FunMaP: Functional Magnetic Particles analysis pipeline for FePt thin films on spherical SiO₂ substrates
Natalia Gonzalez-Vazquez · Andrew K. Schulz
A thesis-linked (soon to be pre-printed) research repository for micromagnetic simulations, SQUID magnetometry analysis, and XRD visualisation of FePt thin films on spherical SiO₂ substrates.
This repository contains three independent Python-based modules developed for the characterisation of FePt thin films on spherical SiO₂ substrates. Together they provide the full computational workflow for micromagnetic simulations, XRD visualisation, and SQUID magnetometry analysis presented in the associated thesis and manuscript.
- Part 1: Micromagnetic simulations of hemispherical FePt caps (ubermag/OOMMF)
- Part 2: Automated visualisation of X-ray diffraction (XRD) data
- Part 3: SQUID magnetometry analysis and SQUID–simulation comparison
Each module is self-contained but designed to function within a unified research workflow.
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FunMaP/
│
├── analysis/ # Experimental data analysis
│ ├── SQUID_analysis_Caps.ipynb # Batch averaging & background correction
│ ├── SQUID-OOMMF-analysis.ipynb # SQUID vs simulation overlay
│ ├── OOMMF-analysis.ipynb # Simulation hysteresis + SFD plots
│ └── XRDplot.ipynb # XRD masked/naked plotting
│
├── simulations/ # Micromagnetic simulation scripts
│ ├── FePt_L10_A1_MultipleCaps_HystLoop_radial_merged.ipynb
│ └── FePt_L10_MultipleCaps_HystLoop_DiameterSweep.ipynb
│
├── sample_data/ # Synthetic demo data (not real measurements)
│ ├── squid/
│ │ ├── sample_3um_measurement_A.dat
│ │ └── sample_3um_measurement_B.dat
│ ├── simulations/
│ │ ├── data_sphere_1.0um_synthetic.csv
│ │ ├── data_sphere_3.0um_synthetic.csv
│ │ ├── data_sphere_5.0um_synthetic.csv
│ │ ├── data_sphere_8.0um_synthetic.csv
│ │ └── data_sphere_10.0um_synthetic.csv
│ └── xrd/
│ └── sample_FePt_SiO2_on_Si.xy
│
├── environment.yml # Conda environment (ubermag_env)
├── .gitignore
└── README.md
| Goal | Notebook | Main output |
|---|---|---|
| Run mixed-phase FePt cap simulations | simulations/FePt_L10_A1_MultipleCaps_HystLoop_radial_merged.ipynb |
Hysteresis data for multiple diameters and phase fractions |
| Run pure L1₀ diameter-sweep simulations | simulations/FePt_L10_MultipleCaps_HystLoop_DiameterSweep.ipynb |
Hysteresis data for pure L1₀ caps |
| Analyse SQUID batches | analysis/SQUID_analysis_Caps.ipynb |
Averaged loops, statistics, corrected plots, CSV export |
| Compare SQUID and simulation results | analysis/SQUID-OOMMF-analysis.ipynb |
Two-panel SQUID–simulation overlay |
| Analyse converted OOMMF simulation files | analysis/OOMMF-analysis.ipynb |
Overlay plots, SFD analysis, per-file reports |
| Plot XRD files | analysis/XRDplot.ipynb |
Publication-ready XRD PNG/SVG plots |
SQUID measurements (.dat)
│
▼
SQUID_analysis_Caps.ipynb
→ background correction (diamagnetic slope subtraction)
→ per-batch averaging + statistics (Hc, Mr/Ms, W_hyst)
→ Averaged_Data_{diam}um_{ts}.csv
│
└──────────────────────────────┐
▼
Simulations (ubermag/OOMMF) SQUID-OOMMF-analysis.ipynb
│ → overlay: SQUID mean vs sims
▼ → two-panel: raw A·m² / M/Msat
[Simulation scripts]
→ CONVERTED CSVs
(B_ext, Mz/Ms, Moment_Am2)
│
▼
OOMMF-analysis.ipynb
→ multi-file overlay plot
→ per-file hysteresis + SFD + report
XRD measurements (.xy)
│
▼
XRDplot.ipynb
→ masked / naked mode
→ reference markers: FePt, Si, SiO₂, Fe–O phases
This repository includes synthetic example files in sample_data/ for testing the plotting and analysis workflow without requiring access to unpublished experimental data.
| Folder | Contents |
|---|---|
sample_data/squid/ |
Demo SQUID-style .dat files (Quantum Design format) |
sample_data/simulations/ |
Synthetic converted simulation CSVs |
sample_data/xrd/ |
Example .xy diffractogram |
These files are intended only for workflow demonstration and code testing — they do not represent the original experimental datasets used in the thesis.
