System Description¶

Parameters describing physical systems¶

system.object¶

key word	:	system.object
possible values	:	a file name of a saved cNA_LCAO object
default value	:	$[\ ]$ (empty)
description	:	If it is not empty, the system is defined by the input
		object. In this case, all other parameters related to
		the system in the input file will not be used.
an example	:	system.object = cNA_LCAO_object.mat

system.hamiltonian¶

key word	:	system.hamiltonian
possible values	:	a file name of an user provided hamiltonian matrix
default value	:	$[\ ]$ (empty)
description	:	If it is not empty, the system is defined by the input
		Hamiltonian matrix. In this case, all other parameters
		related to the system in the input file will not be
		used. In addition, since the real space wavefunction
		basis have not been given explicitly, any calculation
		related to real space wavefunction can not be performed.

		The input file can be either a mat-file or xml-file, or
		text file, but must be in the same format as nanodcal
		output file Hamiltonian.mat or Hamiltonian.xml, or
		Hamiltonian.txt.
an example	:	system.hamiltonian = $[\ ]$

system.name¶

key word	:	system.name
possible values	:	any string
default value	:	NoName
description	:	a string provided by user to label the system and
		it is not used in the calculation.
an example	:	system.name = Si-nanowire

system.spinType¶

key word	:	system.spinType
possible values	:	NoSpin, CollinearSpin, CoplanarSpin, GeneralSpin
default value	:	NoSpin
description	:	within the framework of non-relativistic theory, spin
		should be an intrinsic physical property of the system
		rather than an input parameter. Usually, some knowledge
		about the type of spin is known before the calculation
		and this priori knowledge can be used to save
		computation time. From the computational point of view,
		the parameter spinType is needed.

		We first define a vector of spin polarization which,
		of course, is along the direction of the polarization.
		Its amplitude is defined as a ratio of
		(N_p-N_ap)/(N_p+N_ap), where N_p (N_ap) is the number
		of electrons whose spin are (anti) parallel to the
		spin polarization. By considering the N above as the
		charge density, spin polarization can also be viewed
		as a function of position in the system.

		NoSpin is used for a system in which spin polarization
		is zero; CollinearSpin is used for a system in which
		spin polarizations at different places are all along the
		same direction (either parallel or anti-parallel);
		CoplanarSpin is used for a system in which spin
		polarizations at different places are all within a same
		plane; GeneralSpin is used for a system in which spin
		polarizations at different places have their own
		directions, or there is no a priori knowledge about
		the spins in the system.
an example	:	system.spinType = NoSpin

system.centralCellVectors¶

key word	:	system.centralCellVectors
possible values	:	3$\times$3 or 1$\times$6 or 1$\times$3 double matrix
default value	:	For a system without leads, the system will be
		considered as a molecule when the parameter
		centralCellVectors is not given, and it will be
		determined by nanodcal automatically.
		For a system with leads, the parameter
		centralCellVectors may be automatically determined by
		the geometry of the leads and the buffer layers.
		There is no default value for a periodic system,
		it must be given, otherwise the system will be
		considered as a molecule by nanodcal.
description	:	This parameter defines the three base vectors of the
		central cell, either the primitive or super cell for a
		periodic system or the central scattering region for an
		open system, which is with a shape of parallelepiped.
		When the parameter is a 3$\times$3 double matrix, its each
		column forms one of the three basis vectors. When
		the parameter is a 1$\times$6 double matrix, it defines the
		three basis vectors by their lengths a,b,c; and the
		angles between them, alpha, beta, gamma. The convention
		is that the a-axis is collinear with x-axis, and the
		b-axis lies in the xy-plane. When the parameter is a
		1$\times$3 double matrix, the alpha, beta, gamma angles are
		all equal to $\pi$/2.

		The default unit for angle is degree.
an example	:	system.centralCellVectors = …
		[[1.3 0 0] [0 1.6 0] [0 0 2.5]]

system.centralCellVector1 or system.centralCellVector2¶

key word	:	system.centralCellVector1 or system.centralCellVector2
		or system.centralCellVector3
possible values	:	3$\times$1 or 1$\times$3 double vector
default value	:	no default value
description	:	it is a alternative method to input the
		centralCellVectors. This input value will not be used
		when system.centralCellVectors is provided.
an example	:	system.centralCellVector1 = [1 0 0]
		system.centralCellVector2 = [0 1 0]
		system.centralCellVector3 = [0 0 1]

system.atomBlock¶

key word	:	system.atomBlock
possible values	:	N (the number of atoms in the central cell)
default value	:	no default value, must be input
description	:	all neutral atom properties related to the atoms which
		consist in the central cell are defined in this block.
		This line must immediately be followed by another (N+2)
		lines: one line of headers, N data lines for all of the
		N atoms, and finally a line with a single word end to
		indicate the end of the atomic data block.

		The first four headers in the header line must be (not
		necessarily in order) X, Y, Z, and AtomType. The
		value of [X Y Z] describes the position of each site in
		the system (see also the parameter
		system.atomCoordinateFormat). The value of AtomType
		describes what atomic species is located in that site,
		it is normally the symbol of the atomic element.

		Another header must be given is OrbitalType which
		describes what atomic orbitals of the atoms are used as
		the wavefunction basis in the LCAO calculation. It is
		normally SZ, SZP, DZ, or DZP. While AtomType
		and OrbitalType could be any string specified by an
		user, the pre-calculated data file of the corresponding
		neutral atom must be named as
		AtomType_OrbitalType.nad, or
		AtomType_OrbitalType.mat, and located either in
		directory where the calculation is performed, or in the
		directory $NANODCALROOT/neutralatomdata.
		See manual for more information about the data files
		concerning the neutral atoms.

		The value of OrbitalType of each individual atom can
		be specified differently, i.e., all atoms can have their
		own unique basis different from each other, even if
		they have the same AtomType. If all the atoms have the
		same OrbitalType, the OrbitalType can be specified
		elsewhere in one shot for all the atoms by the
		parameter system.orbitalType.

		Other possible headers are SpinPolarization,
		SpinPolarization_x, SpinPolarization_y,
		SpinPolarization_z; SpinPolarization_r,
		SpinPolarization_theta, SpinPolarization_phi; etc.
		SpinPolarization is used for CollinearSpin system to
		describe the initial polarization of the atom. The set
		of SpinPolarization_x, SpinPolarization_y, and
		SpinPolarization_z and the set of SpinPolarization_r,
		SpinPolarization_theta, and SpinPolarization_phi are
		used for CoplanarSpin or GeneralSpin system to
		describe the initial polarization of the atom. When a
		system is specified as CoplanarSpin, the values of
		SpinPolarization_y or SpinPolarization_phi will
		automatically be set to zero.

