def initialize_parameters(code, width, h):
parameters = {}
if code == 'gpaw':
from gpaw import GPAW as Calculator
from gpaw.mpi import rank
parameters['h'] = h
parameters['width'] = width
parameters['stencils'] = (3, 3)
#parameters['eigensolver'] = 'cg'
conv_param = parameters['h']
elif code == 'dacapo':
from ase.calculators.dacapo import Dacapo as Calculator
rank = 0
parameters['kT'] = width
parameters['planewavecutoff'] = gridspacing2cutoff(h)
parameters['densitycutoff'] = parameters['planewavecutoff'] * 1.2
conv_param = parameters['planewavecutoff']
elif code == 'abinit':
from ase.calculators.abinit import Abinit as Calculator
rank = 0
parameters['width'] = width
parameters['ecut'] = gridspacing2cutoff(h) * 1.4
conv_param = parameters['ecut']
elif code == 'elk':
parameters['swidth'] = width
parameters['stype'] = 3
parameters['autormt'] = True
parameters['tforce'] = True # calulate forces
parameters['nempty'] = 20 # default 5
#parameters['fixspin'] = -1 # default 0
#parameters['evalmin'] = -15.0 # default -4.5
#parameters['autokpt'] = True
#parameters['nosym'] = True
#parameters['radkpt'] = 10.0 # default 40.0
parameters['gmaxvr'] = 16 # default 12 #
parameters['rgkmax'] = 7.0 # default 7 #
#parameters['gmaxvr'] = 19 # default 12
#parameters['rgkmax'] = 9.5 # default 7
parameters['beta0'] = 0.02 # default 0.05
parameters['betamax'] = 0.05 # default 0.5
parameters['maxscl'] = 500 # default 200
#parameters['mixtype'] = 2 # Pulay # default 1
#parameters['deband'] = 0.005 # default 0.0025
#parameters['rmtapm'] = '0.25 0.90' # default (0.25,0.95)
return parameters
def memory_bandwidth(code='gpaw', runs=7):
slab = Atoms([
Atom('Al', (0, 0, 0)),
Atom('Al', (a, 0, 0)),
Atom('Al', (a / 2, d / 2, -d / 2)),
Atom('Al', (3 * a / 2, d / 2, -d / 2)),
Atom('Al', (0, 0, -d)),
Atom('Al', (a, 0, -d)),
Atom('Al', (a / 2, d / 2, -3 * d / 2)),
Atom('Al', (3 * a / 2, d / 2, -3 * d / 2)),
Atom('Al', (0, 0, -2 * d)),
Atom('Al', (a, 0, -2 * d)),
Atom('H', (a / 2 - b / 2, 0, z)),
Atom('H', (a / 2 + b / 2, 0, z))
],
cell=(2 * a, d, 5 * d),
pbc=(1, 1, 1))
h = 0.15
nbands = 28
kpts = (2, 6, 1)
parameters = {}
if code == 'gpaw':
from gpaw import Calculator
from gpaw.mpi import rank
parameters['convergence'] = {'eigenstates': 1e-5}
parameters['h'] = h
elif code == 'dacapo':
from ase.calculators.dacapo import Dacapo as Calculator
parameters['planewavecutoff'] = gridspacing2cutoff(h)
parameters['densitycutoff'] = parameters['planewavecutoff'] * 1.5
rank = 0
t = 0.0
t_runs = []
for n in range(runs):
t0 = time.time()
for i in range(1):
calc = Calculator(nbands=nbands, kpts=kpts, **parameters)
slab.set_calculator(calc)
e = slab.get_potential_energy()
del calc
if exists('out.nc'): remove('out.nc')
t1 = time.time()
t = t + t1 - t0
t_runs.append(t1 - t0)
print 'Run: ', n, ' energy ', e, ' rank: ', str(
rank), ' time: ', time.time() - t0
if rank == 0:
print 'Rank ' + str(rank) + ': time [sec]: avg ' + str(
round(np.average(t_runs), 1)) + ', stddev ' + str(
