[QE-users] QHA Error: from find_min_mur_pol : error # 1 minimum not found

[Sitangshu Bhattacharya]

Dear all,

I am trying to do a QHA analyses of a material with symmorphic group D_3h
with space group P63/mmc. A BZ sampling was done at unshifted 12x12x1 with
q-point sampling as 10x10x1.
I have choosen three geometries (two about the central relaxed one) and
obtained the minimum energy configuration:

# Vol.E_calcE_fit   E_diffPressure  Enthalpy
# a.u.^3Ry   RyRyGPa   Ry
##
 3810.76 -26.83684 -26.83684 0.0   0.05  -26.82358
 3835.17 -26.83688 -26.83688-0.0   0.00  -26.83667
 3859.69 -26.83684 -26.83684-0.0  -0.05  -26.84946

The dynamical matrices were calculated and all the phonon dispersion, free
energy, etc. were done at all geometries. I found that the results upto
this stage are quite convincing.

However during the end, when the anharmonic computation (mur_lc_t) started,
I got this horrible error:

%%
 Error in routine find_min_mur_pol (1):
 minimum not found
 %%

 stopping ...

I used temperature variation from 0K to 1000K with difference of 3K. and
the geometries are seperated by 0.01 angstrom about the central one.
I was using QE-6.1 version. I am not getting any clue wher I am wrong.. Any
suggestion will be greatly appreciated!
Excuse me for writng in the QE forum. I saw that the QHA forum has become
obsolate



Regards,
**
Sitangshu Bhattacharya (সিতাংশু ভট্টাচার্য), Ph.D
Assistant Professor,
Room No. 2221, CC-1,
Nanoscale Electro-Thermal Laboratory,
Department of Electrical and Communication Engineering,
Indian Institute of Information Technology-Allahabad
Uttar Pradesh 211 012
India
Telephone: 91-532-2922000 Extn.: 2131
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/
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Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface

[Venkataramana Imandi]

Dear Ari,

I misunderstood your message.
I ask you whether you got stable O_ad position at a bridge site.

With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.


On Tue, Apr 10, 2018 at 3:50 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:

