[QE-users] CONTCAR to QE-input

[Naseem Hassan]

Dear All !

Would be grateful if somebody can help in converting VASP CONTCAR file to
Quantum Espresso input file. I have already tried using ibrav=0 and ibrav=6
but getting error. I am attaching down below both CONTCAR and my attempted
input file. Kindly point out mistake wherever possible

………

VASP input file

……..

Vasp-file

   1.00

 2.86569538771406580.00   0.0

 0.002.8656953954702842   0.0

 0.00   0.0   14.5687674940416922

   **   **   **

 5 3 3

Direct

  0.192692689512  0.193149041301 -0.0253111824898425

  0.571502138721  0.571328622521  0.065890491135

  0.006585860885  0.005834590312  0.1666816777950017

  0.545513131905  0.544294604946  0.2674877725929466

  0.141020522640  0.139458087178  0.3586520540557601

  0.449082703968  0.443883341108  0.5110114048024905

  0.029386433817  0.030412347271  0.640608352582

  0.507705108729  0.513733071873  0.8222013593108685

 -0.107135629075 -0.110927390669  0.5146809763675351

  0.4999845524255632  0.4999846220443415  0.859792830676

 -0.061006705978 -0.056516248497  0.8186883904105440



  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

  0.E+00  0.E+00  0.E+00

….

Quantum Espresso Input File

….

&CONTROL

calculation='vc-relax'

title='zQ'

prefix='zQ'

verbosity='high'

restart_mode='from_scratch'

nstep=1000

iprint=1

tprnfor=.true.

outdir='./'

disk_io='default'

tstress=.true.

pseudo_dir = './'

wf_collect=.true.,

! forc_conv_thr=1.0d-4

! etot_conv_thr=1.0d-5

/

&SYSTEM

ibrav = 6,

celldm(1) = 3,

celldm(3)=  5.2,

nat = 11,

ntyp = 3,

nspin= 2

ecutwfc = 50.0 ,

ecutrho = 250.0 ,

! input_DFT = 'PBE' ,

occupations = 'smearing' ,

degauss = 0.005 ,

smearing = 'methfessel-paxton' ,

 starting_magnetization(1) = 0.1

 vdw_corr='Grimme-D2'

 lda_plus_u = .true.

 Hubbard_U(1) = 3.0d0

/

&ELECTRONS

electron_maxstep = 100,

! conv_thr = 1.0d-10 ,

mixing_mode = 'plain' ,

! mixing_beta = 0.3d0 ,

/

&IONS

ion_dynamics='bfgs'

! upscale=100

/

&CELL

! press_conv_thr = 0.5D0

! press = 0.D0

! cell_dynamics = 'bfgs',

! cell_dofree = '2Dxy'

! cell_factor = 1.5D0

/

ATOMIC_SPECIES

**  **  **.UPF

**  **  **.UPF

**  **  **.UPF

ATOMIC_POSITIONS{Angstrom}

**0.550.55   14.200015

**1.4328681.4328680.959943

**0.000.002.428347

**1.4328611.4328603.896967

**0.400.405.225119

**1.4328331.4328327.444807

**0.080.099.712474

**1.4328501.432852   11.978460

**   -0.31   -0.327.498268

**1.4328041.4328049.712793

**   -0.17   -0.16   11.927280

K_POINTS automatic

5 5 1 0 0 0


Best Regards

Naseem
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[Pw_forum] (no subject)

[naseem]

Hi

I want to extract the wavefunctions using pw.x -pw2casino. I use PBE+SOC as
implemented in PWSCF v.5.4.0 and also PWSCF v.6.1 code to collect the
wavefunctions.
However I get the error message after the convergence using both versions.

!total energy  =-483.74343066 Ry
 Harris-Foulkes estimate   =-483.74343068 Ry
 estimated scf accuracy<   0.0015 Ry

 total all-electron energy = -9683.110071 Ry

 The total energy is the sum of the following terms:

 one-electron contribution =-996.39203589 Ry
 hartree contribution  = 501.72766193 Ry
 xc contribution   = -42.70749299 Ry
 ewald contribution= 347.74778137 Ry
 one-center paw contrib.   =-294.11934395 Ry
 smearing contrib. (-TS)   =  -0.0113 Ry

 convergence has been achieved in   8 iterations

 %%
 Error in routine pw2casino (2):
 noncollinear/spinorbit magnetism not (yet) implemented
 %%

 stopping ...

  Can somebody help me

Thanks

Naseem Ud Din
Graduate Candidate
University of Central Florida
Orlando USA
Cell # +1-407-683-3016
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[Pw_forum] Difference in band lines.

