diff --git a/.gitignore b/.gitignore
index ce901c07..57e89b0a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,13 +25,7 @@ vtks
# ignore *.so created by cython
-fidimag/extensions/baryakhtar_clib.so
-fidimag/extensions/clib.so
-fidimag/extensions/cvode.so
-fidimag/extensions/dipolar.so
-fidimag/extensions/micro_clib.so
-fidimag/extensions/neb_clib.so
-
+fidimag/extensions/*.so
# ignore output from coverage
htmlcov
@@ -39,3 +33,5 @@ htmlcov
# ignore junit test output
test-reports
+# ignore notebook checkpoint directory
+.ipynb_checkpoints/
diff --git a/install/docker/Dockerfile b/docker/minimal-py2/Dockerfile
similarity index 94%
rename from install/docker/Dockerfile
rename to docker/minimal-py2/Dockerfile
index 4042d8d2..54fe700b 100644
--- a/install/docker/Dockerfile
+++ b/docker/minimal-py2/Dockerfile
@@ -49,6 +49,10 @@ RUN useradd -m -s /bin/bash -G sudo fidimag && \
echo "fidimag ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
RUN chown -R fidimag $FIDIMAG_HOME
+# For bind mounts from host
+RUN mkdir /io
+RUN chown -R fidimag /io
+
USER fidimag
RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
@@ -56,6 +60,5 @@ RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
#COPY WELCOME $FIDIMAG_HOME/WELCOME
-
-WORKDIR $FIDIMAG_HOME
+WORKDIR /io
CMD ["/bin/bash","-i"]
diff --git a/install/docker/Dockerfile.org b/docker/minimal-py2/Dockerfile.org
similarity index 100%
rename from install/docker/Dockerfile.org
rename to docker/minimal-py2/Dockerfile.org
diff --git a/install/docker/Makefile b/docker/minimal-py2/Makefile
similarity index 50%
rename from install/docker/Makefile
rename to docker/minimal-py2/Makefile
index 0751bb27..3a5d4083 100644
--- a/install/docker/Makefile
+++ b/docker/minimal-py2/Makefile
@@ -1,19 +1,16 @@
# to build a new docker image
build:
- time docker build -t fangohr/fidimag:latest .
+ time docker build -t fidimag/minimal-py2:latest .
# to run new image
-run:
- docker run -ti fangohr/fidimag bash
+run: build
+ docker run -v `pwd`:/io -ti fidimag/minimal-py2
# try 'ipython' and then 'import fidimag'
-login:
- docker login
-
# to push the new docker image to dockerhub (need to login first)
-push:
- docker push fangohr/fidimag:latest
+push: build
+ docker push fidimag/minimal-py2:latest
# to fetch image to local machine
pull:
- docker pull fangohr/fidimag:latest
+ docker pull fidimag/minimal-py2:latest
diff --git a/docker/minimal-py2/Readme.md b/docker/minimal-py2/Readme.md
new file mode 100644
index 00000000..a701838c
--- /dev/null
+++ b/docker/minimal-py2/Readme.md
@@ -0,0 +1,31 @@
+# Docker
+
+Run fidimag with Python 2 under Docker.
+
+## Using the docker container
+
+There is a fidimag container available under `fidimag/minimal-py2`.
+
+To use it, you can try this:
+
+1. Install docker
+
+2. Pull the container onto your machine using
+
+ docker pull fidimag/minimal-py2
+
+3. Start the container using
+
+ docker run -ti fidimag/minimal-py2
+
+ This command should show a bash prompt inside the docker container:
+
+
+ bin:docker fangohr$ docker run -v `pwd`:/io -ti fidimag/minimal-py2
+ fidimag@38fdd2a0feb4:/io$
+
+
+## Creating the docker container
+
+The `Makefile` in this directory shows the relevant targets (build, login, push)
+to create a new container and push it to the the cloud.
diff --git a/docker/minimal-py3/Dockerfile b/docker/minimal-py3/Dockerfile
new file mode 100644
index 00000000..037dd152
--- /dev/null
+++ b/docker/minimal-py3/Dockerfile
@@ -0,0 +1,64 @@
+FROM ubuntu:14.04
+
+# packages we need to run fidimag
+RUN apt-get -y update
+RUN apt-get -y install python3-numpy python3-dev python3-scipy
+RUN apt-get -y install python3-pytest ipython3 python3-matplotlib python3-pip
+# standard tools for compilation
+RUN apt-get -y install wget make git
+
+# where to install source
+ENV FIDIMAG_HOME /home/fidimag
+
+RUN mkdir -p $FIDIMAG_HOME
+WORKDIR $FIDIMAG_HOME
+RUN git clone https://github.com/computationalmodelling/fidimag.git
+WORKDIR $FIDIMAG_HOME/fidimag/bin
+
+# install third party libraries from source
+RUN bash install-fftw.sh
+RUN bash install-sundials-2.5.sh
+
+# for pip
+RUN python3 -m pip install --user --upgrade setuptools pip
+# install pyvtk
+RUN python3 -m pip install pyvtk
+# install cython
+RUN python3 -m pip install cython --upgrade
+WORKDIR $FIDIMAG_HOME/fidimag
+
+# compile fidimag
+RUN python3 setup.py build_ext --inplace
+env PYTHONPATH=$FIDIMAG_HOME/fidimag
+env LD_LIBRARY_PATH=$FIDIMAG_HOME/fidimag/local/lib
+WORKDIR $FIDIMAG_HOME/fidimag/tests
+
+# check that tests run okay
+RUN py.test-3 -v
+
+
+# install Jupyter, port exposing doesn't work yet
+#RUN pip install jupyter
+
+# expose jupyter port - not working yet
+#EXPOSE 8888 8888
+
+
+# Set up user so that we do not run as root
+RUN useradd -m -s /bin/bash -G sudo fidimag && \
+ echo "fidimag:docker" | chpasswd && \
+ echo "fidimag ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+RUN chown -R fidimag $FIDIMAG_HOME
+
+# For bind mounts from host
+RUN mkdir /io
+RUN chown -R fidimag /io
+
+USER fidimag
+RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
+
+# Print something nice on entry.
