These scripts are meant to facilitate the execution, tracking, and monitoring of hPIC simulations launced with XGC input. hPIC is a hybrid Particle-in-Cell plasma simulation code written at LCPP at University of Illinois at Urbana-Champaign. XGC is a gyrokinetic particle-in-cell code written at Princeton Plasma Physics Laboratory. This code is meant to be run after XGC simulations. It configures hPIC simulations to be run for each node of interest in the XGC messh.
The output of a completed XGC simulation, including axgc.f0.mesh.bp, xgc.bfield.bp, and xgc.f0.#####.bp, where ##### represents the time step. The hPIC simulation will be configured based on the distribution found in xgc.f0.#####.bp.
Visually inspect the XGC mesh and select individual nodes of interest. One hPIC simulation will be run for each node of interest. In addition, determine the poloidal angle of the surface close to the node you are choosing. theta = 0 represents the D3D divertor (pointing in the +z direction), while +90 indicates a surface pointing in the +R direction, and -90 indicates a surface pointing in the -R direction.
Save the mesh coordinates and angles to a CSV file, for example xgc_nodes.csv. The format of the file must be:
MESH_NODE,SURFACE_ANGLE
6000,0
12345,22.4
36803,11
The first line of this file must contain column names (they can be called anything).
Update all bash fields in configure_hpic_xgc_simulations.sh between the lines ### BEGIN USER MODIFICATION and ### END USER MODIFICATION. For a further
explanation of fields, run ./hpic -xgc to see a print-out of field descriptions.
Once you have modified configure_hpic_xgc_simulations.sh to your liking, run:
./configure_hpic_xgc_simulations.sh xgc.f0.mesh.bp xgc.bfield.bp xgc.f0.#####.bp xgc_nodes.csv.This will create the following:
launch_hpic_simulations_for_<PARENT_SIMULATION_ID>.sh: the parent bash script to launch all simulations. Executing this script will launch one hpic simulation, asynchronously, for each (node_id, surface_theta) pair in xgc_nodes.csv
<PARENT_SIMULATION_ID>_run_scripts: a directory containing one bash script for each hPIC simulation to be run. One script will be created for each line in xgc_nodes.csv
hpic_results: a directory containing one subdirectory for each line in xgc_nodes.csv. Simulations will be run in each subdirectory, and output will be saved here.
Run the following command to launch one hpic simulation, asynchronously, for each line in xgc_nodes.csv:
launch_hpic_simulations_for_<PARENT_SIMULATION_ID>.shTo monitor simulations, run:
./check_status.shTo kill all simulations launched in step 4, modify kill_simulations.sh and set parent_simulation_id to the same value as was used to configure simulations. Then save and execute the script. All simulations will be killed. Note running ./check_status.sh after this step will display failures for each hPIC simulation.