[Pw_forum] (no subject)

[Phillip Nyawere]

Your file has no directory for output data.

On Wed, Sep 7, 2011 at 1:57 PM, Winfred Mulwa wrote:

>   Dear all,
>
> I have tried doing a vc-relax on the attached TiO*2 *rutile
> supercell, but the calculations stop after a few seconds without
> giving any error.  What might be the problem?
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
The Abdus Salam International Center for Theoretical Physics,
Enrico Fermi Building Associate Office 18,
Strada Costiera 11,
34014 Trieste, Italy
Tel +393382213805, or +39 040 2240 567
pnyawere at gmail.com, pnyawere at ictp.it, 

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[Pw_forum] Using a big box model to calculating the energy of isolated atom.

[Phillip Nyawere]

To implement no symmetry use
nosym=.true. at the $system

On Thu, Jul 28, 2011 at 10:12 AM, Gabriele Sclauzero <
gabriele.sclauzero at epfl.ch> wrote:

>
> Il giorno 28/lug/2011, alle ore 01.55, Hongsheng Zhao ha scritto:
>
> Hi all,
>
> I've learned that when using the a large-cell ( i.e., a big box ) to
> calculate the energy of isolated atom, it should be done without
> symmetry.   But I'm not sure what's the meaning of the  "without
> symmetry"  here and how to ensure this when we using a a big box model
> for this purpose.  Any hints on this issue?
>
>
> This is a FAQ on this forum: have you spent some time browsing the
> archives?
>
> OK, I'll give you a hint: "nosym"... but use it with care!
>
> HTH
>
> GS
>
>
> Regards
> --
> Hongsheng Zhao 
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
>
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
The Abdus Salam International Center for Theoretical Physics,
Enrico Fermi Building Associate Office 18,
Strada Costiera 11,
34014 Trieste, Italy
Tel +393895378328, or +39 040 2240 567
pnyawere at gmail.com, pnyawere at ictp.it, 

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[Pw_forum] vacancy defect

[Phillip Nyawere]

Hello all,
I am calculating vacancy formation energy of barium flouride. I am using a
super cell of 96 atoms. When I create barium vacancy and do a relax
calculation, the vacancy energy is positive in sign. When i do the same for
flouride ion, the vacancy energy turns to be negative. This energy is
calculated by the formula E = E(vacancy) + E(single atom) - E(pure crystal).
Both energies I hope should be positive.
Thanks,
-- 
Phillip W. Otieno Nyawere,
Kabarak University,
P.O. Box Private Bag - 20157,
KABARAK
Nakuru Kenya
Tel +254728342054,
pnyawere at gmail.com, potieno at kabarak.ac.ke

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[Pw_forum] Vacancy energy

[Phillip Nyawere]

Dear all,
I am doing vacancy calculation of a flouride but I am obtaining
positive energy for cation and negative energy for anion. The material is
barium floride.
Can someone help me understand this problem?
-- 
Phillip W. Otieno Nyawere,
Kabarak University,
P.O. Box Private Bag - 20157,
KABARAK
Nakuru Kenya
Tel +254728342054,
pnyawere at gmail.com, potieno at kabarak.ac.ke

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[Pw_forum] elastic constant calculations

[Phillip Nyawere]

you can do between -0.02 to 0.02 at intervals of 0.002.
Best wishes,
Nyawere

On Sat, Jan 15, 2011 at 8:55 PM, pikee priya  wrote:

> Hi ,
>
> Can you help me with the strain range to be considered for fitting in
> polynomial curves for finding the bulk modulus and elastic constans(c11, c12
> and c44) for cubic metals.
>
> Regards,
> Pikee.
> IISc, Bangalore.
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
International Center for Theoretical Physics, ICTP,
Strada Costiera, 11 - 34014217,
Leonardo Building,
Office 305,
Trieste,
Italy.
Tel +393382213805 office +39 040 2240 217
pnyawere at gmail.com, potieno at kabarak.ac.ke

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[Pw_forum] Ghost States

[Phillip Nyawere]

