[Pw_forum] transmission calculation

[Gabriele Sclauzero]

Quoting Manoj Srivastava :

> Dear PWSCF users and developers,
>  I have been trying to do the conductance calculation for the twin
> boundary of Cu. I compared my results with previously done calculations
> and for most K points the transmission coefficients match up very well.
> But there are some k points that I get transmission coefficients more than
> 1! This is not reasonable, as the maximum value of transmission
> coefficient could be 1.I am getting 1.000345, and similar for other k
> points.

Which k-points? How many channels are there? Please send me the output  
file or post the relevant part of it.


> Do you think transmission coefficients being more than 1 is just
> numerical error of the code or there is something wrong with my input
> file? Attached is the input file for lead and scatterign region -

Transmission coefficients should be between 0 and 1. In the code there  
are many levels of approximation. Some of them may affect the results.  
Usually the two relevant parameters one needs to adjust are epsproj  
and ewind. Why are you tweaking the others? Have you tried the default?




> ecutwfc =150.0,

Why such a high value? You are using US, aren't you?



> ATOMIC_POSITIONS
>   Cu  0.0   0.00.0
>   Cu -0.5   0.2886751340.81649658
>   Cu -1.0   0.5773502691.632993162
>
> K_POINTS (automatic)
> 6 6 8 1 1 1
> CELL_PARAMETERS {hexagonal}
>  1.0   0.00.0
> -0.5   0.8660254037844386 0.0
>  0.0   0.0 2.449489743

This shouldn't be an issue, but you could try to use ibrav=4 instead  
of ibrav=0 and specify atomic positions such that all atoms are inside  
the first primitive cell (i.e. the one with R=0)





>
>  /
>   6
>   0.500 -0.500   1
>   4.2584095E-17  0.500   1

Why don't you specify 0.0 instead? Should not matter anyway.


Gabriele Sclauzero


SISSA & Democritos


>   0.250000.000   1
>   0.167  0.167   1
>  -1.2775231E-16 -0.250   1
>   0.250 -0.251   1
> 1
> 0.0
>
>
> Regards,
> Manoj Srivastava
> University of Florida,
> Gainesville, FL
>
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[Pw_forum] problem in updating cvs version

[Bipul Rakshit]

Dear Pwscf users,
I am using remote parallel computers for calculation. When I try to update
the cvs version with the following commands

*For sh/ksh/bash, use

export CVS_RSH=ssh
export CVSROOT=:pserver:cvsanon at democritos.sissa.it:/home/cvs
* *
Then:

cvs login

and enter password: /cvsanon/*

it gives me the following error

*cvs [login aborted]: connect to democritos.sissa.it(147.122.10.31):2401
failed: Connection timed out*


-- 
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
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[Pw_forum] Problem with parallel running by mpich2

[Lorenzo Paulatto]

In data 04 giugno 2009 alle ore 10:38:11, loc duong ding  
 ha scritto:
> there is nothing: No error, no announcement.
Dear loc Duong Ding,
doesn't it even print the first dozen of lines? If it does, it may just be  
the usual problem with input redirection: try feeding the input file by  
using the syntax
   mpich2 [...] pw.x -in input.in [...]
which is more parallel safe.

regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
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[Pw_forum] problem in updating cvs version

[Lorenzo Paulatto]

In data 04 giugno 2009 alle ore 09:31:46, Bipul Rakshit  
 ha scritto:
> *cvs [login aborted]: connect to democritos.sissa.it(147.122.10.31):2401
> failed: Connection timed out*

There was a fierce thunderstorm half an hour ago, and this could explain  
the problem connecting to the server; yet I have to advise you that the  
CVS repository has been moved to qe-forge.org a couple of months ago: the  
branch on the democrito server is no longer updated.

Please see this page  for details  
on how to get the cvs version from the forge. I think there is a way to  
transfer the local setting to make a previous cvs directory point to the  
new repository, but I don't know how to do it. You can always get a fresh  
check-out and then replace the files...

best regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] SCF correction problem in relaxation

[Lorenzo Paulatto]

In data 04 giugno 2009 alle ore 05:03:18, Jhon W. Gonz?lez  
 ha scritto:
> and always get the same warning "SCF correction compared to forces is  
> too large, reduce conv_thr"

When the forces are ~zero the SCF correction will always be large compared  
to them. What counts is if the forces are small enough for you to consider  
the calculation converged. Zero +/- zero is still zero.

