Merge branch 'master' of github.com:computationalmodelling/fidimag

Author: rpep

.travis.yml

@@ -6,8 +6,16 @@ group: deprecated-2017Q4
 services:
   - docker
 
-script:
-  - make travis
+before_install:
+  - docker build -t fidimag -f ./docker/travis/Dockerfile .
+  - docker run -ti -d --name fidimag fidimag
+
+jobs:
+  include:
+    - stage: Tests
+      script: make test-docker
+    - stage: Notebooks
+      script: make ipynb-docker
 
 notifications:
   email:

Makefile

@@ -13,6 +13,7 @@ build:
 clean:
 	rm -rf ${EXTENSIONS_DIR}/*
 	touch ${EXTENSIONS_DIR}/__init__.py
+	rm -rf build
 
 docker:
 	docker build -t fidimag -f ./docker/travis/Dockerfile .
@@ -22,13 +23,19 @@ docker:
 # Tests #
 #########
 
-test-docker: docker
+test-docker:
 	docker exec fidimag make test-basic
 	#docker exec fidimag make test-without-run-oommf
 	#docker exec fidimag make test-ipynb
 
-travis: test-docker
+ipynb-docker:
+	while sleep 9m; do echo "===[ Still Running ]===\n"; done &
+	docker exec fidimag make test-ipynb
+	kill %1
+
+travis-test: test-docker
 	docker exec fidimag make codecov
+	docker exec fidimag make test-ipynb
 
 codecov:
 	bash <(curl -s https://codecov.io/bash)

README.md

@@ -2,12 +2,16 @@
 
 
 [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/computationalmodelling/fidimag/master)
-[![Build Status](https://travis-ci.org/computationalmodelling/fidimag.svg?branch=master)](https://travis-ci.org/computationalmodelling/fidimag)
 [![Documentation Status](https://readthedocs.org/projects/fidimag/badge/?version=latest)](http://fidimag.readthedocs.org/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/computationalmodelling/fidimag/branch/master/graph/badge.svg)](https://codecov.io/gh/computationalmodelling/fidimag)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.167858.svg)](https://doi.org/10.5281/zenodo.167858)
 [![Website](https://img.shields.io/website-up-down-green-red/http/shields.io.svg?label=Fidimag-Website)](http://computationalmodelling.github.io/fidimag/)
 
+| Tests Type | Status |
+|:-:|:-:|
+| Tests | ![Tests](https://travis-matrix-badges.herokuapp.com/repos/computationalmodelling/fidimag/branches/master/1)
+| Notebooks | ![Notebooks](https://travis-matrix-badges.herokuapp.com/repos/computationalmodelling/fidimag/branches/master/2)
+
 <img src="http://computationalmodelling.github.io/fidimag/figs/skyrmion.jpg" alt="Fidimag Image" width="400" align="right">
 
 Fidimag solves finite-difference micromagnetic problems and supports atomistic simulations, using Python interface. The interface to both types of simulation is similar.
@@ -71,9 +75,9 @@ The results can be straightforwardly visualised from the outputted VTK files usi
 
 
 ### Attributions
-The code is developed by Weiwei Wang, Marc-Antonio Bisotti, David Cortes, Thomas Kluyver, Mark Vousden, Ryan Pepper, Oliver Laslett, Rebecca Carey, and Hans Fangohr at the University of Southampton.
+The code is currently developed by Weiwei Wang, David Cortes, Ryan Pepper and Hans Fangohr at Anhui University, University of Southampton and European XFEL. Previous developers who have worked on Fidimag are Marc-Antonio Bisotti, Thomas Kluyver, Mark Vousden, Oliver Laslett and Rebecca Carey.
 
-This is an early experimental version; contributions and pull requests to both the code and documentation are welcome.
+Contributions and pull requests to both the code and documentation are welcome.
 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
@@ -82,24 +86,28 @@ Bisotti, M.-A., Cortés-Ortuño, D., Pepper, R., Wang, W., Beg, M., Kluyver, T.
 
 The following publications, in reverse chronological order, have used Fidimag:
 
-[1] [Proposal for a micromagnetic standard problem for materials with Dzyaloshinskii–Moriya interaction](http://iopscience.iop.org/article/10.1088/1367-2630/aaea1c), D. C-Ortuño, M. Beg2, V. Nehruji3, L. Breth1, R. Pepper, T. Kluyver, G. Downing, T. Hesjedal, P. Hatton3, T. Lancaster, R. Hertel5, O. Hovorka and H. Fangohr, New Journal of Physics, Volume 20 (2018)
+[1] [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)
+
+[2] [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)
+
+[3] [Proposal for a micromagnetic standard problem for materials with Dzyaloshinskii–Moriya interaction](http://iopscience.iop.org/article/10.1088/1367-2630/aaea1c), D. C-Ortuño, M. Beg2, V. Nehruji3, L. Breth1, R. Pepper, T. Kluyver, G. Downing, T. Hesjedal, P. Hatton3, T. Lancaster, R. Hertel5, O. Hovorka and H. Fangohr, New Journal of Physics, Volume 20 (2018)
 
-[2] [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,
+[4] [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).
 
-[3] [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)
+[5] [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)
 
-[4] [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)
+[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)
+[7] [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)
 
-[6] [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)
+[8] [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)
 
-[7] [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).
+[9] [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).
 
-[8] [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).
+[10] [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).
 
-[9] [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)
+[11] [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
 We acknowledge financial support from EPSRC’s Centre for Doctoral Training in Next Generation Computational Modelling (EP/L015382/1),  EPSRC’s Doctoral Training Centre in Complex System Simulation (EP/G03690X/1), EPSRC Programme grant on Skyrmionics (EP/N032128/1) and OpenDreamKitHorizon 2020 European Research Infrastructure project (676541).

bin/install-fftw.sh

@@ -33,10 +33,12 @@ download_and_install() {
         tar -xzf ${1}.tar.gz
         cd ${1}
         echo "Configuring "${1}"."
-        ./configure --enable-shared --enable-openmp --enable-sse2 --enable-avx --prefix=${LIBS_DIR}
+        ./configure --quiet --enable-shared --enable-openmp --enable-sse2 --enable-avx --prefix=${LIBS_DIR}
         echo "Compiling and installing "${1}"."
-        make
-        make install
+        {
+            make
+            make install
+        } > /dev/null
         echo "Done."
         cd ${LIBS_DIR}
     fi;