Refactor all Python code so that tests pass with new extensions location

.gitignore

@@ -6,6 +6,11 @@
 *.pdf
 *.tmp
 *.so
+*.o
+*.dSYM
+fidimag/**/*.cpp
+
+
 local/
 *~
 *.bak

Makefile

@@ -3,17 +3,50 @@ EXTENSIONS_DIR = ${PROJECT_DIR}/fidimag/extensions
 PYTHON = python3
 PYTEST = ${PYTHON} -m pytest
 
+CC=g++-8
+
+FFTW_INC=local/include
+FFTW_LIB=local/lib
+
+SUNDIALS_INC=local/include
+SUNDIALS_LIB=local/lib
+
+CPPFLAGS = -fPIC -g -Iinclude/ \
+           -I${FFTW_INC} -L${FFTW_LIB} \
+           -I${SUNDIALS_INC} -L${SUNDIALS_LIB} \
+           -lm \
+           -lfftw3_omp -lfftw3 \
+           -lsundials_cvodes -lsundials_nvecserial -lsundials_nvecopenmp \
+           -lblas -llapack \
+           -fopenmp
+
+LDFLAGS = -shared
+SOURCES = $(shell echo native/src/*.cpp)
+OBJECTS = $(SOURCES:.cpp=.o)
+LIBRARY = local/lib/libfidimag.so
+
+all: $(LIBRARY) build
+
+$(LIBRARY) : $(OBJECTS)
+	$(CXX) $(CPPFLAGS) $(OBJECTS) -o $@ $(LDFLAGS)
+
+
+
 #####################
 # Cython Extensions #
 #####################
 
-build:
+build: $(LIBRARY)
 	${PYTHON} setup.py build_ext --inplace
 
+
+
+
 clean:
 	rm -rf ${EXTENSIONS_DIR}/*
 	touch ${EXTENSIONS_DIR}/__init__.py
 	rm -rf build
+	rm -rf $(OBJECTS) $(TARGET) *.dSYM
 
 docker:
 	docker build -t fidimag -f ./docker/travis/Dockerfile .

fidimag/atomistic/lib/a_clib.pyx → fidimag/atomistic/a_clib.pyx

@@ -4,7 +4,7 @@ import numpy
 cimport numpy as np
 np.import_array()
 
-cdef extern from "fidimag_random.h":
+cdef extern from "a_random.h":
     ctypedef struct mt19937_state:
         pass
 
@@ -20,7 +20,7 @@ cdef extern from "time.h":
     ctypedef int time_t
     time_t time(time_t *timer)
 
-cdef extern from "clib.h":
+cdef extern from "a_clib.h":
     void run_step_mc(mt19937_state *state, double *spin, double *new_spin,
                      int *ngbs, int *nngbs, int n_ngbs,
                      double J, double J1, double D, double D1,

fidimag/atomistic/anisotropy.py

@@ -1,4 +1,4 @@
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 import numpy as np
 from .energy import Energy
 import fidimag.common.helper as helper

fidimag/atomistic/atomistic_driver.py

@@ -3,7 +3,7 @@
 
 from fidimag.common.driver_base import DriverBase
 
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 import fidimag.extensions.cvode as cvode
 from fidimag.common.vtk import VTK
 import fidimag.common.constant as const

fidimag/atomistic/demag_full.py

@@ -1,4 +1,4 @@
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 import numpy as np
 from .energy import Energy
 

fidimag/atomistic/dmi.py

@@ -1,4 +1,4 @@
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 from .energy import Energy
 import numpy as np
 

fidimag/atomistic/exchange.py

@@ -1,4 +1,4 @@
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 import numpy as np
 from .energy import Energy
 

fidimag/atomistic/llg.py

@@ -2,7 +2,7 @@
 from __future__ import print_function
 
 # Use the common C library for the LLG equation in the atomistic case
-import fidimag.extensions.common_clib as clib
+import fidimag.extensions.c_clib as clib
 
 from .atomistic_driver import AtomisticDriver
 

fidimag/atomistic/llg_stt.py

@@ -1,6 +1,5 @@
 from __future__ import division
-
-import fidimag.extensions.common_clib as clib
+import fidimag.extensions.c_clib as clib
 import numpy as np
 
