Skip to content

Commit

Permalink
Merge with main branch
Browse files Browse the repository at this point in the history
  • Loading branch information
@davidcortesortuno
davidcortesortuno committed Mar 6, 2024
2 parents feec815 + ca56c43 commit 1788c81
Show file tree
Hide file tree
Showing 67 changed files with 4,177 additions and 2,056 deletions.
2 changes: 2 additions & 0 deletions .github/workflows/superlinter.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,3 +29,5 @@ jobs:
VALIDATE_ALL_CODEBASE: true
DEFAULT_BRANCH: master
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
FILTER_REGEX_EXCLUDE: .*fidimag/atomistic/fmmlib/*.*
FILTER_REGEX_EXCLUDE: .*fidimag/atomistic/lib/fmmlib/*.*
3 changes: 3 additions & 0 deletions Makefile
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
PROJECT_DIR = $(abspath .)
EXTENSIONS_DIR = ${PROJECT_DIR}/fidimag/extensions
USER_EXTENSIONS_DIR = ${PROJECT_DIR}/fidimag/extensions/user
PYTHON = python3
PYTEST = ${PYTHON} -m pytest

Expand All @@ -12,7 +13,9 @@ build:

clean:
rm -rf ${EXTENSIONS_DIR}/*
mkdir -p ${USER_EXTENSIONS_DIR}
touch ${EXTENSIONS_DIR}/__init__.py
touch ${USER_EXTENSIONS_DIR}/__init__.py
rm -rf build

docker:
Expand Down
71 changes: 71 additions & 0 deletions PUBLICATIONS.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,71 @@
# Publications

The following publications, in reverse chronological order, have used or cited Fidimag:

[32] [Thermal Evolution of Skyrmion Formation Mechanism in Chiral Multilayer Films](https://journals.aps.org/prapplied/abstract/10.1103/PhysRevApplied.17.044039) Phys. Rev. Applied 17, 044039 (2022)

[31] [Mutual conversion between a magnetic Néel hopfion and a Néel toron](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.105.174407) Phys. Rev. B 105, 174407 (2022)

[30] [Unveiling the emergent traits of chiral spin textures in magnetic multilayers](https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202103978) Advanced Science Vol 9, Iss 6 (2022)

[29] [The magnetic genome of two-dimensional van der waals materials](https://pubs.acs.org/doi/full/10.1021/acsnano.1c09150) ACS Nano 16, 5, 6960–7079 (2022)

[28] [L-shaped electrode design for high-density spin–orbit torque magnetic random access memory with perpendicular shape anisotropy](https://iopscience.iop.org/article/10.1088/1361-6463/abf61d/) J. Phys. D: Appl. Phys. 54 285002 (2021)

[27] [Periodically modulated skyrmion strings in Cu2OSeO3](https://doi.org/10.1038/s41535-021-00373-y), npj Quantum Materials volume 6, Article number: 73 (2021)

[26] [Speeding up explicit numerical evaluation methods for micromagnetic simulations using demagnetizing field polynomial extrapolation](https://ieeexplore.ieee.org/document/9737008), IEEE Transactions on Magnetics, Vol 58 Issue 5 (2022)

[25] [A Review of Modelling in Ferrimagnetic Spintronics](https://journals.jps.jp/doi/full/10.7566/JPSJ.90.081001) J. Phys. Soc. Jpn. 90, 081001 (2021)

[24] [Topological defect-mediated skyrmion annihilation in three dimensions](https://www.nature.com/articles/s42005-021-00675-4) Communications Physics 4, 175 (2021)

[23] [Stray Field Calculation for Micromagnetic Simulations Using True Periodic Boundary Conditions](https://doi.org/10.1038/s41598-021-88541-9) Scientific Reports 11, 9202 (2021)

[22] [Field-free spin–orbit torque perpendicular magnetization switching in ultrathin nanostructures](https://doi.org/10.1038/s41524-020-0347-0), npj Computational Materials volume 6, 78 (2020)

[21] [Hybrid FFT algorithm for fast demagnetization field calculations on non-equidistant magnetic layers](https://doi.org/10.1016/j.jmmm.2020.166592)
Journal of Magnetism and Magnetic Materials, Volume 503, 166592 (2020)

