MOLCAS manual:
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Contents
I. Introduction
1. Introduction to
MOLCAS
1.1
MOLCAS
Quantum Chemistry Software
1.2 The
MOLCAS
Manual
1.2.1 Manual in Four Parts
1.2.2 Notation
1.3 New features and updates
1.4 Parallelization efforts for
MOLCAS
modules
1.5 Acknowledgment
1.6 Citation for
MOLCAS
1.7 Web Site
1.8 Disclaimer
II. Installation Guide
2. Installation
2.1 Prerequisites
2.1.1 Prerequisite hardware
2.1.2 Prerequisite software
2.1.3 Preparing the installation
2.1.4 Installation of Molcas and OpenMolcas
2.2 Alternative versions of Molcas
2.3 Advanced configuration of Molcas
2.3.1 Configuring
MOLCAS
2.3.2 Building
MOLCAS
2.4 Parallel Installation
2.4.1 Supported MPI implementations
2.4.2 Using an external Global Arrays installation (optional step)
2.4.3 General overview of the procedure with the configure script (alternative 1)
2.4.4 General overview of the procedure with cmake (alternative 2)
2.4.5 Running
MOLCAS
in parallel
2.5 Installation of CheMPS2–
MOLCAS
interface for DMRG calculations
3. Maintaining the package
3.1 Tailoring
3.1.1 Dynamic memory
3.1.2 Disk usage
3.1.3 Improving CPU performance
3.1.4 Customizing handling of files
3.1.5 Improving I/O performance
3.1.6 Local modifications
III. Short Guide to
MOLCAS
4. Quickstart Guide for
MOLCAS
4.1 Introduction
4.2
MOLCAS
Environment Setup
4.3 Customization of
MOLCAS
Execution
4.4
MOLCAS
Command-Line Help System
4.5 Input Structure and EMIL Commands
4.6 Basic Examples
4.6.1 Simple Calculation on Water
4.6.2 Geometry Optimization
4.6.3 GASSCF method
4.6.4 Solvation Effects
4.7 Analyzing Results: Output Files and the
LUSCUS
Program
4.7.1 LUSCUS: Grid and Geometry Visualization
5. Problem Based Tutorials
5.1 Electronic Energy at Fixed Nuclear Geometry
5.2 Optimizing geometries
5.3 Computing excited states
6. Program Based Tutorials
6.1 8.1 Flowchart
6.2 Environment and EMIL Commands
6.3 GATEWAY - Definition of geometry, basis sets, and symmetry
6.3.1
GATEWAY
Output
6.3.2 Basis Set Superposition Error (BSSE)
6.3.3
GATEWAY
Basic and Most Common Keywords
6.4 SEWARD — An Integral Generation Program
6.5 SCF — A Self-Consistent Field program and Kohn Sham DFT
6.5.1 Running
SCF
6.5.2
SCF
Output
6.5.3 SCF - Basic and Most Common Keywords
6.6 MBPT2 — A Second-Order Many-Body PT RHF Program
6.7 RASSCF — A Multi Configurational SCF Program
6.7.1
RASSCF
Output
6.7.2 Storing and Reading
RASSCF
Orbitals and Wave Functions
6.7.3 RASSCF - Basic and Most Common Keywords
6.8 CASPT2 — A Many Body Perturbation Program
6.8.1
CASPT2
Output
6.8.2 CASPT2 - Basic and Most Common Keywords
6.9 RASSI — A RAS State Interaction Program
6.9.1
RASSI
Output
6.9.2 RASSI - Basic and Most Common Keywords
6.9.3 CASVB — A non-orthogonal MCSCF program
6.9.4
CASVB
input
6.9.5
CASVB
output
6.9.6 Viewing and plotting VB orbitals
6.10 MOTRA — An Integral Transformation Program
6.10.1
motra
Output
6.10.2 MOTRA - Basic and Most Common Keywords
6.11 GUGA — CI Coupling Coefficients Program
6.11.1
GUGA
Output
6.12 MRCI — A Configuration Interaction Program
6.12.1
mrci
Output
6.13 CPF — A Coupled-Pair Functional Program
6.13.1
cpf
Output
6.14 CCSDT — A Set of Coupled-Cluster Programs
6.14.1
CCSDT
Outputs
6.14.2 Example of a CCSD(T) calculation
6.14.3 CCSDT - Basic and Most Common Keywords
