ase merge requestshttps://staging.gitlab.com/ase/ase/-/merge_requests2015-11-09T06:54:21Zhttps://staging.gitlab.com/ase/ase/-/merge_requests/72Update/clarify contributing.rst2015-11-09T06:54:21Zusername-removed-164158Update/clarify contributing.rstMade some clarifying edits on contribute.rst. Nothing too controversial I hope! cc @schiotz Made some clarifying edits on contribute.rst. Nothing too controversial I hope! cc @schiotz https://staging.gitlab.com/ase/ase/-/merge_requests/73Bug fix: contraints.Filter must support same keyword args as Atoms.2015-11-09T12:31:51Zusername-removed-265766Bug fix: contraints.Filter must support same keyword args as Atoms.Bug fix: contraints.Filter did not pass keyword arguments to get_potential_energy() and set_momenta() to the original atoms object, causing MD to crash.Bug fix: contraints.Filter did not pass keyword arguments to get_potential_energy() and set_momenta() to the original atoms object, causing MD to crash.https://staging.gitlab.com/ase/ase/-/merge_requests/74BUG: Fix ase.db strings interpreted as integers or floats2015-11-12T11:08:13Zusername-removed-256065BUG: Fix ase.db strings interpreted as integers or floatsNow there is a test of whether a value in a key value pair is put in as a string but can be interpreted as a integer or float. This is not allowed since you will not be able to search for this key value pair again.Now there is a test of whether a value in a key value pair is put in as a string but can be interpreted as a integer or float. This is not allowed since you will not be able to search for this key value pair again.https://staging.gitlab.com/ase/ase/-/merge_requests/75kpoints changes2015-11-12T14:34:27Zusername-removed-289445kpoints changeshttps://staging.gitlab.com/ase/ase/-/merge_requests/76Make bundletrajectory work in Python 3, and enable the test.2015-11-09T16:19:02Zusername-removed-265766Make bundletrajectory work in Python 3, and enable the test.The bundletrajectory did not work in Python 3, because it did not open files in binary mode.
There is most likely still a compatibility problem between bundletrajctories written with Python 2 and Python 3.
The bundletrajectory did not work in Python 3, because it did not open files in binary mode.
There is most likely still a compatibility problem between bundletrajctories written with Python 2 and Python 3.
https://staging.gitlab.com/ase/ase/-/merge_requests/77ENH: add build interface to manip. atoms tutorial2015-11-10T15:11:09Zusername-removed-256176ENH: add build interface to manip. atoms tutorialENH: add build interface to manip. atoms tutorial
The manipulating atoms tutorial (manipulating_atoms.rst) is extended
with a little tutorial to add a layer of water to a surface.
Two helper python files are included. WL.py creates...ENH: add build interface to manip. atoms tutorial
The manipulating atoms tutorial (manipulating_atoms.rst) is extended
with a little tutorial to add a layer of water to a surface.
Two helper python files are included. WL.py creates WL.traj, which
can be imported using ase.io.read.
interface-h2o.py loads WL.traj and creates the png files for the tutorial.https://staging.gitlab.com/ase/ase/-/merge_requests/78ase-gui read .poscar2015-11-09T18:30:12Zusername-removed-289445ase-gui read .poscarhttps://staging.gitlab.com/ase/ase/-/merge_requests/79Raise on all ranks in parallel2015-11-09T19:49:41Zusername-removed-71423Raise on all ranks in parallelhttps://staging.gitlab.com/ase/ase/-/merge_requests/80BUG: Writing png files now works with matplotlib v.1.5.02015-11-10T11:08:57Zusername-removed-256065BUG: Writing png files now works with matplotlib v.1.5.0The writing of png files now work with matplotlib version 1.5.0 it has also been tested with versions 1.4.0 and 0.99.1.1The writing of png files now work with matplotlib version 1.5.0 it has also been tested with versions 1.4.0 and 0.99.1.1https://staging.gitlab.com/ase/ase/-/merge_requests/81BUG: not able to choose own optimizer in neb idpp, now fixed2015-11-12T11:03:57Zusername-removed-256065BUG: not able to choose own optimizer in neb idpp, now fixedhttps://staging.gitlab.com/ase/ase/-/merge_requests/82Parallel IO2015-11-16T08:22:30Zusername-removed-255251Parallel IOBUG: raise exception also on slavesBUG: raise exception also on slaveshttps://staging.gitlab.com/ase/ase/-/merge_requests/83Castep interface2015-11-16T14:52:26Zusername-removed-253735Castep interfaceSecond merge request due to merge conflicts before.Second merge request due to merge conflicts before.https://staging.gitlab.com/ase/ase/-/merge_requests/84BUG: Bugfix in write_castep_cell()2015-11-17T08:38:31Zusername-removed-253735BUG: Bugfix in write_castep_cell()Actually a new MR. Tiny but crucial bugfix.Actually a new MR. Tiny but crucial bugfix.https://staging.gitlab.com/ase/ase/-/merge_requests/85Feature/remove duplicates - Identify and handle duplicate atoms2015-12-14T10:26:24Zusername-removed-268789Feature/remove duplicates - Identify and handle duplicate atomsThis is Work-In-Progress and needs some discussion.
