Contents
Release 97.2, May 1998
Table of Contents
1. Introduction
- What Is DMol?
- DMol--The Insight and standalone modes of operation
- Comparison of the Insight and standalone modes of DMol
- Starting DMol
- Using this guide
- Additional information
- Notes on command names
2. Theory and Implementation
- Density functional theory (DFT)
- Numerical basis sets
- Numerical integration
- Evaluation of the effective potential
- Computational self-consistent field procedure
- Energy gradients
- Electron gas model
- Point-group symmetry
- Geometry optimization -- The OPTIMIZE suite of algorithms
- Introduction
- Theory and implementation
- The EF algorithm and mode following
- Constrained optimization
- GDIIS
- COSMO--solvation effects
- DMol/COSMO
- Determination of the cavity surface (or solvent-accessible surface)
- Determination of nonelectrostatic contributions to the free energy of solvation
- Electric field gradients
- Fitting atomic point charges to the electrostatic potential (ESP)
- Optical absorption spectra
- Density of states analysis
- Mulliken and Mayer bond orders
- Statistical thermodynamics
- Theory
- Thermodynamic quantities
- Implementation
3. General Methodology
- Choosing a job type
- Energy calculation
- Geometry optimization
- Vibrational frequencies
- Setting up the computation
- Molecule size and hardware requirements
- Outline of basic steps for a DMol calculation
4. Command Summary--The Insight Environment
- Setup pulldown
- Symmetry pulldown
- Optimize pulldown
- Environment pulldown
- Background_Job pulldown
- Run pulldown
- Analyze pulldown
5. Methodology--Insight
- Using DMol in the Insight environment
- Outline of basic steps of a DMol calculation
- Step 1: Defining the molecule
- Step 2: Setting up the calculation parameters
- Step 3: Performing the DMol calculation
- Step 4: Analyzing the results
- Setting up calculations with the commands in the DMol module
- Beginning a DMol session
- Defining the molecule and its point-group symmetry
- Specifying the system and type of calculation
- Finding and adjusting the point-group symmetry
- Specifying parameters that control the calculation
- Using the Setup/Parameters command
- Choosing functionals
- Parameters controlling the basis set
- Electronic state and environment parameters
- SCF parameters
- Properties and population analysis parameters
- COSMO--solvation effects
- Vibrational parameters
- Using OPTIMIZE in the Insight environment
- Volumetric and print parameters
- Setup_Grid_Output command
- Setting up the background job
- Starting the job
- Monitoring a background job
- Visual aids to analyzing results
- Displaying orbital contours
- Displaying charges
- Displaying optical absorption spectra
- Specifying isotopes
- Displaying normal mode vibrations
- Statistical thermodynamics
- Displaying density-of-states information
- Displaying a summary of DMol output
- Using other Insight pulldowns
6. Tutorial--The Insight Environment
- Pilot online tutorials
- Overview of tutorial lessons
7. Command Summary--Standalone Mode
- General keywords for setting up the calculation
- Basis and grid keywords
- Input for SCF calculation
- Specification of electronic state
- Input for geometry optimization
- COSMO--solvation effects
- Specification of optional functions
- Input for calculation of vibrational frequencies
8. Methodology--Standalone Mode
- Using DMol in the standalone mode
- Basics steps for a DMol calculation
- DMol input preparation utility: dmol_master
- Creating a new .input file
- Running dmol_master without any previously existing input files
- Use of the new geometry optimizer/transition state finder in standalone mode
- OPTIMIZE keywords in the .input file
- Fixed Cartesian coordinates
- Dummy atoms
- Constraints
- Point group symmetry in standalone mode
- COSMO--solvation effects
- ESP-fitted charges
- Notes on point charges
APPENDICES
A. References
B. Glossary
C. Files
- Input files
- Sample .input file
- .inmol file
- .car and .arc files
- .pchg file
- COSMO input files
- espfit.inp file
- q_isotopes.dat file
- Input for statistical mechanics analysis
- .coord file (standalone mode only)
- .zmat file (standalone mode only)
- .gzmat file (standalone mode only)
- .symdec file
- Output files
- .sum file
- Short form of summary file
- History Form of Summary File
- .outmol file
- Water example
- HSOH example including ESP-fitted point charges
- .cosmo file
- Occupancy file
- Optical absorption results
- Plot files
- .hess File
- Output from statistical mechanics
- Scratch files
D. Utilities
- Background jobs in the Insight environment
- Shell scripts and utilities
- DAtom utility
- Overview
- Input
- DAtom output
- File management
- Basis set summary
- Memory allocation in DMol
E. Commands--Standalone Mode
- Format for documenting DMol standalone commands
- Keyword specifications
- Basis
- Bond_Order
- Calculate
- Charge
- Constraint
- Cosmo
- DIIS
- Direct
- Displacement_Convergence
- Electric_Field
- Electrostatic_Moments
- ESP_Charges
- Fixed
- Fixoc
- Frozen
- FrqRestart
- Functionals
- GC_Correlation
- GC_Exchange
- GDIIS
- Geometry
- Gradient_Convergence
- Grid
- Hessian_File
- Hessian_Update
- Hirshfeld_Analysis
- Integration_Grid
- Lmax
- Local_Correlation
- Locate
- Lower_Energy_Limit
- Max_Displacement
- Mixing_Alpha
- Mixing_Beta
- Mulliken_Analysis
- NDiff
- Nonlocal
- Nuclear_EFG
- Number_Bad_Steps
- Occupation
- Opt_Coordinate_System
- Opt_Cycles
- Opt_Energy_Convergence
- Opt_Print
- Opt_Use_Symmetry
- Optical _Absorption
- Partial_DOS
- Plot
- Point_Charges
- Population_Analysis
- Print
- Project
- SCF_Density_Convergence
- SCF_Energy_Convergence
- SCF_Iterations
- SCF_Restart
- Smear
- Solvate
- Spin
- Symmetry
- TS_Mode
- Upper_Energy_Limit
- Vibdiff
INDICES
List of Figures
List of Tables
Cross-Index of Old and New Keywords
Index
Last updated January 8, 1998.
Copyright © 1997, 1998, Molecular Simulations, Inc. All rights
reserved.