1.per script

#!perl

#

# Purpose: This script builds a 'correct' methane molecule from scratch

use strict;

use warnings;

use MaterialsScript qw(:all);

#Utility function to create an atom of a specific type in a doc

#  Optionally creates a bond to that atom

sub CreateAtom {

   # Bond information ($bondTo, $bondType) is optional

   my ($doc, $element, $pos, $bondTo, $bondType) = @_;

 

   my $newAtom = $doc->CreateAtom($element, $pos);

 

   # Only build the bond if the bond information is present

   if($bondTo && $bondType) {

       $doc->CreateBond($newAtom, $bondTo, $bondType);

   }

 

   return $newAtom;

}

my $doc = Documents->New("Methane.xsd");

#To demonstrate Forcite Minimization put the H atoms in a planar cross

my $centralC = CreateAtom($doc, "C", Point(X => 1, Y => 1, Z => 1));

CreateAtom($doc, "H", Point(X => 1, Y => 0, Z => 1), $centralC, "Single");

CreateAtom($doc, "H", Point(X => 2, Y => 1, Z => 1), $centralC, "Single");

CreateAtom($doc, "H", Point(X => 1, Y => 2, Z => 1), $centralC, "Single");

CreateAtom($doc, "H", Point(X => 0, Y => 1, Z => 1), $centralC, "Single");

#Minimize the structure

Modules->Forcite->GeometryOptimization->Run($doc);

$doc->Save;

2.CASTEP Energy taskobject = module->EnergyDescription

Computes the single point energy of a structure using the CASTEP server.

Applies to

• CASTEP module

Return type

A task object

Using the CASTEP Energy task

Refer to the top-level CASTEP documentation for more details about CASTEP calculations and their settings.

Configuration

Use ChangeSettings on the CASTEP module, or pass the settings into the Run function. The Energy settings are applicable to all CASTEP tasks. The following settings are specific to the Energy task and fall into 12 categories:

