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.

r70453: ADFinput: DIM/QM charge setup could fail when using aromatic structures.

r70447: ADF: Improved numerical stability of RIHartreeFock for long-range-separated hybrids.

The minimum possible value for the switching distance from range-separated potential to 1/r is now 2 Bohr (before it was 0 Bohr). This seems to fix occasional variational collapses, e.g. for CAMY-B3LYP with very small beta values (\approx 0.001). This fix might lead to small differences in the results of calculations using certain kinds of long-range-separated hybrids.

r70437: Open proper ADFjobs window (and only if needed, and only if not in joblist mode).

r70426: MacOS version: try to avoid that the signature becomes invalid after starting the ADF-GUI application.

This hopefully fixes popups from some virus scanner related to the signature.

70419: Utils: The run_standard_tests script can now run multiple tests simultaneously.

r70352: Reaxff: Fix the "opt%caldat array overflow in ParseTrainSetOneMolecule" error.

r70346: ADFdos: Fix crash with partialdos for dftb.

r70262: Reaxff: Make the MINRES-QLP convergence criteria in ACKS2 more strict.

Besides, the min distance cutoff for ACKS2 has been reduced to be in line with the standalone reax.

r70132: ADFinput: avoid crash when pasting an empty clipboard.

r70082: Reaxff: added pdist command to rxffutil.

See User's Guide for details.

r70067: ADF: bug fix SM12.

The self-consistent part of the SM12 implementation was incorrect. This has been fixed. The incorrect implementation was very close to only include SM12 as a post-SCF energy correction.

r70035: ADF: Save electron smearing status and use it upon restart.

In order to avoid conflicts upon restart, the saved data will not be used if the restart calculation has an Occupations key in the input.

r70001: ADFinput: fix PBE0 with spin-spin couplings run script (input was wrong).

r69981: Reaxff: extended the rxffutil utility with some options

The new options include printing some basic information about known reaxff parameters and preparation of the params file used for reaxff parameter fitting. Some examples:

Prepare params file for optimization of all parameters of the C-O bond block and the first C-O-O-C torsion parameter (both blocks!) in the TiOCHNCl.ff force-field.

$ rxffutil.exe params --ff=$ADFRESOURCES/ForceFields/ReaxFF/TiOCHNCl.ff b%CO t%COOC:1
#     Key          delta         min         max     comment
   3   4   1    1.017360     95.6228    197.3588     # b%CO:1 E(Sigma)
   3   4   2    1.057032     58.4169    164.1201     # b%CO:2 E(Pi)
   3   4   3    1.248792      5.5000    130.3792     # b%CO:3 E(Pi2)
   3   4   4    0.019273     -1.3755      0.5518     # b%CO:4 p_be1
   3   4   5    0.002831     -0.3906     -0.1075     # b%CO:5 p_bo5
   3   4   6    0.000000      1.0000      1.0000     # b%CO:6 13corr flag
   3   4   7    0.094704     10.2503     19.7207     # b%CO:7 p_bo6
   3   4   8    0.007175      0.3796      1.0971     # b%CO:8 p_ovun1
   3   4   9    0.037882      0.3211      4.1093     # b%CO:9 p_be2
   3   4  10    0.003587     -0.5875     -0.2288     # b%CO:10 p_bo3
   3   4  11    0.027827      6.7927      9.5754     # b%CO:11 p_bo4
   3   4  12    0.000000      1.0000      1.0000     # b%CO:12
   3   4  13    0.001969     -0.2877     -0.0908     # b%CO:13 p_bo1
   3   4  14    0.012328      4.5000      5.7328     # b%CO:14 p_bo2
   3   4  15    0.010000      0.0000      1.0000     # b%CO:15 ovcoord flag
   3   4  16    0.012141      0.0000      1.2141     # b%CO:16 p_xel1 (ereax)
   6  16   1    0.055006     -2.0324      3.4682     # t%COOC:1 V1
   6  41   1    0.055006     -2.0324      3.4682     # t%COOC:1 V1

Print some basic info about known H-Pt-H angle parameters (use the first parameter only for clarity), list files where this parameter is present:

