Important Notes

==================================================

Important Notes

Not an official repository:
- This repository is not the official mumax3 repository. The official repository can be found here.
- This repository is not the official mumax3-ME repository. The official repository can be found here.
- This repository is not the official amumax repository. The official repository can be found here.

==================================================

Overview

This repository contains an extended version of Mumax3-ME. The web interface is taken from the amumax repository.
The functions have been mainly tested for researching vortices in magnetic systems. Below are the key extensions and commands.

==================================================

Extended Extraction Variables

Space-resolved Variables (ovf files)

F_melM: Force from the elastic system onto the magnetic system
F_el: Elastic force within the elastic PDE
F_elsys: Reformulation of the elastic PDE such that one side is zero (the side that must be zero)
rhod2udt2: Force of the elastic PDE resulting from the acceleration of displacement
etadudt: Damping force of the elastic PDE resulting from the velocity of displacement
GradMx, GradMy, GradMz: Gradients of the x, y, and z components of the magnetization
ddu: Acceleration of displacement

Space-independent Variables (Table)

CorePosR: Radius to the core position of the vortex

==================================================

Commands for Vortex Functions

VortexAsym: Creates a deformed vortex
Args: int (circulation), int (polarity), float (scaling factor for the FWHM of the out-of-plane Gaussian), float (angle for FWHM change), float (angle defining the width until the FWHM returns to its usual value)
DisplacedVortex: A vortex displaced from the center
Args: int (circulation), int (polarity), float (deltaX), float (deltaY)
DisplacedVortexAsym: A deformed and displaced vortex
Args: int (circulation), int (polarity), float (deltaX), float (deltaY), float (FWHM scaling), float (angle for FWHM change), float (angle defining the width until the FWHM returns to its usual value)
Activate_corePosScriptAccess: Uses the vortex's core position for runWhile methods within the mumax script
- Note: The variable CorePosRT corresponds to this function.
Activate_corePosScriptAccessR: Uses the radius to the core position (from the center) for runWhile methods within the mumax script
- Note: The variable CorePosRTR corresponds to this function.

==================================================

Commands for Loading Data

LoadFileWithoutMem: Loads an ovf file into a variable without memory allocation (needed for strain).
Args: Quantity and file path.
Note: Available for normStrain, shearStrain, normStress, and shearStress.
Best practice: Set all dependencies to zero (see SetQuantityWithoutMemToConfig).
SetQuantityWithoutMemToConfig: Sets a quantity without allocated memory to a configuration (e.g., Uniform(...)).
Args: Quantity and config.
LoadFileVector: Assigns a vector variable with memory using an '='; e.g.,
```
LoadFileVector("path_to_file")
```
Comment: Loading strains is experimental – if you want to use the strain as an initial state, activate loading for one step only, otherwise the newly calculated displacement will not be properly considered.

==================================================

Commands for Saving Data

SaveAsAt: Saves a quantity as an ovf file with a specific name at a provided path.
Args: Quantity, filename, path (string).
AutoSaveAs: Autosaves a quantity and relabels the file.
Args: Quantity, dt (float), and name (string).
AutoSnapshotAs: Similar to AutoSaveAs, but for snapshots.
Args: Quantity, dt (float), and name (string).
ignoreCropName: Set to true to disable automatic range labeling of ovf files when a cropped quantity is saved.
File Numbering Commands:
These commands set the numbering of the ovf files (e.g., if a simulation is to be continued):
- SetAutoNumTo
- SetAutoNumPrefixTo
- SetAutoNumSnapshotTo
- SetAutoNumSnapshotPrefixTo
- SetAutoNumToAs
- SetAutoNumPrefixToAs
- SetAutoNumSnapshotToAs
- SetAutoNumSnapshotPrefixToAs
  All commands require an integer argument.
createNewTable: Set to false to continue the existing table.txt instead of overwriting it.
rewriteHeaderTable: Set to true to append the table header to table.txt if it is continued.

==================================================

Commands for File Checking and Management

IsFile: Checks if a file exists at the given path.
Args: path_to_file (string)
IsFileMyDir: Checks if a file exists in the current mumax directory.
Args: filename (string)
EraseOD: Deletes all files in the current mumax directory.
GSDIR: Since mumax3 does not allow strings in the script by default, this variable can be assigned the path to a folder where ground states are stored. In combination with Suffix and ConcStr, complex ground state ovf files can be stored using schematic names.
Suffix: See GSDIR.