+#COPY WELCOME $FIDIMAG_HOME/WELCOME
+
+WORKDIR /io
+CMD ["/bin/bash","-i"]
diff --git a/docker/minimal-py3/Makefile b/docker/minimal-py3/Makefile
new file mode 100644
index 00000000..659b56a4
--- /dev/null
+++ b/docker/minimal-py3/Makefile
@@ -0,0 +1,16 @@
+# to build a new docker image
+build:
+ time docker build -t fidimag/minimal-py3:latest .
+
+# to run new image
+run: build
+ docker run -v `pwd`:/io -ti fidimag/minimal-py3
+ # try 'ipython3' and then 'import fidimag'
+
+# to push the new docker image to dockerhub (need to login first)
+push: build
+ docker push fidimag/minimal-py3:latest
+
+# to fetch image to local machine
+pull:
+ docker pull fidimag/minimal-py3:latest
diff --git a/docker/minimal-py3/Readme.md b/docker/minimal-py3/Readme.md
new file mode 100644
index 00000000..c83816b7
--- /dev/null
+++ b/docker/minimal-py3/Readme.md
@@ -0,0 +1,31 @@
+# Docker
+
+Run fidimag with Python 3 under Docker.
+
+## Using the docker container
+
+There is a fidimag container available under `fidimag/minimal-py3`.
+
+To use it, you can try this:
+
+1. Install docker
+
+2. Pull the container onto your machine using
+
+ docker pull fidimag/minimal-py3
+
+3. Start the container using
+
+ docker run -ti fidimag/minimal-py3
+
+ This command should show a bash prompt inside the docker container:
+
+
+ bin:docker fangohr$ docker run -v `pwd`:/io -ti fidimag/minimal-py3
+ fidimag@38fdd2a0feb4:/io$
+
+
+## Creating the docker container
+
+The `Makefile` in this directory shows the relevant targets (build, login, push)
+to create a new container and push it to the the cloud.
diff --git a/docker/notebook/Dockerfile b/docker/notebook/Dockerfile
new file mode 100644
index 00000000..91bc2dda
--- /dev/null
+++ b/docker/notebook/Dockerfile
@@ -0,0 +1,37 @@
+FROM jupyter/scipy-notebook
+
+# where to install source
+ENV FIDIMAG_DIR $HOME/work/fidimag
+
+RUN git clone https://github.com/computationalmodelling/fidimag.git
+WORKDIR $FIDIMAG_DIR
+
+# install third party libraries from source
+RUN bash bin/install-fftw.sh
+RUN bash bin/install-sundials-2.5.sh
+
+# install pyvtk
+RUN pip install pyvtk
+# install cython
+RUN pip install cython --upgrade
+
+# compile fidimag
+RUN python3 setup.py build_ext --inplace
+ENV PYTHONPATH=$FIDIMAG_DIR
+ENV LD_LIBRARY_PATH=$FIDIMAG_DIR/local/lib
+WORKDIR $FIDIMAG_DIR/tests
+
+# https://github.com/conda-forge/matplotlib-feedstock/issues/36
+RUN conda install --quiet --yes icu
+
+# check that tests run okay
+RUN conda install --quiet --yes pytest
+RUN py.test -v
+
+# /io will be mounted from the host system
+USER root
+RUN mkdir /io
+RUN chown -R $NB_USER /io
+USER $NB_USER
+
+WORKDIR /io
diff --git a/docker/notebook/Makefile b/docker/notebook/Makefile
new file mode 100644
index 00000000..95caeb39
--- /dev/null
+++ b/docker/notebook/Makefile
@@ -0,0 +1,15 @@
+# to build a new docker image
+build:
+ time docker build -t fidimag/notebook:latest .
+
+# to run new image
+run: build
+ docker run -v `pwd`:/io -d -p 30008:8888 fidimag/notebook
+
+# to push the new docker image to dockerhub (need to login first)
+push: build
+ docker push fidimag/notebook:latest
+
+# to fetch image to local machine
+pull:
+ docker pull fidimag/notebook:latest
diff --git a/docker/notebook/Readme.md b/docker/notebook/Readme.md
new file mode 100644
index 00000000..441338e2
--- /dev/null
+++ b/docker/notebook/Readme.md
@@ -0,0 +1,42 @@
+# Docker
+
+First steps towards running fidimag through Docker.
