def gen_mol_from_fasta(fasta_str):
temp_dir = os.getenv('TEMP_DIR')
if temp_dir:
temp_dir += "/" + fasta_str
else:
temp_dir = os.path.join("/tmp", fasta_str)
try:
os.mkdir(temp_dir)
except:
pass
fdfn = os.path.join(temp_dir, fasta_str)
with open(fdfn + ".fasta", 'w') as f:
f.write(fasta_str + "\n")
mol2out = fdfn + ".mol2"
mol2cout = fdfn + "-cut.mol2"
babel = os.getenv("BABEL_EXE")
subprocess.call(
shlex.split('%s -ifasta %s.fasta --join -omol2 %s' %
(babel, fdfn, mol2out)))
init_mol2 = io.read(mol2out, format="mol2")
nat = init_mol2.get_number_of_atoms()
bonds = init_mol2.get_bonds()
newbonds = []
ie = 18 #this is the atom number of Q
iv = nat - 2 #this is the atom number of the last G
for b in bonds:
if (b[0] > ie - 1 and b[0] < iv) and (b[1] > ie - 1 and b[1] < iv):
newbonds.append([b[0] - ie, b[1] - ie, b[2]])
newmol = init_mol2[ie:iv]
newmol.set_bonds(newbonds)
newmol.set_ffsymbols(init_mol2.get_ffsymbols()[ie:iv])
newmol.write(mol2cout, format="mol2", symbols=newmol.get_ffsymbols())
drei_param = os.path.join(DREI_DIR, "DREI_PARAM")
drei_outdir = os.path.join(temp_dir, "drei")
try:
os.mkdir(drei_outdir)
except:
pass
DFF.create_input(mol2cout, lammpsdrei_template, drei_param, drei_outdir)
drei_comm = os.getenv("LAMMPS_EXE")
#subprocess.call(shlex.split('bash -c "ls %s; cd %s; %s < in.drei |tee out"'%(drei_comm, drei_outdir, drei_comm)))
subprocess.call(
shlex.split('bash -c "cd %s; %s < in.drei > out"' %
(drei_outdir, drei_comm)))
#subprocess.call(shlex.split('bash -c "cp %s ./"' % os.path.join(drei_outdir, relaxed_xyz)))
relaxed_xyz = io.read(os.path.join(drei_outdir, fn_relaxed_xyz), 0)[0]
return relaxed_xyz, init_mol2, fasta_str[1:-1]
def import_atoms(self, filename, cur_frame):
if filename:
filename = filename[0]
old_a = self.get_atoms(cur_frame)
imp_a = read(filename, -1)
new_a = old_a + imp_a
self.initialize([new_a], [filename])
def __init__(self, images, k=0.1, climb=False):
if isinstance(images, str):
# this is a filename
traj = read(images, '0:')
images = []
for atoms in traj:
images.append(atoms)
NEB.__init__(self, images, k, climb, False)
self.calculators = [None] * self.nimages
self.energies_ok = False
def read(self, filenames, index=-1):
images = []
names = []
for filename in filenames:
i = read(filename, index)
if not isinstance(i, list):
i = [i]
images.extend(i)
names.extend([filename] * len(i))
self.initialize(images, names)
def create_input(mol2_input, drei_input_temp, Paramfile, outdir):
mol = io.read(mol2_input, format="mol2")
data, chemical_symbols = CreateLammps(mol, Paramfile)
with open(os.path.join(outdir, "data"), "w") as f:
f.write(data)
if type(drei_input_temp) == type("str"):
lammps_temp = Template(drei_input_temp)
else:
lammps_temp = Template(open(drei_input_temp, 'r').read())
with open(os.path.join(outdir, "in.drei"), "w") as f:
f.write(lammps_temp.substitute(SYM=chemical_symbols))
def vasp_vol_relax():
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
calc = Vasp(xc='LDA', isif=7, nsw=5,
ibrion=1, ediffg=-1e-3, lwave=False, lcharg=False)
calc.calculate(Al)
# Explicitly parse atomic position output file from Vasp
CONTCAR_Al = io.read('CONTCAR', format='vasp')
print('Stress after relaxation:\n', calc.read_stress())
print('Al cell post relaxation from calc:\n', calc.get_atoms().get_cell())
print('Al cell post relaxation from atoms:\n', Al.get_cell())
print('Al cell post relaxation from CONTCAR:\n', CONTCAR_Al.get_cell())
