v2.4.0

Moderate update from 2.3. The main changes are compatibility with deal.II 9.6.0, support for the use of up to 6th order elements, improved testing and continuous integration, code auto-formatting, and bug fixes.

Features

• deal.II 9.2.0 - 9.6.0 compatibility by @landinjm in #226 and #236
• Adding support for 4th, 5th, and 6th order elements by @landinjm in #251
• The local element volume is now available in equations.cc and postprocess.cc for stabilization schemes like PSPG and SUPG by @landinjm in #269
• Fields can be pinned to 0 at any vertex in the mesh. This works in addition to the boundary conditions prescribed in parameters.prm by @landinjm in #275
• Switched Allen-Cahn documentation to markdown by @landinjm in #263

Bug fixes

• Fixed explicit solves for problems with both scalar and vector explicit fields by @landinjm in #208
• Fixed multiple linear/nonlinear solves by @landinjm in #241
• Fixed incomplete refactoring of methods in customPDE override by @landinjm in #256
• Fixed FloodFiller unit test and fixed grainGrowth bug by @zachcroft in #224
• Optimized vtk file read-in behavior by @fractalsbyx in #222
• Better error handling for boundary conditions by @zachcroft in #225
• Better error handling for model constants by @landinjm in #262
• Deleted deprecated applications by @landinjm in #234

Miscellaneous

• Code auto-formatting by @landinjm in #209, #216, #229
• Suppression of warnings by @landinjm in #243 and #235, @arijitroy6 in #239, @gjerdej in #238, and @ellery-hendrix in #237
• Fixed some typos and style by @tkphd in #246

Tests/CI

• Continuous integration via GitHub Actions by @landinjm in #230
• Adding script to check that all applications work by @landinjm in #245
• Update automatic test script to run in parallel by @landinjm in #247

New Contributors

• @zachcroft made their first contribution in #224
• @arijitroy6 made their first contribution in #239
• @ellery-hendrix made their first contribution in #237
• @gjerdej made their first contribution in #238
• @tkphd made their first contribution in #246
• @fractalsbyx made their first contribution in #222

Full Changelog: v2.3...v2.4

PRISMS-PF (Version 2.3)

Moderate update to 2.2, released in July 2021. The main changes are new applications, new postprocessing scripts, improvements in performance, bug fixes and comparibility with the latest version of deal.II.

Added Features:

• New applications:
  • corrosion_microgalvanic: Simulates the evolution of the metal-electrolyte interface during free immersion due to the microgalvanic coupling between anodic and cathodic metals.
  • alloySolidification_uniform: Simulates solidification of a binary alloy at uniform temperature.
  • allenCahn_conserved: Simulates a system undergoing Allen-Cahn dynamics subject to global (as opposed to local) conservation.
• New postprocessing scripts. The following Python scripts for suite post-processing suite were added:
  • plot_and_save.py - This script creates a pseudocolor (in 2D) or contour (in 3D) plot for each outputted time states and saves the serieas of plots as png images.
  • domain_stats.py - This script calculates the following quantities for each of the time states:

    • Number of domains, defined as the number or separate regions based on the values of field variable, "n". Each interconnected region for which n>0.5 is counted as a separate domain.

    • Average domain size (area in 2D and volume in 3D)

    • Standard deviation of the domain sizes

  • splitvtufiles.py - This script splits the output .vtu files into several files, allowing for parallel visualization in VisIt or ParaView.
• New options for nucleation were added: an option to set the time interval for then nucleation is allowed and an option to allow for microstructure evolution before the first nucleation event.
• Improved the method for grain detection when reading data from a DREAM3D microstructure file.
• Added depencency of element degree for time step used in initial smoothing after reading from a DREAM3D microstructure file. This avoids posible numerical instabilities.
• Added Troubleshooting/FAQ page with the most common compilation/runtime errors and the way to fix them.

Bug Fixes:

• Fixed incomplete loop to detect dirichlet boundary conditions in init.cc
• The code now correctly updates time-dependent non-uniform Dirichlet boundary conditions.
• Updated input file parameters.prm for grainGrowth_dream3d application
• Fixed several typos and errors in the documentation of built-in applications

Other Changes:

• Updated comparibility with deal.II version 9.5.x

New Contributors

• @landinjm made their first contribution in #197

Full Changelog: v2.2...v2.3

PRISMS-PF (Version 2.2)

Moderate update to 2.1.2, released in July 2019. The biggest change in this version is the addition of new applications and post-processing scripts.

