From c832d1934a5f4f90377e3a07024cce831af976e7 Mon Sep 17 00:00:00 2001 From: danlwill Date: Wed, 22 Jan 2025 14:42:31 -0500 Subject: [PATCH 01/11] Update app_files.md --- .../user_manual/app_files/app_files.md | 41 +++++++++++++++---- 1 file changed, 34 insertions(+), 7 deletions(-) diff --git a/doc/doxygen/user_manual/app_files/app_files.md b/doc/doxygen/user_manual/app_files/app_files.md index ec43b2f9b..87ab85058 100644 --- a/doc/doxygen/user_manual/app_files/app_files.md +++ b/doc/doxygen/user_manual/app_files/app_files.md @@ -17,16 +17,43 @@ The file ''equations.cc'' contains a list of the variables in the model equation To modify the functions in this file, one needs to be familiar with the weak form of the governing equations. In PRISMS-PF, the governing equations are expressed in two terms. The first is the part of the integrand that is multiplied by the test function (marked by 'eq' with the subscript of the variable in the example below). The second is the part of the integrand that multiplied by the gradient of the test function (marked by 'eqx' with the subscript of the variable in the example below). For the coupled Cahn-Hilliard/Allen-Cahn system, the governing equations are -\f[ -\int_{\Omega} w \eta^{n+1} ~dV =\int_{\Omega} w \left( \underbrace{\eta^{n} - \Delta t M_{\eta}~ ((f_{\beta,c}^n-f_{\alpha,c}^n)H_{,\eta}^n)}_{eq_{\eta}} \right)+ \nabla w \cdot \underbrace{(- \Delta t M_{\eta}\kappa) \nabla \eta^{n}}_{eqx_{\eta}} ~dV -\f] +$$ +\begin{align} +\int_{\Omega} w \eta^{n+1} ~dV =\int_{\Omega} w \left( \eta^{n} - \Delta t M_{\eta}~ ((f_{\beta,c}^n-f_{\alpha,c}^n)H_{,\eta}^n) \right)+ \nabla w \cdot (- \Delta t M_{\eta}\kappa) \nabla \eta^{n} ~dV +\end{align} +$$ + +$$ +\begin{align} +eq_{\eta} &= \eta^{n} - \Delta t M_{\eta}~ ((f_{\beta,c}^n-f_{\alpha,c}^n)H_{,\eta}^n) +\end{align} +$$ + +$$ +\begin{align} +eqx_{\eta} &= (- \Delta t M_{\eta}\kappa) \nabla \eta^{n} +\end{align} +$$ and -\f[ - -]$\int_{\Omega} w c^{n+1} ~dV = \int_{\Omega} w \underbrace{c^{n}}_{eq_c} + \nabla w \underbrace{(-\Delta t M_{c})~ [~(f_{\alpha,cc}^n(1-H^{n+1})+f_{\beta,cc}^n H^{n+1}) \nabla c + ~((f_{\beta,c}^n-f_{\alpha,c}^n)H^{n+1}_{,\eta} \nabla \eta) ] }_{eqx_{c}} ~dV -\f] +$$ +\begin{align} +]$\int_{\Omega} w c^{n+1} ~dV = \int_{\Omega} w c^{n} + \nabla w (-\Delta t M_{c})~ [~(f_{\alpha,cc}^n(1-H^{n+1})+f_{\beta,cc}^n H^{n+1}) \nabla c + ~((f_{\beta,c}^n-f_{\alpha,c}^n)H^{n+1}_{,\eta} \nabla \eta) ] ~dV +\end{align} +$$ + +$$ +\begin{align} +eq_c &= c^{n} +\end{align} +$$ + +$$ +\begin{align} +eqx_{c} &= (-\Delta t M_{c})~ [~(f_{\alpha,cc}^n(1-H^{n+1})+f_{\beta,cc}^n H^{n+1}) \nabla c + ~((f_{\beta,c}^n-f_{\alpha,c}^n)H^{n+1}_{,\eta} \nabla \eta) +\end{align} +$$ for the Allen-Cahn and Cahn-Hilliard equation, respectively. Each of the terms in the governing equation is marked with an underbrace. The terms multiplied by the test function are referred to as the value terms and the terms multiplied by the gradient of the test function are referred to as the gradient terms. From 892e815d1f795e47d6584bb202248401ce72e588 Mon Sep 17 00:00:00 2001 From: danlwill Date: Sat, 25 Jan 2025 21:46:49 -0500 Subject: [PATCH 02/11] Update app_files.md --- .../user_manual/app_files/app_files.md | 44 ++++++++++++++----- 1 file changed, 33 insertions(+), 11 deletions(-) diff --git a/doc/doxygen/user_manual/app_files/app_files.md b/doc/doxygen/user_manual/app_files/app_files.md index 87ab85058..4d3cc697d 100644 --- a/doc/doxygen/user_manual/app_files/app_files.md +++ b/doc/doxygen/user_manual/app_files/app_files.md @@ -166,31 +166,53 @@ The 'nonExplicitEquationRHS' function is where the terms in the RHS of the gover In the coupledCahnHilliardAllenCahn app, the equationLHS function is empty because it is only needed for TIME_INDEPENDENT PDEs (or more specifically, when a non-trivial matrix inversion needs to be performed). Here we go through the equationLHS function from the precipitateEvolution application, where the equation for mechanical equilibrium is TIME_INDEPENDENT. From the formulation file in the precipitateEvolution application, the governing equation for the mechanical displacement is: -\f[ + +$$ +\begin{align} R(u) = \int_{\Omega} \nabla w : C(\eta_1, \eta_2, \eta_3) : \left( \epsilon - \epsilon^0(c,\eta_1, \eta_2, \eta_3)\right) ~dV = 0 -\f] +\end{align} +$$ + In PRISMS-PF, matrix inversion problems are always written as Newton's method iterations. For linear equations, like the one above, the solution is reached in a single Newton step. The reason for this approach is two-fold. First, it provides an identical user interface for linear and nonlinear problems. Second, it enables the efficient handling of constraints for when inhomogeneous Dirichlet boundary conditions are used. -To write the above equations in terms of a Newton iteration, the solution, \f$u\f$, can be written as the sum of an initial guess, \f$u_0\f$, and an update, \f$\Delta u\f$: +To write the above equations in terms of a Newton iteration, the solution, $u$, can be written as the sum of an initial guess, $u_0$, and an update, $\Delta u$: -\f[ +$$ +\begin{align} R(u) = R(u_0 + \Delta u) = R(u_0) + \int_{\Omega} \left. \frac{\delta R(u)}{\delta u}\right|_{u=u_0} \Delta u ~dV = 0 -\f] +\end{align} +$$ In this case, the equation is linear and the variation derivative is trivial: -\f[ +$$ +\begin{align} R(u_0 + \Delta u) = \int_{\Omega} \nabla w : C(\eta_1, \eta_2, \eta_3) : \left( \epsilon(u_0 + \Delta u) - \epsilon^0(c,\eta_1, \eta_2, \eta_3)\right) ~dV = \int_{\Omega} \nabla w : C(\eta_1, \eta_2, \eta_3) : \left( \epsilon(u_0) + \epsilon(\Delta u) - \epsilon^0(c,\eta_1, \eta_2, \eta_3)\right) ~dV = 0 -\f] +\end{align} +$$ Rearranging yields: -\f[ -\int_{\Omega} \nabla w : \underbrace{C : \nabla (\epsilon(\Delta u))}_{eqx_{u}^{LHS}} dV = -\int_{\Omega} \nabla w : \underbrace{C :(\epsilon(u_0)-\epsilon^0)}_{eqx_{u}^{RHS}} ~dV -\f] +$$ +\begin{align} +\int_{\Omega} \nabla w : C : \nabla (\epsilon(\Delta u)) dV = -\int_{\Omega} \nabla w : C :(\epsilon(u_0)-\epsilon^0) ~dV +\end{align} +$$ + +$$ +\begin{align} +eqx_{u}^{LHS} &= C : \nabla (\epsilon(\Delta u)) +\end{align} +$$ + +$$ +\begin{align} +eqx_{u}^{RHS} &= C :(\epsilon(u_0)-\epsilon^0) +\end{align} +$$ -The above values of \f$eqx_{u}^{LHS}\f$ and \f$eqx_{u}^{RHS}\f$ are used to define the residuals in the equations.h file. A similar process can be undertaken for other TIME_INDEPENDENT problems. +The above values of $eqx_{u}^{LHS}$ and $eqx_{u}^{RHS}$ are used to define the residuals in the equations.h file. A similar process can be undertaken for other TIME_INDEPENDENT problems. Here is the 'equationLHS' function from the precipitateEvolution example application: ``` From f2d8b993188f399a574b654de78e876f3e5413cd Mon Sep 17 00:00:00 2001 From: danlwill Date: Sat, 25 Jan 2025 21:51:15 -0500 Subject: [PATCH 03/11] Update input_file.md --- .../user_manual/input_file/input_file.md | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/doc/doxygen/user_manual/input_file/input_file.md b/doc/doxygen/user_manual/input_file/input_file.md index 8520bbcf4..1b00069e4 100644 --- a/doc/doxygen/user_manual/input_file/input_file.md +++ b/doc/doxygen/user_manual/input_file/input_file.md @@ -126,10 +126,10 @@ set [parameter name] = [parameter value] ### Element Parameters | Name | Options | Required | Default | Description | | --------------|---------|----------|---------|----------------------------------------------------| -|Subdivisions X | Any positive integer | no | 1 | The number of mesh subdivisions in the x direction to control the element aspect ratio. The mesh size is \f$2^{(Refine Factor)} \times Subdivisions\f$ in each direction. -Subdivisions Y | Any positive integer | no | 1 | The number of mesh subdivisions in the y direction to control the element aspect ratio.The mesh size is \f$2^{(Refine Factor)} \times Subdivisions\f$ in each direction. -Subdivisions Z | Any positive integer | no | 1 | The number of mesh subdivisions in the z direction to control the element aspect ratio. The mesh size is \f$2^{(Refine Factor)} \times Subdivisions\f$ in each direction. -Refine factor | Any non-negative integer | yes | n/a | The number of initial refinements of the mesh. The mesh size is \f$2^{(Refine Factor)} \times Subdivisions\f$ in each direction. While in principle the mesh could be entirely controlled by the number of subdivisons, computational performance is best when the majority of the refinement is done via the Refine factor. +|Subdivisions X | Any positive integer | no | 1 | The number of mesh subdivisions in the x direction to control the element aspect ratio. The mesh size is $2^{(Refine Factor)} \times Subdivisions$ in each direction. +Subdivisions Y | Any positive integer | no | 1 | The number of mesh subdivisions in the y direction to control the element aspect ratio.The mesh size is $2^{(Refine Factor)} \times Subdivisions$ in each direction. +Subdivisions Z | Any positive integer | no | 1 | The number of mesh subdivisions in the z direction to control the element aspect ratio. The mesh size is $2^{(Refine Factor)} \times Subdivisions$ in each direction. +Refine factor | Any non-negative integer | yes | n/a | The number of initial refinements of the mesh. The mesh size is $2^{(Refine Factor)} \times Subdivisions$ in each direction. While in principle the mesh could be entirely controlled by the number of subdivisons, computational performance is best when the majority of the refinement is done via the Refine factor. Element degree | 1, 2, 3 | no | 1 | The polynomial order of the elements. The spatial order of accuracy is one plus the degree. ### Mesh Adaptivity (optional) @@ -176,7 +176,7 @@ Use Laplace's equation to determine the initial guess | Boolean | no | false | W ### Output (optional) | Name | Options | Required | Default | Description | | --------------|---------|----------|---------|----------------------------------------------------| -Output condition | EQUAL_SPACING, LOG_SPACING, N_PER_DECADE, LIST | no | EQUAL_SPACING | This sets the spacing between the times the simulation outputs the model variables. EQUAL_SPACING spaces them equally, LOG_SPACING spaces them \f$10^{n/(outputs) \log(time steps)}\f$, N_PER_DECADE allows the user to set how many times the simulation outputs per power of ten iterations, and LIST outputs at a user-given list of time step numbers. +Output condition | EQUAL_SPACING, LOG_SPACING, N_PER_DECADE, LIST | no | EQUAL_SPACING | This sets the spacing between the times the simulation outputs the model variables. EQUAL_SPACING spaces them equally, LOG_SPACING spaces them $10^{n/(outputs) \log(time steps)}$, N_PER_DECADE allows the user to set how many times the simulation outputs per power of ten iterations, and LIST outputs at a user-given list of time step numbers. Number of outputs | Any non-negative integer | no | 10 | The number of inputs if the output condition is EQUAL_SPACING. The number of outputs if the output condition is N_PER_DECADE. Ignored for the other output conditions. List of time steps to output | Comma-separated list of non-negative integers | no | 0 | The list of time steps to output, used for the LIST output condition and ignored for the others. Output file name (base) | String | no | solution | The name for the output file, before the time step and processor info are added. @@ -188,7 +188,7 @@ Skip print steps | Any positive integer | no | 1 | The number of time steps betw | Name | Options | Required | Default | Description | | --------------|---------|----------|---------|----------------------------------------------------| Load from a checkpoint | Boolean | no | false | Whether to start the simulation from the checkpoint of another simulation. -Checkpoint condition | EQUAL_SPACING, LOG_SPACING, N_PER_DECADE, LIST | no | EQUAL_SPACING | This sets the spacing between the times the simulation outputs the model variables. EQUAL_SPACING spaces them equally, LOG_SPACING spaces them \f$10^{n/(outputs) \log(time steps)}\f$, N_PER_DECADE allows the user to set how many times the simulation outputs per power of ten iterations, and LIST outputs at a user-given list of time step numbers. +Checkpoint condition | EQUAL_SPACING, LOG_SPACING, N_PER_DECADE, LIST | no | EQUAL_SPACING | This sets the spacing between the times the simulation outputs the model variables. EQUAL_SPACING spaces them equally, LOG_SPACING spaces them $10^{n/(outputs) \log(time steps)}$, N_PER_DECADE allows the user to set how many times the simulation outputs per power of ten iterations, and LIST outputs at a user-given list of time step numbers. Number of checkpoints | Any non-negative integer | no | 1 | The number of inputs if the output condition is EQUAL_SPACING. The number of outputs if the output condition is N_PER_DECADE. Ignored for the other output conditions. List of time steps to save checkpoints | Comma-separated list of non-negative integers | no | 0 | The list of time steps to create checkpoints, used for the LIST output condition and ignored for the others. @@ -210,7 +210,7 @@ Variable names in the files | Comma-separated list of strings | no | [empty] | W | Name | Options | Required | Default | Description | | --------------|---------|----------|---------|----------------------------------------------------| Time steps between nucleation attempts | Any positive integer | no | 100 | The number of time steps between nucleation attempts. This parameter is shared among all nucleating variables. -Minimum allowed distance between nuclei | Any non-negative real number | no | 2\f$\times\f$ the largest nucleus semiaxis | The minimum allowed distance between nuclei centers during a single nucleation attempt. This parameter is shared among all nucleating variables. +Minimum allowed distance between nuclei | Any non-negative real number | no | 2$\times$ the largest nucleus semiaxis | The minimum allowed distance between nuclei centers during a single nucleation attempt. This parameter is shared among all nucleating variables. Order parameter cutoff value | Any non-negative real number | no | 0.01 | The minimum allowed value of the sum of all nucleating variable fields where nucleation is allowed to occur. Implemented to prevent nucleation inside existing particles. This parameter is shared among all nucleating variables. Time steps between nucleation attempts | Any positive integer | no | 100 | The number of time steps between nucleation attempts. This parameter is shared among all nucleating variables. @@ -406,12 +406,12 @@ Each application specifies its own set of model constants. These are most often - TENSOR: For either rank 1 tensors (i.e. vectors) or rank 2 tensors (i.e. matrices) with a size of the number of dimensions. These are assumed to be real numbers. Each row should be given by a comma-separated list in parentheses. For example, a 3D vector would be given as ```(2.5, 1.2, 0.1)``` and a 2D matrix would be given as: ```((4.1, 2.0),(1.6, 5.2))```. - {[symmetry]} ELASTIC CONSTANTS: For sets of elastic constants, given as a vector. The symmetry options are ISOTROPIC, TRANSVERSE, ORTHOTROPIC, or ANISOTROPIC. The number of entries for the different symmetries are given below. PRISMS-PF converts these sets of elastic constants into a stiffness matrix. -The number and order of the entries for the elastic constants are (where \f$C_{ij}\f$ are entries in the stiffness matrix): +The number and order of the entries for the elastic constants are (where $C_{ij}$ are entries in the stiffness matrix): - ISOTROPIC (2D/3D): 2 constants (Young's Modulus, Poisson's Ratio) -- TRANSVERSE (3D): 5 constants (\f$C_{11}\f$, \f$C_{33}\f$, \f$C_{44}\f$, \f$C_{12}\f$, \f$C_{13}\f$) -- ORTHOTROPIC (3D): 9 constants (\f$C_{11}\f$, \f$C_{22}\f$, \f$C_{33}\f$, \f$C_{44}\f$, \f$C_{55}\f$, \f$C_{66}\f$, \f$C_{12}\f$, \f$C_{13}\f$, \f$C_{23}\f$) -- ANISOTROPIC (2D/3D): 21 constants (\f$C_{11}\f$, \f$C_{22}\f$, \f$C_{33}\f$, \f$C_{44}\f$, \f$C_{55}\f$, \f$C_{66}\f$, \f$C_{12}\f$, \f$C_{13}\f$, \f$C_{14}\f$, \f$C_{15}\f$, \f$C_{16}\f$, \f$C_{23}\f$, \f$C_{24}\f$, \f$C_{25}\f$, \f$C_{26}\f$, \f$C_{34}\f$, \f$C_{35}\f$, \f$C_{36}\f$, \f$C_{45}\f$, \f$C_{46}\f$, \f$C_{56}\f$) +- TRANSVERSE (3D): 5 constants ($C_{11}$, $C_{33}$, $C_{44}$, $C_{12}$, $C_{13}$) +- ORTHOTROPIC (3D): 9 constants ($C_{11}$, $C_{22}$, $C_{33}$, $C_{44}$, $C_{55}$, $C_{66}$, $C_{12}$, $C_{13}$, $C_{23}$) +- ANISOTROPIC (2D/3D): 21 constants ($C_{11}$, $C_{22}$, $C_{33}$, $C_{44}$, $C_{55}$, $C_{66}$, $C_{12}$, $C_{13}$, $C_{14}$, $C_{15}$, $C_{16}$, $C_{23}$, $C_{24}$, $C_{25}$, $C_{26}$, $C_{34}$, $C_{35}$, $C_{36}$, $C_{45}$, $C_{46}$, $C_{56}$) Each model constant in `parameters.in' must have a counterpart in the appropriate section of the `customPDE.h' file. From 7366e2659ef4fb6addaa824bac3ae1a6ff4315e8 Mon Sep 17 00:00:00 2001 From: danlwill Date: Sat, 25 Jan 2025 21:51:57 -0500 Subject: [PATCH 04/11] Update installation.md --- doc/doxygen/user_manual/installation/installation.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/doc/doxygen/user_manual/installation/installation.md b/doc/doxygen/user_manual/installation/installation.md index 9c9560305..921d482fd 100644 --- a/doc/doxygen/user_manual/installation/installation.md +++ b/doc/doxygen/user_manual/installation/installation.md @@ -1,9 +1,3 @@ # Installation {#install} -Installing PRISMS-PF consists of three stages: installing prerequisites, installing PRISMS-PF itself, and installing visualization software to view and analyze the results. Each of these steps is discussed in the following sections. -@subpage install_prereqs - -@subpage install_prismspf - -@subpage install_vis From f8f262d1a56fa898eec8e0b590f43d7b73e7d1ba Mon Sep 17 00:00:00 2001 From: danlwill Date: Sat, 25 Jan 2025 21:54:49 -0500 Subject: [PATCH 05/11] Update installation.md --- .../user_manual/installation/installation.md | 112 ++++++++++++++++++ 1 file changed, 112 insertions(+) diff --git a/doc/doxygen/user_manual/installation/installation.md b/doc/doxygen/user_manual/installation/installation.md index 921d482fd..d2f9c87ba 100644 --- a/doc/doxygen/user_manual/installation/installation.md +++ b/doc/doxygen/user_manual/installation/installation.md @@ -1,3 +1,115 @@ # Installation {#install} +## Installing CMake and deal.II {#install_prereqs} +Before downloading and installing PRISMS-PF itself, one should install CMake and deal.II. For MacOS or Linux users, it is likely that your distribution already contains CMake. To test if you have it type: +``` +$ cmake --version +``` + +### Installing CMake +CMake can be downloaded [here](https://cmake.org/download), which also has installation instructions. It is also available through package managers such as homebrew, yum, and apt. + +Once installed, be sure to add CMake to your path by entering: +``` +$ export PATH=/path/to/cmake/Contents/bin:$PATH +``` + +filling in the path to the installation of CMake (for example, on Mac OS, the default installation path is /Applications/CMake.app/Contents/bin). For convenience, we recommend adding this line to your bash profile. Your bash profile can be opened via the following terminal command +``` +$ vi ~/.profile +``` + +### Installing deal.II +deal.II can be downloaded [here](https://www.dealii.org/current_release/download/), which also has installation instructions. The deal.II installation process depends on your operating system. The current PRISMS-PF version has been tested with deal.II versions 9.2.0 through 9.6.1. We recommend using the latest version of deal.II, if possible. Other versions are available [here](https://github.com/dealii/dealii/releases). + +There are three general approaches to installing deal.II: using a binary package, installing from source, and using Docker. For general use on a personal computer, any of these are appropriate. When available, we recommend installing deal.II using a binary package, this should be the most straightforward approach. If a binary package isn't available, installation using Docker is also fairly straightforward. The third option is to install deal.II and its prerequisites from source, which is more difficult than the other options. When using PRISMS-PF on a HPC cluster we recommend installing from source to make full use of the optimized libraries installed on the cluster. + +The process for installing deal.II using these three approaches on Mac OS X, Linux, and Windows is described below. + +#### Binary Package (Mac OS X) +A binary package for the latest version of deal.II (and other versions) is available here. The binary package includes all the libraries that you need (excluding CMake). To install deal.II open the .dmg file and drag ''deal.II.app'' into your Applications folder. Then, open ''deal.II.app'', which will open a Terminal window