[20] [Review – Micromagnetic Simulation Using OOMMF and Experimental Investigations on Nano Composite Magnets](https://doi.org/10.1088/1742-6596/1172/1/012070)
Review – Micromagnetic Simulation Using OOMMF and Experimental Investigations on Nano Composite Magnets, J. Phys.: Conf. Ser. 1172 012070

[19] [Spin waves in thin films and magnonic crystals with Dzyaloshinskii-Moriya interactions](https://arxiv.org/abs/1903.04288), arxiv:1903.04288 (2019)

[18] [Tomorrow's Micromagnetic Simulations](https://doi.org/10.1063/1.5093730), Journal of Applied Physics 125, 180901 (2019)

[17] [Diameter-independent skyrmion Hall angle in the plastic flow regime observed in chiral magnetic
multilayers](https://arxiv.org/pdf/1908.04239.pdf](https://www.nature.com/articles/s41467-019-14232-9), Nature Communications volume 11, Article number: 428 (2020)

[16] [Efficient computation of demagnetising fields for magnetic multilayers using multilayered convolution](https://aip.scitation.org/doi/10.1063/1.5116754), Journal of Applied Physics 126, 103903 (2019)

[15] [Micromagnetics and spintronics: models and numerical methods](https://link.springer.com/article/10.1140%2Fepjb%2Fe2019-90599-6), Eur. Phys. J. B (2019) 92: 120

[14] [Nanoscale magnetic skyrmions and target states in confined geometries](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.214408), Physical Review B 99, 214408 (2019)

[13] [Learning Magnetization Dynamics](https://www.sciencedirect.com/science/article/abs/pii/S0304885319307978?via%3Dihub), Journal of Magnetism and Magnetic Materials
Volume 491, (2019)

[12] [Computational micromagnetics with Commics](https://doi.org/10.1016/j.cpc.2019.106965), Computer Physics Communications, 248 (2020)

[11] [Binding a hopfion in a chiral magnet nanodisk](https://journals.aps.org/prb/pdf/10.1103/PhysRevB.98.174437), Physical Review B 98, 174437 (2018)

[10] [Proposal for a micromagnetic standard problem for materials with Dzyaloshinskii–Moriya interaction](http://iopscience.iop.org/article/10.1088/1367-2630/aaea1c), New Journal of Physics, Volume 20 (2018)

[9] [Driving chiral domain walls in antiferromagnets using rotating magnetic fields](https://link.aps.org/doi/10.1103/PhysRevB.97.184418) Physical Review B 97, 184418 (2018)

[8] [Fidimag - A Finite Difference Atomistic and Micromagnetic Simulation Package](http://doi.org/10.5334/jors.223), Journal of Open Research Software, 6(1), p.22. (2018)

[7] [Topological Spintronics in Confined Geometry](https://escholarship.org/uc/item/8wx626mw), Y. Liu, PhD Thesis, University of California Riverside (2017)

[6] [Thermal stability and topological protection of skyrmions in nanotracks](https://www.nature.com/articles/s41598-017-03391-8), Scientific Reports 7, 4060 (2017)

[5] [Current-induced instability of domain walls in cylindrical nanowires](http://iopscience.iop.org/article/10.1088/1361-648X/aa9698/meta), Journal of Physics: Condensed Matter, 30, 1 (2017)

[4] [Magnonic analog of relativistic Zitterbewegung in an antiferromagnetic spin chain](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.024430), Phys. Rev. B 96 024430 (2017)

[3] [Driving magnetic skyrmions with microwave fields](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.92.020403) Phys. Rev. B 92, 020403 (2015).

[2] [Microwave-induced dynamic switching of magnetic skyrmion cores in nanodots](https://aip.scitation.org/doi/10.1063/1.4914496) Applied Physics Letters 106, 102401 (2015).

[1] [Magnon-Driven Domain-Wall Motion with the Dzyaloshinskii-Moriya Interaction](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.087203) Phys. Rev. Lett. 114, 087203 (2015)
73 changes: 4 additions & 69 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,9 @@
Fidimag solves finite-difference micromagnetic problems and supports atomistic simulations, using Python interface. The interface to both types of simulation is similar.

