"""
#test_what = "contraforce"
# specify which testfunction == first input argument
try:
testfun = argv[1]
except IndexError:
testfun = "zmat"
# The ASE atoms object for calculating the forces
ar4 = Atoms("Ar4")
ar4.set_calculator(LennardJones())
# PES in cartesian coordiantes:
pes = QFunc(ar4, ar4.get_calculator())
# some variables for the starting values
# length
var1 = 1.12246195815
# and angles (in rad)
var3 = 60.0 / 180. * pi
var4 = 70.5287791696 / 180. * pi
var6 = 59.0020784259 / 180. * pi
var7 = 60.4989607871 / 180 * pi
var8 = pi
td_s = var1
def reduce(vec, mask):
def getTrajactory(self, fileobj='result'):
from ase.atoms import Atoms, Atom
from ase import units
from ase.calculators.singlepoint import SinglePointCalculator
"""Reads quantum espresso output text files."""
fileobj = open(fileobj, 'rU')
lines = fileobj.readlines()
#print lines
images = []
lattice = self.getLattices()
for number, line in enumerate(lines):
if 'number of atoms/cell' in line:
numAtom = int(line.split()[-1])
if 'number of atomic types' in line:
numElement = int(line.split()[-1])
if "atomic species valence mass" in line:
elementLines = lines[number + 1:number + 1 + numElement]
elementsInfo = [[(i) for i in l.split()] for l in elementLines]
#print numAtom
if 'lattice parameter (alat)' in line:
line = line.strip().split('=')[1].strip().split()[0]
lattice_parameter = float(line) * units.Bohr
if "crystal axes: (cart. coord. in units of alat)" in line:
ca_line_no = number
cell = np.zeros((3, 3))
for number, line in enumerate(lines[ca_line_no + 1:ca_line_no +
4]):
line = line.split('=')[1].strip()[1:-1]
values = [float(value) for value in line.split()]
cell[number, 0] = values[0]
cell[number, 1] = values[1]
cell[number, 2] = values[2]
cell *= lattice_parameter
if "site n. atom positions (alat units)" in line:
initPositionLines = lines[number + 1:number + 1 + numAtom]
elements = np.array([l.split()[1] for l in initPositionLines])
scaledPositions = np.array([[float(i) for i in l.split()[6:9]]
for l in initPositionLines])
atom = Atoms(symbols=elements,
scaled_positions=scaledPositions,
cell=cell,
pbc=True)
images.append(atom)
cellkey = 'CELL_PARAMETERS (angstrom)'
if cellkey in line:
ca_line_no = number
cell = np.array([[float(num) for num in line.split()]
for line in lines[ca_line_no + 1:ca_line_no +
4]])
# for number, line in enumerate(lines[ca_line_no + 1: ca_line_no + 4]):
# line = line.split('=')[1].strip()[1:-1]
# values = [float(value) for value in line.split()]
# cell[number, 0] = values[0]
# cell[number, 1] = values[1]
# cell[number, 2] = values[2]
posikey = 'ATOMIC_POSITIONS'
if posikey in line:
positionLines = lines[number + 1:number + 1 + numAtom]
elements = np.array([l.split()[0] for l in positionLines])
positions = np.array([[float(i) for i in l.split()[1:]]
for l in positionLines])
if 'angstrom' in line:
atom = Atoms(symbols=elements,
positions=positions,
cell=cell,
pbc=True)
elif 'crystal' in line:
atom = Atoms(symbols=elements,
scaled_positions=positions,
cell=cell,
pbc=True)
images.append(atom)
if "Forces acting on atoms (cartesian axes, Ry/au):" in line:
#print number
atom = images[-1]
forceLines = lines[number + 2:number + 2 + numAtom]
forces = np.array([[float(i) for i in l.split()[-3:]]
for l in forceLines])
forces *= units.Ry / units.Bohr
calc = SinglePointCalculator(atom, forces=forces)
atom.set_calculator(calc)
if "total stress" in line:
#print number
atom = images[-1]
selectLines = lines[number + 1:number + 4]
selectPrperties = np.array([[float(i) for i in l.split()[-3:]]
for l in selectLines])
#forces *= units.Ry / units.Bohr
calc = atom.get_calculator()
#print(selectPrperties)
calc.results['stress'] = selectPrperties
#atom.set_calculator(calc)
filename = 'Trajectory'
from ase.io import write
if len(images) > 1:
write(filename, images[1:], 'traj')
else:
write(filename, images, 'traj')
from ase.io.trajectory import Trajectory
traj = Trajectory(filename)
return traj
# Atoms object needs to have all these in order to be able to run correctly:
PdH.set_calculator(calculator)
PdH.set_pbc(True)
sc = 5.59180042562320832916
cell = [[1.0000000000000000, 0.0000000000000000, 0.0000000000000000],
[0.5000000000000000, 0.8660254037844386, 0.0000000000000000],
[0.0000000000000000, 0.0000000000000000, 1.0000000000000000]]
cell = array(cell) * sc
PdH.set_cell(cell)
# Do calculation in Cartesian coordinates
fun1 = Cartesian()
# PES in cartesian coordiantes:
pes = QFunc(PdH, PdH.get_calculator())
def reduce(vec, mask):
"""
Function for generating starting values.
Use a mask to reduce the complete vector.
"""
vec_red = []
for i, m in enumerate(mask):
if m:
vec_red.append(vec[i])
return array(vec_red)
# The starting geometries in flattened Cartesian coordinates
min1 = array([ 1.3979501064058020, 0.8071068702470560, 1.0232994778890470,
0.0000000000000000, 0.0000000000000000, 0.0000000000000000,