ConcStr: Concatenates as many strings as desired.
Args: strings (string)
Example for GS:

GSDir = "/home/test/GS/"
Suffix = "_GS_3mTX_Vortex_512_512_256_256_eta_300_CoFeB.ovf"
if IsFile(ConcStr(GSDir, ConcStr("m", Suffix))) && IsFile(ConcStr(GSDir, ConcStr("u", Suffix))) && IsFile(ConcStr(GSDir, ConcStr("du", Suffix))) {
      m.LoadFile(ConcStr(GSDir, ConcStr("m", Suffix)))
      u.LoadFile(ConcStr(GSDir, ConcStr("u", Suffix)))
      du = Uniform(0, 0, 0)
} else {
      B_ext = Vector(0, 0.003, 0)
      RelaxFullCoupled = true
      Relax()
      SaveAsAt(m, ConcStr("m", Suffix), GSDir)
      SaveAsAt(u, ConcStr("u", Suffix), GSDir)
      SaveAsAt(du, ConcStr("du", Suffix), GSDir)
      B_ext = Vector(0, 0, 0)
      du = Uniform(0, 0, 0)
}

==================================================

Commands for Fully Elastically Coupled Systems

useBoundaries: Activates boundaries for the elastic system.
AllowInhomogeniousMECoupling: Deactivates the blocking of inhomogeneous B1 and B2 values.

==================================================

Other Useful Commands

RotVector: Rotates a vector around another vector b by an angle c.
Args: b, c (vector)
IDT: Generates a one-sided IDT.
Args: IDTWidthFinger, IDTDistanceFinger, IDTFingerLength (float64), AmountFingers (int)
WriteNUndoneToLog: Writes the number of reversed steps to the log.
absPath: Defines the absolute path to the simulation folder without the folder itself – used in ExecDir.
Exec: Executes a bash command.
Args: cmd (string)
ExecDir: Executes a bash command but appends the absolute path to the output directory as an argument, or replaces all occurrences of %v and %s with the path.
Example:
```
ExecDir("python3 foo.py %v/fee %s/faa")
```
-> Executes:
```
Exec("python3 foo.py path_to_outputdir/fee path_to_outputdir/faa")
```
ExecSweep: Executes a bash command after finishing a sweep from a template- Args: cmd (string)
ExecSweepDir: Executes a bash command after sweep from a template but appends the absolute path to the output directory as an argument, or replaces all occurrences of %v and %s with the path. Args: cmd (string)
string: Casts a float or int to a string.
Args: interface
int: Casts a value to an integer.
Args: value (float)

==================================================

Commands for Relaxation

outputRelax: Set to true to extract ovf files and table data during relaxation (depending on AutoSave etc.).
The files will have a prefix (modifiable with prefix_relax) to avoid conflicts with time evolution.
RelaxFullCoupled: Set to true to relax the fully coupled system (requires FixDt).
useHighEta: Sets eta homogeneously to 1e6 during relaxation (requires RelaxFullCoupled = true).
__printSlope__: Prints the slope or the value of the variable being minimized (requires RelaxFullCoupled = true).
SlopeTresholdEnergyRelax: Threshold from which it can be assumed that the energy slope (over time) is zero (default is 1e-12; may vary depending on the system, requires RelaxFullCoupled = true).
RelaxDDUThreshold: Similar to RelaxTorqueThreshold but for the second derivative in time of displacement (requires RelaxFullCoupled = true).
RelaxDUThreshold: Similar to RelaxTorqueThreshold but for the first derivative in time of displacement (requires RelaxFullCoupled = true).
IterativeHalfing: Runs the minimization process N times and halves FixDt as well as the thresholds (SlopeTresholdEnergyRelax, RelaxDDUThreshold, RelaxDUThreshold) each time (requires RelaxFullCoupled = true).

