def test_Pd_setup(Pd, Pd_copy):
"""Makes sure the initial folders were setup according to the spec.
"""
#raise Exception("RAWR")
Pd.setup()
modelroot = path.join(Pd.root, "Manual", "phonon.manual", "Pd")
#import pdb; pdb.set_trace()
assert Pd["Manual/phonon/Pd/"].root == modelroot
#The matdb.yml file specifies the following database:
dbs = ["Manual/phonon.manual/Pd/"]
#Each one should have a folder for: ["hessian", "modulations"]
#On the first go, the modulations folder will be empty because the DFT
#calculations haven't been performed yet. However, hessian should have DFT
#folders ready to go.
folders = {
"__files__": ["compute.pkl", "jobfile.sh"],
"S1.1": {
"__files__": ["INCAR", "POSCAR", "POTCAR", "PRECALC", "KPOINTS"]
}
}
from matdb.utility import compare_tree
for db in dbs:
dbfolder = path.join(Pd.root, db)
compare_tree(dbfolder, folders)
#import pdb; pdb.set_trace()
#Now we will test some of the border cases of the database __init__ method
Pd_copy.setup()
db = "Manual/phonon.manual/Pd"
dbfolder = path.join(Pd_copy.root, db)
compare_tree(dbfolder, folders)
def test_setup(CoNiTi):
"""Tetsts the setup of the enumerated database.
"""
assert not CoNiTi.collections['prototype'].steps['prototype'].is_setup()
CoNiTi.setup()
db = "Prototypes/prototype.prototype/per-1"
folders = {
"__files__":
["compute.pkl", "jobfile.sh", "prototype_P_uuid.txt", "puuids.pkl"]
}
for i in range(1, 251):
folders["P.{0}".format(i)] = {
"__files__":
["INCAR", "PRECALC", "uuid.txt", "POSCAR", "pre_comp_atoms.h5"]
}
dbfolder = path.join(CoNiTi.root, db)
from matdb.utility import compare_tree
compare_tree(dbfolder, folders)
assert CoNiTi.collections['prototype'].steps['prototype'].is_setup()
prot = CoNiTi.collections['prototype'].steps['prototype']
assert len(prot.sequence['per-1'].puuids) == 250
assert not prot.ready()
# We need to create fake atoms.h5 objects so that the system will
# think that VASP has run and the caculations have been extracted.
dbfolder = path.join(CoNiTi.root, db)
for j in range(1, 251):
src = path.join(dbfolder, "P.{}".format(j), "pre_comp_atoms.h5")
dest = path.join(dbfolder, "P.{}".format(j), "atoms.h5")
symlink(src, dest)
assert len(prot.rset) == 250
assert len(prot.fitting_configs) == 250
# We run the setup one more time to ensure quick returns
assert prot.ready()
prot._setup_configs(False)
def test_not_extractable(Pd_not_extractable):
""" test not extractable
"""
mPd = Pd_not_extractable
tdb = Database("phonon", path.join(mPd.root, "tmp_db"), mPd,
[{
"type": "simple.Manual"
}], {}, 0)
for config in tdb.iconfigs:
assert config is not None
mPd.setup()
mdb = mPd.collections['phonon'].steps['manual']
assert mdb is not None
assert mdb.nconfigs == 1
assert mdb.sub_dict() == {'extractable': False, 'name': 'manual'}
assert not mdb.extractable
assert not mdb._trainable
assert mdb.is_setup()
assert len(mdb.sequence) == 1
assert len(mdb.sequence['Pd'].configs) == 1
assert mdb.ready()
assert mdb.can_extract()
folders = {
"__files__": ["phonon_S1_uuid.txt"],
"Pd": {
"__files__": ["phonon_S1_uuid.txt", "compute.pkl"],
"S1.1": {
"__files__": [
"INCAR", "PRECALC", "POSCAR", "POTCAR", "atoms.h5",
"uuid.txt", "KPOINTS", "ase-sort.dat"
]
}
}
}
dbfolder = mdb.root
compare_tree(dbfolder, folders)
mdb.tarball()
assert path.isfile(path.join(dbfolder, "Pd", "output.tar.gz"))
def test_compare_tree(tmpdir):
"""Tests the folder comparison method.
"""
from os import mkdir
from matdb.utility import touch, compare_tree
test_dir = str(tmpdir.join("comp_tree"))
mkdir(test_dir)
touch(path.join(test_dir,"compute.pkl"))
touch(path.join(test_dir,"jobfile.sh"))
mkdir(path.join(test_dir,"phonopy"))
touch(path.join(test_dir,"phonopy","POSCAR"))
folders = {
"__files__": ["compute.pkl","jobfile.sh"],
"phonopy": {
"__files__": ["POSCAR"]
},
}
compare_tree(test_dir,folders)
def test_AgCu_setup(AgCu):
"""Test the setup of the substitutions database.
