Trunk Changelog

New features and major improvements to the last ADF Modeling Suite release, listing last changes first. The revision number corresponds to that of the development snapshots.

r72775: Heat exchange methods (simple, HEX, eHEX) to study t-NEMD are now available for testing in AMS.

r72747: GFN1-xTB is now available as a new model in DFTB.

Both molecular and periodic calculations are supported for systems containing all elements up until Rn. Molecular orbitals can be visualized in ADFView.

r72297: The AMS molecular dynamics driver can now be combined with the PLUMED library.

PRD or REMD with PLUMED may not work yet.

r72112: Library version of MOPAC engine.

MOPAC has been fully integrated as an Engine in the Amsterdam Modeling Suite; this significantly speeds up the execution of MOPAC via AMS.

r71783: Partial Vibrational DOS (PVDOS) is computed after AMS normal modes calculations.

r71761: Implement Intrinsic Reaction Coordinate (IRC) Scan in AMS.

See User's Guide for details.

r71548: Thermodynamic properties are now computed after AMS normal modes calculations.

r71506: Implement Grand Canonical Monte Carlo (GCMC) in AMS.

See User's Guide for details.

r71278: Tools for mode selective vibrational analysis added to AMS: Mode Scanning, Mode Refinement, and Mode Tracking

Adds some tools for the calculation and analysis of vibrational modes: Mode Scanning (the equivalent to ADF's ScanFreq keyword), Mode Refinement and Mode Tracking (experimental). The latter two methods can be used for the calculation of select modes or select regions of the vibrational spectrum, whereas Mode Scanning can be used to obtain more accurate approximations of the vibrational mode properties. See the vibrational analysis section in the AMS driver manual.

r71065: ADF: Raman icw spin-orbit coupling using AORESPONSE

r71004: The Reaxff CVHD feature has been ported to AMS

r70713: DENSF: Lone pair localization via Coulomb potential minima.

No special input key is required. The Coulpot minima are analyzed automatically by DENSF if "Potential Coul SCF" is requested and the grid is regular and rectangular.

Results are saved in TAPE41 section "Coulpot minima". Variables:
"Number of minima" - number of the found minima;
"Coords 1" - coordinates if the 1st minimum in Bohr;
"Potential 1" - value of the Coulomb potential at this point;
"Eigenvalues 1" - three eigenvalues of the corresponding Coulomb potential Hessian;
"Eigenvectors 1" - corresponding eigenvectors as 3x3 matrix;
"Coords 2" - coordinates if the 2nd minimum in Bohr;

A located minimum of the Coulomb potential is visualized as an ellipsoid at the corresponding position. The size of the ellipsoid corresponds to the magnitude of the eigenvalue in the direction of the corresponding eigenvector.

The simple grid-based method used to find the minima may find false ones in a very shallow valley (for example for atoms with two lone pairs).

r70637: Band: implemented DFT-1/2 method for band gap prediction

r70543: adfprep now can add constraints (-fixdist, -fixangle, -fixdihed)

r70487: AMS: AddMolecules (aka molecule gun) and RemoveMolecules are implemented as part of MolecularDynamics

See the AMS User Guide for details.

r70485: Improved performance of the input handling system

The text input to JSON conversion is now done by a Fortran component instead of through a Python script. This reduces the startup times for the Fortran programs. Furthermore the JSON structure is now traversed more efficiently when it is accessed, improving the performance for very large input files.

r69978: Reaxff: extended the rxffutil utility with some options

The new options include printing some basic information about the known reaxff parameters and preparation of the params files used for reaxff parameter fitting. Some examples:

Prepare params file for optimization of all parameters of the C-O bond block and the first C-O-O-C torsion parameter (both blocks!) in the TiOCHNCl.ff force-field.