and set the necessary environment variables. You may need to modify your security settings so that your operating system will let you open the application (in System Preferences, select Security & Privacy, then under the general tab choose to allow apps downloaded from anywhere; don't click ''Open deal.II.app anyway'', we have found that doing so doesn't actually launch deal.II.app). + +In some cases, deal.II.app will not open, possibly freezing at the ''Verifying...'' stage. If this happens, right click on it and select ''Show Package Contents''. Then go to ''/Contents/Resources/bin/'' and launch ''dealii-terminal''. This should launch the Terminal window that sets the environment variables. + +#### Binary Package (Linux) +Binary packages for deal.II are available for Gentoo, Debian (stretch or newer), Ubuntu (16.10 or newer), and Arch Linux. Please refer to https://www.dealii.org/current_release/download/ for details. + +#### Docker (Mac OS X, Linux, Windows) +Docker is a container platform that can be used to run code identically on any OS X, Linux, or Windows machine. The [PRISMS-PF Docker image](https://hub.docker.com/repository/docker/prismspf/prismspf/) contains a full instantiation of PRISMS-PF and all of its prerequisites. The steps to use it are given in on the [Installing PRISMS-PF page](#install_prismspf). Docker images for deal.II are also posted on [DockerHub](https://hub.docker.com/r/dealii/dealii/). These can be used directly, if so desired. + +#### Installing from Source (Mac OS X, Linux) +##### Manual Installation +Before building deal.II, you will need to install two libraries, MPI and p4est. Make sure you have both libraries installed before installing deal.II, or else you will have to reinstall deal.II! Many computing clusters already have these libraries installed. MPI libraries (such as MPICH2) are often available through package managers (e.g. yum, apt, pkg_add, port, brew), installing it using your package manager of choice is likely the simplest option. If not, you can find binaries and the source code at http://www.mpich.org/downloads/, as well as instructions for installation. The p4est library may also be available through your package manager. If not, you can download the latest release tarball at http://www.p4est.org/. To install, unzip the archive, move to the p4est root directory and enter the following commands at the command line: +``` +$ ./configure --enable-mpi; make; make install +``` +Users have found that this approach works better than the setup script ''p4est-setup.sh'' that is on the deal.ii website. More detailed installation instructions can be found in the ''INSTALL'' and ''README'' files in the p4est root directory. + +With MPI and p4est installed, you are ready to install deal.II. Open the archive you downloaded from the deal.II website. From the root deal.II directory enter the following commands: +``` +$ mkdir build +$ cd build +$ cmake -DP4EST_DIR=/path/to/installation/dir -DDEAL_II_WITH_P4EST=ON +-DDEAL_II_WITH_MPI=ON -DCMAKE_INSTALL_PREFIX=/path/to/install/dir +$ make install +``` + +where ''/path/to/install/dir'' is the path to where you want to install deal.II. After installation is complete (which can take take up to an hour), open the file ''summary.log''. The second section of the log file lists the configured features. Ensure that DEAL_II_WITH_MPI and DEAL_II_WITH_P4EST say either ''set up with bundled packages'' or ''set up with external dependences''. If either is listed as ''OFF'', then deal.II was unable to find MPI or p4est. If this is the case, double check that MPI and p4est were installed correctly. + +### Installation using candi +An alternative route is to use the [candi (compile and install)](https://github.com/koecher/candi) script to install deal.II and its prerequisites. If it works, it should be much simpler than the traditional route described above. While some users have reported success using this approach, it hasn't worked for everyone. + +## Installing PRISMS-PF {#install_prismspf} + +### Traditional Installation (Non-Docker) +#### Downloading PRISMS-PF +PRISMS-PF is available for download at our [GitHub site](https://github.com/prisms-center/phaseField). The recommended method for downloading the PRISMS-PF source code is through git. Using a Linux/Unix terminal, go to the directory where you want PRISMS-PF to be located. To clone the repository, type: +``` +$ git clone https://github.com/prisms-center/phaseField.git +``` +Git will then download the PRISMS-PF source code into a directory entitled ''phaseField''. A resource for learning to use Git can be found [here](https://git-scm.com/book). + +If you prefer not to use Git, a zip file containing the PRISMS-PF source code can be downloaded [here](https://github.com/prisms-center/phaseField/releases). + +### Compiling the Core Library +To compile the core PRISMS-PF library, enter the ```phaseField``` directory: +``` +$ cd phaseField +``` + +Next, use CMake to generate a makefile and then compile the library: +``` +$ cmake . +$ make -j 8 +``` +In the last command, the number following ```-j``` is the number of threads used during compilation. The general rule of thumb is to pick a number 1.5x the number of processors available. This process should take a minute or two and will compile both the ''debug'' and ''release'' versions of the core PRISMS-PF library. + +Note: This step can be skipped and the core library will be compiled the first time that you compile one of the applications. However, the compilation will be on a single thread and thus will take much longer than if you follow the instructions above and use multiple threads. + +### Docker Installation +One option when installing PRISMS-PF is to install it and all of its prerequisites using Docker. Docker is a container platform that can be used to run code identically on any OS X, Linux, or Windows machine. If you aren't familiar with Docker, you can get a quick overview [here](https://opensource.com/resources/what-docker). + +1. [Install Docker](https://docs.docker.com/install/) +2. Create a directory on your computer to hold the PRISMS-PF applications folder (e.g. ```$ mkdir ~/DockerWorkspace```) and go to that directory (e.g. ```$ cd ~/DockerWorkspace```) +3. Clone the PRISMS-PF repository (```$ git clone https://github.com/prisms-center/phaseField```) +4. Get the PRISMS-PF Docker image (```$ docker pull prismspf/prismspf:latest```) +5. Now, launch the Docker container, linking the PRISMS-PF applications folder in the container to your local one: (e.g. ```$ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications prismspf/prismspf:latest```) + +Now you should have a working PRISMS-PF environment. The core library will already be compiled, but you'll need to compile any applications that you want to use. Any changes that you make or output files that you create should be found at ~/DockerWorkspace on your host computer. + +To get out of the container, type: +``` +$ exit +``` + +**Note:** If you only want to update (and use) the new Docker image, follow steps 4 and 5 above. If you want to remove the previous image, simply type: +``` +$ docker rmi stvdwtt/prismspf:prismspf +``` +or +``` +$ docker rmi prismspf/prismspf:2.2 +``` +## Installing Visualization Software {#install_vis} +The output files for PRISMS-PF are follow the VTK format. Two popular programs to read and visualize these files are VisIt (which is used in the remainder of this user manual) and ParaView. Installation instructions for VisIt can be found [here](https://visit-sphinx-github-user-manual.readthedocs.io/en/v3.2.0/gui_manual/Intro/Installing_VisIt.html). Installation instructions for ParaView can be found [here](https://www.paraview.org/download/). From ea4a0e1bebd46e43fca195a3e483ab377de93d3c Mon Sep 17 00:00:00 2001 From: danlwill Date: Sat, 25 Jan 2025 21:56:21 -0500 Subject: [PATCH 06/11] Update running_apps.md --- doc/doxygen/user_manual/running_apps/running_apps.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/doxygen/user_manual/running_apps/running_apps.md b/doc/doxygen/user_manual/running_apps/running_apps.md index 8f586f57d..40474e484 100644 --- a/doc/doxygen/user_manual/running_apps/running_apps.md +++ b/doc/doxygen/user_manual/running_apps/running_apps.md @@ -23,7 +23,7 @@ After deal.II and PRISMS-PF are downloaded, you can run the pre-built PRISMS-PF - grainGrowth_dream3D: An implementation of coupled Allen-Cahn equations simulating grain growth in two dimensions with an initial microstructure imported from Dream3D. (2D) - precipiateEvolution: An implementation of the coupled Cahn-Hilliard/Allen-Cahn/Linear Elasticity equations often used in phase field simulation of precipitate evolution. (2D) - precipiateEvolution_pfunction: Like precipitateEvolution, but loads inputs using PRISMS IntegrationTools. (2D) -- MgNd_precipitate_single_Bppp: Similar to precipiateEvolution, but uses the KKS model rather than the WBM model for the free energy functional. The parameters are set for \f$\beta\f$''' precipitates in an Mg-Nd alloy from [this publication](https://www.sciencedirect.com/science/article/pii/S1359645417305281). (3D) +- MgNd_precipitate_single_Bppp: Similar to precipiateEvolution, but uses the KKS model rather than the WBM model for the free energy functional. The parameters are set for $\beta$''' precipitates in an Mg-Nd alloy from [this publication](https://www.sciencedirect.com/science/article/pii/S1359645417305281). (3D) - nucleationModel: KKS precipitation model that makes use of the PRISMS-PF explicit nucleation capabilities. (2D) - nucleationModel_preferential: Like nucleationModel, but with a zone with an increased nucleation rate to simulate a grain boundary. (2D) From 125a6fa5fdea2c5b097cdbb610bb5a8ea0f8b8b6 Mon Sep 17 00:00:00 2001 From: danlwill Date: Wed, 29 Jan 2025 14:25:47 -0500 Subject: [PATCH 07/11] Delete doc/doxygen/user_manual/installation/install_prereqs.md --- .../installation/install_prereqs.md | 59 ------------------- 1 file changed, 59 deletions(-) delete mode 100644 doc/doxygen/user_manual/installation/install_prereqs.md diff --git a/doc/doxygen/user_manual/installation/install_prereqs.md b/doc/doxygen/user_manual/installation/install_prereqs.md deleted file mode 100644 index f892ec32e..000000000 --- a/doc/doxygen/user_manual/installation/install_prereqs.md +++ /dev/null @@ -1,59 +0,0 @@ -# Installing CMake and deal.II {#install_prereqs} - -Before downloading and installing PRISMS-PF itself, one should install CMake and deal.II. For MacOS or Linux users, it is likely that your distribution already contains CMake. To test if you have it type: -``` -$ cmake --version -``` - -## Installing CMake -CMake can be downloaded [here](https://cmake.org/download), which also has installation instructions. It is also available through package managers such as homebrew, yum, and apt. - -Once installed, be sure to add CMake to your path by entering: -``` -$ export PATH=/path/to/cmake/Contents/bin:$PATH -``` - -filling in the path to the installation of CMake (for example, on Mac OS, the default installation path is /Applications/CMake.app/Contents/bin). For convenience, we recommend adding this line to your bash profile. Your bash profile can be opened via the following terminal command -``` -$ vi ~/.profile -``` - -## Installing deal.II -deal.II can be downloaded [here](https://www.dealii.org/current_release/download/), which also has installation instructions. The deal.II installation process depends on your operating system. The current PRISMS-PF version has been tested with deal.II versions 9.2.0 through 9.6.1. We recommend using the latest version of deal.II, if possible. Other versions are available [here](https://github.com/dealii/dealii/releases). - -There are three general approaches to installing deal.II: using a binary package, installing from source, and using Docker. For general use on a personal computer, any of these are appropriate. When available, we recommend installing deal.II using a binary package, this should be the most straightforward approach. If a binary package isn't available, installation using Docker is also fairly straightforward. The third option is to install deal.II and its prerequisites from source, which is more difficult than the other options. When using PRISMS-PF on a HPC cluster we recommend installing from source to make full use of the optimized libraries installed on the cluster. - -The process for installing deal.II using these three approaches on Mac OS X, Linux, and Windows is described below. - -### Binary Package (Mac OS X) -A binary package for the latest version of deal.II (and other versions) is available here. The binary package includes all the libraries that you need (excluding CMake). To install deal.II open the .dmg file and drag ''deal.II.app'' into your Applications folder. Then, open ''deal.II.app'', which will open a Terminal window and set the necessary environment variables. You may need to modify your security settings so that your operating system will let you open the application (in System Preferences, select Security & Privacy, then under the general tab choose to allow apps downloaded from anywhere; don't click ''Open deal.II.app anyway'', we have found that doing so doesn't actually launch deal.II.app). - -In some cases, deal.II.app will not open, possibly freezing at the ''Verifying...'' stage. If this happens, right click on it and select ''Show Package Contents''. Then go to ''/Contents/Resources/bin/'' and launch ''dealii-terminal''. This should launch the Terminal window that sets the environment variables. - -### Binary Package (Linux) -Binary packages for deal.II are available for Gentoo, Debian (stretch or newer), Ubuntu (16.10 or newer), and Arch Linux. Please refer to https://www.dealii.org/current_release/download/ for details. - -### Docker (Mac OS X, Linux, Windows) -Docker is a container platform that can be used to run code identically on any OS X, Linux, or Windows machine. The [PRISMS-PF Docker image](https://hub.docker.com/repository/docker/prismspf/prismspf/) contains a full instantiation of PRISMS-PF and all of its prerequisites. The steps to use it are given in on the [Installing PRISMS-PF page](#install_prismspf). Docker images for deal.II are also posted on [DockerHub](https://hub.docker.com/r/dealii/dealii/). These can be used directly, if so desired. - -### Installing from Source (Mac OS X, Linux) -#### Manual Installation -Before building deal.II, you will need to install two libraries, MPI and p4est. Make sure you have both libraries installed before installing deal.II, or else you will have to reinstall deal.II! Many computing clusters already have these libraries installed. MPI libraries (such as MPICH2) are often available through package managers (e.g. yum, apt, pkg_add, port, brew), installing it using your package manager of choice is likely the simplest option. If not, you can find binaries and the source code at http://www.mpich.org/downloads/, as well as instructions for installation. The p4est library may also be available through your package manager. If not, you can download the latest release tarball at http://www.p4est.org/. To install, unzip the archive, move to the p4est root directory and enter the following commands at the command line: -``` -$ ./configure --enable-mpi; make; make install -``` -Users have found that this approach works better than the setup script ''p4est-setup.sh'' that is on the deal.ii website. More detailed installation instructions can be found in the ''INSTALL'' and ''README'' files in the p4est root directory. - -With MPI and p4est installed, you are ready to install deal.II. Open the archive you downloaded from the deal.II website. From the root deal.II directory enter the following commands: -``` -$ mkdir build -$ cd build -$ cmake -DP4EST_DIR=/path/to/installation/dir -DDEAL_II_WITH_P4EST=ON --DDEAL_II_WITH_MPI=ON -DCMAKE_INSTALL_PREFIX=/path/to/install/dir -$ make install -``` - -where ''/path/to/install/dir'' is the path to where you want to install deal.II. After installation is complete (which can take take up to an hour), open the file ''summary.log''. The second section of the log file lists the configured features. Ensure that DEAL_II_WITH_MPI and DEAL_II_WITH_P4EST say either ''set up with bundled packages'' or ''set up with external dependences''. If either is listed as ''OFF'', then deal.II was unable to find MPI or p4est. If this is the case, double check that MPI and p4est were installed correctly. - -### Installation using candi -An alternative route is to use the [candi (compile and install)](https://github.com/koecher/candi) script to install deal.II and its prerequisites. If it works, it should be much simpler than the traditional route described above. While some users have reported success using this approach, it hasn't worked for everyone. From 84f8985e217f446edf964a7b98bc569f9fd8e12f Mon Sep 17 00:00:00 2001 From: danlwill Date: Wed, 29 Jan 2025 14:26:11 -0500 Subject: [PATCH 08/11] Delete doc/doxygen/user_manual/installation/install_prismspf.md --- .../installation/install_prismspf.md | 51 ------------------- 1 file changed, 51 deletions(-) delete mode 100644 doc/doxygen/user_manual/installation/install_prismspf.md diff --git a/doc/doxygen/user_manual/installation/install_prismspf.md b/doc/doxygen/user_manual/installation/install_prismspf.md deleted file mode 100644 index b2198f980..000000000 --- a/doc/doxygen/user_manual/installation/install_prismspf.md +++ /dev/null @@ -1,51 +0,0 @@ -# Installing PRISMS-PF {#install_prismspf} - -## Traditional Installation (Non-Docker) -### Downloading PRISMS-PF -PRISMS-PF is available for download at our [GitHub site](https://github.com/prisms-center/phaseField). The recommended method for downloading the PRISMS-PF source code is through git. Using a Linux/Unix terminal, go to the directory where you want PRISMS-PF to be located. To clone the repository, type: -``` -$ git clone https://github.com/prisms-center/phaseField.git -``` -Git will then download the PRISMS-PF source code into a directory entitled ''phaseField''. A resource for learning to use Git can be found [here](https://git-scm.com/book). - -If you prefer not to use Git, a zip file containing the PRISMS-PF source code can be downloaded [here](https://github.com/prisms-center/phaseField/releases). - -### Compiling the Core Library -To compile the core PRISMS-PF library, enter the ```phaseField``` directory: -``` -$ cd phaseField -``` - -Next, use CMake to generate a makefile and then compile the library: -``` -$ cmake . -$ make -j 8 -``` -In the last command, the number following ```-j``` is the number of threads used during compilation. The general rule of thumb is to pick a number 1.5x the number of processors available. This process should take a minute or two and will compile both the ''debug'' and ''release'' versions of the core PRISMS-PF library. - -Note: This step can be skipped and the core library will be compiled the first time that you compile one of the applications. However, the compilation will be on a single thread and thus will take much longer than if you follow the instructions above and use multiple threads. - -## Docker Installation -One option when installing PRISMS-PF is to install it and all of its prerequisites using Docker. Docker is a container platform that can be used to run code identically on any OS X, Linux, or Windows machine. If you aren't familiar with Docker, you can get a quick overview [here](https://opensource.com/resources/what-docker). - -1. [Install Docker](https://docs.docker.com/install/) -2. Create a directory on your computer to hold the PRISMS-PF applications folder (e.g. ```$ mkdir ~/DockerWorkspace```) and go to that directory (e.g. ```$ cd ~/DockerWorkspace```) -3. Clone the PRISMS-PF repository (```$ git clone https://github.com/prisms-center/phaseField```) -4. Get the PRISMS-PF Docker image (```$ docker pull prismspf/prismspf:latest```) -5. Now, launch the Docker container, linking the PRISMS-PF applications folder in the container to your local one: (e.g. ```$ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications prismspf/prismspf:latest```) - -Now you should have a working PRISMS-PF environment. The core library will already be compiled, but you'll need to compile any applications that you want to use. Any changes that you make or output files that you create should be found at ~/DockerWorkspace on your host computer. - -To get out of the container, type: -``` -$ exit -``` - -**Note:** If you only want to update (and use) the new Docker image, follow steps 4 and 5 above. If you want to remove the previous image, simply type: -``` -$ docker rmi stvdwtt/prismspf:prismspf -``` -or -``` -$ docker rmi prismspf/prismspf:2.2 -``` From 7ef31e77820e98f3bfa472696bc1cd7ba1d73080 Mon Sep 17 00:00:00 2001 From: danlwill Date: Wed, 29 Jan 2025 14:26:49 -0500 Subject: [PATCH 09/11] Delete doc/doxygen/user_manual/installation/install_vis.md --- doc/doxygen/user_manual/installation/install_vis.md | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 doc/doxygen/user_manual/installation/install_vis.md diff --git a/doc/doxygen/user_manual/installation/install_vis.md b/doc/doxygen/user_manual/installation/install_vis.md deleted file mode 100644 index 6e69b7f09..000000000 --- a/doc/doxygen/user_manual/installation/install_vis.md +++ /dev/null @@ -1,2 +0,0 @@ -# Installing Visualization Software {#install_vis} -The output files for PRISMS-PF are follow the VTK format. Two popular programs to read and visualize these files are VisIt (which is used in the remainder of this user manual) and ParaView. Installation instructions for VisIt can be found [here](https://visit-sphinx-github-user-manual.readthedocs.io/en/v3.2.0/gui_manual/Intro/Installing_VisIt.html). Installation instructions for ParaView can be found [here](https://www.paraview.org/download/). From 1a94063f0233cec25b9bb86348d7ccb88060862f Mon Sep 17 00:00:00 2001 From: Daniel Williams Date: Wed, 29 Jan 2025 14:37:12 -0500 Subject: [PATCH 10/11] Remove sub headings --- doc/doxygen/user_manual/installation/installation.