Merge branch 'main' of https://github.com/PeriHub/PeriLab.j

.github/workflows/TagBot.yml

@@ -32,9 +32,7 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
           ssh: ${{ secrets.DOCUMENTER_KEY }}
-          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}
   DockerHub:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
@@ -50,10 +48,10 @@ jobs:
         id: get_version
         run: echo "PERILAB_VERSION=$(awk -F'"' '/version/{print $2}' Project.toml)" >> $GITHUB_OUTPUT
       - name: Build Docker image
-        run: docker build -t perihub/perilab:$PERILAB_VERSION .
+        run: docker build -t perihub/perilab:${{ steps.get_version.outputs.PERILAB_VERSION }} .
       - name: Publish to Registry
-        run: docker push perihub/perilab:$PERILAB_VERSION
+        run: docker push perihub/perilab:${{ steps.get_version.outputs.PERILAB_VERSION }}
       - name: Retag latest
-        run: docker tag perihub/perilab:$PERILAB_VERSION perihub/perilab:latest
+        run: docker tag perihub/perilab:${{ steps.get_version.outputs.PERILAB_VERSION }} perihub/perilab:latest
       - name: Publish to Registry
         run: docker push perihub/perilab:latest

.reuse/dep5

@@ -1,7 +1,7 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PeriLab
 Upstream-Contact: Christian Willberg <christian.willberg@dlr.de>, Jan-Timo Hesse <jan-timo.hesse@dlr.de>
-Source: https://gitlab.com/dlr-perihub/perilab
+Source: https://github.com/PeriHub/PeriLab.jl
 
 # Sample paragraph, commented out:
 #

CHANGELOG.md

@@ -8,6 +8,12 @@ SPDX-License-Identifier: BSD-3-Clause
 
 All notable changes to this project will be documented in this file.
 
+## [1.1.2] - 2024-03-25
+
+### Fixed
+
+- Abaqus surface extension
+
 ## [1.1.1] - 2024-03-21
 
 ### Fixed
@@ -137,6 +143,6 @@ All notable changes to this project will be documented in this file.
 
 - First full PeriLab release
 
-[1.0.2]: https://gitlab.com/dlr-perihub/PeriLab.jl/-/compare/v1.0.1...v1.0.2
-[1.0.1]: https://gitlab.com/dlr-perihub/PeriLab.jl/-/compare/v1.0.0...v1.0.1
-[1.0.0]: https://gitlab.com/dlr-perihub/PeriLab.jl/-/tags/v1.0.0
+[1.0.2]: https://github.com/PeriHub/PeriLab.jl/-/compare/v1.0.1...v1.0.2
+[1.0.1]: https://github.com/PeriHub/PeriLab.jl/-/compare/v1.0.0...v1.0.1
+[1.0.0]: https://github.com/PeriHub/PeriLab.jl/-/tags/v1.0.0

Project.toml

@@ -1,7 +1,7 @@
 name = "PeriLab"
 uuid = "2ecefcea-59f0-46dd-9cfd-1d2b8cc5f112"
 authors = ["Christian Willberg <christian.willberg@dlr.de>", "Jan-Timo Hesse <jan-timo.hesse@dlr.de>"]
-version = "1.1.1"
+version = "1.1.2"
 
 [deps]
 AbaqusReader = "bc6b9049-e460-56d6-94b4-a597b2c0390d"
@@ -42,7 +42,7 @@ CSV = "^0.10"
 DataFrames = "^1"
 Dates = "^1"
 Dierckx = "^0.5"
-Exodus = "^0.11, 0.13"
+Exodus = "^0.12"
 FastGaussQuadrature = "^1"
 JSON3 = "^1"
 LibGit2 = "^1"

README.md

@@ -20,8 +20,8 @@ SPDX-License-Identifier: BSD-3-Clause
 Welcome to `PeriLab`, a powerful software solution designed for tackling Peridynamic problems. 
 
