v0.0.1

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>

test4.py

@@ -0,0 +1,64 @@
+#!/opt/local/bin/python3
+
+import sys, math
+from math import pi
+import numpy as np
+from numpy import linalg
+from numpy.random import rand, random
+from copy import deepcopy
+
+from DPpack.MolHandling import *
+from DPpack.PTable import *
+
+
+natoms = input("# of atoms: ")
+natoms = int(natoms)
+file = input("xyz file: ")
+
+molecules=[]
+
+with open(file) as fh:
+	xyzfile = fh.readlines()
+
+file += ".new"
+file2 = file + "2"
+fh = open(file, "w")
+fh2 = open(file2, "w")
+
+total_atoms = int(xyzfile.pop(0).split()[0])
+fh.write("{}\n".format(total_atoms))
+comment = xyzfile.pop(0)
+fh.write("{}".format(comment))
+
+nmols = round(total_atoms/natoms)
+for i in range(nmols):
+	molecules.append([])
+	for j in range(natoms):
+		molecules[i].append({})
+		line = xyzfile.pop(0).split()
+		molecules[i][j]['na'] = int(line[0])
+		molecules[i][j]['rx'] = float(line[1])
+		molecules[i][j]['ry'] = float(line[2])
+		molecules[i][j]['rz'] = float(line[3])
+		molecules[i][j]['mass'] = atommass[molecules[0][j]['na']]
+
+for atom in molecules[0]:
+	fh.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']], 
+													  atom['rx'], atom['ry'], atom['rz']))
+	fh2.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']], 
+													  atom['rx'], atom['ry'], atom['rz']))
+
+for i in range(1, nmols):
+	fh2.write("{}\n".format(natoms))
+	fh2.write("{}".format(comment))
+	rmsd, projected_mol = rmsd_fit(molecules[i], molecules[0])
+	print("{:>9.5f}".format(rmsd))
+	for atom in projected_mol:
+		fh.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']], 
+													  atom['rx'], atom['ry'], atom['rz']))
+		fh2.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']], 
+													  atom['rx'], atom['ry'], atom['rz']))
+	
+fh.close()
+fh2.close()
+