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DISCLAIMER
Contents
1. Introduction
1.1 Citation
1.2 User Feedback
2. Getting Started
2.1 Input File Structure
2.2 Simple Input File -- SCF geometry optimization
2.3 Water Molecule Sample Input File
2.4 Input Format and Syntax for Directives
2.4.1 Input Format
2.4.2 Format and syntax of directives
3. NWChem Architecture
3.1 Database Structure
3.2 Persistence of data and restart
4. Functionality
4.1 Molecular electronic structure
4.2 Relativistic effects
4.3 Pseudopotential plane-wave electronic structure
4.4 Periodic system electronic structure
4.5 Molecular dynamics
4.6 Python
4.7 Parallel tools and libraries (ParSoft)
5. Top-level directives
5.1 START and RESTART -- Start-up mode
5.2 SCRATCH_DIR and PERMANENT_DIR -- File directories
5.3 MEMORY -- Control of memory limits
5.4 ECHO -- Print input file
5.5 TITLE -- Specify job title
5.6 PRINT and NOPRINT -- Print control
5.7 SET -- Enter data in the RTDB
5.8 UNSET -- Delete data in the RTDB
5.9 STOP -- Terminate processing
5.10 TASK -- Perform a task
5.10.1 TASK Directive for Electronic Structure Calculations
5.10.2 TASK Directive for Special Operations
5.10.3 TASK Directive for the Bourne Shell
5.10.4 TASK Directive for QM/MM simulations
5.11 CHARGE -- Total system charge
6. Geometries
6.1 Keywords on the GEOMETRY directive
6.2 Symmetry Group Input
6.3 Cartesian coordinate input
6.4 Z-matrix input
6.5 ZCOORD -- Forcing internal coordinates
6.6 Applying constraints in geometry optimizations
6.7 SYSTEM -- Lattice parameters for periodic systems
7. Basis sets
7.1 Basis set library
7.2 Explicit basis set definition
8. Effective Core Potentials
8.1 Scalar ECPs
8.2 Spin-orbit ECPs
9. Relativistic All-electron Approximations
9.1 Douglas-Kroll approximation
9.2 Dyall's Modified Dirac Hamitonian approximation
10. Hartree-Fock or Self-consistent Field
10.1 Wavefunction type
10.2 SYM -- use of symmetry
10.3 ADAPT - symmetry adaptation of MOs
10.4 TOL2E -- integral screening threshold
10.5 VECTORS -- input/output of MO vectors
10.5.1 Superposition of fragment molecular orbitals
10.5.2 Atomic guess orbitals with charged atoms
10.6 Accuracy of initial guess
10.7 THRESH -- convergence threshold
10.8 MAXITER -- iteration limit
10.9 RI-SCF -- resolution of the identity approximation
10.10 PROFILE -- performance profile
10.11 DIIS -- DIIS convergence
10.12 DIRECT and SEMIDIRECT -- recomputation of integrals
10.12.1 Integral File Size and Format for the SCF Module
10.13 SCF Convergence Control Options
10.14 NR -- controlling the Newton-Raphson
10.15 LEVEL -- level-shifting the orbital Hessian
10.16 Orbtial Localization
10.17 Printing Information from the SCF Module
10.18 Hartree-Fock or SCF, MCSCF and MP2 Gradients
11. DFT for Molecules (DFT)
11.1 Specification of Basis Sets for the DFT Module
11.2 VECTORS and MAX_OVL -- KS-MO Vectors
11.3 XC and DECOMP -- Exchange-Correlation Potentials
11.3.1 Optional Exchange Functionals
11.3.2 Optional Correlation Functionals
11.3.3 Combined Exchange and Correlation Functionals
11.4 ITERATIONS -- Number of SCF iterations
11.5 CONVERGENCE -- SCF Convergence Control
11.6 GRID -- Numerical Integration of the XC Potential
11.6.1 Angular grids
11.6.2 Partitioning functions
11.6.3 Radial grids
11.6.4 Grid Scheme
11.7 TOLERANCES -- Screening tolerances
11.8 DIRECT and NOIO -- Hardware Resource Control
11.9 DFT, ODFT and MULT -- Open shell systems
11.10 SIC -- Self-Interaction Correction
11.11 MULLIKEN -- Mulliken analysis
11.12 Print Control
12. Spin-Orbit DFT (SODFT)
13. COSMO
14. DFT for Periodic Systems (GAPSS)
14.1 Specification of Basis Sets for the GAPSS Module
14.2 CORRELATION and EXCHANGE -- Exchange-Correlation Potentials
14.2.1 Optional Functionals
14.3 Numerical Integration
14.4 Summations and Integrations for a Periodic System
14.5 SCF Iterative Procedure
15. MP2
15.1 Input directives