 <p align="center" style="font-size:0;"><!--
-  PeriLab_crack      --><img align="middle" src="https://gitlab.com/dlr-perihub/PeriLab.jl/-/raw/main/assets/PeriLab_crack.gif" width="50%"><!--
-  PeriLab_additive      --><img align="middle" src="https://gitlab.com/dlr-perihub/PeriLab.jl/-/raw/main/assets/PeriLab_additive.gif" width="50%">
+  PeriLab_crack      --><img align="middle" src="https://raw.githubusercontent.com/PeriHub/PeriLab.jl/main/assets/PeriLab_crack.gif" width="50%"><!--
+  PeriLab_additive      --><img align="middle" src="https://raw.githubusercontent.com/PeriHub/PeriLab.jl/main/assets/PeriLab_additive.gif" width="50%">
 </p>
 
 ## Documentation
@@ -79,17 +79,18 @@ using PeriLab
 PeriLab.get_examples()
 PeriLab.main("examples/DCB/DCBmodel.yaml")
 ```
->Note: More details about the main functionalities in the yaml input deck [here](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/src/Support/Parameters/parameter_handling.jl?ref_type=heads).
+>Note: More details about the main functionalities in the yaml input deck [here](https://github.com/PeriHub/PeriLab.jl/blob/main/src/Support/Parameters/parameter_handling.jl).
 
 ## Parallel Processing with `PeriLab` (MPI)
 
-To handle large-scale problems efficiently, install [MPI](https://juliaparallel.org/MPI.jl/stable/usage/). Run PeriLab with two processors using the following commands:
+To handle large-scale problems efficiently, install [MPI](https://juliaparallel.org/MPI.jl/stable/usage/). Run PeriLab with two processors on a **Linux** system using the following commands:
 
 ```sh
 $ julia
 julia> using MPI
 julia> MPI.install_mpiexecjl()
 ```
+>Note: If you work with **Windows 10 or higher** you can use the [WSL](https://learn.microsoft.com/en-us/windows/wsl/install) environment.
 
 Run PeriLab with two processors:
 ```sh
@@ -122,7 +123,7 @@ Now, you've successfully installed PeriLab using the official Perihub/Perilab Do
 
 ## `PeriLab` on `JuliaHub`
 
-Experience the convenience of using PeriLab as a ready-to-use application on JuliaHub. Simply create an [account](https://juliahub.com), navigate to the [applications page](https://juliahub.com/ui/Applications), and add the repository URL: https://gitlab.com/dlr-perihub/PeriLab.jl.
+Experience the convenience of using PeriLab as a ready-to-use application on JuliaHub. Simply create an [account](https://juliahub.com), navigate to the [applications page](https://juliahub.com/ui/Applications), and add the repository URL: https://github.com/PeriHub/PeriLab.jl.
 
 Configure advanced options, such as _filename_, _dryrun_, _verbosity_, _debug_, and _silence_. Click __Start__ and monitor the job progress. Results will be available in a zipped folder.
 
@@ -157,7 +158,7 @@ We welcome contributions in various forms, including bug reports, documentation
 ### Development
 1. **Clone the repository:**
 ```sh
-git clone https://gitlab.com/dlr-perihub/PeriLab.jl
+git clone https://github.com/PeriHub/PeriLab.jl
 cd PeriLab.jl
 ```
 2. **Activate the environment and install dependencies:**
@@ -177,7 +178,7 @@ For any questions or inquiries about PeriLab.jl, feel free to reach out to the a
 
 ## Authors and acknowledgment
 
-<a href="https://orcid.org/0000-0003-2433-9183"><img src="https://orcid.figshare.com/ndownloader/files/8439032/preview/8439032/preview.jpg" style="height:15px;width:auto;vertical-align: top;background-color:transparent;"> </a>[Dr.-Ing. Christian Willberg](mailto::christian.willberg@dlr.de)
+<a href="https://orcid.org/0000-0003-2433-9183"><img src="https://orcid.figshare.com/ndownloader/files/8439032/preview/8439032/preview.jpg" style="height:15px;width:auto;vertical-align: top;background-color:transparent;"> </a>[Dr.-Ing. Christian Willberg](mailto::christian.willberg@h2.de)
 
 <a href="https://orcid.org/0000-0002-3006-1520"><img src="https://orcid.figshare.com/ndownloader/files/8439032/preview/8439032/preview.jpg" style="height:15px;width:auto;vertical-align: top;background-color:transparent;"> [M.Sc. Jan-Timo Hesse](mailto::jan-timo.hesse@dlr.de)
 
@@ -203,7 +204,7 @@ For any questions or inquiries about PeriLab.jl, feel free to reach out to the a
 ## Partner
 
