Bug-fix changelog

Bug-fixes and improvements to the latest major release, with the latest changes listed first. The revision number corresponds to that of the bug-fixed binaries.

r83359: Fixed retrocompatibility issue for band.rkf results files.

Now it is possible to visualize in ADFView Band results files created with AMS2019.1 using AMS2019.3.

r83255: ADFmovie: Fix handling non-AMS result files that contain systems with different periodicities.

r83177: ADFmovie: Fix map atoms into unit cell for non-AMS/ADF result types.

r83131: ADFspectra: Fix warning message when hovering over the View->Atom Details (and related) menu.

r83026: ADFinput: CV(n)-DFT requires an all electron basis set

r83024: ADFinput: CD requires NOSYM

r82922: SCM menu behaviour changed

Now using the SCM menu will try to open the currently open file first, if possible, instead of trying the main job. This is as it was before r82616, except for fixing opening of explicitly selected files in ADFjobs.

r82879: Corrected an issue in detecting the number of physical cores for Windows machines with more than 64 virtual processors.

r82763: ADFinput: unit labels for repeated fields (like Molecule Gun) did not correctly show after redisplaying the page

r82616: SCM menu: uniform behaviour

In all modules except ADFjobs using the SCM menu will act the same as opening the selected module with the current job.

In ADFjobs with a job selected behaviour is the same, when a file has been explicitly selected that file will be opened.

r82561: ADFjobs SCM menu: when a file is selected in ADFjobs, always open that file (if supported by the module started)

r82559: ADFmovie: Change default movie export to mp4 with x264 encoding.

r82504: ADFmovie: Fix displaying SDF files with different amount of atoms.

r82441: NMR and CPL: Remove the scratch RIHartreeFock file at the end of a calculation.

r82369: ADFmovie: Fix error when displaying a PES scan, introduced by r80628.

r82350: GUI: Removed the OpenGL1 fallback in favour of providing OpenGL libraries that use software rendering.

On Windows, usage of the provided libraries is decided automatically at runtime.
On Linux, the environment variable SCM_OPENGL_SOFTWARE needs to be set in order to use the provided libraries.
The old SCM_OPENGL1_FALLBACK environment variable is no longer used.

r82337: GUI: Fix issues with certain modules (mainly ADFspectra not loading spectra) when used over SSH.

r82164: DFTB/band: prevent issue -- cannot linearize extreme dispersion -- . This was not implemented for 1D and 2D periodic systems. It prevents very high bands picking up small occupations, which coulc happen with very small basis sets.

r82157: GUI: Fixed several issues (e.g. pre-optimizer, field visualization) related to TMPDIR permissions on Windows.

r82142: Fixed a license issue for PES point characterization with BAND

The AMS driver attempted to use the DFTB engine for the calculation of the preconditioning Hessian and guess modes, which failed for users without a DFTB license. It now falls back to UFF in case DFTB is not available.

r82093: Bugfix error histograms for ReaxFF parameter fitting.

A bug in the analyze_errors script used in the ReaxFF fitting tutorial caused error histograms (error_bonds.csv, errors_angle.csv, etc.) to be shifted left by one bin. The count for the leftmost bin was lost, so the sum of all counts did not match the number of corresponding entries in the training set.

r82080: AMS NEB: Improve interpolation in the internal coordinates and add an option to add (valence and/or dihedral) angles to it.

Possible values of the NEB%InterpolationOption key:
1 - only distances,
2 - distances and near-linear valence angles,
3 - distances and all valence angles,
4 - distances and dihedral angles,
99 - all coordinates

r82031: ADF via AMS was not enabled in ADFinput in some cases.

r82010: Densf: add a repulsive NCI region as -3 value of the NCI field.

r81909: (Februari 24th, 2020):AMS2019.303 released

r81700: ADFspectra: fix issue with using the menu on Windows.

r81514: AMS-ReaxFF: Return corrected bond orders by default.

The ReaxFF engine now accepts a new input option "ReturnCorrectedBonds". With the default setting (enabled), the bonds returned to the driver are based on the final bond orders that include valence-dependent correction terms. Disable this if you want to see the raw uncorrected bond orders instead (ReaxFF will still use the corrected bond orders internally to evaluate the potential as usual).

Although classic reaxff defaulted to uncorrected bonds, in practice all our control files always set icobo=1, so most users likely expect seeing corrected bonds (which are also more chemically intuitive). Uncorrected bond orders also make molecule analysis unreliable.

r81511: Pipe engine, ASEPipeWorker: Fix compliance with the protocol specification.

r81425: KFBrowser: fix getting frequency labels from rkf style files

r81414: ADFmovie: Fix some issues with displaying electrons and electron holes (from eReaxff).

r81299: Bugfix XZ and YZ components of the polarizability tensor in the TAPE21 Properties section.

Before the fix, the XZ and YZ components of the tensor were interchanged.

r81277: Bugfix in the MESA SCF acceleration method.