• Basic settings

• K-mesh setup

• Detailed electronic settings

• General property calculations

• General K-mesh setup for property calculations

• Phonon calculation properties

• DOS and band structure properties

• NMR properties

• Optical properties

• Core Level Spectroscopy properties

• Raman properties

• Import fields

• Import Fermi Surface

<!--<variables start here>--><!--<variables end here>-->

Setting	Default	Values	Description
Basic settings
TheoryLevel	GGA	LDA GGA HF HF-LDA sX sX-LDA PBE0 B3LYP	The exchange-correlation functional theory level.
NonLocalFunctional	PBE	PBE RPBE PW91 WC PBESOL	The GGA density functional to use.
LocalFunctional	CA-PZ	CA-PZ	The LDA density functional to use.
SpinPolarized	No	No Yes	If "Yes" different wavefunctions for different spins will be used. If "No" the same orbitals for alpha and beta spins are used.
UseFormalSpin	Yes	No Yes	If "Yes" the initial value for the number of unpaired electrons for each atom will be taken from the formal spin specified for each atom.
UseLDAU	No	No Yes	If "Yes" the LDA+U formalism will be used.
UseDFTD	No	No Yes	If "Yes" the DFT-D correction will be used.
DFTDMethod	TS	OBS TS Grimme	The preferred DFT-D correction method to use (if the method is not supported by the exchange-correlation functional default method for the functional will be used).
UseCoreHoles	No	No Yes	If "Yes" core holes will be included in the calculation.
Charge	0	−9999 to 9999	The total charge on the unit cell.
Quality	Medium	Express Coarse Medium Fine Ultra-fine	The overall quality of the calculation. This should be the first setting modified as changing the quality will modify all quality dependent settings.
UseInsulatorDerivation	No	No Yes	Use coarser setting for insulators.
SCFMinimizationAlgorithm	Density Mixing	Density Mixing All Bands/EDFT	The electronic minimization method to be used for the SCF calculation.
UseBasisCorrection	Smart	Smart Always Never	The finite basis set correction used in the evaluation of energy and stress. If "Smart" the correction is only applied when stress is required.
Smearing	0.1	0.01 to 10.0	The electronic broadening width to use in a variable occupancy calculation.
Pseudopotentials	Ultrasoft	Ultrasoft Norm-conserving On the fly	The type of pseudopotential to be used. "Ultrasoft" is preferred, "Norm-conserving" may be computationally expensive, and "On the fly" is required for calculation of NMR properties.
InitialSpin	0	−9999 to 9999	The initial value for the number of unpaired electrons in a spin-polarized calculation. This starting value will be subsequently optimized during the calculation.
OptimizeTotalSpin	Yes	No Yes	If "Yes" the total spin will be varied for the current SCF state with variable occupancy.
FixOccupancy	Yes	No Yes	If "Yes" the electronic occupation numbers will be fixed during electronic minimization. Only the lowest occupied states will be included in the calculation.
DensityMixingScheme	Pulay	Linear Kerker Pulay Broyden	The method used for mixing the input densities and output densities from the current iteration to obtain the input density for the next iteration in the solution for the SCF.
EmptyBands	20	0 to 9999	The number of additional bands to be included in an electronic minimization as a percentage of the number of occupied bands.
AdjustSymmetry	No	No Yes	If "Yes" the symmetry of the system will be increased or decreased automatically according to the type of calculation.
K-mesh setup
KPointOverallQuality	Medium	Gamma Coarse Medium Fine	Quality of k-point grid, combined with derivation rules.
KPointDerivation	Quality	Quality Separation Gamma ustomGrid	How the k-point grid is derived.
KPointQuality	Medium	Coarse Medium Fine	Quality of k-point grid.
KPointSeparation	0.05	0.001 to 10.0	k-point separation (1/Å).
OriginA	0.0	−0.5 to 0.5	k-point grid offset along a-axis.
OriginC	0.0	−0.5 to 0.5	k-point grid offset along c-axis.
OriginB	0.0	−0.5 to 0.5	k-point grid offset along b-axis.
ParameterA	4	1 to 50	k-point grid parameter along a-axis.
ParameterB	4	1 to 50	k-point grid parameter along b-axis.
ParameterC	4	1 to 50	k-point grid parameter along c-axis.
Detailed electronic settings
EnergyCutoffQuality	Medium	Coarse Medium Fine Ultra-fine	The precision used for the plane wave basis set.
UseCustomEnergyCutoff	No	No Yes	If "Yes" a custom value for the EnergyCutoff can be used.
EnergyCutoff	250.0	10.0 to 99999.0	A custom value for the plane-wave energy cutoff for wavefunction basis. Only available when UseCustomEnergyCutoff => "Yes".
MaximumSCFCycles	100	1 to 9999	The maximum number of SCF cycles.
EnergyTolerancesScope	Atom	Atom Cell	If "Atom" energy convergence tolerances are used per atom, otherwise the energy convergence tolerances per cell are used.
