Changelog bug-fixes Amsterdam Modeling Suite 2021

Revision Description
r103044 AMS: Added a check for normal modes in symmetric displacements in combination with periodicity (which is not supported).
r102736 ADF: bug fix single point gradients dDsC dispersion correction.
r102703 AMS: Fix a few minor bugs in the shared array locking.
r102598 AMS: Work around a bug in Cluster MKL on AMD Zen that may cause AMS to stop with an “Error exit from DistributedMatrix%SVD” message. IRC: save engine rkf files for the final points on the IRC path; enable calculation of optional properties for the initial IRC point.
r102383 AMS: Add a possibility to configure the KF page size (=file size increment) via the SCM_KF_PAGESIZE environment variable (which is in kB).
r102374 AMS: fix a bug in IRC that prevented it from computing optional properties (such various ADF chanrges) at converged reaction path points.
r102161 AMSjobs: avoid crash when the modification time of a job cannot be determined.
r102137 Only compute transition dipole moments between excited states if asked for.
r102050 BAND: bug fix for band NewResponse when using the ActiveXYZ option with the X component disabled.
. ERROR: kfOpenSection: Attempt to open nonexistent section IndDensVec1Re IndDensVec1Re.
r101852 ADF: Fixed a bug that made it impossible to restart a partially done analytical frequencies calculation from TAPE13.
r101126 Windows: Replace the GetNumCores utility with a new version that should work better under Windows 11.
This update should solve issues with AMS crashing inside the Intel-MPI library during initialization.
r101004 ADF: fixed a string overflow when using restart orbitals from a file with a long path name.
r100769 ADF+NBO6: Fixed a bug for writing Fock matrix to file in case of hybrids.
r100583 AMS: Fixed a bug in generation of delocalized coordinates for a highly compressed periodic linear chain.
r100041 AMSinput: Fix checking the correct license target for the Mopac pre-optimizer.
r99925 AMSpackages: bugfix expired modules should no longer be presented as licensed.
r99899 DENSF: bugfix writing cube files for multi-components values such as gradients and spinors.
Before the fix, the x component was used when writing values for x, y, and z components.
r99803 ADF: bugfix input reading and documentation of custom solvent SM12.
r99751 BAND: bugfix for serializing the TAPE10. The last line in the log file would be “saving tape 10”, and the program would crash. This would happen for instance with a QTAIM (bader) calculation.
r99722 Densf: bugfix in MO gradient calculation.
r99350 AMS2021.106 released (December 6th, 2021)
r99329 AMSinput fixes for occupations.
r99169 The TestJob now also checks some floating license details, and produces a more detailed license check output.
r99129 AMSpackages: Fix a warning message.
r99106 Fixed a bug in a common library function dealing with KF files that would not trigger a parallel program (for example, nmr) to exit gracefully if a mandatory KF file was missing.
r99093 AMSinput fix crashing but with settings occupations (the bug was introduced in r98924).
r99076 AMSjobs TestJob: also generate detaile license.log
r98925 AMS2021.105 released (November 29th, 2021)
r98924 AMSinput: Spin and Occupations panel limitted to show only 5 virutals (for speed).
r98918 AMSpackages: Workaround potential issues with parsing of license information.
r98904 AMS pipe on Windows: Work around an Intel Fortran bug that would cause AMS pipe to hang when receiving data larger than 64kB.
r98898 AMSPackages: Improve error message description in GUI.
r98828 DFTB: Add a check for dipoles in System%ElectrostaticEmbedding in combination with periodicity.
r98702 BAND: Prevent (harmless) warnings about wrong arguments in call to zgemm in case of Non-Collinear calculations. Does not affect the results, as this problem was about zero-sized arrays. Th warning looked like
Intel MKL ERROR: Parameter 10 was incorrect on entry to ZGEMM
r98645 AMSpackages: Fix issues with the package mananger when editable python packages are installed by the user.
r98527 AMSinput: Fix license check for running ReaxFF or MLPotential as pre-optimizer.
r98322 Reaxff: Fix a bug that would lead to a segfault in a multithreaded calculation when too many errors are triggered and ignored, for example during a force-field optimization.
