- ase >= ?.?.?
- NumPy >= 1.21
- PyYaml >= 5.1
python basin_hopping.py -f ./config/config.yaml -v
mpirun -n 4 python basin_hopping.py -f config/config.yaml -v
Arguments | Description |
---|---|
-f config/config.yaml |
Run the basin hopping algorithm with settings defined in config.yaml |
-f config/config.json |
Run the basin hopping algorithm with settings defined in config.json |
-f config/config.yaml -v |
Turn on log messages |
-n 10 |
Run the basin hopping algorithm for a cluster with 10 atoms |
-n 10 -m 500 |
Run the basin hopping algorithm for 500 steps |
usage: basin_hopping.py (-f CONFIG | -n CLUSTER_SIZE) [options]
Run the basin hopping algorithm.
required arguments:
One of these arguments must be present
-f CONFIG, --config CONFIG
The location of the config file (default: None)
-n CLUSTER_SIZE, --cluster-size CLUSTER_SIZE
The size of the cluster (default: None)
optional arguments:
-r RADIUS, --radius RADIUS
Radius of the sphere the initial atoms configuration
is uniformly distributed in (default: 1)
-c MAX_RADIUS, --max-radius MAX_RADIUS
The maximum radius of the cube to constrain the atoms
in. If not set, no constraint is placed on the atoms
(default: None)
--temperature TEMPERATURE
The temperature parameter for the Metropolis
acceptance criterion (default: 0.008617330337217212)
--step-size STEP_SIZE
The initial value of the step size (default: 0.5)
--accept-rate ACCEPT_RATE
The desired step acceptance rate (default: 0.5)
--step-size-factor STEP_SIZE_FACTOR
The factor to multiply and divide the step size by
(default: 0.9)
--step-size-interval STEP_SIZE_INTERVAL
The interval for how often to update the step size
(default: 50)
stop conditions:
-m MAX_STEPS, --max-steps MAX_STEPS
The maximum number of steps the algorithm will take
(default: 500)
-ss STOP_STEPS, --stop-steps STOP_STEPS
The number of steps, without there being a new
minimum, the algorithm will take before stopping. If
not set, the algorithm will run for the maximum number
of steps (default: None)
-st STOP_TIME, --stop-time STOP_TIME
The maximum amount of time, in seconds, the algorithm
will run for before stopping. If not set, the
algorithm will run for the maximum number of steps
(default: None)
filter arguments:
-fn, --no-filter Use no filter (default: None)
-fs, --filter-significant-figures
Use significant figures filter (default: None)
-fd, --filter-difference
Use difference filter (default: None)
-sf SIGNIFICANT_FIGURES, --significant-figures SIGNIFICANT_FIGURES
Significant figures to round the potential energy to
to check for uniqueness (default: 2)
-d DIFFERENCE, --difference DIFFERENCE
Minimum potential energy difference between unique
local minima to check for uniqueness (default: 0.1)
logging & help:
-h, --help show this help message and exit
-v, --verbose Print information about each step (default: False)
-vr, --view-results Open ase gui after completion (default: False)
-db DATABASE, --database DATABASE
Database file for storing global minima (default:
None)
-tr TRAJECTORY, --trajectory TRAJECTORY
Trajectory file for storing local minima (default:
None)
-trf FILTERED_TRAJECTORY, --filtered-trajectory FILTERED_TRAJECTORY
Trajectory file for storing filtered local minima. If
None, filtered local minima are stored in the original
trajectory file (default: None)