 from .atomistic_driver import AtomisticDriver

fidimag/atomistic/llg_stt_cpp.py

@@ -2,7 +2,7 @@
 
 import types
 
-import fidimag.extensions.common_clib as clib
+import fidimag.extensions.c_clib as clib
 import numpy as np
 
 from .atomistic_driver import AtomisticDriver

fidimag/atomistic/monte_carlo.py

@@ -2,7 +2,7 @@
 from __future__ import print_function
 import os
 import numpy as np
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 from fidimag.common.fileio import DataSaver
 import fidimag.common.helper as helper
 import fidimag.common.constant as const

fidimag/atomistic/sim.py

@@ -7,7 +7,7 @@
 
 import fidimag.common.skyrmion_number
 import fidimag.common.helper as helper
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 import numpy as np
 
 from fidimag.common.sim_base import SimBase

fidimag/atomistic/sllg.py

@@ -1,6 +1,6 @@
 from __future__ import division
 import numpy as np
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 import fidimag.common.helper as helper
 import fidimag.common.constant as const
 

fidimag/common/lib/common_clib.pyx → fidimag/common/c_clib.pyx

@@ -5,7 +5,7 @@ import numpy as np
 
 # -----------------------------------------------------------------------------
 
-cdef extern from "common_clib.h":
+cdef extern from "c_clib.h":
 
     # From: llg.c
     void llg_rhs(double * dm_dt, double * spin,

fidimag/common/dipolar/dipolar.pyx

@@ -6,7 +6,7 @@ import ctypes
 cimport numpy as np
 np.import_array()
 
-cdef extern from "dipolar.h":
+cdef extern from "c_dipolar.h":
     # used for demag
     ctypedef struct fft_demag_plan:
         int nx, ny, nz
@@ -186,7 +186,7 @@ cdef class FFTDemag(object):
                                     &field[0], &energy[0])
 
 
-cdef extern from "demagcoef.h":
+cdef extern from "c_demagcoef.h":
     double CalculateSDA00(double x, double y, double z, double dx,double dy,double dz)
     double DemagNxxAsymptotic(double x, double y, double z, double dx,double dy,double dz)
 

fidimag/common/gradient_descent.py

@@ -1,6 +1,6 @@
 from __future__ import division
 import numpy as np
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as a_clib
 # import fidimag.common.constant as const
 
 from .minimiser_base import MinimiserBase

fidimag/common/helper.py

@@ -1,8 +1,8 @@
-from fidimag.extensions.common_clib import normalise
-from fidimag.extensions.common_clib import init_scalar
-from fidimag.extensions.common_clib import init_vector
-from fidimag.extensions.common_clib import init_vector_func_fast
-import fidimag.extensions.clib as clib
+from fidimag.extensions.c_clib import normalise
+from fidimag.extensions.c_clib import init_scalar
+from fidimag.extensions.c_clib import init_vector
+from fidimag.extensions.c_clib import init_vector_func_fast
+import fidimag.extensions.a_clib as clib
 import numpy as np
 
 

fidimag/common/neb_method/nebm_clib.pyx

@@ -1,6 +1,6 @@
 # distutils: language = c++
 
-cdef extern from "nebm_lib.h":
+cdef extern from "c_nebm_lib.h":
     void compute_tangents_C(double *tangents,
                             double *y,
                             double *energies,
@@ -59,7 +59,7 @@ cdef extern from "nebm_lib.h":
                                    int n_images,
                                    int n_dofs_image)
 
-cdef extern from "nebm_integrators.h":
+cdef extern from "c_nebm_integrators.h":
     double step_Verlet_C(double * forces,
                          double * forces_prev,
                          double * velocities,
@@ -177,7 +177,7 @@ def compute_dYdt_nc(double [:]  y,
 
 
 
-cdef extern from "nebm_geodesic_lib.h":
+cdef extern from "c_nebm_geodesic_lib.h":
     double compute_geodesic_GreatCircle(double * A, double * B,
                                      int n_dofs_image,
                                      int * material,
@@ -230,7 +230,7 @@ def image_distances_GreatCircle(double [:] distances,
                                    )
 
