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qmcpack/nexus/lib/rmg_input.py

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import numpy as np
from generic import obj
from developer import DevBase,error
from unit_converter import convert
from pseudopotential import pp_elem_label
from structure import generate_structure
from simulation import SimulationInput
class RmgInputSettings(DevBase):
enforce_min_value = True
enforce_max_value = True
enforce_allowed = True
check_on_write = True
#end class RmgInputSettings
# raw input spec below
# taken directly from
# https://github.com/RMGDFT/rmgdft/wiki/Input-File-Options
# changes made from website values
# write_data_period
# Max value: 50 -> 500
# pseudopotential
# Key type : string -> formatted
# Hubbard_U
# Key type : string -> formatted
raw_input_spec = '''
Control options
Key name: a_length
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 0.000000e+00
Description: First lattice constant.
Key name: b_length
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 0.000000e+00
Description: Second lattice constant.
Key name: c_length
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 0.000000e+00
Description: Third lattice constant.
Key name: calculation_mode
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Quench Electrons"
Allowed: "Exx Only" "NEB Relax" "Band Structure Only" "Psi Plot" "Plot"
"Constant Pressure And Energy" "TDDFT" "Dimer Relax" "Constant
Temperature And Energy" "Constant Volume And Energy" "Relax
Structure" "Quench Electrons"
Description: Type of calculation to perform.
Key name: cell_relax
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: flag to control unit cell relaxation
Key name: coalesce_factor
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 1
Max value: 16
Default: 4
Description: Grid coalescing factor.
Key name: coalesce_states
Required: no
Key type: boolean
Expert: Yes
Experimental: No
Default: "false"
Description: Flag indicating whether or not to coalesce states.
Key name: compressed_infile
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: Flag indicating whether or not parallel restart wavefunction file
uses compressed format.
Key name: compressed_outfile
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: Flag indicating whether or not parallel output wavefunction file
uses compressed format.
Key name: description
Required: no
Key type: string
Expert: No
Experimental: No
Default: ""
Allowed:
Description: Description of the run.
Key name: energy_convergence_criterion
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 1.000000e-20
Max value: 1.000000e-07
Default: 1.000000e-10
Description: The RMS value of the estimated change in the total energy per step
where we assume self consistency has been achieved.
Key name: energy_output_units
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Hartrees"
Allowed: "Rydbergs" "Hartrees"
Description: Units to be used when writing energy values to the output file.
Hartrees or Rydbergs are available.
Key name: exx_integrals_filepath
Required: no
Key type: string
Expert: No
Experimental: No
Default: "afqmc_rmg"
Allowed:
Description: File/path for exact exchange integrals.
Key name: exx_mode
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Distributed fft"
Allowed: "Local fft" "Distributed fft"
Description: FFT mode for exact exchange computations.
Key name: exxdiv_treatment
Required: no
Key type: string
Expert: No
Experimental: No
Default: "gygi-baldereschi"
Allowed: "none" "gygi-baldereschi"
Description: Exact exchange method for handling exx divergence at G=0.
Key name: input_tddft_file
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Waves/wave_tddft.out"
Allowed:
Description: Input file/path to read wavefunctions and other binary data from
on a restart.
Key name: input_wave_function_file
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Waves/wave.out"
Allowed:
Description: Input file/path to read wavefunctions and other binary data from
on a restart.
Key name: interpolation_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "FFT"
Allowed: "FFT" "prolong" "Cubic Polynomial"
Description: Interpolation method for transferring data between the potential
grid and the wavefunction grid. Mostly for diagnostic purposes.
Key name: max_exx_steps
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 2147483647
Default: 100
Description: Maximum number of self consistent steps to perform with hybrid
functionals.
Key name: max_scf_steps
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 2147483647
Default: 500
Description: Maximum number of self consistent steps to perform. Inner loop for
hybrid functionals.
Key name: noncollinear
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: if set true, calculate noncollinear
Key name: nvme_orbitals
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag indicating whether or not orbitals should be mapped to disk.
Key name: nvme_orbitals_filepath
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Orbitals/"
Allowed:
Description: File/path for runtime disk storage of orbitals.
Key name: nvme_weights
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag indicating whether or not projector weights should be mapped
to disk.
Key name: nvme_weights_filepath
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Weights/"
Allowed:
Description: File/path for disk storage of projector weights.
Key name: nvme_work
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag indicating whether or not work arrays should be mapped to
disk.
Key name: nvme_work_filepath
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Work/"
Allowed:
Description: File/path for disk storage of workspace.
Key name: omp_threads_per_node
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 64
Default: 0
Description: Number of Open MP threads each MPI process will use. A value of 0
selects automatic setting.
Key name: output_tddft_file
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Waves/wave_tddft.out"
Allowed:
Description: Output file/path to store wavefunctions and other binary data.
Key name: output_wave_function_file
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Waves/wave.out"
Allowed:
Description: Output file/path to store wavefunctions and other binary data.
Key name: pseudo_dir
Required: no
Key type: string
Expert: No
Experimental: No
Default: "."
Allowed:
Description: Directory where pseudopotentials are stored.
Key name: qfunction_filepath
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Qfunctions/"
Allowed:
Description: File/path for runtime disk storage of qfunctions.
Key name: read_serial_restart
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Directs RMG to read from serial restart files. Normally used when
changing the sprocessor topology used during a restart run
Key name: rms_convergence_criterion
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 1.000000e-03
Default: 1.000000e-07
Description: The RMS value of the change in the total potential from step to
step where we assume self consistency has been achieved.
Key name: spinorbit
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: if set true, calculate with spinorbit coupling
Key name: start_mode
Required: no
Key type: string
Expert: No
Experimental: No
Default: "LCAO Start"
Allowed: "Modified LCAO Start" "Restart TDDFT" "Start TDDFT" "Gaussian
Start" "FIREBALL Start" "LCAO Start" "Restart From File" "Random
Start"
Description: Type of run.
Key name: stress
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: flag to control stress cacluation
Key name: stress_convergence_criterion
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 50.000000
Default: 0.500000
Description: The stress criteria
Key name: tddft_steps
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 2147483647
Default: 2000
Description: Maximum number of tddft steps to perform.
Key name: time_reversal
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: if false, no k -> -k symmetry
Key name: vdw_corr
Required: no
Key type: string
Expert: No
Experimental: No
Default: "None"
Allowed: "DFT-D3" "DFT-D2" "Grimme-D2" "None"
Description: Type of vdw correction
Key name: vdwdf_kernel_filepath
Required: no
Key type: string
Expert: No
Experimental: No
Default: "vdW_kernel_table"
Allowed:
Description: File/path for vdW_kernel_table data.
Key name: wannier90
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: set up informations for wannier90 interface
Key name: wannier90_scdm_mu
Required: no
Key type: double
Expert: No
Experimental: No
Min value: -unlimited
Max value: unlimited
Default: 0.000000e+00
Description: when wannier90 is used to build wannier functions, the energy
window parameter
Key name: write_data_period
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 5
Max value: 500
Default: 5
Description: How often to write checkpoint files during the initial quench in
units of SCF steps. During structural relaxations of molecular
dynamics checkpoints are written each ionic step.
Key name: write_eigvals_period
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 100
Default: 5
Description: How often to output eigenvalues in units of scf steps.
Key name: write_pseudopotential_plots
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag to indicate whether or not to write pseudopotential plots.
Key name: write_qmcpack_restart
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: If true then a QMCPACK restart file is written as well as a serial
restart file.
Key name: write_qmcpack_restart_localized
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: If true then a QMCPACK restart file for localized orbitals
Key name: write_serial_restart
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: RMG normally writes parallel restart files. These require that
restarts have the same processor topology. If write_serial_restart
= "true" then RMG will also write a serial restart file that can
be used with a different processor topology
Cell parameter options
Key name: atomic_coordinate_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Absolute"
Allowed: "Absolute" "Cell Relative"
Description: Flag indicated whether or not atomic coordinates are absolute or
cell relative.
Key name: bravais_lattice_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Orthorhombic Primitive"
Allowed: "Tetragonal Primitive" "Cubic Body Centered" "Orthorhombic
Primitive" "Cubic Face Centered" "Hexagonal Primitive" "Cubic
Primitive" "None"
Description: Bravais Lattice Type.
Key name: cell_movable
Required: no
Key type: integer array
Expert: No
Experimental: No
Default: "0 0 0 0 0 0 0 0 0 "
Description: 9 numbers to control cell relaxation
Key name: crds_units
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Bohr"
Allowed: "Angstrom" "Bohr"
Description: Units for the atomic coordinates.
Key name: grid_spacing
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 0.350000
Description: Approximate grid spacing (bohr).
Key name: kpoint_is_shift
Required: no
Key type: integer array
Expert: No
Experimental: No
Default: "0 0 0 "
Description: Three-D layout of the kpoint shift.
Key name: kpoint_mesh
Required: no
Key type: integer array
Expert: No
Experimental: No
Default: "1 1 1 "
Description: Three-D layout of the kpoint mesh.
