Fixing conglict with 1D domain wall notebook

Author: davidcorteso

.gitignore

@@ -1,3 +1,4 @@
+*.txt
 *.pyc
 /local/
 
@@ -35,3 +36,6 @@ test-reports
 
 # ignore notebook checkpoint directory
 .ipynb_checkpoints/
+
+*.npz
+*.npy

.travis.yml

@@ -3,8 +3,8 @@ python:
         - "3.5"
         - "3.4"
         - "2.7"
-sudo: false
-# command to install dependencies
+
+
 before_install:
   # We do this conditionally because it saves us some downloading if the
   # version is the same.
@@ -16,7 +16,7 @@ before_install:
     fi
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH=/home/travis/miniconda/bin:$PATH
-
+  - sudo apt-get install liblapack-dev libblas-dev
 install:
   - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy pytest-cov gcc cmake psutil
   - source activate fidimag-test

Makefile

@@ -1,13 +1,14 @@
 PROJECT_DIR = $(abspath .)
 EXTENSIONS_DIR = ${PROJECT_DIR}/fidimag/extensions
+PYTHON = python
 
 #####################
 # Cython Extensions #
 #####################
 
 
 build:
-	python setup.py build_ext --inplace
+	${PYTHON} setup.py build_ext --inplace
 
 clean:
 	rm -rf ${EXTENSIONS_DIR}/*
@@ -21,6 +22,32 @@ clean:
 test:
 	cd tests && py.test -v -m "not slow and not run_oommf"
 
+test-clean:
+	rm -rf neb*.ndt
+	rm -rf relax_npys
+	rm -rf relax.txt
+	rm -rf skx_number_*
+	rm -rf skx_num_*
+	rm -rf vtks
+	rm -rf spin.txt
+	rm -rf unnamed_npys
+	rm -rf unnamed.txt
+	rm -rf 2dpbc_tensors.npz
+	rm -rf 10spin.txt
+	rm -rf dyn_npys
+	rm -rf dyn_spin.txt
+	rm -rf dyn.txt
+	rm -rf dyn_vtks
+	rm -rf m0.npy
+	rm -rf skx_num.txt
+	rm -rf test_energy.txt
+	rm -rf unnamed_vtks
+	rm -rf dw_cobalt.txt
+	rm -rf mu_s.npy
+	rm -rf npys
+	rm -rf relax_vtks
+	rm -rf m1.npy
+
 test2:
 	# like test, but run also outside the 'tests' directory.
 	# Doesn't work on Hans laptop.

bin/install-fftw.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-
+echo "HELLO"
 # This script installs FFTW locally. It may need to environment
 # variables to work, like 'export CC=gcc' in ARCHER.
 
@@ -9,9 +9,12 @@ set -e
 
 # Create target directory if needed.
 
+
 HERE_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 FIDIMAG_DIR="$(dirname "$HERE_DIR")"
-LIBS_DIR=${FIDIMAG_DIR}/local
+
+if [ -z $LIBS_DIR ]; then LIBS_DIR=${FIDIMAG_DIR}/local; fi
+
 mkdir -p $LIBS_DIR
 cd ${LIBS_DIR}
 echo "Installing FFTW to "$LIBS_DIR"."

bin/install-sundials.sh

@@ -13,7 +13,8 @@ type cmake >/dev/null 2>&1 || { printf "CMake required to build SUNDIALS. You ca
 
 HERE_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 FIDIMAG_DIR="$(dirname "$HERE_DIR")"
-LIBS_DIR=${FIDIMAG_DIR}/local
+
+if [ -z $LIBS_DIR ]; then LIBS_DIR=${FIDIMAG_DIR}/local; fi
 
 echo "Will install SUNDIALS to "${LIBS_DIR}" using CC="${CC}"."
 mkdir -p ${LIBS_DIR}

