Merge

Author: rpep

Diff for: .gitignore

@@ -6,6 +6,8 @@
 *.pdf
 *.tmp
 *.so
+*.o
+
 local/
 *~
 *.bak
@@ -51,3 +53,4 @@ test-reports
 
 *.npz
 *.npy
+fmm.cpp

Diff for: .travis.yml

@@ -7,7 +7,7 @@ services:
   - docker
 
 before_install:
-  - docker build -t fidimag -f ./docker/travis/Dockerfile .
+  - travis_wait 90 docker build -t fidimag -f ./docker/travis/Dockerfile .
   - docker run -ti -d --name fidimag fidimag
 
 jobs:

Diff for: Dockerfile

@@ -1,9 +1,14 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
 
-RUN apt -y update 
-RUN apt install -y git python3 python3-pip gcc psutils cmake wget make
+# Avoid user interaction dialog
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt -y update
+# Binder fails with Cython from pip -> use apt cython3
+RUN apt install -y git python3 python3-pip gcc psutils cmake wget make cython3
 RUN apt install -y gfortran libblas-dev liblapack-dev python3-tk sudo fonts-lato
-RUN pip3 install cython matplotlib pytest scipy psutil pyvtk ipywidgets -U
+RUN pip3 install pip -U
+RUN pip3 install matplotlib pytest scipy psutil pyvtk ipywidgets -U
 RUN pip3 install --no-cache-dir notebook
 
 RUN ln -s /usr/bin/python3 /usr/bin/python
@@ -12,7 +17,7 @@ WORKDIR /usr/local
 RUN git clone https://github.com/computationalmodelling/fidimag.git
 WORKDIR /usr/local/fidimag
 # Work with stable release
-RUN git checkout tags/v2.9
+RUN git checkout tags/v3.0a2
 # Install CVODE and FFTW libraries
 WORKDIR /usr/local/fidimag/bin
 RUN bash install-fftw.sh

Diff for: Makefile

@@ -8,7 +8,7 @@ PYTEST = ${PYTHON} -m pytest
 #####################
 
 build:
-	${PYTHON} setup.py build_ext --inplace
+	${PYTHON} setup.py build_ext --inplace -j2
 
 clean:
 	rm -rf ${EXTENSIONS_DIR}/*

Diff for: README.md

@@ -86,6 +86,12 @@ Bisotti, M.-A., Cortés-Ortuño, D., Pepper, R., Wang, W., Beg, M., Kluyver, T.
 
 The following publications, in reverse chronological order, have used or cited Fidimag:
 
+[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://arxiv.org/abs/1906.00813) S. Lepadatu, arXiv:1906.00813 (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) 

Diff for: bin/install-fftw.sh

@@ -36,7 +36,7 @@ download_and_install() {
         ./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."

Diff for: bin/install-sundials.sh

@@ -39,7 +39,7 @@ download_and_cmake_install() {
 
         echo "Compiling and installing "${1}"."
         {
-            make
+            make -j2
             make install
         } > /dev/null
 

Diff for: docker/travis/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
 
 # To build this image `docker build -t fidimag .`
 # Then you can drop into a live bash shell with `docker run -it fidimag`.

Diff for: examples/micromagnetic/skyrmion/Ku_H/main.py

@@ -3,10 +3,10 @@
 import matplotlib.pyplot as plt
 
 import numpy as np
-from micro import Sim
-from common import CuboidMesh
-from micro import UniformExchange, Demag, DMI, UniaxialAnisotropy
-from micro import Zeeman, TimeZeeman
+from fidimag.micro import Sim
+from fidimag.common import CuboidMesh
+from fidimag.micro import UniformExchange, Demag, DMI, UniaxialAnisotropy
+from fidimag.micro import Zeeman, TimeZeeman
 from fidimag.common.fileio import DataReader
 
 mu0 = 4 * np.pi * 1e-7

Diff for: fidimag/atomistic/__init__.py

@@ -2,7 +2,7 @@
 from .exchange import UniformExchange, Exchange
 from .anisotropy import Anisotropy, CubicAnisotropy
 from .zeeman import Zeeman, TimeZeeman
-from .demag import Demag
+from .demag import Demag, DemagFMM
 from .demag_hexagonal import DemagHexagonal
 from .hexagonal_mesh import HexagonalMesh
 from .demag_full import DemagFull

Diff for: fidimag/atomistic/demag.py

@@ -1,6 +1,12 @@
 import fidimag.extensions.dipolar as clib
 import numpy as np
 from .energy import Energy
+import numpy as np
+import fidimag
+from fidimag.atomistic.energy import Energy
+import fidimag.extensions.fmm as fmm
+import time
+import sys
 
 
 class Demag(Energy):
@@ -41,7 +47,7 @@ def __init__(self, calc_every=0, name='Demag'):
 
     def setup(self, mesh, spin, mu_s, mu_s_inv):
         super(Demag, self).setup(mesh, spin, mu_s, mu_s_inv)
-        
+
         # Ryan Pepper 04/04/2019
         # We *do not* need to scale by mesh.unit_length**3 here!
         # This is because in the base energy class, dx, dy and dz