Key name: lattice_units
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Bohr"
Allowed: "Angstrom" "Alat" "Bohr"
Description: Units for the lattice vectors
Key name: lattice_vector
Required: no
Key type: double array
Expert: No
Experimental: No
Default: "Not done yet"
Description: Lattice vectors, a0, a1, a2
Key name: potential_grid_refinement
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 4
Default: 0
Description: Ratio of the potential grid density to the wavefunction grid
density. For example if the wavefunction grid is (72,72,72) and
potential_grid_refinement = "2" then the potential grid would be
(144,144,144). The default value is 2 but it may sometimes be
beneficial to adjust this. (For USPP the minimum value is also 2
and it cannot be set lower. NCPP can be set to 1).
Key name: processor_grid
Required: no
Key type: integer array
Expert: No
Experimental: No
Default: "1 1 1 "
Description: Three-D (x,y,z) layout of the MPI processes.
Key name: wavefunction_grid
Required: no
Key type: integer array
Expert: No
Experimental: No
Default: "1 1 1 "
Description: Three-D (x,y,z) dimensions of the grid the wavefunctions are
defined on.
Pseudopotential related options
Key name: atomic_orbital_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "delocalized"
Allowed: "delocalized" "localized"
Description: Atomic Orbital Type. Choices are localized and delocalized.
Key name: energy_cutoff_parameter
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.600000
Max value: 1.000000
Default: 0.800000
Description:
Key name: filter_dpot
Required: no
Key type: boolean
Expert: Yes
Experimental: No
Default: "false"
Description: Flag indicating whether or not to filter density dependent
potentials.
Key name: filter_factor
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.060000
Max value: 1.000000
Default: 0.250000
Description: Filtering factor.
Key name: localize_localpp
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: The local potential associated with a particular ion also decays
rapidly in real-space with increasing r. As with beta projectors
truncating the real-space representation for large cells can lead
to significant computational savings with a small loss of accuracy
but it should be set to false for small cells.
Key name: localize_projectors
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: The Beta function projectors for a particular ion decay rapidly in
real-space with increasing r. For large cells truncating the
real-space representation of the projector can lead to significant
computational savings with a small loss of accuracy. For smaller
cells the computational cost is the same for localized or
delocalized projectors so it is better to set localize_projectors
to false.
Key name: max_nlradius
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 2.000000
Max value: 10000.000000
Default: 10000.000000
Description: maximum radius for non-local projectors
Key name: max_qradius
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 2.000000
Max value: 10000.000000
Default: 10000.000000
Description: maximum radius for qfunc in ultra-pseudopotential
Key name: min_nlradius
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 1.000000
Max value: 10000.000000
Default: 2.000000
Description: minimum radius for non-local projectors
Key name: min_qradius
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 1.000000
Max value: 10000.000000
Default: 2.000000
Description: minimum radius for qfunc in ultra-pseudopotential
Key name: projector_expansion_factor
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.500000
Max value: 3.000000
Default: 1.000000
Description: When using localized projectors the radius can be adjusted with
this parameter.
Key name: pseudopotential
Required: no
Key type: formatted
Expert: No
Experimental: No
Default: ""
Allowed:
Description: External pseudopotentials may be specfied with this input key. The
format uses the atomic symbol followed by the pseudopotential file
name. pseudopotential = "Ni Ni.UPF O O.UPF"
Kohn Sham solver options
Key name: davidson_max_steps
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 5
Max value: 20
Default: 8
Description: Maximum number of iterations for davidson diagonalization.
Key name: davidson_multiplier
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 6
Default: 0
Description: The davidson solver expands the eigenspace with the maximum
expansion factor being set by the value of davidson_multiplier.
Larger values often lead to faster convergence but because the
computational cost of the davidson diagonalization step scales as
the cube of the number of eigenvectors the optimal value based on
the fastest time to solution depends on the number of orbitals. If
not specified explicitly or set to 0 RMG uses the following
algorithm to set the value.
Number of orbitals <= 600 davidson_multiplier= "4"
600 < Number of orbitals <= 900 davidson_multiplier = "3"
Number of orbitals > 900 davidson_multiplier = "2"
For very large problems the N^3 scaling makes even a factor of 2
prohibitively costly and the multigrid solver is a better choice.
Key name: kohn_sham_coarse_time_step
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.000000e+00
Max value: 1.200000
Default: 1.000000
Description: Time step to use in the kohn-sham multigrid solver on the coarse
levels.
Key name: kohn_sham_fd_order
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 6
Max value: 10
Default: 8
Description: RMG uses finite differencing to represent the kinetic energy
operator and the accuracy of the representation is controllable by
the kohn_sham_fd_order parameter. The default is 8 and is fine for
most purposes but higher accuracy is obtainable with 10th order at
the cost of some additional computational expense.
Key name: kohn_sham_mg_levels
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: -1
Max value: 6
Default: -1
Description: Number of multigrid levels to use in the kohn-sham multigrid
preconditioner.
Key name: kohn_sham_mg_timestep
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.000000e+00
Max value: 2.000000
Default: 0.666667
Description: timestep for multigrid correction.
Key name: kohn_sham_mucycles
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 6
Default: 2
Description: Number of mu (also known as W) cycles to use in the kohn-sham
multigrid preconditioner.
Key name: kohn_sham_post_smoothing
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 1
Max value: 5
Default: 2
Description: Number of global grid post-smoothing steps to perform after a
multigrid preconditioner iteration.
Key name: kohn_sham_pre_smoothing
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 1
Max value: 5
Default: 2
Description: Number of global grid pre-smoothing steps to perform before a
multigrid preconditioner iteration.
Key name: kohn_sham_solver
Required: no
Key type: string
Expert: No
Experimental: No
Default: "davidson"
Allowed: "davidson" "multigrid"
Description: RMG supports a pure multigrid Kohn-Sham solver as well as a
multigrid preconditioned davidson solver. The davidson solver is
usually better for smaller problems with the pure multigrid solver
often being a better choice for very large problems.
Key name: kohn_sham_time_step
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.000000e+00
Max value: 2.000000
Default: 0.660000
Description: Smoothing timestep to use on the fine grid in the the kohn-sham
multigrid preconditioner.
Key name: unoccupied_tol_factor
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 1.000000
Max value: 100000.000000
Default: 1000.000000
Description: When using the Davidson Kohn-Sham solver unoccupied states are
converged to a less stringent tolerance than occupied orbitals
with the ratio set by this parameter.
Exchange correlation options
Key name: exchange_correlation_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "AUTO_XC"
Allowed: "hartree-fock" "vdw-df-c09" "sla+pw+pbe+vdw1" "VDW-DF" "vdw-df"
"gaupbe" "B3LYP" "hse" "mgga tb09" "AUTO_XC" "m06l" "VDW-DF-CX"
"tpss" "ev93" "optbk88" "sogga" "wc" "HSE" "HCTH" "hcth" "Q2D"
"q2d" "PBESOL" "tb09" "b86bpbe" "PW86PBE" "PBE0" "MGGA TB09"
"pw86pbe" "REVPBE" "pbe" "revpbe" "GGA PBE" "BLYP" "pbe0" "pbesol"
"blyp" "PBE" "GGA XP CP" "pw91" "GGA XB CP" "TB09" "optb86b"
"olyp" "BP" "GGA BLYP" "bp" "b3lyp" "LDA" "vdw-df-cx" "PW91" "PZ"
"pz"
Description: Most pseudopotentials specify the exchange correlation type they
were generated with and the default value of AUTO_XC means that
the type specified in the pseudopotial is what RMG will use. That
can be overridden by specifying a value here.
Key name: exx_convergence_criterion
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 1.000000e-12
Max value: 1.000000e-06
Default: 1.000000e-09
Description: Convergence criterion for the EXX delta from step to step where we
assume EXX consistency has been achieved.
Key name: exx_fraction
Required: no
Key type: double
Expert: No
Experimental: No
Min value: -1.000000
Max value: 1.000000
Default: -1.000000
Description: when hybrid functional is used, the fraction of Exx
Key name: vexx_fft_threshold
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 1.000000e-14
Max value: 0.100000
Default: 1.000000e-14
Description: The value for the EXX delta where we switch from single to double
precision ffts. Single precision ffts are generally accurate
enough.
Key name: x_gamma_extrapolation
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: if set true, use exx extrapolation to gamma
Orbital occupation options
Key name: MP_order
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 5
Default: 2
Description: order of Methefessel Paxton occupation.
Key name: dos_broading
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 1.000000
Default: 0.100000
Description: For DOS with Gaussian broading method
Key name: dos_method
Required: no
Key type: string
Expert: No
Experimental: No
Default: "tetrahedra"
Allowed: "Gaussian" "tetrahedra"
Description: tetrahedra or gauss smearing method for DOS calculation
Key name: occupation_electron_temperature_eV
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 2.000000
Default: 0.040000
Description: Target electron temperature when not using fixed occupations.
