def test_basissets():
from basisset import BasisSets
from basisset import BasisFile
from basisset import gamessBasisFile
# empty initialization
BasisSets()
BasisFile()
gamessBasisFile()
filenames = get_filenames()
files = get_files()
f = [files[fn] for fn in filenames]
# standard initialization
divert_nexus_log()
bf = BasisFile(f[1])
gbf = gamessBasisFile(f[0])
bs = BasisSets(f[2:] + [bf, gbf])
restore_nexus_log()
assert (bf.element == 'Fe')
assert (bf.filename == 'Fe.aug-cc-pwcv5z-dk.0.gbs')
assert (gbf.element == 'Fe')
assert (gbf.filename == 'Fe.aug-cc-pwcv5z-dk.0.bas')
assert (gbf.text.startswith('IRON'))
assert (gbf.text.endswith('1 1.3776500 1.0000000'))
assert (len(gbf.text.strip()) == 21135)
for fn in filenames:
assert (fn in bs)
assert (isinstance(bs[fn], BasisFile))
if fn.endswith('.bas'):
assert (isinstance(bs[fn], gamessBasisFile))
def test_keyspec_groups():
from gamess_input import check_keyspec_groups
divert_nexus_log()
check_keyspec_groups()
restore_nexus_log()
def test_write_splash():
from nexus_base import NexusCore
log = divert_nexus_log()
nc = NexusCore()
assert(not nc.wrote_splash)
nc.write_splash()
assert('Nexus' in log.contents())
assert('Please cite:' in log.contents())
assert(nc.wrote_splash)
restore_nexus_log()
def test_check_dependencies():
from simulation import Simulation
from project_manager import ProjectManager
from test_simulation_module import get_test_workflow
divert_nexus_log()
sims = get_test_workflow(1)
pm = ProjectManager()
pm.add_simulations(sims.list())
idc = id(pm.cascades)
idp = id(pm.progressing_cascades)
pm.check_dependencies()
restore_nexus_log()
Simulation.clear_all_sims()
def test_resolve_file_collisions():
from generic import NexusError
from simulation import Simulation
from project_manager import ProjectManager
from test_simulation_module import get_test_workflow, n_test_workflows
divert_nexus_log()
sims = []
for n in range(n_test_workflows):
sims.extend(get_test_workflow(n).list())
#end for
pm = ProjectManager()
pm.add_simulations(sims)
pm.resolve_file_collisions()
s1 = sims[len(sims) // 2]
s2 = sims[len(sims) // 2 + 1]
s2.locdir = s1.locdir
s2.outfile = s1.outfile
try:
pm.resolve_file_collisions()
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
restore_nexus_log()
Simulation.clear_all_sims()
def test_enter_leave():
import os
from nexus_base import NexusCore
tpath = testing.setup_unit_test_output_directory('nexus_base','test_enter_leave')
cwd = os.getcwd()
log = divert_nexus_log()
nc = NexusCore()
nc.enter(tpath)
tcwd = os.getcwd()
assert(tcwd==tpath)
assert('Entering' in log.contents())
assert(tpath in log.contents())
nc.leave()
assert(os.getcwd()==cwd)
restore_nexus_log()
def test_logging():
from generic import log,message,warn,error
from generic import generic_settings,NexusError
# send messages to object rather than stdout
divert_nexus_log()
logfile = generic_settings.devlog
# test log
# simple message
s = 'simple message'
logfile.reset()
log(s)
assert(logfile.s==s+'\n')
# list of items
items = ['a','b','c',1,2,3]
logfile.reset()
log(*items)
assert(logfile.s=='a b c 1 2 3 \n')
# message with indentation
s = 'a message\nwith indentation'
logfile.reset()
log(s,indent=' ')
