Merge branch 'fmm' of github.com:computationalmodelling/fidimag into fmm

Author: rpep

.gitignore

@@ -5,16 +5,22 @@
 *.swp
 *.pdf
 *.tmp
-/local/
-
+*.so
+local/
+*~
+*.bak
+.DS_Store
+.pytest_cache/
 # ignore automatically generated cython files
 fidimag/atomistic/lib/clib.c
+fidimag/common/lib/common_clib.c
 fidimag/common/dipolar/dipolar.c
 fidimag/common/neb/neb_clib.c
 fidimag/common/neb_method/*clib.c
 fidimag/common/sundials/cvode.c
 fidimag/micro/lib/baryakhtar/baryakhtar_clib.c
 fidimag/micro/lib/micro_clib.c
+fidimag/user/example/example.c
 
 # ignore .cache from pytest
 .cache

.hgignore

@@ -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:

.travis.yml

@@ -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

@@ -0,0 +1,85 @@
+Version 3.0 Alpha
+------------------
+* Changes to the helper functions init_scalar and init_vector (fidimag/common/helper.py)
+  which allow users to pass additional parameters. These are then used within the sim
+  classes to allow 
+  
+  For example:
+
+  ```
+  
+  mesh = CuboidMesh(nx=10, ny=1, nz=1, unit_length=1e-9)
+  sim = Sim(mesh, Ms)
+
+  def init_domain_wall(pos, domain_centre)
+      x, y, z = pos
+
+      if x < domain_centre:
+          return (0, 0, 1)
+
+      else:
+          return (0, 0, -1)
+   
+  # Place a domain wall at 5nm
+  sim.set_m(init_domain_wall, 5)
+  # Place a domain wall at 3nm
+  sim.set_m(init_domain_wall, 3)
+
+  ```
+
+* Setting currents is now more general, and is standardised across the simulation types.
+  This allows us to use more general functions for setting the current.
+  Previously, the current function was set as:
+  ```
+  sim(mesh, driver='llg_stt')
+  sim.driver.jx = 1e14 # A / m^2
+  sim.driver.update_j_fun = lambda t: np.sin(t)
+  ```
+  with the actual current used being multiplicative:
+
+  $ jx * sin(t) $
+
+  For the current-perpendicular to the plane STT ('llg_stt_cpp') driver
+   we would now change this to 
+
+  ```
+  sim.driver(mesh, driver='llg_stt_cpp')
+  sim.driver.j_function = lambda t: 1e14 * np.sin(t)
+  ```
+  and for the standard STT driver:
+
+  ```
+  sim.drive(mesh, driver='llg_stt')
+  sim.driver.jz_function = lambda t: 1e14 * np.sin(t)
+  # Can also set:
+  # sim.driver.jx_function = ...
+  # sim.driver.jy_function = ...
+
+* Similarly, the TimeZeeman interaction is also no longer multiplicative;
+  you can have an arbitrary function of the form:
+ 
+  def time_function(pos, t):
+      x, y, z = pos
+      # some calculation of Bx(pos, t), By(pos, t), Bz(pos, t)
+      return (Bx, By, Bz)
+  zee = TimeZeeman(np.array([0, 0, 0]), time_function)
+  sim.add(zee)
+
+* You can now remove energy classes from the simulation.
+
+  This can be useful in cases where you have an interaction
+  but no longer need to calculate it because the simulation has 
+  reached a certain point, e.g. an applied field has been turned off.
+ 
+  In the data table, the entries corresponding to a given interaction 
+  will be zero everywhere once the interaction is removed.
+ 
+  
+  For example:
+
+  ```
+  sim.add(Zeeman((0, 0, B), name='Zeeman'))
+  
+  sim.run_until(1e-9)
+  sim.remove('Zeeman')
+  ```

CHANGELOG.md

@@ -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

@@ -8,11 +8,12 @@ PYTEST = ${PYTHON} -m pytest
 #####################
 
 build:
-	${PYTHON} setup.py build_ext --inplace
+	${PYTHON} setup.py build_ext --inplace -j2
 
 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)

Makefile

@@ -70,25 +70,40 @@ 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.
+### Attributions
+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:
 
-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] [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] [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] [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] [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] [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)
 
-[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] [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).
+
+[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)
+
+[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)
+
+[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)
+
+[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)
+
+[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).
+
+[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).
+
+[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) 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
 
@@ -33,10 +33,10 @@ download_and_install() {
         tar -xzf ${1}.tar.gz
         cd ${1}
         echo "Configuring "${1}"."
-        ./configure --quiet --enable-shared --enable-openmp --prefix=${LIBS_DIR}
+        ./configure --quiet --enable-shared --enable-openmp --enable-sse2 --enable-avx --prefix=${LIBS_DIR}
         echo "Compiling and installing "${1}"."
         {
-            make
+            make -j2
             make install
         } > /dev/null
         echo "Done."