SCFConvergence	2.0E-6	>1.0E-14	The SCF convergence tolerance per atom, used only if EnergyTolerancesScope => "Atom".
SCFConvergencePerCell	0.0001	>1.0E-14	The SCF convergence tolerance per cell, used only EnergyTolerancesScope => "Cell".
ElectronicConvergenceWindow	3	2 to 5	Convergence tolerance window for SCF.
PseudopotentialRepresentation	Reciprocal Space	Reciprocal Space Real Space	The representation of pseudopotentials.
RealSpaceTransformEnergy	250.0	10.0 to 99999.0	The energy cutoff for real-space transformation of pseudopotentials.
UseCustomRealSpaceTransformEnergy	No	No Yes	If "Yes" a value for the cutoff of the real space transformation energy can be specified by RealSpaceTransformEnergy.
RealSpaceQuality	Medium	Coarse Medium Fine	The tolerance for the transformation.
FFTQuality	Standard	Standard Fine Precise	The quality of the FFT grid.
FFTFineGrid	1.0	≤4.0	The quality of the augmented FFT grid.
BasisSetCorrectionMode	Automatic	Automatic Manual	The method for calculating the finite basis set correction.
NumBasisPoints	3	2 to 9	The number of energy points to use in evaluating the energy derivative required for the finite basis set correction. A converged SCF energy will be evaluated at each point.
BasisSetEnergyDerivative	0.0	≤0.0	The value of the energy derivative required for the finite basis set correction when BasisSetCorrectionMode => "Manual".
TotalSpinOptimizationDelay	6	1 to 99	The number of SCF iterations for which the total electronic spin will remain fixed before being allowed to vary.
ImposeRealSpaceTransformTolerance	Yes	No Yes	If "Yes" the real space pseudopotential transformation will have the quality set by RealSpaceQuality imposed.
DIISHistory	20	1 to 50	The number of previous iterations to be considered in the DIIS for the Pulay or Broyden density mixing method. Only used when DensityMixingScheme => "Broyden" or "Pulay".
DensityMixingAmplitude	0.5	0.001 to 1.0	The amplitude of the output density to mix with the input density to obtain input for the next iteration.
DensityMixingCutoff	1.5	0.01 to 100.0	Density mixing is reduced for Fourier coefficients at reciprocal lattice vectors less than this value.
SpinMixingCutoff	1.5	0.01 to 100.0	Spin mixing is reduced for Fourier coefficients at reciprocal lattice vectors less than about this value. Only used when DensityMixingScheme => "Broyden", "Kerker", or "Pulay".
SpinMixingAmplitude	2.0	0.001 to 10.0	The amplitude of the output spin density to mix with the input spin density to obtain input for the next iteration. Only used when SpinPolarized => "Yes".
RuntimeOptimization	Default	Default Memory Speed	The strategy used to balance memory use and speed during the calculation.
General property calculations
CalculateCharge	None	None Mulliken Hirshfeld	Calculate and assign Mulliken or Hirshfeld atomic charges.
CalculateSpin	None	None Mulliken Hirshfeld	Calculate and assign Mulliken or Hirshfeld spins.
CalculateBondOrder	None	None Mulliken	Calculate and assign Mulliken bond orders.
CalculateStress	No	No Yes	Calculates the stress tensor.
BondPopulationCutoff	3.0	>0.01	The maximum interatomic distance, in Å, to be considered in the bond population calculations.
General K-mesh setup for property calculations
PropertiesKPointQuality	Medium	Coarse Medium Fine	Quality of k(q)-point grid to be used for all properties calculations requested (BandStructure, PhononDispersion, DOS, CalculatePhononDOS, Optics, CoreLevelSpectrum).
PropertiesKPointSeparation	0.05	0.001 to 10.0	k(q)-point separation (1/Å) to be used for all properties calculations requested (BandStructure, PhononDispersion, DOS, CalculatePhononDOS, Optics, CoreLevelSpectrum).
Phonon calculation properties
CalculatePolarizability	None	None Crystal Molecule Linear	Calculate Polarizability.
CalculatePhononDOS	None	None Full Partial	Calculate and plot phonon Full/Partial DOS.
CalculatePhononDispersion	None	None Dispersion DispersionAndDos	Calculate and plot phonon dispersion.
CalculateThermodynamics	None	None Full	Calculate and plot thermodynamic properties with the Debye temperature.
PolarizabilityConvergence	1.0E-5	>1.0E-9	The convergence criterion, in Å3, for the second-order response to the electric fields during a polarizability run.
PhononMethod	Linear response	Linear response Finite displacement	The technique to be used to calculate phonon frequencies.
PhononRcut	5.0	0.0 to 100.0	The real space cutoff radius, in Å, for dynamical matrix calculations.
PhononUseInterpolation	Yes	No Yes	If "Yes" the real space dynamical matrix will be calculated using the Monkhorst-Pack mesh defined by the separation parameter.
PhononInterpolationSpacing	0.05	0.01 to 10.0	The q-point separation parameter, in Å-1, which represents the average distance between Monkhorst-Pack mesh q-points used in the real space dynamical matrix calculations.