[Naseem Hassan]

Dear Users !

I calculated band strcutre of graphene using K-point path in Crystal_b and
tpiba_b format. I see some slight different in the structure of bands. All
other parameters/inputs are same.

Why is there such a difference ?

Second additional question please. After ploting band structure I need to
draw symmetry lines. How will I draw such lines ?

Thanks you for you attention !

N. Hasan
UNIST South Korea.



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[Pw_forum] Complete path of q-points

[Naseem Hassan]

Dear Members,

I would like to calculate phonons via QE.  I know how to setup Phonon
calculations.

Firstly, kindly guide, how to choose complete q-point path (as we give
Kpoint path for band structure) for a specific system such as for MoSe2 ?
Secondly, is primitive cell enough for such calculations ?

I Would be very grateful for your time and help.

Best Regards,
N. Hassan,
UNIST, South Korea.
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Re: [Pw_forum] PWneb reads coordinates of images incorrectly

[naseem]

Thank you Tone  for your help.

Naseem

Naseem Ud Din
Graduate Student
University of Central Florida
Orlando USA
Cell # +1-407-683-3016

On Mon, Jul 4, 2016 at 5:29 AM, Tone Kokalj  wrote:

> On Wed, 2016-06-29 at 13:45 -0400, naseem wrote:
> > Here is the example, where the program reads input for first and last
> > image correctly,
> > while for intermediate images the program reads the atomic
> > coordinates incorrectly.
>
> Note that in NEB only the first and last images are used verbatim,
> whereas intermediate images are used only for "steering". This is how
> they are used:
> first all the images are connected linearly and then the linearized
> "path" length is calculated. For N images, the path is then divided
> into N-1 equidistant segments and the intermediate images are the
> "points" on this equidistant segmented linearized path, which implies
> that the so generated images will not coincide with the input specified
> images, unless you precisely calculated your intermediate input images
> using this algorithm.
>
>
> Best regards, Tone Kokalj
>
> PS: As an illustration a simple example can be done on the sheet of paper,
> i.e., draw several points and connect them with line segments (start at the
> first and finish at the last point); then calculate the linearized "path"
> length. For N points divide the path into N-1 segments and you have found
> the your intermediate points.
>
> --
>
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax: +386-1-251-9385)
> > In this example I have the input files for  4 images and their
> > outputs.
> >
> > Thank you so much
> >
> > Naseem
> >
> >
> >
> >
> >
> > Naseem Ud Din
> > Graduate Student
> > University of Central Florida
> > Orlando USA
> > Cell # +1-407-683-3016
> >
> > On Tue, Jun 28, 2016 at 2:19 PM, naseem  wrote:
> > > Dear Paolo Giannozzi
> > >
> > > The input file, I have shown here only last few coordinates for
> > > comparison.
> > >
> > > &CONTROL
> > > ! .control.settings.
> > > prefix= 'pwneb',
> > > pseudo_dir= '/home/ndin/PP',
> > >
> > > ! .control.io.
> > > verbosity = 'low',
> > > disk_io   = 'low',
> > > wf_collect= .false.,
> > > outdir= './tmp/',
> > >
> > > ! .control.ion_relax.
> > > etot_conv_thr = 0.0001,
> > > forc_conv_thr = 0.001,
> > > nstep = 200,
> > > tprnfor   = .true.,
> > > tstress   = .false.,
> > > /
> > >
> > > &SYSTEM
> > > ! .system.structure.
> > > a = 1.0,
> > > ibrav = 0,
> > > nat   = 56,
> > > ntyp  = 5,
> > >
> > > ! .system.ecut.
> > > ecutwfc   = 50,
> > > ecutrho   = 300,
> > >
> > > ! .system.occupations.
> > > degauss   = 0.007,
> > > smearing  = 'fd',
> > > occupations   = 'smearing',
> > >
> > > ! .system.spin_pol.
> > > nspin = 2,
> > > ! .system.starting_magnetization.
> > > starting_magnetization(1) =  0.0 ,
> > > starting_magnetization(2) =  0.0 ,
> > > starting_magnetization(3) =  0.0 ,
> > > starting_magnetization(4) =  0.5 ,
> > > starting_magnetization(5) =  0.0 ,
> > > /
> > >
> > > &ELECTRONS
> > > ! .electrons.
> > > diagonalization   = 'david',
> > > mixing_mode   = 'plain',
> > > electron_maxstep  = 300,
> > > mixing_beta   = 0.7,
> > > conv_thr  = 1e-06,
> > > /
> > >
> > > &IONS
> > > ! .ions.
> > > pot_extrapolation = 'atomic',
> > > wfc_extrapolation = 'none',
> > > ion_dynamics  = 'bfgs',
> > > /
> > >
> > > ATOMIC_SPECIES
> > > C  12.0110 C.pbe-n-kjpaw_psl.1.0.0.UPF
> > > H   1.0079 H.pbe-kjpaw_psl.1.0.0.UPF
> > > N  14.0070 N.pbe-n-kjpaw_psl.1.0.0.UPF
> > >Mo  95.9500 Mo.pbe-s

Re: [Pw_forum] PWneb reads coordinates of images incorrectly

[naseem]

Thank you for your help.

