Re: [SIESTA-L] how to save EIG or PDOS at every step of MD run?

[Ferran Jovell]

Dear Alex,

I don't know if there's any built-in solution. However I'd go for a bash 
script so you can store all the files that matter and you can save all 
the files in all MD steps.


Ferran
On 30/06/14 20:41, Alexander Vozny wrote:

Any ready-to-use solutions?
I really need to monitor not only the total energy but at least a 
bandgap at every step.

Alex.


--
Ferran Jovell Megias
Tècnic Mitjà de Suport a la Recerca
Departament d'Enginyeria Electrònica
Universitat Autònoma de Barcelona
contact info:
e-mail: ferran.jov...@uab.cat
  telf: +34 93 581 35 29

[SIESTA-L] how to save EIG or PDOS at every step of MD run?

[Alexander Vozny]

Any ready-to-use solutions?
I really need to monitor not only the total energy but at least a bandgap
at every step.
Alex.

Re: [SIESTA-L] one question

[Mostafa Shabani]

I think you have to change split_norm  paramater in your fdf file. its
value is between 0 and 1. it determine how localize is your second zeta


On Sun, Jun 29, 2014 at 2:28 PM, Salami  wrote:

>  Dear Siesta users
>
>
>
> I want to relax the armchair MoS2(10), but after siesta running, I have
> faced to this error. I have took Mo.psf from Siesta web page. Should I
> build Mo.psf file?
>
>  I would be really thankful for your comments and helps.
>
> Thanks in advance,
>
> Kind Regards.
>
> Nadia Salami
>
>
>
>
>
>
>
> atom: Called for Mo(Z =  42)
>
>
>
> read_vps: Pseudopotential generation method:
>
> read_vps: ATM3  Troullier-Martins
>
> Total valence charge:6.0
>
>
>
> read_vps: Pseudopotential includes a core correction:
>
> read_vps: Pseudo-core for xc-correction
>
>
>
> xc_check: Exchange-correlation functional:
>
> xc_check: GGA Perdew, Burke & Ernzerhof 1996
>
> V l=0 = -2*Zval/r beyond r=  3.3612
>
> V l=1 = -2*Zval/r beyond r=  3.3612
>
> V l=2 = -2*Zval/r beyond r=  3.3612
>
> V l=3 = -2*Zval/r beyond r=  3.3612
>
> All V_l potentials equal beyond r=  2.8216
>
> This should be close to max(r_c) in ps generation
>
> All pots = -2*Zval/r beyond r=  3.3612
>
>
>
> VLOCAL1: 99.0% of the norm of Vloc inside  5.452 Ry
>
> VLOCAL1: 99.9% of the norm of Vloc inside 12.426 Ry
>
> atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge3.36125
>
> atom: Maximum radius for r*vlocal+2*Zval:2.96629
>
> GHOST: No ghost state for L =  0
>
> GHOST: No ghost state for L =  1
>
> GHOST: No ghost state for L =  2
>
> GHOST: No ghost state for L =  3
>
>
>
> KBgen: Kleinman-Bylander projectors:
>
>l= 0   rc=  3.761488   el= -0.278904   Ekb=  2.810542   kbcos=  0.286707
>
>l= 1   rc=  3.856712   el= -0.075735   Ekb=  1.630125   kbcos=  0.263456
>
>l= 2   rc=  3.403530   el= -0.293317   Ekb= -4.604863   kbcos= -0.604078
>
>l= 3   rc=  4.004087   el=  0.003037   Ekb= -2.640656   kbcos= -0.020140
>
>
>
> KBgen: Total number of  Kleinman-Bylander projectors:   16
>
> atom:
> -
>
>
>
> atom: SANKEY-TYPE ORBITALS:
>
> atom: Selected multiple-zeta basis: split
>
>
>
> SPLIT: Orbitals with angular momentum L= 0
>
>
>
> SPLIT: Basis orbitals for state 5s
>
>
>
> SPLIT: PAO cut-off radius determined from an
>
> SPLIT: energy shift=  0.02 Ry
>
> p
>
>
>
>izeta = 1
>
>  lambda =1.00
>
>  rc =7.295971
>
>  energy =   -0.258275
>
> kinetic =0.254463
>
> potential(screened) =   -0.512738
>
>potential(ionic) =   -3.626001
>
> WARNING: Minimum split_norm parameter:  0.15392. Will not be able to
> generate orbital with split_norm =  0.15000
>
> See manual for new split options
>
> ERROR STOP from Node:0
>
>
>
>
> =
>
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>
> =   EXIT CODE: 256
>
> =   CLEANING UP REMAINING PROCESSES
>
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>

Re: [SIESTA-L] Non equilibrium density of states in Transiesta

[Jingxian Yu]

Hi Guangping,

Many thanks!  I will have a look at Inelastica. Cheers!

Jin


On 30/06/2014 7:59 PM, zgp121 wrote:

Figure 3a is the dependence of projected DOS on E-Ef.
I never get figures like figure 3b. Figure 3c can be obtained from 
inelastica.