6.15 Other Multiconfigurational and Multireference Methods
6.16 ALASKA and SLAPAF: A Molecular Structure Optimization
6.16.1 SLAPAF - Basic and Most Common Keywords
6.17 MCKINLEY — A Program for Integral Second Derivatives
6.17.1 MCKINLEY - Basic and Most Common Keywords
6.18 MCLR — A Program for Linear Response Calculations
6.18.1 MCLR program - Basic and Most Common Keywords
6.19 GENANO — A Program to Generate ANO Basis Sets
6.20 FFPT — A Finite Field Perturbation Program
6.20.1
ffpt
Output
6.21 VIBROT — A Program for Vibration-Rotation on Diatomic Molecules
6.22 SINGLE_ANISO — A Magnetism of Complexes Program
6.22.1
SINGLE_ANISO
Output
6.22.2 SINGLE_ANISO - Basic and Most Common Keywords
6.23 POLY_ANISO — Semi -
ab initio
Electronic Structure and Magnetism of Polynuclear Complexes Program
6.23.1
POLY_ANISO
Output
6.23.2 POLY_ANISO - Basic and Most Common Keywords
6.24 GRID_IT: A Program for Orbital Visualization
6.24.1 GRID_IT - Basic and Most Common Keywords
6.25 Writing MOLDEN input
6.26 Most frequent error messages found in MOLCAS
6.27 Tools for selection of the active space
6.28 Some practical HINTS
6.28.1 GATEWAY/SEWARD program:
6.28.2 SCF program
6.28.3 RASSCF program:
6.28.4 Selection of active spaces:
6.28.5 CASPT2 program:
6.28.6 RASSI program:
6.28.7 Geometry optimization
6.28.8 Solvent effects
IV. User's Guide
7. The
MOLCAS
environment
7.1 Overview
7.1.1 Programs in the system
7.1.2 Files 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
7.3.4 Customization of molcas input
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
averd
8.2.1 Description
8.2.2 Dependencies
8.2.3 Files
8.2.4 Input
8.3
caspt2
8.3.1 Dependencies
8.3.2 Files
8.3.3 Input
8.4
casvb
8.4.1 Dependencies
8.4.2 Files
8.4.3 Input
8.5
ccsdt
8.5.1 Dependencies
8.5.2 Files
8.5.3 Input
8.5.4 How to run closed shell calculations using ROHF CC codes
8.6
chcc
8.6.1 Dependencies
8.6.2 Files
8.6.3 Input
8.7
cht3
8.7.1 Dependencies
8.7.2 Files
8.7.3 Input
8.8
cmocorr
8.8.1 Description
8.8.2 Dependencies
8.8.3 Files
8.8.4 Input
8.9
cpf
8.9.1 Dependencies
8.9.2 Files
8.9.3 Input
8.9.4
CPF
8.10
dimerpert
8.11
dynamix
8.11.1 Dependencies
8.11.2 Files
8.11.3 Input
8.11.4 Dynamixtools
8.12
embq
8.12.1 Description
8.12.2 Files
8.12.3 Input
8.13
espf (+ QM/MM interface)
8.13.1 Description
8.13.2 ESPF and QM/MM
8.13.3 Dependencies
8.13.4 Files
8.13.5 Input
8.13.6 Examples
8.14
expbas
8.14.1 Dependencies
8.14.2 Files
8.14.3 Input
8.15
falcon
8.15.1 Description
8.15.2 Input
8.16
ffpt
8.16.1 Dependencies
8.16.2 Files
8.16.3 Input
8.17
gateway
8.17.1 Input
8.18
genano
8.18.1 Dependencies
8.18.2 Files
8.18.3 Input
8.19
geo
8.19.1 Description
8.19.2 Dependencies
8.19.3 Files
8.19.4 input
8.20
GRID_IT
8.20.1 Description
8.20.2 Dependencies
8.20.3 Files
8.20.4 Input
8.21
guessorb
8.21.1 Description
8.21.2 Dependencies
8.21.3 Files
8.21.4 Input
8.22
Guga
8.22.1 Dependencies
8.22.2 Files
8.22.3 Input
8.23
GUGACI
8.23.1 Dependencies
8.23.2 Files
8.23.3 Input
8.24
GUGADRT
8.24.1 Dependencies
8.24.2 Files
8.24.3 Input
8.25
localisation
8.25.1 Description
8.25.2 Dependencies
8.25.3 Files
8.25.4 Input
8.26
LoProp
8.26.1 Dependencies
8.26.2 Files
8.26.3 Input
8.27
mbpt2
8.27.1 Description
8.27.2 Dependencies
8.27.3 Files
8.27.4 Input
8.28
mckinley
(a.k.a.
