def test_expand(self):
"""
Testing helper function to extend the convergence grid
"""
self.maxDiff = None
spec = get_spec('GW')
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
tests = SingleAbinitGWWork(struc, spec).convs
tests_out = {'nscf_nbands': {'test_range': (40,),
'control': 'gap', 'method': 'set_bands', 'level': 'nscf'},
'ecut': {'test_range': (50, 48, 46, 44),
'control': 'e_ks_max', 'method': 'direct', 'level': 'scf'},
'ecuteps': {'test_range': (4, 8, 12, 16, 20),
'control': 'gap', 'method': 'direct', 'level': 'sigma'}}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
if "VASP_PSP_DIR" in os.environ:
spec.update_code_interface()
tests = GWG0W0VaspInputSet(struc, spec).convs
tests_out = {'ENCUTGW': {'test_range': (200, 400, 600, 800), 'control': 'gap', 'method': 'incar_settings'}}
self.assertEqual(expand(tests, 1), tests_out)
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_expand(self):
self.maxDiff = None
spec = get_spec('GW')
tests = SingleAbinitGWWork(structure, spec).convs
tests_out = {'nscf_nbands': {'test_range': (40,),
'control': 'gap', 'method': 'set_bands', 'level': 'nscf'},
'ecut': {'test_range': (50, 48, 46, 44),
'control': 'e_ks_max', 'method': 'direct', 'level': 'scf'},
'ecuteps': {'test_range': (4, 8, 12, 16, 20),
'control': 'gap', 'method': 'direct', 'level': 'sigma'}}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
spec.update_code_interface()
tests = GWG0W0VaspInputSet(structure, spec).convs
tests_out = {'ENCUTGW': {'test_range': (200, 400, 600, 800), 'control': 'gap', 'method': 'incar_settings'}}
self.assertEqual(expand(tests, 1), tests_out)
def main(update=True):
"""
main gw setup
"""
spec_in = get_spec('GW')
try:
spec_in.read_from_file('spec.in')
except (IOError, OSError):
try:
spec_in.read_from_file('$HOME/.abinit/abipy/spec.in')
except (IOError, OSError):
pass
pass
if update:
# in testing mode there should not be interactive updating
spec_in.update_interactive()
spec_in.test()
spec_in.write_to_file('spec.in')
spec_in.loop_structures('i')
return 0
def test_expand(self):
self.maxDiff = None
spec = get_spec('GW')
tests = SingleAbinitGWWork(structure, spec).convs
tests_out = {
'nscf_nbands': {
'test_range': (40, ),
'control': 'gap',
'method': 'set_bands',
'level': 'nscf'
},
'ecut': {
'test_range': (50, 48, 46, 44),
'control': 'e_ks_max',
'method': 'direct',
'level': 'scf'
},
'ecuteps': {
'test_range': (4, 8, 12, 16, 20),
'control': 'gap',
'method': 'direct',
'level': 'sigma'
}
}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
spec.update_code_interface()
tests = GWG0W0VaspInputSet(structure, spec).convs
tests_out = {
'ENCUTGW': {
'test_range': (200, 400, 600, 800),
'control': 'gap',
'method': 'incar_settings'
}
}
self.assertEqual(expand(tests, 1), tests_out)
def test_GWget_spec(self):
spec = get_spec('GW')
self.assertIsInstance(spec, GWSpecs)
#!/usr/bin/env python
"""
Script process the GW output generated by GWsetup using VASP or ABINIT.
"""
from __future__ import unicode_literals, division, print_function
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ = "0.9"
__maintainer__ = "Michiel van Setten"
__email__ = "*****@*****.**"
__date__ = "May 2014"
import os
import os.path
from abipy.gw.datastructures import get_spec
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
if __name__ == "__main__":
if os.path.isfile('plots'):
os.remove('plots')
if os.path.isfile('plot-fits'):
os.remove('plot-fits')
spec = get_spec('GW')
spec.read_from_file('spec.in')
print('Found setup for ', spec.get_code())
spec.loop_structures('o')
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ = "0.9"
__maintainer__ = "Michiel van Setten"
__email__ = "*****@*****.**"
__date__ = "May 2014"
import os
import os.path
from abipy.gw.datastructures import get_spec
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
if __name__ == "__main__":
counter = 0
#load_ps()
spec_in = get_spec('GW')
try:
spec_in.read_from_file('spec.in')
except (IOError, OSError):
try:
spec_in.read_from_file('$HOME/.abinit/abipy/spec.in')
except (IOError, OSError):
pass
pass
spec_in.update_interactive()
spec_in.test()
spec_in.write_to_file('spec.in')
spec_in.loop_structures('i')
def test_setup(self):
"""
Testing the main functions called in the abiGWsetup script
"""
spec_in = get_spec('GW')
self.assertIsInstance(spec_in, GWSpecs)
self.assert_equal(spec_in.test(), 0)
self.assert_equal(len(spec_in.to_dict()), 10)
self.assert_equal(spec_in.get_code(), 'ABINIT')
spec_in.data['source'] = 'cif'
self.assert_equal(
spec_in.hash_str(),
"code:ABINIT;source:cifjobs:[u'prep', u'G0W0'];mode:ceci;functional:PBE;kp_grid_dens:500prec:m;tol:0.0001;test:False;converge:False"
)
wdir = tempfile.mkdtemp()
base = os.getcwd()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"),
os.path.join(wdir, 'si.cif'))
shutil.copyfile(
abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'),
os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
spec_in.data['source'] = 'cif'
print('dirpath', abidata.dirpath)
spec_in.write_to_file('spec.in')
self.assertTrue(os.path.isfile(os.path.join(wdir, 'spec.in')))
# broken due to strategy refactoring
# spec_in.loop_structures('i')
os.chdir(base)
shutil.rmtree(wdir)
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
#!/usr/bin/env python
"""
Script to store GW results for VASP and ABINIT in a database.
