Changelog bug-fixes Amsterdam Modeling Suite 2019

r79622: (November 28th, 2019):AMS2019.105 released

This is the last planned 2019.1 release

r79620: ADF: fix Fragments key in case a directory name is used as block header

ADF would give an error: STRINGS TOO LONG. CONCSS.

r79613: Reaxff: Skip charge equilibration for a single-atom system.

r79578: Reaxff: Do not remove atoms on the last MD step to avoid discrepancy between the last saved molsav and fort.90 files.

r79549: Reaxff: catch user mistakes in the restraints input

r79515: Reaxff: Fixed a bug determining frozen atoms when a geo file contains multiple geometries

This bug could result in atoms specified as frozen in one geometry would also be frozen in subsequent geometries

r79288: ADF: Fix a bug that would cause a “Parameter 13 was incorrect on entry to DGEMM” message in MetaGGA calculations.

Apart from this message the results of the computation were not affected by the bug.

r78669: ADFtrain: Fix importing systems with non-orthorhombic lattices.

r78021: ADFjobs: Fix remote job submission issue on Windows related to the ssh key agent.

r78017: ADFspectra: average curve for CD spectra was not showing

r77958: ADFinput: use of preoptimizer left wrong input options enabled in some cases.

r77951: ADFinput: Fix adding a single H to a linear X-Y-Z system.

ADFinput would put the new H along the axes X-Y-Z, often inside X or Y.

r77792: ReaxFF: Fix handling large parameter deltas (exceeding the min-max parameter range) in the CMA-ES optimizer.

r77708: AMS MD: Fix angular momentum removal for 1D/2D-periodic systems.

r77669: AMS-UFF: Fixed a bug that could lead to (very) wrong UFF atom types and bond orders for 1D periodic systems.

r77354: AMS-ReaxFF: Fix picking up the total charge set in the System block.

r77330: BAND: PEDA energy decomposition results were wrong in case that atoms were shifted. Does not affect normal calculations.

r77220: ADFmovie: Fix rotating the camera while playing the movie on MacOS.

r77194: Fix VTK 2D graphs: error in generating X and Y labels.

r77153: ADFmovie: Fix the graphs loaded at startup.

r77035: AMS driver: fixed a bug causing the optimizer to change the lattice in a mu-VT GCMC calculation if the GeometryOptimization%OptimizeLattice option was still on.

r76944: ADFjobs: Fixed ‘$jobname’ substition when used in a remote queue in the runcommand.

r76697: ADFinput: Input unit preferences with non-ascii symbols were saved and retrieved incorrectly.

r76620: (August 14th, 2019):AMS2019.104 released

r76619: Reaxff: Add a check for zero parameter intervals in the CMA-ES optimizer.

r76612: ADFview: problems visualizing when using fragments with band.

r76597: ADFinput: also update geometry when reopening ADFinput when a job is ready if the termination status is NORMAL TERMINATION with some extra text.

For example, NORMAL TERMINATION with warnings would block updating the geometry.

r76475: ADFmovie: Fix for unit issues between left and right axis.

r76458: Bandstructure: Fix unit change via menu.

r76390: GUI: Fix for macOS 10.14.6 update where the WindowServer crashed and the user got sent back to login.

r76310: ADFjobs: Fix ssh-pageant cleanup.

r76249: ReaxFF: Fix control file parsing in the presence of tab characters.

r76247: ReaxFF: Fix CMA-ES startup with parameters on a boundary.

If a parameter was exactly on the edge of the allowed range, CMA-ES would terminate after a single iteration due to numerical issues.

r76246: ReaxFF: Fix incorrect initialization of parameter deltas in the CMA-ES optimizer.

A bug in the CMA-ES parameter optimizer caused the “delta” values specified in a “params” file to be completely ignored. The initial standard deviations for all parameters were thus always estimated using the “mcrxdd” control parameter. This fix makes the optimizer behave as documented in the manual, using the deltas from the params file if they’re positive and falling back to “mcrxdd” otherwise.

r76233: Reaxff: interpret non-positive off-diagonal values in ff files the way as in the original reax.