Cheers.
Guangping
2014-06-30


*发件人：*Jingxian Yu 
*发送时间：*2014-06-30 11:08
*主题：*Re: [SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"zgp121","siesta-l"
*抄送：*
Dear Guangping,

Thanks for your reply!

Yes, it is easy to reproduce Figure 3(a), which just plotted the 
dependence of total DOS on E-Ef.


Would you mind to have some suggestions on how to reproduce Figure 
3(b) and 3(c)? I noticed that you reported similar data in number of 
your publications. Cheers!


Jin


On 30/06/2014 7:25 PM, zgp121 wrote:

Dear Jin,
I don't think you can get the Projected Density of States on the 
particular HOMO/LUMO in current TranSIESTA. You can only get the one 
to the selected atoms. So, you can reproduce Figure 3a in 
Computational Materials Science, 27 (2003) 151, but it needs some 
more work to reproduce Figure 3b.

Cheers.
Guangping
2014-06-30


*发件人：*Jingxian Yu 
*发送时间：*2014-06-30 04:03
*主题：*Re: [SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"siesta-l","zgp121"
*抄送：*

Dear Guangping,

I appreciated that the parameters "TS.TBT.PDOSto' and 
"TS.TBT.PDOSFrom " can generate Projected Density of States (PDOS) on 
a selected atom range.



I understand that the SIESTA package does DFT calculation by using 
linear combination of numerical atomic orbitals. By defining an 
appropriate atom range, one may be able to generate Projected Density 
of States on the particular HOMO/LUMO. But I reckon it is 
time-consuming. /


/

Is it possible to generate Projected Density of States on a selected 
MPSH eigen state, particularly HOMO or LUMO, by a more efficient way? 
Basically, I want to produce a figure similar to Figure 3(a), as 
shown in Computational Materials Science, 27 (2003) 151.

/
/Cheers!

Jin



On 28/06/2014 9:39 PM, zgp121 wrote:

Dear Jin,
Projected density of states at nonequilibrium (under non zero bias) 
in TranSIESTA should be calculated by using the options, (this is 
detailed documented by Nick as attached)

TS.TBT.PDOSto
TS.TBT.PDOSFrom
The total density of states of the device region is calculated by 
default. And transiesta can not give local density of states at this 
moment.
The projected and total density of states are the forth and third 
column, respectively, in *AVTRANS.
The non equilibrium charge density can also be obatined from *RHO or 
*TOCH after the self consistent calculation of transiesta. If you 
want to see the bias effect, you should minus that of zero bias (in 
this case, *RHO, *TOCH or *DRHO are the same to calculate the 
difference).
 If we say a system of which LUMO orbital is lower than the Fermi 
energy of electrodes in the absolute energy scale, I think we should 
make the energy levels of vacumm are the same in the two calculation.

Cheers
Guangping
2014-06-28


*发件人：*Jingxian Yu 
*发送时间：*2014-06-28 01:59
*主题：*[SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"siesta-l"
*抄送：*
Dear All

When I went through the Siesta-L, I found the following message 
posted in February 2013. I am quite interested in the same question. 
Unfortunately, nobody answered it. Can anyone have any suggestion? 
Cheers!


Jin


  [SIESTA-L] Non equilibrium density of states in Transiesta
  



Artem Baskin 
 
Thu, 21 Feb 2013 15:05:31 -0800 



Hey Siesta/Transiesta Users,

I have a question about Transiesta. in particular I am interested in how to
calculate the density of states (total, projected, local) at non
equilibrium (under non zero bias). The problem is that if I include, let's
say, a block "ProjectedDensityOfStates" into the regular Transiesta input
file where I have to choose SolutionMethod as transiesta, then PDOS is not
calculated since it requires the different SolutionMethod, namely, diagon
or norder.
Another question is did anybody try to calculate non equilibrium charge
density (due to the bias) from systemlabel.TSDE using Denchar? I have tried
to input into Denchar the Density Matrix calculated for a system under 1 V
but I did not find any difference compared to the non-biased case. 

Re: [SIESTA-L] Non equilibrium density of states in Transiesta

[zgp121]

Figure 3a is the dependence of projected DOS on E-Ef.

I never get figures like figure 3b. Figure 3c can be obtained from inelastica.

Cheers.

Guangping

2014-06-30 





发件人：Jingxian Yu 
发送时间：2014-06-30 11:08
主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta
收件人："zgp121","siesta-l"
抄送：

Dear Guangping,

Thanks for your reply! 

Yes, it is easy to reproduce Figure 3(a), which just plotted the dependence of 
total DOS on E-Ef.

Would you mind to have some suggestions on how to reproduce Figure 3(b) and 
3(c)? I noticed that you reported similar data in number of your publications. 
Cheers!