		The default unit of angle is degree.
an example	:	system.atomBlock = 2
		AtomType OrbitalType X Y Z SpinPolarization
		Fe DZP 0.000000 0.000000 0.000000 0.200000
		Fe DZP 2.610100 2.610100 2.610100 0.200000
		end

system.atomFile¶

key word	:	system.atomFile
possible values	:	any string representing the name of an input atomfile
default value	:	no default value
description	:	In this alternative input mode, the content of the data
		block of system.atomBlock is written into a separate
		file (See the description of system.atomBlock). The
		file atomFile contains (N+2) lines where N is the
		number of atoms in the central cell. While the first
		line is the integer N, the rest (N+1) lines are
		exactly the same as those defined in the block of
		system.atomBlock. The line of end is needed when there
		are extra data lines after the (N+2) line in the file.
		This input value will not be used when system.atomBlock
		is given.
an example	:	system.atomFile = system.xyz

system.atomPositionShift¶

key word	:	system.atomPositionShift
possible values	:	a 3$\times$1 double matrix
default value	:	[0 0 0]
description	:	In nanodcal calculations, we suggest that users put all
		the atoms inside the central cell box. This parameter
		helps to shift all the coordinates which are defined in
		the system.atomFile or system.atomBlock, by a constant
		vector. In other words, the real coordinates of atoms
		used by nanodcal will be the original ones
		plus this input parameter.
an example	:	system.atomPositionShift = [9 8 7]

system.atomCoordinateFormat¶

key word	:	system.atomCoordinateFormat
possible values	:	cartesian or fractional
default value	:	cartesian
description	:	The format of the atomic coordinates defined in
		system.atomBlock or system.atomFile. If cartesian, the
		coordinates are defined in the normal cartesian system.
		If fractional, the coordinates are defined on the basis
		of system.atomFractionalCoordinateBaseVectors.
an example	:	system.atomCoordinateFormat = fractional

system.atomFractionalCoordinateBaseVectors¶

key word	:	system.atomFractionalCoordinateBaseVectors
possible values	:	3$\times$3 or 1$\times$6 or 1$\times$3 double matrix
default value	:	system.centralCellVectors
description	:	When system.atomCoordinateFormat is fractional, this
		parameter gives the three base vectors with which the
		fractional coordinates are defined.
		When the parameter is a 3$\times$3 double matrix, its each
		column forms one of the three basis vectors. When
		this parameter is a 1$\times$6 double matrix, it defines the
		three basis vectors by giving their lengths, a, b, and
		c, and the angles between them, alpha, beta, and gamma,
		with the convention that the a-axis is collinear with
		the x-axis, and the b-axis lies in the xy-plane. When
		the parameter is a 1$\times$3 double matrix, the alpha, beta,
		and gamma are all assumed to be $\pi$/2.

		The default unit of angle is degree.
an example	:	system.atomFractionalCoordinateBaseVectors = …
		[[1.3 0 0] [0 1.6 0] [0 0 2.5]]

system.atomPositionPrecision¶

key word	:	system.atomPositionPrecision
possible values	:	a small number
default value	:	1e-3 Bohr
description	:	Used as a criterion in symmetry analysis. If the
		distance of two atoms or their images is less than this
		parameter, the atoms are considered to occupy the same
		site.
an example	:	system.atomPositionPrecision = 1e-6

system.orbitalType¶

key word	:	system.orbitalType
possible values	:	any string
default value	:	AtomicData
description	:	orbitalType describes what atomic orbitals of the atoms
		are used as the wavefunction basis in the LCAO
		calculations. See relevant part of the description of
		system.atomBlock. The input value will not be used when
		the information of orbital type has been given in
		system.atomBlock or in the file of system.atomFile.
an example	:	system.orbitalType = DZP

system.neutralAtomDataDirectory¶

key word	:	system.neutralAtomDataDirectory
possible values	:	any string representing the directory where the
		calculated neutral atom data are saved.
default value	:	$NANODCALROOT/neutralatomdata
description	:	This input is for users to apply their own neutral atom
		data.
an example	:	system.neutralAtomDataDirectory = ./neutralatomdata

system.numberOfElectrons¶

key word	:	system.numberOfElectrons
possible values	:	a double value
default value	:	calculated automatically by nanodcal
description	:	the number of electrons in (the central cell of) the
		system. This value will be generated automatically by
		nanodcal and normally, there is no need for an user to
		input it. However, this input offers the opportunity
		to calculate a charged system.
an example	:	system.numberOfElectrons = 88

system.numberOfLeads¶

key word	:	system.numberOfLeads
possible values	:	0, 2 (number of leads in the system)
default value	:	0
description	:	the number of leads (probes) in the system.
an example	:	system.numberOfLeads = 2

system.typeOfLead1, system.typeOfLead2, …¶

key word	:	system.typeOfLead1, system.typeOfLead2, …
possible values	:	top, bottom, front, back, left, and right
default value	:	no default value, must be given
description	:	the value must be given for each of the leads in the
		system. It describes the relative position of the lead
		to the central scattering region. More precisely,
		left means the direction of [ 0 0 -1]
		right means the direction of [ 0 0 1]
		top means the direction of [ 0 1 0]
		bottom means the direction of [ 0 -1 0]
		front means the direction of [-1 0 0]
		back means the direction of [ 1 0 0]

		In two-probe calculations, the pair of left and
		right is recommended for possible better computation
		efficiency.
an example	:	system.typeOfLead1 = left
		system.typeOfLead2 = right

system.voltageOfLead1, system.voltageOfLead2¶

key word	:	system.voltageOfLead1, system.voltageOfLead2
possible values	:	V, a double value
default value	:	0
description	:	the bias voltage applied to the lead, in the unit of
		Volt. The change of chemical potential of the lead due
		to the bias voltage is -eV.
an example	:	system.voltageOfLead1 = 0
		system.voltageOfLead2 = 1.2

system.spinDirectionOfLead1, system.spinDirectionOfLead2¶

key word	:	system.spinDirectionOfLead1, system.spinDirectionOfLead2
possible values	:	a 3$\times$1 array, a 2$\times$1 array, or a number
default value	:	the direction of the total spin of a lead which is
		calculated as a periodic bulk system
description	:	If a lead which is a periodic bulk structure has
		freedom to change the direction of its total spin, this
		input parameter gives the desired direction of the total
		spin of that lead when it is used as a part of the
		device system.

