def print_forces(self):
"""
Print out the forces and stress during calculation
"""
self["FORCE_EVAL"].insert(Section("PRINT", subsections={}))
self["FORCE_EVAL"]["PRINT"].insert(Section("FORCES", subsections={}))
self["FORCE_EVAL"]["PRINT"].insert(Section("STRESS_TENSOR", subsections={}))
def __init__(self,
structure: Union[Structure, Molecule],
max_drift: float = 3e-3,
max_force: float = 4.5e-3,
max_iter: int = 200,
project_name: str = "Relax",
optimizer: str = "BFGS",
override_default_params: Dict = {},
**kwargs):
"""
Args:
structure:
max_drift: Convergence criterion for the maximum geometry change between the current and the
last optimizer iteration. This keyword cannot be repeated and it expects precisely one real.
Default value: 3.00000000E-003
Default unit: [bohr]
max_force (float): Convergence criterion for the maximum force component of the current configuration.
This keyword cannot be repeated and it expects precisely one real.
Default value: 4.50000000E-004
Default unit: [bohr^-1*hartree]
max_iter (int): Specifies the maximum number of geometry optimization steps.
One step might imply several force evaluations for the CG and LBFGS optimizers.
This keyword cannot be repeated and it expects precisely one integer.
Default value: 200
optimizer (str): Specify which method to use to perform a geometry optimization.
This keyword cannot be repeated and it expects precisely one keyword. BFGS is a
quasi-newtonian method, and will best for "small" systems near the minimum. LBFGS
is a limited memory version that can be used for "large" (>1000 atom) systems when
efficiency outweights robustness. CG is more robust, especially when you are far from
the minimum, but it slower.
Default value: BFGS
"""
super().__init__(structure, **kwargs)
self.structure = structure
self.max_drift = max_drift
self.max_force = max_force
self.max_iter = max_iter
self.project_name = project_name
self.optimizer = optimizer
self.override_default_params = override_default_params
self.kwargs = kwargs
global_section = Global(project_name=project_name, run_type="GEO_OPT")
geo_opt_params = {
"TYPE": Keyword("TYPE", "MINIMIZATION"),
"MAX_DR": Keyword("MAX_DR", max_drift),
"MAX_FORCE": Keyword("MAX_FORCE", max_force),
"RMS_DR": Keyword("RMS_DR", 1.5e-3),
"MAX_ITER": Keyword("MAX_ITER", max_iter),
"OPTIMIZER": Keyword("OPTIMIZER", optimizer),
}
geo_opt = Section("GEO_OPT", subsections={}, keywords=geo_opt_params)
if not self.check("MOTION"):
self.insert(Section("MOTION", subsections={}))
self["MOTION"].insert(geo_opt)
self.insert(global_section)
self.modify_dft_print_iters(max_iter + 1, add_last="numeric")
self.update(override_default_params)
def activate_nonperiodic(self):
"""
Activates a calculation with non-periodic calculations by turning of PBC and
changing the poisson solver. Still requires a CELL to put the atoms
"""
kwds = {
"POISSON_SOLVER": Keyword("POISSON_SOLVER", "MT"),
"PERIODIC": Keyword("PERIODIC", "NONE"),
}
self["FORCE_EVAL"]["DFT"].insert(Section("POISSON", subsections={}, keywords=kwds))
if not self.check("FORCE_EVAL/SUBSYS/CELL"):
x = max(s.coords[0] for s in self.structure.sites)
y = max(s.coords[1] for s in self.structure.sites)
z = max(s.coords[2] for s in self.structure.sites)
self["FORCE_EVAL"]["SUBSYS"].insert(Cell(lattice=Lattice([[x, 0, 0], [0, y, 0], [0, 0, z]])))
self["FORCE_EVAL"]["SUBSYS"]["CELL"].add(Keyword("PERIODIC", "NONE"))
def print_motion(self):
"""
Print the motion info (trajectory, cell, forces, stress
"""
if not self.check("MOTION"):
self.insert(Section("MOTION", subsections={}))
self["MOTION"].insert(Section("PRINT", subsections={}))
self["MOTION"]["PRINT"].insert(Section("TRAJECTORY", section_parameters=["ON"], subsections={}))
self["MOTION"]["PRINT"].insert(Section("CELL", subsections={}))
self["MOTION"]["PRINT"].insert(Section("FORCES", subsections={}))
self["MOTION"]["PRINT"].insert(Section("STRESS", subsections={}))
def modify_dft_print_iters(self, iters, add_last="no"):
"""
Modify all DFT print iterations at once. Common use is to set iters to the max
number of iterations + 1 and then set add_last to numeric. This would have the
effect of printing only the first and last iteration, which might be useful for
speeding up/saving space on GEO_OPT or MD runs where you don't need the intermediate
values.