In any case you can get rid of the message by setting i.e. upscale=1.e+5  
which will allow the program to reduce the convergence threshold down to  
insane levels, preventing the message from displaying. But is this what  
you really want?

regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] PAW dataset for Mn, NC PPs for GIPAW for Mn and Li

[Gregor Mali]

Dear PWscf users,

I am studying hyperfine interaction of lithium nuclei in some lithium
manganese silicates. 
I hope that an insight into the interaction could be obtained by
calculating spin-polarization at Li position (or in a small sphere
around Li), or by using the GIPAW module. In the former case
(spin-polarization) I would like to use the PAW approach, since, as far
as I understand, it improves the accuracy on the core.

I kindly ask, whether someone is willing to share a PAW dataset for Mn,
or an input file for generation of such a dataset, as well as
norm-conserving pseudopotentials for Li and Mn, convenient for use with
GIPAW.

Thank you very much in advance.


Gregor Mali
National Institute of Chemistry
Ljubljana, Slovenia

[Pw_forum] SCF correction problem in relaxation

[Jhon W. González]

Thaks, but I have tried several configurations including: 

* mixing_mode =  'local-TF' and 'plain' 
* conv_thr = 1.0D-7, 1.0D-6, 1.0D-5, 1.0D-4, 1.0D-3, 1.0D-2, 1.0D-1
and always get the same warning "SCF correction compared to forces is too 
large, reduce conv_thr"

 

Jhon W. Gonz?lez

Universidad T?cnica Federico Santa Mar?a
Fono (56) (32) 2654623 Fax  (56) (32) 2797656
Casilla 110-VALPARAISO
Avenida Espa?a 1680
239-0123 VALPARAISO
CHILE

for QE forum: http://www.democritos.it/mailman/listinfo/pw_forum


- Mensaje original 
De: Lorenzo Paulatto 
Para: PWSCF Forum 
Enviado: s?bado, 30 de mayo, 2009 6:29:56
Asunto: Re: [Pw_forum] SCF correction problem in relaxation


Dear John,
it means that your convergence threshold is too big:
>   conv_thr = 1.0D-5 ,
it is at least 10 and at most 10 thousand times larger than an acceptable
convergence threshiold. Either increase it or increase the upscale
parameter.

regards

P.S. you could also try and search the mailing list archive:

please note that the same question has been asked and answered no more
than 7 days ago.

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:  http://people.sissa.it/~paulatto/




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[Pw_forum] Problem with parallel running by mpich2

[loc duong ding]

Dear developers and all users,

I use MPICH2 to run PWSCF. I get?a problem. When I?run PWSCF by command:

mpiexec -machinefile /home/loc/machinefile -n 8 pw.x -npool 2 test

there is nothing: No error, no announcement. 
When?I test the input file?( C8OOH_11.txt) by command:

pw.x? test
?
it runs well even though very slow. 
?
To test MPICH2, I use that to run another small structure and no problem.
?
Have any one met this problem??What is the possible reason of this problem?
?
This is my input file:
?
?
? calculation = 'relax',
? prefix='C8OOH_1H2',
? restart_mode = 'restart',
? pseudo_dir ='/home/loc/espresso-4.0/pseudo',
? outdir='./'
? tstress = .true. ,
? tprnfor = .true. ,
? nstep =? 200? ,
? etot_conv_thr = 1.0E-4 ,
? forc_conv_thr = 1.0D-3 ,
? dt = 20 ,
/

? ibrav= 14,? celldm(1) = 18.89399, celldm(2)= 0.99629,celldm(3)= 1.05229, 
celldm(4)= 0.109, celldm(5)= -0.1598,celldm(6)= -0.504, nat = 88, ntyp = 3, 
nspin=2,
? ecutwfc =35, ecutrho = 210, occupations='smearing', degauss=0.0001,
? starting_magnetization(1) = 0.0,
? starting_magnetization(2) = 0.3,
? starting_magnetization(3) = 0.5??? 
/

??? startingwfc = 'atomic'
??? mixing_mode = 'plain'
??? mixing_beta = 0.6
??? conv_thr = 1.0e-6
??? electron_maxstep= 250
/

