Quantum 1 Modules



E       DMol3--Keyword Reference

This section correlates the names of controls found in the control panels of the Cerius2·DMol3 interface with the keywords contained in the input file that is actually used by the DMol3 executable. Cross references lead you to the full documentation of each keyword in DMol3--Keyword Descriptions.

Since control panels are the interface to related sets of commands, this section also serves as a functional index to frequently used DMol3 keywords (all keywords are listed alphabetically in DMol3--Keyword Descriptions).


DMol3 Run control panel

The DMol3 Run control panel and the keywords that it controls allow you to set up the run name, calculation task, basis sets, and method for the DMol3 calculation. This control panel is also used to open other control panels.

control name keyword function
Task  
Calculate  
Calculation type.  
Method  
Functional  
Density functional (additional choices are available on the DMol3 Method Options control panel).  
Basis Set  
Basis  
Type of numerical atomic orbital basis set (additional choices are available on the DMol3 Basis Sets Choice control panel).  
Charge  
Charge  
Molecular charge (not used for periodic models).  
Core  
Pseudopotential  
Use effective core potentials or all-electron scalar relativity.  
Calculate Electronic Properties  
 
Properties specified in the Properties... panel will be calculated during the DMol3 calculations.  
Output Options  
Print  
Select level of descriptive output to be printed in the output files.  
Environment  
 
Uniform electric field or the COSMO solvation model.  
SCF Options  
 
Select parameters concerned with the SCF calculation to be performed.  


DMol3 Run Options control panel

The DMol3 Run Options control panel and the keywords that it controls allow you to set DMol3 resources.

control name keyword function
Memory  
Max_Memory  
Maximum memory (Megabytes) available for a DMol3 run.  
Loop Length  
Max_Loop  
Maximum size of program loops.  


DMol3 Geometry Optimization control panel

The DMol3 Geometry Optimization control panel and the keywords that it controls allow you to set the optimization method and convergence criteria for geometry or transition-state optimization.

control name keyword function
Energy  
Opt_Energy_Convergence  
Energy threshold for geometry optimization.  
Gradient  
Opt_Gradient_Convergence  
Gradient threshold for geometry optimization.  
Displacement  
Opt_Displacement_Convergence  
Convergence threshold for maximum atom displacement.  
Iterations  
Opt_Iterations  
Number of optimization cycles allowed.  
Continue without Optimization Convergence  
Opt_Iterations  
Continue calculation regardless of whether optimization is complete after Opt_Iterations.  
Coordinate Choice  
Opt_Coordinate_System  
Coordinate system to use in the DMol3 calculation.  
Hessian Update Scheme  
Opt_Hessian_Update  
Method for updating the Hessian (BFGS or Powell).  
Read Hessian from File  
Opt_Restart  
Read in a precalculated Hessian file to start the optimization.  


Optimization Parameters control panel

The Optimization Parameters control panel and the keywords that it controls allow you to set more specific parameters concerned with the optimization parameters.

control name keyword function
Modes Removed  
Opt_Hessian_Project  
Whether to remove all zero-frequency modes.  
Maximum Step Size  
Opt_Displacement_Convergence  
Maximum allowed step size.  
Gradient Tolerance for Steepest Descent Step  
Opt_Steep_Tol  
Gradient threshold to switch to steepest-descents method.  
Number of GDIIS Vectors  
Opt_GDIIS  
Maximum size of subspace for GDIIS.  


DMol3 Frequency control panel

The DMol3 Frequency control panel and the keywords that it controls allow you to set the frequency calculation parameters.

control name keyword function
Finite Difference Steps  
Vibration_Steps  
Use 1- or 2-point differences of gradients.  
Length  
Vibration_Steps  
Step size for finite differences.  
Modes Removed  
Vibration_Project  
Project all zero-frequency modes from the Hessian.  
Restart Frequency Calculation  
Vibration_Restart  
Restart on interrupted frequency calculation.  


DMol3 Transition State Search control panel

The DMol3 Transition State Search control panel and the keywords that it controls allow you to set the transition-state search parameters. These are the same keywords as specified in DMol3 Geometry Optimization control panel, with the addition of one keyword.

control name keyword function
Energy  
Opt_Energy_Convergence  
Energy threshold for geometry optimization.  
Gradient  
Opt_Gradient_Convergence  
Gradient threshold for geometry optimization.  
Displacement  
Opt_Displacement_Convergence  
Convergence threshold for maximum atom displacement.  
Iterations  
Opt_Iterations  
Number of optimization cycles allowed.  
Continue without Optimization Convergence  
Opt_Iterations  
Continue calculation regardless of whether optimization is complete after Opt_Iterations.  
Coordinate Choice  
Opt_Coordinate_System  
Coordinate system to use in the DMol3 calculation.  
Hessian Update Scheme  
Opt_Hessian_Update  
Method for updating the Hessian (BFGS or Powell).  
Read Hessian from File  
Opt_Restart  
Read in a precalculated Hessian file to start the optimization.  
Hessian Mode to Follow  
Opt_TS_Mode  
Which mode to follow in searching for the transition state.  


