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

davidcortesortuno · davidcortesortuno · commit 92717492ad38 · 2016-04-29T14:40:08.000+01:00
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,41 @@
 *.pyc
 /local/
+
+# ignore automatically generated cython files
+fidimag/atomistic/lib/clib.c
+fidimag/common/dipolar/dipolar.c
+fidimag/common/neb/neb_clib.c
+fidimag/common/sundials/cvode.c
+fidimag/micro/lib/baryakhtar/baryakhtar_clib.c
+fidimag/micro/lib/micro_clib.c
+
+# ignore .cache from pytest
+.cache
+
+# ignore simulation data
+*_npys
+*_vtks
+
+# ignore output files from NEB method
+npys
+vtks
+
+/build/
+/doc/build/
+
+
+# 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
+
+
+# ignore output from coverage
+htmlcov
+
+# ignore junit test output
+test-reports
+
diff --git a/.travis.yml b/.travis.yml
@@ -17,7 +17,7 @@ before_install:
   - export PATH=/home/travis/miniconda/bin:$PATH
 
 install:
-  - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy
+  - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy pytest-cov
   - source activate fidimag-test
   - pip install pyvtk six
   # Download and compile FFTW & Sundials locally
diff --git a/Makefile b/Makefile
@@ -6,16 +6,12 @@ EXTENSIONS_DIR = ${PROJECT_DIR}/fidimag/extensions
 #####################
 
 
-build: extensions-directory
-	python setup.py build_ext --build-lib ${EXTENSIONS_DIR}
-	touch ${EXTENSIONS_DIR}/__init__.py
-	rm -rf ${PROJECT_DIR}/build
-
-extensions-directory:
-	mkdir -p ${EXTENSIONS_DIR}
+build:
+	python setup.py build_ext --inplace
 
 clean:
-	rm -rf ${EXTENSIONS_DIR}
+	rm -rf ${EXTENSIONS_DIR}/*
+	touch ${EXTENSIONS_DIR}/__init__.py
 
 #########
 # Tests #
@@ -28,7 +24,7 @@ test: create-dirs
 	py.test -v --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml
 
 test-without-run-oommf: create-dirs
-	py.test -v --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml -m "not run_oommf"
+	py.test -v --junitxml=$(PROJECT_DIR)/test-reports/junit/test-pytest.xml -m "not run_oommf" --cov=fidimag --cov-report=html
 
 test-basic:
 	cd tests && py.test -v
diff --git a/README.md b/README.md
@@ -3,6 +3,8 @@ FIDIMAG
 
 [![Build Status](https://travis-ci.org/computationalmodelling/fidimag.svg?branch=master)](https://travis-ci.org/computationalmodelling/fidimag)
 [![Documentation Status](https://readthedocs.org/projects/fidimag/badge/?version=latest)](http://fidimag.readthedocs.org/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/computationalmodelling/fidimag/branch/master/graph/badge.svg)](https://codecov.io/gh/computationalmodelling/fidimag)
+
 
 Fidimag solves finite-difference micromagnetic problems and also
 does atomistic simulations.
diff --git a/doc/ipynb/Spin-polarised-current-driven-skyrmion.ipynb b/doc/ipynb/Spin-polarised-current-driven-skyrmion.ipynb
diff --git a/doc/ipynb/current-driven-domain-wall.ipynb b/doc/ipynb/current-driven-domain-wall.ipynb
diff --git a/examples/atomic/PRL_111_067203/phase_script/phase.py b/examples/atomic/PRL_111_067203/phase_script/phase.py
@@ -5,11 +5,9 @@
 
 import numpy as np
 from fidimag.atomistic import Sim, DMI, UniformExchange, Zeeman
-from fidimag.common import Constant, BatchTasks, DataReader, CuboidMesh
+from fidimag.common import BatchTasks, DataReader, CuboidMesh
 from fidimag.common.helper import plot_m
-
-
-const = Constant()
+import fidimag.common.constant as const
 
 
 def init_m(pos):
diff --git a/examples/atomic/PRL_111_067203/single.py b/examples/atomic/PRL_111_067203/single.py
@@ -3,10 +3,10 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from fidimag.atomistic import Sim, DMI, UniformExchange, Zeeman
-from fidimag.common import Constant, CuboidMesh
+from fidimag.common import constant, CuboidMesh
 