Added Features:

• New application: corrosion. This app simulates the evolution of the metal-electrolyte interface during the anodic corrosion
  reaction. It uses the nonlinear solver functionality to solve for the electrostatic potential field at every time step.
• New application: alloySolidification. This app simulates the dendritic solidification of a binary alloy in the dilute limit.
• New application: spinodalDecomposition. This app simulates the evolution of a two-phase domain system following spinodal decomposition using CahnHilliard dynamics.
• Postprocessing scripts suite. A suite of Python scripts por post-processing the results from PRISMS-PF was added. Three scripts which are integrated with VisIt via the VisIt CLI have been added. These scripts allow for the calculation of the number of domains, interfacial area (or length, in 2D) and phase fraction. A brief documentation page was added.

Bug Fixes:

• Updated precipitate evolution documentation (Issue #134).
• Removed elasticity terms from nucleation application documentation.
• Updated input file parameters.prm for grainGrowth_dream3d application
• Removed some commented lines in the equations.cc file of the alloySolidification app
• Updated application nucleationModel_preferential. Function adaptiveRefineCriterion in customPDE.h was outdated (Issues #144, #159 and #161).

Other Changes:

• The default parameters file name was changed to parameters.prm for compatibility with the newest recent deal.II versions.
• Updated the conversion scripts for the vtk input files for the grainGrowth_dream3d app.

PRISMS-PF (Version 2.1.2)

Minor update to 2.1.1, released in July 2019. The biggest change in this version is a change in how the user
specifies the adaptivity criteria in the parameters file.

Added Functionality:

• Users now specify the adaptivity criteria on a variable-by-variable basis, similar to the nucleation parameters. This new format permits more flexibility in the adaptvity criteria. Gradient-based adaptivity criteria are now supported. (Issue #56)
• Users now have the option to have a timing summary printed out every time the code outputs, controlled via the parameters file. (Issue #132)

Bug Fixes:

• PRISMS-PF will no longer zero out fields if the domain size is smaller than approximately 1e-5. This was related to the calculation of the inverse of the mass matrix. A tolerance to prevent a divide by zero error needs to scale with the minimum element volume. (Issue #119)
• The code will now produce outputs/checkpoints if given a list, regardless of the number of outputs/checkpoints specified for the other frequency types. (Issue #123)

Other Changes:

• Fixed the derivation for the mechanics and eshelbyInclusion apps with respect to surface tractions. (Issue #130)
• Improved the error message for attempted access of a value/gradient/hessian that wasn't requested in variableAttributeLoader::loadVariableAttributes(). (Issue #136)

PRISMS-PF (Version 2.1.1)

Minor update to 2.1.1, released in March 2018. The main purpose for the release was to trigger the creation of a Zenodo DOI. A few lingering bugs were fixed.

Bug Fixes:

• Fixed incorrect file extension for the ICs and BCs file in the fickianDiffusion app (Issue #115)
• Added missing update to a vector containing the past values of integrated postprocessed fields (Issue #120)

Other Changes:

• PRISMS-PF now has a DOI assigned to it (Issue #121)
• The terminology in the output printed to the screen regarding the linear solver was updated

PRISMS-PF (Version 2.1)

Moderate-level update to v2.0, released in August 2018. The largest changes involve a restructuring of the functions in equations.cc and ICs_and_BCs.cc. Grain remapping was also introduced to permit simulations with hundreds/thousands of grains.

Changes to the example applications:

• New application: CHAC_performance_test. This app is very similar to 'coupledCahnHilliardAllenCahn', but is 3D and was designed for scaling and performance comparisons to a finite difference code.
• The grainGrowth app has been overhauled and now uses the grain remapping capabilities (see below). A new grainGrowth_dream3D app was added that reads in a microstructure from dream3D.
• The singlePrecipitateKKS app has been removed in favor of the MgNd_precipitate_single_Bppp app.
• Renamed "preferential_nucleationModel" to "nucleationModel_preferential" so that they are next to each other in file listings.
• The source files in all of the example app directories have been changed to a ".cc" extension instead of ".h" to properly represent their contents.
• Merged 'allenCahn_pfield' into 'allenCahn', just using a different input file.
• Merged 'cahnHilliardWithAdaptivity' into 'cahnHilliard', just using a different input file.
• Added an app for the CHiMaD/PFHub benchmark #3 problem.
• Added a steady-state Allen-Cahn solver that uses the new nonlinear solver.
• Changed the naming convention for the terms in the governing equations.

