Run eDFTpy with input files¶
eDFTpy is a set of python modules. However,you can run it using the edftpy executable. Here’s a quick guide to the available keywords.
Warning
PP is a mandatory input (i.e., no default is avaliable for it).
Note
Defaults work well for most arguments.
When Options is empty, it can accept any value.
JOB¶
Control of the running job.
- task
The task to be performed. Optdensity solves for the electronic structure to selfconsistency. Calculation performs a one-shot evaluation of calctype (see below) without selconsistency.
Options : Optdensity, Calculation, Tddft, Optmix
Default : Optdensity
- calctype
The property to be calculated.
Options : Energy, Potential, Force, Stress
Default : Energy
PATH¶
Specify the path of needed files.
- pp
The path of pseudopotential.
Options :
Default : ./
- cell
The path of input structure.
Options :
Default : ./
MATH¶
Some methods and techniques that make DFTpy really fast.
- linearii
Linear-scaling method to deal with Ion-Ion interactions (PME).
Options : True, False
Default : True
- linearie
Linear-scaling method to deal with Ion-Electron interactions (PME).
Options : True, False
Default : True
PP¶
Control of the running job.
e.g. :
Al = Al_lda.oe01.recpot
OUTPUT¶
Control the output.
- electrostatic_potential
Output of electrostatic potential
Options :
Default : None
- sub_temp
Output all the temporary files of subsystems.
Options : True, False
Default : False
- append
Append the output of all the subsystems.
Options : True, False
Default : False
- time
Output the time information of all parts.
Options : True, False
Default : True
OPT¶
Control the charge density optimization of global system.
- method
Charge density optimization method.
Options : Normal
Default : Normal
- econv
Convergence threshold for energy, it will divided by the number of atoms.
Options :
Default : 1e-05
Unit : a.u./atom
- pconv
Convergence threshold for potential. Default is ‘econv’/1E2.
Options :
Default : None
Unit : a.u/atom
- maxiter
The max steps for optimization.
Options :
Default : 100
- ncheck
How many step satisfy the convergence.
Options :
Default : 2
- olevel
The level of output energy, large will faster.
Options :
Default : 2
Note
Only set 0, the energy of each cycle is useful.
- maxtime
Maximum execution time. Non-positive number means no time limit.
Options :
Default : 0
Unit : second
TD¶
Control the TDDFT.
- maxiter
The max steps for TDDFT.
Options :
Default : 1000
- olevel
The level of output energy, large will faster.
Options :
Default : 2
Note
Only set 0, the energy of each cycle is useful.
- restart
Start the job from new one, scf results or restart from previous run.
Options : initial, scf, restart
Default : initial
- iter
The iteration number of restart.
Options :
Default : 0
- maxtime
Maximum execution time. Non-positive number means no time limit.
Options :
Default : 0
Unit : second
GSYSTEM¶
SUB¶
cell¶
Structure information of system.
- cell-file
The file name of input structure. Many file formats are available. We use ASE’s I/O for some formats.
Options :
Default : None
- cell-split
Cut small cell for each direction (scaled).
Options :
Default : None
- cell-cut
Base on the subsystem atoms build the small cell, and add the vacuum on each direction. 0 means use whole cell.
Options :
Default : 0
- cell-index
The indices of the atoms, support integer and slice.
Options :
Default : None
Note
If not only a slice, you should given the stop for the slice.
- cell-elename
The name of atom.
Options :
Default : None
- cell-zval
The charge of atomic species.
Options :
Default : None
- cell-format
The format of structure file.
Options : pp, vasp, xsf, snpy, …
Default : None
Note
Only snpy format support parallel read and write
- cell-lattice
Three numbers means three lengths of orthogonal cell; Six numbers means three vector lengths and three angles; Nine numbers means unit vector[a, b, c]. Only works for GSYSTEM and when cell-file is not given.
Options :
Default : None
- cell-symbols
A list of symbols for all atoms. Only works for GSYSTEM and when cell-file is not given.