		When it is a 3$\times$1 array, this input is a directional
		vector (not necessarily normalized) defined in cartesian
		coordinates.
		When it is a 2$\times$1 array, this input is a directional
		vector defined in spherical coordinate system, i.e,
		[theta, phi].
		When it is a number s, it means the the direction is
		[0, 0, s].
an example	:	system.spinDirectionOfLead1 = [0 0 1]
		system.spinDirectionOfLead2 = [0 0 -1]

system.objectOfLead1, system.objectOfLead2¶

key word	:	system.objectOfLead1, system.objectOfLead2
possible values	:	a file name of a saved cNA_LCAO object of the lead, or
		an input file name based on which the lead object can
		be calculated
default value	:	no default value, must be input
description	:	The calculation of a system with leads can be performed
		in two steps. The first step is to perform calculation
		for each lead which is considered equivalently as an
		infinite periodic system. In the second step, the
		physical properties (potential, density etc.) of the
		leads are used as boundary conditions applied to the
		central scattering region of the device. In this
		scenario, this input value is normally a filename of
		the calculated and saved results of the leads.
		This input can also be just another input file which
		initiates a complete calculation of the leads. Please
		note that all information about the leads are described
		indirectly by this input file. Please also note
		that if this input is another input file for a lead
		calculation, the current directory will be changed to
		that of the lead input file when performing the
		calculation for the lead.
an example	:	system.objectOfLead1 = ../leftlead/cNA_LCAO_object.mat
		system.objectOfLead2 = ../rightlead/cNA_LCAO_object.mat

system.numberOfGates¶

key word	:	system.numberOfGates
possible values	:	an integer
default value	:	0
description	:	the number of gates in the system. Gates are
		capacitively coupled to the device scattering region.
		They affect the device by providing effective
		boundary conditions to the electrostatic potential.
an example	:	system.numberOfGates = 0

system.typeOfGate1, system.typeOfGate2¶

key word	:	system.typeOfGate1, system.typeOfGate2
possible values	:	top, bottom, front, back, left, and right
default value	:	no default value, must be specified
description	:	the value must be given for each of the gates in the
		system. It describes the relative position of the gate
		to the central scattering region. More precisely,
		left means the direction of [ 0 0 -1]
		right means the direction of [ 0 0 1]
		top means the direction of [ 0 1 0]
		bottom means the direction of [ 0 -1 0]
		front means the direction of [-1 0 0]
		back means the direction of [ 1 0 0]
an example	:	system.typeOfGate1 = top
		system.typeOfGate2 = bottom

system.voltageOfGate1, system.voltageOfGate2¶

key word	:	system.voltageOfGate1, system.voltageOfGate2
possible values	:	Vg, a double value
default value	:	0
description	:	the voltage on the gate located at the boundary
		of the system, the unit is Volt. Note that
		the corresponding energy shift is -eVg.
an example	:	system.voltageOfGate1 = -3
		system.voltageOfGate2 = 0

Parameter describing calculations¶

calculation.name¶

key word	:	calculation.name
possible values	:	one from the following list, or a cell array with
		each cell containing one from the following list.

		init, initial, initialize, initialization;

		NSC, NSCF, nonSelfConsistentField,
		rigidAtomicField, neutralAtomicPotential;

		HarrisField, HarrisEnergyFunctional,
		HarrisFunctional, HarrisEnergy,
		Harris, HarrisApproximation;

		SC, SCF, selfConsistentField, selfConsistent;


		PSC, PSCF, PostSCF, postField,
		postSelfConsistencyField, postSelfConsistentField;



		TE, totalEnergy, energy;

		TP, P, momentum;

		force;

		stress, stressMatrix;

		Hessian, HessianMatrix, dynamicalMatrix;

		BS, bandStructure;


		CBS, complexBandStructure

		FBS, fullBandStructure, fermiSphere, fermiSurface

		eig, eigs, eigen, eigenStates;

		SS, scatteringStates;

		DOS, densityOfStates;

		DOSS, densityOfScatteringStates;

		CH, charge, electron, electrons;

		PO, potential;

		EPhCoupling;


		TR, TM, transmission;

		TRC, TMC, channel, transchannel,
		transmission-channel, transmissionchannel;

		CO, COND, conductance;

		ACCO, ACCOND, acConductance;



		IVC, IVCurve;

		IETS;


		relax, relaxation, structureRelaxation;

		basisOptimization, BO;
default value	:	no default value, must be provided.
description	:	The above list of possible values are divided into
		groups by ;. Values in the same group are all
		equivalent, i.e. they invoke the same calculation.

		Note that when choosing more than one calculation,
		they must be arranged in a physically correct
		(meaningful) order.

		The following are descriptions of each calculation.

		initialization : for construction of the system
		object without calculating any physical property.

		rigidAtomicField : a simple summation of precalculated
		atomic self-consistent fields of all atoms involved in
		the system without any further electronic relaxation.
		This calculation generates the Hamiltonian and the real
		space charge density needed for further calculations.
		This field or potential is not self-consistent. In a DFT
		calculation, this field accounts for those terms of the
		Hamiltonian that need to be computed only once outside
		of the self-consistent loop.

		HarrisField : same as the rigidAtomicField
		calculation but within the Harries functional method.
		The Harris total energy is an approximation of the DFT
		self-consistent total energy.

		The HarrisField calculation can also be used together
		with the SCF option. After 2 or 3 self-consistent
		steps (by setting calculation.SCF.maximumSteps = 2 or
		3), the estimation of total energy may be somewhat
		improved.

		SCF : generates Hamiltonian and density which are
		consistent with each other.


		PostSCF : modify the (self-consistent) Hamiltonian
		by various additional terms, e.g. the terms caused by
		an applied external magnetic field.



		totalEnergy: the total energy of the system as defined
		by the density-functional theory. The total energy can
		also be decomposed into several terms, like kinetic energy,
		band structure energy, short range energy, and so on.

		momentum: calculate total electronic momentum of the
		system and also the electronic momentum matrix.

		force: atomic forces, which can also also be decomposed
		into several terms, like kinetic force, short range
		force, and so on.


		stress: the stress tensor of the system, which is
		defined as the negative derivative of the total energy
		with respect to the strain tensor. The stress tensor can
		also be decomposed into several terms, like kinetic
		stress, short range stress, and so on.

		hessian: the hessian matrix, which is defined as the
		second derivative of the total energy with respect to
		atomic positions.

		The corresponding dynamical matrix can also be
		calculated, with which the phonon spectrum and
		vibrational modes of the system can further be
		determined.