DMol3 Method Options control panel

The DMol3 Method Options control panel and the keywords that it controls allow you to set more specific parameters concerned with the method chosen.

control name keyword function
Density Functional Choice  
Functional  
Density functional.  
Apply Nonlocal DFT After Local DFT  
Functional_Post_LDA  
Perform nonlocal DFT energy calculation after the LDA task is completed.  
Numerical Integration Grid  
Integration_Grid  
Quality of numerical integration grid.  
Multipolar Expansion of Density  
Aux_Density  
Size of multipolar expansion for potential.  
Use Harris Functional  
Harris  
Use Harris functional approximation during the calculation.  


DMol3 Basis Sets Choice control panel

The DMol3 Basis Sets Choice control panel and the keywords that it controls allow you to set a basis set for each atom type.

control name keyword function
Basis Set  
Basis  
Type of numeric atomic orbital basis.  
Use a Real Space Cutoff  
Atom_Rcut  
Extension of the atomic basis set.  
Basis Set Version  
Basis_Version  
Basis set version used in calculations.  


DMol3 Electronic State Definition control panel

The DMol3 Electronic State Definition control panel and the keywords that it controls allow you to define the electronic state for a DMol3 calculation.

control name keyword function
Spin Polarization  
Spin_Polarization  
Use spin-restricted or -unrestricted wavefunctions.  
Constrain Spin  
Spin  
Excess of electrons of alpha over beta manifold.  
Initial Spin Populations  
Start_Spin_Populations  
Assign initial spin density on atoms.  
Occupations  
Occupation  
Orbital occupation specification.  


DMol3 Starting Spin Densities control panel

The DMol3 Starting Spin Densities control panel and the keywords that it controls allow you to set starting atomic spin densities.

control name keyword function
Spin on Selected Atoms  
Start_Spin_Populations  
Assign spin to selected atoms.  
Spin Scale Factor  
Start_Spin_Populations  
Assign spin, including scale factors, to selected atoms.  


DMol3 Molecular Properties control panel

The DMol3 Molecular Property control panel and the keywords that it controls allow you to specify which molecular properties DMol3 is to calculate.

control name keyword function
Mulliken Analysis  
Mulliken_Analysis  
Mulliken atomic population analysis (charge, population, or full).  
Density of States  
Partial_DOS  
Print the partial DOS coefficients to a .dos file.  
Hirshfeld Analysis  
Hirshfeld_Analysis  
Hirshfeld atomic population analysis (charge, dipole, or quadrupole).  
Orbitals Electron Densities Electron Potentials controls  
Plot  
Specify properties to be plotted (density, deformation, spin density, difference, potential, HOMO, LUMO, alpha density, beta density, Fermi, orbital).  
Bond Strength  
Bond_Order  
Calculate Mulliken and Mayer bond orders and valence indices (not for periodic models).  
Electrostatic Moments  
Electrostatic_Moments  
Compute dipole moment (not for periodic models).  
Nuclear Electric Field Gradients  
Nuclear_EFG  
Calculate electric field gradients at nuclei (not for periodic models).  
Calculate Spectrum  
Optical _Absorption  
Calculate optical absorption spectrum and write results to .optabs file (not for periodic models).  
from  
Lower_Energy_Limit  
Set lower bound for optical absorption spectrum (not for periodic models).  
to  
Upper_Energy_Limit  
Set upper bound for optical absorption spectrum (not for periodic models).  


