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- skip QHAA test if in GitHub Actions environment
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@amkrajewski
amkrajewski authored Nov 17, 2023
1 parent 5a7d1c6 commit 11b4441
Showing 1 changed file with 180 additions and 176 deletions.
356 changes: 180 additions & 176 deletions tests/test_QHAAnalysis.py
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Expand Up @@ -47,182 +47,186 @@
from dfttk.analysis.ywutils import get_rec_from_metatag, get_used_pot
from monty.serialization import loadfn, dumpfn

FW_CONFIG_FILE = os.getenv('FW_CONFIG_FILE')
FW_CONFIG_FILE = loadfn(FW_CONFIG_FILE)

CONFIG_FILE_DIR = FW_CONFIG_FILE.get('CONFIG_FILE_DIR',None)
if CONFIG_FILE_DIR is not None:
db_file = os.path.join(CONFIG_FILE_DIR, 'db.json')
if os.getenv("GITHUB_ACTIONS") == "true":
print("Skipping the test when running inside GitHub actions and Yi Wang's MongoDB is not accessible")
else:
head,tail = os.path.split(__file__)
db_file = os.path.join(head,"db.json")

@pytest.mark.QHAAnalysis
def test_QHAAnalysis():
tags = ['700dd9c9-afb0-4a09-a39d-ad77622b3f08']
print(db_file)
for tag in tags:
FW_CONFIG_FILE = os.getenv('FW_CONFIG_FILE')
FW_CONFIG_FILE = loadfn(FW_CONFIG_FILE)

CONFIG_FILE_DIR = FW_CONFIG_FILE.get('CONFIG_FILE_DIR',None)
if CONFIG_FILE_DIR is not None:
db_file = os.path.join(CONFIG_FILE_DIR, 'db.json')
else:
head,tail = os.path.split(__file__)
db_file = os.path.join(head,"db.json")

@pytest.mark.QHAAnalysis
def test_QHAAnalysis():
tags = ['700dd9c9-afb0-4a09-a39d-ad77622b3f08']
print(db_file)
for tag in tags:
vasp_db = VaspCalcDb.from_db_file(db_file, admin=False)
phonon_calculations = list(vasp_db.db['phonon'].find({'$and':[ {'metadata.tag': tag}, {'adopted': True} ]}))
T = phonon_calculations[0]['temperatures']
t_min = min(T)
everyT = 10
t_step = (T[1]-T[0])*everyT
t_max = max(T)
nT = int((t_max-t_min)/t_step)
t_max = t_min + nT*t_step
print ("testing tag=", tag)
proc = QHAAnalysis(phonon=True, t_min=t_min, t_max=t_max,
t_step=t_step, everyT=everyT, db_file=db_file, test=True,
tag=tag)
proc.run_task("")

@pytest.mark.check_points
def test_check_points():
proc = EVcheck_QHA()
volumes = [504.4854780252552, 534.1610477526048, 563.8366733894931, 593.512427132093, 623.1879003769909, 652.8636686613459, 682.5393342833485, 711.6214250632727, 740.703761424463, 769.7858059616457, 798.8678864247061]
energies = [-342.98343642, -344.38954914, -344.89492019, -344.80547287, -344.28500957, -343.47527914, -342.47536783, -341.31384393, -340.16711161, -339.67940075, -338.41924052]
proc.check_points("", "", 0.005, 14, 0.3, volumes, energies, True)

@pytest.mark.check_points_1
def test_check_points_1():
tag = '19c9e217-4159-4bfe-9c3a-940fb40e023e'
tag = 'd054780c-f051-4450-a611-d374d41d1884'
tag = 'ed85a69b-4054-41d4-a724-7373934cdcc6'
proc = EVcheck_QHA()
volumes, energies, _ = proc.get_orig_EV(db_file, tag)
proc.check_points("", "", 0.005, 14, 0.3, volumes, energies, True)
#assert False

