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69 lines
2.2 KiB
69 lines
2.2 KiB
2 years ago
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import warnings
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warnings.filterwarnings("ignore")
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import MDAnalysis
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import MDAnalysis.analysis.rdf
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import numpy as np
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from pymatgen.core import lattice
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import builtins
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import os
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def rdf(traject,latt,pair,endrange,resolution):
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cell = []
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with open(latt, 'r') as f:
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for line in f:
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if 'TV' in line:
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cell.append(list(map(float, line.split()[1:4])))
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box = lattice.Lattice(cell)
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(lx, ly, lz), (a, b, c) = box.lengths_and_angles
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u = MDAnalysis.Universe(traject, format='XYZ')
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u.dimensions = np.array([lx, ly, lz, a, b, c], dtype=np.float32)
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builtins.u = u
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ag1 = None
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ag2 = None
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elems = pair.split('-')
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# Definisi file keluaran
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outfile = open('rdf_{}-{}.dat'.format(elems[0],elems[1]), 'w')
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ag1 = u.select_atoms(f'name {elems[0]}')
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ag2 = u.select_atoms(f'name {elems[1]}')
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nbins = int((endrange - 0.05)/resolution)
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rdf = MDAnalysis.analysis.rdf.InterRDF(ag1, ag2, nbins=nbins, range=(0.05, endrange), verbose=True)
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rdf.run()
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vol = np.power(rdf.edges[1:], 3) - np.power(rdf.edges[:-1], 3)
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vol *= 4/3.0 * np.pi
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box_vol = box.volume
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pair_den = box_vol / (len(ag1.atoms) * len(ag2.atoms))
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integral = rdf.rdf / (pair_den / vol)
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total = 0.0
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step = 0
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for r, v, d in zip(rdf.bins, rdf.rdf, integral):
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step += 1
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total += d/len(ag1.atoms)
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if (step == 1):
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continue
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print('{:8.4f} {:8.4f} {:8.4f}'.format(r, v, total), file=outfile)
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outfile.close()
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with open('rdf_{}-{}.gp'.format(elems[0],elems[1]),'w') as fout:
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print("""set terminal pdf
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set output "rdf_{}-{}.pdf"
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set key
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set yrange [0:10]
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set ytics (0,1,2,3,4,5,6,7,8,9,10)
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set xlabel "Distance [Angstroms]"
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set ylabel "RDF [arb.]"
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set style line 1 lc rgb '#00008b' lt 1 lw 2 pt 7
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set style line 2 lc rgb '#FF0000' lt 1 lw 2 pt 7
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plot 'rdf_{}-{}.dat' u 1:2 with line title "RDF" linestyle 1,\
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'' u 1:3 with line title "Coordination Number" linestyle 2""".format(elems[0],elems[1],elems[0],elems[1]),file=fout)
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os.system('gnuplot rdf_{}-{}.gp'.format(elems[0],elems[1]))
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