doc/ipynb/1d_domain_wall.ipynb

@@ -110,7 +110,7 @@
     "# Set simulation parameters.\n",
     "sim.Ms = Ms\n",
     "sim.alpha = alpha\n",
-    "sim.gamma = gamma\n",
+    "sim.driver.gamma = gamma\n",
     "\n",
     "# Add energies.\n",
     "sim.add(UniformExchange(A=A))\n",
@@ -119,7 +119,7 @@
     "    \n",
     "# Since the magnetisation dynamics is not important in this stage,\n",
     "# the precession term in LLG equation can be set to artificially zero.\n",
-    "sim.do_precession = False"
+    "sim.driver.do_precession = False"
    ]
   },
   {
@@ -385,7 +385,7 @@
     "sim.set_m(m_init)\n",
     "\n",
     "# Relax the system to its equilibrium state.\n",
-    "sim.relax(dt=1e-13, stopping_dmdt=0.01, max_steps=5000, save_m_steps=None, save_vtk_steps=None)"
+    "sim.driver.relax(dt=1e-13, stopping_dmdt=0.01, max_steps=5000, save_m_steps=None, save_vtk_steps=None)"
    ]
   },
   {
@@ -461,7 +461,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",

doc/ipynb/current-driven-domain-wall.ipynb

@@ -115,9 +115,9 @@
     "    sim = Sim(mesh)\n",
     "\n",
     "    # Set simulation parameters.\n",
-    "    sim.set_tols(rtol=1e-8, atol=1e-8)\n",
+    "    sim.driver.set_tols(rtol=1e-8, atol=1e-8)\n",
     "    sim.alpha = alpha\n",
-    "    sim.gamma = gamma\n",
+    "    sim.driver.gamma = gamma\n",
     "    sim.Ms = Ms\n",
     "\n",
     "    # Add energies to the system.\n",
@@ -128,8 +128,8 @@
     "    sim.set_m(init_m)\n",
     "    \n",
     "    # Relax the system and save the state in m0.npy\n",
-    "    sim.relax(dt=1e-14, stopping_dmdt=0.01, max_steps=5000,\n",
-    "              save_m_steps=None, save_vtk_steps=None)\n",
+    "    sim.driver.relax(dt=1e-14, stopping_dmdt=0.01, max_steps=5000,\n",
+    "                     save_m_steps=None, save_vtk_steps=None)\n",
     "\n",
     "    np.save('m0.npy', sim.spin)"
    ]
@@ -190,9 +190,9 @@
     "    sim = Sim(mesh, name='dyn', driver='llg_stt')\n",
     "    \n",
     "    # Set the simulation parameters\n",
-    "    sim.set_tols(rtol=1e-12, atol=1e-14)\n",
+    "    sim.driver.set_tols(rtol=1e-12, atol=1e-14)\n",
     "    sim.alpha = alpha\n",
-    "    sim.gamma = gamma\n",
+    "    sim.driver.gamma = gamma\n",
     "    sim.Ms = Ms\n",
     "\n",
     "    # Add energies to the system.\n",
@@ -203,15 +203,15 @@
     "    sim.set_m(np.load('m0.npy'))\n",
     "\n",
     "    # Set the spin-polarised current in the x direction.\n",
-    "    sim.jx = J\n",
-    "    sim.beta = beta\n",
+    "    sim.driver.jx = J\n",
+    "    sim.driver.beta = beta\n",
     "\n",
     "    # The simulation will run for x ns and save\n",
     "    # 'snaps' snapshots of the system in the process\n",
     "    ts = np.linspace(0, time, snapshots)\n",
     "\n",
     "    for t in ts:\n",
-    "        sim.run_until(t)\n",
+    "        sim.driver.run_until(t)\n",
     "        sim.save_vtk()\n",
     "        sim.save_m()\n"
    ]
@@ -1019,7 +1019,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.6"
+   "version": "2.7.11"
+  },
+  "widgets": {
+   "state": {},
+   "version": "1.1.2"
   }
  },
  "nbformat": 4,

