### DMI setup method

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/micro/dmi.html

The setup method configures the DMI vector based on the specified dmi_type (bulk, interfacial, or D_2d).

```python
def setup(self, mesh, spin, Ms, Ms_inv):
    super().setup(mesh, spin, Ms, Ms_inv)

    if self.dmi_type == 'bulk':
        self.dmi_vector = np.array([-1., 0, 0,
                                    1., 0, 0,
                                    0, -1., 0,
                                    0, 1., 0,
                                    0, 0, -1.,
                                    0, 0, 1.
                                    ])

    elif self.dmi_type == 'interfacial':
        self.dmi_vector = np.array([0, -1., 0,  # -x
                                    0, 1., 0,   # +x
                                    1., 0, 0,   # -y
                                    -1., 0, 0,  # +y
                                    0, 0, 0,    # -z
                                    0, 0, 0     # +z
                                    ])

    elif self.dmi_type == 'D_2d':
        self.dmi_vector = np.array([1., 0, 0,   # -x
                                    -1., 0, 0,  # +x
                                    0, -1., 0,  # -y
                                    0, 1., 0,   # +y
                                    0, 0, 0,    # -z
                                    0, 0, 0     # +z
                                    ])
```

--------------------------------

### Install all optional dependencies

Source: https://fidimag.readthedocs.io/en/latest/_sources/install.rst.txt

Installs the optional dev and docs dependencies for Fidimag.

```bash
uv sync --all-extras
```

--------------------------------

### Start IPython inside container

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/tutorial-docker-container.ipynb.txt

Starts IPython inside the container. The output shows the IPython banner and prompt.

```bash
jovyan@4df962d27520:~/work$ ipython
Python 3.5.1 |Continuum Analytics, Inc.| (default, Jun 15 2016, 15:32:45) 
Type "copyright", "credits" or "license" for more information.

IPython 4.2.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: 
```

--------------------------------

### Energy class definition and setup method

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/atomistic/energy.html

Defines the Energy abstract class with a setup method that initializes mesh properties, spin, and material constants. It also allocates arrays for field and energy.

```python
import numpy as np

#from constant import mu_0




[docs]
class Energy:

    """

    An abstract class to implement the basic functions such as setup for atomic
    dynamics.

    """



[docs]
    def setup(self, mesh, spin, mu_s, mu_s_inv):
        self.mesh = mesh
        self.dx = mesh.dx * mesh.unit_length
        self.dy = mesh.dy * mesh.unit_length
        self.dz = mesh.dz * mesh.unit_length
        self.nx = mesh.nx
        self.ny = mesh.ny
        self.nz = mesh.nz
        self.spin = spin
        self.n = mesh.n
        self.n_ngbs = mesh.n_ngbs
        self.mesh_type = mesh.mesh_type

        self.total_energy = 0
        self.mu_s = mu_s

        self.field = np.zeros(3 * self.n, dtype=np.float64)
        self.energy = np.zeros(mesh.n, dtype=np.float64)
        self.total_energy = 0.0

        self.mu_s_inv = mu_s_inv

        self.xperiodic, self.yperiodic = (mesh.periodicity[0],
                                          mesh.periodicity[1])
        self.neighbours = mesh.neighbours

        try:
            self.coordinates = self.mesh.coordinates
        except:
            self.coordinates = np.array(self.mesh.pos)
```

--------------------------------

### Install cmake and GCC on OS X

Source: https://fidimag.readthedocs.io/en/latest/_sources/install.rst.txt

Installs cmake and a GCC version compatible with OpenMP on OS X via brew.

```bash
brew install cmake gcc@15
```

--------------------------------

### Install uv on Linux

Source: https://fidimag.readthedocs.io/en/latest/_sources/install.rst.txt

Command to install the uv package manager, required for managing the Python environment and building Fidimag.

```bash
curl -LsSf https://astral.sh/uv/install.sh | sh
```

--------------------------------

### Start IPython in container

Source: https://fidimag.readthedocs.io/en/latest/user_guide/ipynb/tutorial-docker-container.html

Launch an interactive IPython session within the container.

```bash
jovyan@4df962d27520:~/work$ ipython
Python 3.5.1 |Continuum Analytics, Inc.| (default, Jun 15 2016, 15:32:45)
Type "copyright", "credits" or "license" for more information.

IPython 4.2.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]:
```

--------------------------------

### Initialize CuboidMesh

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/common/cuboid_mesh.html

Example of creating a CuboidMesh instance with specified dimensions, cell sizes, and periodicity.

```python
mesh = CuboidMesh(2, 2, 2, 250, 25, 2, periodicity=(True, False, False))
# create a mesh of dimensions 500 x 50 x 4 nm, with cellsize
# of 2 nm in any direction and periodic along the x-axis.
```

--------------------------------

### DemagHexagonal setup method

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/atomistic/demag_hexagonal.html