+
+## Using the docker container
+
+There is a fidimag container available under `fangohr/fidimag`.
+
+To use it, you can try this:
+
+1. Install docker
+
+2. Pull the container onto your machine using
+
+ docker pull fidimag/notebook
+
+3. Start the container using
+
+ docker run -v `pwd`:/io -d -p 30008:8888 fidimag/notebook
+
+ This will start a notebook server. You can see it in your browser at
+http://localhost:30008/ on Linux, or http://192.168.99.100:30008/ on Mac (you may
+need to change this IP address if your docker VM is at a different address).
+
+To run a shell instead of the notebook server, run:
+
+ docker run -v `pwd`:/io -ti fidimag/notebook bash
+
+## Shortcomings
+
+- need to share directory between host and container (MOUNT or VOLUME)
+
+
+## Creating the docker container
+
+The `Makefile` in this directory shows the relevant targets (build, login, push)
+to create a new container and push it to the the cloud.
+
+
+
+
+
diff --git a/fidimag/atomistic/anisotropy.py b/fidimag/atomistic/anisotropy.py
index e67a6cf1..a284f0dc 100644
--- a/fidimag/atomistic/anisotropy.py
+++ b/fidimag/atomistic/anisotropy.py
@@ -44,7 +44,7 @@ class Anisotropy(Energy):
"""
- def __init__(self, Ku, axis=(1, 0, 0), name='anis'):
+ def __init__(self, Ku, axis=(1, 0, 0), name='Anisotropy'):
self.Ku = Ku
self.name = name
self.axis = axis
diff --git a/fidimag/atomistic/demag.py b/fidimag/atomistic/demag.py
index e265e4d3..a08d1293 100644
--- a/fidimag/atomistic/demag.py
+++ b/fidimag/atomistic/demag.py
@@ -33,7 +33,7 @@ class Demag(object):
"""
- def __init__(self, name='demag'):
+ def __init__(self, name='Demag'):
self.name = name
self.jac = True
diff --git a/fidimag/atomistic/demag_full.py b/fidimag/atomistic/demag_full.py
index 6e81f75d..fd6514d8 100644
--- a/fidimag/atomistic/demag_full.py
+++ b/fidimag/atomistic/demag_full.py
@@ -14,7 +14,7 @@ class DemagFull(Energy):
the energy density.
"""
- def __init__(self, name='demag_full'):
+ def __init__(self, name='DemagFull'):
self.name = name
self.jac = True
diff --git a/fidimag/atomistic/demag_hexagonal.py b/fidimag/atomistic/demag_hexagonal.py
index e7a99ddb..b5cda137 100644
--- a/fidimag/atomistic/demag_hexagonal.py
+++ b/fidimag/atomistic/demag_hexagonal.py
@@ -47,7 +47,7 @@ class DemagHexagonal(object):
"""
- def __init__(self, name='demag_hex'):
+ def __init__(self, name='DemagHexagonal'):
self.name = name
self.jac = True
diff --git a/fidimag/atomistic/exchange.py b/fidimag/atomistic/exchange.py
index 82c0831b..8f93ce21 100644
--- a/fidimag/atomistic/exchange.py
+++ b/fidimag/atomistic/exchange.py
@@ -41,7 +41,7 @@ class UniformExchange(Energy):
"""
- def __init__(self, J=0, name='exch'):
+ def __init__(self, J=0, name='UniformExchange'):
self.J = J
self.name = name
@@ -142,7 +142,7 @@ def my_exchange(pos):
"""
- def __init__(self, J_fun, name='exch'):
+ def __init__(self, J_fun, name='Exchange'):
self.J_fun = J_fun
self.name = name
self.jac = False
diff --git a/fidimag/atomistic/lib/llg.c b/fidimag/atomistic/lib/llg.c
index 27b71f3e..bd0cd838 100644
--- a/fidimag/atomistic/lib/llg.c
+++ b/fidimag/atomistic/lib/llg.c
@@ -1,70 +1,167 @@
#include "clib.h"
-void llg_rhs(double *dm_dt, double *m, double *h, double *alpha, int *pins,
- double gamma, int n, int do_precession, double default_c) {
+/* The right hand side of the LLG equation for the CVOde solver. This can be
+ * used both for the micromagnetic and atomistic codes since m or S are unitless
+ * and the prefactors keep the same structure.
+ *
+ * The LLG equation has the structure:
+ * ( * is for dot or scalar product)
+ *
+ * dm -gamma
+ * ---- = -------- ( m X H_eff + a * m X ( m x H_eff ) )
+ * dt 2
+ * ( 1 + a )
+ *
+ * where a is the Gilbert damping constant, gamma is the gyromagnetic
+ * ratio ( gamma = 1.76e11 for a free electron; for the micromagnetic
+ * case, we use gamma_0 = mu_0 * gamma = 2.21e5, for a free electron),
+ * m is the magnetisation vector and H_eff is the effective field.
