def _convertNamelists(self, namelists):
for name in namelists.keys():
nl = Namelist(name)
for p in namelists[name]:
nl.add(p[0], p[1])
self.namelists[name] = nl
def setNamelist(self, namelist):
"""
Sets namelist as dictionaty:
namelist: (dict) -- Dictionary of namelist
Format:
{"name": <namelist name>,
"params": {param1: value1,
param2: value2,
...}}
Example:
{"name": "control",
"params": {calculation: 'scf',
restart_mode: 'from_scratch',
tprnfor: .true.}}
"""
if not namelist: # Ignore empty card
return
self._checkDictFormat(namelist, NAMELIST_KEYS, NAMELIST_REQ)
nl = Namelist(namelist["name"])
if namelist.has_key("params"):
for p in namelist["params"].keys():
value = namelist["params"][p]
nl.set(p, value)
self._fnamelists.append(nl)
def setNamelist(self, namelist):
"""
Sets namelist as dictionaty:
namelist: (dict) -- Dictionary of namelist
Format:
{"name": <namelist name>,
"params": {param1: value1,
param2: value2,
...}}
Example:
{"name": "control",
"params": {calculation: 'scf',
restart_mode: 'from_scratch',
tprnfor: .true.}}
"""
if not namelist: # Ignore empty card
return
self._checkDictFormat(namelist, NAMELIST_KEYS, NAMELIST_REQ)
nl = Namelist(namelist["name"])
if namelist.has_key("params"):
for p in namelist["params"].keys():
value = namelist["params"][p]
nl.set(p, value)
self._fnamelists.append(nl)
def _convertNamelists(self, namelists):
"""Converts dictionary to Namelist"""
for name in namelists.keys():
nl = Namelist(name)
for p in namelists[name]:
nl.add(p[0], p[1])
self.namelists[name] = nl
def test_qeinput_namelist(self):
input = QEInput()
nl = Namelist("control")
nl.set("title", "'Ni'")
input.addNamelist(nl)
nl2 = input.namelist("phonon")
self.assertEqual(input.toString(), fixtures.assertNewNamelist)
input.removeNamelist("control")
self.assertEqual(input.toString(), fixtures.assertNewNamelist2)
def test_qeinput_namelist(self):
input = QEInput()
nl = Namelist("control")
nl.set("title", "'Ni'")
input.addNamelist(nl)
nl2 = input.namelist("phonon")
self.assertEqual(input.toString(), fixtures.assertNewNamelist)
input.removeNamelist("control")
self.assertEqual(input.toString(), fixtures.assertNewNamelist2)
def test_namelist_set_get(self):
nl = Namelist("control")
self.assertEqual(nl.get("title"), None)
nl.set("title", "hello")
self.assertEqual(nl.get("title"), "hello")
self.assertEqual(nl.get("title", quotes=True), "hello") # should not add quotes
nl.set("Title", "'hello'")
self.assertEqual(nl.get("titlE", quotes=False), "hello")
self.assertEqual(nl.get("title"), "'hello'")
def _to_str_nml(params):
""" Write with namelist format
"""
# convert to Namelist class
groups = odict()
for k, g in groupby(params, lambda x: x.group):
if k == "":
print list(g)
raise ValueError("Group not defined. Cannot write to namelist. See Parameters' set_group() method.")
groups[k] = odict([(p.name, p.value) for p in g])
nml = Namelist(groups)
string = nml.dump()
return string
def some_opts_extr(self):
try:
names = np.sort(listdir(self.frm.folder_name))
except TypeError:
self.frm.status.set('it seems you should show me the folder, Doc')
return False
for name in names:
if fnmatch(name, '*.in'):
inputname = self.frm.folder_name + '/' + name
No_ion = int(
Namelist(inputname).get('ions').get('par')[0].get('no_ion')[0])
self.frm.n_nod = int(
Namelist(inputname).get('option').get('par')[0].get('nd_para')
[0]) - 1
return No_ion
def test_namelist_remove_exists(self):
nl = Namelist("control")
nl.set("title", "hello")
self.assertTrue(nl.exists("title"))
self.assertTrue(nl.exists("Title"))
nl.remove("title")
self.assertFalse(nl.exists("title"))
def __setitem__(self, key, value):
if key == 'k0':
# convenience variable for harmonic potential
self['rk2'] = float(value)
self['rk3'] = float(value)
elif key == 'r0':
# convenience variable for harmonic potential
self['r2'] = float(value)
self['r3'] = float(value)
self['r1'] = self._r1_harmonic
self['r4'] = self._r4_harmonic
elif key in ['rk2','rk3']:
# some restraints use internal units (e.g. angles)
Namelist.__setitem__(self,key,float(value))
else:
Namelist.__setitem__(self,key,value)
def setParam(self, namelist, param, value=""):
"""
Set parameter of the namelist. If the parameter or namelist do not exist,
it creates them.