Options :
Default : None
- cell-positions
Atomic positions in Cartesian coordinate. Only works for GSYSTEM and when cell-file is not given.
Options :
Default : None
Unit : Angstrom
grid¶
Control the grid.
- grid-ecut
The kinetic energy cutoff.
Options :
Default : None
Unit : eV
- grid-optfft
Optimize the number of grid points.
Options : True, False
Default : True
- grid-spacing
The spacing (or gap) separating nearest real space grid points. If set this, ecut is disabled.
Options :
Default : None
Unit : Angstrom
- grid-gfull
Determines oif the number of grid points in the reciprocal and real space grids are equal. If ‘False’ only use half grid, which will be faster.
Options : True, False
Default : False
Note
gfull=False’ implies that the the number of points of reciprocal space is only half of real space.
- grid-nr
The number of grid points in the direction of the three lattice vectors.
Options :
Default : None
e.g. :
nr = 32 32 32
- grid-maxprime
The max prime of guess best number of grid points for FFT
Options : 3, 5, 7, 11, 13, 17,…, 97
Default : 13
- grid-scale
The minimum scale for guess the best number of grid points
Options :
Default : 0.99
- grid-cplx
The type of real space value
Options : True, False
Default : False
density¶
Control the charge density.
- density-ncharge
Total charge of the system.
Options :
Default : None
- density-file
The input density file for initial density. If set, the density-initial will automatically set to ‘file’.
Options :
Default : None
- density-output
The output file or format of density. The name starts with ‘.’ represent the format.
Options :
Default : None
- density-initial
Default is None, which means engines determine the initial density by themself. ‘temp’ means initial density from engine temporary output. ‘atomic’ means base on the atomic density files or pseudopotentials initialize the density. ‘file’ means use input density file density-file to initialize the density.
Options : None, heg, temp, atomic, file
Default : None
- density-atomic
If density-initial set the Atomic, here can set each elements atomic density.
Options :
Default : {}
- density-use_gaussians
It will replaces the core densities of the surrounding fragments with a gaussian. This is to avoid problems of electrons leaking in the core region of surrounding fragments when hard pseudopotentials are employed.
Options : True, False
Default : False
- density-gaussians_rcut
The cutoff of distance.
Options :
Default : 3
Unit : Angstrom
- density-gaussians_sigma
The sigma of gaussians.
Options :
Default : 0.3
- density-gaussians_scale
The scale of each elements. If not set, will use the number of core electrons.
Options :
Default : {}
exc¶
Control the exchange-correlation functional.
- exc-libxc
The type of exchange-correlation functionals with pylibxc. See available functionals.
Options :
Default : None
- exc-xc
The kind of exchange-correlation functional. If not LDA, must have pylibxc installed. It has higher priority than libxc
Options : LDA, PBE
Default : None
- exc-dftd4
The method of dftd4. If use it, the dftd4 should be installed. See dftd4’s available methods.
Options :
Default : None
Note
If dftd4=’same’, which means dftd4 use same functional as exchange-correlation.
- exc-x_str
See libxc’s available exchange functionals (deprecated).
Options :
Default : None
- exc-c_str
See libxc’s available correlation functionals (deprecated).
Options :
Default : None
kedf¶
Control the kinetic energy density functional (KEDF). DFTpy features most KEDFs, from GGAs to nonlocal to nonlocal with density dependent kernel.
- kedf-kedf
The type of KEDF. GGA functionals are available with keywords GGA and LIBXC_KEDF.
Options : TF, GGA, LIBXC_KEDF, vW, x_TF_y_vW, WT, SM, FP, MGP, MGPA, MGPG, LMGP, LMGPA, LMGPG
Default : WT
- kedf-x
The ratio of TF KEDF.
Options :
Default : 1
- kedf-y
The ratio of vW KEDF.
Options :
Default : 1
- kedf-alpha
The alpha parameter typical in nonlocal KEDF \(\rho^{\alpha}\).