Naseem

Naseem Ud Din
Graduate Student
University of Central Florida
Orlando USA
Cell # +1-407-683-3016

On Thu, Jun 30, 2016 at 8:57 AM, Paolo Giannozzi 
wrote:

> The NEB code performs a linear interpolation of the "images" (routine
> "initial_guess", module "path_base"). This is the expected behavior if
> one provides only the end points. If one provides an already
> interpolated path, it has no effect. If however you provide a path
> that doesn't fall in either cases, intermediate images will be
> modified (actually, overwritten). I am not a big NEB expert so I am
> not sure this is the expected or desired behavior. If you do not like
> such behavior, the only solution I see is to modify the mentioned
> routine in such a way that it doesn't alter the input path if the
> number of input images is equal to the number of desired images
>
> Paolo
>
> On Wed, Jun 29, 2016 at 7:45 PM, naseem  wrote:
> >
> > Dear Paolo Giannozzi
> >
> > Thanks for your help.
> > Here is the example, where the program reads input for first and last
> image
> > correctly,
> > while for intermediate images the program reads the atomic coordinates
> > incorrectly.
> > In this example I have the input files for  4 images and their outputs.
> >
> > Thank you so much
> >
> > Naseem
> >
> >
> >
> >
> >
> > Naseem Ud Din
> > Graduate Student
> > University of Central Florida
> > Orlando USA
> > Cell # +1-407-683-3016
> >
> > On Tue, Jun 28, 2016 at 2:19 PM, naseem  wrote:
> >>
> >> Dear Paolo Giannozzi
> >>
> >> The input file, I have shown here only last few coordinates for
> >> comparison.
> >>
> >> &CONTROL
> >> ! .control.settings.
> >> prefix= 'pwneb',
> >> pseudo_dir= '/home/ndin/PP',
> >>
> >> ! .control.io.
> >> verbosity = 'low',
> >> disk_io   = 'low',
> >> wf_collect= .false.,
> >> outdir= './tmp/',
> >>
> >> ! .control.ion_relax.
> >> etot_conv_thr = 0.0001,
> >> forc_conv_thr = 0.001,
> >> nstep = 200,
> >> tprnfor   = .true.,
> >> tstress   = .false.,
> >> /
> >>
> >> &SYSTEM
> >> ! .system.structure.
> >> a = 1.0,
> >> ibrav = 0,
> >> nat   = 56,
> >> ntyp  = 5,
> >>
> >> ! .system.ecut.
> >> ecutwfc   = 50,
> >> ecutrho   = 300,
> >>
> >> ! .system.occupations.
> >> degauss   = 0.007,
> >> smearing  = 'fd',
> >> occupations   = 'smearing',
> >>
> >> ! .system.spin_pol.
> >> nspin = 2,
> >> ! .system.starting_magnetization.
> >> starting_magnetization(1) =  0.0 ,
> >> starting_magnetization(2) =  0.0 ,
> >> starting_magnetization(3) =  0.0 ,
> >> starting_magnetization(4) =  0.5 ,
> >> starting_magnetization(5) =  0.0 ,
> >> /
> >>
> >> &ELECTRONS
> >> ! .electrons.
> >> diagonalization   = 'david',
> >> mixing_mode   = 'plain',
> >> electron_maxstep  = 300,
> >> mixing_beta   = 0.7,
> >> conv_thr  = 1e-06,
> >> /
> >>
> >> &IONS
> >> ! .ions.
> >> pot_extrapolation = 'atomic',
> >> wfc_extrapolation = 'none',
> >> ion_dynamics  = 'bfgs',
> >> /
> >>
> >> ATOMIC_SPECIES
> >> C  12.0110 C.pbe-n-kjpaw_psl.1.0.0.UPF
> >> H   1.0079 H.pbe-kjpaw_psl.1.0.0.UPF
> >> N  14.0070 N.pbe-n-kjpaw_psl.1.0.0.UPF
> >>Mo  95.9500 Mo.pbe-spn-rrkjus_psl.1.0.0.UPF
> >> O  15.9990 O.pbe-n-kjpaw_psl.1.0.0.UPF
> >>
> >> ATOMIC_POSITIONS  crystal
> >>   N 0.9548502075 0.5635784967 0.4962439034   1
>  1
> >> 1
> >>   N 0.20503544416667 0.6063052660 0.5061812013   1
>  1
> >> 1
> >>   N 0.79510299916667 0.3932039887 0.494546763