 
-cdef extern from "nebm_spherical_lib.h":
+cdef extern from "c_nebm_spherical_lib.h":
     void normalise_spherical(double * a, int n)
     void normalise_images_spherical_C(double * y, int n_images,
                                       int n_dofs_image)

fidimag/common/plt_helper.py

@@ -1,11 +1,8 @@
 from __future__ import division
-# import matplotlib as mpl
-# mpl.use("Agg")
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 import numpy as np
 
 import matplotlib.pyplot as plt
-# from mpl_toolkits.mplot3d import Axes3D
 from matplotlib.colors import colorConverter
 from matplotlib.collections import PolyCollection
 

fidimag/common/simple_minimiser.py

@@ -1,6 +1,6 @@
 from __future__ import division
 import numpy as np
-import fidimag.extensions.clib as clib
+import fidimag.extensions.a_clib as clib
 # import fidimag.common.constant as const
 
 from .minimiser_base import MinimiserBase

fidimag/common/skyrmion_number.py

@@ -1,4 +1,4 @@
-import fidimag.extensions.clib
+import fidimag.extensions.a_clib
 import fidimag.extensions.micro_clib
 import numpy as np
 
@@ -69,7 +69,7 @@ def skyrmion_number_slice(sim, at=None, zIndex=None):
                spinSlice, sim._skx_number, sim.mesh.nx, sim.mesh.ny,
                sim.mesh.nz, sim.mesh.neighbours)
     else:
-        return fidimag.extensions.clib.compute_skyrmion_number(\
+        return fidimag.extensions.a_clib.compute_skyrmion_number(\
                spinSlice, sim._skx_number, sim.mesh.nx, sim.mesh.ny,
                sim.mesh.nz, sim.mesh.neighbours)
 
@@ -104,7 +104,7 @@ def skyrmion_number_lee(sim):
                                   sim.mesh.ny, sim.mesh.nz,
                                   sim.mesh.neighbours)
         else:
-            skyrmionNumbers[zI] = fidimag.extensions.clib.compute_skyrmion_number(\
+            skyrmionNumbers[zI] = fidimag.extensions.a_clib.compute_skyrmion_number(\
                                   spinSlice, sim._skx_number, sim.mesh.nx,
                                   sim.mesh.ny, sim.mesh.nz,
                                   sim.mesh.neighbours, 6)

fidimag/common/steepest_descent.py

@@ -1,8 +1,8 @@
 from __future__ import division
 import numpy as np
-import fidimag.extensions.common_clib as clib
+import fidimag.extensions.c_clib as clib
 # Change int he future to common clib:
-import fidimag.extensions.clib as atom_clib
+import fidimag.extensions.a_clib as atom_clib
 import sys
 from .minimiser_base import MinimiserBase
 

fidimag/common/sundials/cvode.pyx

@@ -176,7 +176,7 @@ cdef extern from "sundials/sundials_iterative.h":
 
 
 
-cdef extern from "../../atomistic/lib/clib.h":
+cdef extern from "a_clib.h":
     void normalise(double * m, int nxyz)
 
 

fidimag/micro/lib/baryakhtar_clib.pyx

@@ -3,7 +3,7 @@ import numpy
 cimport numpy as np
 np.import_array()
 
-cdef extern from "baryakhtar_clib.h":
+cdef extern from "m_baryakhtar_clib.h":
     void compute_laplace_m(double *m, double *field, double *Ms, double dx, double dy, double dz,
         int nx, int ny, int nz)
 

fidimag/micro/lib/micro_clib.pyx

@@ -2,7 +2,7 @@
 import numpy as np
 cimport numpy as np
 
-cdef extern from "micro_clib.h":
+cdef extern from "m_clib.h":
     void compute_exch_field_micro(double *m, double *field,
                                   double *energy, double *Ms_inv,
                                   double A, double dx, double dy, double dz,

fidimag/micro/llg.py

@@ -3,7 +3,7 @@
 
 # We use the common/lib/llg.c file to calculate the LLG equation for
 # the micromagnetic case
-import fidimag.extensions.common_clib as clib
+import fidimag.extensions.c_clib as clib
 
 from .micro_driver import MicroDriver
 

fidimag/micro/llg_stt.py

@@ -1,6 +1,6 @@
 from __future__ import division
 
-import fidimag.extensions.common_clib as clib
+import fidimag.extensions.c_clib as clib
 import numpy as np
 
 from .micro_driver import MicroDriver

fidimag/micro/llg_stt_cpp.py

@@ -2,7 +2,7 @@
 
 from .micro_driver import MicroDriver
 
-import fidimag.extensions.common_clib as clib
+import fidimag.extensions.c_clib as clib
 import numpy as np
 
 import fidimag.common.helper as helper