def test_inline_export(self):
from aiida.orm.data.cif import CifData
from aiida.tools.dbexporters.tcod import export_values
import tempfile
with tempfile.NamedTemporaryFile() as f:
f.write('''
data_test
_cell_length_a 10
_cell_length_b 10
_cell_length_c 10
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C 0 0 0
O 0.5 0.5 0.5
''')
f.flush()
a = CifData(file=f.name)
s = a._get_aiida_structure(store=True)
val = export_values(s)
script = val.first_block()['_tcod_file_contents'][1]
function = '_get_aiida_structure_ase_inline'
self.assertNotEqual(script.find(function), script.rfind(function))
def test_symmetry_reduction(self):
from aiida.tools.dbexporters.tcod import export_values
from ase import Atoms
a = Atoms('BaTiO3', cell=(4., 4., 4.))
a.set_scaled_positions((
(0.0, 0.0, 0.0),
(0.5, 0.5, 0.5),
(0.5, 0.5, 0.0),
(0.5, 0.0, 0.5),
(0.0, 0.5, 0.5),
))
a.set_chemical_symbols(['Ba', 'Ti', 'O', 'O', 'O'])
val = export_values(orm.StructureData(ase=a),
reduce_symmetry=True,
store=True)['0']
self.assertEqual(val['_atom_site_label'], ['Ba1', 'Ti1', 'O1'])
self.assertEqual(val['_symmetry_space_group_name_H-M'], 'Pm-3m')
self.assertEqual(val['_symmetry_space_group_name_Hall'], '-P 4 2 3')
def test_export_trajectory(self):
from aiida.orm.data.structure import StructureData
from aiida.orm.data.array.trajectory import TrajectoryData
from aiida.tools.dbexporters.tcod import export_values
cells = [[[
2.,
0.,
0.,
], [
0.,
2.,
0.,
], [
0.,
0.,
2.,
]], [[
3.,
0.,
0.,
], [
0.,
3.,
0.,
], [
0.,
0.,
3.,
]]]
symbols = [['H', 'O', 'C'], ['H', 'O', 'C']]
positions = [[[0., 0., 0.], [0.5, 0.5, 0.5], [1.5, 1.5, 1.5]],
[[0., 0., 0.], [0.75, 0.75, 0.75], [1.25, 1.25, 1.25]]]
structurelist = []
for i in range(0, 2):
struct = StructureData(cell=cells[i])
for j, symbol in enumerate(symbols[i]):
struct.append_atom(symbols=symbol, position=positions[i][j])
structurelist.append(struct)
td = TrajectoryData(structurelist=structurelist)
with self.assertRaises(ValueError):
# Trajectory index is not specified
v = export_values(td)
expected_tags = [
'_atom_site_fract_x', '_atom_site_fract_y', '_atom_site_fract_z',
'_atom_site_label', '_atom_site_type_symbol',
'_audit_conform_dict_location', '_audit_conform_dict_name',
'_audit_conform_dict_version', '_audit_creation_method',
'_cell_angle_alpha', '_cell_angle_beta', '_cell_angle_gamma',
'_cell_length_a', '_cell_length_b', '_cell_length_c',
'_chemical_formula_sum', '_symmetry_Int_Tables_number',
'_symmetry_equiv_pos_as_xyz', '_symmetry_space_group_name_H-M',
'_symmetry_space_group_name_Hall'
]
tcod_file_tags = [
'_tcod_content_encoding_id', '_tcod_content_encoding_layer_id',
'_tcod_content_encoding_layer_type', '_tcod_file_URI',
'_tcod_file_content_encoding', '_tcod_file_contents',
'_tcod_file_id', '_tcod_file_md5sum', '_tcod_file_name',
'_tcod_file_role', '_tcod_file_sha1sum'
]
# Not stored and not to be stored:
v = export_values(td, trajectory_index=1)
self.assertEqual(sorted(v['0'].keys()), expected_tags)
# Stored, but not expected to be stored:
td = TrajectoryData(structurelist=structurelist)
td.store()
v = export_values(td, trajectory_index=1)
self.assertEqual(sorted(v['0'].keys()), expected_tags + tcod_file_tags)
# Not stored, but expected to be stored:
td = TrajectoryData(structurelist=structurelist)
v = export_values(td, trajectory_index=1, store=True)
self.assertEqual(sorted(v['0'].keys()), expected_tags + tcod_file_tags)
# Both stored and expected to be stored:
td = TrajectoryData(structurelist=structurelist)
td.store()
v = export_values(td, trajectory_index=1, store=True)
self.assertEqual(sorted(v['0'].keys()), expected_tags + tcod_file_tags)
# Stored, but asked not to include DB dump:
td = TrajectoryData(structurelist=structurelist)
td.store()
v = export_values(td, trajectory_index=1, dump_aiida_database=False)
self.assertEqual(sorted(v['0'].keys()), expected_tags)
def test_cif_structure_roundtrip(self):
from aiida.tools.dbexporters.tcod import export_cif, export_values
from aiida.orm import Code
from aiida.orm import JobCalculation
from aiida.orm.data.cif import CifData
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.upf import UpfData
from aiida.orm.data.folder import FolderData
