[QE-users] (no subject)

[fatemeh mahmudi]

​Hello, I used the following commands to install Quantum Espresso on Debian 9. 
Is it correct?









apt-get update
apt-get upgrade
apt-get install gfortran
apt-get install mpich 
apt-get install quantum-espresso
please help me.
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[QE-users] (no subject)

[Pooja Vyas]

Dear users,

Following is my scf input for spin polarised D03 (Fm-3m) structure of V3Al.


  calculation = 'scf'
  prefix = 'v3al'
  outdir = './'
  pseudo_dir = './'
  tprnfor = .true.
  tstress = .true.
  etot_conv_thr =   4.00d-05
  forc_conv_thr =   1.00d-04
  verbosity = 'high'
/


  ibrav = 2
  celldm(1) = 11.512210722
  space_group = 225
  nat = 4
  ntyp = 4
  ecutwfc = 60
  ecutrho = 400
  occupations = 'smearing'
  smearing = 'cold'
  degauss = 0.005
  nspin = 2
  starting_magnetization(1)=1
  starting_magnetization(2)=-1
/


  conv_thr =   8.00d-10
  mixing_beta =   4.00d-01
/

ATOMIC_SPECIES
Al 26.9815 Al.pbe-nl-rrkjus_psl.1.0.0.UPF
V1 50.9415 V.pbe-spnl-rrkjus_psl.1.0.0.UPF
V2 50.9415 V.pbe-spnl-rrkjus_psl.1.0.0.UPF
V3 50.9415 V.pbe-spnl-rrkjus_psl.1.0.0.UPF

ATOMIC_POSITIONS {crystal_sg}
Al 4a
V1 4b
V2 8c
V3 0.25 0.25 0.75

KPOINTS automatic
  20 20 20 0 0 0

-


The output shows the error:

 Error in routine check_atoms (1):
 atoms #   3 and #   6 overlap!
 %%

 stopping ...





What is causing the issue and what should be changed in the input file?
Any kind of help is appreciated.



*Pooja,*
*Research Scholar,*
*Department of Physics,*
*MKBU,*
*Bhavnagar,*
*Gujarat.*
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Re: [QE-users] (no subject)

[Giovanni Cantele]

Dear Nirmal,

there can be several reasons why you find such a (possibly strange) behaviour. 
I give you two possible reasons, that I can easily explain.
One is that one of the two calculations (or both) is (are) wrong, but this 
point might be better assessed if you provide the inputs of both calculation. 
The second is that the two calculations are NOT carried out within the same 
framework. The point is that in plane-waves calculations the total energy is 
meaningless. It is enough that you change pseudopotentials, and the total 
energy might change by many Ry! Again, the inputs could be helpful in 
understanding if this is the case.
Much better, to compare two different calculations, are the energy differences. 
For example, in you MD simulation, you could have an initial and a final 
geometry, and you can compute the energy difference between the two.
You could then input both geometries in a scf calculation, and compute again 
their energy difference.
The two differences, should at least look similar, otherwise you can conclude 
that something wrong is affecting your results.

Giovanni

> On 23 Feb 2022, at 15:55, Nirmal Barman  wrote:
> 
> Dear Quantum Espresso Users and Developers,
> I have calculated scf energy for a graphene sheet and obtained the value 
> -205.39676576 Ry. But this scf energy is not matching or close to the energy 
> obtained at different steps of MD simulation. There is a significant 
> deviation in magnitude as well as energy is positive in case of MD 
> simulation. Could you please tell me the reason? Ideally this scf energy 
> should mimic the MD simulated result.
> 
> Thanking you
> Best regards 
> Nirmal
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[QE-users] (no subject)

[Nirmal Barman]

Dear Quantum Espresso Users and Developers,
I have calculated scf energy for a graphene sheet and obtained the
value -205.39676576 Ry. But this scf energy is not matching or close to the
energy obtained at different steps of MD simulation. There is a significant
deviation in magnitude as well as energy is positive in case of MD
simulation. Could you please tell me the reason? Ideally this scf energy
should mimic the MD simulated result.

Thanking you
Best regards
Nirmal
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[QE-users] (no subject)

[shubham kumar]

Dear sir
I want to post question. Help me related to this.
With Regards
Shubham
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[QE-users] (no subject)

[mohamed maymoun]

Dear users,
I calculate the vacuum energy with the average electrostatic potential
using pwscf, pp.x and average.x.
I wanted to calculate the band edge position with respect to vacuum
Any suggestions on what I do ?

*Best regards,*

*mohammad maymoun*


*PhD Student*
*Laboratoire des sciences des Matériaux, des Milieux et de la Modélisation
(LS3M)*

*Faculté Polydisciplinaire de Khouribga*

*Université Sultan Moulay Slimane*
*Béni Mellal , Maroc*
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[QE-users] (no subject)

[Nirmal Barman]

Dear Sir/mam
I would like to use the quantum espresso package for calculating the NBO
charge for graphene. Can somebody kindly guide me in this regard?
I have optimized the graphene structure and I have also done the scf
calculation, but i don't know how to calculate NBO charge by quantum
espresso? Please help me in this regard.
Thank you in advance

Regards
Nirmal Barman
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[QE-users] (no subject)

[Nirmal Barman]

Dear Sir/mam
I would like to use the quantum espresso package for calculating the NBO
charge for graphene. Can somebody kindly guide me in this regard?
I have optimized the graphene structure and I have also done the scf
calculation, but i don't know how to calculate NBO charge by quantum
espresso? Please help me in this regard.

Thank you in advance

Regards
Nirmal Barman
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[QE-users] (no subject)

[Guangyao Gao]

Dear QE community,


I have difficulty when calculating the band structure for Co3O4. I used the
conventional unit cell and optimized the structure. I performed a band
structure calculation and I got a small bandgap (about 0.6 eV). This makes
sense because Co3O4 is a semi-conductor. Then I performed a band structure
calculation with a Hubbard correction and expecting a bigger bandgap.
However, the band structure diagram looks very strange. The band was gone,
which means the valence band and conduction band are overlapping with each
other. I was expecting the band will be bigger because of the Hubbard
correction and I was surprised because I got the opposite result. Then I
tried to increase the Hubbard value by about 1 eV, the result stays the
same: no gaps. and the diagram for both Hubbard correction calculations
looks very similar.


As I mentioned, I really think the bandgap will be bigger with the Hubbard
correction, I believe there is something wrong with my calculation, but I
just don’t understand where I got wrong and I am not even sure why
the hubbard value is not acting on the metal. How can I explain this
phenomenon? Does anyone ever have this similar issue? Any insights about
how can I possibly figure this out?


Here is the main part of my input file.


Thank you so much!




calculation   = 'scf'

restart_mode  = 'from_scratch'

prefix= ‘$’

pseudo_dir= '$$'

outdir= '$$$'

nstep = 200

max_seconds   = 324000

wf_collect=.FALSE.

/



ibrav=1, celldm(1)=15.1884, nat=56, ntyp=2,

ecutwfc=300.0,ecutrho=1200.0,

occupations = 'smearing',degauss=0.010d0

smearing = 'mp'

nspin = 2

starting_magnetization(1)= 0.1

lda_plus_u=.TRUE.

Hubbard_U(1)=5.9

/



conv_thr=1.0d-6, electron_maxstep=1000,

mixing_mode='plain', mixing_beta=0.1,diagonalization='cg'

/

$ions

ion_dynamics='bfgs'

/



cell_dynamics='bfgs'

/

ATOMIC_SPECIES

  Co  58.933  Co_pbe_v1.2.uspp.F.UPF

  O   15.999  O_pbe_v1.2.uspp.F.UPF

  ATOMIC_POSITIONS crystal

Co0.2409920.2409920.240992

***

***

***

O 0.11470283660.38529693340.1147028366


K_POINTS Automatic

4 4 4 0 0 0


Sincerely,


Yao
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[QE-users] (no subject)

[kh_f_69 via users]

Hi
I have a problem making Supercell for Quantum Espresso. I use Burai software. I 
use CFFs available from two sites 
1-https://materialsproject.org/materials/mp-2/ 
(https://materialsproject.org/materials/mp-2/) 
2-http://rruff.geo.arizona.edu/AMS/minerals/Palladium 
(http://rruff.geo.arizona.edu/AMS/minerals/Palladium). There are 4 formats 
1-computed 2-conventional-3primitive-4-symmetrized for the site 
https://materialsproject.org/materials/mp-2/ 
(https://materialsproject.org/materials/mp-2/). When I made Supercell for iron, 
I realized that if you use any Which of the following formats did the number of 
atoms in Supercell differ from, while copper did not, and all formats gave me a 
Supercell with the same number of atoms?
In order to be more confident, I also tried Palladium, which also had the same 
problem. My question is, which site do you recommend, and also if the second 
site gives me the correct cifs format?
I am a beginner in Quantum Espresso software training. Thank you for your answer
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[QE-users] (no subject)

[kh_f_69 via users]

Hi
I have a problem making Supercell for Quantum Espresso. I use Burai software. I 
use CFFs available from two sites 
1-https://materialsproject.org/materials/mp-2/ 
(https://materialsproject.org/materials/mp-2/) 
2-http://rruff.geo.arizona.edu/AMS/minerals/Palladium 
(http://rruff.geo.arizona.edu/AMS/minerals/Palladium). There are 4 formats 
1-computed 2-conventional-3primitive-4-symmetrized for the site 
https://materialsproject.org/materials/mp-2/ 
(https://materialsproject.org/materials/mp-2/). When I made Supercell for iron, 
I realized that if you use any Which of the following formats did the number of 
atoms in Supercell differ from, while copper did not, and all formats gave me a 
Supercell with the same number of atoms?
In order to be more confident, I also tried Palladium, which also had the same 
problem. My question is, which site do you recommend, and also if the second 
site gives me the correct Sur Sol format?
I am a beginner in Quantum Espresso software training. Thank you for your answer
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Re: [QE-users] (no subject)

[Giuseppe Mattioli]

Dear Mayank Dotiyal
AFAIK epsilon.x works only with norm-conserving pseudopotentials.
HTH
Giuseppe

Quoting Mayank Dotiyal :


Dear QE users,

I am a new user of QE and I have been trying to calculate the dielectric
function of Silicon using the *epsilon.x. *I am using PAW type
pseudopotential and PBE functional.
I ran an SCF and an NSCF calculation with nosym =.true., and noinv =.true.,
and then using the outdirectory of NSCF calculation, I tried running the
epsilon.x, but I am getting an error (listed below).

The *input file *for epsilon.x is:

outdir = './scratch'
prefix = 'Si'
calculation = 'eps'
/
_grid
smeartype = 'gauss'
intersmear = 0.136d0
intrasmear = 0.0d0
wmax = 15.0d0
wmin = 0.0d0
nw = 600
shift = 0.0d0
/

But I am getting the following error after running the epsilon.x:

*Error:*
%%%
 Error in routine grid_build (1):
 USPP are not implemented
 %%%

I would be grateful to you if you could help me understand and solve this
issue.

Best regards,
Mayank Dotiyal
PhD Research Scholar
Materials engineering
IIT Gandhinagar
--
*Regards,*
*MD*




GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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[QE-users] (no subject)

[Mayank Dotiyal]

Dear QE users,

I am a new user of QE and I have been trying to calculate the dielectric
function of Silicon using the *epsilon.x. *I am using PAW type
pseudopotential and PBE functional.
I ran an SCF and an NSCF calculation with nosym =.true., and noinv =.true.,
and then using the outdirectory of NSCF calculation, I tried running the
epsilon.x, but I am getting an error (listed below).

The *input file *for epsilon.x is:

outdir = './scratch'
prefix = 'Si'
calculation = 'eps'
/
_grid
smeartype = 'gauss'
intersmear = 0.136d0
intrasmear = 0.0d0
wmax = 15.0d0
wmin = 0.0d0
nw = 600
shift = 0.0d0
/

But I am getting the following error after running the epsilon.x:

*Error:*
%%%
 Error in routine grid_build (1):
 USPP are not implemented
 %%%

I would be grateful to you if you could help me understand and solve this
issue.

Best regards,
Mayank Dotiyal
PhD Research Scholar
Materials engineering
IIT Gandhinagar
-- 
*Regards,*
*MD*
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[QE-users] (no subject)

[Lenz Fiedler]

Hi users,

I am experiencing a problem with pp.x. I want to calculate the LDOS for a
16 Fe atom supercell using a 560 value energy grid and the 3D grid given by
the DFT calculation (100x100x100 grid points). I have performed the DFT
calculation by first doing a SCF calculation (8x8x8 k-points) and then a
non-SCF calculation (14x14x14 k-points) successfully. Now I am trying to
do:

mpirun -np 160 pp.x -in Fe.pp.ldos.in

but the calculation takes way longer than I anticipated. The entire DFT
calculation took less than a day, while for the LDOS, after about 12 hours,
only 20 tmp files had been written. Am I doing something wrong? Or is this
expected? At this rate, calculating the LDOS would take days, which is why
I am assuming I am doing something wrong.
Please find my output and input files here:

https://drive.google.com/drive/folders/1R-m5jlw1bcNxe3nBXjc4dms-IoMMp4Ir?usp=sharing
(the pp.out file is from a run where I investigated if a lower number of
CPUs helps, but that was slower, as expected.)

Kind regards
Lenz

PhD Student (HZDR / CASUS)
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[QE-users] (no subject)

[Mainak Ghosh]

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Re: [QE-users] (no subject) (Yang Liu)

[liuyang]

Dear Peshal Karki


I've run into similar situation when I did nscf calculation weeks ago. I also 
tried to play with ecutwfc, ecutrho etc, but made no differences. I see 
somewhere that diago_david_ndim in ELECTRONS card determines how many planes to 
use in diagonalization of the central equation system. Default value is 2. Then 
I tried to increase it to 4, 6, 8... and I found that warning getting less and 
less. With diago_david_ndim 12, all warnings disappeared. I thought the warning 
may be due to some numeric issues during the solution processes.  You can try 
it.


Regards


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Re: [QE-users] [External Email] (no subject)

[Peshal Karki]

Hello Hari,
Thank you for your suggestions. I tried all those options but did not help.
If it does not cause a problem , I will try working on it.
Thank you.


On Thu, Nov 12, 2020 at 4:15 PM Hari Paudyal 
wrote:

> Hi Peshal,
>
> You can play with the following four parameters; cut off (ecutwfc and
> hence ecutrho),  conv_thr,  k mesh, and mixing_beta. Usually, I ignore
> this warning and should not cause a problem if it is not present in the
> last step of the scf calculation.
>
> Best,
> Hari Paudyal
>
> On Thu, Nov 12, 2020 at 3:28 PM Peshal Karki 
> wrote:
>
>> Hello,
>> I was doing an nscf calculation after getting  a smooth output from scf
>> calculation of cubic CsPbI3 structure. But I encountered an error in the
>> output file of nscf calculation as below.
>>
>>  Error in routine c_bands (1):
>>  too many bands are not converged
>>
>> Then I tried increasing ecutwfc value and decreasing conv_thr but it did
>> not help. Then I changed the diagonalization from 'david' to 'cg'. Though
>> it finished the nscf calculation and showed the Fermi energy but still many
>> lines in output saying
>>
>>  c_bands:  2 eigenvalues not converged
>>  c_bands:  3 eigenvalues not converged
>>  c_bands:  3 eigenvalues not converged
>>  c_bands:  2 eigenvalues not converged
>>  c_bands:  2 eigenvalues not converged
>>  c_bands:  2 eigenvalues not converged
>>  c_bands:  2 eigenvalues not converged
>>  c_bands:  2 eigenvalues not converged
>>  c_bands:  4 eigenvalues not converged
>>  c_bands:  2 eigenvalues not converged
>>
>> Please help me. What should I do ?
>> I have attached the nscf input file with cg diagonalisation.
>>
>> Thank you.
>>
>> With regards
>> Peshal Karki
>>
>>
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Re: [QE-users] [External Email] (no subject)

[Hari Paudyal]

Hi Peshal,

You can play with the following four parameters; cut off (ecutwfc and hence
ecutrho),  conv_thr,  k mesh, and mixing_beta. Usually, I ignore this
warning and should not cause a problem if it is not present in the last
step of the scf calculation.

Best,
Hari Paudyal

On Thu, Nov 12, 2020 at 3:28 PM Peshal Karki  wrote:

> Hello,
> I was doing an nscf calculation after getting  a smooth output from scf
> calculation of cubic CsPbI3 structure. But I encountered an error in the
> output file of nscf calculation as below.
>
>  Error in routine c_bands (1):
>  too many bands are not converged
>
> Then I tried increasing ecutwfc value and decreasing conv_thr but it did
> not help. Then I changed the diagonalization from 'david' to 'cg'. Though
> it finished the nscf calculation and showed the Fermi energy but still many
> lines in output saying
>
>  c_bands:  2 eigenvalues not converged
>  c_bands:  3 eigenvalues not converged
>  c_bands:  3 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  4 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>
> Please help me. What should I do ?
> I have attached the nscf input file with cg diagonalisation.
>
> Thank you.
>
> With regards
> Peshal Karki
>
>
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[QE-users] (no subject)

[Peshal Karki]

Hello,
I was doing an nscf calculation after getting  a smooth output from scf
calculation of cubic CsPbI3 structure. But I encountered an error in the
output file of nscf calculation as below.

 Error in routine c_bands (1):
 too many bands are not converged

Then I tried increasing ecutwfc value and decreasing conv_thr but it did
not help. Then I changed the diagonalization from 'david' to 'cg'. Though
it finished the nscf calculation and showed the Fermi energy but still many
lines in output saying

 c_bands:  2 eigenvalues not converged
 c_bands:  3 eigenvalues not converged
 c_bands:  3 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  4 eigenvalues not converged
 c_bands:  2 eigenvalues not converged

Please help me. What should I do ?
I have attached the nscf input file with cg diagonalisation.

Thank you.

With regards
Peshal Karki


nscf.in
Description: Binary data
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Re: [QE-users] Subject: RE: Slab doesn't converge

[Omer Mutasim]

Dear Moraga Your feedback is very helpful . I have another questions :Is it 
fine to use the default value (1xe-03) for force-conv-thr ? If i use this 
default value , what is the suitable value conv-thr ? I’m familiar with this 
asymmetric slab, so How to use the dipole background You stated?In order to 
study various monolayer coverages , i have yo place multiple S atoms on the 
surface, ao is there any criteria for placing these atoms on asymmetric slab ? 
How far they should be from each other to avoid lateral interactions between 
Adsorbed atoms ? 
Sulfur (S⁻²) adsorption, should i set the net charge of the system to -1 ? If i 
set it to 0 (default) , does that mean Sulfur will be bonded to two Ni atoms ? 
The Ni2P is paramagnetic, so I didn’t consider spin polarized calculation, is 
this correct ? 