15.1.1 FREEZE -- Freezing orbitals
15.1.2 TIGHT -- Increased precision
15.1.3 PRINT and NOPRINT
15.1.4 VECTORS -- MO vectors
15.1.5 RI-MP2 fitting basis
15.1.6 FILE3C -- RI-MP2 3-center integral filename
15.1.7 RIAPPROX -- RI-MP2 Approximation
15.1.8 Advanced options for RI-MP2
15.2 One-electron properties and natural orbitals
16. Multiconfiguration SCF
16.1 ACTIVE -- Number of active orbitals
16.2 ACTELEC -- Number of active electrons
16.3 MULTIPLICITY
16.4 SYMMETRY -- Spatial symmetry of the wavefunction
16.5 STATE -- Symmetry and multiplicity
16.6 VECTORS -- Input/output of MO vectors
16.7 HESSIAN -- Select preconditioner
16.8 LEVEL -- Level shift for convergence
16.9 PRINT and NOPRINT
17. Selected CI
17.1 Background
17.2 Files
17.3 Configuration Generation
17.3.1 Specifying the reference occupation
17.3.2 Applying creation-annihilation operators
17.3.3 Uniform excitation level
17.4 Number of roots
17.5 Accuracy of diagonalization
17.6 Selection thresholds
17.7 Mode
17.8 Memory requirements
17.9 Forcing regeneration of the MO integrals
17.10 Disabling update of the configuration list
17.11 Orbital locking in ci geometry optimization
18. Coupled Cluster Calculations
18.1 MAXITER -- Maximum number of iterations
18.2 THRESH -- Convergence threshold
18.3 TOL2E -- integral screening threshold
18.4 DIISBAS -- DIIS subspace dimension
18.5 FREEZE -- Freezing orbitals
18.6 IPRT -- Debug printing
18.7 PRINT and NOPRINT
18.8 Methods (Tasks) Recognized
18.9 Debugging and Development Aids
18.9.1 Switching On and Off Terms
19. Geometry Optimization with DRIVER
19.1 Convergence criteria
19.2 Available precision
19.3 Controlling the step length
19.4 Maximum number of steps
19.5 Discard restart information
19.6 Regenerate internal coordinates
19.7 Initial Hessian
19.8 Mode or variable to follow to saddle point
19.9 Optimization history as XYZ files
19.10 Print options
20. Geometry Optimization with STEPPER
20.1 MIN and TS -- Minimum or transition state search
20.2 TRACK -- Mode selection
20.3 MAXITER -- Maximum number of steps
20.4 TRUST -- Trust radius
20.5 CONVGGM, CONVGG and CONVGE -- Convergence criteria
20.6 Backstepping in Stepper
20.7 Initial Nuclear Hessian Options
21. Hybrid Calculations with ONIOM
21.1 Real, model and intermediate geometries
21.1.1 Link atoms
21.1.2 Numbering of the link atoms
21.2 High, medium and low theories
21.2.1 Basis specification
21.2.2 Effective core potentials
21.2.3 General input strings
21.3 Use of symmetry
21.4 Molecular orbital files
21.5 Restarting
21.6 Examples
21.6.1 Hydrocarbon bond energy
21.6.2 Optimization and frequencies
21.6.3 A three-layer example
21.6.4 DFT with and without charge fitting
22. Vibrational frequencies
22.1 Vibrational Module Input
22.1.1 Hessian File Reuse
22.1.2 Redefining Masses of Elements
22.1.3 Animation
22.1.4 An Example Input Deck
23. DPLOT
23.1 GAUSSIAN -- Gaussian Cube format
23.2 TITLE -- Title for Insight
23.3 LIMITXYZ -- Plot limits
23.4 SPIN -- Density to be plotted
23.5 OUTPUT -- Filename for Insight
23.6 VECTORS -- MO vector file name
23.7 WHERE -- Density evaluation
23.8 ORBITAL -- Orbital sub-space
23.9 Examples
24. Properties
24.1 Subdirectives
24.1.1 Nbofile
25. Electrostatic potentials
25.1 Grid specification
25.2 Constraints
25.3 Restraints
26. Prepare
26.1 Default database directories
26.2 System name and coordinate source
26.3 Sequence file generation
26.4 Topology file generation
26.5 Appending to an existing topology file
26.6 Generating a restart file
27. Molecular dynamics
27.1 Introduction
27.1.1 Spacial decomposition
27.1.2 Topology
27.1.3 Files
27.1.4 Databases
27.1.5 Force fields
27.2 Format of fragment files
27.3 Creating segment files
27.4 Creating sequence files
27.5 Creating topology files
27.6 Creating restart files
27.7 Molecular simulations
27.8 System specification
27.9 Parameter set
27.10 Energy minimization algorithms
27.11 Multi-configuration thermodynamic integration