Jin


On 30/06/2014 7:25 PM, zgp121 wrote:

Dear Jin,

I don't think you can get the Projected Density of States on the particular 
HOMO/LUMO in current TranSIESTA. You can only get the one to the selected 
atoms. So, you can reproduce Figure 3a in Computational Materials Science, 27 
(2003) 151, but it needs some more work to reproduce Figure 3b.

Cheers.

Guangping


2014-06-30 





发件人：Jingxian Yu 
发送时间：2014-06-30 04:03
主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta
收件人："siesta-l","zgp121"
抄送：

Dear Guangping,

I appreciated that the parameters "TS.TBT.PDOSto' and "TS.TBT.PDOSFrom " can 
generate Projected Density of States (PDOS) on a selected atom range. 

I understand that the SIESTA package does DFT calculation by using linear 
combination of numerical atomic orbitals. By defining an appropriate atom 
range, one may be able to generate Projected Density of States on the 
particular HOMO/LUMO. But I reckon it is time-consuming. 


Is it possible to generate Projected Density of States on a selected MPSH eigen 
state, particularly HOMO or LUMO, by a more efficient way? Basically, I want to 
produce a figure similar to Figure 3(a), as shown in Computational Materials 
Science, 27 (2003) 151.

Cheers!

Jin


On 28/06/2014 9:39 PM, zgp121 wrote:

Dear Jin,

Projected density of states at nonequilibrium (under non zero bias) in 
TranSIESTA should be calculated by using the options, (this is detailed 
documented by Nick as attached)

TS.TBT.PDOSto
TS.TBT.PDOSFrom

The total density of states of the device region is calculated by default. And 
transiesta can not give local density of states at this moment.

The projected and total density of states are the forth and third column, 
respectively, in *AVTRANS.

The non equilibrium charge density can also be obatined from *RHO or *TOCH 
after the self consistent calculation of transiesta. If you want to see the 
bias effect, you should minus that of zero bias (in this case, *RHO, *TOCH or 
*DRHO are the same to calculate the difference).

 If we say a system of which LUMO orbital is lower than the Fermi energy of 
electrodes in the absolute energy scale, I think we should make the energy 
levels of vacumm are the same in the two calculation.

Cheers

Guangping

2014-06-28 





发件人：Jingxian Yu 
发送时间：2014-06-28 01:59
主题：[SIESTA-L] Non equilibrium density of states in Transiesta
收件人："siesta-l"
抄送：

Dear All

When I went through the Siesta-L, I found the following message posted in 
February 2013. I am quite interested in the same question. Unfortunately, 
nobody answered it. Can anyone have any suggestion? Cheers!

Jin


[SIESTA-L] Non equilibrium density of states in Transiesta 
Artem Baskin Thu, 21 Feb 2013 15:05:31 -0800 
Hey Siesta/Transiesta Users,

I have a question about Transiesta. in particular I am interested in how to
calculate the density of states (total, projected, local) at non
equilibrium (under non zero bias). The problem is that if I include, let's
say, a block "ProjectedDensityOfStates" into the regular Transiesta input
file where I have to choose SolutionMethod as transiesta, then PDOS is not
calculated since it requires the different SolutionMethod, namely, diagon
or norder.
Another question is did anybody try to calculate non equilibrium charge
density (due to the bias) from systemlabel.TSDE using Denchar? I have tried
to input into Denchar the Density Matrix calculated for a system under 1 V
but I did not find any difference compared to the non-biased case. Any
comments on this problem?

One more question. Let's say we have a system whose LUMO orbital is lower
than the Fermi energy of electrodes in the absolute energy scale. I would
expect some charging of the sandwiched molecule due to the contacts with
electrodes. Did anybody tested this effect in Transiesta?

Any info or comments would be greatly appreciated.

Best,

Artem Baskin

Re: [SIESTA-L] Non equilibrium density of states in Transiesta

[zgp121]

Dear Jin and Akshu,

The code has moved the Fermi energy to zero. That is to say the smallest 
positive eigenvalue is LUMO and the biggest negative one is HOMO.

To obtain wavefunctions for HOMO/LUMO and visualise them, you should use 
"EigenChannels" in inelastica package, which is also a free one. EigenChannels 
can read "TS.TBT.PDOSto' and "TS.TBT.PDOSFrom", and then calculated the 
eigenvalues and the eigenstates in a energy range.
About Inelastica, you can download the code from 
http://sourceforge.net/p/inelastica/code/commit_browser. I now can not find the 
link on how to install and use this package. Maybe someone else can help on 
this.

Cheers,

Guangping

2014-06-30 





发件人：Jingxian Yu 
发送时间：2014-06-30 10:50
主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta
收件人："akshu hans","siesta-l"
抄送：

Hi Akshu,

I did a test using Guangping's code. It was fine!

To figure out HOMO and LUMO, you need to count total number of valence 
electrons in the organic molecule. For example, if your molecule contains 200 
valence electrons, simply HOMO is the 100th state. 

