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
r119618 Conformers: fix removing dependency of Crest on DFTB license.
r119207 PLAMS: fix retrieving the CRS database path on Windows by using the SCM_PKG_ADFCRSDIR environment variable.
r119157 AMSinput: fix tracing changing coordinates in Coordinates panel after selecting atoms.
r118995 ADF: bug fix in case of 1 SCF iteration in case of metaGGA or metahybrid functionals.
r118561 AMSinput: saving for QE/VASP was very slow due to generation of atom types by region.
118437 BAND/DFTB: improved text output for thermodynamical data after a Numerical Phonon run. All numbers used to start with a leading zero, giving no information.
r118002 AMS: Fix for BondBoost removing expired restraints.
r117986 AMS: Another fix for BondBoost that did not work with multiple moving restraints.
r117924 AMS: Fixed a bug that affected MD BondBoost when multiple bond boosts were active at the same time. Without the fix, activating a new boost would remove the previously active ones.
r117662 ADF: Small fix for calculation of memory usage to reduce the number of independent tasks for numerical differentiation.
r117573 ADF: Fixed bug excited state gradients in case of zero beta electrons.
r117524 AMS: Fixed a bug in the SCMGO optimizer.
r117437 BAND: New input options for Hubbars, specify for atom (element) or for region. Not yet gui supported.
r117362 BAND: fix illegal memory access issues. This should improve cross platform stabiltiy.
r117256 AMSjobs: never save .pid file with status unknown.
r117239 AMStail: add some error checks, hopefully preventing AMStail hang (not sure, could not reproduce the isssue).
r117220 AMSinput: make sure no empty LoadSystem keys are written.
r116992 AMSspectra: Use "Wavelength" as axis label if a length unit is used as energy equivalent.
r116943 ADF/BAND: Fix some uninitialized variable issues to improve cross platform stability. This may potentially influence results from the tau-HCTH functional. For BAND it is also checked that the non collinear option does not allow for energy gradients.
r116820 Documentation: Fix missing term in the formula for the electron energy density in the band documentation. The code itself included already the term.
r116812 BAND/DFTB: Allow for a larger number of symmetry operators, being useful for periodic calculations with large super cells. This prevents in such cases the error: Failed to detect system symmetry. Falling back to NOSYM....
r116757 AMSjobs: do not start monitoring jobs with status unknown just by getting the job status (caused slow-down in AMSjobs display while not needed).
r116754 AMSjobs: the toggle to switch between job list and directory display caused triple full refreshes, slowing down the joblist mode especially.
r116673 AMSview: fix calculating fields via AMSjobs (for example on some remote machine).
r116663 ADF: resolve a memory leak in the AOResponse code used with a hybrid functional.
r116577 BAND: reduce available memory leaked by band during geometry optimizations. Jobs could crash because running out of memory after many steps.
r116289 GUI: avoid crash when right clicking an input option in some other GUI module than AMSinput.
r116284 AMSinput: fix menu coloring for thermostats and barostats.
r116281 GUI: fix check for plams unit, could cause crash for example when importing run scripts due to unrecognized units.
r116154 Engine ASE: Allow relative path for the specified calculator file.
r116019 e-Reaxff: undo the previous change because it was apparently a bug present only in the version used to obtain published results in the 2016 paper. More recent e-Reaxff version do not contain it.
r116002 e-Reaxff: fix a bug that resulted in the electron-electron repulsion being underestimated. With this fix it should now be possible to reproduce the literature e-Reaxff results.
r115871 ADF: fix in case of CalcOverlapOnly writing the overlap matrix to TAPE15 in Matrices%Smat. This option CalcOverlapOnly may be useful for external programs like SHARC.
r115785 AMS2023.104 released (Oct 9th, 2023)
r115784 AMS: Fix a bug which made the System%SuperCell input key inadvertently change the atom symbols from those specified in the Atoms block. This bug made several MD features (such as Shake constraints) fail to match the expected atoms, causing the simulation to silently run without constraints.
r115782 AMS MD: Fix several bugs in the analyze_cosine_shear script. The script now no longer requires atomic velocities to be stored in the trajectory, relying instead on the precomputed MeanCosineShearVelocity. The reported shear parameter was also previously incorrect, especially for systems with constraints.
r115779 AMS MD: Fix incorrect normalization of the CosineShear FlowDirection vector. The bug only affected simulations using a non-default FlowDirection which was not a unit length vector.
r115750 ADF: Synchronize automatically generated atomic fragment files between MPI rank to avoid generation of invalid fragment orbitals in some types of calculations on some machines. This has not been observed before in the released AMS versions but is theoretically possible.
