Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 1. An introduction to Molpro 2000 by Patrick S. Vogt

Transcription

1 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 1 An introduction to Molpro 2000 by Patrick S. Vogt

2 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 2 Why use Molpro? Molpro is faster than Gaussian. To demonstrate this some calculation with a basis set of cc-pvdz are shown: method CPU time / s Molpro 2000 Gaussian 98 HF MP CCSD CCSD (dimer) The MP2 calculation itself takes 0.02 seconds, the SCF calculation 0.03 seconds and the integral calculation 0.45 seconds

3 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 3 Getting Help The Molpro package includes a complete manual. The manual exists in two formats: PDF $MOLPRO_HOME/doc/manual.pdf HMTL $MOLPRO_HOME/doc/manual/index.html (To find your local $MOLPRO_HOME type which molpro on our UNIX prompt.) Some Molpro locations: xino: Huber Net: $MOLPRO_HOME=/soft/molpro $MOLPRO_HOME=/usr/local/src/molpro2000.1

4 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 4 On-line informations The Molpro Home-page resides at the University of Birmingham: Some topics covered: The current version of the Molpro User s manual. Some Patches correcting bugs of Molpro. The Basis library is a graphical user interface to query the basis sets available for Molpro.

5 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 5 The Input File The following code shows a simple Molpro input file, doing a Hartree-Fock geometry optimisation of water: ***, Water geometry optimisation geometry={!define the geometry O H1 O rh1o H2 O rh2o H1 ah2oh1 } rh1o=0.96 Ang!Bohr is default rh2o=0.96 Ang ah2oh1=104 basis=cc-pvtz!set the basis set hf!do SCF calclation mp2!needed for mp2 optg!optimise geometry ---

6 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 6 Structure of the Input File ***, title marks the beginning of the input file and sets the title. --- marks the end of the input file. var = value Sets a variable. Basisset and geometry are treated as variables. prog Calls a program, methods and optimisations are treated as programs. ; A semicolon marks the end of a statement and is equivalent to a newline., A comma is equivalent to a space.! Everything after a exclamation mark is a comment.

7 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 7 Specification of the Molecular Geometry The geometry variable is used to specify the molecular geometry. It has the following format: geometry={pointgroup options z-matrix or XYZ-format} pointgroup Consist of one or more X, Y or Z which specify the axes that change sign. See Molpro manual section 8.1. If z-matrix input is used Molpro determines the symmetry itself. options See Molpro manual section 8.2. nosym turns of automatic symmetry detection. Alternatively the geometry can be read from a file using GEOMETRY=file.

8 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 8 Setting the basis set There are several ways to specify the basis set: basis=cc-pvdz loads the cc-pvdz basis for all atoms. basis={def=cc-pvdz, H=cc-pvtz} loads the cc-pvtz basis for the hydrogen atoms and the cc-pvdz basis for all other atoms. The existing basis sets can be queried and downloaded at molpro_basis.

9 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 9 Non-existing Atoms Sometimes it is necessary or convenient to define atoms that do not exist. Dummy centers in z-matrices are called Q or X and show up as normal atoms in z-matrices. They are used as a center reference in z-matrices, needed to define linear chains or rings. Dummy centers to hold basis functions for bond orbitals or counterpoise calculations. You can mark an existing atom as a dummy center by writing: dummy atom-label

10 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 10 Implemented Methods Molpro implements the following methods: HF DFT MCSF CI MP2 CCSD SCF Hartree-Fock (see slide 11 or Molpro manual section 12) Density Functional Theory, using the functionals LDA, DIRAC, B88, LYP88,B-LYP, B3LYP (Molpro manual section 13) MCSCF or CASSCF calculations (Molpro manual section 15) Configuration interaction (Molpro manual section 16) Møller-Plesset correlation calculations (see slide 12 or Molpro manual section 18) Coupled-cluster correlation calculations (see slide 13 or Molpro manual section 19)

11 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 11 SCF calculations A Hartree-Fock SCF calculation is started by one of the following keywords: HF or RHF UHF for the restricted version for the unrestricted version In addition, the number of electrons, the symmetry and the spin can be specified by wf elec,sym,spin

12 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 12 Møller-Plesset perturbation theory Molpro implements the following Møller-Plesset methods: MP2, MP3 and MP4 Unlike other packages (e.g. Gaussian) Molpro does not perform a SCF calculation prior to a electron correlation calculation. Therefore the SCF program has to be called explicitly, e.g.: hf; mp2

13 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 13 Coupled-cluster calculations Molpro implements the following coupled-cluster methods, remember to call the SCF program first: CCSD and CCSD(T) perform closed-shell coupled-cluster calculations. CISD performs quadratic configuration interaction calculations. BCCD performs Brückner coupled-cluster calculations. QCI performs a closed-shell configuration interactions calculations.

14 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 14 Linear Scaling Methods The packages local and direct must be installed in order to perform linear scaling calculations. Linear scaling methods have a big over head and will therefore only be useful for big molecules. Linear scaling is achieved by: 1. Reducing disk I/O with the gdirect mode. (Two electron integrals will recomputed when used.) See Chapter 7 of the Molpro Manual. 2. Local correlation treatment with multp. See slide 15 and chapter 21 of the Molpro Manual.

15 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 15 Local Correlation Treatment (LCT) LCT is switched on by the keyword local or multp, the latter turns on some additional approximations that depend on the distance of their orbitals. Since LCT builds up molecular domains the geometry options nosym;noorient must be used. LCT is not a black box method, you should check the molecular domains and the other parameters, and therefore it is highly recommended to read chapter 21 of the Molpro manual. At the moment only local MP2 is available.

16 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 16 Geometry optimisation An automatic geometry optimisation, on the level of the last single point calculation, is started by the command: optg By default all variables are active in respect to the optimisation. The command inactive,variable can be used to exclude a variable from the optimisation. Alternatively, only listed variables can be set active in a calculation by the command active,variable.

17 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 17 The Molpro files Molpro uses the following files to store its information: file name purpose 1 Main file: contains basis set, geometry, one and two electron integrals. 2 Dump file: used to store wavefunction information 3 Auxiliary file: can be used for restarting purposes.

18 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 18 Handling files Molpro provides the following command to handle files: file, file-number, filename, [status ] The file-number refers to the numbers listed in slide 17. The filename is used by the operating system. The optional parameter status is discussed in section 5.1 of the Molpro manual. Creating permanent files for our example on slide 5 could look like: file,1,h2o.int; file,2,h2o.wf;

19 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 19 Restart a Molpro calculation Files of a former Molpro job can be used in a new calculation. The files have to be defined using the file command as shown in slide 18. Once defined, these files can be loaded by the following command: restart [list ] Where list can be empty to load all known files, or list the file-numbers to be loaded.

20 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 20 Allocation of memory Molpro uses the following syntax to allocate memory: memory,n [,scale ] Where n is the number of words and scale is a scaling factor, that can be K for 10 3 or M for Molpro allocates memory in units of words. A word indicates the number of binary digits the processor can handle in parallel. processor word-size / byte DEC Alpha 64 Cray T3e 64 NEC SX/4 64 Intel i Sun E HP N

21 Patrick S. Vogt, Institut für physikalische Chemie der Universität Basel 21 Molpro as Scripting Language Molpro knows some basic programing constructs: Do loops: do variable =start, end [, increment ] [, unit ]... enddo If statments: if (...) then... [else...] endif Procedures: proc name... endproc