namelist: (str) -- Name of the namelist
param: (str) -- Name of the parameter
value: (str) -- Valur of the parameter
"""
for nl in self._fnamelists:
if nl.name() == namelist:
nl.set(param, value)
return
# namelist doesn't exists
nl = Namelist(namelist)
nl.set(param, value)
self._fnamelists.append(nl)
def setParam(self, namelist, param, value=""):
"""
Set parameter of the namelist. If the parameter or namelist do not exist,
it creates them.
namelist: (str) -- Name of the namelist
param: (str) -- Name of the parameter
value: (str) -- Valur of the parameter
"""
for nl in self._fnamelists:
if nl.name() == namelist:
nl.set(param, value)
return
# namelist doesn't exists
nl = Namelist(namelist)
nl.set(param, value)
self._fnamelists.append(nl)
def test_namelist_remove_exists(self):
nl = Namelist("control")
nl.set("title", "hello")
self.assertTrue(nl.exists("title"))
self.assertTrue(nl.exists("Title"))
nl.remove("title")
self.assertFalse(nl.exists("title"))
def _parse_file_nml(cls, string):
nml = Namelist.parse_file(string)
# flatten namelist to store it in the Parameters class
params = cls()
for g in nml.groups:
for nm in nml.groups[g]:
p = Parameter(name=nm, value=nml.groups[g][nm], group=g)
params.append(p)
return params
def __str__(self):
if len(self.keys()) > 0: # Don't print empty namelists.
if self.name is not None:
return Namelist.__str__(self)
else:
# Modify the Namelist print behavior for a NoneType namelist.
# Namely, don't print the "&name" section and ending slash.
return '\n'.join([' %s=%s'%(k,v) for k,v in self.iteritems()])
else:
return ''
def testCreateConfig():
print "Testing creation of config file"
qe = QEInput()
nl = Namelist('control')
nl.add('title', "'Ni'")
nl.add('restart_mode', "'from_scratch'")
print "Adding parameters to namelist:\n%s" % nl.toString()
nl.set('title', "'Fe'")
qe.addNamelist(nl)
print "Adding namelist to QEInput:\n%s" % qe.toString()
c = Card('atomic_species')
c.addLine('Ni 26.98 Ni.pbe-nd-rrkjus.UPF')
print "Adding line to card:\n%s" % c.toString()
qe.addCard(c)
print "Adding card to QEInput:\n%s" % qe.toString()
def _createNamelist(self, name):
"""
Creates namelist specified by name
name: (str) -- Name of the namelist
"""
if not name in self.namelistRef: # If not standard card, ignore it
return None
# Otherwise create a new namelist
nl = Namelist(name)
self.namelists[name] = nl
return nl
def testCreateConfig():
print "Testing creation of config file"
qe = QEInput()
nl = Namelist('control')
nl.add('title', "'Ni'")
nl.add('restart_mode', "'from_scratch'")
print "Adding parameters to namelist:\n%s" % nl.toString()
nl.set('title', "'Fe'")
qe.addNamelist(nl)
print "Adding namelist to QEInput:\n%s" % qe.toString()
c = Card('atomic_species')
c.addLine('Ni 26.98 Ni.pbe-nd-rrkjus.UPF')
print "Adding line to card:\n%s" % c.toString()
qe.addCard(c)
print "Adding card to QEInput:\n%s" % qe.toString()
def __str__(self):
# Convert list values to strings.
self['iat'] = ','.join([str(i) for i in self['iat']])
try:
self['rstwt'] = ','.join([str(i) for i in self['rstwt']])
except KeyError:
pass
txt = Namelist.__str__(self)