r115729 ADF: fix values of the Iring and MCI aromaticity descriptors for the spin-unrestricted case. There was a wrong 2^(n-1) denominator used, where n is the number of atoms in the corresponding ring.
r115718 Params GUI: fix importing issue leading to duplicated system header error, bug was introduced in r114856
r115689 AMSinput: fix check that incorrectly complained about the hyperfine interaction with unrestricted calculations.
r115446 ADF: UnrestrictedFragments cannot be used with ROSCF. ADF will now stop in this case.
r115434 AMS driver: geometry optimizations with FIRE where all atoms are frozen no longer cause errors in AMSmovie
r115380 AMSinput: check M3GNet is installed when trying to use it via AMSinput, and offer to install it if not found (via the package manager).
r115352 ADF and BAND: fix (workaround) Grimme DFT-D4 dispersion for elements with 86 < Z < 95. Incorrectly assumed that DFT-D4 parameters existed for elements with 86 < Z < 95. Like for Z > 94 workaround is to use the parameters of the lighter 6th row homologues (Z=Z-32) and raise a warning.
r115284 AMSinput: fix saving a preset via the main menu in AMSinput, saving via right click on an option did work fine.
r115194 AMS driver: fix bug with BondOrders Method=Guess and engines that would always produce bond orders (FF engine)
r114996 Apple silicon version: the license code did count all cores instead of high-performance cores only.
r114857 FCF: fixed a bug that occured for diatomic molecules.
r114856 Params GUI: fix importing multiple structures via shortcut, did not import the proper coordinates in some cases like basin hopping results.
r114709 ADF: Fix ADF if in AMS Properties%OrbitalsInfo is requested.
r114653 AMSinput: fix issue with New when multiple molecules are present.
r114594 AMSview/BAND: LDOS visualization was problematic with spin unrestricted calculations.
r114570 GUI: Fix an issue with checking installed packages in the GUI (e.g. using QE in AMSinput) when there is a newline character in an environment variable.
r114565 AMSinput: improve PES scan coordinate scans (reordering atoms would break the PES scan setup). If you have saved files using PES scans per coordinate, check to see if your input is still correct (in some cases the wrong atom might be scanned).
r114559 ParAMS GUI: when importing jobs into the ParAMS GUI, reuse an engine if possible.
r114556 ParAMS GUI: Increase default geometry optimization iterations from 20 to 30 to match the Python ResultsImporter default.
r114554 ParAMS GUI: importing multiple jobs with same engine did mess up the engine IDs, now a new engine for each job is made.
r114549 PLAMS/ParAMS: fix incorrect unit when getting results from Cartesian coordinate PES Scans.
r114546 AMSdos: fix bug when showing multiple PDOS curves at the same time using the mirror-beta option.
r114542 GUI: fix error in cleanup after a job when running with SCM_DEBUG set.
r114527 AMSmovie: better handling of showing result from crashed IRC/NEB/PES/GCMC calculations (not switching to accepted geometries only as data to display those will typically be missing).
r114497 ADF fix: LOCORB not implemented in case of spin-orbit coupling. Fix is to ignore the key instead of stopping with unclear error message.
r114487 AMSspectra: fix backwards compatibility with .t21 files.
r114428 AMS: Make MD calculations with lattice deformations fully restartable.
r114344 BAND: Do not disable DOS when using the technical key Programmer%StoreOrbitals is no.
r114274 ADF: Replace dsyevx with dsyevr when creating Lowdin basis with unrestricted molecular fragments. Such calculations sometimes stop with basis orthogonality errors due to faulty MKL's version of dsyevx. The problem is likely caused by a very high degeneracy of the fragment overlap matrix in these calculations.
r114206 AMS2023.103 released (Aug 7th, 2023)
r114170 AMSinput: Fix crash when trying to find the QE pseudo potential dir when there is no local QE installation present.
r114112 AMSmovie: Fix performance issue with graphing molecule counts for MD simulations.
r114032 ADF Fukui descriptors: proper fix for amsreport Fukui descriptors computed using QTAIM partitioning.
r114019 ADF Fukui descriptors: undo the r113961 change below because it breaks QTAIM charges for all other things. A separate fix for the Fukui descriptor is pending.
r114012 GUI: Fix an issue with the Swish-E based search feature on Apple Silicon.
r113998 BAND: Some GTO basis sets did not match those from basissetexchange.org.