Options :
Default : 0.8333333333333333
- kedf-beta
The beta parameter typical in nonlocal KEDF \(\rho^{\beta}\).
Options :
Default : 0.8333333333333333
- kedf-sigma
A parameter used to smooth with a Gaussian convolution FFTs of problematic functions (e.g., invfft of \({G^2\rho(G)}\) ).
Options :
Default : None
- kedf-nsp
The number of \({k_{f}}\) points for splining LWT like nonlocal KEDFs. There are three options to achieve the same goal, the priority is nsp -> delta -> ratio. Default is using ratio.
Options :
Default : None
- kedf-interp
The interpolation method for LWT KEDF’s kernel from the kernel table.
Options :
Default : hermite
- kedf-kerneltype
The kernel for LWT KEDF.
Options : linear, newton, hermite
Default : WT
- kedf-symmetrization
The symmetrization way for MGP KEDF. See MGP_paper.
Options : None, Arithmetic, Geometric
Default : None
- kedf-lumpfactor
The kinetic electron for LWT KEDF.
Options :
Default : None
- kedf-neta
The max number of discrete \(\eta\) for LWT KEDF.
Options :
Default : 50000
- kedf-etamax
The max value of eta for kernel in LWT KEDF.
Options :
Default : 50
- kedf-order
The order for the interpolation of the kernel in LWT KEDF. ‘0’ means using the value of nearest-neighbor point is used.
Options : 1, 2, 3, 4, 5
Default : 3
- kedf-ratio
The ratio of \({k_{f}}\) for spline in LWT KEDF. There are three options to do same thing, the priority is nsp -> delta -> ratio. Default is using ratio.
Options :
Default : 1.2
- kedf-maxpoints
The max number of integration points for the evaluation of the MGP kernel.
Options :
Default : 1000
- kedf-delta
The gap of spline
Options :
Default : None
- kedf-kdd
- The kernel density denpendent for LWT KEDF:
1 : The origin LWT KEDF.
2 : Considers the \(\rho^{\beta}(r')\omega(\rho(r),r-r')\) term in the potential.
3 : Also considers the derivative of kernel which is neglected in LWT. See LMGP_paper.
Options : 1, 2, 3
Default : 3
- kedf-rho0
The ‘average’ density used for the definition of the Fermi momentum. Default is None, which means it calculated based on the total charge and system volume.
Options :
Default : None
- kedf-k_str
Functional type for GGA/LIBXC_KEDF
Options : LKT, DK, LLP, LLP91, OL1, OL, OL2, T92, THAK, B86A, B86, B86B, DK87, PW86, PW91O, PW91, PW91k, LG94, E00, P92, PBE2, PBE3, PBE4, P82, TW02, APBE, APBEK, REVAPBEK, REVAPBE, VJKS00, LC94, VT84F, SMP, TF, VW, X_TF_Y_VW, TFVW, STV, PBE2M, PG
Default : revAPBEK
Warning
GGA invokes DFTpy’s implementation. LIBXC_KEDF invokes libxc’s implementation (discouraged).
- kedf-params
Parameters for GGA KEDF functionals
Options :
Default : None
- kedf-kfmin
Lower limit of kf
Options :
Default : None
- kedf-kfmax
Upper limit of kf
Options :
Default : None
- kedf-rhomax
Maximum/cutoff density
Options :
Default : None
- kedf-ldw
local density weight
Options :
Default : None
- kedf-temperature
The temperature of TF KEDF.
Options :
Default : None
Unit : eV
- kedf-temperature0
The temperature of TF KEDF (analytical approximation).
Options :
Default : None
Unit : eV
decompose¶
The way to decompose the subsystem to more subsystems
- decompose-method
‘manual’ means use the given subsystem; ‘distance’ means base on the distance of atoms to decompose the subsystem.
Options : manual, distance
Default : manual
- decompose-adaptive
The decompose method after first step, ‘manual’ will remove all ‘NSUB’.