Dear pwscf
 I am doing a "relax" calculation by shifting the position of an atom in a
supercell. Some sites appear unfavorable and one of them is hear below
showing the presence of a ghost state. Could anyone give me an idear of how
to remove the ghost sites (energy) in a calculation? Part of the output is
here:

k = 0. 0. 0. ( 36612 PWs)   bands (ev):
  -30.6867 -19.5462 -19.4947 -19.4037 -19.3662 -19.3332 -19.2705 -19.2304
   -19.1717 -19.1681 -19.1466 -19.1386 -19.1164 -19.1036 -19.0976 -19.0943
   -19.0939 -19.0851 -19.0845 -19.0825 -19.0527 -19.0276 -19.0078 -18.9858
   -18.9681 -18.9567 -18.9032 -18.8883 -18.8418 -18.8179 -18.8140 -18.7612
   -16.0244 -16.0133 -15.9881 -15.9532 -15.9512 -15.9385 -15.9291 -15.9228
   -15.9189 -15.9102 -15.9075 -15.8753 -15.8739 -15.8689 -15.8610 -15.8544
   -15.8478 -15.8397 -15.8373 -15.8212 -15.8090 -15.8056 -15.8013 -15.8011
   -15.7823 -15.7817 -15.7715 -15.7649 -15.7627 -15.7584 -15.7468 -15.7436
   -15.7351 -15.7292 -15.7268 -15.7206 -15.7142 -15.7116 -15.6975 -15.6971
   -15.6943 -15.6870 -15.6812 -15.6688 -15.6646 -15.6594 -15.6557 -15.6490
   -15.6428 -15.6409 -15.6229 -15.6099 -15.6036 -15.6026 -15.5933 -15.5905
   -15.5677 -15.4540 -15.2097 -15.0390 -14.9480 -14.9457 -13.8970  -8.5916
-8.4985  -6.7400  -4.8562  -4.8507  -4.7891  -4.7626  -4.7525  -4.7343
-4.6927  -4.6912  -4.6645  -4.6403  -4.6237  -4.6234  -4.6209  -4.6134
-4.6053  -4.5858  -4.5672  -4.5576  -4.5273  -4.5016  -4.4944  -4.4676
-4.4578  -4.4492  -4.4396  -4.4155  -4.4061  -4.3838  -4.3792  -4.3767
-4.3725  -4.3714  -4.3711  -4.3593  -4.3566  -4.3515  -4.3489  -4.3463
-4.3440  -4.3399  -4.3383  -4.3366  -4.3351  -4.3343  -4.3326  -4.3321
-4.3299  -4.3266  -4.3264  -4.3241  -4.3239  -4.3229  -4.3224  -4.3206
-4.3189  -4.3165  -4.3158  -4.3152  -4.3045  -4.3029  -4.2829  -4.2798


-- 
Phillip W. Otieno Nyawere,
International Center for Theoretical Physics, ICTP,
Strada Costiera, 11 - 34014217,
Leonardo Building,
Office 305,
Trieste,
Italy.
Tel +393382213805 office +39 040 2240 217
pnyawere at gmail.com, potieno at kabarak.ac.ke

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[Pw_forum] Giving shift in K points

[Phillip Nyawere]

Giving shift is moving the position from 0 0 0 to say 1 1 1. So the position
you have given below is not shifted. It could be 1 1 1 1 1 1.
Cheers

On Mon, Aug 23, 2010 at 6:28 PM, Dimpy Sharma wrote:

>
> Hi Quantum espresso user,
>
> I have to run plane wave calcuation on a periodic stucture to predict the
> band gap,as my system has 200 atoms (which has 5 unit cells),thus for scf I
> prefer to choose the k point as
>
> K_POINTS automatic
>  1 1 1   0 0 0
>
> where I gave the shift as 0.I would like to ask is it possible to give
> shift in K_Points for periodic system?as the concept is not clear to me ,can
> anyone please suggest me some papers or book ?and I would be very greatfull
> if my question is answered.
>
> Thanks a lot in advance
>
> Dimpy.
> Dimpy Sharma
> ETG-Group
> Tyndall National Institute
> Cork
>
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
International Center for Theoretical Physics, ICTP,
Strada Costriera, 11 - 34014,
Galileo Guest House,
Trieste,
Italy.
Tel +393382213805 office +39 040 2240 234
pnyawere at gmail.com, potieno at kabarak.ac.ke

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[Pw_forum] Band Structure of Graphite

[Phillip Nyawere]

You have not asked any question. Could you please ask the question.