In the previous version, a non-positive value for the VdW-related off-diagonal parameters were used as is. In the original reax they were ignored and values calculated from the atomic parameters were used, as if these off-diagonals were absent. This situation is extremely rare.

r76231: Fixed a bug in the kfoptim feature and re-enabled it.

r76220: ADFmovie: Fix PES scan surface selection marker order.

r76216: Disable kfoptim until all issues are solved.

r76173: Re-enable the kfoptim feature which should save some disk space in ADF geometry optimizations.

r76069: ADFjobs: make sure an empty option field does not unset NSCM

If a user defines NSCM, jobs running should use it. The default queue would unset NSCM if no number of tasks was specified in the options field, and as a result all cores of the machine would be used instead of the NSCM required by the user.

r76042: ADFjobs: Fix issues with Transfer To/From Remote command in the Job menu.

r75980: Reaxff: Added the CHON-2019 force-field.

r75963: ADF: Reintroduce the 2nd argument of SCF Mixing key as a separate Mixing1 keyword

r75936: ADF: Fix in POLTDDFT

For some basis sets the bug would cause incorrect or NaN results.

r75924: ReaxFF: Fix reaxff-ams import scripts for non-orthorhombic lattices

The bgf2ams and vels2ams scripts in scripting/standalone/reaxff-ams accidentally transposed the cell matrix.

r75923: DFTB: Fix missing neighbors in non-periodic directions

A bug in the generation of neighbor lists for DFTB integrals caused some pairs to be lost if they had a large enough distance in a non-periodic cell direction. In the worst case (system extent in a non-periodic direction just slightly over twice the cutoff), this affected pairs separated by >2/3*cutoff in the non-periodic direction.

r75805: Too many timers. Could happen with MD calculations with for instance band

r75748: All codes: avoid a false “license invalid” alarm when the MPI initialization fails

r75671: GUI: fixed reading strings from KF files

r75624: ADFtrain: do not crash when reading malformed ffield files

The error and the line in the force field file that causes the error are reported.

r75604: GUI Preferences: fix saving preferences after using the Apply button first

Also some timing debug output was removed.

r75596: ADFinput: Crystal Builder tool only worked correctly for the first invokation (per ADFinput run)

r75512: ADFspectra: Fix exporting tdcdft values.

r75461: GUI: If clicking on atoms is not working, try setting the environment variable SCM_SELECTION_BUG

r75460: AMS: Fixed a bug in CGMC that was messing up atom indices when removing molecules

r75337: ADFmovie: Molecule Fractions for ReaxFF (.rxkf) files Show button was broken

r75332: GUI: Atom and bond selection with the OpenGL1 fallback mode fixed

r75331: Reaxff: Correct units for FBMC energies in the output file

r75281: (June 4th, 2019):AMS2019.103 released

r75280: ADFinput: conformers panel listed menus like Model and Properties etc that were not used

r75199: Sources: include the dftd3 library

r75085: Bandstructure: Enable exporting DOS values as xy

r75036: ADFspectra: Fix exporting negf values

r74977: AMS MD: Fix using wrong lattice to convert molecule gun positions from fractionals

The AddMolecules feature in AMS incorrectly used the (possibly undefined) lattice of the bullet instead of the main system to evaluate FractionalCoords/FractionalCoordsBox.

r74968: Fix documentation search for MOPAC in ADFinput

r74953: ADFspectra: fix LFDFT excited state spectrum

r74936: AMS MD: Fix a bug that caused unnecessary calculations of the stress tensor when using PLUMED

r74931: Importing CIF files. Some would fail because due to whitespace issues.

r74911: ADFjobs: Fix ssh multiplexing when adfjobs was killed abnormally

A quick manual fix for this issue is to delete the scmmux* files in your /.scm_gui/ dir and restart ADFjobs.

r74895: Reaxff: Fixed a bug in geometry optimizer

Normally, after geometry optimization the calling program should perform a single-point calculation for the last geometry. The reaxff program (not to be confused with the reaxff engine in AMS) didn’t do this so the final reported energy was corresponding not to the final geometry but to the previous one. However, the difference between the two energies is significant only when the geometry optimization is stopped far from convergence.

r74851: ADFview: give error message when used with DFTB results without basis information

r74845: PLUMED/AMS: Fixed a bug that was preventing the use of PLUMED with engines other than reaxff and enable it for non-periodic systems

r74839: Reaxff: Fixed a bug related to the FIXATOMS key in a multi-molecule geo file

r74830: ADF: cpl: fix non-default magneto-gyric ratio gamma input for spin-spin couplings

r74765: Added SCM_MPIOPTIONS environment variable

The SCM_MPIOPTIONS environment variable can be used to pass additional arguments to the mpirun/srun/aprun command.

r74699: AMS ModeTracking: improved convergence stability and speed

With these improvements the ModeTracking task in AMS is no longer considered an experimental feature.

r74648: ADFmovie: restarting a job while it is shown in ADFmovie wil cause ADFmovie to reopen the result file.