+ *
+ * In our calculation, we usually compute:
+
+ * m x (m x H_eff) = ( m * H_eff) m - (m * m) H_eff
+
+ * Then, if we define the perpendicular component of the effective
+ * field as:
+
+ * H_perp = H_eff - ( m * H_eff) m
+
+ * we can write
+
+ * dm -gamma
+ * ---- = -------- ( m X H_perp - a * H_perp )
+ * dt 2
+ * ( 1 + a )
+
+ * since m X m = 0 and, theoretically, m * m = 1 (at zero temperature m has
+ * fixed length). However, for the second term to the right hand side,
+ * proportional to a, it is better to keep the m X ( m x H_eff ) term with (m *
+ * m) for stability purposes, thus we use
+ *
+
+ * H_perp = (m * m) H_eff - ( m * H_eff) m
+
+ * for both terms.
+ *
+ * Additionally, to preserve the magnetisation length, we need to correct the
+ * dm / dt term for every time step, adding the following term to the right
+ * hand size expression of the LLG:
+
+ * dm dm 2
+ * ---- ---> ---- + c * ( 1 - m ) m
+ * dt dt
+
+ * with
+ _________
+ * / 2
+ * c = 6 * / ( dm )
+ * / ( ---- )
+ * \/ ( dt )
+
+ * The correction must be introduced since numerically, m can change length
+ * during a step of the integration (which would not occur if the integration
+ * step is infinitely small), deviating from the real answer. If we just
+ * rescaled m, we would have to recompute the effective field (m changes) and
+ * also the solution would present jumps due to the rescaling. With the term
+ * specified above, m stays close to 1, giving a more continuous solution, and
+ * also the term stays as zero if m is exactly 1 (notice that if m increases,
+ * the correction is negative and it decreases m length; similarly if m
+ * decreases). The prefactor c must be specified because the correction term
+ * must be sufficiently strong to affect the solution. Accordingly, we can
+ * think of dm/dt as a kind of velocity that is proportional to the change of
+ * rate of m, hence using its magnitude, the correction is stronger for large
+ * deviations and weak for small deviations. The factor 6 is added ad-hoc,
+* which seems to work well when computing the solutions, but its specification
+* stills requires a more strict proof. It is worth mentioning that the norm of
+* dm/dt changes the time scaling by a factor proportional to 1/t, therefore in
+* the future we could try to estimate its
+ * influence with more mathematical/numerical rigour and analyse an optimal
+ * value for the prefactor (6).
+ */
+
+void llg_rhs(double * dm_dt, double * m, double * h, double * alpha, int * pins,
+ double gamma, int n, int do_precession, double default_c) {
- int i, j, k;
+ int i, j, k;
double coeff, mm, mh, c;
- double hpi,hpj,hpk;
-
- #pragma omp parallel for private(i,j,k,coeff,mm, mh, c, hpi,hpj,hpk)
- for (int id = 0; id < n; id++) {
- i = 3*id;
- j = i+1;
- k = i+2;
-
- if (pins[id]>0){
- dm_dt[i] = 0;
- dm_dt[j] = 0;
- dm_dt[k] = 0;
- continue;
- }
-
- coeff = -gamma/(1.0+alpha[id]*alpha[id]);
-
- mm = m[i]*m[i] + m[j]*m[j] + m[k]*m[k];
- mh = m[i]*h[i] + m[j]*h[j] + m[k]*h[k];
-
- //suppose m is normalised, i.e., mm=1; hp=mm.h-mh.m=-mx(mxh)
- hpi = mm*h[i] - mh*m[i];
- hpj = mm*h[j] - mh*m[j];
- hpk = mm*h[k] - mh*m[k];
- //IMPORTANT: never ignore mm!!!
- //what we found is that if we igonre mm, i.e. using
- // hpi = h[i] - mh*m[i]
- // hpj = h[j] - mh*m[j];
- // hpk = h[k] - mh*m[k];
- //then the standard problem 4 failed to converge ?!!
- double mth0=0, mth1=0, mth2=0;
+ double hpi, hpj, hpk;
+
+ #pragma omp parallel for private(i,j,k,coeff,mm, mh, c, hpi,hpj,hpk)
+ for (int id = 0; id < n; id++) {
+ // Indexes for the 3 components of the spin (magnetic moment)
+ // at the i-th lattice (mesh) site --> x, y, z
+ i = 3 * id;
+ j = i + 1;
+ k = i + 2;
+
+ // Pinned spins do not follow the dynamical equation
+ if (pins[id] > 0) {
+ dm_dt[i] = 0;
+ dm_dt[j] = 0;
+ dm_dt[k] = 0;
+ continue;
+ }
+ coeff = -gamma / (1.0 + alpha[id] * alpha[id]);
+
+ // Dot products
+ mm = m[i] * m[i] + m[j] * m[j] + m[k] * m[k];
+ mh = m[i] * h[i] + m[j] * h[j] + m[k] * h[k];
+
+ // Usually, m is normalised, i.e., mm=1;
+ // so hp = mm.h - mh.m = -m x (m x h)
+ // We set here the perpendicular componenet of the field
+ // but using the (m * m) product
+ hpi = mm * h[i] - mh * m[i];
+ hpj = mm * h[j] - mh * m[j];
+ hpk = mm * h[k] - mh * m[k];
+
+ // IMPORTANT: do not ignore mm !!