		In addition, the derivative of the Hamiltonian matrix
		with respect to atomic positions can also be calculated,
		which could be used to study the phonon and electron
		interactions.

		bandStructure: the normal band structure calculation
		which gives the band energies as a function of a series
		of k-points. The k-points are normally along a line
		segment(s) in the k-space.


		complexBandStructure: the complex-band structure
		calculation. Comparing to normal band structure which
		displays a band energy as a function of a k-point, i.e.,
		e = e(k1,k2,k3), the complex-band structure displays a
		k-coordinate, e.g. k3, as a function of band energy and
		other k-coordinates, i.e., k3 = k3(e;k1,k2) where the
		value of k3 is normally a complex number.

		fullBandStructure: this calculation gives the band
		energies at all k-points whin the Brillouin zone. The
		fermi surface can also be determined and visualized, with
		which electronic transmission properties of a lead can
		be studied.

		eigenStates: this calculation is used for molecular or
		periodic bulk systems, which gives eigen energies and
		also corresponding wave functions as a vector of the
		coefficients of a set of atomic basis and/or as a
		real-space function, for a set of states specified by
		an user.

		scatteringStates: this calculation is used for systems
		with probes, which gives transmission and reflection
		coefficients and also the real-space wave function, for
		a set of states specified by an user.

		densityOfStates: the density of electronic states
		(dos), which can also be decomposed in various ways to
		obtain projected dos, local dos, and so on.

		densityOfScatteringStates: the density of electronic
		scattering states (dos), which can also be decomposed in
		various ways to obtain projected dos, local dos, and so
		on. Comparing to the normal dos, doss only counts for
		the scattering states associated to a specific lead and
		washes out all other states.

		charge: analysis of the total charge of the system in
		various ways, such as projected to some particular atomic
		orbitals, localized to a particular real-space region,
		projected to the spin-polarization direction, and so on.

		potential: this calculation is to obtain and also
		display or visualize a real-space potential function of
		Vdh, Vxc, Vna, or Veff, where Vdh is the delta_Hartree
		potential, Vxc is the exchange-correlation potential,
		Vna is the neutral atomic potential, and Veff = Vdh+Vxc.

		Note that the difference of two Vdh calculated with and
		without a bias voltage gives the detailed information
		about how the voltage drops across the structure.

		EPhCoupling: the electron-phonon couplings.

		transmission: transmission coefficients calculation,
		which can be used to determine the conductance of the
		structure.

		channel: the number of transmission channels of a
		system when being used as a lead, which is given as a
		function of energy, transverse wave vectors.

		conductance: the conductance. The current with the
		applied voltage is also calculated.

		acConductance: the ac conductance when an ac bias
		voltage is applied.



		IVCurve: this calculation gives the current as a
		function of applied voltages, and the intermediate data
		of conductance is also given.

		IETS: The inelastic electron tunneling spectroscopy.


		relaxation: structure relaxation with or without
		change of the central cell. Various constrains can be
		applied during the relaxation.

		basisOptimization: used to optimize the atomic basis
		for a particular system(s). This is normally a key step
		to a reliable result with high precision.
an example	:	calculation.name = {scf, bs}

Control parameters for the calculation¶

calculation.control.lengthUnit¶

key word	:	calculation.control.lengthUnit
possible values	:	au, a.u., atomic unit, Bohr,
		an, ang, angstrom,
		nm, nanometer,
		where au a.u., and atomic unit are for Bohr,
		an and ang for angstrom, and nm for nanometer.
default value	:	angstrom
description	:	the unit of length used in the input file. For example,
		it will be used as the unit of the x-, y-, and
		z-coordinates of the atoms, the unit of
		centralCellVectors or the group of centralCellVector1,
		centralCellVector2, and centralCellVector3.
		Note: 1 Bohr = 0.529177208319 Angstrom
an example	:	calculation.control.lengthUnit = au

calculation.control.energyUnit¶

key word	:	calculation.control.energyUnit
possible values	:	au, a.u., atomic unit, Hartree,
		Ryd, Ryd., Rydberg,
		eV,
		where au a.u., and atomic unit are for Hartree,
		Ryd and Ryd. for Rydberg.
default value	:	eV
description	:	the unit of energy used in the input file.
		Note: 1 Hartree = 27.211383411 eV = 2 Rydberg.
an example	:	calculation.control.energyUnit = au

calculation.control.angleUnit¶

key word	:	calculation.control.angleUnit
possible values	:	d, deg, deg., degree,
		r, rad, rad., radian,
		where d, deg, deg., and degree are for degree,
		and r, rad, rad., and radian are for radian.
default value	:	degree
description	:	the unit of angle used in the input file.
an example	:	calculation.control.angleUnit = r

calculation.control.precision¶

key word	:	calculation.control.precision
possible values	:	high, normal, low
default value	:	normal
description	:	used to control default values of the following
		parameters:
		calculation.realspacegrids.E_cutoff
		low — 20 Hartree
		normal — 50 Hartree
		high — 150 Hartree
		calculation.k_spacegrids.L_cutoff
		low — 20 Bohr
		normal — 40 Bohr
		high — 80 Bohr
		calculation.complexEcontour.numberOfPoints
		low — 20
		normal — 40
		high — 60
		calculation.complexEcontour.numberOfPoints2
		low — 4
		normal — 8
		high — 16
		calculation.realEcontour.interval
		low — 2e-3 Hartree
		normal — 5e-4 Hartree
		high — 1e-4 Hartree
		calculation.realEcontour.eta
		low — 5e-4 Hartree
		normal — 2e-5 Hartree
		high — 1e-6 Hartree
		calculation.SCF.convergenceCriteria
		low — 1e-3 Hartree for hamiltonian matrix
		and 1e-3 for density matrix
		normal — 1e-4 Hartree for hamiltonian matrix
		and 1e-4 for density matrix
		high — 1e-5 Hartree for hamiltonian matrix
		and 1e-5 for density matrix
an example	:	calculation.control.precision = normal

calculation.control.parallel¶

key word	:	calculation.control.parallel
possible values	:	1, true, 0, false
default value	:	false
description	:	If it is true or 1, the calculator will work in a
		parallel calculation mode. Otherwise, it will work in a
		serial calculation mode. Note that for parallel
		computations, MPICH2 needs to be set up first.
an example	:	calculation.control.parallel = false

calculation.control.dataFormat¶

key word	:	calculation.control.dataFormat
possible values	:	compact, distributed
default value	:	compact
description	:	If compact, all calculated data will be saved in the
		class object; if distributed, calculated data will be
		saved separately.
an example	:	calculation.control.dataFormat = distributed

