Changelog bug-fixes ADF 2012

ADF2012 bug-fixes

r36542: Fix background color for images in HTML reports via ADFjobs

r36316: Fix potential problem with ADFjobs, changes to the options field were sometimes not sticking

r36152: Fix conversion of ReaxFF rxkf files to gromacs trajectories via adfreport

r36127: Add StepSize key for phonon calculations with BAND in GUI

r36110: Bug with band when doing optimization with one k-point

r36077: Mopac binaries updated

r36026: Avoid crash with display of angles in GUI of 180 degrees

r36004: Fix Builder in ADFinput

When using the builder and selecting a molecule via the file select icon, the builder would crash.

r35815: Crystal builder: atoms created in the same position

For some space groups (between 149 and 194) and some wyckoff positions the generated postions were incorrect.The affected groups are 149, 151, 153, 156, 160, 162-166, 177-183, 186-188, 191-194. At the same time the special handling of space groups with the Trigonal-R lattice was reverted (introduced at revision r33879).

r35547: Read ReaxFF lattice vectors after a minimization via ReaxFF

r35508: ADF2012.01d released

r35497: Add an option to store individual covalent bond energies to the kf file

To use the feature, set dumpcb to 1 in the control file. To get a list of bonds at iteration 100 after a calculation, use the following commands:
adfreport reaxout.kf “History%strong bond atoms 100#6d##2”
adfreport reaxout.kf “History%strong bond energy 100#12.5f##1”
The first command will get you atom pairs for each bond and the 2nd command will get you the corresponding energies, in kcal/mol. Which bonds are listed is controlled by the cutof3 parameter in the control file, which specifies the minimum bond order and is equal to 0.3.

r35507: ADFinput: make Crystal menu commands more rubust

Some of them could fail when given without atoms present.

r35436: ADFinput: force use of coulomb fit derivatives (FITAODERIV) when ORD is cacluated with GIAO via AORESPONSE

r35408: ADFinput now update lattice vectors after ReaxFF run

r35369: ReaxFF bugfix for fixed connectivity (iconne not 0) and pi bonds

Fixed a bug in srtbon2 used with non-zero iconne in the control file. This bug would result in incorrect bond order for pi-bonds.

r35361: Fix info for CaSiAlO ReaxFF force field file

Due to a typo this force field file did not show up in the force field menu in ReaxFF GUI.

r35327: ADFlevels: fix hang and interaction lines drawing

Sometimes ADFlevels could end up hanging when selecting a level.

Interaction lines were sometimes incorrectly drawn (sometimes not taking the extended width of degenerate levels into account).

r35321: Reaxff: Fix run-time updates of the rxkf file

Now it should again be possible to watch the progress of a reaxff calculation in ADFmovie.

r35265: Minor change to BAND run script

Now the RUNKF result file is copyied back by the .job script, no longer the .run script.

r35261: Fix SimpleMM license message when using SimpleMM preoptimizer in ADFinput

r35201: BugFix ADF: Restarting QMMM calculations from a file without QMMM restart data.

In such a case, the QMMM will be initialized from scratch.

r35173: BugFix ADF: ORD with numerical integrals

r35146: Fix ADFjobs on Mac OS X Mountain Lion: killing local jobs was broken

r35087: Fix builder (broken in previous fix)

r35059: Fix sequential queue

Sometimes multiple jobs started running, hopefully fixed

r35043: Fix Report Tool for NMR shieldings in ADFjobs

r35040: Fix Prepare Tool in ADFjobs

If the integration option was used, the produced files would have overlapping names (for integragtion 2.0 and 2.5 etc)

The XC potential menu has been fixed: it is different for ADF and BAND. Only the BAND options were shown, thus the hybrids did not show up for ADF calculations.

r34965: Mopac binaries updated

r34960: Do not copy kf file to vels file for ReaxFF restarts

The GUI only supports restarts from the KF result file

r34907: ADFmovie with lattice optimizations in BAND fixed

The lattice vectors history (only in adfmovie) where incorrectly read (transposed).

r34889: ADFjobs click in job-icon fixed

In rare cases periodic systems were opened in non-periodic mode

r34843: ADF: bug fix g-tensor spin-orbit metaGGAs and meta-hybrids

Fix a bug in unrestricted collinear spin-orbit coupled calculations of the g-tensor in case of metaGGA’s and meta-hybrids. Note that still no GIAO’s are used in this case.

