def pileg(taut, plam=0.5):
therm = xml.make_node('thermostat', {'mode': 'pile_g'})
lam_node = xml.make_node('pile_lambda', text=str(plam))
tnode = xml.make_node('tau', {'units': 'femtosecond'}, str(taut))
therm.append(lam_node)
therm.append(tnode)
return therm
def ensemble(tkel, pgpa=None):
ens = xml.make_node('ensemble')
tnode = xml.make_node('temperature', {'units': 'kelvin'}, str(tkel))
ens.append(tnode)
if pgpa is not None:
pnode = xml.make_node('pressure', {'units': 'gigapascal'}, str(pgpa))
ens.append(pnode)
return ens
def barostat(taup, taut):
baro = xml.make_node('barostat', {'mode': 'isotropic'})
cell_thermo = xml.make_node('thermostat', {'mode': 'langevin'})
tnode = xml.make_node('tau', {'units': 'femtosecond'}, str(taut))
cell_thermo.append(tnode)
pnode = xml.make_node('tau', {'units': 'femtosecond'}, str(taup))
baro.append(pnode)
baro.append(cell_thermo)
return baro
def properties(props=None, **kwargs):
if props is None:
quantum = kwargs.pop('quantum', False)
props = default_properties(quantum=quantum)
text = text_arr(np.array(props))
# defaults
attrib = {
'stride': str(kwargs.pop('stride', '1')),
'flush': str(kwargs.pop('flush', '1')),
'filename': str(kwargs.pop('filename', 'out')),
}
prop = xml.make_node('properties', attrib, text)
return prop
def classical_qe(temp, pgpa=None, **kwargs):
ens_name = 'nvt'
if pgpa is not None:
ens_name = 'npt'
# defaults
prefix = kwargs.pop('prefix', 'qemd')
ntherm = kwargs.pop('ntherm', 2) # property output
nconf = kwargs.pop('nconf', 20) # conf. output
dtfs = kwargs.pop('dtfs', 0.5) # timestep in fs
taut = kwargs.pop('taut', 100) # fs
taup = kwargs.pop('taup', 100) # fs
# make input pieces
sim = xml.make_node('simulation', {'verbosity': 'high'})
# <system>: init, forces, ensemble, dynamics
system = xml.make_node('system')
init = xml.make_node('initialize', {'nbeads': '1'})
fnode = xml.make_node('file', {'mode': 'xyz'}, 'init.xyz')
vnode = xml.make_node('velocities', {
'mode': 'thermal', 'units': 'kelvin'}, str(temp))
xml.append(init, [fnode, vnode])
forces = xml.make_node('forces')
forces.append(xml.make_node('force', {'forcefield': 'qe'}))
mot = xml.make_node('motion', {'mode': 'dynamics'})
dyn = xml.make_node('dynamics', {'mode': ens_name})
ts = xml.make_node('timestep', {'units': 'femtosecond'}, str(dtfs))
tnode = pileg(taut)
dnodes = [ts, tnode]
if pgpa is not None:
baro = barostat(taup, taut)
dnodes.append(baro)
xml.append(dyn, dnodes)
mot.append(dyn)
ens = ensemble(temp, pgpa=pgpa)
xml.append(system, [init, forces, mot, ens])
# <output>: properties, trajectory, checkpoint
output = xml.make_node('output', {'prefix': prefix})
props = properties(quantum=False, stride=ntherm)
ptraj = xml.make_node('trajectory', {
'filename': 'pos',
'stride': str(nconf),
'flush': '1',
'cell_units': 'angstrom',
}, text='positions{angstrom}')
ftraj = xml.make_node('trajectory', {
'filename': 'frc',
'stride': str(nconf),
'flush': '1',
'cell_units': 'angstrom',
}, text='forces{ev/ang}')
check = xml.make_node('checkpoint', {'stride': str(nconf)})
xml.append(output, [props, ptraj, ftraj, check])
# assemble
xml.append(sim, [system, output])
doc = xml.etree.ElementTree(sim)
# ??? <ffsocket>
# ??? <prng>
# ??? <total_steps>
return doc