        
-| <img src="https://gitlab.com/dlr-perihub/PeriLab.jl/-/raw/main/assets/dlr.jpg" height="200" title="German Aerospace Center"> | <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Logo_h2.svg/1280px-Logo_h2.svg.png" height="200" title="Magdeburg-Stendal University of Applied Science"> |
+| <img src="https://raw.githubusercontent.com/PeriHub/PeriLab.jl/main/assets/dlr.jpg" height="200" title="German Aerospace Center"> | <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Logo_h2.svg/1280px-Logo_h2.svg.png" height="200" title="Magdeburg-Stendal University of Applied Science"> |
 |:------------------------------------------------------------------------------------------------------------------------------:|:-------------------------------------------------------------------------------------------------------------------------------------:|
 | [German Aerospace Center](http://www.dlr.de/sy)                                                                               | [Magdeburg-Stendal University of Applied Science](http://www.h2.de)                                                                  |
 
@@ -215,22 +216,22 @@ For any questions or inquiries about PeriLab.jl, feel free to reach out to the a
 
 <p align="center" style="font-size:0;"><!--
   <!--
-  DFG      --><img align="middle" src="https://gitlab.com/dlr-perihub/PeriLab.jl/-/raw/main/assets/dfg.jpg" height="120">
+  DFG      --><img align="middle" src="https://raw.githubusercontent.com/PeriHub/PeriLab.jl/main/assets/dfg.jpg" height="120">
 </p>
 
 This project has benefited from funding by the [Deutsche
 Forschungsgemeinschaft](https://www.dfg.de/) (DFG, German Research Foundation)
 through the following grant ''Gekoppelte Peridynamik-Finite-Elemente-Simulationen zur Schädigungsanalyse von Faserverbundstrukturen''. <br/><br/>Grant number: [WI 4835/5-1](https://gepris.dfg.de/gepris/projekt/456427423)
 <p align="center" style="font-size:0;"><!--
-  SACHSEN  --><img align="middle" src="https://gitlab.com/dlr-perihub/PeriLab.jl/-/raw/main/assets/sachsen.jpg" height="120">
+  SACHSEN  --><img align="middle" src="https://raw.githubusercontent.com/PeriHub/PeriLab.jl/main/assets/sachsen.jpg" height="120">
 </p>
 
 [M-ERA.NET](https://www.m-era.net/) funded project ''Exploring Multi-Method Analysis of composite structures and joints under consideration of uncertainties engineering and processing (EMMA)''
 
 This measure is co-financed with tax funds on the basis of the budget passed by the [Saxon state parlament](https://www.landtag.sachsen.de/de). <br/><br/>Grant number: [3028223](https://www.m-era.net/materipedia/2020/emma).
 
 <p align="center" style="font-size:0;"><!--
-  HyTank  --><img align="middle" src="https://gitlab.com/dlr-perihub/PeriLab.jl/-/raw/main/assets/hytank.jpg" height="120"><!--
+  HyTank  --><img align="middle" src="https://raw.githubusercontent.com/PeriHub/PeriLab.jl/main/assets/hytank.jpg" height="120"><!--
   -->
 </p>
 

bin/main.jl

@@ -28,8 +28,9 @@ dryrun = get(ENV, "dryrun", "false") == "true"
 verbose = get(ENV, "verbose", "false") == "true"
 debug = get(ENV, "debug", "false") == "true"
 silent = get(ENV, "silent", "false") == "true"
+reload = get(ENV, "reload", "false") == "true"
 
-PeriLab.main(filename, "./results", dryrun, verbose, debug, silent)
+PeriLab.main(filename; output_dir="./results", dryrun=dryrun, verbose=verbose, debug=debug, silent=silent, reload=reload)
 
 zip_filename = "results.zip"
 zip_folder(output_dir, zip_filename)

docs/make.jl

@@ -13,9 +13,10 @@ makedocs(
     doctest=true,
     checkdocs=:none, # :all, :exports, :none
     sitename="PeriLab",
-    repo=Documenter.Remotes.GitLab("dlr-PeriHub", "PeriLab"),
+    repo=Documenter.Remotes.GitHub("PeriHub", "PeriLab.jl"),
+
     format=Documenter.HTML(
-        canonical="https://gitlab.com/dlr-perihub/perilab",
+        canonical="https://github.com/PeriHub/PeriLab.jl",
         assets=["assets/favicon.ico"],
         edit_link="main"
     ),

docs/src/index.md

@@ -31,18 +31,18 @@ cannot figure out how to do, please reach out with questions in Domains/Data on
 [Discourse](https://github.com/PeriHub/PeriLab.jl/discussions).
 
 Please report bugs by
-[opening an issue](https://gitlab.com/dlr-perihub/PeriLab.jl/-/issues/new).
+[opening an issue](https://github.com/PeriHub/PeriLab.jl/issues/new/choose).
 