Key name: occupation_number_mixing
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 1.000000
Default: 1.000000
Description: Mixing parameter for orbital occupations when not using fixed
occupations.
Key name: occupations_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Fermi Dirac"
Allowed: "Error Function" "Gaussian" "Fermi Dirac" "MethfesselPaxton" "Cold
Smearing" "Fixed"
Description: RMG supports several different ways of specifying orbital
occupations. For a spin polarized system one may specify the
occupations for up and down separately. In the case of a non-zero
electronic temperature these will be adjusted as the calculation
proceeds based on this setting.
Key name: states_count_and_occupation
Required: no
Key type: string
Expert: No
Experimental: No
Default: ""
Allowed:
Description: Occupation string for states. Format for a system with 240
electrons and 20 unoccupied states would be. "120 2.0 20 0.0"
Key name: states_count_and_occupation_spin_down
Required: no
Key type: string
Expert: No
Experimental: No
Default: ""
Allowed:
Description: Occupation string for spin down states. Format is the same as for
states_count_and_occupation. Total number of states must match
spin up occupation string.
Key name: states_count_and_occupation_spin_up
Required: no
Key type: string
Expert: No
Experimental: No
Default: ""
Allowed:
Description: Occupation string for spin up states. Format is the same as for
states_count_and_occupation. Total number of states must match
spin down occupation string.
Key name: unoccupied_states_per_kpoint
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 2147483647
Default: 10
Description: The number of unoccupied orbitals. A value that is 15-20% of the
number of occupied orbitals generally works well.
Charge density mixing options
Key name: charge_broyden_order
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 10
Default: 5
Description: Number of previous steps to use when Broyden mixing is used to
update the charge density.
Key name: charge_broyden_scale
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 1.000000
Default: 0.500000
Description:
Key name: charge_density_mixing
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 1.000000
Default: 0.500000
Description: Proportion of the current charge density to replace with the new
density after each scf step when linear mixing is used.
Key name: charge_mixing_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Pulay"
Allowed: "Broyden" "Pulay" "Linear"
Description: RMG supports Broyden, Pulay and Linear mixing When the davidson
Kohn-Sham solver is selected Broyden or Pulay are preferred. For
the multigrid solver Linear with potential acceleration is often
(but not always) the best choice.
Key name: charge_pulay_Gspace
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: if set true, charge density mixing the residual in G space
Key name: charge_pulay_order
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 10
Default: 5
Description: Number of previous steps to use when Pulay mixing is used to
update the charge density.
Key name: charge_pulay_refresh
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 2147483647
Default: 100
Description:
Key name: charge_pulay_scale
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 1.000000
Default: 0.500000
Description:
Key name: potential_acceleration_constant_step
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 4.000000
Default: 0.000000e+00
Description: When set to a non-zero value this parameter causes RMG to perform
a band by band update of the self-consistent potential during the
course of an SCF step when the multigrid kohn_sham_solver is
chosen. This means that updates to the lower energy orbitals are
incorporated into the SCF potential seen by the higher energy
orbitals as soon as they are computed. This can lead to faster
convergence and better stability for many systems. The option
should only be used with Linear mixing. Even when the davidson
solver is chosen this parameter may be used since the first few
steps with davidson usually uses the multigrid solver.
Relaxation and Molecular dynamics options
Key name: dynamic_time_counter
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 0
Default: 0
Description:
Key name: dynamic_time_delay
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 5
Max value: 5
Default: 5
Description:
Key name: force_grad_order
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 12
Default: 8
Description: Atomic forces may be computed to varying degrees of accuracy
depending on the requirements of a specific problem. A value of 0
implies highest accuracy which is obtained by using FFTs in place
of finite differencing.
Key name: ionic_time_step
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 50.000000
Description: Ionic time step for use in molecular dynamics and structure
optimizations.
Key name: ionic_time_step_decrease
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 1.000000
Default: 0.500000
Description: Factor by which ionic timestep is decreased when dynamic timesteps
are enabled.
Key name: ionic_time_step_increase
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 1.000000
Max value: 3.000000
Default: 1.100000
Description: Factor by which ionic timestep is increased when dynamic timesteps
are enabled.
Key name: max_ionic_time_step
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 150.000000
Default: 150.000000
Description: Maximum ionic time step to use for molecular dynamics or
structural optimizations.
Key name: max_md_steps
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 2147483647
Default: 100
Description: Maximum number of molecular dynamics steps to perform.
Key name: md_integration_order
Required: no
Key type: string
Expert: No
Experimental: No
Default: "5th Beeman-Velocity Verlet"
Allowed: "5th Beeman-Velocity Verlet" "3rd Beeman-Velocity Verlet" "2nd
Velocity Verlet"
Description: Integration order for molecular dynamics.
Key name: md_nose_oscillation_frequency_THz
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 15.590000
Description:
Key name: md_number_of_nose_thermostats
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 5
Max value: 5
Default: 5
Description: Number of Nose thermostats to use during Constant Volume and
Temperature MD.
Key name: md_randomize_velocity
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: The initial ionic velocities for a molecular dyanamics run are
randomly initialized to the target temperature.
Key name: md_temperature
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 300.000000
Description: Target MD Temperature.
Key name: md_temperature_control
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Nose Hoover Chains"
Allowed: "Anderson Rescaling" "Nose Hoover Chains"
Description: Type of temperature control method to use in molecular dynamics.
Key name: relax_dynamic_timestep
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag indicating whether or not to use dynamic timesteps in
relaxation mode.
Key name: relax_mass
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Atomic"
Allowed: "Equal" "Atomic"
Description: Mass to use for structural relaxation, either atomic masses, or
the mass of carbon for all atoms.
Key name: relax_max_force
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 2.500000e-03
Description: Force value at which an ionic relaxation is considered to be
converged.
Key name: relax_method
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Fast Relax"
Allowed: "LBFGS" "MD Min" "Quick Min" "FIRE" "Fast Relax"
Description: Type of relaxation method to use for structural optimizations.
Key name: renormalize_forces
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: Flag indicating whether or not to renormalize forces.
Key name: tddft_time_step
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 0.200000
Description: TDDFT time step for use in TDDFT mode
Diagonalization options
Key name: extra_random_lcao_states
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 2147483647
Default: 0
Description: LCAO (Linear Combination of Atomic Orbitals) is the default
startup method for RMG. The atomic orbitals are obtained from the
pseudpotentials but in some cases better convergence may be
obtained by adding extra random wavefunctions in addition to the
atomic orbitals.
Key name: folded_spectrum
Required: no
Key type: boolean
Expert: Yes
Experimental: No
Default: "false"
Description: When the number of eigenvectors is large using folded_spectrum is
substantially faster than standard diagonalization. It also tends
to converge better for metallic systems. It works with the
multigrid kohn_sham_solver but not the davidson solver.
Key name: folded_spectrum_iterations
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 0
Max value: 20
Default: 2
Description: Number of folded spectrum iterations to perform.
Key name: folded_spectrum_width
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.100000
Max value: 1.000000
Default: 0.300000
Description: Submatrix width to use as a fraction of the full spectrum. The
folded spectrum width ranges from 0.10 to 1.0. For insulators and
semiconductors a value of 0.3 is appropriate. For metals values
between 0.15 to 0.2 tend to be better. The default value is 0.3
Key name: initial_diagonalization
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: Perform initial subspace diagonalization.
Key name: period_of_diagonalization
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 2147483647
Default: 1
Description: Diagonalization period (per scf step). Mainly for debugging and
should not be changed for production.
Key name: scalapack_block_factor
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 4
Max value: 512
Default: 32
Description: Block size to use with scalapack. Optimal value is dependent on
matrix size and system hardware.
Key name: subdiag_driver
Required: no
Key type: string
Expert: No
Experimental: No
Default: "auto"
Allowed: "elpa" "cusolver" "auto" "scalapack" "magma" "lapack"
Description: Driver type used for subspace diagonalization of the eigenvectors.
Performance related options
Key name: mpi_queue_mode
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: Use mpi queue mode.
Key name: non_local_block_size
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 64
Max value: 40000
Default: 512
Description: Block size to use when applying the non-local and S operators.
Key name: preconditioner_threshold
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 1.000000e-09
Max value: 0.100000
Default: 0.100000
Description: The RMS value of the change in the total potential where we switch
the preconditioner from single to double precision.
Key name: require_huge_pages
Required: no
Key type: boolean
Expert: No
Experimental: Yes
Default: "false"
Description: If set RMG assumes that sufficient huge pages are available. Bad
things may happen if this is not true.
Key name: spin_manager_thread
Required: no
Key type: boolean
Expert: Yes
Experimental: No
Default: "true"
Description: When mpi_queue_mode is enabled the manager thread spins instead of
sleeping.
Key name: spin_worker_threads
Required: no
Key type: boolean
Expert: Yes
Experimental: No
Default: "true"
Description: When mpi_queue_mode is enabled the worker threads spin instead of
sleeping.
