Update geometry dialog

When opening AMSinput for a finished job, or if the AMSinput window is open when the job finishes, the following dialog pops up if there have been changes to the geometry:

_images/update_dialog.png

If you click

  • No: AMSinput is unchanged..

  • Yes: AMSinput is updated according to your selection.

The data in the .ams file is only changed when saving. As there are results present, you will get a Save As dialog when saving the input. Thus the data in the current .ams file is never changed unless you explicitly select it in the Save As dialog to overwrite it.

Alternatively, use the File → Restart From Results… menu command, it will bring up the same dialog even if the geometry did not change.

Meaning of restart options

If you put your mouse on an option and do not move it, a balloon will pop up showing more information about the options. It also lists which input keys are set if you enable that particular option.

Not all options will be enabled. It depends on the kind of information found on the result files which restart options are possible.

At the top of the dialog you can see which job (and thus which ams.rkf file) will be used for AMS restarts. Next the current engine file is shown, if present. In some cases there may be multiple engine files, use the file select button to select the engine file you want to use if you want to restart using engine results.

  • Update coordinates and bonds in AMSinput with data from AMS results: The geometry in AMSinput is updated from the results file. This option is only available when the geometry has been changed.

The following options specify how to use engine results. In the text ADF is used as an example.

  • Replace molecule in AMSinput with System from ADF engine results: Replace the molecule in AMSinput by importing the System from the engine results. This option is useful if there are multiple engine results files (like after an IRC calculation).

  • Use Hessian from results from ADF engine results: If you calculated the hessian, normal modes, or vibrational frequencies in the original job, you can reuse the calculated hessian in a new job. This can help, for example, to converge a geometry optimization or transition state search faster.

  • Restart ADF with engine results: If you select the option, then on the Model → Restart panel, the Engine restart keyword is set to the engine.rkf file from the original job. How the engine uses this restart information depends on the engine.

  • Properties Only job using ADF engine results: For ADF there are a number of property programs like NMR, CPL, and more. These need the results of the ADF engine to run. You can run them after your job is completed using the Properties Only task.

The following options are to set up some restart based on the AMS result file (ams.rkf).

  • Use MD velocities from results for AMS MD restart: If the original job is a molecular dynamics simulation, this option will load the velocities from the final frame from the original job, allowing you to continue an MD simulation. Note that if you use thermostats or barostats, the continuation trajectory will not perfectly match the trajectory which “would have” taken place if the original job was longer.

  • Restart MD using AMS results: Restart the MD run.

  • Restart GCMC using AMS results: Restart the GCMC run.

  • Restart IRC using AMS results: Restart the IRC run.

  • Restart NEB using AMS results: Restart the NEB run.

  • Replay: recompute frames from AMS results: Select the ams.rkf result file as a source to recalculate selected frames. On the Model → Replay panel you can specify which frames to recalculate.