> Dear Ari,
>
> What shall i do now. The wrong in the input file coordinates or system
> description.
> Can you give more hints. Even increasing system size (present 24 atoms to
> 48 Pt atoms), the results remain same.
>
> With best regards
> Venkataramana Imandi
> Postdoctoral fellow
> IIT Madras, India.
>
>
> On Tue, Apr 10, 2018 at 3:08 PM, Venkataramana Imandi <
> venkataramana.ima...@gmail.com> wrote:
>
>> Dear Ari,
>>
>> Sorry, I didn't mention that I also tried by fixing coordinate of O_ad at
>> a bridge position.
>> It resulted the Pt atoms moving, in such way that O_ad becomes three-fold
>> site(either fcc or hcp).
>>
>> With best regards
>> Venkataramana Imandi
>> Postdoctoral fellow
>> IIT Madras, India.
>>
>>
>> On Tue, Apr 10, 2018 at 2:44 PM, Venkataramana Imandi <
>> venkataramana.ima...@gmail.com> wrote:
>>
>>>
>>> Dear QE community,
>>>
>>> I am a new user of Quantum espresso simulation package. I installed
>>> 6.2.1 Quantum espresso in the Linux-X86_64-INTEL-MPI. I want to find out
>>> the binding energy of O_ad at various sites(top,bridge,hcp and fcc) on
>>> Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried on
>>> Pt-surface, and I got O_ad at top, hcp and fcc sites on Pt-surface,
>>> however, i couldn't find O_ad at bridge position.
>>> I have tried all possible ways of getting O_ad at the bridge
>>> position(between Pt-Pt). None of them were given succussful results, and
>>> the resulted O_ad comes to either fcc or hcp position. All possible ways:
>>> using with and without spin-polarization, davidson diagonalization anc cg,
>>> option (nosym = .TRUE. and .FALSE.), mixing mode(plain, local-TF and TF),
>>> changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative charge(-2) and
>>> different simulation setup (present 24 atoms to 48 Pt atoms). The last
>>> option, i used different pseudopotential(Pt.pw91-n-van.UPF and
>>> O.pw91-van_ak.UPF), herein, i got error as follows (Error in
>>> scalartorealdp  Too few elements found). Now i stopped trials.
>>> I ask you can anyone do calculation in your simulation setup with the
>>> given input file, tell me the where the problem is.
>>>
>>> I really thanks to you in advance for any suggestions regarding this.
>>> For information, i used VASP in the last year, therein, i obtained O_ad
>>> at all sites on Pt-surface.
>>>
>>>  
>>> calculation='relax'
>>> restart_mode='from_scratch',
>>> pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
>>> prefix='pt'
>>> tprnfor = .true.,
>>> nstep = 200
>>>  /
>>>  
>>> ibrav=0,
>>> nat=25,
>>> ntyp=2,
>>> ! nspin = 2,
>>> ! starting_magnetization(1)=0.7,
>>> ecutwfc = 32.0,
>>> ecutrho = 320.0,
>>> occupations='smearing',
>>> smearing='methfessel-paxton',
>>> degauss=0.02
>>>! tot_charge = -2,
>>> nosym = .TRUE.
>>>  /
>>>  
>>> diagonalization='cg'
>>> conv_thr = 1.0e-6
>>> mixing_beta = 0.3
>>>electron_maxstep = 1000
>>>  /
>>> 
>>> ion_dynamics='bfgs',
>>>  /
>>> ATOMIC_SPECIES
>>> Pt  195.084  Pt.pbe-nd-rrkjus.UPF
>>> O15.999  O.pbe-rrkjus.UPF
>>>
>>> ATOMIC_POSITIONS {angstrom}
>>> O 3.45091550  1.17466050 13.69732100  1 1 1
>>> Pt4.84778787  1.20016667 12.44963917  1 1 1
>>> Pt3.46185858  3.60066659 12.44963917  1 1 1
>>> Pt2.07592929  1.20016667 12.44963917  1 1 1
>>> Pt0.6900  3.60066659 12.44963917  1 1 1
>>> Pt3.46185858  0.4000 10.18642611  1 1 1
>>> Pt4.84778787  2.80049996 10.18642611  1 1 1
>>> Pt0.6900  0.4000 10.18642611  1 1 1
>>> Pt2.07592929  2.80049996 10.18642611  1 1 1
>>> Pt3.46185858  2.0000  7.92321305  1 1 1
>>> Pt4.84778787  4.40083326  7.92321305  1 1 1
>>> Pt0.6900  2.0000  7.92321305  1 1 1
>>> Pt2.07592929  4.40083326  7.92321305  1 1 1
>>> Pt4.84778787  1.20016667  5.6600  1 1 1
>>> Pt3.46185858  3.60066659  5.6600  1 1 1
>>> Pt2.07592929  1.20016667  5.6600  1 1 1
>>> Pt0.6900  3.60066659  5.6600  1 1 1
>>> Pt3.46185858  0.4000  3.39678694  0 0 0
>>> Pt4.84778787  2.80049996  3.39678694  0 0 0
>>> Pt0.6900  0.4000  3.39678694  0 0 0
>>> Pt2.07592929  2.80049996  3.39678694  0 0 0
>>> Pt3.46185858  2.0000  1.13357388  0 0 0
>>> Pt4.84778787  4.40083326  1.13357388  0 0 0
>>> 

Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface

[Venkataramana Imandi]

Dear Ari,

What shall i do now. The wrong in the input file coordinates or system
description.
Can you give more hints. Even increasing system size (present 24 atoms to
48 Pt atoms), the results remain same.

With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.


