Comments (6)
I think I've figured out that the nextIndexI code in operation.chain doesn't consider cases where the nextIndexI is part of the current molecule1 and not molecule2.
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What's happening is chain is used assuming that the next molecule is being attached to molecule2 of the last attachment.
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Maybe we should resort to using _combine for non-successive attachments? But I like the idea of forcing a Molecule.configure call when the process is completed. [.configure is] Totally wasteful in a multi-attachment process and takes a considerable amount of time with this large molecules like CNTs.
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I could keep chain but switch between the use of nextIndexI with the use of a keyword argument that defaults to not using it? Ultimately a question of design I think.
Maybe _configure should only be called when it is explicitly needed, or make the user call it when needed and want access to those generated attributes. define_energy/gradient_routine is (atm) supposed to be called when needed (like preceeding energy minimization).
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I could do something where if the inputted indices are negative, then attach them to molecule1. But that would require the user to know this. It may be more straightforward, however more cluttered, to use a keyword argument that defaults to to something.
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Going to close the issue. Documentation should reflect this specific use of .chain now. It was more important to be aware of the function, it was not actually an issue with the code.
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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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