Changelog bug-fixes ADF Modeling Suite 2016

r57324: ADFinput: now chain results of a job as input to ReaxFF works

It did complain about forcefield files and lattice vectors incorrectly.

r56024: Reaxff: fixed an important bug for non-orthorombic lattice

There was an error in the calculation of forces (for a non-orthorombic unit cell) in the situation where the lattice parameters were specified in the control but not in the BGF geo file. The users who prepare their input using the GUI should not encounter the bug because ADFinput always saves the lattice parameters in the BGF geo file.

r55741: Reaxff: Fixed a bug that would cause spurious reactions near the unit cell edges for non-orthorombic cells.

The bug could only be triggered by using a non-zero value for the range parameter in the control file

r55352: Bugfix ADFjobs: now ADFjobs should be able to deal with remote hosts that print stuff on stderr when logging in.

Preferably the ssh connection to the remote host should be clean (nothing printed). Some hosts print stuff to stderr, which was causing trouble. Hopefully fixed now.

r55044: Bugfix ADFinput QMMM: incorrect check for spin and charge has been removed

Only the warning generated was misleading, this has no effect on the actual run script.

r55002: Bugfix ADFspectra: ignore shifts for elements that have not been calculated

In spectra and tables they were visible with a shielding of 9876543210.0, leading to unusable spectra.

r54991: Bugfix ADFinput: fix incorrect check for NMR calculations

Fixes error message: WARNING: NMR output requested, but no atoms selected for which to calculate NMR shieldings"

r54956: Bugfix ADFmovie: issue with displaying lattice info in the graph when the file is not completely loaded.

The displayed error would be: AIMCriticalPointsModule::ncp too large. It was observed in a bulk calculation (NaCl) with band. It is less likely to affect ADF.

r54794: Update TclTk version used in the GUI, hopefully fixing a memory issue with ADFjobs

On MacOS the fonts have been modified due to this change.

r54725: Fix reaxff when the order of atom types in the ffield dihedrals and angles sections does not comply with the original reax convention.

The original reax requires that the order of atom indices in the dihedrals section of the ff file complies with the following 2 rules: i(2) ≤ i(3), and i(1) ≤ i(4) if i(2)==i(3). Similarly for angles i(2) must be ≤ i(3). Reaxff will now flip the order of atom types for such angles and dihedrals.

r54713: Improve performance of the KF subsystem

This change should make long reaxff calculations much faster.

r54293: Bugfix for GCMC ReaxFF calculations

The noinsr keyword was working in reverse mode. From now on a value of 1 turns ON noinsr, meaning the species will not insert.

r54291: Bugfix UFF via ADFinput and adfprep: the previous fix (r54266) changed (incorrectly) all uff jobs into SP jobs

This also broke the pre-optimizer

r54208: Bugfix ADF: excitation energies icw singleorbtrans icw fractional occupations

The subkeyword SINGLEORBTRANS in the block key EXCITATIONS, will calculate excitation energies as Kohn-Sham orbital energy differences. It was meant to be working also in case of fractional occupation numbers, this has been fixed now. Workaround for previous ADF2016 releases is to include the keyword KSSPECTRUM.

r54143: Bugfix ADFinput: region dependent basis sets for BAND produced wrong run scripts

The basis files in the run script were pointing to ADF basis sets instead of BAND basis sets.

r53667: Bugfix ADFinput: atom coordinate conversion for ReaxFF non-orthogonal cells was done after creating the run script

Sevaral bugs were fixed in CVnDFT. CVnDFT icw GGA’s was not working. The CV_DFT and SCF_CV_DFT methods gave incorrect numbers. ALLPOINTS was required for calculations that use symmetry, now automatically set in case of CVnDFT. EXACTDENSITY was required for precision reasons, now automatically set in case of CVnDFT.

r53439: Bugfix ADFview: fix crash when using AIM to display bondpaths, but no bondpaths are present

