Improve serialization of settings

[mhoeijm]

The settings subpackage heavily relies on stdlib dataclasses to manage the various settings and material configurations. However, serialization and validation of incoming settings is tedious and error prone. pydantic offers a flexible framework to manage serialization and validation.

[mhoeijm]

In #1259 and related PRs such as #1244 , #1233, #1242 pydantic is introduced for serialization and validating simulation settings data.