round(np.std(t_runs), 1)) + ', min ' + str(
round(min(t_runs), 1)) + ', max ' + str(
round(max(t_runs), 1))
def memory_bandwidth(code='gpaw', runs=7):
slab = Atoms([Atom('Al', (0, 0, 0)),
Atom('Al', (a, 0, 0)),
Atom('Al', (a/2, d/2, -d/2)),
Atom('Al', (3*a/2, d/2, -d/2)),
Atom('Al', (0, 0, -d)),
Atom('Al', (a, 0, -d)),
Atom('Al', (a/2, d/2, -3*d/2)),
Atom('Al', (3*a/2, d/2, -3*d/2)),
Atom('Al', (0, 0, -2*d)),
Atom('Al', (a, 0, -2*d)),
Atom('H', (a/2-b/2, 0, z)),
Atom('H', (a/2+b/2, 0, z))],
cell=(2*a, d, 5*d), pbc=(1, 1, 1))
h = 0.15
nbands = 28
kpts = (2, 6, 1)
parameters = {}
if code == 'gpaw':
from gpaw import Calculator
from gpaw.mpi import rank
parameters['convergence'] = {'eigenstates': 1e-5}
parameters['h'] = h
elif code == 'dacapo':
from ase.calculators.dacapo import Dacapo as Calculator
parameters['planewavecutoff'] = gridspacing2cutoff(h)
parameters['densitycutoff'] = parameters['planewavecutoff']*1.5
rank = 0
t = 0.0
t_runs = []
for n in range(runs):
t0 = time.time()
for i in range(1):
calc = Calculator(
nbands=nbands,
kpts=kpts,
**parameters)
slab.set_calculator(calc)
e = slab.get_potential_energy()
del calc
if exists('out.nc'): remove('out.nc')
t1 = time.time()
t = t + t1 - t0
t_runs.append(t1 - t0)
print 'Run: ', n, ' energy ', e, ' rank: ', str(rank), ' time: ', time.time() - t0
if rank == 0:
print 'Rank '+str(rank)+': time [sec]: avg '+str(round(np.average(t_runs),1))+', stddev '+str(round(np.std(t_runs),1))+', min '+str(round(min(t_runs),1))+', max '+str(round(max(t_runs),1))
def memory_bandwidth(code="gpaw", runs=7):
slab = Atoms(
[
Atom("Al", (0, 0, 0)),
Atom("Al", (a, 0, 0)),
Atom("Al", (a / 2, d / 2, -d / 2)),
Atom("Al", (3 * a / 2, d / 2, -d / 2)),
Atom("Al", (0, 0, -d)),
Atom("Al", (a, 0, -d)),
Atom("Al", (a / 2, d / 2, -3 * d / 2)),
Atom("Al", (3 * a / 2, d / 2, -3 * d / 2)),
Atom("Al", (0, 0, -2 * d)),
Atom("Al", (a, 0, -2 * d)),
Atom("H", (a / 2 - b / 2, 0, z)),
Atom("H", (a / 2 + b / 2, 0, z)),
],
cell=(2 * a, d, 5 * d),
pbc=(1, 1, 1),
)
h = 0.15
nbands = 28
kpts = (2, 6, 1)
parameters = {}
if code == "gpaw":
from gpaw import Calculator
from gpaw.mpi import rank
parameters["convergence"] = {"eigenstates": 1e-5}
parameters["h"] = h
elif code == "dacapo":
from ase.calculators.dacapo import Dacapo as Calculator
parameters["planewavecutoff"] = gridspacing2cutoff(h)
parameters["densitycutoff"] = parameters["planewavecutoff"] * 1.5
rank = 0
t = 0.0
t_runs = []
for n in range(runs):
t0 = time.time()
for i in range(1):
calc = Calculator(nbands=nbands, kpts=kpts, **parameters)
slab.set_calculator(calc)
e = slab.get_potential_energy()
del calc
if exists("out.nc"):
remove("out.nc")
t1 = time.time()
t = t + t1 - t0
t_runs.append(t1 - t0)
print("Run: ", n, " energy ", e, " rank: ", str(rank), " time: ", time.time() - t0)
if rank == 0:
print(
"Rank "
+ str(rank)
+ ": time [sec]: avg "
+ str(round(np.average(t_runs), 1))
+ ", stddev "
+ str(round(np.std(t_runs), 1))
+ ", min "
+ str(round(min(t_runs), 1))
+ ", max "
+ str(round(max(t_runs), 1))
)