r34824: Fix adfmovie window sizes with graphs present

r34780: FIx crash on windows when using the scroll wheel outside a GUI window

r34757: Fix ADFinput BUILDER when selecting molecule with a space in its name

r34747: Try to fix ADFmovie opening logfile when result files are available, and improve resize behaviour

r34679: Add an option to store individual hydrogen bond parameters to the kf file

To use the feature, set dumphb to 1 in the control file. To get a list of hydrogen bonds at iteration 100 after a calculation, use the following commands:
adfreport reaxout.kf “History%strong Hbond atoms XHO 100#6d##3”
adfreport reaxout.kf “History%strong Hbond energy 100#12.5f##1”
The first command will get you atom triples for each hydrogen bond and the 2nd command will get you the corresponding energies, in kcal/mol. In each atom triple, the 1st atoms is the acceptor, 2nd – the H and the 3rd atom is the atom bonded to H.

r34675: ADF, and Band: option to set k3 parameter for D3 dispersion correction

Occasionally the D3 dispersion correction may yield a bumpy potential energy surface. In such cases lowering the k3 parameter will smoothen the surface. The input key is Dispersion%k3. The default is 4, the advised alternative is 3. This effectively defines a new functional.

r34654: MOPAC binaries updated

r34646: Fix (hopefully) adfmovie save movie via ffmpeg

The command line arguments passed to ffmpeg have been changed to make them compatible with the latest ffmpeg. Also, on windwos the default movie type is now .avi, on other platforms .mp4. Note that you can specify the file name with an extension, and that the extension actually determines the file format to be produced (via ffmpeg).

r34579: Check for new version in ADFinput did not work properly (not finding new versions)

r34566: Fix Help menu Rotate and Select items in ADFview and ADFmovie

r34562: The GUI uses now gedit as default editor on Linux

If EDITOR is set in the environment, that editor will be used. Otherwise gedit is the default. If gedit is not found, vi inside an xterm window is the default.

r34542: Use of MetaGGA postSCF option in BANDinput together with MetaGGA XC produced non-working input for BAND

r34499: Use of MegaGGA:revTPSS via ADFinput fixed (gave error when saving the job)

r34444: ADFmovie: fix graphs after Open

When you were viewing a movie with a graph, and then used the Open command to open a different file to view, the graph data was not properly reset. As a result the graph shown was incorrect. This has been fixed.

A minor new feature: when using the Open command in ADFmovie, now all recognized files are listed.

r34443: ESC-key in some GUI modules (like ADFmovie)

In some GUI modules pressing the ESC key caused an error message.

r34436: ADF: bugfix hybrids icw EDIIS

r34403: ADF2012.01c released.

r34402: Fix adfprep -m option with rkf files (from DFTB or MOPAC)

r34357: MOPAC binaries updated

r34345: Fix reading MOPAC results in the GUI when using the MOPAC mozyme option

r34250: Fix running MOPAC from the ADF-GUI for windows

r34245: Reaxff: Bugfix for the change in r34235 and a fix for non-reactive reaxff.

Users who downloaded a r34238 version should update to r34245 or later. The change introduced with r34235 causes rxkf files to be corrupted.

Another fixed bug is related to non-reactive part of reaxff. Without the fix the number of molecules can still change with time. Note however, that even though the bonds identified at the first step of simulation are kept throughout the non-reactive steps, their bond orders do change over time. This means that analysis of molecules based on the updated bond orders may result in molecules different from the 1st step.

r34350: Band: prevent InitialPMat: qqq=0 error.