On Tue, Apr 10, 2018 at 3:08 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:

> Dear Ari,
>
> Sorry, I didn't mention that I also tried by fixing coordinate of O_ad at
> a bridge position.
> It resulted the Pt atoms moving, in such way that O_ad becomes three-fold
> site(either fcc or hcp).
>
> With best regards
> Venkataramana Imandi
> Postdoctoral fellow
> IIT Madras, India.
>
>
> On Tue, Apr 10, 2018 at 2:44 PM, Venkataramana Imandi <
> venkataramana.ima...@gmail.com> wrote:
>
>>
>> Dear QE community,
>>
>> I am a new user of Quantum espresso simulation package. I installed 6.2.1
>> Quantum espresso in the Linux-X86_64-INTEL-MPI. I want to find out the
>> binding energy of O_ad at various sites(top,bridge,hcp and fcc) on
>> Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried on
>> Pt-surface, and I got O_ad at top, hcp and fcc sites on Pt-surface,
>> however, i couldn't find O_ad at bridge position.
>> I have tried all possible ways of getting O_ad at the bridge
>> position(between Pt-Pt). None of them were given succussful results, and
>> the resulted O_ad comes to either fcc or hcp position. All possible ways:
>> using with and without spin-polarization, davidson diagonalization anc cg,
>> option (nosym = .TRUE. and .FALSE.), mixing mode(plain, local-TF and TF),
>> changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative charge(-2) and
>> different simulation setup (present 24 atoms to 48 Pt atoms). The last
>> option, i used different pseudopotential(Pt.pw91-n-van.UPF and
>> O.pw91-van_ak.UPF), herein, i got error as follows (Error in
>> scalartorealdp  Too few elements found). Now i stopped trials.
>> I ask you can anyone do calculation in your simulation setup with the
>> given input file, tell me the where the problem is.
>>
>> I really thanks to you in advance for any suggestions regarding this.
>> For information, i used VASP in the last year, therein, i obtained O_ad
>> at all sites on Pt-surface.
>>
>>  
>> calculation='relax'
>> restart_mode='from_scratch',
>> pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
>> prefix='pt'
>> tprnfor = .true.,
>> nstep = 200
>>  /
>>  
>> ibrav=0,
>> nat=25,
>> ntyp=2,
>> ! nspin = 2,
>> ! starting_magnetization(1)=0.7,
>> ecutwfc = 32.0,
>> ecutrho = 320.0,
>> occupations='smearing',
>> smearing='methfessel-paxton',
>> degauss=0.02
>>! tot_charge = -2,
>> nosym = .TRUE.
>>  /
>>  
>> diagonalization='cg'
>> conv_thr = 1.0e-6
>> mixing_beta = 0.3
>>electron_maxstep = 1000
>>  /
>> 
>> ion_dynamics='bfgs',
>>  /
>> ATOMIC_SPECIES
>> Pt  195.084  Pt.pbe-nd-rrkjus.UPF
>> O15.999  O.pbe-rrkjus.UPF
>>
>> ATOMIC_POSITIONS {angstrom}
>> O 3.45091550  1.17466050 13.69732100  1 1 1
>> Pt4.84778787  1.20016667 12.44963917  1 1 1
>> Pt3.46185858  3.60066659 12.44963917  1 1 1
>> Pt2.07592929  1.20016667 12.44963917  1 1 1
>> Pt0.6900  3.60066659 12.44963917  1 1 1
>> Pt3.46185858  0.4000 10.18642611  1 1 1
>> Pt4.84778787  2.80049996 10.18642611  1 1 1
>> Pt0.6900  0.4000 10.18642611  1 1 1
>> Pt2.07592929  2.80049996 10.18642611  1 1 1
>> Pt3.46185858  2.0000  7.92321305  1 1 1
>> Pt4.84778787  4.40083326  7.92321305  1 1 1
>> Pt0.6900  2.0000  7.92321305  1 1 1
>> Pt2.07592929  4.40083326  7.92321305  1 1 1
>> Pt4.84778787  1.20016667  5.6600  1 1 1
>> Pt3.46185858  3.60066659  5.6600  1 1 1
>> Pt2.07592929  1.20016667  5.6600  1 1 1
>> Pt0.6900  3.60066659  5.6600  1 1 1
>> Pt3.46185858  0.4000  3.39678694  0 0 0
>> Pt4.84778787  2.80049996  3.39678694  0 0 0
>> Pt0.6900  0.4000  3.39678694  0 0 0
>> Pt2.07592929  2.80049996  3.39678694  0 0 0
>> Pt3.46185858  2.0000  1.13357388  0 0 0
>> Pt4.84778787  4.40083326  1.13357388  0 0 0
>> Pt0.6900  2.0000  1.13357388  0 0 0
>> Pt2.07592929  4.40083326  1.13357388  0 0 0
>>
>> K_POINTS {automatic}
>> 3 3 1 0 0 0
>> CELL_PARAMETERS {angstrom}
>> 5.5437171600 0.00 0.00
>> 0.00 4.800000 0.00
>> 0.00 0.0025.5792783300
>>
>>
>> With best regards
>> Venkataramana Imandi
>> 

Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface

[Ari P Seitsonen]

Dear Venkataramana Imandi,

  Since you have fixed the lowest layers of the substrate, it sounds quasi 
impossible that only few layers would have moved that much (the 
interaction between the layers should be larger than the corrugation of 
the potential energy surface of the oxygen). Of course the coverage is 
quite high (1/2), but still I am surprised... Otherwise, I do not see 
anything "obviously wrong" in your input now.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 10 Apr 2018, Venkataramana Imandi wrote:


Dear Ari,

Sorry, I didn't mention that I also tried by fixing coordinate of O_ad at a 
bridge position.
It resulted the Pt atoms moving, in such way that O_ad becomes three-fold 
site(either fcc or hcp).

With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.


On Tue, Apr 10, 2018 at 2:44 PM, Venkataramana Imandi 
 wrote:

  Dear QE community,

  I am a new user of Quantum espresso simulation package. I installed 6.2.1 
Quantum espresso
  in the Linux-X86_64-INTEL-MPI. I want to find out the binding energy of 
O_ad at various
  sites(top,bridge,hcp and fcc) on Pt-surface and Pt-Ni alloy surface. In 
the beginning, i
  have tried on Pt-surface, and I got O_ad at top, hcp and fcc sites on 
Pt-surface, however,
  i couldn't find O_ad at bridge position.
  I have tried all possible ways of getting O_ad at the bridge 
position(between Pt-Pt). None
  of them were given succussful results, and the resulted O_ad comes to 
either fcc or hcp
  position. All possible ways: using with and without spin-polarization, 
davidson
  diagonalization anc cg, option (nosym = .TRUE. and .FALSE.), mixing 
mode(plain, local-TF
  and TF), changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative 
charge(-2) and different
  simulation setup (present 24 atoms to 48 Pt atoms). The last option, i 
used different
  pseudopotential(Pt.pw91-n-van.UPF and O.pw91-van_ak.UPF), herein, i got 
error as follows
  (Error in scalartorealdp  Too few elements found). Now i stopped trials.
  I ask you can anyone do calculation in your simulation setup with the 
given input file,
  tell me the where the problem is.

  I really thanks to you in advance for any suggestions regarding this.
  For information, i used VASP in the last year, therein, i obtained O_ad 
at all sites on
  Pt-surface.

   
      calculation='relax'
      restart_mode='from_scratch',
      pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
      prefix='pt'
      tprnfor = .true.,
      nstep = 200
   /
   
      ibrav=0,
      nat=25,
      ntyp=2,
      ! nspin = 2,
      ! starting_magnetization(1)=0.7,
      ecutwfc = 32.0,
      ecutrho = 320.0,
      occupations='smearing',
      smearing='methfessel-paxton',
      degauss=0.02
     ! tot_charge = -2,
      nosym = .TRUE.
   /
   
      diagonalization='cg'
      conv_thr = 1.0e-6
      mixing_beta = 0.3
     electron_maxstep = 1000
   /
  
  ion_dynamics='bfgs',
   /
  ATOMIC_SPECIES
  Pt  195.084  Pt.pbe-nd-rrkjus.UPF
  O    15.999  O.pbe-rrkjus.UPF

