def HEA(f_file, verbose=3):
""" Helium approach
Calculate porosity using celllist
f_file ... file name
verbose ... verbosity
"""
#print('----------------')
#print('HEA: calculation')
#print('----------------')
print('f_file : {}'.format(f_file))
t1 = time.time()
# read the structure
struct = read(f_file)
p_framework = struct.get_positions()
s_framework = struct.get_chemical_symbols()
cell = struct.get_cell()
Lx = numpy.linalg.norm(cell[:][0, :])
Ly = numpy.linalg.norm(cell[:][1, :])
Lz = numpy.linalg.norm(cell[:][2, :])
# Guess for M
M0 = get_M(Lx=Lx, Ly=Ly, Lz=Lz, m='high')
# Optimize d for M0
dopt = get_opt_r(Lx=Lx, Ly=Ly, Lz=Lz, Mx=M0[0], My=M0[1], Mz=M0[2])
# Optimize M for dopt
M = get_M(Lx=Lx, Ly=Ly, Lz=Lz, m='high', d=dopt)
Mx, My, Mz = M
# Celllist = get_subcells(cell, M, p_framework)
# Get COMs of Celllist
p_insert = get_COMs_celllist(cell, M)
# Species we are inserting
s_insert = ['He'] * len(p_insert)
# Remove atoms an the insertion grid overlapping with the framework
ropt = dopt / 2.
print('r_opt: {:10.5f} A'.format(ropt))
p_insert_red, s_insert_red = prune_points(p_framework=p_framework,
p_insert=p_insert,
s_framework=s_framework,
s_insert=s_insert,
r_i=ropt)
# Calculate number of atoms
N_insert = len(p_insert)
N_insert_red = len(p_insert_red)
P_points = N_insert_red / N_insert
print('N_insert: {:10d}'.format(N_insert))
print('N_insert_reduced: {:10d}'.format(N_insert_red))
# Calculate volumes
struct_subcell = Atoms(cell=cell)
cell_subcell = struct_subcell.get_cell()
cell_subcell[:][0, :] = cell_subcell[:][0, :] / Mx
cell_subcell[:][1, :] = cell_subcell[:][1, :] / My
cell_subcell[:][2, :] = cell_subcell[:][2, :] / Mz
struct_subcell.set_cell(cell_subcell)
V_subcell = struct_subcell.get_volume() * N_insert_red
V_insert = 4 / 3. * numpy.pi * ropt**3. * N_insert_red
V_framework = struct.get_volume()
P_subcell = V_subcell / V_framework
print('optimal M: {:10d} {:10d} {:10d}'.format(Mx, My, Mz))
# simple cubic packing
f_sc = 0.52
f_calc = V_insert / V_subcell
print('------------------')
print('packing fraction f')
print('------------------')
print('f_sc: {:15.5f}'.format(f_sc))
print('f_calc: {:15.5f}'.format(f_calc))
P_volume = V_insert / (V_framework * f_calc)
print('----------------------')
print('HEA porosity P [%]')
print('----------------------')
print('P_subcell: {:15.5f}'.format(P_subcell * 100.0))
print('P_points: {:15.5f}'.format(P_points * 100.0))
print('P_volume: {:15.5f}'.format(P_volume * 100.0))
print('---------------')
print(' Volume V [A^3]')
print('---------------')
print('V_framework: {:15.5f}'.format(V_framework))
print('V_subcell: {:15.5f}'.format(V_subcell))
print('V_He: {:15.5f}'.format(V_insert))
t2 = time.time()
print('Total CPU time: {:15.5f} s'.format(t2 - t1))
print('\n')
if verbose > 3:
get_ase(f_file, p_insert_red, s_insert_red)
return [
P_points * 100.0, P_subcell * 100.0, P_volume * 100.0, V_framework,
V_subcell, V_insert, N_insert, N_insert_red, f_calc, ropt
]
class execution(object):
def __init__(self, executionInput, xyz=None, stateFile='state.json'):
'''
Setup a new execution
Name: input file
xyz: xyz coordinates (for future automated execution)
stateFile: state file to use for tracking of executions
TODO:
- only ground state in non-periodic cell supported NOW, more to add!