"""
assert not AgCu.collections['substitution'].steps['Substitution'].is_setup(
)
AgCu.setup()
dbs = "Substitution/substitution.Substitution/Ag1Cu5"
folders = {
"__files__": ["compute.pkl", "suids.pkl", "jobfile.sh", "index.json"],
"S.1": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.2": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.3": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.4": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.5": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.6": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.7": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.8": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.9": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.10": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.11": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.12": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.13": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.14": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"S.15": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
}
}
from matdb.utility import compare_tree
dbfolder = path.join(AgCu.root, dbs)
compare_tree(dbfolder, folders)
assert AgCu.collections['substitution'].steps['Substitution'].is_setup()
# test the suid and index creation for the entire database.
assert path.isfile(
path.join(AgCu.root,
"Substitution/substitution.Substitution/suids.pkl"))
assert path.isfile(
path.join(AgCu.root,
"Substitution/substitution.Substitution/index.json"))
sub = AgCu.collections['substitution'].steps['Substitution']
assert len(sub.index) == 15
assert len(sub.suids) == 15
assert sub.ready()
src = relpath(
"./tests/data/Pd/complete/OUTCAR__DynMatrix_phonon_Pd_dim-2.00")
dbfolder = path.join(AgCu.root, dbs)
for j in range(1, 16):
dest = path.join(dbfolder, "S.{}".format(j), "OUTCAR")
symlink(src, dest)
dbfolder = path.join(AgCu.root, dbs)
for j in range(1, 16):
src = path.join(dbfolder, "S.{}".format(j), "POSCAR")
dest = path.join(dbfolder, "S.{}".format(j), "CONTCAR")
symlink(src, dest)
assert len(sub.atoms_paths()) == 15
assert len(sub.rset()) == 15
def test_all(Pd):
"""Tetsts setup/extract/ready of the simple.Manual database.
"""
Pd.setup()
mdb = Pd.collections['phonon'].steps['manual']
assert Pd is not None
assert mdb is not None
assert mdb.is_setup()
assert len(mdb.sequence) == 3
assert len(mdb.sequence['Pd1'].configs) == 1
folders = {
"__files__": ["phonon_S1_uuid.txt"],
"Pd1": {
"__files__": ["phonon_S1_uuid.txt", "jobfile.sh", "compute.pkl"],
"S1.1": {
"__files__": [
"INCAR", "PRECALC", "POSCAR", "POTCAR",
"pre_comp_atoms.h5", "uuid.txt", "KPOINTS", "ase-sort.dat"
]
}
},
"Pd2": {
"__files__": ["phonon_S1_uuid.txt", "jobfile.sh", "compute.pkl"],
"S1.1": {
"__files__": [
"INCAR", "PRECALC", "POSCAR", "POTCAR",
"pre_comp_atoms.h5", "uuid.txt", "KPOINTS", "ase-sort.dat"
]
}
},
"Pd3": {
"__files__": ["phonon_S1_uuid.txt", "jobfile.sh", "compute.pkl"],
"S1.1": {
"__files__": [
"INCAR", "PRECALC", "POSCAR", "POTCAR",
"pre_comp_atoms.h5", "uuid.txt", "KPOINTS", "ase-sort.dat"
]
}
}
}
dbfolder = mdb.root
compare_tree(dbfolder, folders)
assert mdb.is_setup()
assert not mdb.ready()
src = relpath("./tests/data/Pd/basic_fail/S.4/OUTCAR")
dbfolder = mdb.root
for j in range(1, 4):
dest = path.join(dbfolder, "Pd{}".format(j), "S1.1", "OUTCAR")
symlink(src, dest)
assert mdb.is_executing()
assert mdb.is_setup()
# should not be executable, because it's been executing
assert not mdb.execute()
# We need to fake some VASP output so that we can cleanup the
# database and get the rset
src = relpath(
"./tests/data/Pd/complete/OUTCAR__DynMatrix_phonon_Pd_dim-2.00")
dbfolder = mdb.root
for j in range(1, 4):
dest = path.join(dbfolder, "Pd{}".format(j), "S1.1", "OUTCAR")
remove(dest)
symlink(src, dest)
dbfolder = mdb.root
for j in range(2, 4):
src = path.join(dbfolder, "Pd{}".format(j), "S1.1", "POSCAR")
dest = path.join(dbfolder, "Pd{}".format(j), "S1.1", "CONTCAR")
symlink(src, dest)
assert not mdb.ready()
# execute should return false, because not all atoms can execute(Pd1 is lacking of POSCAR file)
assert not mdb.execute()
src = path.join(dbfolder, "Pd1", "S1.1", "POSCAR")
dest = path.join(dbfolder, "Pd1", "S1.1", "CONTCAR")
symlink(src, dest)
assert not mdb.execute()
mdb.extract()
assert not mdb.execute()
assert len(mdb.sequence) == 3
assert len(mdb.sequence['Pd1'].config_atoms) == 1
assert len(mdb.sequence['Pd2'].config_atoms) == 1
assert len(mdb.sequence['Pd3'].config_atoms) == 1
assert len(mdb.sequence['Pd1'].configs) == 1
assert len(mdb.sequence['Pd2'].configs) == 1
assert len(mdb.sequence['Pd3'].configs) == 1
assert len(mdb.fitting_configs) == 3
assert len(mdb.rset) == 3
assert not mdb.is_executing()
assert mdb.ready()
# setup again(with rerun=True) on an already ready database
Pd.setup(rerun=True)
assert mdb.is_setup()
assert mdb.ready()
assert len(mdb.sequence) == 3
assert len(mdb.sequence['Pd1'].config_atoms) == 1
assert len(mdb.fitting_configs) == 3
assert len(mdb.rset) == 3
def test_AlMg_setup(AlMg):
"""Test the setup of the distortion database.
