Auto cell scaling function

[qzhu2017]

Find a direction with large spacing and then make the direction shorter.

[qzhu2017]

from pyxtal import pyxtal
from pyxtal.molecule import pyxtal_molecule

asp = pyxtal_molecule('CC(=O)OC1=CC=CC=C1C(=O)O.smi', active_sites=[(11), (12)])
xtal = pyxtal(molecular=True)
xtal.from_random(3, 14, [asp], sites=[["4e"]])
print(xtal)
print(xtal.get_separations([[1, 0, 0], [0, 1, 0], [0, 0, 1]]))
xtal.to_file('init.cif')

# Iteratively reduce the empty space
xtal.cut_lattice(2.0, True)
xtal.cut_lattice(2.0, True)
xtal.cut_lattice(2.0, True)
xtal.to_file('cut.cif')

site = xtal.mol_sites[0]
print(site.get_energy())
site.optimize_orientation_by_energy(20)#, verbose=True)
print(site.get_energy())
xtal.to_file('opt.cif')
print(xtal)

[qzhu2017]

[qzhu2017]

from pyxtal import pyxtal
from pyxtal.molecule import pyxtal_molecule

# Acceptor, Donor, H
asp = pyxtal_molecule('CC(=O)OC1=CC=CC=C1C(=O)O.smi', active_sites=[[11], [12], [20]])
xtal = pyxtal(molecular=True)

#xtal.from_random(3, 14, [asp], sites=[["4e"]])
xtal.from_random(3, 14, [asp], [8], sites=[["4e", "4e"]])
print(xtal); xtal.to_file('init.cif'); print(xtal.get_orientation_energy())
xtal.optimize_lattice_and_rotation()
print(xtal); xtal.to_file('opt.cif'); print(xtal.get_orientation_energy())

# BT: XXV
m1 = pyxtal_molecule('OC(=O)c1cc(cc(c1)N(=O)=O)N(=O)=O.smi', active_sites=[[], [0], [15]])
m2 = pyxtal_molecule('Cc1ccc2N3CN(Cc2c1)c1ccc(C)cc1C3.smi', active_sites=[[5], [], []])
xtal.from_random(3, 14, [m1, m2], [4, 4], sites=[["4e"], ["4e"]])
print(xtal); xtal.to_file('init.cif'); print(xtal.get_orientation_energy())
xtal.optimize_lattice_and_rotation()
print(xtal); xtal.to_file('opt.cif'); print(xtal.get_orientation_energy())