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Running from the command line
koopmans automatically installs the command koopmans. See koopmans --help for
usage details.
koopmans
Automated Koopmans functional calculations and workflows.
Usage
koopmans [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
- --pdb
Drop into ipdb debugger on unhandled exceptions.
- -l, --logging
Enable logging to koopmans.log file.
backend
Manage the AiiDA backend.
Usage
koopmans backend [OPTIONS] COMMAND [ARGS]...
codes
List all registered codes.
Usage
koopmans backend codes [OPTIONS]
daemon
Manage the AiiDA daemon.
Usage
koopmans backend daemon [OPTIONS] COMMAND [ARGS]...
restart
Restart the AiiDA daemon.
Usage
koopmans backend daemon restart [OPTIONS]
Options
- --cache, --no-cache
Enable AiiDA caching to reuse results from previous identical calculations.
start
Start the AiiDA daemon.
Usage
koopmans backend daemon start [OPTIONS]
Options
- --cache, --no-cache
Enable AiiDA caching to reuse results from previous identical calculations.
status
Check if the AiiDA daemon is running.
Usage
koopmans backend daemon status [OPTIONS]
stop
Stop the AiiDA daemon.
Usage
koopmans backend daemon stop [OPTIONS]
hq
Manage the HyperQueue worker that runs your calculations.
Usage
koopmans backend hq [OPTIONS] COMMAND [ARGS]...
restart
Restart the HyperQueue worker, optionally resizing its CPU pool.
Without –max-procs the replacement keeps the pool it had. Starts the HyperQueue server too if it is down. The caution under ‘stop’ about work in flight applies here as well.
Usage
koopmans backend hq restart [OPTIONS]
Options
- --max-procs <max_procs>
Total MPI ranks allowed concurrently across all running calcs. Default: physical core count.
start
Start the HyperQueue worker.
Brings the HyperQueue server up first if it is down. Does nothing if a worker is already running; use ‘restart’ to change its CPU pool.
Usage
koopmans backend hq start [OPTIONS]
Options
- --max-procs <max_procs>
Total MPI ranks allowed concurrently across all running calcs. Default: physical core count.
status
Show the state of the HyperQueue server and worker.
Usage
koopmans backend hq status [OPTIONS]
stop
Stop the HyperQueue worker.
Leaves the HyperQueue server up, so the queue is not discarded. ‘koopmans backend uninstall’ removes the server as well.
Check ‘hq job summary’ first if work is in flight: a task whose worker disappears may be retried on the next one, in the same directory.
Usage
koopmans backend hq stop [OPTIONS]
status
Show the status of the AiiDA installation.
Usage
koopmans backend status [OPTIONS]
uninstall
Completely remove the AiiDA backend.
This will delete the AiiDA profile and all associated data including: - The database (all calculation history) - The file repository - Registered computers and codes
This action cannot be undone!
Usage
koopmans backend uninstall [OPTIONS]
Options
- -y, --yes
Skip confirmation prompt.
install
Auto-install the AiiDA backend.
This command: 1. Creates an AiiDA profile with SQLite storage (or PostgreSQL with –use-postgres) 2. Downloads the bundled HyperQueue binary and starts the HQ server + worker 3. Configures the localhost computer (HyperQueue scheduler) 4. Detects and registers the executables koopmans runs on PATH 5. Starts the AiiDA daemon with caching enabled
Use –code to specify a custom executable path for a code, e.g.:
koopmans install –code pw=/opt/qe/bin/pw.x –code wannier90=/usr/local/bin/wannier90.x
Whether each code is launched under mpirun is decided by inspecting its binary. Use –serial/–parallel to overrule that, e.g.:
koopmans install –parallel wannier90
Rerunning this command also replaces codes registered earlier that run the wrong way, which orphans the results cached against them; –no-migrate leaves them alone.
Usage
koopmans install [OPTIONS]
Options
- --use-postgres
Use PostgreSQL instead of SQLite for storage (recommended for production).
- --procs-per-calc <procs_per_calc>
MPI ranks each calc launches (default: auto-detect physical cores).
- --code <NAME=PATH>
Specify an executable path for a code, e.g. –code pw=/opt/qe/bin/pw.x
- --serial <NAME>
Register a code to run without mpirun, overriding what its binary declares.
- --parallel <NAME>
Register a code to run under mpirun, overriding what its binary declares.
- --migrate, --no-migrate
Replace already-registered codes that run the wrong way. Replacing a code orphans the results cached against it; –no-migrate leaves them as they are.
- --max-procs <max_procs>
Total MPI ranks allowed concurrently across all running calcs. Default: physical core count.
- --cache, --no-cache
Enable AiiDA caching to reuse results from previous identical calculations.
plot
Draw a figure from one or more finished runs.
Usage
koopmans plot [OPTIONS] COMMAND [ARGS]...
bandstructure
Draw the band structures of finished runs on one set of axes.
FOLDERS are directories koopmans run wrote. Every band structure across all of them is drawn, so a DFT run and a Koopmans run given together overlay, referenced to a single energy zero.
To export one band structure in Grace, gnuplot or dat form instead, use verdi data core.bands export: those exporters take one node at a time, and so lose both the overlay and its shared zero.
Usage
koopmans plot bandstructure [OPTIONS] FOLDERS...
Options
- -o, --output <output_path>
Where to write the figure; the extension sets the format.
- --show
Open an interactive window instead of writing a file (-o still writes one).
- --zero <zero>
Which energy to put at zero. One shift, from the first series that reports it, is applied to every series on the axes.
- Default:
'vbm'- Options:
vbm | fermi | none
- --data <data_path>
Also write the series the figure was drawn from, as JSON.
- --label <labels>
Rename a series; repeat to rename several, in order.
Arguments
- FOLDERS
Required argument(s)
run
Run a koopmans calculation from an input file.
INPUT_FILE is the path to a YAML or JSON input file describing the calculation.
Usage
koopmans run [OPTIONS] INPUT_FILE
Arguments
- INPUT_FILE
Required argument