 
-const = Constant()
+const = constant
 
 """
 If we only consider the exchange, dmi and external field, 
diff --git a/examples/atomic/demag_field/demag_field.py b/examples/atomic/demag_field/demag_field.py
@@ -5,11 +5,9 @@
 import numpy as np
 from pc import Sim, Demag
 from fidimag.common import CuboidMesh
-from pc import Constant
+import fidimag.common.constant as const
 from pc.save_vtk import SaveVTK
 
-const = Constant()
-
 
 def mu_s(pos):
     x, y, z = pos
diff --git a/examples/atomic/dmi/interfacial_dmi_dw/dw.py b/examples/atomic/dmi/interfacial_dmi_dw/dw.py
@@ -3,11 +3,9 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from fidimag.atomistic import Sim, DMI, UniformExchange, Anisotropy
-from fidimag.common import Constant, CuboidMesh
+from fidimag.common import constant, CuboidMesh
 
 
-const = Constant()
-
 def m_init_dw(pos):
 
     x = pos[0]
@@ -34,14 +32,14 @@ def analytical(xs, A=1.3e-11, D=4e-4, K=8e4):
 def relax_system(mesh):
 
     sim = Sim(mesh, name='relax')
-    sim.set_default_options(gamma=const.gamma)
+    sim.set_default_options(gamma=constant.gamma)
     sim.alpha = 0.5
-    sim.mu_s = const.mu_s_1
+    sim.mu_s = constant.mu_s_1
     sim.do_precession = False
 
     sim.set_m(m_init_dw)
 
-    J = 50.0 * const.k_B
+    J = 50.0 * constant.k_B
     exch = UniformExchange(J)
     sim.add(exch)
 
diff --git a/examples/atomic/heat/compute_energy.py b/examples/atomic/heat/compute_energy.py
@@ -1,14 +1,9 @@
 import numpy as np
 import scipy.integrate as integrate
-from pccp.pc import Constant
-
-const = Constant()
-
 import matplotlib as mpl
 mpl.use("Agg")
 import matplotlib.pyplot as plt
-
-
+import fidimag.common.constant as const
 """
 compute the figure 2 in the paper at dx.doi.org/10.1063/1.2169472
 Note: it seems that the volume given in the paper is not correct, 
diff --git a/examples/atomic/skyrmion_demag/single_ku.py b/examples/atomic/skyrmion_demag/single_ku.py
@@ -5,12 +5,9 @@
 from pccp.pc import UniformExchange
 from pccp.pc import Demag
 from pccp.pc import Anisotropy
-from pccp.pc import Constant
-
+import fidimag.common.constant as const
 from pccp.pc.batch_task import BatchTasks
 
-const = Constant()
-
 
 def mu_s(pos):
     x, y, z = pos
diff --git a/examples/neb_atomistic/1D_spin_chain/neb_helicoid-fm.py b/examples/neb_atomistic/1D_spin_chain/neb_helicoid-fm.py
@@ -38,10 +38,7 @@
 from fidimag.atomistic import UniformExchange
 from fidimag.atomistic import Zeeman
 from fidimag.atomistic import Anisotropy
-from fidimag.atomistic import Constant
-
-# Import constants from fidimag
-const = Constant()
+import fidimag.common.constant as const
 
 # Import NEB library
 from fidimag.common.neb_cartesian import NEB_Sundials
diff --git a/examples/neb_atomistic/1D_spin_chain/relaxation/1D_spin_chain.py b/examples/neb_atomistic/1D_spin_chain/relaxation/1D_spin_chain.py
@@ -6,10 +6,7 @@
 from fidimag.atomistic import UniformExchange
 from fidimag.atomistic import Zeeman
 from fidimag.atomistic import Anisotropy
-from fidimag.atomistic import Constant
-
-# Import constants from fidimag
-const = Constant()
+import fidimag.common.constant as const
 
 # Number of spins and lattice spacing (see mesh)
 nx = 50
diff --git a/examples/neb_atomistic/1D_spin_chain/relaxation/1D_spin_chain_fm.py b/examples/neb_atomistic/1D_spin_chain/relaxation/1D_spin_chain_fm.py
@@ -6,10 +6,7 @@
 from fidimag.atomistic import UniformExchange
 from fidimag.atomistic import Zeeman
 from fidimag.atomistic import Anisotropy
-from fidimag.atomistic import Constant
-
-# Import constants from fidimag
-const = Constant()
+import fidimag.common.constant as const
 