Args
iters (int): print each "iters" iterations.
add_last (str): Whether to explicitly include the last iteration, and how to mark it.
numeric: mark last iteration with the iteration number
symbolic: mark last iteration with the letter "l"
no: do not explicitly include the last iteration
"""
assert add_last.lower() in ["no", "numeric", "symbolic"]
if self.check("FORCE_EVAL/DFT/PRINT"):
run_type = (
self["global"].get("run_type", Keyword("run_type", "energy")).values[0]
)
for k, v in self["force_eval"]["dft"]["print"].subsections.items():
if v.name.upper() in [
"ACTIVE_SPACE",
"BAND_STRUCTURE",
"GAPW",
"IMPLICIT_PSOLVER",
"SCCS",
"WFN_MIX",
]:
continue
v.insert(
Section(
"EACH",
subsections=None,
keywords={run_type: Keyword(run_type, iters)},
)
)
v.keywords["ADD_LAST"] = Keyword("ADD_LAST", add_last)
def activate_hybrid(
self,
hybrid_functional: str = "PBE0",
hf_fraction: float = 0.25,
gga_x_fraction: float = 0.75,
gga_c_fraction: float = 1,
max_memory: int = 2000,
cutoff_radius: float = 8.0,
potential_type: str = None,
omega: float = 0.2,
aux_basis: Union[Dict, None] = None,
admm: bool = True,
eps_schwarz: float = 1e-6,
eps_schwarz_forces: float = 1e-6,
screen_on_initial_p: bool = True,
screen_p_forces: bool = True,
):
"""
Basic set for activating hybrid DFT calculation using Auxiliary Density Matrix Method.
Note 1: When running ADMM with cp2k, memory is very important. If the memory requirements exceed
what is available (see max_memory), then CP2K will have to calculate the 4-electron integrals
for HFX during each step of the SCF cycle. ADMM provides a huge speed up by making the memory
requirements *feasible* to fit into RAM, which means you only need to calculate the integrals
once each SCF cycle. But, this only works if it fits into memory. When setting up ADMM
calculations, we recommend doing whatever is possible to fit all the 4EI into memory.
Note 2: This set is designed for reliable high-throughput calculations, NOT for extreme
accuracy. Please review the in-line comments in this method if you want more control.
Args:
hybrid_functional (str): Type of hybrid functional. This set supports HSE (screened) and PBE0
(truncated). Default is PBE0, which converges easier in the GPW basis used by
cp2k.
hf_fraction (float): fraction of exact HF exchange energy to mix. Default: 0.25
gga_x_fraction (float): fraction of gga exchange energy to retain. Default: 0.75
gga_c_fraction (float): fraction of gga correlation energy to retain. Default: 1.0
max_memory (int): Maximum memory available to each MPI process (in Mb) in the calculation.
Most modern computing nodes will have ~2Gb per core, or 2048 Mb, but check for
your specific system. This value should be as large as possible while still leaving
some memory for the other parts of cp2k. Important: If this value is set larger
than the memory limits, CP2K will likely seg-fault.
Default: 2000
cutoff_radius (float): for truncated hybrid functional (i.e. PBE0), this is the cutoff
radius. The default is selected as that which generally gives convergence, but
maybe too low (if you want very high accuracy) or too high (if you want a quick
screening). Default: 8 angstroms
potential_type (str): what interaction potential to use for HFX. Available in CP2K are
COULOMB, GAUSSIAN, IDENTITY, LOGRANGE, MIX_CL, MIX_CL_TRUNC, MIX_LG, SHORTRANGE,
and TRUNCATED. Default is None, and it will be set automatically depending on the
named hybrid_functional that you use, but setting it to one of the acceptable
values will constitute a user-override.
omega (float): For HSE, this specifies the screening parameter. HSE06 sets this as
0.2, which is the default.