PhononDOSCalcLOTO	Yes	No Yes	If "Yes" a non-analytical correction to the dynamical matrix will be applied. The LO-TO phonon frequency splitting at the G-point will be calculated for phonon DOS calculations.
PhononDOSConvergence	1.0E-5	>1.0E-9	The convergence criterion, in eV Å-2, for the electronic eigenvalues during a phonon DOS run.
PhononDispCalcLOTO	Yes	No Yes	If "Yes" a non-analytical correction to the dynamical matrix will be applied. The LO-TO phonon frequency splitting at the G-point will be calculated for phonon dispersion calculations.
PhononDispConvergence	1.0E-5	>1.0E-9	The convergence criterion, in eV Å-2, for the electronic eigenvalues during a phonon dispersion run.
ImportHessian	No	No Yes	Imports the Hessian (Dynamical matrix for G-point).
PhononDOSNormalization	1	1 3N	The normalization style for phonon DOS.
PhononDOSInterpolationBroadening	0.05	0.001 to 100	The instrumental broadening effects (in THz).
PhononDOSIntegrationMethod	Smearing	Smearing Interpolation	The preferred method for DOS generation.
PhononDOSSmearingWidth	0.1	0.001 to 100	The width of Gaussian smearing (in THz).
PhononDOSInterpolationAccuracy	Coarse	Coarse Medium Fine	The required interpolation accuracy.
PhononUnits	THz	meV THz cm-1	The frequency units to be used for the phonon dispersion graph.
PhononDispersionLineStyle	Line	Points Line	The line style for phonon dispersion graphs.
StartTemperature	5.0	>0.1	The lower limit for the temperature scale for plotting thermodynamics.
EndTemperature	1000.0	>0.1	The upper limit for the temperature scale for plotting thermodynamics.
DOS and band structure properties
CalculateBandStructure	None	None Dispersion DispersionAndDos	Calculate and plot dispersion.
BandStructureNumExtraBands	12	0 to 999	The number of additional bands to use in eigenvalue calculation.
BandStructureEnergyTolerance	1.0E-5	>1.0E-8	The convergence criterion for electronic eigenvalues during the band structure calculation.
BandStructureUseNewXC	No	No Yes	If "Yes" a different exchange-correlation functional is used for the band structure calculation.
BandStructureTheoryLevel	GGA	LDA GGA HF HF-LDA sX sX-LDA PBE0 B3LYP	The exchange-correlation functional theory level to use for the band structure calculation.
BandStructureLocalFunctional	CA-PZ	CA-PZ	The LDA density functional to use for the band structure calculation.
BandStructureNonLocalFunctional	PBE	PBE RPBE PW91 WC PBESOL	The GGA density functional to use for the band structure calculation.
BandStructureLineStyle	Line	Points Line	The line style for band graphs.
CalculateDOS	None	None Full Partial	Calculate and plot Full/Partial DOS.
DOSNumExtraBands	12	0 to 999	The number of additional bands to use in eigenvalue calculation.
DOSEnergyTolerance	1.0E-5	>1.0E-8	The convergence criterion for electronic eigenvalues during the DOS calculation.
DOSUseNewXC	No	No Yes	If "Yes" a different exchange-correlation functional is used for the band structure calculation.
DOSTheoryLevel	GGA	LDA GGA HF HF-LDA sX sX-LDA PBE0 B3LYP	The exchange-correlation functional theory level to use for the DOS calculation.
DOSLocalFunctional	CA-PZ	CA-PZ	The LDA density functional to use for the DOS calculation.
DOSNonLocalFunctional	PBE	PBE RPBE PW91 WC PBESOL	The GGA density functional to use for the DOS calculation.
DOSInterpolationBroadening	0.05	0.0 to 100	The instrumental broadening effects (in eV).
DOSPreferredIntegrationMethod	Smearing	Smearing Interpolation	The preferred method for DOS generation.
DOSSpinDisplay	Total	Total Alpha Beta Alpha and Beta Spin Total and Spin	The type of DOS to plot.
DOSorTOS	DOS	DOS Integrated DOS	Whether to plot DOS or Integrated DOS (Number of States).
DOSSmearingWidth	0.2	0.005 to 100	The width of Gaussian smearing (in eV).
DOSInterpolationAccuracy	Coarse	Coarse Medium Fine	The required interpolation accuracy.
PartialS	Yes	No Yes	If "Yes" includes the S angular momentum term of the partial DOS.
PartialP	Yes	No Yes	If "Yes" includes the P angular momentum term of the partial DOS.
PartialD	Yes	No Yes	If "Yes" includes the D angular momentum term of the partial DOS.
PartialF	Yes	No Yes	If "Yes" includes the F angular momentum term of the partial DOS.
PartialSum	Yes	No Yes	If "Yes" includes the sum of angular momentum terms of the partial DOS.
NMR properties
CalculateNMR	None	None Crystal Molecule	Calculate and assign NMR shielding and electric field gradients.
NMRCalculation	Shielding and EFG	Shielding EFG Shielding and EFG	The type of NMR properties calculated.
NMRMaxSteps	250	1 to 999	The maximum number of conjugate gradient steps taken for each electronic band in the electronic minimizer during an NMR calculation.
Optical properties
CalculateOptics	None	None Full	Calculate and plot various optical properties.