Key name: state_block_size
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 1
Max value: 2147483647
Default: 64
Description: state_block used in nlforce.
Key name: use_alt_zgemm
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag indicating whether or not to use alternate zgemm
implementation.
Key name: use_async_allreduce
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: Use asynchronous allreduce if available.
Key name: use_hwloc
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Use internal hwloc setup if available. If both this and use_numa
are true hwloc takes precedence.
Key name: use_numa
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: Use internal numa setup if available.
LDAU options
Key name: Hubbard_U
Required: no
Key type: formatted
Expert: No
Experimental: No
Default: ""
Allowed:
Description: Hubbard U parameter for each atomic species using the format
Hubbard_U="Ni 6.5"
Key name: ldaU_mode
Required: no
Key type: string
Expert: No
Experimental: No
Default: "None"
Allowed: "Simple" "None"
Description: Type of lda+u implementation.
Key name: ldaU_radius
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 1.000000
Max value: 12.000000
Default: 9.000000
Description: Max radius of atomic orbitals to be used in LDA+U projectors.
Poisson solver options
Key name: hartree_max_sweeps
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 5
Max value: 100
Default: 10
Description: Maximum number of hartree iterations to perform per scf step.
Key name: hartree_min_sweeps
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 5
Default: 5
Description: Minimum number of hartree iterations to perform per scf step.
Key name: hartree_rms_ratio
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 1000.000000
Max value: unlimited
Default: 100000.000000
Description: Ratio between target RMS for get_vh and RMS total potential.
Key name: poisson_coarse_time_step
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.400000
Max value: 1.000000
Default: 0.800000
Description: Time step to use in the poisson multigrid solver on the coarse
levels.
Key name: poisson_coarsest_steps
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 10
Max value: 100
Default: 25
Description: Number of smoothing steps to use on the coarsest level in the
hartree multigrid solver.
Key name: poisson_finest_time_step
Required: no
Key type: double
Expert: Yes
Experimental: No
Min value: 0.400000
Max value: 1.000000
Default: 1.000000
Description: Time step to use in the poisson multigrid solver on the finest
level.
Key name: poisson_mucycles
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 1
Max value: 4
Default: 3
Description: Number of mu (also known as W) cycles to use in the hartree
multigrid solver.
Key name: poisson_post_smoothing
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 1
Max value: 6
Default: 1
Description: Number of global hartree grid post-smoothing steps to perform
after a multigrid iteration.
Key name: poisson_pre_smoothing
Required: no
Key type: integer
Expert: Yes
Experimental: No
Min value: 1
Max value: 6
Default: 2
Description: Number of global hartree grid pre-smoothing steps to perform
before a multigrid iteration.
Key name: poisson_solver
Required: no
Key type: string
Expert: No
Experimental: No
Default: "pfft"
Allowed: "pfft" "multigrid"
Description: poisson solver.
Testing options
Key name: test_energy
Required: no
Key type: double
Expert: No
Experimental: No
Min value: -1000000000.000000
Max value: 1000000000.000000
Default: nan
Description: Expected final energy for testing.
Key name: test_energy_tolerance
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 1.000000e-08
Max value: 1.000000e-04
Default: 1.000000e-07
Description: Test final energy tolerance.
Miscellaneous options
Key name: E_POINTS
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 201
Max value: 201
Default: 201
Description:
Key name: Emax
Required: no
Key type: double
Expert: No
Experimental: No
Min value: -100.000000
Max value: 100.000000
Default: 0.000000e+00
Description:
Key name: Emin
Required: no
Key type: double
Expert: No
Experimental: No
Min value: -100.000000
Max value: 100.000000
Default: -6.000000
Description:
Key name: ExxCholMax
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 64
Default: 8
Description: maximum number of Exx integral cholesky vectors
Key name: ExxIntCholosky
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: if set true, Exx integrals are Cholesky factorized to 3-index
Key name: alt_laplacian
Required: no
Key type: boolean
Expert: Yes
Experimental: No
Default: "true"
Description: Flag indicating whether or not to use alternate laplacian weights
for some operators.
Key name: boundary_condition_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Periodic"
Allowed: "Periodic"
Description: Boundary condition type Only periodic is currently implemented.
Key name: charge_analysis
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Voronoi"
Allowed: "Voronoi" "None"
Description: Type of charge analysis to use. Only Voronoi deformation density
is currently available.
Key name: charge_analysis_period
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 500
Default: 0
Description: How often to perform and write out charge analysis.
Key name: cube_pot
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: if set true, total potential is printed out in cube format
Key name: cube_rho
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: if set true, charge density is printed out in cube format
Key name: cube_states_list
Required: no
Key type: string
Expert: No
Experimental: No
Default: ""
Allowed:
Description: plot the states listed here
Key name: cube_vh
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: if set true, hatree potential is printed out in cube format
Key name: dftd3_version
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 2
Max value: 6
Default: 3
Description: Grimme's DFT-D3 versions,
Key name: dipole_correction
Required: no
Key type: integer array
Expert: No
Experimental: No
Default: "0 0 0 "
Description: (1,1,1) for molecule, dipole correction in all directions.
Key name: dipole_moment
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Turns on calculation of dipole moment for the entire cell.
Key name: ecutrho
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 10000.000000
Default: 0.000000e+00
Description: ecut for rho in unit of Ry.
Key name: ecutwfc
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: 10000.000000
Default: 0.000000e+00
Description: ecut for wavefunctions in unit of Ry.
Key name: electric_field_magnitude
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 0.000000e+00
Description: Magnitude of external electric field.
Key name: electric_field_vector
Required: no
Key type: double array
Expert: No
Experimental: No
Default: "Not done yet"
Description: Components of the electric field.
Key name: equal_initial_density
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Specifies whether to set initial up and down density to be equal.
Key name: exx_int_flag
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: if set true, calculate the exact exchange integrals
Key name: fast_density
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: Use a faster but less accurate method to generate the charge
density from the electronic wavefunctions. As the cutoff
(grid-density) increases this method improves in accuracy. This
option should be set to false if you receive warnings about
negative charge densities after interpolation.
Key name: fd_allocation_limit
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1024
Max value: 262144
Default: 65536
Description: Allocation sizes in finite difference routines less than this
value are stack rather than heap based.
Key name: frac_symmetry
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: For supercell calculation, one can disable the fractional
translation symmetry
Key name: freeze_occupied
Required: no
Key type: boolean
Expert: No
Experimental: Yes
Default: "false"
Description: Flag indicating whether or not to freeze the density and occupied
orbitals after a restart.
Key name: gw_residual_convergence_criterion
Required: no
Key type: double
Expert: No
Experimental: Yes
Min value: 1.000000e-14
Max value: 4.000000e-04
Default: 1.000000e-06
Description: The max value of the residual for unoccupied orbitals when
performing a GW calculation.
Key name: gw_residual_fraction
Required: no
Key type: double
Expert: No
Experimental: Yes
Min value: 0.000000e+00
Max value: 1.000000
Default: 0.900000
Description: The residual value specified by gw_residual_convergence_criterion
is applied to this fraction of the total spectrum.
Key name: kohn_sham_ke_fft
Required: no
Key type: boolean
Expert: Yes
Experimental: No
Default: "false"
Description: Special purpose flag which will force use of an FFT for the
kinetic energy operator.
Key name: kpoint_distribution
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: -2147483647
Max value: 2147483647
Default: -1
Description:
Key name: laplacian_autocoeff
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: if set to true, we use LaplacianCoeff.cpp to generate coeff
Key name: laplacian_offdiag
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: if set to true, we use LaplacianCoeff.cpp to generate coeff
Key name: lcao_use_empty_orbitals
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Some pseudopotentials contain unbound atomic orbitals and this
flag indicates whether or not they should be used for LCAO starts.
Key name: md_steps_offset
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 0
Default: 0
Description:
Key name: num_wanniers
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 2147483647
Default: 0
Description: number of wannier functions to be used in wannier90
Key name: output_rho_xsf
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Generate xsf format for electronic density.
Key name: poisson_mg_levels
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: -1
Max value: 6
Default: -1
Description: Number of multigrid levels to use in the hartree multigrid solver.
Key name: restart_tddft
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: restart TDDFT
Key name: rmg2bgw
Required: no
Key type: boolean
Expert: No
Experimental: Yes
Default: "false"
Description: Write wavefunction in G-space to BerkeleyGW WFN file.
Key name: rmg_threads_per_node
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 64
Default: 0
Description: Number of Multigrid/Davidson threads each MPI process will use. A
value of 0 means set automatically.
Key name: scf_steps_offset
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 0
Default: 0
Description:
Key name: sqrt_interpolation
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag indicating whether or not to use square root technique for
density interpolation.
Key name: system_charge
Required: no
Key type: double
Expert: No
Experimental: No
Min value: -unlimited
Max value: unlimited
Default: 0.000000e+00
Description: Number of excess holes in the system (useful for doped systems).
