MOLCAS manual:
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Contents
List of Figures
List of Tables
1. Introduction to
MOLCAS
1.1
MOLCAS
, a quantum chemistry software
1.2 The
MOLCAS
Manuals
1.2.1 The three parts of the manual
1.2.2 Notation
1.2.3 Molcas documentation
1.3
MOLCAS-7
, new features and updates
1.4 Acknowledgment
1.5 Citation for
MOLCAS
1.6 Web addresses
1.7 Disclaimer
2. Introduction to the
MOLCAS
manual
I. Tutorials and Examples
3. How to run
MOLCAS
in a nutshell
3.1 Introduction
3.2 Environment Setup
3.3 Customization of molcas execution
3.4
MOLCAS
Command-Line Help System
3.5 Input Structure and EMIL Commands
3.6 Basic Examples
3.6.1 A simple calculation on water
3.6.2 Using a z-Matrix
3.6.3 Running a geometry optimization
3.6.4 Solvation effects
3.7 Basic and More Common Keywords
3.7.1 Environment and EMIL commands
3.7.2 GATEWAY - Definition of geometry, basis sets, and symmetry
3.7.3 SEWARD - An integral generation program
3.7.4 SCF - An SCF and DFT program
3.7.5 RASSCF - A multiconfigurational MCSCF program
3.7.6 CASPT2 - A second-order multiconfigurational perturbation program
3.7.7 RASSI - A state-interaction properties program
3.7.8 MCLR program - A multiconfigurational linear-response program
3.7.9 SLAPAF - A geometry-relaxation program
3.7.10 GRID_IT - A program to compute densities and graphical interface
3.7.11 MBPT2 - An MP2 program
3.7.12 MOTRA - A molecular-basis transformation program
3.7.13 CCSDT - A coupled-cluster program
3.8 Getting Information: Outputs and GUI
3.8.1 MING: a Graphical Molcas Input Generator
3.8.2 GV: Grid an Geometry visualization
4. Tutorials
4.1 Problem-based tutorials
4.1.1 Computing the electronic energy at fixed nuclear geometry
4.1.2 Optimizing geometries: minima, transition states, crossings, and minimum energy paths
4.1.3 Computing excited states
4.2 Program-based tutorials
4.2.1 GATEWAY -- A Molecule Handling Program
4.2.2 SEWARD -- An Integral Generation Program
4.2.3 SCF -- A Self-Consistent Field program and Kohn Sham DFT
4.2.4 RASSCF -- A Multi Configurational SCF Program
4.2.5 RASSI -- A RAS State Interaction Program
4.2.6 CASPT2 -- A Many Body Perturbation Program
4.2.7 CASVB -- A non-orthogonal MCSCF program
4.2.8 MOTRA -- An Integral Transformation Program
4.2.9 GUGA -- CI Coupling Coefficients Program
4.2.10 MRCI -- A Configuration Interaction Program
4.2.11 CPF -- A Coupled-Pair Functional Program
4.2.12 CCSDT -- A Set of Coupled-Cluster Programs
4.2.13 MBPT2 -- A Second-Order Many-Body PT RHF Program
4.2.14 FFPT -- A Finite Field Perturbation Program
4.2.15 VIBROT -- A Program for Vibration-Rotation on Diatomic Molecules
4.2.16 GENANO -- A Program to Generate ANO Basis Sets
4.2.17 ALASKA -- A Program for Integral Derivatives
4.2.18 SLAPAF -- A Program for Geometry Optimizations, Transition States, etc.
4.2.19 MCKINLEY -- A Program for Integral Second Derivatives
4.2.20 MCLR -- A Program for Linear Response Calculations
4.2.21 A Molecular Structure Optimization
4.2.22 Core and Embedding Potentials within the SEWARD Program
4.2.23 GRID_IT: A Program for Orbital Visualization
4.3 MOLCAS grid and geometry viewer
4.3.1 Editing molecular structures using the
GV
program.
