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
r109774 AMSinput: fix EXCITATIONS, SELECTEXCITATIONS and MODIFYEXCITATIONS keys in fragment runs (incorrectly present).
r109670 Fix APPLE&P to ignore angles whose initial value if off by 60 degrees or more. This is necessary to avoid problems with molecules like PF6
r109572 AMSinput: Add Contact distance option to the Molecule Gun options
r109530 AMSinput: fix ETSNOCV input for the fragment runs (incorrectly contained the ETSNOCV block)
r109417 AMSinput: generate proper run script for fragment calculations with atoms not assigned to a fragment (like the Ni(CO)4 tutorial).
r109325 ADF: bugfix POLTDDFT basis sets icw PBE.
r109211 AMS MD: Do not remove motion in directions where ApplyVelocity is zero. Prior to this fix, ApplyVelocity cannot coexist with ApplyForce on the same region because it overrides all components of the net velocity, effectivelly cancelling any effect of ApplyForce. If you need to recover the old behaviour (forcing a particular velocity component to zero), just set it to a tiny value like 1e-300.
r109186 AMSmovie: Show the FFMPEG error information when exporting a movie failed.
r108958 AMS MD: Fix a bug which caused the force applied by ApplyForce to be 904 times smaller than requested.
r108926 ADF: restore the ALLOW BADSCF option, which was no longer having any effect.
r108919 BAND: bug with EngineRestart. This would delete the restart file, and also occasionally crash.
r108797 PLAMS: bugfix reading System blocks with [Units] in the header of the Atoms or Lattice subblocks
r108691 AMSinput: Autografs less strict topology and sbu matching.
r108682 GUI: Fix scmd startup on Windows with named pipe, related to bugfix revision 108550.
r108661 GUI: Fix the autografs builder for certain topologies and centers.
r108639 AMS driver: fixed a crash with the combination of PES scan gap filling and GeometryOptimization%KeepIntermediateResults
r108638 AMS driver: fixed a bug where KeepIntermediateResults only worked with the FIRE optimizer
r108618 AMSinput: do not prevent the user from combining IQA and D4 dispersion correction.
r108550 GUI: On Windows, use the named pipe method for inter GUI communaction by default (previously via SCM_SCMD_PIPE). Use SCM_SCMD_NOPIPE to use the old method with sockets and a random port, or use SCM_SCMD_PORT to set a fixed port.
r108388 AMSinput: Fix enabling input options for the COSMO-RS Compound template.
r108131 OLED workflows: Fix issue when using @include with relative paths in the input.
r107932 GUI: Load the environment variables SCM_SCMD_PORT and SCM_SCMD_PIPE from the preferences before starting scmd.
r107924 AMSlevels: Fix SFO coefficients display in MO tooltip for frozen core results.
r107677 GUI: Unit conversion between energy (or wavenumber) and wavelength is less strict now, in particular for relative energy spectra (FCF).
r107600 AMS MD: Fix hang in fbMC molecular translation for molecules with vanishing net force.
r107599 AMS: Fix parsing input containing @include with inline blocks and fix performance issues handling big @include files.
r107597 AMSinput: Fix displayed default mass for eReaxFF El/Eh particles.
r107554 PLAMS: Fix crash when calling AMSJob.load_external() after finish().
r107334 AMS: Fix a performance bug in APPLE&P, which may make it much faster (up to a few times).
Fix an issue in Reaxff that could result in NaNs in the VdW energy when using atoms with incompatible inner core parameters.
r107334 Molecule gun: fix a bug that caused AMS to ignore atomic info (such as the region) in the added system if the main system did not have any.
r107326 AMSinput: when updating the geometry after opening a finished job, proplery update the lattice vector panel.
r107316 AMSinput: avoid crash trying to select atoms with same PDB name if no atoms selected.
r107303 BAND: Prevent error VOCOrthogonalizerModule: no current k point. This could happen for MetaGGAs with more than one k-point.
r107180 AMS: Solved performance issue for geometry optimizations of very large systems with a fast engine.
