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.

r62318 (November 20th, 2017): ADF2017.110 released

r62317: Avoid saving GUI preferences when nothing changed.

r62261: Fixed a bug in the dmpkf utility that would cause the same variable to be printed more than once.

r61992: ADF: Fixed stack overflow in InducedPotMatElts on very large calculations.

r61969: Bugfix band. Combination of spin-orbit and the use of the xc%libxc key gave incorrect bonding energies.

r61921: The ADF-GUI did sometimes not show the Tutorial when starting the first time after an update.

r61908: ADFspectra: sometimes when switching between spectra types the molecule frame was retained (while it should have been removed).

r61878: ADFinput: for DFTB the constraints were not included

The bug was introduced in r60718, and thus is present in the 2017.108 and 2017.109 release.

r61814: Reaxff: An important bugfix for the r62775 below.

In r61775, the torsion angle value is incorrectly adjusted by 2*PI while the angle is given in the units of degree and not in radians as it was assumed.

r61812: Bugfix ADFspectra for MCD spectra

Clicking in the table below the spectrum would highlight the wrong peak (off by one).

r61794: small improvement for the adfbashrc.sh environment setup script.

r61775: Reaxff: small change for handling dihedral angles in the training set.

When calculating a difference between the optimized dihedral angle theta and its reference counterpart theta_0 the minimum of theta-theta_0, theta+2pi-theta_0, and theta-2pi-theta_0 is selected. This will make sure that, for example, two diherdals -pi and +pi will be considered equal.

r61728: GUI: fix double Preferences entry in SCM-popup menu on non-OSX

r61708 (October 16th, 2017): ADF2017.109 released

r61707: ADFjobs: fix SCM-popup menu on Linux

Using a right click on a job in ADFjobs will show the SCM menu. On linux in some cases it would lead to an error.

r61681: ADFmovie: use bond energy instead of SCF bond energy to display energy curves of optimizations.

r61580: ADFinput: OCCUPATIONS key now sums full shells to avoid problems with the OCCUPATIONS line being too long for ADF.

This is mainly useful for excitations from a core level.

r61567: ADFinput: fix issue with replaced constrained atoms.

r61513: ADFinput: fix crash on missing chain info.

Fixes errors like can't read "data(-,ribbon)": no such element in array

r61452: ADFinput: fix typo in XC help balloon.

r61430: ADFinput: fix the units in the ETS-NOCV panel.

r61386: GUIPrefs: fix Reset Defaults command.

r61380: BAND: avoid crash when /tmp has no write permissions.

This should fix the error couldn't create error file for command: permission denied.

r61347: Bandstructure: Fix default path.

r61319: ADFinput: fix dependencies for fragment jobs when fragment files are explicitly set.

r61273: ReaxFF, ChemTraYzer: Fixed a bug in image generation causing the "can't read widthstring" error.

r61215: ADFinput: make slider input for changing distance or angle have a resolution of 0.1, to make it consistent with info shown.

r61213: ADFinput: fix error with interactive optimizer on Windows.

r61206: Add new debug tool to code

r61155 (September 12th, 2017): ADF2017.108 released

r61154: Bandstructure: Fix exporting to csv and gnuplot.

r61103: ADFinput: NEB and MD via ASE calculations saved with the GUI can now be run from the commandline.

r61063: ADFspectra, ADFmovie: atom labels were not working any more

r61057: ADFspectra: PVDOS spectra with multiple molecules of different sizes would crash

Fixes errors like can't read "data(1,pvdos,9,1)": no such element in array

r61028: ADFinput: fix bond display issue that could happen after using New

Fixes errors like can't read "::Mol::bid ..."

r61017: ADFmovie: avoid problems getting molecule fraction data wirh ReaxFF

Fixes error can't read "molnumber(Iteration)" ...

r60954: ADF: BugFix ZORA SAPA

A bug was fixed for the non-default ZORA SAPA method. In ADF2017 in case of ZORA the ZORA MAPA method is default.

r60935: ADFinput: avoid scrolling crashes when windows no longer available.