- inputs from a dict to better handle automated executions
'''
if isinstance(executionInput, str):
self.inp = self.json(executionInput)
self.inputFileName = executionInput
if isinstance(executionInput, dict):
self.inp = executionInput
self.inputFileName = 'dict' # TODO: generate meaningful name here (how?)
self.setup()
def setup(self):
'''setup'''
self.functional = self.inp.get('functional') or 'LDA'
self.runtype = self.inp.get('runtype') or 'calc'
# this actually can't be none!
_xyz = self.inp.get('xyz')
if isinstance(_xyz, str):
self.inputXYZ = _xyz
self.atoms = read(self.inputXYZ)
else:
# support reading frm a dict (TODO: other type of objects - ?)
from ase.atoms import Atoms
from ase.atom import Atom
self.atoms = \
Atoms([Atom(a[0],(a[1],a[2],a[3])) for a in _xyz])
# TODO: support multiple cell types
self.atoms.cell = (self.inp['cell']['x'], self.inp['cell']['y'],
self.inp['cell']['z'])
# Mixer setup - only "broyden" supported
self.mixer = self.inp.get('mixer')
if self.mixer is None:
self.mixer = Mixer
else:
self.mixer = BroydenMixer
# Custom ID: allow to trace parameter set using a custom id
self.custom_id = self.inp.get('custom_id')
# Periodic Boundary Conditions
self.atoms.pbc = False
# This should not be done always
self.atoms.center()
self.nbands = self.inp.get('nbands')
self.gpts = None
self.setup_gpts()
self.max_iterations = self.inp.get('maxiter') or 333
# Name: to be set by __str__ first time it is run
self.name = None
#
self.logExtension = 'txt'
self.dataExtension = 'gpw'
# Timing / statistics
self.lastElapsed = None
#
def get_optimizer(self, name='QuasiNewton'):
from importlib import import_module
name = name.lower()
_optimMap = \
{
'mdmin': 'MDMin',
'hesslbfgs': 'HessLBFGS',
'linelbfgs': 'LineLBFGS',
'fire': 'FIRE',
'lbfgs': 'LBFGS',
'lbfgsls': 'LBFGSLineSearch',
'bfgsls': 'BFGSLineSearch',
'bfgs': 'BFGS',
'quasinewton': 'QuasiNewton'
}
_class = _optimMap[name]
_m = import_module('ase.optimize')
return getattr(_m, _class)
#
def setup_gpts(self):
self.gpts = h2gpts(self.inp.get('spacing') or 0.20,
self.atoms.get_cell(),
idiv=self.inp.get('idiv') or 8)
def filename(self, force_id=None, extension='txt'):
'''to correctly support this:
stateFile support must be completed
as it isn't just add "_0" to __str__() for now
'''
base = self.__str__()
if self.custom_id is not None:
base = base + '_' + self.custom_id
if force_id is None:
_fn = base + '_0.' + extension
else:
_fn = '{}_{}.{}'.format(base, force_id, extension)
return _fn
#
@property
def xyz(self):
return self.inp['xyz']
#
@property
def spacegroup(self):
'''international ID of determined spacegroup'''
sg = spglib.get_symmetry_dataset(spglib.refine_cell(
self.atoms))['international']
return sg.replace('/', ':')
#
def __str__(self):
'''get execution name - to be used for log filename
Components:
- Number atoms
- Volume
- Spacegroup number
- Functional name
'''
if self.name is None:
self.name = '{}_{}_{}_{}'.format(
len(self.atoms), int(self.atoms.get_volume() * 100),
self.spacegroup, self.functional)
_gpaw = os.environ['GPAW']
_pwd = os.environ['PWD']
self.procname = '{} ({})'.format(self.name,
_pwd.replace(_gpaw + '/', ''))
setproctitle(self.procname)
return self.name
##
def print(self, *args, **kwargs):
'''print wrapper - initial step before logger'''