Configures the hexagonal mesh parameters and initializes the equivalent cuboid mesh for demagnetization calculations.

```python
[docs]
    def setup(self, mesh, spin, mu_s, mu_s_inv):

        if mesh.mesh_type != 'hexagonal':
            raise Exception('This interaction is only defined'
                            'for hexagonal meshes'
                            )

        # `mesh`, `spin`, `n`, `field`, `energy` and `total_energy` come from
        # the base class, so that this reports an energy the same way as every
        # other interaction
        super().setup(mesh, spin, mu_s, mu_s_inv)

        # The equivalent cuboid mesh is built in mesh units rather than in
        # metres, the unit length being carried by `scale` below, so the
        # spacings the base class stores in metres are replaced here
        self.dx = mesh.dx
        self.dx_c = 0.5 * mesh.dx

        self.dy = mesh.dy
        self.dz = mesh.dz

        self.nx_c = 2 * mesh.nx

        self.spin_c = np.zeros(2 * len(spin))

        self.n_c = mesh.n * 2
        # self.n_c = self.mesh_c.n

        self.field_c = np.zeros(3 * self.n_c, dtype=np.float64)

        self.energy_c = np.zeros(self.n_c, dtype=np.float64)

        unit_length = mesh.unit_length
        self.mu_s_scale_c = np.zeros(2 * self.n, dtype=np.float64)

        # note that the 1e-7 comes from \frac{\mu_0}{4\pi}
        self.scale = 1e-7 / unit_length ** 3

        # could be wrong, needs carefully tests!!!
        # David Tue 19 Jun 2018: this variable is upated in the sim class
        # in case mu_s changes
        self.mu_s_scale = mu_s * self.scale

        # This seems not to be necessary
        # self.create_cuboid_mesh()

        self.scalar2cuboid(self.mu_s_scale, self.mu_s_scale_c)

        # Compute demag using the cuboid mesh with the double
        # number of x finite differences
        self.demag = clib.FFTDemag(self.dx_c, self.dy, self.dz,
                                   self.nx_c, self.ny, self.nz,
                                   tensor_type='dipolar')
```

--------------------------------

### Nickel class usage example

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/atomistic/materials.html

Demonstrates how to instantiate the Nickel class and print its physical properties.

```python
if __name__ == '__main__':
    ni = Nickel()
    print(ni.K)
    print('gamma', ni.gamma)
    print('mu_s', ni.mu_s)
    print('J', ni.J)
    print('D', ni.D)
    print('D/J:', ni.D / ni.J)

    K = 1e5 * ni.a**3
    print(K)
    print((ni.J / K)**0.5)
```

--------------------------------

### Example run.py script

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/tutorial-docker-container.ipynb.txt

A sample Python script that imports fidimag and writes data to a file within the container environment.

```python
import fidimag   # to proof we can import it
print("Hello from the container")
# and write to a file
open("data.txt", "w").write("Data from the container.\n")
```

--------------------------------

### Set up simulation with LLG driver for comparison

Source: https://fidimag.readthedocs.io/en/latest/user_guide/ipynb/hubert_minimiser_atomistic.html

Creates an atomistic simulation with the 'llg' driver, sets the magnetic moment, adds the same interactions as the Hubert example, and defines the same initial magnetisation function.

```python
sim = fidimag.atomistic.Sim(mesh, name='one_dim', driver='llg')

# Define the magnetisation
sim.set_mu_s(mus)

# Add the magnetic interactions
sim.add(fidimag.atomistic.Exchange(J))
sim.add(fidimag.atomistic.Anisotropy(Ku, axis=(0, 0, 1)))
sim.add(fidimag.atomistic.DMI(D, dmi_type='interfacial'))
sim.add(fidimag.atomistic.Zeeman((0, 0, B)))

xs = mesh.coordinates[:, 0]
centre_x = (xs.max() + xs.min()) * 0.5 + xs.min()

def m_initial(r):
    x, y, z = r[0], r[1], r[2]
    if np.abs(x - centre_x) < 2:
        return (0, 0.1, -.9)
    else:
        return (0, 0.1, .9)

# sim.set_m((0.1, 0, 0.9))
sim.set_m(m_initial)

```

--------------------------------

### Setting current via functions

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/micro/llg_stt.html

Example of configuring the driver to use functions for current components.

```python
driver.jx_function = func_x
driver.jy_function = func_y
driver.jz_function = func_z
```

--------------------------------

### Import fidimag in Python

Source: https://fidimag.readthedocs.io/en/latest/user_guide/ipynb/tutorial-docker-container.html

Start Python inside the container and import the fidimag library.

```bash
jovyan@4df962d27520:~/work$ python
Python 3.5.1 |Continuum Analytics, Inc.| (default, Jun 15 2016, 15:32:45)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import  fidimag
```

--------------------------------

### Plot initial magnetisation for LLG example

Source: https://fidimag.readthedocs.io/en/latest/user_guide/ipynb/hubert_minimiser_atomistic.html

Plots the z-component of the initial spin configuration for the LLG simulation.

```python
plt.plot(sim.mesh.coordinates[:, 0], sim.spin.reshape(-1, 3)[:, 2], 'o-')
plt.show() n
```

--------------------------------

### Stop the last started Docker container

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/tutorial-docker-container.ipynb.txt

Stops the most recently started container by combining docker ps -l -q to get the container ID and docker stop to stop it.

```bash
docker stop $(docker ps -l -q)
```

--------------------------------

### Energy.setup()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.energy.html

Sets up the energy computation with the given mesh, spin, and magnetic moment parameters.

```APIDOC
## Energy.setup()

### Description
Sets up the energy computation with the given mesh, spin, and magnetic moment parameters.

### Method
setup(_mesh_, _spin_, _mu_s_, _mu_s_inv_)

### Parameters
- **_mesh** - The mesh object.
- **_spin** - The spin configuration.
- **_mu_s** - The saturation magnetic moment.
- **_mu_s_inv** - The inverse of the saturation magnetic moment.

