# Changelog bug-fixes ADF Modeling Suite 2012

### 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).

# 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.

### 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.

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

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

### r35059: Fix sequential queue

Sometimes multiple jobs started running, hopefully fixed

### 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.

### 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.

### 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.

### 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).

### 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.

### 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.

# r34403: ADF2012.01c released.

### 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.

# r34160: ADF2012.01b released.

### 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.

### 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.

### 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.

### 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.

### 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

### 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.

### 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

### 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.

### 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.

### r32828: BANDinput should allow empty fields for most options

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

### 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.

### 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.

### 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)

### 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/

### 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.

### 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.

### 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.

### 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.

# r32106: ADF2012.01a released

### 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).

### 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.

### r31969: Bugfix HF exchange

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

### r31855: Fix bug when transfering files from remote machines

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

### 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.

### 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.

### 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).

### 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.

### 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.