Changelog bug-fixes ADF 2013

ADF2013 bug-fixes

r42814: Bugfix handling some MOPAC result files

Sometime MOPAC does not write the SCF symmetry labels to the result file. This caused problems when reading the result file by the GUI, for example ADFmovie would then not work properly.

r42367: Bugfix mol2 import in ADFinput

The import would crash when some special mol2 bond types were used (nc, un, …)

r42156: Added a SPACING parameter to the BADER keyword in ADF.

The parameter specifies spacing of the initial grid in Angstrom, for example:
BADER Spacing=0.1

r42030: bugfix ADFmovie

Clicking in graphs sometimes could lead to errors

r41780: bugfix KFBrowser

When showing sections with an extreme amount of information in one section (more then 1 GB) the KFBrowser would crash

r41755: bugfix for ADF-GUI startup

The ADF-GUI package did not properly handle SCMLICENSE when it is defined in your shell startup script.

r41607: bugfix for importing cif files

Some cif files define the contents of a loop on a single line, as a result the import would fail.

r41525: bugfix for revPBE functional in band

When using the revPBE functional, the program would print in the logfile and RUNKF file the PBE rather than the revPBE energy. The correct energy can be found in the output in the Energy section. One can also see in the same section the PBE value used in the logfile and RUNKF file.

r41490: bugfix GUI: adflevels could read wrong SFO contributions

Sometimes (especially when using the degeneracy key) ADFlevels did not read the contributions properly, leading to either a crash or strange interaction lines.<h3

You can now force this index to be in the location you like using the SCM_DOCINDEXDIR environment variable. This is mainly useful for use with central installations with many users, then the index may be put on some shared disk. Either set SCM_DOCINDEXDIR in your shell, or use the GUIPrefs Environment tab to set it. Obviously the first time the user needs write permission to create the index.

r40851: bugfix GUI: color of labels next to color bars were not properly updated when chaning (via info style)

r40783: bugfix GUI: colors of atoms with special types (C.Region_1 etc) were not displayed correctly

r40782: bugfix dmpkf/udmpkf to avoid problems caused by huge integers

r40694: bugfix GUI: coloring of atoms by scalar value was broken

r40639: bugfix reading MOPAC frequencies results with MOZYME option activated

r40589: bugfix spin and occupation panel in ADFinput

Switching unrestricted option and running a guess again would cause a crash

r40553: bugfix for importing cif files containing element names with quotes

r40476: bugfix for periodic DFTB, leading to inaccurate results

When using more than one k-point with big unit cells, the results were inaccurate leading to for instance bad phonone curves.

r40456: bugfix for EFG in band, the printed values for Vzz and Eta could be wrong

r40291: Added the missing libiomp5md.dll library needed to run MOPAC2012 on Windows

r40265: bugfix for adf unrestricted calculation of transferintegrals (print FMATSFO)

r40239: bugfix for adf beckegrid for alternative elements with partial nuclear charges smaller than one

r40205: fix running densf job via ADFjobs (via the progress dialog in ADFview)

r40118: fix the option to hide distances in the GUI

r40108: bugfix for band and periodic dftb

Sometimes the error lattice displacement breaks symmetry occurs usually due to inexact coordinates. Even when disabeling symmetry the error persists. This has now been fixed.

r40040: bugfix for band, NaN in bond energy

Sometimes the printed bond energy would be NaN. This was due to small negative densities in the calculation of the atomic reference inergies in the molecular grid.

r40025: Bugfix unrestricted NOCV deformation densities: beta component did not work properly in adfview

r40009: ADF2013.01d released

r40005: bugfix adfjobs: Generate Test-Job did not show test job in global list in adfjobs

r39999: bugfix nbo6: allow for the nbo6.exe full path name to be longer than 80 characters, which should solve the NBO execusion problem on the MacOS X

r39953: bugfix GGA and analytical frequencies

An issue has been resolved that would sometimes lead to CPKS non-convergence during analytical frequency calculations with GGAs.

r39946: bugfix adfreport: pdbtrajectories did not correctly read molecule info from rxkf result file

r39895: bugfix adfinput: bonds disappeared for periodic structures when changing periodicity

The bug had effect only on the display in the GUI, not on any calculation result.

r39568: bugfix uff, problem with periodic structure geometry optimization.