doc/ipynb/isolated_skyrmion.ipynb

@@ -168,7 +168,7 @@
     "sim = Sim(mesh)\n",
     "sim.Ms = Ms_function(Ms)\n",
     "sim.alpha = alpha\n",
-    "sim.gamma = gamma\n",
+    "sim.driver.gamma = gamma\n",
     "\n",
     "# Add energies.\n",
     "sim.add(UniformExchange(A=A))\n",
@@ -177,7 +177,7 @@
     "\n",
     "# Since the magnetisation dynamics is not important in this stage,\n",
     "# the precession term in LLG equation can be set to artificially zero.\n",
-    "sim.do_precession = False\n",
+    "sim.driver.do_precession = False\n",
     "\n",
     "# Initialise the system.\n",
     "sim.set_m(init_m)"
@@ -559,7 +559,7 @@
    "source": [
     "# PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "# Relax the system to its equilibrium.\n",
-    "sim.relax(dt=1e-13, stopping_dmdt=0.01, max_steps=5000, save_m_steps=None, save_vtk_steps=None)"
+    "sim.driver.relax(dt=1e-13, stopping_dmdt=0.01, max_steps=5000, save_m_steps=None, save_vtk_steps=None)"
    ]
   },
   {
@@ -650,6 +650,10 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
    "version": "2.7.11"
+  },
+  "widgets": {
+   "state": {},
+   "version": "1.1.2"
   }
  },
  "nbformat": 4,

doc/ipynb/spin-polarised-current-driven-skyrmion.ipynb

@@ -113,8 +113,8 @@
     "# Set parameters.\n",
     "sim.Ms = Ms\n",
     "sim.alpha = alpha\n",
-    "sim.gamma = gamma\n",
-    "sim.do_precession = False\n",
+    "sim.driver.gamma = gamma\n",
+    "sim.driver.do_precession = False\n",
     "\n",
     "# Add energies.\n",
     "sim.add(UniformExchange(A=A))\n",
@@ -174,7 +174,7 @@
    "outputs": [],
    "source": [
     "%%capture\n",
-    "sim.relax(dt=1e-13, stopping_dmdt=0.1, max_steps=5000, save_m_steps=None, save_vtk_steps=None)\n",
+    "sim.driver.relax(dt=1e-13, stopping_dmdt=0.1, max_steps=5000, save_m_steps=None, save_vtk_steps=None)\n",
     "np.save('m0.npy', sim.spin)"
    ]
   },
@@ -252,21 +252,21 @@
     "# Set parameters.\n",
     "sim2.Ms = Ms\n",
     "sim2.alpha = alpha\n",
-    "sim2.gamma = gamma\n",
+    "sim2.driver.gamma = gamma\n",
     "\n",
     "# Add energies.\n",
     "sim2.add(UniformExchange(A=A))\n",
     "sim2.add(DMI(D))\n",
     "sim2.add(Zeeman(H))\n",
     "\n",
-    "sim2.jx = -5e12\n",
+    "sim2.driver.jx = -5e12\n",
     "sim2.alpha = 0.2\n",
-    "sim2.beta = 0.2\n",
+    "sim2.driver.beta = 0.2\n",
     "\n",
     "sim2.set_m(np.load('m0.npy'))\n",
     "\n",
     "for t in [0, 0.1, 0.2]:\n",
-    "    sim2.run_until(t*1e-9)\n",
+    "    sim2.driver.run_until(t*1e-9)\n",
     "    plot_magnetisation(sim2.spin.copy(), mesh, title='t=%g ns'%t)"
    ]
   }
@@ -287,7 +287,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "version": "2.7.11"
+  },
+  "widgets": {
+   "state": {},
+   "version": "1.1.2"
   }
  },
  "nbformat": 4,

doc/ipynb/spin-waves-in-periodic-system.ipynb

@@ -88,7 +88,7 @@
     "# Set parameters.\n",
     "sim.Ms = Ms\n",
     "sim.alpha = alpha\n",
-    "sim.gamma = gamma\n",
+    "sim.driver.gamma = gamma\n",
     "\n",
     "# Add energies.\n",
     "sim.add(UniformExchange(A=A))\n",
@@ -262,7 +262,7 @@
     "t_array = np.arange(dt, t_sim, dt)\n",
     "\n",
     "for t in t_array:\n",
-    "    sim.run_until(t)\n",
+    "    sim.driver.run_until(t)\n",
     "    plot_magnetisation(np.copy(sim.spin))"
    ]
   },
@@ -290,7 +290,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.6"
+   "version": "2.7.11"
+  },
+  "widgets": {
+   "state": {},
+   "version": "1.1.2"
   }
  },
  "nbformat": 4,