Re: [SIESTA-L] DM_out and segmentation error

[Nick Papior]

Could you please follow the instructions on this page:

https://answers.launchpad.net/siesta/+faq/2779

This would help in tracking down the problem.

2017-11-14 13:17 GMT+01:00 王亮 :

> Hello,
>
>  I tried examples from siesta official page （Files-Latcon-SrTiO3，
> File-Si-structure...）,after scf, I always got segmentation error:
>
> Using DM_out to compute the final energy and forces
> No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps:
> 26 161
> ...forrtl: severe (174): SIGSEGV, segmentation fault occurred
>
> Does anyone know how to fix it?
>
> Ps: siesta-4.1b3 and 24 cpus or 1 cpu
>
> Regards
>
>
>
> --
> Liang WANG
> Center for Nanofabrication and System Integration
> Chongqing Institute of Green and Intelligent Technology, Chinese Academy
> of Science
> 266 Fangzheng Ave
> ,
> ShuiTu technology development zone, Beibei District, Chongqing, P. R. China
> Tel: +86-23-65935570 <+86%2023%206593%205570>
>



-- 
Kind regards Nick

Re: [SIESTA-L] Defining periodic structure

[Mostafa Shabani]

Dear HarsH

A1- For making a structure you need lattice vectors and atomic position
coordinates of your unit cell structure to put in your input fdf file that
you can find in the papers or some material structure databases.

A2- You can check it by 3D structure visualization programs like VESTA
or *XCrySDen
*to see whether the structure is periodic or not

A3- After optimize some crucial parameter values  like (k-point and
Mesh-Cutoff) by set MD.MaxForceTol in your input fdf file you can optimize
your structure by MD (Molecular Dynamic) procedure.

Best regards,

)

On Tue, Nov 14, 2017 at 3:03 AM, Harsh Shah  wrote:

> Dear Siesta user,
>
> I am really new to this siesta software & I am just getting started with
> it.
>
> I had a few basic questions:
> 1.Which is the best software to use with siesta for making structures?
> 2.How can we define whether the structure is periodic or not and where
>  to define it?
> 3.How to optimize a structure?
>
> I would really appreciate if you could help me out.
>
> With Best Wishes,
> Harsh
>

Re: [SIESTA-L] Molecular Adsorption on Material Surfaces

[Lukas Deuchler]

Hey Rishi,

the adsorption site is defined as the energy minimum. What people usually do is 
they try out different heights, fit a curve to the energy - height plot and by 
this determine the adsorption site.
good luck

Lukas


--
Lukas Deuchler


> Am 14.11.2017 um 06:16 schrieb Rishi Sreedhar :
> 
> 
> Dear Lukas, 
> 
> Thank you for your logical insights. Also, how to determine at what best 
> height above the material surface the adsorbate should be initialized? Is 
> this data only available from experiments? 
> 
> Thank you for your time.
> Warm Regards,
> Rishi
> 
> 
> On Mon, Nov 13, 2017 at 12:41 PM, Lukas Deuchler 
> > 
> wrote:
> Dear Rishi,
> 
> a good starting point is experimental data of the system you want to study, 
> in case of halides on metals this could besides many more Magnussen, O. M., 
> Ordered anion adlayers on metal electrode surfaces, Chem Rev, Vol. 102, 
> (2002).
> Another starting point is the so called „chemical intuition“ where you guess 
> minimum energy configurations due to symmetry arguments and experience how 
> the considered atoms would behave in other situations (eg in a molecule). If 
> you have knowledge of chemically similar elements in a similar situation, 
> this may be a starting point (but be aware that they may behave completely 
> different). In Principle, the space of possible minimum energy configurations 
> is huge.
> Good luck in finding them
> Cheers,
> 
> Lukas
> 
> --
> Lukas Deuchler
> 
> 
>> Am 12.11.2017 um 18:59 schrieb Rishi Sreedhar > >:
>> 
>> 
>> 
>> Dear SIESTA users,
>> 
>> I am quite inexperienced in the area of molecular simulations and my query 
>> may not be particular to SIESTA and be on computational chemistry in general 
>> (I do hope that is fine).
>> 
>>  I wish to study molecular adsorption on to surfaces and wanted to know what 
>> are the methods used to find the final minimal energy orientation of the 
>> adsorbate on/near the adsorbent surface. Is the only way relaxing the system 
>> from different initial configurations and then choosing the one with minimum 
>> energy? If so,
>> how can one come up with relevant initial configurations? 
>> 
>> Many thanks for your time.
>> Warm Regards,
>> Rishi.
> 
> 

Re: [SIESTA-L] Defining periodic structure

[Nick Papior]

Dear Harsh,

2017-11-14 0:33 GMT+01:00 Harsh Shah :

> Dear Siesta user,
>
> I am really new to this siesta software & I am just getting started with
> it.
>
> I had a few basic questions:
> 1.Which is the best software to use with siesta for making structures?
>
There are many options, VNL for academics is becoming quite popular.

> 2.How can we define whether the structure is periodic or not and where
>  to define it?
>
Siesta always uses periodicity in all directions.

> 3.How to optimize a structure?
>
Please look in the manual for various optimization methods (see under
MD.TypeofRun)

>
> I would really appreciate if you could help me out.
>
> With Best Wishes,
> Harsh
>



-- 
Kind regards Nick