Example, 2 means system is missing two electrons
Key name: tddft_mode
Required: no
Key type: string
Expert: No
Experimental: No
Default: "electric field"
Allowed: "point charge" "electric field"
Description: TDDFT mode
Key name: tddft_qgau
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 1.000000
Description: Gaussian parameter for point charge to Gaussian charge
Key name: tddft_qpos
Required: no
Key type: double array
Expert: No
Experimental: No
Default: "Not done yet"
Description: cartesian coordinate of the point charge for tddft
Key name: total_scf_steps_offset
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 0
Max value: 0
Default: 0
Description:
Key name: use_cpdgemr2d
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: if set to true, we use Cpdgemr2d to change matrix distribution
Key name: use_symmetry
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "true"
Description: For non-gamma point, always true, for gamma point, optional
Key name: vdwdf_grid_type
Required: no
Key type: string
Expert: No
Experimental: No
Default: "Coarse"
Allowed: "Fine" "Coarse"
Description: Type of grid to use when computing vdw-df correlation.
Key name: verbose
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag for writing out extra information
Key name: vxc_diag_nmax
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 10000
Default: 1
Description: Maximum band index for diagonal Vxc matrix elements.
Key name: vxc_diag_nmin
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: 1
Max value: 10000
Default: 1
Description: Minimum band index for diagonal Vxc matrix elements.
Key name: wannier90_scdm
Required: no
Key type: integer
Expert: No
Experimental: No
Min value: -2147483647
Max value: 2
Default: 0
Description: use scdm method to set the trial wannier functions
Key name: wannier90_scdm_sigma
Required: no
Key type: double
Expert: No
Experimental: No
Min value: 0.000000e+00
Max value: unlimited
Default: 1.000000
Description: when wannier90 is used to build wannier functions, the energy
window parameter
Key name: write_orbital_overlaps
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: If true the orbital overlap matrix from successive MD steps is
written.
Key name: write_pdos
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Description: Flag to write partial density of states.
Key name: z_average_output_mode
Required: no
Key type: string
Expert: No
Experimental: No
Default: "None"
Allowed: "potential and charge density" "wave functions" "None"
Description: z_average_output_mode.
'''
undocumented_options = '''
Undocumented options
Key name: use_bessel_projectors
Required: no
Key type: boolean
Expert: No
Experimental: No
Default: "false"
Key name: kpoints
Required: no
Key type: formatted
Expert: No
Experimental: No
Key name: kpoints_bandstructure
Required: no
Key type: formatted
Expert: No
Experimental: No
Key name: atoms
Required: no
Key type: formatted
Expert: No
Experimental: No
'''
deprecated_options = '''
Deprecated options
Key name: alpha
Required: no
Key type: double
Expert: No
Experimental: No
Key name: beta
Required: no
Key type: double
Expert: No
Experimental: No
Key name: gamma
Required: no
Key type: double
Expert: No
Experimental: No
Key name: length_units
Required: no
Key type: string
Allowed: "Angstrom" "Bohr"
Expert: No
Experimental: No
Key name: projector_mixing
Required: no
Key type: double
Expert: No
Experimental: No
'''
raw_input_spec += undocumented_options
raw_input_spec += deprecated_options
def read_string(v):
return v.strip().strip('"')
#end def read_string
truefalse_read = {'"true"':True,'"false"':False,'true':True,'false':False}
def read_boolean(v):
return truefalse_read[v.lower()]
#end def read_boolean
def read_integer(v):
return int(v.strip().strip('"'))
#end def read_integer
def read_double(v):
return float(v.strip().strip('"'))
#end def read_double
def read_integer_array(v):
return np.array(v.strip().strip('"').split(),dtype=int)
#end def read_integer_array
def read_double_array(v):
return np.array(v.strip().strip('"').split(),dtype=float)
#end def read_double_array
def write_string(v):
return '"'+v.strip()+'"'
#end def write_string
truefalse_write = {True:'"true"',False:'"false"'}
def write_boolean(v):
return truefalse_write[v]
#end def write_boolean
def write_integer(v):
return '"{}"'.format(v)
#end def write_integer
double_fmt = '{: 16.8f}'
double_fmt_exp = '{: 16.8e}'
def write_double(v):
vs = double_fmt.format(v).strip()
if abs((float(vs)-v))>1e-6*abs(v):
vs = double_fmt_exp.format(v).strip()
#end if
return '"'+vs+'"'
#end def write_double
def write_integer_array(v):
s = '"'
if isinstance(v,np.ndarray):
v = v.flatten()
#end if
for i in v:
s+='{} '.format(i)
#end for
return s[:-1]+'"'
#end def write_integer_array
def write_double_array(v):
s = '"'
if isinstance(v,np.ndarray):
v = v.flatten()
#end if
for d in v:
s+=double_fmt.format(d).strip()+' '
#end for
return s[:-1]+'"'
#end def write_double_array
rmg_value_types = obj({
'string' : (str , np.string_),
'boolean' : (bool , np.bool_ ),
'integer' : (int , np.int_ ),
'double' : (float, np.float_ ),
'integer array' : (tuple,list,np.ndarray),
'double array' : (tuple,list,np.ndarray),
})
read_functions = obj({
'string' : read_string,
'boolean' : read_boolean,
'integer' : read_integer,
'double' : read_double,
'integer array' : read_integer_array,
'double array' : read_double_array,
})
write_functions = obj({
'string' : write_string,
'boolean' : write_boolean,
'integer' : write_integer,
'double' : write_double,
'integer array' : write_integer_array,
'double array' : write_double_array,
})
rmg_array_dtypes = obj({
'integer array' : int,
'double array' : float,
})
class RmgKeyword(DevBase):
def __init__(self,key_spec,section_name):
self.key_name = None
self.key_type = None
self.default = None
self.allowed = None
self.min_value = None
self.max_value = None
self.required = None
self.expert = None
self.experimental = None
self.description = None
self.value_type = None
self.array_dtype = None
self.section_name = section_name
spec = obj()
name = None
value = None
for line in key_spec.strip().splitlines():
if ':' in line:
if name is not None:
spec[name] = value
#end if
name,value = line.split(':',1)
name = name.strip().lower().replace(' ','_')
value = value.strip()
else:
value += ' '+line.strip()
#end if
#end for
if name is not None:
spec[name] = value
else:
self.error('Invalid keyword specification text received.\nNo field names are present.\nInvalid spec: {}'.format(key_spec))
#end if
for name,value in spec.items():
if name not in self:
kname = 'unknown'
if 'key_name' in spec:
kname = spec.key_name
#end if
self.error('Unrecognized keyword specification field.\nKeyword: {}\nField name: {}\nField value: {}'.format(kname,name,value))
#end if
self[name] = value
#end for
if self.key_name is None:
self.error('Invalid keyword specification received.\nKey name must be defined.\nInvalid spec: {}'.format(key_spec))
#end if
if self.key_type is None:
self.error('Invalid keyword specification received.\nKey type must be defined.\nInvalid spec: {}'.format(key_spec))
#end if
if self.key_type=='formatted':
return
#end if
if self.key_type not in read_functions:
self.error('Read function has not been implemented for key type "{}".'.format(self.key_type))
#end if
if self.key_type not in write_functions:
self.error('Write function has not been implemented for key type "{}".'.format(self.key_type))
#end if
read_function = read_functions[self.key_type]
yesno = dict(yes=True,no=False)
if self.required is None:
self.required = False
else:
self.required = yesno[self.required.lower()]
#end if
if self.expert is None:
self.expert = False
else:
self.expert = yesno[self.expert.lower()]
#end if
if self.experimental is None:
self.experimental = False
else:
self.experimental = yesno[self.experimental.lower()]
#end if
if self.min_value is not None:
if 'unlimited' in self.min_value:
self.min_value = None
else:
self.min_value = self.read(self.min_value)
#end if
#end if
if self.max_value is not None:
if 'unlimited' in self.max_value:
self.max_value = None
else:
self.max_value = self.read(self.max_value)
#end if
#end if
if self.default is not None and self.default!='"Not done yet"':
self.default = self.read(self.default)
#end if
if self.allowed is not None:
tokens = []
i1 = -1
i2 = -1
for i,c in enumerate(self.allowed):
if c=='"':
if i1==-1:
i1 = i