 You can follow the **source** links throughout the documentation to jump right
 to the source files on GitHub to make pull requests for improving the
 documentation and function capabilities.
 
 Please review [PeriLab contributing
-guidelines](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/CONTRIBUTING.md)
+guidelines](https://github.com/PeriHub/PeriLab.jl/blob/main/CONTRIBUTING.md)
 before submitting your first PR!
 
 Information on specific versions can be found on the [Release
-page](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/CHANGELOG.md).
+page](https://github.com/PeriHub/PeriLab.jl/blob/main/CHANGELOG.md).
 
 ## Package Manual
 
@@ -59,4 +59,4 @@ loading the PeriLab.jl package with `using PeriLab`) types and functions
 are considered a part of the public API of the PeriLab.jl package. In general
 all such objects are documented in this manual (in case some documentation is
 missing please kindly report an issue
-[here](https://gitlab.com/dlr-perihub/PeriLab.jl/-/issues/new)).
+[here](https://github.com/PeriHub/PeriLab.jl/-/issues/new)).

docs/src/lib/faq.md

@@ -24,7 +24,7 @@ There are multiple options to generate your own input mesh:
 
 - Use the [Perihub](https://gitlab.com/dlr-perihub/Perihub.jl) framework to generate your own input mesh.
 
-- Generate your own input mesh with julia, [here](https://gitlab.com/dlr-perihub/PeriLab.jl/-/tree/main/examples/Training/meshing/mesh.jl?ref_type=heads) is an example.
+- Generate your own input mesh with julia, [here](https://github.com/PeriHub/PeriLab.jl/-/tree/main/examples/Training/meshing/mesh.jl?ref_type=heads) is an example.
 
 - Use an existing Abaqus Inputfile (.inp).
 
@@ -52,4 +52,4 @@ If your question is not addressed here, please feel free to [contact us](mailto:
 
 ## Contributions
 
-Contributions are always welcomed, take a look at the [Contributing Guidelines](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/CONTRIBUTING.md)
+Contributions are always welcomed, take a look at the [Contributing Guidelines](https://github.com/PeriHub/PeriLab.jl/blob/main/CONTRIBUTING.md)

docs/src/lib/functions.md

@@ -64,6 +64,7 @@ set_max_rank
 set_synch
 switch_NP1_to_N
 synch_manager
+clear_data_manager
 ```
 
 ```@meta

docs/src/man/input_yaml.md

@@ -85,7 +85,7 @@ The PeriLab configuration file is a YAML file used to specify the parameters for
       - **_Own_Name_**: Numeric value representing interblock damage. (Float64 or Int64, required)
     - **Anisotropic Damage**: Dictionary of anisotropic damage parameters.
       - **Critical Value X/Y**: Numeric values representing critical values in X and Y directions. (Float64 or Int64, required)
-- **Material Models**: Dictionary of material models. (optional)
+- **Material Models**: Dictionary of [material models](material_manual.md). (optional)
   - **_Own_Name_**: List of material model configurations.
     - **Material Model**: String representing the material model.
     - **Symmetry**: String representing the symmetry. (optional)

docs/src/manual.md → docs/src/man/material_manual.md

@@ -1,67 +1,16 @@
-# Model defintion
-A basic PeriLab model exists two files. A mesh file and a yaml file.
+# Material Models
 