Fixes error message: can/t read "mins": no such variable by adfview (from ShowBondPaths)

r53437: Bugfix ADFinput: fix crash when imorting PDB files

Fixes error message: expected integer bug got "" from GetResidues

r53411: Bugfix ADFinput: multiple molecule mode fixes

• If you had more then two molecules (via Edit → New Molecule) only the first two were selectable
• The periodic info was not updated correctly in the right side panel when switching molecules

The periodicity of the system with multiple molecules could be wrong with 5 or more molecules

r53291: Bugfix ADFmovie: avoid crash when someone clicks the play controls with no file loaded

Fixes error message: can't read "tFilename": no such variable

r52180: BugFix BandStructure (bzstruct) in Band with MetaGGAs and Hybrids

BandStructure plot in Band can now be used in combination with MetaGGA and Hybrid functionals. Before the bug fix, bzstruct would either produce a wrong band-structure or not work at all in combination with MetaGGAs and Hybrids

r52179: Modified the bin/start script for IntelMPI to make it compatible with Cray XC systems

Now it should be possible to run IntelMPI binaries on Cray systems using the Cray MPT. This has become possible because both IntelMPI (starting from v5.0) and Cray MPT (starting from v7.1.3) are ABI-compatible with MPICH2. To use this compatibility mode it might be necessary to load the cray-mpich-abi module.

r52174: Bugix ADFinput: avoid crash in Align command

Fixes error message: ERROR r3angl: zero vector

Fixes error message: can't read "tasks(...)": no such element in array

r52166: Bugfix ADFinput: avoid crash in GEOVARS key when saving run script

Fixes error message: can't read "gin(geometry.branch.used)": no such element in array

r52100: Molecular dynamics with ASE: zero total linear and angular momentum. New scripting examples.

After randomizing the initial velocity with a Maxwell-Boltzmann distribution, the total linear and angular momentum is now set to zero (before this fix you could have a non-zero total overall linear and angular momentum). We also added a few scripting examples for PLAMS and ASE.

r51990: ReaxFF/ChemTraYzer: improved generation of 2D molecule pictures

Fixing Errors: "can't read widthstring" and "can't read maxconcentration"

r51946: ADFview: fix Select within distance command

Fixes error message: invalid command name "RealDlg"

For example this avoids errors in the Spin and Occupation panel)

r51901: MacOSX ADF-GUI environment variables changed

If a user defines ADFHOME or so in their shell startup file the ADF-GUI application would use that version insted of the bundled version. That lead to confusion and problems.

Now the shell startup scripts are ignored when starting the ADF-GUI application on MacOSX.

Instead you can make a \$HOME/.scmenv file and define the environment in there (using bash shell syntax).

r51889: bugfix ADFinput: make sure a known pre-optimizer is used

Fixes error message: can't read "gin(mm.runtype)": no such element in array, probably caused by preferences from an old ADFinput version

r51864: bugfix ADFview: changing the isovalue for a multi-ioso surface could crash

Fixes error message: can't read "VTK(id_7,type)": no such element in array

r51859: bugfix ADFspectra: for periodic systems a crash could occur when switching spectra types

Fixes error message: can't read "VTK(wignerseitz.0,ids)": no such element in array

r51856: bugix BANDstructure: avoid crash when dragging while nothing has been loaded yet

Fixes error message: can't read "t21::kuniqu": no such variable

r51800: Improved analytical lattice gradients in band.

By now symmetry does not need to be disabled. Also sensible defaults have been chosen. Here is an example input

GeoOpt
OptimizeLattice true
end

xc
libxc pbe
end

End

Analytical true
end


Note that for a GGA one needs to use the libxc key rather than the normal gga key. A speedup of 2-3 is realistic compared to using the default numerical lattice gradients. It does not work for metaGGAs and hybrids.

r51773: Reaxff: revert unintentional change in the bond order cutoffs when searching for torsion angles.