assert(logfile.s==' a message\n with indentation\n')
logfile.reset()
log(s,indent='msg: ')
assert(logfile.s=='msg: a message\nmsg: with indentation\n')
# writing to separate log files
logfile2 = FakeLog()
s1 = 'message to log 1'
s2 = 'message to log 2'
logfile.reset()
logfile2.reset()
log(s1)
assert(logfile.s==s1+'\n')
assert(logfile2.s=='')
logfile.reset()
logfile2.reset()
log(s2,logfile=logfile2)
assert(logfile.s=='')
assert(logfile2.s==s2+'\n')
# test warn
logfile.reset()
s = 'this is a warning'
warn(s)
so = '''
warning:
this is a warning
'''
assert(logfile.s==so)
logfile.reset()
s = 'this is a warning'
warn(s,header='Special')
so = '''
Special warning:
this is a warning
'''
assert(logfile.s==so)
# test error
# in testing environment, should raise an error
try:
error('testing environment')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# in standard/user environment, should print message
generic_settings.raise_error = False
logfile.reset()
error('this is an error',header='User',exit=False)
so = '''
User error:
this is an error
'''
assert(logfile.s==so)
generic_settings.raise_error = True
# in testing environment, should raise an error
try:
error('testing environment')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
restore_nexus_log()
def test_intrinsics():
# test object_interface functions
import os
from generic import obj,object_interface
from generic import generic_settings,NexusError
from numpy import array,bool_
tpath = testing.setup_unit_test_output_directory('generic','test_intrinsics')
# test object set/get
# make a simple object
o = obj()
o.a = 1
o.b = 'b'
o['c'] = (1,1,1)
o[3,4,5] = (5,6,7)
# test member values
assert(o.a==1)
assert(o.b=='b')
assert(o.c==(1,1,1))
assert(o[3,4,5]==(5,6,7))
# test member presence and length
assert('a' in o)
assert(2 not in o)
assert(len(o)==4)
del o.a
assert('a' not in o)
assert(len(o)==3)
try:
del o.d
raise FailedTest
except AttributeError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test add/access failures
try: # add unhashable type
o[{1:2,3:4}] = 5
raise FailedTest
except TypeError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try: # access missing member
v = o.d
raise FailedTest
except AttributeError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try: # access missing member
v = o['d']
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test iterability
# test list-like iterability
l = list()
for v in o:
l.append(v)
#end for
l = set(l)
l2 = {'b', (1, 1, 1), (5, 6, 7)}
assert(l2==l)
# test dict-like iterability
d = dict()
for k,v in o.items():
d[k] = v
#end for
o2 = obj()
o2.__dict__ = d
assert(object_eq(o,o2))
assert(set(o.keys())==set(d.keys()))
assert(set(o.values())==set(d.values()))
assert(set(o.items())==set(d.items()))
# test repr
ro = '''
b str
c tuple
(3, 4, 5) tuple
'''
assert(repr(o)==ro[1:])
o2 = obj(
a = obj(a1=1,a2=2,a3=3),
b = obj(b1='b1',b2='b2'),
c = obj(c1=5,c2=('a',3,4)),
d = array([3,4,5],dtype=int),
)
ro2 = '''
a obj
b obj
c obj
d ndarray
'''
assert(repr(o2)==ro2[1:])
# test str
so = '''
b = b
c = (1, 1, 1)
(3, 4, 5) = (5, 6, 7)
'''
assert(str(o)==so[1:])
so2 = '''
d = [3 4 5]
a
a1 = 1
a2 = 2
a3 = 3
end a
b
b1 = b1
b2 = b2
end b
c
c1 = 5
c2 = ('a', 3, 4)
