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

Author: rpep

.travis.yml

@@ -1,53 +1,14 @@
-language: python
-python:
-        - "3.6"
-        - "3.5"
-        - "3.4"
-        - "2.7"
+sudo: required
 
+dist: trusty
+group: deprecated-2017Q4
 
-before_install:
-  # We do this conditionally because it saves us some downloading if the
-  # version is the same.
-  - deactivate  # Deactivate virtualenv
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH=/home/travis/miniconda/bin:$PATH
-  - sudo apt-get install liblapack-dev libblas-dev
-install:
-  - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy pytest-cov gcc cmake psutil
-  - source activate fidimag-test
-  - pip install pyvtk six nbval
-  - pip install pyvtk six ipywidgets
-  - pip install git+https://github.com/computationalmodelling/nbval.git
-  # Download and compile FFTW & Sundials locally
-  - bash bin/install-sundials.sh
-  - bash bin/install-fftw.sh
+services:
+  - docker
 
-before_script:
-        - conda list
-        - make build
-        - export PYTHONPATH="$TRAVIS_BUILD_DIR:$PYTHONPATH"
-        - export LD_LIBRARY_PATH="$TRAVIS_BUILD_DIR/local/lib:$LD_LIBRARY_PATH"
-        - export LD_RUN_PATH="$TRAVIS_BUILD_DIR/local/lib:$LD_RUN_PATH"
-        - export OMP_NUM_THREADS=1
-        - export MPLBACKEND=Agg
-        # Tells matplotlib (?) to use PyQt class v2 APIs (I think)
-        - export QT_API=pyqt
-
-# command to run tests
 script:
-  - make test-without-run-oommf
-  - make test-ipynb
-
+  - make travis
 
 notifications:
   email:
     on_failure: always
-
-after_success:
-  - bash <(curl -s https://codecov.io/bash)

Dockerfile

@@ -0,0 +1,53 @@
+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 --no-cache-dir notebook
+
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
+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
+# Install CVODE and FFTW libraries
+WORKDIR /usr/local/fidimag/bin
+RUN bash install-fftw.sh
+RUN bash install-sundials.sh
+
+ENV PYTHONPATH="/usr/local/fidimag:$PYTHONPATH"
+ENV LD_LIBRARY_PATH="/usr/local/fidimag/local/lib:$LD_LIBRARY_PATH"
+
+WORKDIR /usr/local/fidimag
+RUN python3 setup.py build_ext --inplace
+RUN python3 -c "import matplotlib"
+# Headless Matplotlib:
+ENV MPLBACKEND=Agg
+
+# Headless Matplotlib:
+ENV MPLBACKEND=Agg
+
+# Set threads for OpenMP:
+ENV OMP_NUM_THREADS=2
+# WORKDIR /io
+
+# User to make Binder happy
+ENV NB_USER magnetism
+ENV NB_UID 1000
+ENV HOME /home/${NB_USER}
+
+RUN adduser --disabled-password \
+    --gecos "Default user" \
+    --uid ${NB_UID} \
+    ${NB_USER}
+
+# Make sure the contents of our repo are in ${HOME}
+COPY . ${HOME}
+USER root
+RUN chown -R ${NB_UID} ${HOME}
+USER ${NB_USER}
+
+WORKDIR /home/${USER}/magnetism/doc/ipynb

Makefile

@@ -1,26 +1,44 @@
 PROJECT_DIR = $(abspath .)
 EXTENSIONS_DIR = ${PROJECT_DIR}/fidimag/extensions
-PYTHON = python
+PYTHON = python3
+PYTEST = py.test-3
 
 #####################
 # Cython Extensions #
 #####################
 
-
 build:
 	${PYTHON} setup.py build_ext --inplace
 
 clean:
 	rm -rf ${EXTENSIONS_DIR}/*
 	touch ${EXTENSIONS_DIR}/__init__.py
 
+docker:
+	docker build -t fidimag -f ./docker/travis/Dockerfile .
+	docker run -ti -d --name fidimag fidimag
+
 #########
 # Tests #
 #########
 