aux_basis (dict): If you want to specify the aux basis to use, specify it as a dict of
the form {'specie_1': 'AUX_BASIS_1', 'specie_2': 'AUX_BASIS_2'}
admm (bool): Whether or not to use the auxiliary density matrix method for the exact
HF exchange contribution. Highly recommended. Speed ups between 10x and aaa1000x are
possible when compared to non ADMM hybrid calculations. Default: True
eps_schwarz (float): Screening threshold for HFX, in Ha. Contributions smaller than this
will be screened. The smaller the value, the more accurate, but also the more
costly. Default value is 1e-6, which is quite aggressive. Aggressive screening
can also lead to convergence issues. 1e-7 should be a safe value if 1e-6 is too
aggressive.
eps_schwarz_forces (float): Same as for eps_schwarz, but for screening contributions to
forces. Convergence is not as sensitive with respect to eps_schwarz forces as
compared to eps_schwarz, and so 1e-6 should be good default.
screen_on_initial_p (bool): If an initial density matrix is provided, in the form of a
CP2K wfn restart file, then this initial density will be used for screening. This
is generally very computationally efficient, but, as with eps_schwarz, can lead to
instabilities if the initial density matrix is poor.
screen_p_forces (bool): Same as screen_on_initial_p, but for screening of forces.
"""
if admm:
aux_basis = aux_basis if aux_basis else {}
aux_basis = {
s: aux_basis[s] if s in aux_basis else None
for s in self.structure.symbol_set
}
basis = get_aux_basis(basis_type=aux_basis)
if isinstance(
self["FORCE_EVAL"]["DFT"]["BASIS_SET_FILE_NAME"], KeywordList
):
self["FORCE_EVAL"]["DFT"]["BASIS_SET_FILE_NAME"].extend(
[
Keyword("BASIS_SET_FILE_NAME", k)
for k in ["BASIS_ADMM", "BASIS_ADMM_MOLOPT"]
],
)
for k, v in self["FORCE_EVAL"]["SUBSYS"].subsections.items():
if "KIND" == v.name.upper():
kind = v["ELEMENT"].values[0]
v.keywords["BASIS_SET"] += Keyword(
"BASIS_SET", "AUX_FIT", basis[kind]
)
# Don't change unless you know what you're doing
# Use NONE for accurate eigenvalues (static calcs)
aux_matrix_params = {
"ADMM_PURIFICATION_METHOD": Keyword("ADMM_PURIFICATION_METHOD", "NONE"),
"METHOD": Keyword("METHOD", "BASIS_PROJECTION"),
}
aux_matrix = Section(
"AUXILIARY_DENSITY_MATRIX_METHOD",
keywords=aux_matrix_params,
subsections={},
)
self.subsections["FORCE_EVAL"]["DFT"].insert(aux_matrix)
# Define the GGA functional as PBE
pbe = PBE("ORIG", scale_c=gga_c_fraction, scale_x=gga_x_fraction)
xc_functional = XC_FUNCTIONAL("PBE", subsections={"PBE": pbe})
screening = Section(
"SCREENING",
subsections={},
keywords={
"EPS_SCHWARZ": Keyword("EPS_SCHWARZ", eps_schwarz),
"EPS_SCHWARZ_FORCES": Keyword("EPS_SCHWARZ_FORCES", eps_schwarz_forces),
"SCREEN_ON_INITIAL_P": Keyword(
"SCREEN_ON_INITIAL_P", screen_on_initial_p
),
"SCREEN_P_FORCES": Keyword("SCREEN_P_FORCES", screen_p_forces),
},
)
ip_keywords = {}
if hybrid_functional == "HSE06":
potential_type = potential_type if potential_type else "SHORTRANGE"
xc_functional.insert(
Section(
"XWPBE",
subsections={},
keywords={
"SCALE_X0": Keyword("SCALE_X0", 1),
"SCALE_X": Keyword("SCALE_X", -hf_fraction),
"OMEGA": Keyword("OMEGA", omega),
},
)
)
ip_keywords.update(
{
"POTENTIAL_TYPE": Keyword("POTENTIAL_TYPE", potential_type),
"OMEGA": Keyword("OMEGA", omega),
}
)
elif hybrid_functional == "PBE0":
potential_type = potential_type if potential_type else "TRUNCATED"
ip_keywords.update(
{
"POTENTIAL_TYPE": Keyword("POTENTIAL_TYPE", potential_type),
"CUTOFF_RADIUS": Keyword("CUTOFF_RADIUS", cutoff_radius),
"T_C_G_DATA": Keyword("T_C_G_DATA", "t_c_g.dat"),
}
)
interaction_potential = Section(
"INTERACTION_POTENTIAL", subsections={}, keywords=ip_keywords
)
# Unlikely for users to override
load_balance = Section(
"LOAD_BALANCE",
keywords={"RANDOMIZE": Keyword("RANDOMIZE", True)},
subsections={},
)