"""
assert not AlMg.collections[
'distortion'].steps['distortion'].is_setup()
AlMg.setup()
dbs = "Distortion/distortion.distortion/Al6Mg4"
folders = {
"__files__": ["compute.pkl", "duids.pkl", "jobfile.sh", "index.json"],
"D.1": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.2": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.3": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.4": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.5": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.6": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.7": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.8": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.9": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.10": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.11": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.12": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.13": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.14": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"D.15": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
}
}
from matdb.utility import compare_tree
dbfolder = path.join(AlMg.root, dbs)
compare_tree(dbfolder, folders)
assert AlMg.collections['distortion'].steps[
'distortion'].is_setup()
# test the duid and index creation for the entire database.
assert path.isfile(path.join(AlMg.root,
"Distortion/distortion.distortion/duids.pkl"))
assert path.isfile(path.join(AlMg.root,
"Distortion/distortion.distortion/index.json"))
dist = AlMg.collections['distortion'].steps['distortion']
assert len(dist.duids) == 50
assert len(dist.index) == 50
assert dist.ready()
def test_setup(AgPd):
"""Tetsts the setup of the enumerated database.
"""
assert not AgPd.collections['enumerated'].steps['enum'].is_setup()
assert AgPd.collections['enumerated'].steps['enum'].fitting_configs == []
AgPd.setup()
dbs = ["Enum/enumerated.enum/lat-{}".format(i) for i in (1, 2)]
folders = {
"__files__": [
"compute.pkl", "euids.pkl", "jobfile.sh", "enum.out", "lattice.in",
"index.json"
],
"E.1": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.2": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.3": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.4": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.5": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.6": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.7": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.8": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.9": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"E.10": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
}
}
from matdb.utility import compare_tree
for db in dbs:
dbfolder = path.join(AgPd.root, db)
compare_tree(dbfolder, folders)
assert AgPd.collections['enumerated'].steps['enum'].is_setup()
# test the euid and index creation for the entire database.
assert path.isfile(path.join(AgPd.root, "Enum/enumerated.enum/euids.pkl"))
assert path.isfile(path.join(AgPd.root, "Enum/enumerated.enum/index.json"))
enum = AgPd.collections['enumerated'].steps['enum']
assert len(enum.index) == 20
assert len(enum.euids) == 20
assert not enum.ready()
# We need to fake some VASP output so that we can cleanup the
# database and get the rset
src = relpath("./tests/files/outcars/4_atom")
for db in dbs:
dbfolder = path.join(AgPd.root, db)
for j in range(1, 11):
dest = path.join(dbfolder, "E.{}".format(j), "OUTCAR")
symlink(src, dest)
for db in dbs:
dbfolder = path.join(AgPd.root, db)
for j in range(1, 11):
src = path.join(dbfolder, "E.{}".format(j), "POSCAR")
dest = path.join(dbfolder, "E.{}".format(j), "CONTCAR")
symlink(src, dest)
enum.extract()
assert len(enum.rset) == 20
def test_all_active(Act):
"""Tetsts the setup of the Active database.