# All the cells should be the same.
assert (calc.get_atoms().get_cell() == CONTCAR_Al.get_cell()).all()
assert (Al.get_cell() == CONTCAR_Al.get_cell()).all()
return Al
import numpy as np
from ase_ext.io import read, PickleTrajectory
from ase_ext.structure import bulk
from ase_ext.calculators.emt import EMT
a0 = 3.52 / np.sqrt(2)
c0 = np.sqrt(8 / 3.0) * a0
print('%.4f %.3f' % (a0, c0 / a0))
for i in range(3):
traj = PickleTrajectory('Ni.traj', 'w')
eps = 0.01
for a in a0 * np.linspace(1 - eps, 1 + eps, 4):
for c in c0 * np.linspace(1 - eps, 1 + eps, 4):
ni = bulk('Ni', 'hcp', a=a, covera=c / a)
ni.set_calculator(EMT())
ni.get_potential_energy()
traj.write(ni)
configs = read('Ni.traj@:')
energies = [config.get_potential_energy() for config in configs]
ac = [(config.cell[0, 0], config.cell[2, 2]) for config in configs]
from ase_ext.optimize import polyfit
p = polyfit(ac, energies)
from scipy.optimize import fmin_bfgs
a0, c0 = fmin_bfgs(p, (a0, c0))
print('%.4f %.3f' % (a0, c0 / a0))
assert abs(a0 - 2.469) < 0.001
assert abs(c0 / a0 - 1.624) < 0.005
a.z)
return strc
if len(sys.argv) != 5:
print(
"""\n Converts a coordinate file (xyz, pdb, mol2 ...) into lammps reax input \n\nUsage: \n\t> python3%s xyz reaxtemplateFile xyzmodelid outputdir \n\n\te.g. python3 %s molecule.xyz in.reax.temp 0 Reax-relax\n"""
% (sys.argv[0], sys.argv[0]))
exit()
finxyz = sys.argv[1]
finp = sys.argv[2]
nm = int(sys.argv[3])
fdir = sys.argv[4]
mol = read(finxyz, nm)
pos = mol.get_positions()
mins = pos.min(axis=0)
maxs = pos.max(axis=0)
#cell = get_cell(pos)
#maxs = (maxs - mins)/2
symlist = set(mol.get_chemical_symbols())
symlist = sorted(symlist)
syms = ase.Atoms(symlist)
indatoms = syms.get_atomic_numbers()
masses, chemical_symbols = get_masses(syms)
with open(os.path.join(fdir, "data"), "w") as f:
f.write(reax_data_temp.substitute(NAT=mol.get_number_of_atoms(),\
from ase_ext import Atoms
from ase_ext.io import read, write
atoms = Atoms('HH', [[.0,.0,.0], [.0,.0,.74]], pbc=True, cell=[5, 5, 5])
atoms.set_initial_magnetic_moments([1, -1])
moms = atoms.get_initial_magnetic_moments()
write('test.traj',atoms)
atoms = read('test.traj')
assert (atoms.get_initial_magnetic_moments() == moms).all()
except ImportError:
pass
else:
w += ['png', 'eps']
for format in w:
print(format, 'O', end=' ')
fname1 = 'io-test.1.' + format
fname2 = 'io-test.2.' + format
write(fname1, atoms, format=format)
if format not in ['cube', 'png', 'eps', 'cfg', 'struct']:
write(fname2, images, format=format)
if format in r:
print('I')
a1 = read(fname1)
assert np.all(
np.abs(a1.get_positions() - atoms.get_positions()) < 1e-6)
if format in ['traj', 'cube', 'cfg', 'struct']:
assert np.all(np.abs(a1.get_cell() - atoms.get_cell()) < 1e-6)
if format in ['cfg']:
assert np.all(
np.abs(a1.get_array('extra') -
atoms.get_array('extra')) < 1e-6)
if format not in ['cube', 'png', 'eps', 'cfg', 'struct']:
a2 = read(fname2)
a3 = read(fname2, index=0)
a4 = read(fname2, index=slice(None))