end c
'''
assert(str(o2)==so2[1:])
o3 = o2
# test tree
# not committed to output, only check execution
assert(isinstance(o2.tree(),str))
assert(isinstance(o2.tree(depth=1),str))
assert(isinstance(o2.tree(types=True),str))
assert(isinstance(o2.tree(all=True),str))
assert(isinstance(o2.tree(nindent=2),str))
# test deepcopy
o2 = o.copy()
assert(id(o)!=id(o2))
assert(object_eq(o,o2))
o2.a=1
assert(object_neq(o,o2))
# test eq
assert(o==o2)
o4 = o3.copy()
v = o3==o4
assert(isinstance(v,bool_))
assert(bool(v))
assert(object_eq(o3,o4))
# test clear
o2.clear()
assert(len(o2)==0)
assert('a' not in o2)
# test save/load
save_file = os.path.join(tpath,'o.p')
o.save(save_file)
o2 = obj()
o2.load(save_file)
assert(object_eq(o,o2))
# test class-level set/get methods
class objint(object_interface):
a = 1
b = 'b'
c = (1,1,1)
#end class objint
# test class_has
assert(objint.class_has('c'))
# test class_get
assert(objint.class_get('c')==(1,1,1))
try:
val = objint.class_get('d')
raise FailedTest
except AttributeError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test class_keys
ck = objint.class_keys()
for v in 'abc':
assert(v in ck)
#end for
# test class_set_single
objint.class_set_single('d',1.34)
assert(objint.class_has('d'))
# test class_set
objint.class_set(
e = 45,
f = 'a phrase',
g = {4:6,'a':2}
)
for v in 'efg':
assert(objint.class_has(v))
#end for
# test class_set_optional
objint.class_set_optional(h=2)
assert(objint.class_has('h'))
assert(objint.class_get('h')==2)
objint.class_set_optional(a=6)
assert(objint.class_get('a')==1)
# test logging functions
# test open log, write, close log
o = obj()
o.open_log('log.out')
s = 'log output'
o.write(s)
o.close_log()
f = open('log.out','r')
so = f.read()
f.close()
os.remove('log.out')
assert(so==s)
# send messages to object rather than stdout
divert_nexus_log()
logfile = object_interface._logfile
# simple message
class DerivedObj(obj):
None
#end class DerivedObj
o = DerivedObj()
s = 'simple message'
logfile.reset()
o.log(s)
assert(logfile.s==s+'\n')
# list of items
items = ['a','b','c',1,2,3]
logfile.reset()
o.log(*items)
assert(logfile.s=='a b c 1 2 3 \n')
# message with indentation
s = 'a message\nwith indentation'
logfile.reset()
o.log(s,indent=' ')
assert(logfile.s==' a message\n with indentation\n')
logfile.reset()
o.log(s,indent='msg: ')
assert(logfile.s=='msg: a message\nmsg: with indentation\n')
# writing to separate log files
logfile2 = FakeLog()
s1 = 'message to log 1'
s2 = 'message to log 2'
logfile.reset()
logfile2.reset()
o.log(s1)
assert(logfile.s==s1+'\n')
assert(logfile2.s=='')
logfile.reset()
logfile2.reset()
o.log(s2,logfile=logfile2)
assert(logfile.s=='')
assert(logfile2.s==s2+'\n')
# test warn
logfile.reset()
s = 'this is a warning'
o.warn(s)
so = '''
DerivedObj warning:
this is a warning
'''
assert(logfile.s==so)
logfile.reset()
s = 'this is a warning'
o.warn(s,header='Special')
so = '''
Special warning:
this is a warning
'''
assert(logfile.s==so)
# test error
# in testing environment, should raise an error
try:
o.error('testing environment')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# in standard/user environment, should print message
generic_settings.raise_error = False