r39471: bugfix for band dispersion corrected calculations on molecules (nonperiodic).

r39399: Workaround bug spin-orbit part ADF2008 – ADF2013

In the ADF2008.01 a bug was introduced in the spin-orbit part of the calculated chemical shielding, which caused the calculated chemical shielding to be gauge dependent. This bug is relevant for spin-orbit coupled calculations for ADF versions ADF2008-ADF2013. The workaround with ZSOAO2007 is now the default. To get the (wrong) gauge dependent results back, use NOZSOAO2007 in the input for nmr.

r39199: ADF2013.01c released

r39197: Fix typo in bond detection in GuessBonds

Bug spin-orbit part ADF2008 – ADF2013

In the ADF2008.01 a bug was introduced in the spin-orbit part of the calculated chemical shielding, which caused the calculated chemical shielding to be gauge dependent. This bug is relevant for spin-orbit coupled calculations for ADF versions ADF2008-ADF2013. Workaround is to include the keyword ZSOAO2007 in the NMR part of the input:

ZSOAO2007

r39028: Update MOPAC binaries

The MOPAC binaries now match the binaries from the OpenMOPAC web site of October 29, 2013. Most importantly, the linux version is statically linked, which should resolve problems running on recent linux systems.

r38906: ADFinput fix bug with Occupations panel

If you would have moved ADFinput off the (main) screen ADFinput could crash when trying to show the Guess results

r38896: ADFinput should respect saved DFTB setup when reading .adf file

r38819: BANDgui: fixed lattice constant of GaN

The wrong value was 5.45 and changed it to 4.52.

r38603: ADFview color of labels next to color bars

Now if you change the Info Color the labels next to the color bars will also be adjusted

r38585: bug fix open shell calculations with NBO6

Depending on the platform, the NBO6 calculations of open shell molecules could produce wrong results.

r38583: GuessBonds improved

A minor change has been made to the routine in the GUI that determines bonds, to make sure H-H and similar diatomics are bonded.

r38561: fix permissions problem

r38447: make Mopac aux file parser more robust

When very big numbers were present in the MOPAC aux file, they are not separated by spaces. This broke the parser that converted the MOPAC aux file to rkf.

r38402: bugfix for adfinput pasting non-periodic stuff in periodic stuff

Now you can copy your molecule and paste it on top of a surface, for example.

r38376: bugfix for band, NaN in Hirshfeld charges

r38373: bugfix for band when using the pw91 potential

When using the Perdew-Wang 91 xc functional there could be a numerical issue. The program would either stop after the first SCF cycle.

r38359: Remove requirement of the GLIBC version 2.7

At some point in the past a call to the sscanf C library function was added. After upgrading the build machine to CentoOS 6 this resulted all binaries requiring the minimal glibc version 2.7. This has been fixed now and the minimum required glibc version should be 2.3 again.

r38281: ADF2013.01b released

r38277: fix reading preferences for first-time users (leading to error when starting scmd for the GUI)

r38273: ADF improve output excitation energies with perturbative inclusion of spin-orbit coupling

More output options are included for excitation energies that are calculated with the perturbative method for inclusion of spin-orbit coupling, that can be used for a closed shell ground state.

SOPERT
RELATIVISTIC SCALAR ZORA
EXCITATIONS
END
PRINT SOMATRIX

If one includes PRINT SOMATRIX the spin-orbit matrix on basis of singlet and triplet excited states will be printed. On the diagonal the singlet or triplet energies is added. The spin-orbit matrix has a real and imaginary part. This spin-orbit matrix is the one that is diagonalized to get the spin-orbit coupled excitation energies.

GSCORR

If one includes GSCORR the singlet ground state is included, which means that spin-orbit cupling can also have some effect on energy of the ground state. The spin-orbit matrix in this case is on basis of the ground state and the singlet and triplet excited states.

r38205: fix check for numerical frequencies for some metaggas when running frequencies after the geometry optimization

r38155: scmd process now reads GUI prefs for environment

Note that if you make changes to the environment via GUIPrefs (SCM -> Prefs) you need to quit the full GUI, make sure scmd is no longer running, and then start a GUI module again.

r38149: MOPAC binaries updated (to the version of MOPAC on Aug 1, 2013)

r38063: bugfix for band bulk jobs with a long axis

The norms of the functions (especially core functions) would be inaccurate and the program would stop with FROZEN CORE SEEMS TO BE TOO LARGE.