+test-docker: docker
+	docker exec fidimag make test-basic
+	#docker exec fidimag make test-without-run-oommf
+	#docker exec fidimag make test-ipynb
+
+travis: test-docker
+	docker exec fidimag make codecov
+
+codecov:
+	bash <(curl -s https://codecov.io/bash)
+codecov: SHELL:= /bin/bash
+# or the recipe fails with /bin/sh complaining
+# `/bin/sh: 1: Syntax error: "(" unexpected`.
+
 # Quick tests, also not using OOMMF tests
 test:
-	cd tests && py.test -v -m "not slow and not run_oommf"
+	cd tests && ${PYTEST} -v -m "not slow and not run_oommf"
 
 test-clean:
 	rm -rf neb*.ndt
@@ -51,16 +69,16 @@ test-clean:
 test2:
 	# like test, but run also outside the 'tests' directory.
 	# Doesn't work on Hans laptop.
-	py.test -v -m "not slow and not run_oommf"
+	${PYTEST} -v -m "not slow and not run_oommf"
 
 test-all: create-dirs
-	py.test -v --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml
+	${PYTEST} -v --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml
 
 test-without-run-oommf: create-dirs
-	py.test -v -m "not run_oommf" --cov=fidimag --cov-report=html --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml
+	${PYTEST} -v -m "not run_oommf" --cov=fidimag --cov-report=html --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml
 
 test-basic:
-	cd tests && py.test -v
+	cd tests && ${PYTEST} -v
 
 # Convenience name for commonly used quick running of tests
 tq:
@@ -71,10 +89,10 @@ test-quick:
 
 
 test-ipynb: create-dirs
-	cd doc/ipynb && py.test . -v --current-env --nbval --sanitize-with sanitize_file --junitxml=$(PROJECT_DIR)/test-reports/junit/test-ipynb-pytest.xml
+	cd doc/ipynb && ${PYTEST} . -v --current-env --nbval --sanitize-with sanitize_file --junitxml=$(PROJECT_DIR)/test-reports/junit/test-ipynb-pytest.xml
 
 test-oommf:
-	py.test -v -m "oommf"
+	${PYTEST} -v -m "oommf"
 
 create-dirs:
 	mkdir -p test-reports/junit
@@ -93,4 +111,4 @@ doc-%:
 	@echo $*
 	make -C doc $*
 
-.PHONY: extensions-directory build clean create-dirs test test-basic test-ipynb doc doc-clean doc-html doc-latexpdf doc-singlehtml
+.PHONY: extensions-directory build clean create-dirs test test-basic test-ipynb doc doc-clean doc-html doc-latexpdf doc-singlehtml docker test-docker travis codecov

README.md

@@ -1,6 +1,7 @@
 FIDIMAG
 =======
 
+[![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)
@@ -42,11 +43,12 @@ BibTeX:
 }
 </pre>
 
-# Acknowledgement 
+# Acknowledgements
 
 We acknowledge financial support from
 
 - EPSRC’s Centre for Doctoral Training in Next Generation
-  Computational Modelling, http://ngcm.soton.ac.uk (#EP/L015382/1) and
-  EPSRC’s Doctoral Training Centre in Complex System Simulation
-  ((EP/G03690X/1), http://icss.soton.ac.uk
+  Computational Modelling, (EP/L015382/1)
+  
+- EPSRC’s Doctoral Training Centre in Complex System Simulation
+  (EP/G03690X/1)

doc/core_eqs.rst

@@ -79,7 +79,7 @@ effective field is
 In the continuum limit the exchange energy can be written as
 
 .. math::
-   E_{ex} = \int_{V} A (\nabla \vec{m})^2 dx
+   E_{ex} = \int_{V} A (\nabla \vec{m})^2 \mathrm{d}V
 
 with :math:`V` as the volume of the system and :math:`A` the anisotropy constant
 in :math:`\text{J m}^{-1}`. Correspondingly, the effective
@@ -176,27 +176,34 @@ For bulk materials :math:`\vec{D}_{ij} = D \vec{r}_{ij}` and for interfacial DMI
 In the continuum limit the bulk DMI energy is written as 
 
 .. math::
-   E_{dmi} = \int_\Omega D_a \vec{m} \cdot (\nabla \times \vec{m}) dx
+   E_{\text{DMI}} = \int_V D_a \vec{m} \cdot (\nabla \times \vec{m}) \, \mathrm{d}V
 
-where :math:`D_a = -D/a^2` and the effective field is
+where :math:`V` is the volume of the sample and :math:`D_a = -D/a^2`. The corresponding
+effective field is
 
 .. math::
    \vec{H}=-\frac{2 D_a}{\mu_0 M_s} (\nabla \times \vec{m})
 
 
-
 For the interfacial case, the effective field becomes,
 
 .. math::
-   \vec{H}=\frac{2 D}{M_s a^2} (\vec{e}_x \times \frac{\partial \vec{m}}{\partial y} - \vec{e}_y \times \frac{\partial \vec{m}}{\partial x} )
+   \vec{H}=\frac{2 D}{M_s a^2} (\hat{x} \times \frac{\partial \vec{m}}{\partial y} - \hat{y} \times \frac{\partial \vec{m}}{\partial x} )
 
 Compared with the effective field [PRB 88 184422]
 
 .. math::
-   \vec{H}=\frac{2 D_a}{\mu_0 M_s} ((\nabla \cdot \vec{m}) \vec{e}_z - \nabla m_z)
+   \vec{H}=\frac{2 D_a}{\mu_0 M_s} ((\nabla \cdot \vec{m}) \hat{z} - \nabla m_z)
 
 where :math:`D_a = D/a^2`. Notice that there is no negative sign for the interfacial case.
 