# EPS_STORAGE_SCALING squashes the integrals for efficient storage
# Unlikely for users to override.
memory = Section(
"MEMORY",
subsections={},
keywords={
"EPS_STORAGE_SCALING": Keyword("EPS_STORAGE_SCALING", 0.1),
"MAX_MEMORY": Keyword("MAX_MEMORY", max_memory),
},
)
hf = Section(
"HF",
keywords={"FRACTION": Keyword("FRACTION", hf_fraction)},
subsections={
"SCREENING": screening,
"INTERACTION_POTENTIAL": interaction_potential,
"LOAD_BALANCE": load_balance,
"MEMORY": memory,
},
)
xc = Section("XC", subsections={"XC_FUNCTIONAL": xc_functional, "HF": hf})
self.subsections["FORCE_EVAL"]["DFT"].insert(xc)
def __init__(
self,
structure: Union[Structure, Molecule],
ot: bool = True,
band_gap: float = 0.01,
eps_default: float = 1e-12,
eps_scf: float = 1e-7,
max_scf: Union[int, None] = None,
minimizer: str = "DIIS",
preconditioner: str = "FULL_ALL",
algorithm: str = "STRICT",
linesearch: str = "2PNT",
cutoff: int = 1200,
rel_cutoff: int = 80,
ngrids: int = 5,
progression_factor: int = 3,
override_default_params: Dict = {},
wfn_restart_file_name: str = None,
kpoints: Union[Kpoints, None] = None,
smearing: bool = False,
**kwargs
):
"""
Args:
structure: Pymatgen structure or molecule object
ot (bool): Whether or not to use orbital transformation method for matrix diagonalization. OT is the
flagship scf solver of CP2K, and will provide huge speed-ups for this part of the calculation,
but the system must have a band gap for OT to be used (higher band-gap --> faster convergence).
Band gap is also used by the preconditioner for OT, and should be set as a value SMALLER than the true
band gap to get good efficiency. Generally, this parameter does not need to be changed from
default of 0.01
band_gap (float): The band gap can also be specified in order to determine if ot should be turned on.
eps_default (float): Replaces all EPS_XX Keywords in the DFT section (NOT its subsections!) to have this
value, ensuring an overall accuracy of at least this much.
eps_scf (float): The convergence criteria for leaving the SCF loop in Hartrees. Default is 1e-7. Should
ensure reasonable results for all properties. Smaller than 1e-7 is generally not needed unless
you need very high precision. 1e-6 may be used for difficult systems, and should still give
reasonable results for most properties.
max_scf (int): The max number of SCF cycles before terminating the solver. NOTE: With the OT solver, this
corresponds to the max number of INNER scf loops, and then the outer loops are set with outer_max_scf,
while with diagnolization it corresponds to the overall (INNER*OUTER) number of SCF steps, with the
inner loop limit set by
minimizer (str): The minimization scheme. DIIS can be as much as 50% faster than the more robust conjugate
gradient method, and so it is chosen as default. Switch to CG if dealing with a difficult system.
preconditioner (str): Preconditioner for the OT method. FULL_ALL is the most reliable, and is the
default. Though FULL_SINGLE_INVERSE has faster convergence according to our internal tests. Should
only change from theses two when simulation cell gets to be VERY large,
in which case FULL_KINETIC might be preferred.
cutoff (int): Cutoff energy (in Ry) for the finest level of the multigrid. A high cutoff will allow you to
have very accurate calculations PROVIDED that REL_CUTOFF is appropriate.
rel_cutoff (int): This cutoff decides how the Guassians are mapped onto the different levels of the
multigrid. From CP2K: A Gaussian is mapped onto the coarsest level of the multi-grid, on which the
function will cover number of grid points greater than or equal to the number of grid points
will cover on a reference grid defined by REL_CUTOFF.
progression_factor (int): Divisor of CUTOFF to get the cutoff for the next level of the multigrid.
