Esempio n. 1
0
def test_read_struct():
    struct = Atoms(
        'H4', pbc=[True, True, True],
        cell=[[4.00759, 0.0, 0.0],
              [-2.003795, 3.47067475, 0.0],
              [3.06349683e-16, 5.30613216e-16, 5.00307]],
        positions=[[-2.003795e-05, 2.31379473, 0.875437189],
                   [2.00381504, 1.15688001, 4.12763281],
                   [2.00381504, 1.15688001, 3.37697219],
                   [-2.003795e-05, 2.31379473, 1.62609781]],
    )
    struct.info = {'dataset': 'deltatest', 'kpoints': np.array([28, 28, 20]),
                   'identifier': 'deltatest_H_1.00',
                   'unique_id': '4cf83e2f89c795fb7eaf9662e77542c1'}
    ase.io.write('tmp.xyz', struct)
Esempio n. 2
0
C         -1.15405        2.86652       -1.26699
C         -5.53758        3.70936        0.63504
C         -7.28250        4.71303       -3.82016

""")
f.close()
a = ase.io.read('structure.xyz')
os.unlink('structure.xyz')

# read xyz with / in key value
f = open('slash.xyz', 'w')
f.write("""4
key1=a key2=a/b
Mg        -4.25650        3.79180       -2.54123
C         -1.15405        2.86652       -1.26699
C         -5.53758        3.70936        0.63504
C         -7.28250        4.71303       -3.82016
""")
f.close()
a = ase.io.read('slash.xyz')
assert a.info['key1'] == r'a'
assert a.info['key2'] == r'a/b'
os.unlink('slash.xyz')

struct = Atoms('H4', pbc=[True, True, True],
                cell=[[4.00759, 0.0, 0.0], [-2.003795, 3.47067475, 0.0], [3.06349683e-16, 5.30613216e-16, 5.00307]], positions=[[-2.003795e-05, 2.31379473, 0.875437189], [2.00381504, 1.15688001, 4.12763281], [2.00381504, 1.15688001, 3.37697219], [-2.003795e-05, 2.31379473, 1.62609781]])
struct.info = {'key_value_pairs': {'dataset': 'deltatest', 'kpoints': np.array([28, 28, 20]), 'identifier': 'deltatest_H_1.00'}, 'unique_id': '4cf83e2f89c795fb7eaf9662e77542c1'}

ase.io.write('tmp.xyz', struct)
os.unlink('tmp.xyz')
Esempio n. 3
0
assert a.info['key3'] == r'a@b'
assert a.info['key4'] == r'a@b'
os.unlink('slash.xyz')

struct = Atoms('H4',
               pbc=[True, True, True],
               cell=[[4.00759, 0.0, 0.0], [-2.003795, 3.47067475, 0.0],
                     [3.06349683e-16, 5.30613216e-16, 5.00307]],
               positions=[[-2.003795e-05, 2.31379473, 0.875437189],
                          [2.00381504, 1.15688001, 4.12763281],
                          [2.00381504, 1.15688001, 3.37697219],
                          [-2.003795e-05, 2.31379473, 1.62609781]])
struct.info = {
    'key_value_pairs': {
        'dataset': 'deltatest',
        'kpoints': np.array([28, 28, 20]),
        'identifier': 'deltatest_H_1.00'
    },
    'unique_id': '4cf83e2f89c795fb7eaf9662e77542c1'
}

ase.io.write('tmp.xyz', struct)
os.unlink('tmp.xyz')

# Complex properties line. Keys and values that break with a regex parser.
# see https://gitlab.com/ase/ase/issues/53 for more info

complex_xyz_string = (
    ' '  # start with a separator
    'str=astring '
    'quot="quoted value" '
    u'quote_special="a_to_Z_$%%^&*\xfc\u2615" '
Esempio n. 4
0
def read_lammps_dump(fileobj, index=-1):
    """Method which reads a LAMMPS dump file."""
    if isinstance(fileobj, str):
        f = paropen(fileobj)
    else:
        f = fileobj