On Thu, Aug 19, 2010 at 2:19 PM, Masoud Nahali wrote:

> Dear Quantum Espresso Users
>
> I take a wrong band from the input which is placed below.
> I have selected 4 essential points in the K_POINTS {crystal} section, which
> are P (0.3,0.3,0.0) , Q(0.0,0.5,0.0) , Gamma (0.0,0.0,0.0) , and
> again
> P (0.3,0.3,0.0) to plot the band-structure and compare it with
> PRB,4,8,2441,1971. The distance between every two essential points is
> divided to 50 parts
> I would appreciate your help.
>
> Band input:
>
> &CONTROL
>   calculation  = "bands",
>   pseudo_dir   = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
>   outdir   = "/home/koa/Graphite(2010-08-16)-A/Bulk/Band-DOS/tmp",
>   prefix='bulk'
>   /
> &SYSTEM
>   ibrav = 4,
>   a = 2.457917036,
>   b = 2.457917036,
>   c = 6.302440996,
>   cosab = -0.5,
>   cosac = 1.0,
>   cosbc = 1.0,
>   nat   = 4,
>   ntyp  = 1,
>   ecutwfc   = 40.D0,
>   ecutrho   = 480.D0,
>   occupations = 'smearing'
>   smearing ='mp',
>   degauss = 0.03,
>   nspin = 2,
>   starting_magnetization(1)= 0.01,
>   london=.true.,
>   /
> &ELECTRONS
>   conv_thr= 1.D-6,
>   mixing_beta = 0.7D0,
>   diagonalization = "david",
> /
> ATOMIC_SPECIES
> C  12.0107  C.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
> C0.0   0.0   0.0
> C0.0   1.419079061   0.0
> C0.0   0.0   3.151220498
> C1.228958518   0.709539531   3.151220498
> K_POINTS {crystal}
> 151
> 0.300.300.001
> 0.3266630.3266630.002
> 0.3199970.3199970.003
> 0.3133300.3133300.004
> 0.3066640.3066640.005
> 0.270.270.006
> 0.2933300.2933300.007
> 0.2866640.2866640.008
> 0.2799970.2799970.009
> 0.2733310.2733310.0010
> 0.240.240.0011
> 0.2599970.2599970.0012
> 0.2533310.2533310.0013
> 0.2466640.2466640.0014
> 0.2399980.2399980.0015
> 0.210.210.0016
> 0.2266640.2266640.0017
> 0.2199980.2199980.0018
> 0.2133310.2133310.0019
> 0.2066650.2066650.0020
> 0.180.180.0021
> 0.1933310.1933310.0022
> 0.1866650.1866650.0023
> 0.1799980.1799980.0024
> 0.1733320.1733320.0025
> 0.150.150.0026
> 0.1599980.1599980.0027
> 0.1533320.1533320.0028
> 0.1466650.1466650.0029
> 0.130.130.0030
> 0.120.120.0031
> 0.1266650.1266650.0032
> 0.110.110.0033
> 0.1133320.1133320.0034
> 0.100.100.0035
> 0.090.090.0036
> 0.0933320.0933320.0037
> 0.080.080.0038
> 0.070.070.0039
> 0.070.070.0040
> 0.060.060.0041
> 0.050.050.0042
> 0.050.050.0043
> 0.040.040.0044
> 0.040.040.0045
> 0.030.030.0046
> 0.020.020.0047
> 0.020.020.0048
> 0.010.010.0049
> 0.0066670.0066670.0050
> 0.000.000.0051
> 0.000.010.0052
> 0.000.020.0053
> 0.000.030.0054
> 0.000.040.0055
> 0.000.050.0056
> 0.000.060.0057
> 0.000.070.0058
> 0.000.080.0059
> 0.000.090.0060
> 0.000.100.0061
> 0.000.110.0062
> 0.000.120.0063
> 0.000.130.0064
> 0.000.140.0065
> 0.000.150.0066
> 0.000.160.0067
> 0.000.170.0068
> 0.000.180.0069
> 0.000.190.0070
> 0.000.200.0071
> 0.000.210.0072
> 0.000.220.0073
> 0.000.230.0074
> 0.000.240.0075
> 0.000.250.0076
> 0.000.260.0077
> 0.000.270.0078
> 0.000.280.0079
> 0.000.290.0080
> 0.000.300.0081
> 0.000.310.0082
> 0.000.320.00 

[Pw_forum] bad Fermi energy

[Phillip Nyawere]

Hi,
Could you increase your Kpoint mesh to a denser one instead of 5x5x5 and
find out if the code still complains.
Best regards,

On Tue, Aug 10, 2010 at 9:31 AM, Hagai Eshet  wrote:

> *Dear all,
> **
> **I'm trying to calculate the electronic DOS for liquid sodium at high 
> pressure.
> The scf calculation is going well, but the nscf stops with the following 
> message:
>
> Message from routine efermit:
>  internal error, cannot braket Ef
>
>  
> %%
>  from tweights : error # 1
>  bad Fermi energy
>
>
>  
> %%**
> **  **
> **I search for this problem in the forum and found few suggestions.
> **So I tried to change nbnd, k-points grid, mixing_mode**
>
> and smearing but it doesn't work.
>
> Does anyone have suggestion?
>
> **Best regards,
> Hagai Eshet**
>
> P.S I attached my input files
> *
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
International Center for Theoretical Physics, ICTP,
Strada Costriera, 11 - 34014,
Galileo Guest House,
Trieste,
Italy.
Tel +393382213805
pnyawere at gmail.com, potieno at kabarak.ac.ke

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[Pw_forum] error: q not allowed

[Phillip Nyawere]

I am working on the same now and I think your title should read 'phonons for
mnas' and prefix to be 'PHmnas'
Nyawere

On Wed, Aug 4, 2010 at 12:41 PM, eli  wrote:

>
>
> Elahe Teimouri
> Computational Condensed Matter Research Lab
> Physics Department, Isfahan University of Technology, Isfahan, Iran
> Tel lab: +98 311 391 3731 Fax Office: +98311 391 3746
>
>
>
>
> dear Karthik
>
> I had 
> visited
> first solution of Prof. Eyvaz:
>
> 1) use >v3.0 where you can directly put  nq1, nq2, nq3
> and everything will go smoothly
>
>  I used espresso-4.0.5. and my input is
>
>  &inputph
>   tr2_ph=1.0d-14,
>   prefix='MnAs',
>   ldisp=.true.,
>   nq1=1 , nq2=1 , nq3=8
>   amass(1)=54.938,
>   amass(2)=74.922,
>   outdir='/home/teimouri/scratch/scf4' ,
>   fildyn='MnAs.dyn',
>  /
> but there was error yet?
>
> I am presently working on some phonon calculations for Nanowire of MnAs and I 
> got an error message from the q2r:
>
> %%
>   from init : error # 1
>   q not allowed
>
> %%
>
>
> I did some phonons on a 1x1x8 grid and my input is
>  &input
>fildyn='MnAs.dyn' , zasr='simple' , flfrc='MnAs.fc'
>  /
>  Plz give me some suggestion
>  on how to correct this error.
> Best Regards.
>
> Elahe Teimouri
> Computational Condensed Matter Research Lab
> Physics Department, Isfahan University of Technology, Isfahan, Iran
> Tel lab: +98 311 391 3731 Fax Office: +98311 391 3746
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
International Center for Theoretical Physics, ICTP,
Strada Costriera, 11 - 34014,
Galileo Guest House,
Trieste,
Italy.
Tel +393382213805
pnyawere at gmail.com, potieno at kabarak.ac.ke

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[Pw_forum] problem with vc-relax

[Phillip Nyawere]

Try cell_dynamics='bfgs' and not 'damp'
Success

On Tue, Jul 27, 2010 at 12:42 PM, Olga Sedelnikova
wrote:

> Dear All,
> I have a problem with 'vc-relax' option for graphene. I have used david
> and cg diagonalization proceedures, different types of smearing and ion and
> cell dynamics but all calculations were crashed.
> One of my input file:
>
> &CONTROL
>  calculation = 'vc-relax',
>  prefix = 'graphene',
>  restart_mode='from_scratch'
>  tstress=.true.,
>  tprnfor=.true.,
>  nstep=45,
>   etot_conv_thr = 1.0E-4 ,
>   forc_conv_thr = 1.0D-3 ,
>   max_seconds = 36000 ,
>   dt = 100,
>/
> &SYSTEM
>  ibrav = 4,
>  celldm(1)= 4.64833
>  celldm(3)=5.447621
>nat = 2,
>ntyp = 1,
>ecutwfc = 18.0,
>nbnd =8,
>  occupations='smearing'
>  smearing = 'mv'
>  degauss = 0.005
>/
> &ELECTRONS
>  conv_thr = 1.0d-7
>  electron_maxstep = 70
>  diagonalization='cg'
>/
> &IONS
>  ion_dynamics='damp'
> /
> &CELL
> cell_dynamics = 'damp-w' ,
> press=0.00 ,
> wmass=0.0015 ,
> /
>
> ATOMIC_SPECIES
>  C   12.01100 C.pz-vbc.UPF
> ATOMIC_POSITIONS crystal
> C  0.0.0.5000
> C  0.0.0.5000
> K_POINTS {automatic}
>6 6 6 0 0 0
> Inthis cause:
>
> from electrons : error # 1
>  charge is wrong
> Maybe somebody has already dealed with this problem and can advice the
> correct options for graphene.
> Any suggestion will be appreciated.
>
> --
> Best wishes,
> Olga Sedelnikova
> Nikolaev Institute of Inorganic Chemistry of SB RAS
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
Kabarak University,
Dept of Physics & Mathematics,
P.O Box Private Bag - 20157,
Kabarak, Kenya.
Tel +254728342054
pnyawere at gmail.com, potieno at kabarak.ac.ke