4.3.2 Visualization of orbitals with gv.
4.3.3 Writing MOLDEN input
4.4 Most frequent error messages found in MOLCAS
5. Examples
5.1 Computing high symmetry molecules.
5.1.1 A diatomic heteronuclear molecule: NiH
5.1.2 A diatomic homonuclear molecule: C
2
5.1.3 A transition metal dimer: Ni
2
5.1.4 High symmetry systems in
MOLCAS
5.2 Geometry optimizations and Hessians.
5.2.1 Ground state optimizations and vibrational analysis
5.2.2 Excited state optimizations
5.2.3 Restrictions in symmetry or geometry.
5.2.4 Optimizing with Z-Matrix.
5.2.5 CASPT2 optimizations
5.3 Computing a reaction path.
5.3.1 Studying a reaction
5.4 High quality wave functions at optimized structures
5.5 Excited states.
5.5.1 The vertical spectrum of thiophene.
5.5.2 Influence of the Rydberg orbitals and states. One example: guanine.
5.5.3 Other cases.
5.6 Solvent models.
5.6.1 Kirkwood model.
5.6.2 PCM
5.6.3 Calculation of solvent effects: Kirkwood model.
5.6.4 Solvation effects in ground states. PCM model in formaldehyde.
5.6.5 Solvation effects in excited states. PCM model and acrolein.
5.7 Computing relativistic effects in molecules.
5.7.1 Scalar relativistic effects
5.7.2 Spin-Orbit coupling (SOC)
5.7.3 The PbO molecule
6. Acknowledgment
II. User's Guide
7. The
MOLCAS
environment
7.1 Overview
7.1.1 Programs in the system
7.2 Commands and environment variables
7.2.1 Commands
7.2.2 Project name and working directory
7.2.3 Input
7.2.4 Preparing a job
7.2.5 System variables
7.3 General input structure. EMIL commands
7.3.1 Molcas input
7.3.2 EMIL commands
7.3.3 Use of shell parameters in input
7.4
MOLCAS-7
Flowchart
8. Programs
8.1
alaska
8.1.1 Analytic Gradients
8.1.2 Description
8.1.3 Numerical gradients
8.1.4 Dependencies
8.1.5 Files
8.1.6 Input
8.2
caspt2
8.2.1 Dependencies
8.2.2 Files
8.2.3 Input
8.3
casvb
8.3.1 Dependencies
8.3.2 Files
8.3.3 Input
8.4
ccsdt
8.4.1 Dependencies
8.4.2 Files
8.4.3 Input
8.4.4 How to run closed shell calculations using ROHF CC codes
8.5
chcc
8.5.1 Dependencies
8.5.2 Files
8.5.3 Input
8.6
cht3
8.6.1 Dependencies
8.6.2 Files
8.6.3 Input
8.7
ciiscmng
8.7.1 Description
8.7.2 Dependencies
8.7.3 Files
8.7.4 CI search, analytical gradients
8.7.5 CI search, numerical gradients
8.7.6 ISC search, analytical gradients
8.7.7 ISC search, numerical gradients
8.8
cpf
8.8.1 Dependencies
8.8.2 Files
8.8.3 Input
8.8.4
CPF
8.9 General input structure. EMIL commands
8.9.1 Molcas input
8.9.2 EMIL commands
8.9.3 Use of shell parameters in input
8.10
MOLCAS-7
Flowchart
8.11
espf (+ QM/MM interface)
8.11.1 Description
8.11.2 Dependencies
8.11.3 Files
8.11.4 Input
8.12
expbas
8.12.1 Dependencies
8.12.2 Files
8.12.3 Input
8.13
ffpt
8.13.1 Dependencies
8.13.2 Files
8.13.3 Input
8.14
gateway
8.14.1 Input
8.15
genano
8.15.1 Dependencies
8.15.2 Files
8.15.3 Input
8.16
GRID_IT
8.16.1 Description
8.16.2 Dependencies
8.16.3 Files
8.16.4 Input
8.17
guessorb
8.17.1 Description
8.17.2 Dependencies
8.17.3 Files
8.17.4 Input
8.18
Guga
8.18.1 Dependencies
8.18.2 Files
8.18.3 Input
8.19
localisation
8.19.1 Description
8.19.2 Dependencies
8.19.3 Files
8.19.4 Input
8.20
LoProp
8.20.1 Dependencies
8.20.2 Files
8.20.3 Input
8.21
m2so
8.21.1 Running
M2SO
for
EPCISO
8.21.2 Running
M2SO
for
MOTRA
8.21.3 Dependencies
8.21.4 Files
8.21.5 Output file
8.21.6 Input
8.22
mbpt2
8.22.1 Description
8.22.2 Dependencies
8.22.3 Files
8.22.4 Input
8.23
mckinley
8.23.1 Description
8.23.2 Dependencies
8.23.3 Files
8.23.4 Input
8.24
mclr
8.24.1 Dependencies
8.24.2 Files
8.24.3 Input
8.25
motra
8.25.1 Dependencies
8.25.2 Files
8.25.3 Input
8.26
MRCI
8.26.1 Dependencies
8.26.2 Files
8.26.3 Input
8.27
Mula
8.27.1 Dependencies
8.27.2 Files
8.27.3 Input
8.28
numerical_gradient
8.28.1 Dependencies
8.28.2 Files
8.28.3 Input
8.29
paralleltest
8.29.1 Description
8.29.2 Files
8.30
rasscf
8.30.1 Dependencies
8.30.2 Files
8.30.3 Input
8.31
rassi
8.31.1 Dependencies
8.31.2 Files
8.31.3 Input
8.32
scf
8.32.1 Description
8.32.2 Dependencies
8.32.3 Files
8.32.4 Input
8.33
seward
8.33.1 Analytic integration
8.33.2 Numerical integration
8.34
SlapAf
8.34.1 Description
8.34.2 Dependencies
8.34.3 Files
8.34.4 Input
8.35
vibrot
8.35.1 Dependencies
8.35.2 Files
8.35.3 Input
8.36 The Basis Set Libraries
9. GUI
9.1 MOLCAS grid and geometry viewer
9.2 Writing GV/MOLDEN input
III. Installation Guide
10. Installation
10.1 Prerequisites
10.1.1 Prerequisite hardware
10.1.2 Prerequisite software
10.1.3 Preparing the installation
10.2 Configuring
MOLCAS
10.3 Building
MOLCAS
10.3.1 Building GUI and documentation
10.3.2 Verifying the
MOLCAS
installation
10.4 Installing and running in parallel environments
10.4.1 Overview of the procedure
10.5 Utilities and special considerations
10.5.1 Global Arrays
10.5.2 ``MPICH'' - public-domain implementation of MPI
10.5.3 Distributed-memory architectures with MPI
11. Maintaining the package
11.1 Tailoring
11.1.1 Dynamic memory
11.1.2 Disk usage
11.1.3 Improving performance
11.2 Applying patches
11.2.1 Local modifications
Bibliography
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