Some basis sets have empty numerical orbitals. In combination with spin-unrestricted calculations the error message InitialPMat: qqq=0 would appear.

r34235: Reaxff: improve performance of writing the rxkf file during long calculations.

r34160: ADF2012.01b released.

r34149: Fix SCF convergence with ExactDensity

r34108: Fix MOPAC2012 distribution

The MOPAC2012 executable was not included in the distribution by mistake

r33991: adfreport converts .rxkf to xmol or pdb trajectories

The PDB trajectories are an experimental feature for now, feedback and suggestions welcome.

r33879: BAND-GUI: lattice for some space groups wrong

For the space groups 146, 148, 155, 160, 161, 166, and 167 the wrong lattice vectors were used.

r33854: ADF-GUI: bug fix saving .coskf file

r33841: Bugfix NMR: unscaled ZORA spinorbit coupling icw hybrids

This non-default use of unscaled ZORA spinor energies produsced incorrect results for spinorbit coupled NMR icw hybrids.

r33801: Bugfix: stop if a CONSTRAINTS input block is used with the OLD branch.

r33779: ADF COSMO: bug fix Delley surface construction

Fixed a bug that (on some platforms) could cause ignoring of some of the COSMO surface points.

r33736: Bugfix QM/MM geometry optimization.

The energy function during geometry optimization contained the MM energy twice. This has been fixed now. The bug existed in all ADF versions.

r33728: bugfix for band NMR single-dipole calculations

Any calculation done with the NMR single-dipole method with more early band 2012 versions should be considered wrong. For NMR supercell method there is now an option that will make the result independent of lattice translations of the NMR atom, so that the user does not need to worry whether or not the probed nmr atom is central in the unit cell.

r33723: Mopac updated to MOPAC2012, PM7 and PM7-TS added in the MOPAC-GUI

r33684: When using DFTB parameter sets that need to be enabled in your license, warn about this in the GUI

The DFTB.org parameters need to be enabled explicitly in the license file. Currently by default they are not.

Now the GUI will warn users of the problem.

r33552: Running ADF or any other computational task will now prevent Windows from sleeping.

r33548: ADFinput fix multiple marquee selectons

When making a slection by dragging a rectangle (with left mouse and shift key), doing this again will now extend the selection with the new items (as it did in ADF2010).

r33499: CIF file importer error (operators could be wrong).

In some cif file the translational part of the operators is given as a floating point number rather than as a fraction. This was not properly recognized.

r33463: ADF: removed incorrect warning for SSB-D functional

When using the SSB-D funtional this incorrect warning appeared— WARNING: Unknown GGA used. Dispersion added with factor 1.0

r33427: ADF: bug fix COSMO spin-unrestricted TDDFT excitations

r33422: Start ADFjobs via command line did not use proper module for t21 files

The t21 files now are opened in ADFview, not in the KFbrowser, when giving them as cmd line argument to adfjobs.

This should also fix opening by drag-and-drop on top of ADFLaunch.

r33392: Some ReaxFF force fields have been updated/corrected

The …-water force fields have been renamed to …-H2O, some force fields have additional elements (based on the references shown). The old NiCH force field contained also parameters for other elements, but the origin of these parameters is not known. So it has been moved to undocumented, and the new NiCH force field has only the Ni C H atoms, matching the references.

r33364: Bugfix for band AIM calculation: all electron or too many critical points.

The GridBasesAIM keyword did not work when there were no frozen core electrons. The AIMBondPaths keyword did not work when the number of critical points exceeded 128.

r33355: CIF file importer error when lattice angles not 90 degrees.

The lattice vectors were wrong when not all angles were 90 degrees.

r33333: In ADFspectra the units in the popup balloon for match the units selected by the user (for the X axes)

r33327: Fix final energy reported by SimpleMM in ADFinput

r33320: Add information in lgofile when ReaxFF runs in serial mode due to small system size

r33291: Fix reading .coskf and other non-t21 files in ADFview

ADFview would present an error about ::t21::nProperties

r33256: Fix reading .adf files for protein data

Fix the “can’t read “data( C,ribbon)”: no such element” in array error

r33149: Diagonalization error

During a geometry optimization with constraints the diagonalization of the Hessian could fail in a low level routine DSTEGR2A.

r33093: Fix the warning about a senseless unrestricted run

It actually might make sense to have spin polarization 0 when specifying occupations.

r33078: Fix ESR.EPR menu in ADFinput

Selecting None did not do anything, and some consistency checks have been added

r33072: Fixed Laplacian value in the AIM critical points output.

r33068: Fix crystal structures for Perovskite and NiAs (lattice parameters were wrong)

r33019: Keep more precision in lattice vectors when removing noise

r33012: ADF: bug fix NBO analysis unrestricted

Bug fix in writing Fock matrix on AOs for beta spin.

