Frequently Asked Questions

General

  • My workflow/simulation crashed (marked as red).
    • In the Jobs&Workflows panel, double click on the workflow to identify the crashed (red) module. Double click on it and download the *.stdout and *.stderr files.
    • In special cases it may be that a job is marked red, although all required output is produced. We are working on an improved reporting system to circumvent this.
  • Can I restart a crashed workflow?
    • We are working on automated restarts. For the time being, please 1) download the required output of the last successful module 2) re-construct the workflow starting with the crashed module 3) load the input of the last successful module from your harddrive.

Deposit

Postprocessing morphologies

  • How can I expand a morphology periodically in x-y direction, e.g. in order to create sufficient environment for QuantumPatch calculations? There are two options for this:
    • If you ran Deposit using an integer box size and a rectangular box (which you probably did, non-rectangular box shapes are only available in the command line version of Deposit), then the periodic extension can be done using the "AddPeriodicCopies.py" tool in the MolecularTools folder of QuantumPatch:

      source $NANOMATCH/$NANOVER/configs/quantumpatch.config

      $SHREDDERPATH/MolecularTools/AddPeriodicCopies.py <cmlfile> <outfilename> [<lowest_layer_cutoff>]

      Here <cmlfile> is the structure.cml of Deposit, <outfilename> is set by the user, and <lowest_layer_cutoff> can be set to e.g. 7A when you wish to cut the lowest layer of the deposited structure, which may have artifacts by forcing the first layer to be smooth.

    • Another way that works for any morphology but requires the runtime folder of Deposit is the following: cd into the Deposit runtime directory (containing the settings file and a folder with all deposited_*.pdb.gz) and do

      source $NANOMATCH/$NANOVER/configs/deposit.config

      $DEPOSITPATH/Tools/add_periodic_copies.py <lowest_layer_cutoff>

      Here, lowest_layer_cutoff is same as above.

Lightforge

PLQ measurements

  • PLQ measurements and excitonic statistics look fishy, i.e. wrong type of quenching observed: During PLQ measurements, high exciton density at the beginning of the measurement may lead to strong exciton-exciton quenching, dominating the analysis although only happening in the first fraction of the simulation. To cut the first part of the simulation from the exciton analysis, you can re-run the LightForge analysis (not the full simulation - this only takes a couple of minutes usually) by including the following lines in the settings:
    • analysis_autorun: True
    • autorun_start: 0.1 These settings re-run the analysis only on the last 90% of KMC simulation steps. To estimate the fraction to cut, have a look at the first column in results/experiments/photoluminescence_transients/all_data_points/pl_phots_X.dat where X is the id of your walker (if you run several simulations for statistics). This column contains the physical time and each line is printed after a specific number of simulation steps. E.g., if you want to start the analysis at 1e-6 sec and this time is reached in line 100/800, set the value in autorun_start to 0.125.
  • PLQ measurements run much longer than expected: Individual LightForge PLQ runs terminate, when no exciton or charge carrier is left in the system. Due to charge separation and/or traps, however, it may occur that single separated charges keep the simulation going. To avoid this, you can set a maximal "physical" time for your simulation to e.g. 10mus by including "max_time: 1.e-5" in your settings file.

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