$ rxffutil.exe params --ff=$ADFRESOURCES/ForceFields/ReaxFF/TiOCHNCl.ff b%CO t%COOC:1
#     Key          delta         min         max     comment
   3   4   1    1.017360     95.6228    197.3588     # b%CO:1 E(Sigma)
   3   4   2    1.057032     58.4169    164.1201     # b%CO:2 E(Pi)
   3   4   3    1.248792      5.5000    130.3792     # b%CO:3 E(Pi2)
   3   4   4    0.019273     -1.3755      0.5518     # b%CO:4 p_be1
   3   4   5    0.002831     -0.3906     -0.1075     # b%CO:5 p_bo5
   3   4   6    0.000000      1.0000      1.0000     # b%CO:6 13corr flag
   3   4   7    0.094704     10.2503     19.7207     # b%CO:7 p_bo6
   3   4   8    0.007175      0.3796      1.0971     # b%CO:8 p_ovun1
   3   4   9    0.037882      0.3211      4.1093     # b%CO:9 p_be2
   3   4  10    0.003587     -0.5875     -0.2288     # b%CO:10 p_bo3
   3   4  11    0.027827      6.7927      9.5754     # b%CO:11 p_bo4
   3   4  12    0.000000      1.0000      1.0000     # b%CO:12
   3   4  13    0.001969     -0.2877     -0.0908     # b%CO:13 p_bo1
   3   4  14    0.012328      4.5000      5.7328     # b%CO:14 p_bo2
   3   4  15    0.010000      0.0000      1.0000     # b%CO:15 ovcoord flag
   3   4  16    0.012141      0.0000      1.2141     # b%CO:16 p_xel1 (ereax)
   6  16   1    0.055006     -2.0324      3.4682     # t%COOC:1 V1
   6  41   1    0.055006     -2.0324      3.4682     # t%COOC:1 V1

Print some basic info about known H-Pt-H angle parameters (use first parameter only for clarity), list files where this parameter is present:

$ rxffutil.exe minmax -vv v%HPtH:1
Key                   N         min         max     average
Found v%HPtH:1               95.0000 in c:/adf2018.205/atomicdata/ForceFields/ReaxFF/CHONSFPtClNi.ff block 69
Found v%HPtH:1               57.3916 in c:/adf2018.205/atomicdata/ForceFields/ReaxFF/PtCH.ff block 14
v%HPtH:1              2     57.3916     95.0000     76.1958

r69746: DFTB now uses the exact same methods and input for the k-space integration as BAND does

r69550: ADFinput: shortcut cmd/ctrl-shift-R added to show the Run Script panel

r69545: ADFinput: support for geometry optimization using internal coordinates (Z-Matrix) has been removed

r69200: AMS MD: Default to Random initial velocities

r69117: ReaxFF AMS engine: Fix missing interactions and stress tensor for small periodic cells

A bug in the Verlet list generation in ReaxFFEngine caused some potentially missing long-range interactions for small periodic cells (thinner than 5 Å in some direction). Additionally, the stress tensor cannot be evaluated analytically for small cells. The engine will automatically fall back to calculating the stress tensor by numerical differentiation if necessary.

r69000: AMS geometry optimizations now try to continue even if engine fails to solve for a geometry

This can happen if there are for example SCF convergence problems in the engine. The energy/gradients might then not be quite correct, but it is probably safe to continue the optimization and hope that things are fine again for the next step. Note that this fix also applies to PES scans, transition state searches, and any other applications that use geometry optimizations internally (e.g. elastic property calculations).

r68755: AMS MD: Fix integration with the Berendsen barostat, make BulkModulus configurable

r68747: ReaxFF: Fix a GCMC bug that led to crashes like "Error when moving molecule!"

r68743: ADFinput: only write lastatom in AMS MD THERMOSTAT key when non-system-wide thermostats are used

r68738: ADFinput: use PM7_solids and ADF molecules from the .tgz files (to reduce the number of files in the distribution)

The ADF and PM7_solids folders are no longer in Molecules, they are avaiable as tgz files if you want to get the individual files.