Sent from Yahoo Mail for iPhone


On Sunday, August 16, 2020, 11:19 PM, Lucas Nicolás Lodeiro Moraga 
 wrote:

Hi!
I am not an expert in adsorption, but I thought your input has some 
deficiencies.
Firstly, forc_conv_thr is set for the maximum force for each relax-frame, the 
value that you use is too low, compared with your conv_thr (which define how 
accurate are your scf forces). Also, for relax, stress is not necessary and you 
could save some time neglecting it (I assume your slab is converged after for 
vc-relax).
About the electronic parameters... 25 Ry for ecutwfc seems to me too low for 
USPPs. The fermi-dirac smearing is slower than others and the results do not 
change appreciably. Another thing is the vdW approach, you are using a 
vdW-functional plus the grimme's vdW-corrections... this does not seem correct. 
If you use a vdW-functional you are accounting the vdW interactions by the 
non-local correlation term, and the grimme's empirical correction is not 
needed, and vice versa, if you use the grimme's empirical corrections, you have 
to use a non vdw-functional as LDA,GGA or hybrid.
A value of 0.7 for mixing_beta could be problematic for bad behaved systems. 
When I have problems on the first scf, I change this value to lower values like 
0.5 or 0.3 to prevent long jumps in the scf solutions.
Finally, something about the system-structure is weird to me. Your distances 
between S-P and S-Ni are too short, ~1.5 A. Those distances are too short to 
heavier atoms, and seems to me a bad guess for the first geometry (but I 
remember, I am not an expert in adsorptions, you know more about the 
system).Moreover, as you are putting the adsorbate only on one face of the 
system, you have a net dipole in the system. If you print the electrostatic 
potential profile along z, on vacuum space you will have a slope on the 
profile. It can be fixed, using a dipole background or using symmetrical 
adsorbates and surfaces on both sides of the slab.

Also, you are simulating the adsorption of neutral atoms (in principle) of S. 
If you want to simulate Sulfur (S⁻²) adsorption, your system has to be a total 
negative charge, this requires some 2-D method to neglect the interactions 
between both sides of slab.

Regards

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Re: [QE-users] Subject: RE: Slab doesn't converge

[Omer Mutasim]

Dear Moraga Your feedback is very helpful . I have another questions :Is it 
fine to use the default value (1xe-03) for force-conv-thr ? If i use this 
default value , what is the suitable value conv-thr ? I’m familiar with this 
asymmetric slab, so How to use the dipole background You stated?In order to 
study various monolayer coverages , i have yo place multiple S atoms on the 
surface, ao is there any criteria for placing these atoms on asymmetric slab ? 
How far they should be from each other to avoid lateral interactions between 
Adsorbed atoms ? 
Sulfur (S⁻²) adsorption, should i set the net charge of the system to -1 ? If i 
set it to 0 (default) , does that mean Sulfur will be bonded to two Ni atoms ? 
The Ni2P is paramagnetic, so I didn’t consider spin polarized calculation, is 
this correct ? 


Sent from Yahoo Mail for iPhone


On Sunday, August 16, 2020, 11:19 PM, Lucas Nicolás Lodeiro Moraga 
 wrote:

Hi!
I am not an expert in adsorption, but I thought your input has some 
deficiencies.
Firstly, forc_conv_thr is set for the maximum force for each relax-frame, the 
value that you use is too low, compared with your conv_thr (which define how 
accurate are your scf forces). Also, for relax, stress is not necessary and you 
could save some time neglecting it (I assume your slab is converged after for 
vc-relax).
About the electronic parameters... 25 Ry for ecutwfc seems to me too low for 
USPPs. The fermi-dirac smearing is slower than others and the results do not 
change appreciably. Another thing is the vdW approach, you are using a 
vdW-functional plus the grimme's vdW-corrections... this does not seem correct. 
If you use a vdW-functional you are accounting the vdW interactions by the 
non-local correlation term, and the grimme's empirical correction is not 
needed, and vice versa, if you use the grimme's empirical corrections, you have 
to use a non vdw-functional as LDA,GGA or hybrid.
A value of 0.7 for mixing_beta could be problematic for bad behaved systems. 
When I have problems on the first scf, I change this value to lower values like 
0.5 or 0.3 to prevent long jumps in the scf solutions.
Finally, something about the system-structure is weird to me. Your distances 
between S-P and S-Ni are too short, ~1.5 A. Those distances are too short to 
heavier atoms, and seems to me a bad guess for the first geometry (but I 
remember, I am not an expert in adsorptions, you know more about the 
system).Moreover, as you are putting the adsorbate only on one face of the 
system, you have a net dipole in the system. If you print the electrostatic 
potential profile along z, on vacuum space you will have a slope on the 
profile. It can be fixed, using a dipole background or using symmetrical 
adsorbates and surfaces on both sides of the slab.

Also, you are simulating the adsorption of neutral atoms (in principle) of S. 
If you want to simulate Sulfur (S⁻²) adsorption, your system has to be a total 
negative charge, this requires some 2-D method to neglect the interactions 
between both sides of slab.

Regards

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[QE-users] Subject: RE: Slab doesn't converge

[Lucas Nicolás Lodeiro Moraga]

Hi!

I am not an expert in adsorption, but I thought your input has some
deficiencies.

Firstly, forc_conv_thr is set for the maximum force for each relax-frame,
the value that you use is too low, compared with your conv_thr (which
define how accurate are your scf forces). Also, for relax, stress is not
necessary and you could save some time neglecting it (I assume your slab is
converged after for vc-relax).

About the electronic parameters... 25 Ry for ecutwfc seems to me too low
for USPPs. The fermi-dirac smearing is slower than others and the results
do not change appreciably. Another thing is the vdW approach, you are using
a vdW-functional plus the grimme's vdW-corrections... this does not seem
correct. If you use a vdW-functional you are accounting the vdW
interactions by the non-local correlation term, and the grimme's empirical
correction is not needed, and vice versa, if you use the grimme's empirical
corrections, you have to use a non vdw-functional as LDA,GGA or hybrid.

A value of 0.7 for mixing_beta could be problematic for bad behaved
systems. When I have problems on the first scf, I change this value to
lower values like 0.5 or 0.3 to prevent long jumps in the scf solutions.

Finally, something about the system-structure is weird to me. Your
distances between S-P and S-Ni are too short, ~1.5 A. Those distances are
too short to heavier atoms, and seems to me a bad guess for the first
geometry (but I remember, I am not an expert in adsorptions, you know more
about the system).
Moreover, as you are putting the adsorbate only on one face of the system,
you have a net dipole in the system. If you print the electrostatic
potential profile along z, on vacuum space you will have a slope on the
profile. It can be fixed, using a dipole background or using symmetrical
adsorbates and surfaces on both sides of the slab.

Also, you are simulating the adsorption of neutral atoms (in principle) of
S. If you want to simulate Sulfur (S⁻²) adsorption, your system has to be a
total negative charge, this requires some 2-D method to neglect the
interactions between both sides of slab.

Regards
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[QE-users] (no subject)

[Chemam faïçal]

Dear Users
im new in this QE, ill like know how to obtain a lattice parameters (a,b,c
and beta angle)  and atomic position  in monoclinic structure in file.out ,
after used a ibrav=-12 in "vc-relax" .
regards
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[QE-users] (no subject)

[Malathe Khalil]

Greetings:
How can I get the standard deviation of the total energy for my scf
calculations ? is it reported in the output file?


Thanks
Malathe
Khalifa Univeristy
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Re: [QE-users] (no subject)

[Baer, Bradly]

Malathe,

I usually use vc-relax, so I dont know if it is the same in the relaxation 
calculation you are using, but the last step of vc-relax is a scf calculation 
with the relaxed structure.  I just checked an old output file and you can 
check for this line in your relax output:

End of BFGS Geometry Optimization

 Final enthalpy =-395.6714252266 Ry
[...]

 A final scf calculation at the relaxed structure.
 The G-vectors are recalculated for the final unit cell
 Results may differ from those at the preceding step.

[...]

!total energy  =-395.66904355 Ry

The energies are slightly different.  If you are not satisfied with this energy 
you could of course perform a scf calculation on the relaxed structure and 
check that the energy is the same.

Good luck,
Brad

Bradly Baer
Graduate Research Assistant, Walker Lab
Interdisciplinary Materials Science
Vanderbilt University



From: users  on behalf of Malathe 
Khalil 
Sent: Sunday, May 17, 2020 11:43 AM
To: Quantum ESPRESSO users Forum 
Subject: Re: [QE-users] (no subject)

Dear Fabrizio
I want to calculate the adsorption energy of a molecule on a surface.
So I need the total energy of the clean slab.
Can I just take the total energy from relax calculations output or I have to 
run scf ?

Thanks
Malathe

On Sun, 17 May 2020, 6:04 pm Fabrizio Cossu, 
mailto:fabrizio.co...@apctp.org>> wrote:


On Sun, 17 May 2020 at 22:19, Malathe Khalil 
mailto:malathe.ze...@gmail.com>> wrote:
Dear QE users
What is the difference between the total energy generated by relax calculations 
and scf calculations?
A structural relaxation is a scf calculation. Perhaps you mean a fixed point 
scf calculation, i.e. without updating the positions.

When I do relax calculations do I need to do scf calculations also?
It depends on what you want to do. Do you want to compute some quantity 
self-consistently? AFAIK, some calculations require a different parameter set 
WRT the relaxation.

Thanks
Malathe

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Re: [QE-users] (no subject)

[Malathe Khalil]

Dear Fabrizio
I want to calculate the adsorption energy of a molecule on a surface.
So I need the total energy of the clean slab.
Can I just take the total energy from relax calculations output or I have
to run scf ?

Thanks
Malathe

On Sun, 17 May 2020, 6:04 pm Fabrizio Cossu, 
wrote:

>
>
> On Sun, 17 May 2020 at 22:19, Malathe Khalil 
> wrote:
>
>> Dear QE users
>> What is the difference between the total energy generated by relax
>> calculations and scf calculations?
>>
> A structural relaxation is a scf calculation. Perhaps you mean a fixed
> point scf calculation, i.e. without updating the positions.
>
>>
>> When I do relax calculations do I need to do scf calculations also?
>>
> It depends on what you want to do. Do you want to compute some quantity
> self-consistently? AFAIK, some calculations require a different parameter
> set WRT the relaxation.
>
>>
>> Thanks
>> Malathe
>>
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>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
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Re: [QE-users] (no subject)

[Fabrizio Cossu]

On Sun, 17 May 2020 at 22:19, Malathe Khalil 
wrote:

> Dear QE users
> What is the difference between the total energy generated by relax
> calculations and scf calculations?
>
A structural relaxation is a scf calculation. Perhaps you mean a fixed
point scf calculation, i.e. without updating the positions.

>
> When I do relax calculations do I need to do scf calculations also?
>
It depends on what you want to do. Do you want to compute some quantity
self-consistently? AFAIK, some calculations require a different parameter
set WRT the relaxation.

>
> Thanks
> Malathe
>
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[QE-users] (no subject)

[Malathe Khalil]

Dear QE users
What is the difference between the total energy generated by relax
calculations and scf calculations?

When I do relax calculations do I need to do scf calculations also?

Thanks
Malathe
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[QE-users] (no subject)

[Malathe Khalil]

Greetings
Does anyone know how to excute vdw-BEEF function?

Thanks
Malathe
Khalifa University
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[QE-users] (no subject)

[Malathe Khalil]

Greetings
I received the error below
[48:c040.cm.cluster] unexpected disconnect completion event from
[26:c050.cm.cluster]
INTERNAL ERROR: invalid error code  (Ring Index out of range) in
MPIR_Alltoall_intra:204
Fatal error in PMPI_Alltoall: Other MPI error, error stack:
PMPI_Alltoall(974)..: MPI_Alltoall(sbuf=0x4537fd0, scount=40,
MPI_DOUBLE_COMPLEX, rbuf=0x23f7270, rcount=40, MPI_DOUBLE_COMPLEX,
comm=0xc400) failed
MPIR_Alltoall_intra(204): fail failed



How can I solve it
I am attaching the input file
Thanks
Malathe


inp2.in
Description: Binary data
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[QE-users] (no subject)

[Malathe Khalil]

Greetings :
I am trying to use this function "BEEF-vdW"
I am following the link below for instructions
https://github.com/vossjo/ase-espresso/wiki

As per my understanding ase-espresso will generate the input file with the
custom espsite.py and as I know adding input_dft="BEEF-vdW" to the input
file will not help.
I need to know how to generate the input file with espsite.py or with
cubecutperiodic / pwlog2trajectory ?"

Thanks
Malathe
Khalifa University
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Re: [QE-users] (no subject)

[Fabrizio Cossu]

Dear Malathe,
isn't CoP orthorhombic? In that case, I'd use ibrav=8, specify celldm(1-3)
then place the atoms as
Co 0 0 0
P .5 .5 .5


On Sun, 10 May 2020 at 23:42, Malathe Khalil 
wrote:

> Greetings
> I am trying to optimize CoP (B31) orthorhombic unit cell with the
> following specifications :
> https://materialsproject.org/materials/mp-22270/
> Hermann Mauguin Pnma [62]
> Point Group
> mmm
> Hall
> -P 2ac 2n
> I checked this link but I didn't find the suitable ibrav option
> https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm199
> Ibrav =0 broke the symmetry of the lattice
>
> Please advise
>
> Thanks
> Malathe
> MSc in Materials science and engineering
> Khalifa University
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[QE-users] (no subject)

[Malathe Khalil]

Greetings
I am trying to optimize CoP (B31) orthorhombic unit cell with the following
specifications :
https://materialsproject.org/materials/mp-22270/
Hermann Mauguin Pnma [62]
Point Group
mmm
Hall
-P 2ac 2n
I checked this link but I didn't find the suitable ibrav option
https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm199
Ibrav =0 broke the symmetry of the lattice

Please advise

Thanks
Malathe
MSc in Materials science and engineering
Khalifa University
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Re: [QE-users] (no subject)

[Paolo Giannozzi]

For versions previous to 6.5: run the appropriate executable
generate_*_kernel_table.x, move the file it produces where pseudopotentials
are
For version 6.5, there is no need to do anything

Paolo

On Thu, Jan 16, 2020 at 2:54 AM 角野 樹 
wrote:

> Can you tell me the steps to create the interaction kernel file needed to
> apply vdW-DF?
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-- 
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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[QE-users] (no subject)

[角野 樹]

Can you tell me the steps to create the interaction kernel file needed to apply 
vdW-DF?
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[QE-users] (no subject)

[Christian Crisostomo]

-- 
Regards,

Christian P. Crisostomo, PhD
Associate Professor
​Department of Physical Sciences
University of the Philippines Baguio
Contact info:
crisostomo96...@gmail.com
+639367389400
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[QE-users] (no subject)

[Pooja Vyas]

I want to calculate energy due to vacancy. I opened the following input
file in x-crysden.


calculation = 'scf',
prefix = '9.1334'
tstress= .true.
tprnfor= .true.
outdir = '/home/user/cao.oct/'
pseudo_dir = '/home/user/cao.oct/pseudo/'
/

ibrav = 2,
celldm(1) = 9.1334,
nat = 2,
ntyp = 2,
ecutwfc = 100,
/

mixing_beta = 0.7
/

ATOMIC_SPECIES

Ca 40.078 Ca.pbe-nsp-van.UPF
O 15.999 O.pbe-van_ak.UPF

ATOMIC_POSITIONS
Ca 0.0 0.0 0.0
O 0.50 0.50 0.50
K_POINTS (automatic)
11 11 11 1 1 1

when I opened this structure in x-crysden, it showed me around 27 atoms.
Now I planned to create one vacancy by removing an atom and included rest
all the atomic position in my input file and gave a run. But at that time I
faced an error.

Following are the atomic positions which I read from x-crysden
Ca 0.0 0.0 0.0
O 0.5 0.0 0.0
O 0.0 0.5 0.0
O 0.0 0.0 0.5
Ca 0.5 0.5 0.0
Ca 0.5 0.0 0.5
Ca 0.0 0.5 0.5
O 0.5 0.5 0.5
Ca 0.5 0.5 1.0
Ca 0.0 0.0 1.0
O 0.0 0.5 1.0
O 0.5 0.0 1.0
Ca 0.0 1.0 0.0
Ca 0.5 1.0 0.5
O 0.0 1.0 0.5
O 0.5 1.0 0.0
Ca 0.0 1.0 1.0
O 0.5 1.0 1.0
Ca 1.0 0.0 0.0
Ca 1.0 0.5 0.5
O 1.0 0.0 0.5
O 1.0 0.5 0.0
Ca 1.0 0.0 1.0
O 1.0 0.5 1.0
Ca 1.0 1.0 0.0
O 1.0 1.0 0.5
Ca 1.0 1.0 1.0

Out of all these positions only
Ca 0.0 0.0 0.0
O 0.5 0.5 0.5
are needed. rest are automatically ignored by quantum espresso. Then how do
I create vacancy?
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[QE-users] (no subject)

[ANKITA SINGH Res. Scholar, School of Mat. Sci. & Tech. IIT (BHU)]

I am performing CPMD in quantum espresso . But to see the output of my
result, some of the tabs are not active like "Energy plot(evp), animation
(pos),.". So please direct me for making these tabs active???
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[QE-users] (no subject)

[Fabrizio Cossu]

   Dear QE users,
I have massive problems with converging the phonon scf for a layered TMD
(bulk calculation).
Here are the last lines of the PHONON output

 **
  iter #  95 total cpu time :  3975.1 secs   av.it.:   8.3
  thresh= 4.694E-07 alpha_mix =  0.300 |ddv_scf|^2 =  6.601E-12

  iter #  96 total cpu time :  3987.5 secs   av.it.:   8.3
  thresh= 2.569E-07 alpha_mix =  0.300 |ddv_scf|^2 =  7.102E-12

  iter #  97 total cpu time :  3999.9 secs   av.it.:   9.1
  thresh= 2.665E-07 alpha_mix =  0.300 |ddv_scf|^2 =  2.096E-11

  iter #  98 total cpu time :  4011.2 secs   av.it.:   8.4
  thresh= 4.579E-07 alpha_mix =  0.300 |ddv_scf|^2 =  1.120E-12

  iter #  99 total cpu time :  4023.8 secs   av.it.:  10.8
  thresh= 1.058E-07 alpha_mix =  0.300 |ddv_scf|^2 =  8.827E-12

  iter # 100 total cpu time :  4035.6 secs   av.it.:   8.9
  thresh= 2.971E-07 alpha_mix =  0.300 |ddv_scf|^2 =  1.223E-11

 End of self-consistent calculation

 No convergence has been achieved
 **

The scf hits |ddv_scf|^2 =  7.292E-11 at iteration # 30.
Single layer calculations never had this problem.
The structure has been relaxed up to"forc_conv_thr =
2.0D-5".
This problem never comes out at Gamma, and trying coarser meshes usually
gives no problems with the convergence.
I attach the input and output of the PHONON for reference.
Any help will be highly appreciated.

