Supporting information (calculation outputs, structures)

Overview

10.1021/acs.jpca.1c03061

Supporting information (calculation outputs, structures) for https://doi.org/10.1021/acs.jpca.1c03061

The folder structure is method, basis set, then "standard" calculations. Variations are in further subfolders.

folder description of contents
b3lyp/methane Calculations for establishing spring and angle force coefficients for methane, B3LYP/6-31G(d)
m05-2x/def2-tzvp All calculations based on M05-2X/def2-TZVP structures.
wb97x-d/def2-tzvp All calculations based on wB97X-D/def2-TZVP structures, including SAPT.
wb97x-d/def2-tzvp/swap_metals Placing magnesium in the calcium-bound structure and vice-versa

Mapping to text in SI document

Originally, some of the calculations were combined geometry optimization and vibrational frequency calculations in the same input. These inputs and outputs have all been split. (As a result, some of the frequency inputs repeated in their respective outputs have $molecule read, where the extracted input has been modified to work standalone.)

  • methane.out is really the entire contents of b3lyp/methane.
  • {apo,ca,mg}_opt_freq_{m,w}.out are {m05-2x,wb97x-d}/def2-tzvp/{apo,ca_ct,mg_ct}_{opt,freq}.out, where the optimization and frequency parts have been split as described above.
  • {ca,mg}_{eda_w,sapt}.out are wb97x-d/def2-tzvp/{ca,mg}_ct_{eda,sapt_gas}.out.
  • {cainmg,mginca}_{eda_w,sapt}.out are wb97x-d/def2-tzvp/swap_metals/{cainmg,mginca}_ct_{eda,sapt_gas}.out.

Analysis notes

The script to make EDA/SAPT analysis tables is also provided under wb97x-d/def2-tzvp/analysis.py. It depends on cclib, pydantic, and pylatex.

You might also like...
 Some problems of SSLC ( High School ) before outputs and after outputs
Some problems of SSLC ( High School ) before outputs and after outputs

Some problems of SSLC ( High School ) before outputs and after outputs 1] A Python program and its output (output1) while running the program is given

This tool for beginner and help those people they gather information about Email Header Analysis, Instagram Information, Instagram Username Check, Ip Information, Phone Number Information, Port Scan

This tool for beginner and help those people they gather information about Email Header Analysis, Instagram Information, Instagram Username Check, Ip Information, Phone Number Information, Port Scan. This tool shows your hostname and public IP first, then user give input and according to option this tool work. This tool work diffrent Oprating system.

Data Structures and Algorithms Python - Practice data structures and algorithms in python with few small projects

Data Structures and Algorithms All the essential resources and template code nee

nptsne is a numpy compatible python binary package that offers a number of APIs for fast tSNE calculation.

nptsne nptsne is a numpy compatible python binary package that offers a number of APIs for fast tSNE calculation and HSNE modelling. For more detail s

nptsne is a numpy compatible python binary package that offers a number of APIs for fast tSNE calculation.

nptsne nptsne is a numpy compatible python binary package that offers a number of APIs for fast tSNE calculation and HSNE modelling. For more detail s

CoCalc: Collaborative Calculation in the Cloud
CoCalc: Collaborative Calculation in the Cloud

logo CoCalc Collaborative Calculation and Data Science CoCalc is a virtual online workspace for calculations, research, collaboration and authoring do

FID calculation with proper image resizing and quantization steps
FID calculation with proper image resizing and quantization steps

clean-fid: Fixing Inconsistencies in FID Project | Paper The FID calculation involves many steps that can produce inconsistencies in the final metric.

Python Library for Secp256k1 Bitcoin curve to do fast ECC calculation

secp256k1 Python Library for Secp256k1 Bitcoin curve to do fast ECC calculation Example Usage import secp256k1 as ice print('[C]',privatekey_to_addres

A course-planning, course-map rendering and GPA-calculation web service, designed for the SFU (Simon Fraser University) student.

SFU Course Planner What is the overall goal of the project (i.e. what does it do, or what problem is it solving)? As the title suggests, this project

Regression Metrics Calculation Made easy

Regression Metrics Mean Absolute Error Mean Square Error Root Mean Square Error Root Mean Square Logarithmic Error Root Mean Square Logarithmic Error

Regression Metrics Calculation Made easy for tensorflow2 and scikit-learn

Regression Metrics Installation To install the package from the PyPi repository you can execute the following command: pip install regressionmetrics I

Two fast AUC calculation implementations for python
Two fast AUC calculation implementations for python

fastauc Two fast AUC calculation implementations for python: python-based is approximately 5X faster than the default sklearn.metrics.roc_auc_score()

This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot.

superSFS This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot. It is easy-to-use and runing fast. What you s

Finite-temperature variational Monte Carlo calculation of uniform electron gas using neural canonical transformation.

CoulombGas This code implements the neural canonical transformation approach to the thermodynamic properties of uniform electron gas. Building on JAX,

A web-based analysis toolkit for the System Usability Scale providing calculation, plotting, interpretation and contextualization utility
A web-based analysis toolkit for the System Usability Scale providing calculation, plotting, interpretation and contextualization utility

System Usability Scale Analysis Toolkit The System Usability Scale (SUS) Analysis Toolkit is a web-based python application that provides a compilatio

torchsummaryDynamic: support real FLOPs calculation of dynamic network or user-custom PyTorch ops

torchsummaryDynamic Improved tool of torchsummaryX. torchsummaryDynamic support real FLOPs calculation of dynamic network or user-custom PyTorch ops.