The change was introduced in r39550 (2013) when removing discontinuty in the torsion angles for BO->0

r51762: Double sided numerical differentiation for Phonons (BAND and DFTB)

Using double-sided sided numerical differentiation improves the precision of phonon calculations, and in many cases this solves the negative frequencies issue.

r51753: bugfix BAND: strange results for big 3D systems such as MOFs

Due to a bug strange things could happen for large unit cells. One of the indications would be not so accurate norms for some of the basis functions. In the end a geometry optimization would behave strangely.

r51684: ADF: TD-DFT+TB, sTDA and sTDDFT: restrict SOT space

For excitation energies calculated with the fast approximate methods: TD-DFT+TB, sTDA or sTDDFT, by default the maximum number of the lowest single orbital transitions (SOTs) that are used (which have the lowest orbital energy differences) is restricted, in order to save memory and computation time. For TD-DFT+TB the lowest 100000 SOTs are included by default.

MODIFYEXCITATION
UseOccVirtNumbers 1 100000
END


For sTDA or sTDDFT the lowest 10000 are included by default.

MODIFYEXCITATION
UseOccVirtNumbers 1 10000
END


One can override this by using a different value for the subkey UseOccVirtNumbers of the key MODIFYEXCITATION.

r51683: ADF excitation energies RS functional LibXC: RS ALDA + HF kernel

For the LibXC range separated (RS) functionals, like CAM-B3LYP, the exchange-correlation kernel used in the excitation energy calculation is approximate. This approximation has been improved to use the RS ALDA + RS exact exchange kernel. (It was using a 100% ALDA + RS exact exchange kernel). Note that this is not the full kernel.

r51670: bugfix ADF: sTDA or sTDDFT icw NOGRIMMEPERTC

The perturbative correction GRIMMEPERTC could not be switched off. Fixed.

r51623: ADF: sTDA or sTDDFT icw range separated functionals

The alpha and beta parameters in Table 1 of a paper by Risthaus et al. Phys. Chem. Chem. Phys. 16, 14408 (2014), should be switched. Thus for CAM-B3LYP use

MODIFYEXCITATION
GrimmeAlpha 0.9
GrimmeBeta 1.86
GrimmeAex 0.38
END


r51549: Performance improvement for the D3 dispersion correction.

In particular for BAND the calculation of the nuclear gradient of the dispersion term could be very slow.

r51522: SCM-ASE-MD: Allow correct tracking of ASE MD calculation at runtime.

MD trajectory can now be expected at runtime by marking the calculation in the GUI (adfjobs) by marking the job of interest and selecting “movie”.

r51446: ADF-GUI: bug fix selecting XC functional CAMY-B3LYP

The ADF-GUI would make an input that would be correct for ADF 2014. However, in ADF 2016 for CAMY-B3LYP the .run file should have

XC
HYBRID CAMY-B3LYP
XCFUN
RANGESEP
END


r51438: Bugfix for band, issues with the k-grid key

Sometimes the requested k-grid (such as “5 1 1”) breaks the symmetry, leading after some time to an error “unexpected nvert”. This is now detected more early on with a better message.

Another problem was that a grid like “4 1 1” would not be accepted, because of the mixing odd and even numbers. However, in this example the the “1 1” means to neglect dispersion, which is not the same using an odd number for k-space integration in those directions.

r51405: Change GUI preference: default min/max for radii when scaling atom spheres by scalar values has been adjusted

Only for fresh installs. For example, when scaling the atom radii by atom charge in ADFview.

r51401: Bugfix permission issue ADF package for MacOSX

Only relevant if you are installing the software to be used by another user.

r51356: ADF NMR: improved kernel possible for spin-orbit coupled calculations

One can include an improved exchange-correlation kernel, as was implemented by J. Autschbach, Molecular Physics 111, 2544 (2013). This is an important option that should be seriously considered. Important only in case of spin-orbit coupled calculations. This may give some (small) gauge dependent results when using this.

The improved exchange-correlation kernel will be included if one uses the subkey USE FXC with the NMR module, for example:

NMR
USE FXC
U1K BEST
END


The example shows how to change atom types in a script, or how to attach different ligands in a script.