r32999: ADFinput: Fix Set Center Cell

For periodic systems you can translate the system with respect to the cell. This was broken.

r32964: Bugfix cif importer

Some CIF files have multiple DATA elements. The importer searches for the first one that contains atoms.

r32943: Bugfix ADFinput when making an ADF input with periodic bonds

If you first make a crystal with bonds across unit cells (using the BANDinput mode), next switch to ADFinput, the resulting ADF job script contains a malformed GUIBONDS key. This causes ADF to crash. A work-around is to delete the GUIBONDS block key from the run script.

r32906: Bugfix ADFmovie reactivate window with logfile visible

r32853: Bugfix ADF bond energy analysis for metaGGA and metahybrids

Fixed a bug in the bond energy analysis (EDA) for the Pauli term in case of metaGGA’s and metahybrids, which could result in large numbers. The final bond energy was correct.

r32839: Fix the ADF optimizer: Quild option in ADFinput

r32836: ADFinput Scanfreq now included with a geometry optimization, followed by frequencies

r32828: BANDinput should allow empty fields for most options

After making it non-empty the user was unable to make a field empty again.

r32815: Fix Cristobalite lattice paramter in the BANDinput crystal builder

r32805: Fix deleting periodic selections in BANDinput

In some situations deleting atoms in a periodic system could break the GUI (non-existent bonds were deleted).

r32797: Fixed errors in ReaxFF forcefield files.

Errors in the following forcefield files have been fixed: AB, CHO, ZnHO. ReaxFF users who run calculations with these forcefields should update their ADF distribution. The errors in AB and CHO forcefields mainly deal with hydrogen bonds, which is probably not that important in the systems for which these forcefields are targeted. The errors in the ZnHO file were more severe so one should repeat their calculation using this forcefield.

r32792: Fix bug in making a scratch dir in GUI

r32773: ADF COSMO: ignore problematic points in Delley surface construction

Instead of stopping of ADF, ADF will now print warning messages like: “WARNING: COSMO delley program error …”, and ignore problematic surface points in the COSMO Delley surface construction.

r32760: Fix detection of clicks on bonds in GUI

In rare cases, a click on a bond would select a different bond.

r32744: Fix ADFMovie Save Movie Coordinates for big systems

r32736: Bugfix ADFview bondcolors with multiple files open

r32730: Bugfix in ADFview user interface code

r32701: Fix reading .adf files for periodic systems (incorrect bond information)

Use GuessBonds if you are opening an old file that still gives troubles.

Note bonds are not used in the calculations (they are for display only)

r32698: Fix display of periodic frequencies

r32685: BANDinput no longer writes DIIS and CONVERGENCE blocks, and dependency left at default value

r32634: Fix bonds after mapping back to unit cell

r32629: Fix undo/redo for periodic systems

r32624: Fix import (or paste) of periodic structures

Now the lattice vectors are correctly pasted for example when copying a structure out of a BAND-logfile.

r32619: Fix ADFmovie reading of logfile

For periodic systems, when reading a logfile of a calculation where the lattice was optimized: only the lattice vectors for the last iteration were used.

r32616: Fix coordinate-editing bug in ADFinput

The bug was introduced in r32444

r32555: Fix saving ex-periodic structures in ADFinput in ADF mode

If you have a periodic structure first with bonds between cells, and then switch to ADF, you could not save the run script. This has been fixed/

r32538: Fix select commands in ADFinput for periodic systems

r32500: Fix SMILES pasting in ADFinput

r32468: Fix ADFmovie bug: startup flashses, and now properly desplsy the regions

r32455: Fix ADFmovie bug: chaning the periodic repetition left ghost atoms

r32444: Fix update problem of the coordinates panel in ADFinput

r32403: Fix atom reordering bug in ADFinput

r32373: Fix slow update of ReaxFF jobs in input after minimization

r32313: Do not show stderr output when a job has been killed

r32296: Fix display of Cube files in ADFview

r32283: BugFix ADF: Cm.4f atomic basis set

The input file Cm.4f for the auxiliary program dirac, which calculates the frozen core potential for the basis set Cm.4f has been fixed.

r32262: Fix ADFdos: fermi level was wrong after unit change

r32256: Fix bug in ADFlevels when after changing the units opening or adding more stacks

r32252: Fix bug in ADFmovie when saving a mp4 movie

The first frame would contain the wrong atom positions. This has been fixed, and now also the gradient background is retained.

