Tortuosity Histogram Bugfix

This update fixes a bug that was causing the tortuosity probability histogram output to be missing data for the first bin of the histogram. For a detailed account of all changes, please see the Changelog.

This release was developed under the financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD).

Tomogram Import Bugfix Update

This update fixes a few bugs that were occurring when importing tomogram data. For a detailed account of all changes, please see the Changelog.

This release was developed under the financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD).

v4.0.0 Final Release

This is the final stable release of Ising_OPV v4.0.0 that is published in the Journal of Open Source Software here:

This release only changes documentation files and does not contain modifications to the operation of the source code. For a detailed account of the changes, please see the Changelog.

This release was developed under the financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD).

v4.0.0 Release Candidate 2

This minor update adds some additional documentation to the README and introduces the examples.md file with a fairly detailed walk-through of how to create a morphology set using the Ising-based phase separation simulation. A draft of the v4.0 release paper to be submitted to the Journal of Open Source Software has also been added.

v4.0.0 Release Candidate 1

New and Updated Features in v4.0:

• Updated/refactored large portions of codebase using C++11 features to create a more well-organized and object-oriented software design with a clean API and remove the Boost library dependency
• Updated README with more information about how to install and use Ising_OPV and information about build and testing status
• Added ability to import and interpret large 3D tomography data sets to create experimentally-derived morphology sets for KMC simulations
• Added ability to interpolate imported tomogram data to generate morphologies with a desired lattice unit size that is smaller than the pixel size of the image data
• Added ability to set the volume fraction and composition of the mixed phase when interpreting tomogram data to allow users to compare 2-phase and 3-phase interpretations of the morphology image data
• Updated domain size correlation data calculation to output standard autocorrelation function that decays to zero at large distances
• Updated domain size calculation to allow use of a new faster and more generally effective 1/e method
• Added calculation and output of film depth dependent blend composition, domain size, and interfacial volume fraction data
• Added calculation and output of composition and tortuosity areal map data
• Updated the output morphology data file format to contain information about the compression format in the file header instead of in the filename
• Simplified how users run simulations with different options by putting all options in the parameter file
• Added a Parameters class to handle parameter file import and checking for parameter validity with output of detailed error messages to users when using invalid parameters
• Added googletest submodule for software testing
• Added continuous integration testing using TravisCI and test code coverage assessment using Coveralls
• Added unit and systems tests for all functional features of the software
• Added API documentation pages using Doxygen
• Added API documentation for all public functions and class members
• Added link to new analysis tool, Ising_OPV_Analysis, that is being developed in a separate repository

NOTE: This software release candidate is still undergoing final development and testing, and there may still be bugs that need to be fixed. Please report any bugs in the Issues section.

This release was developed under the financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD).

v4.0 First Beta Release - Codebase Modernization and Tomogram Import

This beta release contains the vast majority of the new features that are planned for v4.0

New and Updated Features in v4.0:

• Updated/refactored large portions of codebase using C++11 features to create a more well-organized object-oriented software design and remove the Boost library dependency
• Updated README with more information about how to install and use Ising_OPV and information about build and testing status
• Added ability to import and interpret large 3D tomography data sets to create morphology sets for KMC simulations
• Added ability to interpolate imported tomogram data to generate morphologies with a desired lattice unit size that is smaller than the pixel size in the image data
• Updated domain size calculation algorithm to a new simpler and faster method
• Updated domain size correlation data calculation to output standard autocorrelation function that decays to zero for large distances
• Added calculation of film depth dependent blend composition, domain size, and interfacial volume fraction data
• Added generation of composition and tortuosity areal map data
• Updated the output morphology data file format to contain information about the compression format in the file header instead of in the filename
• Added googletest submodule for unit testing
• Added continuous integration testing using TravisCI and test code coverage assessment using Coveralls
• Added public API documentation pages using Doxygen
• Added link to new analysis tool Ising_OPV_Analysis that is being developed in a separate repository

NOTE: This software is still in the pre-release beta phase of development, and as such, there may still be bugs that need to be fixed. Please report any bugs or submit feature requests in the Issues section.