-## Mesh file
-The mesh file is an ASCII file and has the following structure for 2D.
-| header: x | y | block_id | volume |
-|:---|:---|:---|:---|
-|-1.5| 0 | 1 | 1.e-01 |
-|-0.5| 0 | 1 | 1.e-01 |
-|0.5 | 0 | 1 | 1.e-01 |
-|1.5 | 0 | 1 | 1.e-01 |
-|-1.5| 1 | 1 | 1.e-01 |
-
-and 3D 
-
-| header: x | y | z | block_id | volume |
-|:---|:---|:---|:---|:---|
-|-1.5| 0 | 2 | 1 | 1.e-01 |
-|-0.5| 0 | 2 | 1 | 1.e-01 |
-|0.5 | 0 | 2 | 1 | 1.e-01 |
-|1.5 | 0 | 0 | 1 | 1.e-01 |
-|-1.5| 1 | 1 | 1 | 1.e-01 |
-
-The difference is found automatically. If no z occurs PeriLab identifies it as 2D problem and requests a plane stress or plane strain definition.
-
-Additional parameter can be applied in the header. They will be added in the datamanager and can be used in the programm. If you add x,y,z to the parameter a multidimensional field will be created, e.g.
-MyVarx, MyVary will be created as field MyVar with 2 degrees of freedom.
-
-
-**Variable definition**
-| Parameter | Datamanager name | Header name 2D | Header name 3D | Type | 
-|:---|:---|:---|:---|:---|
-|x, y, z (optional) coordinate of the node | Coordinates | x, y | x, y, z | Float64, Int64|
-| Definition to which block the node corresponds. Is needed in the Yaml file to define properties | Block_Id | block_id | block_id | Int64|
-| Volume the node represents. | Volume | volume | volume | Float64, Int64|
-
-
-**Optional**
-| Parameter | Datamanager name | Header name 2D | Header name 3D | Type | 
-|:---|:---|:---|:---|:---|
-| Orientation of a Node | Angles | Angles | Anglesx, Anglesy, Anglesz | Float64, Int64|
-| Activation time of a node, e.g. used for additive manufacturing to define when the node will be acativated | Activation_Time | Activation_Time | Activation_Time | Float64, Int64|
-| Status of the node. If it is false the node is deactivated, but exists. This variable is automatically created if additive models are used and set everywhere to false, if it is not predefined | Active | Active | Active | Bool |
-
-## Yaml file
-
-tbd
-
-## Node set file (optional)
-
-
-# Existing Models
+## Existing Models
 The physics related functions can be found [here](
 https://perihub.github.io/PeriLab.jl/stable/lib/physics_functions/
 ).
-## Material Models
-
 | Method | Related Model in PeriLab |
 |---|---|
 | [Bond-based](theory/basics.md#Bond-based) | [Bond-based Elastic](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/src/Physics/Material/BondBased/Bondbased_Elastic.jl) |
 | [Ordinary state-based](theory/basics.md#PD_Solind) | [PD Solid Elastic](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/src/Physics/Material/Material_Models/PD_Solid_Elastic.jl) [PD Solid Plastic](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/src/Physics/Material/Material_Models/PD_Solid_Plastic.jl) |
 |[Non-ordinary state-based](theory/basics.md#Correspondence)| [Correspondence Elastic](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/src/Physics/Material/Material_Models/Correspondence_Elastic.jl) [Correspondence Plastic](https://gitlab.com/dlr-perihub/PeriLab.jl/-/blob/main/src/Physics/Material/Material_Models/Correspondence_Plastic.jl)|
 
-**Bond-based Elastic**
+## Bond-based Elastic
 
 The theory of the bond-based elastic material can be found [here](theory/basics.md#Bond-based)
 
@@ -78,7 +27,7 @@ tabelle
 One of theses parameters have to be defined. 
 >Note: In the bond-based formulation the Poisson's ratio is fixed by [0.25 for 2D plane strain and 1/3 for 3D and 2D plane stress](https://link.springer.com/article/10.1007/s42102-019-00021-x), respectively.
 
-**PD Solid Elastic**
+## PD Solid Elastic
 
 | Parameter | Unit | Description |
 |---|---|---|
@@ -89,14 +38,14 @@ One of theses parameters have to be defined.
 
 Two of these parameters have to be defined. The other two are determined automatically and can be used in the model if needed.
 
-**PD Solid Plastic**
+## PD Solid Plastic
 
 | Parameter | Unit | Description |
 |---|---|---|
 |Yield Stress | $\left[N/m^2\right]$| [Yield stress](https://en.wikipedia.org/wiki/Yield_(engineering))
 
 
-**Correspondence Elastic**
+## Correspondence Elastic
 
 
 | Parameter | Unit | Description |
@@ -113,19 +62,18 @@ For Correspondence Elastic you can provide all 27 elastic parameters if you like
 
 >Note 2: If you define a field "Angles" for 2D or "Anglesx", "Anglesy" and "Anglesz" for 3D in the mesh file your material will be rotated. This helps to create an arbitrary material orientation.
 
-
-**Correspondence Plastic**
+## Correspondence Plastic
 
 | Parameter | Unit | Description |
 |---|---|---|
 |Yield Stress | $\left[N/m^2\right]$| [Yield stress](https://en.wikipedia.org/wiki/Yield_(engineering))
 
-**Correspondence UMAT**
+## Correspondence UMAT
 
 in developement
 
 
-**Model merging**
+## Model merging
 
 In PeriLab you are able to combine models with each other, by simply adding a +. Therefore, modules can be merged and double coding can be avoided.