27.12 Time and integration algorithm directives
27.13 Ensemble selection
27.14 Velocity reassignments
27.15 Cutoff radii
27.16 Polarization
27.17 External electrostatic field
27.18 Constraints
27.19 Long range interaction corrections
27.20 Fixing coordinates
27.21 Autocorrelation function
27.22 Print options
27.23 Periodic updates
27.24 Recording
27.25 Program control options
28. Analysis
28.1 Reference coordinates
28.2 File specification
28.3 Selection
28.4 Coordinate analysis
28.5 Essential dynamics analysis
28.6 Trajectory format conversion
28.7 Electrostatic potentials
29. Combined quantum and molecular mechanics
29.1 EATOMS
30. File formats
31. Pseudopotential Plane-Wave DFT (PSPW)
31.1 PSPW Tasks
31.1.1 STEEPEST_DESCENT
31.1.2 CONJUGATE_GRADIENT
31.1.3 Car-Parrinello
31.1.4 PSP_FORMATTER
31.1.5 WAVEFUNCTION_INTITIALIZER
31.1.6 V_WAVEFUNCTION_INITIALIZER
31.1.7 WAVEFUNCTION_EXPANDER
31.1.8 PSP_GENERATOR
31.2 PSPW RTDB Entries and DataFiles
31.2.1 Ion Positions
31.2.2 Ion Velocities
31.2.3 Simulation Cell
31.2.4 Analysis: Mulliken RTDB data
31.2.5 Wavefunction Datafile
31.2.6 Velocity Wavefunction Datafile
31.2.7 Formatted Pseudopotential Datafile
31.2.8 One-Dimensional Pseudopotential Datafile
31.2.9 PSPW Car-Parrinello Output Datafiles
31.3 Minimizing the DFT Energy Functional
31.3.1 Steepest Descent Equations
31.3.2 Conjugate Gradient with Curvature: Grassmann Manifold
31.4 Car-Parrinello Scheme for Ab Initio Molecular Dynamics
31.4.1 Verlet Algorithm for Integration
31.4.2 Constant Temperature Simulations: Nose-Hoover Thermostats
31.5 PSPW Tutorial 1: Minimizing the one-electron orbitals by Running a Steepest Descent and Conjuagate Gradient Simulation in Tandem
31.6 PSPW Tutorial 2: Running a Car-Parrinello Simulation
31.7 PSPW Capabilities and Limitations
31.8 Questions and Difficulties
32. Controlling NWChem with Python
32.1 How to input and run a Python program inside NWChem
32.2 NWChem extensions
32.3 Examples
32.3.1 Hello world
32.3.2 Scanning a basis exponent
32.3.3 Scanning a basis exponent revisited.
32.3.4 Scanning a geometric variable
32.3.5 Scan using the BSSE counterpoise corrected energy
32.3.6 Scan the geometry and compute the energy and gradient
32.3.7 Reaction energies varying the basis set
32.3.8 Using the database
32.3.9 Handling exceptions from NWChem
32.3.10 Accessing geometry information -- a temporary hack
32.3.11 Scaning a basis exponent yet again -- plotting and handling child processes
32.4 Troubleshooting
33. Interfaces to Other Programs
33.1 NBO -- Natural Bond Orbital Analysis
34. Acknowledgments
A. Standard Basis Sets
B. Sample input files
B.1 Water SCF calculation and geometry optimization in a 6-31g basis
B.1.1 Job 1. Single point SCF energy
B.1.2 Job 2. Restarting and perform a geometry optimization
B.2 Compute the polarizability of Ne using finite field
B.2.1 Job 1. Compute the atomic energy
B.2.2 Job 2. Compute the energy with applied field
B.3 SCF energy of HCO using ECPs for C and O
B.4 MP2 optimization and CCSD(T) on nitrogen
C. Examples of geometries using symmetry
C.1 methanol
C.2 water
C.3 acetylene
C.4 ethylene
C.5 methane
C.6 buckminsterfullerene
C.7 porphyrin
C.8 iron penta-carbonyl
C.9 sodium crown ether
C.10 ammonia
C.11 benzene
C.12
C.13 ferrocene
C.14
C.15 trans-dichloroethylene
C.16
C.17 cyclopentadiene anion
C.18 gold tetrachloride
D. Running NWChem
D.1 Sequential execution
D.2 Parallel execution on UNIX-based parallel machines including workstation clusters using TCGMSG
D.3 Parallel execution on UNIX-based parallel machines including workstation clusters using MPI
D.4 Parallel execution on MPPs
D.5 IBM SP
D.6 Cray T3E
D.7 Linux
D.8 Alpha systems with Quadrics switch
D.9 Windows 98 and NT
D.10 Tested Platforms and O/S versions
Next:
1. Introduction
Up:
user
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DISCLAIMER
Jorge Garza Olguin 2003-04-28