Re: [Pw_forum] PWneb reads coordinates of images incorrectly

[naseem]

Dear Paolo Giannozzi

Thanks for your help.
*Here is the example, where the program reads input for first and last
image correctly,*
*while for intermediate images the program reads the atomic coordinates
incorrectly.*
*In this example I have the input files for  4 images and their outputs.*

*Thank you so much *

*Naseem *





Naseem Ud Din
Graduate Student
University of Central Florida
Orlando USA
Cell # +1-407-683-3016

On Tue, Jun 28, 2016 at 2:19 PM, naseem  wrote:

> Dear Paolo Giannozzi
>
> The input file, I have shown here only last few coordinates for comparison.
>
> &CONTROL
> ! .control.settings.
> prefix= 'pwneb',
> pseudo_dir= '/home/ndin/PP',
>
> ! .control.io.
> verbosity = 'low',
> disk_io   = 'low',
> wf_collect= .false.,
> outdir= './tmp/',
>
> ! .control.ion_relax.
> etot_conv_thr = 0.0001,
> forc_conv_thr = 0.001,
> nstep = 200,
> tprnfor   = .true.,
> tstress   = .false.,
> /
>
> &SYSTEM
> ! .system.structure.
> a = 1.0,
> ibrav = 0,
> nat   = 56,
> ntyp  = 5,
>
> ! .system.ecut.
> ecutwfc   = 50,
> ecutrho   = 300,
>
> ! .system.occupations.
> degauss   = 0.007,
> smearing  = 'fd',
> occupations   = 'smearing',
>
> ! .system.spin_pol.
> nspin = 2,
> ! .system.starting_magnetization.
> starting_magnetization(1) =  0.0 ,
> starting_magnetization(2) =  0.0 ,
> starting_magnetization(3) =  0.0 ,
> starting_magnetization(4) =  0.5 ,
> starting_magnetization(5) =  0.0 ,
> /
>
> &ELECTRONS
> ! .electrons.
> diagonalization   = 'david',
> mixing_mode   = 'plain',
> electron_maxstep  = 300,
> mixing_beta   = 0.7,
> conv_thr  = 1e-06,
> /
>
> &IONS
> ! .ions.
> pot_extrapolation = 'atomic',
> wfc_extrapolation = 'none',
> ion_dynamics  = 'bfgs',
> /
>
> ATOMIC_SPECIES
> C  12.0110 C.pbe-n-kjpaw_psl.1.0.0.UPF
> H   1.0079 H.pbe-kjpaw_psl.1.0.0.UPF
> N  14.0070 N.pbe-n-kjpaw_psl.1.0.0.UPF
>Mo  95.9500 Mo.pbe-spn-rrkjus_psl.1.0.0.UPF
> O  15.9990 O.pbe-n-kjpaw_psl.1.0.0.UPF
>
> ATOMIC_POSITIONS  crystal
>   N 0.9548502075 0.5635784967 0.4962439034   1   1
>   1
>   N 0.20503544416667 0.6063052660 0.5061812013   1   1
>   1
>   N 0.79510299916667 0.3932039887 0.4945467630   1   1
>   1
>   N 0.9005930546 0.5040479798 0.4954070975   1   1
>   1
>  Mo 0.2500019781 0.528125 0.5038506950   1   1
>   1
>  Mo 0.759711 0.496645 0.4949650590   1   1
>   1
>   O 0.2785712690 0.5237995800 0.7873582690   1   1
>   1
>   O 0.2191770950 0.4751825040 0.7883099620   1   1
>   1
> CELL_PARAMETERS
>13.967476 0.00 0.00
> 0.0019.29957382133830 0.00
> 0.00 0.0015.00
>
> K_POINTS automatic
>311   0   0   0
>
>
> The out put reads like this
>
>
>  coordinates at iteration   0
>
>
> ATOMIC_POSITIONS (crystal)
> N0.957544089   0.564108314   0.491040077
> N0.206819548   0.605649544   0.515574286
> N0.796628928   0.393825710   0.491616776
> N0.902045066   0.504897968   0.488557042
> Mo   0.24821   0.50792   0.503850698
> Mo   0.749998615   0.48178   0.494965059
> O0.278571269   0.523799580   0.690302740
> O0.219177095   0.475182504   0.690540490
>
>
>
>Info: using nr1, nr2, nr3 values from input
>
>Info: using nr1s, nr2s, nr3s values from input
>
>  Parallelization info
>  
>  sticks:   dense  smooth PW G-vecs:dense   smooth  PW
>  Min  89  59 15 9347 5072 655
>  Max  90  60 16 9360 5110 662
>  Sum   22973   15343   3923  2394473  1303361  168491
>
>
> Thank you in advance for your help.
>
> Naseem
>
> Naseem Ud Din
> Graduate Student
> University of Central Florida

[Pw_forum] PWneb reads coordinates of images incorrectly

[naseem]

Dear All

I am trying to calculate reaction barrier using neb. The program doesn't
read the coordinates correctly for intermediate image. It reads correctly
the coordinates of initial and final image.

Any help is really appreciated.

thanks.

Here I put the input and output coordinates.


Input coordinates   Program NEB v.5.2.0


 ATOMIC_POSITIONS  crystal
  N 0.0458087269 0.4357101372 0.5012321465   1   1
  1
  N 0.0995362024 0.4949877337 0.5040735278   1   1
  1
  N 0.9544776551 0.5634852461 0.4969233258   1   1
  1
  N 0.20455961416665 0.6065336165 0.50715900716668   1   1
  1
  N 0.7948911295 0.3934361415 0.4963889690   1   1
  1
  N 0.9002404209 0.50402929283332 0.4965848249   1   1
  1
 Mo0.24999891816665 0.4971083334 0.5173825696   1   1
1
 Mo0.75000210116668 0.517712 0.4956577359   1   1
1
  O 0.24998766383334 0.4970916667 0.7455726474   1   1
  1
  C 0.24998865416667 0.501217 0.6672466500   1   1
  1

OUTPUT

coordinates at iteration   0

ATOMIC_POSITIONS  crystal
N0.045791964   0.435746632   0.501695225
N0.099568664   0.495144336   0.503660926
N0.954391613   0.563630181   0.497000916
N0.204742419   0.606524793   0.505858492
N0.794822904   0.393434607   0.497139846
N0.900260428   0.504122574   0.497178183
Mo  0.25072   0.50453   0.508613877
Mo  0.750001857   0.51752   0.497483220
O0.249987954   0.49100   0.778497829
C0.249980974   0.49925   0.701865784


Naseem Ud Din
Graduate Student
University of Central Florida
Orlando USA
Cell # +1-407-683-3016
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Re: [Pw_forum] PWneb reads coordinates of images incorrectly

[naseem]

Dear Paolo Giannozzi

The input file, I have shown here only last few coordinates for comparison.

&CONTROL
! .control.settings.
prefix= 'pwneb',
pseudo_dir= '/home/ndin/PP',

! .control.io.
verbosity = 'low',
disk_io   = 'low',
wf_collect= .false.,
outdir= './tmp/',

! .control.ion_relax.
etot_conv_thr = 0.0001,
forc_conv_thr = 0.001,
nstep = 200,
tprnfor   = .true.,
tstress   = .false.,
/

&SYSTEM
! .system.structure.
a = 1.0,
ibrav = 0,
nat   = 56,
ntyp  = 5,

! .system.ecut.
ecutwfc   = 50,
ecutrho   = 300,

! .system.occupations.
degauss   = 0.007,
smearing  = 'fd',
occupations   = 'smearing',

! .system.spin_pol.
nspin = 2,
! .system.starting_magnetization.
starting_magnetization(1) =  0.0 ,
starting_magnetization(2) =  0.0 ,
starting_magnetization(3) =  0.0 ,
starting_magnetization(4) =  0.5 ,
starting_magnetization(5) =  0.0 ,
/

&ELECTRONS
! .electrons.
diagonalization   = 'david',
mixing_mode   = 'plain',
electron_maxstep  = 300,
mixing_beta   = 0.7,
conv_thr  = 1e-06,
/

&IONS
! .ions.
pot_extrapolation = 'atomic',
wfc_extrapolation = 'none',
ion_dynamics  = 'bfgs',
/

