DFT calculations with ADF

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					DFT calculations with ADF
      Density Functional Theory
• A detailed description of DFT will not be included in this
  presentation.
• Notes which help to explain what keywords correspond
  to will be included, but in a very loose, unrigourous way.
• For further details about DFT, the following books are
  recommended. I also recommend you attend an
  appropriate lecture series
   – A chemists guide to DFT, W. Koch, M. C. Holthausen, Wiley-
     VCH, ISBN: 3-527-30372-3
   – Computational Chemistry, G.H. Grant, W. G. Richards, OUP
     (Oxford Primer), ISBN: 978-0198557401
   – Introduction to computational chemistry, F. Jensen, Wiley, ISBN:
     0-470-01187-4
 Amsterdam Density Functional
• ADF is a program used to do DFT
  calculations
• www.scm.com is the website for the
  program and includes
  – Manual (under the documentation heading)
  – Forum where people post problems and
    others reply (under community)
• Also look on ccl.net, although this is more
  general and ADF issues tend to get
  directed to the ADF website.
        Example input file
$ADFBIN/adf -n 1 <<eor

TITLE H2O

BASIS
TYPE TZP
CORE Small
END

SCF
ITERATIONS 99
CONVERGE 0.000001
END

GEOMETRY
optim
END

INTEGRATION 6.0

XC
GRADIENT OPBE
END

CHARGE 0 0

ATOMS
O           0.000000    0.000000    0.012976
H           0.000000   -0.754442   -0.589982
H           0.000000    0.754442   -0.589982
END

ENDINPUT
eor
            Example input file - explained
$ADFBIN/adf -n 1 <<eor                  This line needs to be included in all ADF calculations


TITLE H2O
                   Folder where            Use ADF executable                    Use one processor
BASIS              ADF binaries            (there are others for
TYPE TZP                                                                         (irrelevant for machines
CORE Small         are kept                different programs
END                                                                              with only 1 cpu)
                                           and utilities)
SCF
ITERATIONS 99
CONVERGE 0.000001
END
                           Read this file until
GEOMETRY                   you reach “eor”
optim
END

INTEGRATION 6.0

XC
GRADIENT OPBE
END

CHARGE 0 0

ATOMS
O            0.000000     0.000000    0.012976
H            0.000000    -0.754442   -0.589982
H            0.000000     0.754442   -0.589982
END

ENDINPUT                Specifies the input file is finished
eor
                        Stop reading the file (see first line)
           Example input file - explained
$ADFBIN/adf -n 1 <<eor

TITLE H2O                      You can give your calculation whatever title you like or
                               exclude this keyword altogether
BASIS
TYPE TZP
CORE Small
                               BASIS keyword specifies what type of basis set you want
END                            to use.
SCF                            TYPE can be lower case but TZP (or whatever you
ITERATIONS 99                  choose) must be capitals as it points to a directory
CONVERGE 0.000001              CORE specifies how large your frozen core is, case
END
                               specific
GEOMETRY
optim
                               END specifies that this is the end of this section
END
                               SCF specifies the conditions for putting the electron
INTEGRATION 6.0
                               density correctly
XC
GRADIENT OPBE
                               Iterations says how many cycles it has to converge in
END                            Converge says how much the energy is allowed to change
CHARGE 0 0                     by to be considered converged
ATOMS
O            0.000000    0.000000    0.012976
H            0.000000   -0.754442   -0.589982
H            0.000000    0.754442   -0.589982
END

ENDINPUT
eor
              Some definitions
• BASIS SET
  – These are mathematical functions which describe
    where the electron density is allowed to go. The
    proportion of each function can be varied until the
    energy provided by the electron density is minimised.
    In ADF the basis functions are the shape of s, p, d etc
    orbitals
• FROZEN CORE
  – The innermost electrons of an element contribute a
    great deal to the overall energy but are largely
    unaffected by the overall environment of the atom.
    Therefore they can be optimised once and then kept
    the same throughout the calculation as the valence
    electrons are the ones which change most.
             Some definitions
• Self Consistent Field (SCF)
  – This is how the electron density is distributed
    within the field of the nuclei and other
    electrons. An iterative procedure is used to
    assign the electron density until it is internally
    consistent, and changing the position of one
    electron a tiny bit does not change the energy
    overall.
            Example input file - explained
$ADFBIN/adf -n 1 <<eor

