subject:"\[QE\-users\] \(no subject\)"

Re: [QE-users] (no subject)

2022-02-23 Thread 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)

2022-02-23 Thread 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)

2022-01-24 Thread 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)

2021-12-03 Thread 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)

2021-09-19 Thread 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)

2021-09-19 Thread 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)

2021-08-03 Thread 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)

2021-07-12 Thread 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)

2021-07-12 Thread 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)

2021-03-21 Thread 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)

2021-03-21 Thread 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)

2021-03-15 Thread 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)

2020-12-19 Thread Mainak Ghosh


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

2020-11-16 Thread 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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[QE-users] (no subject)

2020-11-12 Thread 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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[QE-users] (no subject)

2020-07-03 Thread 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)

2020-05-31 Thread 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)

2020-05-18 Thread 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)

2020-05-17 Thread 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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Re: [QE-users] (no subject)

2020-05-17 Thread 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)

2020-05-17 Thread 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)

2020-05-14 Thread Malathe Khalil

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

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

2020-05-14 Thread 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)

2020-05-11 Thread 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)

2020-05-10 Thread 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)

2020-05-10 Thread 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)

2020-01-17 Thread 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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-- 
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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)

2020-01-15 Thread 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)

2020-01-14 Thread 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)

2020-01-07 Thread 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)

2019-06-11 Thread 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)

2019-05-26 Thread 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)

2019-04-11 Thread 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)

2019-04-08 Thread 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)

2019-04-08 Thread 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)

2019-03-29 Thread 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)

2019-03-19 Thread 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)

2019-03-19 Thread 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)

2019-02-25 Thread 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)

2019-02-24 Thread 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)

2018-09-16 Thread 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)

2018-09-06 Thread 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)

2018-09-06 Thread 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
> ___
> 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)

2018-09-06 Thread 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)

2018-09-06 Thread 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
> -
>
> ___
> users mailing list
> users@lists.quantum-espresso.org
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[QE-users] (no subject)

2018-09-06 Thread 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)

2018-08-27 Thread 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)

2018-08-27 Thread 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)

2018-08-27 Thread 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)

2018-08-27 Thread 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)

2018-08-24 Thread 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)

2018-08-24 Thread 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)

2018-07-23 Thread 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)

2018-03-07 Thread Nuttachai Jutong


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