Now my trouble is how to obtain wavefunctions for HOMO/LUMO and visualise them. 
Anyone can help? Guangping suggested Inelastica. Would anyone like to share any 
any tutorial with me? Cheers!

Jin


On 30/06/2014 6:05 PM, akshu hans wrote:

Hi Jin
Yes i did set the file correctly...but there is only one non-zero eigen 
value...how can i get homo and lumo of the molecule  


Regards
Akshu



On Monday, June 30, 2014 2:01 PM, Jingxian Yu  
wrote:




Hi Akshu

These numbers are a set of eigenvalues for the organic molecule in your 
scattering region. Did you set your atom_list.txt file correctly?

In you atom_list.txt file, the first line is the total number of atoms 
contained in the organic molecule. The following lines list atom numbers (one 
number per line) of the organic molecule, as specified in the fdf file. cheers!

Jin






 On 30/06/2014 5:28 PM, akshu hans wrote:


Dear Guangping

Thank you for sharing the code with all of us. Could you please explain its 
outputi got one eigen value and remaining all zeroes.


Regards
Akshu



On Saturday, June 28, 2014 6:42 PM, zgp121  wrote:




Yes, it is possible. But in TranSIESTA itself not. You can achive this in 
inelastica package. But if you are only interested in the eigenvaule not the 
eigenvector(wavefunction), you can use the attached fortran code by myself to 
calculate the eigenvalues from *TSHS file of the scattering region. 

It is welcome for anyone, who is familar with the basis set of SIESTA, to 
extended this code to calculate the eigenvector.

Cheers,

Guangping

2014-06-28 





发件人：Akshu 
发送时间：2014-06-28 19:21
主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta
收件人："siesta-l@uam.es"
抄送：



Hi, 
Is it possible to calculate homo and lumo (mpsh eigen states) of the molecule 
sandwiched between two
Electrodes using transiesta ??

On 28-Jun-2014, at 5:39 pm, "zgp121" wrote:


Dear Jin,

Projected density of states at nonequilibrium (under non zero bias) in 
TranSIESTA should be calculated by using the options, (this is detailed 
documented by Nick as attached)

TS.TBT.PDOSto
TS.TBT.PDOSFrom

The total density of states of the device region is calculated by default. And 
transiesta can not give local density of states at this moment.

The projected and total density of states are the forth and third column, 
respectively, in *AVTRANS.

The non equilibrium charge density can also be obatined from *RHO or *TOCH 
after the self consistent calculation of transiesta. If you want to see the 
bias effect, you should minus that of zero bias (in this case, *RHO, *TOCH or 
*DRHO are the same to calculate the difference).

 If we say a system of which LUMO orbital is lower than the Fermi energy of 
electrodes in the absolute energy scale, I think we should make the energy 
levels of vacumm are the same in the two calculation.

Cheers

Guangping

2014-06-28 





发件人：Jingxian Yu 
发送时 间：2014-06-28 01:59
主题：[SIESTA-L] Non equilibrium density of states in Transiesta
收件人："siesta-l"
抄送：

Dear All

When I went through the Siesta-L, I found the following message posted in 
February 2013. I am quite interested in the same question. Unfortunately, 
nobody answered it. Can anyone have any suggestion? Cheers!

Jin


[SIESTA-L] Non equilibrium density of states in Transiesta 
Artem Baskin Thu, 21 Feb 2013 15:05:31 -0800 
Hey Siesta/Transiesta Users,

I have a question about Transiesta. in particular I am interested in how to
calculate the density of states (total, projected, local) at non
equilibrium (under non zero bias). The problem is that if I include, let's
say, a block "ProjectedDensityOfStates" into the regular Transiesta input
file where I have to choose SolutionMethod as transiesta, then PDOS is not
calculated since it requires the different SolutionMethod, namely, diagon
or norder.
Another question is did anybody try to calculate non equilibrium charge
density (du

Re: [SIESTA-L] Non equilibrium density of states in Transiesta

[Jingxian Yu]

Dear Guangping,

Thanks for your reply!

Yes, it is easy to reproduce Figure 3(a), which just plotted the 
dependence of total DOS on E-Ef.


Would you mind to have some suggestions on how to reproduce Figure 3(b) 
and 3(c)? I noticed that you reported similar data in number of your 
publications. Cheers!


Jin


On 30/06/2014 7:25 PM, zgp121 wrote:

Dear Jin,
I don't think you can get the Projected Density of States on the 
particular HOMO/LUMO in current TranSIESTA. You can only get the one 
to the selected atoms. So, you can reproduce Figure 3a in 
Computational Materials Science, 27 (2003) 151, but it needs some more 
work to reproduce Figure 3b.

Cheers.
Guangping
2014-06-30


*发件人：*Jingxian Yu 
*发送时间：*2014-06-30 04:03
*主题：*Re: [SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"siesta-l","zgp121"
*抄送：*

Dear Guangping,

I appreciated that the parameters "TS.TBT.PDOSto' and "TS.TBT.PDOSFrom 
" can generate Projected Density of States (PDOS) on a selected atom 
range.