r32233: Fix display of lattice vectors when switching between periodic and non-periodic mode in ADFinput

Another bug fixed is where switching could cause drawing problems when the selection was not empty.

r32228: Changed dependency criterion default for band

The basis set dependency criterion was changed from 1e-5 to 1e-8, thus avoiding often encountered (unneeded) dependent basis errors.

r32227: Bugfix for CIF reader

There was a problem with short loops that had a string value at the same line as the key.

r32195: Fix display of Amber types in Atom Details in GUI

r32192: Fix GUI (bug introduced in r32180)

r32190: Fix BANDinput

It was impossible to save a BAND job with the GUI.

r32187: XC Dispersion: possibility to set PAR to zero

There was a bug in ADF for parsing of Grimme DFT-D3 correction parameters: when a parameter was explicitly set to zero, ADF incorrectly replaced it with the PBE value. This has been fixed. This can be a problem for the Minnesota M06 family where the s8 parameter (PAR3 in ADF) needs to be zero. Setting it to 1e-99 is a workaround.

r32180: No more new-style LT for band (via ntransit in constraints)

r32177: Linear Transit preset for Band removed

r32151: Bugfix display of Wigner-Seitz cell

ADFview offered to display the WS cell even if the data for it is not available. When a users used the menu, ADFview would crash.

r32144: Bugfix ADF: icosahedral symmetry number for thermodynamical analysis included

r32106: ADF2012.01a released

r32102: Fix hanging ADFjobs when running in background, introduced in r31915

r32087: ADFView: bug fix NBO analysis unrestricted

r32078: ADF: g-tensor common gauge collinear spin-orbit metaGGAs and hybrids

Unrestricted collinear spin-orbit coupled calculations of the g-tensor in case of metaGGA’s and hybrids and metahybrids now uses common gauge, which makes them dependent on the origin of the molecule. Thus the GIAO formalism for the unrestricted collinear spin-orbit coupled calculations of the g-tensor is only implemented for LDA and GGA’s. Note that the g-tensor calculation that perturbatively includes spin-orbit coupling does use GIAO’s for hybrids (and LDA and GGA’s).

r32065: ADFjobs: remove the rest job info command

r32054: Bugfix remote jobs monitoring for windows

r32048: ADF bug fix unrestricted spin-orbit coupled hybrid calculations

Fixed a bug for unrestricted spin-orbit coupled hybrid calculations in the collinear and noncollinear approximation. This bug still exists in older versions of ADF.

r32014: Bugfix ADFjobs; fix calculations using restarts

r32012: Bugfix ADFinput: frequency jobs for some dispersion corrected functionals were incorrectly refused

r31972: Bugfix ADFjobs for fragment calculations on remote machines with explicitly specified fragment files

r31969: Bugfix HF exchange

Communicate the amount of memory between nodes to make sure all nodes calculate the same number of passes

r31944: Fix visualization of MOPAC results

r31930: Bugfix ADFjobs: renaming or deleting jobs could crash ADFjobs

r31915: Bugfix ADFjobs: on remote machine tail processes could be left-over

r31909: Bugfix: when reading a .xyz file with lattice vectors in non-periodic mode, ADFinput should stay in non-periodic mode

r31869: Bugfix: Disable automatic electron smearing in case of excited state optimization

r31855: Fix bug when transfering files from remote machines

The transfered files could end up in the home directory instead of the job directory.

r31814: ADF analytical second derivatives: fix origin dependence IR intensities

r31794: Fix GuessBonds for periodic systems other then bulk (chains and slabs)

r31789: ADFmovie bonds in first frame were based on coordinates of last frame

r31778: Bugfix ADFmovie/ADFinput after transfer of coordinates

When using the transfer coordinate feature (where you push the coordinates of some selected frame in ADFmovie to ADFinput), the bonds could be wrong in cases of periodic systems when molecules cross the unit cell boundary.

r31774: GUI periodic implementation

This is a significant rewrite of the code that handles periodic details, both for setting up jobs and for visualizing results. For the user the effect is that display of periodic systems is much faster, bonds between periodic cells are now visible (created by GuessBonds), and many bugs have been fixed that had to do with periodicity.

