From d2de40bb1f0f79e250cec3ec352ae363316826a5 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 11:48:04 +0100
Subject: [PATCH 01/12] Add docker file using Python 3

---
 install/docker-py3/Dockerfile | 62 +++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 install/docker-py3/Dockerfile

diff --git a/install/docker-py3/Dockerfile b/install/docker-py3/Dockerfile
new file mode 100644
index 00000000..17a7ec0f
--- /dev/null
+++ b/install/docker-py3/Dockerfile
@@ -0,0 +1,62 @@
+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
+
+USER fidimag
+RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
+
+# Print something nice on entry.
+#COPY WELCOME $FIDIMAG_HOME/WELCOME
+
+
+
+WORKDIR $FIDIMAG_HOME
+CMD ["/bin/bash","-i"]

From 00887c9ae9f8134cd527367caf8bb9de682dfac5 Mon Sep 17 00:00:00 2001
From: davidcortesortuno <david.cortes.o@gmail.com>
Date: Fri, 8 Jul 2016 14:50:53 +0100
Subject: [PATCH 02/12] Documented C code for the calculation of the right hand
 side of the LLG equation. Since this code is both used by atomistic and
 micromagnetic evolvers, we should move it to the common folder in the future

---
 fidimag/atomistic/lib/llg.c | 227 +++++++++++++++++++++++++-----------
 1 file changed, 162 insertions(+), 65 deletions(-)

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]);
         }
 
-	}
+    }
 
 }

From 8b9c50ab316686750d9396a3546314fed1c2878e Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 14:51:57 +0100
Subject: [PATCH 03/12] Dockerfile based on jupyter/scipy-notebook

---
 install/docker-nb/Dockerfile | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 install/docker-nb/Dockerfile

diff --git a/install/docker-nb/Dockerfile b/install/docker-nb/Dockerfile
new file mode 100644
index 00000000..a4e6db37
--- /dev/null
+++ b/install/docker-nb/Dockerfile
@@ -0,0 +1,32 @@
+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
+
+
+WORKDIR $HOME/work

From a8f8c47ad972551a4b4dc62bedff8636061a8df5 Mon Sep 17 00:00:00 2001
From: davidcortesortuno <david.cortes.o@gmail.com>
Date: Fri, 8 Jul 2016 15:52:56 +0100
Subject: [PATCH 04/12] Commented and improved some variable names in Cuboid
 mesh

---
 fidimag/common/cuboid_mesh.py | 72 +++++++++++++++++++----------------
 1 file changed, 40 insertions(+), 32 deletions(-)

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:

From ff5a93441138c87e531936ccf67b97eb1fb169fe Mon Sep 17 00:00:00 2001
From: davidcortesortuno <david.cortes.o@gmail.com>
Date: Fri, 8 Jul 2016 16:21:04 +0100
Subject: [PATCH 05/12] Updated interactions/fields names

---
 fidimag/atomistic/anisotropy.py      |  2 +-
 fidimag/atomistic/demag.py           |  2 +-
 fidimag/atomistic/demag_full.py      |  2 +-
 fidimag/atomistic/demag_hexagonal.py |  2 +-
 fidimag/atomistic/exchange.py        |  4 +--
 fidimag/micro/anisotropy.py          |  2 +-
 fidimag/micro/demag.py               | 23 +++++++++-------
 fidimag/micro/dmi.py                 |  2 +-
 fidimag/micro/exchange.py            |  2 +-
 tests/test_demag_libraries.py        | 40 ++++++++++++++--------------
 10 files changed, 42 insertions(+), 39 deletions(-)

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/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/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__':

From 17ae8ba49f8d4707ccbc9561488be66e4123d92e Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 16:22:07 +0100
Subject: [PATCH 06/12] Rearrange docker files

---
 {install/docker => docker/minimal}/Dockerfile |  0
 .../docker => docker/minimal}/Dockerfile.org  |  0
 {install/docker => docker/minimal}/Makefile   |  0
 {install/docker => docker/minimal}/Readme.md  |  0
 .../docker-nb => docker/notebook}/Dockerfile  |  0
 docker/notebook/Makefile                      | 18 ++++++++
 docker/notebook/Readme.md                     | 42 +++++++++++++++++++
 7 files changed, 60 insertions(+)
 rename {install/docker => docker/minimal}/Dockerfile (100%)
 rename {install/docker => docker/minimal}/Dockerfile.org (100%)
 rename {install/docker => docker/minimal}/Makefile (100%)
 rename {install/docker => docker/minimal}/Readme.md (100%)
 rename {install/docker-nb => docker/notebook}/Dockerfile (100%)
 create mode 100644 docker/notebook/Makefile
 create mode 100644 docker/notebook/Readme.md