Thank you in advance,
Fabrizio


-- 

*Fabrizio Cossupostdoctoral fellow at APCTP (Asia Pacific Center for
Theoretical Physics)*,

   |
  .. .. .. |  ..   ===
  ,| || |  |  ||   http://www.apctp.org/?JrgId=16
  `^ |' `' `' |'   ===
 ||


uc-elph.in
Description: Binary data


elph.out.gz
Description: application/gzip
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[QE-users] (no subject)

[Mauricio Rincón Bonilla]

Hi!
I'm relatively new to QE, but have been able to run small systems without
any problem so far. However, I'm having issues with all of the Lithium PPs
from the PS library. For some reason, the iotk routine is unable to
correctly read these PP, and always ends with the error message:

# ERROR IN: iotk_scan_begin (iotk_scan.f90:182)
# CVS Revision: 1.23
# FROM IOTK LIBRARY, VERSION 1.2.0
# CVS Revision: 1.23
# CVS Revision: 1.23
# UNRECOVERABLE ERROR (ierr=-1)
# Tag not found
# Tag not found
# Tag not found
# CVS Revision: 1.23
namel=PP_GIPAW_CORE_ORBITALS

This is for a simple vc-relax calculation for Li2O. I see the Oxygen PP is
read correctly, but when the Li PP is going to be read (regardless of which
one I choose), this error comes up. Here's a sample input file:


  calculation  = 'vc-relax'
  restart_mode = 'from_scratch'
  prefix   = 'Li2O'
  pseudo_dir   = '/home/espresso/pseudo'
  outdir   = '.'
  wf_collect   = .true.
  tprnfor  = .true.
  tstress  = .true.
/


  nat = 12
  ntyp = 2
  ibrav =0
  ecutwfc =  40
  ecutrho = 320
  occupations = 'smearing'
  smearing= 'gauss'
  degauss =   0.001
/

   Li  4.062306154.062306151.35410205

K_POINTS automatic
 3 3 3   0 0 0

  diagonalization  = 'david'
  electron_maxstep = 100
  conv_thr_init=   1.0e-3
  conv_thr =   1.0e-6
/


   ion_dynamics = 'bfgs' ,
/


   cell_dynamics = 'bfgs' ,
   press = 500.00
/

ATOMIC_SPECIES
O  15.9994  O.pbe-n-kjpaw_psl.1.0.0.UPF
Li  6.44Li.pbe-s-kjpaw_psl.1.0.0.UPF

CELL_PARAMETERS (Angstrom)
5.416408200.0.
0.5.416408200.
0.0.5.41640820


ATOMIC_POSITIONS (Angstrom)
   O   2.708204102.708204100.
   O   2.708204100.2.70820410
   O   0.2.708204102.70820410
   O   0.0.0.
   Li  4.062306151.354102054.06230615
   Li  1.354102051.354102054.06230615
   Li  1.354102054.062306151.35410205
   Li  4.062306154.062306154.06230615
   Li  4.062306151.354102051.35410205
   Li  1.354102051.354102051.35410205
   Li  1.354102054.062306154.06230615
   Li  4.062306154.062306151.35410205

K_POINTS automatic
 3 3 3   0 0 0

Thanks!!

Cheers,
Mauricio


-- 
Mauricio Rincon Bonilla
Postdoc Fellow
*BCAM - *Basque Center for Applied Mathematics
Alameda de Mazarredo, 14
E-48009 Bilbao, Basque Country - Spain
Tel. +34 946 567 842
mrin...@bcamath.org | www.bcamath.org/mrincon

*(**matematika mugaz bestalde)*
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Re: [QE-users] (no subject)

[Paolo Giannozzi]

On Mon, Apr 8, 2019 at 9:40 AM as gj  wrote:

>
> So i have a question : GWL treats only gamma point
>

yes

or it could done calculation for various kpoints ?
>

no, without major work on the code

Paolo
-- 
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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[QE-users] (no subject)

[as gj]

 Dear all QE users,
i am new user;
i would like to calculate InSb band structure by GW PBE. i tried it with
GWL and i have a result on gamma point only and i would all the band
structure.
So i have a question : GWL treats only gamma point or it could done
calculation for various kpoints ? If yes how it does ?

in another part,i am trying SternheimerGW application linked with QE.
currently, i work with QE6.2.0. And when i launch gw.x after scf
calculation (which runs and converges well)  from tutorial for Si, i have
the following error (in attached fil i put the gw.out):

 evaluate self energy for k = (  0.  0.  0. )

 Error in routine sigma.f90 (2):
 error opening ./tmp/_gw0/si.coul1
 stopping ...
i obtained the same for the second Li example and the another found in
examples folder.

I tried also on QE6.3 with the same Si tutorial abd i have the following
error which is different and i don't know why ?

 T E R N H E I M E R
http://www.sternheimergw.org/
   ### ###
  ###   ##  ###
#  #
  ### ##   ### #
##  #
   ###  ### #
## #
#  # #   #  #
#
   /// #  \\\ #  #   #  #
#
  ///  \\\#   # ## #
 ///### \\\   # # # ## #
(((  ### )))  # #  #   #  #   #
 \\\###  ###///##  #   #  #   #
  \\\######///  #  ## ## #
   \\\###  ###///#   ## ######
   ## ####  #


 Program SternheimerGW v.0.15 starts on  5Apr2019 at 10:52:17

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
 "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
  URL http://www.quantum-espresso.org;,
 in publications or presentations arising from this work. More details
at
 http://www.quantum-espresso.org/quote

 Serial version

 Please cite SternheimerGW as:
 M. Schlipf, H. Lambert, N. Zibouche, and F. Giustino,
SternheimerGW,
 paper in preparation, URL http://www.sternheimergw.org

 To increase the reproducibility of your results you can mention the
 git description of this version: unknown

 other relevant papers:
 H. Lambert and F. Giustino, Phys. Rev. B 88, 075117 (2013)
 F. Giustino, M. L. Cohen, and S. G. Louie, Phys. Rev. B 81, 115105
(201
0)

 Reading data from directory:
 ./tmp/si.save/

 IMPORTANT: XC functional enforced from input :
 Exchange-correlation  = PZ ( 1  1  0  0 0 0)
 Any further DFT definition will be discarded
 Please, verify this is what you really want


 G-vector sticks info
 
 sticks:   dense  smooth PW G-vecs:dense   smooth  PW
 Sum 235 235 85 2277 2277 531



 Coulomb Perturbations for ( 4, 4, 4,)  uniform grid of q-points
 (   8q-points):
   N xq(1) xq(2) xq(3)
   1   0.0   0.0   0.0
   2  -0.25000   0.25000  -0.25000
   3   0.5  -0.5   0.5
   4   0.0   0.5   0.0
   5   0.75000  -0.25000   0.75000
   6   0.5   0.0   0.5
   7   0.0  -1.0   0.0
   8  -0.5  -1.0   0.0

 %%
 Error in routine ggens (2):
 mismatch in number of G-vectors
 %%


someone can explain at what these errors are due to ?

thanks in advance for your answer,
Anne-Sophie
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[QE-users] (no subject)

[Suman sarkar]

Dear QE Users and developers,
I am trying to do Hubbard U correction for Gd atom according to an article
https://doi.org/10.1016/j.commatsci.2014.07.030  where Hubbard_U correction
is suggested for d as well as f orbitals of Gd.

The available tag for Quantum espresso is Hubbard_U(i), i=1,ntyp : Real. I
do not find any tag for specifying orbital also for U correction. Is it not
implemented in qe-6.4 yet ??
or If I do U correction for f orbital of Gd that will be sufficient and I
do not need to do correction for d orbital.
Please elaborate this correction to me.

Thank you,
Suman
IIT Madras
India
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Re: [QE-users] (no subject)

[Pietro Davide Delugas]

Dear Yasmin

in the output there are these lines

DEPRECATED: no units specified in ATOMIC_POSITIONS card

and
Warning: card K_POINTS(AUTOMATIC) ignored
Warning: card  12 12 12 0 0 0 ignored

which seem to be unrelated to your input
could you check please. It would be also useful to have a look to the 
output of the scf calculation to understand what happened.

Pietro

On 03/19/2019 10:50 AM, yasmin kani wrote:
when i am running band structure for InSb. i have error "error opening 
xml data file". i attached my input and output file



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[QE-users] (no subject)

[yasmin kani]

when i am running band structure for InSb. i have error "error opening xml
data file". i attached my input and output file


insb.band.in
Description: Binary data


insbbandout
Description: Binary data
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Re: [QE-users] (no subject)

[Paolo Giannozzi]

Try to run the code interactively, or on a single processor: this should
tell you something more on why the code crashes. Also try a smaller number
of k-points. Note that by default all Kohn-Sham orbitals are stored in
memory.

Paolo

On Mon, Feb 25, 2019 at 1:31 AM Bharat Thapa  wrote:

> Dear developers,
>
> I am running a scf calculation to test the cutoff convergence with respect
> to the total energy. My plan is then to test k points and lattice constant
> convergence test and then doing vc-relax. The system is Hf7O8N4. However,
> surprising, it stops after printing:
>
> k(  763) = (   0.4375000  -0.4375000  -0.3125000), wk =
> 0.0026042
> k(  764) = (  -0.4375000   0.000  -0.4375000), wk =   0.0026042
> k(  765) = (   0.4375000  -0.000  -0.4375000), wk =   0.0026042
> k(  766) = (   0.000  -0.4375000   0.4375000), wk =   0.0026042
> k(  767) = (   0.000   0.4375000   0.4375000), wk =   0.0026042
> k(  768) = (   0.4375000  -0.4375000  -0.4375000), wk =   0.0026042
>
>  Dense  grid:  1146249 G-vectors FFT dimensions: ( 144, 144, 135)
>
>  Smooth grid:   220527 G-vectors FFT dimensions: (  81,  81,  75)
>
>  Largest allocated arrays est. size (Mb) dimensions
> Kohn-Sham Wavefunctions 1.19 Mb ( 457,  170)
> NL pseudopotentials 1.55 Mb ( 457,  222)
> Each V/rho on FFT grid  0.95 Mb (   62208)
> Each G-vector array 0.14 Mb (   17913)
> G-vector shells 0.06 Mb (8140)
>  Largest temporary arrays est. size (Mb) dimensions
> Auxiliary wavefunctions 4.74 Mb ( 457,  680)
> Each subspace H/S matrix0.28 Mb ( 136,  136)
> Each  matrix  0.58 Mb ( 222,  170)
> Arrays for rho mixing   9.49 Mb (   62208,   10)
>
>  Initial potential from superposition of free atoms
>
>  starting charge  151.98640, renormalised to  152.0
>  Starting wfc are  118 randomized atomic wfcs +   52 random wfc
>
> 1763,6Bot
>
> I am not sure what happened and why it stopped without any error message.
> What should I do? I am running this parallel on 64 cores. I have never
> found such strange situation before and was able to solve it via googling
> but this time I am helpless.
>
> Please help me!
> *Bharat Thapa*
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-- 
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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[QE-users] (no subject)

[Bharat Thapa]

Dear developers,

I am running a scf calculation to test the cutoff convergence with respect
to the total energy. My plan is then to test k points and lattice constant
convergence test and then doing vc-relax. The system is Hf7O8N4. However,
surprising, it stops after printing:

k(  763) = (   0.4375000  -0.4375000  -0.3125000), wk =   0.0026042
k(  764) = (  -0.4375000   0.000  -0.4375000), wk =   0.0026042
k(  765) = (   0.4375000  -0.000  -0.4375000), wk =   0.0026042
k(  766) = (   0.000  -0.4375000   0.4375000), wk =   0.0026042
k(  767) = (   0.000   0.4375000   0.4375000), wk =   0.0026042
k(  768) = (   0.4375000  -0.4375000  -0.4375000), wk =   0.0026042

 Dense  grid:  1146249 G-vectors FFT dimensions: ( 144, 144, 135)

 Smooth grid:   220527 G-vectors FFT dimensions: (  81,  81,  75)

 Largest allocated arrays est. size (Mb) dimensions
Kohn-Sham Wavefunctions 1.19 Mb ( 457,  170)
NL pseudopotentials 1.55 Mb ( 457,  222)
Each V/rho on FFT grid  0.95 Mb (   62208)
Each G-vector array 0.14 Mb (   17913)
G-vector shells 0.06 Mb (8140)
 Largest temporary arrays est. size (Mb) dimensions
Auxiliary wavefunctions 4.74 Mb ( 457,  680)
Each subspace H/S matrix0.28 Mb ( 136,  136)
Each  matrix  0.58 Mb ( 222,  170)
Arrays for rho mixing   9.49 Mb (   62208,   10)

 Initial potential from superposition of free atoms

 starting charge  151.98640, renormalised to  152.0
 Starting wfc are  118 randomized atomic wfcs +   52 random wfc

1763,6Bot

I am not sure what happened and why it stopped without any error message.
What should I do? I am running this parallel on 64 cores. I have never
found such strange situation before and was able to solve it via googling
but this time I am helpless.

Please help me!
*Bharat Thapa*
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[QE-users] (no subject)

[Sabike Ghasemi]

thank you for reply, 
but when ocupation = smearing then i face wiht an error: 
Berry Phase/electric fields only for insulators! 

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Re: [QE-users] (no subject)

[문태환]

Dear Minho Lee,

As you mentioned, we looked at the quota of 'swap' memory through the 'file' 
command.

The SWAP memory was allocated at 32 GB, but the actual memory was only 3 GB.

While checking the SCF's log file, I found something different from the 
previous one.

Processes (MPI) and Threads (openMP) used in the calculation are the same as 8 
and 4 respectively,

Successful calculations before reinstalling the computer include the following:

 Parallel version (MPI & OpenMP), running on 32 processor cores
 Number of MPI processes: 8
 Threads / MPI process: 4
 R & G space division: proc / nbgrp / npool / nimage = 32
 Reading input from espresso.in

However, in the current log file, there are four nodes separated as follows.

 Parallel version (MPI & OpenMP), running on 4 processor cores
 Number of MPI processes: 1
 Threads / MPI process: 4

 MPI processes distributed on 1 nodes

This seems to be the cause of exceeding the memory of my computer .. Do you 
know why this happens?

Thank you!



-

Moon TaeHwan

Chung-Ang University

th4...@cau.ac.kr

-



보낸 사람: Minho Lee  대신 users 

보낸 날짜: 2018년 9월 7일 금요일 오전 10:29:00
받는 사람: Quantum Espresso users Forum
제목: Re: [QE-users] (no subject)

Dear TaeHwan Moon,

I’m sorry for the typo(ion_positions->atomic_positions )

Did you check your output?

In the standard output, you can find “estimated …..RAM ….” lines.

and you can check real memory usage of your computer via linux command “free”

If physical memory of your computer is not enough, “Swap” will be increased

Sincerly,

Minho Lee

Minho Lee
CEO/Developer
T. 02-3293-0204 | C. 010-2770-4080
E. m...@virtuallab.co.kr | H. http://www.virtuallab.co.kr

On-demand Materials Simulation
https://www.materialssquare.com
On 7 Sep 2018, 9:51 AM +0900, 문태환 , wrote:

Dear Minho Lee,

Thank you for your kind reply.

If you are talking about ATOMIC_POSITIONS, I thought I took a lot of text, so I 
excluded it when I wrote!

I have run the calculations by reducing the Processes (MPI) to 4, but the 
calculations are still going smoothly without exceeding the memory.

But my PC does not use CPU well and calculation speed is slow.

Like the Gaussian program,

Do you know how to control the memory while allocating a lot of CPU in the 
calculation?



-

Moon TaeHwan

Chung-Ang University

th4...@cau.ac.kr

-



보낸 사람: Minho Lee  대신 users 

보낸 날짜: 2018년 9월 6일 목요일 오후 8:17:16
받는 사람: users@lists.quantum-espresso.org; Quantum Espresso users Forum
제목: Re: [QE-users] (no subject)

Dear Taehwan Moon,

I can’t find the  namelist in your script,

I think you need to set ion_positions

Sincerely,

Minho Lee

Minho Lee
CEO/Developer
T. 02-3293-0204 | C. 010-2770-4080
E. m...@virtuallab.co.kr | H. http://www.virtuallab.co.kr

On-demand Materials Simulation
https://www.materialssquare.com
On 2018년 9월 6일 PM 7:48 +0900, 문태환 , wrote:

Hello! Quantum espresso users.
I am a beginner user of QE and Linux, and I am having a lot of computation 
difficulties.
I need to calculate the SCF, DOS, and Band structure using a CIF file with 
zero-dimensional organic-inorganic hybrid materials.
However, when the SCF calculation starts and after an hour or so has elapsed, 
the memory problem causes an error.
My computer has 32 core CPU and 64GB of memory.  In the case of the CPU, there 
is room for using 8 cores when executing calculations.
(Processes (MPI) and Threads (openMP) use 8 and 4, respectively.)

The input file looks like this:

Can you give me advice to solve this problem?
Please help me .. Thank you.



calculation  = "scf"
max_seconds  =  8.64000e+04
pseudo_dir   = "/home/user/.burai/.pseudopot"
restart_mode = "from_scratch"
tprnfor  = .FALSE.
tstress  = .FALSE.
/


a =  1.19962e+01
b =  1.46765e+01
c =  1.38899e+01
constrained_magnetization = "none"
cosac = -5.92053e-02
degauss   =  1.0e-02
ecutrho   =  5.06000e+02
ecutwfc   =  5.62066e+01
ibrav = -12
lda_plus_u= .FALSE.
nat   = 192
nosym = .FALSE.
nspin = 1
ntyp  = 5
occupations   = "smearing"
smearing  = "guassian"
starting_magnetization(1) =  0.0e+00
/


conv_thr =  1.0e-06
diago_david_ndim = 4
diagonalization  = "david"
electron_maxstep = 100
mixing_beta  =  7.0e-01
mixing_mode  = "plai

Re: [QE-users] (no subject)

[Minho Lee]

Dear TaeHwan Moon,

I’m sorry for the typo(ion_positions->atomic_positions )

Did you check your output?

In the standard output, you can find “estimated …..RAM ….” lines.

and you can check real memory usage of your computer via linux command “free”

If physical memory of your computer is not enough, “Swap” will be increased

Sincerly,

Minho Lee

Minho Lee
CEO/Developer
T. 02-3293-0204 | C. 010-2770-4080
E. m...@virtuallab.co.kr | H. http://www.virtuallab.co.kr

On-demand Materials Simulation
https://www.materialssquare.com
On 7 Sep 2018, 9:51 AM +0900, 문태환 , wrote:
> Dear Minho Lee,
>
> Thank you for your kind reply.
>
> If you are talking about ATOMIC_POSITIONS, I thought I took a lot of text, so 
> I excluded it when I wrote!
>
> I have run the calculations by reducing the Processes (MPI) to 4, but the 
> calculations are still going smoothly without exceeding the memory.
>
> But my PC does not use CPU well and calculation speed is slow.
>
> Like the Gaussian program,
>
> Do you know how to control the memory while allocating a lot of CPU in the 
> calculation?
>
>
> -
> Moon TaeHwan
> Chung-Ang University
> th4...@cau.ac.kr
> -
>
> 보낸 사람: Minho Lee  대신 users 
> 
> 보낸 날짜: 2018년 9월 6일 목요일 오후 8:17:16
> 받는 사람: users@lists.quantum-espresso.org; Quantum Espresso users Forum
> 제목: Re: [QE-users] (no subject)
>
> Dear Taehwan Moon,
>
> I can’t find the  namelist in your script,
>
> I think you need to set ion_positions
>
> Sincerely,
>
> Minho Lee
> 
> Minho Lee
> CEO/Developer
> T. 02-3293-0204 | C. 010-2770-4080
> E. m...@virtuallab.co.kr | H. http://www.virtuallab.co.kr
>
> On-demand Materials Simulation
> https://www.materialssquare.com
> On 2018년 9월 6일 PM 7:48 +0900, 문태환 , wrote:
> > Hello! Quantum espresso users.
> > I am a beginner user of QE and Linux, and I am having a lot of computation 
> > difficulties.
> > I need to calculate the SCF, DOS, and Band structure using a CIF file with 
> > zero-dimensional organic-inorganic hybrid materials.
> > However, when the SCF calculation starts and after an hour or so has 
> > elapsed, the memory problem causes an error.
> > My computer has 32 core CPU and 64GB of memory.  In the case of the CPU, 
> > there is room for using 8 cores when executing calculations.
> > (Processes (MPI) and Threads (openMP) use 8 and 4, respectively.)
> >
> > The input file looks like this:
> >
> > Can you give me advice to solve this problem?
> > Please help me .. Thank you.
> >
> >
> > 
> >     calculation  = "scf"
> >     max_seconds  =  8.64000e+04
> >     pseudo_dir   = "/home/user/.burai/.pseudopot"
> >     restart_mode = "from_scratch"
> >     tprnfor      = .FALSE.
> >     tstress      = .FALSE.
> > /
> >
> > 
> >     a                         =  1.19962e+01
> >     b                         =  1.46765e+01
> >     c                         =  1.38899e+01
> >     constrained_magnetization = "none"
> >     cosac                     = -5.92053e-02
> >     degauss                   =  1.0e-02
> >     ecutrho                   =  5.06000e+02
> >     ecutwfc                   =  5.62066e+01
> >     ibrav                     = -12
> >     lda_plus_u                = .FALSE.
> >     nat                       = 192
> >     nosym                     = .FALSE.
> >     nspin                     = 1
> >     ntyp                      = 5
> >     occupations               = "smearing"
> >     smearing                  = "guassian"
> >     starting_magnetization(1) =  0.0e+00
> > /
> >
> > 
> >     conv_thr         =  1.0e-06
> >     diago_david_ndim = 4
> >     diagonalization  = "david"
> >     electron_maxstep = 100
> >     mixing_beta      =  7.0e-01
> >     mixing_mode      = "plain"
> >     mixing_ndim      = 8
> >     startingpot      = "atomic"
> >     startingwfc      = "atomic+random"
> > /
> >
> > K_POINTS {automatic}
> >  3  3  3  0 0 0
> >
> > ATOMIC_SPECIES
> > Bi    208.98038  Bi.pbe-dn-kjpaw_psl.1.0.0.UPF
> > Br     79.90400  Br.pbe-dn-kjpaw_psl.1.0.0.UPF
> > N      14.00674  N.pbe-n-kjpaw_psl.1.0.0.UPF
> > H       1.00794  H.pbe-kjpaw_psl.1.0.0.UPF
> > C      12.01070  C.pbe-n-kjpaw_psl.1.0.0.UPF
> >
> >
> >
> > -
> > Moon TaeHwan
> > Chung-Ang University
> > th4...@cau.ac.kr
> > -
> >
> > ___
> > users mailing list
> > users@lists.quantum-espresso.org
> > https://lists.quantum-espresso.org/mailman/listinfo/users
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Re: [QE-users] (no subject)

[문태환]

Dear Minho Lee,

Thank you for your kind reply.