The battle belongs to the Lord.
CURRENTLY IN CAPE TOWN, SOUTH AFRICA
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[Pw_forum] Supercells

[Phillip Nyawere]

If the cell spacing was 1 unit for the unit cell then divide it by two for 2
unit cells. Place the atoms manually at this new spacing and then view in
the xcrysden. It requires a lot of practice but after sometime you will be
used to it.
Cheers

On Fri, May 21, 2010 at 2:23 PM, Bertrand SITAMTZE wrote:

> Dear all,
>
> I wanted to built a supercell for my system in QE. I went through the forum
> and saw some procedures. I followed this:
>
> 1. Upload the unit cell in XcrySDen, display the asymmetric unit, modify
> the number of unit drawn to fit the shape of the desired supercell (2*2*2)
> and then save the XSF file.
>
> 2. From the XSF file, the coordinates of atoms in the supercell are
> obtained, in angstrom.
>
> But the problem is with the CELL. How should I built the CELL parameters
> and read the final structure with XCrySDen?
>
>
> Note: I choosed the same ibrav as for the unit cell, then multiply the
> celldm by 2, but the structure does'nt look fine in XCrySDen.
>
> Thans for your help
>
>
>
> *
> Bertrand SITAMTZE YOUMBI
> Laboratory of Material Sciences
> Department of Physics
> University of Yaounde I-Cameroon
> 
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
Kabarak University,
Dept of Physics & Mathematics,
P.O Box Private Bag - 20157,
Kabarak, Kenya.
Tel +254728342054
pnyawere at gmail.com, potieno at kabarak.ac.ke

The battle belongs to the Lord.
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[Pw_forum] Low speed

[Phillip Nyawere]

You need high speed computer. I tried with 96 atoms and it was taking even
longer.
Success.

On Wed, May 12, 2010 at 10:07 PM, mohsen modaresi  wrote:

> Dear Developers and users,
> I run a SCF calculation with 71 atoms on a camputer with 8 cpu and 8GB RAM,
> i expect it run in some minutes, But it take 3 hours to run.
> Is it regular?
>
>
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>


-- 
Phillip W. Otieno Nyawere,
Kabarak University,
Dept of Physics & Mathematics,
P.O Box Private Bag - 20157,
Kabarak, Kenya.
Tel +254728342054
pnyawere at gmail.com, potieno at kabarak.ac.ke

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[Pw_forum] Visualization of Results

[Phillip Nyawere]

To visualize you need to use XCrysDen which you can install in your
computer. I have not used pp.x but I shall check and see if I can offer any
meaningful help.

On Wed, May 19, 2010 at 9:09 PM, Vikas Varshney  wrote:

> Dear Developers,
> I am a new user of QE and currently going through various examples (along
> with tutorials) to understand the software. I have few questions regarding
> how I can visualize some results.
>
> I have VMD installed on my machine but do not have XCrySDen. Is it possible
> to input the output files (.out format as outputted from the calculations)
> directly somehow to VMD to visualize molecular relaxation (like example03).
> Or do I need to install XCrySDen?
>
> I also tried to visualize the output of example02 (phonon spectra) using
> PP/pp.x but was totally unsuccessful. Any help will be highly appreciated
>
> Thanks in advance.
>
> Best Regards,
> Vikas
>
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> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
Kabarak University,
Dept of Physics & Mathematics,
P.O Box Private Bag - 20157,
Kabarak, Kenya.
Tel +254728342054
pnyawere at gmail.com, potieno at kabarak.ac.ke

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