"""
from __future__ import unicode_literals, division, print_function
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ = "0.9"
__maintainer__ = "Michiel van Setten"
__email__ = "*****@*****.**"
__date__ = "May 2014"
import os
import os.path
from abipy.gw.datastructures import get_spec
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
if __name__ == "__main__":
counter = 0
spec_in = get_spec('GW')
spec_in.read_from_file('spec.in')
spec_in.loop_structures('s')
def test_GWget_spec(self):
"""
Testing the factory function get_specs()
"""
spec = get_spec('GW')
self.assertIsInstance(spec, GWSpecs)
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
#wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"),
os.path.join(wdir, 'si.cif'))
shutil.copyfile(
abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers',
'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'),
os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open(os.path.join(wdir, 'extra_abivars'), 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc),
work.get_electrons(struc) / 2,
'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow[0][0].__class__, ScfTask)
self.assertEqual(flow[0][1].__class__, ScfTask)
self.assertEqual(flow[0][2].__class__, ScfTask)
self.assertEqual(flow[0][3].__class__, ScfTask)
self.assertEqual(flow[0][4].__class__, NscfTask)
self.assertEqual(flow[0][5].__class__, ScrTask)
self.assertEqual(flow[0][6].__class__, SigmaTask)
ecuts = [
dict(task.input.as_dict()['abi_args'])['ecut'] for task in flow[0]
]
print('ecuts:', ecuts)
# it is essential that the first four are diffent, this is for the convergence study of ecut, and that
# after that is stays the same
self.assertEqual(ecuts, [
50, 48, 46, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44,
44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44,
44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44
])
nbands = [
dict(task.input.as_dict()['abi_args'])['nband'] for task in flow[0]
]
print('nbands:', nbands)
# the firs 4 should be 'low' these are self consistent
# the fifth should be the maximum of what follows
# the 6th and on should always be pairs that are the same, they are combinations of scr and sigma tasks
self.assertEqual(nbands, [
26, 26, 26, 26, 180, 30, 30, 60, 60, 120, 120, 180, 180, 30, 30,
60, 60, 120, 120, 180, 180, 30, 30, 60, 60, 120, 120, 180, 180, 30,
30, 60, 60, 120, 120, 180, 180, 30, 30, 60, 60, 120, 120, 180, 180
])
ecuteps = [
dict(task.input.as_dict()['abi_args']).get('ecuteps', None)
for task in flow[0]
]
print('ecuteps:', ecuteps)
self.assertEqual(ecuteps, [
None, None, None, None, None, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8,
8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16,
16, 16, 20, 20, 20, 20, 20, 20, 20, 20
])
inplens = [len(task.input.as_dict()['abi_args']) for task in flow[0]]
print(inplens)
self.assertEqual(inplens, [
17, 17, 17, 17, 18, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30,
27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27,
30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30
])
ngkpts = [
dict(task.input.as_dict()['abi_args'])['ngkpt'] for task in flow[0]
]
for ngkpt in ngkpts:
self.assertEqual(ngkpt, [2, 2, 2])
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
#!/usr/bin/env python
# coding: utf-8
"""
Script process the GW output generated by GWsetup using VASP or ABINIT.
"""
from __future__ import unicode_literals, division, print_function
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ = "0.9"
__maintainer__ = "Michiel van Setten"
__email__ = "*****@*****.**"
__date__ = "May 2014"
import os
import os.path
from abipy.gw.datastructures import get_spec
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
if __name__ == "__main__":
if os.path.isfile('plots'):
os.remove('plots')
if os.path.isfile('plot-fits'):
os.remove('plot-fits')
spec = get_spec('GW')
spec.read_from_file('spec.in')
print('Found setup for ', spec.get_code())
spec.loop_structures('o')
def test_GWget_spec(self):
"""
Testing the factory function get_specs()
"""
spec = get_spec('GW')
self.assertIsInstance(spec, GWSpecs)
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open('extra_abivars', 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc), work.get_electrons(struc) / 2, 'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_expand(self):
"""
Testing helper function to extend the convergence grid
"""
self.maxDiff = None
spec = get_spec('GW')
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"),
os.path.join(wdir, 'si.cif'))
shutil.copyfile(
abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'),
os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
tests = SingleAbinitGWWork(struc, spec).convs
tests_out = {
'nscf_nbands': {
'test_range': (40, ),
'control': 'gap',
'method': 'set_bands',
'level': 'nscf'
},
'ecut': {
'test_range': (50, 48, 46, 44),
'control': 'e_ks_max',
'method': 'direct',
'level': 'scf'
},
'ecuteps': {
'test_range': (4, 8, 12, 16, 20),
'control': 'gap',
'method': 'direct',
'level': 'sigma'
}
}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
if "VASP_PSP_DIR" in os.environ:
spec.update_code_interface()
tests = GWG0W0VaspInputSet(struc, spec).convs
tests_out = {
'ENCUTGW': {
'test_range': (200, 400, 600, 800),
'control': 'gap',
'method': 'incar_settings'
}
}
self.assertEqual(expand(tests, 1), tests_out)
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
#wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open(os.path.join(wdir, 'extra_abivars'), 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc), work.get_electrons(struc) / 2, 'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS