[Octopus-users] Time Dependent wave-functions

[Conn O'Rourke]

Hi All,

So I have output the time-dependent wavefunctions with octopus (thanks to
emily). I just have a question about the output format.

I output the wavefunctions in DX format, and then used VMD to visualise them
- although when I do a time dependent run the wf files have two columns in
the output - the second being the wavefunction. The question is what is in
the first column? This is what was confusing me, as I was plotting this
first column and thinking they were the wavefunctions.

Incidentally anyone wanting to visualise DX format with VMD should remove
the initial blank spaces from the first few lines, so:

object 1 class gridpositions counts     55     55     55
 origin   -4.050000   -4.050000   -4.050000
 delta     0.150000    0.000000    0.000000
 delta     0.000000    0.150000    0.000000
 delta     0.000000    0.000000    0.150000
object 2 class gridconnections counts     55     55     55
object 3 class array type float category complex rank 0 items 166375

should be:

object 1 class gridpositions counts     55     55     55
origin   -4.050000   -4.050000   -4.050000
delta     0.150000    0.000000    0.000000
delta     0.000000    0.150000    0.000000
delta     0.000000    0.000000    0.150000
object 2 class gridconnections counts     55     55     55
object 3 class array type float category complex rank 0 items 166375

or VMD won't be able to read the file.

Cheers,
Conn


On Tue, Mar 9, 2010 at 11:30 AM, Conn O'Rourke
<conn.orourke at googlemail.com>wrote:

> Hi Emily,
>
> Thanks again for the help - I thought Output was only for gs calculations.
> I had used it and found the td wave-functions looked nothing like the gs
> ones, even if I wasn't perturbing them. I'm just starting dynamic td
> simulations, and what I wanted to do was perturb the ground state of a
> simple molecule and then have a look at how the wave-functions evolve.
>
> I'll have another look.
>
> Cheers,
> Conn
>
>
> On Mon, Mar 8, 2010 at 2:23 PM, Emily <listemily at eml.cc> wrote:
>
>> Hi Conn,
>> Yes, use OutputEvery, and there will be directories called td.00000000,
>> td.00000010, etc which have all the files that you specify with Output.
>> I'm not sure what your aim is, but you could make OutputEvery 1 to get
>> the wavefunction at every step (that would
>> be a lot of data).
>>
>> Good luck!
>> Emily
>>
>> Output = wfs
>> OutputHow = dx
>> OutputEvery = 1
>>
>> from:
>>
>> http://www.tddft.org/programs/octopus/doc/3.2.0/html/vars.php?section=Output&name=Output
>>
>> Output
>> Section: Output
>> Type: flag
>> Default: no
>>
>> Specifies what to print. The output files go into the static directory,
>> except when running a time-dependent simulation, when the directory
>> td.XXXXXXX is used.
>> wfs (4): Outputs wavefunctions. Which wavefunctions are to be printed is
>> specified by the variable OutputWfsNumber -- see below. The output file
>> is called wf-, or lr_wf- in linear response.
>>
>> OutputEvery
>> Section: Output
>> Type: integer
>> Default: 50
>>
>> The output is saved when the iteration number is a multiple of the
>> OutputEvery variable. This works for the ground-state and time-dependent
>> runs.
>>
>> OutputHow
>> Section: Output
>> Type: flag
>>
>> Describes the format of the output files (see Output). Example: axis_x +
>> plane_x + dx
>> dx (64): For printing three-dimensional information, the open-source
>> program visualization tool OpenDX (http://www.opendx.org/) can be used.
>> The string .dx is appended to previous file names.
>>
>> ----- Original message -----
>> From: "Conn O'Rourke" <conn.orourke at googlemail.com>
>> To: octopus-users at tddft.org
>> Date: Mon, 8 Mar 2010 10:43:57 +0000
>> Subject: [Octopus-users] Time Dependent wave-functions
>>
>> Dear Octopus users,
>>
>> Is it possible to get octopus to output the time dependent wave
>> functions so
>> I visualise them using DX?
>> I can't see how to go about doing it from looking at the variable list.
>>
>> Thanks in advance,
>>
>> Conn
>>
>
>
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