Changelog¶

r241119: AMS2024.105 released (Nov 20th, 2024)¶

r241119

• PLAMS: update AMSCalculator to support ase==3.23.0 and Molecule to support networkx>=3

r241114

• AMSinput QE: bandstructure detail options were not correctly activated.

• QE: Bug fixed in band structure calculations when users specified explicit k-points and their corresponding labels (K_Points and K_PointsLabels) in the input file.

r241105

• AMS driver: bug fix for numerical phonons when symmetry is disabled and the number of lattice vectors is less than 3. This would lead indirectly to an internal error in plgirr.

r241030

• AMSinput: modify start potential is only supported when (non-basic atom) fragments are present.

r241028

• AMSbands: allow opening kf result files from almost all AMS engines.

r241023

• ParAMS GUI: fix crash when reading saved files with complicated expressions, error: couldn’t compile regular expression pattern: quantifier operand invalid.

r241023

• AMSinput Hybrid: fix a crashing bug when going to the ADF/BAND Basis panel when they are used as a subengine.

• AMSinput Hybrid: fix coloring of menus on the right side when editing a subengine.

• AMSdos: Fix opening BAND result files that contain both bandstructure and partial-DOS results.

• ADF: Fixed a bug in the spin-unrestricted ETS-NOCV analysis that could sometimes lead to a segmentation fault.

r241022

• GUI: Fix a bug introduced in AMS2024.103, where ams packages installations are incorrectly detected by the GUI. This mainly affects the ADFCRS-2018 database for the COSMO-RS GUI module. Setting the SCM_ADFCRSDIR environment variable to the database path works around the issue.

r241017: AMS2024.104 released (Oct 21th, 2024)¶

r241017

• Fix a bug introduced in AMS2024.103, where python venvs and ams packages installations are incorrectly named/detected.

r241016

• AMSinput: the default unit when using the unit change popup menus (the option selected by default) was often incorrect.

r241009

• AMS: Raman and VROA calculations give more output regarding polarizability derivatives in case a frequency range is used.

r241004: AMS2024.103 released (Oct 7th, 2024)¶

r241004:

• AMSview: Add option to the View menu to change the bond source between the result file or guessed bonds.

r241003:

• AMSinput: Fix importing runscripts or system blocks containing the fractionalcoords key with a ‘Yes’ value.

r240930:

• Third-party software license information is now summarized in third-party-software.txt inside the AMS distribution.

• AIMNet2 calculations no longer crash when the number of atoms is changed.

r240927:

• MOPAC: avoid ERROR: Solvent radius too large - reduce RSOLV

r240924:

• GUI startup: add diagnostic code and changing timing to startup of scmd, to solve issue on MacOS Sequoia.

r240923:

• AMS: Fix a bug which caused atomic properties like ForceField.Charge to be lost in some situations during GCMC, Replay, or PESExploration runs.

• Fix encoding of logical values on KF files which caused issues when moving RKF files between Apple Silicon systems and other platforms.

• ForceField: Bugfix the UFF valence angle term for linear angles. Our previous implementation deviated from the UFF paper by making the barrier four times too low and also creating a spurious minimum at 0 degrees.

• AMSinput: charge was missing if multiple System blocks were present in all but first System block. For example with charged NEB calculations.

r240917:

• AMSinput: switching modules (from ADF to BAND for example) would clear the Dirty flag, thus closing would not ask to save your setup.

• AMSinput: make the Edit -> Crystal -> From Space Group… menu command also work if ADF mode is active, by automatically switching to a module supporting periodic systems.

r240911:

• AMSview: fix offscreen drawing on MacOS (the -batch command line flag)

r240911:

• PLAMS: A bug in AMSResults.get_density_along_axis was patched.

• AMSview: make sure fields are available when loading a VTK file

r240911:

• AMSPython: A bug causing a runtime error in RDKit was patched.

r240910:

• APPLE&P packmol interface: ensure integer molecular charges.

r240906:

• AMSview: when BAND fragment files have been moved, or are the result of a remote job, try to guess their new location when visualizing result:

  1. search for the fragment .results folder inside the main .results folder (the fragment .results folder should have the original name)

  2. search for the fragment .results folder on the same level as the main jobs .results folder

r240828:

• AMSinput: when editing with multiple molecules visible, stop the bonding mode when activating another molecule.

