MOLCAS manual: 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 2.3.1.1 Fetching extra programs 2.3.1.2 Advanced configuration with the configure script 2.3.2 Building MOLCAS 2.3.2.1 Verifying the MOLCAS installation 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 Self-Consistent Field 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 — A Configuration Interaction 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 8.1.5.1 Input files 8.1.5.2 Output files 8.1.6 Input 8.2 averd 8.2.1 Description 8.2.2 Dependencies 8.2.3 Files 8.2.3.1 Input files 8.2.3.2 Output files 8.2.4 Input 8.2.4.1 Input example 8.3 caspt2 8.3.1 Dependencies 8.3.2 Files 8.3.2.1 Input files 8.3.2.2 Output files 8.3.3 Input 8.3.3.1 Keywords 8.3.3.2 Input example 8.4 casvb 8.4.1 Dependencies 8.4.2 Files 8.4.2.1 Input files 8.4.2.2 Output files 8.4.3 Input 8.4.3.1 Keywords 8.4.3.2 Input example 8.4.3.3 Viewing and plotting VB orbitals 8.5 ccsdt 8.5.1 Dependencies 8.5.2 Files 8.5.2.1 Input files 8.5.2.2 Output 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 8.6.2.1 Input files 8.6.2.2 Output files 8.6.3 Input 8.7 cht3 8.7.1 Dependencies 8.7.2 Files 8.7.2.1 Input files 8.7.2.2 Intermediate files 8.7.2.3 Output files 8.7.3 Input 8.8 cmocorr 8.8.1 Description 8.8.2 Dependencies 8.8.3 Files 8.8.3.1 Input files 8.8.3.2 Output files 8.8.4 Input 8.8.4.1 Input examples 8.9 cpf 8.9.0.1 Orbital subspaces 8.9.1 Dependencies 8.9.2 Files 8.9.2.1 Input files 8.9.2.2 Output files 8.9.3 Input 8.9.4 CPF 8.9.4.1 Optional keywords 8.9.4.2 Input example 8.10 dimerpert 8.11 dynamix 8.11.1 Dependencies 8.11.2 Files 8.11.2.1 Input files 8.11.2.2 Output files 8.11.3 Input 8.11.3.1 General keywords 8.11.3.2 Input examples 8.11.4 Dynamixtools 8.12 embq 8.12.1 Description 8.12.2 Files 8.12.2.1 Input files 8.12.2.2 Intermediate files 8.12.2.3 Output files 8.12.3 Input 8.12.3.1 Compulsory keywords 8.12.3.2 Optional keywords 8.12.3.3 Limitations 8.12.3.4 Input example 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 8.13.4.1 Intermediate files 8.13.4.2 Output files 8.13.5 Input 8.13.6 Examples 8.13.6.1 ESPF example 8.13.6.2 MOLCAS/Tinker example 8.13.6.3 MOLCAS/Gromacs example 8.14 expbas 8.14.1 Dependencies 8.14.2 Files 8.14.2.1 Input files 8.14.2.2 Output files 8.14.3 Input 8.14.3.1 Input example 8.14.3.2 Optional general keywords 8.15 falcon 8.15.1 Description 8.15.2 Input 8.15.2.1 Keywords 8.15.2.2 Input examples 8.16 ffpt 8.16.1 Dependencies 8.16.2 Files 8.16.2.1 Input files 8.16.2.2 Output files 8.16.3 Input 8.16.3.1 General keywords 8.16.3.2 Input example 8.17 gateway 8.17.1 Input 8.17.1.1 General keywords 8.17.1.2 Molecular structure: coordinates, symmetry and basis sets 8.17.1.3 Constraints 8.17.1.4 Explicit auxiliary basis sets 8.17.1.5 Reaction field calculations 8.17.1.6 Keywords associated to one-electron integrals 8.17.1.7 Keywords associated with nuclear charge distribution models 8.17.1.8 The Saddle method for transition state optimization 8.17.1.9 Geometry optimization using constrained internal coordinates 8.17.1.10 QM/MM calculations with MOLCAS/Gromacs 8.18 genano 8.18.1 Dependencies 8.18.2 Files 8.18.2.1 Input files 8.18.2.2 Output files 8.18.3 Input 8.19 geo 8.19.1 Description 8.19.1.1 Creating the z-matrix 8.19.2 Dependencies 8.19.3 Files 8.19.3.1 Input files 8.19.3.2 Geo communication files 8.19.4 input 8.20 GRID_IT 8.20.1 Description 8.20.2 Dependencies 8.20.3 Files 8.20.3.1 Input files 8.20.3.2 Output files 8.20.4 Input 8.20.4.1 Optional general keywords 8.20.4.2 Input example 8.21 guessorb 8.21.1 Description 8.21.2 Dependencies 8.21.3 Files 8.21.3.1 Input files 8.21.3.2 Output files 8.21.4 Input 8.21.4.1 Keywords 8.21.4.2 Input examples 8.22 Guga 8.22.1 Dependencies 8.22.2 Files 8.22.2.1 Input files 8.22.2.2 Output files 8.22.3 Input 8.22.3.1 Keywords. 