??? upscale = 15
/

?? cell_dynamics = 'bfgs' ,
?? press = 0.00 ,
?? wmass =? 0.0015? ,
?? press_conv_thr = 0.5,
/
ATOMIC_SPECIES
?C? 12.011? C.pbe-rrkjus.UPF
?O? 15.9994 O.pbe-rrkjus.UPF 
?H? 1.008?? H.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C??? 2.97500??? 1.96900??? 7.98400 
C??? 0.44200??? 1.99500??? 8.00700 
C??? 1.74300?? -0.16900??? 7.98800 
C??? 1.70600??? 2.71300??? 7.63300 
C??? 2.93300??? 0.57400??? 8.01100 
C??? 0.48500??? 0.56000??? 8.20500 
O??? 1.62100??? 2.83300??? 6.18300 
C?? -0.80500?? -0.17900??? 8.19100 
O?? -0.18900??? 0.06300??? 9.47200 
C?? -0.15900??? 1.96900?? 13.18800 
C??? 1.14200?? -0.19400?? 13.16500 
C??? 2.33300??? 0.54800?? 13.18600 
C?? -1.40500?? -0.20600?? 13.36700 
C?? -0.11700??? 0.53400?? 13.38400 
O?? -0.79200??? 0.02000?? 14.65100 
C??? 1.10500??? 2.68600?? 12.80800 
O??? 1.01600??? 2.79700?? 11.35900 
C??? 4.22300??? 2.69000??? 8.01100 
C??? 2.37500??? 1.94400?? 13.15900 
C??? 3.62200??? 2.66500?? 13.18700 
H??? 2.43200??? 3.27000??? 5.83300 
H??? 1.77600??? 3.31500?? 11.00400 
C??? 7.97200??? 1.96900??? 7.98400 
C??? 5.43900??? 1.99500??? 8.00700 
C??? 6.74100?? -0.16900??? 7.98800 
C??? 6.70300??? 2.71300??? 7.63300 
C??? 7.93100??? 0.57400??? 8.01100 
C??? 5.48200??? 0.56000??? 8.20500 
O??? 6.61800??? 2.83300??? 6.18300 
C??? 4.19300?? -0.17900??? 8.19100 
O??? 4.80800??? 0.06300??? 9.47200 
C??? 4.83800??? 1.96900?? 13.18800 
C??? 6.14000?? -0.19400?? 13.16500 
C??? 7.33100??? 0.54800?? 13.18600 
C??? 3.59300?? -0.20600?? 13.36700 
C??? 4.88000??? 0.53400?? 13.38400 
O??? 4.20600??? 0.02000?? 14.65100 
C??? 6.10200??? 2.68600?? 12.80800 
O??? 6.01300??? 2.79700?? 11.35900 
C??? 9.22000??? 2.69000??? 8.01100 
C??? 7.37200??? 1.94400?? 13.15900 
C??? 8.62000??? 2.66500?? 13.18700 
H??? 7.43000??? 3.27000??? 5.83300 
H??? 6.77400??? 3.31500?? 11.00400 
C??? 5.46300??? 6.27000??? 7.98400 
C??? 2.93000??? 6.29500??? 8.00700 
C??? 4.23100??? 4.13100??? 7.98800 
C??? 4.19400??? 7.01300??? 7.63300 
C??? 5.42100??? 4.87400??? 8.01100 
C??? 2.97300??? 4.86000??? 8.20500 
O??? 4.10900??? 7.13300??? 6.18300 
C??? 1.68300??? 4.12100??? 8.19100 
O??? 2.29900??? 4.36300??? 9.47200 
C??? 2.32900??? 6.26900?? 13.18800 
C??? 3.63000??? 4.10600?? 13.16500 
C??? 4.82100??? 4.84800?? 13.18600 
C??? 1.08300??? 4.09400?? 13.36700 
C??? 2.37100??? 4.83400?? 13.38400 
O??? 1.69600??? 4.32000?? 14.65100 
C??? 3.59300??? 6.98600?? 12.80800 
O??? 3.50400??? 7.09700?? 11.35900 
C??? 6.71100??? 6.99100??? 8.01100 
C??? 4.86300??? 6.24400?? 13.15900 
C??? 6.11000??? 6.96600?? 13.18700
H??? 4.92000??? 7.57000??? 5.83300
H??? 4.26400??? 7.61500?? 11.00400
C??? 0.46500??? 6.27000??? 7.98400
C?? -2.06800??? 6.29500??? 8.00700
C?? -0.76600??? 4.13100??? 7.98800
C?? -0.80400??? 7.01300??? 7.63300
C??? 0.42400??? 4.87400??? 8.01100
C?? -2.02500??? 4.86000??? 8.20500
O?? -0.88900??? 7.13300??? 6.18300
C?? -3.31400??? 4.12100??? 8.19100
O?? -2.69900??? 4.36300??? 9.47200
C?? -2.66900??? 6.26900?? 13.18800
C?? -1.36700??? 4.10600?? 13.16500
C?? -0.17600??? 4.84800?? 13.18600
C?? -3.91400??? 4.09400?? 13.36700
C?? -2.62600??? 4.83400?? 13.38400
O?? -3.30100??? 4.32000?? 14.65100
C?? -1.40500??? 6.98600?? 12.80800
O?? -1.49300??? 7.09700?? 11.35900
C??? 1.71300??? 6.99100??? 8.01100
C?? -0.13400??? 6.24400?? 13.15900
C??? 1.11300??? 6.96600?? 13.18700
H?? -0.07700??? 7.57000??? 5.83300
H?? -0.73300??? 7.61500?? 11.00400
K_POINTS {automatic}
4 4 1 0 0 0