else:
i2 = i
tokens.append(self.read(self.allowed[i1:i2+1]))
i1 = -1
i2 = -1
#end if
#end if
#end for
self.allowed = set(tokens)
if len(self.allowed)==0:
self.allowed = None
#end if
#end if
self.value_type = rmg_value_types[self.key_type]
if self.key_type in rmg_array_dtypes:
self.array_dtype = rmg_array_dtypes[self.key_type]
#end if
#end def __init__
def read(self,value):
return read_functions[self.key_type](value)
#end def read
def write(self,value):
return write_functions[self.key_type](value)
#end def write
def assign(self,value):
if not isinstance(value,self.value_type):
self.error('cannot assign RMG keyword "{}".\nInvalid type encountered.\nType encoutered: {}\nType(s) expected: {}'.format(self.key_name,value.__class__.__name__,self.value_type))
#end if
if self.array_dtype is not None:
return np.array(value,dtype=self.array_dtype)
else:
return value
#end if
#end def assign
def valid(self,value,message=False):
msg = ''
if not isinstance(value,self.value_type):
msg += 'Keyword "{}" has the wrong type.\n Type expected: {}\n Type provided: {}\n'.format(self.key_name,self.key_type,value.__class__.__name__)
else:
if RmgInputSettings.enforce_min_value:
if self.min_value is not None and value<self.min_value:
msg += 'Value for keyword "{}" is smaller than allowed.\n Minimum value allowed: {}\n Value provided: {}\n'.format(self.key_name,self.min_value,value)
#end if
#end if
if RmgInputSettings.enforce_max_value:
if self.max_value is not None and value>self.max_value:
self.warn('Value for keyword "{}" is larger than allowed.\n Maximum value allowed: {}\n Value provided: {}\n'.format(self.key_name,self.max_value,value))
#end if
#end if
if RmgInputSettings.enforce_allowed:
if self.allowed is not None and value not in self.allowed:
msg += 'Value for keyword "{}" is not allowed.\n Value provided: {}\n Allowed values: {}'.format(self.key_name,value,list(sorted(self.allowed)))
#end if
#end if
#end if
if not message:
return len(msg)==0
else:
return len(msg)==0,msg
#end if
#end def valid
#end class RmgKeyword
class FormattedRmgKeyword(RmgKeyword):
def read(self,value):
self.not_implemented()
#end def read
def write(self,value):
self.not_implemented()
#end def write
def assign(self,value):
self.not_implemented()
#end def assign
def valid(self,value,message=False):
valid = self.valid_no_msg(value)
if not message:
return valid
else:
return valid,'Data for keyword "{}" is invalid.\nInvalid value: {}'.format(self.key_name,value)
#end if
#end def valid
def valid_no_msg(self,value):
self.not_implemented()
#end def valid_no_msg
#end class FormattedRmgKeyword
class FormattedTableRmgKeyword(FormattedRmgKeyword):
array_options = None
array_types = None
exclude_fields = set()
def assign(self,value):
if isinstance(value,str):
return value
elif isinstance(value,(dict,obj)):
for k,v in value.items():
if isinstance(v,(tuple,list)):
value[k] = np.array(v)
#end if
#end for
return value
else:
self.error('cannot assign RMG keyword "{}".\nInvalid type encountered.\nType encoutered: {}\nType(s) expected: str,dict,obj'.format(self.key_name,value.__class__.__name__))
#end if
#end def assign
def valid_no_msg(self,value):
cls = self.__class__
if not isinstance(value,obj):
return False
#end if
keys = set(value.keys())-set(cls.exclude_fields)
match = False
for key_set in cls.array_options:
if keys==key_set:
match = True
break
#end if
#end if
if not match:
return False
#end if
lengths = [len(value[k]) for k in keys]
if lengths[0]==0:
return False
#end if
if len(set(lengths))!=1:
return False
#end if
for k in keys:
v = value[k]
if not isinstance(v,np.ndarray):
return False
elif not isinstance(v.flatten()[0],cls.array_types[k]):
return False
#end if
#end for
return True
#end def valid_no_msg
#end class FormattedTableRmgKeyword
class PseudopotentialKeyword(FormattedTableRmgKeyword):
array_options = [
set(('species','pseudos')),
]
array_types = obj(
species = rmg_value_types.string,
pseudos = rmg_value_types.string,
)
def read(self,value):
d = np.array(value.split(),dtype=str)
d.shape = len(d)//2,2
species = d[:,0].flatten()
pseudos = d[:,1].flatten()
return obj(species=species,pseudos=pseudos)
#end def read
def write(self,value):
v = value
s = '"\n'
for (sp,p) in zip(v.species,v.pseudos):
s += '{:<4} {}\n'.format(sp,p)
#end for
s += '"'
return s
#end def write
#end class PseudopotentialKeyword
class KpointsKeyword(FormattedTableRmgKeyword):
array_options = [
set(('kpoints','weights')),
]
array_types = obj(
kpoints = rmg_value_types.double,
weights = rmg_value_types.double,
)
def read(self,value):
d = np.array(value.split(),dtype=float)
d.shape = len(d)//4,4
kpoints = d[:,:3]
weights = d[:,-1].flatten()
return obj(kpoints=kpoints,weights=weights)
#end def read
def write(self,value):
v = value
s = '"\n'
for (kp,w) in zip(v.kpoints,v.weights):
s += '{: 16.12f} {: 16.12f} {: 16.12f} {: 16.12f}\n'.format(kp[0],kp[1],kp[2],w)
#end for
s += '"'
return s
#end def write
#end class KpointsKeyword
class KpointsBandstructureKeyword(FormattedTableRmgKeyword):
array_options = [
set(('kpoints','counts','labels')),
]
array_types = obj(
kpoints = rmg_value_types.double,
counts = rmg_value_types.integer,
labels = rmg_value_types.string,
)
def read(self,value):
d = np.array(value.split(),dtype=str)
d.shape = len(d)//4,5
kpoints = np.array(d[:,:3],dtype=float)
counts = np.array(d[:,3],dtype=int).flatten()
labels = d[:,-1].flatten()
return obj(kpoints=kpoints,counts=counts,labels=labels)
#end def read
def write(self,value):
v = value
s = '"\n'
for (kp,c,l) in zip(v.kpoints,v.counts,v.labels):
s += '{: 16.12f} {: 16.12f} {: 16.12f} {:>3} {}\n'.format(kp[0],kp[1],kp[2],c,l)
#end for
s += '"'
return s
#end def write
#end class KpointsBandstructureKeyword
class AtomsKeyword(FormattedTableRmgKeyword):
formats = ('basic','movable','movable_moment','moment','spin_ratio','full_spin')
array_options = [
set(('atoms','positions')),
set(('atoms','positions','movable')),
set(('atoms','positions','moments')),
set(('atoms','positions','movable','moments')),
set(('atoms','positions','movable','spin_ratio')),
set(('atoms','positions','movable','spin_ratio','spin_theta','spin_phi')),
]
array_types = obj(
atoms = rmg_value_types.string,
positions = rmg_value_types.double,
movable = rmg_value_types.boolean,
moments = rmg_value_types.double,
spin_ratio = rmg_value_types.double,
spin_theta = rmg_value_types.double,
spin_phi = rmg_value_types.double,
)
exclude_fields = ['format']
def read(self,value):
# check if input data is empty
value = value.strip()
if len(value)==0:
self.error('No data provided for "atoms".')
#end if
# determine the number of values per line
if '\n' in value:
first,rest = value.split('\n',1)
else:
first = value
#end if
nvals = len(first.split())
# initial array parse of value table
d = np.array(value.split(),dtype=str)
d.shape = len(d)//nvals,nvals
# extract universal atom labels and positions
atom_labels = d[:,0]
atom_labels = atom_labels.flatten()
positions = np.array(d[:,1:4],dtype=float)
# extract remaining data and determine format
v = obj(
format = None,
atoms = atom_labels,
positions = positions,
)
boolset = set(['0','1'])
invalid_format = False
if nvals==4:
v.format = 'basic'
elif nvals==5:
if len(set(d[:,4])-boolset)==0:
v.movable = np.array(d[:,4],dtype=bool)
v.format = 'movable'
else:
try:
v.moments = np.array(d[:,4],dtype=float)
v.format = 'moment'
except:
invalid_format = True
#end try
#end if
elif nvals==6:
try:
v.movable = np.array(d[:,4],dtype=bool)
v.moments = np.array(d[:,5],dtype=float)
v.format = 'movable_moment'
except:
invalid_format = True
#end try
elif nvals==8:
try:
assert(len(set(d[:,4:7].flatten())-boolset)==0)
v.movable = np.array(d[:,4:7],dtype=bool)
v.spin_ratio = np.array(d[:,7],dtype=float)
v.format = 'spin_ratio'
except:
invalid_format = True
#end try
elif nvals==10:
try:
assert(len(set(d[:,4:7].flatten())-boolset)==0)
v.movable = np.array(d[:,4:7],dtype=bool)
v.spin_ratio = np.array(d[:,7],dtype=float)
v.spin_theta = np.array(d[:,8],dtype=float)
v.spin_phi = np.array(d[:,9],dtype=float)
v.format = 'full_spin'
except:
invalid_format = True
#end try
#end if
if invalid_format:
self.error('Failed to read atoms data.\nPlease check the formatting:\n{}'.format(value))
elif v.format is None or v.format not in AtomsKeyword.formats:
self.error('Failed to read atoms data.\nThis is a developer error.\nPlease contact the developers.')