r = print(*args, *kwargs)
return r
#
def pretty(self):
'''pretty print original parameters'''
_p = pformat(self.inp)
self.print(_p)
#
def json(self, filename):
'''load parameters from json'''
with open(filename, 'rb') as f:
s = f.read()
j = json.loads(s)
return j
#
def run(self, force_id=None, runtype=None):
'''
perform execution - only calc or optim supported now
'''
_lastStart = time.time()
if runtype is None and self.runtype is 'calc':
_f = self.calc
else:
_f = self.optim
# calculate
try:
result = _f(force_id)
finally:
_lastEnd = time.time()
self.lastElapsed = _lastEnd - _lastStart
return result
#
def calc(self, force_id=None, functional=None):
'''prepare and launch execution
force_id: use this id for filename generation
'''
# Allow to override the funtional
_fnl = functional or self.functional
# generate filenames
_fn = self.filename(force_id)
_dn = self.filename(force_id, extension=self.dataExtension)
self.print('Calculation with {} log and Input: {}.'.format(
_fn, self.inputFileName))
if self.nbands is None:
_calc = GPAW(xc=_fnl,
txt=self.filename(force_id),
mixer=self.mixer(),
maxiter=self.max_iterations,
gpts=self.gpts)
else:
_calc = GPAW(xc=_fnl,
txt=self.filename(force_id),
nbands=self.nbands,
mixer=self.mixer(),
maxiter=self.max_iterations,
gpts=self.gpts)
self.atoms.set_calculator(_calc)
self.atoms.get_potential_energy()
# write out wavefunctions
_calc.write(_dn, 'all')
return _calc
#####
def optim(self, force_id=None, functional=None):
'''prepare and launch execution
force_id: use this id for filename generation
'''
_optim_name = self.inp.get('optimizer') or 'QuasiNewton'
optimizer = self.get_optimizer(_optim_name)
# Allow to override the funtional
_fnl = functional or self.functional
# generate filenames
_fn = self.filename(force_id)
_dn = self.filename(force_id, extension=self.dataExtension)
self.print('Optimization with {} log and Input: {}.'.format(
_fn, self.inputFileName))
if self.nbands is None:
_calc = GPAW(xc=_fnl,
txt=self.filename(force_id),
mixer=self.mixer(),
maxiter=self.max_iterations,
gpts=self.gpts)
else:
_calc = GPAW(xc=_fnl,
txt=self.filename(force_id),
nbands=self.nbands,
mixer=self.mixer(),
maxiter=self.max_iterations,
gpts=self.gpts)
self.atoms.set_calculator(_calc)
self.opt = optimizer(self.atoms,
trajectory=self.__str__() + '_emt.traj')
self.opt.run(fmax=0.05)
# write out wavefunctions
_calc.write(_dn, 'all')
return _calc
class TestCalculator_SW_Potential(quippytest.QuippyTestCase):
def setUp(self):
self.xml = """
<SW_params n_types="2" label="PRB_31_plus_H">
<comment> Stillinger and Weber, Phys. Rev. B 31 p 5262 (1984), extended for other elements </comment>
<per_type_data type="1" atomic_num="1" />
<per_type_data type="2" atomic_num="14" />
<per_pair_data atnum_i="1" atnum_j="1" AA="0.0" BB="0.0"
p="0" q="0" a="1.0" sigma="1.0" eps="0.0" />
<per_pair_data atnum_i="1" atnum_j="14" AA="8.581214" BB="0.0327827"
p="4" q="0" a="1.25" sigma="2.537884" eps="2.1672" />
<per_pair_data atnum_i="14" atnum_j="14" AA="7.049556277" BB="0.6022245584"
p="4" q="0" a="1.80" sigma="2.0951" eps="2.1675" />
<!-- triplet terms: atnum_c is the center atom, neighbours j and k -->