logfile.reset()
o.error('this is an error',exit=False)
so = '''
DerivedObj error:
this is an error
'''
assert(logfile.s==so)
logfile.reset()
o.error('this is an error',header='User',exit=False)
so = '''
User error:
this is an error
'''
assert(logfile.s==so)
generic_settings.raise_error = True
# in testing environment, should raise an error
try:
o.error('testing environment')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# restore logging function
restore_nexus_log()
def test_optimization_analysis():
import os
from numpy import array
from generic import obj
from qmcpack_analyzer import QmcpackAnalyzer
tpath = testing.setup_unit_test_output_directory(
test='qmcpack_analyzer',
subtest='test_optimization_analysis',
file_sets=['diamond_gamma'],
)
divert_nexus_log()
infile = os.path.join(tpath, 'diamond_gamma/opt/opt.in.xml')
qa = QmcpackAnalyzer(infile, analyze=True, equilibration=5)
qa_keys = 'info wavefunction opt qmc results'.split()
assert (set(qa.keys()) == set(qa_keys))
qmc = qa.qmc
qmc_keys = range(6)
assert (set(qmc.keys()) == set(qmc_keys))
le_opt = obj()
for n in qmc_keys:
le_opt[n] = qmc[n].scalars.LocalEnergy.mean
#end for
le_opt_ref = obj({
0: -10.449225495355556,
1: -10.454263886688889,
2: -10.459916961266668,
3: -10.4583030738,
4: -10.462984807955555,
5: -10.460860545622223,
})
assert (object_eq(le_opt, le_opt_ref))
results = qa.results
results_keys = ['optimization']
assert (set(results.keys()) == set(results_keys))
opt = results.optimization
opt_keys = '''
all_complete
any_complete
energy
energy_error
energy_weight
failed
info
optimal_file
optimal_series
optimal_wavefunction
optimize
opts
series
unstable
variance
variance_error
variance_weight
'''.split()
assert (set(opt.keys()) == set(opt_keys))
from qmcpack_input import wavefunction
assert (isinstance(opt.optimal_wavefunction, wavefunction))
opt_wf = opt.optimal_wavefunction
opt_wf_text = opt_wf.write()
opt_wf_text_ref = '''
<wavefunction name="psi0" target="e">
<sposet_builder type="bspline" href="../scf/pwscf_output/pwscf.pwscf.h5" tilematrix="1 0 0 0 1 0 0 0 1" twistnum="0" source="ion0" version="0.1" meshfactor="1.0" precision="float" truncate="no">
<sposet type="bspline" name="spo_ud" size="4" spindataset="0"> </sposet>
</sposet_builder>
<determinantset>
<slaterdeterminant>
<determinant id="updet" group="u" sposet="spo_ud" size="4"/>
<determinant id="downdet" group="d" sposet="spo_ud" size="4"/>
</slaterdeterminant>
</determinantset>
<jastrow type="Two-Body" name="J2" function="bspline" print="yes">
<correlation speciesA="u" speciesB="u" size="8" rcut="2.3851851232">
<coefficients id="uu" type="Array">
0.2576630369 0.1796686015 0.1326653657 0.09407180823 0.06267013118 0.03899100023
0.02070235604 0.009229775746
</coefficients>
</correlation>
<correlation speciesA="u" speciesB="d" size="8" rcut="2.3851851232">
<coefficients id="ud" type="Array">
0.4385891515 0.3212399072 0.2275448261 0.1558506324 0.1009589176 0.06108433554
0.03154274436 0.01389485975
</coefficients>
</correlation>
</jastrow>
</wavefunction>
'''
opt_wf_text_ref = opt_wf_text_ref.replace('"', ' " ')
opt_wf_text = opt_wf_text.replace('"', ' " ')
assert (text_eq(opt_wf_text, opt_wf_text_ref))
