Set up and run a simulation

Let’s first show how to set up a single simulation. The basic work-flow consists of several steps. First we have to prepare the simulation, then we run the main simulation program. This gives us a data file with the simulation results. Then we can apply various post processing steps, for example the computation of energies, plotting of norms and many more.

The first step is to create a configuration file and set the simulation parameters. We use the file examples/harmonic_oscillators/harmonic_1D_p.py from the examples collection. The full content of this file is printed below:

algorithm = "hagedorn"
propagator = "semiclassical"
splitting_method = "Y4"

T = 12
dt = 0.01

dimension = 1
ncomponents = 1

eps = 0.1

potential = "quadratic"

# The parameter set of the initial wavepacket
Q = [[1.0]]
P = [[1.0j]]
q = [[1.0]]
p = [[0.0]]
S = [[0.0]]

# What it takes to specify a wavepacket!
wp0 = {
    "type": "HagedornWavepacket",
    "dimension": 1,
    "ncomponents": 1,
    "eps": eps,
    "Pi": [q, p, Q, P, S],
    "basis_shapes": [{
        "type": "HyperbolicCutShape",
        "K": 10,
        "dimension": 1
    }],
    "coefficients": [[((0,), 1.0)]],
    "innerproduct": {
        "type": "HomogeneousInnerProduct",
        "delegate": {
            "type": "DirectHomogeneousQuadrature",
            'qr': {
                'type': 'TensorProductQR',
                'dimension': 1,
                'qr_rules': [{'dimension': 1, 'order': 14, 'type': 'GaussHermiteQR'}]
            }
        }
    }
}

# Which wavepackets are initial values
initvals = [wp0]

leading_component = 0

# How often do we write data to disk
write_nth = 5

matrix_exponential = "pade"

Now we have to run the main simulation program. This is done by the following command:

Main.py harmonic_1D_p.py

where we have to provide the configuration file as command line option of the Main.py program. The Main.py command (like all other commands) supports an online help listing the available options and switches:

Main.py --help

usage: Main.py [-h] [-o OUTPUTFILE] [-r [RESULTSPATH]] parametersfile

positional arguments:
  parametersfile        The simulation configuration parameters file.

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUTFILE, --outputfile OUTPUTFILE
                        The data file to write the transformed data.
  -r [RESULTSPATH], --resultspath [RESULTSPATH]
                        Path where to put the results.

When the program terminates, it leaves a file called simulation_results.hdf5 which contains all the simulation data. This hdf results file is stored in the local directory where the script was called (unless specified otherwise by the -o or -r switches) and not in the directory where the configuration file was loaded from. The script refuses to run if it would overwrite an existing hdf file. This measure is in place to prevent you from data loss.

We can use the program hdfview for example to gain some insight of the contents of the file. More tools for manipulating hdf files can be found on the web-page of the [hdfgroup]. Two very useful command line tools are h5ls and h5dump.

[hdfgroup]

http://www.hdfgroup.org/products/hdf5_tools/