This prevents ADFmovie showing old results when rerunning a job.

r74641: ADFspectra: fix clicking in spectra after scaling, and baselinemarkers with scaling and/or offset

When the scaling was not 1.0, clicking on a peak would not work properly (the click coordinate was not scaled, thus the peak typically was not found). Also, the markers at the baseline were not updated after scaling or changing the offset.

r74558: KFBrowser: Fix saving graphs.

r74540: Correct units for stress and elastic tensors and the Hessian in AMSResults and the GUI.

r74538: KFBrowser: Fix units usage when plotting variables as graphs.

r74468: AMS GCMC: bugfix uninitialized Mu-PT parameters in Mu-VT simulation.

r74452: e-Reaxff: fix asymptotics of the electron interaction at very short distances.

r74392: ADFmovie: fix issues with reading properties from a running job with adfmovie.

r74351: (April 26th, 2019):AMS2019.102 released

AMS2019 has been released. Please see Release notes for a list of new features and improvements.

r74320: partial fix for left-over icons in Mac Dock

When Show recent applications in Dock was enabled on MacOS, launching ADF-GUI modules would leave defunct icons in the Dock. Clicking on them would result in an error message in the terminal. This fix sometimes helps, sometimes not, still work in progress…

r74318: fix atom reording issue with BAND results

r74299: fix issues causing the “SharedArrays error(): Permission denied” error.

r74222: ADFjobs: fix issues with the ssh agent (ssh-pageant) on Windows.

r74208: COSMO-RS: Fast Sigma for polymers

Fast Sigma can produce an ‘average monomer’ that can be used in polymer calculations. Input SMILES string should be a CurlySmiles, like C{-}C{n+} for poly(ethylene).

r74199: COSMO-RS GUI: 2D visualization polymers

Approximate 2D visualization of a CurlySmiles shows a biradical. For example, C{-}C{n+} is shown as [CH2][CH2].

r74194: Avoid crashing adfmovie when following a remote KF file.

r74116: ADFview: when showning pairs of NTOs via the Properties menu, properly show the NTOs already available in the table.

r74105: ADF: fix AOresponse icw Solvation and CSMRSP

r74103: ADFoutput: proper search for K-space info in BAND output.

r74091: ADFjobs timeout for remote jobs default increased from 5 to 10 seconds.

The new default will only have effect for first time users (or when users remove the .scm_guirc file).

r74061: ADFjobs: make the trace commands to remote option in the Help menu produce more useful output.

r74046: ADFjobs: when starting ADFmovie for a running remote job, do not delete the local ams.rkf file

Not deleting the file makes the file transfer much faster as rsync is used.

r74026: ADFjobs: make click on remote job to transfer work again

r74017: ADFjobs: improve TransferFromRemote performance

r74001: ADFinput: Fix coskf atoms when generating a trimer from the Solvation panel.

r73996: ADF-GUI: improve TIMEOUT handling in file transfer routines

r73978: ADFmovie: avoid showing the GeoProgress dialog (for showing distances and so) when fewer than 100 extra frames are needed.

When more frames need updating the progress dialog is still shown to allow users to Cancel.

r73974: ADFjobs: running remote jobs for the first time would generate a progress dialog that would not go away.

r73967: ADF: Small changes in the ConceptualDFT Domains

r73963: ADF-GUI: improve error handling for remote job submission.

r73956: ADF: resolve the Failed to open inputmodel.plist error when running ADF from a long ADFHOME path

r73946: ADF-GUI: add SCM_NO_DIRAC_CHECKS option.

r73944: ADFjobs: Modified rsync command for use with older versions.

r73940: ADFjobs: Renaming a job with spaces would remove it from the list of displayed jobs.

The job does not really disappear, ADFjobs would just forget about it.

r73933: ADFjobs: Rewrote the scripts to start/kill jobs

Fix issues with remote jobs with spaces.

r73921: ADFjobs: Fixed issue with remote jobs when spaces are used in the path.

r73883: ADFinput: Fixed polymer builder search panel placement on Windows

r73864: ADFjobs: Fixed issue with remote job submission on platforms where ‘sh’ is not ‘bash’

r73848: COSMO-RS: fixes for polymers

Fixed incorrect reading bond energy in GUI for polymers. Added Flory-Huggins parameter calcuation in miscibility gap. Fixed binary miscibility issues for polymers.

r73838: ADF-GUI: launching a browser on linux could fail (complaints about missing or non-matching libraries)

r73835: ADFinput: adjust label on TS panel in ADF to make it more evident how to set an initial hessian

r73833: ADFjobs: fix an issue causing a crash when renaming a random (not ADF/AMS related) file

r73831: fix typo in ReadMe in MacOS install image

r73810: (April 10th, 2019):AMS2019.101 released