@pytest.mark.check_points_2
def test_check_points_2():
tag = '19c9e217-4159-4bfe-9c3a-940fb40e023e'
tag = 'd054780c-f051-4450-a611-d374d41d1884'
tag = 'ed85a69b-4054-41d4-a724-7373934cdcc6'
tag = '8e7b216d-c6b6-4da4-905e-e7afd44195aa'
vasp_db = VaspCalcDb.from_db_file(db_file, admin=False)
phonon_calculations = list(vasp_db.db['phonon'].find({'$and':[ {'metadata.tag': tag}, {'adopted': True} ]}))
T = phonon_calculations[0]['temperatures']
t_min = min(T)
everyT = 10
t_step = (T[1]-T[0])*everyT
t_max = max(T)
nT = int((t_max-t_min)/t_step)
t_max = t_min + nT*t_step
print ("testing tag=", tag)
proc = QHAAnalysis(phonon=True, t_min=t_min, t_max=t_max,
t_step=t_step, everyT=everyT, db_file=db_file, test=True,
tag=tag)
proc.run_task("")

@pytest.mark.check_points
def test_check_points():
proc = EVcheck_QHA()
volumes = [504.4854780252552, 534.1610477526048, 563.8366733894931, 593.512427132093, 623.1879003769909, 652.8636686613459, 682.5393342833485, 711.6214250632727, 740.703761424463, 769.7858059616457, 798.8678864247061]
energies = [-342.98343642, -344.38954914, -344.89492019, -344.80547287, -344.28500957, -343.47527914, -342.47536783, -341.31384393, -340.16711161, -339.67940075, -338.41924052]
proc.check_points("", "", 0.005, 14, 0.3, volumes, energies, True)

@pytest.mark.check_points_1
def test_check_points_1():
tag = '19c9e217-4159-4bfe-9c3a-940fb40e023e'
tag = 'd054780c-f051-4450-a611-d374d41d1884'
tag = 'ed85a69b-4054-41d4-a724-7373934cdcc6'
proc = EVcheck_QHA()
volumes, energies, _ = proc.get_orig_EV(db_file, tag)
proc.check_points("", "", 0.005, 14, 0.3, volumes, energies, True)
#assert False

@pytest.mark.check_points_2
def test_check_points_2():
tag = '19c9e217-4159-4bfe-9c3a-940fb40e023e'
tag = 'd054780c-f051-4450-a611-d374d41d1884'
tag = 'ed85a69b-4054-41d4-a724-7373934cdcc6'
tag = '8e7b216d-c6b6-4da4-905e-e7afd44195aa'
vasp_db = VaspCalcDb.from_db_file(db_file, admin=False)
EV, POSCAR, INCAR = get_rec_from_metatag(vasp_db, tag, test=True)
structure = Structure.from_str(POSCAR, fmt='POSCAR')
proc = EVcheck_QHA(db_file=db_file, metadata={'tag':tag}, structure=structure, deformations = np.linspace(0.94,1.06,7), test=True)
proc.run_task({})
#assert False

POSCAR_STR = """STa1
4.10
0 .5 .5
.5 0 .5
.5 .5 0
Al
1
direct
0.000000 0.000000 0.000000 Al"""


@pytest.mark.check_points_3
def test_check_points_3():
settings = {'deformation_fraction': [-0.05, 0.05], 'num_deformations': 3, 'deformation_scheme': 'volume', 'run_isif': 4, 'phonon': True, 'phonon_supercell_matrix': [[-2, 2, 2], [2, -2, 2], [2, 2, -2]], 'override_default_vasp_params': {'user_incar_settings': {'EDIFF_PER_ATOM': 1e-07, 'Relax_settings': {'PREC': 'HIGH', 'grid_density': 1000}, 'Static_settings': {'PREC': 'HIGH', 'grid_density': 1000}}, 'user_kpoints_settings': {'grid_density': 1000}}, 'metadata': {'tag': '67783198-6d5a-40c2-8d49-4f03e50ac130'}}

################ PARAMETERS FOR WF #############################
#str, the absolute path of db.json file, e.g. /storage/home/mjl6505/atomate/config/db.json
# If None, it will use the configuration in fireworks
#db_file = settings.get('db_file', DB_FILE)
db_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
#str, the vasp command, if None then find in the FWorker configuration
vasp_cmd = settings.get('vasp_cmd', VASP_CMD)
#dict, metadata to be included, this parameter is useful for filter the data, e.g. metadata={"phase": "BCC_A2", "tag": "AFM"}
metadata = settings.get('metadata',{})
tag = metadata.get('tag', '{}'.format(str(uuid4())))
metadata.update({'tag': tag})

