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cmelab / polybinder

Initialization of thermoplastic polymer systems to simulate thermal welding
GNU General Public License v3.0
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Divide final box lengths by the reference distance #9

Closed chrisjonesBSU closed 3 years ago

chrisjonesBSU commented 3 years ago

The box edge length that is calculated for our final target volume needs to be divided by the reference distance used in hoomd_simulation.py and hoomd_snapshot.py. The best way might be to just use the same method used in those mBuild files

    if auto_scale:
        ref_mass = max([atom.mass for atom in structure.atoms])
        pair_coeffs = list(set((atom.type,
                                atom.epsilon,
                                atom.sigma) for atom in structure.atoms))
        ref_energy = max(pair_coeffs, key=operator.itemgetter(1))[1]
        ref_distance = max(pair_coeffs, key=operator.itemgetter(2))[2]
chrisjonesBSU commented 3 years ago

Fixed by pull request #11