Changelog bug-fixes Amsterdam Modeling Suite 2019-3

r90329(January 4th, 2021): AMS2019.306 released
This is the last scheduled subrelease for AMS2019.3
r89916ADF: Fix rotational entropy value after frequency scan (it was incorrect due to using a lower symmetry).
r89776ADF: fix quadrupole intensities XAS in unrestricted calculations.
r89619 GUI: Fix issues with automatic OpenGL check and software fallback on Windows.
r89467 ADFjobs: Fix remote file retrieval on Windows when SCM_NO_RSYNC is set.
r89466 ADFspectra: Better error handling when determining rotational equivalent atoms for NMR.
r88181 ADFtrain: fix handling of ReaxFF ffield header flags like ereaxff, acks2 and lgDispersion.
r88018 (October 6th, 2020): AMS2019.305 released
r87916 Band: XC_orb term wrong in PEDA analysis when using the libxc key.
r87902 Band: Prevent stop with ERROR: KMatrixIOModule: inconsistent dim, during a band structure calculation.
r87843 ADF: bug fix: sometimes too few frequencies were calculated for linear molecules.
In case of linear molecules of more than 2 atoms, the number of frequencies calculated with symmetric displacements was incorrect in case of hybrids or range-separated hybrids.
r87820 ADF: bug fix: bond energy in case of numerical frequncies may be incorrect.
In some cases, instead of the bond energy of the molecule at the central geometry, the bond energy may be given of the molecule at the last geometry step.
r87814 ADFInput, avoid hang when creating a slab from bulk material (slicing tool).
r87672 Write atoms to a CUB file in the input order instead of the internal ADF one.
r87527 Reduce the amount of disk space used by ADF analytical frequencies code.
r87495 ReaxFF: fix a few bugs related to force-field fitting.
Multiple geometries with the same name in a geo file will now trigger an error message. Only one of these geometries will be used to calculate the cost function contribution.
The RUTYPE NORMAL RUN key will turn off any previously specified CELL OPT flag in the same geo file. Before, a NO CELL OPT key was required to achieve this.
r87276 ADFview on MacOS: color mapping for cutplanes and colored contour lines had color issues after interacting, looking like random colors
r87218 ADF: Save some scratch space by not saving AOResponse restart data to TAPE13 files belonging to MPI slave processes.
r87155 Band: Error StrainDerElstat: nOper different at perturbed geo, could happen when disabling symmetry.
r87147 Band: growing memory usage when using the NewResponse option (when COApproach is true, the default).
r87003 Reaxff: Fixed a bug in readbgf that resets some settings to default values after reading the geo file.
This, for example, results in “RUTYPE CELL OPT 0” being written to the fort.90 instead of a non-zero value from the geo file.
r86771 Band: Crash on windows in PrepareBas for calculation on large systems without frozen core.
r86722 ADFtrain: Fix error when saving force fields with lgDispersion enabled.
r86720 AMS-ReaxFF: Bugfix potentially lost interactions in highly skewed cells.
Non-reactive runs could lose some of the bonds crossing PBC boundaries when the unit cell was significantly non-orthorhombic. Similarly, reactive runs in such lattices could lose some long-range nonbonded interactions (near the cutoff distance), but the effect on results should be small.
r86682 AMS MD: Fix a bug that caused the CalcPressure input option to be ignored.
r86681 AMS-ReaxFF: Bugfix crashes in non-reactive mode.
Non-reactive runs would crash when the number of the atoms in the system changed (such as in combination with the molecule gun) or in combination with multilevel parallelism (such as when calculating the elastic tensor.
r86606 DFTB: Erroneous behavior for some elements, like Ba, when using the GFN1-xTB model, due to a too short function range.
r86531 Band: special basis sets set by adfinput ignored. Now the ByAtomType Path subkey is no longer ignored by band.
r86141 AMSinput: add warning when saving an MD run with DFTB with multiple K points: no bond info, and thus no molcule info, will be calculated.
r86082 Make sure the floating license is released for crashed and killed DFTB and BAND calculations.
r86035 Improve prediction of the next energy during quasi-Newton optimization with constraints.
r86033 adfreport: fixed a bug that would cause the program to crash when processing many (over 60) files at once.
r85941 GUI: running remote jobs left tail processes on the remote machine for showing the logfile, cleanup code fixed.
r85848 BAND: When using the explicit Occupation options, the occupations would be wrong in the GUI.
r85685 ADFinput: Avoid endless warning popups when saving a job with the Run Script window open.
r85679 ADFinput: Builder could add an incorrect number of molecules due to round-off errors (one too many or few).
r85668 ADF: bug fix workaround Grimme4 dispersion for (trans-)actinides.