+ // What we've found is that if we igonre mm, i.e. using
+ // hpi = h[i] - mh * m[i];
+ // hpj = h[j] - mh * m[j];
+ // hpk = h[k] - mh * m[k];
+ // the micromagnetic standard problem 4 failed to converge (?)
+ //
+ // NOTE (Fri 08 Jul 2016 13:58): In fact, the problem converges but with 2 less
+ // decimals of accuracy, compared with the OOMMF calculation
+ double mth0 = 0, mth1 = 0, mth2 = 0;
+
+ // The first term: m x H_eff = m x H_perp
if (do_precession){
- mth0 = cross_x(m[i],m[j],m[k],hpi,hpj,hpk);
- mth1 = cross_y(m[i],m[j],m[k],hpi,hpj,hpk);
- mth2 = cross_z(m[i],m[j],m[k],hpi,hpj,hpk);
+ mth0 = cross_x(m[i], m[j], m[k], hpi, hpj, hpk);
+ mth1 = cross_y(m[i], m[j], m[k], hpi, hpj, hpk);
+ mth2 = cross_z(m[i], m[j], m[k], hpi, hpj, hpk);
}
- dm_dt[i] = coeff*(mth0 - hpi * alpha[id]);
- dm_dt[j] = coeff*(mth1 - hpj * alpha[id]);
- dm_dt[k] = coeff*(mth2 - hpk * alpha[id]);
-
- // in future, we will try the new method to integrate the LLG equation,
- // A mixed mid-point Runge-Kutta like scheme for the integration of Landau-Lifshitz equation
- // Journal of Applied Physics 115, 17D101 (2014)
- // if possible, we can combine it with adaptive step size, don't know how to do but it's worth a try.
-
- if (default_c<0){
- c = 6*sqrt(dm_dt[i]*dm_dt[i]+dm_dt[j]*dm_dt[j]+dm_dt[k]*dm_dt[k]);
- }else{
- c = default_c;
+ // The RHS term of the LLG equation
+ dm_dt[i] = coeff * (mth0 - hpi * alpha[id]);
+ dm_dt[j] = coeff * (mth1 - hpj * alpha[id]);
+ dm_dt[k] = coeff * (mth2 - hpk * alpha[id]);
+
+ // In future, we will try the new method to integrate the LLG equation,
+ // A mixed mid-point Runge-Kutta like scheme for the integration of
+ // Landau-Lifshitz equation Journal of Applied Physics 115, 17D101
+ // (2014) if possible, we can combine it with adaptive step size, don't
+ // know how to do but it's worth a try.
+
+ if (default_c < 0){
+ c = 6 * sqrt(dm_dt[i] * dm_dt[i] +
+ dm_dt[j] * dm_dt[j] +
+ dm_dt[k] * dm_dt[k]
+ );
+ } else {
+ c = default_c;
}
//printf("%0.15g %0.15g\n", c, default_c);
- dm_dt[i] += c*(1-mm)*m[i];
- dm_dt[j] += c*(1-mm)*m[j];
- dm_dt[k] += c*(1-mm)*m[k];
+ // Correct the RHS term to keep m normalised
+ dm_dt[i] += c * (1 - mm) * m[i];
+ dm_dt[j] += c * (1 - mm) * m[j];
+ dm_dt[k] += c * (1 - mm) * m[k];
- }
+ }
}
@@ -106,9 +203,9 @@ void llg_rhs_jtimes(double *jtn, double *m, double *h, double *mp, double *hp, d
/*
if (default_c>0){
- jtn[i] += default_c *((1-mm)*mp[i]-2*mmp*m[i]);
- jtn[j] += default_c *((1-mm)*mp[j]-2*mmp*m[j]);
- jtn[k] += default_c *((1-mm)*mp[k]-2*mmp*m[k]);
+ jtn[i] += default_c *((1-mm)*mp[i]-2*mmp*m[i]);
+ jtn[j] += default_c *((1-mm)*mp[j]-2*mmp*m[j]);
+ jtn[k] += default_c *((1-mm)*mp[k]-2*mmp*m[k]);
}*/
}
@@ -118,16 +215,16 @@ void llg_rhs_jtimes(double *jtn, double *m, double *h, double *mp, double *hp, d
void llg_s_rhs(double *dm_dt, double *m, double *h, double *alpha, double *chi, double gamma, int n) {
- int i, j, k;
+ int i, j, k;
- double mth0, mth1, mth2;
- double coeff = - gamma;
+ double mth0, mth1, mth2;
+ double coeff = - gamma;
double mm, c;
double hpi,hpj,hpk,mh;
- for (i = 0; i < n; i++) {
- j = i + n;
- k = j + n;
+ for (i = 0; i < n; i++) {
+ j = i + n;
+ k = j + n;
if (chi[i] > 0.0){
mth0 = coeff * (m[j] * h[k] - m[k] * h[j]);
@@ -147,7 +244,7 @@ void llg_s_rhs(double *dm_dt, double *m, double *h, double *alpha, double *chi,
}else{ //do LL equation, similiar to the function of llg_rhs
- mm = m[i] * m[i] + m[j] * m[j] + m[k] * m[k];
+ mm = m[i] * m[i] + m[j] * m[j] + m[k] * m[k];
