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Francois Gygi committed
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   Calculation of vibrational frequencies

1) Generate a Qbox input script "fdmoves.i" using the script ""

   $ O1 O2 H1 H2 H3 H4 > fdmoves.i

   Note: the atom names must appear in the same order as they are printed in
   the <atomset> element in Qbox output. This may not correspond to the order
   in which they were defined with the atom command.

2) Run Qbox using the following input file:

   A sample file describing a relaxed structure must be available (in the
   following example: "relaxed_sample.xml")

   # finite difference calculation of the dynamical matrix
   load relaxed_sample.xml
   set xc PBE
   set wf_dyn PSDA
   set ecutprec 4

   Save the result in "fdmoves.r"

3) Extract all the <force> elements from the file "fdmoves.r"

   $ grep '<force>' fdmoves.r > force.dat

4) Run the dynmat program using "force.dat"

   use: ./dynmat force.dat h Nat1 mass1 [Nat2 mass2] ...
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   where Nat1 is the number of atoms of mass mass1 
   Nat2 is the number of atoms of mass mass2, etc.
   The mass parameters are in amu (C=12)

   Example for the water dimer (with oxygen atoms first, hydrogen last)
   Two oxygen atoms of mass 16, four hydrogen atoms of mass 1
   Displacements used to compute forces are 0.01 (a.u.)
   $ ./dynmat force.dat 0.01 2 16 4 1 
Francois Gygi committed
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   The frequencies are printed twice in order of increasing magnitude.
   The first six frequencies should be zero. Deviations from zero give
   an estimate of the lower bound on the error in frequencies.
   The dynamical matrix computed from finite-difference force calculations
   is not exactly symmetric due to errors in the forces and imperfect 
   relaxation of the original structure. The dynmat program prints two sets
   of eigenvalues. The first is computed using the upper triangle of the 
   dynamical matrix and the second using the lower triangle. The difference
   between the two sets gives an indication of the error due to the lack
   of symmetry of the dynamical matrix.

   Note: For calculations involving different isotopes, only step 4 must be 
   repeated with modified mass arguments. The file force.dat can be reused.