basis missing wrong removed
CC-PVQZ Mg, Zn, Kr Z>Kr
CC-PV5Z Mg,Zn,Kr Z>Kr
CC-PWCVQZ Ar,Br,Co,Cr,Cu,Fe,Mn,Ni,Sc,Ti,V,Zn Si,S,P,O,N,F,Cl,C,B,Al
r113992 GUI: Fix the location for temporary files inside SCM_TMPDIR for different users on Windows (e.g. AMScrs temporary results could clash between users).
r113961 ADF Fukui descriptors: Fix a bug with atom order of Fukui descriptors when the internal order of atoms is different from the input one.
r113872 GUI: Fix an issue with Packmol on Apple Silicon.
r113869 ADF: Do not stop calculation in case of spin-orbit coupled calculation in which BondOrders are requested, instead only show warning.
r113752 AMS2023.102 released (Jul 17th, 2023)
r113744 AMSinput: BAND NEGF: treat empty bias potential as 0.0, did lead to weird unit conversion error.
r113600 AMSinput: with multiple molecules, make sure the active molecule is properly shown (in bold and bigger letters in the label).
r113537 AMS MD: Shorten variable names written to the trajectory by ApplyVelocity (from MeanEngineXForceRegionName to MeanEngXFrcRgnName) to support region names up to eight characters long. Longer region names will be truncated. The original title of the variable including the full region name is written to a separate metadata variable with a (title) suffix.
r113521 Workflows: Fixed opening HDF5 OLED workflow result files in AMSview on Windows.
r113499 ADF NCI: Fixed a bug that resulted in DenSigned having the wrong sign.
r113466 GUI: refine previous change: let user select where to save examples with Help->Copy Examples (and renamed to Copy And Show Examples). No more SCM_EXAMPLES env var.
r113461 GUI: the Help -> Examples menu has been modified to Help -> Copy Examples. This avoids messing with the distribution, especially on macOS. The Examples will be copied to $HOME/AMS_Examples with a version number appended. You can select your own prefered location using the SCM_EXAMPLES env var.
r113438 AMSview: when recalculating fields, update related defaults (like color ranges), unless user made changes to them.
r113359 Fix an issue with including files >4Mb using the @include directive in input files.
r113349 OLED properties: fix a bug with ions not having an actual charge when using the Relax "None" and "Neutral" option for calculating vertical IP/EA
r113327 AMSmovie: Fix the sign for the volume graph.
r113282 ParAMS GUI: Fix cmd window popup on Windows when importing certain job types.
r113256 Windows: Fix result file conversion via PLAMS for some formats, used for example when importing jobs in ParAMS.
r113227 MLPotential: M3GNet no longer uses all available GPU memory and parallel settings are improved.
r113219 AMSview: Add two fields in case of doing a charged periodic system with band (Neutralizing density and Homogeneous density).
r113201 AMSinput: NBOs and NLMOs will be saved on a file name nbo-nlmo-adf.rkf.
r113195. BAND: Increase maximum number of semaphores. Relevant for machines with 128 cores or more per Shared Memory node. (Physical nodes may be split into several Shared memory nodes).
r113183 Windows: Force MKL to use 1 thread because Intel OMP has a CPU affinity bug on Windows with more than 64 cores.
r113153 AMSinput: when opening a fragment job, ignore that it is a fragment so occupations etc can be modified.
r113082 ADF: Improve error message regarding SOPERT in case of Excitations%OnlySing or Excitations%OnlyTrip. In case of perturbative inclusion of spin-orbit coupling for excited states both singlet and triplet excited states should be calculated.
r113062 AMSinput: when opening an old .ams file with info for multiple molecules, properly update the charge.
r113034 AMSview: the default grid should extent 4 Angstrom. The Grid Details extent was correct (but you needed to change something to use that).
r113020 AMSinput: fix run script when using NBO analysis of EFG/NMR, the original adf.rkf file was deleted. Now it is present (or present as 1-adf.rkf, check the run script).
r113004 Increase the limit on the number of shared arrays to avoid a "Too many shared arrays" error when uding AMS with rdkit.
r112990 BAND: Error when using regions and stress. The final message would be ERROR: KMatrixIOModule: matrix not shared. The error was caused by A1LatticeStrainsModule: lattice strain breaks symmetry.
r112930 AMSinput: Avoid incorrect newresponse block in BAND run scripts with hybrid engine.
r112920 AMSinput: Fix issue with switching from and back to the Hybrid engine main panel.
r112912 AMSinput: Avoid crash after using Edit -> Delete Molecule when the Coordinates panel is visible.
r112894 AMSinput: CDFT excited state reference ground state file could not be selected.
r112842 AMSmovie: Fix gradient and force atom vectors.