r107062 AMSinput: added extra checks for a correct setup for a CPL calculation.
r107032 AMSinput: fix NEB with atom constraints.
r107010 AMSinput undo fix for NEB with atom constraints, it breaks handling of multiple molecules.
r106986 AMSspectra: handle reading results with no spectra info without crash.'
r106978 AMSinput: fix NEB with atom constraints.
r106965 AMS: prevent symmetry error: no equivalent error found opratm, in case of a numerical phonon run on a linear 1D periodic system.
r106929 AMSinput: Fix the pre-optimizer when dependencies (such as forcefield files) are needed.
r106905 ForceField engine: Fix crash when running with only one CPU per (NUMA) node.
r106801 Bugfix: Fixed an issue with python modules being unusable together with a cloud license.
r106799 amsbashrc.sh: Check if /scratch is also writable, to use as SCM_TMPDIR.
r106641 AMSmovie: Fix exporting ffmpeg movies when -loop is used (e.g. normal modes or phonons).
r106600 ADF: bug fix velocity-gauge oscillator strengths icw TDA for LDA or GGA XC functionals. The velocity-gauge oscillator strengths icw TDA for hybrids does not produce correct results.
r106318 AMS: In the file amsresults/output.xyz element names were truncted to two characters.
r106112 ADF: Fix calculating bond energy in case of 1 SCF iteration for range separated and hybrid XC functionals.
r106048 AMSinput: Fixed the runscript generation for hyperpolarizability calculations with ADF. A space was missing between the frequencies keyword and the value.
r105877 AMS input reader (fortran) can now do conversion between inverse units. E.g. it can convert 1/bohr to 1/angstrom. This solves a bug where AMSInput would write the unit [1/angstrom] for the option BandStructure%DeltaK (Band and DFTB) if you changed the default unit.
r105796 AMSinput: On Linux, fix window popup on startup.
r105759 AMSjobs: Fix 'kill' to kill jobs that are incorrectly marked queued.
r105719 Bugfix reaxff: avoid calling Frotran write() statement by more than one thread at once.
r105521 ParAMS: Update ReaxFF parameter database
r105444 BAND: for spin unrestricted calculations sometimes a band gap was reported whereas there was none. This happened when only one the spins had fractional occupations.
r105211 AMSspectra: fix markers for NMR spin-spin splitted spectra
r105172 ADF: fix input handling CDFT in case of ChargeAndSpin.
r105018 BAND: Voronoi (deformation) charges now relative to fragments used. They used to be independent of the choice of fragments.
r104886 AMS2022.103 released (Jun 21th, 2022)
r104885 ReaxFF: Fix incorrect formatting of the force field FeOCHCl.ff
r104851 ParAMS GUI: fix clearing ref values (which should revert to proper ref value if defined), and adding reference values if they don't already exist.
r104821 AMS MD: Fix a bug in the molecule sink (RemoveMolecules) where a successful removal of some molecules caused other MD features executing during the same timestep (other sinks, CVHD, fbMC molecular moves) to work with invalid bonds and molecule data.
r104792 Params: Replace non-ASCII characters with ASCII equivalents in the ReaxFF forcefield files, to avoid encoding issues on Windows.
r104666 QE: Fix parsing the Fermi energy from spin polarized QE results.
r104660 AMSinput: Avoid crash with Fuse Atoms if no atoms selected.
r104656 AMSdos: Fix reading spin polarized QE results.
r104499 AMSinput: Store the molecule styles used when saving.
r104472 AMSmovie: Fix "Select atom close to origin" in AMSmovie.
r104470 QE: Fix parsing the QE CP results and converting to a kf result file that is readable by the GUI.
r104458 BAND,DFTB: Allow for EngineAutomations during an NEB calculation. This can help to avoid non converging SCF (or SCC) problems while the gradients are still large. The error message was "ERROR: Energy calculation failed. Stopping optimization"
r104456 BAND: Error when calculating the band structure if the parent directory name had a space in it. The error message contained "-c: error: unrecognized arguments:"
r104440 AMSpackages: Fix potential gui hanging issue when installing an invalid package.