#list/tuple(min, max) or float(-max, max), the maximum amplitude of deformation, e.g. (-0.15, 0.15) means (0.95, 1.1) in volume
deformation_fraction = settings.get('deformation_fraction', (-0.15, 0.20))
#int, the number of initial deformations, e.g. 7
num_deformations = settings.get('num_deformations', 8)
if num_deformations==1:
deformation_fraction[1] = deformation_fraction[0]
#bool, run phonon(True) or not(False)
phonon = settings.get('phonon', False)
#list(3x3), the supercell matrix for phonon, e.g. [[2.0, 0, 0], [0, 2.0, 0], [0, 0, 2.0]]
phonon_supercell_matrix = settings.get('phonon_supercell_matrix', None)
phonon_supercell_matrix_min = settings.get('phonon_supercell_matrix_min', None)
phonon_supercell_matrix_max = settings.get('phonon_supercell_matrix_max', None)
optimize_sc = settings.get('optimize_sc', False)
#The tolerance for phonon stable
stable_tor = settings.get('stable_tor', 0.01)
#float, the mimimum of temperature in QHA process, e.g. 5
t_min = settings.get('t_min', 5)
#float, the maximum of temperature in QHA process, e.g. 2000
t_max = settings.get('t_max', 2000)
#float, the step of temperature in QHA process, e.g. 5
t_step = settings.get('t_step', 5)
#float, acceptable value for average RMS, recommend >= 0.005
eos_tolerance = settings.get('eos_tolerance', 0.01)

#Global settings for all vasp job, e.g.
#override_default_vasp_params = {'user_incar_settings': {}, 'user_kpoints_settings': {}, 'user_potcar_functional': str}
#If some value in 'user_incar_settings' is set to None, it will use vasp's default value
override_default_vasp_params = settings.get('override_default_vasp_params', {})

#dict, dict of class ModifyIncar with keywords in Workflow name. e.g.
modify_incar_params = settings.get('modify_incar_params', {})

#check if fworker_name is assigned
powerups = settings.get('powerups', {})
if len(powerups)>0:
if 'user_incar_settings' not in override_default_vasp_params:
override_default_vasp_params.update({'user_incar_settings':{}})
override_default_vasp_params['user_incar_settings'].update({'powerups':powerups})
modify_incar_params.update({'powerups':powerups})

#dict, dict of class ModifyKpoints with keywords in Workflow name, similar with modify_incar_params
modify_kpoints_params = settings.get('modify_kpoints_params', {})
#bool, print(True) or not(False) some informations, used for debug
verbose = settings.get('verbose', False)
#Save the volume data or not ("chgcar", "aeccar0", "aeccar2", "elfcar", "locpot")
store_volumetric_data = settings.get('store_volumetric_data', False)

if phonon:
if isinstance(phonon_supercell_matrix, str):
if phonon_supercell_matrix=='Yphon':
phonon_supercell_matrix = supercell_scaling_by_Yphon(structure,
supercellsize=phonon_supercell_matrix_max)
else:
phonon_supercell_matrix = supercell_scaling_by_atom_lat_vol(structure, min_obj=phonon_supercell_matrix_min,
max_obj=phonon_supercell_matrix_max, scale_object=phonon_supercell_matrix,
target_shape='sc', lower_search_limit=-2, upper_search_limit=2,
verbose=verbose, sc_tolerance=1e-5, optimize_sc=optimize_sc)

_deformations = _get_deformations(deformation_fraction, num_deformations)
if num_deformations > 1: vol_spacing = _deformations[1]-_deformations[0]
else: vol_spacing=0.05

structure = Structure.from_str(POSCAR_STR, fmt='POSCAR')
t_kwargs = {'t_min': t_min, 't_max': t_max, 't_step': t_step}
common_kwargs = {'vasp_cmd': vasp_cmd, 'db_file': db_file, "metadata": metadata, "tag": tag,
'override_default_vasp_params': override_default_vasp_params}
vasp_kwargs = {'modify_incar_params': modify_incar_params, 'modify_kpoints_params': modify_kpoints_params}
eos_kwargs = {'deformations': _deformations, 'vol_spacing': vol_spacing, 'eos_tolerance': eos_tolerance, 'threshold': 14}
a_kwargs = {"structure":structure, "settings":settings, "eos_kwargs":eos_kwargs,
"static": True, "phonon":phonon, "phonon_supercell_matrix":phonon_supercell_matrix}

proc = Crosscom_EVcheck_QHA(verbose=verbose, stable_tor=stable_tor,
run_num = 0,
store_volumetric_data=store_volumetric_data, a_kwargs=a_kwargs,
**eos_kwargs, **vasp_kwargs, **t_kwargs, **common_kwargs, test=True)
proc.run_task({})
assert False