If you are talking about ATOMIC_POSITIONS, I thought I took a lot of text, so I 
excluded it when I wrote!

I have run the calculations by reducing the Processes (MPI) to 4, but the 
calculations are still going smoothly without exceeding the memory.

But my PC does not use CPU well and calculation speed is slow.

Like the Gaussian program,

Do you know how to control the memory while allocating a lot of CPU in the 
calculation?



-

Moon TaeHwan

Chung-Ang University

th4...@cau.ac.kr

-



보낸 사람: Minho Lee  대신 users 

보낸 날짜: 2018년 9월 6일 목요일 오후 8:17:16
받는 사람: users@lists.quantum-espresso.org; Quantum Espresso users Forum
제목: Re: [QE-users] (no subject)

Dear Taehwan Moon,

I can’t find the  namelist in your script,

I think you need to set ion_positions

Sincerely,

Minho Lee

Minho Lee
CEO/Developer
T. 02-3293-0204 | C. 010-2770-4080
E. m...@virtuallab.co.kr | H. http://www.virtuallab.co.kr

On-demand Materials Simulation
https://www.materialssquare.com
On 2018년 9월 6일 PM 7:48 +0900, 문태환 , wrote:

Hello! Quantum espresso users.
I am a beginner user of QE and Linux, and I am having a lot of computation 
difficulties.
I need to calculate the SCF, DOS, and Band structure using a CIF file with 
zero-dimensional organic-inorganic hybrid materials.
However, when the SCF calculation starts and after an hour or so has elapsed, 
the memory problem causes an error.
My computer has 32 core CPU and 64GB of memory.  In the case of the CPU, there 
is room for using 8 cores when executing calculations.
(Processes (MPI) and Threads (openMP) use 8 and 4, respectively.)

The input file looks like this:

Can you give me advice to solve this problem?
Please help me .. Thank you.



calculation  = "scf"
max_seconds  =  8.64000e+04
pseudo_dir   = "/home/user/.burai/.pseudopot"
restart_mode = "from_scratch"
tprnfor  = .FALSE.
tstress  = .FALSE.
/


a =  1.19962e+01
b =  1.46765e+01
c =  1.38899e+01
constrained_magnetization = "none"
cosac = -5.92053e-02
degauss   =  1.0e-02
ecutrho   =  5.06000e+02
ecutwfc   =  5.62066e+01
ibrav = -12
lda_plus_u= .FALSE.
nat   = 192
nosym = .FALSE.
nspin = 1
ntyp  = 5
occupations   = "smearing"
smearing  = "guassian"
starting_magnetization(1) =  0.0e+00
/


conv_thr =  1.0e-06
diago_david_ndim = 4
diagonalization  = "david"
electron_maxstep = 100
mixing_beta  =  7.0e-01
mixing_mode  = "plain"
mixing_ndim  = 8
startingpot  = "atomic"
startingwfc  = "atomic+random"
/

K_POINTS {automatic}
 3  3  3  0 0 0

ATOMIC_SPECIES
Bi208.98038  Bi.pbe-dn-kjpaw_psl.1.0.0.UPF
Br 79.90400  Br.pbe-dn-kjpaw_psl.1.0.0.UPF
N  14.00674  N.pbe-n-kjpaw_psl.1.0.0.UPF
H   1.00794  H.pbe-kjpaw_psl.1.0.0.UPF
C  12.01070  C.pbe-n-kjpaw_psl.1.0.0.UPF




-

Moon TaeHwan

Chung-Ang University

th4...@cau.ac.kr

-


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Re: [QE-users] (no subject)

[Minho Lee]

Dear Taehwan Moon,

I can’t find the  namelist in your script,

I think you need to set ion_positions

Sincerely,

Minho Lee

Minho Lee
CEO/Developer
T. 02-3293-0204 | C. 010-2770-4080
E. m...@virtuallab.co.kr | H. http://www.virtuallab.co.kr

On-demand Materials Simulation
https://www.materialssquare.com
On 2018년 9월 6일 PM 7:48 +0900, 문태환 , wrote:
> Hello! Quantum espresso users.
> I am a beginner user of QE and Linux, and I am having a lot of computation 
> difficulties.
> I need to calculate the SCF, DOS, and Band structure using a CIF file with 
> zero-dimensional organic-inorganic hybrid materials.
> However, when the SCF calculation starts and after an hour or so has elapsed, 
> the memory problem causes an error.
> My computer has 32 core CPU and 64GB of memory.  In the case of the CPU, 
> there is room for using 8 cores when executing calculations.
> (Processes (MPI) and Threads (openMP) use 8 and 4, respectively.)
>
> The input file looks like this:
>
> Can you give me advice to solve this problem?
> Please help me .. Thank you.
>
>
> 
>     calculation  = "scf"
>     max_seconds  =  8.64000e+04
>     pseudo_dir   = "/home/user/.burai/.pseudopot"
>     restart_mode = "from_scratch"
>     tprnfor      = .FALSE.
>     tstress      = .FALSE.
> /
>
> 
>     a                         =  1.19962e+01
>     b                         =  1.46765e+01
>     c                         =  1.38899e+01
>     constrained_magnetization = "none"
>     cosac                     = -5.92053e-02
>     degauss                   =  1.0e-02
>     ecutrho                   =  5.06000e+02
>     ecutwfc                   =  5.62066e+01
>     ibrav                     = -12
>     lda_plus_u                = .FALSE.
>     nat                       = 192
>     nosym                     = .FALSE.
>     nspin                     = 1
>     ntyp                      = 5
>     occupations               = "smearing"
>     smearing                  = "guassian"
>     starting_magnetization(1) =  0.0e+00
> /
>
> 
>     conv_thr         =  1.0e-06
>     diago_david_ndim = 4
>     diagonalization  = "david"
>     electron_maxstep = 100
>     mixing_beta      =  7.0e-01
>     mixing_mode      = "plain"
>     mixing_ndim      = 8
>     startingpot      = "atomic"
>     startingwfc      = "atomic+random"
> /
>
> K_POINTS {automatic}
>  3  3  3  0 0 0
>
> ATOMIC_SPECIES
> Bi    208.98038  Bi.pbe-dn-kjpaw_psl.1.0.0.UPF
> Br     79.90400  Br.pbe-dn-kjpaw_psl.1.0.0.UPF
> N      14.00674  N.pbe-n-kjpaw_psl.1.0.0.UPF
> H       1.00794  H.pbe-kjpaw_psl.1.0.0.UPF
> C      12.01070  C.pbe-n-kjpaw_psl.1.0.0.UPF
>
>
>
> -
> Moon TaeHwan
> Chung-Ang University
> th4...@cau.ac.kr
> -
>
> ___
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> users@lists.quantum-espresso.org
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[QE-users] (no subject)

[문태환]

Hello! Quantum espresso users.
I am a beginner user of QE and Linux, and I am having a lot of computation 
difficulties.
I need to calculate the SCF, DOS, and Band structure using a CIF file with 
zero-dimensional organic-inorganic hybrid materials.
However, when the SCF calculation starts and after an hour or so has elapsed, 
the memory problem causes an error.
My computer has 32 core CPU and 64GB of memory.  In the case of the CPU, there 
is room for using 8 cores when executing calculations.
(Processes (MPI) and Threads (openMP) use 8 and 4, respectively.)

The input file looks like this:

Can you give me advice to solve this problem?
Please help me .. Thank you.



calculation  = "scf"
max_seconds  =  8.64000e+04
pseudo_dir   = "/home/user/.burai/.pseudopot"
restart_mode = "from_scratch"
tprnfor  = .FALSE.
tstress  = .FALSE.
/


a =  1.19962e+01
b =  1.46765e+01
c =  1.38899e+01
constrained_magnetization = "none"
cosac = -5.92053e-02
degauss   =  1.0e-02
ecutrho   =  5.06000e+02
ecutwfc   =  5.62066e+01
ibrav = -12
lda_plus_u= .FALSE.
nat   = 192
nosym = .FALSE.
nspin = 1
ntyp  = 5
occupations   = "smearing"
smearing  = "guassian"
starting_magnetization(1) =  0.0e+00
/


conv_thr =  1.0e-06
diago_david_ndim = 4
diagonalization  = "david"
electron_maxstep = 100
mixing_beta  =  7.0e-01
mixing_mode  = "plain"
mixing_ndim  = 8
startingpot  = "atomic"
startingwfc  = "atomic+random"
/

K_POINTS {automatic}
 3  3  3  0 0 0

ATOMIC_SPECIES
Bi208.98038  Bi.pbe-dn-kjpaw_psl.1.0.0.UPF
Br 79.90400  Br.pbe-dn-kjpaw_psl.1.0.0.UPF
N  14.00674  N.pbe-n-kjpaw_psl.1.0.0.UPF
H   1.00794  H.pbe-kjpaw_psl.1.0.0.UPF
C  12.01070  C.pbe-n-kjpaw_psl.1.0.0.UPF




-

Moon TaeHwan

Chung-Ang University

th4...@cau.ac.kr

-

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Re: [QE-users] (no subject)

[Dan Gil]

Thanks, I'll make sure to try those options out!

Dan

On Mon, Aug 27, 2018 at 2:53 PM Paolo Giannozzi 
wrote:

> Reducing mixing_ndim should actually reduce a bit (but not much) the
> needed memory.  in the very likely case of slow scf convergence, use
> mixing_mode='local-TF' and increase the initial scf threshold to 10^-6 or
> so.
>
> Paolo
>
> On Tue, Aug 28, 2018 at 12:34 AM, Dan Gil  wrote:
>
>> Thank you Paolo,
>>
>> I wasn't initially sure that it was really a RAM problem, because I tried
>> reducing mixing_ndim but this didn't have any impact on the "Estimated
>> total dynamical RAM." I am sorry that this seemed thoughtless.
>>
>> I tried again with K_POINTS gamma - it is running now without any
>> problems so far!
>>
>> Thanks as always,
>>
>> Dan
>>
>> On Mon, Aug 27, 2018 at 11:21 AM Paolo Giannozzi 
>> wrote:
>>
>>> On Sat, Aug 25, 2018 at 2:00 AM, Dan Gil  wrote:
>>>
>>> [...] With the input format shown below, I get the following error from
 the HPC.

 - - - - -
 /tmp/slurm/job8327489/slurm_script: line 11: 111713
 Killed  pw.x < sapphire.pw.in > sapphire.pw.out
 slurmstepd: error: Exceeded step memory limit at some point.
 - - - - -

 When I run it on my personal computer

>>>
>>> let me understand: your HPC says "exceeded memory", and you try to run
>>> it on your PC?
>>> In your output, there should be a line saying something like
>>>
>>>  Estimated total dynamical RAM >  67.08 GB
>>>
>>> By setting
>>>K_POINTS gamma
>>> instead of
>>>   K_POINTS automatic
>>>   1 1 1 1 1 1
>>> you can cut the RAM into half (results are the same), by the way. You
>>> should also consider reducing the cell length along c (95 A!) and starting
>>> with smaller cutoffs.
>>>
>>> Paolo
>>>
>>> I get this error:

 - - - - -
  task # 0
  from diropn : error #10
  error opening sapphire/pwscf.wfc1
 - - - - -

 And indeed, there is no pwscf.wfc1 to be seen.

 Here is the input:

 - - - - -
 
 calculation='relax',
 wf_collect = .true. ,
 outdir = 'sapphire' ,
 restart_mode = 'from_scratch' ,
 pseudo_dir = 'pseudo' ,
 disk_io = 'low' ,
 verbosity = 'low' ,
 max_seconds = 72000 ,
  /
  
 ibrav = 4 ,
 celldm(1)=17.99085377,
 celldm(3)=10,
 nat = 168 ,
 ntyp = 3 ,
 ecutwfc =50,
 ecutrho =400,
 smearing='mp',
 occupations='smearing',
 degauss=0.03,
  /
  
 diagonalization='david',
 conv_thr = 1.d-9,
 mixing_mode = 'plain',
  /
  
  /
 ATOMIC_SPECIES
 Al   26.981539   Al.pbe-n-rrkjus_psl.0.1.UPF
 O15.999000   O.pbe-n-rrkjus_psl.0.1.UPF
 H 1.000800   H.pbe-rrkjus_psl.0.1.UPF
 ATOMIC_POSITIONS crystal
 Al   0.0   0.0   0.095697893
 Al   0.0   0.0   0.177259148
 Al   0.0   0.0   0.040053860
 Al   0.0   0.0   0.232903158
 Al   0.33311   0.16621   0.187801968
 Al   0.33311   0.16621   0.270721823
 Al   0.33311   0.16621   0.131337383
 Al   0.33311   0.16621   0.045832216
 Al   0.16682   0.33364   0.002235215
 Al   0.16682   0.33364   0.085155073
 Al   0.16682   0.33364   0.227124825
 Al   0.16682   0.33364   0.141619636
 Al   0.5   0.0   0.095697893
 Al   0.5   0.0   0.177259148
 Al   0.5   0.0   0.040053860
 Al   0.5   0.0   0.232903158
 Al   0.83311   0.16621   0.187801968
 Al   0.83311   0.16621   0.270721823
 Al   0.83311   0.16621   0.131337383
 Al   0.83311   0.16621   0.045832216
 Al   0.66682   0.33364   0.002235215
 Al   0.66682   0.33364   0.085155073
 Al   0.66682   0.33364   0.227124825
 Al   0.66682   0.33364   0.141619636
 Al   0.5   0.5   0.095697893
 Al   0.5   0.5   0.177259148
 Al   0.5   0.5   0.040053860
 Al   0.5   0.5   0.232903158
 Al   0.83311   0.66621   0.187801968
 Al   0.83311   0.66621   0.270721823
 Al   0.83311   0.66621   0.131337383
 Al   0.83311   0.66621   0.045832216
 Al   0.66682   0.83364   0.002235215
 Al   0.66682   0.83364   

Re: [QE-users] (no subject)

[Paolo Giannozzi]

Reducing mixing_ndim should actually reduce a bit (but not much) the needed
memory.  in the very likely case of slow scf convergence, use
mixing_mode='local-TF' and increase the initial scf threshold to 10^-6 or
so.

Paolo

On Tue, Aug 28, 2018 at 12:34 AM, Dan Gil  wrote:

> Thank you Paolo,
>
> I wasn't initially sure that it was really a RAM problem, because I tried
> reducing mixing_ndim but this didn't have any impact on the "Estimated
> total dynamical RAM." I am sorry that this seemed thoughtless.
>
> I tried again with K_POINTS gamma - it is running now without any problems
> so far!
>
> Thanks as always,
>
> Dan
>
> On Mon, Aug 27, 2018 at 11:21 AM Paolo Giannozzi 
> wrote:
>
>> On Sat, Aug 25, 2018 at 2:00 AM, Dan Gil  wrote:
>>
>> [...] With the input format shown below, I get the following error from
>>> the HPC.
>>>
>>> - - - - -
>>> /tmp/slurm/job8327489/slurm_script: line 11: 111713
>>> Killed  pw.x < sapphire.pw.in > sapphire.pw.out
>>> slurmstepd: error: Exceeded step memory limit at some point.
>>> - - - - -
>>>
>>> When I run it on my personal computer
>>>
>>
>> let me understand: your HPC says "exceeded memory", and you try to run it
>> on your PC?
>> In your output, there should be a line saying something like
>>
>>  Estimated total dynamical RAM >  67.08 GB
>>
>> By setting
>>K_POINTS gamma
>> instead of
>>   K_POINTS automatic
>>   1 1 1 1 1 1
>> you can cut the RAM into half (results are the same), by the way. You
>> should also consider reducing the cell length along c (95 A!) and starting
>> with smaller cutoffs.
>>
>> Paolo
>>
>> I get this error:
>>>
>>> - - - - -
>>>  task # 0
>>>  from diropn : error #10
>>>  error opening sapphire/pwscf.wfc1
>>> - - - - -
>>>
>>> And indeed, there is no pwscf.wfc1 to be seen.
>>>
>>> Here is the input:
>>>
>>> - - - - -
>>> 
>>> calculation='relax',
>>> wf_collect = .true. ,
>>> outdir = 'sapphire' ,
>>> restart_mode = 'from_scratch' ,
>>> pseudo_dir = 'pseudo' ,
>>> disk_io = 'low' ,
>>> verbosity = 'low' ,
>>> max_seconds = 72000 ,
>>>  /
>>>  
>>> ibrav = 4 ,
>>> celldm(1)=17.99085377,
>>> celldm(3)=10,
>>> nat = 168 ,
>>> ntyp = 3 ,
>>> ecutwfc =50,
>>> ecutrho =400,
>>> smearing='mp',
>>> occupations='smearing',
>>> degauss=0.03,
>>>  /
>>>  
>>> diagonalization='david',
>>> conv_thr = 1.d-9,
>>> mixing_mode = 'plain',
>>>  /
>>>  
>>>  /
>>> ATOMIC_SPECIES
>>> Al   26.981539   Al.pbe-n-rrkjus_psl.0.1.UPF
>>> O15.999000   O.pbe-n-rrkjus_psl.0.1.UPF
>>> H 1.000800   H.pbe-rrkjus_psl.0.1.UPF
>>> ATOMIC_POSITIONS crystal
>>> Al   0.0   0.0   0.095697893
>>> Al   0.0   0.0   0.177259148
>>> Al   0.0   0.0   0.040053860
>>> Al   0.0   0.0   0.232903158
>>> Al   0.33311   0.16621   0.187801968
>>> Al   0.33311   0.16621   0.270721823
>>> Al   0.33311   0.16621   0.131337383
>>> Al   0.33311   0.16621   0.045832216
>>> Al   0.16682   0.33364   0.002235215
>>> Al   0.16682   0.33364   0.085155073
>>> Al   0.16682   0.33364   0.227124825
>>> Al   0.16682   0.33364   0.141619636
>>> Al   0.5   0.0   0.095697893
>>> Al   0.5   0.0   0.177259148
>>> Al   0.5   0.0   0.040053860
>>> Al   0.5   0.0   0.232903158
>>> Al   0.83311   0.16621   0.187801968
>>> Al   0.83311   0.16621   0.270721823
>>> Al   0.83311   0.16621   0.131337383
>>> Al   0.83311   0.16621   0.045832216
>>> Al   0.66682   0.33364   0.002235215
>>> Al   0.66682   0.33364   0.085155073
>>> Al   0.66682   0.33364   0.227124825
>>> Al   0.66682   0.33364   0.141619636
>>> Al   0.5   0.5   0.095697893
>>> Al   0.5   0.5   0.177259148
>>> Al   0.5   0.5   0.040053860
>>> Al   0.5   0.5   0.232903158
>>> Al   0.83311   0.66621   0.187801968
>>> Al   0.83311   0.66621   0.270721823
>>> Al   0.83311   0.66621   0.131337383
>>> Al   0.83311   0.66621   0.045832216
>>> Al   0.66682   0.83364   0.002235215
>>> Al   0.66682   0.83364   0.085155073
>>> Al   0.66682   0.83364   0.227124825
>>> Al   0.66682   0.83364   0.141619636
>>> Al   0.0   0.5   0.095697893
>>> Al   0.0   0.5   0.177259148

Re: [QE-users] (no subject)

[Dan Gil]

Thank you Paolo,

I wasn't initially sure that it was really a RAM problem, because I tried
reducing mixing_ndim but this didn't have any impact on the "Estimated
total dynamical RAM." I am sorry that this seemed thoughtless.