Fixes errors like bad window path name ...

r60915: ADF: Remove GEOMETRY from the list of blocks for which the content is parsed to avoid substitution in file names.

r60898: Reaxff: Reduce memory usage by the MCFFOptimizer module.

r60870: Bandstructure: Fatbands uses less memory. In addition, a warning is given to avoid excessive loading times.

r60859: BAND: problem assigning fragment: geometryFragmentGeomCheck: FragmentGeometryCheck failed.

r60822: Reaxff: Increase the max number of restraints to 10000.

r60818: DFTB: Fix a bug that would cause DFTB to hang at the end of a geometry optimization in delocalized coordinates.

r60808: ADFspectra: saving regions in VCD analysis would crash if the .results folder is not present.

r60802: ADFmovie could freeze when resizing while playing and graphs are visible.

r60793: SDF file handling: the rms filtering via RDKit has been changed to ignore H's connected to C atoms. This makes the filter very, very much faster.

r60772: ADFinput: As PZ and lDA are identical, give them one name in QE so they may be mixed.

r60768: ADFinput: make filtering of conformers faster.

r60763: ADF: Bugfix misinterpreting input strings that resemble (but don't exactly match) numbers

r60761: GUI: The GUI will warn and avoid scratch dir names with a blank space. This avoids issues with certain utilities (e.g. PackMol)

r60718: ADFinput: constraints for ADF are not checked and written to the ADF input file when a Singel Point run is requested.

r60714: ADFinput: add Hirshfeld analysis of NOCV results.

r60700: ADFinput: BAND restart DOS option is no longer available

r60697: ADFinput: no Raman in combination with scanning of frequencies.

r60689: GUI: the option to show distances in the molecule window was broken.

r60674: ADFinput: fix dihedral editing when not all selected atoms are connected.

r60637: ADFmovie: stop/pause buttons did not work any more

r60634: ADFjobs: catch problem trying to make a folder without sufficient permissions.

r60624: ADFinput: Builder did not work any more

A line of debug code broke the builder for all users (except the developer ...), fixed.

r60590: Reaxff: Extend the molecule gun.

A NUMADD option has been added to the addmol.bgf file format. The NUMADD keyword has one integer argument that sets a limit on the number of molecules added.

r60570: bugfix ADFinput: slider for geometry changes fixed.

If you would click outside the thumb in the slider for geometry adjustments, it would keep changing the value as if you kept clicking.

r60549: bugfix BAND: restart SCF would fail for some basis sets.

60538: Reaxff: Fix a long-standing bug: the external electric field component entering the EEM equations is now treated properly in eV/A units.

Before this fix, the field was multiplied additionally with the 1/(4*pi*epsilon_0) factor (=332.0638 kcal/mol*A/e^2), which was erroneous in two ways. First, the electric field should already contain the 1/(4*pi*epsilon_0) (=14.40 eV*A/e^2) factor when specified in eV/A. Second, the EEM system of linear equations is solved in the eV units, which means that no conversion from eV to kcal/mol should be done for the EEM right-hand side term due to the external electric field.

60517: Band: big fix: do not compute partial DOS and fat-bands for spin-orbit coupling

Bug Fix band: Band will not compute the partial DOS and fat-bands in case of spin-orbit coupling (it used to calculate those properties, but they were incorrect).

60500: Band: bug fix for hybrids

Fixed a bug that caused band to crash in case of hybrid calculations with large cells (where only 1 k-point is used)

60479: Reaxff: Fix a bug that could cause a segmentation fault for a long and narrow simulation box.

r60454 (July 21, 2017): ADF2017.107 released

60451: Update IntelMPI runtime to 5.1.2, and disable CMA for intra-node communication.

60405: Add SCM_PYTHONPATH variable, which allows users to put their own code into the pythonpath.

r60395: Bugfix in DFTB+Band: Geometry optimization with frozen atom constraints are more reliable

There was a mistake in the code which led to the rigid motions being projected out in optimizations with frozen atoms constraints. This moved the atoms which were supposed to be frozen, causing all kind of problems, e.g. failure to converge at all.

r60381: Bugfix ADFinput: Builder could break molecules added with non-orthogonal unit cells.

r60376: Bugfix ADFinput: fix forcefield check in ReaxFF jobs with frozen atoms.

r60372: Bugfix ADFinput: Export Z-matrix atom numbering should start at 1 instead of 0.

r60363: Band problem with badly normalized charge in a phonon run.

The program would stop with: WARNING: BADLY NORMALIZED AT. CHARGE.

r60310: Fix one cause of slow GUI with poor/misconfigured networks.

r60208: ADF does not calculate VV10 dependent LibXC functionals

ADF can not calculate VV10 dependent LibXC functionals, like VV10, LC-VV10, B97M-V, WB97X-V.

r60199: ADFview: fix saving a picture of contour fields at the highest resolution.

r60160: Bugfix ReaxFF: fix the scaling factor determining the force acting on a charged atom in the electric field.

r60098: 32bit Windows GUI now OpenGL1 compatible, 64bit Windows GUI now build in 64bit mode

