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

Author: Weiwei Wang

.travis.yml

@@ -1,5 +1,6 @@
 language: python
 python:
+        - "3.6"
         - "3.5"
         - "3.4"
         - "2.7"

examples/micromagnetic/baryakhtar/relax_system.py

@@ -12,8 +12,9 @@
 
 def relax_system(mesh):
 
-    sim = Sim(mesh, chi=1e-3, name='relax', driver='llbar_full')
+    sim = Sim(mesh, name='relax', driver='llbar_full')
 
+    sim.driver.chi = 1e-3
     sim.driver.set_tols(rtol=1e-7, atol=1e-7)
     sim.Ms = 8.0e5
     sim.driver.alpha = 0.1

fidimag/common/cuboid_mesh.py

@@ -27,7 +27,7 @@
 
 """
 from __future__ import print_function
-from psutil import 	virtual_memory
+from psutil import virtual_memory
 import numpy as np
 from textwrap import dedent
 from six.moves import range
@@ -53,6 +53,12 @@ def __init__(self, dx=1, dy=1, dz=1, nx=1, ny=1, nz=1, x0=0, y0=0, z0=0,
             # of 2 nm in any direction and periodic along the x-axis.
 
         """
+
+        if (np.array([nx, ny, nz]) <= 0).any():
+            raise ValueError("nx, ny and nz must be integers >= 1")
+        if (np.array([dx, dy, dz]) <= 0).any():
+            raise ValueError("dx, dy and dz must be greater than 0")
+
         self.dx = dx
         self.dy = dy
         self.dz = dz
@@ -279,7 +285,7 @@ def check_size(self, system_memory_fake_for_testing=None):
 
         if 2 * size_coordinates_GiB > mem_GiB:
             # print because no logging yet
-            print("Warning! Size of mesh coordinates i {} GiB.".format(
+            print("Warning! Size of mesh coordinates is {} GiB.".format(
                 size_coordinates_GiB))
             print(
                 "You have {} GiB system memory. Possible halt.".format(mem_GiB))

fidimag/common/nebm_cartesian.py

@@ -8,6 +8,7 @@
 from .nebm_tools import spherical2cartesian, cartesian2spherical, compute_norm
 from .nebm_tools import linear_interpolation_spherical
 from .nebm_tools import interpolation_Rodrigues_rotation
+from .nebm_tools import m_to_zero_nomaterial
 
 from .nebm_base import NEBMBase
 
@@ -235,6 +236,10 @@ def generate_initial_band(self, method='linear'):
                         self.sim._pins
                         )
 
+                interpolation = np.apply_along_axis(lambda m: m_to_zero_nomaterial(m, self.sim),
+                                                    axis=1,
+                                                    arr=interpolation)
+
                 # We then set the interpolated spins fields at once
                 self.band[i_initial_images[i] + 1:
                           i_initial_images[i + 1]] = interpolation

fidimag/common/nebm_geodesic.py

@@ -9,6 +9,7 @@
 from .nebm_tools import spherical2cartesian, cartesian2spherical, compute_norm
 from .nebm_tools import linear_interpolation_spherical
 from .nebm_tools import interpolation_Rodrigues_rotation
+from .nebm_tools import m_to_zero_nomaterial
 
 from .nebm_base import NEBMBase
 
@@ -247,6 +248,10 @@ def generate_initial_band(self, method='linear'):
                         self.sim._pins
                         )
 
+                interpolation = np.apply_along_axis(lambda m: m_to_zero_nomaterial(m, self.sim),
+                                                    axis=1,
+                                                    arr=interpolation)
+
                 # We then set the interpolated spins fields at once
                 self.band[i_initial_images[i] + 1:
                           i_initial_images[i + 1]] = interpolation

fidimag/common/nebm_tools.py

@@ -213,3 +213,19 @@ def interpolation_Rodrigues_rotation(y_initial, y_final, n, pins=None):
     y_final.shape = (-1)
 
     return interpolations
+
+def m_to_zero_nomaterial(image_cartesian, sim):
+    """
+    For spins in sites with no material, we set its spin
+    direction to [0, 0, 0]
+    
+    Input is an image in Cartesian coordinates:
+        [mx_0 my_0 mz_0 mx_1 my_1 ... mz_(P-1)]
+
+    sim is a fidimag simulation object from which we extract
+    the Ms or mu_s to filter the spin directions
+    """
+    image_reshape = np.copy(image_cartesian.reshape(-1, 3))
+    _filter = sim._magnetisation == 0  
+    image_reshape[_filter] = np.array([0., 0., 0.])
+    return image_reshape.reshape(-1)

fidimag/common/sim_base.py

@@ -275,3 +275,17 @@ def compute_energy(self):
             energy += obj.compute_energy()
 
         return energy
+
+    def get_field_array(self, interaction):
+        """
+        Returns the field array corresponding to the interaction given:
+
+        e.g.
+            compute_interaction_field('Demag')
+        returns a numpy array containing the Demag field.
+        """
+        field = self.get_interaction(interaction)
+        # Copy here to avoid destroying the field accidentally
+        # e.g. through reshaping
+        f = field.field.copy()
+        return f

fidimag/micro/baryakhtar.py

@@ -7,7 +7,7 @@
 
 class LLBarFull(MicroDriver):
 
