[Pw_forum] tot_charge in nano structures

[Zara Nosh]

Dear all,
Thanks for reading it.
I would like to add some charge to graphene layer by adding tot_charge in
SYSTEM window.
My problem is energy convergence versus vacuum, it isn't converge  even at
high vacuum (~30Ang and more), is there any trick to solve this problem?
Thank you,
Zara
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] QE-GPU (installation)

[Phanikumar Pentyala]

Here I am attaching my SERVER architecture and GPU device enquiry (text
file)

After whole long day I found some reasons (I don't know whether they are
correct or not ):

Initially I written my GPU was Tesla K40, but it is not. Actual series name
was *NVIDIA Tesla K40m. *Sorry for that, that was my mistake

>From "README" file in software, *NVIDIA Tesla K40m *was not mentioned. Is
that any problem?

If I try compilation with QE-5.3.0, It was different error (*config.status:
error: cannot find input file: ../include/fft_defs.h.in
*)

Also, Intel® math kernel library (MKL) and Intel® Message Passing Interface
(MPI) library installation required or not?



Thank you once again


Regarrds
Phanikumar

On Tue, Dec 6, 2016 at 12:02 AM, Filippo SPIGA <
filippo.sp...@quantum-espresso.org> wrote:

> On Dec 5, 2016, at 2:11 PM, Phanikumar Pentyala 
> wrote:
> > After change the compilation command:  ./configure --enable-parallel
> --enable-openmp --with-scalapack --enable-cuda --with-gpu-arch=sm_35
> --with-cuda-dir=/usr/local/cuda-8.0/bin --without-magma --with-phigemm
> (now I changed with scalapack)
>
> You have a single server with 2 K40 right? No point of using ScaLAPACK for
> only 2 MPI processes, please disable scaLAPACk and enable MAGMA.
>
>
> > configure: error: Cannot compile against this version of Quantum
> ESPRESSO. Use v5.4
>
> Weird, it shoudl work. I tested it multiple time a month ago in my system.
> I will look into this or this night or tomorrow and get back to you.
>
> --
> Filippo SPIGA ~ Quantum ESPRESSO Foundation ~ http://www.quantum-espresso.
> org
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
##

SERVER architecture information (from "lscpu" command in terminal)

##

Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):40
On-line CPU(s) list:   0-39
Thread(s) per core:2
Core(s) per socket:10
Socket(s): 2
NUMA node(s):  2
Vendor ID: GenuineIntel
CPU family:6
Model: 79
Model name:Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
Stepping:  1
CPU MHz:   1200.000
BogoMIPS:  4788.53
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  25600K
NUMA node0 CPU(s): 0-9,20-29
NUMA node1 CPU(s): 10-19,30-39


##

After I run device quiry in CUDA_samples I got this information about my GPU 
accelerators

##

Detected 2 CUDA Capable device(s)

Device 0: "Tesla K40m"
  CUDA Driver Version / Runtime Version  8.0 / 8.0
  CUDA Capability Major/Minor version number:3.5
  Total amount of global memory: 11440 MBytes (11995578368 
bytes)
  (15) Multiprocessors, (192) CUDA Cores/MP: 2880 CUDA Cores
  GPU Max Clock rate:745 MHz (0.75 GHz)
  Memory Clock rate: 3004 Mhz
  Memory Bus Width:  384-bit
  L2 Cache Size: 1572864 bytes
  Maximum Texture Dimension Size (x,y,z) 1D=(65536), 2D=(65536, 65536), 
3D=(4096, 4096, 4096)
  Maximum Layered 1D Texture Size, (num) layers  1D=(16384), 2048 layers
  Maximum Layered 2D Texture Size, (num) layers  2D=(16384, 16384), 2048 layers
  Total amount of constant memory:   65536 bytes
  Total amount of shared memory per block:   49152 bytes
  Total number of registers available per block: 65536
  Warp size: 32
  Maximum number of threads per multiprocessor:  2048
  Maximum number of threads per block:   1024
  Max dimension size of a thread block (x,y,z): (1024, 1024, 64)
  Max dimension size of a grid size(x,y,z): (2147483647, 65535, 65535)
  Maximum memory pitch:  2147483647 bytes
  Texture alignment: 512 bytes
  Concurrent copy and kernel execution:  Yes with 2 copy engine(s)
  Run time limit on kernels: No
  Integrated GPU sharing Host Memory:No
  Support host page-locked memory mapping:   Yes
  Alignment requirement for Surfaces:Yes
  Device has ECC support:

Re: [Pw_forum] QE-GPU (installation)

[Filippo SPIGA]

On Dec 5, 2016, at 2:11 PM, Phanikumar Pentyala  wrote:
> After change the compilation command:  ./configure --enable-parallel 
> --enable-openmp --with-scalapack --enable-cuda --with-gpu-arch=sm_35 
> --with-cuda-dir=/usr/local/cuda-8.0/bin --without-magma --with-phigemm (now I 
> changed with scalapack)

You have a single server with 2 K40 right? No point of using ScaLAPACK for only 
2 MPI processes, please disable scaLAPACk and enable MAGMA.