r38044: Reaxff: specifying total system charge via geo file is now possible

A total system charge specified via the MOLCHARGE key in the geo file is now treaded correctly. This is done for compatibility with geo files used for forcefield fitting. Before this change, only the value specified by the syscha key in the control file used.

r37971: bugfix band: COSMO with spin-polarization

It was not possible to run COSMO with the spin unrestricted option. The error would be: ERROR DETECTED: BlockPropertyModule: inconsistent dimensioning for var rho.

r37966: bugfix for lattice optimizations with band and periodic DFTB

The program might stop with ERROR DETECTED: CheckIdempotentMatrixModule: too bad. Also not all lattice displacements might be found.

r37959: bugfix NMR analysis scalar ZORA

r37907: bugfix ADFjobs for jobs with spaces in their name

r37897: bugfix for band COSMO calculations

When applying COSMO to a slab with the RemovePointsWithNegativeZ option, sometimes the solvation energy could be way too large. Another issue that was solved that the cvec=fitpot option was restored.

r37886: ADFinput: write pressure for ReaxFF to control file with 12.6 format

Note the input is not compatible with older ReaxFF executables.

r37856: ADFinput: units of pressure in ReaxFF are MPa (not GPa)

r37830: bugfix adfprep: did not work for dftb jobs

r37819: bugfix adfreport

When using adfreport via the command line, the generic key energy would not report the energy from a .rkf file written via MOPAC.

37762: bugfix band: NMR single-dipole method (with the correct_r option)

When doing a NMR calculation with the single-dipole method the resulting shielding would be nonsensical (NaN).

37744: bugfix band: NMR2MatrixEvaluatorModule::dk/dBas

When doing a NMR calculation with the single-dipole method the program could stop with a technical error, triggered by inconsistent handling of the sparseness of functions. The results of calculations that did not trigger this error will not be affected by this bug fix.

r37736: revision ADF example Franck-Condon factors

In the example $ADFHOME/example/adf/FranckCondon_NO2 the open shell molecule Nitrogen dioxide was treated as if it was closed shell, and the closed shell molecule Nitrite as if it was open shell. This has been fixed.

r37727: bugfix ADFjobs remote jobs directory

The remote jobs directory was sometimes not determined correctly.

r37724: bugfix ADFjobs

Procces ID number from the script starting remote jobs could appear in the error output, leading to a wrong job status.

37705: Performance band: improved SCF convergence

An adaptable scheme has been devised to determine on-the-fly the SCF%mixing and DIIS%DIIS parameters based on the observed SCF behavior. Before these two parameters had to be tweaked by the user. To disable set DIIS%ADAPTABLE to FALSE.

r37687: ADFjobs: unset NSCM before starting local job

The NSCM value from your environment will be ignored (even if defined via the GUIprefs).

r37685: bugfix GUI: showing hidden bonds (unhiding them) was broken

37673: Performance band: restart SCF during geometry optimization when possible

During a geometry optimization the starting guess can be based on the solution of the previous geometry. Due to an error this did not become active in the first but in the second geometry step.

r37672: COSMO-RS: improve convergence solubility calculations

r37669: Bugfix band: nmr crash on windows and mac

NMR calculations could crash due to the limited stack size. Also a part of the code was made parallel, speeding up nmr calculations when using more cores.

r37661: Bugfix ADF DIM/QM: force field file was not in distribution

An error could occur like: DimQMReadCOORDParameters:ErrorOpening..adf2013/adf/dimqm/forcefld/vdWParameters.ff. The vdWParameters.ff file has now been moved to $ADFRESOURCES/atomicdata/ForceFields/dimqm/vdWParameters.ff.

r37649: Bugfix ADFinput: Atom dependent Becke integration key weak should be basic

r37646: Make cleanup.cmd script more error proof

r37637: Bugfix ADFjobs job archiving, removed job import/export

On windows the job archiving, and job import/export did not work. This has been fixed for job archiving, for now the the job import/export options have been removed.

r37618: adfreport and adfprep no longer require a GUI license

r37597: Fix ADFinput raman range option

In the input for ADF the RESPONSE block was always added, but it is not always needed.