• AMSinput: make sure to show proper default directory with file Save As boxes, for example Apple&P atom typing was messing with it.

• ParAMS GUI: improve editting engines via AMSinput (would fail wit some engine IDs).

r240826:

• BAND: write PEDA terms to band.rkf, which can be useful for scripting.

• AMSview: make Grid Full Unit Cell work also when changing grids.

• AMSinput: preoptimize should not pick up atom properties, just changed coordinates.

r240823:

• Autolicense: change wording of error message when the license server cannot be reached.

• AMSinput: More button to the left of the BAND task should lead to Fragments panel when the task is Single Point.

• AMSinput: speed up display of BAND Fragments panel.

• BAND: stop when a negative valence count is requested when determining the fermi energy. This can be caused by requesting a spin polarization exceeding the number of valence electrons.

r240821:

• AMSinput: fix BGF export.

r240820:

• License checking: use improved machine ID on Mac also for clould licenses.

• AMSinput: importing from SMILES now handles inputs that do not generate atoms or bonds.

r240815:

• AMS: Undo the r240805 change because it may cause problems with some geometry optimizations and increase performance of constrained optimizations in delocalized coordinates.

r240809:

• BAND: The option Programmer%UpdateStdVec=’No’ was not working.

• BAND/amsview When using Grid%UserDefined, the grid will be with respect to the input molecule. Now consistent coordinates between gui and band, there is no longer a shift or remapping of the atoms to the unit cell.

• ADF: removed undocumented NOTOTEN key from example adf/Energy_H2O, which may lead to an AMS error output.

r240805:

• AMS: Improve convergence of the back-transformation of the delocalized step to Cartesian coordinates.

r240731:

• ParAMS: M3GNet fitting can now be interrupted with asking for an early stop.

r240730:

• Scripting: Deleted placeholder “acerxn” module. Developers should use “scm.acerxn” to import acerxn into scripts.

r240725

• ADF: fixed NOCV in case of a spin-polarized calculation with zero spin-polarization and no FRAGOCCUPATIONS keyword used with spin-restricted fragments. Remark: better option is to use a spin-restricted calculation in this case, and that was working also before this bug fix.

r240723

• AMSinput: fixed writing ACE Reaction Network system blocks to the run script

r240722

• ADF: fixed bug reading INTEGRATION block key

r240716

• Fixed a bug in the Reaxff-lg dispersion correction that would lead to too short inter-molecule distances and too high densities.

r240715

• GUI: do not use updatevtk in exported version

• MacOS: improve the machine ID used for license checking

• e-Reaxff: Fixed a bug that could lead to MPI errors for large systems with relatively few explicit electrons/holes.

r240712

• PLAMS: fix packmol interface if molecule charges were read in from system.in file

r240710

• Params GUI: when trying to use suggested weights after a sensitivity run without selecting training entries to update, give some informative dialog.

r240705

• AMSinput: fix importing / opening of files with .poscar or .contcar extension.

• Documentation(BAND): Added missing 1s frozen core for for Al-Ar.

r240704

AMSinput: fix importing multiple molecules at once.

r240703

• AMSinput: do not use fragoccupations key for repeated fragments, and if the total charge check in that case.

• AMSinput: items were not properly enabled for MLPotential.

r240627

COSMO-RS manual: Fix in documenting how Henry’s law dimensionless constant is calculated.

r240621

• AMS MD: Fix checking of Deformation input options TargetLength and LengthVelocity. Negative values of TargetLength were silently ignored instead of causing an error, and using LengthVelocity could potentially make AMS crash on start-up.

• Fix issue with symlinks to a missing lstopo executable.