A minor detail is that for more atoms colors have been defined, and the default color has changed. If you do not like the new colors, you can change them via the Preferences (in the SCM menu).

r31757: ADFjobs remote job monitoring with bad connections

When you have internet connection troubles while running a job, the .pid file could disappear. This should be solve (but is hard to test…).

r31722: ADF bug fix parallel unrestricted spin-orbit coupled hybrid calculations

Fixed a bug for unrestricted spin-orbit coupled hybrid calculations in the collinear and noncollinear approximation, in case the calculation was performed in parallel. Note this bug is fixed only in ADF2012 and the development snapshots. This bug still exists in older versions of ADF.

r31710: Fix ADFjobs remote job monitoring

After the previous fix, tail commands could still be around after a job has finished.

r31704: Band/periodic-DFTB – symmetry detection

The program occasionally detects a too low symmetry. With lattice vector optimizations this could lead to the error: mode break symmtry.

r31700: ADF analysis hybrid excitation energies: avoid negative MO→MO contributions

Slightly modify analysis of Mo→Mo contributions for TDHF, such that no negative contributions appear.

r31692: Minor fixes for ADFjobs remote job monitoring

r31685: Fix ADFjobs job monitoring issues

r31673: ADFmovie had trouble with logfiles of big molecules

r31665: ADFjobs job error status often was lost, typically after quitting ADFjobs

r31653: ADFjobs job monitoring could be confused after kill

r31644: MOPAC binaries updated to the latest available from OpenMOPAC

r31624: Fixed a bug in ETS-NOCV with hybrid XC functionals

r31618: bug fix ADF excited GO and input amount of Hartree-Fock exchange

For hybrids it is possible to change the amount of Hartree-Fock exchange in the input.

XC
  Hybrid B3LYP HF=0.25
END

However, for excited state optimizations, the HF percentage was not recognized, and an error messaage was produced: ‘Error in SetHybridStrings: kernel of this hybrid functional not available’. This has been fixed.

r31606: Fix typo in reading of RKF files

r31602: Fix ADFmovie Open menu (would still show traces of previous molecule)

r31596: Fix Molecule visualization style (Balls&Sticks) menu command

Often the main menu did not work properly, fixed. The alternative of changing the molecule view option via the regions details was not broken.

r31591: When visualizing .rkf files (from DFTB for example) the lattice vectors were read transposed

Thus for periodic calculations with DFTB or UFF the lattice vectors were incorrect in the visualization of the results if the lattice vectors are not symmetric.

r31582: Fix Band/dftb lattice optimization bug

The program might stop with: check idempotent too bad. This occurred for systems with a non symmorphic space group.

r31567: Fix GUI license problem when licence file contains expired options

The most common occurance will be if your MOPAC license is expired while you still have a valid license for other GUI modules.

A work-around is to delete the expired license targets manually from the license file (remove also the encrypted lines for these targets, otherwise your license file will be corrupt).

r31537: Fix PVDOS in ADFspectra

r31528: Bug fix in ADFspectra for FCF visualization

ADFspectra required a .t21, .runkf or .rkf extension when opening a file. This requirement has been removed, so users can now easily open a result from from an FCF calculation.

r31514: Important bugfix in shared arrays

ADF may hang due to a deadlock in situations when running in parallel on multiple nodes. The deadlock occurs when some nodes have only one process of a job running while other nodes have more than one process from the same job. The case when all nodes have either multiple processes or a single process from the same job running is not affected by the bug.

r31505: fix bug in Mopac visualization

A tool to read the Mopac results (tokf) was not properly included in the distribution. As a result, visualization of Mopac results did not work.

r31491: GUI slicer minor bug fixed

When slicing a crystal, making a slab, the resulting atoms would have their number of connectors reset to 1. This has only effects on the visual display of slabs.

r31471: Bandstructure: show K points fixed

r31410: ADF: 2 examples added for non-self-consistent Green’s function calculations

Two example .run files for the use of the green module (non-self-consistent Green’s function method) are added in $ADFHOME/examples/adf/green_Al.

r31403: GUI: add Cancel option when using the New command with ADFinput

r31330: GUI: add Cancel option when quitting ADFinput

ADF2012.01 released

ADF2012.01 has been released. Please see Release notes for a list of new features and improvements.