def scaled_structure(structure, scale):
new_structure = StructureData(cell=numpy.array(structure.cell)*float(scale))
for site in structure.sites:
new_structure.append_atom(position=numpy.array(site.position)*float(scale), \
symbols=structure.get_kind(site.kind_name).symbol,\
name=site.kind_name)
new_structure.label = 'auxiliary structure for stress tensor'
new_structure.description = "created from the original structure with PK=%i, "\
"lattice constant scaling: %f"%(structure.pk, float(scale))
return new_structure
def scaled_structure(structure, scale):
new_structure = StructureData(cell=np.array(structure.cell)*scale)
for site in structure.sites:
new_structure.append_atom(position=np.array(site.position)*scale, \
symbols=structure.get_kind(site.kind_name).symbol,\
name=site.kind_name)
new_structure.label = 'created inside stress tensor run'
new_structure.description = "auxiliary structure for stress tensor "\
"created from the original structure with PK=%i, "\
"lattice constant scaling: %f"%(structure.pk, scale)
return new_structure
def load_example_structures():
""" Read input structures into the database
Structures are read from subfolder "example-structures"
and stored in the group "example-structures".
:return: group of available structures
"""
from aiida.orm.group import Group
try:
group = Group.get(name=group_name)
except NotExistent:
import glob
import os
from ase.io import read
from aiida.orm.data.structure import StructureData
paths = glob.glob(group_name + '/*.cif')
structure_nodes = []
for path in paths:
fname = os.path.basename(path)
name = os.path.splitext(fname)[0]
structure = StructureData(ase=read(path))
if "ML" in name:
# surface normal of monolayers should be oriented along z
structure.set_pbc([True, True, False])
else:
structure.set_pbc([True, True, True])
structure.label = name
print("Storing {} in database".format(name))
structure.store()
structure_nodes.append(structure)
group = Group(name=group_name)
group.store()
group.description = "\
Set of atomic structures used by examples for AiiDA plugins of different codes"
group.add_nodes(structure_nodes)
return group
from aiida.common.example_helpers import test_and_get_code # noqa
from aiida.orm.data.structure import StructureData # noqa
from aiida.orm.data.parameter import ParameterData # noqa
from aiida.orm.data.base import Str
from aiida.work.run import submit
import ase.build
from aiida_cp2k.workflows import Cp2kGeoOptWorkChain
atoms = ase.build.molecule('H2O')
atoms.center(vacuum=2.0)
structure = StructureData(ase=atoms)
structure.label = 'H2O'
structure.store()
options_dict = {
"resources": {
"num_machines": 1,
"num_mpiprocs_per_machine": 2,
},
"max_wallclock_seconds": 3 * 60 * 60,
}
options = ParameterData(dict=options_dict)
params_dict = {
'FORCE_EVAL': {
'DFT': {
'UKS': True,
},
},
}
def test_6(self):
"""
This test checks that nodes belonging to user A (which is not the
default user) can be correctly exported, imported, enriched with nodes
from the default user, re-exported & re-imported and that in the end
all the nodes that have been finally imported belonging to the right
users.
"""
import os
import shutil
import tempfile
from aiida.orm import load_node
from aiida.orm.calculation.job import JobCalculation
from aiida.orm.data.structure import StructureData
from aiida.orm.importexport import export
from aiida.common.datastructures import calc_states
from aiida.common.links import LinkType
from aiida.common.utils import get_configured_user_email
from aiida.orm.user import User
# Creating a folder for the import/export files
temp_folder = tempfile.mkdtemp()
try:
# Create another user
new_email = "[email protected]"
user = User(email=new_email)
user.force_save()
# Create a structure data node that has a calculation as output
sd1 = StructureData()
sd1.dbnode.user = user._dbuser
sd1.label = 'sd1'
sd1.store()
jc1 = JobCalculation()
jc1.set_computer(self.computer)
jc1.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
jc1.dbnode.user = user._dbuser
jc1.label = 'jc1'
jc1.store()
jc1.add_link_from(sd1)
jc1._set_state(calc_states.PARSING)
# Create some nodes from a different user
sd2 = StructureData()
sd2.dbnode.user = user._dbuser
sd2.label = 'sd2'
sd2.store()
sd2.add_link_from(jc1, label='l1', link_type=LinkType.RETURN)
# Set the jc1 to FINISHED
jc1._set_state(calc_states.FINISHED)
# At this point we export the generated data
filename1 = os.path.join(temp_folder, "export1.tar.gz")
export([sd2.dbnode], outfile=filename1, silent=True)
uuids1 = [sd1.uuid, jc1.uuid, sd2.uuid]
self.clean_db()
self.insert_data()
import_data(filename1, silent=True)
# Check that the imported nodes are correctly imported and that
# the user assigned to the nodes is the right one
for uuid in uuids1:
self.assertEquals(load_node(uuid).get_user().email, new_email)
# Now we continue to generate more data based on the imported
# data
sd2_imp = load_node(sd2.uuid)
jc2 = JobCalculation()
jc2.set_computer(self.computer)
jc2.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
jc2.label = 'jc2'
jc2.store()
jc2.add_link_from(sd2_imp, label='l2')
jc2._set_state(calc_states.PARSING)
sd3 = StructureData()
sd3.label = 'sd3'
sd3.store()
sd3.add_link_from(jc2, label='l3', link_type=LinkType.RETURN)
# Set the jc2 to FINISHED
jc2._set_state(calc_states.FINISHED)
# Store the UUIDs of the nodes that should be checked
# if they can be imported correctly.
uuids2 = [jc2.uuid, sd3.uuid]
filename2 = os.path.join(temp_folder, "export2.tar.gz")
export([sd3.dbnode], outfile=filename2, silent=True)
self.clean_db()
self.insert_data()
import_data(filename2, silent=True)
# Check that the imported nodes are correctly imported and that
# the user assigned to the nodes is the right one
for uuid in uuids1:
self.assertEquals(load_node(uuid).get_user().email, new_email)
for uuid in uuids2:
self.assertEquals(load_node(uuid).get_user().email,
get_configured_user_email())
finally:
# Deleting the created temporary folder
shutil.rmtree(temp_folder, ignore_errors=True)
def test_5(self):
"""
This test checks that nodes belonging to different users are correctly
exported & imported.