The 32bit Windows GUI is now compiled in OpenGL1 compatibility mode. This disables some of the performance improvements introduced into the GUI with ADF2017, but allows for using the GUI on older hardware. The 64bit Windows GUI still contains all the performance improvements (using OpenGL 3.2), and is now compiled in proper 64bit mode.

r60049: Bugfix ADFinput: fixed constraints introduce 1 extra type per element instead of 1 per atom

BAND was running out of types. Also reset the atom type if the fix constraint is removed.

r60042: Try to make the GUI more robust agains virus scanners blocking file deletion

Fixes error messages like: error deleting "W:/SCMTMP/user/cmd185880.err": permission denied from ADFview.

r59992: Bugfix ADF: do not require occupations to match charge key in 12 decimals (now 9).

r59978: Bugfix: allow more time to start up scmd process (on some machines it is slow to start for unknown reasons, probably network related)

r59945: BugFix: scm-ase calculator: replaced NotImplementedError with PropertyNotImplementedError

r59890: ADF-GUI: saving postscript files on arch linux could have zero fontsize.

r59882: ADF-GUI: when showing information via a browser, give a proper error message when no browser found (on linux).

r59848: ReaxFF: added new forcefield file CHOFeAlNiCuSCrSiGe.ff.

r59831: ADFinput: Saving a DRF calculation with manual charges and no charges set will now give a warning instead of crash.

r59815: GUI: visually, parts of bonds and atoms could be missing. Especially when saving high resolution pictures this gave issues.

r59798: ADFinput: fix auto-update toggle for Quild and QMMM jobs.

r59763 (June 13, 2017): ADF2017.106 released

r59762: ADFinput: fix Quild ADF setup: quality should be used instead of integration.

r59748: ADFview: when a result file has been invalidated by resaving a job, still handle it (without re-running the job).

r59736: ADFinput: saving a fragment job sometimes produced wrong job references.

The result was that the fragments did not run automatically, and that fragment files were not found.

r59728: ADFinput: when a fragment file has been specified for a fragment, no fragment job should be created and/or run

This is relevant only when you explicitly select a fragment file to use in the fragments panel.

r59718: ADFinput support KT1 and KT2 GGA XCs.

r59712: ADFinput ReaxFF: molecule gun should not start during non-reactive iterations.

r59710: Reaxff: Save job termination status to the rxkf file.

r59708: Reaxff: Fixed a bug in the unit cell gradients for a non-orthorombic unit cell.

r59706: Bugfix ADFinput: the Spin and Occupation panel did not recognize a t21 with occupation info when non-standard atom types were used.

r59701: Bugfix adfprep: using a template file with gradients turned on in the template file did not work.

r59692: BugFix: Fixed molecular dynamics calculations via ASE.

The driver script for MD via ASE was not updated after we upgraded to ASE 3.11. This effectively broke the MD functionality for Band and ADF. Fixed now.

r59687: ADF: bugfix dDsC dispersion correction for functions it has not been parametrized for

The density dependent dispersion correction (dDsC) was giving errors for XC functionals it was not parametrized for. Now it does calculate a dispersion energy, however, using non-optimized parameters. One can set the dDsC parameters ATT0 and BTT0 with

XC
 ...
  DISPERSION dDsC ATT0=att0 BTT0=btt0
END

r59671: ADFjobs: Running remote on windows with a space in the username could give problems.

r59645: Reaxff: Added a column with the calculation's elapsed time to the logfile (a.k.a. summary.txt).

r59605: Reaxff: Fix a bug writing output.pdb file with complex PDB atom names.

r59587: ADFinput: added the E-Regime option for ReaxFF as a special option for experts only.

r59556: Conductance: Changed the license requirement from DFTB to Utils

r59550: ADFmovie: reading energies from sdf files with adfmovie fix

r59505: ADFinput: remove E-Regime option for ReaxFF as it does not work reliably.

r59502: DFTB: Fixed a crash in DFTB density matrix purification when running on >1 node.

r59463: BAND: Added an option for a charged system. Works only for non-periodic systems. The keyword is simply CHARGE.

r59443: Reaxff: Fix a bug with VdW energy not being added to the total in a single-point calculation.

r59441: UFF: Fixed the hybrid scheme for geometry optimizations.

When the hybrid scheme is used, the nonbonded interactions are excluded at the start and get included once the system is getting close to convergence.

r59431: Reaxff: Change again the way atom names in bgf input are interpreted.

Now element names in either in the two entries should be recognized automatically.

r59424: Reaxff: Save intermediate geometries every iout2 steps during energy minimization.

r59411: Reaxff: Change the way atom names in bgf input are interpreted.

