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.

Revision Description
r91038 AMSspectra: interacting with offset or scaling would show all conformer curves when only average curve should be shown
r91028 AMSspectra: fix remembering the width of the broadening function. Opening the same spectrum again could generate a different value, depending on the units used on the X axes.
r91018 BAND/AMSinput: Allow the user not to store the DOS per basis function. For large super cells this may be very expensive. See storeDosPerBas in band Band Expert panel.
r91014 AMSinput: fix name displayed in preoptimizer (would shoow ReaxAMS instead of ReaxFF, etc)
r91010 AMSinput: fix packmol builder with non-orthogonal cells, removing too many atoms in the final step.
r90976 AMSinput: update DIM/QM GUI panel on method change. No longer ask to update the full system after a DIM/QM calculation.
r90965 AMS: Geometry optimizations with the quasi-Newton optimizer will be performed in Cartesian coordinates by default when a fast engine is used.
The delocalized coordinates can be very expensive compared to the engine.
r90956 AMS driver: fix issue with input reading of the NEB%Parallel block during NEB restarts
r90919 AMSinput: avoid crash in Z-matrix panel when less then three atoms are present.
r90912 GUI: fix opening KFBrowser via the SCM menu, and AMSmovie now will not open logfiles any more for AMS jobs.
r90880 GUI: starting a module that was already open sometimes started a new module with the same file open. Fixed.
r90861 AMSspectra: fix reading old raman spectra (from .t21 files)
r90821 AMS2020.102 released (Januari 12th, 2021)
r90820 AMSinput: input key names for most keys were missing in the AMSinput search database.
r90802 DFTB: the fix r90772 introduced a bug for response DFTB when using more than one node.
r90790 AMSinput: fix test when using dispersion correction with heavy elements (did produce an incorrect warning message when saving the job).
r90782 GUI: When using the Intel Ice Lake integrated GPU, clicking on atoms or bonds can select the wrong ones. This change attempts to fix this.
An alternative solution is to use software rendering, which can be enabled by adding SCM_OPENGL_SOFTWARE to your Windows environment variables with value 1.
r90772. DFTB: Orbitals coefficients wrong for systems with multiple k-points when using more than one node. This affects only the plotting in amsview of the orbitals and density. It also affect QTAIM for DFTB.
r90744 GUI on non-MacOS: on macos Big Sur dark/light mode fix only for mac version.
r90738 BAND: low level kf-error about reading occup variable. Only observed for DTB-1/2 calculations.
r90736 GUI: on macos Big Sur the GUI was only usable (readable) in light mode.
r90719 AMS driver: fixed size of the Gradients variable in the ams.rkf History section for geometry optimizations with constraints using the Quasi-Newton optimizer
r90642 AMSoutput: make sure to open the main output file instead of CreateOutputs when started via the SCM menu (with no local file selected)
r90612 KFBrowser: the reported size of a variable is now the actual numer of elements (instead of the reserved size).
r90603 KF library: Update the number of used elements in a KF variable after writing less data than there was.
Before this change, writing n elements to a pre-existing variable of length m (n < m) did not update its used elements count if it was already larger than n. After the change it will be set to n regardless of its previous value. This should, for example, fix issues when performing a restart from an ams.rkf file from MD calculation in which some atoms were removed from the system.
r90572 DFTB: Orbital coefficients possibly wrong when using more than one node. TDDFTB results would always be wrong when using more than one node. (A node is not a core, but rather a physical computer)
r90559 AMSinput: when setting up a job for the Hybrid engine, # dependencies lines where missing (if needed for a restart).
r90528 AMS MD: Fix fractional coordinate handling in the AddMolecule feature (molecule gun) for non-3D-periodic systems.
This affects the FractionalCoords and FractionalCoordsBox input options. The components corresponding to non-periodic dimensions are now correctly interpreted as absolute values in Ångströms as documented. This also includes a fix to performance issues with large values of NumAttempts.
r90525 ReaxFF: Re-enable OpenMP parallelization in AMS.