  ATOMIC_POSITIONS {angstrom}
  O 3.45091550  1.17466050 13.69732100  1 1 1
  Pt    4.84778787  1.20016667 12.44963917  1 1 1
  Pt    3.46185858  3.60066659 12.44963917  1 1 1
  Pt    2.07592929  1.20016667 12.44963917  1 1 1
  Pt    0.6900  3.60066659 12.44963917  1 1 1
  Pt    3.46185858  0.4000 10.18642611  1 1 1
  Pt    4.84778787  2.80049996 10.18642611  1 1 1
  Pt    0.6900  0.4000 10.18642611  1 1 1
  Pt    2.07592929  2.80049996 10.18642611  1 1 1
  Pt    3.46185858  2.0000  7.92321305  1 1 1
  Pt    4.84778787  4.40083326  7.92321305  1 1 1
  Pt    0.6900  2.0000  7.92321305  1 1 1
  Pt    2.07592929  4.40083326  7.92321305  1 1 1
  Pt    4.84778787  1.20016667  5.6600  1 1 1
  Pt    3.46185858  3.60066659  5.6600  1 1 1
  Pt    2.07592929  1.20016667  5.6600  1 1 1
  Pt    0.6900  3.60066659  5.6600  1 1 1
  Pt    3.46185858  0.4000  3.39678694  0 0 0
  Pt    4.84778787  2.80049996  3.39678694  0 0 0
  Pt    0.6900  0.4000  3.39678694  0 0 0
  Pt    

Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface

[Venkataramana Imandi]

Dear Ari,

Sorry, I didn't mention that I also tried by fixing coordinate of O_ad at a
bridge position.
It resulted the Pt atoms moving, in such way that O_ad becomes three-fold
site(either fcc or hcp).

With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.


On Tue, Apr 10, 2018 at 2:44 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:

>
> Dear QE community,
>
> I am a new user of Quantum espresso simulation package. I installed 6.2.1
> Quantum espresso in the Linux-X86_64-INTEL-MPI. I want to find out the
> binding energy of O_ad at various sites(top,bridge,hcp and fcc) on
> Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried on
> Pt-surface, and I got O_ad at top, hcp and fcc sites on Pt-surface,
> however, i couldn't find O_ad at bridge position.
> I have tried all possible ways of getting O_ad at the bridge
> position(between Pt-Pt). None of them were given succussful results, and
> the resulted O_ad comes to either fcc or hcp position. All possible ways:
> using with and without spin-polarization, davidson diagonalization anc cg,
> option (nosym = .TRUE. and .FALSE.), mixing mode(plain, local-TF and TF),
> changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative charge(-2) and
> different simulation setup (present 24 atoms to 48 Pt atoms). The last
> option, i used different pseudopotential(Pt.pw91-n-van.UPF and
> O.pw91-van_ak.UPF), herein, i got error as follows (Error in
> scalartorealdp  Too few elements found). Now i stopped trials.
> I ask you can anyone do calculation in your simulation setup with the
> given input file, tell me the where the problem is.
>
> I really thanks to you in advance for any suggestions regarding this.
> For information, i used VASP in the last year, therein, i obtained O_ad at
> all sites on Pt-surface.
>
>  
> calculation='relax'
> restart_mode='from_scratch',
> pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
> prefix='pt'
> tprnfor = .true.,
> nstep = 200
>  /
>  
> ibrav=0,
> nat=25,
> ntyp=2,
> ! nspin = 2,
> ! starting_magnetization(1)=0.7,
> ecutwfc = 32.0,
> ecutrho = 320.0,
> occupations='smearing',
> smearing='methfessel-paxton',
> degauss=0.02
>! tot_charge = -2,
> nosym = .TRUE.
>  /
>  
> diagonalization='cg'
> conv_thr = 1.0e-6
> mixing_beta = 0.3
>electron_maxstep = 1000
>  /
> 
> ion_dynamics='bfgs',
>  /
> ATOMIC_SPECIES
> Pt  195.084  Pt.pbe-nd-rrkjus.UPF
> O15.999  O.pbe-rrkjus.UPF
>
> ATOMIC_POSITIONS {angstrom}
> O 3.45091550  1.17466050 13.69732100  1 1 1
> Pt4.84778787  1.20016667 12.44963917  1 1 1
> Pt3.46185858  3.60066659 12.44963917  1 1 1
> Pt2.07592929  1.20016667 12.44963917  1 1 1
> Pt0.6900  3.60066659 12.44963917  1 1 1
> Pt3.46185858  0.4000 10.18642611  1 1 1
> Pt4.84778787  2.80049996 10.18642611  1 1 1
> Pt0.6900  0.4000 10.18642611  1 1 1
> Pt2.07592929  2.80049996 10.18642611  1 1 1
> Pt3.46185858  2.0000  7.92321305  1 1 1
> Pt4.84778787  4.40083326  7.92321305  1 1 1
> Pt0.6900  2.0000  7.92321305  1 1 1
> Pt2.07592929  4.40083326  7.92321305  1 1 1
> Pt4.84778787  1.20016667  5.6600  1 1 1
> Pt3.46185858  3.60066659  5.6600  1 1 1
> Pt2.07592929  1.20016667  5.6600  1 1 1
> Pt0.6900  3.60066659  5.6600  1 1 1
> Pt3.46185858  0.4000  3.39678694  0 0 0
> Pt4.84778787  2.80049996  3.39678694  0 0 0
> Pt0.6900  0.4000  3.39678694  0 0 0
> Pt2.07592929  2.80049996  3.39678694  0 0 0
> Pt3.46185858  2.0000  1.13357388  0 0 0
> Pt4.84778787  4.40083326  1.13357388  0 0 0
> Pt0.6900  2.0000  1.13357388  0 0 0
> Pt2.07592929  4.40083326  1.13357388  0 0 0
>
> K_POINTS {automatic}
> 3 3 1 0 0 0
> CELL_PARAMETERS {angstrom}
> 5.5437171600 0.00 0.00
> 0.00 4.800000 0.00
> 0.00 0.0025.5792783300
>
>
> With best regards
> Venkataramana Imandi
> Postdoctoral fellow
> IIT Madras, India.
>
>
>
>
>
>
>