I understand that the SIESTA package does DFT calculation by using 
linear combination of numerical atomic orbitals. By defining an 
appropriate atom range, one may be able to generate Projected Density 
of States on the particular HOMO/LUMO. But I reckon it is 
time-consuming. /


/

Is it possible to generate Projected Density of States on a selected 
MPSH eigen state, particularly HOMO or LUMO, by a more efficient way? 
Basically, I want to produce a figure similar to Figure 3(a), as shown 
in Computational Materials Science, 27 (2003) 151.

/
/Cheers!

Jin



On 28/06/2014 9:39 PM, zgp121 wrote:

Dear Jin,
Projected density of states at nonequilibrium (under non zero bias) 
in TranSIESTA should be calculated by using the options, (this is 
detailed documented by Nick as attached)

TS.TBT.PDOSto
TS.TBT.PDOSFrom
The total density of states of the device region is calculated by 
default. And transiesta can not give local density of states at this 
moment.
The projected and total density of states are the forth and third 
column, respectively, in *AVTRANS.
The non equilibrium charge density can also be obatined from *RHO or 
*TOCH after the self consistent calculation of transiesta. If you 
want to see the bias effect, you should minus that of zero bias (in 
this case, *RHO, *TOCH or *DRHO are the same to calculate the 
difference).
 If we say a system of which LUMO orbital is lower than the Fermi 
energy of electrodes in the absolute energy scale, I think we should 
make the energy levels of vacumm are the same in the two calculation.

Cheers
Guangping
2014-06-28


*发件人：*Jingxian Yu 
*发送时间：*2014-06-28 01:59
*主题：*[SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"siesta-l"
*抄送：*
Dear All

When I went through the Siesta-L, I found the following message 
posted in February 2013. I am quite interested in the same question. 
Unfortunately, nobody answered it. Can anyone have any suggestion? 
Cheers!


Jin


  [SIESTA-L] Non equilibrium density of states in Transiesta
  



Artem Baskin 
 
Thu, 21 Feb 2013 15:05:31 -0800 



Hey Siesta/Transiesta Users,

I have a question about Transiesta. in particular I am interested in how to
calculate the density of states (total, projected, local) at non
equilibrium (under non zero bias). The problem is that if I include, let's
say, a block "ProjectedDensityOfStates" into the regular Transiesta input
file where I have to choose SolutionMethod as transiesta, then PDOS is not
calculated since it requires the different SolutionMethod, namely, diagon
or norder.
Another question is did anybody try to calculate non equilibrium charge
density (due to the bias) from systemlabel.TSDE using Denchar? I have tried
to input into Denchar the Density Matrix calculated for a system under 1 V
but I did not find any difference compared to the non-biased case. Any
comments on this problem?

One more question. Let's say we have a system whose LUMO orbital is lower
than the Fermi energy of electrodes in the absolute energy scale. I would
expect some charging of the sandwiched molecule due to the contacts with
electrodes. Did anybody tested this effect in Transiesta?

Any info or comments would be greatly appreciated.

Best,

Artem Baskin

Re: [SIESTA-L] Non equilibrium density of states in Transiesta

[zgp121]

Dear Akshu,

What Jin has mentioned is totally right. Indeed, to make a better agreement 
with the transmission peak, you can include some neighbouring electrodes atoms. 
Furthermore, these atoms are not necessarily successive.


Cheers,

Guangping
2014-06-30 





发件人：Jingxian Yu 
发送时间：2014-06-30 10:30
主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta
收件人："akshu hans","siesta-l"
抄送：

Hi Akshu

These numbers are a set of eigenvalues for the organic molecule in your 
scattering region. Did you set your atom_list.txt file correctly?

In you atom_list.txt file, the first line is the total number of atoms 
contained in the organic molecule. The following lines list atom numbers (one 
number per line) of the organic molecule, as specified in the fdf file. cheers!

Jin





 On 30/06/2014 5:28 PM, akshu hans wrote:


Dear Guangping

Thank you for sharing the code with all of us. Could you please explain its 
outputi got one eigen value and remaining all zeroes.


Regards
Akshu



On Saturday, June 28, 2014 6:42 PM, zgp121  wrote:




Yes, it is possible. But in TranSIESTA itself not. You can achive this in 
inelastica package. But if you are only interested in the eigenvaule not the 
eigenvector(wavefunction), you can use the attached fortran code by myself to 
calculate the eigenvalues from *TSHS file of the scattering region. 

It is welcome for anyone, who is familar with the basis set of SIESTA, to 
extended this code to calculate the eigenvector.

Cheers,

Guangping

2014-06-28 





发件人：Akshu 
发送时间：2014-06-28 19:21
主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta
收件人："siesta-l@uam.es"
抄送：



Hi, 
Is it possible to calculate homo and lumo (mpsh eigen states) of the molecule 
sandwiched between two
Electrodes using transiesta ??