### Features
* Optimal LLG equation integration using modern [Sundial's v6](https://github.com/LLNL/sundials/) CVODE solver
* Offers LLG and LLG with spin torque terms (Zhang-Li and Sloncewski)
* Calculations using the Nudged-Elastic-Band method to compute energy barriers.
* Calculations using the Geodesic-Nudged-Elastic-Band and String methods to compute energy barriers.
* Exchange, Zeeman, Demagnetising, Uniaxial Anisotropy energy classes.
* Parallelised using OpenMP.
* Easily extensible to add new features.
Expand Down Expand Up @@ -71,7 +72,9 @@ The results can be straightforwardly visualised from the outputted VTK files usi
<img src="http://computationalmodelling.github.io/fidimag/figs/target.png" alt="Target Skyrmion State" width="250">
</p>

### Publications

A list tracking publications that cite FIDIMAG can be found in the [Publications](PUBLICATIONS.md) document.


### Attributions
Expand All @@ -82,75 +85,7 @@ If you use Fidimag, please cite as:

Bisotti, M.-A., Cortés-Ortuño, D., Pepper, R., Wang, W., Beg, M., Kluyver, T. and Fangohr, H., 2018. Fidimag – A Finite Difference Atomistic and Micromagnetic Simulation Package. Journal of Open Research Software, 6(1), p.22. DOI: http://doi.org/10.5334/jors.223

### Publications

The following publications, in reverse chronological order, have used or cited Fidimag:

[28] [L-shaped electrode design for high-density spin–orbit torque magnetic random access memory with perpendicular shape anisotropy](https://iopscience.iop.org/article/10.1088/1361-6463/abf61d/) K. Chi, Y. Shi, Z. Li, W. Zhang, Y. Xing, X. Feng, Y. Ma, H. Meng, B. Liu, J. Phys. D: Appl. Phys. 54 285002 (2021)

[27] [Periodically modulated skyrmion strings in Cu2OSeO3](https://doi.org/10.1038/s41535-021-00373-y) D. M. Burn, R. Brearton, K. J. Ran, S. L. Zhang, G. van der Laan, T. Hesjedal, npj Quantum Materials volume 6, Article number: 73 (2021)

[26] [Speeding up explicit numerical evaluation methods for micromagnetic simulations using demagnetizing field polynomial extrapolation](https://arxiv.org/abs/2107.06729) S. Lepadatu, arXiv:2107.06729 (2021)

[25] [A Review of Modelling in Ferrimagnetic Spintronics](https://journals.jps.jp/doi/full/10.7566/JPSJ.90.081001) Joseph Barker, Unai Atxitia, J. Phys. Soc. Jpn. 90, 081001 (2021)

[24] [Topological defect-mediated skyrmion annihilation in three dimensions](https://www.nature.com/articles/s42005-021-00675-4) M. T. Birch, D. Cortés-Ortuño, N. D. Khanh, S. Seki, A. Štefančič, G. Balakrishnan, Y. Tokura & P. D. Hatton, Communications Physics 4, 175 (2021)

[23] [Stray Field Calculation for Micromagnetic Simulations Using True Periodic Boundary Conditions](https://doi.org/10.1038/s41598-021-88541-9) F. Bruckner, A. Ducevic, P. Heistracher, C. Abert & D. Suess, Scientific Reports 11, 9202 (2021)

[22] [Field-free spin–orbit torque perpendicular magnetization switching in ultrathin nanostructures](https://doi.org/10.1038/s41524-020-0347-0)
M. Dai, J-M. Hu, npj Computational Materials volume
6, 78 (2020)

[21] [Hybrid FFT algorithm for fast demagnetization field calculations on non-equidistant magnetic layers](https://doi.org/10.1016/j.jmmm.2020.166592)
P. Heistracher, F. Bruckner, C. Abert, C. Vogler, D. Suess, Journal of Magnetism and Magnetic Materials
Volume 503, 166592 (2020)

[20] [Review – Micromagnetic Simulation Using OOMMF and Experimental Investigations on Nano Composite Magnets](https://doi.org/10.1088/1742-6596/1172/1/012070)
Review – Micromagnetic Simulation Using OOMMF and Experimental Investigations on Nano Composite Magnets
S. Sundara Mahalingam, B. V. Manikandan, S. Arockiaraj, J. Phys.: Conf. Ser. 1172 012070