r112756 QuantumEspresso: do not overwrite OMP_NUM_THREADS variable if it is already set
r112680 AMSinput: fix error about crs(savedruntype) not found that could pop-up when saving a job.
r112671 AMSjobs: status for fragment jobs was not properly updated for extremely fast jobs.
r112639 MLPotential engine, ForceField LAMMPSOffload: Fix message decoding errors on Windows.
r112627 Conformers: fixed a startup crash for users with non-ASCII characters in their license file.
r112552 BAND: Smaller threshold for atomic potenial. The bonding curve for very heavy elements (Z=100) could look bumpy. Also solves wrong implementation of the NuclearModel=Gaussian. In fact this used to be a Uniform model.
r112549 ADF: Fixed a bug with the storing of GW energies into the rkf file.
r112518 IRC: Fix a bug that causes a "File already exists" error at the end of IRC job.
r112501 AMSview: enable opening of explicit vtk file with .rkf file (open the .vtk file first).
r112483 AMSpackages: Prevent UnicodeDecodeErrors when installing python packages.
r112481 AMSinput: make --help work (not crash).
r112453 AMSinput: add IntegerAufbau option in SCF convergence details, and hide occupations key from expert options (as it will be ignored if used).
r112437 Quantum Espresso engine: fix default for occupations.
r112314 AMSmovie: MD analysis graphs which include many atoms now have a more reasonable name in the legend.
r112288 AMSmovie ChemTraYzer2: headers for the bottom table could be missing on some systems (depending on screen layout)
r112282 BAND: Print AIM deformation Charges when available and make them depend on the fragment setup.
r112277 AMSinput: fix the regions option "Add region in same way to identical molecules" when non-standard molecules are used.
r112268 AMSinput: fix bonds for small unit cells when using the "Map Atoms To ..." feature.
r112249 ADF: GW bug fix. Incorrect Fermi energy was used. Also affects BSE.
r112242 AMSinput: fix typo in new preset code leading to the preset code not to recognize the task used.
r112227 BAND: Prevent crash when using Basis%Foder in band with an absolute path.
r112209 AMSinput: option to avoid question about only pre-optimizing selected atoms each time.
r112200 AMSinput: fix generating non-trivial 2D supercells.
r112199 AMSinput: preset handling improved (no longer overwrites user changes, much easier to use). Check the GUI documentation for details.
r112181 BAND: With AIMCriticalPoints do not only calculatte the deformation AIM charges (derived from the deformation density), but also the total ones (calculated from the total density).
r112173 ForceField/OLED-deposition: Fix LAMMPS neighbor list overflows for large cutoffs with UseGPU.
r112147 chemtrayzer2: made reaction filtering criteria stricter: now, to remove a reaction from the set, it must have the same reactants and products (previously true) and also each reactant-product pair must contain the same atom indices. this prevents a subtle issue related to when a reaction takes place within another reaction.
r112140 AMS: Fixed a bug that would cause a 'ERROR: Multiple instances of the singleton engine' error with a TransitionState task.
r112136 AMSinput: when a preset is defined setting the XC, do switch to this preset value when switching modules (instead of switching to LDA).
r112109 AMSmovie: analysis legends were not complete, missing atom names.
r112091 AMSinput: suggest better name when saving a preset.
r112080 BAND/DFTB: Initialize variable in MultiStepper. No known effects.
r112077 AMSinput/ParAMS GUI: make sure always a full file path is used pointing to the ReaxFF force field file.
r112075 ParAMS GUI: avoid crash when reading an unexpected formatted ReaxFF force field file.
r112021 AMSview: fix display of KPoints in orbital labels for periodic systems.
r112012 AMSmovie: Fix Chemtrayzer2 on Windows to generate useable csv files./td>
r112008 AMSmovie: Fix unit conversion for the energylandscape plot when using the relative energy option.
r112002 AMS: Fix the FIRE optimizer so it can work with a fully frozen system.
r111998 GUI: Fix atom label resizing with a multiview enabled (e.g. AMSinput multiview or AMSmovie energylandscape).
r111996 AMSinput: allow fixed region constraints also for GCMC jobs.
r111942 AMSinput: Improve feedback of running the APPLE&P atomtyper.
r111918 AMSmovie: Fix visualization issue when El and Eh ReaxFF elements were shown in combination with regions.
r111911 AMSspectra: Unit inversion for the broadening value is improved and reversible.
r111908 GUI: Handle invalid input in the graph options when the Enter-key is used to confirm.
r111868 AMS2023.101 released (Apr 4th, 2023)