 # Number of spins and lattice spacing (see mesh)
 nx = 50
diff --git a/fidimag/__init__.py b/fidimag/__init__.py
@@ -15,3 +15,5 @@
 
 
 citation = common.citation
+
+__version__ = '0.2'
diff --git a/fidimag/atomistic/__init__.py b/fidimag/atomistic/__init__.py
@@ -6,5 +6,5 @@
 from .demag_hexagonal import DemagHexagonal
 from .demag_full import DemagFull
 from .dmi import DMI
-from fidimag.common.constant import Constant
+import fidimag.common.constant as const
 from .materials import UnitMaterial, Nickel
diff --git a/fidimag/atomistic/lib/clib.pyx b/fidimag/atomistic/lib/clib.pyx
@@ -98,7 +98,7 @@ def random_number(np.ndarray[double, ndim=1, mode="c"] v):
 
 
 
-def compute_skymrion_number(np.ndarray[double, ndim=1, mode="c"] spin,
+def compute_skyrmion_number(np.ndarray[double, ndim=1, mode="c"] spin,
                             np.ndarray[double, ndim=1, mode="c"] charge,
                             nx, ny, nz,
                             np.ndarray[int, ndim=2, mode="c"] ngbs
diff --git a/fidimag/atomistic/llg.py b/fidimag/atomistic/llg.py
@@ -7,9 +7,7 @@
 import fidimag.common.helper as helper
 from fidimag.common.fileio import DataSaver
 from fidimag.common.save_vtk import SaveVTK
-from fidimag.common.constant import Constant
-
-const = Constant()
+import fidimag.common.constant as const
 
 
 class LLG(object):
@@ -290,7 +288,7 @@ def skyrmion_number(self):
         nx = self.mesh.nx
         ny = self.mesh.ny
         nz = self.mesh.nz
-        number = clib.compute_skymrion_number(
+        number = clib.compute_skyrmion_number(
             self.spin, self._skx_number, nx, ny, nz, self.mesh.neighbours)
         return number
 
diff --git a/fidimag/atomistic/sllg.py b/fidimag/atomistic/sllg.py
@@ -3,9 +3,7 @@
 import fidimag.extensions.clib as clib
 import fidimag.common.helper as helper
 from .llg import LLG
-from fidimag.common.constant import Constant
-
-const = Constant()
+import fidimag.common.constant as const
 
 
 class SLLG(LLG):
diff --git a/fidimag/common/__init__.py b/fidimag/common/__init__.py
@@ -1,4 +1,3 @@
-from .constant import Constant
 from .fileio import DataSaver
 from .fileio import DataReader
 from .batch_task import BatchTasks
diff --git a/fidimag/common/constant.py b/fidimag/common/constant.py
@@ -1,18 +1,15 @@
-import numpy as np
+from math import pi
 
-mu_0 = 4 * np.pi * 1e-7
-
-class Constant(object):
-    mu_0 = mu_0
-    mu_B = 9.27400949e-24
-    k_B = 1.3806505e-23
-    c_e = 1.602176565e-19
-    eV = 1.602176565e-19
-    meV = 1.602176565e-22
-    m_e = 9.10938291e-31
-    g_e = 2.0023193043737
-    h_bar = 1.05457172647e-34
-    h = h_bar * 2. * np.pi
-    gamma = g_e * mu_B / h_bar
-    mu_s_1 = g_e * mu_B * 1.0  # for S=1, 1.856952823077189e-23
-    h_bar_gamma = h_bar * gamma
+mu_0 = 4 * pi * 1e-7
+mu_B = 9.27400949e-24
+k_B = 1.3806505e-23
+c_e = 1.602176565e-19
+eV = 1.602176565e-19
+meV = 1.602176565e-22
+m_e = 9.10938291e-31
+g_e = 2.0023193043737
+h_bar = 1.05457172647e-34
+h = h_bar * 2. * pi
+gamma = g_e * mu_B / h_bar
+mu_s_1 = g_e * mu_B * 1.0  # for S=1, 1.856952823077189e-23
+h_bar_gamma = h_bar * gamma
diff --git a/fidimag/common/neb_spherical.py b/fidimag/common/neb_spherical.py
@@ -1,8 +1,8 @@
 import os
 import fidimag.extensions.cvode as cvode
 import numpy as np
-from fileio import DataSaver, DataReader
-from save_vtk import SaveVTK
+from .fileio import DataSaver, DataReader
+from .save_vtk import SaveVTK
 import fidimag.extensions.neb_clib as neb_clib
 