    # load everything into memory
    lines = f.readlines()

    natoms = 0
    images = []

    while len(lines) > natoms:
        line = lines.pop(0)

        if 'ITEM: TIMESTEP' in line:
            natoms = 0
            lo = []
            hi = []
            tilt = []
            #id = [] ; types = []
            positions = None
            velocities = None
            forces = None
            quaternions = None
            charges = None

        if 'ITEM: NUMBER OF ATOMS' in line:
            line = lines.pop(0)
            natoms = int(line.split()[0])

        if 'ITEM: BOX BOUNDS' in line:
            # save labels behind "ITEM: BOX BOUNDS" in triclinic case (>=lammps-7Jul09)
            tilt_items = line.split()[3:]
            for i in range(3):
                line = lines.pop(0)
                fields = line.split()
                lo.append(float(fields[0]))
                hi.append(float(fields[1]))
                if (len(fields) >= 3):
                    tilt.append(float(fields[2]))

            # determine cell tilt (triclinic case!)
            if (len(tilt) >= 3):
                # for >=lammps-7Jul09 use labels behind "ITEM: BOX BOUNDS" to assign tilt (vector) elements ...
                if (len(tilt_items) >= 3):
                    xy = tilt[tilt_items.index('xy')]
                    xz = tilt[tilt_items.index('xz')]
                    yz = tilt[tilt_items.index('yz')]
                # ... otherwise assume default order in 3rd column (if the latter was present)
                else:
                    xy = tilt[0]
                    xz = tilt[1]
                    yz = tilt[2]
            else:
                xy = xz = yz = 0
            xhilo = (hi[0] - lo[0]) - abs(xy) - abs(xz)
            yhilo = (hi[1] - lo[1]) - abs(yz)
            zhilo = (hi[2] - lo[2])
            celldispx = lo[0] - min(0, xy) - min(0, xz)
            celldispy = lo[1] - min(0, yz)
            celldispz = lo[2]

            cell = [[xhilo, 0, 0], [xy, yhilo, 0], [xz, yz, zhilo]]
            celldisp = [[celldispx, celldispy, celldispz]]

        if 'ITEM: ATOMS' in line:
            atom_attributes = {}
            for (i, x) in enumerate(line.split()[2:]):
                atom_attributes[x] = i

            positions = np.zeros((natoms, 3)) * np.nan
            types = np.empty(natoms, dtype=int)
            if 'vx' in atom_attributes:
                velocities = np.zeros((natoms, 3)) * np.nan

            if 'fx' in atom_attributes:
                forces = np.zeros((natoms, 3)) * np.nan

            if 'c_q[1]' in atom_attributes:
                quaternions = np.zeros((natoms, 4)) * np.nan

            if 'q' in atom_attributes:
                charges = np.zeros(natoms)

            def get_values(fields, keys):
                return [float(fields[atom_attributes[key]]) for key in keys]

            for n in range(natoms):
                line = lines.pop(0)
                fields = line.split()
                id = int(fields[atom_attributes['id']])
                #id.append( int(fields[atom_attributes['id']]) )
                types[id - 1] = int(fields[atom_attributes['type']])
                try:
                    positions[id - 1] = get_values(fields, ['x', 'y', 'z'])
                except:
                    print id, positions.shape, n_atoms, line
                    raise
                if velocities != None:
                    velocities[id - 1] = get_values(fields, ['vx', 'vy', 'vz'])
                if forces != None:
                    forces[id - 1] = get_values(fields, ['fx', 'fy', 'fz'])
                if quaternions != None:
                    quaternions[id - 1] = get_values(
                        fields, ['c_q[1]', 'c_q[2]', 'c_q[3]', 'c_q[4]'])
                if charges != None:
                    charges[id - 1] = get_values(fields, 'q')[0]

            #if len(quaternions):
            #    images.append(Quaternions(symbols=types,
            #                              positions=positions,
            #                              cell=cell, celldisp=celldisp,
            #                              quaternions=quaternions, info=info))

            atoms = Atoms(symbols=types, positions=positions, cell=cell)
            if velocities != None:
                atoms.set_velocities(velocities)
            if charges != None:
                atoms.set_charges(charges)
            info = dict(celldisp=celldisp)
            if forces != None:
                info['forces'] = forces
            atoms.info = info
            images.append(atoms)

    return images[index]
Esempio n. 5
0
def read_lammps_dump(fileobj, index=-1):
	"""Method which reads a LAMMPS dump file."""
	if isinstance(fileobj, str):
		f = paropen(fileobj)
	else:
		f = fileobj