r104339 Densf: bug fix: avoid reading number of atoms from CUBINPUT file if it is only used for grid definition.
r104318 ParAMS GUI: avoid hanging gui when job crashes/finishes very quickly.
r104206 AMSinput: fix saving regions if defined for multiple molecules, and handling of All region for multiple molecules.
r104158 AMSinput: fix reading multiple molecules from .ams files (the order was not guaranteed, causing issues for jobs pointing to multiple molecules_.
r104123 AMSinput: fix importing multiple system blocks from run script
r103978 BAND: Changed the default value of Dependency%Core from 0.98 to 0.80, thus making the "FROZEN CORE SEEMS TO BE TOO LARGE" error much less likely.
r103939 Params gui: fix saving adjusted AMS settings for a job in a jobcollection (the change was ignored).
r103907 Params: Fix importing VASP OUTCAR jobs on Windows.
r103881 Params: Fix losing atom selection on menu use on Windows.
r103878 AMSinput: fix capitalization of Params -> ParAMS.
r103851 Update the download_repository.py utility script.
r103841 GUI: Fix the initial value for the periodic cell range view, after having it changed once.
r103794 AMSjobs: Add extra check for jobs marked killed by the GUI, in case they were finished correctly. This can happen on slower Networked File Systems. Requires the env var SCM_CHECK_JOBSTATUS to be set.
r103784 ADF/BAND: QTAIM might warn "PSearch37 WARNING: More critical points found than can fit", especially when using many cores. Potentially critical points could be missed.
r103759 AMSmovie: change startup to avoid wrong window layout in rare cases.
r103709 PLAMS: Fix a filename clash for jobs whose name explicitly ends with the counting suffix (e.g. ".002"). A manually supplied counting suffix is now ignored. Also fix a potential race condition in the JobManager class.
r103692 AMS (Linux/Mac only): Try to delete temporary files when the program receives a segmentation fault (program bug) or a bus error (full disk) signal.
r103678 AMSinput: if opening very old AMS jobs, result dialog asking what to import was misbehaving (prog not found).
r103675 AMSinput: avoid unneeded traces (effect was to slow down AMSinput).
r103649 Add a possibility to use InfiniBand adapter info for licensing as the last resort.
r103598 AMS2022.102 released (Apr 26th, 2022)
r103597 BAND: All printed band energy ranges would be zero if using a finite electronic temperature and a single k-point. Energy and gradients not affected, only the table was wrong.
r103468 AMSinput: pre-optimizers now run in serial mode by default. This can be adjusted with a toggle in AMSpreferences.
r103443 ADF: BugFix: LibXC meta-GGA and meta-hybrid functionals can not be combined with analytical frequencies.
r103363 AMSbands: Fix display of bonds and lattice for phonons results.
r103346 AMSjobs: fix display of warning messages in the two-line summary below the jobs
r103342 AMSspectra: Fix opening BAND phonons results in AMSspectra.
r103324 ParAMS GUI: properly resize graph windows when changing window size.
r103281 AMSinput: fix graphics glitch in Notebook toolbar on some machines.
r103270 GUI: Fix issue with certain GUI modules (mainly AMSinput) where the window was previously on a second monitor which is no longer connected.
r103258 AMS MD: Make Deformation raise an error when TargetLength contains negative components instead of ignoring them silently.
r103257 ReaxFF: Fix handling lattices with negative diagonal components.
r103230 Documentation: Fix broken link in AWS parallelcluster installation guide.
r103223 BAND: When using band as an engine for the MD molecular gun the program woudl stop with NAODataModule: unexpected spherHarmonicType.
r103217 MOPAC: Remove MOPAC single-point output files created by slave processes (there can be many of them during MD).
r103143 AMSinput: Fix the fuse atoms function when there are bonds across the periodic boundary.