diff --git a/install/docker/Dockerfile b/docker/minimal/Dockerfile
similarity index 100%
rename from install/docker/Dockerfile
rename to docker/minimal/Dockerfile
diff --git a/install/docker/Dockerfile.org b/docker/minimal/Dockerfile.org
similarity index 100%
rename from install/docker/Dockerfile.org
rename to docker/minimal/Dockerfile.org
diff --git a/install/docker/Makefile b/docker/minimal/Makefile
similarity index 100%
rename from install/docker/Makefile
rename to docker/minimal/Makefile
diff --git a/install/docker/Readme.md b/docker/minimal/Readme.md
similarity index 100%
rename from install/docker/Readme.md
rename to docker/minimal/Readme.md
diff --git a/install/docker-nb/Dockerfile b/docker/notebook/Dockerfile
similarity index 100%
rename from install/docker-nb/Dockerfile
rename to docker/notebook/Dockerfile
diff --git a/docker/notebook/Makefile b/docker/notebook/Makefile
new file mode 100644
index 00000000..65a7f0d4
--- /dev/null
+++ b/docker/notebook/Makefile
@@ -0,0 +1,18 @@
+# to build a new docker image
+build:
+	time docker build -t fidimag/notebook:latest .
+
+# to run new image
+run:
+	docker run -ti fidimag/notebook bash
+
+login:
+    docker login
+
+# to push the new docker image to dockerhub (need to login first)
+push: build login
+	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..acd85844
--- /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 -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 -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.
+
+
+
+
+

From de544d3481ce13f0b059bef6260eacc55dbbde6e Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 16:24:03 +0100
Subject: [PATCH 07/12] Remove login from Makefile

---
 docker/notebook/Makefile | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/docker/notebook/Makefile b/docker/notebook/Makefile
index 65a7f0d4..ab05f33f 100644
--- a/docker/notebook/Makefile
+++ b/docker/notebook/Makefile
@@ -6,11 +6,8 @@ build:
 run:
 	docker run -ti fidimag/notebook bash
 
-login:
-    docker login
-
 # to push the new docker image to dockerhub (need to login first)
-push: build login
+push: build
 	docker push fidimag/notebook:latest
 
 # to fetch image to local machine

From 3bbd6f7149553d5a7cb45fd947c1ce9dc6c4cdd6 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 16:26:21 +0100
Subject: [PATCH 08/12] Rename minimal -> minimal-py2

---
 docker/{minimal => minimal-py2}/Dockerfile     | 0
 docker/{minimal => minimal-py2}/Dockerfile.org | 0
 docker/{minimal => minimal-py2}/Makefile       | 0
 docker/{minimal => minimal-py2}/Readme.md      | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename docker/{minimal => minimal-py2}/Dockerfile (100%)
 rename docker/{minimal => minimal-py2}/Dockerfile.org (100%)
 rename docker/{minimal => minimal-py2}/Makefile (100%)
 rename docker/{minimal => minimal-py2}/Readme.md (100%)

diff --git a/docker/minimal/Dockerfile b/docker/minimal-py2/Dockerfile
similarity index 100%
rename from docker/minimal/Dockerfile
rename to docker/minimal-py2/Dockerfile
diff --git a/docker/minimal/Dockerfile.org b/docker/minimal-py2/Dockerfile.org
similarity index 100%
rename from docker/minimal/Dockerfile.org
rename to docker/minimal-py2/Dockerfile.org
diff --git a/docker/minimal/Makefile b/docker/minimal-py2/Makefile
similarity index 100%
rename from docker/minimal/Makefile
rename to docker/minimal-py2/Makefile
diff --git a/docker/minimal/Readme.md b/docker/minimal-py2/Readme.md
similarity index 100%
rename from docker/minimal/Readme.md
rename to docker/minimal-py2/Readme.md

From 2791d93fdd77777713ec121c1be8709c8a1fdc7b Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 16:39:36 +0100
Subject: [PATCH 09/12] Update Makefiles and READMEs

---
 docker/minimal-py2/Makefile                   | 15 +++---
 docker/minimal-py2/Readme.md                  | 30 ++++-------
 .../minimal-py3}/Dockerfile                   |  0
 docker/minimal-py3/Makefile                   | 16 ++++++
 docker/minimal-py3/Readme.md                  | 53 +++++++++++++++++++
 5 files changed, 86 insertions(+), 28 deletions(-)
 rename {install/docker-py3 => docker/minimal-py3}/Dockerfile (100%)
 create mode 100644 docker/minimal-py3/Makefile
 create mode 100644 docker/minimal-py3/Readme.md

diff --git a/docker/minimal-py2/Makefile b/docker/minimal-py2/Makefile
index 0751bb27..a8ed6cb5 100644
--- a/docker/minimal-py2/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 -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
index ca7662e8..38598bb4 100644
--- a/docker/minimal-py2/Readme.md
+++ b/docker/minimal-py2/Readme.md
@@ -1,10 +1,10 @@
 # Docker
 
-First steps towards running fidimag through Docker.
+Run fidimag with Python 2 under Docker.
 