denali
)
8.28.1 Description
8.28.2 Dependencies
8.28.3 Files
8.28.4 Input
8.29
mclr
8.29.1 Dependencies
8.29.2 Files
8.29.3 Input
8.30
MCPDFT
8.30.1 Dependencies
8.30.2 Files
8.30.3 Input
8.31
mknemo
8.31.1 Description
8.31.2 Files
8.31.3 Dependencies
8.32
motra
8.32.1 Dependencies
8.32.2 Files
8.32.3 Input
8.33
mpprop
8.33.1 Description
8.33.2 Dependencies
8.33.3 Files
8.33.4 Input
8.34
MRCI
8.34.1 Dependencies
8.34.2 Files
8.34.3 Input
8.35
Mula
8.35.1 Dependencies
8.35.2 Files
8.35.3 Input
8.36
nemo
8.36.1 Description
8.36.2 Dependencies
8.36.3 Files
8.36.4 Input
8.37
numerical_gradient
8.37.1 Dependencies
8.37.2 Files
8.38
poly_aniso
8.38.1 Input
8.39
qmstat
8.39.1 Description
8.39.2 Dependencies
8.39.3 Files
8.39.4 Input
8.40
quater
8.40.1 Dependencies
8.40.2 Files
8.40.3 Input
8.41
rasscf
8.41.1 GASSCF method
8.41.2 MC-PDFT method
8.41.3 Dependencies
8.41.4 Files
8.41.5 Input
8.42
rassi
8.42.1 Dependencies
8.42.2 Files
8.42.3 Input
8.43
rpa
8.44
scf
8.44.1 Description
8.44.2 Dependencies
8.44.3 Files
8.44.4 Input
8.45
seward
8.45.1 Analytic integration
8.45.2 Numerical integration
8.45.3 Relativistic operators
8.46
single_aniso
8.46.1 Dependencies
8.46.2 Files
8.46.3 Input
8.47
SlapAf
8.47.1 Description
8.47.2 Dependencies
8.47.3 Files
8.47.4 Input
8.48
surfacehop
8.48.1 Input
8.49
vibrot
8.49.1 Dependencies
8.49.2 Files
8.49.3 Input
8.50
wfa
8.50.1 Installation
8.50.2 Dependencies
8.50.3 Files
8.50.4 Input
8.50.5 Output
8.51 The Basis Set Libraries
9. GUI
9.1 Writing LUSCUS/MOLDEN input
V. Advanced Examples and Annexes
10. Examples
10.1 Computing high symmetry molecules.
10.1.1 A diatomic heteronuclear molecule: NiH
10.1.2 A diatomic homonuclear molecule: C
2
10.1.3 A transition metal dimer: Ni
2
10.1.4 High symmetry systems in
MOLCAS
10.2 Geometry optimizations and Hessians.
10.2.1 Ground state optimizations and vibrational analysis
10.2.2 Excited state optimizations
10.2.3 Restrictions in symmetry or geometry.
10.2.4 Optimizing with Z-Matrix.
10.2.5 CASPT2 optimizations
10.3 Computing a reaction path.
10.3.1 Studying a reaction
10.3.2 Finding the reaction path - an IRC study
10.4 High quality wave functions at optimized structures
10.5 Excited states.
10.5.1 The vertical spectrum of thiophene.
10.5.2 Influence of the Rydberg orbitals and states. One example: guanine.
10.5.3 Other cases.
10.6 Solvent models.
10.6.1 Kirkwood model.
10.6.2 PCM
10.6.3 Calculation of solvent effects: Kirkwood model.
10.6.4 Solvation effects in ground states. PCM model in formaldehyde.
10.6.5 Solvation effects in excited states. PCM model and acrolein.
10.7 Computing relativistic effects in molecules.
10.7.1 Scalar relativistic effects
10.7.2 Spin-Orbit coupling (SOC)
10.7.3 The PbO molecule
10.8 Extra information about basis sets and integrals
10.9 Core and Embedding Potentials within the SEWARD Program
10.9.1
seward
input for Effective Core Potential calculations
10.9.2
seward
input for Embedded Cluster calculations
Bibliography
List of Figures
List of Tables
Index
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