8.22.3.2 Input example 8.23 GUGACI 8.23.0.1 Orbital subspaces 8.23.1 Dependencies 8.23.2 Files 8.23.2.1 Input files 8.23.2.2 Output files 8.23.2.3 Local files 8.23.3 Input 8.23.3.1 Keywords 8.23.3.2 Input example 8.24 GUGADRT 8.24.1 Dependencies 8.24.2 Files 8.24.2.1 Input files 8.24.2.2 Output files 8.24.3 Input 8.24.3.1 Keywords. 8.24.3.2 Input example 8.25 localisation 8.25.1 Description 8.25.2 Dependencies 8.25.3 Files 8.25.3.1 Input files 8.25.3.2 Output files 8.25.4 Input 8.25.4.1 Optional general keywords 8.25.4.2 Limitations 8.25.4.3 Input examples 8.26 LoProp 8.26.1 Dependencies 8.26.2 Files 8.26.2.1 Input files 8.26.2.2 Output files 8.26.3 Input 8.26.3.1 Keywords 8.26.3.2 Input example 8.27 mbpt2 8.27.1 Description 8.27.2 Dependencies 8.27.3 Files 8.27.3.1 Input files 8.27.3.2 Output files 8.27.4 Input 8.27.4.1 Optional keywords 8.27.4.2 Optional keywords specific to Cholesky calculations 8.27.4.3 Limitations 8.27.4.4 Input example 8.28 mckinley (a.k.a. denali) 8.28.1 Description 8.28.2 Dependencies 8.28.3 Files 8.28.3.1 Input files 8.28.3.2 Output files 8.28.4 Input 8.29 mclr 8.29.1 Dependencies 8.29.2 Files 8.29.2.1 Input files 8.29.2.2 Output files 8.29.2.3 Scratch files 8.29.3 Input 8.29.3.1 Optional keywords 8.29.3.2 Input example 8.30 MCPDFT 8.30.1 Dependencies 8.30.2 Files 8.30.2.1 Input files 8.30.2.2 Output files 8.30.3 Input 8.30.3.1 Input example 8.31 mknemo 8.31.1 Description 8.31.2 Files 8.31.2.1 Standard input 8.31.2.2 Input files 8.31.2.3 Output files 8.31.3 Dependencies 8.32 motra 8.32.1 Dependencies 8.32.2 Files 8.32.2.1 Input files 8.32.2.2 Output files 8.32.3 Input 8.32.3.1 Compulsory keywords 8.32.3.2 Optional keywords 8.32.3.3 Input example 8.33 mpprop 8.33.1 Description 8.33.2 Dependencies 8.33.3 Files 8.33.3.1 Input files 8.33.3.2 Output files 8.33.4 Input 8.33.4.1 Optional general keywords 8.33.4.2 Limitations 8.33.4.3 Input examples 8.34 MRCI 8.34.0.1 Orbital subspaces 8.34.1 Dependencies 8.34.2 Files 8.34.2.1 Input files 8.34.2.2 Output files 8.34.3 Input 8.34.3.1 Keywords 8.34.3.2 Input example 8.35 Mula 8.35.1 Dependencies 8.35.2 Files 8.35.2.1 Input files 8.35.2.2 Output files 8.35.3 Input 8.35.3.1 Keywords 8.35.3.2 Input example 8.36 nemo 8.36.1 Description 8.36.2 Dependencies 8.36.3 Files 8.36.3.1 Input files 8.36.3.2 Columns in the ATOMPAR file 8.36.3.3 Output files 8.36.4 Input 8.36.4.1 Optional general keywords 8.36.4.2 Optional RETY paramters 8.36.4.3 Optional NEMO paramters 8.36.4.4 Optional FITPar specific keywords 8.36.4.5 Optional WEIGht paramters 8.36.4.6 Optional ERROr paramters 8.36.4.7 Optional DIMEr specific keywords 8.36.4.8 Optional POTSurf specific keywords 8.36.4.9 Optional TRANslation paramters 8.36.4.10 Optional SIMPar specific keywords 8.36.4.11 Limitations 8.37 numerical_gradient 8.37.1 Dependencies 8.37.2 Files 8.38 poly_aniso 8.38.0.1 Input files 8.38.0.2 Output files 8.38.1 Input 8.38.1.1 Mandatory keywords defining the calculation 8.38.1.2 