 ## Using the docker container
 
-There is a fidimag container available under `fangohr/fidimag`.
+There is a fidimag container available under `fidimag/minimal-py2`.
 
 To use it, you can try this:
 
@@ -12,18 +12,18 @@ To use it, you can try this:
 
 2. Pull the container onto your machine using
 
-`docker pull fangohr/fidimag`
+       docker pull fidimag/minimal-py2
 
 3. Start the container using
 
-`docker run -ti fangohr/fidimag`
+       docker run -ti fidimag/minimal-py2
 
-This command should show a bash prompt inside the docker container:
+   This command should show a bash prompt inside the docker container:
 
-<pre>
-bin:docker fangohr$ docker run -ti fangohr/fidimag
-fidimag@38fdd2a0feb4:~$
-</pre>
+    <pre>
+    bin:docker fangohr$ docker run -ti fidimag/minimal-py2
+    fidimag@38fdd2a0feb4:~$
+    </pre>
 
 One way to test the installation is to run the unit tests:
 
@@ -47,15 +47,7 @@ test_anis.py:7: test_anis PASSED
 
 - 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.
-
-
-
-
-
+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/install/docker-py3/Dockerfile b/docker/minimal-py3/Dockerfile
similarity index 100%
rename from install/docker-py3/Dockerfile
rename to docker/minimal-py3/Dockerfile
diff --git a/docker/minimal-py3/Makefile b/docker/minimal-py3/Makefile
new file mode 100644
index 00000000..27d4e4cc
--- /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 -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..ad4f72c7
--- /dev/null
+++ b/docker/minimal-py3/Readme.md
@@ -0,0 +1,53 @@
+# 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:
+
+    <pre>
+    bin:docker fangohr$ docker run -ti fidimag/minimal-py3
+    fidimag@38fdd2a0feb4:~$
+    </pre>
+
+One way to test the installation is to run the unit tests:
+
+<pre>
+fidimag@38fdd2a0feb4:~$ cd fidimag/tests/
+fidimag@38fdd2a0feb4:~/fidimag/tests$ py.test-3 -v
+========== test session starts =======================
+platform linux2 -- Python 3.4.3 -- pytest-2.5.1 -- /usr/bin/python3
+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
+.
+.
+.
+</pre>
+
+## 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.

From 87af3df871f143b07d973e8c3050ae0ca7d87aaf Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 16:39:51 +0100
Subject: [PATCH 10/12] Add some things to .gitignore

---
 .gitignore | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

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/

From 43256c1839028cc046c14c4b2d264c503a0cfe67 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 17:09:41 +0100
Subject: [PATCH 11/12] Bind mount working directory into docker containers

---
 docker/minimal-py2/Dockerfile |  7 +++++--
 docker/minimal-py2/Makefile   |  2 +-
 docker/minimal-py2/Readme.md  | 26 ++------------------------
 docker/minimal-py3/Dockerfile |  4 ++++
 docker/minimal-py3/Makefile   |  2 +-
 docker/minimal-py3/Readme.md  | 26 ++------------------------
 docker/notebook/Dockerfile    |  7 ++++++-
 docker/notebook/Makefile      |  4 ++--
 docker/notebook/Readme.md     |  4 ++--
 9 files changed, 25 insertions(+), 57 deletions(-)

diff --git a/docker/minimal-py2/Dockerfile b/docker/minimal-py2/Dockerfile
index 4042d8d2..54fe700b 100644
--- a/docker/minimal-py2/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/docker/minimal-py2/Makefile b/docker/minimal-py2/Makefile
index a8ed6cb5..3a5d4083 100644
--- a/docker/minimal-py2/Makefile
+++ b/docker/minimal-py2/Makefile
@@ -4,7 +4,7 @@ build:
 
 # to run new image
 run: build
-	docker run -ti fidimag/minimal-py2
+	docker run -v `pwd`:/io -ti fidimag/minimal-py2
 	# try 'ipython' and then 'import fidimag'
 
