Awesome-Agent-Skills-for-Empirical-Research numerical-methods-guide
Apply numerical methods and scientific computing techniques
install
source · Clone the upstream repo
git clone https://github.com/brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/43-wentorai-research-plugins/skills/domains/math/numerical-methods-guide" ~/.claude/skills/brycewang-stanford-awesome-agent-skills-for-empirical-research-numerical-methods-2612b0 && rm -rf "$T"
manifest:
skills/43-wentorai-research-plugins/skills/domains/math/numerical-methods-guide/SKILL.mdsource content
Numerical Methods Guide
A skill for applying numerical methods in scientific computing and research. Covers root finding, numerical integration, ODE solvers, optimization, interpolation, and error analysis with practical implementations in Python.
Root Finding
Newton's Method and Alternatives
import numpy as np def newton_method(f, df, x0: float, tol: float = 1e-10, max_iter: int = 100) -> dict: """ Newton's method for finding roots of f(x) = 0. Args: f: Function whose root we seek df: Derivative of f x0: Initial guess tol: Convergence tolerance max_iter: Maximum iterations """ x = x0 history = [x] for i in range(max_iter): fx = f(x) dfx = df(x) if abs(dfx) < 1e-15: return {"root": x, "converged": False, "reason": "Zero derivative encountered"} x_new = x - fx / dfx history.append(x_new) if abs(x_new - x) < tol: return { "root": x_new, "converged": True, "iterations": i + 1, "f_at_root": f(x_new), "convergence": "quadratic" } x = x_new return {"root": x, "converged": False, "reason": "Max iterations reached"}
Method Selection Guide
| Method | Convergence | Requires | Robustness |
|---|---|---|---|
| Bisection | Linear (slow) | Bracketing interval | Very robust |
| Newton | Quadratic (fast) | Derivative | May diverge |
| Secant | Superlinear (~1.62) | Two initial guesses | Moderate |
| Brent | Superlinear | Bracketing interval | Very robust |
Numerical Integration
Quadrature Methods
from scipy import integrate def numerical_integration_comparison(f, a: float, b: float) -> dict: """ Compare numerical integration methods. Args: f: Function to integrate a: Lower bound b: Upper bound """ # Adaptive Gaussian quadrature (recommended default) quad_result, quad_error = integrate.quad(f, a, b) # Simpson's rule (fixed-point) n_points = 101 x = np.linspace(a, b, n_points) simps_result = integrate.simpson(f(x), x=x) # Romberg integration romb_result = integrate.romberg(f, a, b) return { "quad": {"value": quad_result, "error_estimate": quad_error}, "simpson": {"value": simps_result, "n_points": n_points}, "romberg": {"value": romb_result}, "recommendation": ( "Use scipy.integrate.quad for most cases. " "It adaptively chooses points for accuracy." ) }
Ordinary Differential Equations
Solving Initial Value Problems
from scipy.integrate import solve_ivp def solve_ode_system(f, t_span: tuple, y0: list, method: str = "RK45") -> dict: """ Solve a system of ODEs: dy/dt = f(t, y). Args: f: Right-hand side function f(t, y) t_span: (t_start, t_end) y0: Initial conditions method: Solver method (RK45, RK23, Radau, BDF, LSODA) """ sol = solve_ivp( f, t_span, y0, method=method, dense_output=True, rtol=1e-8, atol=1e-10 ) return { "success": sol.success, "message": sol.message, "t": sol.t, "y": sol.y, "n_evaluations": sol.nfev, "method_used": method } # Example: Lorenz system (chaotic dynamics) def lorenz(t, state, sigma=10, rho=28, beta=8/3): x, y, z = state return [ sigma * (y - x), x * (rho - z) - y, x * y - beta * z ] result = solve_ode_system(lorenz, (0, 50), [1.0, 1.0, 1.0])
Solver Selection
Non-stiff problems: RK45 (default): 4th/5th order Runge-Kutta, adaptive step RK23: Lower order, useful for less smooth problems DOP853: High-order, excellent for smooth problems Stiff problems: Radau: Implicit Runge-Kutta, good for stiff systems BDF: Backward differentiation formula (classic stiff solver) LSODA: Automatically switches between non-stiff and stiff How to tell if your problem is stiff: - RK45 takes many tiny steps or fails to converge - The system has widely separated time scales - Chemical kinetics, circuit simulations often stiff
Optimization
Minimization Methods
from scipy.optimize import minimize def optimize_with_comparison(f, x0: np.ndarray, bounds: list = None) -> dict: """ Compare optimization methods on a given objective function. Args: f: Objective function to minimize x0: Initial guess bounds: List of (min, max) tuples for each variable """ results = {} # Gradient-free res_nm = minimize(f, x0, method="Nelder-Mead") results["Nelder-Mead"] = {"x": res_nm.x, "fun": res_nm.fun, "nfev": res_nm.nfev} # Gradient-based (quasi-Newton) res_bfgs = minimize(f, x0, method="L-BFGS-B", bounds=bounds) results["L-BFGS-B"] = {"x": res_bfgs.x, "fun": res_bfgs.fun, "nfev": res_bfgs.nfev} return results
Error Analysis
Sources of Numerical Error
1. Rounding error: Finite precision arithmetic (float64 has ~16 significant digits) Accumulates in long computations 2. Truncation error: Error from approximating continuous math with discrete formulas Example: Finite difference df/dx ~ (f(x+h) - f(x)) / h 3. Conditioning: Sensitivity of the result to perturbations in input Condition number quantifies this amplification Best practice: Always compare your numerical solution against analytical solutions (when available) or use convergence studies (refine the discretization and check if the answer converges).
When publishing numerical results, report the method used, convergence criteria, error tolerances, grid resolution (for PDEs), and validate against known test cases. Provide code so readers can reproduce your computations.