If the 1st name contains a number or an apostroph then it is ignored and the 2nd one is used. Otherwise the 2nd one is ignored, unless it is also more complicated than just one or two letters.

r59403: ADFinput: fix layout of More button in FDE panel.

r59387: ADFinput: allow VCD with Geometry & Frequencies task (as well as the Frequencies task).

r59372: Reaxff: Fixed a bug reading temperature regimes with more than 2 temperature zones

r59310: ADF: Increase the number of MBH blocks to 100 and add a check for when the limit is exceeded.

r59308: Fixed a bug in ppdistrib_area that would cause ADF SCF convergence issues for very small molecules/atoms on multiple nodes (unlileky to happen)

r59293: Fixed a typo in the ReaxFF Readme file for the eReaxFF forcefield file

r59271 (May 15, 2017): ADF2017.105 released

r59257: UFF / GUI preoptimizer: Change the default for computing the non-bonded interactions with UFF to always

r59254: UFF: add General%termination status to the uff.rkf file

r59239: ADF: Restore the printing of Voronoi charges

r59234: Reaxff: fix a bug in the new molecule gun feature that would produce NaNs in some situations.

r59229: GUIprefs: fix ADFjobs status window auto-refresh preference setting.

The preference value was ignored.

r59206: ADFspectra: fix zooming and translating issue with imported (experimental) spectra

r59202: ADFjobs: faster adfjobs loading on windows with antivirus on.

r59200: ADFmovie: reading energies from rkf files went wrong for running calculations.

59195: QE: Detect binaries and pseudopotentials seperately. This allows 32bit Windows users to set up remote calculations by only installing the pseudo potentials. Running QE locally on 32bit Windows is not supported.

59194: FlexMD: changed the input and reference output for the hydroxide example. Two hydrogen atoms were sitting very close together in the old input which can cause ReaxFF issues.

r59191: ADFinput: checkbuttons had wrong font.

r59184: ADFinput: list of frozen atoms for MOPAC calculation was not displayed after reopening saved job.

This issue had no effect on the calculation itself.

r59181: ADFview: when both t21 and t41 are present, t21 is opened by default with the SCM menu (even if the t41 is newer).

This prevents problems after calculating a NOCV charge displacement function (which is saved on t41).

To open a .t41 file: select specifically the t41 file in ADFjobs, and use the SCM menu.

r59170: ADF: Fix the bug in SCF triggered when KeepOrbitals is used together with explicit orbital populations

r59168: Foray: Workaround for a python 3 issue with nfs4 filesystems

The python shutil.copy2 command fails on nfs4 filesystems, which causes the compilation from source to stop.

r59155: ADFinput: saving a fragment job would no longer track certain input options.

r59154: ADF: avoid stack overflow on windows in AOresponse

r59151: ADF/BAND: bug fix for high integration quality

When requesting Lebedev angular integration grids of order > 59, return 59 instead of stopping

r59144: ADF: Make it possible to specify the list of nucleii for analytical frequencies on multiple lines

It is now possible to specify the NUC sub-key multiple times within the AnalyticalFreq block. The lists will be concatenated.

r59132: ADFspectra: less strict xy data parsing.

r59124: mecp: switching to python 3 and resolving bugs.

r59121: FlexMD: Bugfix for the Reaxff2Forcejob module, and a bugfix for restarts.

r59117: ADFinput: fix typo in frequency units.

459115: ADFinput: NEGF needs number of points on transmission energy grid,

instead of number of steps.

r59098: Reaxff: Do not move center of mass to origin during GCMC.

r59078: MacOS ADF application now also gets environment from /Library/Application Support/SCM/scmenv if it exists.

r59071: Reaxff: Print more accurate info when an error in the geo file is detected. Accept crystal lattice parameters in a free format.

r59067: DENSF: Bugfix saving atomic coordinate projections for the NOCV profile. Now they are in the internal order like all other data.

r59065: ADFinput: when adding old style LT-coordinates generate a message when no range is specified.

r59058: FlexMD Added an example for the Reaxff2Forcejob module, which uses named pipes to speed up FlexMD with ReaxFF.

r59012(May 2, 2017): ADF2017.104 released

r59048: re-enable lattice optimizations with ASE.

r58999: MacOS: improve double click on ADF application and its documents.

Double clicking on a document (like a .adf or .t21 file) would open in the GUI, but only when the GUI was not yet running.

And it was impossible to open the GUI by multiple users (on the same mac) at the same time.

r58995: MacOS: fixed dylib reference paths in the pythonstack and openbabel to solve MacOS signing issues.

r58993: ADFmovie: fix the Scale Displacements menu command.

