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
r96372 GUI: Fix display of the angle when atoms are overlapping, which is more likely to happen with periodic systems displaying the shortest pbc angle.
r96221 GUI: Bond guessing involving metallic atoms and hydrogen would in too many cases skip those bonds.
r96179 AMSjobs: Right clicking on empty space would create a popup menu that could not be dismissed.
r96174 AMSinput: Bugfix for presets to make super cells in the 2D case: The sqrt(3) x sqrt(3) preset was not shown when the angle between the lattice vectors was 120 degrees, rather than 60 degrees.
r96145 AMSinput: QTAIM and IQA now availble with relativity, except for atomic energies.
r96122 GUI: on Linux when the new file dialog encounters an error (due to too old system libraries) it now automatically sets SCM_DEFAULT_DIALOG to 1 in the prefernces to fall back to the old file dialog.
r96111 AMSinput: importing specific step from MD RKF files would import wrong lattice and bonds.
96093 AMSinput: constraints for MD offered the option to constrain regions, but this is not supported in AMS. These are now converted to atomlist constraints.
96089 AMSmovie: fix exporting 1D and 2D system trajectory to BGF format. Add check for other formats when atoms are added or removed during the trajectory, this is currently not handled.
96060 BAND: two extra fields available for :plotting laplacian[rho(valence)] and laplacian[rho(deformation/fit)].
r95991 AMSpackages: better error message for download failures.
r95984 AMSpackages: provide more information for repository errors.
r95877 ADF: Fix RPA correlation energy.
The RPA correlation energy was calculated a factor 2 too large.
r95870 AMSinput: remove the option to delete the only system block in AMS expert keys.
r95860 BAND: Improvements for non-collinear calculations. For big systems the memory footprint is reduced, avoiding a crash. Furthermore a change has been made to the SCF procedure improving the convergence. Still converging a non collinear calculation is often difficult.
r95857 AMSinput: do not add the coords key for the molecule gun when a fractional coords box has been defined.
r95854 AMSbands: the BZ would be invisible due to wrong camera positioning (for example in the phonons tutorial).
r95840 AMSinput: molecule sink should accept * as formula, fixed.
r95787 AMS: Fixed a bug in the molecule gun that could result in NaN velocities if EnergySigma was too large.
95783 AMSpackages: Bugfix. package manager can now find licenses even when AMSBIN is not in path.
r95768 ReaxFF documentation: mention force-bias Monte Carlo support.
r95737 All: improve messages produced in case of license issues, add license debug mode
r95692 AMSpackages: Bugfix. No longer produce an unhandled exception when an installation is attempted without a valid license.
95621 BAND: Error "Fragments cannot be assigned by a simple translation" when visualizing from amsview.
r95566 DFTB: Bugfix. The finite electronic temperature (300K) should also be the default for periodic calculations usig more than one k-point. This improves the SCC convergence for such systems.
r95509 AMSpackages: Bugfix. When updating a package, new dependencies will no longer be skipped.
r95464 In case of license errors print out the #user line as found in the license file.
r95424 BAND: Added expert keys SCF%PrintAllOccupiedBands and SCFPrintAllVirtualBands. Affects only the text output where the ranges of the bands are printed.
r95409 AMS: Add a VaryTrustRadius input option to the GeometryOptimization%Quasi-Newton%Step input block.
Setting this option will override the default behavior, which is to allow the TR to change during energy minimization but not during a transition state search.
r95387 ADF: QM/FQ fix: include screening of interaction between MM atoms and QM density.
This fix is to avoid unstable results in case numerical integration points are accidentilly close to MM atoms.
r95383 AMSmovie: Avoid segfault on MacOS with NVIDIA drivers.
r95337 AMSpackages: Use of "~" to refer to home directory inside configuration files now works as intended.
r95332 Doc: Mention SCM_SHAR_NONUMA in the installation manual.
See below for a description.
r95222 BAND: Bug fixes for NewResponse. The results were not the same as for OldResponse, even if converged with k-space integration. The main effect of the bugfixes is that the susceptibilty is roughly twice as large. However, it is possible that the spectrum is changed in a less trivial way. The dielectric function is also affected as it depends on the susceptibility.
As the induced density is larger, the self-consistent procedure for each frequency tends to take more iterations.
r95211 AMS MD: Fix bugs in the ContactDistance option of the AddMolecules feature (molecule gun) leading to atom clashes and explosions.
r95202 Documentation: Added documentation for the "update geometry" dialog in AMSinput.
r95194 AMSinput: remove debug output for 2D cell conversion.
r95086 AMSinput: fix the check for available Hessian when opening an input that has previously been run.
r95074 AMSpreferences: the default pre-optimizer should be ForceField instead of UFF (though both do the same so the change is cosmetic).
r95042 AMS2021.102 released (June 8th, 2021)
r95023 AMSspectra: fix NMR atom selection with multiple results open.
r94996 Provide more documentation for installing Quantum ESPRESSO and the COSMO-RS Database
r94972 AMSspectra: fix NMR splitting bug introduced in r94876.