On 28-Jun-2014, at 5:39 pm, "zgp121" wrote:


Dear Jin,

Projected density of states at nonequilibrium (under non zero bias) in 
TranSIESTA should be calculated by using the options, (this is detailed 
documented by Nick as attached)

TS.TBT.PDOSto
TS.TBT.PDOSFrom

The total density of states of the device region is calculated by default. And 
transiesta can not give local density of states at this moment.

The projected and total density of states are the forth and third column, 
respectively, in *AVTRANS.

The non equilibrium charge density can also be obatined from *RHO or *TOCH 
after the self consistent calculation of transiesta. If you want to see the 
bias effect, you should minus that of zero bias (in this case, *RHO, *TOCH or 
*DRHO are the same to calculate the difference).

 If we say a system of which LUMO orbital is lower than the Fermi energy of 
electrodes in the absolute energy scale, I think we should make the energy 
levels of vacumm are the same in the two calculation.

Cheers

Guangping

2014-06-28 





发件人：Jingxian Yu 
发送时 间：2014-06-28 01:59
主题：[SIESTA-L] Non equilibrium density of states in Transiesta
收件人："siesta-l"
抄送：

Dear All

When I went through the Siesta-L, I found the following message posted in 
February 2013. I am quite interested in the same question. Unfortunately, 
nobody answered it. Can anyone have any suggestion? Cheers!

Jin


[SIESTA-L] Non equilibrium density of states in Transiesta 
Artem Baskin Thu, 21 Feb 2013 15:05:31 -0800 
Hey Siesta/Transiesta Users,

I have a question about Transiesta. in particular I am interested in how to
calculate the density of states (total, projected, local) at non
equilibrium (under non zero bias). The problem is that if I include, let's
say, a block "ProjectedDensityOfStates" into the regular Transiesta input
file where I have to choose SolutionMethod as transiesta, then PDOS is not
calculated since it requires the different SolutionMethod, namely, diagon
or norder.
Another question is did anybody try to calculate non equilibrium charge
density (due to the bias) from systemlabel.TSDE using Denchar? I have tried
to input into Denchar the Density Matrix calculated for a system under 1 V
but I did not find any difference compared to the non-biased case. Any
comments on this problem?

One more question. Let's say we have a system whose LUMO orbital is lower
than the Fermi energy of electrodes in the absolute energy scale. I would
expect some charging of the sandwiched molecule due to the contacts with
electrodes. Did anybody tested this effect in Transiesta?

Any info or comments would be greatly appreciated.

Best,

Artem Baskin

Re: [SIESTA-L] Non equilibrium density of states in Transiesta

[Jingxian Yu]

Hi Akshu,

I did a test using Guangping's code. It was fine!

To figure out HOMO and LUMO, you need to count total number of valence 
electrons in the organic molecule. For example, if your molecule 
contains 200 valence electrons, simply HOMO is the 100th state.


Now my trouble is how to obtain wavefunctions for HOMO/LUMO and 
visualise them. Anyone can help? Guangping suggested Inelastica. Would 
anyone like to share any any tutorial with me? Cheers!


Jin



On 30/06/2014 6:05 PM, akshu hans wrote:

Hi Jin
Yes i did set the file correctly...but there is only one non-zero 
eigen value...how can i get homo and lumo of the molecule

Regards
Akshu


On Monday, June 30, 2014 2:01 PM, Jingxian Yu 
 wrote:



Hi Akshu

These numbers are a set of eigenvalues for the organic molecule in 
your scattering region. Did you set your atom_list.txt file correctly?


In you atom_list.txt file, the first line is the total number of atoms 
contained in the organic molecule. The following lines list atom 
numbers (one number per line) of the organic molecule, as specified in 
the fdf file. cheers!


Jin





 On 30/06/2014 5:28 PM, akshu hans wrote:

Dear Guangping

Thank you for sharing the code with all of us. Could you please 
explain its outputi got one eigen value and remaining all zeroes.

Regards
Akshu


On Saturday, June 28, 2014 6:42 PM, zgp121  
 wrote:



Yes, it is possible. But in TranSIESTA itself not. You can achive this 
in inelastica package. But if you are only interested in the 
eigenvaule not the eigenvector(wavefunction), you can use the 
attached fortran code by myself to calculate the eigenvalues from 
*TSHS file of the scattering region.
It is welcome for anyone, who is familar with the basis set 
of SIESTA, to extended this code to calculate the eigenvector.

Cheers,
Guangping
2014-06-28


*发件人：*Akshu  
*发送时间：*2014-06-28 19:21
*主题：*Re: [SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"siesta-l@uam.es"  


*抄送：*


Hi,
Is it possible to calculate homo and lumo (mpsh eigen states) of the 
molecule sandwiched between two

Electrodes using transiesta ??

