Rohit Goswami HaoZeke

`PYSEAMS` : Python bindings for d-SEAMS

d-SEAMS (Deferred Structural Elucidation Analysis for Molecular Simulations), a free and open-source post-processing engine for the analysis of molecular dynamics trajectories, which is specifically able to qualitatively classify ice structures, in both strong confinement and bulk systems.

The objective of my project was to create Python bindings to the seams-core C++ engine of d-SEAMS. I named my bindings repository and project as pyseams with the importable name cyoda in keeping with yodaStruct and yodaLib from d-SEAMS. The d-SEAMS project provided lua bindings which many users may find difficult. I wrote bindings with pybind11 for the functions and classes present in d-SEAMS. Each basic example has it's own file in pyseams, which users can run. Initially, d-SEAMS didn't support the latest version of Macos but I worked to ensure M1-Macos users can use d-SEAMS as well.

Beyond th

Installing Doom Emacs on Windows

More guides:

Installing Emacs

The easiest way to install Emacs is by using Chocolatey:

Purpose

To benchmark Python (Numpy) default procedure to find all eigenvalues and eigenvectors of a complex (hermitian) matrix and compare the results with Fortran using either MKL and OpenBLAS libraries.

Python code

import time
import numpy as np

An attempt to make Windows 10/11 work for me by customizing/personalizing it

Why gist not dotfiles?

I use dotfiles to personalize *nix type of machines. But I'm new to personalizing Windows 10. So I'm collecting information here first before adding these to the dotfiles. I'm not sure if these will ever move to dotfiles though.

Enable WSL2

Zathura on Mac

I want to open PDF files with Zathura on Mac. Problem is - Zathura does not have a proper App Bundle. So you cannot go in Finder to a pdf file, navigate to ‘Get Info’ and set pdf files to be opened with Zathura.

Luckily, you can create a custom App Bundle that wraps up a script that does that

But that is not as straightforward as you think it is, you can’t just execute a shell script. What if the file already opened with one of the instances of zathura process? Since Zathura is not a native OSX app, it will create a new process instance every time you open it.

The following script opens a file in Zathura, and if it was already opened, it would only activate the right window.

How to use it

The current version of this document is here.

This document contains additional supporting material for the claims in this post (published 1 September 2019), in response to a cease and desist letter from John De Goes that I received on 6 July 2020.

Please see also this post for more information about De Goes deleting the FCoP repository on GitHub shortly before sending the cease and desist letter.

	// ==UserScript==
	// @name Medium Paywall Bypass
	// @namespace Violentmonkey Scripts
	// @run-at document-start
	// @match ://.medium.com/*
	// @match ://medium.com/
	// @match :///*
	// @grant none
	// @version 2.4
	// @inject-into content

	#!/usr/bin/env python3

	# See https://github.com/Nakiami/MultithreadedSimpleHTTPServer/blob/master/MultithreadedSimpleHTTPServer.py

	# Python 3.x
	from socketserver import ThreadingMixIn
	from http.server import SimpleHTTPRequestHandler, HTTPServer

	class ThreadingSimpleServer(ThreadingMixIn, HTTPServer):
	pass

	# This isn't supposed to run as a bash script, i named it with ".sh" for syntax highlighting.

	# https://developer.nvidia.com/nsight-systems
	# https://docs.nvidia.com/nsight-systems/profiling/index.html

	# My preferred nsys (command line executable used to create profiles) commands
	#
	# In your script, write
	# torch.cuda.nvtx.range_push("region name")
	# ...

	<< MaTeX`
	SetOptions[MaTeX, "Preamble" -> {"\\usepackage{color,txfonts}"}];
	SetDirectory[NotebookDirectory[]];

	Clear[drawLadder];
	drawLadder[n_, l_, m_, imsize_: 500] := Module[{maxrungs = 5, mag = 4},
	Graphics[{
	White, Opacity[1], Thickness[.02], Dashing[None],
	Table[Line[{{0, k}, {1, k}}], {k, maxrungs}], (draw n lines)