All scripts run in a single conda environment based on ubermag.
| Dependency | Version | Purpose |
|---|---|---|
| Python | ≥ 3.9 | Core execution |
| Ubermag | Latest stable | Micromagnetic simulation interface |
| OOMMF | ≥ 1.2 | Micromagnetic solver backend |
| NumPy | ≥ 1.20 | Numerical operations |
| pandas | ≥ 1.3 | Data I/O and tabulation |
| Matplotlib | ≥ 3.5 | Visualisation |
| scipy | ≥ 1.7 | Signal processing |
git clone https://github.com/nagova/FunMaP.git
cd FunMaP
conda env create -f environment.yml
conda activate ubermag_env
jupyter notebookVerify OOMMF is available:
oommf.tcl +versionAfter installation, open Jupyter Notebook inside the ubermag_env environment and choose the notebook matching your task:
- Run micromagnetic hysteresis simulations
simulations/FePt_L10_A1_MultipleCaps_HystLoop_radial_merged.ipynbsimulations/FePt_L10_MultipleCaps_HystLoop_DiameterSweep.ipynb
- Analyse SQUID measurements →
analysis/SQUID_analysis_Caps.ipynb - Compare SQUID data with simulations →
analysis/SQUID-OOMMF-analysis.ipynb - Plot XRD diffractograms →
analysis/XRDplot.ipynb - Analyse converted simulation files →
analysis/OOMMF-analysis.ipynb
Recommended order for first-time users:
- Create and activate the conda environment
- Verify OOMMF is available (
oommf.tcl +version) - Open Jupyter Notebook
- Start from the notebook matching your workflow goal
Click to expand
This module models the intrinsic magnetic switching behaviour of hemispherical FePt shells deposited on diamagnetic SiO₂ spheres. The SiO₂ substrate is treated as magnetically inactive (Ms = 0) and is excluded from the computational mesh.
The simulations explicitly account for:
- Curvature-dependent demagnetising effects
- Competition between exchange and magnetocrystalline anisotropy energies
- Phase composition (ordered L1₀ vs mixed L1₀/A1 FePt)
- Size-dependent discretisation for numerical convergence
FePt_L10_A1_MultipleCaps_HystLoop_radial_merged.ipynb
Hysteresis loops for diameters 1, 3, 5, 8, 10, 20 µm (60 nm cap). Mixed L1₀/A1 phase with radial anisotropy. Runtime prompts select temperature (MinDriver at 0 K / TimeDriver at T > 0 K). Supports checkpoint-based resume.
FePt_L10_MultipleCaps_HystLoop_DiameterSweep.ipynb
Same diameter sweep but pure L1₀ phase — no A1 soft fraction. Runtime prompts select temperature and anisotropy mode (Radial or Uniaxial_Vertical). Supports checkpoint-based resume.
Note on notation: Throughout this repository,
L10in file names and code refers to the L1₀ (L1-zero) ordered intermetallic phase of FePt.
| Parameter | Value | Units |
|---|---|---|
| Ms (saturation magnetisation) | 1 × 10⁶ | A/m |
| A (exchange stiffness) | 1 × 10⁻¹¹ | J/m |
| Ku (L1₀ hard phase) | 6.6 × 10⁶ | J/m³ |
| Ku (A1 soft phase) | 1 × 10⁴ | J/m³ |
| B_max (field sweep range) | ±18 | T |
| Cap thickness | 60 | nm |
| Sphere diameters | 1, 3, 5, 8, 10, 20 | µm |
- Single isolated hemispherical FePt cap; no inter-particle dipolar coupling
- Zero-temperature approximation for static driver (no thermal activation)
- Open boundary conditions; self-consistent magnetostatic field within the cap
- Homogeneous material parameters within each defined phase
Click to expand
Automated visualisation of Cu Kα XRD diffractograms of FePt films on SiO₂ sphere monolayers, enabling rapid structural phase assessment and L1₀ ordering evaluation.