Fixes error message: can't read "gui(DTMvectors)": no such element in array from ADFmovie.

r58987: ADFinput: if installation of QE or LFDFT database failed, ADFinput could run into an error.

Fixes error message: can't unset "installchecked": no such variable from ADFinput.

r58983: GUI on MacOS: remove check that DISPLAY env var is set

The current version does not use X11 on a mac. Nevertheless the GUI would refuse to start on MacOS when the DISPLAY environment variable has not been set. If XQuartz has been installed DISPLAY will be set, so then there is no problem.

r59853: Linux with OpenMPI start script simplification

r58947: ADFinput: change where the i button on the LFDFT panel points.

r58945: ADFinput: properly remove modifystartpotential settings when not used.

If removed (turned off) ADFinput still insisted (incorrectly) to turn on unrestricted.

r58940: ADFinput: less strict SDF importing

r85938: ADFinput: using constraints with BAND for symmetric systems fix

r58934: ADF: Added warning message in case of diagonalization errors in davidson

r58927: ADF: bugfix excitation energies icw SINGLEORBTRANS icw XAS

r58923: ReaxFF: added a new forcefield that uses eReaxFF and ACKS2

r58917: ADFjobs: fix remote fragment jobs

r58914: ADFjobs: make sure error info is updated

r58911: ADFjobs: running jobs with dependencies sometimes would forget the queue information, and old error results were not cleared when started via a dependency.

r58907: ADFspectra: fix domain error when zooming in adfspectra

r58904: ADFjobs: update of error and warning status made more robust

r58901: ADFinput: fix ... button after task in DFTB

It was disabled permanently when selecting the Single Point option.

r58887: ADFinput: compatibility fix with old saved NPT ReaxFF runs

r58884: ADFinput: when saving fragment jobs, make sure they are all saved in the same folder.

In some rare cases the fragment jobs would be saved in a different location (the location of the previous job), causing issues.

r58881: Make Builder work more reliably.

On some systems like Ubuntu the Builder (using packmol) did not work.

r58869: Improve the fix for jobs with dependencies (now a job must have either a job or a run file).

r58863: ADFjobs avoid deadlocks in sequential queue

r58858: ADFjobs sometimes did not update the (error) status of jobs.

r58851: Jobs with dependencies (like the multiple methods tutorial) could in some cases fail to run.

r58851: Reaxff: bugfix for reptx|repty|reptz.

r58846: ADFjobs: jobs could not be renamed, fixed.

r58813(April 13, 2017): ADF2017.103 released

r58812: ADFjobs: job options field could not be edited, fixed.

r58793: ADFjobs: make monitoring and handling of remote jobs more robust

This solves the issue that sometimes remote files were not automatically updated on the local machine.

r58788: ADF: solvent radii for Am-Og

Include somewhat arbitrary default COSMO radii for the heavy elements Am-Og (Z=95-118), equal to 2.1 Angstrom for all these elements, like in r58763, but now in the ADF program. This is relevant only for COSMO and if one does not specify a COSMO radius for such heavy element.

r58766: ADF2017.102 released

r58763: ADF-GUI: solvent radii for Am-Og

Somewhat arbitrary COSMO radii are included for the heavy elements Am-Og (Z=95-118), equal to 2.1 Angstrom for all these elements (in the ADF-GUI). Reason is that such value is better than 0.0 Angstrom. COSMO radii of 0.0 Angstrom may crash the calculation, or give NaNs (not a numbers).

r58755: Lowered GLIBC dependencies for Linux

The compute engines and python stack now require a minimal GLIBC version of 2.4, the GUI requires GLIBC 2.7 or higher.

r58745: ADFjobs job monitoring issue solved

ADFjobs monitoring jobs that take more then 10 minutes lead to scmjobd.exe processes getting stuck (and using one full core continuously).

r58706: ADFjobs improve display of error status

The warning and error messages of jobs were not always shown in ADFjobs, even when warnings or errors were present. This should be fixed. This issue has no effect other then the display in ADFjobs.

r58661: Plasmons in Molecules

In [J. Phys. Chem. C 117 (2013) 1863], a scaling approach was used to identify plasmons in molecules. This is now documented in the ADF manual.

r58634: ADFjobs job monitoring might cause duplicate dependency lines in pid file

Fixed, did not cause any problems.

r58623: ADFjobs monitoring of jobs started via dependencies (like fragment jobs) fixed.

The jobs and dependencies did run fine, but the status (of the jobs started automatically via dependencies) in ADFjobs would not update.

Note that this fix requires your remote ADF installation to be updated as well (this fix is actually on the remote site)!

ADF2017 released

ADF2017 has been released. Please see Release notes for a list of new features and improvements.