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

Author: rpep

.gitignore

@@ -6,8 +6,11 @@
 *.pdf
 *.tmp
 *.so
-/local/
-
+local/
+*~
+*.bak
+.DS_Store
+.pytest_cache/
 # ignore automatically generated cython files
 fidimag/atomistic/lib/clib.c
 fidimag/common/lib/common_clib.c

.hgignore

@@ -1 +1 @@
-Weiwei Wang, Marc-Antonio Bisotti, David Cortes, Mark Vousden, Beckie Carey, Marijan Beg, Hans Fangohr
+Weiwei Wang, Marc-Antonio Bisotti, David Cortes, Thomas Kluyver, Mark Vousden, Ryan Pepper, Oliver Laslett, Rebecca Carey, and Hans Fangohr

AUTHORS.txt

@@ -3,7 +3,7 @@ FROM ubuntu:16.04
 RUN apt -y update 
 RUN apt install -y git python3 python3-pip gcc psutils cmake wget make
 RUN apt install -y gfortran libblas-dev liblapack-dev python3-tk sudo fonts-lato
-RUN pip3 install cython matplotlib pytest scipy psutil pyvtk ipywidgets
+RUN pip3 install cython matplotlib pytest scipy psutil pyvtk ipywidgets -U
 RUN pip3 install --no-cache-dir notebook
 
 RUN ln -s /usr/bin/python3 /usr/bin/python

Dockerfile

@@ -70,25 +70,36 @@ The results can be straightforwardly visualised from the outputted VTK files usi
 
 
 
-### Attributions 
+### 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.
 
 This is an early experimental version; contributions and pull requests to both the code and documentation are welcome.
 If you use Fidimag, please cite as:
 
-David Cortés-Ortuño, Weiwei Wang, Ryan Pepper, Marc-Antonio Bisotti, Thomas Kluyver, Mark Vousden, & Hans Fangohr. (2016). Fidimag v2.0 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.167858A bib file is provided in the repository.
+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 Fidimag:
 
-[1] [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)
+[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)
 
-[2] [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)
+[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,
+Physical Review B 97, 184418 (2018).
 
-[3] [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 (2017)
+[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)
 
-[4] [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)
+[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)
+
+[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)
+
+[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)
+
+[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).
+
+[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).
+
+[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)
 
 ### Acknowledgements
-We acknowledge financial support from EPSRC’s Centre for Doctoral Training in Next Generation Computational Modelling (EP/L015382/1) and EPSRC’s Doctoral Training Centre in Complex System Simulation (EP/G03690X/1)
+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).

README.md

@@ -20,12 +20,13 @@
 def extract_library(so_file):
     cmd = ('otool', '-L', so_file)
     output = subprocess.check_output(cmd)
-    for line in output.split('\t'):
+    for line in output.decode().split('\t'):
         m = patten.match(line)
+        print(m, line)
         if m:
             lib_name =  m.group()
             full_name = os.path.join(LIB_DIR, lib_name)
-            #print lib_name, full_name
+            print(lib_name, full_name)
             cmd = ('install_name_tool', '-change',
                  lib_name, full_name, so_file
                  )

bin/fix_load_path_mac.py

@@ -1,9 +1,9 @@
 #!/bin/bash
-echo "HELLO"
+
 # This script installs FFTW locally. It may need to environment
 # variables to work, like 'export CC=gcc' in ARCHER.
 
-FFTW=fftw-3.3.4
+FFTW=fftw-3.3.8
 
 set -e
 
@@ -33,12 +33,10 @@ download_and_install() {
         tar -xzf ${1}.tar.gz
         cd ${1}
         echo "Configuring "${1}"."
-        ./configure --quiet --enable-shared --enable-openmp --prefix=${LIBS_DIR}
+        ./configure --enable-shared --enable-openmp --enable-sse2 --enable-avx --prefix=${LIBS_DIR}
         echo "Compiling and installing "${1}"."
-        {
-            make
-            make install
-        } > /dev/null
+        make
+        make install
         echo "Done."
         cd ${LIBS_DIR}
     fi;

bin/install-fftw.sh

@@ -31,6 +31,7 @@ Contents:
    ipynb/spin-polarised-current-driven-skyrmion
    ipynb/spin-waves-in-periodic-system
    ipynb/FMR-stdprob
+   ipynb/steepest_descent_atomistic
 
 .. toctree::
    :maxdepth: 2