I appreciate your help!
---
Loc Duong Dinh
Ms-Ph.D Student
Sungkyunkwan Advanced Institute of Nanotechnology,
Sungkyunkwan University,
Suwon, 440-746, Korea 
Email: mambom1902 at yahoo.com


  

[Pw_forum] transmission calculation

[Manoj Srivastava]

Dear PWSCF users and developers,
 I have been trying to do the conductance calculation for the twin
boundary of Cu. I compared my results with previously done calculations
and for most K points the transmission coefficients match up very well.
But there are some k points that I get transmission coefficients more than
1! This is not reasonable, as the maximum value of transmission
coefficient could be 1.I am getting 1.000345, and similar for other k
points. Do you think transmission coefficients being more than 1 is just
numerical error of the code or there is something wrong with my input
file? Attached is the input file for lead and scatterign region -

SCF for the LEFT lead-

calculation='scf'
pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo',
outdir='./',
prefix='lcu',
 /
 
ibrav =0,
celldm(1)=4.82,
nat= 3,
ntyp= 1,
ecutwfc =150.0,
occupations='smearing',
smearing='gaussian',
degauss=0.02,
ecutrho=500
 /
 
conv_thr = 1.0e-8
mixing_beta=0.7
 /
ATOMIC_SPECIES
 Cu 63.55  Cu.pz-d-rrkjus.UPF
ATOMIC_POSITIONS
  Cu  0.0   0.00.0
  Cu -0.5   0.2886751340.81649658
  Cu -1.0   0.5773502691.632993162

K_POINTS (automatic)
6 6 8 1 1 1
CELL_PARAMETERS {hexagonal}
 1.0   0.00.0
-0.5   0.8660254037844386 0.0
 0.0   0.0 2.449489743
>>
SCF for the RIGHT lead-

calculation='scf'
pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo',
outdir='./',
prefix='rcu',
 /
 
ibrav =0,
celldm(1)=4.82,
nat= 3,
ntyp= 1,
ecutwfc =150.0,
occupations='smearing',
smearing='gaussian',
degauss=0.02,
ecutrho=500
 /
 
conv_thr = 1.0e-8
mixing_beta=0.7
 /
ATOMIC_SPECIES
 Cu 63.55  Cu.pz-d-rrkjus.UPF
ATOMIC_POSITIONS
  Cu 0.0   0.00.0
  Cu 0.5  -0.2886751340.81649658
  Cu 1.0  -0.5773502691.632993162

K_POINTS (automatic)
6 6 8 1 1 1
CELL_PARAMETERS {hexagonal}
 1.0  0.00.0
-0.5  0.8660254037844386  0.0
 0.0   0.0 2.449489743

>
SCF for SCATTERING region-

calculation='scf'
pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo',
outdir='./',
prefix='scu',
 /
 
ibrav =0,
celldm(1)=4.82,
nat= 12,
ntyp= 1,
ecutwfc =150.0,
occupations='smearing',
smearing='gaussian',
degauss=0.02,
ecutrho=500
 /
 
conv_thr = 1.0e-8
mixing_beta=0.7
/
ATOMIC_SPECIES
 Cu 63.55  Cu.pz-d-rrkjus.UPF
ATOMIC_POSITIONS
  Cu  0.0   0.0 0.0
  Cu -0.5   0.288675134 0.816496581
  Cu -1.0   0.577350269 1.632993162
  Cu -0.5   0.288675134 2.449489743
  Cu  0.0   0.0 3.265986324
  Cu  0.5  -0.288675134 4.082482905
  Cu  1.0  -0.577350269 4.898979486
  Cu  1.5  -0.866025404 5.715476066
  Cu  2.0  -1.154700538 6.531972647
  Cu  1.5  -0.866025404 7.348469228
  Cu  1.0  -0.577350269 8.164965809
  Cu  0.5  -0.288675134 8.981462390

K_POINTS (automatic)
6 6 4 1 1 1
CELL_PARAMETERS {hexagonal}
 1.0   0.0 0.0
-0.5   0.866025403 0.0
 0.0   0.0 9.797958971

>>
input file for conductance part-


outdir='./'
prefixs='scu'
prefixl='lcu'
prefixr='rcu'
tran_file ='trans.twin'
ikind=2
ecut2d=200
energy0=0.0
denergy=0.0
ewind=101.d0
epsproj=1.d-6
nz1=25
bds=3.265986324

 /
  6
  0.500 -0.500   1
  4.2584095E-17  0.500   1
  0.250000.000   1
  0.167  0.167   1
 -1.2775231E-16 -0.250   1
  0.250 -0.251   1
1
0.0


Regards, 
Manoj Srivastava 
University of Florida, 
Gainesville, FL