When reading experimental crystal structures (for example .cifs from the Cambridge Structural Database) often (H)-atoms are defined multiple times, due to uncertainties in the experi...This is Work-In-Progress and needs some discussion.
When reading experimental crystal structures (for example .cifs from the Cambridge Structural Database) often (H)-atoms are defined multiple times, due to uncertainties in the experimental Xray data. The ase.io.cif module will read all atoms, leading to unphysical structures with overlapping atoms.
The proposed method (get_duplicate_atoms) allows efficient identification of duplicate atoms within an Atoms-object using a cutoff radius. In addition, it is possible to directly delete one set of duplicates. This can be useful not only for the .cif issue, but also for other cases when one needs to test if atoms are too close within a system.
[Issue 1] - I added this method to ase.atoms since I felt it would be a natural addition to the existing atoms-methods. But of course it could be added as some routine that just takes atoms objects as inputs.
[Issue 2] - scipy.spatial.distance.pdist: I know there is a neighbourlist calculator, but I'm not sure if I understand why it is implemented in pure Python - it is quite slow compared to alternatives? Unfortunately I couldn't find some kind of core guidelines on what imports are acceptable for which parts of ASE.https://staging.gitlab.com/ase/ase/-/merge_requests/86Castep interface2015-11-18T06:22:21Zusername-removed-253735Castep interfaceFixed CASTEP interface test failing with (ancient) Python 2.6 -- basically replaced subprocess.check_output() with subprocess.Popen()
Includes further minor bugfix regarding the dryrun functionality of the CASTEP calculator.Fixed CASTEP interface test failing with (ancient) Python 2.6 -- basically replaced subprocess.check_output() with subprocess.Popen()
Includes further minor bugfix regarding the dryrun functionality of the CASTEP calculator.https://staging.gitlab.com/ase/ase/-/merge_requests/87Exclude emacs backup files2015-11-18T09:00:40Zusername-removed-255251Exclude emacs backup filesDEVDEVhttps://staging.gitlab.com/ase/ase/-/merge_requests/88ENH: Rraman2015-11-19T11:58:22Zusername-removed-255251ENH: RramanResonant Raman spectra.
Would like to introduce a test to gpaw-test suite where this checkin is neededResonant Raman spectra.
Would like to introduce a test to gpaw-test suite where this checkin is neededhttps://staging.gitlab.com/ase/ase/-/merge_requests/90Fix for old psycopg22015-12-03T14:16:01Zusername-removed-71423Fix for old psycopg2https://staging.gitlab.com/ase/ase/-/merge_requests/91reading of atomic elements in espresso input-files adapted2015-12-04T10:07:31Zusername-removed-291783reading of atomic elements in espresso input-files adaptedUp to now only the first character of either the -periodic element number- or the -elements abbreviation- was read in; hence -atoms- could not convert the espresso input correctly. This is accounted for now.Up to now only the first character of either the -periodic element number- or the -elements abbreviation- was read in; hence -atoms- could not convert the espresso input correctly. This is accounted for now.https://staging.gitlab.com/ase/ase/-/merge_requests/92DEP: Warned about future removal of raw score methods attached to the atoms o...2015-12-09T20:07:40Zusername-removed-256065DEP: Warned about future removal of raw score methods attached to the atoms objectAdded warnings when using the methods being added to the atoms object in ase.ga. That is the get and set methods for raw_score, parametrization and neighbor_list. Now there is regular functions in ase.ga.__init__ (imported by e.g. from a...Added warnings when using the methods being added to the atoms object in ase.ga. That is the get and set methods for raw_score, parametrization and neighbor_list. Now there is regular functions in ase.ga.__init__ (imported by e.g. from ase.ga import get_raw_score) that takes an atoms object as an argument and does the same as the old functions.