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/doxygen/user_manual/installation/installation.md b/doc/doxygen/user_manual/installation/installation.md index d2f9c87ba..30dc17273 100644 --- a/doc/doxygen/user_manual/installation/installation.md +++ b/doc/doxygen/user_manual/installation/installation.md @@ -1,6 +1,6 @@ # Installation {#install} -## Installing CMake and deal.II {#install_prereqs} +## Installing CMake and deal.II Before downloading and installing PRISMS-PF itself, one should install CMake and deal.II. For MacOS or Linux users, it is likely that your distribution already contains CMake. To test if you have it type: ``` @@ -60,7 +60,7 @@ where ''/path/to/install/dir'' is the path to where you want to install deal.II. ### Installation using candi An alternative route is to use the [candi (compile and install)](https://github.com/koecher/candi) script to install deal.II and its prerequisites. If it works, it should be much simpler than the traditional route described above. While some users have reported success using this approach, it hasn't worked for everyone. -## Installing PRISMS-PF {#install_prismspf} +## Installing PRISMS-PF ### Traditional Installation (Non-Docker) #### Downloading PRISMS-PF From 4e83002835b2e611f96ad0abe74097ff062b8ea8 Mon Sep 17 00:00:00 2001 From: Daniel Williams Date: Mon, 3 Feb 2025 17:51:00 -0500 Subject: [PATCH 11/11] Added copyright heading to all .h and .cc files in applications. --- applications/CHAC_anisotropy/ICs_and_BCs.cc | 3 +++ applications/CHAC_anisotropy/customPDE.h | 3 +++ applications/CHAC_anisotropy/equations.cc | 3 +++ applications/CHAC_anisotropy/postprocess.cc | 3 +++ .../CHAC_anisotropyRegularized/ICs_and_BCs.cc | 3 +++ .../CHAC_anisotropyRegularized/customPDE.h | 3 +++ .../CHAC_anisotropyRegularized/equations.cc | 3 +++ .../CHAC_anisotropyRegularized/postprocess.cc | 3 +++ .../CHAC_performance_test/ICs_and_BCs.cc | 3 +++ .../CHAC_performance_test/customPDE.h | 3 +++ .../CHAC_performance_test/equations.cc | 3 +++ .../CHAC_performance_test/postprocess.cc | 3 +++ .../CHiMaD_benchmark1a/ICs_and_BCs.cc | 3 +++ .../CHiMaD_benchmark1a/customPDE.h | 3 +++ .../CHiMaD_benchmark1a/equations.cc | 3 +++ .../CHiMaD_benchmark1a/postprocess.cc | 3 +++ .../CHiMaD_benchmark1b/ICs_and_BCs.cc | 3 +++ .../CHiMaD_benchmark1b/customPDE.h | 3 +++ .../CHiMaD_benchmark1b/equations.cc | 3 +++ .../CHiMaD_benchmark1b/postprocess.cc | 3 +++ .../CHiMaD_benchmark1c/ICs_and_BCs.cc | 3 +++ .../CHiMaD_benchmark1c/customPDE.h | 5 +++- .../CHiMaD_benchmark1c/equations.cc | 3 +++ .../CHiMaD_benchmark1c/postprocess.cc | 3 +++ .../CHiMaD_benchmark2a/ICs_and_BCs.cc | 3 +++ .../CHiMaD_benchmark2a/customPDE.h | 3 +++ .../CHiMaD_benchmark2a/equations.cc | 3 +++ .../CHiMaD_benchmark2a/postprocess.cc | 3 +++ .../CHiMaD_benchmark3a/ICs_and_BCs.cc | 3 +++ .../CHiMaD_benchmark3a/customPDE.h | 3 +++ .../CHiMaD_benchmark3a/equations.cc | 3 +++ .../CHiMaD_benchmark3a/postprocess.cc | 3 +++ .../CHiMaD_benchmark6a/ICs_and_BCs.cc | 3 +++ .../CHiMaD_benchmark6a/customPDE.h | 3 +++ .../CHiMaD_benchmark6a/equations.cc | 3 +++ .../CHiMaD_benchmark6a/postprocess.cc | 3 +++ .../CHiMaD_benchmark6b/ICs_and_BCs.cc | 3 +++ .../CHiMaD_benchmark6b/customPDE.h | 3 +++ .../CHiMaD_benchmark6b/equations.cc | 3 +++ .../CHiMaD_benchmark6b/postprocess.cc | 3 +++ .../CHiMaD_benchmark7a/ICs_and_BCs.cc | 3 +++ .../CHiMaD_benchmark7a/customPDE.h | 3 +++ .../CHiMaD_benchmark7a/equations.cc | 3 +++ .../CHiMaD_benchmark7a/postprocess.cc | 3 +++ .../ICs_and_BCs.cc | 3 +++ .../MgNd_precipitate_single_Bppp/customPDE.h | 3 +++ .../MgNd_precipitate_single_Bppp/equations.cc | 3 +++ .../postprocess.cc | 3 +++ applications/allenCahn/ICs_and_BCs.cc | 3 +++ applications/allenCahn/customPDE.h | 3 +++ applications/allenCahn/equations.cc | 3 +++ applications/allenCahn/postprocess.cc | 3 +++ .../allenCahn_conserved/ICs_and_BCs.cc | 3 +++ applications/allenCahn_conserved/customPDE.h | 26 ++++++++++++++----- applications/allenCahn_conserved/equations.cc | 3 +++ .../allenCahn_conserved/postprocess.cc | 3 +++ .../alloySolidification/ICs_and_BCs.cc | 3 +++ applications/alloySolidification/customPDE.h | 3 +++ applications/alloySolidification/equations.cc | 3 +++ .../alloySolidification/postprocess.cc | 3 +++ .../ICs_and_BCs.cc | 3 +++ .../alloySolidification_uniform/customPDE.h | 3 +++ .../alloySolidification_uniform/equations.cc | 3 +++ applications/anisotropyFacet/ICs_and_BCs.cc | 3 +++ .../anisotropyFacet/anisotropy_facet.h | 3 +++ applications/anisotropyFacet/customPDE.h | 3 +++ applications/anisotropyFacet/equations.cc | 3 +++ applications/anisotropyFacet/postprocess.cc | 3 +++ applications/cahnHilliard/ICs_and_BCs.cc | 3 +++ applications/cahnHilliard/customPDE.h | 3 +++ applications/cahnHilliard/equations.cc | 3 +++ applications/cahnHilliard/postprocess.cc | 3 +++ applications/corrosion/ICs_and_BCs.cc | 3 +++ applications/corrosion/customPDE.h | 3 +++ applications/corrosion/equations.cc | 3 +++ .../corrosion_microgalvanic/ICs_and_BCs.cc | 3 +++ .../corrosion_microgalvanic/customPDE.h | 3 +++ .../corrosion_microgalvanic/equations.cc | 3 +++ .../ICs_and_BCs.cc | 3 +++ .../coupledCahnHilliardAllenCahn/customPDE.h | 3 +++ .../coupledCahnHilliardAllenCahn/equations.cc | 3 +++ .../postprocess.cc | 3 +++ .../dendriticSolidification/ICs_and_BCs.cc | 3 +++ .../dendriticSolidification/customPDE.h | 3 +++ .../dendriticSolidification/equations.cc | 3 +++ applications/eshelbyInclusion/ICs_and_BCs.cc | 3 +++ applications/eshelbyInclusion/customPDE.h | 3 +++ applications/eshelbyInclusion/equations.cc | 3 +++ applications/fickianDiffusion/ICs_and_BCs.cc | 3 +++ applications/fickianDiffusion/customPDE.h | 3 +++ applications/fickianDiffusion/equations.cc | 3 +++ applications/grainGrowth/ICs_and_BCs.cc | 3 +++ applications/grainGrowth/customPDE.h | 3 +++ applications/grainGrowth/equations.cc | 3 +++ applications/grainGrowth/postprocess.cc | 3 +++ .../grainGrowth_dream3d/ICs_and_BCs.cc | 3 +++ applications/grainGrowth_dream3d/customPDE.h | 3 +++ applications/grainGrowth_dream3d/equations.cc | 3 +++ .../grainGrowth_dream3d/postprocess.cc | 3 +++ applications/main.cc | 3 +++ applications/mechanics/ICs_and_BCs.cc | 3 +++ applications/mechanics/customPDE.h | 3 +++ applications/mechanics/equations.cc | 3 +++ applications/nucleationModel/ICs_and_BCs.cc | 3 +++ applications/nucleationModel/customPDE.h | 3 +++ applications/nucleationModel/equations.cc | 3 +++ applications/nucleationModel/nucleation.cc | 3 +++ .../ICs_and_BCs.cc | 3 +++ .../nucleationModel_preferential/customPDE.h | 3 +++ .../nucleationModel_preferential/equations.cc | 3 +++ .../nucleation.cc | 3 +++ .../precipitateEvolution/ICs_and_BCs.cc | 3 +++ applications/precipitateEvolution/customPDE.h | 3 +++ .../precipitateEvolution/equations.cc | 3 +++ .../precipitateEvolution/postprocess.cc | 3 +++ .../spinodalDecomposition/ICs_and_BCs.cc | 3 +++ .../spinodalDecomposition/customPDE.h | 3 +++ .../spinodalDecomposition/equations.cc | 3 +++ .../spinodalDecomposition/postprocess.cc | 3 +++ 119 files changed, 374 insertions(+), 8 deletions(-) diff --git a/applications/CHAC_anisotropy/ICs_and_BCs.cc b/applications/CHAC_anisotropy/ICs_and_BCs.cc index 6bfac8aab..6e25b8173 100644 --- a/applications/CHAC_anisotropy/ICs_and_BCs.cc +++ b/applications/CHAC_anisotropy/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHAC_anisotropy/customPDE.h b/applications/CHAC_anisotropy/customPDE.h index d68af692b..dff5e158c 100644 --- a/applications/CHAC_anisotropy/customPDE.h +++ b/applications/CHAC_anisotropy/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHAC_anisotropy/equations.cc b/applications/CHAC_anisotropy/equations.cc index a8a365caf..0be7bc01b 100644 --- a/applications/CHAC_anisotropy/equations.cc +++ b/applications/CHAC_anisotropy/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHAC_anisotropy/postprocess.cc b/applications/CHAC_anisotropy/postprocess.cc index 9a9b9e3de..1a0b0fb73 100644 --- a/applications/CHAC_anisotropy/postprocess.cc +++ b/applications/CHAC_anisotropy/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHAC_anisotropyRegularized/ICs_and_BCs.cc b/applications/CHAC_anisotropyRegularized/ICs_and_BCs.cc index 75b1d8324..1a6c323a6 100644 --- a/applications/CHAC_anisotropyRegularized/ICs_and_BCs.cc +++ b/applications/CHAC_anisotropyRegularized/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHAC_anisotropyRegularized/customPDE.h b/applications/CHAC_anisotropyRegularized/customPDE.h index b39bc9701..b7454f2e0 100644 --- a/applications/CHAC_anisotropyRegularized/customPDE.h +++ b/applications/CHAC_anisotropyRegularized/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHAC_anisotropyRegularized/equations.cc b/applications/CHAC_anisotropyRegularized/equations.cc index 3237df286..f43d0a25c 100644 --- a/applications/CHAC_anisotropyRegularized/equations.cc +++ b/applications/CHAC_anisotropyRegularized/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHAC_anisotropyRegularized/postprocess.cc b/applications/CHAC_anisotropyRegularized/postprocess.cc index 769433fa9..e92e713c6 100644 --- a/applications/CHAC_anisotropyRegularized/postprocess.cc +++ b/applications/CHAC_anisotropyRegularized/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHAC_performance_test/ICs_and_BCs.cc b/applications/CHAC_performance_test/ICs_and_BCs.cc index 1dab9766c..8a161decf 100644 --- a/applications/CHAC_performance_test/ICs_and_BCs.cc +++ b/applications/CHAC_performance_test/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHAC_performance_test/customPDE.h b/applications/CHAC_performance_test/customPDE.h index c87307e06..c4d805a24 100644 --- a/applications/CHAC_performance_test/customPDE.h +++ b/applications/CHAC_performance_test/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHAC_performance_test/equations.cc b/applications/CHAC_performance_test/equations.cc index 1207100e7..631507d0d 100644 --- a/applications/CHAC_performance_test/equations.cc +++ b/applications/CHAC_performance_test/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHAC_performance_test/postprocess.cc b/applications/CHAC_performance_test/postprocess.cc index 33a4da316..96b101a16 100644 --- a/applications/CHAC_performance_test/postprocess.cc +++ b/applications/CHAC_performance_test/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the postprocessing variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/ICs_and_BCs.