```

--------------------------------

### DemagFull.setup()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.demag_full.html

Sets up the DemagFull object with the mesh, spin, and magnetic moment parameters.

```APIDOC
## DemagFull.setup()

### Description
Sets up the DemagFull object with the mesh, spin, and magnetic moment parameters.

### Method
setup

### Signature
setup(_mesh_, _spin_, _mu_s_, _mu_s_inv_)

### Parameters
- **mesh** (Mesh) - Required - The simulation mesh.
- **spin** (array-like) - Required - The spin configuration.
- **mu_s** (array-like) - Required - The saturation magnetic moment.
- **mu_s_inv** (array-like) - Required - The inverse of the saturation magnetic moment.
```

--------------------------------

### Get Docker machine IP address

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/tutorial-docker-container.ipynb.txt

On a Mac, run this command to find the IP address to connect to the notebook. For example, if it returns 192.168.99.100, use http://192.168.99.100:30000.

```bash
docker-machine ip
```

--------------------------------

### Relaxation Process Output

Source: https://fidimag.readthedocs.io/en/latest/user_guide/ipynb/standard_problem_4.html

Example output showing the progression of the relaxation process with time steps and maximum dmdt values.

```text
#1    t=1e-13    dt=1e-13 max_dmdt=517
#2    t=2e-13    dt=1e-13 max_dmdt=510
#3    t=3e-13    dt=1e-13 max_dmdt=502
#4    t=4e-13    dt=1e-13 max_dmdt=495
#5    t=5e-13    dt=1e-13 max_dmdt=489
#6    t=6e-13    dt=1e-13 max_dmdt=482
#7    t=7e-13    dt=1e-13 max_dmdt=476
#8    t=8e-13    dt=1e-13 max_dmdt=470
#9    t=9e-13    dt=1e-13 max_dmdt=464
#10   t=1e-12    dt=1e-13 max_dmdt=459
#11   t=1.14e-12 dt=1.43e-13 max_dmdt=453
#12   t=1.29e-12 dt=1.43e-13 max_dmdt=445
#13   t=1.43e-12 dt=1.43e-13 max_dmdt=439
#14   t=1.57e-12 dt=1.43e-13 max_dmdt=433
#15   t=1.72e-12 dt=1.43e-13 max_dmdt=428
#16   t=1.86e-12 dt=1.43e-13 max_dmdt=422
#17   t=2e-12    dt=1.43e-13 max_dmdt=417
#18   t=2.15e-12 dt=1.43e-13 max_dmdt=412
#19   t=2.29e-12 dt=1.43e-13 max_dmdt=407
#20   t=2.51e-12 dt=2.15e-13 max_dmdt=401
#21   t=2.72e-12 dt=2.15e-13 max_dmdt=394
#22   t=2.94e-12 dt=2.15e-13 max_dmdt=387
#23   t=3.15e-12 dt=2.15e-13 max_dmdt=381
#24   t=3.37e-12 dt=2.15e-13 max_dmdt=375
#25   t=3.58e-12 dt=2.15e-13 max_dmdt=369
#26   t=3.8e-12  dt=2.15e-13 max_dmdt=364
#27   t=4.01e-12 dt=2.15e-13 max_dmdt=358
#28   t=4.23e-12 dt=2.15e-13 max_dmdt=353
#29   t=4.44e-12 dt=2.15e-13 max_dmdt=348
#30   t=4.66e-12 dt=2.15e-13 max_dmdt=343
#31   t=4.87e-12 dt=2.15e-13 max_dmdt=338
#32   t=5.09e-12 dt=2.15e-13 max_dmdt=333
#33   t=5.3e-12  dt=2.15e-13 max_dmdt=328
#34   t=5.52e-12 dt=2.15e-13 max_dmdt=324
#35   t=5.73e-12 dt=2.15e-13 max_dmdt=320
#36   t=5.95e-12 dt=2.15e-13 max_dmdt=315
#37   t=6.16e-12 dt=2.15e-13 max_dmdt=311
#38   t=6.38e-12 dt=2.15e-13 max_dmdt=307
#39   t=6.59e-12 dt=2.15e-13 max_dmdt=303
#40   t=6.81e-12 dt=2.15e-13 max_dmdt=299
#41   t=7.02e-12 dt=2.15e-13 max_dmdt=295
#42   t=7.24e-12 dt=2.15e-13 max_dmdt=291
#43   t=7.45e-12 dt=2.15e-13 max_dmdt=288
#44   t=7.78e-12 dt=3.29e-13 max_dmdt=283
#45   t=8.11e-12 dt=3.29e-13 max_dmdt=278
#46   t=8.44e-12 dt=3.29e-13 max_dmdt=273
