Re: [SIESTA-L] Continuation Run

[Seyed Mohammad Tabatabaei]

Do you mean that visualizing a .XV file after completing a relaxation run
does not correctly show the relaxed structure and I should visualize the
SystemLabel.STRUCT_OUT file?


On Tue, Jan 31, 2017 at 4:08 PM, Seyed Mohammad Tabatabaei  wrote:

> Thank you. But for a system that is fully relaxed, what does the data for
> the next step really mean? My systems are fully relaxed and I always
> thought that the .XV file contains the relaxed coordinates. There is even a
> tool named xv2xsf for the relaxed .XV file. There is no such tool for
> SystemLabel.STRUCT_OUT file. Nevertheless, thank you for your help.
>
> On Mon, Jan 30, 2017 at 6:38 PM, Alberto Garcia  wrote:
>
>> Hi, Mohammad,
>>
>> Depending on the Siesta version that you are using, and the options used,
>> the XV file might contain the coordinates
>> predicted for the next molecular-dynamics or relaxation step, so they
>> will not be same as those for which the electronic structure (the DM) was
>> computed.
>> If you want to preserve the coordinates, use the SystemLabel.STRUCT_OUT
>> file, renaming it to SystemLabel.STRUCT_IN, and use
>> the option
>>
>> Use.Struct.File T
>>
>>  Alberto
>>
>>
>> > On 27 Jan 2017, at 02:25, Seyed Mohammad Tabatabaei 
>> wrote:
>> >
>> > Dear all,
>> >
>> > I have a converged .DM file from a previous calculation with 300 Ry
>> cutoff and DM.Tolerance=0.0001. When I copy this .DM file along with the
>> corresponding .XV file (I have no .CG file) to a second folder and do not
>> change any settings in my input .fdf file, a few SCF iterations are still
>> computed (I expect only 1 SCF iteration). I think this is abnormal because
>> my .DM is already converged and I do not change any settings like cutoff
>> energy, kgrid, DM.Tolerance, etc in the second run.
>> >
>> > I have these lines at the end of my input file to do a continuation run:
>> >
>> > UseSaveData T
>> > DM.UseSaveDM T
>> > ON.UseSaveLWFT
>> > MD.UseSaveXV  T
>> > MD.UseSaveCG  T
>> >
>> > Any comments on this issue is highly appreciated.
>> >
>> > Bests,
>> > Mohammad,
>>
>>
>

Re: [SIESTA-L] Error in parallel siesta 4.1b1

[Nick Papior]

Could you please try the latest beta release 4.1-b2, it should have fixed
this problem.

2017-01-30 19:05 GMT+01:00 RAJAN SINGH :

> Dear Dr Nick
>
> after this step I have this error
>
> Error: Different types in pointer assignment at (1); attempted assignment
> of UNKNOWN to REAL(8)
> Fatal Error: Error count reached limit of 25.
> make: *** [m_mixing.o] Error 1
>
> kindly give me some directions to remove this one.
>
> Regards
> Rajan
>



-- 
Kind regards Nick

[SIESTA-L] Structure setup for transiesta calculations

[Ankita Joshi]

Dear All,

Hi. I am new to SIESTA and TRANSEISTA. I want to perform transport calculations 
with transiesta for the system in which carbon nanotube act as scattering 
region and graphene act as electrodes. Please anyone suggest how to start with 
the modelling of the structure. 

Thanks

Regards 
Ankita

Re: [SIESTA-L] Error in the end of simulation Siesta 4.1 b1

[Nick Papior]

This is the last call before siesta stops. So if this is the only "error"
you get, you may disregard it completely.
I will fix this in the 4.1-b3 release so that it simply creates a file.

May I suggest you to try 4.1-b2 instead of b1? Numerous bug-fixes has
already been added to the 4.1 release series. And with 4.1 still being in
beta it is imperative to stay updated.

2017-01-30 10:11 GMT+01:00 Riya Rogers :

> Dear All
>
> I am using siesta 4.1 b1 in parallel mode, everything is fine but I am
> getting following errors in the end:
>
> sh: /usr/bin/touch: No such file or directory
>
> what should i do for such error?
>
> Thanks
>
> Regards
> Riya
>



-- 
Kind regards Nick

Re: [SIESTA-L] NETCDF error

[Alberto Garcia]

Hi,

In your arch.make, replace -DNCDF by -DCDF, type “make clean” and “make”.

 Alberto

> On 30 Jan 2017, at 11:33, RAJAN SINGH  wrote:
> 
> Dear Siesta users
> 
> I am facing following errors while trying to install 4.1-b1 in parallel mode 
> with NETCDF:
> 
> Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No such 
> file or directory
> make[2]: *** [nf_ncdf.o] Error 1
> make[2]: Leaving directory `/home/rajan.singh/siesta-4.1-b1ncdf/Obj/NCDF/src'
> make[1]: *** [lib] Error 2
> make[1]: Leaving directory `/home/rajan.singh/siesta-4.1-b1ncdf/Obj/NCDF'
> make: *** [libncdf.a] Error 2
> 
> 
> can anyone tell me what is wrong?
> my arch file is attached with mail.
> 
> thanking you
> 
> regards
> Rajan
> 
> 

Re: [SIESTA-L] NETCDF error

[Nick Papior]

You are trying to compile with netcdf, however, the compiler cannot find
the appropriate netcdf module.

Either:
1) You have added -DCDF erroneously, or
2) You have forgotten to add the netcdf include directory.

2017-01-30 11:33 GMT+01:00 RAJAN SINGH :

> Dear Siesta users
>
> I am facing following errors while trying to install 4.1-b1 in parallel
> mode with NETCDF:
>
> Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No
> such file or directory
> make[2]: *** [nf_ncdf.o] Error 1
> make[2]: Leaving directory `/home/rajan.singh/siesta-4.1-
> b1ncdf/Obj/NCDF/src'
> make[1]: *** [lib] Error 2
> make[1]: Leaving directory `/home/rajan.singh/siesta-4.1-b1ncdf/Obj/NCDF'
> make: *** [libncdf.a] Error 2
>
>
> can anyone tell me what is wrong?
> my arch file is attached with mail.
>
> thanking you
>
> regards
> Rajan
>
>


-- 
Kind regards Nick