r37594: Change limits for the max number of SCF and geometry optimization steps

The default max number of SCF steps has been increased to 300. For geometry optimization the max number of steps is set by default to max(30,2*Nfree), where Nfree is the number of free variables. The typical value will thus be equal to six times the number of atoms.

r37579: bugfix GUI: termination status on TAPE21 properly handled

If ADF ended with an error exit the GUI would crash on trying to read the resulting TAPE21 file.

r37564: bugfix RamanRange feature in ADF: mark the a1 irreducible representation as active.

r37553: ADFinput: add check against mixing LT constraints with Frequencies/IRC/TS runs

r37539: Bugfix ADFinput: New command could fail if Restraints panel was visible

r37532: ADF: possibility to use ADF2012 settings for HF exchange

In ADF2013 use is made of distance cut-offs for the calculation of the HF exchange integrals. By default the cut-off criteria for the use of distance effects in HF exchange integrals are automatically made more strict if a higher numerical integration accuracy is chosen. Included is the possiblility to set manually the distance cut-off threshold for the calculation of the HF exchange integrals. A value of 99 for hffit virtually excludes the possibility that something will be neglected.:

LINEARSCALING
  HF_FIT hffit
END

In the simplest application of the LINEARSCALING keyword, if only one parameter is provided, hffit will get the value of linscal:

LINEARSCALING linscal

Note that ADF2013 also has a new default numerical integration scheme. The Voronoi numerical integration scheme, that was default in ADF2012, will be used in ADF2013 if one includes the key NOBECKEGRID.

r37519: Bugfix ADFview: when started via ADFlevels the grid could not be changed

r37503: ADFspectra handling of FCF improved

Now if after the calculation of Franck-Condon factors you have an FCF spectrum on a t21 file that also contains other spectra, the other spectra are also available in ADFspectra.

r37494: Bugfix B95 functional

There is now a shortcut for the B95 metagga functional (for correlation) with:

XC
  MetaGGA B95
  xcfun
END

This means the Becke88 functional icw with B95c correlation. This functional could already be used with:

XC
  MetaGGA Becke88 B95c
  xcfun
END

r37491: Fix ADFSpectra repeated activation of NMR spectra

r37487: Fix SCM Input command

In ADFjobs, the SCM→New Input command always starts a new empty ADFinput.

In other GUI modules, the SCM→Input command opens the current job in ADFinput (the matching .adf file). To reflect this changed behaviour, the name of the command has changed. When the GUI module does not have a file open yet, the SCM menu will still have a New Input command that starts a new empty ADFinput

r37475: Bugfix ADFinput for DFTB phonon runs

If you specified the stepsize or interpol parameters for a DFTB phonon run, the input was incorrect (missing =).

r37461: Bugfix ADFjobs remote jobs directory

When running remote jobs with ADFjobs, all remote jobs would be stored in the same remote job directory, which was determined by the first remote job running per ADFjobs session. This behaviour is incorrect, if you are saving jobs in different directories. The remote job directory is now properly determined per job.

r37451: Bugfix job monitoring

Job monitoring was confused when the ps command gave output on stderr (for example when remote system is a Mac with Mountain Lion, and DYLD path adjusted).

r37440: Bugfix band: reduce memory usage in initial phase

For bulk systems with a long unit cell one could get a memory allocation error.

r37438: Bugfix band: symmetry issue with phonon calculation

At the end of a phonon run, the program might stop in the symops routine: TRANSLATION ERROR. SYMOPS.

r37407: Bug fix ADF: Bader atomic energies Hartree-Fock

r37403: Bugfix running remote jobs

Fix job monitoring for remote jobs, fixing leftover processes for some users

r37400: Domain-wide license files can now also be used under Windows

Customers with a site license can now also use their domain-wide license file on Windows. Separate entry for each Windows machine is no longer necessary. For the domain-wide license to work, all of the following conditions must be satisfied:

  • the netbios name of the machine matches its hostname in the DNS domain for which the license file is issued,
  • the computer is connected to the network, and
  • the computer specified as a DNS server on the Windows machine is reachable from it.

r37393: Change (increase) numerical precision used within GUI modules

As a result real numbers displayed in some GUI modules may be different (not in ADFinput, and only after 6 digits).

r37390: Fix opening GUI reference manual via Help menu in ADFspectra

r37368: Bug fix ADFview when plotting unrestricted BAND orbtials

r37362: Bug fix ReaxFF: allow more than 9999999 MD steps

The number of MD steps specified must still be less than 231=2147483648

r37313: Bug fix ADFinput for BAND accuracy

When the Becke grid was used the overall accuracy parameter was missing.