$ rxffutil.exe minmax -vv v%HPtH:1
....
Key                   N         min         max     average
Found v%HPtH:1               95.0000 in c:/adf2018.105/atomicdata/ForceFields/ReaxFF/CHONSFPtClNi.ff block 69
Found v%HPtH:1               57.3916 in c:/adf2018.105/atomicdata/ForceFields/ReaxFF/PtCH.ff block 14
v%HPtH:1              2     57.3916     95.0000     76.1958

r69963: ADFspectra: Fix edge case for unit inversion with non-convoluted spectra.

r69959: ADFinput: Searching for non-existent basissets for POLTDDFT no longer gives an error.

r69931: ReaxFF: Add CVHD analysis scripts.

r69920: ADF: bug fix CAM(Y)-B3LYP calculation where short range HF percentage is higher than long range HF percentage

r69908: ADFreport: Fix handling atoms outside unit cells.

r69881: GUI: The 3D visualization options would crash in combination with anti-aliasing.

r69847: ADFmovie, ADFinput, adfreport: make import of BGF files more robust.

r69817: AMS PESScan will no longer crash in the gap filling step if the system is periodic.

r69816: Reaxff: Add a possibility to write optimized geometries obtained by MCFFOptimizer for the latest best ffield.

This is triggered by setting fort90 to 1 in the control file.

r69783: AMS will no longer hang if one of the kid processes fails to create its scratch directory.

r69762: BAND: results wrong for when using UserOccupations in a fragment calculation.

r69752: ADFmovie: ReaxFF export trajectory menu commands now allow selection of destination file.

Previously it would always be the jobname with a new extension.

r69712: Add scripts to ADFBIN for ReaxFF Parameter Optimization.

r69710: ADFinput: The SaveAs dialog now shows the current filename as default.

r69707: Resolve issue that would sometimes cause PDORMTR error messages.

The "PDORMTR parameter number 1403 had an illegal value" message may appear in ADF with OldSCF but it does not affect the computation results.

r69698: GUI: On Windows the OpenGL detection could fail.

The environment variable SCM_OPENGL1_FALLBACK could be set manually to avoid this detection.

r69692: ADFmovie: Moving a curve to the x-axis could lead to issues.

r69678: AddCoordinates command added, to add for example bgf frames to a file.

Replaces the Trainset command. Note names after DESCR in bgf format are trunated after 20 characters and are NOT automatically unique.

r69627: GUI: Starting a commandline window from the GUI on Windows will no longer block the GUI.

r69620: ADFinput: Trainset command added, with subcommands to add to selected/last used train set.

Note this is very experimental and should really not be in the 2018 version, it may disappear or change ...

r69598: ADFinput: calculating frequencies in the same run as a Transition state search did not work via ADFinput.

r69586: ADFinput EFG NBO analysis input generation could crash when no EFG atom has been set

r69558: ADF command line on Windows: fixed the backspace issue existing in adf2018.104.

r69557: ADFinput: Changes in Atom Details panel were not always used.

Only when input focus was changed explicitly by clicking outside the field being changed the value was used.

r69541: ADFinput: Run Script window did not live update when molecule was modified

r69467: Removed SSE4.2 instructions from the binaries

ADF now has optimized code paths for SSE2, AVX and AVX512 in the normal binaries.

r69466: (October 8th, 2018):AMS2018.104 released

r69396: ADF: fixed a bug related to using restart orbitals in a calculation with linearly dependent Lowdins.

r69366: ADF: fixed a bug in Becke grid that could lead to segmentation faults for large system and high quality settings.

r69322: Documentation: add IQA tutorial

r69288: AMS: Better restarting of crashed geometry optimizations.