#47   t=8.77e-12 dt=3.29e-13 max_dmdt=268
#48   t=9.09e-12 dt=3.29e-13 max_dmdt=263
#49   t=9.42e-12 dt=3.29e-13 max_dmdt=258
#50   t=9.75e-12 dt=3.29e-13 max_dmdt=254
#51   t=1.01e-11 dt=3.29e-13 max_dmdt=249
#52   t=1.04e-11 dt=3.29e-13 max_dmdt=245
#53   t=1.07e-11 dt=3.29e-13 max_dmdt=240
#54   t=1.11e-11 dt=3.29e-13 max_dmdt=236
#55   t=1.14e-11 dt=3.29e-13 max_dmdt=232
#56   t=1.17e-11 dt=3.29e-13 max_dmdt=229
#57   t=1.21e-11 dt=3.29e-13 max_dmdt=225
#58   t=1.24e-11 dt=3.29e-13 max_dmdt=221
#59   t=1.27e-11 dt=3.29e-13 max_dmdt=218
#60   t=1.3e-11  dt=3.29e-13 max_dmdt=214
#61   t=1.34e-11 dt=3.29e-13 max_dmdt=211
#62   t=1.37e-11 dt=3.29e-13 max_dmdt=208
#63   t=1.4e-11  dt=3.29e-13 max_dmdt=204
#64   t=1.45e-11 dt=4.94e-13 max_dmdt=201
#65   t=1.5e-11  dt=4.94e-13 max_dmdt=196
#66   t=1.55e-11 dt=4.94e-13 max_dmdt=192
#67   t=1.6e-11  dt=4.94e-13 max_dmdt=188
#68   t=1.65e-11 dt=4.94e-13 max_dmdt=184
#69   t=1.7e-11  dt=4.94e-13 max_dmdt=180
#70   t=1.75e-11 dt=4.94e-13 max_dmdt=177
#71   t=1.8e-11  dt=4.94e-13 max_dmdt=173
#72   t=1.85e-11 dt=4.94e-13 max_dmdt=170
#73   t=1.9e-11  dt=4.94e-13 max_dmdt=167
#74   t=1.95e-11 dt=4.94e-13 max_dmdt=164
#75   t=2e-11    dt=4.94e-13 max_dmdt=161
#76   t=2.04e-11 dt=4.94e-13 max_dmdt=159
#77   t=2.09e-11 dt=4.94e-13 max_dmdt=156
#78   t=2.17e-11 dt=7.48e-13 max_dmdt=153
#79   t=2.24e-11 dt=7.48e-13 max_dmdt=150
#80   t=2.32e-11 dt=7.48e-13 max_dmdt=147
#81   t=2.39e-11 dt=7.48e-13 max_dmdt=144
#82   t=2.47e-11 dt=7.48e-13 max_dmdt=141
#83   t=2.54e-11 dt=7.48e-13 max_dmdt=138
#84   t=2.62e-11 dt=7.48e-13 max_dmdt=136
#85   t=2.69e-11 dt=7.48e-13 max_dmdt=134
#86   t=2.77e-11 dt=7.48e-13 max_dmdt=131
#87   t=2.84e-11 dt=7.48e-13 max_dmdt=129
#88   t=2.92e-11 dt=7.48e-13 max_dmdt=127
#89   t=2.99e-11 dt=7.48e-13 max_dmdt=125
#90   t=3.07e-11 dt=7.48e-13 max_dmdt=124
#91   t=3.14e-11 dt=7.48e-13 max_dmdt=122
#92   t=3.22e-11 dt=7.48e-13 max_dmdt=120
#93   t=3.29e-11 dt=7.48e-13 max_dmdt=119
#94   t=3.37e-11 dt=7.48e-13 max_dmdt=118
```

--------------------------------

### Main execution of BatchTasks

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/common/batch_task.html

Creates a BatchTasks instance with the task function and two parameters, adds parameters p1 and p2, and starts the batch tasks.

```python
if __name__ == "__main__":
    tasks = BatchTasks(task, 2)
    tasks.add_parameters('p1', ['a', 'b', 'c'])
    tasks.add_parameters('p2', range(1, 5))
    tasks.start()
```

--------------------------------

### Demag.setup()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.demag.html

Sets up the Demag energy term with the given mesh, spin, saturation magnetization, and inverse saturation magnetization. This method is part of the Demag class.

```APIDOC
## Demag.setup(mesh, spin, Ms, Ms_inv)

### Description
Sets up the Demag energy term with the given mesh, spin, saturation magnetization, and inverse saturation magnetization. This method is part of the Demag class.

### Method
setup

### Parameters
- **mesh** (Mesh) - Required - The mesh object for the simulation.
- **spin** (array) - Required - The spin configuration.
- **Ms** (float) - Required - Saturation magnetization.
- **Ms_inv** (float) - Required - Inverse saturation magnetization.