• Changed development versioning scheme to rYYMMDD

r122243

PLAMS: Apply fix to AMSRedoxScreeningJob disable rerun prevention for ADFCOSMORSCompoundJob.

r122217

ADF: fix memory leak in ADF engine that could cause out-of-memory issues for jobs that called the ADF engine many times (e.g. MD). Also improved performance of input reading for the ADF engine.

r122119

ParAMS GUI: Fix potential issue with the unit preferences used for importing results.

r122055: AMS2024.102 released (Jun 10th, 2024)¶

r122022

QE: Fix a bug in the startqe script which made QuantumESPRESSO property calculations fail to start when running across several nodes under SLURM. Non-SLURM systems are still affected by a related issue, causing QE to use too many OpenMP threads for the property programs in multi-node runs, slowing them down. This can be worked around by setting the OMP_NUM_THREADS environment variable appropriately.

r121911

ParAMS GUI: do not modify the ParAMS engine when one is defined but no parameters are used.

r121906

PLAMS: Fix a crash in the AMSRedoxScreeningJob recipe.

r121893

• QE: Fixed an issue with the QuantumESPRESSO engine giving wrong results if the symmetry of a system broke during the lifetime of a worker. The underlying issue was that the QE engine did not redetermine the k-points upon symmetry breaking. The actual bug has been fixed in the 7.1-115 version of the QuantumESPRESSO package installable via AMSpackages, so updating the package will fix the issue also in AMS2024.101. This revision only updates the reference output of the LatticeOptimization example, which has changed slightly due to the changes in QE.

• AMSdriver: Fixed an issue with the EngineDebugging%ForceContinous PES not working anymore.

r121878

AMSinput: QE DOS panel was only reachable via the More button, the menu entry was missing.

r121858

APPLE&P: fixed a bug that would make assignment of atom sub-type incorrect in some rare cases.

r121845

• Engine ASE: PerformanceClass is no longer initialised randomly when not present in the input.

• Engine ASE: The File keyword in the Engine ASE block now works with any filename, while previously an error was reported if the extension was not .py.

• ParAMS: Fitting with NequIP now works also for jobs with different numbers of atoms.

r121831

ADF and Band: Show printed atomic coordinates in input order in case of QTAIM.

r121827

AMSview: Show QTAIM CP and BP coordinates in balloon text in Angstrom (instead of Bohr).

r121748

AMSinput: Fix the “Builder” that fills a periodic box with molecules, which would give an integer overflow error.

r121739

PLAMS: Allow small deviations from orthorhombic cells in the packmol_on_slab function.

r121731

AMSmovie: Fix the Filter Categories menu option for Reaction Discovery results on Windows.

r121698

AMSdriver: CopyRestartTrajectory was broken in combination with molecular gun.

r121687

AMSinput: DFTB NEGF remove potential button was broken.

r121666

AMSinput: make molecule gun work with simple active learning.

r121572

Active Learning: Decreased default value of MinR2 gradient checker to 0.2. This helps to prevent the AL loop from getting stuck when starting from geometry-optimized structures.

r121505

Active Learning: Prevent TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' crash for failed reference calculations when evaluating gradient accuracy.

r121499

AMSkinetics: fix help balloon for temperature runs.

r121492

AMSmovie: For EON results with an energy profile, for fragmented states, show the correct amount of molecules in the molecule formula label.

r121477

AMSspectra: Fix opening multiple files that are similarly named.

r121446

AMSinput: options called _Space where showing that should be blank lines.

r121436

GUI: Save with the correct extension on Linux when more options are possible (e.g. when exporting images).

r121375

AMSinput: Fix flickering issue when using the new Show Info Axes and Planes info panel.

r121343

AMSinput: Fix keybindings, such as the delete and element hotkeys, after changing certain visualization options (e.g. the 3D view options).

r121331

ADF and BAND: fix for OPBE Grimme3 zero-damping.

r121326

Params gui: make sure copy of molecule structure works when using Copy with focus on the molecule window.

r121288

Params gui: fix display of datapoint markers in plots on Windows.

r121277

BAND: Reduce non shared memory usage for BAND MetaGGA gradients. Band could crash during xc part of the energy gradients for systems with many atoms.

r121275

AMSview: fix picking up atomic vectors automatically.

r121256

AMSinput: allow spinflip spin-orbit calculations with BAND.

r121211

BAND: For non collinear calculation print the atomic magnetization (using Hirshfeld weights) in the text output.

r121187

AMSmovie: Fixed plotting the MD Property -> Step curve.

r121175

FlexMD: Fixed some bugs. Can now compute RDF for big systems.

r121172

Analysis: Fixed an overflow bug in the RDF

r121099: AMS2024.101 released (Apr 25th, 2024)¶