yangyushi’s gists

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 / 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 / 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 / parse_xyz.cpp

Last active April 7, 2022 14:55

Parse .xyz file and load to std::vector

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 / 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 / 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 / compile Vim.txt

Created March 15, 2020 23:37

	./configure --with-features=huge \
	--enable-multibyte \
	--enable-rubyinterp=yes \
	--enable-python3interp=yes \
	--with-python3-config-dir=$(python3-config --configdir) \
	--enable-perlinterp=yes \
	--enable-luainterp=yes \
	--enable-cscope \
	--prefix=/usr/local

yangyushi / reform.py

Last active May 16, 2020 11:35

format the entry key names in your bib file to please your supervisor

	#!/usr/bin/env python
	import re
	import sys
	from textwrap import dedent

	STOPWORDS = [ # common stop words from package nltk
	"i", "me", "my", "myself", "we", "our", "ours", "ourselves", "you", "you're", "you've", "you'll",
	"you'd", "your", "yours", "yourself", "yourselves", "he", "him", "his", "himself", "she", "she's",
	"her", "hers", "herself", "it", "it's", "its", "itself", "they", "them", "their", "theirs",
	"themselves", "what", "which", "who", "whom", "this", "that", "that'll", "these", "those", "am",

yangyushi / compile python3.7.7 macOS with homebrew openssl.sh

Last active April 24, 2020 14:40

	ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers/X11 /usr/local/include/X11
	./configure\
	--enable-optimizations\
	--prefix=/usr/local\
	--enable-shared\
	--with-openssl=$(brew --prefix openssl)\
	CPPFLAGS="-I/usr/local/opt/openssl/include"\
	LDFLAGS="-L/usr/local/opt/openssl/lib"

Yushi Yang yangyushi