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I'm doing science and I'm still alive.

David W.H. Swenson dwhswenson

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I'm doing science and I'm still alive.
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dwhswenson / shorten_runs.py
Created October 11, 2023 15:11
A script to modify OpenFE transformation JSON files
import argparse
import pathlib
import logging
import json
# this takes about 9 minutes to run on my Mac
SHORT_CONFIG = {
'integrator_settings.n_steps.magnitude': 10,
'simulation_settings.checkpoint_interval.magnitude': 10,
'simulation_settings.equilibration_length.magnitude': 40,
@dwhswenson
dwhswenson / contracted_networks.ipynb
Created November 23, 2021 20:17
A quick analysis of contracting networks in NetworkX
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dwhswenson / code_style.rst
Last active November 4, 2021 13:58
In-development code style guide for OpenPathSampling projects

Code Style

Code style should be mostly PEP-8.

The easiest way to get good code is to pass it through Black (with an 80 column maximum). Our code style isn't exactly Black, but Black code will almost always be acceptable, and it is easy for contributors to reformat with Black. Just install black (pip or the conda-forge channel of conda) and run the command black -l 80 $filename on your files.

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dwhswenson / PythonHashing.ipynb
Last active October 6, 2021 22:05
Hashing in Python
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dwhswenson / simstore_numpy_fix.ipynb
Last active July 11, 2021 23:20
SimStore NumPy Array Storage Fix
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dwhswenson / COVID-19 Expert Reanalysis.ipynb
Created March 24, 2020 13:33
Analysis of expert predictions of COVID-19 cases and fatalities in the US
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dwhswenson / ENS_Temperature.ipynb
Created July 9, 2019 15:17
Notebook looking at the temperature of offices at the ENS. It was way too hot.
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dwhswenson / what_is_nucleic.ipynb
Last active April 13, 2019 21:13
Which residues are "nucleic"?
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dwhswenson / double_well_examples.ipynb
Created January 27, 2019 23:35
Examples for using the Double Well Dimer testsystems in OpenMMTools
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dwhswenson / lammps_lj_analysis.ipynb
Created October 2, 2018 21:24
Simple OPS LAMMPS example
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