Added functionality:

• To reflect their generality, the equation type PARABOLIC is now EXPLICIT_TIME_DEPENDENT and the equation type ELLIPTIC is now TIME_INDEPENDENT.
• A new equation type AUXILIARY has been introduced to handle time independent equations that don't require a (non)linear solve (e.g. the chemical potential for the split form of the Cahn-Hilliard equation).
• The core solver loop has been overhauled. AUXILIARY and TIME_INDEPENDENT equations are now updated before the EXPLICIT_TIME_DEPENDENT equations so that the EXPLICIT_TIME_DEPENDENT equations have up-to-date values for the other fields.
• A nonlinear solver has been added. It uses Newton's method to solve for each equation and Picard's method to handle coupling between equations.
• A grain remapping algorithm has been added so that arbitrary numbers of grains can be stored on a few order parameters. When grains are close to coming into contact, one is reassigned to a new order parameter. The initial grain structure can be read in from dream3D (or any voxelated dataset of grain ids).
• The user can now specify a parameters file other than 'parameters.in'. The syntax is: './main -i other_parameters_file.in'

Bug fixes:

• A typo has been fixed in the expression for 'faccV' in the precipitateEvolution app

Other changes:

• The pdf user guide has been removed as well as the Doxygen files. A Doxygen-based user guide is now hosted on a separate site to provide a more interactive experience. The repo for the new user guide can be found here.
• Changed how the equation dependencies are input, making them more specific and more intuitive.
• Previously, there were separate initial condition functions and non-uniform Dirichlet BC functions for scalar fields and vector fields. These have been merged so that there is one initial condition function and one non-uniform Dirichlet BC function. These functions are now part of customPDE and have direct access to the model parameters declared in customPDE.h.
• Renamed the functions in the equation file, removing references to 'residuals'. Instead, everything is referred to as a term in the governing equation.
• The source file names in the app folders have been changed to .cc extensions instead of .h extensions.
• The deal.II headers in the core library have been pruned so there aren't unneeded ones in many of the classes.

Known issues:

• The grain remapping algorithm does not currently obey periodic BCs. This will be patched soon.
• The CHiMaD benchmark problem 6b fails when run with more than 5 MPI processes. This might be due to the size of the coarse mesh (being too small). We're looking into it. There is no problem for benchmark 6a, which is identical except for the domain shape.
• (Inherited from v2.0) PFields only work for scalar fields and only work when the variable with index zero is a scalar field.
• (Inherited from v2.0) Postprocessing only works for scalar fields and only when the variable with index zero is a scalar field.

PRISMS-PF (Version 2.0.2)

Minor updates to v2.0.1, released in May 2018.

Added functionality:

• Nucleation parameters can now be set separately for each nucleating variable. Thus, the input for nucleation in parameters.in has changed. A new core library function "weightedDistanceFromNucleusCenter" has been created to streamline the introduction of nuclei in equations.h (as well streamlining some areas of the core library). See the "nucleationModel" app to view the changes.
• A single vtu file can now be simultaneously written by all MPI processes. This is the new default, but can be changed back to separate output files for each process in the parameters file.
• The simulated time is now included in the vtu file, and for example is now visible in VisIt.

Bug fixes:

• Fixed a bug that prevented the checkpoint system from working in simulations with nucleation.
• The MatrixFreePDE destructor was fixed so it doesn't fail if an exception is caught while a vectors of pointers are being initialized.

Other changes:

• PRISMS-PF is now compatible with deal.II version 9.0 (and still is compatible with version 8.4 and 8.5).
• Changed the file name convention so that when the maximum number of time steps is between powers of 10, it isn't padded by an extra 0 in front (e.g. solution-02000.pvtu becomes solution-2000.pvtu).
• A comprehensible error message is now given if a simulation is set to read a checkpoint file but can't find it.
• The description of how to implement time independent equations in the user guide has been improved.

PRISMS-PF (Version 2.0.1)

Minor update to v2.0, released in November 2017. The biggest change is the introduction of a checkpoint/restart system.

Added functionality:

• A checkpoint/restart system has been added. It allows runs to be restarted if they fail or you want the run to continue for more simulated time.
• The parser to load in VTK files for initial conditions has been generalized so that it can read files generated from ParaView

Changes to the example applications:

• Fixed numerous errors in the documentation for the 'dendriticSolidification' app and edited the 'equations.h' file to use the notation from the documentation.
• Fixed typos in the documentation for the 'coupledCahnHilliardAllenCahn' app.

Bug fixes:

• Fixed the subscriptor bug that appeared at the end of simulations in debug mode.

Other changes:

• Some minor updates to the user guide, including adding a new PRISMS-PF logo.