> configure: error: Cannot compile against this version of Quantum ESPRESSO. 
> Use v5.4

Weird, it shoudl work. I tested it multiple time a month ago in my system. I 
will look into this or this night or tomorrow and get back to you.

--
Filippo SPIGA ~ Quantum ESPRESSO Foundation ~ http://www.quantum-espresso.org


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

Re: [Pw_forum] QE-GPU (installation)

[Phanikumar Pentyala]

Thank you for quick reply

So I downloaded QE-GPU version 5.4 and updated my CUDA version to 8.0.

After change the compilation command:  *./configure --enable-parallel
--enable-openmp --with-scalapack --enable-cuda --with-gpu-arch=sm_35
--with-cuda-dir=/usr/local/cuda-8.0/bin --without-magma --with-phigemm*
(now I changed with scalapack)

but it is showing *new error *that is:

checking build system type... x86_64-unknown-linux-gnu
checking Quantum ESPRESSO version... grep:
/root/Quantum-Espresso/QE-GPU-5.4/..//Modules/version.f90: No such file or
directory

configure: error: Cannot compile against this version of Quantum ESPRESSO.
Use v5.4

Is there any other prerequisites I missed?


Regards
Phanikumar


On Mon, Dec 5, 2016 at 2:25 PM, Filippo SPIGA <
filippo.sp...@quantum-espresso.org> wrote:

> Dear Phanikumar,
>
> upgrade to QE v5.4 and upgrade to the latest QE-GPU from GIT (
> https://github.com/fspiga/QE-GPU/archive/5.4.tar.gz). I've just create a
> tag to simplify checkout operations).
>
> Moreover you want to use MAGMA if you do not use ScaLAPACK. if you disable
> both, most likely you will run single core LAPACK and there will be no gain
> there in having GPU.
>
> On Dec 5, 2016, at 5:57 AM, Phanikumar Pentyala 
> wrote:
> > I am trying to install QE-GPU-14.10.0 in my server (details below).
> while configuration it's not generating files and showing some error
> (config.status: error: cannot find input file: ../include/fft_defs.h.in).
> I am new to linux OS, please help me for successful installation of GPU
> version.
> >
> > Command I used for configuration: ./configure --enable-parallel
> --enable-openmp --enable-cuda --without-scalapack --with-gpu-arch=sm_35
> --with-cuda-dir=/usr/local/cuda-7.5/bin --without-magma --with-phigemm
>
> --
> Filippo SPIGA ~ Quantum ESPRESSO Foundation ~ http://www.quantum-espresso.
> org
>
>
> ___
> 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] Negative Phonon Frequencies - Numerical instability or unstable structure

[Pietro Delugas]

Sorry forgot half of the answer


acustic branches should be flat along k_z direction, I would check that 
is so. If it is not so, maybe you are adding non physical interactions 
between periodic images and this can cause the numerical instabilities. 
  I don't know whether your program is able to clean spurious 
interactions due to fake periodicity.

 I hope this helps - pietro

On 05/12/2016 09:52, Pietro Delugas wrote:


Then one of the 3 acustic branches ( probably the one you gave 
problems with ) should be flat.


I don't know how this phononpy works,  maybe there is a way to deal 
directly with 2D systems, otherwise just find a way to set to 0 all 
the interatomic force constants that  correspond to interactions 
between atoms staying in different periodic images of the slab.



pietro



On 05/12/2016 09:33, Mohammed Ghadiyali wrote:


Hi,


The structure is two dimensional similar to bi-layer graphene.


Regards,


Ghadiyali Mohammed Kader


Research Scholar


University of Mumbai.



___
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] (no subject)

[Σωτήρης Φράγκος]

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

Re: [Pw_forum] Negative Phonon Frequencies - Numerical instability or unstable structure

[Mohammed Ghadiyali]

Respected Sir.


I have computed the force for the super cell and used the parameter --dim="2 2 
1" .


Regards,


Ghadiyali Mohammed Kader


Research Scholar


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

Re: [Pw_forum] QE-GPU (installation)

[Filippo SPIGA]

Dear Phanikumar,

upgrade to QE v5.4 and upgrade to the latest QE-GPU from GIT 
(https://github.com/fspiga/QE-GPU/archive/5.4.tar.gz). I've just create a tag 
to simplify checkout operations).

Moreover you want to use MAGMA if you do not use ScaLAPACK. if you disable 
both, most likely you will run single core LAPACK and there will be no gain 
there in having GPU.