"""
import os
import shutil
import tempfile
from aiida.orm import load_node
from aiida.orm.calculation.job import JobCalculation
from aiida.orm.data.structure import StructureData
from aiida.orm.importexport import export
from aiida.common.datastructures import calc_states
from aiida.common.links import LinkType
from aiida.orm.user import User
from aiida.common.utils import get_configured_user_email
# Creating a folder for the import/export files
temp_folder = tempfile.mkdtemp()
try:
# Create another user
new_email = "[email protected]"
user = User(email=new_email)
user.force_save()
# Create a structure data node that has a calculation as output
sd1 = StructureData()
sd1.dbnode.user = user._dbuser
sd1.label = 'sd1'
sd1.store()
jc1 = JobCalculation()
jc1.set_computer(self.computer)
jc1.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
jc1.dbnode.user = user._dbuser
jc1.label = 'jc1'
jc1.store()
jc1.add_link_from(sd1)
jc1._set_state(calc_states.PARSING)
# Create some nodes from a different user
sd2 = StructureData()
sd2.dbnode.user = user._dbuser
sd2.label = 'sd2'
sd2.store()
sd2.add_link_from(jc1, label='l1', link_type=LinkType.RETURN)
jc2 = JobCalculation()
jc2.set_computer(self.computer)
jc2.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
jc2.label = 'jc2'
jc2.store()
jc2.add_link_from(sd2, label='l2')
jc2._set_state(calc_states.PARSING)
sd3 = StructureData()
sd3.label = 'sd3'
sd3.store()
sd3.add_link_from(jc2, label='l3', link_type=LinkType.RETURN)
uuids_u1 = [sd1.uuid, jc1.uuid, sd2.uuid]
uuids_u2 = [jc2.uuid, sd3.uuid]
filename = os.path.join(temp_folder, "export.tar.gz")
export([sd3.dbnode], outfile=filename, silent=True)
self.clean_db()
import_data(filename, silent=True)
# Check that the imported nodes are correctly imported and that
# the user assigned to the nodes is the right one
for uuid in uuids_u1:
self.assertEquals(load_node(uuid).get_user().email, new_email)
for uuid in uuids_u2:
self.assertEquals(load_node(uuid).get_user().email,
get_configured_user_email())
finally:
# Deleting the created temporary folder
shutil.rmtree(temp_folder, ignore_errors=True)
from aiida.common.example_helpers import test_and_get_code # noqa
from aiida.orm.data.structure import StructureData # noqa
from aiida.orm.data.parameter import ParameterData # noqa
from aiida.orm.data.base import Str
from aiida.work.run import submit
from ase.io import read
from aiida_cp2k.workflows import Cp2kRobustGeoOptWorkChain
atoms = read(
'/home/daniele/Programs/aiida-database/frameworks/test/Cu-MOF-74_h211.cif')
structure = StructureData(ase=atoms)
structure.label = 'Cu-MOF-74'
structure.store()
options_dict = {
"resources": {
"num_machines": 2,
},
"max_wallclock_seconds": 1 * 60 * 60,
'prepend_text': '#SBATCH --partition=debug',
}
options = ParameterData(dict=options_dict)
params_dict = {
'MOTION': {
'MD': {
'STEPS': 5,
},
'GEO_OPT': {
from aiida.common.example_helpers import test_and_get_code # noqa
from aiida.orm.data.structure import StructureData # noqa
from aiida.orm.data.parameter import ParameterData # noqa
from aiida.work.run import submit
from ase.io import read
from aiida_lsmo_workflows.geoopt_charges import Cp2kGeoOptDdecWorkChain
atoms = read('Fe-MOF-74.cif')
structure = StructureData(ase=atoms)
structure.label = 'Fe-MOF-74'
structure.store()
cp2k_options = {
"resources": {
"num_machines": 2,
},
"max_wallclock_seconds": 1 * 60 * 60,
}
params_dict = {
'MOTION': {
'MD': {
'STEPS': 5,
},
'GEO_OPT': {
'MAX_ITER': 5,
},
'CELL_OPT': {
'MAX_ITER': 5,
},
from aiida.common.example_helpers import test_and_get_code # noqa
from aiida.orm.data.structure import StructureData # noqa
from aiida.orm.data.parameter import ParameterData # noqa
from aiida.orm.data.base import Str
from aiida.work.run import submit
from ase.io import read
from aiida_cp2k.workflows import Cp2kRobustGeoOptWorkChain
atoms = read(
'/home/daniele/Dropbox (LSMO)/proj44_studycasesCP2K/CELL_OPT/13150N_CoRE-COF_4layers.cif'
)
structure = StructureData(ase=atoms)
structure.label = '13150Nx4layers'
structure.store()
options_dict = {
"resources": {
"num_machines": 2,
},
"max_wallclock_seconds": 3 * 60 * 60,
}
options = ParameterData(dict=options_dict)
params_dict = {}
parameters = ParameterData(dict=params_dict)
code = test_and_get_code('cp2k@fidis', expected_code_type='cp2k')
submit(
Cp2kRobustGeoOptWorkChain,
code=code,
structure=structure,