Known issues:

• PFields only work for scalar fields and only work when the variable with index zero is a scalar field.
• Postprocessing only works for scalar fields and only when the variable with index zero is a scalar field.
• An extraneous error can appear under the following circumstances: in debug mode, with multiple cores, with adaptive meshing, using deal.II v8.4.2 or earlier. The error message includes something similar to: "Called compress(VectorOperation::insert), but the element received from a remote processor, value -2.944283206211677e-10, does not match with the value -2.944283206213795e-10 on the owner processor 60". This is a deal.II issue that they fixed in v8.5 where the tolerance for comparing numbers between processors is too tight and can be triggered by standard round-off error. It doesn't effect simulation results.

PRISMS-PF (Version 2.0)

Major update to PRISMS-PF, released in August 2017. The core library is very similar to v1.2, but the user interface is substantially changed. Most importantly, input parameters are now read from a text file, instead of via #define statements. All of the individual interface changes are not listed here, see the User Guide for the new file structure and syntax.

Added functionality:

• New option for non-uniform Dirichlet BCs (either non-uniform in space or time)
• The integral of any postprocessed field can be calculated
• Non-rectangular meshes (implemented in the new application CHiMaD_benchmark6b)

Changes to the example applications:

• New application: dendriticSolidification, solidification of a pure material, accounting for temperature evolution
• New application: anisotropyFacet, demonstrates a simple way to specify facets for strong interfacial energy anisotropy
• New applications: CHiMaD_benchmark6a and CHiMaD_benchmark6b, the new CHiMaD electrochemistry benchmark problems, with a coupled Cahn-Hilliard-Poisson system of equations

Performance improvements:

• New containers for getting variables into and residuals out of the equations.h functions yields ~15% speedup

Bug fixes:

• Unit tests now run in debug mode
• The variables that can be accessed in postprocess.h are now unrelated to those for residualRHS in equations.h

Other changes:

• Changed the syntax for accessing variables and submitting residuals in equations.h, indices are now error-checked
• To be more accurate mathematically, renamed the "ZERO_DERIVATIVE" to "NATURAL"
• User guide overhauled to use tables instead of long blocks of text, when possible
• Free energies are now treated as just another postprocessing variable
• The postprocessing.h and nucleation.h files are now optional
• Updated the README, including a link to a repository for training materials
• Version changes file changed from a general text file to markdown

Known issues:

• PFields only work for scalar fields and only work when the variable with index zero is a scalar field.
• Postprocessing only works for scalar fields and only when the variable with index zero is a scalar field.
• The formulation file for the dendriticSolidifiation application may have errors.

PRISMS-PF (Version 1.2)

Update to v1.1, released in June 2017. The core library was substantially reorganized and nucleation and postprocessing
capabilities were added.

Added functionality:

• Add postprocessing capabilities, which can be accessed in the new "postprocess.h" file in each application folder.
• New applications "nucleationModel" and "_preferential_nucleationModel" were added and include new nucleation capabilities.

Changes to the pre-built applications:

• New applications "nucleationModel" and "_preferential_nucleationModel" were added and include new nucleation capabilities.
• Changed the initial conditions for the Allen-Cahn and the Cahn-Hilliard applications to have smooth initial profiles.
• The elastic constants are now accessed by "userInputs.CIJ_List" instead of just "CIJ_List" in the functions in equations.h.
• Updated the gradient energy coefficient, the time step, and the mesh resolution of the Allen-Cahn application. Increased the
  time step for CHAC_anisotropy to its maximum stable level. Changed the mesh resolution and time step for the coupled
  Allen-Cahn/Cahn-Hilliard application. Changed the convergence tolerance, time step, and number of iterations for the precipitate
  evolution application.
• The Fickian diffusion application was overhauled to be more conceptually straightforward.
• Changed to a simpler way of specifying the initial conditions, calculating the distances by hand instead of using a pre-built,
  deal.II method.

Performance improvements:

• Removed unnecessary applications of constraints, improving run times by up to 30%.
• Updated how Dirichlet constraints are implemented, reducing the number of solver iterations for non-zero Dirichlet BCs.

Bug fixes:

• Dirichlet BCs now work for parabolic PDEs.
• Users can now load in ICs with PFields in 3D and with adaptive meshes.

Other changes:

• Restructured much of the core library. Model files were completely eliminated, pushing many of those functions into MatrixFreePDE.
  Each application now has a subclass of MatrixFreePDE called customPDE where member variables and methods can be implemented for
  specific applications.
• A wall was put in place between the define macros in the input files and the core solver code. The inputs are now housed in the
  new "userInputParameters" class.
• The core library is now linked instead of "included" in the apps. This increases the compile time the first time an app is compiled
  but decreases it substantially afterward.
• Added more in-app explanation of how to set the BCs (more comments in each ICs_and_BCs.h file)

Known issues:

• PFields only work for scalar fields and only work when the variable with index zero is a scalar field.