On Dec 5, 2016, at 5:57 AM, Phanikumar Pentyala  wrote:
> I am trying to install QE-GPU-14.10.0 in my server (details below). while 
> configuration it's not generating files and showing some error 
> (config.status: error: cannot find input file: ../include/fft_defs.h.in). I 
> am new to linux OS, please help me for successful installation of GPU version.
> 
> Command I used for configuration: ./configure --enable-parallel 
> --enable-openmp --enable-cuda --without-scalapack --with-gpu-arch=sm_35 
> --with-cuda-dir=/usr/local/cuda-7.5/bin --without-magma --with-phigemm

--
Filippo SPIGA ~ Quantum ESPRESSO Foundation ~ http://www.quantum-espresso.org


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

Re: [Pw_forum] Negative Phonon Frequencies - Numerical instability or unstable structure

[Pietro Delugas]

Then one of the 3 acustic branches ( probably the one you gave problems 
with ) should be flat.


I don't know how this phononpy works,  maybe there is a way to deal 
directly with 2D systems, otherwise just find a way to set to 0 all the 
interatomic force constants that  correspond to interactions between 
atoms staying in different periodic images of the slab.



pietro



On 05/12/2016 09:33, Mohammed Ghadiyali wrote:


Hi,


The structure is two dimensional similar to bi-layer graphene.


Regards,


Ghadiyali Mohammed Kader


Research Scholar


University of Mumbai.



___
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] Negative Phonon Frequencies - Numerical instability or unstable structure

[ulrich.aschauer]

Dear Mohammed,

Have you computed your force constants for a supercell or are you 
inter/extrapolating q≠Gamma from the --dim=“1 1 1” force constants? If it’s 1 1 
1, try to make a supercell that will give you access to the zone-boundary 
points so that your interpolation becomes better.

Best regards,
-uli
--
SNF Prof. Dr. Ulrich Aschauer
Universität Bern
Departement für Chemie und Biochemie
Freiestrasse 3
CH-3012 Bern
Tel. +41 (0)31 631 5629
ulrich.ascha...@dcb.unibe.ch
www.dcb.unibe.ch
Büro: N431
--



On 5 Dec 2016, at 09:25, Pietro Delugas 
> wrote:

Hello Mohammed

If the phonon were computed with phononpy for any numerical problem maybe you 
will find more help in the forum of phononpy users.

Could you provide more information about the structure ?  Is it 3D or 2D ?


greetings - pietro

On 05/12/2016 08:23, Mohammed Ghadiyali wrote:
Dear All,

I am working on a bilayer tin system and has performed geometry relaxation 
using Quantum Espresso 5.4.0 of the structure via:


1. One relax calculation - for coordinate relaxation

2. One vc-relax calculation with cell_do_free as 2Dxy - for coordinate and cell 
shape relaxation

3. Two vc-relax calculation with cell_do_free as shape - for coordinate and 
cell shape relaxation with constant volume.


these calculations were performed with, ecutwfc = 60 Ry and K-point mesh as 10 
10 1, 1 1 1.

Further, phonon calculations were performed using the phononpy 1.11.0 package 
with the same parameters. The

structure seem to gotten relaxed but it still has some negative frequencies 
near the Gamma point, are these's negative

frequencies numerical instabilities or the structure is unstable.


I am attaching the phonon dispersion file. Please advice.


Regards,

Ghadiyali Mohammed Kader.

Research Scholar,

University of Mumbai.




___
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

Re: [Pw_forum] Negative Phonon Frequencies - Numerical instability or unstable structure

[Mohammed Ghadiyali]

Hi,


The structure is two dimensional similar to bi-layer graphene.


Regards,


Ghadiyali Mohammed Kader


Research Scholar


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

Re: [Pw_forum] Negative Phonon Frequencies - Numerical instability or unstable structure

[Pietro Delugas]

Hello Mohammed


If the phonon were computed with phononpy for any numerical problem 
maybe you will find more help in the forum of phononpy users.



Could you provide more information about the structure ?  Is it 3D or 2D ?



greetings - pietro


On 05/12/2016 08:23, Mohammed Ghadiyali wrote:


Dear All,


I am working on a bilayer tin system and has performed geometry 
relaxation using Quantum Espresso 5.4.0 of the structure via:




1. One relax calculation - for coordinate relaxation


2. One vc-relax calculation with cell_do_free as 2Dxy - for coordinate 
and cell shape relaxation



3. Two vc-relax calculation with cell_do_free as shape - for 
coordinate and cell shape relaxation with constant volume.




these calculations were performed with, ecutwfc = 60 Ry and K-point 
mesh as 10 10 1, 1 1 1.



Further, phonon calculations were performed using the phononpy 1.11.0 
package with the same parameters. The



structure seem to gotten relaxed but it still has some negative 
frequencies near the Gamma point, are these's negative



frequencies numerical instabilities or the structure is unstable.



I am attaching the phonon dispersion file. Please advice.



Regards,


Ghadiyali Mohammed Kader.


Research Scholar,


University of Mumbai.




___
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