Input/Output

Input file

The text input file of a simulation should be precised using the method initialize which will instantiate the static Parser object of Akantu. This section explains how to manipulate at Parser objects to input data in Akantu.

Akantu Parser

Akantu file parser has a tree organization.

Parser, the root of the tree, can be accessed using:
```
auto & parser = getStaticParser();
```
ParserSection, branch of the tree, contains map a of sub-sections (ParserType, ParserSection) and a ParserSection * pointing to the parent section. The user section of the input file can directly be accessed by:
```
const auto & usersect = getUserParser();
```
ParserParameter, the leaf of the tree, carries data of the input file which can be cast to the correct type with the assignment operator:
```
Real mass = usersect.getParameter("mass");
```
or used directly within an expression

Grammar

The structure of text input files consists of different sections containing a list of parameters. As example, the file parsed in the previous section will look like:

user parameters [
  mass = 10.5
]

Basically every standard arithmetic operations can be used inside of input files as well as the constant pi and e and the exponent operator ^. Operations between ParserParameter are also possible with the convention that only parameters of the current and the parent sections are available. Vector and Matrix can also be read according to the NumPy [num] writing convention (a.e. cauchy_stress_tensor = [[\(\sigma_{xx}\), \(\sigma_{xy}\)],[\(\sigma_{yx}\),\(\sigma_{yy}\)]]). An example illustrating how to parse the following input file can be found in example\io\parser\example_parser.cc:

user parameters [
    spatial_dimension = 2
    mesh_file     = swiss_cheese.msh
    inner_holes   = holes
    outter_crust  = crust
    lactostatic_p = 30e3
    stress        = [[lactostatic_p, 0            ],
                     [0,             lactostatic_p]]
    max_nb_iterations = 100
    precision     = 1e-9
]

Material section

The input file should also be used to specify material characteristics (constitutive behavior and material properties). The dedicated material section is then read by initFull method of SolidMechanicsModel which initializes the different materials specified with the following convention:

material constitutive_law [
  name = value
  rho = value
  ...
]

where constitutive_law is the adopted constitutive law, followed by the material properties listed one by line in the bracket (e.g., name and density :math:rho. Some constitutive laws can also have an optional flavor. More information can be found in sections relative to material Constitutive Laws.

Output data

Generic data

In this section, we address ways to get the internal data in human-readable formats. The models in Akantu handle data associated to the mesh, but this data can be split into several Arrays. For example, the data stored per element type in a ElementTypeMapArray is composed of as many Arrays as types in the mesh.

In order to get this data in a visualization software, the models contain a object to dump VTK files. These files can be visualized in software such as ParaView [par], ViSit [vis] or Mayavi [may].

The internal dumper of the model can be configured to specify which data fields are to be written. This is done with the addDumpField method. By default all the files are generated in a folder called paraview/:

model.setBaseName("output"); // prefix for all generated files
model.addDumpField("displacement"); model.addDumpField("stress"); ...
model.dump()

The fields are dumped with the number of components of the memory. For example, in 2D, the memory has Vectors of 2 components, or the \(2^{nd}\) order tensors with \(2\times2\) components. This memory can be dealt with addDumpFieldVector which always dumps Vectors with 3 components or addDumpFieldTensor which dumps \(2^{nd}\) order tensors with \(3\times3\) components respectively. The routines addDumpFieldVector and addDumpFieldTensor were introduced because of ParaView which mostly manipulate 3D data.

Those fields which are stored by quadrature point are modified to be seen in the VTK file as elemental data. To do this, the default is to average the values of all the quadrature points.

The list of fields depends on the models (for SolidMechanicsModel see table List of dumpable fields for SolidMechanicsModel..

Table 7 List of dumpable fields for `SolidMechanicsModel`.
key	type	support
displacement	`Vector<Real>`	nodes
mass	`Vector<Real>`	nodes
velocity	`Vector<Real>`	nodes
acceleration	`Vector<Real>`	nodes
force	`Vector<Real>`	nodes
residual	`Vector<Real>`	nodes
increment	`Vector<Real>`	nodes
blocked_dofs	`Vector<bool>`	nodes
partitions	`Real`	elements
material_index	variable	elements
strain	`Matrix<Real>`	quadrature points
Green strain	`Matrix<Real>`	quadrature points
principal strain	`Vector<Real>`	quadrature points
principal Green strain	`Vector<Real>`	quadrature points
grad_u	`Matrix<Real>`	quadrature points
stress	`Matrix<Real>`	quadrature points
Von Mises stress	`Real`	quadrature points
material_index	variable	quadrature points

Cohesive elements’ data

Cohesive elements and their relative data can be easily dumped thanks to a specific dumper contained in SolidMechanicsModelCohesive. In order to use it, one has just to add the string cohesive elements when calling each method already illustrated. Here is an example on how to dump displacement and damage:

model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");

Fragmentation data

Whenever the SolidMechanicsModelCohesive is used, it is possible to dump additional data about the fragments that get formed in the simulation both in serial and parallel. This task is carried out by the FragmentManager class, that takes care of computing the following quantities for each fragment:

index;
mass;
moments of inertia;
velocity;
number of elements.

These computations can be realized at once by calling the function computeAllData, or individually by calling the other public functions of the class. The data can be dumped to be visualized in ParaView, or can be accessed within the simulation. An example of usage is:

At the end of this example the velocities of the fragments are accessed with a reference to a const Array<Real>. The size of this array is the number of fragments, and its number of components is the spatial dimension in this case.

Advanced dumping

Arbitrary fields

In addition to the predetermined fields from the models and materials, the user can add any data to a dumper as long as the support is the same. That is to say data that have the size of the full mesh on if the dumper is dumping the mesh, or of the size of an element group if it is a filtered dumper.

For this the easiest is to use the “external” fields register functions

The simple case force nodal and elemental data are to pass directly the data container itself if it as the good size.

For nodal fields:

It is assumed that the array as the same size as the number of nodes in the mesh
For elemental fields:

It is assumed that the arrays in the map have the same sizes as the element numbers in the mesh for element types of dimension spatial_dimension.

If some changes have to be applied on the data as for example a padding for ParaView vectors, this can be done by using the field interface.

All these functions use the default dumper registered in the mesh but also have the ToDumper variation with the dumper name specified. For example:

An example of code presenting this interface is present in the examples/io/dumper. This interface is part of the Dumpable class from which the Mesh inherits.

Creating a new dumper

You can also create you own dumpers, Akantu uses a third-party library in order to write the output files, IOHelper. Akantu supports the ParaView format and a Text format defined by IOHelper.

This two files format are handled by the classes DumperParaview and DumperText.

In order to use them you can instantiate on of this object in your code. This dumper have a simple interface. You can register a mesh registerMesh, registerFilteredMesh or a field, registerField.

An example of code presenting this low level interface is present in the examples/io/dumper. The different types of Field that can be created are present in the source folder src/io/dumper.