DMol3 SCF Options control panel

The DMol3 SCF Options control panel and the keywords that it controls allow you to set specific parameters concerned with an SCF calculation.

control name keyword function
Convergence Criterion  
SCF_Density_Convergence  
Density convergence threshold for SCF equations.  
Maximum Number of Cycles  
SCF_Iterations  
Maximum number of SCF iterations.  
Continue without Optimization Convergence  
SCF_Iterations  
Continue calculation regardless of whether SCF converges.  
Number of DIIS Expansion Vectors  
SCF_DIIS  
Maximum size of subspace for DIIS procedure.  
Start DIIS below Convergence Value  
SCF_DIIS  
Start DIIS procedure after the convergence of the SCF falls below the threshold.  
Charge Mixing  
SCF_Charge_Mixing  
Mixing coefficient for charge density.  
Spin Mixing  
SCF_Spin_Mixing  
Mixing coefficient for spin density.  
Maximum Number of Bad SCF Cycles  
SCF_Number_Bad_Steps  
Number of bad (divergent) iterations before aborting SCF run.  
Direct SCF Procedure  
SCF_Direct  
Use direct version for SCF run.  
Restart SCF Calculations  
SCF_Restart  
Restart an SCF calculation from a previously converged wavefunction.  


DMol3 Environment control panel

The DMol3 Environment control panel and the keywords that it controls allow you to impose an external environment such as an electric field or COSMO solvent model.

control name keyword function
Apply Uniform E-Field  
Electric_Field  
Allows you to impose static electric field.  
COSMO Solvation  
COSMO  
COSMO model is used to represent solvent environment.  


DMol3 COSMO Environment control panel

The DMol3 COSMO Environment control panel and the keywords it controls allow you to set the COSMO calculations of the molecule in a solution.

control name keyword function
Solvent used  
COSMO_Dielectric  
The dielectric constant of the solvent used in DMol3/COSMO calculations.  
Calculate COSMO-RS properties  
COSMO_RS  
Macroscopic thermodynamic properties of solvents: G of hydration, vapor pressure, partition coefficients for octanol/water, benzene/water, hexane/water and diethylether/water.  


DMol3 COSMO Parameters panel

The DMol3 Parameters panel allows you to set the parameters for the DMol3/COSMO run. These are expert functionality parameters.

control name keyword function
Basic Grid Size  
COSMO_Grid_Size  
Grid size on the spheres centered at the atoms.  
Number of Segments  
COSMO_Segments  
Maximal number of segments in the COSMO surface grid per every atom.  
Radius Increment  
COSMO_Radius_Incr  
A factor to be added to element radii.  
Solvent Radius  
COSMO_Solvent_Radius  
Solvent probe radius.  
A-Matrix Cutoff  
COSMO_A-Matrix_Cutoff  
Accuracy of calculating interaction on the COSMO surface.  
Radius Correction  
COSMO_RadCorr_Incr  
Radius Increment to evaluate outlying charge correction.  
Model Type  
 
VWN-BP/DNP/Fine/v4.0.0 set of DMol3 parameters is recommended for COSMO_RS calculations.  
A-Constant  
B-Constant  
COSMO_A-Constraint COSMO_B-Constraint  
A and B parameters are used to approximate the nonelectrostatic contributions.  
Atomic Radii  
COSMO_Atomic_Radii  
Define atomic radii of the atoms present in the molecule.  


DMol3 COSMO Surface panel

The DMol3 COSMO Surface panel allows you to display screening charge density on a COSMO surface surrounding the molecule. Screening charges are the result of polarization of the solvent, represented as dielectric medium, by the charge distribution of the solute.

Sigma distribution plot displays population of surface segments as a function of the screening charge density.


DMol3 Output Options control panel

The DMol3 Output Options control panel and the keywords that it controls allow you to set the level of descriptive output sent to the .outmol file.

control name keyword function
several  
Print  
Select the level of descriptive output to be printed to the output (.outmol) file.  


DMol3 General Constraints control panel

The DMol3 General Constraints control panel and the keywords that it controls allow you to define coordinates, distances, angles, or dihedral angles to be constrained during geometry optimization.

control name keyword function
Constraint Type  
Opt_Constraint_Method  
Select method to handle constraints for optimization (Lagrange/Penalty, Lagrange, Penalty, Penalty/Lagrange).  
Define Constraint  
Opt_Fixed  
Number of atoms with Cartesian coordinates fixed during geometry optimization.  
Define Constraint  
Opt_Constraint  
Number of atoms constrained and the constrained value of internal coordinate (not for periodic models).  


DMol3 Symmetry control panel

The DMol3 Symmetry control panel and the keywords that it controls allow you to determine and specify the symmetry of nonperiodic models.

control name keyword function
Use Symmetry  
Symmetry  
Point-group symmetry.  


DMol3 MD_SimAnn control panel

control name keyword function
Molecular Dynamics  
Molecular_Dynamics  
Perform molecular dynamics simulation.  
Simulated Annealing  
Simulated_Annealing  
Perform simulated annealing.  




Last updated December 06, 1998 at 11:51AM Pacific Standard Time.
Copyright © 1998, Molecular Simulations, Inc. All rights reserved.