@pytest.mark.EVcheck_QHA_2
def test_EVcheck_QHA_2():
tag = '19c9e217-4159-4bfe-9c3a-940fb40e023e'
wf = Firework(EVcheck_QHA(db_file=db_file,vasp_cmd=">>vasp_cmd<<",tag="test",metadata={'tag':tag}, test=True))
print(wf.as_dict())
#assert False

@pytest.mark.get_static_calculations
def test_get_static_calculations():
tag = '8e7b216d-c6b6-4da4-905e-e7afd44195aa'
vasp_db = VaspCalcDb.from_db_file(db_file=db_file, admin = True)
volumes, energies, dos_objs, _ = get_static_calculations(vasp_db,tag)
#print(volumes, energies)
assert False
EV, POSCAR, INCAR = get_rec_from_metatag(vasp_db, tag, test=True)
structure = Structure.from_str(POSCAR, fmt='POSCAR')
proc = EVcheck_QHA(db_file=db_file, metadata={'tag':tag}, structure=structure, deformations = np.linspace(0.94,1.06,7), test=True)
proc.run_task({})
#assert False

POSCAR_STR = """STa1
4.10
0 .5 .5
.5 0 .5
.5 .5 0
Al
1
direct
0.000000 0.000000 0.000000 Al"""


@pytest.mark.check_points_3
def test_check_points_3():
settings = {'deformation_fraction': [-0.05, 0.05], 'num_deformations': 3, 'deformation_scheme': 'volume', 'run_isif': 4, 'phonon': True, 'phonon_supercell_matrix': [[-2, 2, 2], [2, -2, 2], [2, 2, -2]], 'override_default_vasp_params': {'user_incar_settings': {'EDIFF_PER_ATOM': 1e-07, 'Relax_settings': {'PREC': 'HIGH', 'grid_density': 1000}, 'Static_settings': {'PREC': 'HIGH', 'grid_density': 1000}}, 'user_kpoints_settings': {'grid_density': 1000}}, 'metadata': {'tag': '67783198-6d5a-40c2-8d49-4f03e50ac130'}}

################ PARAMETERS FOR WF #############################
#str, the absolute path of db.json file, e.g. /storage/home/mjl6505/atomate/config/db.json
# If None, it will use the configuration in fireworks
#db_file = settings.get('db_file', DB_FILE)
db_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
#str, the vasp command, if None then find in the FWorker configuration
vasp_cmd = settings.get('vasp_cmd', VASP_CMD)
#dict, metadata to be included, this parameter is useful for filter the data, e.g. metadata={"phase": "BCC_A2", "tag": "AFM"}
metadata = settings.get('metadata',{})
tag = metadata.get('tag', '{}'.format(str(uuid4())))
metadata.update({'tag': tag})

#list/tuple(min, max) or float(-max, max), the maximum amplitude of deformation, e.g. (-0.15, 0.15) means (0.95, 1.1) in volume
deformation_fraction = settings.get('deformation_fraction', (-0.15, 0.20))
#int, the number of initial deformations, e.g. 7
num_deformations = settings.get('num_deformations', 8)
if num_deformations==1:
deformation_fraction[1] = deformation_fraction[0]
#bool, run phonon(True) or not(False)
phonon = settings.get('phonon', False)
#list(3x3), the supercell matrix for phonon, e.g. [[2.0, 0, 0], [0, 2.0, 0], [0, 0, 2.0]]
phonon_supercell_matrix = settings.get('phonon_supercell_matrix', None)
phonon_supercell_matrix_min = settings.get('phonon_supercell_matrix_min', None)
phonon_supercell_matrix_max = settings.get('phonon_supercell_matrix_max', None)
optimize_sc = settings.get('optimize_sc', False)
#The tolerance for phonon stable
stable_tor = settings.get('stable_tor', 0.01)
#float, the mimimum of temperature in QHA process, e.g. 5
t_min = settings.get('t_min', 5)
#float, the maximum of temperature in QHA process, e.g. 2000
t_max = settings.get('t_max', 2000)
#float, the step of temperature in QHA process, e.g. 5
t_step = settings.get('t_step', 5)
#float, acceptable value for average RMS, recommend >= 0.005
eos_tolerance = settings.get('eos_tolerance', 0.01)