I tried again with K_POINTS gamma - it is running now without any problems
so far!

Thanks as always,

Dan

On Mon, Aug 27, 2018 at 11:21 AM Paolo Giannozzi 
wrote:

> On Sat, Aug 25, 2018 at 2:00 AM, Dan Gil  wrote:
>
> [...] With the input format shown below, I get the following error from
>> the HPC.
>>
>> - - - - -
>> /tmp/slurm/job8327489/slurm_script: line 11: 111713
>> Killed  pw.x < sapphire.pw.in > sapphire.pw.out
>> slurmstepd: error: Exceeded step memory limit at some point.
>> - - - - -
>>
>> When I run it on my personal computer
>>
>
> let me understand: your HPC says "exceeded memory", and you try to run it
> on your PC?
> In your output, there should be a line saying something like
>
>  Estimated total dynamical RAM >  67.08 GB
>
> By setting
>K_POINTS gamma
> instead of
>   K_POINTS automatic
>   1 1 1 1 1 1
> you can cut the RAM into half (results are the same), by the way. You
> should also consider reducing the cell length along c (95 A!) and starting
> with smaller cutoffs.
>
> Paolo
>
> I get this error:
>>
>> - - - - -
>>  task # 0
>>  from diropn : error #10
>>  error opening sapphire/pwscf.wfc1
>> - - - - -
>>
>> And indeed, there is no pwscf.wfc1 to be seen.
>>
>> Here is the input:
>>
>> - - - - -
>> 
>> calculation='relax',
>> wf_collect = .true. ,
>> outdir = 'sapphire' ,
>> restart_mode = 'from_scratch' ,
>> pseudo_dir = 'pseudo' ,
>> disk_io = 'low' ,
>> verbosity = 'low' ,
>> max_seconds = 72000 ,
>>  /
>>  
>> ibrav = 4 ,
>> celldm(1)=17.99085377,
>> celldm(3)=10,
>> nat = 168 ,
>> ntyp = 3 ,
>> ecutwfc =50,
>> ecutrho =400,
>> smearing='mp',
>> occupations='smearing',
>> degauss=0.03,
>>  /
>>  
>> diagonalization='david',
>> conv_thr = 1.d-9,
>> mixing_mode = 'plain',
>>  /
>>  
>>  /
>> ATOMIC_SPECIES
>> Al   26.981539   Al.pbe-n-rrkjus_psl.0.1.UPF
>> O15.999000   O.pbe-n-rrkjus_psl.0.1.UPF
>> H 1.000800   H.pbe-rrkjus_psl.0.1.UPF
>> ATOMIC_POSITIONS crystal
>> Al   0.0   0.0   0.095697893
>> Al   0.0   0.0   0.177259148
>> Al   0.0   0.0   0.040053860
>> Al   0.0   0.0   0.232903158
>> Al   0.33311   0.16621   0.187801968
>> Al   0.33311   0.16621   0.270721823
>> Al   0.33311   0.16621   0.131337383
>> Al   0.33311   0.16621   0.045832216
>> Al   0.16682   0.33364   0.002235215
>> Al   0.16682   0.33364   0.085155073
>> Al   0.16682   0.33364   0.227124825
>> Al   0.16682   0.33364   0.141619636
>> Al   0.5   0.0   0.095697893
>> Al   0.5   0.0   0.177259148
>> Al   0.5   0.0   0.040053860
>> Al   0.5   0.0   0.232903158
>> Al   0.83311   0.16621   0.187801968
>> Al   0.83311   0.16621   0.270721823
>> Al   0.83311   0.16621   0.131337383
>> Al   0.83311   0.16621   0.045832216
>> Al   0.66682   0.33364   0.002235215
>> Al   0.66682   0.33364   0.085155073
>> Al   0.66682   0.33364   0.227124825
>> Al   0.66682   0.33364   0.141619636
>> Al   0.5   0.5   0.095697893
>> Al   0.5   0.5   0.177259148
>> Al   0.5   0.5   0.040053860
>> Al   0.5   0.5   0.232903158
>> Al   0.83311   0.66621   0.187801968
>> Al   0.83311   0.66621   0.270721823
>> Al   0.83311   0.66621   0.131337383
>> Al   0.83311   0.66621   0.045832216
>> Al   0.66682   0.83364   0.002235215
>> Al   0.66682   0.83364   0.085155073
>> Al   0.66682   0.83364   0.227124825
>> Al   0.66682   0.83364   0.141619636
>> Al   0.0   0.5   0.095697893
>> Al   0.0   0.5   0.177259148
>> Al   0.0   0.5   0.040053860
>> Al   0.0   0.5   0.232903158
>> Al   0.33311   0.66621   0.187801968
>> Al   0.33311   0.66621   0.270721823
>> Al   0.33311   0.66621   0.131337383
>> Al   0.33311   0.66621   0.045832216
>> Al   0.16682   0.83364   

Re: [QE-users] (no subject)

[Paolo Giannozzi]

On Sat, Aug 25, 2018 at 2:00 AM, Dan Gil  wrote:

[...] With the input format shown below, I get the following error from the
> HPC.
>
> - - - - -
> /tmp/slurm/job8327489/slurm_script: line 11: 111713
> Killed  pw.x < sapphire.pw.in > sapphire.pw.out
> slurmstepd: error: Exceeded step memory limit at some point.
> - - - - -
>
> When I run it on my personal computer
>

let me understand: your HPC says "exceeded memory", and you try to run it
on your PC?
In your output, there should be a line saying something like

 Estimated total dynamical RAM >  67.08 GB

By setting
   K_POINTS gamma
instead of
  K_POINTS automatic
  1 1 1 1 1 1
you can cut the RAM into half (results are the same), by the way. You
should also consider reducing the cell length along c (95 A!) and starting
with smaller cutoffs.

Paolo

I get this error:
>
> - - - - -
>  task # 0
>  from diropn : error #10
>  error opening sapphire/pwscf.wfc1
> - - - - -
>
> And indeed, there is no pwscf.wfc1 to be seen.
>
> Here is the input:
>
> - - - - -
> 
> calculation='relax',
> wf_collect = .true. ,
> outdir = 'sapphire' ,
> restart_mode = 'from_scratch' ,
> pseudo_dir = 'pseudo' ,
> disk_io = 'low' ,
> verbosity = 'low' ,
> max_seconds = 72000 ,
>  /
>  
> ibrav = 4 ,
> celldm(1)=17.99085377,
> celldm(3)=10,
> nat = 168 ,
> ntyp = 3 ,
> ecutwfc =50,
> ecutrho =400,
> smearing='mp',
> occupations='smearing',
> degauss=0.03,
>  /
>  
> diagonalization='david',
> conv_thr = 1.d-9,
> mixing_mode = 'plain',
>  /
>  
>  /
> ATOMIC_SPECIES
> Al   26.981539   Al.pbe-n-rrkjus_psl.0.1.UPF
> O15.999000   O.pbe-n-rrkjus_psl.0.1.UPF
> H 1.000800   H.pbe-rrkjus_psl.0.1.UPF
> ATOMIC_POSITIONS crystal
> Al   0.0   0.0   0.095697893
> Al   0.0   0.0   0.177259148
> Al   0.0   0.0   0.040053860
> Al   0.0   0.0   0.232903158
> Al   0.33311   0.16621   0.187801968
> Al   0.33311   0.16621   0.270721823
> Al   0.33311   0.16621   0.131337383
> Al   0.33311   0.16621   0.045832216
> Al   0.16682   0.33364   0.002235215
> Al   0.16682   0.33364   0.085155073
> Al   0.16682   0.33364   0.227124825
> Al   0.16682   0.33364   0.141619636
> Al   0.5   0.0   0.095697893
> Al   0.5   0.0   0.177259148
> Al   0.5   0.0   0.040053860
> Al   0.5   0.0   0.232903158
> Al   0.83311   0.16621   0.187801968
> Al   0.83311   0.16621   0.270721823
> Al   0.83311   0.16621   0.131337383
> Al   0.83311   0.16621   0.045832216
> Al   0.66682   0.33364   0.002235215
> Al   0.66682   0.33364   0.085155073
> Al   0.66682   0.33364   0.227124825
> Al   0.66682   0.33364   0.141619636
> Al   0.5   0.5   0.095697893
> Al   0.5   0.5   0.177259148
> Al   0.5   0.5   0.040053860
> Al   0.5   0.5   0.232903158
> Al   0.83311   0.66621   0.187801968
> Al   0.83311   0.66621   0.270721823
> Al   0.83311   0.66621   0.131337383
> Al   0.83311   0.66621   0.045832216
> Al   0.66682   0.83364   0.002235215
> Al   0.66682   0.83364   0.085155073
> Al   0.66682   0.83364   0.227124825
> Al   0.66682   0.83364   0.141619636
> Al   0.0   0.5   0.095697893
> Al   0.0   0.5   0.177259148
> Al   0.0   0.5   0.040053860
> Al   0.0   0.5   0.232903158
> Al   0.33311   0.66621   0.187801968
> Al   0.33311   0.66621   0.270721823
> Al   0.33311   0.66621   0.131337383
> Al   0.33311   0.66621   0.045832216
> Al   0.16682   0.83364   0.002235215
> Al   0.16682   0.83364   0.085155073
> Al   0.16682   0.83364   0.227124825
> Al   0.16682   0.83364   0.141619636
> O0.155404208   0.001886947   0.067662578
> O0.344595898  -0.001886947   0.205294440
> O   -0.001886987   0.153517181   0.067662578
> O0.001886979   0.346482804   0.205294440
> O0.346482772   0.344595857   0.067662578
> O0.153517221   0.155404128   

Re: [QE-users] (no subject)

[Fariba Nazari]

Hi 
I have run the in put on my mac with no problem.
The only change was the introducing the path for out directory.
outdir = '/Users/./tmp' ,

regards
Fariba
IASBS


On Fri, 24/08/2018 08:00 PM, Dan Gil  wrote:
> 
Hi, 
> 

> 
I am using pwscf v6.3, and running into some issues that I could not resolve.

> 
I first ran simulations with hydroxylated sapphire (0001) surface with only 42 
atoms successfully. Now I am trying to run an identical simulation with the 
same surface with 168 atoms (2x2 supercell) and here is where I am running into 
issues.

> 
I've tried various settings, and I've gotten a variety of error messages. With 
the input format shown below, I get the following error from the HPC.

> 
- - - - -
/tmp/slurm/job8327489/slurm_script: line 11: 111713 Killed  
pw.x < sapphire.pw.in > sapphire.pw.out
> slurmstepd: error: Exceeded step memory limit at some point.
- - - - -

> 
When I run it on my personal computer, I get this error:

> 
- - - - -
 task # 0
>  from diropn : error #10
>  error opening sapphire/pwscf.wfc1
> 
- - - - -

> 
And indeed, there is no pwscf.wfc1 to be seen.

> 
Here is the input:

> 
- - - - - 
> 

> calculation='relax',
> wf_collect = .true. ,
> outdir = 'sapphire' ,
> restart_mode = 'from_scratch' ,
> pseudo_dir = 'pseudo' ,
> disk_io = 'low' ,
> verbosity = 'low' ,
> max_seconds = 72000 ,
>  /
>  
> ibrav = 4 ,
> celldm(1)=17.99085377,
> celldm(3)=10,
> nat = 168 ,
> ntyp = 3 ,
> ecutwfc =50,
> ecutrho =400,
> smearing='mp',
> occupations='smearing',
> degauss=0.03,
>  /
>  
> diagonalization='david',
> conv_thr = 1.d-9,
> mixing_mode = 'plain',
>  /
>  
>  /
> ATOMIC_SPECIES
> Al   26.981539   Al.pbe-n-rrkjus_psl.0.1.UPF
> O15.999000   O.pbe-n-rrkjus_psl.0.1.UPF
> H 1.000800   H.pbe-rrkjus_psl.0.1.UPF
> ATOMIC_POSITIONS crystal
> Al   0.0   0.0   0.095697893
> Al   0.0   0.0   0.177259148
> Al   0.0   0.0   0.040053860
> Al   0.0   0.0   0.232903158
> Al   0.33311   0.16621   0.187801968
> Al   0.33311   0.16621   0.270721823
> Al   0.33311   0.16621   0.131337383
> Al   0.33311   0.16621   0.045832216
> Al   0.16682   0.33364   0.002235215
> Al   0.16682   0.33364   0.085155073
> Al   0.16682   0.33364   0.227124825
> Al   0.16682   0.33364   0.141619636
> Al   0.5   0.0   0.095697893
> Al   0.5   0.0   0.177259148
> Al   0.5   0.0   0.040053860
> Al   0.5   0.0   0.232903158
> Al   0.83311   0.16621   0.187801968
> Al   0.83311   0.16621   0.270721823
> Al   0.83311   0.16621   0.131337383
> Al   0.83311   0.16621   0.045832216
> Al   0.66682   0.33364   0.002235215
> Al   0.66682   0.33364   0.085155073
> Al   0.66682   0.33364   0.227124825
> Al   0.66682   0.33364   0.141619636
> Al   0.5   0.5   0.095697893
> Al   0.5   0.5   0.177259148
> Al   0.5   0.5   0.040053860
> Al   0.5   0.5   0.232903158
> Al   0.83311   0.66621   0.187801968
> Al   0.83311   0.66621   0.270721823
> Al   0.83311   0.66621   0.131337383
> Al   0.83311   0.66621   0.045832216
> Al   0.66682   0.83364   0.002235215
> Al   0.66682   0.83364   0.085155073
> Al   0.66682   0.83364   0.227124825
> Al   0.66682   0.83364   0.141619636
> Al   0.0   0.5   0.095697893
> Al   0.0   0.5   0.177259148
> Al   0.0   0.5   0.040053860
> Al   0.0   0.5   0.232903158
> Al   0.33311   0.66621   0.187801968
> Al   0.33311   0.66621   0.270721823
> Al   0.33311   0.66621   0.131337383
> Al   0.33311   0.66621   0.045832216
> Al   0.16682   0.83364   0.002235215
> Al   0.16682   0.83364   0.085155073
> Al   0.16682   0.83364   0.227124825
> Al   0.16682   0.83364   0.141619636
> O0.155404208   0.001886947   0.067662578
> O0.344595898  -0.001886947   0.205294440
> O   -0.001886987   0.153517181   0.067662578
> O0.001886979  

[QE-users] (no subject)

[Dan Gil]

Hi,

I am using pwscf v6.3, and running into some issues that I could not
resolve.

I first ran simulations with hydroxylated sapphire (0001) surface with only
42 atoms successfully. Now I am trying to run an identical simulation with
the same surface with 168 atoms (2x2 supercell) and here is where I am
running into issues.

I've tried various settings, and I've gotten a variety of error messages.
With the input format shown below, I get the following error from the HPC.

- - - - -
/tmp/slurm/job8327489/slurm_script: line 11: 111713 Killed
pw.x < sapphire.pw.in > sapphire.pw.out
slurmstepd: error: Exceeded step memory limit at some point.
- - - - -

When I run it on my personal computer, I get this error:

- - - - -
 task # 0
 from diropn : error #10
 error opening sapphire/pwscf.wfc1
- - - - -

And indeed, there is no pwscf.wfc1 to be seen.

Here is the input:

- - - - -

calculation='relax',
wf_collect = .true. ,
outdir = 'sapphire' ,
restart_mode = 'from_scratch' ,
pseudo_dir = 'pseudo' ,
disk_io = 'low' ,
verbosity = 'low' ,
max_seconds = 72000 ,
 /
 
ibrav = 4 ,
celldm(1)=17.99085377,
celldm(3)=10,
nat = 168 ,
ntyp = 3 ,
ecutwfc =50,
ecutrho =400,
smearing='mp',
occupations='smearing',
degauss=0.03,
 /
 
diagonalization='david',
conv_thr = 1.d-9,
mixing_mode = 'plain',
 /
 
 /
ATOMIC_SPECIES
Al   26.981539   Al.pbe-n-rrkjus_psl.0.1.UPF
O15.999000   O.pbe-n-rrkjus_psl.0.1.UPF
H 1.000800   H.pbe-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS crystal
Al   0.0   0.0   0.095697893
Al   0.0   0.0   0.177259148
Al   0.0   0.0   0.040053860
Al   0.0   0.0   0.232903158
Al   0.33311   0.16621   0.187801968
Al   0.33311   0.16621   0.270721823
Al   0.33311   0.16621   0.131337383
Al   0.33311   0.16621   0.045832216
Al   0.16682   0.33364   0.002235215
Al   0.16682   0.33364   0.085155073
Al   0.16682   0.33364   0.227124825
Al   0.16682   0.33364   0.141619636
Al   0.5   0.0   0.095697893
Al   0.5   0.0   0.177259148
Al   0.5   0.0   0.040053860
Al   0.5   0.0   0.232903158
Al   0.83311   0.16621   0.187801968
Al   0.83311   0.16621   0.270721823
Al   0.83311   0.16621   0.131337383
Al   0.83311   0.16621   0.045832216
Al   0.66682   0.33364   0.002235215
Al   0.66682   0.33364   0.085155073
Al   0.66682   0.33364   0.227124825
Al   0.66682   0.33364   0.141619636
Al   0.5   0.5   0.095697893
Al   0.5   0.5   0.177259148
Al   0.5   0.5   0.040053860
Al   0.5   0.5   0.232903158
Al   0.83311   0.66621   0.187801968
Al   0.83311   0.66621   0.270721823
Al   0.83311   0.66621   0.131337383
Al   0.83311   0.66621   0.045832216
Al   0.66682   0.83364   0.002235215
Al   0.66682   0.83364   0.085155073
Al   0.66682   0.83364   0.227124825
Al   0.66682   0.83364   0.141619636
Al   0.0   0.5   0.095697893
Al   0.0   0.5   0.177259148
Al   0.0   0.5   0.040053860
Al   0.0   0.5   0.232903158
Al   0.33311   0.66621   0.187801968
Al   0.33311   0.66621   0.270721823
Al   0.33311   0.66621   0.131337383
Al   0.33311   0.66621   0.045832216
Al   0.16682   0.83364   0.002235215
Al   0.16682   0.83364   0.085155073
Al   0.16682   0.83364   0.227124825
Al   0.16682   0.83364   0.141619636
O0.155404208   0.001886947   0.067662578
O0.344595898  -0.001886947   0.205294440
O   -0.001886987   0.153517181   0.067662578
O0.001886979   0.346482804   0.205294440
O0.346482772   0.344595857   0.067662578
O0.153517221   0.155404128   0.205294440
O0.171949672   0.170609214   0.023055667
O0.333498557   0.320107131   0.159438914
O0.329390758   0.001340470   0.023055667
O0.179892883   0.013391458   0.159438914
O0.328050321   0.329390771   0.249901352
O0.013391439   0.333498589   

[QE-users] (no subject)

[Priyanka Makkar]

Dear Experts,
I am facing a problem in opening a PWscf output file for vc-relax in
Xcrysden. In the output file I am getting all the parameters zero when run
on server which are as follows:
Executing: sh /opt/apps/xcrysden/scripts/dummy.sh
/home/p20170414/MnF-Slab/MnF-slab-vc-relax.pw.out
Number of Atoms:  0
Number of Frames: 0
Estimated number of bonds = 0
sInfo(dim) = 0; periodic(dim) = 0

but in input file I am getting the following parameters
Executing: sh /opt/apps/xcrysden/scripts/pwi2xsf.sh
/home/p20170414/MnF-Slab/MnF-slab-vc-relax.pw.in
reading PRIMCOORD
Number of Atoms:  0
Number of Frames: 0
Estimated number of bonds = 0
sInfo(dim) = 3; periodic(dim) = 3
Executing: /opt/apps/xcrysden/bin/gengeom 0 1 11 1 1 1 1 xc_gengeom.31035
/tmp/xc_31035/pwi2xsf.xsf_out.raw
Executing: /opt/apps/xcrysden/bin/gengeom 2 1 11 1 1 1 1
/tmp/xc_31035/xc_struc.31035 /tmp/xc_31035/pwi2xsf.xsf_out.raw
reading PRIMCOORD
reading CONVCOORD
Number of Atoms:  46
Number of Frames: 12
natoms: 46 , ndel: 0
Filtered number of atoms: 46
Estimated number of bonds = 118
sInfo(dim) = 3; periodic(dim) = 3




 Anyone facing the same issue, please help me to solve this difficulty. I
will be waiting for the response.

