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)