<per_triplet_data atnum_c="1" atnum_j="1" atnum_k="1"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="1" atnum_j="1" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="1" atnum_j="14" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="1" atnum_k="1"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="1" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="14" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
</SW_params>
"""
quippy.system_module.system_reseed_rng(2065775975)
self.pot_calculator = Potential('IP SW', param_str=self.xml)
self.at = Atoms('Si8',
positions=diamond_pos,
pbc=True,
cell=[5.44, 5.44, 5.44])
self.f = np.zeros((3, len(self.at)), order='F')
self.df = np.zeros((3, len(self.at)), order='F')
self.v = np.zeros((3, 3), order='F')
self.energy_ref = -34.5038375509
self.forces_ref = np.array([[0.89920374, -0.38025157, -0.38727027],
[0.36623356, -0.52403757, 0.7200206],
[-0.36952654, 0.12899529, 0.00458111],
[-0.19912365, -0.1632057, 1.08509495],
[-0.67565314, -0.59410498, -0.47921521],
[0.17097454, 0.5847822, -0.31088749],
[0.43613712, 0.90811269, 0.1600328],
[-0.62824563, 0.03970963, -0.79235649]])
self.virial_ref = np.array([[-0.34103601, 0.60925144, -0.02138795],
[0.60925144, -0.36145702, -0.19375487],
[-0.02138795, -0.19375487, -0.34640615]]).T
# Voigt notation by hand from virial
self.stress_ref = -np.array([
-0.34103601, -0.36145702, -0.34640615, -0.19375487, -0.02138795,
0.60925144
]) / self.at.get_volume()
self.at.set_calculator(self.pot_calculator)
def test_energy(self):
self.assertAlmostEqual(self.at.get_potential_energy(), self.energy_ref)
def test_forces(self):
self.assertArrayAlmostEqual(self.at.get_forces(),
self.forces_ref,
tol=1E-06)
def test_stress(self):
self.assertArrayAlmostEqual(self.at.get_stress(), self.stress_ref)
def test_virial(self):
self.assertArrayAlmostEqual(self.pot_calculator.get_virial(self.at),
self.virial_ref,
tol=1E-06)
def test_calc_args_1(self):
self.pot_calculator.calculate(self.at,
propertes=["forces"],
calc_args="do_rescale_E E_scale=1.01")
f = self.pot_calculator.results['forces']
self.assertArrayAlmostEqual(f, self.forces_ref * 1.01, tol=1E-06)
def test_calc_args_2(self):
self.pot_calculator.calculate(self.at,
properties=["forces"],
do_rescale_E=True,
E_scale=1.01)
f = self.pot_calculator.results['forces']
self.assertArrayAlmostEqual(f, self.forces_ref * 1.01, tol=1E-06)
def test_calc_args_3(self):
pot2 = Potential('IP SW',
param_str=self.xml,
calc_args="do_rescale_E E_scale=1.01")
f = pot2.get_forces(self.at)
self.assertArrayAlmostEqual(f, self.forces_ref * 1.01, tol=1E-06)
def test_calc_args_4(self):
pot2 = Potential('IP SW',
param_str=self.xml,
calc_args={
'do_rescale_E': True,
'E_scale': 1.01
})
f = pot2.get_forces(self.at)
self.assertArrayAlmostEqual(f, self.forces_ref * 1.01, tol=1E-06)
'sme/method': 'fermi_dirac',
'ELECTRONIC_TEMPERATURE': 300,
'DIA/ALGORITHM': 'STANDARD',
'mix/METHOD': 'BROYDEN_MIXING',
'ALPHA': 0.1,
'BETA': 1.5,
'NBUFFER': 8,
'cpu': 24,
'cutoff': 300,
'run_type': 'cell_opt',
'atoms': atoms,
}
calc = CP2K(**kwargs)
atoms.set_calculator(calc)
s = time.time()
e = atoms.get_potential_energy()
t = time.time() - s
v = atoms.get_volume()
print('*=================================================*')
print('volume time energy (eV)')
print('{0:1.2f} {1:1.1f} {2:1.4f} '.format(v, t, e))
print('cell:')
print(atoms.cell)