Thanks and regards

*Priyanka Makkar*
*Research Scholar *

*Department of Chemistry*

*BITS PILANI K K BIRLA GOA CAMPUS  *
*+91-9650393163*
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[QE-users] (no subject)

[Nuttachai Jutong]

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Re: [Pw_forum] (no subject)

[Mitsuaki Kawamura]

Dear Yuhit

You forgot to write the subject and your affiliation.
The following things may help you.

Examples of QE
http://qe-forge.org/gf/download/frsrelease/244/1115/qe-6.2-examples.tar.gz
Tutorial slides
http://www.quantum-espresso.org/tutorials/
List of schools, workshops, and tutorials
http://www.quantum-espresso.org/complete-qe-schools-workshops-and-tutorials/

If some school of QE will be held in your country (or somewhere), you should 
join that.

Best regards,
Mitsuaki Kawamura

--
--
Dr. Mitsuaki Kawamura
Software Advancement Team
Supercomputer Section
Materials Design and Characterization Laboratory
The Institute for Solid State Physics, Kashiwa, Japan
e-mail : mkawam...@issp.u-tokyo.ac.jp
--

From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf 
Of Yuhit Gupta
Sent: Sunday, December 3, 2017 12:05 AM
To: pw_forum@pwscf.org
Subject: [Pw_forum] (no subject)

I want to learn the Quantum espresso for doing pw,ph and pp.x calculation 
please suggest how to start


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[Pw_forum] (no subject)

[Yuhit Gupta]

I want to learn the Quantum espresso for doing pw,ph and pp.x calculation
please suggest how to start
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[Pw_forum] (no subject)

[wils...@gmail.com]

hello Pw



http://bit.ly/2AmSGcx


Thx

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[Pw_forum] (no subject)

[Nayana Devaraj]

Respected QE Users,

How to choose kpoints for a  hexagonal structure while using wannier
transport (wanT)? I have done with k points obtained using kmesh.pl
utility. But the band structure thus obtained is different from the actual
band structure. Using quantum espresso I have got a good band diagrom.
There I selected k points using Xcrysden. But if I use the same k points in
wanT it's showing error.

-- 


*Regards,*
*Nayana Devaraj*
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[Pw_forum] (no subject)

[Nayana Devaraj]

Dear QE users,
  How to choose k points of a hexagonal structure for wannier transport
calculation?
It is showing error when i use k points generated using utilities like
kmesh.pl , kgrid and kpoints.x .
-- 
*Nayana Devaraj*
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Re: [Pw_forum] (no subject)

[Lorenzo Paulatto]

JUts run plotrho interactively, and answer the questions manually as 
they come

kind regards

On 24/08/17 22:26, baizid kabir wrote:
> dear all
> thanks for yours reply.I modified the input file & run again. the output is
> attached.
> is it normal termination or not?
> after this calculation i run ./plotrho to give charge density image. but i
> saw tihs error in terminal:
> 
> 
> 
>   At line 114 of file plotrho.f90 (unit = 5, file = 'stdin')
> Fortran runtime error: Bad integer for item 3 in list input.
> 
> 
> 
>   and output of ./plotrho is :
> 
> Input file > r0   :   0.  0.  0.
> tau1 :   1.  1.  0.
> tau2 :   0.  0.  1.
> read   2 atomic positions
> output file > Read  56 * 40  grid
> Logarithmic scale (y/n)? > Bounds: 0.0014110.087440
> min, max, # of levels >
> 
> what i can do?
> 
> 
> 
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-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
phone: +33 (0)1 442 79822 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/423 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
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[Pw_forum] (no subject)

[baizid kabir]

dear all
thanks for yours reply.I modified the input file & run again. the output is
attached.
is it normal termination or not?
after this calculation i run ./plotrho to give charge density image. but i
saw tihs error in terminal:



 At line 114 of file plotrho.f90 (unit = 5, file = 'stdin')
Fortran runtime error: Bad integer for item 3 in list input.



 and output of ./plotrho is :

Input file > r0   :   0.  0.  0.
tau1 :   1.  1.  0.
tau2 :   0.  0.  1.
read   2 atomic positions
output file > Read  56 * 40  grid
Logarithmic scale (y/n)? > Bounds: 0.0014110.087440
min, max, # of levels >

what i can do?
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[Pw_forum] (no subject)

[baizid kabir]

hi i am calculating the charge density of hexagonal SiC
and um using plotrho.x
input:
moissanite.rho.dat
moissanite.rho.ps
n
0 0.09 6

but tere is an fortran error in this case.what value should i change
thanks in advance
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[Pw_forum] (no subject)

[baizid kabir]

  line 114 of file plotrho.f90 (unit = 5, file = 'stdin')
Fortran runtime error: Bad real number in item 1 of list input error how
can  i solve it?
sic.rho.dat
sic.rho.ps
n
0 0.09 7
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Re: [Pw_forum] (no subject)

[Taiwo Oginni]

Thanks

On Aug 10, 2017 11:47, "Taiwo Oginni"  wrote:

>  I am trying to get transport properties of GaAs using boltztrap but I was
> encountering this error.
>
>   "stop error in opening file (look in output) > 0.000u 0.004s 0:00.00
> 0.0% 0+0k"".
>
>
>  Pls.help if you can in solving this,I have searched for solution but to
> no avail,thanks.
>
>
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[Pw_forum] (no subject)

[Taiwo Oginni]

 I am trying to get transport properties of GaAs using boltztrap but I was
encountering this error.

  "stop error in opening file (look in output) > 0.000u 0.004s 0:00.00
0.0% 0+0k"".


 Pls.help if you can in solving this,I have searched for solution but to no
avail,thanks.
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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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Re: [Pw_forum] (no subject)

[Sonu Kumar]

Kindly, use appropriate subject for the post.


*===*
With kind regards,
Dr. S Kumar, Post doctoral fellow
Physical Sciences and Engineering  Divison,
IBN Sina Building, KAUST,
Thuwal, KSA
*===*

On Thu, Jul 20, 2017 at 9:46 AM, Rajesh <creativeidlemi...@gmail.com> wrote:

> It will be better to run on 6
>
> On Thu, Jul 20, 2017 at 9:18 AM, Shishir Timilsena <expressgu...@gmail.com
> > wrote:
>
>> suppose we have octa-core processor, can we run QE code as
>> mpirun -np 8 ..
>> or we have to use less no. of processors than we have for QE code like
>> mpirun -np 7
>>
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>
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Re: [Pw_forum] (no subject)

[Titusi Forum]

Just to clarify, loosing internet connection does not break your
simulation. Your simulation will continue to run even if you close your
browser or shut down your laptop. You can go back to same model and click
on "Visulaizer" button to reconnect to your job.

On Thu, Jul 20, 2017 at 8:08 AM, Isaiah Moses  wrote:

> It will be great if that can be checked for the sake of people like me
> whose internet connection is not too good.
>
> Thanks a lot,
> Isaiah
>
> On Thu, Jul 20, 2017 at 4:02 PM, Titusi Forum 
> wrote:
>
>> That happens when your internet connection keeps breaking.
>> Let me take a look if we really need to do that even if connection breaks.
>>
>> On Jul 20, 2017 8:00 AM, "Isaiah Moses"  wrote:
>>
>>> Great Titusi!
>>> I appreciate your response.
>>>
>>> I shall give it a trial.
>>>
>>> But I'm being logged out too frequently.
>>>
>>> In a minute or two I will have to log in again and again.
>>>
>>> Is there a way of disallowing that?
>>>
>>> Kind regards,
>>> Isaiah
>>>
>>> On Thu, Jul 20, 2017 at 3:43 PM, Titusi Forum 
>>> wrote:
>>>
 Easiest way to get started with Kogence might be to "Copy" an existing
 example first. For example, you might want to copy this example :-
 https://kogence.com/app/jobs/files/dashboard/-316%5EBand_str
 ucture_and_charge_density_in_110_plane_of_Si

 After copying, click on the "Files" tab. Now double-click on the
 run_example.sh file in that example. This will open the file in a code
 editor. Now you can edit that file.

 Look at line #98. cat > si.scf.in << EOF. From this line to line #131,
 we are creating *.in file. You can replace these files with your *.in file
 content here. Make sure you don't change the file paths such as path to
 pseudo etc. Leave those lines as it is.

 This is hsould get you going. Let me know if this does not work.

 Answer to your specific questions:-

 For uploading your input file you clicked on the "+" button, right? The
 same "+" button shows options for creating a directory as well.
 See instructions here :-
 https://kogence.com/app/category/Quantum_Espresso
 Look at Section: "Create a New Quantum Espresso Project from Scratch"
 -> "Step 2"

 For the software command, click on "Settings" in top/right toolbar
 (third level). It will open a forth level of toolbar with two subtabs --
 one for "Machines" and other for "Software". In the "Software" subtab,
 select "Quantum Espresso" from the dropdown and type "./run_example.sh" in
 the empty text box. We run QE through shell script. Your *.in file is
 inside our *.sh file. Open any *.sh file on Kogence to see where *.in goes.





 On Jul 20, 2017 5:39 AM, "Isaiah Moses"  wrote:

 Hi Titusi Forum,
 I'm trying to run calculations on Kogence.com using quantum espresso
 but I'm not getting what command to give.

 For instance, if I want to run an scf calculation?

 Also, after uploading my input file, how do I create a 'directory'
 where I can save other files like pseudo potentials.

 I shall appreciate your comment


 On Thu, Jul 20, 2017 at 2:16 AM, Titusi Forum 
 wrote:

> Try running your simulations on kogence.com.
> You would avoid dealing with all these issues.
>
> On Tue, Jul 18, 2017 at 7:33 PM, Rajesh 
> wrote:
>
>> This may help
>> https://www.physicsforums.com/threads/fortran-runtime-error-
>> end-of-file.716352/
>>
>> On Tue, Jul 18, 2017 at 11:33 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> may i know what is this error about ??
>>>
>>> On Tue, Jul 18, 2017 at 11:19 PM, Rajesh <
>>> creativeidlemi...@gmail.com> wrote:
>>>
 These are libraries you should install. You can Google how to
 install these

 On Jul 18, 2017 22:58, "Shishir Timilsena" 
 wrote:

> what about scalapack ??? do we need to install it too ???
>
>
>
> On Tue, Jul 18, 2017 at 10:13 PM, Rajesh <
> creativeidlemi...@gmail.com> wrote:
>
>> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
>> i-2.1.1.tar.gz
>>
>> Steps to install
>>
>> Step – 1 :Download the latest openmpi package from here ;
>>
>> Step- 2: Extract the openmpi package and open the directory ;
>>
>> Step – 3: Configure the installation file
>>
>> ./configure --prefix="/home/user/.openmpi"
>>
>> Step – 4: Install the program
>>
>> make && sudo make install
>>
>> Step – 5: Setup environment path and test mpirun

Re: [Pw_forum] (no subject)

[Isaiah Moses]

It will be great if that can be checked for the sake of people like me
whose internet connection is not too good.

Thanks a lot,
Isaiah

On Thu, Jul 20, 2017 at 4:02 PM, Titusi Forum  wrote:

> That happens when your internet connection keeps breaking.
> Let me take a look if we really need to do that even if connection breaks.
>
> On Jul 20, 2017 8:00 AM, "Isaiah Moses"  wrote:
>
>> Great Titusi!
>> I appreciate your response.
>>
>> I shall give it a trial.
>>
>> But I'm being logged out too frequently.
>>
>> In a minute or two I will have to log in again and again.
>>
>> Is there a way of disallowing that?
>>
>> Kind regards,
>> Isaiah
>>
>> On Thu, Jul 20, 2017 at 3:43 PM, Titusi Forum 
>> wrote:
>>
>>> Easiest way to get started with Kogence might be to "Copy" an existing
>>> example first. For example, you might want to copy this example :-
>>> https://kogence.com/app/jobs/files/dashboard/-316%5EBand_str
>>> ucture_and_charge_density_in_110_plane_of_Si
>>>
>>> After copying, click on the "Files" tab. Now double-click on the
>>> run_example.sh file in that example. This will open the file in a code
>>> editor. Now you can edit that file.
>>>
>>> Look at line #98. cat > si.scf.in << EOF. From this line to line #131,
>>> we are creating *.in file. You can replace these files with your *.in file
>>> content here. Make sure you don't change the file paths such as path to
>>> pseudo etc. Leave those lines as it is.
>>>
>>> This is hsould get you going. Let me know if this does not work.
>>>
>>> Answer to your specific questions:-
>>>
>>> For uploading your input file you clicked on the "+" button, right? The
>>> same "+" button shows options for creating a directory as well.
>>> See instructions here :-
>>> https://kogence.com/app/category/Quantum_Espresso
>>> Look at Section: "Create a New Quantum Espresso Project from Scratch" ->
>>> "Step 2"
>>>
>>> For the software command, click on "Settings" in top/right toolbar
>>> (third level). It will open a forth level of toolbar with two subtabs --
>>> one for "Machines" and other for "Software". In the "Software" subtab,
>>> select "Quantum Espresso" from the dropdown and type "./run_example.sh" in
>>> the empty text box. We run QE through shell script. Your *.in file is
>>> inside our *.sh file. Open any *.sh file on Kogence to see where *.in goes.
>>>
>>>
>>>
>>>
>>>
>>> On Jul 20, 2017 5:39 AM, "Isaiah Moses"  wrote:
>>>
>>> Hi Titusi Forum,
>>> I'm trying to run calculations on Kogence.com using quantum espresso but
>>> I'm not getting what command to give.
>>>
>>> For instance, if I want to run an scf calculation?
>>>
>>> Also, after uploading my input file, how do I create a 'directory' where
>>> I can save other files like pseudo potentials.
>>>
>>> I shall appreciate your comment
>>>
>>>
>>> On Thu, Jul 20, 2017 at 2:16 AM, Titusi Forum 
>>> wrote:
>>>
 Try running your simulations on kogence.com.
 You would avoid dealing with all these issues.

 On Tue, Jul 18, 2017 at 7:33 PM, Rajesh 
 wrote:

> This may help
> https://www.physicsforums.com/threads/fortran-runtime-error-
> end-of-file.716352/
>
> On Tue, Jul 18, 2017 at 11:33 PM, Shishir Timilsena <
> expressgu...@gmail.com> wrote:
>
>> may i know what is this error about ??
>>
>> On Tue, Jul 18, 2017 at 11:19 PM, Rajesh > > wrote:
>>
>>> These are libraries you should install. You can Google how to
>>> install these
>>>
>>> On Jul 18, 2017 22:58, "Shishir Timilsena" 
>>> wrote:
>>>
 what about scalapack ??? do we need to install it too ???



 On Tue, Jul 18, 2017 at 10:13 PM, Rajesh <
 creativeidlemi...@gmail.com> wrote:

> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
> i-2.1.1.tar.gz
>
> Steps to install
>
> Step – 1 :Download the latest openmpi package from here ;
>
> Step- 2: Extract the openmpi package and open the directory ;
>
> Step – 3: Configure the installation file
>
> ./configure --prefix="/home/user/.openmpi"
>
> Step – 4: Install the program
>
> make && sudo make install
>
> Step – 5: Setup environment path and test mpirun
> add these lines to bash.bashrc and profile in /etc folder
>
> PATH="$PATH:/home/user/.openmpi/bin"
> LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
>
> To test
> run command mpirun and you should get te output
>
> If everything goes fine, then you should see the following message
> :
>
> mpirun could not find anything to do
>
>
> On Tue, 

Re: [Pw_forum] (no subject)

[Titusi Forum]

That happens when your internet connection keeps breaking.
Let me take a look if we really need to do that even if connection breaks.

