https://github.com/cmelab/forcefields
Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (7.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: cmelab
- Language: Jupyter Notebook
- Default Branch: main
- Size: 110 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 2
- Open Issues: 5
- Releases: 0
Metadata Files
README.md
forcefields
This repo is designed to aid in the proccess of creating forcefield files from scratch using the Espaloma Program written by the Chodera Lab (https://github.com/choderalab/espaloma).
Installing Environment
For Apple Silicon Mac (ARM):
CONDA_SUBDIR=osx-64 conda create -n ff_generation python
conda activate ff_generation
conda env config vars set CONDA_SUBDIR=osx-64
conda deactivate
conda activate ff_generation
conda install 'espaloma=0.3.2' mbuild "python=3.10.14" foyer openbabel py3dmol
pip install notebook
Example
from functions import MonToSmiles
from functions.MonToSmiles import mon_to_smiles
you can either import a preexisting monomer class:
from monclasses.py import P3HT
or you can build the monomer class:
class P3HT(mb.Compound):
def __init__(self):
super(P3HT,self).__init__()
self.add(mb.load("CCCCCCC1=C(SC(=C1))",smiles=True))
self.bond_indices = [24,25]
self.orientations = [[0,0,1],[0,0,-1]]
self.separation = 0.14
self.replace = True
The monomer class must include the atomic indices where the polymerizing bonds will be formed as well as the orientations of the #bonds, the bond separation, and whether you are replacing the atoms where the bond will be formed or not.
smiles = montosmiles(fragment=P3HT())[1] #this line must be run before importing the espaloma function.
The montosmiles function returns both the mbuild compound including both the monomer and dimer as well as the smiles string of the monomer and dimer
``` from functions import EspalomaFxn from functions.EspalomaFxn import espaloma
espaloma(SMILES=smiles, #from montosmiles function XMLFILEPATH='INSERT DESIRED XML FILEPATH', TYPEDFILEPATH='INSERT DESIRED MOL2 FILEPATH') ```
Owner
- Name: Computational Materials Engineering Laboratory
- Login: cmelab
- Kind: organization
- Location: Boise, ID
- Website: https://coen.boisestate.edu/cmelab/
- Repositories: 22
- Profile: https://github.com/cmelab
GitHub Events
Total
- Push event: 2
Last Year
- Push event: 2
Dependencies
- notebook *