Changelog bug-fixes Amsterdam Modeling Suite 2020

Revision Description
r94495 AMS: Fix a problem on Windows when an ams sub-process tries to write to the logfile of the parent ams process pointed to by the SCM_LOGFILE environment variable.
r94419 ADF: revert 94016 for one file in Dirac Ac, used in ADF, which should not have been changed.
r94388 BAND: Bugfix for band on windows for big systems at the start of the SCF. Last message in the log file would be “Initial density from psi”.
r94177 AMSPipe: Fix occasional corruption of pipe messages causing AMS to exit with a communication error.
94016 BAND: Basis sets for the element Ac changed. They used to include the unoccupied numerical 5f orbital, which was not intended as already the expected number of STOs were included. Technically, no solution could be found when using spin-poribt coupling, leading the error message “TOO MANY TRIES in didif”.
93896 AMSinput: Fix issues with setting the solvent radius for atoms.
93884 CifReader: Allow for a quote in the element name in a .cif file.
r93543 AMS: Fixed a bug in BondBoost that could lead to a crash.
r93523 ADF: Bug fix VROA
The electric dipole-electric quadrupole polarizability contribution was taken into account incorrectly
r93379 ADF: Fix a performance issue in COSMO, which should make it faster.
r93373 Reaxff: Fix a bug that could lead to memory corruption and a program crash in a long non-reactive calculation in NPT ensemble.
r93137 AMS2020.103 released (April 15th, 2021)
r93118 ADF: Bug fix analytical frequencies open shell PBEc
The bug affects the analytical frequency calculation of spin-polarized systems with PBE, OPBE, RPBE, revPBE, and S12g. This bug was present in all ADF releases starting from ADF2006. Analytical frequencies using LibXC are not affected.
Workaround is to use numerical frequencies.
r93101 COSMO-RS: fixed saving multipleform compound with only conformers.
r93086 AMSjobs: closing AMSjobs could give an error during cleanup when checking the mtime of certain jobs.
r93075 Plumed on Linux: on builds with MKL2021+, we use a plumed that was also compiled with MKL2021.
r93007 AMSmovie: fix angle graph for results other than .rkf and .t21.
r92948 Reaxff Classic: add a shortb control flag that allows ignoring short bonds, similar to the System%AllowCloseAtoms setting in AMS.
r92910 COSMO-RS: fixed several numerical issues related to small numbers.
r92905 Reaxff: fix a bug finding random initial guesses with FFOptimizer.
r92888 Prepare AMS2020 for switching to Intel MKL 2021.1.1
r92695 AMSjobs: fix previous bug fix regarding job monitoring
r92657 AMSjobs: detecting jobs that were no longer running (and thus are missing) were not properly detected.
r92506 AMStrain: importing via SDF file failed if pointing to engine files, now matching AMS result file is used.
r92479 AMS: Automatic atomtyping in the ForceField engine would fail if antechamber created new atomtypes.
r92394 AMSjobs: moving a remote job to a directory that exists locally but not remetly would fail on the remote side.
r92393 AMS: Fix the path length for the last point in the ams.rkf file after IRC scan.
r92361. BAND: bug with EnforcedSpinPolarization. Would give wrong occupations when one of the occupations should be zero.
For instance a Hydrogen atom with enforced polarization of one would give occupations 1//1 rather than the intended 1//0.>
r92342 AMSjobs: fix crash when trying to rename a job without selecting one job first.
r92339 AMSinput: improve reading of old Quild setup (system read, switched to Hybrid engine but no options read).
r92308 DFTB: possible segfault after message “reducing k-group size to the nr. of k-points used during the SCC”.
r92291 AMSinput: avoid pre-optimizer failure due to AMS properties requested in current module.
r92266 AMS IRC: Fix small bugs in the output of IRC scan.
Switch forward and backward barriers in the IRC summary so they are more chemically intuitive (energy change on the path backwards equals to negative of the barrier of the forward reaction and vice versa). Fix values for arc lengths on the rkf file and the final path length in the printed output.
r92245 ADF and BAND: Again workaround precision issues LibXC REVSCAN and REVSCAN0 functional.
r92225 AMSjobs: avoid potential crash when deleting files in a directory in which hidden files are present.
92222 AMSinput: fix menu coloring for some panels like the Expert ReaxFF panel.
92213 BAND/amsview: plotting of orbitals could fail with a techical “section name too large” error.
For a bulk system with the unrestricted key only the first 99 oribtals could be plotted.
92203 AMS: Fix a bug that can cause symmetry be distorted during geometry optimization with delocalized coordinates.
The fix does not apply to periodic systems when optimizing lattice.
