Make fidimag great again

.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
 
-#####################
-# Cython Extensions #
-#####################
+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} \
+           -Inative/include \
+           -lm \
+           -lfftw3_omp -lfftw3 \
+           -lsundials_cvodes -lsundials_nvecserial -lsundials_nvecopenmp \
+           -lblas -llapack \
+           -fopenmp \
+           -std=c++14
+
+LDFLAGS = -shared
+SOURCES = $(shell echo native/src/*.cpp)
+OBJECTS = $(SOURCES:.cpp=.o)
+LIBRARY = local/lib/libfidimag.so
+
+########
+# Build
+########
+
+
+all: $(LIBRARY) build
+
+
+$(LIBRARY) : $(OBJECTS)
+	$(CXX) $(CPPFLAGS) $(OBJECTS) -o $@ $(LDFLAGS)
+
+
+build: $(LIBRARY)
+	CC=${CC} CXX=${CXX} CPPFLAGS="${CPPFLAGS}" ${PYTHON} setup.py build_ext --inplace
 
-build:
-	${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 .

docker/travis/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
 
 # To build this image `docker build -t fidimag .`
 # Then you can drop into a live bash shell with `docker run -it fidimag`.

fidimag/__init__.py

@@ -48,6 +48,3 @@
          Processor: {}
          """
     print(message.format(FIDIMAG_DIR, e, platform.machine(), platform.platform(), platform.processor()))
-
-
-__version__ = '0.2'

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

@@ -1,8 +1,12 @@
+# distutils: language = c++
 import numpy
 cimport numpy as np
+cimport fidimag.common.vectormath as vmath
 np.import_array()
 
-cdef extern from "fidimag_random.h":
+
+
+cdef extern from "a_random.h":
     ctypedef struct mt19937_state:
         pass
 
@@ -18,7 +22,7 @@ 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,
@@ -95,8 +99,6 @@ cdef extern from "clib.h":
 
     # -------------------------------------------------------------------------
 
-    void normalise(double *m, int *pins, int n)
-
     # used for sllg
     void llg_rhs_dw_c(double *m, double *h, double *dm, double *T, double *alpha,
                       double *mu_s_inv, int *pins, double *eta, int n,
@@ -270,7 +272,7 @@ def compute_demag_full(double [:] spin,
 
 def normalise_spin(np.ndarray[double, ndim=1, mode="c"] spin,
               np.ndarray[int, ndim=1, mode="c"] pins, n):
-    normalise(&spin[0], &pins[0], n)
+    vmath.normalise(&spin[0], &pins[0], n)
 
 def compute_llg_rhs_dw(double [:] dm,
                        double [:] spin,

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/hexagonal_mesh.py

@@ -1,5 +1,4 @@
-
-"""
+r"""
 Represent hexagonal 2D mesh.
 
 The hexagons are pointy topped (as against flat topped). We use axial
@@ -38,6 +37,7 @@
 Coordinates a
 
 """
+
 import numpy as np
 from math import sqrt
 

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