==================================================

Commands for Defining Regions

homogeniousRegionZ: When set to true, defines a region for only one z-layer and copies it to the other layers.
LimitRenderRegionX: Limits the area in x where rendering is performed.
Args: from, to (int, in cells)
LimitRenderRegionY: Similar to x, but for y.
Args: from, to (int, in cells)
LimitRenderRegionZ: Similar to x, but for z.
Args: from, to (int, in cells)
ReDefRegion: Reassigns cells of one region to a different one (0 to remove the region).
Args: oldRegion, newRegion (int)
EraseAllRegions: Erases all regions – resets all cells to region 0 (more efficient than redefining each region separately).

==================================================

Commands for expanding Quantities

Expand: Expands the array of a quantity and fills the new created entries with constant (default 0). Args: q (Quantity), fromX, toX, fromY, toY, fromZ, toZ, shiftX, shiftY, shiftZ (int, in cells), value to set for the expanded area (optional, can be set componentwise, but does not have to. Default is 0. float)
ExpandX: Same as Expand but only for x dimension Args: q (Quantity), fromX, toX, shiftX (int, in cells), value to set for the expanded area (optional, can be set componentwise, but does not have to. Default is 0. float)
ExpandY: Same as Expand but only for y dimension Args: q (Quantity), fromY, toY, shiftY (int, in cells), value to set for the expanded area (optional, can be set componentwise, but does not have to. Default is 0. float)
ExpandZ Same as Expand but only for z dimension Args: q (Quantity), fromZ, toZ, shiftZ (int, in cells), value to set for the expanded area (optional, can be set componentwise, but does not have to. Default is 0. float)

==================================================

Commands for generating Operators

Crop

CropOperator: Returns a function with the cropping area being defined already but the quantity missing. Args: fromX, toX, fromY, toY, fromZ, toZ (int, in cells)
CropXOperator: Same as CropOperator but only for x dimension Args: fromX, toX (int, in cells)
CropYOperator: Same as CropOperator but only for y dimension Args: fromY, toY (int, in cells)
CropZOperator: Same as CropOperator but only for z dimension Args: fromZ, toZ (int, in cells)

Expand

ExpandOperator: Returns a function with the expanding area being defined already but the quantity missing: Args: fromX, toX, fromY, toY, fromZ, toZ, shiftX, shiftY, shiftZ (int, in cells), value to set for the expanded area (optional, can be set componentwise, but does not have to. Default is 0. float)
ExpandXOperator: Same as ExpandOperator but only for x dimension Args: fromX, toX, shiftX (int, in cells), value to set for the expanded area (optional, can be set componentwise, but does not have to. Default is 0. float)
ExpandYOperator: Same as ExpandOperator but only for y dimension Args: fromY, toY, shiftY (int, in cells), value to set for the expanded area (optional, can be set componentwise, but does not have to. Default is 0. float)
ExpandZOperator: Same as ExpandOperator but only for z dimension Args: fromZ, toZ, shiftZ (int, in cells), value to set for the expanded area (optional, can be set componentwise, but does not have to. Default is 0. float)

Example

operator := CropXOperator(0, 32)
Save(operator(m))
Save(operator(B_ext))

==================================================

FFT Functions

FFT3D

FFT3D: Computes a 3D FFT (x, y, z) and, for example, saves it to an ovf file.
When this command is run, the real and imaginary parts of the FFT are visible in the Web UI.
Methods on the result:
- .Abs() – Length of the complex FFT value
- .Phi() – Angle of the complex FFT value
- .ToPolar() – Exports length and angle alternately along x (saves computation time if .Abs() and .Phi() are not called separately)
- .Real() and .Imag()
Example:
```
Save(FFT3D(m).Abs())
```

