Frequently Asked Questions
- 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.
- 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:
$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
Here, lowest_layer_cutoff is same as above.
- 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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