mh = m[i]*h[i] + m[j]*h[j] + m[k]*h[k];
hpi = mm*h[i] - mh*m[i];
@@ -163,6 +260,6 @@ void llg_s_rhs(double *dm_dt, double *m, double *h, double *alpha, double *chi,
dm_dt[k] = coeff*(mth2 - hpk * alpha[i]);
}
- }
+ }
}
diff --git a/fidimag/common/cuboid_mesh.py b/fidimag/common/cuboid_mesh.py
index cf69bb20..9ea0eeed 100644
--- a/fidimag/common/cuboid_mesh.py
+++ b/fidimag/common/cuboid_mesh.py
@@ -137,36 +137,44 @@ def init_neighbours(self):
for i in range(self.nz):
for j in range(self.ny):
for k in range(self.nx):
+ # Unique index for the current lattice site
cell = self._index(k, j, i)
- ngbs = [other for other in [
+ neighbours = [
self.index(k - 1, j, i), # left
self.index(k + 1, j, i), # right
self.index(k, j - 1, i), # behind
self.index(k, j + 1, i), # in front
self.index(k, j, i - 1), # under
self.index(k, j, i + 1), # over
- ]]
+ ]
- nngbs = [other for other in [
+ # If one of the neighbours is the cell itself, we
+ # set its index to -1
+ # neighbours = [other if other != cell
+ # else -1 for other in neighbours]
+
+ next_neighbours = [
self.index(k - 2, j, i), # left
self.index(k + 2, j, i), # right
self.index(k, j - 2, i), # behind
self.index(k, j + 2, i), # in front
self.index(k, j, i - 2), # under
self.index(k, j, i + 2), # over
- ]]
-
- # July 1st, 2016 Weiwei: I think it's okay for a cell with its neighbour is itself
- # if periodic boundary conditions are used. For example, if we only have cell and enable
- # periodic boundary condition in x-direction, then we got a rod.
- # therefore, I commented two lines below.
+ ]
+
+ # July 1st, 2016 Weiwei: I think it's okay for a cell with
+ # its neighbour is itself if periodic boundary conditions
+ # are used. For example, if we only have one cell and
+ # enable periodic boundary condition in x-direction, then
+ # we got a rod. therefore, I commented two lines below.
# no cell should be its own neighbour
- # neighbours = [other if other != cell
- # else -1 for other in ngbs]
- connectivity.append(ngbs)
- connectivity_next.append(nngbs)
-
- return np.array(connectivity, dtype=np.int32), np.array(connectivity_next, dtype=np.int32)
+
+ connectivity.append(neighbours)
+ connectivity_next.append(next_neighbours)
+
+ return (np.array(connectivity, dtype=np.int32),
+ np.array(connectivity_next, dtype=np.int32)
+ )
def index(self, i, j, k):
"""
@@ -176,22 +184,22 @@ def index(self, i, j, k):
i, j, k are the positions in the x, y and z directions, respectively
"""
- if self.periodicity[0]: # if mesh is periodic in x-direction
- if i < 0: # then wrap the left side
- i += self.nx # to the right
- elif i >= self.nx: # and wrap the right side
- i -= self.nx # to the left
-
- if self.periodicity[1]:
- if j < 0:
- j += self.ny
- elif j >= self.ny:
- j -= self.ny
-
- if self.periodicity[2]:
- if k < 0:
- k += self.nz
- elif k >= self.nz:
+ if self.periodicity[0]: # if mesh is periodic in x-direction
+ if i < 0: # then wrap the left side
+ i += self.nx # to the right
+ elif i >= self.nx: # and wrap the right side
+ i -= self.nx # to the left
+
+ if self.periodicity[1]:
+ if j < 0:
+ j += self.ny
+ elif j >= self.ny:
+ j -= self.ny
+
+ if self.periodicity[2]:
+ if k < 0:
+ k += self.nz
+ elif k >= self.nz:
k -= self.nz
return self._index(i, j, k)
@@ -199,7 +207,7 @@ def index(self, i, j, k):
def _index(self, i, j, k):
"""
Returns the index for the cell with ordinals i, j, k
- or False if that cell would be out of bounds.
+ or -1 if that cell would be out of bounds.