 # to push the new docker image to dockerhub (need to login first)
diff --git a/docker/minimal-py2/Readme.md b/docker/minimal-py2/Readme.md
index 38598bb4..a701838c 100644
--- a/docker/minimal-py2/Readme.md
+++ b/docker/minimal-py2/Readme.md
@@ -21,32 +21,10 @@ To use it, you can try this:
    This command should show a bash prompt inside the docker container:
 
     <pre>
-    bin:docker fangohr$ docker run -ti fidimag/minimal-py2
-    fidimag@38fdd2a0feb4:~$
+    bin:docker fangohr$ docker run -v `pwd`:/io -ti fidimag/minimal-py2
+    fidimag@38fdd2a0feb4:/io$
     </pre>
 
-One way to test the installation is to run the unit tests:
-
-<pre>
-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
-.
-.
-.
-</pre>
-
-## 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)
diff --git a/docker/minimal-py3/Dockerfile b/docker/minimal-py3/Dockerfile
index 17a7ec0f..773895cb 100644
--- a/docker/minimal-py3/Dockerfile
+++ b/docker/minimal-py3/Dockerfile
@@ -50,6 +50,10 @@ 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
 
diff --git a/docker/minimal-py3/Makefile b/docker/minimal-py3/Makefile
index 27d4e4cc..659b56a4 100644
--- a/docker/minimal-py3/Makefile
+++ b/docker/minimal-py3/Makefile
@@ -4,7 +4,7 @@ build:
 
 # to run new image
 run: build
-	docker run -ti fidimag/minimal-py3
+	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)
diff --git a/docker/minimal-py3/Readme.md b/docker/minimal-py3/Readme.md
index ad4f72c7..c83816b7 100644
--- a/docker/minimal-py3/Readme.md
+++ b/docker/minimal-py3/Readme.md
@@ -21,32 +21,10 @@ To use it, you can try this:
    This command should show a bash prompt inside the docker container:
 
     <pre>
-    bin:docker fangohr$ docker run -ti fidimag/minimal-py3
-    fidimag@38fdd2a0feb4:~$
+    bin:docker fangohr$ docker run -v `pwd`:/io -ti fidimag/minimal-py3
+    fidimag@38fdd2a0feb4:/io$
     </pre>
 
-One way to test the installation is to run the unit tests:
-
-<pre>
-fidimag@38fdd2a0feb4:~$ cd fidimag/tests/
-fidimag@38fdd2a0feb4:~/fidimag/tests$ py.test-3 -v
-========== test session starts =======================
-platform linux2 -- Python 3.4.3 -- pytest-2.5.1 -- /usr/bin/python3
-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
-.
-.
-.
-</pre>
-
-## 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)
diff --git a/docker/notebook/Dockerfile b/docker/notebook/Dockerfile
index a4e6db37..91bc2dda 100644
--- a/docker/notebook/Dockerfile
+++ b/docker/notebook/Dockerfile
@@ -28,5 +28,10 @@ RUN conda install --quiet --yes icu
 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 $HOME/work
+WORKDIR /io
diff --git a/docker/notebook/Makefile b/docker/notebook/Makefile
index ab05f33f..95caeb39 100644
--- a/docker/notebook/Makefile
+++ b/docker/notebook/Makefile
@@ -3,8 +3,8 @@ build:
 	time docker build -t fidimag/notebook:latest .
 
 # to run new image
-run:
-	docker run -ti fidimag/notebook bash
+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
diff --git a/docker/notebook/Readme.md b/docker/notebook/Readme.md
index acd85844..441338e2 100644
--- a/docker/notebook/Readme.md
+++ b/docker/notebook/Readme.md
@@ -16,7 +16,7 @@ To use it, you can try this:
 
 3. Start the container using
 
-       docker run -d -p 30008:8888 fidimag/notebook
+       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
@@ -24,7 +24,7 @@ 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 -ti fidimag/notebook bash
+    docker run -v `pwd`:/io -ti fidimag/notebook bash
 
 ## Shortcomings
 

From 49a4d004ac0bd7895fd0f041df25f1dbea97c4eb Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 8 Jul 2016 17:11:20 +0100
Subject: [PATCH 12/12] Set working directory to bind mount

---
 docker/minimal-py3/Dockerfile | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/docker/minimal-py3/Dockerfile b/docker/minimal-py3/Dockerfile
index 773895cb..037dd152 100644
--- a/docker/minimal-py3/Dockerfile
+++ b/docker/minimal-py3/Dockerfile
@@ -60,7 +60,5 @@ RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
 # Print something nice on entry.
 #COPY WELCOME $FIDIMAG_HOME/WELCOME
 
-
-
-WORKDIR $FIDIMAG_HOME
+WORKDIR /io
 CMD ["/bin/bash","-i"]