# 4.1.1. Overview¶

Molcas contains a set of ab initio quantum chemical programs. These programs are essentially separate entities, but they are tied together by a shell. The exchange of information between the programs is through files. The shell is designed to allow ease of use with a minimum amount of specifications in a “run of the mill” case. The shell is flexible and allows the user to perform any calculation possible within the limitations of the various codes supplied with Molcas.

To make a calculation using Molcas you have to decide on which programs you need to use, prepare input for these, and construct a command procedure file to run the various programs. This command procedure file is submitted for batch execution. The following two subsections describe the programs available and the files used in Molcas.

## 4.1.1.1. Programs in the system¶

Below is a list of the available programs given. The programs are tied together with a shell and the inter-program information is passed through files. These files are also specified in this list to indicate the program module interdependencies.

- ALASKA
- This program computes the first derivatives of the one- and two-electron integrals with respect to the nuclear positions. The derivatives are not stored on files, but contracted immediately with the one- and two-electron densities to form the molecular gradients.
- CASPT2
- This program computes the second order Many Body Perturbation Theory correction to CASSCF or RASSCF wave function.
- CASVB
- This program performs various types of valence bond calculations. It may be called directly (for VB interpretation of CASSCF wave functions), or within the RASSCF program (for fully variational VB calculations). In the former case it requires the information in the JOBIPH file generated by the RASSCF program, possibly also the integral files ONEINT and ORDINT.
- CCSDT
- This program performs the iterative ROHF CCSD procedure, optionally followed by the (T) calculation contribution. It requires the JOBIPH file produced by RASSCF, and TRAONE and TRAINT files produced by MOTRA.
- CHCC
- This program performs Closed-Shell Coupled-Clusters Singles and Doubles calculations based exclusively on the Cholesky (or RI) decomposed 2-electron integrals.
- CMOCORR
- This program compares the orbital spaces of two orbitals files.
- CPF
- This program produces a CPF, MCPF or ACPF wave function from a single reference configuration.
- DYNAMIX
- This program allows to do molecular dynamics simulations using the velocity Verlet algorithm. It has also the capability to detect non-adiabatic transition using a surface hopping algorithm.
- ESPF
- The ElectroStatic Potential Fitted (ESPF) method adds some one-electron operators to the one-electron hamiltonian in order to compute the interaction between the charge distribution and any kind of external electrostatic potential, field, and field derivatives.
- EXPBAS
- This program takes one orbital file generated with a smaller basis set (ANO) and expands it to a larger basis set.
- GATEWAY
- This program collects all information about computed system, including geometry, basis sets and symmetry, and stores the data for a future use.
- GENANO
- This program is used to construct ANO type basis sets.
- GRID_IT
- This program calculates densities and molecular orbitals in a set of cartesian grid points, and produce a file for visualisation of MO’s and densities.
- FFPT
- This program applies perturbations to the one-electron Hamiltonian for finite field perturbation calculations.
- GUGA
- This program generates the coupling coefficients required by the MRCI and CPF programs.
- LOCALISATION
- This program generates localised occupied orbitals according to one of the following procedures: Pipek–Mezey, Boys, Edmiston–Ruedenberg, or Cholesky. Orthonormal, linearly independent, local virtual orbitals may also be generated from projected atomic orbitals (Cholesky PAOs).
- LOPROP
- This program computes molecular properties based on the one-electron density or transition-density and one-electron integrals like charges, dipole moments and polarizabilities
- MBPT2
- This program computes the second order Many Body Perturbation Theory correction to an SCF wave function.
- MCKINLEY
- This program calculates the second and first order derivatives of integrals that are used for calculating second order derivatives of the energies with perturbation dependent basis sets.
- MCLR
- This program calculates the response of the wave function and related second order properties.
- MOTRA
- This program transforms one- and two-electron integrals from AO basis to MO basis. The integrals that are transformed are the one-electron Hamiltonian and the two-electron repulsion integrals.
- MRCI
- This program produces a Multi Reference CI wave function from an arbitrary set of reference configurations. Alternatively the program can produce an Averaged CPF wave function.
- MULA
- This program calculates intensities of vibrational transitions between electronic states.
- NEMO
- A set of computational modules for calculation of interaction energies between molecules.
- RASSCF
- This program generates CASSCF, RASSCF and GASSCF type wave functions.
- RASSI
- This program computes the interaction between several RASSCF wave functions. A spin-orbit Hamiltonian can be used.
- SCF
- This program generates Closed Shell SCF or Unrestricted SCF, and Kohn–Sham DFT wave functions.
- SEWARD
- This program generates one- and two-electron integrals needed by other programs. If requested the two-electron integrals are computed in the form of Cholesky decomposed vectors.
- SINGLE_ANISO
- This program allows the non-perturbative calculation of effective spin (pseudospin) Hamiltonians and static magnetic properties of mononuclear complexes and fragments completely ab initio, including the spin-orbit interaction.
- SLAPAF
- This program is a general purpose facility for geometry optimization, transition state search, MEP, conical intersections, intersystem crossings, etc. using analytical or numerical gradients produced by ALASKA.
- VIBROT
- This program computes the vibrational-rotational spectrum of a diatomic molecule. Spectroscopic constants are computed. The program can also compute transition moments, life times, etc. for excited state potentials.

## 4.1.1.2. Files in the system¶

The following is a list of the most common files in Molcas that are used to exchange information between program modules. The names given in this list are the FORTRAN file names, defined in the source code. Actual file names are constructed from so called prgm tables, specific for each individual module. (More information about PRGM files can be found in the Molcas Programming Guide).

- RUNFILE
- This file contains general information of the calculation. All programs read from it and write to it. GATEWAY creates a new RUNFILE corresponding to a new calculation.
- ONEINT
- This file contains the one-electron integrals generated by the program SEWARD.
- ORDINT
- This file contains the ordered two-electron integrals generated by the program SEWARD.
- RYSRW
- Data base for the fast direct evaluation of roots and weights of the Rys polynomials. This file is a part of the program system and should not be manipulated by the user.
- ABDATA
- Data base for the evaluation of roots and weights of high order Rys polynomial. This file is a part of the program system and should not be manipulated by the user.
- CHVEC
- This file contains the Cholesky vectors representing the two-electron integrals as generated by the program SEWARD.
- CHORST
- This file contains information about each of the Cholesky vectors generated by the program SEWARD.
- CHRED
- This file contains information about the storage mode of the Cholesky vectors generated by the program SEWARD.
- CHOR2F
- File containing the mapping between Cholesky vector storage and the canonical orbital ordering.
- TRAINT
- This file contains the transformed two-electron integrals generated by the program MOTRA.
- TRAONE
- This file contains the transformed one-electron integrals generated by the program MOTRA.
- INPORB
A generic name for an orbital file. Different programs uses and/or generates INPORB files with a specific name:

- GSSORB generated by the program GUESSORB.
- SCFORB generated by the program SCF.
- RASORB generated by the program RASSCF.
- CIORB generated by the program MRCI
- CPFORB generated by the program CPF.
- SIORB generated by the program RASSI.
- PT2ORB generated by the program CASPT2.

- JOBIPH
- This file contains the RASSCF wave function information generated by the RASSCF program.
- JOBOLD
- This file contains the RASSCF wave function information generated by the RASSCF program in the file JOBIPH, and is used as input for a subsequent RASSCF calculation.
- JOBMIX
- This file contains the multi-state CASPT2 wave function information generated by the CASPT2 program, and is used as input for a subsequent RASSI calculation.
- GRID
- This file contains binary or ASCII data generated by GRID_IT program for visualization of density or molecular orbitals.