2021-10-29 Windows: Fixed a bug in the installer that would make it partially ignore a different location for the ADF_DATA folder set by the user.
r98093 AMSspectra: Fix the unit conversion when updating the ‘Bias steps’ for NEGF current plots.
r98020 Fix a bug that would cause programs of the AMS package (including the GUI) to crash with a segmentation fault when opening a corrupted rkf file, instead of returning with an error message.
r97937 AMS Reaxff: Fix a bug that would cause Reaxff to stop when trying to combine molecule gun and charge constraints.
r97918 AMSinput: minimum value in distance input (next to slider) reduced to 1 pm
r97908 ADF: fix crash spin-polarized G0W0
However, spin-polarized G0W0 is still not implemented correctly.
r97906 AMSPackages: Fix utf-8 encoding errors when installing/checking packages.
r97864 AMStrain: fix import of remote SDF results
r97709 AMSinput: Preoptimizer now checks the engine license before running to generate better visible error message.
r97610 AMSinput: Fix ‘couldn’t open config’ when saving the runscript.
r97600 Reaxff-AMS: Fix a bug in ACKS2 charge constraints (important for e-Reaxff with AMS).
With the bug, the charge is always constrained to zero instead of the value provided in the input. Users who run e-Reaxff calculations with AMS should install an updated version. The Reaxff Classic is not affected by the bug.
r97577 BAND: NEGF error: “types do not match for left lead”. Could happen with a self consistent NEGF calculation on a lead with multiple atom types.
r97566 BAND: Spin-flip option would do nothing for the case of Spin-Orbit coupling.
r97517 Reaxff Classic: fix a bug that would ignore the optcel control flag. With the bug, the only way to optimize the unit cell was to set the RUTYPE in the geo file.
r97472 Bugfix ADF: do not use A-DIIS when AccelerationMethod is set to SDIIS.
r97386 AMS driver: fix an issue with the xyz-files written by the AMS driver for elements with three character symbols (e.g. Uue)
r97254 AMSpackages: Update documentation, provide a python script for downloading repository copies more easily.
r97178 AMSinput: Use the minimum image convention for the initial values of constraints and restraints with periodic boundary conditions. This relates to fix 96331.
r97169 AMSspectra: Fix export NEGF transmission curve as XY values. Give a warning and refuse to write an empty file if no peak data is available when using export XY peaks.
r97106 AMS2021.104 released (September 14th, 2021)
r97105 BAND: Improved printing of the total energy (print totalenergy) for band. For heavy systems or systems with many atoms stars (***) would be printed rather than total energies.
r97007 Windows: fix missing components for using AMSJobs with remote queues. This was broken in the 2021.103 release.
r96996 GetLicense dialog: first line (no valid license found) has been removed as it caused confusion.
r96797 AMS2021.103 released (August 26th, 2021)
r96783 Python: The version of ipython was updated to 7.16.1 to solve an issue with Qt5 and matplotlib.
r96776 Windows: Update and deduplicate MKL inside of the python stack, just like it is done on Linux and MacOS. This saves some space in the installer and on disk, and also avoids some conflicts when running python code from within AMS, or vice versa
r96745 AMSinput: avoid coordinates check when verifying t21 for use with occupations.
r96740 AMS MD: Fix molecule gun insertion failures in non-3D-PBC systems with the ContactDistance option.
r96704 AMSlevels: Fix crash when viewing specific unrestricted results, introduced by r94802.
r96649 AMSpackages: Fix compatibility issue with cloud licenses./td>
r96556 ADF: Fix Md finite nucleus.
The so called dirac calculation for Md with a finite nucleus would fail.
r96537 IRC: Fix a compatibility issue between IRC and the external electric field.
r96533 AMSinput: Warn the user when trying to use the Write history “All” option. Because of the severe performance impact, this option should only be used for testing.
r96454 GUI: Shortest pbc angle and dihedral are now independent of ordering (e.g. A-B-C or C-B-A).
r96425 AMSspectra: Show spin info for transitions for unrestricted excitation calculations.
r96416 AMSinput: Don’t force unrestricted when fragment spin is 0 instead of empty.
r96406 AMSinput: Fix progation of the diagonal input in the supercell dialog, bug introduced in revision 96174.
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.
r96331 AMS: Fix a bug in geometric constraints in combination with periodic boundary conditions. The constraints now use the minimum image convention.
Before the fix they would always use atoms from the same unit cell, which would lead to wrong results for constraints crossing a unit cell boundary.
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.
r96093 AMSinput: constraints for MD offered the option to constrain regions, but this is not supported in AMS. These are now converted to atomlist constraints.
r96089 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.
r96060 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 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 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 saved, 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 file (located in the AMS home folder), type the command ‘$AMSBIN/amspython –install_venv’