del opt.info
del opt.opts
del opt.optimal_wavefunction
opt_ref = obj(
all_complete=True,
any_complete=True,
energy=array([
-10.45426389, -10.45991696, -10.45830307, -10.46298481,
-10.46086055
],
dtype=float),
energy_error=array(
[0.00320561, 0.00271802, 0.00298106, 0.00561322, 0.00375811],
dtype=float),
energy_weight=None,
failed=False,
optimal_file='opt.s003.opt.xml',
optimal_series=3,
optimize=(1.0, 0.0),
series=array([1, 2, 3, 4, 5], dtype=int),
unstable=False,
variance=array(
[0.40278743, 0.39865602, 0.38110459, 0.38927957, 0.39354343],
dtype=float),
variance_error=array(
[0.01716415, 0.00934316, 0.00529809, 0.01204068, 0.00913372],
dtype=float),
variance_weight=None,
)
assert (object_eq(opt.to_obj(), opt_ref, atol=1e-8))
restore_nexus_log()
def test_input():
# imports
import os
import numpy as np
import pwscf_input as pwi
from generic import obj
from structure import read_structure
from physical_system import generate_physical_system
from pwscf_input import check_new_variables,check_section_classes
from pwscf_input import PwscfInput,generate_pwscf_input
# directories
tpath = testing.setup_unit_test_output_directory('pwscf_input','test_input')
# files
files = get_files()
# divert logging function
divert_nexus_log()
# definitions
def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'):
pw_same = object_eq(pw1_,pw2_,int_as_float=True)
if not pw_same:
d,d1,d2 = object_diff(pw1_,pw2_,full=True,int_as_float=True)
diff = obj({l1:obj(d1),l2:obj(d2)})
failed(str(diff))
#end if
#end def check_pw_same
# test internal spec
check_new_variables(exit=False)
check_section_classes(exit=False)
# test compose
compositions = obj()
# based on sample_inputs/Fe_start_ns_eig.in
pw = PwscfInput()
pw.control.set(
calculation = 'scf' ,
restart_mode = 'from_scratch' ,
wf_collect = True ,
outdir = './output' ,
pseudo_dir = '../pseudo/' ,
prefix = 'fe' ,
etot_conv_thr = 1.0e-9 ,
forc_conv_thr = 1.0e-6 ,
tstress = True ,
tprnfor = True ,
)
pw.system.set(
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100 ,
ecutrho = 300 ,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005 ,
smearing = 'methfessel-paxton' ,
nspin = 2 ,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True ,
)
pw.system.set({
'celldm(1)' : 15,
'starting_magnetization(1)' : 0.9,
'hubbard_u(1)' : 3.1,
'starting_ns_eigenvalue(1,2,1)' : 0.0,
'starting_ns_eigenvalue(2,2,1)' : 0.0476060,
'starting_ns_eigenvalue(3,2,1)' : 0.0476060,
'starting_ns_eigenvalue(4,2,1)' : 0.9654373,
'starting_ns_eigenvalue(5,2,1)' : 0.9954307,
})
pw.electrons.set(
conv_thr = 1.0e-9 ,
mixing_beta = 0.7 ,
diagonalization = 'david' ,
mixing_fixed_ns = 500,
)
pw.atomic_species.set(
atoms = ['Fe'],
masses = obj(Fe=58.69000),
pseudopotentials = obj(Fe='Fe.pbe-nd-rrkjus.UPF'),
)
pw.atomic_positions.set(
specifier = 'angstrom',
atoms = ['Fe','Fe'],
positions = np.array([
[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000],
]),
)
pw.k_points.set(
specifier = 'automatic',
grid = np.array((1,1,1)),
shift = np.array((1,1,1)),
)
compositions['Fe_start_ns_eig.in'] = pw
# test read
pwr = PwscfInput(files['Fe_start_ns_eig.in'])
pwc = pw.copy()
pwc.standardize_types()
check_pw_same(pwc,pwr,'compose','read')