On Jul 20, 2017 8:00 AM, "Isaiah Moses"  wrote:

> Great Titusi!
> I appreciate your response.
>
> I shall give it a trial.
>
> But I'm being logged out too frequently.
>
> In a minute or two I will have to log in again and again.
>
> Is there a way of disallowing that?
>
> Kind regards,
> Isaiah
>
> On Thu, Jul 20, 2017 at 3:43 PM, Titusi Forum 
> wrote:
>
>> Easiest way to get started with Kogence might be to "Copy" an existing
>> example first. For example, you might want to copy this example :-
>> https://kogence.com/app/jobs/files/dashboard/-316%5EBand_str
>> ucture_and_charge_density_in_110_plane_of_Si
>>
>> After copying, click on the "Files" tab. Now double-click on the
>> run_example.sh file in that example. This will open the file in a code
>> editor. Now you can edit that file.
>>
>> Look at line #98. cat > si.scf.in << EOF. From this line to line #131,
>> we are creating *.in file. You can replace these files with your *.in file
>> content here. Make sure you don't change the file paths such as path to
>> pseudo etc. Leave those lines as it is.
>>
>> This is hsould get you going. Let me know if this does not work.
>>
>> Answer to your specific questions:-
>>
>> For uploading your input file you clicked on the "+" button, right? The
>> same "+" button shows options for creating a directory as well.
>> See instructions here :-
>> https://kogence.com/app/category/Quantum_Espresso
>> Look at Section: "Create a New Quantum Espresso Project from Scratch" ->
>> "Step 2"
>>
>> For the software command, click on "Settings" in top/right toolbar (third
>> level). It will open a forth level of toolbar with two subtabs -- one for
>> "Machines" and other for "Software". In the "Software" subtab, select
>> "Quantum Espresso" from the dropdown and type "./run_example.sh" in the
>> empty text box. We run QE through shell script. Your *.in file is inside
>> our *.sh file. Open any *.sh file on Kogence to see where *.in goes.
>>
>>
>>
>>
>>
>> On Jul 20, 2017 5:39 AM, "Isaiah Moses"  wrote:
>>
>> Hi Titusi Forum,
>> I'm trying to run calculations on Kogence.com using quantum espresso but
>> I'm not getting what command to give.
>>
>> For instance, if I want to run an scf calculation?
>>
>> Also, after uploading my input file, how do I create a 'directory' where
>> I can save other files like pseudo potentials.
>>
>> I shall appreciate your comment
>>
>>
>> On Thu, Jul 20, 2017 at 2:16 AM, Titusi Forum 
>> wrote:
>>
>>> Try running your simulations on kogence.com.
>>> You would avoid dealing with all these issues.
>>>
>>> On Tue, Jul 18, 2017 at 7:33 PM, Rajesh 
>>> wrote:
>>>
 This may help
 https://www.physicsforums.com/threads/fortran-runtime-error-
 end-of-file.716352/

 On Tue, Jul 18, 2017 at 11:33 PM, Shishir Timilsena <
 expressgu...@gmail.com> wrote:

> may i know what is this error about ??
>
> On Tue, Jul 18, 2017 at 11:19 PM, Rajesh 
> wrote:
>
>> These are libraries you should install. You can Google how to install
>> these
>>
>> On Jul 18, 2017 22:58, "Shishir Timilsena" 
>> wrote:
>>
>>> what about scalapack ??? do we need to install it too ???
>>>
>>>
>>>
>>> On Tue, Jul 18, 2017 at 10:13 PM, Rajesh <
>>> creativeidlemi...@gmail.com> wrote:
>>>
 https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
 i-2.1.1.tar.gz

 Steps to install

 Step – 1 :Download the latest openmpi package from here ;

 Step- 2: Extract the openmpi package and open the directory ;

 Step – 3: Configure the installation file

 ./configure --prefix="/home/user/.openmpi"

 Step – 4: Install the program

 make && sudo make install

 Step – 5: Setup environment path and test mpirun
 add these lines to bash.bashrc and profile in /etc folder

 PATH="$PATH:/home/user/.openmpi/bin"
 LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"

 To test
 run command mpirun and you should get te output

 If everything goes fine, then you should see the following message :

 mpirun could not find anything to do


 On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena <
 expressgu...@gmail.com> wrote:

> ok i will try to install it
> can u provide the link for it.
> m using ubunut
>
> On Tue, Jul 18, 2017 at 9:56 PM, Rajesh <
> creativeidlemi...@gmail.com> wrote:
>
>> openmpi is a software that you will have 

Re: [Pw_forum] (no subject)

[Isaiah Moses]

Great Titusi!
I appreciate your response.

I shall give it a trial.

But I'm being logged out too frequently.

In a minute or two I will have to log in again and again.

Is there a way of disallowing that?

Kind regards,
Isaiah

On Thu, Jul 20, 2017 at 3:43 PM, Titusi Forum  wrote:

> Easiest way to get started with Kogence might be to "Copy" an existing
> example first. For example, you might want to copy this example :-
> https://kogence.com/app/jobs/files/dashboard/-316%5EBand_
> structure_and_charge_density_in_110_plane_of_Si
>
> After copying, click on the "Files" tab. Now double-click on the
> run_example.sh file in that example. This will open the file in a code
> editor. Now you can edit that file.
>
> Look at line #98. cat > si.scf.in << EOF. From this line to line #131, we
> are creating *.in file. You can replace these files with your *.in file
> content here. Make sure you don't change the file paths such as path to
> pseudo etc. Leave those lines as it is.
>
> This is hsould get you going. Let me know if this does not work.
>
> Answer to your specific questions:-
>
> For uploading your input file you clicked on the "+" button, right? The
> same "+" button shows options for creating a directory as well.
> See instructions here :-
> https://kogence.com/app/category/Quantum_Espresso
> Look at Section: "Create a New Quantum Espresso Project from Scratch" ->
> "Step 2"
>
> For the software command, click on "Settings" in top/right toolbar (third
> level). It will open a forth level of toolbar with two subtabs -- one for
> "Machines" and other for "Software". In the "Software" subtab, select
> "Quantum Espresso" from the dropdown and type "./run_example.sh" in the
> empty text box. We run QE through shell script. Your *.in file is inside
> our *.sh file. Open any *.sh file on Kogence to see where *.in goes.
>
>
>
>
>
> On Jul 20, 2017 5:39 AM, "Isaiah Moses"  wrote:
>
> Hi Titusi Forum,
> I'm trying to run calculations on Kogence.com using quantum espresso but
> I'm not getting what command to give.
>
> For instance, if I want to run an scf calculation?
>
> Also, after uploading my input file, how do I create a 'directory' where I
> can save other files like pseudo potentials.
>
> I shall appreciate your comment
>
>
> On Thu, Jul 20, 2017 at 2:16 AM, Titusi Forum 
> wrote:
>
>> Try running your simulations on kogence.com.
>> You would avoid dealing with all these issues.
>>
>> On Tue, Jul 18, 2017 at 7:33 PM, Rajesh 
>> wrote:
>>
>>> This may help
>>> https://www.physicsforums.com/threads/fortran-runtime-error-
>>> end-of-file.716352/
>>>
>>> On Tue, Jul 18, 2017 at 11:33 PM, Shishir Timilsena <
>>> expressgu...@gmail.com> wrote:
>>>
 may i know what is this error about ??

 On Tue, Jul 18, 2017 at 11:19 PM, Rajesh 
 wrote:

> These are libraries you should install. You can Google how to install
> these
>
> On Jul 18, 2017 22:58, "Shishir Timilsena" 
> wrote:
>
>> what about scalapack ??? do we need to install it too ???
>>
>>
>>
>> On Tue, Jul 18, 2017 at 10:13 PM, Rajesh > > wrote:
>>
>>> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
>>> i-2.1.1.tar.gz
>>>
>>> Steps to install
>>>
>>> Step – 1 :Download the latest openmpi package from here ;
>>>
>>> Step- 2: Extract the openmpi package and open the directory ;
>>>
>>> Step – 3: Configure the installation file
>>>
>>> ./configure --prefix="/home/user/.openmpi"
>>>
>>> Step – 4: Install the program
>>>
>>> make && sudo make install
>>>
>>> Step – 5: Setup environment path and test mpirun
>>> add these lines to bash.bashrc and profile in /etc folder
>>>
>>> PATH="$PATH:/home/user/.openmpi/bin"
>>> LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
>>>
>>> To test
>>> run command mpirun and you should get te output
>>>
>>> If everything goes fine, then you should see the following message :
>>>
>>> mpirun could not find anything to do
>>>
>>>
>>> On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena <
>>> expressgu...@gmail.com> wrote:
>>>
 ok i will try to install it
 can u provide the link for it.
 m using ubunut

 On Tue, Jul 18, 2017 at 9:56 PM, Rajesh <
 creativeidlemi...@gmail.com> wrote:

> openmpi is a software that you will have to install first. Then
> compile qe with command
>  ./configure -enable-opennmpi. Only then you can use parallel
> version of qe. value is the number of processor you want to run  the
> process.
>
> On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
> expressgu...@gmail.com> wrote:
>

Re: [Pw_forum] (no subject)

[Titusi Forum]

Easiest way to get started with Kogence might be to "Copy" an existing
example first. For example, you might want to copy this example :-
https://kogence.com/app/jobs/files/dashboard/-316%5EBand_structure_and_charge_density_in_110_plane_of_Si

After copying, click on the "Files" tab. Now double-click on the
run_example.sh file in that example. This will open the file in a code
editor. Now you can edit that file.

Look at line #98. cat > si.scf.in << EOF. From this line to line #131, we
are creating *.in file. You can replace these files with your *.in file
content here. Make sure you don't change the file paths such as path to
pseudo etc. Leave those lines as it is.

This is hsould get you going. Let me know if this does not work.

Answer to your specific questions:-

For uploading your input file you clicked on the "+" button, right? The
same "+" button shows options for creating a directory as well.
See instructions here :-
https://kogence.com/app/category/Quantum_Espresso
Look at Section: "Create a New Quantum Espresso Project from Scratch" ->
"Step 2"

For the software command, click on "Settings" in top/right toolbar (third
level). It will open a forth level of toolbar with two subtabs -- one for
"Machines" and other for "Software". In the "Software" subtab, select
"Quantum Espresso" from the dropdown and type "./run_example.sh" in the
empty text box. We run QE through shell script. Your *.in file is inside
our *.sh file. Open any *.sh file on Kogence to see where *.in goes.





On Jul 20, 2017 5:39 AM, "Isaiah Moses"  wrote:

Hi Titusi Forum,
I'm trying to run calculations on Kogence.com using quantum espresso but
I'm not getting what command to give.

For instance, if I want to run an scf calculation?

Also, after uploading my input file, how do I create a 'directory' where I
can save other files like pseudo potentials.

I shall appreciate your comment


On Thu, Jul 20, 2017 at 2:16 AM, Titusi Forum  wrote:

> Try running your simulations on kogence.com.
> You would avoid dealing with all these issues.
>
> On Tue, Jul 18, 2017 at 7:33 PM, Rajesh 
> wrote:
>
>> This may help
>> https://www.physicsforums.com/threads/fortran-runtime-error-
>> end-of-file.716352/
>>
>> On Tue, Jul 18, 2017 at 11:33 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> may i know what is this error about ??
>>>
>>> On Tue, Jul 18, 2017 at 11:19 PM, Rajesh 
>>> wrote:
>>>
 These are libraries you should install. You can Google how to install
 these

 On Jul 18, 2017 22:58, "Shishir Timilsena" 
 wrote:

> what about scalapack ??? do we need to install it too ???
>
>
>
> On Tue, Jul 18, 2017 at 10:13 PM, Rajesh 
> wrote:
>
>> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
>> i-2.1.1.tar.gz
>>
>> Steps to install
>>
>> Step – 1 :Download the latest openmpi package from here ;
>>
>> Step- 2: Extract the openmpi package and open the directory ;
>>
>> Step – 3: Configure the installation file
>>
>> ./configure --prefix="/home/user/.openmpi"
>>
>> Step – 4: Install the program
>>
>> make && sudo make install
>>
>> Step – 5: Setup environment path and test mpirun
>> add these lines to bash.bashrc and profile in /etc folder
>>
>> PATH="$PATH:/home/user/.openmpi/bin"
>> LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
>>
>> To test
>> run command mpirun and you should get te output
>>
>> If everything goes fine, then you should see the following message :
>>
>> mpirun could not find anything to do
>>
>>
>> On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> ok i will try to install it
>>> can u provide the link for it.
>>> m using ubunut
>>>
>>> On Tue, Jul 18, 2017 at 9:56 PM, Rajesh >> > wrote:
>>>
 openmpi is a software that you will have to install first. Then
 compile qe with command
  ./configure -enable-opennmpi. Only then you can use parallel
 version of qe. value is the number of processor you want to run  the
 process.

 On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
 expressgu...@gmail.com> wrote:

> may i know what is openmpi and [value]  ???
>
> On Tue, Jul 18, 2017 at 9:29 PM, Rajesh <
> creativeidlemi...@gmail.com> wrote:
>
>> for openmpi it is mpirun -np [value] pw.xscf.out
>>
>>
>> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> May i know what are the quantum espresso codes in Parallel
>>> machine ??
>>> in 

Re: [Pw_forum] (no subject)

[Isaiah Moses]

Hi Titusi Forum,
I'm trying to run calculations on Kogence.com using quantum espresso but
I'm not getting what command to give.

For instance, if I want to run an scf calculation?

Also, after uploading my input file, how do I create a 'directory' where I
can save other files like pseudo potentials.

I shall appreciate your comment


On Thu, Jul 20, 2017 at 2:16 AM, Titusi Forum  wrote:

> Try running your simulations on kogence.com.
> You would avoid dealing with all these issues.
>
> On Tue, Jul 18, 2017 at 7:33 PM, Rajesh 
> wrote:
>
>> This may help
>> https://www.physicsforums.com/threads/fortran-runtime-error-
>> end-of-file.716352/
>>
>> On Tue, Jul 18, 2017 at 11:33 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> may i know what is this error about ??
>>>
>>> On Tue, Jul 18, 2017 at 11:19 PM, Rajesh 
>>> wrote:
>>>
 These are libraries you should install. You can Google how to install
 these

 On Jul 18, 2017 22:58, "Shishir Timilsena" 
 wrote:

> what about scalapack ??? do we need to install it too ???
>
>
>
> On Tue, Jul 18, 2017 at 10:13 PM, Rajesh 
> wrote:
>
>> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
>> i-2.1.1.tar.gz
>>
>> Steps to install
>>
>> Step – 1 :Download the latest openmpi package from here ;
>>
>> Step- 2: Extract the openmpi package and open the directory ;
>>
>> Step – 3: Configure the installation file
>>
>> ./configure --prefix="/home/user/.openmpi"
>>
>> Step – 4: Install the program
>>
>> make && sudo make install
>>
>> Step – 5: Setup environment path and test mpirun
>> add these lines to bash.bashrc and profile in /etc folder
>>
>> PATH="$PATH:/home/user/.openmpi/bin"
>> LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
>>
>> To test
>> run command mpirun and you should get te output
>>
>> If everything goes fine, then you should see the following message :
>>
>> mpirun could not find anything to do
>>
>>
>> On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> ok i will try to install it
>>> can u provide the link for it.
>>> m using ubunut
>>>
>>> On Tue, Jul 18, 2017 at 9:56 PM, Rajesh >> > wrote:
>>>
 openmpi is a software that you will have to install first. Then
 compile qe with command
  ./configure -enable-opennmpi. Only then you can use parallel
 version of qe. value is the number of processor you want to run  the
 process.

 On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
 expressgu...@gmail.com> wrote:

> may i know what is openmpi and [value]  ???
>
> On Tue, Jul 18, 2017 at 9:29 PM, Rajesh <
> creativeidlemi...@gmail.com> wrote:
>
>> for openmpi it is mpirun -np [value] pw.xscf.out
>>
>>
>> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> May i know what are the quantum espresso codes in Parallel
>>> machine ??
>>> in serial i use, pw.x  scf.out what is in parallel ??
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Shishir Timilsena, M.Sc
>>> St.xavier's College
>>> Kathmandu,Nepal
>>> e-mail: shishir.timils...@gmail.com
>>> phone: +977 9845196469 <+977%20984-5196469>
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>


 ___
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 Pw_forum@pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>

Re: [Pw_forum] (no subject)

[Rajesh]

It will be better to run on 6

On Thu, Jul 20, 2017 at 9:18 AM, Shishir Timilsena 
wrote:

> suppose we have octa-core processor, can we run QE code as
> mpirun -np 8 ..
> or we have to use less no. of processors than we have for QE code like
> mpirun -np 7
>
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>
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[Pw_forum] (no subject)

[Shishir Timilsena]

suppose we have octa-core processor, can we run QE code as
mpirun -np 8 ..
or we have to use less no. of processors than we have for QE code like
mpirun -np 7
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Re: [Pw_forum] (no subject)

[Titusi Forum]

Try running your simulations on kogence.com.
You would avoid dealing with all these issues.

On Tue, Jul 18, 2017 at 7:33 PM, Rajesh  wrote:

> This may help
> https://www.physicsforums.com/threads/fortran-runtime-error-
> end-of-file.716352/
>
> On Tue, Jul 18, 2017 at 11:33 PM, Shishir Timilsena <
> expressgu...@gmail.com> wrote:
>
>> may i know what is this error about ??
>>
>> On Tue, Jul 18, 2017 at 11:19 PM, Rajesh 
>> wrote:
>>
>>> These are libraries you should install. You can Google how to install
>>> these
>>>
>>> On Jul 18, 2017 22:58, "Shishir Timilsena" 
>>> wrote:
>>>
 what about scalapack ??? do we need to install it too ???



 On Tue, Jul 18, 2017 at 10:13 PM, Rajesh 
 wrote:

> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
> i-2.1.1.tar.gz
>
> Steps to install
>
> Step – 1 :Download the latest openmpi package from here ;
>
> Step- 2: Extract the openmpi package and open the directory ;
>
> Step – 3: Configure the installation file
>
> ./configure --prefix="/home/user/.openmpi"
>
> Step – 4: Install the program
>
> make && sudo make install
>
> Step – 5: Setup environment path and test mpirun
> add these lines to bash.bashrc and profile in /etc folder
>
> PATH="$PATH:/home/user/.openmpi/bin"
> LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
>
> To test
> run command mpirun and you should get te output
>
> If everything goes fine, then you should see the following message :
>
> mpirun could not find anything to do
>
>
> On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena <
> expressgu...@gmail.com> wrote:
>
>> ok i will try to install it
>> can u provide the link for it.
>> m using ubunut
>>
>> On Tue, Jul 18, 2017 at 9:56 PM, Rajesh 
>> wrote:
>>
>>> openmpi is a software that you will have to install first. Then
>>> compile qe with command
>>>  ./configure -enable-opennmpi. Only then you can use parallel
>>> version of qe. value is the number of processor you want to run  the
>>> process.
>>>
>>> On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
>>> expressgu...@gmail.com> wrote:
>>>
 may i know what is openmpi and [value]  ???

 On Tue, Jul 18, 2017 at 9:29 PM, Rajesh <
 creativeidlemi...@gmail.com> wrote:

> for openmpi it is mpirun -np [value] pw.xscf.out
>
>
> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
> expressgu...@gmail.com> wrote:
>
>> May i know what are the quantum espresso codes in Parallel
>> machine ??
>> in serial i use, pw.x  scf.out what is in parallel ??
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Shishir Timilsena, M.Sc
>> St.xavier's College
>> Kathmandu,Nepal
>> e-mail: shishir.timils...@gmail.com
>> phone: +977 9845196469 <+977%20984-5196469>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>


 ___
 Pw_forum mailing list
 Pw_forum@pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
> ___
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> http://pwscf.org/mailman/listinfo/pw_forum
>


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 Pw_forum mailing list
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>>>
>>> ___
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>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
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>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
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> 

[Pw_forum] (no subject)

[VineetKumar Pandey]

dear users
   how can we calculate the weight of phonon  inequivalent q
wave vectors what we've got in output of ph.x executable ?


