def workflow(self, model):
"""
@brief Create a FireWorks Workflow object performing initialisation.
@details
The workflow
@param model surrogate model object.
@return Workflow object
"""
## Call the newPoints method to receive a list of dictionaries each
# dictionary representing one data point.
p = self.newPoints(model)
if len(p):
wf = model.exactTasks(p)
wf.append_wf(
model.parameterFittingStrategy().workflow(model),
wf.leaf_fw_ids
)
return wf
elif not len(p) and len(model.substituteModels):
wf = Workflow([])
for sm in model.substituteModels:
wf.append_wf(
sm.initialisationStrategy().workflow(sm),
[]
)
return wf
else:
return Workflow([])
def workflow(self, model):
"""
@brief Create a FireWorks Workflow object performing initialisation.
@details
The workflow
@param model surrogate model object.
@return Workflow object
"""
## Call the newPoints method to receive a list of dictionaries each
# dictionary representing one data point.
p = self.newPoints(model)
if len(p):
wf = model.exactTasks(p)
wf.append_wf(model.parameterFittingStrategy().workflow(model),
wf.leaf_fw_ids)
return wf
elif not len(p) and len(model.substituteModels):
wf = Workflow([])
for sm in model.substituteModels:
wf.append_wf(sm.initialisationStrategy().workflow(sm), [])
return wf
else:
return Workflow([])
def workflow(self, model):
"""
"""
# Get initial data
points = self.newPoints(model)
# Save initial data in database
model.updateFitDataFromFwSpec(points)
model.updateMinMax()
model.save()
wf = Workflow( [], name='initialising to dataset')
wf.append_wf( model.parameterFittingStrategy().workflow(model),
wf.leaf_fw_ids)
return wf
def workflow(self, model):
"""
"""
# Get initial data
points = self.newPoints(model)
# Save initial data in database
model.updateFitDataFromFwSpec(points)
model.updateMinMax()
model.save()
wf = Workflow([], name='initialising to dataset')
wf.append_wf(model.parameterFittingStrategy().workflow(model),
wf.leaf_fw_ids)
return wf
def get_wf_slab(slab,
include_bulk_opt=False,
adsorbates=None,
ads_structures_params=None,
ads_site_finder_params=None,
vasp_cmd="vasp",
db_file=None,
add_molecules_in_box=False,
user_incar_settings=None):
"""
Gets a workflow corresponding to a slab calculation along with optional
adsorbate calcs and precursor oriented unit cell optimization
Args:
slabs (list of Slabs or Structures): slabs to calculate
include_bulk_opt (bool): whether to include bulk optimization,
this flag sets the slab fireworks to be TransmuterFWs based
on bulk optimization of oriented unit cells
adsorbates ([Molecule]): list of molecules to place as adsorbates
ads_structures_params (dict): parameters to be supplied as
kwargs to AdsorbateSiteFinder.generate_adsorption_structures
add_molecules_in_box (boolean): flag to add calculation of
adsorbate molecule energies to the workflow
db_file (string): path to database file
vasp_cmd (string): vasp command
Returns:
Workflow
"""
fws, parents = [], []
if adsorbates is None:
adsorbates = []
if ads_structures_params is None:
ads_structures_params = {}
# Add bulk opt firework if specified
if include_bulk_opt:
oriented_bulk = slab.oriented_unit_cell
vis = MPSurfaceSet(oriented_bulk, bulk=True)
fws.append(
OptimizeFW(structure=oriented_bulk,
vasp_input_set=vis,
vasp_cmd=vasp_cmd,
db_file=db_file))
parents = fws[-1]
name = slab.composition.reduced_formula
if getattr(slab, "miller_index", None):
name += "_{}".format(slab.miller_index)
# Create slab fw and add it to list of fws
slab_fw = get_slab_fw(slab,
include_bulk_opt,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=parents,
name="{} slab optimization".format(name))
fws.append(slab_fw)
for adsorbate in adsorbates:
ads_slabs = AdsorbateSiteFinder(
slab, **ads_site_finder_params).generate_adsorption_structures(
adsorbate, **ads_structures_params)
for n, ads_slab in enumerate(ads_slabs):
# Create adsorbate fw
ads_name = "{}-{} adsorbate optimization {}".format(
adsorbate.composition.formula, name, n)
adsorbate_fw = get_slab_fw(ads_slab,
include_bulk_opt,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=parents,
name=ads_name,
user_incar_settings=user_incar_settings)
fws.append(adsorbate_fw)
if isinstance(slab, Slab):
name = "{}_{} slab workflow".format(
slab.composition.reduced_composition, slab.miller_index)
else:
name = "{} slab workflow".format(slab.composition.reduced_composition)
wf = Workflow(fws, name=name)
# Add optional molecules workflow
if add_molecules_in_box:
molecule_wf = get_wf_molecules(adsorbates,
db_file=db_file,
vasp_cmd=vasp_cmd)
wf.append_wf(molecule_wf)
return wf
def get_wf_hubbard_hund_linresp(structure,
user_incar_settings=None,
relax_nonmagnetic=True,
spin_polarized=True,
applied_potential_range=(-0.2, 0.2),
num_evals=9,
site_indices_perturb=None,
species_perturb=None,
find_nearest_sites=True,
parallel_scheme=0,
ediff_tight=None,
c=None):
"""
Compute Hubbard U (and Hund J) on-site interaction values using GGA+U
linear response method proposed by Cococcioni et. al.
