ase merge requestshttps://staging.gitlab.com/ase/ase/-/merge_requests2017-03-07T12:59:31Zhttps://staging.gitlab.com/ase/ase/-/merge_requests/135WIP: Connectivity diagram2017-03-07T12:59:31Zusername-removed-284116WIP: Connectivity diagramENH connectivity plotting
This adds a module utils/connectivities.py for easy listing and plotting of connectivities. It also adds a tools menuitem in the gui for plotting of connectivity diagrams.
The connectivities module works f...ENH connectivity plotting
This adds a module utils/connectivities.py for easy listing and plotting of connectivities. It also adds a tools menuitem in the gui for plotting of connectivity diagrams.
The connectivities module works fine, but would benefit from some cleanup. Especially would it be nice to use covertree.py for finding nearest neighbours, which make the search for nearest neighbours much faster for large systems.username-removed-284116username-removed-284116https://staging.gitlab.com/ase/ase/-/merge_requests/259ENH: added a read function for VASP's hessian2016-09-13T14:33:41Zusername-removed-478503ENH: added a read function for VASP's hessianA reader function for the VASP hessian.A reader function for the VASP hessian.username-removed-249965username-removed-249965https://staging.gitlab.com/ase/ase/-/merge_requests/300ENH: Atoms.get_spacegroup() method which determines the spacegroup from the A...2017-05-30T15:18:51Zusername-removed-646258ENH: Atoms.get_spacegroup() method which determines the spacegroup from the Atoms.positionsAdd a get_spacegroup method to Atoms, in a way similar to pyspglib.
Methodology: Test space groups from highest to lowest symmetry, and return the first match which keeps the cell unaffected by applying symmetry operators.
Merge requ...Add a get_spacegroup method to Atoms, in a way similar to pyspglib.
Methodology: Test space groups from highest to lowest symmetry, and return the first match which keeps the cell unaffected by applying symmetry operators.
Merge request from a cleaned (recent) repo which has testing pipeline OK.
This is a re-submission after a few failures. Sorry for that. ;-)
Emmanuel.https://staging.gitlab.com/ase/ase/-/merge_requests/330WIP: Implement band structure functionality in CP2K2017-03-06T23:52:26Zusername-removed-249965WIP: Implement band structure functionality in CP2KCP2K supports band structure calculations using the CP2K_INPUT/FORCE_EVAL/DFT/KPOINTS/BAND_STRUCTURE. I have added some bare minimum functionality to expose this to the CP2K calculator. Some internal cleanup is needed before this can be ...CP2K supports band structure calculations using the CP2K_INPUT/FORCE_EVAL/DFT/KPOINTS/BAND_STRUCTURE. I have added some bare minimum functionality to expose this to the CP2K calculator. Some internal cleanup is needed before this can be merged.https://staging.gitlab.com/ase/ase/-/merge_requests/337WIP: Added I-V curve function to tansport module2016-12-02T15:12:10Zusername-removed-837831WIP: Added I-V curve function to tansport moduleAdded a function to calculators.py which gives the current as a function of the bias for the transport module of ASE. I am not quite sure, if I worked out the units correctly though and would appreciate some help with this.Added a function to calculators.py which gives the current as a function of the bias for the transport module of ASE. I am not quite sure, if I worked out the units correctly though and would appreciate some help with this.username-removed-406082username-removed-406082https://staging.gitlab.com/ase/ase/-/merge_requests/362Symmetric surface2017-06-08T17:40:18Zusername-removed-265993Symmetric surfaceFirst attempt at a merge request to ase.
Enhancement to add adsorbates to slab symmetrically.First attempt at a merge request to ase.
Enhancement to add adsorbates to slab symmetrically.https://staging.gitlab.com/ase/ase/-/merge_requests/364WIP: lammpslib.py2017-04-27T13:51:51Zusername-removed-261087WIP: lammpslib.pylammpslib.py provides a Calculator interface to LAMMPS via it's bundled Python interface.
Interpretations of the licences previously prevented the code being distributed with ase, however this has now been resolved in Issue #37
This i...lammpslib.py provides a Calculator interface to LAMMPS via it's bundled Python interface.
Interpretations of the licences previously prevented the code being distributed with ase, however this has now been resolved in Issue #37
This is a modified version that was developed as part of https://github.com/libAtoms/pymatnest and has extended functionality, including bonds.