Options : manual, distance
Default : manual
- decompose-rcut
The cutoff for decompose the subsystems.
Options :
Default : 3
Unit : Angstrom
- decompose-radius
The radius of each elements for decompose the subsystems.
Options :
Default : {}
Unit : Angstrom
- decompose-rtol
The tolerance of distance for adaptive simulation.
Options :
Default : 0.0
Unit : Angstrom
mix¶
Control the charge density mixing.
- mix-scheme
Density mixing scheme, default is with driver’s own scheme.
Options : Pulay, Linear
Default : None
- mix-predtype
The preconditioning method.
Options : kerker, inverse_kerker, resta
Default : kerker
- mix-predcoef
The parameters for preconditioning.
Options :
Default : 1.0 1.0 1.0
- mix-predecut
The preconditioning energy cutoff.
Options :
Default : None
Unit : eV
- mix-maxm
Maximum of iterations used for mixing.
Options :
Default : 7
mix-coef
Options : The mixing parameter.
Default : 0.7
- mix-delay
Delay several step to mixing the density.
Options :
Default : 2
- mix-restarted
Restart the mixer after several step.
Options : True, False
Default : False
- mix-kf
Similar as predcoef, not use now.
Options :
Default : auto
opt¶
Control the charge density optimization for subsystem.
- opt-maxiter
The max steps for optimization
Options :
Default : 800
- opt-update_sleep
Subsystem will wait several steps then update.
Options :
Default : 0
- opt-update_delay
Delay several steps to evaluate the update frequency.
Options :
Default : 0
- opt-update_freq
The update frequency of subsystem.
Options :
Default : 1
- opt-method
The density optimization method.
Options : TN, LBFGS, CG-HS, CG-DY, CG-CD, CG-LS, CG-FR, CG-PR
Default : CG-HS
- opt-algorithm
The direct minimization method : Energy (EMM) or Residual (RMM).
Options : EMM, RMM
Default : EMM
- opt-vector
The scheme to deal with search direction.
Options : Orthogonalization, Scaling
Default : Orthogonalization
- opt-c1
The wolfe parameters c1
Options :
Default : 0.0001
- opt-c2
The wolfe parameters c2
Options :
Default : 0.2
- opt-maxls
The max steps for line search.
Options :
Default : 10
- opt-econv
The energy convergence for last three steps (a.u./atom).
Options :
Default : 1e-06
Unit : a.u./atom
- opt-maxfun
The max steps for function calls. For TN density optimization method its the max steps for searching direction.
Options :
Default : 50
- opt-xtol
Relative tolerance for an acceptable step.
Options :
Default : 1e-12
- opt-h0
The initial approximation for the inverse Hessian needed by LBFGS.
Options :
Default : 1
kpoints¶
Set the kpoints for subsystem.
- kpoints-method
The method for generate the kpoints.
Options :
Default : auto
- kpoints-grid
The grid of kpoints.
Options :
Default : None
- kpoints-offset
The offset of kpoints.
Options :
Default : None
- calculator
The SCF driver of subsystem.
Options : dftpy, castep, qe
Default : dftpy
- technique
The technique (OF|KS) of the driver.
Options :
Default : OF
- nprocs
The number of processors for the subsystem.
Options :
Default : 1
Note
If the minimum of all subsystems is 1, can also be used as ratio of number of processors for each subsystem.
- embed
The embedding potential.
Options : KE, XC
Default : KE XC
- embedpot
The output file or format of embedding potential. The name starts with ‘.’ represent the format.
Options :
Default : None
- basefile
The base input file for subsystem.
Options :
Default : None
- prefix
The prefix of each subsystem. If not set, it’s same as the name of subsystem.
Options :
Default : None
- task
The task to be performed for subsystem. Only works for JOB-task = Optmix.
Options : scf, optical
Default : None
MOL¶
The information of molecules.
- charge
The charge of molecules or atoms.
Options :
Default : {}
- magmom
The magnetic moment of molecules or atoms.
Options :
Default : {}