-    def __init__(self, mesh, spin, Ms, field, alpha, pins,
+    def __init__(self, mesh, spin, Ms, field, pins,
                  interactions,
                  name,
                  data_saver,
@@ -18,18 +18,36 @@ def __init__(self, mesh, spin, Ms, field, alpha, pins,
 
         # Inherit from the driver class
         super(LLBarFull, self).__init__(mesh, spin, Ms, field,
-                                        alpha, pins, interactions, name,
+                                        pins, interactions, name,
                                         data_saver,
                                         integrator=integrator,
                                         use_jac=use_jac
                                         )
 
-        self.chi = chi
+        self._chi = 1e-3
+        add(Relaxation(self.chi, name='chi_relax'),
+            self.interactions, self.data_saver,
+            self.mesh, self.spin, self._Ms)
+
         self.lap = Laplace(mesh)
-        self.add(Relaxation(chi))
+        # OLD: self.add(Relaxation(chi))
 
         self.beta = 0
 
+    def get_chi(self):
+        """
+        """
+        return self._chi
+
+    def set_chi(self, chi):
+        """
+        """
+        for i in self.interactions:
+            if i.name == 'chi_relax':
+                i.chi = chi
+
+    chi = property(get_chi, set_chi)
+
     def sundials_rhs(self, t, y, ydot):
 
         self.t = t
@@ -58,7 +76,7 @@ def sundials_rhs(self, t, y, ydot):
 
 class LLBar(MicroDriver):
 
-    def __init__(self, mesh, spin, Ms, field, alpha, pins,
+    def __init__(self, mesh, spin, Ms, field, pins,
                  interactions,
                  name,
                  data_saver,
@@ -68,7 +86,7 @@ def __init__(self, mesh, spin, Ms, field, alpha, pins,
 
         # Inherit from the driver class
         super(LLBar, self).__init__(mesh, spin, Ms, field,
-                                    alpha, pins, interactions, name,
+                                    pins, interactions, name,
                                     data_saver,
                                     integrator='sundials',
                                     use_jac=False
@@ -107,3 +125,54 @@ def sundials_rhs(self, t, y, ydot):
         #ydot[:] = self.dm_dt[:]
 
         return 0
+
+
+def add(interaction, interactions_list, data_saver,
+        mesh, spin, magnetisation, save_field=False):
+
+    """
+
+    Add an interaction to the interaction list.
+    This function is based on the Sim class *add* method
+    (it is likely that this function will be moved to the common
+     helpers in the future)
+
+    OPTIONAL ARGUMENTS:
+
+    save_field      :: Set True to save the average values of this
+                       interaction field when relaxing the system
+
+    """
+
+    # magnetisation is Ms for the micromagnetic Sim class, and it is
+    # mu_s for the atomistic Sim class
+    interaction.setup(mesh, spin, magnetisation)
+
+    # TODO: FIX  --> ??
+    # When adding an interaction that was previously added, using
+    # the same name, append a '_2' to the new interaction name (?)
+    for i in interactions_list:
+        if i.name == interaction.name:
+            interaction.name = i.name + '_2'
+
+    interactions_list.append(interaction)
+
+    # Specify a name for the energy of the interaction, which will
+    # appear in a file with saved values
+    # When saving the energy values, we call the compute_energy() method
+    # from the (micromagnetic/atomistic) Energy class (overhead?)
+    energy_name = 'E_{0}'.format(interaction.name)
+    data_saver.entities[energy_name] = {
+        'unit': '<J>',
+        'get': lambda sim: sim.get_interaction(interaction.name).compute_energy(),
+        'header': energy_name}
+
+    # Save the average values of the interaction vector field components
+    if save_field:
+        fn = '{0}'.format(interaction.name)
+        data_saver.entities[fn] = {
+            'unit': '<>',
+            'get': lambda sim: sim.get_interaction(interaction.name).average_field(),
+            'header': ('%s_x' % fn, '%s_y' % fn, '%s_z' % fn)}
+
+    data_saver.update_entity_order()

tests/test_mesh.py

@@ -1,5 +1,5 @@
 from fidimag.common import CuboidMesh
-
+import unittest
 
 def test_mesh1():
     mesh = CuboidMesh(nx=5, ny=3, nz=2, dx=0.23, dy=0.41)
@@ -9,5 +9,11 @@ def test_mesh1():
     assert tuple(mesh.coordinates[mesh.index(3, 2, 1)]) == (
         (3 + 0.5) * 0.23, (2 + 0.5) * 0.41, 1 + 0.5)
 
+
+class Mesh_TestCase(unittest.TestCase):
+    def test_mesh_input_args(self):
+        self.assertRaises(ValueError, CuboidMesh, 1, 1, 0, 1, 1, 1)
+        self.assertRaises(ValueError, CuboidMesh, 1, 1, 1, 0, 1, 1)
+
 if __name__ == '__main__':
     test_mesh1()