ATOMIC_SPECIES
C  12.0110 C.pbe-n-kjpaw_psl.1.0.0.UPF
H   1.0079 H.pbe-kjpaw_psl.1.0.0.UPF
N  14.0070 N.pbe-n-kjpaw_psl.1.0.0.UPF
   Mo  95.9500 Mo.pbe-spn-rrkjus_psl.1.0.0.UPF
O  15.9990 O.pbe-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS  crystal
  N 0.9548502075 0.5635784967 0.4962439034   1   1
  1
  N 0.20503544416667 0.6063052660 0.5061812013   1   1
  1
  N 0.79510299916667 0.3932039887 0.4945467630   1   1
  1
  N 0.9005930546 0.5040479798 0.4954070975   1   1
  1
 Mo 0.2500019781 0.528125 0.5038506950   1   1
  1
 Mo 0.759711 0.496645 0.4949650590   1   1
  1
  O 0.2785712690 0.5237995800 0.7873582690   1   1
  1
  O 0.2191770950 0.4751825040 0.7883099620   1   1
  1
CELL_PARAMETERS
   13.967476 0.00 0.00
0.0019.29957382133830 0.00
0.00 0.0015.00

K_POINTS automatic
   311   0   0   0


The out put reads like this


 coordinates at iteration   0


ATOMIC_POSITIONS (crystal)
N0.957544089   0.564108314   0.491040077
N0.206819548   0.605649544   0.515574286
N0.796628928   0.393825710   0.491616776
N0.902045066   0.504897968   0.488557042
Mo   0.24821   0.50792   0.503850698
Mo   0.749998615   0.48178   0.494965059
O0.278571269   0.523799580   0.690302740
O0.219177095   0.475182504   0.690540490



   Info: using nr1, nr2, nr3 values from input

   Info: using nr1s, nr2s, nr3s values from input

 Parallelization info
 
 sticks:   dense  smooth PW G-vecs:dense   smooth  PW
 Min  89  59 15 9347 5072 655
 Max  90  60 16 9360     5110 662
 Sum   22973   15343   3923  2394473  1303361  168491


Thank you in advance for your help.

Naseem

Naseem Ud Din
Graduate Student
University of Central Florida
Orlando USA
Cell # +1-407-683-3016

On Mon, Jun 27, 2016 at 1:34 PM, Paolo Giannozzi 
wrote:

> Please support your claim with some data, such as e.g. input and output
> files
>
> Paolo
>
> On Mon, Jun 27, 2016 at 6:32 PM, naseem  wrote:
> > Dear All
> >
> > I am trying to calculate reaction barrier using neb. The program doesn't
> > read the coordinates correctly for intermediate image. It reads correctly
> > the coordinates of initial and final image.
> >
> > Any help is really appreciated.
> >
> > thanks
> >
> > Naseem Ud Din
> > Graduate Student
> > University of Central Florida
> > Orlando USA
> > Cell # +1-407-683-3016
> >
> > ___
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> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> ___
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Re: [Pw_forum] PWneb reads coordinates of images incorrectly

[naseem]

Dear Paolo Giannozzi

*here is my input file and out put. the program reads from input and write
the coordinates in output before starting any calculations. *
*But the coordinates in output  are all different.*

*Thank you for your help.*

*Naseem*

Naseem Ud Din
Graduate Student
University of Central Florida
Orlando USA
Cell # +1-407-683-3016

On Mon, Jun 27, 2016 at 1:34 PM, Paolo Giannozzi 
wrote:

> Please support your claim with some data, such as e.g. input and output
> files
>
> Paolo
>
> On Mon, Jun 27, 2016 at 6:32 PM, naseem  wrote:
> > Dear All
> >
> > I am trying to calculate reaction barrier using neb. The program doesn't
> > read the coordinates correctly for intermediate image. It reads correctly
> > the coordinates of initial and final image.
> >
> > Any help is really appreciated.
> >
> > thanks
> >
> > Naseem Ud Din
> > Graduate Student
> > University of Central Florida
> > Orlando USA
> > Cell # +1-407-683-3016
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum@pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>


test.in
Description: Binary data


test.out
Description: Binary data
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[Pw_forum] PWneb reads coordinates of images incorrectly

[naseem]

Dear All

I am trying to calculate reaction barrier using neb. The program doesn't
read the coordinates correctly for intermediate image. It reads correctly
the coordinates of initial and final image.

Any help is really appreciated.

thanks

Naseem Ud Din
Graduate Student
University of Central Florida
Orlando USA
Cell # +1-407-683-3016
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[Pw_forum] Structure collapse during relaxation

[Naseem Hassan]

Dear Members,

I took a 3-layer Ni-111 surface structure and checked it via xcrysden and
chemcraft. The structure is fine and also my friend is using same structure
in VASAP without any problem. But when I run the relaxation for this system
in QE 5.1. The structure starts spreading/collapsing. I tried other ways
but not sure why this structure is not stable in QE during relaxation.

Kindly provide some input for overcoming this problem. The input file is
shown Below.