On 28-Jun-2014, at 5:39 pm, "zgp121"> wrote:


Dear Jin,
Projected density of states at nonequilibrium (under non zero bias) in 
TranSIESTA should be calculated by using the options, (this is 
detailed documented by Nick as attached)

TS.TBT.PDOSto
TS.TBT.PDOSFrom
The total density of states of the device region is calculated by 
default. And transiesta can not give local density of states at this 
moment.
The projected and total density of states are the forth and third 
column, respectively, in *AVTRANS.
The non equilibrium charge density can also be obatined from *RHO or 
*TOCH after the self consistent calculation of transiesta. If you want 
to see the bias effect, you should minus that of zero bias (in this 
case, *RHO, *TOCH or *DRHO are the same to calculate the difference).
 If we say a system of which LUMO orbital is lower than the Fermi 
energy of electrodes in the absolute energy scale, I think we should 
make the energy levels of vacumm are the same in the two calculation.

Cheers
Guangping
2014-06-28


*发件人：*Jingxian Yu >

*发送时 间：*2014-06-28 01:59
*主题：*[SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"siesta-l"mailto:siesta-l@uam.es>>
*抄送：*
Dear All

When I went through the Siesta-L, I found the following message posted 
in February 2013. I am quite interested in the same question. 
Unfortunately, nobody answered it. Can anyone have any suggestion? Cheers!


Jin


  [SIESTA-L] Non equilibrium density of states in Transiesta
  



Artem Baskin 
 
Thu, 21 Feb 2013 15:05:31 -0800 


Hey Siesta/Transiesta Users,

I have a question about Transiesta. in particular I am interested in how to
calculate the density of states (total, projected, local) at non
equilibrium (under non zero bias). The problem is that if I include, let's
say, a block "ProjectedDensityOfStates" into the regular Transiesta input
file where I have to choose SolutionMethod as transiesta, then PDOS is not
calculated since it requires the different SolutionMethod, namely, diagon
or norder.
Another question is did anybody try to calculate non equilibrium charge
density (due to the bias) from systemlabel.TSDE using Denchar

Re: [SIESTA-L] Non equilibrium density of states in Transiesta

[Jingxian Yu]

Hi Akshu

These numbers are a set of eigenvalues for the organic molecule in your 
scattering region. Did you set your atom_list.txt file correctly?


In you atom_list.txt file, the first line is the total number of atoms 
contained in the organic molecule. The following lines list atom numbers 
(one number per line) of the organic molecule, as specified in the fdf 
file. cheers!


Jin





 On 30/06/2014 5:28 PM, akshu hans wrote:


Dear Guangping

Thank you for sharing the code with all of us. Could you please 
explain its outputi got one eigen value and remaining all zeroes.

Regards
Akshu


On Saturday, June 28, 2014 6:42 PM, zgp121  wrote:


Yes, it is possible. But in TranSIESTA itself not. You can achive this 
in inelastica package. But if you are only interested in the 
eigenvaule not the eigenvector(wavefunction), you can use the 
attached fortran code by myself to calculate the eigenvalues from 
*TSHS file of the scattering region.
It is welcome for anyone, who is familar with the basis set 
of SIESTA, to extended this code to calculate the eigenvector.

Cheers,
Guangping
2014-06-28


*发件人：*Akshu 
*发送时间：*2014-06-28 19:21
*主题：*Re: [SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"siesta-l@uam.es"
*抄送：*


Hi,
Is it possible to calculate homo and lumo (mpsh eigen states) of the 
molecule sandwiched between two

Electrodes using transiesta ??

On 28-Jun-2014, at 5:39 pm, "zgp121"> wrote:


Dear Jin,
Projected density of states at nonequilibrium (under non zero bias) in 
TranSIESTA should be calculated by using the options, (this is 
detailed documented by Nick as attached)

TS.TBT.PDOSto
TS.TBT.PDOSFrom
The total density of states of the device region is calculated by 
default. And transiesta can not give local density of states at this 
moment.
The projected and total density of states are the forth and third 
column, respectively, in *AVTRANS.
The non equilibrium charge density can also be obatined from *RHO or 
*TOCH after the self consistent calculation of transiesta. If you want 
to see the bias effect, you should minus that of zero bias (in this 
case, *RHO, *TOCH or *DRHO are the same to calculate the difference).
 If we say a system of which LUMO orbital is lower than the Fermi 
energy of electrodes in the absolute energy scale, I think we should 
make the energy levels of vacumm are the same in the two calculation.

Cheers
Guangping
2014-06-28


*发件人：*Jingxian Yu >

*发送时 间：*2014-06-28 01:59
*主题：*[SIESTA-L] Non equilibrium density of states in Transiesta
*收件人：*"siesta-l"mailto:siesta-l@uam.es>>
*抄送：*
Dear All

When I went through the Siesta-L, I found the following message posted 
in February 2013. I am quite interested in the same question. 
Unfortunately, nobody answered it. Can anyone have any suggestion? Cheers!