calculation.control.networkFileSystem¶

key word	:	calculation.control.networkFileSystem
possible values	:	1, true, 0, false
default value	:	true
description	:	Network File System (NFS) is a protocol allowing a
		computer to access files over a network as easily as if
		the network device was attached to the local disks of
		the computer. In a parallel calculation, when
		control.networkFileSystem is set to true, only one copy
		of calculated data is saved, and each processor will use
		the same copy through the network. When
		control.networkFileSystem is false, each processor saves
		its own copy of the calculated data.
an example	:	calculation.control.networkFileSystem = true

calculation.control.logOutputLevel¶

key word	:	calculation.control.logOutputLevel
possible values	:	an integer array
default value	:	[1 1]
description	:	logOutputLevel is designed to control both the log
		output to screen and to files. If the length of the
		logOutputLevel is n, there will be n-1 log files
		generated. logOutputLevel(1) is for screen control and
		logOutputLevel(ii+1) is for the control of the iith
		file. The higher the value of logOutputLevel is, the
		more detailed information will be written into the log
		file.
		Note: If only one log file is requested, it is named as
		log.txt. If more than one log files are requested, their
		names will be named like log3.txt or log5.txt, where the
		integer 3 or 5 in the name is the corresponding output
		level.
an example	:	calculation.control.logOutputLevel = [1 1]

calculation.control.txtResultsOutputLevel¶

key word	:	calculation.control.txtResultsOutputLevel
possible values	:	an integer
default value	:	1
description	:	Some calculated results may be given in files of *.mat
		(also in .xml, some also in .txt) format.
		txtResultsOutputLevel is used to control the output of
		those files.

		if it is 0,
		no *.mat file will be saved

		if it is >= 1,
		Hamiltonian.mat (Hamiltonian matrix of the whole system)
		DensityMatrix.mat (density matrix of the part related to
		the central region) are saved.

		if it is >= 2, in addition,
		DensityFunction.mat (real space charge density, the part
		within the central box)
		PotentialFunctionVeff.mat (real space potential function
		Veff, i.e. sum of the potential functions
		delta-hartree and exchange-correlation, the part
		within the central box)

		if it is >= 3, in addition,
		HamiltonianMatrixT.mat (the kinetic component of the
		hamiltonian matrix, the part related to the
		central region)
		HamiltonianMatrixVna.mat (the neutral-atom component of
		the Hamiltonian matrix, the part related to the
		central region)
		HamiltonianMatrixVnl.mat (the nonlocal pseudopotential
		component of the Hamiltonian matrix, the part
		related to the central region)
		HamiltonianMatrixVeff.mat (the effective potential
		component, i.e. sum of delta-Hartree and
		exchange-correlation components of the
		Hamiltonian matrix, the part related to the
		central region)
		HamiltonianMatrixVhubbard.mat (the Hubbard component of
		the Hamiltonian matrix, the part related to the
		central region)
		HamiltonianMatrixVso.mat (the spin-orbit-interaction
		component of the Hamiltonian matrix, the part
		related to the central region)

		if it is >= 4, in addition,
		DensityFunctionRna.mat (real space neutral-atom charge
		density, the part within the central box)
		PotentialFunctionVna.mat (real space neutral-atom
		potential function Vna, i.e. sum of the
		neutral-atom Coulomb potential and
		local pseudopotential, the part within the
		central box)
		PotentialFunctionVdh.mat (real space delta-Hartree
		potential function Vdh, the part within the
		central box)
		PotentialFunctionVxc.mat (real space exchange-correlation
		potential function Vxc, the part within the
		central box)

		if it is >= 5, in addition,
		HamiltonianMatrixStaticPartOfH.mat (the static part of
		the Hamiltonian matrix, the part related to the
		central region)

		if it is >= 6, in addition,
		DensityFunctionRpc.mat (real space partial-core charge
		density, the part within the central box)
		DensityFunctionReffna.mat (real space effective
		neutral-atom charge density, i.e. an effective
		charge density which produces a Coulomb
		potential that is exactly same as Vna, the part
		within the central box)
an example	:	calculation.control.txtResultsOutputLevel = 1

calculation.control.largeSystem¶

key word	:	calculation.control.largeSystem
possible values	:	1, true, 0, false
default value	:	determined by nanodcal.
description	:	If it is true or 1, nanodcal will use some special
		algorithms for saving memory, otherwise, it will use
		other algorithms for saving time.
an example	:	calculation.control.largeSystem = false

calculation.control.byPassCentralCellCheck¶

key word	:	calculation.control.byPassCentralCellCheck
possible values	:	1, true, 0, false
default value	:	false
description	:	Only used for open system. If it is false or 0, the
		code will automatically check the consistency between
		the central cell vectors and lead cell vectors, and the
		positions of the atoms in the central cell and in the
		lead cells. If it is true or 1, nanodcal will pass by
		the check for saving time.
an example	:	calculation.control.byPassCentralCellCheck = true

calculation.control.temporaryDirectory¶

key word	:	calculation.control.temporaryDirectory
possible values	:	any string representing the directory where some
		temporary data generated during the calculation will be
		saved.
default value	:	./temporarydata
description	:	This input is for the user to redirect the temporary
		data generated during a calculation.
an example	:	calculation.control.temporaryDirectory = ./tmp1

Pseudopotential parameters¶

This section summarizes the parameters of the pseudopotential.

calculation.pseudoPotential.nonOverlapInteractionMode¶

key word	:	calculation.pseudoPotential.nonOverlapInteractionMode
possible values	:	0, 1, 2
default value	:	2
description	:	A non-local pseudo-potential matrix ($V_{nl}$) element
		$<\phi_i \| V_{nl} \| \phi_j>$ can be non-zero even when the two
		atomic orbital functions $\|\phi_i>$ and $\|\phi_j>$ do not
		overlap. This parameter is for controlling the
		calculation of those non-overlapping Vnl elements.
		If nonOverlapInteractionMode is 0, all non-overlapping
		Vnl elements will be set to zero. If it is 2, none of
		the non-overlapping Vnl elements will be set to zero.
		If it is 1, the element $<\phi_i \| V_{nl} \| \phi_j>$ will be
		set to zero when and only when there is no orbital in
		the cell which contains $\|\phi_i>$ overlap with any orbital
		in the image cell which contains $\|\phi_j>$.
an example	:	calculation.pseudoPotential.nonOverlapInteractionMode = 1

calculation.pseudoPotential.Lmax4Vnl¶

key word	:	calculation.pseudoPotential.Lmax4Vnl
possible values	:	an integer
default value	:	2
description	:	The highest angular momentum used in the
		Kleinman-Bylander Vnl projector. Namely, those
		projectors having angular momentum higher than Lmax4Vnl
		will not be used in the calculation of Vnl.
an example	:	calculation.pseudoPotential.Lmax4Vnl = 3

Spin-orbit interaction parameters¶

calculation.spinOrbitInteraction.isIncluded¶

key word	:	calculation.spinOrbitInteraction.isIncluded
possible values	:	1, true, 0, false
default value	:	false
description	:	If it is true or 1, the effect of spin-orbit
		interaction will be taken into account. Only used for
		systems having the spinType of GeneralSpin.
an example	:	calculation.spinOrbitInteraction.isIncluded = true
feature status	:	experimental.

