Extract continuous and discrete relaxation spectra from G(t)

Overview

pyReSpect-time

Extract continuous and discrete relaxation spectra from stress relaxation modulus G(t). The papers which describe the method and test cases are:

  • Shanbhag, S., "pyReSpect: A Computer Program to Extract Discrete and Continuous Spectra from Stress Relaxation Experiments", Macromolecular Theory and Simulations, 2019, 1900005 [doi: 10.1002/mats.201900005].
  • Takeh, A. and Shanbhag, S. "A computer program to extract the continuous and discrete relaxation spectra from dynamic viscoelastic measurements", Appl. Rheol. 2013, 23, 24628.

Files

Code Files

This repository contains two python modules contSpec.py discSpec.py. They extract the continuous and discrete relaxation spectra from a stress relaxation data. (t versus G(t) experiment or simulation).

It containts a third module common.py which contains utilities required by both contSpec.py and discSpec.py.

In addition to the python modules, a jupyter notebook interactContSpec.ipynb is also provisionally included. This allows the user to experiment with parameter settings interactively.

Input Files

The user is expected to supply two files:

  • inp.dat is used to control parameters and settings
  • Gt.dat which contains two columns of data t and G(t)

Output Files

Text files containting output from the code are stored in a directory output/. These include a fit of the data, the spectra, and other files relevant to the continuous or discrete spectra calculation.

Graphical and onscreen output can be suppressed by appropriate flags in inp.dat.

Test Files

A bunch of test files are supplied in the folder tests/. These data are described in the paper: Shanbhag, S., "pyReSpect: A Computer Program to Extract Discrete and Continuous Spectra from Stress Relaxation Experiments" which will appear in Macromolecular Theory and Simulations in 2019.

Usage

Once inp.dat and Gt.dat are furnished, running the code is simple.

To get the continuous spectrum:

python3 contSpec.py

The continuous spectrum must be extracted before the discrete spectrum is computed. The discrete spectrum can then be calculated by

python3 discSpec.py

Interactive Mode

The interactive mode offers a "GUI" for exploring parameter settings. To launch use jupyter notebook interactContSpec.ipynb.

Pre-requisites

The numbers in parenthesis show the version this has been tested on.

python3 (3.5.2) numpy (1.14.2) scipy (1.0.1)

For interactive mode:

jupyter (4.3) ipywidgets (6.0.0)

History

The code is based on the Matlab program ReSpect, which extract the continuous and discrete relaxation spectra from frequency data, G*(w). Work was supported by National Science Foundation DMR grants number 0953002 and 1727870.

Major Upgrade: March-April 2019

  • added ability to infer plateau modulus G0; modified all python routines and reorganized inp.dat
  • use a Bayesian formulation to infer uncertainty in the continuous spectrum
  • currently keeping old method to determine critical lambda, but using a far more efficient method (3-4x savings in compute time)
  • made discSpec.py compliant with G0

Major Upgrade: December 2018

  • moved all common imports and definitions to common; made completely visible
  • in discSpec(): added a NLLS routine to optimize tau; use previous optima as initial guesses for final tau; this greatly improved the quality of fits.

Major Upgrade: August 2018

Continuous Spectrum

  • orignal program with n = 100 and lambda = 20 pts with clean 1 mode data took ~33s.
  • prestore kernMat: evaluation of kernel (meshgrid S, T, and hs) by prestoring kernMat ~12.5s (~3x speed gain)
  • improved least_squares setting by incorporating jacobianLM; ~6s (2x gain)
  • lcurve coarser (auto) mesh, robust criterion, and interpolation ~3.5s (~1.75x gain)
  • Total gain in speed as a consequence of these improvements is 33s -> 3.5s a nearly 10x gain!
  • making jupyter interact compliant

Discrete Spectrum

  • AutoMagic Mode: need only par verbose and plotting flags; auto Nopt
  • switching to nnls as default fitting engine
  • changed older MaxwellModes and LLS -> nnls
  • some printing modifications
  • hardcoding prune = True everywhere; doesn't seem to be use case otherwise
  • making jupyter interact compliant
Repository for DNN training, theory to practice, part of the Large Scale Machine Learning class at Mines Paritech

DNN Training, from theory to practice This repository is complementary to the deep learning training lesson given to les Mines ParisTech on the 11th o

Alexandre Défossez 6 Nov 14, 2022
Implemented Exploratory Data Analysis (EDA) using Python.Built a dashboard in Tableau and found that 45.87% of People suffer from heart disease.