	# load everything into memory
	lines = f.readlines()

	natoms = 0
	images = []

	while len(lines) > natoms:
		line = lines.pop(0)

		if 'ITEM: TIMESTEP' in line:
			natoms = 0
			lo = [] ; hi = [] ; tilt = []
			#id = [] ; types = []
			positions = None
			velocities = None
			forces = None
			quaternions = None
			charges = None

		if 'ITEM: NUMBER OF ATOMS' in line:
			line = lines.pop(0)
			natoms = int(line.split()[0])
			
		if 'ITEM: BOX BOUNDS' in line:
			# save labels behind "ITEM: BOX BOUNDS" in triclinic case (>=lammps-7Jul09)
			tilt_items = line.split()[3:]
			for i in range(3):
				line = lines.pop(0)
				fields = line.split()
				lo.append(float(fields[0]))
				hi.append(float(fields[1]))
				if (len(fields) >= 3):
					tilt.append(float(fields[2]))

			# determine cell tilt (triclinic case!)
			if (len(tilt) >= 3):
				# for >=lammps-7Jul09 use labels behind "ITEM: BOX BOUNDS" to assign tilt (vector) elements ...
				if (len(tilt_items) >= 3):
					xy = tilt[tilt_items.index('xy')]
					xz = tilt[tilt_items.index('xz')]
					yz = tilt[tilt_items.index('yz')]
				# ... otherwise assume default order in 3rd column (if the latter was present)
				else:
					xy = tilt[0]
					xz = tilt[1]
					yz = tilt[2]
			else:
				xy = xz = yz = 0
			xhilo = (hi[0] - lo[0]) - abs(xy) - abs(xz)
			yhilo = (hi[1] - lo[1]) - abs(yz)
			zhilo = (hi[2] - lo[2])
			celldispx = lo[0] - min(0, xy) - min(0, xz)
			celldispy = lo[1] - min(0, yz)
			celldispz = lo[2]

			cell = [[xhilo,0,0],[xy,yhilo,0],[xz,yz,zhilo]]
			celldisp = [[celldispx, celldispy, celldispz]]
				
		if 'ITEM: ATOMS' in line:
			atom_attributes = {}
			for (i, x) in enumerate(line.split()[2:]):
				atom_attributes[x] = i
			
			positions = np.zeros((natoms, 3))*np.nan
			types = np.empty(natoms, dtype=int)
			if 'vx' in atom_attributes:
				velocities = np.zeros((natoms, 3))*np.nan
			
			if 'fx' in atom_attributes:
				forces = np.zeros((natoms, 3))*np.nan
			
			if 'c_q[1]' in atom_attributes:
				quaternions = np.zeros((natoms, 4))*np.nan
			
			if 'q' in atom_attributes:
				charges = np.zeros(natoms)
			
			def get_values(fields, keys):
				return [float(fields[atom_attributes[key]]) for key in keys]
			
			for n in range(natoms):
				line = lines.pop(0)
				fields = line.split()
				id = int(fields[atom_attributes['id']])
				#id.append( int(fields[atom_attributes['id']]) )
				types[id-1] = int(fields[atom_attributes['type']])
				try:
					positions[id-1] = get_values(fields, ['x', 'y', 'z'])
				except:
					print id, positions.shape, n_atoms, line
					raise
				if velocities != None:
					velocities[id-1] = get_values(fields, ['vx', 'vy', 'vz'])
				if forces != None:
					forces[id-1] = get_values(fields, ['fx', 'fy', 'fz'])
				if quaternions != None:
					quaternions[id-1] = get_values(fields, ['c_q[1]', 'c_q[2]', 'c_q[3]', 'c_q[4]'])
				if charges != None:
					charges[id-1] = get_values(fields, 'q')[0]

			#if len(quaternions):
			#    images.append(Quaternions(symbols=types,
			#                              positions=positions,
			#                              cell=cell, celldisp=celldisp,
			#                              quaternions=quaternions, info=info))

			atoms = Atoms(symbols=types, positions=positions, cell=cell)
			if velocities != None: 
				atoms.set_velocities(velocities)
			if charges != None:
				atoms.set_charges(charges)
			info = dict(celldisp=celldisp)
			if forces != None:
				info['forces'] = forces
			atoms.info = info
			images.append(atoms)

	return images[index]