https://github.com/sheepforce/hchem
Tools for working on chemical Data
https://github.com/sheepforce/hchem
Last synced: 12 months ago
JSON representation
Tools for working on chemical Data
- Host: GitHub
- URL: https://github.com/sheepforce/hchem
- Owner: sheepforce
- License: gpl-3.0
- Created: 2017-07-16T10:47:03.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2018-12-07T10:20:32.000Z (over 7 years ago)
- Last Synced: 2025-03-03T16:26:55.381Z (over 1 year ago)
- Language: Haskell
- Size: 2.19 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# HChem -- Tools for working on chemical data
## Installation
Install the Glasgow Haskell compiler, BLAS and cabal and/or stack as system dependencies, for example on Debian:
aptitude install ghc cabal haskell-stack libopenblas-dev
You can use cabal to install the packages. First install the dependencies
cabal install hmatrix either-unwrap attoparsec text
and then install the [chemical data for Haskell](https://github.com/sheepforce/Haskell_Data.Chemistry) and the HChem package with cabal
# install HChem-libs
git clone https://github.com/sheepforce/Haskell_Data.Chemistry.git
cd Haskell_Data.Chemistry/
cabal configure && cabal build
cabal install
# install HChem
cd $HOME
git clone https://github.com/sheepforce/HChem.git
cd HChem
cabal configure && cabal build
cabal install
Or (to avoid version conflicts) use stack
git clone https://github.com/sheepforce/HChem.git
cd HChem
stack setup
stack install
## Usage
HChem is able to
- align structure in a specific orientation
- align trajectory
- interpolate structures in cartesian coordinates
- convert basis set formats (NWChem & GAMESS-US -> BAGELs JSON)
- recontract a basis set from a atomic calculation
Calling is easy
hchem [command] [option]
If you enter help or non existing commands it prints info text. You get more specific help if you just enter the command. For example
- to align a structure in `Molecule.xyz` so that atom 2 has x, y, z = 0, atom 4 has x, y = 0 and atom 5 has z = 0 enter
hchem align Molecule.xyz 2 4 5
- to find contraction coefficients from am molden file `Molecule.molden`, where the molecular orbitals 0,1,2 are used to find contraction coefficients for the basis functions 4,5 without renormalisation
hchem bascont [0,1,2] [4,5] False Molecule.molden