r68711: ADF: Implemented spin polarization optimization

The spin polarization can be optimized by minimizing the difference between Fermi level values for spin-alpha and spin-beta MOs. This method works reliably only when a reasonably large finite electron temperature is used (300K is found to be sufficiently large for small transition metal clusters). The polarization value is optimized up to a specified tolerance (fractional values are allowed) by step-wise reduction of the root-braketing interval for the objective function f=FermiLevel(alpha)-FermiLevel(beta). The SCF procedure is converged for each spin polarization. When the interval becomes smaller than the tolerance the optimization is considered converged. After that the SCF may optionally be repeated with the spin polarization set to the nearest even or odd number (depending on the total number of electrons in the system) or, in other words, with the total number of electrons per spin rounded to the nearest integer. The method is invoked by using one of the following Occupations keys:

OCCUPATIONS  ElectronicTemperature=300 OptimizeSpinRound=0.05
OCCUPATIONS  ElectronicTemperature=300 OptimizeSpin=0.05

Here, the ElectronicTemperature sets the electronic temperature, in Kelvin, for calculating the Fermi MO occupations. The OptimizeSpin and OptimizeSpinRound argument specifies the tolerance value. The OptimizeSpinRound key specifies that after convergence the SCF must be completed with the total number of electrons per spin rounded to the nearest integer.

It should be noted that as usual the Unrestricted and Charge keys must be specified as for any other spin-unrestricted calculation. The second argument of the Charge key sets the initial spin polarization value from which the optimization is started. The result of the optimization may depend on the initial value as the objective function may have more than one root.

r68708: ADF: Fixed a bug related to atoms order in IQA input/output

r68698: Band: much better running of big fragments

Band used to disable Shared Arrays for fragment related calculations, slowing down significantly the calculations. Big systems might even crash.

r68688: Windows: Update intelmpi runtime to 2018.0.3

r68672: ADFinput: add check that fragments do not overlap for BAND

r68588: ADFinput: report proper error when property estimation fails

r68583: ADFjobs: when starting by double clicking the icon, make sure the initial directory is writable (if not, switch to $HOME)

r68577: ADFinput: when saving fails, do not set job name in window

For example, when trying to save your setup in a location where you have no write permission.

r68519: Fix floating license issue with AMS (DFTB/BAND/...)

r68514: ADFspectra: fix issues caused by NMR spectra updating too quickly in succession

r68513: ADFspectra: Boltzmann weights caused issues with large energy differences

r68502: AMS MD: Rename the "NHC" barostat to MTK

It should have always been called MTK as it implements the Martyna-Tobias-Klein equations, but it accidentally ended up under the confusing "NHC" name.

r68497: AMS MD: Disable Preserve CenterOfMass by default

It only makes sense in rare situations (long free-boundary simulations or 3D periodic inhomogeneous systems with one heavy component surrounded by solvent where the Brownian drift of the CoM may be annoying) and leads to surprising spurious translation of all other systems.

r68493: ADF: Fixed a bug in RamanRange with hybrid XC functionals

Before the fix, the Raman intensities were calculated using the Response module, which resulted in incorrect results. With this fix, the AOResponse module is used instead, which does work with hybrids.

r68489: ADFspectra: fix processing peakwidths with nonvalid values for NMR spectra

r68487: ADFmovie: converged geometries only for an IRC calculation will show all final IRC geometries

If not converged, it will be mentioned in the label (if that info is available, ie ADF2018 or later).

r68474: ChemTraYzer: Fixed issues with SMILES strings that cannot be handled by RDKit

r68439: ADFdos: Restricted BAND calculations would show the DOS per spin

r68434: ADFinput: Metahybrid functional accuracy requirement wasn't checked correctly

r68433: Velocities from file for AMS MD, fix rare problem of ADFjobs hanging, fix ADFjobs for non-job files

The option to select the file with AMD MD velocities was in expert options, moved to the AMD MD panel.

The scmd daemon could crash when generating the errors file when a job finishes due to a race condition. This lead to ADFjobs hanging.

ADFjobs had visual update issues with jobs that are actually not jobs (like just a .xyz file).

r68432: Bandstructure: Fix COOP window size for MacOS

r68390: AMS2018.101 released

AMS2018 has been released. Please see Release notes for a list of new features and improvements.