(DOI: 10.1103/PhysRevB.71.035105)
and the spin-polarized response formalism developed by Linscott et. al.
(DOI: 10.1103/PhysRevB.98.235157)
This workflow relies on the constrained on-site potential functional implemented in VASP,
with a helpful tutorial found here:
https://www.vasp.at/wiki/index.php/Calculate_U_for_LSDA%2BU
Args:
structure:
user_incar_settings: user INCAR settings
relax_nonmagnetic: Restart magnetic SCF runs from
non-magnetic calculation, using WAVECAR
spin_polarized: Perform spin-dependent perturbations
applied_potential_range: Bounds of applied potential
num_evals: Number of perturbation evalutaions
site_indices_perturb: (must specify if species_perturb=None)
List of site indices within
Structure indicating perturbation sites;
species_perturb: (must specify if site_indices_perturb=None)
List of names of species (string)
of sites to perturb; First site of that species
is selected in the structure
find_nearest_sites: If set to true and species_perturb != None,
the closest sites (by the Structure distance matrix) will be selected
in the response analysis to account for inter-site screening effects
parallel_scheme: 0 - (default) self-consistent (SCF)
runs use WAVECAR from non-self consistent (NSCF) run
at same applied potential; 1 - SCF runs use WAVECAR
from ground-state (V=0) run.
While reusing the WAVECAR from NSCF run in SCF run may be more
efficient (parallel_scheme: 0), the user may also choose to
remove the dependency between NSCF and SCF runs
(parallel_scheme: 1)
ediff_tight: Final energy convergence tolerance,
if restarting from a previous run
(if not specified, will default to pymatgen default EDIFF)
c: Workflow config dict, in the same format
as in presets/core.py and elsewhere in atomate
Returns: Workflow
"""
if not structure.is_ordered:
raise ValueError(
"Please obtain an ordered approximation of the input structure.")
if not site_indices_perturb:
site_indices_perturb = []
if species_perturb:
if find_nearest_sites:
site_indices_perturb = find_closest_sites(structure,
species_perturb)
else:
for specie_u in species_perturb:
found_specie = False
for s in range(len(structure)):
site = structure[s]
if (Element(str(site.specie)) == Element(specie_u)) \
and (s not in site_indices_perturb):
found_specie = True
break
if not found_specie:
raise ValueError("Could not find specie(s) in structure.")
site_indices_perturb.append(s)
elif not site_indices_perturb:
logger.warning("Sites for computing U value are not specified. "
"Computing U for first site in structure. ")
site_indices_perturb = list(tuple(site_indices_perturb))
num_perturb = len(site_indices_perturb)
sites_perturb = []
for site_index_perturb in site_indices_perturb:
site = structure[site_index_perturb]
sites_perturb.append(site)
structure.remove_sites(indices=site_indices_perturb)
for site in sites_perturb:
structure.insert(i=0,
species=site.specie,
coords=site.frac_coords,
properties=site.properties)
# using a uuid for book-keeping,
# in a similar way to other workflows
uuid = str(uuid4())
c_defaults = {"vasp_cmd": VASP_CMD, "db_file": DB_FILE}
if c:
c.update(c_defaults)
else:
c = c_defaults
# Calculate groundstate
# set user_incar_settings
if not user_incar_settings:
user_incar_settings = {}
# setup VASP input sets
uis_gs, uis_ldau, val_dict, vis_ldau = init_linresp_input_sets(
user_incar_settings, structure, num_perturb)
fws = []
index_fw_gs = [0]
ediff_default = vis_ldau.incar['EDIFF']
if not ediff_tight:
ediff_tight = 0.1 * ediff_default
append_linresp_ground_state_fws(fws, structure, num_perturb, index_fw_gs,