#end if
return v
#end def read
def write(self,value):
v = value
s = '"\n'
if v.format=='basic':
for (a,p) in zip(v.atoms,v.positions):
s += '{:<4} {: 16.12f} {: 16.12f} {: 16.12f}\n'.format(a,p[0],p[1],p[2])
#end for
elif v.format=='movable':
for (a,p,m) in zip(v.atoms,v.positions,v.movable):
s += '{:<4} {: 16.12f} {: 16.12f} {: 16.12f} {}\n'.format(a,p[0],p[1],p[2],int(m))
#end for
elif v.format=='moment':
for (a,p,m) in zip(v.atoms,v.positions,v.moments):
s += '{:<4} {: 16.12f} {: 16.12f} {: 16.12f} {: 6.4f}\n'.format(a,p[0],p[1],p[2],m)
#end for
elif v.format=='movable_moment':
for (a,p,mv,mo) in zip(v.atoms,v.positions,v.movable,v.moments):
s += '{:<4} {: 16.12f} {: 16.12f} {: 16.12f} {} {: 6.4f}\n'.format(a,p[0],p[1],p[2],int(mv),mo)
#end for
elif v.format=='spin_ratio':
for (a,p,m,s) in zip(v.atoms,v.positions,v.movable,v.spin_ratio):
s += '{:<4} {: 16.12f} {: 16.12f} {: 16.12f} {} {} {} {: 6.4f}\n'.format(a,p[0],p[1],p[2],int(m[0]),int(m[1]),int(m[2]),s)
#end for
elif v.format=='full_spin':
for (a,p,m,sr,st,sp) in zip(v.atoms,v.positions,v.movable,v.spin_ratio,v.spin_theta,v.spin_phi):
s += '{:<4} {: 16.12f} {: 16.12f} {: 16.12f} {} {} {} {: 6.4f} {: 6.2f} {: 6.2f}\n'.format(a,p[0],p[1],p[2],int(m[0]),int(m[1]),int(m[2]),sr,st,sp)
#end for
else:
self.error('Invalid atoms format encountered on write.\nInvalid format: {}\nValid options are: {}'.format(v.format,self.formats))
#end if
s += '"'
return s
#end def write
#end class AtomsKeyword
class HubbardUKeyword(RmgKeyword):
def read(self,value):
v = obj()
tokens = read_string(value).split()
for a,u in zip(tokens[::2],tokens[1::2]):
v[a] = float(u)
#end for
return v
#end def read
def write(self,value):
s = ''
for a in sorted(value.keys()):
s += ' {} {}'.format(a,value[a])
#end for
return write_string(s)
#end def write
def assign(self,value):
if isinstance(value,str):
return value
elif isinstance(value,(dict,obj)):
return obj(value)
else:
self.error('cannot assign RMG keyword "{}".\nInvalid type encountered.\nType encoutered: {}\nType(s) expected: str,dict,obj'.format(self.key_name,value.__class__.__name__))
#end if
#end def assign
def valid(self,value,message=False):
valid = True
for k,v in value.items():
if not isinstance(k,rmg_value_types.string):
valid = False
break
elif not isinstance(v,rmg_value_types.double):
valid = False
break
#end if
#end for
if not message:
return valid
else:
return valid,'Data for keyword "{}" is invalid.\nInvalid value: {}'.format(self.key_name,value)
#end if
#end def valid
#end class HubbardUKeyword
formatted_keywords = obj(
pseudopotential = PseudopotentialKeyword,
kpoints = KpointsKeyword,
kpoints_bandstructure = KpointsBandstructureKeyword,
atoms = AtomsKeyword,
Hubbard_U = HubbardUKeyword,
)
class RmgInputSpec(DevBase):
def __init__(self):
spec = raw_input_spec.strip()
blocks = spec.split('\n\n')
self.section_order = []
self.section_labels = obj()
self.section_contents = obj()
self.keywords = obj()
section = None
sec_cont = None
for b in blocks:
if ':' not in b:
b = b.strip().lower()
if b.endswith('options'):
sec_cont = []
section = b.replace(' options','').strip().replace(' ',' ').replace(' ','_')
self.section_order.append(section)
self.section_labels[section] = b
self.section_contents[section] = sec_cont
#end if
else:
k = RmgKeyword(b,section)
if k.key_type=='formatted':
if k.key_name not in formatted_keywords:
self.error('unrecognized formatted keyword: "{}"'.format(k.key_name))
#end if
k = formatted_keywords[k.key_name](b,section)
#end if
self.keywords[k.key_name] = k
sec_cont.append(k.key_name)
#end if
#end for
#end def __init__
#end class RmgInputSpec
input_spec = RmgInputSpec()
class RmgCalcModes(DevBase):
def __init__(self):
self.full_calc = obj(
scf = 'Quench Electrons',
exx = 'Exx Only',
neb = 'NEB Relax',
band = 'Band Structure Only',
relax = 'Relax Structure',
dimer_relax = 'Dimer Relax',
md_PE = 'Constant Pressure And Energy',
md_TE = 'Constant Temperature And Energy',
md_VE = 'Constant Volume And Energy',
tddft = 'TDDFT',
plot = 'Plot',
psi_plot = 'Psi Plot',
)
self.short_calc = obj()
for k,v in self.full_calc.items():
self.short_calc[v] = k
#end for
self.full_calc_modes = set(self.full_calc.values())
self.short_calc_modes = set(self.short_calc.values())
#end def __init__
def is_full_mode(self,mode):
return mode in self.full_calc_modes
#end def is_full_mode
def is_short_mode(self,mode):
return mode in self.short_calc_modes
#end def is_short_mode
def full_mode(self,short_mode):
mode = None
if short_mode in self.full_calc:
mode = self.full_calc[short_mode]
#end if
return mode
#end def full_mode
def short_mode(self,full_mode):
mode = None
if full_mode in self.short_calc:
mode = self.short_calc[full_mode]
#end if
return mode
#end def short_mode
def mode_match(self,text,short=False):
mode = None
text = text.lower()
for full_mode in self.full_calc_modes:
if full_mode.lower() in text:
if not short:
mode = full_mode
else:
mode = self.short_mode(full_mode)
#end if
break
#end if
#end for
return mode
#end def mode_match
#end class RmgCalcModes
rmg_modes = RmgCalcModes()
class RmgInput(SimulationInput):
def __init__(self,filepath=None):
if filepath is not None:
self.read(filepath)
#end if
#end def __init__
def assign(self,**values):
unrecognized = []
for k,v in values.items():
if k in input_spec.keywords:
if isinstance(v,(str,np.string_)):
self[k] = input_spec.keywords[k].read(v)
else:
self[k] = input_spec.keywords[k].assign(v)
#end if
else:
unrecognized.append(k)
#end if
#end for
if len(unrecognized)>0:
unrec = obj(values).obj(unrecognized)
self.error('Unrecognized keywords encountered during assignment.\nUnrecognized keywords: {}\nCorresponding values:\n{}'.format(list(sorted(unrecognized)),unrec))
#end if
#end def assign
def read_text(self,contents,filepath=None):
# remove comments and whitespace
text = ''
for line in contents.splitlines():
i = line.find('#')
if i!=-1:
line = line[:i]
#end if
ls = line.strip()
if len(ls)>0:
text += ls+'\n'
#end if
#end for
text = text.strip()
# separate keywords and values
values = obj()
whitespace = ' \t\n'
icur = 0
k = 'some key'
while k is not None:
k = None
ie = text.find('=',icur)
if ie!=-1:
k = text[icur:ie].strip()
iv1 = text.find('"',ie)
if iv1!=-1:
iv2 = text.find('"',iv1+1)
if iv2!=-1:
v = text[iv1+1:iv2]
values[k] = v
icur = iv2+1
#end if
#end if
#end if
#end while
# read the keyword values, checking for unrecognized ones
self.assign(**values)
#end def read_text
def write_text(self,filepath=None):
if RmgInputSettings.check_on_write:
self.check_valid()
#end if
text = ''
for section_name in input_spec.section_order:
present = False
for k in input_spec.section_contents[section_name]:
if k in self:
if not present:
text += '\n\n# '+input_spec.section_labels[section_name]+'\n\n'
present = True
#end if
kw = input_spec.keywords[k]
text += '{:<22} = {}\n'.format(kw.key_name,kw.write(self[k]))
#end if
#end for
#end for
return text.lstrip()
#end def write_text
def check_valid(self,exit=True):
msg = ''
allowed = set(input_spec.keywords.keys())
present = set(self.keys())
unrecognized = present-allowed
if len(unrecognized)>0:
msg += 'Unrecognized keywords encountered.\n Unrecognized keywords: {}\n Valid keywords are: {}\n'.format(list(sorted(unrecognized)),list(sorted(allowed)))
#end if
recognized = present-unrecognized
for k in sorted(recognized):
kval,m = input_spec.keywords[k].valid(self[k],message=True)
if not kval:
msg += m+'\n'
#end if
#end if
if len(msg)>0 and exit:
self.log(msg)
self.error('Input is invalid.\nPlease see messages above for specific issues.')