"""
if i < 0 or j < 0 or k < 0 or k >= self.nz or j >= self.ny or i >= self.nx:
diff --git a/fidimag/micro/anisotropy.py b/fidimag/micro/anisotropy.py
index c44a500b..eea40056 100644
--- a/fidimag/micro/anisotropy.py
+++ b/fidimag/micro/anisotropy.py
@@ -11,7 +11,7 @@ class UniaxialAnisotropy(Energy):
compute the anisotropy field with the energy density E = K[1- (m.u)^2]
"""
- def __init__(self, Ku, axis=(1, 0, 0), name='anis'):
+ def __init__(self, Ku, axis=(1, 0, 0), name='Anisotropy'):
self.Ku = Ku
self.name = name
self.jac = True
diff --git a/fidimag/micro/demag.py b/fidimag/micro/demag.py
index ee2a0e37..8ced3f44 100644
--- a/fidimag/micro/demag.py
+++ b/fidimag/micro/demag.py
@@ -6,15 +6,17 @@
default_options={
- 'pbc_2d_error':1e-10,
- 'sample_repeat_nx':-1,
- 'sample_repeat_ny':-1,
- 'tensor_file_name':'2dpbc_tensors',
+ 'pbc_2d_error': 1e-10,
+ 'sample_repeat_nx': -1,
+ 'sample_repeat_ny': -1,
+ 'tensor_file_name': '2dpbc_tensors',
}
+
class Demag(object):
- def __init__(self, name='demag', pbc_2d=False, pbc_options=default_options):
+ def __init__(self, name='Demag', pbc_2d=False,
+ pbc_options=default_options):
self.name = name
self.oommf = True
self.pbc_2d = pbc_2d
@@ -36,7 +38,7 @@ def setup(self, mesh, spin, Ms):
if self.pbc_2d is True:
- self.demag = clib.FFTDemag(self.dx, self.dy, self.dz,
+ self.demag = clib.FFTDemag(self.dx, self.dy, self.dz,
self.nx, self.ny, self.nz, tensor_type='2d_pbc')
nxyz = self.nx*self.ny*self.nz
@@ -65,7 +67,7 @@ def setup(self, mesh, spin, Ms):
if len(tensor_file_name) > 0 :
if not (os.path.exists(tensor_file_name+'.npz')):
-
+
self.demag.compute_tensors_2dpbc(tensors, pbc_2d_error, sample_repeat_nx, sample_repeat_ny, dipolar_radius)
else:
npzfile = np.load(tensor_file_name+'.npz')
@@ -82,14 +84,15 @@ def setup(self, mesh, spin, Ms):
else:
self.demag.compute_tensors_2dpbc(tensors, pbc_2d_error, sample_repeat_nx, sample_repeat_ny, dipolar_radius)
-
+
#print tensors
self.demag.fill_demag_tensors(tensors)
-
+
else:
self.demag = clib.FFTDemag(self.dx, self.dy, self.dz,
- self.nx, self.ny, self.nz, tensor_type='demag')
+ self.nx, self.ny, self.nz,
+ tensor_type='demag')
diff --git a/fidimag/micro/dmi.py b/fidimag/micro/dmi.py
index d5b1bf2e..d282fc0d 100644
--- a/fidimag/micro/dmi.py
+++ b/fidimag/micro/dmi.py
@@ -12,7 +12,7 @@ class DMI(Energy):
compute the DMI field in micromagnetics
"""
- def __init__(self, D, name='dmi', dmi_type='bulk'):
+ def __init__(self, D, name='DMI', dmi_type='bulk'):
"""
type could be 'interfacial' or 'bulk'
"""
diff --git a/fidimag/micro/exchange.py b/fidimag/micro/exchange.py
index bcb958a2..3f187f89 100644
--- a/fidimag/micro/exchange.py
+++ b/fidimag/micro/exchange.py
@@ -9,7 +9,7 @@ class UniformExchange(Energy):
Compute the exchange field in micromagnetics.
"""
- def __init__(self, A, name='exch'):
+ def __init__(self, A, name='UniformExchange'):
self.A = A
self.name = name
self.jac = True
diff --git a/install/docker/Readme.md b/install/docker/Readme.md
deleted file mode 100644
index ca7662e8..00000000
--- a/install/docker/Readme.md
+++ /dev/null
@@ -1,61 +0,0 @@
-# Docker
-
-First steps towards running fidimag through Docker.
-
-## Using the docker container
-
-There is a fidimag container available under `fangohr/fidimag`.
-
-To use it, you can try this:
-
-1. Install docker
-
-2. Pull the container onto your machine using
-
-`docker pull fangohr/fidimag`
-
-3. Start the container using
-
-`docker run -ti fangohr/fidimag`
-
-This command should show a bash prompt inside the docker container:
-
-
-bin:docker fangohr$ docker run -ti fangohr/fidimag
-fidimag@38fdd2a0feb4:~$
-
-
-One way to test the installation is to run the unit tests:
-
-
-fidimag@38fdd2a0feb4:~$ cd fidimag/tests/
-fidimag@38fdd2a0feb4:~/fidimag/tests$ py.test -v
-========== test session starts =======================
-platform linux2 -- Python 2.7.6 -- pytest-2.5.1 -- /usr/bin/python
-collected 63 items
-
-field_test.py:7: test_initialise_scalar PASSED
-field_test.py:13: test_initialise_vector PASSED
-test_2dpbc_cube.py:10: test_compute_field PASSED
-test_anis.py:7: test_anis PASSED
-.
-.
-.
-
-
-## Shortcomings
-
-- need to share directory between host and container (MOUNT or VOLUME)
-
-- make use of jupyter notebook work (as we have seen in FEniCS course): connect port in container to port on host machine (EXPOSE)
-
-
-
-## Creating the docker container
-
-The `Makefile` in this directory shows the relevant targets (build, login, push) to create a new container and push it to the the cloud.