Hubbard parameters¶

The parameters in this section are for LDA+U calculations.

calculation.Hubbard.isIncluded¶

key word	:	calculation.Hubbard.isIncluded
possible values	:	1, true, 0, false
default value	:	false
description	:	If it is true or 1, a Hubbard-like term, the so called
		LDA+U, is added to the potential.
an example	:	calculation.Hubbard.isIncluded = true
feature status	:	experimental.

calculation.Hubbard.parameterBlock¶

key word	:	calculation.Hubbard.parameterBlock
possible values	:	N (the number of atomic species whose Hubbard U
		values needs to be re-defined.)
default value	:	no default value, must input when Hubbard.isIncluded is
		true
description	:	This block is used to overwrite the default Hubbard U
		values of specified atomic basis. There must be
		exactly N lines in the block, and followed by a line of
		end used as a end mark of the block. Each line
		has two strings, which specify the AtomType and
		OrbitalType of the atomic basis respectively, and
		enough U values for s, p, d, and f orbitals,
		respectively.
		Note that the unit of the U values is defined by the
		parameter calculation.control.energyUnit.
an example	:
		calculation.Hubbard.parameterBlock = 3
		Fe DZP 0 0 2
		Co DZP 0 0 4
		Ni DZP 0 0 3 6
		end
feature status	:	experimental.

Occupation function parameters¶

The parameters here are for setting up the distribution function.

calculation.occupationFunction.name¶

key word	:	calculation.occupationFunction.name
possible values	:	a string to describe the occupation function:
		FermiDirac: Fermi-Dirac distribution
default value	:	FermiDirac
description	:	The given function is used to determines the occupation
		of the electronic states.
an example	:	calculation.occupationFunction.name = FermiDirac

calculation.occupationFunction.temperature¶

key word	:	calculation.occupationFunction.temperature
possible values	:	a double value
default value	:	0 for open systems and 100 for closed systems.
description	:	electronic temperature of the system, in the unit of K.
		Although it is a physical property of the system, it is
		often used as a parameter to stabilize calculations in
		some cases.
		Note: the Boltzmann constant k = 8.617342e-05(eV/K) /
		27.2113834(eV/Hartree) = 3.1668151e-06 (Hartree/K).
an example	:	calculation.occupationFunction.temperature = 100

Real space grid parameters¶

The parameters here are for generating real space numerical grids.

calculation.realspacegrids.number¶

key word	:	calculation.realspacegrids.number
possible values	:	3$\times$1 integer vector or a integer number
default value	:	determined from the value of realspacegrids.E_cutoff
description	:	the small grid number in each direction. It is used
		to divide the central cell into the input number of
		small grids.
an example	:	calculation.realspacegrids.number = [64 64 64]

calculation.realspacegrids.E_cutoff¶

key word	:	calculation.realspacegrids.E_cutoff
possible values	:	a double number with proper energy unit such as
		eV,
		Ryd, Ryd., Rydberg,
		au, a.u., atomic unit, Hartree,
		where au a.u., and atomic unit are for Hartree,
		Ryd, Ryd. for Rydberg.
default value	:	20, 50, or 150 Hartree, depending on the value of the
		parameter calculation.control.precision.
description	:	the equivalent energy cut-off of the grid density.
		E_cutoff ~ (1/2)($\pi$/grid_length) $^{2}$.
		This input parameter is not used when
		realspacegrids.number is given.
		Note that if the number part of the input is missing, it
		will be considered as 1, and if the unit part is
		missing, it will be considered to use the unit defined
		by calculation.control.energyUnit.
an example	:	calculation.realspacegrids.E_cutoff = 50

calculation.realspacegrids.clusterfactor¶

key word	:	calculation.realspacegrids.clusterfactor
possible values	:	an integer number
default value	:	5
description	:	Defines the number of grid points in each direction
		which are grouped into a cluster for saving index
		storage on the grids.
an example	:	calculation.realspacegrids.clusterfactor = 5

k_space grid parameters¶

The parameters here are for generating Fourier space numerical grids.

calculation.k_spacegrids.number¶

key word	:	calculation.k_spacegrids.number
possible values	:	3$\times$1 integer array
default value	:	determined by the value of k_spacegrids.L_cutoff
description	:	the small k-space grid number in each direction. It is
		used to divide the Brillouin zone into the input
		number of small grids.
an example	:	calculation.k_spacegrids.number = [8 8 8]

calculation.k_spacegrids.L_cutoff¶

key word	:	calculation.k_spacegrids.L_cutoff
possible values	:	a double number with proper length unit such as
		au, a.u., atomic unit, Bohr
		an, ang, angstrom,
		nm, nanometer,
		where au a.u., and atomic unit are for Bohr,
		an and ang for angstrom, and nm for nanometer.
default value	:	20, 40, or 80 Bohr, depending on the value of the
		parameter calculation.control.precision.
description	:	the equivalent length cut-off of the k-space grid
		density. k-space grid length ~ ($\pi$/L_cutoff).
		The input parameter will not be used when
		k_spacegrids.number is given.
		Note that if the number part of the input is missing, it
		will be considered as 1, and if the unit part is
		missing, it will be considered to use the unit defined
		by calculation.control.lengthUnit.
an example	:	calculation.k_spacegrids.L_cutoff = 40

calculation.k_spacegrids.shift¶

key word	:	calculation.k_spacegrids.shift
possible values	:	3$\times$1 or 1$\times$3 array, [s$_1$, s$_2$, s$_3$], with each s$_i$ a
		double number between 0 and 1.
default value	:	[0 0 0]
description	:	k-space grid point shift. While all s$_i$ are set to be 0,
		the Gamma point is always among the k-space grid points
		being generated; otherwise, the k-space grid points will
		be shifted s$_1$, s$_2$, and s$_3$ grid length along their
		grid vector directions, respectively.
an example	:	calculation.k_spacegrids.shift = [1/2 1/2 1/2]

Energy contour parameters¶

The parameters here are for setting up the contour integration over energy for calculating the density matrix from the Green’s functions.