# Convert back to lists.
self['iat'] = [int(i) for i in self['iat'].split(',')]
try:
self['rstwt'] = [float(i) for i in self['rstwt'].split(',')]
except KeyError:
pass
return txt
def get_pv(forcing, output, n1=0, n2=10000, option="timeseries"):
""" forcing : nc file assumed to be located in Forcings/ e.g. "SIRTA_all"
output : name of output file containing PV production, stored in PV_Outputs directory
n1 and n2 : left and right indicess for partial computations along timeseries
option : specify the type of forcing to optimize vectorial computations
"""
print("----------Namelist loading----------------")
nam = Namelist(
) # all options should be hardcoded in the Namelist() attributes
print("----------Atmosphere loading----------------")
# build an Atmosphere object from an nc file. Such object can be built directly from np.arrays
atm = Atmosphere(*tools.get_atm_from_ncfile(
forcing=forcing, albedo=nam.albedo, n1=n1, n2=n2))
atm.compute_sun() # to compute the full series of sza, saa, sw_toa
# define PV panel from information contained in Namelist
print("----------Module initialization----------------")
panel = Panel(
name=nam.panel_name,
technology=nam.panel_technology,
beta=nam.panel_beta,
gamma=nam.panel_gamma,
method_FF=nam.method_FF,
SR_method=nam.SR_method,
namelist=nam
) # get physical characteristics of the panel from a description file - here SIRTA panel used for consistency
# call pv_interface to handle large arrays and successive (and possibly multi-thread) calls to pv_production
t1 = time.time()
if option == "timeseries":
power_simul = pv_interface_timeseries(nam, atm, panel)
elif option == "atlas":
power_simul = pv_interface_atlas(nam, atm, panel)
# save PV outputs
np.savetxt("PV_Outputs/%s.dat" % output, power_simul)
t2 = time.time()
print("Time to run the PV code = %s seconds" % (t2 - t1))
return atm.dates, power_simul, atm.lat, atm.lon
def __getitem__(self, key):
try:
return Namelist.__getitem__(self,key)
except KeyError:
self[key] = value = self.default(key)
return value
def test_namelist_name(self):
nl = Namelist("Control")
self.assertEqual(nl.name(), "control")
nl.setName("SyStem")
self.assertEqual(nl.name(), "system")
def __init__(self, *args, **kwargs):
Namelist.__init__(self,'rst',' ','=',' ',72,72,*args,**kwargs)
def createNamelist(self, name):
"""Creates namelist and adds to QEInput. """
nl = Namelist(name)
self.namelists[name] = nl
def test_namelist_set_get(self):
nl = Namelist("control")
self.assertEqual(nl.get("title"), None)
nl.set("title", "hello")
self.assertEqual(nl.get("title"), "hello")
self.assertEqual(nl.get("title", quotes=True),
"hello") # should not add quotes
nl.set("Title", "'hello'")
self.assertEqual(nl.get("titlE", quotes=False), "hello")
self.assertEqual(nl.get("title"), "'hello'")
def test_namelist_tostring(self):
nl = Namelist("control")
nl.set("title", "hello")
self.assertEqual(nl.toString(), fixtures.assertNL)
self.assertEqual(nl.toString(indent=3), fixtures.assertNL_space_3)
def test_namelist_name(self):
nl = Namelist("Control")
self.assertEqual(nl.name(), "control")
nl.setName("SyStem")
self.assertEqual(nl.name(), "system")
def __init__(self, name, engine, *args, **kwargs):
Namelist.__init__(self,name,line_prefix=' ',name_value_separator=' = ',
value_separator=', ',max_namevalues_per_line=72,
max_chars_per_line=72,*args,**kwargs)
self.engine = engine
#!/usr/bin/env python3
from namelist import Namelist
control = Namelist(name="CONTROL")
control.set_val("calculation", 'scf')
control.set_val("prefix", "scf.pbe.ecut-80")
control.set_val("outdir", "./scratch/")
control.set_val("pseudo_dir", "/home/altoidnerd/.data/PSEUDOPOTENTIALS/")
control.set_val("verbosity", "high")
control.set_val("title", "p-dichlorobenzene-efg")
control.set_val("restart_mode", "from_scratch")
control.set_val("forc_conv_thr", 1.0e-4)
control.set_val("disk_io", "low")
control.set_val("wfcollect", ".false.")
for key in ["tstress", "tprnfor", "lorbm", "lberry", "ikpoint_dir"]:
control.set_val(key, ".true.")
system = Namelist("SYSTEM")
key_value_pairs = [("ibrav", 0), ('a', 9.558), ('c', "8.981"), ("ecutwfc", 60),
("ecutrho", 600), ("occupations", 'smearing'),
('smearing', 'fermi-dirac'), ('degauss', .00367),
('nat', 70), ('ntyp', '6')]
for (key, value) in key_value_pairs:
system.set_val(key, value)
electrons_dict = {
"conv_thr": 1e-7,
"diago_thr_init": 1e-4,
def test_namelist_tostring(self):
nl = Namelist("control")
nl.set("title", "hello")
self.assertEqual(nl.toString(), fixtures.assertNL)
self.assertEqual(nl.toString(indent=3), fixtures.assertNL_space_3)
def p_subroutine_statement_namelist(p): 'subroutine_statement : NAMELIST SLASH ID SLASH namelist_variables' p[0] = Namelist(p[3], p[5])