Vineet Kumar Pandey
IISER PUNE, INDIA
PINCODE-411008

Phone: +91 8853094275
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Re: [Pw_forum] (no subject)

[Rajesh]

This may help
https://www.physicsforums.com/threads/fortran-runtime-error-end-of-file.716352/

On Tue, Jul 18, 2017 at 11:33 PM, Shishir Timilsena 
wrote:

> may i know what is this error about ??
>
> On Tue, Jul 18, 2017 at 11:19 PM, Rajesh 
> wrote:
>
>> These are libraries you should install. You can Google how to install
>> these
>>
>> On Jul 18, 2017 22:58, "Shishir Timilsena" 
>> wrote:
>>
>>> what about scalapack ??? do we need to install it too ???
>>>
>>>
>>>
>>> On Tue, Jul 18, 2017 at 10:13 PM, Rajesh 
>>> wrote:
>>>
 https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
 i-2.1.1.tar.gz

 Steps to install

 Step – 1 :Download the latest openmpi package from here ;

 Step- 2: Extract the openmpi package and open the directory ;

 Step – 3: Configure the installation file

 ./configure --prefix="/home/user/.openmpi"

 Step – 4: Install the program

 make && sudo make install

 Step – 5: Setup environment path and test mpirun
 add these lines to bash.bashrc and profile in /etc folder

 PATH="$PATH:/home/user/.openmpi/bin"
 LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"

 To test
 run command mpirun and you should get te output

 If everything goes fine, then you should see the following message :

 mpirun could not find anything to do


 On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena <
 expressgu...@gmail.com> wrote:

> ok i will try to install it
> can u provide the link for it.
> m using ubunut
>
> On Tue, Jul 18, 2017 at 9:56 PM, Rajesh 
> wrote:
>
>> openmpi is a software that you will have to install first. Then
>> compile qe with command
>>  ./configure -enable-opennmpi. Only then you can use parallel version
>> of qe. value is the number of processor you want to run  the process.
>>
>> On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> may i know what is openmpi and [value]  ???
>>>
>>> On Tue, Jul 18, 2017 at 9:29 PM, Rajesh >> > wrote:
>>>
 for openmpi it is mpirun -np [value] pw.xscf.out


 On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
 expressgu...@gmail.com> wrote:

> May i know what are the quantum espresso codes in Parallel machine
> ??
> in serial i use, pw.x  scf.out what is in parallel ??
>
>
>
>
>
>
>
>
>
>
>
> Shishir Timilsena, M.Sc
> St.xavier's College
> Kathmandu,Nepal
> e-mail: shishir.timils...@gmail.com
> phone: +977 9845196469 <+977%20984-5196469>
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>


 ___
 Pw_forum mailing list
 Pw_forum@pwscf.org
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>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
> ___
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>


 ___
 Pw_forum mailing list
 Pw_forum@pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
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>
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Re: [Pw_forum] (no subject)

[Shishir Timilsena]

may i know what is this error about ??

On Tue, Jul 18, 2017 at 11:19 PM, Rajesh 
wrote:

> These are libraries you should install. You can Google how to install these
>
> On Jul 18, 2017 22:58, "Shishir Timilsena"  wrote:
>
>> what about scalapack ??? do we need to install it too ???
>>
>>
>>
>> On Tue, Jul 18, 2017 at 10:13 PM, Rajesh 
>> wrote:
>>
>>> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
>>> i-2.1.1.tar.gz
>>>
>>> Steps to install
>>>
>>> Step – 1 :Download the latest openmpi package from here ;
>>>
>>> Step- 2: Extract the openmpi package and open the directory ;
>>>
>>> Step – 3: Configure the installation file
>>>
>>> ./configure --prefix="/home/user/.openmpi"
>>>
>>> Step – 4: Install the program
>>>
>>> make && sudo make install
>>>
>>> Step – 5: Setup environment path and test mpirun
>>> add these lines to bash.bashrc and profile in /etc folder
>>>
>>> PATH="$PATH:/home/user/.openmpi/bin"
>>> LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
>>>
>>> To test
>>> run command mpirun and you should get te output
>>>
>>> If everything goes fine, then you should see the following message :
>>>
>>> mpirun could not find anything to do
>>>
>>>
>>> On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena <
>>> expressgu...@gmail.com> wrote:
>>>
 ok i will try to install it
 can u provide the link for it.
 m using ubunut

 On Tue, Jul 18, 2017 at 9:56 PM, Rajesh 
 wrote:

> openmpi is a software that you will have to install first. Then
> compile qe with command
>  ./configure -enable-opennmpi. Only then you can use parallel version
> of qe. value is the number of processor you want to run  the process.
>
> On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
> expressgu...@gmail.com> wrote:
>
>> may i know what is openmpi and [value]  ???
>>
>> On Tue, Jul 18, 2017 at 9:29 PM, Rajesh 
>> wrote:
>>
>>> for openmpi it is mpirun -np [value] pw.xscf.out
>>>
>>>
>>> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
>>> expressgu...@gmail.com> wrote:
>>>
 May i know what are the quantum espresso codes in Parallel machine
 ??
 in serial i use, pw.x  scf.out what is in parallel ??











 Shishir Timilsena, M.Sc
 St.xavier's College
 Kathmandu,Nepal
 e-mail: shishir.timils...@gmail.com
 phone: +977 9845196469 <+977%20984-5196469>


 ___
 Pw_forum mailing list
 Pw_forum@pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

>>>
>>>
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Re: [Pw_forum] (no subject)

[Rajesh]

These are libraries you should install. You can Google how to install these

On Jul 18, 2017 22:58, "Shishir Timilsena"  wrote:

> what about scalapack ??? do we need to install it too ???
>
>
>
> On Tue, Jul 18, 2017 at 10:13 PM, Rajesh 
> wrote:
>
>> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmp
>> i-2.1.1.tar.gz
>>
>> Steps to install
>>
>> Step – 1 :Download the latest openmpi package from here ;
>>
>> Step- 2: Extract the openmpi package and open the directory ;
>>
>> Step – 3: Configure the installation file
>>
>> ./configure --prefix="/home/user/.openmpi"
>>
>> Step – 4: Install the program
>>
>> make && sudo make install
>>
>> Step – 5: Setup environment path and test mpirun
>> add these lines to bash.bashrc and profile in /etc folder
>>
>> PATH="$PATH:/home/user/.openmpi/bin"
>> LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
>>
>> To test
>> run command mpirun and you should get te output
>>
>> If everything goes fine, then you should see the following message :
>>
>> mpirun could not find anything to do
>>
>>
>> On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> ok i will try to install it
>>> can u provide the link for it.
>>> m using ubunut
>>>
>>> On Tue, Jul 18, 2017 at 9:56 PM, Rajesh 
>>> wrote:
>>>
 openmpi is a software that you will have to install first. Then compile
 qe with command
  ./configure -enable-opennmpi. Only then you can use parallel version
 of qe. value is the number of processor you want to run  the process.

 On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
 expressgu...@gmail.com> wrote:

> may i know what is openmpi and [value]  ???
>
> On Tue, Jul 18, 2017 at 9:29 PM, Rajesh 
> wrote:
>
>> for openmpi it is mpirun -np [value] pw.xscf.out
>>
>>
>> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> May i know what are the quantum espresso codes in Parallel machine ??
>>> in serial i use, pw.x  scf.out what is in parallel ??
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Shishir Timilsena, M.Sc
>>> St.xavier's College
>>> Kathmandu,Nepal
>>> e-mail: shishir.timils...@gmail.com
>>> phone: +977 9845196469 <+977%20984-5196469>
>>>
>>>
>>> ___
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>>
>>
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Re: [Pw_forum] (no subject)

[Shishir Timilsena]

what about scalapack ??? do we need to install it too ???



On Tue, Jul 18, 2017 at 10:13 PM, Rajesh 
wrote:

> https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.gz
>
> Steps to install
>
> Step – 1 :Download the latest openmpi package from here ;
>
> Step- 2: Extract the openmpi package and open the directory ;
>
> Step – 3: Configure the installation file
>
> ./configure --prefix="/home/user/.openmpi"
>
> Step – 4: Install the program
>
> make && sudo make install
>
> Step – 5: Setup environment path and test mpirun
> add these lines to bash.bashrc and profile in /etc folder
>
> PATH="$PATH:/home/user/.openmpi/bin"
> LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
>
> To test
> run command mpirun and you should get te output
>
> If everything goes fine, then you should see the following message :
>
> mpirun could not find anything to do
>
>
> On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena  > wrote:
>
>> ok i will try to install it
>> can u provide the link for it.
>> m using ubunut
>>
>> On Tue, Jul 18, 2017 at 9:56 PM, Rajesh 
>> wrote:
>>
>>> openmpi is a software that you will have to install first. Then compile
>>> qe with command
>>>  ./configure -enable-opennmpi. Only then you can use parallel version of
>>> qe. value is the number of processor you want to run  the process.
>>>
>>> On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
>>> expressgu...@gmail.com> wrote:
>>>
 may i know what is openmpi and [value]  ???

 On Tue, Jul 18, 2017 at 9:29 PM, Rajesh 
 wrote:

> for openmpi it is mpirun -np [value] pw.xscf.out
>
>
> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
> expressgu...@gmail.com> wrote:
>
>> May i know what are the quantum espresso codes in Parallel machine ??
>> in serial i use, pw.x  scf.out what is in parallel ??
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Shishir Timilsena, M.Sc
>> St.xavier's College
>> Kathmandu,Nepal
>> e-mail: shishir.timils...@gmail.com
>> phone: +977 9845196469 <+977%20984-5196469>
>>
>>
>> ___
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>> http://pwscf.org/mailman/listinfo/pw_forum
>>
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>
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Re: [Pw_forum] (no subject)

[Rajesh]

https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.gz

Steps to install

Step – 1 :Download the latest openmpi package from here ;

Step- 2: Extract the openmpi package and open the directory ;

Step – 3: Configure the installation file

./configure --prefix="/home/user/.openmpi"

Step – 4: Install the program

make && sudo make install

Step – 5: Setup environment path and test mpirun
add these lines to bash.bashrc and profile in /etc folder

PATH="$PATH:/home/user/.openmpi/bin"
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"

To test
run command mpirun and you should get te output

If everything goes fine, then you should see the following message :

mpirun could not find anything to do


On Tue, Jul 18, 2017 at 9:53 PM, Shishir Timilsena 
wrote:

> ok i will try to install it
> can u provide the link for it.
> m using ubunut
>
> On Tue, Jul 18, 2017 at 9:56 PM, Rajesh 
> wrote:
>
>> openmpi is a software that you will have to install first. Then compile
>> qe with command
>>  ./configure -enable-opennmpi. Only then you can use parallel version of
>> qe. value is the number of processor you want to run  the process.
>>
>> On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> may i know what is openmpi and [value]  ???
>>>
>>> On Tue, Jul 18, 2017 at 9:29 PM, Rajesh 
>>> wrote:
>>>
 for openmpi it is mpirun -np [value] pw.xscf.out


 On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
 expressgu...@gmail.com> wrote:

> May i know what are the quantum espresso codes in Parallel machine ??
> in serial i use, pw.x  scf.out what is in parallel ??
>
>
>
>
>
>
>
>
>
>
>
> Shishir Timilsena, M.Sc
> St.xavier's College
> Kathmandu,Nepal
> e-mail: shishir.timils...@gmail.com
> phone: +977 9845196469 <+977%20984-5196469>
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>


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>>>
>>>
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Re: [Pw_forum] (no subject)

[Shishir Timilsena]

ok i will try to install it
can u provide the link for it.
m using ubunut

On Tue, Jul 18, 2017 at 9:56 PM, Rajesh  wrote:

> openmpi is a software that you will have to install first. Then compile qe
> with command
>  ./configure -enable-opennmpi. Only then you can use parallel version of
> qe. value is the number of processor you want to run  the process.
>
> On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena  > wrote:
>
>> may i know what is openmpi and [value]  ???
>>
>> On Tue, Jul 18, 2017 at 9:29 PM, Rajesh 
>> wrote:
>>
>>> for openmpi it is mpirun -np [value] pw.xscf.out
>>>
>>>
>>> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
>>> expressgu...@gmail.com> wrote:
>>>
 May i know what are the quantum espresso codes in Parallel machine ??
 in serial i use, pw.x  scf.out what is in parallel ??











 Shishir Timilsena, M.Sc
 St.xavier's College
 Kathmandu,Nepal
 e-mail: shishir.timils...@gmail.com
 phone: +977 9845196469 <+977%20984-5196469>


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 http://pwscf.org/mailman/listinfo/pw_forum

>>>
>>>
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Re: [Pw_forum] (no subject)

[Rajesh]

openmpi is a software that you will have to install first. Then compile qe
with command
 ./configure -enable-opennmpi. Only then you can use parallel version of
qe. value is the number of processor you want to run  the process.

On Tue, Jul 18, 2017 at 9:20 PM, Shishir Timilsena 
wrote:

> may i know what is openmpi and [value]  ???
>
> On Tue, Jul 18, 2017 at 9:29 PM, Rajesh 
> wrote:
>
>> for openmpi it is mpirun -np [value] pw.xscf.out
>>
>>
>> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena <
>> expressgu...@gmail.com> wrote:
>>
>>> May i know what are the quantum espresso codes in Parallel machine ??
>>> in serial i use, pw.x  scf.out what is in parallel ??
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Shishir Timilsena, M.Sc
>>> St.xavier's College
>>> Kathmandu,Nepal
>>> e-mail: shishir.timils...@gmail.com
>>> phone: +977 9845196469 <+977%20984-5196469>
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> ___
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>
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Re: [Pw_forum] (no subject)

[Shishir Timilsena]

may i know what is openmpi and [value]  ???

On Tue, Jul 18, 2017 at 9:29 PM, Rajesh  wrote:

> for openmpi it is mpirun -np [value] pw.xscf.out
>
>
> On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena  > wrote:
>
>> May i know what are the quantum espresso codes in Parallel machine ??
>> in serial i use, pw.x  scf.out what is in parallel ??
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Shishir Timilsena, M.Sc
>> St.xavier's College
>> Kathmandu,Nepal
>> e-mail: shishir.timils...@gmail.com
>> phone: +977 9845196469 <+977%20984-5196469>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
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Re: [Pw_forum] (no subject)

[Rajesh]

for openmpi it is mpirun -np [value] pw.xscf.out


On Tue, Jul 18, 2017 at 8:29 PM, Shishir Timilsena 
wrote:

> May i know what are the quantum espresso codes in Parallel machine ??
> in serial i use, pw.x  scf.out what is in parallel ??
>
>
>
>
>
>
>
>
>
>
>
> Shishir Timilsena, M.Sc
> St.xavier's College
> Kathmandu,Nepal
> e-mail: shishir.timils...@gmail.com
> phone: +977 9845196469 <+977%20984-5196469>
>
>
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[Pw_forum] (no subject)

[Shishir Timilsena]

May i know what are the quantum espresso codes in Parallel machine ??
in serial i use, pw.x  scf.out what is in parallel ??











Shishir Timilsena, M.Sc
St.xavier's College
Kathmandu,Nepal
e-mail: shishir.timils...@gmail.com
phone: +977 9845196469
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[Pw_forum] (no subject)

[Shishir Timilsena]

how to use  tran_prefix  ???









Shishir Timilsena, M.Sc
St.xavier's College
Kathmandu,Nepal
e-mail: shishir.timils...@gmail.com
phone: +977 9845196469
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Re: [Pw_forum] (no subject)

[Rita Maji]

Dear Paolo,
You may not have seen such error, but I'm facing same problem repeatedly, I
don't know whether it is input parameter that I have used or machine
dependent problem, I am trying to find out that .
Here I'm attaching input and output file .
Any kind of suggestion will be helpful for me .

Thanks,
Rita Maji
Research Scholar
NISER,Bhubaneswar
INDIA

On Thu, Jul 6, 2017 at 5:26 PM, Paolo Giannozzi 
wrote:

> On Thu, Jul 6, 2017 at 7:25 AM, Rita Maji  wrote:
>
>
>> I am getting the following error in some calculations
>>  " ERROR: Problem contains processor column with zero width"
>>
>
> I don't see any such error anywhere in QE
>
> Paolo
> --
> 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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scf.in
Description: Binary data


scf.out
Description: Binary data
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Re: [Pw_forum] (no subject)

[Paolo Giannozzi]

On Thu, Jul 6, 2017 at 7:25 AM, Rita Maji  wrote:


> I am getting the following error in some calculations
>  " ERROR: Problem contains processor column with zero width"
>

I don't see any such error anywhere in QE

Paolo
-- 
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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[Pw_forum] (no subject)

[Rita Maji]

Hi all.
I am getting the following error in some calculations
 " ERROR: Problem contains processor column with zero width"
 According to my understanding it is related to parallel file system
machine dependent  problem ,
can anybody help me to short out this error.

Thanks,
Rita
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Re: [Pw_forum] (no subject)

[Paolo Giannozzi]

>From the header of next version of average.f90:

  !  The planar average is defined as
  ! p(k) = \sum_{i=1}^{N_1} \sum_{j=1}^{N_2} Q(i,j,k) / (N_1 N_2)
  !  along direction 3, and the like for directions 1 and 2;
  !  N_1, N_2, N_3 are the three dimensions of the 3D FFT.
  !  Note that if Q is a charge density whose integral is Z_v:
  ! Z_v = \int p(z) dV = \sum_k p(k) \Omega/N_3
  !  where \Omega is the size of the unit cell (or supercell)

P.

On Tue, Jul 4, 2017 at 12:02 PM, VineetKumar Pandey <
vineetkumar.pan...@students.iiserpune.ac.in> wrote:

> dear sir, when we do average.x, we get charge per unit surface, I want to
> know unit of charge , I mean it's in electronic unit or coulomb. and sir I
> multiplied it by area. it's coming half of the charge in comparison with
> what it should be.
>
>
> thank you
>
> Vineet Kumar Pandey
> IISER PUNE, INDIA
> PINCODE-411008
>
> Phone: +91 8853094275 <+91%2088530%2094275>
>
>
> On Tue, Jul 4, 2017 at 2:49 PM, Thomas Brumme <
> thomas.bru...@uni-leipzig.de> wrote:
>
>> Dear Vineet Kumar,
>>
>> if you average the charge over a surface you'll get the charge per unit
>> surface. Integrating this will give you the total charge per unit surface...
>>
>> I think the output of average.x is just this... Thus, you'll need to
>> multiply by the xy-area of your unit cell...
>>
>> Regards
>>
>> Thomas
>>
>> On 07/04/17 11:08, VineetKumar Pandey wrote:
>>
>> I am trying to calculate charge density(rho)  as a function of z axis.
>> what I did by using pp.x and then average.x. but when I am integrating
>> rho(z)  with respect to z. I am not getting the total charge, that I have
>> in my system. can anybody help me to get out of it?  actually, my system is
>> PbI2. and it has 18 e- in a unit cell.
>> Vineet Kumar Pandey
>> IISER PUNE, INDIA
>> PINCODE-411008
>>
>> Phone: +91 8853094275 <+91%2088530%2094275>
>>
>>
>>
>> ___
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>>
>>
>> --
>> Dr. rer. nat. Thomas Brumme
>> Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
>> Leipzig University
>> Phillipp-Rosenthal-Strasse 31
>> 04103 Leipzig
>>
>> Tel:  +49 (0)341 97 36456 <+49%20341%209736456>
>>
>> email: thomas.bru...@uni-leipzig.de
>>
>>
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-- 
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] (no subject)

[VineetKumar Pandey]

dear sir, when we do average.x, we get charge per unit surface, I want to
know unit of charge , I mean it's in electronic unit or coulomb. and sir I
multiplied it by area. it's coming half of the charge in comparison with
what it should be.


thank you

Vineet Kumar Pandey
IISER PUNE, INDIA
PINCODE-411008

Phone: +91 8853094275


On Tue, Jul 4, 2017 at 2:49 PM, Thomas Brumme 
wrote:

> Dear Vineet Kumar,
>
> if you average the charge over a surface you'll get the charge per unit
> surface. Integrating this will give you the total charge per unit surface...
>
> I think the output of average.x is just this... Thus, you'll need to
> multiply by the xy-area of your unit cell...
>
> Regards
>
> Thomas
>
> On 07/04/17 11:08, VineetKumar Pandey wrote:
>
> I am trying to calculate charge density(rho)  as a function of z axis.
> what I did by using pp.x and then average.x. but when I am integrating
> rho(z)  with respect to z. I am not getting the total charge, that I have
> in my system. can anybody help me to get out of it?  actually, my system is
> PbI2. and it has 18 e- in a unit cell.
> Vineet Kumar Pandey
> IISER PUNE, INDIA
> PINCODE-411008
>
> Phone: +91 8853094275
>
>
>
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> --
> Dr. rer. nat. Thomas Brumme
> Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
> Leipzig University
> Phillipp-Rosenthal-Strasse 31
> 04103 Leipzig
>
> Tel:  +49 (0)341 97 36456
>
> email: thomas.bru...@uni-leipzig.de
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