-
-
-
-
-
diff --git a/tests/test_demag_libraries.py b/tests/test_demag_libraries.py
index 99e34ece..37cbc2d1 100644
--- a/tests/test_demag_libraries.py
+++ b/tests/test_demag_libraries.py
@@ -67,9 +67,9 @@ def test_hexagonal_demags_1Dchain():
# Brute force demag calculation
sim.add(DemagFull())
- sim.get_interaction('demag_full').compute_field()
- sim.get_interaction('demag_full').field
- demag_full_energy = sim.compute_energy() / const.meV
+ sim.get_interaction('DemagFull').compute_field()
+ sim.get_interaction('DemagFull').field
+ DemagFull_energy = sim.compute_energy() / const.meV
# Demag using the FFT approach and a larger mesh
sim2 = Sim(mesh)
@@ -78,13 +78,13 @@ def test_hexagonal_demags_1Dchain():
sim2.set_m(lambda pos: m_init_dw(pos, N, a))
sim2.add(DemagHexagonal())
- sim2.get_interaction('demag_hex').compute_field()
+ sim2.get_interaction('DemagHexagonal').compute_field()
sim2.compute_energy()
demag_2fft_energy = sim2.compute_energy() / const.meV
# We compare both energies scaled in meV
- assert (demag_full_energy - demag_2fft_energy) < 1e-10
+ assert (DemagFull_energy - demag_2fft_energy) < 1e-10
def test_cuboid_demags_1Dchain():
@@ -108,9 +108,9 @@ def test_cuboid_demags_1Dchain():
# Brute force demag calculation
sim.add(DemagFull())
- sim.get_interaction('demag_full').compute_field()
- # print sim.get_interaction('demag_full').field
- demag_full_energy = sim.compute_energy() / const.meV
+ sim.get_interaction('DemagFull').compute_field()
+ # print sim.get_interaction('DemagFull').field
+ DemagFull_energy = sim.compute_energy() / const.meV
# Demag using the FFT approach
sim2 = Sim(mesh)
@@ -119,13 +119,13 @@ def test_cuboid_demags_1Dchain():
sim2.set_m(lambda pos: m_init_dw(pos, N, a))
sim2.add(Demag())
- sim2.get_interaction('demag').compute_field()
+ sim2.get_interaction('Demag').compute_field()
sim2.compute_energy()
demag_fft_energy = sim2.compute_energy() / const.meV
# We compare both energies scaled in meV
- assert (demag_full_energy - demag_fft_energy) < 1e-10
+ assert (DemagFull_energy - demag_fft_energy) < 1e-10
def test_cuboid_demags_2D():
@@ -154,9 +154,9 @@ def test_cuboid_demags_2D():
# Brute force demag calculation
sim.add(DemagFull())
- sim.get_interaction('demag_full').compute_field()
- # print sim.get_interaction('demag_full').field
- demag_full_energy = sim.compute_energy() / const.meV
+ sim.get_interaction('DemagFull').compute_field()
+ # print sim.get_interaction('DemagFull').field
+ DemagFull_energy = sim.compute_energy() / const.meV
# Demag using the FFT approach
sim2 = Sim(mesh)
@@ -165,13 +165,13 @@ def test_cuboid_demags_2D():
sim2.set_m(lambda pos: m_init_2Dvortex(pos, (xc, yc)))
sim2.add(Demag())
- sim2.get_interaction('demag').compute_field()
+ sim2.get_interaction('Demag').compute_field()
sim2.compute_energy()
demag_fft_energy = sim2.compute_energy() / const.meV
# We compare both energies scaled in meV
- assert (demag_full_energy - demag_fft_energy) < 1e-10
+ assert (DemagFull_energy - demag_fft_energy) < 1e-10
def test_hexagonal_demags_2D():
@@ -202,9 +202,9 @@ def test_hexagonal_demags_2D():
# Brute force demag calculation
sim.add(DemagFull())
- sim.get_interaction('demag_full').compute_field()
- sim.get_interaction('demag_full').field
- demag_full_energy = sim.compute_energy() / const.meV
+ sim.get_interaction('DemagFull').compute_field()
+ sim.get_interaction('DemagFull').field
+ DemagFull_energy = sim.compute_energy() / const.meV
# Demag using the FFT approach and a larger mesh
sim2 = Sim(mesh)
@@ -213,13 +213,13 @@ def test_hexagonal_demags_2D():
sim2.set_m(lambda pos: m_init_2Dvortex(pos, (xc, yc)))
sim2.add(DemagHexagonal())
- sim2.get_interaction('demag_hex').compute_field()
+ sim2.get_interaction('DemagHexagonal').compute_field()
sim2.compute_energy()
demag_2fft_energy = sim2.compute_energy() / const.meV
# We compare both energies scaled in meV
- assert (demag_full_energy - demag_2fft_energy) < 1e-10
+ assert (DemagFull_energy - demag_2fft_energy) < 1e-10
if __name__ == '__main__':