All optimizers (Quasi-Newton, FIRE, SCMGO) now write intermediate geometries to the Molecule section on ams.rkf, enabling easy restarting using the LoadSystem keyword. Previously only the FIRE optimizer was doing that, so crashed geometry optimizations with the other optimizers were not easily restartable.

r69287: Reaxff: Remove hard-coded limit on the number of entries in the training set.

r69284: ADFinput: fix reading .adf files from older versions.

r69273: Band: bug fix for long range part of the Coulomb potential for bulk systems. This bug affected small, highly symmetric bulk systems (e.g. diamond).

r69254: Reaxff: Bugfix for the iremove feature running in parallel.

r69252: ADF: Add a stop for ETSNOCV in combination with a non-NOSYM symmetry.

r69233: Bandstructure: Fixed default range for DOS-only in bandstructure.

r69204: AMS MD: Default to Random initial velocities.

r69181: ADFinput: improve link to documentation in AMS MD page

r69174: Fixed a memory leak that caused long-running BAND jobs to run out of memory.

r69169: Bandstructure: Loading of COOP data made faster.

r69167: ADFinput: AMS MD calculate pressure option moved to AMS expert options.

r69159: ReaxFF AMS engine: Fix missing interactions and stress tensor for small periodic cells.

A bug in the Verlet list generation in ReaxFFEngine caused some potentially missing long-range interactions for small periodic cells (thinner than 5 Å in some direction). Additionally, the stress tensor cannot be evaluated analytically for small cells. The engine will automatically fall back to calculating the stress tensor by numerical differentiation if necessary.

r69123: COSMO-RS GUI: ADF Lei 2018 COSMO-RS parameters

Added a popup menu to use the reparametrized COSMO-RS parmeters for systems containing ionic liquids (ILs), see [J. Han, C. Dai, G. Yu, Z. Lei, Green Energy & Environment 3, 247 (2018)].

r69091: ADFinput: fix update glitch (bonds not drawn correctly) after Edit -> Symmetrize.

r69000: AMS geometry optimizations now try to continue even if engine fails to solve for a geometry.

This can happen if there are for example SCF convergence problems in the engine. The energy/gradients might then not be quite correct, but it is probably safe to continue the optimization and hope that things are fine again for the next step. Note that this fix also applies to PES scans, transition state searches, and any other applications that use geometry optimizations internally (e.g. elastic property calculations).

r68955: ADFinput and ADFoutput: minor IQA details.

Make sure IQA is not used for unrestricted calculations, and add a link to the IQA output section in the Output browser.

r68924: AMS2018.103 released

r68904: ADFinput: fix molecule search for older windows machines

r68887: ADFjobs: automatically run jobs on which a job depends (like fragment runs) if those jobs ended with an error.

A dependency will now run if its state is ready with an error. This could happen for example if the input is correct, but the disk is full, executables are missing or things like that. Previously, dependencies would only run automatically when their state was not in queued,running or ready.

r68863: COSMO-RS GUI: bug fix .xyz to SMILES search

The search entry for adding an estimated sigma-profile with .xyz files could create the message 'XYZ file: not found', even though it was present. Fixed.

r68862: COSMO-RS GUI: bug fix pure compound density estimate

The pure compound density estimate could give a NaN or Inf in case the density of the compound could not be estimated with the QSPR method. Fixed.

r68854: ADFinput: add/fix minor details for IQA.

  • only single point,
  • warning ADF will run in serial mode,
  • no empty atomstodo.
  • r68800: AMS2018.102 released

    r68755: AMS MD: Fix integration with the Berendsen barostat, make BulkModulus configurable.

    r68747: ReaxFF: Fix a GCMC bug that led to crashes like "Error when moving molecule!".

    r68743: ADFinput: only write lastatom in AMS MD THERMOSTAT key when non-system-wide thermostats are used.

    r68738: ADFinput: use PM7_solids and ADF molecules from the .tgz files (to reduce the number of files in the distribution)

    The ADF and PM7_solids folders are no longer in Molecules, they are avaiable as tgz files if you want to get the individual files.

    r68711: ADF: Implemented spin polarization optimization.