-- 
venkataramana
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[QE-users] Subscription

[Pablo García Risueño]

Dear friend

I would like to know if I am actually subscribed to the list; if not, may
you register me?

Thank you very much. Best regards.

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Dr. Pablo García Risueño
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Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface

[Ari P Seitsonen]

Dear Venkataramana Imandi,

  Possibly the bridge site is a saddle point but the symmetry is not 
perfect, so the symmetry constrain does not fix the atom from moving 
toward a lower-energy site. I would try arranging the surface so that for 
example the x axis is the reaction coordinate for diffusion from a 
three-fold site to the other three-fold site, and then fixing the value of 
that coordinate (well, I do not remember if the fixed coordinates in the 
input are for relative or Cartesian coordinates, but you could try fixing 
a Cartesian one). If the bridge would be, however, a in-principle fully 
symmetric coordinate it does not get fixed because the symmetries are not 
found.


Greetings from Rüschlikon (ZH),

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 10 Apr 2018, Venkataramana Imandi wrote:



Dear QE community,

I am a new user of Quantum espresso simulation package. I installed 6.2.1 
Quantum espresso in the
Linux-X86_64-INTEL-MPI. I want to find out the binding energy of O_ad at 
various sites(top,bridge,hcp
and fcc) on Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried 
on Pt-surface, and I got
O_ad at top, hcp and fcc sites on Pt-surface, however, i couldn't find O_ad at 
bridge position.
I have tried all possible ways of getting O_ad at the bridge position(between 
Pt-Pt). None of them were
given succussful results, and the resulted O_ad comes to either fcc or hcp 
position. All possible ways:
using with and without spin-polarization, davidson diagonalization anc cg, 
option (nosym = .TRUE. and
.FALSE.), mixing mode(plain, local-TF and TF), changing mixing-beta(0.2, 0.3 
and 0.5), neutral,
negative charge(-2) and different simulation setup (present 24 atoms to 48 Pt 
atoms). The last option,
i used different pseudopotential(Pt.pw91-n-van.UPF and O.pw91-van_ak.UPF), 
herein, i got error as
follows (Error in scalartorealdp  Too few elements found). Now i stopped trials.
I ask you can anyone do calculation in your simulation setup with the given 
input file, tell me the
where the problem is.