else:
print()
from string import Template
from numpy import *
from scipy import spatial
import sys, os
PYYAEHMOP_DIR = os.getenv("PYYAEHMOP_DIR")
YAEHMOP_DIR = os.getenv("YAEHMOP_DIR")
sys.path.append(PYYAEHMOP_DIR)
from Yaehmop import *
ASE_DIR = os.getenv("ASE_DIR")
sys.path.append(ASE_DIR)
from ase_ext.io import read
import ase_ext as ase
if len(sys.argv) != 3:
print(
"""\n Converts a coordinate file (xyz, pdb, mol2 ...) into YAEHMOP input \n\nUsage: \n\t> python3%s xyz xyzmodelid \n\n\te.g. python3 %s molecule.xyz 0 \n"""
% (sys.argv[0], sys.argv[0]))
exit()
fn = sys.argv[1]
id = sys.argv[2]
mol = read(fn, id)
ymol = Yaehmop(mol=mol,
yaehmop_binary=os.path.join(YAEHMOP_DIR, "bind"),
param_file=os.path.join(YAEHMOP_DIR, "eht_param.dat"))
ymol.create_input(just_matrices=False)
ymol.run()
import numpy as np
from ase_ext import Atoms
from ase_ext.units import fs
from ase_ext.calculators.test import TestPotential
from ase_ext.calculators.emt import EMT
from ase_ext.md import VelocityVerlet
from ase_ext.io import PickleTrajectory, read
from ase_ext.optimize import QuasiNewton
np.seterr(all='raise')
a = Atoms('4X',
masses=[1, 2, 3, 4],
positions=[(0, 0, 0), (1, 0, 0), (0, 1, 0), (0.1, 0.2, 0.7)],
calculator=TestPotential())
print(a.get_forces())
md = VelocityVerlet(a, dt=0.5 * fs, logfile='-', loginterval=500)
traj = PickleTrajectory('4N.traj', 'w', a)
md.attach(traj.write, 100)
e0 = a.get_total_energy()
md.run(steps=10000)
del traj
assert abs(read('4N.traj').get_total_energy() - e0) < 0.0001
qn = QuasiNewton(a)
qn.run(0.001)
assert abs(a.get_potential_energy() - 1.0) < 0.000002
from ase_ext import Atoms
from ase_ext.io import read, write
from ase_ext.calculators import Exciting
from ase_ext.units import Bohr, Hartree
from ase_ext.test import NotAvailable
try:
import lxml
except ImportError:
raise NotAvailable('This test need lxml module.')
a = Atoms('N3O',
[(0, 0, 0), (1, 0, 0), (0, 0, 1), (0.5, 0.5, 0.5)],
pbc=True)
raise NotAvailable('Problem with lxml module.')
write('geo.exi', a)
b = read('geo.exi')
print(a)
print(a.get_positions())
print(b)
print(b.get_positions())
calculator = Exciting(dir='excitingtestfiles',
kpts=(4, 4, 3),
maxscl=3,
#bin='/fshome/chm/git/exciting/bin/excitingser'
)
from ase_ext import Atoms
from ase_ext.calculators.lj import LennardJones
from ase_ext.optimize.basin import BasinHopping
from ase_ext.io import PickleTrajectory, read
from ase_ext.units import kB
N = 7
R = N**(1. / 3.)
pos = np.random.uniform(-R, R, (N, 3))
s = Atoms('He' + str(N), positions=pos)
s.set_calculator(LennardJones())
ftraj = 'lowest.traj'
traj = PickleTrajectory(ftraj, 'w', s)
bh = BasinHopping(s, temperature=100 * kB, dr=0.5, optimizer_logfile=None)
bh.attach(traj)
bh.run(10)
Emin, smin = bh.get_minimum()
# recalc energy
smin.set_calculator(LennardJones())
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
traj.close()
smim = read(ftraj)
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
#view(smin)