r94963 AMSpackages now presents the user with documentation upon connection errors.
r94939 AMSinput: fix update issue (like coordinates not updating) when opening a .ams file for a system with 1 atom only.
r94926 AMSinput: undo previous fix in r94919, causing issues with Edit-Clear on linux.
r94919 AMSinput: selection in region panel text was not cleared when clicking somewhere else, leading to visual confusion.
r94901 AMSmovie: fix screen update issue when starting without file
r94896 AMSinput: fix deleting atoms with Atom Details panel open.
r94880 Densf: fix conversion of cub files.
r94876 AMSspectra: fix handling of multiple NMR spectra.
r94866 AMSjobs: prepare tool now works when spaces are in the path to the source job(s).
r94862 AMSspectra: avoid crash when opening AMSspectra after conversion to inverted units in the previous run.
r94855 Spreadsheet export: fixed an issue where the formula character limit was exceeded for large jobs.
r94802 AMSlevels: improved memory consumption which allows larger systems and basis sets to be viewed.
r94786 AMSinput: centroids attached to two atoms did not drag correctly.
r94783 AMSinput: after using the Builder with a non-periodic program, make sure to remove periodic images.
r94775 AMSinput: input option to select molecule source (in Coordinates panel) now is disabled when not used.
r94766 AMSinput: changing modules will not change lattice vectors (it may change the periodicity if needed).
r94746 AMSinput: when updating geometry after an optimization, only update the lattice for periodic systems.
r94728 AMSinput: when many irreps are present, the occupations panel needs scrolling. Align left the Show Levels button, and list irreps to make user aware of this.
r94726 BAND: two uninialized variable issues. This may affect NewResponse and Voronoi spin polarization charge analysis. The issues wer most likely harmless however.
r94721 AMSinput: disable some properties that MLPotential could not handle, like bond orders.
r94716 AMSview: avoid crash when changing grid type with non-specified fields present.
r94712 AMSview: avoid crash when changing grid type with non-specified fields present.
r94695/td> AMSspectra: fix sorting of the VCD details table when selecting an entry and fix scale stored vectors when there are no vectors stored yet.
r94683/td> BAND: DOS was wrong (huge) when using a finite electronic temperature.
r94675 AMSspectra: fix crash that could sometimes happen when adding multiple curves to AMSspectra
r94657 PLAMS: fix RKF trajectory reader for non-periodic and 1D/2D periodic systems.
r94653 Analysis: fix autocorrelation velocity vector with non-existent indices 4 5 6 did not raise error.
r94648 AMSmovie: fix reading energies for a running MD calculation when skipping through frames.
r94611 AMSpackages: fix AMSpackages gui being named "Python" on MacOS, reliability improvements.
r94549 AMSinput: fix molecule name after undo of delete molecule when having multiple molecules
r94539 AMSinput: fix converting 2D cells to primitive or conventional.
r94538 AMS: Added an SCM_SHAR_NONUMA option to disable splitting machine into NUMA nodes.
Set the SCM_SHAR_NONUMA environment variable to a non-empty string to disable NUMA.
This option may be useful to speed up large calculation with a hybrid XC functional (which normally uses a lot of shared memory) on a dual-socket machine with not so many cores (say less than 32-64) and limited RAM.
r94530 AMSmovie: Fix crash on certain machines or wrong graph background when using software rendering, caused by an anti-aliasing issue.
r94527 AMSjobs: Fix potential errors during joblist cleanup of remote jobs at exit.
r94518 AMSinput: POLTDDFT in ADF had issue when number of frequencies was changed from the default.
r94512 AMS: Fix a problem causing errors writing to logfile on Windows. Fix the size of the shared memory used by AMS in multi-socket Linux configurations using NUMA (use the NUMA node's memory size instead of the machine's).
r94490 BAND: Improvements for DOS. The total DOS is now always calculated and save, the PDOS by default not. Also the option IntegrateDeltaE=no works, to use the exact delta function for the DOS, rather than the histogram-style (integrated over the energy intervals).
r94482 BAND: Error "Fragments cannot be assigned by a simple translation". Could also happen when visualizing from amsview.
r94455 AMSpython: fixed a bug where the user's python virtual environment would sometimes not find the Python packages included with AMS.
r94442 Fix a bug in the periodic HF exchange.
r94438 AMSpackages: Bugfix for package manager for MacOS GUI
The package manager GUI on MacOS may produce an error message and freeze when installing packages. This can occur if it is started from GUI windows that were opened directly from the MacOS dock.
This bug has been fixed in AMS2021.102.
r94406 AMS2021.101 released (May 18th, 2021)
List of known issues and bugs in AMS2021.101
  • MacOS only: The package manager GUI on MacOS may produce an error message and freeze when installing packages. This can occur if it is started from GUI windows that were opened directly from the MacOS dock. Workaround: open a new AMSinput window and start up the package manager from that window.
  • The python virtual environment would sometimes not find the Python packages included with AMS. Workaround: In a terminal, after sourcing the amsbashrc.sh file (located in the AMS home folder), type the command '$AMSBIN/amspython --install_venv'