[19] [Spin waves in thin films and magnonic crystals with Dzyaloshinskii-Moriya interactions](https://arxiv.org/abs/1903.04288)
R. A. Gallardo, D. Cortés-Ortuño, R. E. Troncoso, P. Landeros, arxiv:1903.04288 (2019)

[18] [Tomorrow's Micromagnetic Simulations](https://doi.org/10.1063/1.5093730)
J. Leliaert, J. Mulkers, Journal of Applied Physics 125, 180901 (2019)

[17] [Diameter-independent skyrmion Hall angle in the plastic flow regime observed in chiral magnetic
multilayers](https://arxiv.org/pdf/1908.04239.pdf)
K. Zeissler, S. Finizio, C. Barton, A. Huxtable, J. Massey, J. Raabe, A. V. Sadovnikov, S. A. Nikitov, R. Brearton, T. Hesjedal, G. van der Laan, M. C. Rosamond, E. H. Linfield, G. Burnell, C. H. Marrows, arXiv:1908.04239 (2019)

[16] [Efficient computation of demagnetising fields for magnetic multilayers using multilayered convolution](https://aip.scitation.org/doi/10.1063/1.5116754) S. Lepadatu, Journal of Applied Physics 126, 103903 (2019)

[15] [Micromagnetics and spintronics: models and numerical methods](https://link.springer.com/article/10.1140%2Fepjb%2Fe2019-90599-6) C. Abert, Eur. Phys. J. B (2019) 92: 120

[14] [Nanoscale magnetic skyrmions and target states in confined geometries](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.214408), D. Cortés-Ortuño, N. Romming, M. Beg, K. von Bergmann, A. Kubetzka, O. Hovorka, H. Fangohr, R. Wiesendanger, Physical Review B 99, 214408 (2019)

[13] [Learning Magnetization Dynamics](https://arxiv.org/abs/1903.09499), A. Kovacs, J. Fischbacher, H. Oezelt, M. Gusenbauer, L. Exl, F. Bruckner, D.Suess, T.Schrefl, arXiV (2019)

[12] [Computational micromagnetics with Commics](https://arxiv.org/abs/1812.05931), C.-M. Pfeiler, M. Ruggeri, B. Stiftner, L. Exl, M. Hochsteger, G. Hrkac, J. Schöberl, N. J. Mauser, D. Praetorius, arXiV (2018)

[11] [Binding a hopfion in a chiral magnet nanodisk](https://journals.aps.org/prb/pdf/10.1103/PhysRevB.98.174437), Y. Liu, R. K. Lake, and J. Zang, Physical Review B 98, 174437 (2018)

[10] [Proposal for a micromagnetic standard problem for materials with Dzyaloshinskii–Moriya interaction](http://iopscience.iop.org/article/10.1088/1367-2630/aaea1c), D. Cortés-Ortuño, M. Beg, V. Nehruji, L. Breth, R. Pepper, T. Kluyver, G. Downing, T. Hesjedal, P. Hatton, T. Lancaster, R. Hertel, O. Hovorka and H. Fangohr, New Journal of Physics, Volume 20 (2018)

[9] [Driving chiral domain walls in antiferromagnets using rotating magnetic fields](https://link.aps.org/doi/10.1103/PhysRevB.97.184418) K.Pan, L.Xing, H.Y.Yuan, and W.Wang, Physical Review B 97, 184418 (2018)

[8] [Fidimag - A Finite Difference Atomistic and Micromagnetic Simulation Package](http://doi.org/10.5334/jors.223), Bisotti, M.-A., Cortés-Ortuño, D., Pepper, R., Wang, W., Beg, M., Kluyver, T. and Fangohr, H., Journal of Open Research Software, 6(1), p.22. (2018)

[7] [Topological Spintronics in Confined Geometry](https://escholarship.org/uc/item/8wx626mw), Y. Liu, PhD Thesis, University of California Riverside (2017)

[6] [Thermal stability and topological protection of skyrmions in nanotracks](https://www.nature.com/articles/s41598-017-03391-8), D. Cortés-Ortuño, W. Wang, M. Beg, R.A. Pepper, M-A. Bisotti, R. Carey, M. Vousden, T. Kluyver, O. Hovorka & H. Fangohr, Scientific Reports 7, 4060 (2017)

