27 lines
974 B
Python
27 lines
974 B
Python
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import numpy as np
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import mdevaluate as md
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import mdevaluate.extra.free_energy_landscape as fel
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data_dir = "/data/skloth/python_packages/mdevaluate_examples/plots"
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path_to_sim = (
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"/data/skloth/sim/silica_pore/tip4p2005/D3_L6_S4.9_R0/T300_isochor/T250_nvt_long"
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)
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trajectory = md.open(path_to_sim, topology="run.tpr", trajectory="out/traj_full.xtc")
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OW = trajectory.subset(atom_name="OW")
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box = np.diag(trajectory[0].box)
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box_voxels = (box // [0.05, 0.05, 0.05] + [1, 1, 1]) * [0.05, 0.05, 0.05]
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occupation_matrix = fel.occupation_matrix(OW, skip=0, segments=len(OW))
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maxima_matrix = fel.find_maxima(occupation_matrix, box=box_voxels, edge_length=0.05)
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maxima_matrix = fel.add_distances(maxima_matrix, "cylindrical", box / 2)
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r_bins = np.arange(0, 2, 0.02)
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distance_bins = np.arange(0.05, 1.55, 0.1)
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energy_df = fel.distance_resolved_energies(
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maxima_matrix, distance_bins, r_bins, box, 225
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)
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result = fel.find_energy_maxima(energy_df, r_min=0.05, r_max=0.15)
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