- GUI file selector → one or more
.xyfiles - Terminal prompt: masked (apply angular masks) or naked (raw data)
- log₁₀ intensity axis by default (switchable to linear)
- Colour-coded vertical reference markers with (hkl) + 2θ labels in an external legend:
- FePt L1₀ — orange
- Si substrate — gray
- SiO₂ amorphous hump — blue
- Fe–O phases (magnetite / hematite / maghemite) — green (togglable)
- Angular masks configurable via
MASKSlist at the top of the script - Outputs: PNG (600 dpi) + SVG per file →
xrd_outputs/
Click to expand
This module bridges experimental SQUID magnetometry data and micromagnetic simulation results, enabling direct comparison between ensemble-averaged experimental hysteresis loops and single-cap simulated loops.
Processes raw SQUID .dat files (Quantum Design format) for a single particle batch.
- GUI file selector → ≥2
.datfiles per batch - Prompts: sphere diameter [µm], cap thickness [nm], substrate area [mm²]
- Optional diamagnetic background subtraction (slope fitted to ±95% saturation tails independently, then averaged)
- Averaging by branch (descending and ascending separately) → proper closed mean loop
- Extracts: Hc [T], Mr/Ms, hysteresis loss W_hyst [J/kg]
- Outputs: PNG + SVG two-panel plot,
.txtstatistical report, averaged CSV
Plot layout:
- Top panel: raw emu — individual curves + mean ± 1 SD
- Bottom panel: background-corrected M/Msat — individual curves + mean ± 1 SD
Averaged CSV columns: Field_T, M_norm_desc, M_norm_asc, M_emu_desc, M_emu_asc
Two-panel overlay of averaged SQUID data and simulation results.
- Step 1: select averaged SQUID CSV (output of
SQUID_analysis_Caps) - Step 2: select one or more CONVERTED simulation CSVs
- Outputs: PNG + SVG →
Comparison_Results_{ts}/
Plot layout:
- Top panel: physical moment [A·m²] — SQUID (emu → A·m² converted) + sim
Moment_Am2 - Bottom panel: normalised M/Msat — SQUID
M_norm+ simMz/Ms
Multi-file simulation overlay and per-file SFD analysis.
- GUI file selector → any number of CONVERTED simulation CSVs
- Terminal prompt: sphere diameter + cap thickness per file
- Outputs per session:
Overlay_{ts}.png/.svg— all files on one two-panel figure- Per-file
{name}_{ts}.png/.svg+_report.txt(Hc, Mr/Ms, SFD FWHM)
If you use this repository, please cite:
@misc{gonzalezvazquez_funmap_2026,
title = {FunMaP: Customizable simulations for Janus particles' magnetic properties
with associated visualizations},
author = {Gonzalez-Vazquez, Natalia and Schulz, Andrew K.},
year = {2026},
note = {In preparation},
}For thesis citation or exact reproducibility, users are encouraged to reference a tagged repository release when available.
This repository was developed as a research workflow accompanying a thesis and associated manuscript. The notebooks are intended for transparent scientific analysis rather than as a general-purpose software package.
- Micromagnetic models treat the SiO₂ substrate as magnetically inactive (Ms = 0)
- Simulations represent isolated hemispherical caps — no inter-particle dipolar coupling
- Static simulations use a zero-temperature approximation unless thermal drivers are explicitly selected
- Material properties are homogeneous within each defined phase region
- Sample files included in the repository are synthetic demonstration data only
These assumptions should be considered when comparing simulation outputs with ensemble-averaged experimental measurements.
This project is licensed under the GNU General Public License v3.0.
See the LICENSE file for details.
We thank G. Richter for scientific feedback and discussion.
Maintained by:
- Natalia Gonzalez-Vazquez — https://github.com/nagova
- Andrew K. Schulz — https://github.com/Aschulz94
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