The ABINIT Users Mailing List ( CLOSED )

["Zhenhua Zeng" <myid520@163.com>]

Hi  Matteo,

Your routine work well. Thank you very much. 
I still have several questions, which are given below.

Best Wishes                      
Zhenhua Zeng

-------------------------------------------------------------
From：Matteo Giantomassi
sent:：2008-12-04 00:19:23
To：forum@abinit.org
Subject：Re: Re: [abinit-forum] projected Phonon DOS

>
>
>
>>> You have to do this by hand for the moment. The idea is that for each
>>> mode
>>> you calculate the contribution in the phonon eigenvectors (normalized)
>>> which
>>> is due to a given atom, e.g.
>>>
>>> weight(lambda, q, tau) = sum_i  |u_lambda,q (i, tau)|^2
>>>
>>> for direction i, atom tau, phonon mode lambda and qpoint q. The sum of
>>> these
>>> over all tau gives 1 (for a given lambda,q), so you have a weight.
>>> Multiply
>>> this by the phonon dos, and you get a PDOS. This also works fine for
>>> crystals and any other system.
>>>
>>> PDOS_tau (omega) = sum_q,lambda  weight(lambda, q, tau)
>>> delta(omega-omega_q,lambda)
>>>
>>> It should be fairly easy to add this to the anaddb output at some point
>>> -
>>> someone may even have already done it! I notice Matteo Giantomassi has a
>>> routine mkphdos with similar functionality: Matteo does this work yet?
>>
>>  Hi Matthieu,
>>
>>  Well, it should work but some hacking is needed to enter this part of the
>> code (see below)
>>  I wrote the routine some time ago and I've used it for one of my
>>  applications. It provides the PHDOS calculated either with tetrahedrons
>> or
>>  standard gaussian smearing. Type-projected contributions to the total
>> PHDOS
>>  are also available.
>>  Atom-projected contributions are not directly available because the
>> different
>>  contributions arising from atoms of the same type are summed up.
>>  Anyway calculating atom-projected contributions is just a matter of
>> changing a bit the routine (17ddb/mkphdos.F90).
>
---------------------------------
>  I had a look at my implementation and it seems that I took into
>  account the possibility of calculating atom-projected PHDOS
>   The array pjdos is indeed defined as
>
> pjdos(nomega,3,natom)
>
> so it contains the partial projected PHDOS for each atom and for
> each cartesian direction. One can easily extract from this array
> the contribution to the PHDOS given by a particular atom.
>
----------------------------------------
Zhenhua: It seem not like that. I found the  PJDOSs are given type by type, 
no atom by atom.
If I want to get PJDOS atom by atom, I have to trick the routine by setting 
'ntypat 2  znucl  13  13'
I use V5.6.4 now. I don't know whether the problem is improved in the version 
going on.

I found there is a file 'out_PHFRQ' generated when done PHDOS calcualtion, 
whose second line is 
'phonon frequencies (in Ha) on qph1l list of qpoints'
However, the just one line date in this file. So I want to know whether the 
output of this file is ok.
BTW: It seem the purpose of this file is to include the projected PHDOS of 
particular Qpoint, which is also very useful, interesting, and original drive 
of this post. 


>
>>
>>  No example and reference output files are provided yet (I know, I know,
>> shame on me!).
>>  Digging into my files I found an anaddb input that can be used to
>> calculate the PHDOS,
>>  The flags that have to be added in the input file are:
>>
>> ifcflag  1  #IFC's are needed
>>
>> #DOS related variables
>> prtdos  1              # 1 for gaussian, 2 for tetrahedrons
>> ng2qpt  35 35 7        # Dense q-mesh for Fourier interpolation
>> q2shft  0.0 0.0 0.0    # Shift for the dense mesh
>> dosdeltae  9.112670E-7 # 0.1 cm-1  frequency step for PHDOS
>> dosmear    1.366900E-5 # 3 cm-1    broadening (only for Gaussian method)
>>
>> At the end of the calculation the results are stored in the PHDOS file
>> There are several columns:
>>
>>  # omega     PHDOS    IPHDOS   PJDOS[1]  IPJDOS[1] ..
>>
>>  PHDOS refers to the total phonon DOS, IPHDOS is the integrated DOS, then
>> we have the
>>  contribution due to all the atoms of the first type as well as the
>> corresponding integrated dos.
>>
>> 3 Comments:
>>
>> 1) To call mkphdos you have to modify a bit 17ddb/invars9
>>   commenting out the call to leave_new in the following piece of code
>>
>>  if(anaddb_dtset%prtdos/=0 .and. anaddb_dtset%ifcflag/=1) then
>>   write(message, '(5a)' )&
>> &  ' invars9 : ERROR -',ch10,&
>> &  '  ifcflag must be 1 when the calculation of the phonon DOS is required
>> ',ch10,&
>> &  '  Action : correct ifcflag in your input file.'
>>   call wrtout(6,message,'COLL')
>>   call leave_new('COLL')
>>  end if
>>
>>
>> 2) If I remember well in old versions of abinit there's a small bug (just
>> a missing factor)
>>    in the calculation of the integrated type-projected PHDOS. So don't
>> rely on the columns
>>    reporting the type-projected IPHDOS. If you need, you can easily
>> integrate the curve using
>>    a plotting software such as xmgrace.
>>
>> 3) Be careful when using the tetrahedron method. The CPU time doesn't
>> scale well wrt
>>    to the number of Fourier interpolated q-points. This is a general
>> problem I found also
>>    in case of electronic DOS calculations. One should do some serious
>> profiling of the tetrahedron
>>    routines and the fortran loops to individuate the bottleneck.
>>
>> Hope it helps.
>> Best Regards
>> Matteo Giantomassi
>>
>>
>
Best Wishes!
Zhenhua Zeng