Thank You
Naseem Hassan
Universiti Tecknologi Malaysia

 &control
calculation='relax'
restart_mode='from_scratch'
pseudo_dir = '/share/QE_pseudo'
outdir='./'
prefix='Graphane'
forc_conv_thr=1.0D-4
!   dt = 20
!   tefield = .true.
nstep=3000
/
 &system
ibrav=  0
nat=  12,  ntyp= 1
ecutwfc =60.0
occupations='smearing'
degauss=0.002
 /
 &electrons
!   conv_thr=1.0D-8
mixing_mode='plain'
scf_must_converge=.false.
!   electron_maxstep=400
 /
&ions
   ion_dynamics = 'damp'
/
CELL_PARAMETERS {angstrom}
 4.936344760.0.
 2.468172384.27540.
 0.0.12.
ATOMIC_SPECIES
 Ni 58.6934 Ni.pbe-mt_fhi.UPF
ATOMIC_POSITIONS {angstrom}
Ni   6.593779744  3.831146919  0.900942199
Ni   2.878171463  0.325256336  2.566767175
Ni   4.149708943  1.089021759  4.449272572
Ni   4.125469394  3.831006729  0.901201599
Ni   0.410161483  0.325286326  2.566708045
Ni   1.681648933  1.089091799  4.448872032
Ni   5.359329404  1.693546849  0.901062359
Ni   4.112411513  2.462676226  2.566528755
Ni   5.383949003  3.226741749  4.449081832
Ni   2.891459644  1.693646869  0.901031849
Ni   1.644121543  2.462456406  2.566627935
Ni   2.915678933  3.226781799  4.448881562
K_POINTS {automatic}
  3 3 1 0 0 0
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[Pw_forum] How to identify different types of normal modes in example 15 for RAMMAN and IR Spectroscopy ?

[Naseem Hassan]

Dear Members

I have a no experience with experimental spectroscopic techniques. Kindly
guide, *How to identify/read different types of normal modes (bending,
**symmetric
stretching, **symmetric stretching etc.) in example 15 for RAMMAN and IR
Spectroscopy.*

The text is mentioned below indicating different modes.

Example#15 (ph.x)
"The obtained results for CO2 show normal modes at 604.82 (bending),
1362.90 (symmetric stretching) and 2441.15 cm-1 (antisymmetric stretching)"

Best Regards
Naseem
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Re: [Pw_forum] Avoiding vacuum and obtaining a periodic relaxed structure

[Naseem Hassan]

 %%
 stopping ...
 %%
 %%
 %%
 Error in routine scale_h (1):
 Error in routine scale_h (1):
 %%
 Error in routine scale_h (1):
 Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
 Error in routine scale_h (1):
 Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
 Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
 %%
 %%
 Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
 %%
 %%




 stopping ...
 Error in routine scale_h (1):
 stopping ...
 Error in routine scale_h (1):
 stopping ...
 Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.


Many Thanks
Naseem Hassan


On Wed, Jan 14, 2015 at 10:12 PM, Pascal Boulet 
wrote:

