Changelog bug-fixes Amsterdam Modeling Suite 2018

r74330: fix atom reording issue with BAND results

r74086: (April 18th, 2019):AMS2018.106 released

This subrelease of AMS2018 is the last planned release of AMS2018.


r73926: ReaxFF: Fix PBC handling in CVHD

There was a bug in the way the CVHD bond distance calculation handles periodic boundary conditions. This led to an incorrect periodic image being selected instead of the nearest one when a bond crossed the cell boundary. This was a minor issue for simulations in orthorhombic boxes (only causing many spurious CVHD messages about “waiting ON, waiting OFF”). However, for non-orthorhombic cells it often led to no bias getting deposited at all, effectively disabling CVHD.

r73733: ADF: metahybrids PW6B95 and PWB6K using XCFUN do not agree with LibXC

The metahybrids PW6B95 PWB6K using XCFUN should not be used.

r73488: AMS MD: Fix corruption of ConservedEnergy stats in MD restart files

When an ams.rkf file was supplied to the MD driver through the Restart key, the conserved energy statistics on this file would accidentally get overwritten.

r73344: ADFspectra: fix normal mode display (in case of symmetry the wrong mode would be shown)

The bug was introduced in r72922.

r73140: Fixed a race condition that could lead to ADFMovie failing to correctly visualize running geometry optimizations and PES scans with AMS.

r72973: GUI: Fix issues with empty environment variables in the preferences on Windows.

r72946: ReaxFF: Bugfix in GCMC

Atom names of added molecules should now appear in the geo_MC* files.

r72922: ADFspectra: reading modes from TAPE21 could fail depending on symmetry

The TAPE21 file was closed too soon, which may lead to trying to read from a closed unit which gives an error.

r72919: ADFinput: EFG NBO anaylsys atom index issue

The atom index might be wrong if the molecule has been edited (atoms deleted).

r72907: ADFinput, GUIprefs: avoid crash when mainpages not defined

Fixes the error can't read "mainpages": no such variable

r72892: Fix GUI update and version dialogs

Giving a new update or version info command (from the Help menu) without closing the dialog first would generate an error (window name "updatedlg"already exists

r72887: Fix ADFmovie logfile parsing

Should fix the can't read "eprint": no such variable error

r72858: Try to fix a ‘unmatched close-brace in file name’ error when quitting on mac

Not sure if it is fixed, as the issue (reported by several users) could not be reproduced.

r72836: Fix rare event where the matching ams.rkf file could not be found

This caused ADFinput not to ask to update coordinates after re-running a job (without closing ADFinput in between) in some cases.

r72754 XC functionals: boost numerical integration grid for LibXC SCAN functional

r72746 ADFinput: use full path for fragments and require rkf instead of runkf files for BAND.

r72743 ADFjobs: garbage in .err file could freeze ADFjobs

r72698: ADFmovie: bugfix showing local atom properties for ReaxFF runs with changing number of atoms

r72666: ReaxFF: Bugfixes in molecule gun and e-Reaxff

Fixed a bug in the molecule gun that was causing the temperature calculation to be incorrect because the number of degrees of freedom was not updated properly.

Fixed a bug in e-Reaxff that was causing electron-electron interaction to be ignored if there were no electron-atom interactions present in the system.

r72590: GUI: Bugfix y-axis inverse unit change.

r72570: ReaxFF: Bugfix molecule removal in combination with molecule gun

r72542: ADF: fix POLTDDFT Ag.4p TZP basis set file

The ZORA/TZP/REDFIT/Ag.4p basis set file was in fact a DZ basis set file. This has been fixed. Note that the basis set files in the REDFIT directories should be used only in POLTDDFT calculations.

r72400: ADFinput: improve/fix conversion of old .adf files

The conversion now only happens with pre-2018 files, and when data is converted a message is shown to the user that the options should be checked.

A symptom was that some fields like the charge of the molecule did not stick in non-ADF programs.

r72388: ADF: Change the default SFO printing so that for large molecules only the initial SFO table is omitted but the SFO analysis of MOs is still performed.

r72372: fixed a bug in DFTB that causes calculations with long absolute paths to the results directory to stop with a KF error

r72341: ReaxFF, AMS MD: Fix shape-changing MTK barostat with some unscaled axes.