92164 AMSinput: When importing an .ams or .adf file via File->Import Coordinates, the lattice vectors were not imported.
92149 GUI: Avoid potential issue with couldinfo missing when pid files are removed (which you should not do…).
92075 AMSinput: Fix handling of ghost atoms and other atom properties.
92065 GUI: fix crash in AMSmovie and AMSspectra when VROA results are present without the CID results.
92050 DFTB: fix hanging while saving orbitals for periodic systems with multiple k-points.
r92045 AMSbands: Fix using custom colors for bands colored by character.
r92037 AMSinput: Fix typo froze core for ADF.
r92033 AMSinput: Fix issue with FCF when files have special characters (quotes added).
r92029 GUI: Fix issues with display of Geometry Info->Distances.
r91998 AMSinput: COSMO-RS setup job made more portable.
r91957 ADF and BAND: for some of the M06 functionals find automatically values for Grimme dispersion.
91872 Hybrid engine: new option TweakRequestForSubEngines, with default true. Disabling it leads to more printing by subengines such as ADF and BAND, in particular charge analysis.
r91851 AMSinput: do not create .fixed atom types when fixing atoms during an optimization.
r91833 DFTB: Crash during calculation of bandstructure for large systems, due to exsessive memory usage. The same could also happen for the Effective Mass calculation, although less likely.
r91788 GUI: Fix atom selection of periodic images, bug introduced in r91186.
r91760 AMSprefs: Default engine in AMSinput ReaxFF uses AMS ReaxFF, and old ReaxFF can not be set as default.
r91711 AMSinput: setting up a molecule gun input, and next switching to a non-MD task, would crash on saving.
r91680 amsprep: include new ams modules like MLPotential and Hybrid
r91607 AMSinput: enable the use of FCF for properties-only calculations.
r91569 AMS driver: charges and atom types for the ForceField engine no longer cause extra atomic species to be created
The enormous number of atomic species caused issues when the ForceField engine was used together with ADF in a QM/MM calculation through the HybridEngine. This resulted in ADF stopping with a “too many fit sets over types” error. For some exotic cases this may change the symmetry detection behavior on AMS, since the ForceField engine’s atomic charges and atom types are now ignored in determining the system symmetry.
r91501 AMSview: avoid crash when changing the Grid when a colored isosurface has been added but with no fields specified.
r91476 AMSinput: when setting up a properties only ADF calculation, make sure results are selected to start from (which may not be the job itself).
r91473 AMSinput: fix converting a non-scanning PES constraint into a proper Geometry constraint (the target was specified twice in the input)
r91459 AMSjobs: make sure every job has a queue assigned. This avoid overwriting the options field for new jobs when running.
r91443 AMSview: fix for visualization NCI and DORI.
Visualization of NCI: use ‘Isosurface:with phase’ isosurface of property NCI (at 0.5). Alternative visualization of NCI: use colored isosurface with isosurface of property RDGforNCI (at 0.5) colored with NCI (range -0.5 to 0.5). The value of RDGforNCI is the same as RDG (reduced density gradient) except in regions where the density is larger than 0.05, in order to get rid of surfaces around atoms, that one would see if one is using an isosurface of RDG. Visualization of DORI: use colored isosurface with isosurface of property DORI (at 0.9) colored with DenSigned (range -0.02 to 0.02). For both NCI and DORI one may need a medium or fine grid for best visualization.
r91402 ParAMS: Fix inadvertent case-sensitive handling of the Task input key for AMS.
The AMSWorker interface in PLAMS used by ParAMS incorrectly interpreted the value of the Task key in the AMS input, so that any value other than “geometryoptimization” led to a single point calculation.
r91318 Windows: force using the shm fabric in Intel-MPI because using OFI introduces a memory leak.
Also remove some smaller memory leaks due to a Intel Fortran compiler bug.
r91251 ADF: Fix a problem passing SCF convergence failure from the ADF engine back to AMS.
The problem could result in geometry optimizations and other tasks producing nonsense for difficult non-converging cases.
r91242 ReaxFF: Fix problems in the calculation of per-atom stress tensors for symmetric structures.
r91226 ReaxFF: Fix a memory leak bug in the calculation of per-atom stress tensors.
r91186 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.
r91184 Analysys: fix in Fourier transform in trajectory analysis tool. Before, the spectrum was shifted to the left by one frequency point.
r91148 GUI: fix importing lattice vectors for 3D systems from geo files. This would cause for example AMStrain to show the lattice incorrectly for 3D systems.
r91120 AMSview: when exporting fields to Cube files show the proper location where they are saved to the user.
r91046 AMS: Reduce the threshold on the initial Euclidian distance between end points for the NEB.
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 (January 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 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)