Takeaway for the cutoffs: https://www.cp2k.org/howto:converging_cutoff
If CUTOFF is too low, then all grids will be coarse and the calculation may become inaccurate; and if
REL_CUTOFF is too low, then even if you have a high CUTOFF, all Gaussians will be mapped onto the coarsest
level of the multi-grid, and thus the effective integration grid for the calculation may still be too
coarse.
"""
super().__init__(structure, **kwargs)
self.structure = structure
self.ot = ot
self.band_gap = band_gap
self.eps_default = eps_default
self.eps_scf = eps_scf
self.max_scf = max_scf
self.minimizer = minimizer
self.preconditioner = preconditioner
self.algorithm = algorithm
self.linesearch = linesearch
self.cutoff = cutoff
self.rel_cutoff = rel_cutoff
self.ngrids = ngrids
self.progression_factor = progression_factor
self.override_default_params = override_default_params
self.wfn_restart_file_name = wfn_restart_file_name
self.kpoints = kpoints
self.smearing = smearing
self.kwargs = kwargs
# Build the QS Section
qs = QS(eps_default=eps_default)
max_scf = (
max_scf if max_scf else 20 if ot else 400
) # If ot, max_scf is for inner loop
scf = Scf(eps_scf=eps_scf, max_scf=max_scf, subsections={})
# If there's a band gap, use OT, else use Davidson
if ot:
if band_gap <= 0:
warnings.warn(
"Orbital Transformation method is being used for"
"a system without a bandgap. OT can have very poor"
"convergence for metallic systems, proceed with caution.",
UserWarning,
)
scf.insert(
OrbitalTransformation(
minimizer=minimizer,
preconditioner=preconditioner,
energy_gap=band_gap,
algorithm=algorithm,
linesearch=linesearch,
)
)
scf.insert(
Section(
"OUTER_SCF",
subsections={},
keywords={
"MAX_SCF": Keyword("MAX_SCF", kwargs.get("outer_max_scf", 20)),
"EPS_SCF": Keyword(
"EPS_SCF", kwargs.get("outer_eps_scf", eps_scf)
),
},
)
)
else:
scf.insert(Section("DIAGONALIZATION", subsections={}))
mixing_kwds = {
"METHOD": Keyword("METHOD", "BROYDEN_MIXING"),
"ALPHA": Keyword("ALPHA", 0.2),
"NBUFFER": Keyword("NBUFFER", 5),
}
mixing = Section("MIXING", keywords=mixing_kwds, subsections=None)
scf.insert(mixing)
davidson_kwds = {"PRECONDITIONER": Keyword("PRECONDITIONER", "FULL_ALL")}
davidson = Section("DAVIDSON", keywords=davidson_kwds, subsections=None)
scf["DIAGONALIZATION"].insert(davidson)
# Create the multigrid for FFTs
mgrid = Mgrid(
cutoff=cutoff,
rel_cutoff=rel_cutoff,
ngrids=ngrids,
progression_factor=progression_factor,
)
# Set the DFT calculation with global parameters
dft = Dft(
MULTIPLICITY=self.multiplicity,
CHARGE=self.charge,
basis_set_filenames=self.basis_set_file_names,
potential_filename=self.potential_file_name,
subsections={"QS": qs, "SCF": scf, "MGRID": mgrid},
wfn_restart_file_name=wfn_restart_file_name,
)
if kpoints:
dft.insert(Kpoints.from_kpoints(kpoints))
if smearing or (band_gap <= 0.0):
scf.kwargs["ADDED_MOS"] = 100
scf["ADDED_MOS"] = 100 # TODO: how to grab the appropriate number?
scf.insert(Smear())
# Create subsections and insert into them
self["FORCE_EVAL"].insert(dft)
xc_functional = XC_FUNCTIONAL(functional=kwargs.get("functional", "PBE"))
xc = Section("XC", subsections={"XC_FUNCTIONAL": xc_functional})
self["FORCE_EVAL"]["DFT"].insert(xc)
self["FORCE_EVAL"]["DFT"].insert(Section("PRINT", subsections={}))
if isinstance(structure, Molecule):
self.activate_nonperiodic()
if kwargs.get("print_pdos", True):
self.print_pdos()
if kwargs.get("print_ldos", False):
self.print_ldos()
if kwargs.get("print_mo_cubes", True):
self.print_mo_cubes()
if kwargs.get("print_hartree_potential", False):
self.print_hartree_potential()
if kwargs.get("print_e_density", False):
self.print_e_density()
self.update(self.override_default_params)