All calculationd done using the ReaxFF engine in 2020.101 accidentally ran with disabled OpenMP parallelization.
r90523 ReaxFF: Reset charge solver when running with disabled predictor and no previous calculation to restart from.
This affects calculations done through the pipe interface (AMSWorker class in PLAMS). Before this change, running multiple independent calculations through the same AMSWorker object caused minor numerical noise in the calculated charges. Setting ReaxFF.Charges.Predictor.Type to "None" now guarantees that the results will be exactly reproducible regardless of any previous calculations.
r90510 AMSview: Fix opening non-kf files, issue was introduced in r90305.
r90485 License code improvement.
r90483 AMSmovie: Fix error with active MD replica graphs when no other graphs are present.
r90458 Reaxff: Fix a bug triggering ACKS2 error for the Eh pseudo-atom.
r90431 AMSinput: Fix polymerbuilder cap with a structure (other than H or None).
r90428 ADF and BAND: Workaround precision issues LibXC REVSCAN and REVSCAN0 functional.
However, this does not solve all numerical issues for these functionals calculated with LibXC.
r90415 AMSmovie: Fix issue when reading MD properties for non-rkf result files (error message: can't read "ix").
r90405 AMSmovie: Fix graphs of PBC distance, angle and dihedral for lattice optimizations.
r90338 AMS: Print names of the molecules removed during molecular dynamics
r90321 AMSinput: resolve a problem with basis set info not working without the corresponding (ADF or BAND) license
r90309 Band: remove memory leak in NewResponse
r90305 AMSmovie, AMSview: display regions if defined in AMSinput, also for single point jobs
r90300 AMSspectra: click in empty space in excitation details would (incorrectly) be handled like clicking on the last line, opening unexpected AMSview windows.
r90291 Linux: improvements and a bugfix for the create_linux_icon.sh script.
r90253 AMSmovie: Fix x units when adding a Molecule Fractions graph to an empty graph window.
r90195 AMSjobs: fix issue with sorting by type for some types (like conformers, hybrid, mlpot)
r90186 AMSpython: Fixed incorrect TCL_LIBRARY path on Windows.
r90135 AMSjobs: Fix Job Requirements filter found in the View menu.
r90008 AMSinput: Fix performance regression of 'Select Within Radius' and 'Select Molecule' atom selection commands
r89994 GUI: Fix several issues with periodic bond guessing.
r89947 AMSinput: avoid warning popups in basis panel for ADF and BAND when no local license for ADF or BAND is available
r89944 AMSinput: handle opening old .adf files using the no longer supported AMS via ADF module without crashing
r89931 AMSmovie: Fix reading region info from result file.
r89924 AMSinput: Fix charge and spin checks when using FDE fragments. Fix region label for FDE.
r89909 AMSinput: avoid check for non-default solvent when no solvent is used.
r89899 ReaxFF forcefields: fix typo in CHO-radiation.ff (element O instead of element 0)
r89887 AMSinput: Fixed field names in Parallel details
r89880 AMSinput: avoid crash when saving a Hybrid job that is missing engine information
r89868 AMSinput: fix crash when activating ETS-NOCV before activating the Fragments option
r89830 AMSinput: Fix FDE uninitialized region charge error and relaxcycles key. Fix FragOccupations block generation when all electrons get paired.
r89826 Windows: switch to using mpiexec from the Intel-MPI legacy directory that supports the -bootstrap fork command line option.
This allows to kill running jobs easier.
r89800 AMSmovie: fix displaying (e.g. Color Atoms By) properties for non-AMS result files.
r89793 AMSoutput: fix displaying UTF-8 characters, fix zero-point energy menu link.
r89774 ADF: fix quadrupole intensities XAS in unrestricted calculations.
r89752 COSMO-RS: fixed COSMO-SAC Enthalpy calculation.
r89746 AMSinput: fix potential issue that could block detecting clicks in the molecule editing window while the bonding indicator is showing.
r89738 AMS & ADF: The EngineRestart keyword can now be used to restart the ADF engine from TAPE21 and TAPE13 files written by ADF2019
r89718 AMSprefs: Add SCM_NO_RSYNC to the list of available environment variables, it could already be added as custom before.