FFT4D / FFT_T

FFT4D / FFT_T:
- FFT4D: Computes a 3D FFT (x, y, z) and performs an incremental Fourier transform in time. Args: q Quantity, period float
- FFT_T: Performs a Fourier transform in time only (using real-space data). Args: q Quantity, period float
- FFT_T_IN_MEM – if set to false, required data is stored continuously in ovf files (lower GPU memory consumption but slower)
- minFrequency, maxFrequency, dFrequency (floats)
- FFT4D_Label – a string to use instead of the quantity name
- negativeKx - set to false to not get negtative kx values
- operatorsKSpace - fuse as many operators (e.g. ExpandOperator or CropOperator) as wished together with MergeOperators(...) and assign the result to this variable to crop or expand the k-space before performing the fouriertransform in time Example:
```
operatorsKSpace = MergeOperators(CropXOperator(0, 64), ExpandXOperator(0, 128, -32)) //only consider everything in the area from x = 0 to x = 64, and then expand to the right side
```
- interpolate - set to true - interpolate between time steps for fouriertransform - need when FixDt not set or the calculation period not a multiple from the calculation period (experimental)
- Methods on the result: .SaveAbs(), .SavePhi(), .ToPolar()
Examples:
```
FFT4D(m, 10e-10).SaveAbs().SavePhi()  //10e-10 is the calculation period - like in AutoSave, but for incremental updating fouriertransform data in time. Saves Length and Angle of complex number in distincted ovf files
FFT4D(m, 10e-10).ToPolar() //saves complex number in polar form in single ovf file
FFT4D(m, 10e-10) //saves complex number in single ovf file
```

Note: The FFT4D code creates twice as many values for kx to hold the imaginary and real parts.
It can be imported into xarray using mumaxXR. Please do not mix non-FFT data with FFT data.

==================================================

RenderFunctions

RenderFunction: Converts a string into a function (using CreateFunction(...)) and renders it as a scalar excitation or parameter (excluding exchange and DMI).
Available variables: All variables defined in the script and standard mathematical functions in mumax3.
x, y, and z are coordinates in the mesh, and t is replaced with the current simulation time.
Important: Do not use the internally used variables (x_factor, y_factor, z_factor, x_length, y_length, and z_length).
Args: StringFunction
Examples:
```
B_ext.RenderFunction(CreateFunction("", "amplitude*1e7*sin(2*pi*t*freq*1e6)", ""))
exx.RenderFunction(CreateFunction("amplitude*1e7*sin(2*pi*t*freqElastic*1e6)"))
```
RenderFunctionLimit: Same as RenderFunction, but spatially limited (mesh still starts at 0 for x, y, z).
Args: StringFunction, startX (int), endX (int), startY (int), endY (int), startZ (int), endZ (int)

RenderFunctionLimitX / LimitY / LimitZ:
Similar functions that limit only in x, y, or z respectively.
Example:

alpha.RenderFunctionLimitX(CreateFunction("alphaLow+(alphaHigh-alphaLow)*tanh((128*dx-x)/(128*dx))"), 0, 128)

RenderFunctionShape: Same es RenderFunction, but the shape, given as an argument is layed over the result, of the individual function and is being merged with prior defintions. Args: StringFunction, Shape

==================================================

Queue

When a queue is started in mumax, it cannot be paused by default. An environment variable "MumaxQueue_%d" is created (with %d being the queue index if multiple queues are running).

Queue Control:
- When the queue starts, the environment variable is set to "running".
- Setting this environment variable to "pause" prevents new simulations from starting until it is set back to "running".
- Removing the environment variable resumes the queue.

==================================================

Template Strings

The following section originates from the amumax repository and has been slightly modified.

Syntax

Template strings are placeholders within your .mx3 files that define how parameters should vary across generated files.
The syntax is:

"{key1=value1;key2=value2;...}"

Each template string is enclosed in quotes and curly braces and contains key-value pairs separated by semicolons.

Available Keys

array: Define a specific set of values
Example: array=[1,2,3]
start, end, step: Define a range of values (similar to numpy.arange)
Example: start=0;end=1;step=0.1
start, end, count: Define a range of values with a specific count (similar to numpy.linspace)
Example: start=0;end=1;count=5
prefix: A string to be added before the value in the generated filenames
Example: prefix=param_
suffix: A string to be added after the value in the generated filenames
Example: suffix=_test
format: Specifies the formatting of the value in the filename (must be a float format like %f)
Example: format=%.2f

Examples

Example 1: Varying a Single Parameter

Template File (template.mx3):

Aex := "{start=0;end=2;step=1}"

Command:

mumax3 --template template1.mx3 template2.mx3 template3.mx3

Generated Files:

0.mx3
1.mx3
2.mx3

Explanation: The placeholder {start=0;end=2;step=1} is replaced with values from 0 to 2 in steps of 1, generating a new .mx3 file for each value.