calculation.complexEcontour.type¶

key word	:	calculation.complexEcontour.type
possible values	:	smallSemiCircle, middleSemiCircle,
		largeSemiCircle, doubleSemiCircle
default value	:	smallSemiCircle
description	:	Type of energy contour to be used in the integration of
		the equilibrium part of lesser Greens function. See
		user manual for more information about the choice of
		complex contour.
an example	:	calculation.complexEcontour.type = smallSemiCircle
		largeSemiCircle, doubleSemiCircle

calculation.complexEcontour.numberOfPoints¶

key word	:	calculation.complexEcontour.numberOfPoints
possible values	:	an integer
default value	:	20, 40, or 60, depending on the value of the
		parameter calculation.control.precision.
description	:	Number of energy points used on the complex energy
		contour for integrating the equilibrium part of
		the lesser Greens function.
		(Note: if the system temperature is not
		zero, numberOfPoints is the number of energy points on
		the circle part of the contour.)
an example	:	calculation.complexEcontour.numberOfPoints = 40

calculation.complexEcontour.lowestEnergyPoint¶

key word	:	calculation.complexEcontour.lowestEnergyPoint
possible values	:	a double number with proper energy unit such as
		eV,
		Ryd, Ryd., Rydberg,
		au, a.u., atomic unit, Hartree,
		where au a.u., and atomic unit are for Hartree,
		Ryd, Ryd. for Rydberg.
default value	:	determined by nanodcal
description	:	The lowest energy point on the complex energy contour.
		Note that if the number part of the input is missing, it
		will be considered as 1; if the unit part is
		missing, it will be considered as using the unit defined
		by calculation.control.energyUnit.
an example	:	calculation.complexEcontour.lowestEnergyPoint = 40

calculation.complexEcontour.Delta¶

key word	:	calculation.complexEcontour.Delta
possible values	:	an integer
default value	:	10
description	:	Used only in the finite temperature case. The number of
		poles of the Fermi function which are enclosed in the
		complex energy contour.
an example	:	calculation.complexEcontour.Delta = 10

calculation.complexEcontour.gamma¶

key word	:	calculation.complexEcontour.gamma
possible values	:	an integer
default value	:	20
description	:	Used only in the finite temperature case. The length (in
		unit kT) of the straight portion of the complex energy
		contour that is below the Fermi energy.
an example	:	calculation.complexEcontour.gamma = 20

calculation.complexEcontour.numberOfPoints2¶

key word	:	calculation.complexEcontour.numberOfPoints2
possible values	:	an integer
default value	:	4, 8, or 16, depending on the value of the
		parameter calculation.control.precision.
description	:	Used only in cases of finite temperature. The number of
		energy points on the straight part of the complex
		energy contour for integrating the equilibrium part
		of lesser Greens function.
an example	:	calculation.complexEcontour.numberOfPoints2 = 6

calculation.realEcontour.numberOfPoints¶

key word	:	calculation.realEcontour.numberOfPoints
possible values	:	an integer
default value	:	determined using the value of realEcontour.interval
description	:	Number of energy points on the real energy axis
		for integrating the non-equilibrium part of
		lesser Greens function.
an example	:	calculation.realEcontour.numberOfPoints = 40

calculation.realEcontour.interval¶

key word	:	calculation.realEcontour.interval
possible values	:	a double number
default value	:	2e-3, 5e-4, or 1e-4 Hartree, depending on the value of the
		parameter calculation.control.precision.
description	:	Energy interval used to determine the number of energy
		points for integrating the non-equilibrium part
		of lesser Greens function on the real energy axis. This
		input is not used when realEcontour.numberOfPoints is
		given.
an example	:	calculation.realEcontour.interval = 5e-4

calculation.realEcontour.etaSigma¶

key word	:	calculation.realEcontour.etaSigma
possible values	:	a small double number
default value	:	1e-6 Hartree
description	:	the small eta used in the calculation of self-energy
		along the real energy contour. In analytical Greens
		function theory, the eta is a positive infinitesimal.
an example	:	calculation.realEcontour.etaSigma = 1e-4

calculation.realEcontour.etaGF¶

key word	:	calculation.realEcontour.etaGF
possible values	:	a small double number
default value	:	1e-6 Hartree
description	:	the small eta used in the calculation of Greens function
		along the real energy contour. In analytical Greens
		function theory, this is a positive infinitesimal.
an example	:	calculation.realEcontour.etaGF = 1e-4

calculation.realEcontour.eta¶

key word	:	calculation.realEcontour.eta
possible values	:	a small double number
default value	:	5e-4, 2e-5, or 1e-6 Hartree, depending on the value of the
		parameter calculation.control.precision.
description	:	the small eta used in the calculation of self-energy
		and/or Greens function along the real energy contour.
		This parameter is not used when the parameter
		realEcontour.etaSigma and/or realEcontour.etaGF is
		given.
an example	:	calculation.realEcontour.eta = 1e-4

Exchange-correlation functional parameters¶

The parameters here are used in various exchange-correlation (XC) functionals. In nanodcal, XC functional calculation is done by plug-in calculators. Several XC functionals can be chosen by the user. On the other hand, the users can input their own XC functionals by plug-in their calculators to nanodcal.

calculation.xcFunctional.calculator¶

key word	:	calculation.xcFunctional.calculator
possible values	:	a structure with two fields of class and parameter
default value	:	determined by nanodcal
description	:	This input parameter defines a plug-in calculator,
		where the field class clarifies the name of the
		calculator, and the field parameter gives its
		construction parameter. The constructor of the plug-in
		calculator will be called in the following manner:
		calculator = constructor([cp])
		where
		[cp] = calculation.xcFunctional.calculator.parameter

		For information about how to replace this plug-in
		calculator, type nanodcal -help plug-in and nanodcal -api.
an example	:	calculation.xcFunctional.calculator.class = XC_cell
		calculation.xcFunctional.calculator.parameter.Type …
		= LDA_VWN80

calculation.xcFunctional.Type¶

key word	:	calculation.xcFunctional.Type
possible values	:	LDA_PZ81, LDA_VWN80, LDA_PW92, GGA_PBE96,
		GGA_REVPBE98, GGA_RPBE99, mixed
default value	:	LDA_PZ81
description	:	The type of exchange-correlation functional to be
		used. While LDA_PZ81, LDA_VWN80, LDA_PW92,
		GGA_PBE96, GGA_REVPBE98, and GGA_RPBE99 are
		well-known functionals, the option mixed is
		for users to mix different types of
		exchange and/or correlation functionals.

