from ase import Atoms
from ase.constraints import FixBondLengths
from ase.calculators.tip3p import TIP3P, rOH, angleHOH
from ase.md import Langevin
import ase.units as units
from ase.io.trajectory import Trajectory
import numpy as np


# Set up water box at 20 deg C density
x = angleHOH * np.pi / 180 / 2
pos = [[0, 0, 0],
       [0, rOH * np.cos(x), rOH * np.sin(x)],
       [0, rOH * np.cos(x), -rOH * np.sin(x)]]
atoms = Atoms('OH2', positions=pos)

vol = ((18.01528 / 6.022140857e23) / (0.9982 / 1e24))**(1 / 3.)
atoms.set_cell((vol, vol, vol))
atoms.center()

atoms = atoms.repeat((3, 3, 3))
atoms.set_pbc(True)

# RATTLE-type constraints on O-H1, O-H2, H1-H2.
atoms.constraints = FixBondLengths([(3 * i + j, 3 * i + (j + 1) % 3)
                                    for i in range(3**3)
                                    for j in [0, 1, 2]])

tag = 'tip3p_27mol_equil'
atoms.calc = TIP3P(rc=4.5)
md = Langevin(atoms, 1 * units.fs, temperature=300 * units.kB,
              friction=0.01, logfile=tag + '.log')

traj = Trajectory(tag + '.traj', 'w', atoms)
md.attach(traj.write, interval=1)
md.run(4000)

# Repeat box and equilibrate further.
tag = 'tip3p_216mol_equil'
atoms.set_constraint()  # repeat not compatible with FixBondLengths currently.
atoms = atoms.repeat((2, 2, 2))
atoms.constraints = FixBondLengths([(3 * i + j, 3 * i + (j + 1) % 3)
                                    for i in range(len(atoms) / 3)
                                    for j in [0, 1, 2]])
atoms.calc = TIP3P(rc=7.)
md = Langevin(atoms, 2 * units.fs, temperature=300 * units.kB,
              friction=0.01, logfile=tag + '.log')

traj = Trajectory(tag + '.traj', 'w', atoms)
md.attach(traj.write, interval=1)
md.run(2000)