# test write
infile = os.path.join(tpath,'pwscf.in')
pw.write(infile)
pw2 = PwscfInput()
pw2.read(infile)
check_pw_same(pw2,pwr)
# test read/write/read
reads = obj()
for infile in input_files:
read_path = files[infile]
write_path = os.path.join(tpath,infile)
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw = PwscfInput(read_path)
pw.write(write_path)
pw2 = PwscfInput(write_path)
check_pw_same(pw,pw2,'read','write/read')
reads[infile] = pw
#end for
# test generate
generations = obj()
# based on sample_inputs/VO2_M1_afm.in
infile = 'VO2_M1_afm.in'
struct_file = files['VO2_M1_afm.xsf']
read_path = files[infile]
write_path = os.path.join(tpath,infile)
s = read_structure(struct_file)
s.elem[0] = 'V1'
s.elem[1] = 'V2'
s.elem[2] = 'V1'
s.elem[3] = 'V2'
vo2 = generate_physical_system(
structure = s,
V1 = 13,
V2 = 13,
O = 6,
)
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
disk_io = 'low',
verbosity = 'high',
wf_collect = True,
input_dft = 'lda',
hubbard_u = obj(V1=3.5,V2=3.5),
ecutwfc = 350,
bandfac = 1.3,
nosym = True,
occupations = 'smearing',
smearing = 'fermi-dirac',
degauss = 0.0001,
nspin = 2,
start_mag = obj(V1=1.0,V2=-1.0),
diagonalization = 'david',
conv_thr = 1e-8,
mixing_beta = 0.2,
electron_maxstep = 1000,
system = vo2,
pseudos = ['V.opt.upf','O.opt.upf'],
kgrid = (6,6,6),
kshift = (0,0,0),
# added for reverse compatibility
celldm = {1:1.0},
cell_option = 'alat',
positions_option = 'alat',
)
generations[infile] = pw
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw2 = PwscfInput(read_path)
pw3 = PwscfInput(write_path)
check_pw_same(pw2,pw3,'generate','read')
# based on sample_inputs/Fe_start_ns_eig.in
infile = 'Fe_start_ns_eig.in'
read_path = files[infile]
write_path = os.path.join(tpath,infile)
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
restart_mode = 'from_scratch',
wf_collect = True,
outdir = './output',
pseudo_dir = '../pseudo/',
prefix = 'fe',
etot_conv_thr = 1.0e-9,
forc_conv_thr = 1.0e-6,
tstress = True,
tprnfor = True,
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100,
ecutrho = 300,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005,
smearing = 'methfessel-paxton',
nspin = 2,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True,
conv_thr = 1.0e-9,
mixing_beta = 0.7,
diagonalization = 'david',
mixing_fixed_ns = 500,
mass = obj(Fe=58.69000),
pseudos = ['Fe.pbe-nd-rrkjus.UPF'],
elem = ['Fe','Fe'],
pos = [[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000]],
pos_specifier = 'angstrom',
kgrid = np.array((1,1,1)),
kshift = np.array((1,1,1)),
)
pw.system.set({
'celldm(1)' : 15,
'starting_magnetization(1)' : 0.9,
'hubbard_u(1)' : 3.1,
'starting_ns_eigenvalue(1,2,1)' : 0.0,
'starting_ns_eigenvalue(2,2,1)' : 0.0476060,
'starting_ns_eigenvalue(3,2,1)' : 0.0476060,
'starting_ns_eigenvalue(4,2,1)' : 0.9654373,
'starting_ns_eigenvalue(5,2,1)' : 0.9954307,
})
generations[infile] = pw
pw2 = compositions[infile]
check_pw_same(pw,pw2,'generate','compose')
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw3 = PwscfInput(write_path)
pw4 = reads[infile]
check_pw_same(pw3,pw4,'generate','read')
# based on sample_inputs/Fe_start_ns_eig.in
# variant that uses direct pwscf array input
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