In rare situation the bug could result in an "All MOs have zero eigenvalue" error. With the fix, the method that produced an invalid Fock matrix will be discarded at the current step.

r81217: Updated the python stack on Windows to 3.6.9 to match MacOS

This also includes pip 19

r81125: ADFinput: Charge key added for Mopac and DFTB when used within Quild

r81085: ADFinput: Fix dragging centroids.

r81055: ADFInput: GGA:S12g-D3 does not require integration Good for frequencies.

r81024: ADFinput: GGA:S12g-D3 can handle analytical frequencies.

r81015: ADFinput: Show Elastic wall restraint with old style ReaxFF

r81005: ADFinput: Fix unresponsive ADFinput GUI on certain Windows systems.

r80965: Updated the python stack on Linux to 3.6.9 to match MacOS

This also includes pip 19

r80941: Updated python stack on MacOS to avoid notarization errors on MacOS Catalina

Updated the python stack to 3.6.9. This includes pip 19. Also removed the pyxenon package, as it gives an error during notarization.

r80902: Make changes to avoid notarization errors on MacOS Catalina

Changes are only in packaging, app structure bundle and corresponding initialization code.

r80812: ADFINPUT: changed the Hcp crystal structure in the database (second basis vector).

r80775: DFTB: bugfix for very large systems. Reduce memory requirement (once more).

r80701: AMS NEB: Fix a segmentation fault trying to use results of an unconverged SCF.

r80690: DFTB: bugfix for very large systems. Reduce memory requirement.

r80628: GUI: Fix the initial legend position in certain plots.

r80612: AMS: Fix a problem with long interpolation path for periodic NEB.

If you intend to move an atom across more than half the unit cell in a periodic NEB, set the NEB%InterpolateShortest option to False.

r80597: ADF: fix issues with ghost atoms and dummy atoms for COSMO

If radius is not specified ghost atoms will get zero COSMO radii. Fixed bug in Delley surface construction in case of zero COSMO radii, relevant for dummy atoms and ghost atoms.

r80528: ADFinput: Fix error when using the element chooser on Windows, introduced by r79967.

r80234: ADF: Optimize memory usage by ETS-NOCV.

r80231: Fix issue that could cause ADFjobs to quit very slowly after running many jobs that have errors

r80156: DFTB: fixed a crash when calculating effective electron masses in parallel

r80089: (December 12th, 2019):AMS2019.302 released

r80088: ADFmovie: Show MD charges from AMS MD calculations (only when not using Fast mode).

r80071: ADFinput: Automatically update POTCAR references when changing POTCAR library dir.

r80065: ADFinput: Fix unit labels on conformers main page.

r80049: ADFmovie: Handle click on PES and NEB surfaces.

r79967: ADFtrain: Fix rxffutil options on Windows.

r79914: ADFmovie: improve the tab order in the RDF panel.

r79890: ADFinput: DFTB does not handle fractional charges, add a check for this.

r79775: ADFmovie: fix 'accepted geometries only' for Linear Transit ADF results.

r79758: ADFmovie: fix atom label positions.

r79683: ADFspectra: fix opening .sdf file with conformer spectra which has been moved from its original location.

r79673: ADFspectra: clicks were not handled as expected (bug was introduced in r79599)

r79669: The SCM menu could in some cases (with subjobs from quild or conformers) open another file than intended.

r79659: ADF: Fix a crash at the very numerical frequencies code after thermo() call

r79620: ADF: fix Fragments key in case a directory name is used as block header

ADF would give an error: STRINGS TOO LONG. CONCSS.

r79615: ADFspectra: fix initial range of some plots

r79613: Reaxff: Skip charge equilibration for a single-atom system.

r79609: ADFspectra: reset graph range after chaning Boltzman/T averaging

r79606: ADF-GUI graphs: only show legend for curves that are visible

r79599: ADFspectra: make visualization of spectra of multiple conformers much faster.

r79587: ADFspectra: make handling multiple conformers much faster

r79586: ADF-GUI: make render blocking work nested

r79578: Reaxff: Do not remove atoms on the last MD step to avoid discrepancy between the last saved molsav and fort.90 files.

r79576: ADFmovie: Fix display issues with qkf/runkf or non-movie result files.

r79563: ADFinput: remove ghost atoms when switching to any method other than ADF or BAND

r79560: ADFjobs: icon for VASP jobs is now blank

r79554: ADF-GUI: reposition Microkinetics in the SCM menu

r79548: Reaxff: catch user mistakes in the restraints input

r79545: The default perspective for viewing is now set properly in all modules, not just in ADFinput

r79524: Conformers filtering was broken

The Filter by rms option for SDF files was broken (causing a crash with a pythin error about a wrong index)

r79521: ADFmovie: Fix IRC trajectory reordering for adf results.

r79513: Reaxff: Fixed a bug determining frozen atoms when a geo file contains multiple geometries

This bug could result in atoms specified as frozen in one geometry would also be frozen in subsequent geometries

r79494: GUI SCM menu: show warning if nothing can be opened (instead of silently doing nothing)

r79479: ADFtrain: add Delete Selection menu commands with indicator that Backspace can be used for the same purpose

r79477: ADFtrain: save params file with hash sign in front of disabled parameter optimziation data to avoid them being optimized

r79461: Tutorials: add minor instructions to the generating molecules tutorial

r79445: DFTB: removed output spam for periodic D2 dispersion correction

r79439: include minor version number (301) in printed header of all programs

r79438: ADFmovie: Show graph markers for Replica Exchange MD.

r79421: ADFmovie: Fix selection issues with trajectories involving added/removed atoms.

r79399: Added examples/AMS to the binary distribution.

r79394: AMS: Fixed a bug in the NEB that would ignore frozen atom constraints.

Pass the constraints to the optimizer for end images optimization. Disable interpolation in internals and initial alignment of end images if frozen atoms are present.

r79386: Fix issues with conformer generation caused by wrong (aromatic) bonds.

r79304: DFTB: fixed a bug that could cause NaNs in the DFTB stress tensor for large systems.

r78301: (November 11th, 2019):AMS2019.301 released

AMS2019.3 has been released. Please see Release notes for a list of new features and improvements.