Quick start

Installation

GaPFlow can be installed via

pip install GaPFlow

A serial build of LAMMPS is provided for most platforms which allows testing all of GaPFlow’s functionality. For production simulations it is however recommended to build GaPFlow with parallel LAMMPS on your system. You need to have MPI installed (e.g. via apt install openmpi-bin libopenmpi-dev on Debian-based systems).

To compile for your specific platform, run

pip install --no-binary GaPFlow GaPFlow[parallel]

You can check your installation by running gpf_info from the command line.

==========
GaPFlow
==========
Version: ...

==========
LAMMPS
==========
Version: ...
Shared lib: <path-to-your-python-env>/lib/python3.X/site-packages/GaPFlow/_vendor/lammps/liblammps_mpi.[so,dylib]
MPI: True
mpi4py: True
packages: ['EXTRA-FIX', 'MANYBODY', 'MOLECULE']

==========
muGrid
==========
Version:  ...
NetCDF4: True
MPI: False

We currently do not use parallel functionalities of µGrid, so MPI support is not required.

Minimal example

Simulation inputs are commonly provided in YAML files. A typical input file might look like this:

# examples/journal.yaml
options:
    output: data/journal
    write_freq: 10
grid:
    dx: 1.e-5
    dy: 1.
    Nx: 100
    Ny: 1
    xE: ['D', 'N', 'N']
    xW: ['D', 'N', 'N']
    yS: ['P', 'P', 'P']
    yN: ['P', 'P', 'P']
    xE_D: 877.7007
    xW_D: 877.7007
geometry:
    type: journal
    CR: 1.e-2
    eps: 0.7
    U: 0.1
    V: 0.
numerics:
    tol: 1e-9
    dt: 1e-10
    max_it: 200
properties:
    shear: 0.0794
    bulk: 0.
    EOS: DH
    P0: 101325
    rho0: 877.7007
    T0: 323.15
    C1: 3.5e10
    C2: 1.23

Note that this example uses fixed-form constitutive laws without GP surrogate models or MD data. More example input files can be found in the examples directory.

The input files can be used to start a simulation from the command line

python -m GaPFlow -i my_input_file.yaml

or from a Python script

from GaPFlow.problem import Problem

myProblem = Problem.from_yaml('my_input_file.yaml')
myProblem.run()

Simulation output is stored under the location specified in the input file. After successful completion, you should find the following files. - config.yml: A sanitized version of your simulation input. - topo.nc: NetCDF file containing the gap height and gradients. - sol.nc: NetCDF file containing the solution and stress fields. - history.csv: Contains the time series of scalar quantities (step, Ekin, residual, …) - gp_[xz,yz,zz].csv (Optional): Contains the time series of GP hyperparameters, database size, etc. - Xtrain.npy (Optional): Training data inputs - Ytrain.npy (Optional): Training data observations - Ytrain_err.npy (Optional): Training data observation error

GaPFlow also provides command line tools for visualizing and animating simulation results. See Visualization for details.