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/ICs_and_BCs.cc index 05b0d2774..3567400ee 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/ICs_and_BCs.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h index 77d36eb36..8c3852b8f 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/equations.cc index 205d73881..69b766911 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/equations.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/postprocess.cc index cbc7cd89f..d057b40c4 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/postprocess.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/ICs_and_BCs.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/ICs_and_BCs.cc index 05b0d2774..3567400ee 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/ICs_and_BCs.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/customPDE.h index 77d36eb36..8c3852b8f 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/customPDE.h +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/equations.cc index 205d73881..69b766911 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/equations.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/postprocess.cc index cbc7cd89f..d057b40c4 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/postprocess.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/ICs_and_BCs.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/ICs_and_BCs.cc index 05b0d2774..3567400ee 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/ICs_and_BCs.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h index 15ec0da88..06579ccd9 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; @@ -181,4 +184,4 @@ customPDE::create_triangulation( } } } -} \ No newline at end of file +} diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/equations.cc index 205d73881..69b766911 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/equations.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/postprocess.cc index cbc7cd89f..d057b40c4 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/postprocess.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/ICs_and_BCs.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/ICs_and_BCs.cc index dd9c52c97..70cce7209 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/ICs_and_BCs.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/customPDE.h index 98526cacc..4dd2782c8 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/customPDE.h +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/equations.cc index b859670c6..4da88fc0f 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/equations.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/postprocess.cc index 274fb2973..332325764 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/postprocess.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/ICs_and_BCs.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/ICs_and_BCs.cc index 15bd1ab6e..bd0b36f96 100755 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/ICs_and_BCs.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/customPDE.h index 4d9845395..861854972 100755 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/customPDE.h +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/equations.cc index e49caba5c..6b2f18c58 100755 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/equations.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/postprocess.cc index 5230390bb..49c56406f 100755 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/postprocess.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/ICs_and_BCs.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/ICs_and_BCs.cc index 8617db09c..da9d84a90 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/ICs_and_BCs.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/customPDE.h index 5f4e54371..487dbefd2 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/customPDE.h +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/equations.cc index 5578eb062..74695ec3a 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/equations.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/postprocess.cc index f761890f1..f741eaa29 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/postprocess.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/ICs_and_BCs.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/ICs_and_BCs.cc index 8617db09c..da9d84a90 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/ICs_and_BCs.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h index 9e08e5c71..db08d2405 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include #include diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/equations.cc index 1f10a131b..1a558b32d 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/equations.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/postprocess.cc index f761890f1..f741eaa29 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/postprocess.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/ICs_and_BCs.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/ICs_and_BCs.cc index f39719f47..08e825733 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/ICs_and_BCs.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/customPDE.h index 272eef523..84e2683ec 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/customPDE.h +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/equations.cc index b231d3637..cca752c36 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/equations.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/postprocess.cc index c7d71cdca..a95ac22f4 100644 --- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/postprocess.cc +++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/MgNd_precipitate_single_Bppp/ICs_and_BCs.cc b/applications/MgNd_precipitate_single_Bppp/ICs_and_BCs.cc index ef9f52544..56dec369f 100644 --- a/applications/MgNd_precipitate_single_Bppp/ICs_and_BCs.cc +++ b/applications/MgNd_precipitate_single_Bppp/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/MgNd_precipitate_single_Bppp/customPDE.h b/applications/MgNd_precipitate_single_Bppp/customPDE.h index 8d1655cfd..26900cb76 100644 --- a/applications/MgNd_precipitate_single_Bppp/customPDE.h +++ b/applications/MgNd_precipitate_single_Bppp/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/MgNd_precipitate_single_Bppp/equations.cc b/applications/MgNd_precipitate_single_Bppp/equations.cc index 6f3da9890..5a4e336eb 100644 --- a/applications/MgNd_precipitate_single_Bppp/equations.cc +++ b/applications/MgNd_precipitate_single_Bppp/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/MgNd_precipitate_single_Bppp/postprocess.cc b/applications/MgNd_precipitate_single_Bppp/postprocess.cc index 49ed8b80b..5ba328941 100644 --- a/applications/MgNd_precipitate_single_Bppp/postprocess.cc +++ b/applications/MgNd_precipitate_single_Bppp/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/allenCahn/ICs_and_BCs.cc b/applications/allenCahn/ICs_and_BCs.cc index e68550084..68ad43f23 100644 --- a/applications/allenCahn/ICs_and_BCs.cc +++ b/applications/allenCahn/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/allenCahn/customPDE.h b/applications/allenCahn/customPDE.h index 5bf769a15..95c08491a 100644 --- a/applications/allenCahn/customPDE.h +++ b/applications/allenCahn/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/allenCahn/equations.cc b/applications/allenCahn/equations.cc index 5b09a18c2..a4c835606 100644 --- a/applications/allenCahn/equations.cc +++ b/applications/allenCahn/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/allenCahn/postprocess.cc b/applications/allenCahn/postprocess.cc index eecfce5b1..4a47ba665 100644 --- a/applications/allenCahn/postprocess.cc +++ b/applications/allenCahn/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the postprocessing variables // ================================================================================= diff --git a/applications/allenCahn_conserved/ICs_and_BCs.cc b/applications/allenCahn_conserved/ICs_and_BCs.cc index 16567f4f6..3fc9e9473 100644 --- a/applications/allenCahn_conserved/ICs_and_BCs.cc +++ b/applications/allenCahn_conserved/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/allenCahn_conserved/customPDE.h b/applications/allenCahn_conserved/customPDE.h index cab5ba3af..142312278 100644 --- a/applications/allenCahn_conserved/customPDE.h +++ b/applications/allenCahn_conserved/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; @@ -123,7 +126,8 @@ customPDE::solveIncrement(bool skip_time_dependent) if (this->currentIncrement % userInputs.skip_print_steps == 0) { - snprintf(buffer, sizeof(buffer), "Integrated mu is %12.6e\n", integrated_mu); + snprintf(buffer, sizeof(buffer), "Integrated mu is %12.6e +", integrated_mu); this->pcout << buffer; } @@ -155,7 +159,8 @@ customPDE::solveIncrement(bool skip_time_dependent) snprintf(buffer, sizeof(buffer), "field '%2s' [explicit solve]: current solution: " - "%12.6e, current residual:%12.6e\n", + "%12.6e, current residual:%12.6e +", this->fields[fieldIndex].name.c_str(), solution_L2_norm, this->residualSet[fieldIndex]->l2_norm()); @@ -165,7 +170,9 @@ customPDE::solveIncrement(bool skip_time_dependent) { snprintf(buffer, sizeof(buffer), - "ERROR: field '%s' solution is NAN. exiting.