OpticsNumExtraBands	12	1 to 999	The number of additional bands to use in eigenvalue calculation.
OpticalEnergyTolerance	1.0E-5	>1.0E-8	The convergence criterion for electronic eigenvalues during the optical properties calculation.
OpticsUseNewXC	No	No Yes	If "Yes" a different exchange-correlation functional is used for the optical properties calculation.
OpticsTheoryLevel	GGA	LDA GGA HF HF-LDA sX sX-LDA PBE0 B3LYP	The exchange-correlation functional theory level to use for the optical properties calculation.
OpticsNonLocalFunctional	PBE	PBE RPBE PW91 WC PBESOL	The GGA density functional to use for the optical properties calculation.
OpticsLocalFunctional	CA-PZ	CA-PZ	The LDA density functional to use for the optical properties calculation.
ScissorsOperator	0.0	>0.0	The scissors operator to be used in plotting the band structure for insulators.
OpticsSmearing	0.5	>0.0001	The Gaussian broadening to be used for calculating the dielectric function.
OpticsGeometry	Polarized	Polarized Unpolarized Polycrystalline	the type of optical properties calculation.
PlasmaFrequency	0.0	>0.0	The Omg plasma value required to calculate the Drude term.
DrudeDamping	0.05	0.0001 to 10	The lifetime broadening value required to calculate the Drude term.
OpticsUnits	eV	eV nm cm-1	The frequency units used for the display of optical properties.
Polarization1	1.0		First coordinate of the polarization (or incident direction) vector.
Polarization2	0.0		Second coordinate of the polarization (or incident direction) vector.
Polarization3	0.0		Third coordinate of the polarization (or incident direction) vector.
Core Level Spectroscopy properties
CalculateCoreLevelSpectrum	None	None Absorption Emission	Calculate and plot core level spectra of the chosen type.
EELSEmax	25	0.0 to 100.0	The energy limit above the Fermi level for which core level spectra will be calculated.
EELSEnergyTolerance	1.0E-5	>1.0E-8	The convergence criterion for electronic eigenvalues during the core level spectra calculation.
EELSSpectrum	1s	1s 2s ... 4d	The core level.
EELSUseSpinOrbit	Yes	No Yes	If "Yes" spin-orbit splitting for the core level is added to the spectrum.
EELSBroadening	0.2	0.02 to 10.0	The Gaussian broadening from the instrument to be used.
EELSUseLifetime	Yes	No Yes	If "Yes" lifetime broadening effects will be taken into account.
EELSCalculation	Unpolarized	Polarized Unpolarized	The polarization of the incident radiation for the core level spectroscopy calculation.
EELSPolarization1	1.0		The direction of the polarization of the incident radiation in fractional (lattice) coordinates. Only available when EELSCalculation => "Polarized".
EELSPolarization2	0.0		The direction of the polarization of the incident radiation in fractional (lattice) coordinates. Only available when EELSCalculation => "Polarized".
EELSPolarization3	0.0		The direction of the polarization of the incident radiation in fractional (lattice) coordinates. Only available when EELSCalculation => "Polarized".
Raman properties
CalculateRaman	None	None Activity Intensity	Calculate and plot Raman intensity.
RamanUnits	cm-1	meV THz cm-1	The units for the X axis of the spectrum.
RamanSmearing	10.0	0.1 to 100.0	The Gaussian broadening to be used in cm-1.
RamanWaveLength	514.5	0.001 to 1000000.	The incident light wavelength in nm when CalculateRaman => "Intensity".
RamanTemperature	10.0	0.1 to 10000.0	The temperature in K when CalculateRaman => "Activity".
RamanInverseEnergy	No	No Yes	If "Yes" the values on the X axis (energy) will decrease from right to left.
RamanInverseIntensity	No	No Yes	If "Yes" the values on the Y axis (intensity) will decrease from bottom to top.
Import fields
CalculateChargeDensity	None	None Field FieldAndIsosurface	Calculate Charge Density and import results.
CalculateSpinDensity	None	None Field FieldAndIsosurface	Calculate Spin Density and import results.
CalculateDensityDifference	None	None Field FieldAndIsosurface	Calculate Density Difference and import results.
CalculatePotential	None	None Field FieldAndIsosurface	Calculate Potential and import results.
CalculateSTMprofile	None	None Field FieldAndIsosurface	Calculate STM profile and import results.
CalculateELF	None	None Field FieldAndIsosurface	Calculate ELF and import results.
Import Fermi Surface
ImportFermiSurface	No	No Yes	If "Yes" all the sheets of Fermi surface will be imported in the document.

Running

The calculation is started using the Run function on this task.

Examples

The following example shows how to run an Energy calculation on the document NaCl.xsd with coarse quality.

my $doc = $Documents{"NaCl.xsd"}; my $outputData = Modules->CASTEP->Energy->Run($doc, Settings(Quality => "Coarse" ) ); See also

Run
Modules collection
CASTEP module

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