Data collection, enhancement, and metrics calculation.

l3_data_collection Data collection, enhancement, and metrics calculation. Summary Repository containing code for QuantDAO's JDT data collection task.

Extract gene length based on featureCount calculation gene nonredundant exon length method.

Extract gene length based on featureCount calculation gene nonredundant exon length method.

IPV4 network calculation project in Python
IPV4 network calculation project in Python

Curso de Python 3 do Básico ao Avançado Desafio: Calculando redes IPV4 Criar um programa que obtem um numero de IP com o prefixo da mascara de rede. O

Releases(v1.0.0)
Owner
Eric Berquist
https://stackoverflow.com/story/berquist
Eric Berquist
Datastructures such as linked list, trees, graphs etc

datastructures datastructures such as linked list, trees, graphs etc Made a public repository for coding enthusiasts. Those who want to collaborate on

0 Dec 01, 2021
Python Data Structures and Algorithms

No non-sense and no BS repo for how data structure code should be in Python - simple and elegant.

Prabhu Pant 1.9k Jan 08, 2023
A HDF5-based python pickle replacement

Hickle Hickle is an HDF5 based clone of pickle, with a twist: instead of serializing to a pickle file, Hickle dumps to an HDF5 file (Hierarchical Data

Danny Price 450 Dec 21, 2022
Supporting information (calculation outputs, structures)

Supporting information (calculation outputs, structures)

Eric Berquist 2 Feb 02, 2022
Data Structure With Python

Data-Structure-With-Python- Python programs also include in this repo Stack A stack is a linear data structure that stores items in a Last-In/First-Ou

Sumit Nautiyal 2 Jan 09, 2022
nocasedict - A case-insensitive ordered dictionary for Python

nocasedict - A case-insensitive ordered dictionary for Python Overview Class NocaseDict is a case-insensitive ordered dictionary that preserves the or

PyWBEM Projects 2 Dec 12, 2021
An esoteric data type built entirely of NaNs.

NaNsAreNumbers An esoteric data type built entirely of NaNs. Installation pip install nans_are_numbers Explanation A floating point number is just co

Travis Hoppe 72 Jan 01, 2023
This repository is for adding codes of data structures and algorithms, leetCode, hackerrank etc solutions in different languages

DSA-Code-Snippet This repository is for adding codes of data structures and algorithms, leetCode, hackerrank etc solutions in different languages Cont

DSCSRMNCR 3 Oct 22, 2021
A DSA repository but everything is in python.

DSA Status Contents A: Mathematics B: Bit Magic C: Recursion D: Arrays E: Searching F: Sorting G: Matrix H: Hashing I: String J: Linked List K: Stack

Shubhashish Dixit 63 Dec 23, 2022
Programming of a spanning tree algorithm with Python : In depth first with a root node.

ST Algorithm Programming of a spanning tree algorithm with Python : In depth first with a root node. Description This programm reads informations abou

Mathieu Lamon 1 Dec 16, 2021
Simple spill-to-disk dictionary

Chest A dictionary that spills to disk. Chest acts likes a dictionary but it can write its contents to disk. This is useful in the following two occas

Blaze 59 Dec 19, 2022
A simple tutorial to use tree-sitter to parse code into ASTs

A simple tutorial to use py-tree-sitter to parse code into ASTs. To understand what is tree-sitter, see https://github.com/tree-sitter/tree-sitter. Tr

Nghi D. Q. Bui 7 Sep 17, 2022
Google, Facebook, Amazon, Microsoft, Netflix tech interview questions

Algorithm and Data Structures Interview Questions HackerRank | Practice, Tutorials & Interview Preparation Solutions This repository consists of solut

Quan Le 8 Oct 04, 2022
A Python implementation of red-black trees

Python red-black trees A Python implementation of red-black trees. This code was originally copied from programiz.com, but I have made a few tweaks to

Emily Dolson 7 Oct 20, 2022
Array is a functional mutable sequence inheriting from Python's built-in list.

funct.Array Array is a functional mutable sequence inheriting from Python's built-in list. Array provides 100+ higher-order methods and more functiona

182 Nov 21, 2022
My notes on Data structure and Algos in golang implementation and python

My notes on DS and Algo Table of Contents Arrays LinkedList Trees Types of trees: Tree/Graph Traversal Algorithms Heap Priorty Queue Trie Graphs Graph

Chia Yong Kang 0 Feb 13, 2022
Webtesting for course Data Structures & Algorithms

Selenium job to automate queries to check last posts of Module Data Structures & Algorithms Web-testing for course Data Structures & Algorithms Struct

1 Dec 15, 2021
This Repository consists of my solutions in Python 3 to various problems in Data Structures and Algorithms

Problems and it's solutions. Problem solving, a great Speed comes with a good Accuracy. The more Accurate you can write code, the more Speed you will

SAMIR PAUL 1.3k Jan 01, 2023
A JSON-friendly data structure which allows both object attributes and dictionary keys and values to be used simultaneously and interchangeably.

A JSON-friendly data structure which allows both object attributes and dictionary keys and values to be used simultaneously and interchangeably.

Peter F 93 Dec 01, 2022
This repo is all about different data structures and algorithms..

Data Structure and Algorithm : Want to learn data strutrues and algorithms ??? Then Stop thinking more and start to learn today. This repo will help y

Priyanka Kothari 7 Jul 10, 2022