Heart_Disease_Diagnostic_Analysis Objective 🎯 The aim of this project is to use the given data and perform ETL and data analysis to infer key metrics

Sultan Shaikh 4 Jan 28, 2022
Anki Addon idea by gbrl.sc to see previous ratings of a card in the reviewer

Card History At A Glance Stop having to press card browser and ctrl+i for every card and then WINCING to see it's history of reviews FEATURES Visualiz

Jerry Zhou 11 Dec 19, 2022
emoji-math computes the given python expression and returns either the value or the nearest 5 emojis as measured by cosine similarity.

emoji-math computes the given python expression and returns either the value or the nearest 5 emojis as measured by cosine similarity.

Andrew White 13 Dec 11, 2022
Pre-commit hook for upgrading type hints

This is a pre-commit hook configured to automatically upgrade your type hints to the new native types implemented in PEP 585.

snok 54 Nov 14, 2022
Checkers Project Built Using Python

Checkers Project Built Using Python

Meekness Anyaeche 1 Nov 08, 2021
This is an online course where you can learn and master the skill of low-level performance analysis and tuning.

Performance Ninja Class This is an online course where you can learn to find and fix low-level performance issues, for example CPU cache misses and br

Denis Bakhvalov 1.2k Dec 30, 2022
Find virtual hosts (vhosts) from IP addresses and hostnames

Features Enumerate vhosts from a list of IP addresses and domain names. Virtual Hosts are enumerated using the following process: Supplied domains are

3 Jul 09, 2022
A tool for study using pomodoro methodology, while study mode spotify or any other .exe app is opened and while resting is closed.

Pomodoro-Timer-With-Spotify-Connection A tool for study using pomodoro methodology, while study mode spotify or any other .exe app is opened and while

2 Oct 23, 2022
IDA Pro plugin that shows the comments in a database

ShowComments A Simple IDA Pro plugin that shows the comments in a database Installation Copy the file showcomments.py to the plugins folder under IDA

Fernando Mercês 32 Dec 10, 2022
Opendrop - An open Apple AirDrop implementation written in Python

OpenDrop: an Open Source AirDrop Implementation OpenDrop is a command-line tool that allows sharing files between devices directly over Wi-Fi. Its uni

Secure Mobile Networking Lab 7.5k Jan 03, 2023
Funchacks - Fun module which is a small set of utilities

funchacks 👋 Introduction Funchacks is a fun module that provides a small packag

DenyS 6 Aug 04, 2022
External Network Pentest Automation using Shodan API and other tools.

Chopin External Network Pentest Automation using Shodan API and other tools. Workflow Input a file containing CIDR ranges. Converts CIDR ranges to ind

Aditya Dixit 9 Aug 04, 2022
Test to grab m3u from YouTube live.

YouTube_to_m3u https://raw.githubusercontent.com/benmoose39/YouTube_to_m3u/main/youtube.m3u Updated m3u links of YouTube live channels, auto-updated e

136 Jan 06, 2023
Apache Superset out of box version(Windows 64-bit)

superset_app Apache Superset out of box version (Windows 64bit) prepare job download 3 files python-3.8.10-embed-amd64.zip get-pip.py python_geohash‑0

Steven Lee 9 Oct 02, 2022
Animations made using manim-ce

ManimCE Animations Animations made using manim-ce The code turned out to be a bit complicated than expected.. It can be greatly simplified, will work

sparshg 17 Jan 06, 2023
A module to prevent invites and joins to Matrix rooms by checking the involved server(s)' domain.

Synapse Domain Rule Checker A module to prevent invites and joins to Matrix rooms by checking the involved server(s)' domain. Installation From the vi

matrix.org 4 Oct 24, 2022
An esoteric programming language that supports concurrency, regex, and web requests.

The Hofstadter Esoteric Programming Language Hofstadter's Law: It always takes longer than you expect, even when you take into account Hofstadter's La

Austin Henley 19 Dec 27, 2022
A faster Python generator that get function results from multi-process workers

multiyield This package implements a Python generator that get function results from multi-process workers. The faster_fifo Queue (instead of the stan

Xin Du 1 Nov 18, 2021
A Python library for inspecting JVM class files (.class)

lawu Lawu is a human-friendly library for assembling, disassembling, and exploring JVM class files. It's highly suitable for automation tasks. Documen

Tyler Kennedy 45 Oct 23, 2022