restart_mode = 'from_scratch',
wf_collect = True,
outdir = './output',
pseudo_dir = '../pseudo/',
prefix = 'fe',
etot_conv_thr = 1.0e-9,
forc_conv_thr = 1.0e-6,
tstress = True,
tprnfor = True,
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100,
ecutrho = 300,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005,
smearing = 'methfessel-paxton',
nspin = 2,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True,
conv_thr = 1.0e-9,
mixing_beta = 0.7,
diagonalization = 'david',
mixing_fixed_ns = 500,
mass = obj(Fe=58.69000),
pseudos = ['Fe.pbe-nd-rrkjus.UPF'],
elem = ['Fe','Fe'],
pos = [[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000]],
pos_specifier = 'angstrom',
kgrid = np.array((1,1,1)),
kshift = np.array((1,1,1)),
starting_ns_eigenvalue = {(1,2,1) : 0.0,
(2,2,1) : 0.0476060,
(3,2,1) : 0.0476060,
(4,2,1) : 0.9654373,
(5,2,1) : 0.9954307,},
celldm = {1 : 15 },
starting_magnetization = {1 : 0.9},
hubbard_u = {1 : 3.1},
)
pwg = pw.copy()
pwg.standardize_types()
generations[infile] = pw
pw2 = compositions[infile].copy()
pw2.standardize_types()
check_pw_same(pwg,pw2,'generate','compose')
pw3 = reads[infile]
check_pw_same(pwg,pw3,'generate','read')
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw4 = PwscfInput(write_path)
check_pw_same(pwg,pw3,'generate','write')
# restore logging function
restore_nexus_log()
def test_pseudopotentials():
from pseudopotential import Pseudopotentials
from pseudopotential import PseudoFile
from pseudopotential import gamessPPFile
filenames = get_filenames()
files = get_files()
filepaths = [files[fn] for fn in filenames]
# empty initialization
Pseudopotentials()
PseudoFile()
gamessPPFile()
# standard initialization
divert_nexus_log()
pps = Pseudopotentials(filepaths)
restore_nexus_log()
for fn in filenames:
assert (fn in pps)
pp = pps[fn]
assert (isinstance(pp, PseudoFile))
if fn.endswith('.gms'):
assert (isinstance(pp, gamessPPFile))
#end if
assert (pp.element == 'C')
assert (pp.element_label == 'C')
assert (pp.filename == fn)
#end for
basis_ref = '''s 9 1.00
1 0.051344 0.013991
2 0.102619 0.169852
3 0.205100 0.397529
4 0.409924 0.380369
5 0.819297 0.180113
6 1.637494 -0.033512
7 3.272791 -0.121499
8 6.541187 0.015176
9 13.073594 -0.000705
s 1 1.00
1 0.098302 1.000000
s 1 1.00
1 0.232034 1.000000
s 1 1.00
1 0.744448 1.000000
s 1 1.00
1 1.009914 1.000000
p 9 1.00
1 0.029281 0.001787
2 0.058547 0.050426
3 0.117063 0.191634
4 0.234064 0.302667
5 0.468003 0.289868
6 0.935757 0.210979
7 1.871016 0.112024
8 3.741035 0.054425
9 7.480076 0.021931
p 1 1.00
1 0.084047 1.000000
p 1 1.00
1 0.216618 1.000000
p 1 1.00
1 0.576869 1.000000
p 1 1.00
1 1.006252 1.000000
d 1 1.00
1 0.206619 1.000000
d 1 1.00
1 0.606933 1.000000
d 1 1.00
1 1.001526 1.000000
d 1 1.00
1 1.504882 1.000000
f 1 1.00
1 0.400573 1.000000
f 1 1.00
1 1.099564 1.000000
f 1 1.00
1 1.501091 1.000000
g 1 1.00
1 0.797648 1.000000
g 1 1.00
1 1.401343 1.000000
h 1 1.00
1 1.001703 1.000000'''
pp_ref = '''C-QMC GEN 2 1
3
4.00000000 1 8.35973821
33.43895285 3 4.48361888
-19.17537323 2 3.93831258
1
22.55164191 2 5.02991637'''
pp = pps['C.BFD.gms']
assert (pp.basis_text == basis_ref)
assert (pp.pp_text == pp_ref)