README.md

Library: AutoIO

Andreas V. Copan, Kevin B. Moore III, Sarah N. Elliott, and Stephen J. Klippenstein

Input writing, output parsing, and job submission tools created as part of the AutoMech package. This repository contains the following python packages: elstruct, autoparse, autoio, and autorun.

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Package: elstruct

Installation

>>> conda install elstruct -c auto-mech

Description

The elstruct package handles input writing and output reading for electronic structure jobs. Current modules available:

• Single point calculation: CFOUR(v2), Gaussian(v09, v16), Molpro(v2015), Orca(v4), PSI4
• Geometry calculation: CFOUR(v2), Gaussian(v09, v16), Molpro(v2015), Orca(v4), PSI4
• Gradients calculation: CFOUR(v2), Gaussian(v09, v16), Molpro(v2015), Orca(v4), PSI4
• Frequency calculation: CFOUR(v2), Gaussian(v09, v16), Molpro(v2015), Orca(v4), PSI4
• VPT2 anharmonic analysis: Gaussian(v09, v16)
• IRC: Gaussian(v09, v16), PSI4

Usage

Our pytest tests serve as an example for building filesystems

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Package: autoparse

Installation

>>> conda install autoparse -c auto-mech

Description

Set of wrappers for python.re that allow for more intelligible regular expressions syntax.

Usage

Our pytest tests serve as an example for building filesystems

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Package: autoio

Installation

>>> conda install autoio -c auto-mech

Description

AutoIO generates the input and reads the output for C++ and Fortran codes used by the AutoMech suite. Interfaces for codes distributed alongside AutoMech:

• MESS: Master Equation System Solver The scope of this master equation solver code is described in Reformulation and Solution of the Master Equation for Multiple-Well Chemical Reactions.

  >>> conda install mess -c auto-mech

• ProjRot: Rotational Projections Projects rotational frequencies from the hessian and generates the resulting projected frequencies

  >>> conda install projrot -c auto-mech

• ThermP: Thermochemistry Properties Converts partition function to thermochemical proprties

  >>> conda install thermps -c auto-mech

• PAC99: Nasa Polynomials Converts thermochemical properties into a polynomial representation

  >>> conda install pac99 -c auto-mech

• PAC99: Nasa Polynomials Converts thermochemical properties into a polynomial representation

  >>> conda install pac99 -c auto-mech

• OneDMin:
• VareCof:
• Polyrate:

External Codes

• CHEMKIN: i

Usage

Our pytest tests serve as an example for building filesystems

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Package: autorun

Installation

>>> conda install autorun -c auto-mech

Description

AutoRUN submits jobs and extracts relevant output through calls to autoio for C++ and Fortran codes used by the AutoMech suite. Interfaces for codes distributed alongside AutoMech:

• MESS: Master Equation System Solver The scope of this master equation solver code is described in Reformulation and Solution of the Master Equation for Multiple-Well Chemical Reactions.

  >>> conda install mess -c auto-mech

• ProjRot: Rotational Projections Projects rotational frequencies from the hessian and generates the resulting projected frequencies

  >>> conda install projrot -c auto-mech

• ThermP: Thermochemistry Properties Converts partition function to thermochemical proprties

  >>> conda install thermps -c auto-mech

• PAC99: Nasa Polynomials Converts thermochemical properties into a polynomial representation

  >>> conda install pac99 -c auto-mech

• PAC99: Nasa Polynomials Converts thermochemical properties into a polynomial representation

  >>> conda install pac99 -c auto-mech

• OneDMin:
• VareCof:

Usage

Our pytest tests serve as an example for building filesystems