#end if
return len(msg)==0
#end def check_valid
def is_valid(self):
return self.check_valid(exit=False)
#end def is_valid
def return_structure(self,units='B'):
axes = self.get('lattice_vector',None)
axes_unit = self.get('lattice_units','bohr')
lattice = self.get('bravais_lattice_type','orthorhombic primitive')
a = self.get('a_length',0.0)
b = self.get('b_length',0.0)
c = self.get('c_length',0.0)
coord_type = self.get('atomic_coordinate_type','absolute')
coord_unit = self.get('crds_units','bohr')
atom_data = self.get('atoms',obj())
atoms = atom_data.get('atoms',None)
positions = atom_data.get('positions',None)
unit_dict = dict(angstrom='A',bohr='B')
coord_unit = unit_dict[coord_unit.lower()]
axes_unit = unit_dict[axes_unit.lower()]
if axes is not None:
axes = np.array(axes,dtype=float)
else:
lattice_orig = lattice
lattice = lattice.lower()
if lattice=='cubic primitive':
axes = np.diag((a,a,a))
elif lattice=='tetragonal primitive':
axes = np.diag((a,a,c))
elif lattice=='orthorhombic primitive':
axes = np.diag((a,b,c))
elif lattice=='cubic body centered':
axes = 0.5*a*np.array([[ 1, 1,-1],
[-1, 1, 1],
[ 1,-1, 1]],dtype=float)
elif lattice=='cubic face centered':
axes = 0.5*a*np.array([[ 1, 1, 0],
[ 0, 1, 1],
[ 1, 0, 1]],dtype=float)
elif lattice=='hexagonal primitive':
axes = np.array([[ a, 0, 0],
[-a/2, np.sqrt(3)/2*a, 0],
[ 0, 0, c]],dtype=float)
else:
# cubic body centered, hexagonal primitive not yet supported
self.error('Structure extraction failed.\nLattice type "{}" is currently unsupported.'.format(lattice_orig))
#end if
#end if
axes = convert(axes,axes_unit,units)
if atoms is None or positions is None:
self.error('Structure extraction failed.\nEither atoms or positions could not be obtained.')
#end if
atoms = np.array(atoms,dtype=object)
positions = np.array(positions,dtype=float)
if coord_type.lower()=='cell relative':
positions = np.dot(positions,axes)
else:
positions = convert(positions,coord_unit,units)
#end if
s = generate_structure(
units = units,
axes = axes,
elem = atoms,
pos = positions,
)
return s
#end def return_structure
#end class RmgInput
def generate_rmg_input(**kwargs):
selector = kwargs.pop('input_type','generic')
if selector=='generic':
return generate_any_rmg_input(**kwargs)
else:
RmgInput.class_error('Input type "{}" has not been implemented for RMG input generation.'.format(selector))
#end if
#end def generate_rmg_input
generate_any_defaults = obj(
none = obj(),
basic = obj(
use_folded = True,
virtual_frac = 0.20,
),
#qmc = obj(
# use_folded = True,
# ),
)
def generate_any_rmg_input(**kwargs):
loc = 'generate_rmg_input'
# set default values
defaults = kwargs.pop('defaults','basic')
kw = obj(**kwargs)
kw.set_optional(generate_any_defaults[defaults])
# extract keywords not appearing in RMG input file
text = kw.delete_optional('text' , None )
wf_grid_spacing = kw.delete_optional('wf_grid_spacing', None )
pseudos = kw.delete_optional('pseudos' , None )
system = kw.delete_optional('system' , None )
copy_system = kw.delete_optional('copy_system' , True )
use_folded = kw.delete_optional('use_folded' , False )
virtual_frac = kw.delete_optional('virtual_frac' , None )
spin_polarized = kw.delete_optional('spin_polarized' , None )
default_units = kw.delete_optional('default_units' , 'bohr' )
default_units = dict(
a = 'angstrom',
b = 'bohr',
angstrom = 'angstrom',
bohr = 'bohr'
)[default_units.lower()]
rmg_units_map = obj(
angstrom = 'Angstrom',
bohr = 'Bohr',
alat = 'Alat',
a = 'Angstrom',
b = 'Bohr',
)
# generate RMG input
ri = RmgInput()
if text is not None:
ri.read_text(text)
#end if
ri.assign(**kw)
# incorporate pseudopotentials details provided via "pseudos"
if pseudos is not None:
species = []
pps = []
for ppname in pseudos:
label,element = pp_elem_label(ppname,guard=True)
species.append(element)
pps.append(ppname)
#end for
ri.pseudopotential = obj(
species = np.array(species),
pseudos = np.array(pps),
)
#end if
# incorporate system details, if provided
if system is not None:
# add system details
if copy_system:
system = system.copy()
#end if
if use_folded:
system = system.get_smallest()
#end if
system.check_folded_system()
system.update_particles()
# set atomic species, positions, magnetic moments and mobility
if 'atomic_coordinate_type' not in ri:
ri.atomic_coordinate_type = 'Absolute'
#end if
if 'crds_units' not in ri:
cu = default_units
else:
cu = ri.crds_units.lower()
#end if
if cu=='angstrom':
system.change_units('A')
elif cu=='bohr':
system.change_units('B')
else:
error('Invalid crds_units.\nExpected "Angstrom" or "Bohr".\nReceived: {}'.format(cu),loc)
#end if
rmg_length_units = rmg_units_map[cu]
if 'crd_units' not in ri and 'atomic_coordinate_type' in ri and ri.atomic_coordinate_type=='Absolute':
ri.crd_units = rmg_length_units
#end if
s = system.structure
elem = np.array(s.elem)
act = ri.atomic_coordinate_type.lower()
if act=='absolute':
pos = s.pos.copy()
elif act=='cell relative':
pos = s.pos_unit().copy()
else:
error('Invalid atomic_coordinate_type.\nExpected "Absolute" or "Cell Relative".\nReceived: {}'.format(cu),loc)
#end if
movable = None
if s.frozen is not None:
movable = ~s.is_frozen()
#end if
moments = None
if s.mag is not None:
moments = np.array(s.mag,dtype=float)
#end if
if movable is not None and moments is not None:
ri.atoms = obj(
format = 'movable_moment',
atoms = elem,
positions = pos,
movable = movable,
moments = moments,
)
elif movable is not None:
ri.atoms = obj(
format = 'movable',
atoms = elem,
positions = pos,
movable = movable,
)
else:
ri.atoms = obj(
format = 'basic',
atoms = elem,
positions = pos,
)
#end if
# set lattice vectors
if 'a_length' not in ri:
ri.lattice_units = rmg_length_units
ri.lattice_vector = s.axes.copy()
#end if
# set kpoints
if len(s.kpoints)>0 and 'kpoint_mesh' not in ri:
kpu = s.kpoints_unit()
ri.kpoints = obj(
kpoints = kpu.copy(),
weights = s.kweights.copy(),
)
if 'kpoint_is_shift' in ri:
del ri.kpoint_is_shift
#end if
#end if
# set wavefunction grid
if wf_grid_spacing is not None:
wf_grid = []
for a in system.structure.axes:
g = int(np.ceil(np.linalg.norm(a)/wf_grid_spacing))
wf_grid.append(g)
#end for
ri.assign(wavefunction_grid=wf_grid)
#end if
if spin_polarized is None and 'noncollinear' not in ri:
spin_polarized = system.spin_polarized_orbitals()
elif spin_polarized is None and 'noncollinear' in ri:
if not ri.noncollinear:
spin_polarized = system.spin_polarized_orbitals()
#end if
#end if
# set occupations
has_states = False
has_states |= 'states_count_and_occupation' in ri
has_states |= 'states_count_and_occupation_up' in ri and 'states_count_and_occupation_down' in ri
if not has_states and virtual_frac is not None:
states_keys = [
'states_count_and_occupation',
'states_count_and_occupation_up',
'states_count_and_occupation_down',
]
for k in states_keys:
if k in ri:
del ri[k]
#end if
#end for
nup,ndn = system.particles.electron_counts()
nvirt = int(np.ceil(virtual_frac*max(nup,ndn)))
nptot = max(nup,ndn) + nvirt
nup_virt = nptot-nup
ndn_virt = nptot-ndn
if nup==ndn and not spin_polarized:
occ_up = '{} 2.0 {} 0.0'.format(nup,nup_virt)
ri.states_count_and_occupation = occ_up
else:
occ_up = '{} 1.0 {} 0.0'.format(nup,nup_virt)
occ_dn = '{} 1.0 {} 0.0'.format(ndn,ndn_virt)
ri.states_count_and_occupation_spin_up = occ_up
ri.states_count_and_occupation_spin_down = occ_dn
#end if
#end if
#end if
if spin_polarized is not None and spin_polarized:
if 'states_count_and_occupation_spin_up' not in ri:
error('System is spin polarized, but occupations not provided for up and down spins.',loc)
#end if
#end if
return ri
#end def generate_any_rmg_input
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