Grimme4 dispersion is not available for (trans-)actinides (Z>86). Workaround in ADF is to use the parameters for the lighter 6th row homologs (Z = Z – 32) instead However, this workaround was incorrectly implemented for elements with Z=87-94.
r85660 COSMO-RS GUI: Allow space in name QSPR COSMO result file.
r85509 ADFinput: Fix polymer builder performance issue and ‘Orient link’ ‘UFF Scan’ option.
r85473 ADFinput: use of sumdiff constraint generated SumDist instead of SumDiff constraint in run script.
r85329 Reaxff: Fixed format when writing restraints to the result geo file.
r85314 AMS NEB: Fixed a small glitch related to NEB restart fix in r84969.
r85191 ADFmovie: When opening a GCMC result file, do not disable the Show Accepted Geometries menu (so user can select to show all geometries).
r85061 AMS: The InitialHessian option in GeometryOptimization and IRC can now accept a ADF t21 file as input.
r84969 AMS NEB: Fix a bug that would cause problems restarting an NEB calculation.
r84927 BAND: Fix a bug that would caused noise on the gradients, especially when using many cores, hampering geometry convergence.
r84703 AMS CVHD: Fix a bug that would cause problems restarting CVHD MD.
r84685 ADFmovie: The labels for the X and Y axes for 2D PES graphs were switched, and show marker in 2D PES graph corresponding to current frame.
r84674 AMS driver: The Quasi-Newton optimizer now uses Cartesian coordinates for linear systems with >2 atoms by default.
r84625 ADFjobs: Fix cloudmachines error. This can be manually fixed by removing the .scm_gui/CloudMachines file found in your userdir, e.g $HOME/.scm_gui/.
r84609 ADFspectra: Moving through frequency peaks with arrow keys would crash after highest frequency when imaginary freqs were present.
r84573 ADFinput: Slicer did show slice plane incorrectly. The fix has no effect on the actual slab generated.
r84542 ADFmovie: Fix the initial MD Molecules window position when there is not enough room.
r84404 ADF: Fix ADF input order versus internal order for Vibrations section on TAPE21.
r84340 ADFmovie: Fixed the Graph->Lattice Vectors menu command for systems with dim < 3.
r84303 ADF: Fixed a bug in SumDist and DifDist constraints, which should make them more stable.
r84219 ADFinput DIMQM: MDC-m charges were used if MDC-D charges were requested, and Hirshfeld charges used for DIMQM could be in wrong order.
r84175 (May 11th, 2020): AMS2019.304 released
This version includes numerous bug fixes, as well as a new software rendering option for the GUI to replace the OpenGL1 fallback mode. For more info see
r84174 AMS MD: Fix a bug related to combining CVHD and RemoveMolecules.
r84139 ADFinput: fix NEGF jobs for ADF (they did not run because of incorrect fragment blocks).
r83937 ADF: allow for B97-D with different Grimme dispersion.
r83768 ADFspectra: Fix issue with switching modes on Windows, introduced in r83131.
r83570 GUI: Fix issue with hanging modules, observed on some macOS machines, related to installed fonts.
r83563 Windows: Fixed an issue in figuring out the number of cores in the machine.
The problem was introduced in r82879 and it affects the number of parallel processes spawned for local Windows jobs.
r83528 ADFjobs: Fix remote jobs with parentheses in the path.
r83523 DFTB: improved performance of serial calculations for large systems
r83487 ADF: fix unrestricted calculation of PM localized MOs.
r83403 Windows: upgrade Putty to v0.73 (64-bit).
The new version Putty version is a 64-bit binary. The default RSA key size has been increased to 2048 which should help with “TIMEOUT” errors when running remote jobs. If you are still using a 1023-bit key you may have to create a new, 2048-bit one.
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 (February 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 AMS2019.302 released (December 12th, 2019)
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 AMS2019.301 released (November 11th, 2019)