 import logging
diff --git a/fidimag/common/sundials/cvode.pyx b/fidimag/common/sundials/cvode.pyx
@@ -77,7 +77,7 @@ cdef class CvodeSolver(object):
     cdef public np.ndarray y
     cdef double rtol, atol
     cdef int cvode_already_initialised
-    cdef np.ndarray spin
+    cdef np.ndarray y0
     cdef np.ndarray dm_dt
     cdef np.ndarray mp
     cdef np.ndarray Jmp
@@ -95,7 +95,7 @@ cdef class CvodeSolver(object):
 
     def __cinit__(self, spins, rhs_fun, jtimes_fun=None, linear_solver="spgmr", rtol=1e-8, atol=1e-8):
         self.t = 0
-        self.spin = spins
+        self.y0 = spins
         self.dm_dt = np.copy(spins)
         self.y = np.copy(spins)
         self.mp = np.copy(spins)
@@ -117,7 +117,7 @@ cdef class CvodeSolver(object):
             self.has_jtimes = 1
 
         self.user_data = cv_userdata(<void*>self.callback_fun,
-                                     <void *>self.spin, <void *>self.dm_dt,
+                                     <void *>self.y0, <void *>self.dm_dt,
                                      <void *>self.jtimes_fun,
                                      <void *>self.mp,<void *>self.Jmp)
 
diff --git a/fidimag/common/vtk_test.py b/fidimag/common/vtk_test.py
@@ -6,7 +6,6 @@
 from fidimag.common.vtk import VTK
 
 MODULE_DIR = os.path.realpath(os.path.dirname(__file__))
-OUTPUT_DIR = os.path.join(MODULE_DIR, "temp")
 REF_DIR = os.path.join(os.path.dirname(os.path.dirname(MODULE_DIR)), "tests", "vtk_refs")
 
 
@@ -22,25 +21,25 @@ def same_as_ref(filepath, ref_dir):
     return ret == 0  # 0 means files are the same, c.f. man diff exit codes
 
 
-def test_save_scalar_field():
+def test_save_scalar_field(tmpdir):
     mesh = CuboidMesh(4, 3, 2, 4, 3, 2)
     s = scalar_field(mesh, lambda r: r[0] + r[1] + r[2])
-    vtk = VTK(mesh, directory=OUTPUT_DIR, filename="save_scalar")
+    vtk = VTK(mesh, directory=str(tmpdir), filename="save_scalar")
     vtk.save_scalar(s, name="s")
     assert same_as_ref(vtk.write_file(), REF_DIR)
 
 
-def test_save_vector_field():
+def test_save_vector_field(tmpdir):
     mesh = CuboidMesh(4, 3, 2, 4, 3, 2)
     s = vector_field(mesh, lambda r: (r[0], r[1], r[2]))
-    vtk = VTK(mesh, directory=OUTPUT_DIR, filename="save_vector")
+    vtk = VTK(mesh, directory=str(tmpdir), filename="save_vector")
     vtk.save_vector(s, name="s")
     assert same_as_ref(vtk.write_file(), REF_DIR)
 
 
-def test_save_scalar_field_hexagonal_mesh():
+def test_save_scalar_field_hexagonal_mesh(tmpdir):
     mesh = HexagonalMesh(1, 3, 3)
     s = scalar_field(mesh, lambda r: r[0] + r[1])
-    vtk = VTK(mesh, directory=OUTPUT_DIR, filename="scalar_hexagonal")
+    vtk = VTK(mesh, directory=str(tmpdir), filename="scalar_hexagonal")
     vtk.save_scalar(s, name="s")
     assert same_as_ref(vtk.write_file(), REF_DIR)
diff --git a/fidimag/extensions/__init__.py b/fidimag/extensions/__init__.py
diff --git a/fidimag/micro/llg.py b/fidimag/micro/llg.py
diff --git a/fidimag/micro/llg_stt.py b/fidimag/micro/llg_stt.py
diff --git a/fidimag/micro/oommf.py b/fidimag/micro/oommf.py
diff --git a/sandbox/relaxation_test/skyrmion.py b/sandbox/relaxation_test/skyrmion.py
diff --git a/setup.py b/setup.py
diff --git a/tests/test_demag_libraries.py b/tests/test_demag_libraries.py
diff --git a/tests/test_dw_atomistic.py b/tests/test_dw_atomistic.py
diff --git a/tests/test_neb_spherical.py b/tests/test_neb_spherical.py
