Hi, Ankush
Thank you for your kind reply. I have encountered a problem when I run the
executable eggbox_checker.py.
$ ./eggbox_checker.py H.psf 50 H_dzp.OUT
Where the H_dzp.OUT is the basis file I have produced by gen-basis.sh. The
errors are followed:
./eggbox_checker.py: line 20: import: command not found
./eggbox_checker.py: line 21: syntax error near unexpected token
`"$HOME/lib/python/Siesta"'
./eggbox_checker.py: line 21: `sys.path.append("$HOME/lib/python/Siesta")'
So, what is the problem and how to fix it? Any comment or suggestion is
appreciated.
Best
Fei Mao
-----原始邮件-----
发件人: "Ankush Rai" <[email protected]>
发送时间: 2012年11月14日 星期三
收件人: [email protected]
抄送:
主题: Re: Re: [SIESTA-L] How to fix the eggbox-effect?
Hi,
To run the python script file. Follow the given steps:
1. open terminal & go to your file system.
2. Copy the script to your folder.
3. chmod +x eggbox_checker.py
4. ./eggbox_checker.py PseudoFile.psf [Cutoff] [basis file]
Provide the name & values of the parameters such as cutoff & basis file(without
square brackets). This script will make calculation in temporary folder. Now,
plot a graph between Energy v/s Mesh Shift (See attached file) for each value
of cutoff that you will run until relaxation is acheived.
------------------------------------------------------------------------------------------------------------------------------
In addition, you suggested the use of the block of GridCellSampling. So is
there any relationships between these two variables? And do I have to use the
two variables together?
--------------------------------------------------------------------------------------------------------------------------------
you shouldn't combine two things at once & there is no relation between above
variables.
If you intend to use grid cell sampling then use it solitarily & plot the
graph as shown in example to notice the changes.
Before you perform this steps care should be taken that you must have already
performed sampling for mesh cutoff.
Ankush
On Tue, Nov 13, 2012 at 2:22 PM, 毛飞 <[email protected]> wrote:
Hi, Emilio
Actually, I have defined the variable FilterCutoff in my input file, but I do
not know how to choose the value for it. I just know it should be smaller than
the value of MeshCutoff (for example, if I choose 400 Ry for MeshCutoff, then
how about the FilterCutoff).
So, the same situation for the variable of FitlerTol, how can I choose a value
for it. The input and output files are attached in my former email.
Any comment or suggestion is appreciated.
Best
Fei Mao
-----原始邮件-----
发件人: "Emilio Artacho" <[email protected]>
发送时间: 2012年11月13日 星期二
收件人:[email protected]
抄送:
主题: Re: [SIESTA-L] How to fix the eggbox-effect?
Dear Fei
You could also use filtering (see e.g. FilterTol)
Emilio
On 13 Nov 2012, at 11:11, 毛飞 wrote:
Hi, all
Thank you for your kind reply. I also have learned the script eggbox_checker.py
in the user’s guide, but I do not know how to use it. Can it be compiled and to
be generated as a executable? In the guide, it does not talk too much about how
to use this script, I do not know. And when I obtain the Fourier components for
each species by the script, I have to define the variable EggboxRemove.
In addition, you suggested the use of the block of GridCellSampling. So is
there any relationships between these two variables? And do I have to use the
two variables together?
Any comment or suggestion is appreciated. Thank you in advance.
Fei Mao
Beijing Normal University, China
-----原始邮件-----
发件人: "Ankush Rai" <[email protected]>
发送时间: 2012年11月13日 星期二
收件人:[email protected]
抄送:
主题: Re: [SIESTA-L] How to fix the eggbox-effect?
Use the attached script to diagnose the eggbox effect.
You can also use grid sampling. Add following lines to your .fdf file
%block GridCellSampling
0.5 0.5 0.0
0.5 0.0 0.5
0.0 0.5 0.5
%endblock GridCellSampling
care should be taken that grid sampling will need to be modified as per the
system.
I hope it will help. Best regard.....
On Mon, Nov 12, 2012 at 8:24 AM, 毛飞 <[email protected]> wrote:
Hi, all
Have you ever met the eggbox effect problem before when you do the geometry
optimization with Siesta, and how do you fix it.
When I optimize the geometry of graphene which is absorbed with a Mg
（Magnesium） atom, I encounter the problem, In my case, the value of Max force
vibrates up and down, which do not go to convergence. I learn to the user’s
guide, it is said that it may fix the problem just by defining the variable
FilterCutoff, but I do not know how to define the suitable value for that
variable (As I know, it should lower than the MeshCutoff. In my case, the
MeshCutoff is 360 Ry, so how about the FilterCutoff? I have attached the input
file and output file).
Any comment or suggestion is appreciated. Thank you.
Fei Mao
Beijing Normal University, China
--
Emilio Artacho
CIC nanoGUNE Consolider, and Cavendish Laboratory, University of Cambridge
Tolosa Hiribidea 76, E-20018 Donostia - San Sebastián, Spain,
[email protected], +34 943 574039, http://theory.nanogune.eu