\n\n", + "ERROR: field '%s' solution is NAN. exiting. + +", this->fields[fieldIndex].name.c_str()); this->pcout << buffer; exit(-1); @@ -209,7 +216,8 @@ customPDE::solveIncrement(bool skip_time_dependent) snprintf(buffer, sizeof(buffer), "field '%2s' [nonlinear solve]: current " - "solution: %12.6e, current residual:%12.6e\n", + "solution: %12.6e, current residual:%12.6e +", this->fields[fieldIndex].name.c_str(), this->solutionSet[fieldIndex]->l2_norm(), this->residualSet[fieldIndex]->l2_norm()); @@ -252,7 +260,8 @@ customPDE::solveIncrement(bool skip_time_dependent) snprintf(buffer, sizeof(buffer), "field '%2s' [auxiliary solve]: current solution: " - "%12.6e, current residual:%12.6e\n", + "%12.6e, current residual:%12.6e +", this->fields[fieldIndex].name.c_str(), this->solutionSet[fieldIndex]->l2_norm(), this->residualSet[fieldIndex]->l2_norm()); @@ -314,7 +323,9 @@ customPDE::solveIncrement(bool skip_time_dependent) { snprintf(buffer, sizeof(buffer), - "ERROR: field '%s' solution is NAN. exiting.\n\n", + "ERROR: field '%s' solution is NAN. exiting. + +", this->fields[fieldIndex].name.c_str()); this->pcout << buffer; exit(-1); @@ -327,7 +338,8 @@ customPDE::solveIncrement(bool skip_time_dependent) if (this->currentIncrement % userInputs.skip_print_steps == 0) { - this->pcout << "wall time: " << time.wall_time() << "s\n"; + this->pcout << "wall time: " << time.wall_time() << "s +"; } // log time this->computing_timer.leave_subsection("matrixFreePDE: solveIncrements"); diff --git a/applications/allenCahn_conserved/equations.cc b/applications/allenCahn_conserved/equations.cc index 0391fc2f1..f740d85e6 100644 --- a/applications/allenCahn_conserved/equations.cc +++ b/applications/allenCahn_conserved/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/allenCahn_conserved/postprocess.cc b/applications/allenCahn_conserved/postprocess.cc index cc8796fbe..aedb31502 100644 --- a/applications/allenCahn_conserved/postprocess.cc +++ b/applications/allenCahn_conserved/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the postprocessing variables // ================================================================================= diff --git a/applications/alloySolidification/ICs_and_BCs.cc b/applications/alloySolidification/ICs_and_BCs.cc index f683b1c9b..8b9c099ad 100644 --- a/applications/alloySolidification/ICs_and_BCs.cc +++ b/applications/alloySolidification/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/alloySolidification/customPDE.h b/applications/alloySolidification/customPDE.h index c57453744..4ccaa6d9c 100644 --- a/applications/alloySolidification/customPDE.h +++ b/applications/alloySolidification/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/alloySolidification/equations.cc b/applications/alloySolidification/equations.cc index a5e5422dd..642588f6e 100644 --- a/applications/alloySolidification/equations.cc +++ b/applications/alloySolidification/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/alloySolidification/postprocess.cc b/applications/alloySolidification/postprocess.cc index dd7a22757..06a52a4ba 100644 --- a/applications/alloySolidification/postprocess.cc +++ b/applications/alloySolidification/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/alloySolidification_uniform/ICs_and_BCs.cc b/applications/alloySolidification_uniform/ICs_and_BCs.cc index d621343c9..98f915e30 100644 --- a/applications/alloySolidification_uniform/ICs_and_BCs.cc +++ b/applications/alloySolidification_uniform/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/alloySolidification_uniform/customPDE.h b/applications/alloySolidification_uniform/customPDE.h index 030117880..c7ab44e55 100644 --- a/applications/alloySolidification_uniform/customPDE.h +++ b/applications/alloySolidification_uniform/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/alloySolidification_uniform/equations.cc b/applications/alloySolidification_uniform/equations.cc index 5e7396e8a..e80655aa0 100644 --- a/applications/alloySolidification_uniform/equations.cc +++ b/applications/alloySolidification_uniform/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/anisotropyFacet/ICs_and_BCs.cc b/applications/anisotropyFacet/ICs_and_BCs.cc index 75b1d8324..1a6c323a6 100644 --- a/applications/anisotropyFacet/ICs_and_BCs.cc +++ b/applications/anisotropyFacet/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/anisotropyFacet/anisotropy_facet.h b/applications/anisotropyFacet/anisotropy_facet.h index 474479b7e..2ceb26d4b 100644 --- a/applications/anisotropyFacet/anisotropy_facet.h +++ b/applications/anisotropyFacet/anisotropy_facet.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // Number of orientation vectors used to generate anisotropy #define n_orients 3 diff --git a/applications/anisotropyFacet/customPDE.h b/applications/anisotropyFacet/customPDE.h index 4778c29ae..ff4c571b1 100644 --- a/applications/anisotropyFacet/customPDE.h +++ b/applications/anisotropyFacet/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/anisotropyFacet/equations.cc b/applications/anisotropyFacet/equations.cc index 29b871a1a..5beeca625 100644 --- a/applications/anisotropyFacet/equations.cc +++ b/applications/anisotropyFacet/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include "anisotropy_facet.h" // ================================================================================= diff --git a/applications/anisotropyFacet/postprocess.cc b/applications/anisotropyFacet/postprocess.cc index 4ccfc2f44..99b121c50 100644 --- a/applications/anisotropyFacet/postprocess.cc +++ b/applications/anisotropyFacet/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/cahnHilliard/ICs_and_BCs.cc b/applications/cahnHilliard/ICs_and_BCs.cc index 659087692..c5d567676 100644 --- a/applications/cahnHilliard/ICs_and_BCs.cc +++ b/applications/cahnHilliard/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/cahnHilliard/customPDE.h b/applications/cahnHilliard/customPDE.h index 96e6e324b..7efb9a18e 100644 --- a/applications/cahnHilliard/customPDE.h +++ b/applications/cahnHilliard/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/cahnHilliard/equations.cc b/applications/cahnHilliard/equations.cc index 50958e855..573f788da 100644 --- a/applications/cahnHilliard/equations.cc +++ b/applications/cahnHilliard/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/cahnHilliard/postprocess.cc b/applications/cahnHilliard/postprocess.cc index 37de70929..b3986ed51 100644 --- a/applications/cahnHilliard/postprocess.cc +++ b/applications/cahnHilliard/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/corrosion/ICs_and_BCs.cc b/applications/corrosion/ICs_and_BCs.cc index 37357f318..bb375e128 100644 --- a/applications/corrosion/ICs_and_BCs.cc +++ b/applications/corrosion/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/corrosion/customPDE.h b/applications/corrosion/customPDE.h index c07b7219b..36fa30f4b 100644 --- a/applications/corrosion/customPDE.h +++ b/applications/corrosion/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/corrosion/equations.cc b/applications/corrosion/equations.cc index 34af0a3c1..8faae6e95 100644 --- a/applications/corrosion/equations.cc +++ b/applications/corrosion/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/corrosion_microgalvanic/ICs_and_BCs.cc b/applications/corrosion_microgalvanic/ICs_and_BCs.cc index 63501011d..697242ab7 100644 --- a/applications/corrosion_microgalvanic/ICs_and_BCs.cc +++ b/applications/corrosion_microgalvanic/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/corrosion_microgalvanic/customPDE.h b/applications/corrosion_microgalvanic/customPDE.h index a4edcbf5d..a69c77f79 100644 --- a/applications/corrosion_microgalvanic/customPDE.h +++ b/applications/corrosion_microgalvanic/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include #include #include diff --git a/applications/corrosion_microgalvanic/equations.cc b/applications/corrosion_microgalvanic/equations.cc index f987ea625..5343c6253 100644 --- a/applications/corrosion_microgalvanic/equations.cc +++ b/applications/corrosion_microgalvanic/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/coupledCahnHilliardAllenCahn/ICs_and_BCs.cc b/applications/coupledCahnHilliardAllenCahn/ICs_and_BCs.cc index 5993e873c..4418b06ba 100644 --- a/applications/coupledCahnHilliardAllenCahn/ICs_and_BCs.cc +++ b/applications/coupledCahnHilliardAllenCahn/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/coupledCahnHilliardAllenCahn/customPDE.h b/applications/coupledCahnHilliardAllenCahn/customPDE.h index c87307e06..c4d805a24 100644 --- a/applications/coupledCahnHilliardAllenCahn/customPDE.h +++ b/applications/coupledCahnHilliardAllenCahn/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/coupledCahnHilliardAllenCahn/equations.cc b/applications/coupledCahnHilliardAllenCahn/equations.cc index 752672590..b63a82ca0 100644 --- a/applications/coupledCahnHilliardAllenCahn/equations.cc +++ b/applications/coupledCahnHilliardAllenCahn/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/coupledCahnHilliardAllenCahn/postprocess.cc b/applications/coupledCahnHilliardAllenCahn/postprocess.cc index d76620548..392edfbcd 100644 --- a/applications/coupledCahnHilliardAllenCahn/postprocess.cc +++ b/applications/coupledCahnHilliardAllenCahn/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the postprocessing variables // ================================================================================= diff --git a/applications/dendriticSolidification/ICs_and_BCs.cc b/applications/dendriticSolidification/ICs_and_BCs.cc index 3cb996c73..c44ab952c 100644 --- a/applications/dendriticSolidification/ICs_and_BCs.cc +++ b/applications/dendriticSolidification/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/dendriticSolidification/customPDE.h b/applications/dendriticSolidification/customPDE.h index 4d9845395..861854972 100644 --- a/applications/dendriticSolidification/customPDE.h +++ b/applications/dendriticSolidification/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/dendriticSolidification/equations.cc b/applications/dendriticSolidification/equations.cc index cf90c9f9d..5cc52bbc8 100644 --- a/applications/dendriticSolidification/equations.cc +++ b/applications/dendriticSolidification/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/eshelbyInclusion/ICs_and_BCs.cc b/applications/eshelbyInclusion/ICs_and_BCs.cc index ff9cead6a..102f09518 100644 --- a/applications/eshelbyInclusion/ICs_and_BCs.cc +++ b/applications/eshelbyInclusion/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/eshelbyInclusion/customPDE.h b/applications/eshelbyInclusion/customPDE.h index df8fc6ae3..24238b55a 100644 --- a/applications/eshelbyInclusion/customPDE.h +++ b/applications/eshelbyInclusion/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/eshelbyInclusion/equations.cc b/applications/eshelbyInclusion/equations.cc index 2b0268ef5..26c9be979 100644 --- a/applications/eshelbyInclusion/equations.cc +++ b/applications/eshelbyInclusion/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/fickianDiffusion/ICs_and_BCs.cc b/applications/fickianDiffusion/ICs_and_BCs.cc index ffce45fef..4ce27bef0 100644 --- a/applications/fickianDiffusion/ICs_and_BCs.cc +++ b/applications/fickianDiffusion/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/fickianDiffusion/customPDE.h b/applications/fickianDiffusion/customPDE.h index abe5fb20c..4a9ffd429 100644 --- a/applications/fickianDiffusion/customPDE.h +++ b/applications/fickianDiffusion/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/fickianDiffusion/equations.cc b/applications/fickianDiffusion/equations.cc index 8b37e5d76..c8ab1f4b8 100644 --- a/applications/fickianDiffusion/equations.cc +++ b/applications/fickianDiffusion/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/grainGrowth/ICs_and_BCs.cc b/applications/grainGrowth/ICs_and_BCs.cc index a0db76df7..774929efa 100644 --- a/applications/grainGrowth/ICs_and_BCs.cc +++ b/applications/grainGrowth/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/grainGrowth/customPDE.h b/applications/grainGrowth/customPDE.h index 38a1580a0..594183ad9 100644 --- a/applications/grainGrowth/customPDE.h +++ b/applications/grainGrowth/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/grainGrowth/equations.cc b/applications/grainGrowth/equations.cc index 9a3f41fa7..e525c26a2 100644 --- a/applications/grainGrowth/equations.cc +++ b/applications/grainGrowth/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/grainGrowth/postprocess.cc b/applications/grainGrowth/postprocess.cc index 4c7bc605d..ec0b823d1 100644 --- a/applications/grainGrowth/postprocess.cc +++ b/applications/grainGrowth/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the postprocessing variables // ================================================================================= diff --git a/applications/grainGrowth_dream3d/ICs_and_BCs.cc b/applications/grainGrowth_dream3d/ICs_and_BCs.cc index 7103514e3..7c2a5a27f 100644 --- a/applications/grainGrowth_dream3d/ICs_and_BCs.cc +++ b/applications/grainGrowth_dream3d/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/grainGrowth_dream3d/customPDE.h b/applications/grainGrowth_dream3d/customPDE.h index 38a1580a0..594183ad9 100644 --- a/applications/grainGrowth_dream3d/customPDE.h +++ b/applications/grainGrowth_dream3d/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/grainGrowth_dream3d/equations.cc b/applications/grainGrowth_dream3d/equations.cc index 492d05f80..943f175f7 100644 --- a/applications/grainGrowth_dream3d/equations.cc +++ b/applications/grainGrowth_dream3d/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/grainGrowth_dream3d/postprocess.cc b/applications/grainGrowth_dream3d/postprocess.cc index 1bf9dbc4a..61bd8f4f6 100644 --- a/applications/grainGrowth_dream3d/postprocess.cc +++ b/applications/grainGrowth_dream3d/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the postprocessing variables // ================================================================================= diff --git a/applications/main.cc b/applications/main.cc index f5526507c..529dd65e3 100644 --- a/applications/main.cc +++ b/applications/main.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // Header files #include "customPDE.h" diff --git a/applications/mechanics/ICs_and_BCs.cc b/applications/mechanics/ICs_and_BCs.cc index 0572c1ec8..702081574 100644 --- a/applications/mechanics/ICs_and_BCs.cc +++ b/applications/mechanics/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/mechanics/customPDE.h b/applications/mechanics/customPDE.h index df8fc6ae3..24238b55a 100644 --- a/applications/mechanics/customPDE.h +++ b/applications/mechanics/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/mechanics/equations.cc b/applications/mechanics/equations.cc index 02fb54377..4056682ba 100644 --- a/applications/mechanics/equations.cc +++ b/applications/mechanics/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // List of variables and residual equations for the mechanics example // application diff --git a/applications/nucleationModel/ICs_and_BCs.cc b/applications/nucleationModel/ICs_and_BCs.cc index 0a1a20799..af2fa7f35 100644 --- a/applications/nucleationModel/ICs_and_BCs.cc +++ b/applications/nucleationModel/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/nucleationModel/customPDE.h b/applications/nucleationModel/customPDE.h index 542600a51..36ab4bee3 100644 --- a/applications/nucleationModel/customPDE.h +++ b/applications/nucleationModel/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/nucleationModel/equations.cc b/applications/nucleationModel/equations.cc index c50567705..3249754cb 100644 --- a/applications/nucleationModel/equations.cc +++ b/applications/nucleationModel/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/nucleationModel/nucleation.cc b/applications/nucleationModel/nucleation.cc index 7a3c1fae0..a0d14d393 100644 --- a/applications/nucleationModel/nucleation.cc +++ b/applications/nucleationModel/nucleation.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // NUCLEATION FUNCTIONS // ================================================================================= diff --git a/applications/nucleationModel_preferential/ICs_and_BCs.cc b/applications/nucleationModel_preferential/ICs_and_BCs.cc index 0a1a20799..af2fa7f35 100644 --- a/applications/nucleationModel_preferential/ICs_and_BCs.cc +++ b/applications/nucleationModel_preferential/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/nucleationModel_preferential/customPDE.h b/applications/nucleationModel_preferential/customPDE.h index 0775b79f7..bf4aacb81 100644 --- a/applications/nucleationModel_preferential/customPDE.h +++ b/applications/nucleationModel_preferential/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/nucleationModel_preferential/equations.cc b/applications/nucleationModel_preferential/equations.cc index 3230ca1cb..7fc194c50 100644 --- a/applications/nucleationModel_preferential/equations.cc +++ b/applications/nucleationModel_preferential/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/nucleationModel_preferential/nucleation.cc b/applications/nucleationModel_preferential/nucleation.cc index 4a5638f58..ad7300db6 100644 --- a/applications/nucleationModel_preferential/nucleation.cc +++ b/applications/nucleationModel_preferential/nucleation.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // NUCLEATION FUNCTIONS // ================================================================================= diff --git a/applications/precipitateEvolution/ICs_and_BCs.cc b/applications/precipitateEvolution/ICs_and_BCs.cc index bfb3b7a84..b3780cfd9 100644 --- a/applications/precipitateEvolution/ICs_and_BCs.cc +++ b/applications/precipitateEvolution/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/precipitateEvolution/customPDE.h b/applications/precipitateEvolution/customPDE.h index 3c72a72e1..ae3dacd42 100644 --- a/applications/precipitateEvolution/customPDE.h +++ b/applications/precipitateEvolution/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include using namespace dealii; diff --git a/applications/precipitateEvolution/equations.cc b/applications/precipitateEvolution/equations.cc index 6c0cc483a..817144f54 100644 --- a/applications/precipitateEvolution/equations.cc +++ b/applications/precipitateEvolution/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/precipitateEvolution/postprocess.cc b/applications/precipitateEvolution/postprocess.cc index c20ffbfda..be08309de 100644 --- a/applications/precipitateEvolution/postprocess.cc +++ b/applications/precipitateEvolution/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables diff --git a/applications/spinodalDecomposition/ICs_and_BCs.cc b/applications/spinodalDecomposition/ICs_and_BCs.cc index 95046044b..6a38f7f17 100644 --- a/applications/spinodalDecomposition/ICs_and_BCs.cc +++ b/applications/spinodalDecomposition/ICs_and_BCs.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // =========================================================================== // FUNCTION FOR INITIAL CONDITIONS // =========================================================================== diff --git a/applications/spinodalDecomposition/customPDE.h b/applications/spinodalDecomposition/customPDE.h index f6affd946..4742f7422 100644 --- a/applications/spinodalDecomposition/customPDE.h +++ b/applications/spinodalDecomposition/customPDE.h @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + #include #include diff --git a/applications/spinodalDecomposition/equations.cc b/applications/spinodalDecomposition/equations.cc index a50154610..a201f4bee 100644 --- a/applications/spinodalDecomposition/equations.cc +++ b/applications/spinodalDecomposition/equations.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ================================================================================= // Set the attributes of the primary field variables // ================================================================================= diff --git a/applications/spinodalDecomposition/postprocess.cc b/applications/spinodalDecomposition/postprocess.cc index b1e5a4c7f..1ddf9d838 100644 --- a/applications/spinodalDecomposition/postprocess.cc +++ b/applications/spinodalDecomposition/postprocess.cc @@ -1,3 +1,6 @@ +//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan +//SPDX-License-Identifier: GNU Lesser General Public Version 2.1 + // ============================================================================================= // loadPostProcessorVariableAttributes: Set the attributes of the postprocessing // variables