Use this variable if you encounter issues (mainly on Windows) with using rsync to submit remote jobs.
r89709 Windows: Update the IntelMPI runtime to 2019 update 9 to fix issues where a job could stay running in the background when it gets killed
r89707 AMSinput: total charge automatically adjusting when editing the occupations now also works for unrestricted Spin-Orbit inputs.
rr89703 AMSjobs try to fix the error list doesnt contain element 500, in the cleanup of the joblist when quitting.
r89682 Python scripting: optimize calculation of inter-molecular distances in oledtools.
r89670 AMSjobs: the job list mode will not keep a list of jobs in $ADFHOME (you should not save anything in that folder), and will remove jobs that have no longer a .pid file.
r89665 COSMO-RS: fixed volume of compound in liquid phase used in calculation.
This could have an effect, for example, on the calculated Henry coefficient, or on the calculated g/(L solution) solubility calculation.
r89661 COSMO-RS GUI: add a saved multiple form automatically to the list of compounds.
r89648 Introduce @include directive for including external files in the input
This replaces the INLINE keyword from ADF, which was accidentally removed when ADF was integrated into the AMS driver.
r89644 DFTB: Symmetrize the DFTB stress tensor. This will not be done when useSymmetry in the DFTB engine input block is set to false.
r89623 GUI: Fix issue with automatic OpenGL detection and fallback on Windows.
r89600 DFTB: hanging code when storing the orbitals for periodic systems with multiple k-points, using more than one node.
r89568 PLAMS: Fix a typo in handling of the settings.runscript.stdout_redirect option by AMS jobs.
r89510 AMSinput: Import Coordinates now also shows files with .run extension.
Importing from an AMS run script often works (including lattice).
r89490 Documentation: change references to ADFinput to AMSinput.AMS.
r89478 AMS: Fix order of atoms in the DifDist PESSCan coordinate.
r89470 AMSjobs: Fix file transfer from remote on Windows with SCM_NO_RSYNC set.
r89462 Band: disable analytical gradients and stress with the Hubbard option (gga+U), because they were incorrect.
r89452 Hybrid engine: do some sanity checking on the regions. Engine will stop when it is not happy. Use AllowSanityCheckWarnings to force the engine to continue.
r89435 COSMO-RS GUI: allow for making dissociated dimer and dissociated compound+solvent as one of the multiple forms of a compound.
r89358 BAND is now able to calculate charges without calculating also all other properties
This inability lead to the engine failing in rare circumstances, e.g. when the charges were requested via the AMSWorker interface in PLAMS.
r89354 BAND: TOO MANY TRIES in didif, for some GGA functionals.
Still three remaining combinations fail: Ac-BLYP, Ac-HTBS, and Lr-OLYP. For the HTBS and OLYP functionals the RadialDefaults%RMin is made larger for light atoms.
r89351 AMSinput: prevent the Save As question when nothing has changed (would show just by starting and quitting AMSinput).
r89345 AMSdos: partial dos (per basis function) in AMSdos could be wrong for BAND calculations.
The partial DOS shown in AMSbandstructure was correct.
r89343 BAND stops earlier when the D4 dispersion correction is used with periodic systems
Before, BAND only stopped after the first SCF, wasting computational time before stopping with an error.
r89319 AMS driver: better logfile output for parallelized numerical derivatives
The AMS driver now prints more information on the automatic parallelization of the numerical derivatives loop to the logfile: the total number of displacements, the number of displacements skipped due to symmetry equivalence, the number of worker groups created, the number of processes per group, as well as the task scheduling strategy (static or dynamic).
r89302 AMSinput: fix changing the angle of three atoms that were all on one line.
r89299 AMSinput: backwards compatibility: convert Frequencies runtype, fix default file name when saving.
r89295 AMSinput: coloring vector input fields (multiple numbers on one line) fixed.
r89291 Fix startup problem for AMSinput and amsprep when starting more than one at the same time
r89258 AMS2020.101 released (November 2, 2020)