Raman Fitting

Overview

This skill guides the analysis and curve fitting of Raman spectroscopy data, particularly for materials like graphene where characteristic peaks (G, D, 2D bands) must be accurately extracted. The primary challenge in these tasks is ensuring correct data ingestion before any analysis begins.

Critical First Step: Data Parsing Verification

Before any fitting or analysis, verify data is parsed correctly. This is the most common source of failure in spectroscopic data analysis.

Data File Inspection Protocol

Read raw file content first - Examine the first 5-10 lines of the raw data file to understand the actual format
Identify potential format issues:
- Line number prefixes (e.g., "1→", "2→" before actual data)
- Decimal separators (comma vs period - European vs US format)
- Column delimiters (tab, comma, semicolon, whitespace)
- Header lines that need to be skipped
- Encoding issues (UTF-8, ISO-8859-1, etc.)

Parse and print first few values - After parsing, print the first 3-5 data points to verify they match expectations:

# Always verify parsing immediately
print(f"First 5 wavenumbers: {wavenumbers[:5]}")
print(f"First 5 intensities: {intensities[:5]}")
print(f"Wavenumber range: {min(wavenumbers)} to {max(wavenumbers)} cm⁻¹")

Sanity check against physical expectations:
- Raman wavenumbers typically range from 100-4000 cm⁻¹
- If values fall outside this range, parsing is likely incorrect
- Graphene G peak should appear near 1580 cm⁻¹
- Graphene 2D peak should appear near 2700 cm⁻¹

Common Parsing Pitfalls

Issue	Example Raw Data	Correct Handling
Line number prefix	`1→1580.5,12345`	Strip prefix before delimiter split
Comma decimal	`1580,5\t12345,7`	Replace comma with period
Mixed delimiters	`1580.5, 12345`	Handle both tab and comma
BOM character	`\ufeff1580.5`	Strip BOM from file start

Physical Constraints for Raman Spectroscopy

Graphene/Carbon Materials

Apply these domain-specific constraints when fitting:

Peak	Expected Position (cm⁻¹)	Typical Width (FWHM)	Physical Meaning
D band	~1350	20-50	Defects/disorder
G band	~1580	10-20	sp² carbon vibration
2D band	~2700	25-60	Second-order D band
D+G	~2940	30-60	Combination mode

Fitting Parameter Bounds

Set physically reasonable bounds to avoid nonsensical fits:

# Example bounds for graphene G peak
bounds_lower = [1560, 5, 0]      # [x0, gamma, amplitude]
bounds_upper = [1600, 50, 1e6]

# Example bounds for graphene 2D peak
bounds_lower = [2650, 10, 0]
bounds_upper = [2750, 100, 1e6]

Fitting Approach

Step 1: Visual Identification of Peaks

Before fitting, identify peaks visually:

Plot the full spectrum to see all features
Note approximate peak positions and relative intensities
Identify baseline behavior (flat, sloped, curved)

Step 2: Baseline Correction

Consider baseline subtraction before peak fitting:

Linear baseline for simple cases
Polynomial baseline for curved backgrounds
Iterative methods for complex baselines

Step 3: Peak Function Selection

Common peak shapes for Raman:

Lorentzian: Natural line shape, use when peaks are sharp
Gaussian: Use when instrumental broadening dominates
Voigt: Convolution of both, most physically accurate
Pseudo-Voigt: Computationally efficient approximation

Lorentzian function:

I(x) = amplitude * (gamma²) / ((x - x0)² + gamma²)

Step 4: Initial Parameter Estimation

Use visual inspection or automatic peak finding to set initial guesses:

from scipy.signal import find_peaks

# Find peaks in the data
peaks, properties = find_peaks(intensity, height=threshold, distance=min_distance)

# Use found peak positions as initial guesses
for peak_idx in peaks:
    x0_guess = wavenumber[peak_idx]
    amplitude_guess = intensity[peak_idx]

Step 5: Fitting and Validation

After fitting, validate results:

Check R² value - Should be > 0.95 for good fits
Check parameter boundaries - Parameters hitting bounds indicate problems
Visual inspection - Plot data with fitted curve overlay
Physical plausibility - Do fitted parameters make physical sense?

Verification Strategies

Red Flags That Indicate Problems

R² < 0.9: Poor fit quality, investigate cause
Parameters at bounds: Fit is constrained, not converged
Peak positions far from expected: Data parsing or assignment error
Negative amplitudes: Physically impossible, check data/model
Very large/small widths: Outside physical expectations

Systematic Debugging Checklist

Raw data file examined line by line
Parsing verified by printing first few values
Wavenumber range is physically reasonable (100-4000 cm⁻¹)
Peaks visible in plotted data at expected positions
Initial guesses based on actual data, not assumptions
Fit quality metrics (R², residuals) calculated and checked
Fitted parameters compared to literature values

When Fits Fail

If fitting produces poor results:

Go back to data parsing - Most common source of error
Narrow the fitting window - Fit one peak at a time
Improve initial guesses - Use values closer to peak maximum
Check for overlapping peaks - May need multi-peak model
Examine residuals - Systematic patterns indicate model issues

Output Format

When reporting fitted parameters, include:

Peak position (x0) with uncertainty
Width parameter (gamma or FWHM)
Amplitude or integrated intensity
Goodness of fit metric (R², chi-squared)
Comparison to expected/literature values if available

raman-fitting