TODO: add tests
TODO: make code functional with Python 2.6, 2.7 and 3.xhttps://staging.gitlab.com/ase/ase/-/merge_requests/373WIP: hide search words2016-12-07T12:51:37Zusername-removed-406082WIP: hide search wordshttps://staging.gitlab.com/ase/ase/-/merge_requests/382WIP: Fix writing Wannier functions to file2017-09-27T16:45:54Zusername-removed-270410WIP: Fix writing Wannier functions to fileThere was an error where the wannier code expected a string as fname, but ase expected a file object. Worked around that.There was an error where the wannier code expected a string as fname, but ase expected a file object. Worked around that.username-removed-270410username-removed-270410https://staging.gitlab.com/ase/ase/-/merge_requests/404ENH: Constraints additive2017-04-14T22:43:35Zusername-removed-265993ENH: Constraints additiveSecond try at this. This is cleaner version and includes an additional to tests that should make the purpose clear.Second try at this. This is cleaner version and includes an additional to tests that should make the purpose clear.https://staging.gitlab.com/ase/ase/-/merge_requests/427WIP: Phonons write: Added write_as_json method to class Phonons2017-02-22T12:53:01Zusername-removed-1133030WIP: Phonons write: Added write_as_json method to class PhononsThis addition is useful for other programs that can plot or use the calculated phonon dispersion.This addition is useful for other programs that can plot or use the calculated phonon dispersion.https://staging.gitlab.com/ase/ase/-/merge_requests/464Simple set_initial_magnetic_moments2017-04-18T14:45:01Zusername-removed-517026Simple set_initial_magnetic_momentshttps://staging.gitlab.com/ase/ase/-/merge_requests/465Move structure in gui2017-09-05T12:05:21Zusername-removed-256065Move structure in guiIn ase-gui: Allow the entire structure to be moved using shift + right mouse button (and then move the mouse)
It contains an odd line to determine from a tkinter event that shift is pressed. Therefore it needs to be tested on Mac also...In ase-gui: Allow the entire structure to be moved using shift + right mouse button (and then move the mouse)
It contains an odd line to determine from a tkinter event that shift is pressed. Therefore it needs to be tested on Mac also.
Update: It still has the strange behavior on Mac, where the structure moves much more than the mouse is moved. This will be fixed eventually.https://staging.gitlab.com/ase/ase/-/merge_requests/481Lammps multistep2017-11-27T09:02:05Zusername-removed-580823Lammps multistepENH: Implemented Multistep usage of LAMMPSrun calculator. Multistep means that LAMMPSrun do not read/write atomic coordinates after each step of molecular dynamics or minimization procedure, but multiple steps are performed by LAMMPS its...ENH: Implemented Multistep usage of LAMMPSrun calculator. Multistep means that LAMMPSrun do not read/write atomic coordinates after each step of molecular dynamics or minimization procedure, but multiple steps are performed by LAMMPS itself. It significantly speeds up calculations but user have to specify all system constraints as LAMMPS parameters. Tests of typical use cases added. There is a need of this functionality:
https://listserv.fysik.dtu.dk/pipermail/ase-users/2017-April/003636.html
https://listserv.fysik.dtu.dk/pipermail/ase-users/2017-March/003585.htmlhttps://staging.gitlab.com/ase/ase/-/merge_requests/526WIP: ENH: Polished Turbomole, Amber, qmmm calculators2017-09-28T18:50:10Zusername-removed-1380022WIP: ENH: Polished Turbomole, Amber, qmmm calculatorshttps://staging.gitlab.com/ase/ase/-/merge_requests/536WIP: Pipek-Mezey Wannier functions2017-06-15T00:21:16Zusername-removed-572630WIP: Pipek-Mezey Wannier functionsWorking Pipek-Mezey module - unitary optimization of KS-DFT states to form highly
localized orbitals (in a similar fashion as maximally localized Wannier functions).
Supports GPAW calc - fd, lcao and pw basis, as well as pbc.
Includes ...Working Pipek-Mezey module - unitary optimization of KS-DFT states to form highly
localized orbitals (in a similar fashion as maximally localized Wannier functions).
Supports GPAW calc - fd, lcao and pw basis, as well as pbc.
Includes a general unitary optimization code (which comes with its own test class).
TODO:
Make a common module for this code and the current Wannier code, since they
share many of the same operations.
Tests.
Documentation.https://staging.gitlab.com/ase/ase/-/merge_requests/560WIP: ENH: Added three keywords in vasp caculator: langevin_gamma, langevin_ga...2017-09-27T16:48:57Zusername-removed-443576WIP: ENH: Added three keywords in vasp caculator: langevin_gamma, langevin_gamma_l and pmassI added few missing keywords to vasp calculator. Also I marked it with WIP, if I found that something else is missing.I added few missing keywords to vasp calculator. Also I marked it with WIP, if I found that something else is missing.https://staging.gitlab.com/ase/ase/-/merge_requests/565Stringbuilder class for O(N) string building with +=.2017-07-08T16:07:44Zusername-removed-71312asklarsen@gmail.comStringbuilder class for O(N) string building with +=.GULP will now use the string builder.GULP will now use the string builder.https://staging.gitlab.com/ase/ase/-/merge_requests/569WIP: Vasp with FileIOCalculator2017-10-05T15:51:13Zusername-removed-473205WIP: Vasp with FileIOCalculatorModule to implement VASP with the FileIOCalculator, as discussed in issue #143Module to implement VASP with the FileIOCalculator, as discussed in issue #143https://staging.gitlab.com/ase/ase/-/merge_requests/580WIP: More consistent Atom class2017-07-14T20:51:01Zusername-removed-71312asklarsen@gmail.comWIP: More consistent Atom classAtom class will now instantiate an internal Atoms of length 1 if it does not refer to another Atoms object.
This guarantees that it will behave the same always.
This also fixes one or more errors related to writing back into Atom o...Atom class will now instantiate an internal Atoms of length 1 if it does not refer to another Atoms object.
This guarantees that it will behave the same always.
This also fixes one or more errors related to writing back into Atom objects (momenta).
Fixes: #3, #23