TITLE H2O

BASIS                    Geometry keyword specifies whether you want to optimise
TYPE TZP
CORE Small
                         the geometry, do a single point, or do frequencies. It can
END                      also specify convergence criteria.
SCF
ITERATIONS 99
CONVERGE 0.000001
                         Integration relates to the accuracy of the calculation.
END

GEOMETRY                  The XC keyword is used to select the functional to be used
optim
END

INTEGRATION 6.0
                         The charge keyword specifies the charge of the molecule and
                         the number of unpaired electrons. If there are unpaired
XC
GRADIENT OPBE
                         electrons another keyword, UNRESTRICTED, needs to be
END                      included on another line
CHARGE 0 0

ATOMS
O            0.000000    0.000000    0.012976
H            0.000000   -0.754442   -0.589982
H            0.000000    0.754442   -0.589982
END

ENDINPUT
eor
               Some definitions
• Functional
  – A functional is a function that acts on the basis
    functions to return the energy. It can be thought of
    that in the Schrödinger equation the Hamiltonian acts
    on the wavefunction to give the energy multiplied by
    the wavefunction. In DFT, the functional acts on the
    electron density (in the form of basis sets) to give the
    energy multiplied by the electron density. However,
    the exact form the functional should take is unknown
    so many different functionals have been created
    which all give slightly different results.
            Some definitions
• RESTRICTED/UNRESTRICTED
 – In a calculation where there are no unpaired
   electrons, the spin-up and spin-down
   electrons are energetically and spatially
   identically.
 – In a calculation where there are unpaired
   electrons (multiplicity > 1), the spin-up and
   spin-down electrons need to be able to have
   different energetic and spatial properties, and
   the UNRESTRICTED keyword allows this.
            Example input file - explained
$ADFBIN/adf -n 1 <<eor

TITLE H2O

BASIS
TYPE TZP
CORE Small
END

SCF
ITERATIONS 99
CONVERGE 0.000001                    Atoms keyword is where the geometry of the
END
                                     molecule (location of nuclei) is included.
GEOMETRY                             Can be xyz file or z-matrix (in which case the
optim
END                                  word internal or zmat needs to be included
INTEGRATION 6.0                      after word atoms)
XC
GRADIENT OPBE
END

CHARGE 0 0

ATOMS
O            0.000000     0.000000     0.012976
H            0.000000    -0.754442    -0.589982
H            0.000000     0.754442    -0.589982
END

ENDINPUT
eor
                          Example output file
• Output files are rather large so here is a summary of what is in an output
  file
• Energy
Summary of Bonding Energy (energy terms are taken from the energy decomposition above)
======================================================================================

  Electrostatic Energy:               -0.256031610040912        -6.9670         -160.66        -672.21
  Kinetic Energy:                      0.447024581673579        12.1642          280.51        1173.66
  Coulomb (Steric+OrbInt) Energy:     -0.247468564515559        -6.7340         -155.29        -649.73
  XC Energy:                          -0.468398583755849       -12.7458         -293.92       -1229.78
                                    --------------------    -----------      ----------    -----------
  Total Bonding Energy:               -0.524874176638742       -14.2826         -329.36       -1378.06


                                        Hartree            Electron Volt      Kcal mol-1     kJ mol-1


  If you want to see which structures are more stable then it is the energies you
  want to compare.
  You can only compare energies from the same method (functional, basis set,
  level of integration) and number of atoms/atom types.
  ADF calculates the energy of bringing different atoms together, i.e. the bonding
  energy.
            Looking at results
• Chemcraft (www.chemcraftprog.com)
  – Still need to double check that this can read
    ADF2008 output correctly (It does read it but I
    am not sure if it reads the last geometry)
• Can view iccg wiki too for some general
  details (www.warwick.ac.uk/go/iccg)
• Open up file.output using chemcraft
• Last structure in optimisation displayed
• Can also display frequencies

				
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posted:8/9/2011
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