Optional general keywords to control the input 8.39 qmstat 8.39.1 Description 8.39.2 Dependencies 8.39.3 Files 8.39.3.1 Input files 8.39.3.2 Output files 8.39.4 Input 8.39.4.1 Input example 8.40 quater 8.40.1 Dependencies 8.40.2 Files 8.40.2.1 Input files 8.40.3 Input 8.40.3.1 Keywords 8.40.3.2 Input example 8.41 rasscf 8.41.1 GASSCF method 8.41.2 MC-PDFT method 8.41.2.1 RASSCF output orbitals 8.41.3 Dependencies 8.41.4 Files 8.41.4.1 Input files 8.41.4.2 Output files 8.41.5 Input 8.41.5.1 Optional keywords 8.41.5.2 Input example 8.42 rassi 8.42.1 Dependencies 8.42.2 Files 8.42.2.1 Input files 8.42.2.2 Output files 8.42.3 Input 8.42.3.1 Keywords 8.42.3.2 Input example 8.43 rpa 8.44 scf 8.44.1 Description 8.44.2 Dependencies 8.44.3 Files 8.44.3.1 Input files 8.44.3.2 Output files 8.44.4 Input 8.44.4.1 Basic general keywords 8.44.4.2 Advanced general keywords 8.44.4.3 Keywords for direct calculations 8.44.4.4 Limitations 8.44.4.5 Input examples 8.45 seward 8.45.1 Analytic integration 8.45.1.1 Description 8.45.1.2 Dependencies 8.45.1.3 Files 8.45.1.4 Input 8.45.2 Numerical integration 8.45.2.1 Description 8.45.2.2 Input 8.45.3 Relativistic operators 8.45.3.1 Using the Douglas–Kroll–Hess Hamiltonian 8.45.3.2 Douglas–Kroll–Hess transformed properties 8.45.3.3 Using the X2C/Barysz–Sadlej–Snijders Hamiltonian 8.45.3.4 Local approximation to relativistic decoupling 8.46 single_aniso 8.46.1 Dependencies 8.46.2 Files 8.46.2.1 Input files 8.46.2.2 Restart files & options 8.46.2.3 Output files 8.46.3 Input 8.46.3.1 Optional general keywords to control the input 8.46.3.2 An input example 8.47 SlapAf 8.47.1 Description 8.47.2 Dependencies 8.47.3 Files 8.47.3.1 Input files 8.47.3.2 Output files 8.47.4 Input 8.47.4.1 Definition of internal coordinates or constraints 8.48 surfacehop 8.48.0.1 Output files 8.48.1 Input 8.48.1.1 General keywords 8.48.1.2 Input examples 8.49 vibrot 8.49.1 Dependencies 8.49.2 Files 8.49.2.1 Input files 8.49.2.2 Output files 8.49.3 Input 8.49.3.1 Keywords 8.49.3.2 Input example 8.50 wfa 8.50.1 Installation 8.50.2 Dependencies 8.50.3 Files 8.50.3.1 Input files 8.50.3.2 Output files 8.50.4 Input 8.50.4.1 Keywords 8.50.4.2 Input example 8.50.5 Output 8.50.5.1 State/difference density matrix analysis (SCF/RASSCF/RASSI) 8.50.5.2 Transition density matrix analysis (RASSI) 8.51 The Basis Set Libraries 8.51.0.1 Dummy atoms 8.51.0.2 The All Electron Basis Set Library 8.51.0.3 Structure of the all electron basis set library 8.51.0.4 The ECP Library 8.51.0.5 Structure of the ECP 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: C2 10.1.3 A transition metal dimer: Ni2 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. 10.2.3.1 Optimizing with geometrical constraints. 10.2.3.2 Optimizing with symmetry restrictions. 10.2.4 Optimizing with Z-Matrix. 10.2.5 CASPT2 optimizations 10.3 Computing a reaction path. 10.3.1 Studying a reaction 10.3.1.1 Reactant and product 10.3.1.2 Transition state optimization 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. 10.5.1.1 Planning the calculations. 10.5.1.2 Generating Rydberg basis functions 10.5.1.3 SEWARD and CASSCF calculations. 10.5.1.4 CASPT2 calculations. 10.5.1.5 Transition dipole moment calculations. 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 10.8.0.1 One-Electron Integral Labels 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 About this document ...