I really thanks to you in advance for any suggestions regarding this.
For information, i used VASP in the last year, therein, i obtained O_ad at all 
sites on Pt-surface.

 
    calculation='relax'
    restart_mode='from_scratch',
    pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
    prefix='pt'
    tprnfor = .true.,
    nstep = 200
 /
 
    ibrav=0,
    nat=25,
    ntyp=2,
    ! nspin = 2,
    ! starting_magnetization(1)=0.7,
    ecutwfc = 32.0,
    ecutrho = 320.0,
    occupations='smearing',
    smearing='methfessel-paxton',
    degauss=0.02
   ! tot_charge = -2,
    nosym = .TRUE.
 /
 
    diagonalization='cg'
    conv_thr = 1.0e-6
    mixing_beta = 0.3
   electron_maxstep = 1000
 /

ion_dynamics='bfgs',
 /
ATOMIC_SPECIES
Pt  195.084  Pt.pbe-nd-rrkjus.UPF
O    15.999  O.pbe-rrkjus.UPF

ATOMIC_POSITIONS {angstrom}
O 3.45091550  1.17466050 13.69732100  1 1 1
Pt    4.84778787  1.20016667 12.44963917  1 1 1
Pt    3.46185858  3.60066659 12.44963917  1 1 1
Pt    2.07592929  1.20016667 12.44963917  1 1 1
Pt    0.6900  3.60066659 12.44963917  1 1 1
Pt    3.46185858  0.4000 10.18642611  1 1 1
Pt    4.84778787  2.80049996 10.18642611  1 1 1
Pt    0.6900  0.4000 10.18642611  1 1 1
Pt    2.07592929  2.80049996 10.18642611  1 1 1
Pt    3.46185858  2.0000  7.92321305  1 1 1
Pt    4.84778787  4.40083326  7.92321305  1 1 1
Pt    0.6900  2.0000  7.92321305  1 1 1
Pt    2.07592929  4.40083326  7.92321305  1 1 1
Pt    4.84778787  1.20016667  5.6600  1 1 1
Pt    3.46185858  3.60066659  5.6600  1 1 1
Pt    2.07592929  1.20016667  5.6600  1 1 1
Pt    0.6900  3.60066659  5.6600  1 1 1
Pt    3.46185858  0.4000  3.39678694  0 0 0
Pt    4.84778787  2.80049996  3.39678694  0 0 0
Pt    0.6900  0.4000  3.39678694  0 0 0
Pt    2.07592929  2.80049996  3.39678694  0 0 0
Pt    3.46185858  2.0000  1.13357388  0 0 0
Pt    4.84778787  4.40083326  1.13357388  0 0 0
Pt    0.6900  2.0000  1.13357388  0 0 0
Pt    2.07592929  4.40083326  1.13357388  0 0 0

K_POINTS {automatic}
3 3 1 0 0 0
CELL_PARAMETERS {angstrom}
5.5437171600 0.00 0.00
0.00 4.800000 0.00
0.00 0.00    25.5792783300


With best regards
Venkataramana 

[QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface

[Venkataramana Imandi]

Dear QE community,

I am a new user of Quantum espresso simulation package. I installed 6.2.1
Quantum espresso in the Linux-X86_64-INTEL-MPI. I want to find out the
binding energy of O_ad at various sites(top,bridge,hcp and fcc) on
Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried on
Pt-surface, and I got O_ad at top, hcp and fcc sites on Pt-surface,
however, i couldn't find O_ad at bridge position.
I have tried all possible ways of getting O_ad at the bridge
position(between Pt-Pt). None of them were given succussful results, and
the resulted O_ad comes to either fcc or hcp position. All possible ways:
using with and without spin-polarization, davidson diagonalization anc cg,
option (nosym = .TRUE. and .FALSE.), mixing mode(plain, local-TF and TF),
changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative charge(-2) and
different simulation setup (present 24 atoms to 48 Pt atoms). The last
option, i used different pseudopotential(Pt.pw91-n-van.UPF and
O.pw91-van_ak.UPF), herein, i got error as follows (Error in
scalartorealdp  Too few elements found). Now i stopped trials.
I ask you can anyone do calculation in your simulation setup with the given
input file, tell me the where the problem is.

