import matplotlib.pyplot as plt import re, sys import numpy as np from AnalyzeTrj import get_data from Molecule import Molecule from math import pi gen = get_data("md_tsh.trj", start=0.0) t_ary = [] x_ary = [] v_ary = [] lim = 100000 for a in gen: t, x, v = a if t > lim: break t_ary.append(t) x_ary.append(x[0][0]) v_ary.append(v[0][0]) plt.plot(t_ary, x_ary) #plt.plot(t_ary,v_ary) plt.show()
import matplotlib.pyplot as plt import re import numpy as np from Constants import hartree2kj, hartree2ev from AnalyzeTrj import get_data from Molecule import Molecule from math import pi import sys gen = get_data("md_tsh_qmmm.trj", start=0.0) mol = Molecule(["C","H","O","O","H"]) t_ary = [] l_ary = [] l2_ary = [] l3_ary = [] lim = 1200 for a in gen: t, x, v = a if t > lim: break mol.set_positions(x,unit="bohr") #print t, mol.get_bond_length(1,2,unit="ang") t_ary.append(t) l_ary.append(mol.get_bond_length(3,4,unit="ang")) l2_ary.append(mol.get_bond_length(0,1,unit="ang")) l3_ary.append(mol.get_bond_length(1,4,unit="ang")) #l_ary.append(mol.get_dihedral(1,0,2,4)*180/pi) f, (ax1, ax2) = plt.subplots(2, sharex=True)
import matplotlib.pyplot as plt import re, sys import numpy as np from AnalyzeTrj import get_data from Molecule import Molecule from math import pi gen = get_data("md_tsh.trj", start=0.0) t_ary = [] x_ary = [] v_ary = [] lim = 100000 for a in gen: t, x, v = a if t > lim: break t_ary.append(t) x_ary.append(x[0][0]) v_ary.append(v[0][0]) plt.plot(t_ary,x_ary) #plt.plot(t_ary,v_ary) plt.show()
import matplotlib.pyplot as plt import re import numpy as np from Constants import hartree2kj, hartree2ev from AnalyzeTrj import get_data from Molecule import Molecule from math import pi import sys gen = get_data("md_tsh_qmmm.trj", start=0.0) mol = Molecule(["C", "H", "O", "O", "H"]) t_ary = [] l_ary = [] l2_ary = [] l3_ary = [] lim = 1200 for a in gen: t, x, v = a if t > lim: break mol.set_positions(x, unit="bohr") #print t, mol.get_bond_length(1,2,unit="ang") t_ary.append(t) l_ary.append(mol.get_bond_length(3, 4, unit="ang")) l2_ary.append(mol.get_bond_length(0, 1, unit="ang")) l3_ary.append(mol.get_bond_length(1, 4, unit="ang")) #l_ary.append(mol.get_dihedral(1,0,2,4)*180/pi) f, (ax1, ax2) = plt.subplots(2, sharex=True)