+In the micromagnetic code, it is also implemented the DMI for materials with
+:math:`D_{2d}` symmetry. The energy of this interaction reads
+
+.. math::
+    E_{\text{DMI}} = \int_V D_a \vec{m} \cdot \left( \frac{\partial \vec{m}}{\partial x} \times \hat{x} - \frac{\partial \vec{m}}{\partial y} \times \hat{y} \right) \, \mathrm{d}V
+
+where :math:`D_a` is the DMI constant.
 
 .. Similar to the exchange case, the effective field in the continuum case
 .. can be computed by the same codes with 

docker/travis/Dockerfile

@@ -0,0 +1,43 @@
+FROM ubuntu:16.04
+
+# To build this image `docker build -t fidimag .`
+# Then you can drop into a live bash shell with `docker run -it fidimag`.
+ENTRYPOINT ["/bin/bash"]  
+SHELL ["/bin/bash", "-c"] 
+
+RUN apt-get update -y
+RUN apt-get install -y build-essential cmake cython3 python3-dev python3-pip \
+    python3-psutil python3-pytest python3-pytest-cov \
+    python3-matplotlib python3-numpy python3-scipy \
+    liblapack-dev libopenblas-dev \
+    wget
+# next line for codecov target
+RUN apt-get install -y curl git
+
+# ----------
+# hack to fix sudden breakage in CI
+# (fix from https://github.com/getsentry/sentry/issues/3143)
+# (first occurance of fail at https://travis-ci.org/computationalmodelling/fidimag/builds/319708056?utm_source=github_status&utm_medium=notification)
+# (which is part of this pull request: https://github.com/computationalmodelling/fidimag/pull/106)
+RUN pip3 install --upgrade setuptools==20.4
+# ----------
+
+# ----------
+# hack to fix sudden breakage in CI
+# (fix from https://github.com/getsentry/sentry/issues/3143)
+# (first occurance of fail at https://travis-ci.org/computationalmodelling/fidimag/builds/319708056?utm_source=github_status&utm_medium=notification)
+# (which is part of this pull request: https://github.com/computationalmodelling/fidimag/pull/106)
+RUN pip3 install --upgrade setuptools==20.4
+# ----------
+
+RUN pip3 install ipywidgets nbval pyvtk six
+
+WORKDIR /fidimag
+ADD . /fidimag
+RUN ./bin/install-sundials.sh
+RUN ./bin/install-fftw.sh
+RUN make build
+
+ENV PYTHONPATH=/fidimag \
+    LD_LIBRARY_PATH=/fidimag/local/lib LD_RUN_PATH=/fidimag/local/lib \
+    OMP_NUM_THREADS=1 MPLBACKEND=Agg QT_API=pyqt

examples/mc/skx.py

@@ -5,27 +5,18 @@
 import numpy as np
 from fidimag.atomistic import MonteCarlo
 from fidimag.common import DataReader, CuboidMesh
-
-
-def init_m(pos):
-    x,y,z = pos
-
-    return (0,0,1)
+import fidimag.common.constant as const
 
 def random_m(pos):
     return np.random.random(3) - 0.5
 
-
 def run(mesh):
-    
     mc = MonteCarlo(mesh, name='test1')
     mc.set_m(random_m)
-    mc.set_options(H=[0,0,0.0], J=50.0, D=0.27*50, T=5.0, Kc=50*0.1)
-    mc.run(steps=20000, save_m_steps=None, save_vtk_steps=1000, save_data_steps=10)
+    J = 50*const.k_B
+    mc.set_options(H=[0,0,0.0], J=J, D=0.27*J, T=4.0)
+    mc.run(steps=100000, save_m_steps=None, save_vtk_steps=50000, save_data_steps=50000)
 
 if __name__=='__main__':
-
-    #mesh = CuboidMesh(nx=174,ny=150, nz=1, pbc='2d')
-    mesh = CuboidMesh(nx=100, ny=100, nz=1, periodicity = (True, True, False))
-
-    run(mesh)
+    mesh = CuboidMesh(nx=58, ny=33, nz=1, periodicity = (True, True, False))
+    run(mesh)