r103137 AMSinput: Fix issue with the atom fftype check when not all atoms have an fftype, when switching forcefield types.
r103128 ParAMS GUI: do not save empty training or validation set.
r103096 GUI: Fix issue with nested busy indicators.
r103090 AMS MD: Fix several bugs in the ReflectiveWall feature.
r103071 AMSreport: Fix exporting history frame in SDF format.
r103066 AMSreport: Fix using history frames where atoms were added or removed, where e.g. a molecule gun or sink was used.
r103061 Fix bug in configure script for source distribution.
r103043 AMS: Added a check for normal modes in symmetric displacements in combination with periodicity (which is not supported).
r102975 BAND: Improved handling of Frozen Core too large error. There was a bug that the core/core overlap matrix was tested for the first k-point, rather than the intended gamma k-point. Also the feedback has been improved about which element is causing the problem.
r102971 AMSmove chemtrayzer2: fix chemtrayzer2 name (no space in front of 2)
r102966 AMSinput fix coloring of some fields on the Hybrid panel.
r102963 AMSmovie chemtrayzer2: proper coloring of input fields.
r102949 AMSmovie: Enable Select Molecule and Select Connected from the Selection menu.
r102943 AMSmovie: fix the Details panel for atom details (colors, selecting atoms, ...)
r102932 3D-RISM: Correct an error in the coordinates of the 3D-RISM methanol solvent.
r102865 AMSpackages: GUI now refreshes the package overview after aborting an operation.
r102813 AMSmovie: Fix periodic view change for trajectory files in xyz format.
r102808 BAND: clean up semaphores at the end of a calculation. On the MaxOS this could lead to problems when running many calculations, because the system would run out of available semaphores/mutexes. This does not affect any of the results.
r102797 BAND: prevent warning "WARNING: Nr of shared arrays ..." when doing a restart (orbital/densityplot).
r102768 AMSinput: Add busy indicator for saving larger jobs.
r102751 Tutorials: Make stress_strain_curve.py compatible with AMS2020.
r102734 ADF: bug fix single point gradients dDsC dispersion correction.
r102719 OLED material DB updated to v2022.1-1: Switched alpha- and beta-MADN. Our names were wrong for these compounds. Outliers with a modified Z-score >16 are now removed prior to calculating mean and sigma of IP/EA.
r102701 AMS: Fix a few minor bugs in the shared array locking.
r102700 AMScrs: Fix default window size with screen scaling or larger font, and remember the size on startup like the other GUI modules.
r102672 AMSinput: fix 3d-rism when the path to AMSHOME contains capitals.
r102658 GUI: Avoid issue caused by rapid inputs that create or update a graph window.
r102655 AMSinput: Avoid All-type constraints as scan coordinate.
r102653 AMSinput: Preoptimize with GFN1-xTB now also clears the parameter directory.
r102649 IRC: Converged IRC geometries, including end points, should now have all the requested properties calculated.
r102631 AMSinput: Clarify and add import button for the OLED materials database.
r102629 ParAMS: Handle PES reference values with incorrect shape inside Logger.
r102626 AMSmovie: Better handling of incorrect kf files from remote running jobs.
r102606 ParAMS documentation: Fix some incorrect parameter names starting with 'n/a'.
r102604 AMSinput: remove Excellent numerical quality option from menu as it is ridiculously expensive and sometimes has numerical issues.
r102597 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.
r102585 AMSinput: reading in older input files (ADF2019 or earlier) could have duplicate periodic bonds.
r102580 AMSjobs: transfer of all job files from remote systems would fail if the path contains spaces.
r102575 AMS: fix a bug related to a combination of frozen atoms and RemoveMolecules during molecular dynamics.
r102550 ACErxn: Make it work for very simple systems very simple reactions.
r102536 AMSinput: improve stability of feedback of pre-optimization.
r102533 ParAMS GUI: improve stability for monitoring running jobs.
r102512 AMS: Speed up calculation of the induced dipole moments by caching moment-independent pre-factors in the electric field calculation.
r102487 AMSinput: when parsing input (for example via the ParAMS GUI), switch to proper engine before handling AMS options as the engine switching could reset AMS options like the task.
r102484 BAND: small performance improvement for calculation with Core=None.
r102481 ReaxFF: fixed a bug that resulted in errors in the valence angle contributions to the force and the virial for a small unit cell.