The shape-changing MTK barostat produced incorrect results when it wasn’t applied to all coordinate axes (using the Scale input option in AMS or the inpt control parameter for ReaxFF). This mainly led to incorrect equilibrium temperature and compromised energy conservation.

r72340: Fix calculation of cell parameters in reaxff-ams scripts for non-orthorhombic cells.

r72269: Bandstructure: Show the phonon supercell for BAND results.

r72216: ADFview: the Fukui calculated fields no longer take up unneccesary space.

r72149: ADFmovie: using atom info would crash if Amber info was requested.

r72147: Reaxff: fix a bug in valence angle term that would produce NaNs in very rare situations (highly compressed structures).

r72131: Add Hide All option for Atom info in GUI

r72008: Grimme D3 dispersion was wrong for systems containing Ba atoms.

r71648: COSMO-RS GUI: bugfix COSMO-SAC-DHB

r71517: Band engine, use numerical strain derivatives in the case of spin orbit coupling, because analytical one not implmented.

r71382: ADFinput: avoid crash when drawing bonds between atoms that are almost on top of each other.

r71380: ADFinput: With ‘adjust atoms when changing lattice vectors’ enabled, switching to no periodicity would put atoms in wrong positions.

r71352: ADFinput: make aligning molecules faster when two atoms are selected.

r71299: ADFinput: prevent rare crash when using ADFinput 2018 after using ADFinput from the current development version

r71281: ADFinput: Improve Raman consistency check (generated unneeded warning messages in some cases)

r71274: ADF-GUI: Properly handle AMS-jobs with spaces in their name when re-running such a job.

r71271: ADFinput: Fix use of files with coordinates that have spaces in their name (via the Coordinates panel)

r71266: ADFinput: Fix error text when trying to use AORESPONSE with SPINORBIT.

r71263: ADFinput: Add MESA SCF convergence method.

r71254: ADFinput: Atoms would disappear for fragment runs with BAND, when the RunScript window is used.

r71237: ADFinput: fix handling modified run script (in ADFinput, was not updated in GUI after reading the .adf file again)

r71191: Reaxff: Fixed a bug in computation of the CVHD hyper-time.

The hyper-time values should now be more consistent with published data

r71165: ADFInput: bug fix for ADF hyperpolarizability calculations icw AOResponse

ADFInput was writing the obsolete keyword ‘AOResponse%NoSymmetry’ to the input file, which triggered an error in the ADF calculation.

r71124: ADF: bug fix Raman icw spin-orbit coupling icw RESPONSE

r71062: ADFinput QE: fix HubbardU key

r71033: Reaxff: allow more freedom for comment usage in the geo file.

r70993: AMS MD driver: fix a “singular lattice” error when using the MTK barostat.

r70952: Band: charge error too serious.

Could happen for some 3D periodic systems. Program would detect the problem and stop with the TOO SERIOUS message.

r70841: A few Reaxff-related changes:

Reduce the number of VdW and EEM warnings in reaxff. The warnings are now printed only for atom types that are used in the particular simulation.

Add an alternative way of removing molecules. If iremov is negative then the mass of the removed molecules must be within +/-0.5 of vmamin, vmami2 or vmami3. When iremov is positive then any molecule with the mass between vmamin and vmami2 is removed.

r70806: ADFinput: Fix DRF input when using a large DIM region (>4000 atoms).

r70798: Fix leaking MPI communicators and fix a bug in DIM/QM.

r70767: Bug in band with error message: nOper different at perturbed geo.

r70765: ADF: Optimize in Cartesian coords by default When there is external electric field.

r70700: rxffutil: small bugfix related to general parameters.

r70682: Bandstructure: Fix COOP display (was introduced in r69169).

r70630: (November 27th, 2018):AMS2018.105 released

r70629: adfreport: Energy for UFF was not found

r70613: AMS ReaxFF engine: Improve performance to the level of standalone ReaxFF.

r70607: ReaxFF: Fix handling vval3 and valf during FF optimization.

ReaxFF normally forces the vval3 parameter to be equal to the valf parameter for elements with atomic mass less than 21. This didn’t work in AMS2018 during force field optimization, so the vval3 parameter was changed separately. The optimized force field would thus behave differently when used after optimization.

r70600: ADFview: Wrong default isovalues could be used, leading to a crash.

r70568: Reaxff: Add min/max values for general parameters 40 and 41 to the RxParRange.txt file.

r70481: Improve saving of preferences

This should avoid most cases where quitting a module overwrites prefs saved by another module.

r70476: 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.