/ase/-/merge_requests/562Made the PBSQueueRun object in ase.ga python3 compatible2017-06-30T13:15:26Zusername-removed-256065Made the PBSQueueRun object in ase.ga python3 compatibleadded universal_newlines=Trueadded universal_newlines=Trueusername-removed-256065username-removed-256065https://staging.gitlab.com/ase/ase/-/merge_requests/561ENH: Use initial charges if charges are not available.2017-09-13T04:55:37Zusername-removed-255251ENH: Use initial charges if charges are not available.small changesmall changeusername-removed-71312asklarsen@gmail.comusername-removed-71312asklarsen@gmail.comhttps://staging.gitlab.com/ase/ase/-/merge_requests/559band structure plot legend with spins2017-06-29T11:17:25Zusername-removed-302375band structure plot legend with spinsAdded label = 'Spin up' or 'Spin down' for cmr band structure plots.Added label = 'Spin up' or 'Spin down' for cmr band structure plots.https://staging.gitlab.com/ase/ase/-/merge_requests/558Find command2017-07-31T11:12:42Zusername-removed-71423Find commandusername-removed-71423username-removed-71423https://staging.gitlab.com/ase/ase/-/merge_requests/557Wrapped atoms in read_atoms_from_outmol in order to assure…2017-06-28T11:18:02Zusername-removed-581020Wrapped atoms in read_atoms_from_outmol in order to assure…Wrapped atoms in read_atoms_from_outmol in order to assure find_dmol_transformation works for periodic structures.Wrapped atoms in read_atoms_from_outmol in order to assure find_dmol_transformation works for periodic structures.https://staging.gitlab.com/ase/ase/-/merge_requests/556BUG: Return list instead of map2017-07-12T00:46:33Zusername-removed-473205BUG: Return list instead of mapReading reciprocal or cartesian KPOINTS file would return list of map objects instead of list of lists.
Also, we only need to have a single call to `set(kpts=kpts)`, as we will always get to that statement, in either case in the for-else...Reading reciprocal or cartesian KPOINTS file would return list of map objects instead of list of lists.
Also, we only need to have a single call to `set(kpts=kpts)`, as we will always get to that statement, in either case in the for-else statement.
As a side effect, Pyflakes found a few spaces here and there.https://staging.gitlab.com/ase/ase/-/merge_requests/555ENH: Read eigenvectors and eigenvalues in the nwchem calculator2017-07-08T23:39:09Zusername-removed-709664ENH: Read eigenvectors and eigenvalues in the nwchem calculatorMigrated the relevant methods into the NWChem class as promised here https://listserv.fysik.dtu.dk/pipermail/ase-users/2017-June/003803.html. Also added the ``print`` keyword to the table of parameters in the documentation. The data read...Migrated the relevant methods into the NWChem class as promised here https://listserv.fysik.dtu.dk/pipermail/ase-users/2017-June/003803.html. Also added the ``print`` keyword to the table of parameters in the documentation. The data read can be used also in the ``get_occupation_numbers()`` and ``get_eigenvalues()`` methods, which are currently not working for non-periodic calculations (not yet implemented).https://staging.gitlab.com/ase/ase/-/merge_requests/554attempt to fix windows scroll wheel in ase gui. Closes: #1322017-07-12T00:43:38Zusername-removed-71312asklarsen@gmail.comattempt to fix windows scroll wheel in ase gui. Closes: #132https://staging.gitlab.com/ase/ase/-/merge_requests/553display index numbers as 1..N instead of 0..(N-1) in the gui.2017-07-20T11:36:33Zusername-removed-71312asklarsen@gmail.comdisplay index numbers as 1..N instead of 0..(N-1) in the gui.Last image will now be shown as 5/5 instead of 4/5.Last image will now be shown as 5/5 instead of 4/5.https://staging.gitlab.com/ase/ase/-/merge_requests/552ENH: Vasp XML import missing info: spin channels, k-point weightings2017-07-18T11:23:12Zusername-removed-282459ENH: Vasp XML import missing info: spin channels, k-point weightingsCurrently the Vasp XML importer only reads the eigenvalues and occupancies of one spin channel.
It also does not grab the information about k-point weightings, which may be needed for applying energy corrections. As the SinglePointCalcul...Currently the Vasp XML importer only reads the eigenvalues and occupancies of one spin channel.
It also does not grab the information about k-point weightings, which may be needed for applying energy corrections. As the SinglePointCalculator has an API for these properties and they are in the XML file, they should be included.https://staging.gitlab.com/ase/ase/-/merge_requests/551Highlight row on mouse hover2017-06-21T10:04:21Zusername-removed-415345Highlight row on mouse hover