"""
assert (Act.last_iteration is None) or (len(Act.last_iteration) == 0)
assert (Act.last_config_atoms is None) or (len(Act.last_config_atoms) == 0)
add_configs(Act, 1)
assert not Act.can_extract()
assert Act.iter_file == path.join(Act.root, "iter_1.pkl")
assert Act.nconfigs == 3
assert not Act.is_executing()
Act.setup()
assert len(Act.last_iteration) == 3
folders = {
"__files__": ["compute.pkl", "auids.pkl", "jobfile.sh", "index.json", "iter_1.pkl",
"active_Ac_uuid.txt"],
"Ac.1": {
"__files__": ["INCAR", "PRECALC", "POSCAR", "POTCAR", "pre_comp_atoms.h5",
"uuid.txt"]
},
"Ac.2": {
"__files__": ["INCAR", "PRECALC", "POSCAR", "POTCAR", "pre_comp_atoms.h5",
"uuid.txt"]
},
"Ac.3": {
"__files__": ["INCAR", "PRECALC", "POSCAR", "POTCAR", "pre_comp_atoms.h5",
"uuid.txt"]
}
}
dbfolder = Act.root
compare_tree(dbfolder,folders)
assert Act.is_setup()
assert not Act.ready()
# We need to fake some VASP output so that we can cleanup the
# database and get the rset
src = relpath("./tests/data/Pd/complete/OUTCAR__DynMatrix_phonon_Pd_dim-2.00")
dbfolder = Act.root
for j in range(1,4):
dest = path.join(dbfolder,"Ac.{}".format(j),"OUTCAR")
symlink(src,dest)
dbfolder = Act.root
for j in range(1,4):
src = path.join(dbfolder,"Ac.{}".format(j),"POSCAR")
dest = path.join(dbfolder,"Ac.{}".format(j),"CONTCAR")
symlink(src,dest)
remove(path.join(Act.root, "Ac.1", "pre_comp_atoms.h5"))
Act.extract()
assert len(Act.config_atoms) == 3
assert len(Act.configs) == 3
assert len(Act.last_config_atoms) == 3
assert len(Act.rset) == 3
assert not Act.is_executing()
remove(path.join(Act.root, "Ac.1", "OUTCAR"))
dest = path.join(Act.root, "Ac.1", "OUTCAR")
src = relpath("./tests/data/Pd/basic_fail/S.4/OUTCAR")
symlink(src,dest)
assert Act.is_executing()
# should not be executable, because it's been executing
assert not Act.execute()
# test the addition of a second set of new configs
# first config is to test if the exclusion of duplicates works.
configs = []
atSi = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43])
configs.append(atSi)
atSi = Atoms("Si",positions=[[0,0,0]],
cell=[3,3,3])
configs.append(atSi)
atSi = Atoms("Si2",positions=[[0,0,0], [0.5,0.75,0.25]],
cell=[3.43,3.43,3.43])
configs.append(atSi)
Act.add_configs(configs, 2)
assert Act.iter_file == path.join(Act.root, "iter_2.pkl")
assert Act.nconfigs == 6
assert not Act.is_executing()
Act.setup()
for cfg in Act.iconfigs:
assert "Si" in cfg.get_chemical_symbols()
assert Act.nconfigs == 5
assert len(Act.last_config_atoms) == 2
Act.iter_file = path.join(Act.root, "iter_1.pkl")
Act._load_last_iter()
assert len(Act.last_iteration) == 3
def test_AlTi_setup(AlTi):
"""Test the setup of the vacancy database.
"""
assert not AlTi.collections['vacancy'].steps['Vacancy'].is_setup()
AlTi.setup()
dbs = "Vacancy/vacancy.Vacancy/Al14Ti6"
folders = {
"__files__": ["compute.pkl", "vuids.pkl", "jobfile.sh", "index.json"],
"V.1": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"V.2": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"V.3": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"V.4": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"V.5": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"V.6": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
},
"V.7": {
"__files__": ["INCAR", "PRECALC", "POSCAR"]
}
}
from matdb.utility import compare_tree
dbfolder = path.join(AlTi.root, dbs)
compare_tree(dbfolder, folders)
assert AlTi.collections['vacancy'].steps['Vacancy'].is_setup()
# test the vuid and index creation for the entire database.
assert path.isfile(
path.join(AlTi.root, "Vacancy/vacancy.Vacancy/vuids.pkl"))
assert path.isfile(
path.join(AlTi.root, "Vacancy/vacancy.Vacancy/index.json"))
vac = AlTi.collections['vacancy'].steps['Vacancy']
assert len(vac.index) == 50
assert len(vac.vuids) == 50
assert vac.ready()
# We need to fake some VASP output so that we can cleanup the
# database and get the rset
src = relpath(
"./tests/data/Pd/complete/OUTCAR__DynMatrix_phonon_Pd_dim-27.00")
dbfolder = path.join(AlTi.root, dbs)
for j in range(1, 51):
dest = path.join(dbfolder, "V.{}".format(j), "OUTCAR")
symlink(src, dest)
dbfolder = path.join(AlTi.root, dbs)
for j in range(1, 51):
src = path.join(dbfolder, "V.{}".format(j), "POSCAR")
dest = path.join(dbfolder, "V.{}".format(j), "CONTCAR")
symlink(src, dest)
assert len(vac.atoms_paths()) == 50
assert len(vac.rset()) == 50