from aiida.common.folders import SandboxFolder
from aiida.common.datastructures import calc_states
import tempfile
with tempfile.NamedTemporaryFile() as f:
f.write('''
data_test
_cell_length_a 10
_cell_length_b 10
_cell_length_c 10
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C 0 0 0
O 0.5 0.5 0.5
''')
f.flush()
a = CifData(file=f.name)
c = a._get_aiida_structure()
c.store()
pd = ParameterData()
code = Code(local_executable='test.sh')
with tempfile.NamedTemporaryFile() as f:
f.write("#/bin/bash\n\necho test run\n")
f.flush()
code.add_path(f.name, 'test.sh')
code.store()
calc = JobCalculation(computer=self.computer)
calc.set_resources({'num_machines': 1, 'num_mpiprocs_per_machine': 1})
calc.add_link_from(code, "code")
calc.set_environment_variables({
'PATH': '/dev/null',
'USER': '******'
})
with tempfile.NamedTemporaryFile(prefix="Fe") as f:
f.write("<UPF version=\"2.0.1\">\nelement=\"Fe\"\n")
f.flush()
upf = UpfData(file=f.name)
upf.store()
calc.add_link_from(upf, "upf")
with tempfile.NamedTemporaryFile() as f:
f.write("data_test")
f.flush()
cif = CifData(file=f.name)
cif.store()
calc.add_link_from(cif, "cif")
calc.store()
calc._set_state(calc_states.SUBMITTING)
with SandboxFolder() as f:
calc._store_raw_input_folder(f.abspath)
fd = FolderData()
with open(
fd._get_folder_pathsubfolder.get_abs_path(
calc._SCHED_OUTPUT_FILE), 'w') as f:
f.write("standard output")
f.flush()
with open(
fd._get_folder_pathsubfolder.get_abs_path(
calc._SCHED_ERROR_FILE), 'w') as f:
f.write("standard error")
f.flush()
fd.store()
fd.add_link_from(calc, calc._get_linkname_retrieved(), LinkType.CREATE)
pd.add_link_from(calc, "calc", LinkType.CREATE)
pd.store()
with self.assertRaises(ValueError):
export_cif(c, parameters=pd)
c.add_link_from(calc, "calc", LinkType.CREATE)
export_cif(c, parameters=pd)
values = export_values(c, parameters=pd)
values = values['0']
self.assertEquals(values['_tcod_computation_environment'],
['PATH=/dev/null\nUSER=unknown'])
self.assertEquals(values['_tcod_computation_command'],
['cd 1; ./_aiidasubmit.sh'])
def test_cif_structure_roundtrip(self):
from aiida.tools.dbexporters.tcod import export_cif, export_values
from aiida.common.folders import SandboxFolder
import tempfile
with tempfile.NamedTemporaryFile(mode='w+') as tmpf:
tmpf.write('''
data_test
_cell_length_a 10
_cell_length_b 10
_cell_length_c 10
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C 0 0 0
O 0.5 0.5 0.5
''')
tmpf.flush()
a = orm.CifData(filepath=tmpf.name)
c = a.get_structure()
c.store()
pd = orm.Dict()
code = orm.Code(local_executable='test.sh')
with tempfile.NamedTemporaryFile(mode='w+') as tmpf:
tmpf.write("#/bin/bash\n\necho test run\n")
tmpf.flush()
code.put_object_from_filelike(tmpf, 'test.sh')
code.store()
calc = orm.CalcJobNode(computer=self.computer)
calc.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
calc.add_incoming(code, LinkType.INPUT_CALC, "code")
calc.set_option('environment_variables', {
'PATH': '/dev/null',
'USER': '******'
})
with tempfile.NamedTemporaryFile(mode='w+', prefix="Fe") as tmpf:
tmpf.write("<UPF version=\"2.0.1\">\nelement=\"Fe\"\n")
tmpf.flush()
upf = orm.UpfData(filepath=tmpf.name)
upf.store()
calc.add_incoming(upf, LinkType.INPUT_CALC, "upf")
with tempfile.NamedTemporaryFile(mode='w+') as tmpf:
tmpf.write("data_test")
tmpf.flush()
cif = orm.CifData(filepath=tmpf.name)
cif.store()
calc.add_incoming(cif, LinkType.INPUT_CALC, "cif")
with SandboxFolder() as fhandle:
calc.put_object_from_tree(fhandle.abspath)
calc.store()
fd = orm.FolderData()
with fd.open('_scheduler-stdout.txt', 'w') as fhandle:
fhandle.write(u"standard output")
with fd.open('_scheduler-stderr.txt', 'w') as fhandle:
fhandle.write(u"standard error")
fd.store()
fd.add_incoming(calc, LinkType.CREATE, calc.link_label_retrieved)
pd.add_incoming(calc, LinkType.CREATE, "create1")
pd.store()
with self.assertRaises(ValueError):
export_cif(c, parameters=pd)
c.add_incoming(calc, LinkType.CREATE, "create2")
export_cif(c, parameters=pd)
values = export_values(c, parameters=pd)
values = values['0']
self.assertEquals(values['_tcod_computation_environment'],
['PATH=/dev/null\nUSER=unknown'])
self.assertEquals(values['_tcod_computation_command'],
['cd 1; ./_aiidasubmit.sh'])
