Output Data

CLI Usage

This documentation page is intended for the Command Line Interface (CLI). If you're new to DuneCopasi, we recommend starting with our Tutorials.

Several output data files in the dune-copasi program are possible:

Simulation Results (VTK Format)

Config Options:

• model.writer.vtk.path={prefix}

Writes a set vtu files with the scalar field solution of the problem in the file system under {prefix}-{cmp} directory for each {cmp} compartment. Additionally, a compendium of all timesteps for each compartment is written in a pvd file on the same directory. The resulting vtu and pvd files can be opened by ParaView or VisiIt to visualize their results.

Simulation Trace (Perfetto Format)

Config Options:

• trace.path={prefix}

Writes a trace file with the timing information of the simulation on the current directory. To visualize the trace, use Perfetto Trace Viewer. Only available if binary is built with Perfetto.

Matrix Layout (SVG Format)

Config Options:

• model.time_step_operator.linear_solver.layout.writer.svg.path={prefix}

Writes a svg file with the matrix layout of the jacobian of the system in the current directory.

There are a number of parameters that affect the resulting layout:

• The model.blocked_layout.[compartments|scalar_fields]=<bool> options affect the hierarchal structure of the matrix.
• The number of scalar fields in model.scalar_field.{var}.* and the compartment {cmp} where the belong (i.e., model.scalar_field.{var}.compartment={cmp}) affacts the position of the matrix entries.
• The grid connectivity affects the position of the matrix entries.
• The jacobian options of the reaction operator (i.e. model.scalar_field.{var}.reaction.jacobian.{wrt}.expression) affects the appearance of many entries in the matrix.

To visualize the results of this option use your web browser, GIMP, Inkscape, Affinity Designer or another vector graphics editor.

This option will only have effect when the a matrix is created, (e.g., matrix-free computation won't write any file).

output size

The SVG format is helpful to understand the sparsity pattern and hierarchy of the matrix, however, this format is not particularly efficient to represent matrices. Hence, use this option only with small and medium problem sizes.

tip

If the resulting SVG file turns out to be too big, try converting the file into another format like png or jpeg with Inkscape or similar:

inkscape -z -w 20000 -h 20000 matrix.svg -e matrix.png

example output

Random Field (VTK Format)

Config Options:

• parser_context.{tkn}.type=random_field
• parser_context.{tkn}.writer.vtk.path={prefix}

Writes a vtu file with the contents of the generated random field in the filesystem with the {tkn} keyword as a base name. This option can only be used together with parser_context.{tkn}.type=random_field. The resulting vtu files can be opened by ParaView or VisiIt to visualize their results.