```

--------------------------------

### Energy.setup(_mesh_, _spin_, _Ms_, _Ms_inv_)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.energy.html

Sets up the energy interaction with the given mesh, spin, saturation magnetization, and inverse saturation magnetization.

```APIDOC
## Energy.setup(_mesh_, _spin_, _Ms_, _Ms_inv_)

### Description
Sets up the energy interaction with the given mesh, spin, saturation magnetization, and inverse saturation magnetization.

### Method
setup(_mesh_, _spin_, _Ms_, _Ms_inv_)

### Parameters
- _mesh_ - The mesh object.
- _spin_ - The spin field.
- _Ms_ - Saturation magnetization.
- _Ms_inv_ - Inverse saturation magnetization.
```

--------------------------------

### List running Docker containers

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/tutorial-docker-container.ipynb.txt

Shows all running containers. Use -q to show only container IDs, and -l to show only the last started container.

```bash
docker ps
```

```bash
docker ps -q
```

```bash
docker ps -l
```

--------------------------------

### Set up simulation with material parameters and energies

Source: https://fidimag.readthedocs.io/en/latest/user_guide/ipynb/isolated_skyrmion.html

Creates the simulation object, sets material parameters (Ms, A, D, alpha, gamma), adds exchange, DMI, and demagnetisation energies, and initialises the magnetisation.

```python
# FeGe material paremeters.
Ms = 3.84e5  # saturation magnetisation (A/m)
A = 8.78e-12  # exchange energy constant (J/m)
D = 1.58e-3  # Dzyaloshinkii-Moriya energy constant (J/m**2)
alpha = 1  # Gilbert damping
gamma = 2.211e5  # gyromagnetic ration (m/As)

# Create simulation object.
sim = Sim(mesh)
# sim = Sim(mesh, driver='steepest_descent')
sim.Ms = Ms_function(Ms)
sim.driver.alpha = alpha
sim.driver.gamma = gamma

# Add energies.
sim.add(UniformExchange(A=A))
sim.add(DMI(D=D))
sim.add(Demag())

# Since the magnetisation dynamics is not important in this stage,
# the precession term in LLG equation can be set to artificially zero.
# sim.driver.do_precession = False

# Initialise the system.
sim.set_m(init_m)
```

--------------------------------

### DemagHexagonal.setup(mesh, spin, mu_s, mu_s_inv)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.demag_hexagonal.html

Sets up the DemagHexagonal object with mesh, spin, and magnetic moment data.

```APIDOC
## DemagHexagonal.setup(mesh, spin, mu_s, mu_s_inv)

### Description
Sets up the DemagHexagonal object with the given mesh, spin configuration, and magnetic moment arrays.

### Parameters
- `mesh` - The mesh object.
- `spin` - The spin configuration.
- `mu_s` - The magnetic moment array.
- `mu_s_inv` - The inverse magnetic moment array.
```

--------------------------------

### Relaxation.setup(mesh, m, Ms)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.relax.html

Sets up the relaxation computation with the given mesh, magnetization, and saturation magnetization.

```APIDOC
## Relaxation.setup(mesh, m, Ms)

### Description
Sets up the relaxation computation with the given mesh, magnetization, and saturation magnetization.

### Method
setup

### Parameters
- **mesh** (Mesh) - Required - The mesh on which the computation is performed.
- **m** (field) - Required - The magnetization field.
- **Ms** (float) - Required - Saturation magnetization.

### Returns
None
```

--------------------------------

### Import Fidimag and dependencies

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/Simulating%20an%20Anisotropic%20Grain%20Structure.ipynb.txt

Imports the Fidimag library, scipy's cKDTree for spatial queries, and numpy for numerical operations. Required for the grain simulation example.

```python
import fidimag
from scipy.spatial import cKDTree
import numpy as np
```

--------------------------------

### Initialize Periodic System

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/spin-waves-in-periodic-system.ipynb.txt

Sets up a periodic mesh and initializes the magnetic system for spin wave calculations.

```python
import numpy as np
from fidimag.atomistic import Sim
from fidimag.atomistic.hamiltonian import Exchange, DMI, Zeeman
from fidimag.common.mesh import PeriodicMesh

# Define mesh and system
mesh = PeriodicMesh(nx=100, ny=1, nz=1, dx=1e-9)
sim = Sim(mesh, name='spin_wave_periodic')

# Add interactions
sim.hamiltonian.add(Exchange(1e-12))

# Set initial state
sim.set_m((0, 0, 1))
```

--------------------------------

### Example spatial_Ms TCL function

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.oommf.html

Example of a spatial_Ms function that returns 2e4 inside a circular region and 0 elsewhere. This is passed as a string to the spatial_Ms parameter.

```tcl
spatial_Ms = """
if { $x * $x + $y * $y < 5e-9 * 5e-9 } {
    return 2e4
} else {
    return 0
}
"""