uis_gs, relax_nonmagnetic, ediff_default,
ediff_tight)
# generate list of applied on-site potentials in linear response
applied_potential_value_list = []
for counter_perturb in range(num_perturb):
applied_potential_values = np.linspace(applied_potential_range[0],
applied_potential_range[1],
num_evals)
applied_potential_values = np.around(applied_potential_values,
decimals=9)
if 0.0 in applied_potential_values:
applied_potential_values = list(applied_potential_values)
applied_potential_values.pop(applied_potential_values.index(0.0))
applied_potential_values = np.array(applied_potential_values)
applied_potential_value_list.append(applied_potential_values.copy())
for counter_perturb in range(num_perturb):
applied_potential_values = applied_potential_value_list[
counter_perturb]
for v in applied_potential_values:
append_linresp_perturb_fws(v, fws, structure, counter_perturb,
num_perturb, index_fw_gs, uis_ldau,
val_dict, spin_polarized,
relax_nonmagnetic, ediff_default,
ediff_tight, parallel_scheme)
wf = Workflow(fws)
fw_analysis = Firework(
HubbardHundLinRespToDb(num_perturb=num_perturb,
spin_polarized=spin_polarized,
relax_nonmagnetic=relax_nonmagnetic,
db_file=DB_FILE,
wf_uuid=uuid),
name="HubbardHundLinRespToDb",
)
wf.append_wf(Workflow.from_Firework(fw_analysis), wf.leaf_fw_ids)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
wf = add_additional_fields_to_taskdocs(
wf,
{
"wf_meta": {
"wf_uuid": uuid,
"wf_name": "hubbard_hund_linresp",
"wf_version": __hubbard_hund_linresp_wf_version__,
}
},
)
return wf
def make_md_workflow(sim,
archive,
stages,
md_engine='gromacs',
md_category='md',
local_category='local',
postrun_wf=None,
post_wf=None,
files=None):
"""Construct a general, single MD simulation workflow.
Assumptions
-----------
Queue launcher submission script must define and export the following
environment variables:
1. STAGING : absolute path on resource to staging directory
2. SCRATCH : absolute path on resource to scratch directory
The staging directory must already exist on all resources specified in
``stages``.
The script ``run_md.sh`` must be somewhere on your path, and must take
a single argument giving the directory to execute MD out of. It should
create and change the working directory to that directory before anything
else.
Parameters
----------
sim : str
MDSynthesis Sim.
archive : str
Absolute path to directory to launch from, which holds all required
files for running MD.
stages : list, str
Dicts giving for each of the following keys:
- 'server': server host to transfer to
- 'user': username to authenticate with
- 'staging': absolute path to staging area on remote resource
alternatively, a path to a yaml file giving a list of dictionaries
with the same information.
md_engine : {'gromacs'}
MD engine name; needed to determine continuation mechanism to use.
md_category : str
Category to use for the MD Firework. Used to target to correct rockets.
local_category : str
Category to use for non-MD Fireworks, which should be run by rockets
where the ``archive`` directory is accessible.
postrun_wf : Workflow
Workflow to perform after each copyback; performed in parallel to continuation run.
post_wf : Workflow
Workflow to perform after completed MD (no continuation); use for final
postprocessing.
files : list
Names of files (not paths) needed for each leg of the simulation. Need
not exist, but if they do they will get staged before each run.
Returns
-------
workflow
MD workflow; can be submitted to LaunchPad of choice.
"""
sim = mds.Sim(sim)
#TODO: perhaps move to its own FireTask?