>
> Hello,
>
> My brute force suggestion:
> 1. Select a chemically consistent axis so that the bond length is around
> 1.5 angstrom.
> 2. Optimize the cell parameters and atomic positions using vc-relax
>
> Pascal
>
>
> Le 14 janv. 2015 à 09:16, Naseem Hassan  a écrit :
>
> Dear All
>
> I have made a structure similar to propylene using chemcraft. Then I
> picked the Cartesian coordinates and made an input file for relaxation. But
> I am not sure How long a Cell vector I should select along z-axis (along
> the Carbon chain). I want this structure to be periodic along the chain
> only. I selected 9 and 10 Angstrom of lattice vector along Z-axis and
> obtained C-C distance 5 and 6 Angstrom (Approx) respectively. It seems with
> 10 Angstrom a little vacuum is added and C-C bonds are elongated more. if I
> give small lattice vector (say 7 Ang) then C-C bond shrinks.
> *How to obtain an optimized C-C bond length ? What is proper method of
> avoiding vacuum and obtaining a perfect periodic relaxed structure. *
> Kindly have a look at the input file.
>
>   &control
> calculation='relax'
> restart_mode='from_scratch'
> pseudo_dir = '/share/QE_pseudo'
> outdir='./'
> prefix='Graphane'
> forc_conv_thr=1.0D-4
> nstep=3000
> /
>  &system
> ibrav=  0
> nat=  24,  ntyp= 2
> ecutwfc =60.0
> occupations='smearing'
> degauss=0.002
>  /
>  &electrons
> scf_must_converge = .false.
> mixing_mode='plain'
>  /
>  &ions
> ion_dynamics = 'damp'
> !   ion_temperature='not_controlled'
>  /
> CELL_PARAMETERS {angstrom}
>   10.000   0.   0.000
>   0.00   10.00   0.000
>   0.   0.  10.0
> ATOMIC_SPECIES
> H  1.0079 H.pw-mt_fhi.UPF
> C  12.0111 C.pw-mt_fhi.UPF
> ATOMIC_POSITIONS {angstrom}
> C5.367107970   4.716603635   1.053018481
> C6.255850131   5.148617707   2.197431688
> C5.604070962   5.956723221   3.300642187
> C5.221138074   5.110436404   4.489234599
> C4.929412403   5.933432549   5.718863005
> C4.751718300   5.084706368   6.956077606
> C5.325054303   5.689729332   8.206876709
> C4.097184203   4.164227727   4.168731293
> H6.706474032   4.257638763   2.659887322
> H4.344006686   3.515258124   3.319860376
> H3.854647824   3.519241858   5.021187742
> H3.190910142   4.727029043   3.904250319
> H3.696251345   4.818294626   7.110426161
> H4.348967601   4.517546557   1.417990955
> H5.731392495   3.757052353   0.655098847
> H7.101013257   5.709772742   1.774202810
> H    6.288921269   6.743142271   3.648137411
> H4.714167633   6.481058689   2.916034182
> H6.110659580   4.502596625   4.738962908
> H4.050783951   6.573507244   5.541152210
> H5.775952152   6.619568616   5.878615758
> H4.786163229   6.607591885   8.486624196
> H6.356503452   6.007847752   7.983988564
> H5.270145007   4.125317908   6.789870671
> K_POINTS {automatic}
>   3 3 1 0 0 0
> Many thanks
> Naseem
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[Pw_forum] Avoiding vacuum and obtaining a periodic relaxed structure

[Naseem Hassan]

Dear All

I have made a structure similar to propylene using chemcraft. Then I picked
the Cartesian coordinates and made an input file for relaxation. But I am
not sure How long a Cell vector I should select along z-axis (along the
Carbon chain). I want this structure to be periodic along the chain only. I
selected 9 and 10 Angstrom of lattice vector along Z-axis and obtained C-C
distance 5 and 6 Angstrom (Approx) respectively. It seems with 10 Angstrom
a little vacuum is added and C-C bonds are elongated more. if I give small
lattice vector (say 7 Ang) then C-C bond shrinks.
*How to obtain an optimized C-C bond length ? What is proper method of
avoiding vacuum and obtaining a perfect periodic relaxed structure. *
Kindly have a look at the input file.

  &control
calculation='relax'
restart_mode='from_scratch'
pseudo_dir = '/share/QE_pseudo'
outdir='./'
prefix='Graphane'
forc_conv_thr=1.0D-4
nstep=3000
/
 &system
ibrav=  0
nat=  24,  ntyp= 2
ecutwfc =60.0
occupations='smearing'
degauss=0.002
 /
 &electrons
scf_must_converge = .false.
mixing_mode='plain'
 /
 &ions
ion_dynamics = 'damp'
!   ion_temperature='not_controlled'
 /
CELL_PARAMETERS {angstrom}
  10.000   0.   0.000
  0.00   10.00   0.000
  0.   0.  10.0
ATOMIC_SPECIES
H  1.0079 H.pw-mt_fhi.UPF
C  12.0111 C.pw-mt_fhi.UPF
ATOMIC_POSITIONS {angstrom}
C5.367107970   4.716603635   1.053018481
C6.255850131   5.148617707   2.197431688
C5.604070962   5.956723221   3.300642187
C5.221138074   5.110436404   4.489234599
C4.929412403   5.933432549   5.718863005
C4.751718300   5.084706368   6.956077606
C5.325054303   5.689729332   8.206876709
C4.097184203   4.164227727   4.168731293
H6.706474032   4.257638763   2.659887322
H4.344006686   3.515258124   3.319860376
H3.854647824   3.519241858   5.021187742
H3.190910142   4.727029043   3.904250319
H3.696251345   4.818294626   7.110426161
H4.348967601   4.517546557   1.417990955
H5.731392495   3.757052353   0.655098847
H7.101013257   5.709772742   1.774202810
H6.288921269   6.743142271   3.648137411
H4.714167633   6.481058689   2.916034182
H6.110659580   4.502596625   4.738962908
H4.050783951   6.573507244   5.541152210
H5.775952152   6.619568616   5.878615758
H4.786163229   6.607591885   8.486624196
H6.356503452   6.007847752   7.983988564
H5.270145007   4.125317908   6.789870671
K_POINTS {automatic}
  3 3 1 0 0 0
Many thanks
Naseem
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