This release was developed under the financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD).

v4.0 First Alpha Release!

This alpha release offers a first look at a number of the new features that are planned for v4.0

Major New Updates in v4.0-alpha.1:

• Updated codebase to C++11 so now the Boost library is not required
• Import and interpret large tomography data sets to create morphology sets for KMC simulations
• New simpler and faster domain size calculation method
• Film depth dependent blend composition and domain size calculation
• Simplified software design using the new Lattice class
• Generalized the implementation of the Morphology class to allow more than 2 components in the blend

NOTE: This software is still in the alpha phase of development, and as such, there may still be bugs that need to be squashed. Please report any bugs or submit feature requests in the Issues section.

This release was developed under the financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD).

Morphology Info Update

What's new?

The first line of the morphology file now contains information about the version of Ising_OPV used to generate the morphology and whether the file is in the compressed or uncompressed data format.

Compatibility:

Morphologies created using older versions of Ising_OPV can still be imported into Ising_OPV v3.2.
Morphologies created using Ising_OPV v3.2 cannot be imported into previous versions.

Morphology Correlation Function Update

This small update adds a new feature, enhances feedback to the user, and corrects a small bug.

New Feature:
As an addition to the average correlation function data that is currently calculated and output for the entire morphology set, the correlation function data each individual morphology is now also output to separate files with the naming scheme correlation_data_#.txt

Feedback to the User:
The software will now output a warning message to the user when the lateral dimensions (Length or Width) might be too small for the domain size and domain anisotropy obtained with the provided input parameters. The warning will be given when the Length or Width of the lattice is not greater than 4 times the x- or y-direction correlation length, respectively. Anisotropic morphologies with domains elongated in the x-y plane will require larger Length and Width dimension to prevent finite size effects from altering the features of the morphology. Ideally, the lattice should large enough so that the features of the morphology are independent of the lattice size. More information about how the finite lattice size affects anisotropic morphologies will be presented in an upcoming publication.

Bug Fixes:
Corrected a small bug in the calculateAdditionalEnergyChange function that affected how the swapping energy was calculated for sites across the z-direction periodic boundary.

Ising_OPV v3.0

What's New in v3.0?

Version 3.0 fixes a significant bug present in the previous versions, adds several exciting new features, and contains several major performance improvements.

Major New Features:

• Added the ability to shrink the lattice by a specified integer factor
• Added the ability to use a 3D checkerboard starting configuration instead of a random blend
• Added the ability to modify the interaction energy in one of the directions to allow anisotropic domain growth
• Improved the analysis file output to include a list of the properties of all morphologies in the set
• Added output of the average correlation function for the morphology set to the correlation_data_avg.txt file

Minor New Features:

• Added the ability to extend the correlation function calculation out to the second correlation maximum
• Added characterization of domain anisotropy as a standard metric
• Improved the analysis file to include a header that specifies which version of the software was used to generate the morphology set
• Improved the analysis file output to also specify which morphology has the median domain size and the median tortuosity

Performance Improvements:

• Increased the speed of the phase separation process by increasing the speed of the energy calculation during the Ising swapping stage
• Improved the speed of the tortuosity calculation by increasing the the speed of the pathfinding and path distance calculations
• Added the ability to enable a reduced memory usage tortuosity calculation algorithm. This algorithm is significantly slower, but it is useful when simulating very large lattices where memory limits are reached.

Bug Fixes:

• Corrected a major bug with the random number generator used to choose which neighboring site to use for a swapping attempt (This bug caused anisotropic domain growth in the previous versions of Ising_OPV)
• Improved the correlation function to catch rare cases where the correlation function does not cross the mix fraction value, and in these cases the domain size is set to the position of the first correlation minimum