The help info has been adjusted to make it clear what the value of the overall accuracy parameter will be when using the Becke grid (or the teVelde grid).

r37285: Bug fix deleting too close atoms after guessing bonds

r37272: Bug fix conversion of MOPAC results to RKF

For bigger systems the conversion of the normal mode labels would fail

r37243: Bug fix conversion of cube files for visualization in ADFview

r37239: Bug fix exporting cube files from ADFview

r37212: Update MOAPC executables

2013-04-24: Fixed an issue with the license code ignoring a network card if it is not connected to a network.

r37172: Bugfix deadlock in long linear transit optimizations with constraints.

An issue was resolved that could lead to a deadlock in a long linear transit calculation for a medium to large molecule

r37101: Bugfix band: spin-unrestricted calculations failed with the direct option

The program would stop with ERROR DETECTED: kfrdnr: Attempt to read too many reals basis%H(VOC/VOC). This would occur when doing a spin unrestricted calculation in combination with either the so-called direct option, band interpolation or the effective mass option.

r37145: Bugfix Builder in ADFinput

When you have a non-orthogonal cell in the Builder then newly added atoms were mapped back into the cell. Next, they were too close to other atoms and stuff was deleted, leading to problems. Now the newly added atoms are not mapped back into the cell (that should not have happened anyhow).

r37125: Avoid errors in ADFlevels when handling MOPAC results

r37122 Fix ADFlevels license check, now MOPAC with ADFlevels needs only MOPAC license

r37101: Bugfix band: TB-mBJ potential for non-bulk systems

For non bulk systems the TB-mBJ potential had problems in regions of space where the density was very small.

r37095: Bugfix band: GLLB-SC potential

Depending on the band structure the results of the GLLB-SC potential were wrong. The problem was that the homo and lumo energies could be wrong.

r37083: Fix missing URL routines, sometimes leading to errors in ADFtail and ADFoutput

r37079: Fix ADFjobs problem with renaming jobs

r37063: Fix license check for BANDstructure with DFTB without BANDGUI license

r37050: Fix orientation of molecule and calculated field in cube files calculated by densf.

Before this fix the X and Z axes had their places switched. Now the orientation should be the same as displayed by ADFview.

r37035: Bugfix included documentation

The pull-down menus with keywords and index etc were not working correctly.

r37008: Bugfix bandstructure showing degenerate phonons

r36996: ADF2013.01a released

r36992: Bugfix band: lattice optimization issue

When doing a lattice optimization the geometry in the final single point calculation was wrong. One of the symptoms can be a complaint about bad normalization. Also the symmetry was broken.

r36982: Bugfix ADFspectra: make sure the baseline is always visible in NMR spectra

r36979: Bugfix ADFspectra: VCD spectra could not be zoomed in

r36975: Bugfix symmetry handling dispersion dDsC icw hybrids

Results with the density dependent dispersion correction (dDsC) could be incorrect or produce NaN in case of symmetric molecules, for example, if hybrids were used.

r36971: Bugfix ADFspectra handling FCF spectra

r36967: Bugfix MOPAC license

If the path to your license file contains spaces, there was a problem installing the MOPAC license.

r36955: Bugfix ADFinput: screen update issue when switching from BAND to ADF without atoms

r36952: Bugfix ADFmovie swapping IRC path from t21

r36949: Bugfix ADFmovie reading logfiles

ADFmovie could not handle logfiles made by ADF2013 due to the coordinates in the logfile for the Create runs

r36943: Bugfix spin-unrestricted AIM analysis

r36904: Handle BAND atom types

If you change the atom type in ADFinput via Atom details, this now works properly for BAND as well. You can use it for example to assign different basis sets to similar atoms, or to break symmetry.

r36897: Fix saving jobs with incorrect inputs in ADFinput

When incompatible options are used, the user still has the option to save the input. This sometimes lead to a crash of ADFinput, depending on which conflicting options were present.

ADF2013.01 released

ADF2013.01 has been released. Please see Release notes for a list of new features and improvements.