[5] [Current-induced instability of domain walls in cylindrical nanowires](http://iopscience.iop.org/article/10.1088/1361-648X/aa9698/meta), W. Wang, Z. Zhang, R.A. Pepper, C. Mu, Y. Zhou & Hans Fangohr, Journal of Physics: Condensed Matter, 30, 1 (2017)

[4] [Magnonic analog of relativistic Zitterbewegung in an antiferromagnetic spin chain](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.024430), W. Wang, C. Gu, Y. Zhou & H. Fangohr, Phys. Rev. B 96 024430 (2017)

[3] [Driving magnetic skyrmions with microwave fields](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.92.020403) W. Wang, M. Beg, B. Zhang, W. Kuch, and H. Fangohr, Phys. Rev. B 92, 020403 (2015).

[2] [Microwave-induced dynamic switching of magnetic skyrmion cores in nanodots](https://aip.scitation.org/doi/10.1063/1.4914496) B. Zhang, W. Wang, M. Beg, H. Fangohr, and W. Kuch, Applied Physics Letters 106, 102401 (2015).

[1] [Magnon-Driven Domain-Wall Motion with the Dzyaloshinskii-Moriya Interaction](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.087203) W. Wang, M. Albert, M. Beg, M-A. Bisotti, D. Chernyshenko, D. Cortés-Ortuño, I. Hawke & H. Fangohr, Phys. Rev. Lett. 114, 087203 (2015)

### Acknowledgements

Expand Down
41 changes: 23 additions & 18 deletions bin/install-sundials.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,10 @@ set -e
# when SUNDIALS moved to a CMake-based installation. Will install locally.
# It may need environment variables to work, like `export CC=gcc` in ARCHER.

SUNDIALS=sundials-2.6.2
# Github release from Sundials repository
# https://github.com/LLNL/sundials
SUNDIALS_TAG=v6.6.1
SUNDIALS=sundials-6.6.1

# Make sure CMake is installed, since SUNDIALS requires it.
type cmake >/dev/null 2>&1 || { printf "CMake required to build SUNDIALS. You can install it by typing: \nsudo apt install cmake\n"; exit 1;}
Expand All @@ -21,39 +24,41 @@ mkdir -p ${LIBS_DIR}
cd ${LIBS_DIR}

download_and_cmake_install() {
# $1 name of the package
# $2 URL where ${1}.tar.gz can be obtained
# $3 configure options
if [ ! -e ${1}.tar.gz ]; then
echo "Downloading "${1}"."
wget -q ${2}/${1}.tar.gz
# $1 tag of the package
# $2 name of the package
# $3 URL where ${1}.tar.gz can be obtained
# $4 configure options
if [ ! -e ${1}/${2}.tar.gz ]; then
echo "Downloading "${3}/${1}/${2}.tar.gz"."
wget -q -O ${2}.tar.gz ${3}/${1}/${2}.tar.gz
fi;

if [ ! -e ${1} ]; then
tar -xzf ${1}.tar.gz
if [ ! -e ${2} ]; then
tar -xzf ${2}.tar.gz

echo "Configuring "${1}"."
mkdir ${1}_build
cd ${1}_build
cmake ${3} ../${1}
echo "Configuring "${2}"."
mkdir ${2}_build
cd ${2}_build
cmake ${4} ../${2}

echo "Compiling and installing "${1}"."
echo "Compiling and installing "${2}"."
{
make -j2
make install
} > /dev/null

echo "Cleaning up."
cd ..
rm -rf ${1}
rm -rf ${1}_build
rm -rf ${2}
rm -rf ${2}_build

cd ${HERE_DIR}
echo "Done."
fi;
}

download_and_cmake_install \
${SUNDIALS_TAG} \
${SUNDIALS} \
http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download \
"-DBUILD_STATIC_LIBS=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX="${LIBS_DIR}" -DEXAMPLES_ENABLE=OFF -DLAPACK_ENABLE=ON -DOPENMP_ENABLE=ON"
https://github.com/LLNL/sundials/releases/download \
"-DBUILD_STATIC_LIBS=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX="${LIBS_DIR}" -DEXAMPLES_ENABLE=OFF -DENABLE_LAPACK=ON -DENABLE_OPENMP=ON"
Loading

0 comments on commit 1788c81

Please sign in to comment.