def setup_calculator(self):
parameters = dict(
neighbor = '2.0 nsq',
)
calc = ReaxFF(ff_file_path=self.ff_file_path, parameters=parameters)
return calc
from multiasecalc.utils import get_datafile
import numpy as np
dimer_name = "2-pyridoxine_2-aminopyridine_complex"
atoms = s22.create_s22_system(dimer_name) # full system
atom_counts = s22.get_number_of_dimer_atoms(dimer_name)
Mixer.set_atom_ids(atoms) # sequence of numbers in same order as positions
# were given above, index starts from 0
atoms_m1 = atoms[:atom_counts[0]] # first molecule
atoms_m2 = atoms[atom_counts[0]:] # second molecule
calc_gpaw = GPAW(nbands=-2, txt="h2_1.txt")
calc_reaxff = ReaxFF(ff_file_path=get_datafile("ffield.reax.new"),
implementation="C")
reaxff_cell = (100.0, 100.0, 100.0)
gpaw_cell = (10.0, 10.0, 10.0)
filter_full_system = AtomListSelector(
range(len(atoms)), dict(zip(range(len(atoms)), [1.0] * len(atoms))))
filter_qm_region = AtomListSelector(
range(atom_counts[0]),
dict(zip(range(atom_counts[0]), [1.0] * atom_counts[0])))
forces_full_system = ForceCalculation("forces_full_sys",
selector=filter_full_system,
calculator=calc_reaxff,
cell=reaxff_cell)
from ase import Atoms
from multiasecalc.lammps.reaxff import ReaxFF
from multiasecalc.utils import get_datafile
d = 0.74
#d = 3.0
a = 6.0
atoms_all = Atoms("H3",
positions=[(0, 0, 0), (0, 0, d), (0, 0, 2 * d)],
cell=(100 * a, 100 * a, 100 * a))
atoms_all.center()
calc_1 = ReaxFF(specorder=("C", "H", "O", "N", "S"),
implementation="C",
ff_file_path=get_datafile("ffield.reax"))
atoms_all.set_calculator(calc_1)
print(atoms_all.get_forces())
print(atoms_all.get_potential_energy())
def calculate_charges(atoms):
from multiasecalc.lammps.reaxff import ReaxFF
atoms.center(vacuum=1)
atoms.calc = ReaxFF(ff_file_path=get_datafile('ffield.reax'), parameters = dict(neighbor='2.0 nsq'))
atoms.get_potential_energy()
from ase.data import s22
from ase import units
import numpy as np
import ase.io
from ase.io.trajectory import PickleTrajectory
atoms = s22.create_s22_system('Methane_dimer')
atoms.center(vacuum=10.0)
print atoms.positions
atoms.calc = COMPASS(ff_file_path=get_datafile('compass.frc'), debug=True)
optimizer = LAMMPSOptimizer(atoms)
optimizer.run()
print atoms.positions
atoms.calc = ReaxFF(ff_file_path=get_datafile('ffield.reax'), debug=True)
dyn = LAMMPS_NVT(atoms,
1 * units.fs,
100,
trajectory='test.traj',
traj_interval=2)
dyn.run(5)
atoms.calc = COMPASS(ff_file_path=get_datafile('compass.frc'), debug=True)
dyn.run(10)
trj = PickleTrajectory('test.traj', 'r')
for t in trj:
print t.positions