yangyushi’s gists

yangyushi / check_tracking_example.py

Last active August 31, 2020 14:58

Handy function to check 3D particle tracking results

	import numpy as np
	import matplotlib.pyplot as plt
	from scipy import ndimage
	from matplotlib.pyplot import plot, scatter, imshow


	def get_fake(size, number, radius, blur):
	"""
	Generate a fake image for ideal gas (random positions).

yangyushi / neighbour_list.py

Last active April 3, 2020 18:07

Algorithm of neighbour list introduced in book "computer simulation of liquids" chapter 5

	#!/usr/bin/env python3
	import math
	from itertools import product
	import numpy as np
	from numba import njit
	from numba.typed import List


	@njit
	def build_verlet_nlist(nlist: List, point: List, particles: np.ndarray, rl:float):

yangyushi / rotation_opt.py

Last active March 31, 2020 12:15

This gist shows a `numba.njit` accelerated code is faster than its `einsum` equivalent for composing/applying a lot of rotation matrices

	from time import time
	import numpy as np
	from numba import njit, prange


	@njit(parallel=True)
	def ndot1(A, B):
	"""
	Calculate C with
	C[i, j, k] = sum_q( A[i, j, q] · B[i, q, k] )

yangyushi / parse_xyz.cpp

Last active April 7, 2022 14:55

Parse .xyz file and load to std::vector

yangyushi / random_sphere_surface.py

Last active May 13, 2020 22:56

generate random points on the surface of a sphere

	import numpy as np
	import matplotlib.pyplot as plt
	from matplotlib.pyplot import plot, scatter, imshow
	from mpl_toolkits.mplot3d import Axes3D

	N = 1000

	z = np.random.uniform(-1, 1, N)
	phi = np.random.uniform(-np.pi, np.pi, N)
	rxy = np.sqrt(1 - z**2)

yangyushi / basis_transform.py

Last active May 15, 2020 12:16

	import numpy as np
	import matplotlib.pyplot as plt
	from mpl_toolkits.mplot3d import Axes3D

	fig = plt.figure()
	ax = fig.add_subplot(111, projection='3d')

	b1 = np.array([
	[1, 0, 0],
	[0, 1, 0],

yangyushi / join_pairs.cpp

Last active July 13, 2020 15:19

Join overlapped labels recursively, eg [(2, 3), (3, 5), (2, 6), (8, 9), (9, 10)] → [(2, 3, 5, 6), (8, 9, 10)]

yangyushi / xyz.py

Last active July 4, 2020 09:52

get all the frames from an xyz file

	import numpy as np
	import re


	def get_frames_from_xyz(filename, use_cols):
	"""
	Get all data from different frames from an xyz file

	Args:
	filename (str): the path of the xyz file to parse

yangyushi / tcc_analysis.ipynb

Last active June 12, 2020 10:39

demonstration on using TCC to analyse a LAMMPS dumped file

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yangyushi / vicsek_order_theory.py

Last active June 19, 2020 00:28

	import numpy as np
	import matplotlib.pyplot as plt
	from scipy import ndimage
	from matplotlib.pyplot import plot, scatter, imshow

	def simulate_2d(N):
	theta = np.random.uniform(-np.pi, np.pi, (1000, N))
	x = np.cos(theta).mean(-1) # shape (1000,)
	y = np.sin(theta).mean(-1) # shape (1000,)
	order = np.linalg.norm((x, y), axis=0)

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