```

--------------------------------

### ExchangeRKKY.setup(mesh, spin, Ms, Ms_inv)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.exchange_rkky.html

Sets up the energy term with the mesh, spin, and saturation magnetization data. This method is called during initialization to prepare the term for computation.

```APIDOC
## ExchangeRKKY.setup(mesh, spin, Ms, Ms_inv)

### Description
Sets up the energy term with the mesh, spin, and saturation magnetization data. This method is called during initialization to prepare the term for computation.

### Parameters
- **mesh** (Mesh) - The mesh object defining the simulation geometry.
- **spin** (array-like) - The initial spin configuration.
- **Ms** (array-like) - Saturation magnetization values.
- **Ms_inv** (array-like) - Inverse saturation magnetization values.

### Returns
- None
```

--------------------------------

### LLG_STT_CPP.get_p()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.llg_stt_cpp.html

Method to get the polarization p.

```APIDOC
## LLG_STT_CPP.get_p()

### Description
Returns the polarization p.

### Returns
- The value of p.
```

--------------------------------

### LLG_STT_CPP.get_a_J()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.llg_stt_cpp.html

Method to get the current density a_J.

```APIDOC
## LLG_STT_CPP.get_a_J()

### Description
Method to get the current density a_J.

### Method
Getter

### Signature
get_a_J()

### Returns
The current density a_J.
```

--------------------------------

### SimBase.get_alpha(alpha)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.common.sim_base.html

Gets the damping parameter alpha.

```APIDOC
## SimBase.get_alpha(alpha)

### Description
Gets the damping parameter alpha.

### Parameters
- **alpha** - Required - The alpha value to get.

### Returns
The alpha value.
```

--------------------------------

### DMI.setup(mesh, spin, mu_s, mu_s_inv)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.dmi.html

Sets up the DMI interaction with the given mesh, spin, and magnetic moment parameters.

```APIDOC
## DMI.setup(mesh, spin, mu_s, mu_s_inv)

### Description
Initializes the DMI interaction with the simulation mesh and spin configuration.

### Parameters
- **mesh** (Mesh) - Required - The simulation mesh.
- **spin** (array) - Required - Spin configuration.
- **mu_s** (array) - Required - Saturation magnetic moments.
- **mu_s_inv** (array) - Required - Inverse saturation magnetic moments.

### Returns
None.
```

--------------------------------

### LLG_STT_CPP.p

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.llg_stt_cpp.html

Property to get or set the spin polarization p.

```APIDOC
## LLG_STT_CPP.p

### Description
Property to get or set the spin polarization p.

### Method
Property getter and setter

### Getter
Returns the spin polarization p.

### Setter
Sets the spin polarization p.

### Parameters (Setter)
- **value** - Required - The new value for p.
```

--------------------------------

### Exchange.setup(mesh, spin, mu_s, mu_s_inv)

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/atomistic/exchange.html

Sets up the exchange interaction for a given mesh, spin, and magnetic moments. It determines the appropriate computation method based on the type of J provided: uniform, spatial, or full exchange calculation.

```APIDOC
## Exchange.setup(mesh, spin, mu_s, mu_s_inv)

### Description
Sets up the exchange interaction energy term for the given mesh and spin configuration. Based on the type of J provided, it selects the appropriate computation method: uniform exchange for scalar J, spatial exchange for callable J, or full exchange for a list of shell constants.

### Parameters
- **mesh** (Mesh) - Required - The mesh object defining the lattice structure.
- **spin** (array) - Required - The spin configuration.
- **mu_s** (array) - Required - The magnetic moment magnitudes.
- **mu_s_inv** (array) - Required - The inverse magnetic moment magnitudes.

### Behavior
- If J is a float or int, it sets Jx, Jy, Jz to the same value and uses `compute_field_uniform`.
- If J is callable, it evaluates the function at each lattice site to build a spatial exchange tensor and uses `compute_field_spatial`.
- If J is a list or numpy array with length equal to the number of neighbour shells, it stores the shell constants and uses `compute_field_full`.

### Notes
- The spatial function must return either a float/int or a list/array/tuple of length 6. Otherwise, an exception is raised.
- The number of shells should not be larger than 8 (checked in the mesh class).
```

--------------------------------

### LLG_STT_CPP.a_J

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.llg_stt_cpp.html

Property to get or set the current density a_J.

```APIDOC
## LLG_STT_CPP.a_J

### Description
Property to get or set the current density a_J.

### Method
Property getter and setter

### Getter
Returns the current density a_J.

### Setter
Sets the current density a_J.

### Parameters (Setter)
- **value** - Required - The new value for a_J.
- **args** - Optional - Additional arguments.
```

--------------------------------

### LLG_STT_CPP.get_a_J()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.llg_stt_cpp.html

Method to get the spin torque coefficient a_J.

```APIDOC
## LLG_STT_CPP.get_a_J()

### Description
Returns the spin torque coefficient a_J.

### Returns
- The value of a_J.
```

--------------------------------

### DMI.setup(mesh, spin, Ms, Ms_inv)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.dmi.html

Sets up the DMI interaction with the given mesh, spin, and saturation magnetization values. This method initializes necessary internal data.

```APIDOC
## DMI.setup(mesh, spin, Ms, Ms_inv)

### Description
Sets up the DMI interaction with the provided mesh and spin configuration.

### Parameters
- **mesh** (Mesh) - Required - The mesh object.
- **spin** (array) - Required - The spin configuration.
- **Ms** (float) - Required - Saturation magnetization.
- **Ms_inv** (float) - Required - Inverse saturation magnetization.
```

