Algorithms developed by me

• Cone algorithm: a generic algorithm identifying surface particles for nano clusters.
• Plane fit and bond curvature: Find normal vectors of local optimized planes of surface particles and calculate the bond curvatures.
• Local parabolic curvature: Fit local surface particles with parabolic ellipsoids.
• Mackay icosahedron structure generator: A small program to generate Mackay icosahedron structure with designated number of layers.
• Shape averaging with icosahedral symmetry: Averaging the fluctuating nanocluster surfaces to get the equilibrium shape of the nanocluster.

Basic random walk algorithms

• Monte Carlo
• Molecular Dynamics

Enchance computational speed

• Cell Index Method

Optimum searching algorithms

• Conjugate Gradient Optimization
• Simulated Annealing
• Parallel Tempering
• Genetic Algorithms

Artificial and biased simulation algorithms

• Umbrella Sampling
• Multicanonical Ensemble Sampling
• Transition Path Sampling

Crystal structure quantification algorithms

• Bond Order Parameters
• CNA Signature

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