The bug existed in all ReaxFF versions and it was the main reason for not allowing small unit cells. With this fix, also the way the stress tensor is calculated has been changed, so the size of the unit cell should be less likely to cause issues.
r102478 Params GUI: click in scatter plot on distances, angles and dihedrals: give feedback by selectig proper atoms.
r102475 BAND: reduce memory footprint for metaGGA (force) calculations, and also make them faster for bigger systems.
r102465 Quantum Espresso: Fix bug in qerc.sh.
r102457 ParAMS GUI: avoid change of shape for 1-d array values when editting.
r102452 GUI: Show Selection Only would fail to show anything if all atoms selected.
r102447 ParAMS GUI: Show correct atom when clicking in a scatter plot with forces.
r102427 AMSinput: Better handling of explicit forcefield files for the ForceField engine (expert option).
r102424 ParAMS GUI: try to fix stability issues while monitoring running calculations.
r102411 ParAMS: Fix bug when reading an lgDispersion ReaxFF force field
r102395 ParAMS GUI: fix stability issue when displaying results of a running optimization (error about xxmin).
r102387 Update repository download python script for AMSpackages offline usage.
r102382 AMS: Add a possibility to configure the KF page size (=file size increment) via the SCM_KF_PAGESIZE environment variable (which is in kB).
r102373 AMS: fix a bug in IRC that prevented it from computing optional properties (such various ADF chanrges) at converged reaction path points.
r102364 AMSinput: fix the Add Region In Same Way To Identical Molecules option on the Regions panel.
r102341 ParAMS GUI: validation set results should be from training set best parameters, and make that explicit with the label.
r102338 ParAMS GUI: fix/change color for errors and validation set in table
r102315 AMSinput: fix 'Add region in same way to identical molecules' command on Regions panel.
r102305 Fix division by zero in WallPotential when an atom is located exactly at the origin.
102269 Update AWS parallelcluster guide with information about multi-node jobs.
r102258 AMSinput: fix protein controls on Regions panel.
r102257 AMScrs: fix: .multipleform file should not contain density in one of its forms, only at the compound level.
r102252 AMSdos: show bonds for BAND results.
r102245 Tutorials: Fix images for Young's modulus, yield point, Poisson's ratio.
r102235 AMSinput: fix several screen dpi issues related to the notebook bar and dropdown menubuttons.
r102231 AMSjobs: update Job Clean Up menu comamnd to handle Params results, and show only files present.
r102226 Fix Fukui tutorial: AMSoutput command is now called Conceptual DFT (FDL)
r102220 AMSmovie: fix 2D Histograms for MD, with non-symmetric bin counts.
r102215 Remove old ReaxFF ParAMS example.
r102208 Add a description for the APPLE&P force field file format.
r102207 The pressure should now always be calculated during MD when using the ForceField engine.
r102192 Update versions of QE in documentation for GUI.
r102189 Update default value of QE_VERSION to 7.0 in qerc.sh.
r102186 Remove pytest-qt from amspython environment.
r102176 AMSinput: fix graphic glitch in notebook bar.
r102170 Params gui: avoid crash by using Graph menus when no results are present.
r102167 AMSinput: fix writing the ElectricField input key to the run script.
r102163 AMSinput: fix unit conversion when the user changed the default and opens a .ams file without explicit units set.
r102158 AMSjobs: avoid crash when the modification time of a job cannot be determined.
r102146 AMSmovie: display molecule for non-trajectory results.
r102135 Only compute transition dipole moments between excited states if asked for.
r102128 Update the reference for Quantum Espresso 7.0 in documentation
r102085 AMS2022.101 released (Feb 28th, 2022)