# Bug-fix changelog

Bug-fixes and improvements to the latest major release, with the latest changes listed first. The revision number corresponds to that of the bug-fixed binaries.

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

### 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.

### 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.

### 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.

### 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.

### r75671: GUI: fixed reading strings from KF 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.

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

### 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.

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

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.

### 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.

# 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...

### 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].

### 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).

### 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.

### 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.

### 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.

### 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.

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

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