Jin


  [SIESTA-L] Non equilibrium density of states in Transiesta
  



Artem Baskin 
 
Thu, 21 Feb 2013 15:05:31 -0800 


Hey Siesta/Transiesta Users,

I have a question about Transiesta. in particular I am interested in how to
calculate the density of states (total, projected, local) at non
equilibrium (under non zero bias). The problem is that if I include, let's
say, a block "ProjectedDensityOfStates" into the regular Transiesta input
file where I have to choose SolutionMethod as transiesta, then PDOS is not
calculated since it requires the different SolutionMethod, namely, diagon
or norder.
Another question is did anybody try to calculate non equilibrium charge
density (due to the bias) from systemlabel.TSDE using Denchar? I have tried
to input into Denchar the Density Matrix calculated for a system under 1 V
but I did not find any difference compared to the non-biased case. Any
comments on this problem?

One more question. Let's say we have a system whose LUMO orbital is lower
than the Fermi energy of electrodes in the absolute energy scale. I would
expect some charging of the sandwiched molecule due to the contacts with
electrodes. Did anybody tested this effect in Transiesta?

Any info or comments would be greatly appreciated.

Best,

Artem Baskin

Re: [SIESTA-L] Non equilibrium density of states in Transiesta

[akshu hans]

Dear Guangping

Thank you for sharing the code with all of us. Could you please explain its 
outputi got one eigen value and remaining all zeroes.

 
Regards
Akshu


On Saturday, June 28, 2014 6:42 PM, zgp121  wrote:
 


Yes, it is possible. But in TranSIESTA itself not. You can achive this in 
inelastica package. But if you are only interested in the eigenvaule not 
the eigenvector(wavefunction), you can use the 
attached fortran code by myself to calculate the eigenvalues from 
*TSHS file of the scattering region. 
 
It is welcome for anyone, who is familar with the basis set 
of SIESTA, to extended this code to calculate the eigenvector.
 
Cheers,
 
Guangping
 
2014-06-28 

 

 
发件人：Akshu 
发送时间：2014-06-28 19:21
主题：Re: [SIESTA-L] Non equilibrium density of states in 
Transiesta
收件人："siesta-l@uam.es"
抄送：
 


Hi, 
Is it possible to calculate homo and lumo (mpsh eigen states) of the 
molecule sandwiched between two
Electrodes using transiesta ??

On 28-Jun-2014, at 5:39 pm, "zgp121" wrote:


Dear Jin,
 
Projected density of states at nonequilibrium (under non zero bias) in  
TranSIESTA should be calculated by using the options, (this is detailed  
documented by Nick as attached)
 
TS.TBT.PDOSto
TS.TBT.PDOSFrom
 
The total density of states of the device region is calculated by  default. And 
transiesta can not give local density of states at this  moment.
 
The projected and total density of states are the forth and  third column, 
respectively, in *AVTRANS.
 
The non equilibrium charge density can also be obatined from *RHO or  *TOCH 
after the self consistent calculation of transiesta. If you want to  see the 
bias effect, you should minus that of zero bias (in this case,  *RHO, *TOCH or 
*DRHO are the same to calculate the difference).
 
 If we say a system of which LUMO orbital is lower than the  Fermi energy of 
electrodes in the absolute energy scale, I think we should  make the energy 
levels of vacumm are the same in the two calculation.
 
Cheers
 
Guangping
 
2014-06-28 

 

 
发件人：Jingxian Yu 
发送时间：2014-06-28 01:59
主题：[SIESTA-L] Non equilibrium density of states in  Transiesta
收件人："siesta-l"
抄送：
 
Dear All

When I went through the Siesta-L, I found the following 
  message posted in February 2013. I am quite interested in the same question. 
  Unfortunately, nobody answered it. Can anyone have any suggestion? 
  Cheers!

Jin


[SIESTA-L] Non equilibrium density of  states in Transiesta 
Artem Baskin Thu, 21 Feb 2013 15:05:31  -0800 
Hey Siesta/Transiesta Users, I have a question about Transiesta. in particular 
I am interested in how to
calculate the density of states (total, projected, local) at non
equilibrium (under non zero bias). The problem is that if I include, let's
say, a block "ProjectedDensityOfStates" into the regular Transiesta input
file where I have to choose SolutionMethod as transiesta, then PDOS is not
calculated since it requires the different SolutionMethod, namely, diagon
or norder.
Another question is did anybody try to calculate non equilibrium charge
density (due to the bias) from systemlabel.TSDE using Denchar? I have tried
to input into Denchar the Density Matrix calculated for a system under 1 V
but I did not find any difference compared to the non-biased case. Any
comments on this problem? One more question. Let's say we have a system whose 
LUMO orbital is lower
than the Fermi energy of electrodes in the absolute energy scale. I would
expect some charging of the sandwiched molecule due to the contacts with
electrodes. Did anybody tested this effect in Transiesta? Any info or comments 
would be greatly appreciated. Best, Artem Baskin