Example 2: Using an Array of Values and Formatting

Template File (template.mx3):

x := "{array=[1,2,3];format=%02.0f}"

Command:

mumax3 --template template.mx3

Generated Files:

01.mx3
02.mx3
03.mx3

Explanation: The placeholder is replaced with the values from the array, and format=%02.0f ensures that the values in the filenames are formatted with at least two digits (padded with zeros if necessary).

Example 3: Combining Multiple Template Strings

Template File (template.mx3):

x := "{prefix=alpha; array=[1,2];format=%02.0f}"
y := "{prefix=beta; array=[3,4];format=%.0f}"

Command:

mumax3 --template template.mx3

Generated Files:

alpha01/beta3.mx3
alpha01/beta4.mx3
alpha02/beta3.mx3
alpha02/beta4.mx3

Explanation: All combinations of x and y values are generated. Each combination results in a new .mx3 file with the corresponding values.

Example 4: Using Flat Output

Template File (template.mx3):

x := "{array=[1,2];format=%02.0f}"
y := "{array=[3,4];format=%.0f}"

Command:

mumax --template --flat template.mx3

Generated Files:

013.mx3
014.mx3
023.mx3
024.mx3

Explanation: The --flat option generates files without creating subdirectories. The filenames are concatenated with the formatted values.

Example 5: Using Prefix and Suffix

Template File (template.mx3):

Temperature := "{prefix=T; array=[300,350]; suffix=K; format=%.0f}"

Command:

mumax3 --template template.mx3

Generated Files:

T300K.mx3
T350K.mx3

Explanation: The keys prefix and suffix add strings before and after the value in the filename, with format=%.0f ensuring no decimal places.

Notes

Formatting: Only %f float formats (e.g., %.2f, %03.0f) are allowed. Formats like %d are not permitted.
Error Handling: The template parser will report errors if the syntax is incorrect or required keys are missing.
Variable Replacement: Within the .mx3 files, placeholders are replaced with numerical values.

Advanced Example

Template File (template.mx3):

alpha := "{prefix=alpha_; array=[0.01, 0.02, 0.03]; format=%.2f}"
beta := "{prefix=beta_; start=0.1; end=0.3; step=0.1; format=%.1f}"

Command:

mumax3 --template template.mx3

Generated Files (excerpt):

alpha_0.01/beta_0.1.mx3
alpha_0.01/beta_0.2.mx3
alpha_0.01/beta_0.3.mx3
alpha_0.02/beta_0.1.mx3
...

Explanation: Generates all combinations of alpha and beta values. Each generated file contains the corresponding replaced values.

==================================================

Final Note

This README provides a comprehensive overview of the extended functions, commands, and template strings in this repository. For questions or issues, please refer to the respective official repositories or the documentation of the individual functions.

Happy simulating!

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bench		bench
cmd		cmd
cuda		cuda
data		data
deploy		deploy
doc		doc
draw		draw
dump		dump
engine		engine
freetype		freetype
frontend		frontend
goptuna		goptuna
govaluate		govaluate
gui		gui
httpfs		httpfs
logUI		logUI
mag		mag
odeint		odeint
oommf		oommf
script		script
svgo		svgo
test		test
timer		timer
util		util
.gitattributes		.gitattributes
.gitignore		.gitignore
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
go.mod		go.mod
go.sum		go.sum
post-commit		post-commit
pre-commit		pre-commit
testfrontend		testfrontend

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timvgl/Mumax3Mod

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Important Notes

Overview

Extended Extraction Variables

Space-resolved Variables (ovf files)

Space-independent Variables (Table)

Commands for Vortex Functions

Commands for Loading Data

Commands for Saving Data

Commands for File Checking and Management

Commands for Fully Elastically Coupled Systems

Other Useful Commands

Commands for Relaxation

Commands for Defining Regions

Commands for expanding Quantities

Commands for generating Operators

Crop

Expand

FFT Functions

FFT3D

FFT4D / FFT_T

RenderFunctions

Queue

Template Strings

Syntax

Available Keys

Examples

Example 1: Varying a Single Parameter

Example 2: Using an Array of Values and Formatting

Example 3: Combining Multiple Template Strings

Example 4: Using Flat Output

Example 5: Using Prefix and Suffix

Notes

Advanced Example

Final Note

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