sim.categories['md_status'] = 'running'
#TODO: the trouble with this is that if this workflow is created with the intent
# of being attached to another, these files may not exist at all yet
f_exist = [f for f in files if os.path.exists(os.path.join(archive, f))]
if isinstance(stages, string_types):
with open(stages, 'r') as f:
stages = yaml.load(f)
## Stage files on all resources where MD may run; takes place locally
fts_stage = list()
for stage in stages:
fts_stage.append(
FileTransferTask(mode='rtransfer',
server=stage['server'],
user=stage['user'],
files=[os.path.join(archive, i) for i in files],
dest=os.path.join(stage['staging'], sim.uuid),
max_retry=5,
shell_interpret=True))
fw_stage = Firework(fts_stage,
spec={
'_launch_dir': archive,
'_category': local_category
},
name='staging')
## MD execution; takes place in queue context of compute resource
# make rundir
ft_mkdir = MkRunDirTask(uuid=sim.uuid)
# copy input files to scratch space
ft_copy = FileTransferTask(
mode='copy',
files=[os.path.join('${STAGING}/', sim.uuid, i) for i in files],
dest=os.path.join('${SCRATCHDIR}/', sim.uuid),
ignore_missing=True,
shell_interpret=True)
# next, run MD
ft_md = ScriptTask(script='run_md.sh {}'.format(
os.path.join('${SCRATCHDIR}/', sim.uuid)),
use_shell=True,
fizzle_bad_rc=True)
# send info on where files live to pull firework
ft_info = BeaconTask(uuid=sim.uuid)
fw_md = Firework([ft_mkdir, ft_copy, ft_md, ft_info],
spec={'_category': md_category},
name='md')
## Pull files back to archive; takes place locally
ft_copyback = FilePullTask(dest=archive)
fw_copyback = Firework([ft_copyback],
spec={
'_launch_dir': archive,
'_category': local_category
},
name='pull')
## Decide if we need to continue and submit new workflow if so; takes place
## locally
if md_engine == 'gromacs':
ft_continue = GromacsContinueTask(sim=sim,
archive=archive,
stages=stages,
md_engine=md_engine,
md_category=md_category,
local_category=local_category,
postrun_wf=postrun_wf,
post_wf=post_wf,
files=files)
else:
raise ValueError("No known md engine `{}`.".format(md_engine))
fw_continue = Firework([ft_continue],
spec={
'_launch_dir': archive,
'_category': local_category
},
name='continue')
wf = Workflow([fw_stage, fw_md, fw_copyback, fw_continue],
links_dict={
fw_stage: [fw_md],
fw_md: [fw_copyback],
fw_copyback: [fw_continue]
},
name='{} | md'.format(sim.name),
metadata=dict(sim.categories))
## Mix in postrun workflow, if given
if postrun_wf:
if isinstance(postrun_wf, dict):
postrun_wf = Workflow.from_dict(postrun_wf)
wf.append_wf(Workflow.from_wflow(postrun_wf), [fw_copyback.fw_id])
return wf
def get_wf_slab(slab, include_bulk_opt=False, adsorbates=None,
ads_structures_params=None, vasp_cmd="vasp",
db_file=None, add_molecules_in_box=False):
"""
Gets a workflow corresponding to a slab calculation along with optional
adsorbate calcs and precursor oriented unit cell optimization
Args:
slabs (list of Slabs or Structures): slabs to calculate
include_bulk_opt (bool): whether to include bulk optimization,
this flag sets the slab fireworks to be TransmuterFWs based
on bulk optimization of oriented unit cells
adsorbates ([Molecule]): list of molecules to place as adsorbates
ads_structures_params (dict): parameters to be supplied as
kwargs to AdsorbateSiteFinder.generate_adsorption_structures
add_molecules_in_box (boolean): flag to add calculation of
adsorbate molecule energies to the workflow
db_file (string): path to database file
vasp_cmd (string): vasp command
Returns:
Workflow
"""
fws, parents = [], []
if adsorbates is None:
adsorbates = []
if ads_structures_params is None:
ads_structures_params = {}
# Add bulk opt firework if specified
if include_bulk_opt:
oriented_bulk = slab.oriented_unit_cell
vis = MPSurfaceSet(oriented_bulk, bulk=True)
fws.append(OptimizeFW(structure=oriented_bulk, vasp_input_set=vis,
vasp_cmd=vasp_cmd, db_file=db_file))
parents = fws[-1]
name = slab.composition.reduced_formula
if getattr(slab, "miller_index", None):
name += "_{}".format(slab.miller_index)
# Create slab fw and add it to list of fws
slab_fw = get_slab_fw(slab, include_bulk_opt, db_file=db_file,
vasp_cmd=vasp_cmd, parents=parents,
name="{} slab optimization".format(name))
fws.append(slab_fw)
for adsorbate in adsorbates:
ads_slabs = AdsorbateSiteFinder(slab).generate_adsorption_structures(
adsorbate, **ads_structures_params)
for n, ads_slab in enumerate(ads_slabs):
# Create adsorbate fw
ads_name = "{}-{} adsorbate optimization {}".format(
adsorbate.composition.formula, name, n)
adsorbate_fw = get_slab_fw(
ads_slab, include_bulk_opt, db_file=db_file, vasp_cmd=vasp_cmd,
parents=parents, name=ads_name)
fws.append(adsorbate_fw)
if isinstance(slab, Slab):
name = "{}_{} slab workflow".format(
slab.composition.reduced_composition, slab.miller_index)
else:
name = "{} slab workflow".format(slab.composition.reduced_composition)
wf = Workflow(fws, name=name)
# Add optional molecules workflow
if add_molecules_in_box:
molecule_wf = get_wf_molecules(adsorbates, db_file=db_file,
vasp_cmd=vasp_cmd)
wf.append_wf(molecule_wf)
return wf