I really thanks to you in advance for any suggestions regarding this.
For information, i used VASP in the last year, therein, i obtained O_ad at
all sites on Pt-surface.

 
calculation='relax'
restart_mode='from_scratch',
pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
prefix='pt'
tprnfor = .true.,
nstep = 200
 /
 
ibrav=0,
nat=25,
ntyp=2,
! nspin = 2,
! starting_magnetization(1)=0.7,
ecutwfc = 32.0,
ecutrho = 320.0,
occupations='smearing',
smearing='methfessel-paxton',
degauss=0.02
   ! tot_charge = -2,
nosym = .TRUE.
 /
 
diagonalization='cg'
conv_thr = 1.0e-6
mixing_beta = 0.3
   electron_maxstep = 1000
 /

ion_dynamics='bfgs',
 /
ATOMIC_SPECIES
Pt  195.084  Pt.pbe-nd-rrkjus.UPF
O15.999  O.pbe-rrkjus.UPF

ATOMIC_POSITIONS {angstrom}
O 3.45091550  1.17466050 13.69732100  1 1 1
Pt4.84778787  1.20016667 12.44963917  1 1 1
Pt3.46185858  3.60066659 12.44963917  1 1 1
Pt2.07592929  1.20016667 12.44963917  1 1 1
Pt0.6900  3.60066659 12.44963917  1 1 1
Pt3.46185858  0.4000 10.18642611  1 1 1
Pt4.84778787  2.80049996 10.18642611  1 1 1
Pt0.6900  0.4000 10.18642611  1 1 1
Pt2.07592929  2.80049996 10.18642611  1 1 1
Pt3.46185858  2.0000  7.92321305  1 1 1
Pt4.84778787  4.40083326  7.92321305  1 1 1
Pt0.6900  2.0000  7.92321305  1 1 1
Pt2.07592929  4.40083326  7.92321305  1 1 1
Pt4.84778787  1.20016667  5.6600  1 1 1
Pt3.46185858  3.60066659  5.6600  1 1 1
Pt2.07592929  1.20016667  5.6600  1 1 1
Pt0.6900  3.60066659  5.6600  1 1 1
Pt3.46185858  0.4000  3.39678694  0 0 0
Pt4.84778787  2.80049996  3.39678694  0 0 0
Pt0.6900  0.4000  3.39678694  0 0 0
Pt2.07592929  2.80049996  3.39678694  0 0 0
Pt3.46185858  2.0000  1.13357388  0 0 0
Pt4.84778787  4.40083326  1.13357388  0 0 0
Pt0.6900  2.0000  1.13357388  0 0 0
Pt2.07592929  4.40083326  1.13357388  0 0 0

K_POINTS {automatic}
3 3 1 0 0 0
CELL_PARAMETERS {angstrom}
5.5437171600 0.00 0.00
0.00 4.800000 0.00
0.00 0.0025.5792783300


With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.
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Re: [QE-users] cholesky Error

[Laurens Siemons]

If your sure there's nothing wrong with your structure or your input 
parameters, then you can try to  add 'nd 1' to your script when you submit it 
like:

pw.x -nd 1 -inp name.rx.in > name.rx.out

This worked for me.
 Laurens Siemons

Van: users  namens Amin Mirzai 

Verzonden: maandag 9 april 2018 12:49
Aan: Quantum Espresso users Forum
Onderwerp: Re: [QE-users] cholesky Error


Thanks for the hint, I understand this topic has already been discussed. 
However, after doing all possible variations I still get the same error.

Anyhow, I believe there is not any explicit answer to this issue.


Regards,

Amin



From: users  on behalf of Lorenzo 
Paulatto 
Sent: Monday, April 9, 2018 10:00:13 AM
To: users@lists.quantum-espresso.org
Subject: Re: [QE-users] cholesky Error

On 09/04/18 09:57, Amin Mirzai wrote:
>   %%
>   Error in routine  cdiaghg (251):
>problems computing cholesky
>   %
>
This is one of the most regularly asked questions. This error typically
comes from bad geometry (i.e. ions core regions overlapping), bad
pseudopotentials (should not happen with anything from usual libraries)
or problematic input parameters with advanced features (i.e. lda+U, exx,...)

kind regards


--
Lorenzo Paulatto - Paris
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