		If calculation.xcFunctional.calculator is given, this
		parameter will not be used.
an example	:	calculation.xcFunctional.Type = LDA_PZ81
		GGA_REVPBE98, GGA_RPBE99, mixed

calculation.xcFunctional.Weight¶

key word	:	calculation.xcFunctional.Weight
possible values	:	2$\times$2 cell array when a well-known exchange and
		correlation functional is used; n X 2 cell array, with n
		a integer, when the mixed type of exchange and
		correlation functional is used.
default value	:	{X,1.0;C,1.0} for regular type; no default value for
		mixed type.
description	:	When a well-known exchange and correlation functional is
		used, it gives weights for the exchange energy and the
		correlation energy. When mixed type is used, it
		specifies the exchange and/or correlation functionals
		to be mixed and the corresponding mixing weights.
		All exchange and correlation functionals which may be
		used in the mixing is listed as follows with a short
		description:
		xLDA — LDA exchange
		cPZ81 — PZ correlation (Phys. Rev. B 23, 5048)
		cVWN80 — VWN correlation (Can. J. Phys. 58, 1200)
		cPW92 — PW92 correlation (Phys. Rev. B 45, 13244)
		xPBE96 — PBE exchange (Phys. Rev. Lett. 77, 3865)
		xREVPBE98 — REVPBE exchange (Phys. Rev. Lett. 80, 890)
		xRPBE99 — RPBE exchange (Phys. Rev. B 59, 7413)
		xEV93 — EV exchange (Phys. Rev. B 47, 13164)
		cPBE96 — PBE correlation (Phys. Rev. Lett. 77, 3865)

		If calculation.xcFunctional.calculator is given, this
		parameter will not be used.
an example	:	(for regular type)
		calculation.xcFunctional.Weight = {X,1.0;C,1.0}
another example	:	(for mixed type):
		calculation.xcFunctional.Weight = …
		{xLDA,0.2;cVWN80,1.0;xPBE96,0.8}

calculation.xcFunctional.Lagrange¶

key word	:	calculation.xcFunctional.Lagrange
possible values	:	an integer
default value	:	3
description	:	Lagrange parameter is for 2N+1 Point Lagrange polynomial
		interpolation to calculate charge density gradient.

		If calculation.xcFunctional.calculator is given, this
		parameter will not be used.
an example	:	calculation.xcFunctional.Lagrange = 3

External Hamiltonian modifier parameters¶

Nanodcal allows users to add/replace terms to the Kohn-Sham Hamiltonian by using plug-in calculators. Parameters here specify the Hamiltonian modifier.

calculation.hExternalModifier.isIncluded¶

key word	:	calculation.hExternalModifier.isIncluded
possible values	:	1, true, 0, false
default value	:	false
description	:	If it is true or 1, the external Hamiltonian modifier
		defined in calculation.hExternalModifier.calculator will
		be used.
an example	:	calculation.hExternalModifier.isIncluded = true

calculation.hExternalModifier.calculator¶

key word	:	calculation.hExternalModifier.calculator
possible values	:	a structure with two fields of class and parameter
default value	:	no default value, must be input when
		hExternalModifier.isIncluded is true.
description	:	This input parameter defines a plug-in calculator,
		where the field class clarifies the name of the
		calculator, and the field parameter gives its
		construction parameter. The constructor of the plug-in
		calculator will be called in the following manner:
		calculator = constructor([cp])
		where
		[cp] = calculation.hExternalModifier.calculator.parameter

		Only used when hExternalModifier.isIncluded is true.

		For information about how to replace this plug-in
		calculator, type nanodcal -help plug-in and nanodcal -api.
an example	:	calculation.hExternalModifier.calculator.class …
		= cHModifierByB
		calculation.hExternalModifier.calculator.parameter.B …
		= [0 0 10] Tesla

External self-energy modifier parameters¶

Nanodcal allows users to calculate self-energy of the device leads using methods of their own - instead of using the methods of nanodcal. The parameters here are for this purpose.

calculation.sigmaExternalModifier.isIncluded¶

key word	:	calculation.sigmaExternalModifier.isIncluded
possible values	:	1, true, 0, false
default value	:	false
description	:	If it is true or 1, the external self-energy modifier
		defined in calculation.sigmaExternalModifier.calculator
		will be used.
an example	:	calculation.sigmaExternalModifier.isIncluded = true

calculation.sigmaExternalModifier.calculator¶

key word	:	calculation.sigmaExternalModifier.calculator
possible values	:	a structure with two fields of class and parameter
default value	:	no default value, must be input when
		sigmaExternalModifier.isIncluded is true.
description	:	This input parameter defines a plug-in calculator,
		where the field class clarifies the name of the
		calculator, and the field parameter gives its
		construction parameter. The constructor of the plug-in
		calculator will be called in the following manner:
		calculator = constructor([cp])
		where
		[cp] = calculation.sigmaExternalModifier.calculator.parameter

		Only used when sigmaExternalModifier.isIncluded is true.

		For information about how to replace this plug-in
		calculator, type nanodcal -help plug-in and nanodcal -api.
an example	:	calculation.sigmaExternalModifier.calculator.class …
		= cAbstractSelfEnergyModifier
		calculation.sigmaExternalModifier.calculator.parameter …
		= $[\ ]$

External real-space density modifier parameters¶

Nanodcal allows users to modify real-space charge density. Parameters here are for this function.

calculation.rhoExternalModifier.isIncluded¶

key word	:	calculation.rhoExternalModifier.isIncluded
possible values	:	1, true, 0, false
default value	:	false
description	:	If it is true or 1, the external real space density
		modifier defined in rhoExternalModifier.calculator will
		be used.
an example	:	calculation.rhoExternalModifier.isIncluded = true

calculation.rhoExternalModifier.calculator¶

key word	:	calculation.rhoExternalModifier.calculator
possible values	:	a structure with the two fields of class and parameter
default value	:	no default value, must be input when
		rhoExternalModifier.isIncluded is true.
description	:	This input parameter defines a plug-in calculator,
		where the field class clarifies the name of the
		calculator, and the field parameter gives its
		construction parameter. The constructor of the plug-in
		calculator will be called in the following manner:
		calculator = constructor([cp])
		where
		[cp] = calculation.rhoExternalModifier.calculator.parameter

		Only used when rhoExternalModifier.isIncluded is true.

		For information about how to replace this plug-in
		calculator, type nanodcal -help plug-in and nanodcal -api.
an example	:	calculation.rhoExternalModifier.calculator.class …
		= cAbstractRealspaceDensityModifier
		calculation.rhoExternalModifier.calculator.parameter …
		= $[\ ]$