Comments (3)
tab10
commented on September 28, 2024
It'd be helpful to create an examples folder with how to generate some molecule like graphene, maybe write the steps in a txt file?
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ajkerr0
commented on September 28, 2024
Yes, it would be nice to have a tutorial up at some point. I can send you something I showed Dr. Mullen and Dr. Glatzhofer before.
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ajkerr0
commented on September 28, 2024
Maybe this is pedantic but since we haven't actually merged the files yet I don't want to close this issue at this time. Should it be closed when we merge into master or into some other branch? I honestly don't know the best practices.
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Related Issues (20)
- Missing simple repeated molecule combination function
- Calculations using kappa HOT 5
- Program crashes on CNT generation for tubes with length != 3 and radius != 1 HOT 1
- Consider a different recursive algorithm to accumulate the desired number of valence states in bond type assignment
- Redundant build code in molecule.py
- Should be able to remove zero modes more easily
- Major rework of forcefields needed
- Redundant functions in atom type parsing
- Forcefield object is not needed in Molecule instantiation HOT 1
- Missing forcefield parameter file implementation from AmberTools HOT 1
- Missing analytical Hessian calculation HOT 1
- Inconsistent kappa values calculated HOT 4
- Missing consideration of improper torsionals in energy calculations
- Consider hydrogenating every carbon base structure HOT 1
- Memory problem storing parameters from parsing, particular dihedral parameters. HOT 1
- Consider performing green's function coefficient calculation in separate package HOT 2
- Missing special consideration of special chemical groups in parameter assignment HOT 3
- Need to store 'grid' values based on parameterization, allow for plotting. HOT 1
- CNTs (armchair) have one section deformed initially
- Dihedral ff parameters do not get assigned as intended in some molecules
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