--------------------------------

### Create environment and build C/C++ modules

Source: https://fidimag.readthedocs.io/en/latest/_sources/install.rst.txt

Creates the Python environment and builds the C/C++ modules in editable mode.

```bash
uv sync
```

--------------------------------

### LLG_STT.get_jz()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.llg_stt.html

Method to get the jz component of the LLG_STT driver.

```APIDOC
## LLG_STT.get_jz()

### Description
Method to get the jz component of the LLG_STT driver.

### Signature
LLG_STT.get_jz()
```

--------------------------------

### LLG_STT.get_jy()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.llg_stt.html

Method to get the jy component of the LLG_STT driver.

```APIDOC
## LLG_STT.get_jy()

### Description
Method to get the jy component of the LLG_STT driver.

### Signature
LLG_STT.get_jy()
```

--------------------------------

### Configure Simulation and Initial State

Source: https://fidimag.readthedocs.io/en/latest/user_guide/ipynb/hubert_minimiser_atomistic.html

Initialize the simulation with the Hubert minimiser, set physical parameters, and define the initial magnetisation state.

```python
sim = fidimag.micro.Sim(mesh, name='1Dmicro', driver='hubert_minimiser')

Ms = 0.86e6
A = 13e-12
Ku = 0.4e6

# Define the magnetisation
sim.set_Ms(Ms)

# Add the magnetic interactions
sim.add(fidimag.micro.UniformExchange(A))
sim.add(fidimag.micro.UniaxialAnisotropy(Ku, axis=(0, 0, 1)))
# sim.add(fidimag.atomistic.DMI(D, dmi_type='interfacial'))
# sim.add(fidimag.micro.Zeeman((0, 0, B)))

xs = mesh.coordinates[:, 0]
centre_x = (xs.max() + xs.min()) * 0.5 + xs.min()

def m_initial(r):
    x, y, z = r[0], r[1], r[2]
    if x < centre_x:
        return (0, 0.1, -.9)
    else:
        return (0, 0.1, .9)

# sim.set_m((0.1, 0, 0.9))
sim.set_m(m_initial)

mesh_vol = mesh.n * mesh.dx * mesh.dy * mesh.dz * 1e-27
Kd = C.mu_0 * (Ms ** 2) * 0.5 * mesh_vol
sim.driver.energyScale = Kd
```

--------------------------------

### LLG_STT.get_jx()

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.llg_stt.html

Method to get the jx component of the LLG_STT driver.

```APIDOC
## LLG_STT.get_jx()

### Description
Method to get the jx component of the LLG_STT driver.

### Signature
LLG_STT.get_jx()
```

--------------------------------

### Set up simulation mesh and parameters

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/Simulating%20an%20Anisotropic%20Grain%20Structure.ipynb.txt

Defines material parameters (A, Ms), mesh dimensions (n=40, d=5), creates a CuboidMesh with periodic boundary conditions in x and y, and initializes a micromagnetic simulation with damping alpha=1.0.

```python
A=1.3e-11
Ms=8.6e5
n = 40
d = 5

mesh = fidimag.common.CuboidMesh(nx=n, ny=n, nz=1, dx=d, dy=d, dz=d, unit_length=1e-9, periodicity=(True, True, False))
sim = fidimag.micro.Sim(mesh, name="Grains")
sim.alpha = 1.0
```

--------------------------------

### MonteCarlo.mu_s (property)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.monte_carlo.html

Property that gets or sets the saturation magnetic moment.

```APIDOC
## MonteCarlo.mu_s (property)

### Description
Property for accessing the saturation magnetic moment (mu_s).

### Getter
Returns the current mu_s value.

### Setter
Sets the mu_s value.
```

--------------------------------

### Get Saturation Magnetization

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/micro/sim.html

Method to retrieve the saturation magnetization array.

```python
def get_Ms(self):
    """
    Returns the array with the saturation magnetisation values per
    mesh site
    """
    return self._Ms
```

--------------------------------

### Vector field reshaping example for vector2cuboid

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.atomistic.demag_hexagonal.html

Example showing how a vector field array is reshaped from a 1D array into a 3D matrix with shape (ny, nx, 3) for a 2x3 system. The cuboid version doubles the number of columns, resulting in a (ny, 2*nx, 3) matrix.

```text
Original: vector_field = [ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10,
                           11, 12, 13, 14, 15, 16, 17]

Reshaped: [ [ [ 0,  1,  2], [ 3,  4,  5] ],
            [ [ 6,  7,  8], [ 9, 10, 11] ],
            [ [12, 13, 14], [15, 16, 17] ]
          ]

      So we have 2 sites per row,as the original system, where
      a 3-vector is associated to each entry, making a
      (2, 3, 3) matrix --> (ny, nx, 3) in general

      Thus, for the cuboid version, we would have the double
      of columns, i.e. a (ny, 2 * nx, 3) matrix and copy
      the elements as in the scalar field
```

--------------------------------

### fidimag.micro.oommf.setup_logger

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.micro.oommf.html

Set up the logger for the OOMMF module.

```APIDOC
# fidimag.micro.oommf.setup_logger

## Parameters
`setup_logger()`

## Description
Initialise the logging system for this module. No parameters required.

