[MAIN PR] Read the 3D Mesh (Issue #390)

[lsawade]

Description

Implementation of the 3D mesh reader, and associated updates to the codebase.

Main tracking branch: Branch issue-390

PRs

New implementations

• Issue 457 -- Implement Meshfem Parameter writer #460
• Issue 461 -- Implement Parameter Reader  #462
• Issue 472 -- Implement templated array reading for multidimensional fortran arrays. Reading ibool, coordinates, partials #475
• Issue 484/498/499/500 -- Implements reading of ispec_is_<medium>, materials, and mass matrices. #501
• Issue 502 - Implements new read_array templates dim3 absorbing boundaries write/read #503
• Issue 504 - Implement the reading of coupled interfaces. #505

Restructure

• Updated the save_database function to write element by element #392
• Make the directory structure for 3D mesher flexible #430
• Separate mesher and generate databases par file #431
• Issue 455 - Refactor IO/mesh/impl/fortran -> IO/mesh/impl/fortran/dim2 & create barebone specfem3d.cpp #456
• Issue 398 - Implement dynamic testing #464
• Issue 463 -- Making header files configuration files  #467
• Issue 482 - Fix cuda compilation + new presets #483
• Issue 485 -- Refactor of mesh struct to split it in dim2 and dim3 folders #486
• [Issue 502 - Implements new read_array templates dim3 absorbing boundaries write/read #503]
• Issue 506 - Addressing comments on previous few commits #510
• Issue 508 -- Implement final bout of structus to read in the 3D mesh #519
• Issue 529 - Fixes the array ordering in the specfem++ arrays #532

Issue Number

For the related issues, please see the PRs

Checklist

Please make sure to check developer documentation on specfem docs.

• I ran the code through pre-commit to check style
• My code passes all the integration tests
• I have added sufficient unittests to test my changes
• I have added/updated documentation for the changes I am proposing
• I have updated CMakeLists to ensure my code builds
• My code builds across all platforms

[lsawade]

ooof I see there are conflict nowwwwww

[lsawade]

Yay!!!

[Rohit-Kakodkar]

Approved! Assuming I saw all previous PRs