    The spin polarization can be optimized by minimizing the difference between Fermi level values for spin-alpha and spin-beta MOs. This method works reliably only when a reasonably large finite electron temperature is used (300K is found to be sufficiently large for small transition metal clusters). The polarization value is optimized up to a specified tolerance (fractional values are allowed) by step-wise reduction of the root-braketing interval for the objective function f=FermiLevel(alpha)-FermiLevel(beta). The SCF procedure is converged for each spin polarization. When the interval becomes smaller than the tolerance the optimization is considered converged. After that the SCF may optionally be repeated with the spin polarization set to the nearest even or odd number (depending on the total number of electrons in the system) or, in other words, with the total number of electrons per spin rounded to the nearest integer. The method is invoked by using one of the following Occupations keys:

    OCCUPATIONS  ElectronicTemperature=300 OptimizeSpinRound=0.05
    OCCUPATIONS  ElectronicTemperature=300 OptimizeSpin=0.05
    

    Here, the ElectronicTemperature sets the electronic temperature, in Kelvin, for calculating the Fermi MO occupations. The OptimizeSpin and OptimizeSpinRound argument specifies the tolerance value. The OptimizeSpinRound key specifies that after convergence the SCF must be completed with the total number of electrons per spin rounded to the nearest integer.

    It should be noted that as usual the Unrestricted and Charge keys must be specified as for any other spin-unrestricted calculation. The second argument of the Charge key sets the initial spin polarization value from which the optimization is started. The result of the optimization may depend on the initial value as the objective function may have more than one root.

    r68708: ADF: Fixed a bug related to atoms order in IQA input/output.

    r68698: Band: much better running of big fragments.

    Band used to disable Shared Arrays for fragment related calculations, slowing down significantly the calculations. Big systems might even crash.

    r68688: Windows: Update intelmpi runtime to 2018.0.3

    r68672: ADFinput: add check that fragments do not overlap for BAND

    r68588: ADFinput: report proper error when property estimation fails

    r68583: ADFjobs: when starting by double clicking the icon, make sure the initial directory is writable (if not, switch to $HOME)

    r68577: ADFinput: when saving fails, do not set job name in window.

    For example, when trying to save your setup in a location where you have no write permission.

    r68519: Fix floating license issue with AMS (DFTB/BAND/...)

    r68514: ADFspectra: fix issues caused by NMR spectra updating too quickly in succession.

    r68513: ADFspectra: Boltzmann weights caused issues with large energy differences.

    r68502: AMS MD: Rename the "NHC" barostat to MTK.

    It should have always been called MTK as it implements the Martyna-Tobias-Klein equations, but it accidentally ended up under the confusing "NHC" name.

    r68497: AMS MD: Disable Preserve CenterOfMass by default.

    It only makes sense in rare situations (long free-boundary simulations or 3D periodic inhomogeneous systems with one heavy component surrounded by solvent where the Brownian drift of the CoM may be annoying) and leads to surprising spurious translation of all other systems.

    r68493: ADF: Fixed a bug in RamanRange with hybrid XC functionals.

    Before the fix, the Raman intensities were calculated using the Response module, which resulted in incorrect results. With this fix, the AOResponse module is used instead, which does work with hybrids.

    r68489: ADFspectra: fix processing peakwidths with nonvalid values for NMR spectra.

    r68487: ADFmovie: converged geometries only for an IRC calculation will show all final IRC geometries.

    If not converged, it will be mentioned in the label (if that info is available, ie ADF2018 or later).

    r68474: ChemTraYzer: Fixed issues with SMILES strings that cannot be handled by RDKit.

    r68439: ADFdos: Restricted BAND calculations would show the DOS per spin.

    r68434: ADFinput: Metahybrid functional accuracy requirement wasn't checked correctly.

    r68433: Velocities from file for AMS MD, fix rare problem of ADFjobs hanging, fix ADFjobs for non-job files

    The option to select the file with AMD MD velocities was in expert options, moved to the AMD MD panel.

    The scmd daemon could crash when generating the errors file when a job finishes due to a race condition. This lead to ADFjobs hanging.

    ADFjobs had visual update issues with jobs that are actually not jobs (like just a .xyz file).

    r68432: Bandstructure: Fix COOP window size for MacOS.

    r68390: AMS2018.101 released

    AMS2018 has been released. Please see Release notes for a list of new features and improvements.