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vibrational_modes

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Vibrational modes

In this section we describe how to calculatethe vibrational modes of molecules using dynamical matrix. Vibrational modes are obtained from eigen values of the dynamical matrix. The elements of the matrix are defined as second derivastives of energy with respect to geometry. The first derivatives with respect to geometry are forces.The second derivatives are obtained from the different of two forces and displacement. At first calculate optimization structure of the molecule and then move with atom in first direction and do SCF calculation, after that move with the same atom but in opposite direction and do again SCF calculation. Then evaluate the matrix element as different of this two forces devided by displacement. This procedure repeat for each direction and each atom of molecule. In order to calculate vibrational modes the dynamical matrix is mass weighted. Vibrational modes are calculated from eigen values of dynamical matrix.

Dynamical matrix calculation set the keywords idynmat in section &OPTION& in input file fireball in

fireball.in:

&OPTION
basisfile = answer.bas 
icluster = 1
nstepf = 1
sigmatol = 0.00000001
max_scf_iterations = 100
dt = 0.5
iqout = 1
idynmat = 1
&END

Parametters of dynamical matrix calculation are set in file dyn.optional placed in work directory.

Calculation of all vibrational modes

dyn.optional:

0.03              !elementary displacement
1 1 1             !dimension vector
dyn.dat           !output file  
.false.            !flag on when only some of atoms are moved, otherwise move all atoms
                     

Calculation of vibrational modes only for selected atoms

dyn.optional:

0.03              !elementary displacement
1 1 1             !dimension vector
dyn.dat           !output file  
.true.            !flag on when only some of atoms are moved, otherwise move all atoms
2                 !number of free atoms
3                 !list of free atoms 
4                        

The vibrational modes are writen into file out.

vibrational modes

vibrational_modes.1371812499.txt.gz · Last modified: 2013/06/21 13:01 (external edit)