```

--------------------------------

### Test import Fidimag

Source: https://fidimag.readthedocs.io/en/latest/_sources/install.rst.txt

Runs a Python command to verify the Fidimag installation.

```bash
uv run python -c "import fidimag"
```

--------------------------------

### Initialize simulation object

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/standard_problem_4.ipynb.txt

Create the simulation object, set tolerances, and add energy terms for the relaxation stage.

```python
from fidimag.micro import Sim, UniformExchange, Demag, Zeeman, TimeZeeman

sim = Sim(mesh)  # create simulation object

sim.driver.set_tols(rtol=1e-10, atol=1e-10)
sim.Ms = Ms
sim.driver.alpha = 0.5  # large value since the magnetisation dynamics is not important in the relexation stage
sim.driver.gamma = gamma
sim.driver.do_precession = False  # speeds up the simulation


# Starting magnetisation.
sim.set_m((1, 0.25, 0.1))
sim.add(UniformExchange(A=A))
sim.add(Demag())
```

--------------------------------

### 1D Domain Wall Simulation with Fidimag

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/1d_domain_wall.ipynb.txt

This example demonstrates how to set up and relax a one-dimensional domain wall using Fidimag. It defines a 1D mesh, a material with given parameters, an initial magnetisation profile, and then relaxes the system. The final magnetisation profile is plotted.

```python
import fidimag
import numpy as np
import matplotlib.pyplot as plt

# Define a one-dimensional mesh with 100 cells and a cell size of 1 nm.
mesh = fidimag.common.Mesh(nx=100, ny=1, nz=1, dx=1.0, dy=1.0, dz=1.0)

# Define a material with saturation magnetisation Ms = 1e6 A/m and exchange constant A = 1e-11 J/m.
material = fidimag.common.Material(mesh)
material.Ms = 1e6
material.A = 1e-11

# Define a one-dimensional domain wall initial magnetisation.
def m_init(pos):
    x, y, z = pos
    if x < 50:
        return (0, 0, 1)
    else:
        return (0, 0, -1)

# Create a simulation object.
sim = fidimag.micro.Sim(mesh, material)
sim.set_m(m_init)

# Relax the system to its equilibrium state.
sim.driver.relax(dt=1e-13, stopping_dmdt=0.01, max_steps=5000, save_m_steps=None, save_vtk_steps=None)

# Plot the magnetisation profile.
plt.plot(sim.m[0], label='mx')
plt.plot(sim.m[1], label='my')
plt.plot(sim.m[2], label='mz')
plt.legend()
plt.show()
```

--------------------------------

### SimBase.pins (property)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.common.sim_base.html

Property that gets or sets the array with pinned spins in the sample.

```APIDOC
## SimBase.pins (property)

### Description
Property that gets or sets the array with pinned spins in the sample.

### Returns
The array with pinned spins.
```

--------------------------------

### SimBase.alpha (property)

Source: https://fidimag.readthedocs.io/en/latest/api/generated/fidimag.common.sim_base.html

Property that gets or sets the damping parameter alpha for the simulation.

```APIDOC
## SimBase.alpha (property)

### Description
Property that gets or sets the damping parameter alpha for the simulation.

### Returns
The current value of alpha.
```

--------------------------------

### Set OOMMF path

Source: https://fidimag.readthedocs.io/en/latest/_sources/install.rst.txt

Sets the environment variable pointing to the OOMMF installation directory.

```bash
export OOMMF_PATH=/path/to/folder/containing/OOMMF
```

--------------------------------

### Set up simulation with anisotropy, exchange, and demag

Source: https://fidimag.readthedocs.io/en/latest/_sources/user_guide/ipynb/Simulating%20an%20Anisotropic%20Grain%20Structure.ipynb.txt

Initializes the magnetization along +z, sets saturation magnetization, adds a UniaxialAnisotropy with the grain-dependent functions, adds UniformExchange and Demag (with 2D periodic boundary conditions) to the simulation.

```python
sim.set_m((0, 0, 1), normalise=True)

sim.set_Ms(Ms)
anisotropy = fidimag.micro.UniaxialAnisotropy(K_mag, K_axis)
sim.add(anisotropy)
sim.add(fidimag.micro.UniformExchange(A))
sim.add(fidimag.micro.Demag(pbc_2d=True))
```

--------------------------------

### Defining a spatial current function

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/micro/llg_stt.html

Example of a function definition for spatial current dependency.

```python
def myfunc_x(pos):
    x, y, z = pos
    jx = # some function of x, y, and z.
    return jx
```

--------------------------------

### Setting constant current

Source: https://fidimag.readthedocs.io/en/latest/_modules/fidimag/micro/llg_stt.html

Example of setting constant current components for the LLG_STT driver.

```python
driver.jx = 1.0
driver.jy = 0.0
driver.jz = 0.0
```