#Global settings for all vasp job, e.g.
#override_default_vasp_params = {'user_incar_settings': {}, 'user_kpoints_settings': {}, 'user_potcar_functional': str}
#If some value in 'user_incar_settings' is set to None, it will use vasp's default value
override_default_vasp_params = settings.get('override_default_vasp_params', {})

#dict, dict of class ModifyIncar with keywords in Workflow name. e.g.
modify_incar_params = settings.get('modify_incar_params', {})

#check if fworker_name is assigned
powerups = settings.get('powerups', {})
if len(powerups)>0:
if 'user_incar_settings' not in override_default_vasp_params:
override_default_vasp_params.update({'user_incar_settings':{}})
override_default_vasp_params['user_incar_settings'].update({'powerups':powerups})
modify_incar_params.update({'powerups':powerups})

#dict, dict of class ModifyKpoints with keywords in Workflow name, similar with modify_incar_params
modify_kpoints_params = settings.get('modify_kpoints_params', {})
#bool, print(True) or not(False) some informations, used for debug
verbose = settings.get('verbose', False)
#Save the volume data or not ("chgcar", "aeccar0", "aeccar2", "elfcar", "locpot")
store_volumetric_data = settings.get('store_volumetric_data', False)

if phonon:
if isinstance(phonon_supercell_matrix, str):
if phonon_supercell_matrix=='Yphon':
phonon_supercell_matrix = supercell_scaling_by_Yphon(structure,
supercellsize=phonon_supercell_matrix_max)
else:
phonon_supercell_matrix = supercell_scaling_by_atom_lat_vol(structure, min_obj=phonon_supercell_matrix_min,
max_obj=phonon_supercell_matrix_max, scale_object=phonon_supercell_matrix,
target_shape='sc', lower_search_limit=-2, upper_search_limit=2,
verbose=verbose, sc_tolerance=1e-5, optimize_sc=optimize_sc)

_deformations = _get_deformations(deformation_fraction, num_deformations)
if num_deformations > 1: vol_spacing = _deformations[1]-_deformations[0]
else: vol_spacing=0.05

structure = Structure.from_str(POSCAR_STR, fmt='POSCAR')
t_kwargs = {'t_min': t_min, 't_max': t_max, 't_step': t_step}
common_kwargs = {'vasp_cmd': vasp_cmd, 'db_file': db_file, "metadata": metadata, "tag": tag,
'override_default_vasp_params': override_default_vasp_params}
vasp_kwargs = {'modify_incar_params': modify_incar_params, 'modify_kpoints_params': modify_kpoints_params}
eos_kwargs = {'deformations': _deformations, 'vol_spacing': vol_spacing, 'eos_tolerance': eos_tolerance, 'threshold': 14}
a_kwargs = {"structure":structure, "settings":settings, "eos_kwargs":eos_kwargs,
"static": True, "phonon":phonon, "phonon_supercell_matrix":phonon_supercell_matrix}

proc = Crosscom_EVcheck_QHA(verbose=verbose, stable_tor=stable_tor,
run_num = 0,
store_volumetric_data=store_volumetric_data, a_kwargs=a_kwargs,
**eos_kwargs, **vasp_kwargs, **t_kwargs, **common_kwargs, test=True)
proc.run_task({})
assert False

@pytest.mark.EVcheck_QHA_2
def test_EVcheck_QHA_2():
tag = '19c9e217-4159-4bfe-9c3a-940fb40e023e'
wf = Firework(EVcheck_QHA(db_file=db_file,vasp_cmd=">>vasp_cmd<<",tag="test",metadata={'tag':tag}, test=True))
print(wf.as_dict())
#assert False

@pytest.mark.get_static_calculations
def test_get_static_calculations():
tag = '8e7b216d-c6b6-4da4-905e-e7afd44195aa'
vasp_db = VaspCalcDb.from_db_file(db_file=db_file, admin = True)
volumes, energies, dos_objs, _ = get_static_calculations(vasp_db,tag)
#print(volumes, energies)
assert False

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