Re: [Pw_forum] Error related to "radial FFT during vc-relax" calculations

[stefano de gironcoli]

what type of vc-relax are you doing ?
I mean: it's a CNT... if you don't fix the xy lattice spacing the cell 
will shrink significantly and the code will beg for a larger 
cell_factor... which you could try to give it if this is really what you 
want to do ... but is it ?

HTH
stefano

On 28/10/2016 08:51, Sai Phani wrote:

Dear all,
I am trying to perform "vc-relax" pwscf calculations for the 54 atomed 
Carbon Nanotube (CNT) molecule. I had performed these calculations at 
various k-points of 5*5*1, 9*9*1, 11*11*1 and 20*20*1 using 
Monkhorst-Pack grid scheme.


But, every time the calculations were stopped in a midway with 
generating the CRASH file.

The CRASH file consists of the following error:

%%
 task # 0
 from scale_h : error # 1
 Not enough space allocated for radial FFT: try restarting with a 
larger cell_factor.

 %%

 %%
 task # 3
 from scale_h : error # 1
 Not enough space allocated for radial FFT: try restarting with a 
larger cell_factor.

 %%

 %%
 task # 1
 from scale_h : error # 1
 Not enough space allocated for radial FFT: try restarting with a 
larger cell_factor.

 %%

I am currently using Ecutwfc = 30 Ry and rhocut_wfc = 300 Ry for this 
system.



Could any of you tell me the reason for the error and what k-points 
and Ecut_wfc and rho_wfc values should I use in my input file?





Thanks & Regards,
Sai Phani Kumar,
Research Scholar (PhD),
Quantum and Molecular Engineering Laboratory,
Department of Chemical Engineering,
Indian Institute of Technology Kharagpur.
West Bengal, India-721302.




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Re: [Pw_forum] LSDA calculation with Hybrid functional

[Lorenzo Paulatto]

Dear Rita,
please provide more details.

kind regards

On Friday, October 28, 2016 11:01:09 AM CEST Rita Maji wrote:
> Dear all,
> during LSDA calcultion with hybrid functional (PBE0) it is not writing
> total and absolute magnetization and also all the contribution to total
> energy, can anybody help me .
> 
> 
> Thanking You,
> Rita Maji
> NISER, Bhubaneswar


-- 
Dr. Lorenzo Paulatto 
IdR @ IMPMC -- CNRS & Université Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05

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[Pw_forum] Charge on individual atom

[Amita Sihag]

Dear all
How can i find charge value on individual atom in Quantum Espresso with
nonmagnetic calculations i.e. taking nspin=1 .Please suggest the necessary.


Thank you
Amita
Dept of Chemistry
Indian Institute of Technology Gandhinagar
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Re: [Pw_forum] Charge on individual atom

[Giuseppe Mattioli]

Dear Amita
Use the projwfc.x postprocessing tool. At the end of its output you'll find 
Lowdin charges and a spilling parameter indicating how much of the total 
charge density does not fit into the Lowdin partitioning.
N.B.: the "on-the-fly" estimates of atomic charge you see in pw.x output when 
you perform nspin=2 calculations are not accurate! Use always projwfc.x, 
or other external tools like, e.g., Bader analysis, see 
http://theory.cm.utexas.edu/henkelman/code/bader/
HTH
Giuseppe

On Friday, October 28, 2016 02:32:34 PM Amita Sihag wrote:
> Dear all
> How can i find charge value on individual atom in Quantum Espresso with
> nonmagnetic calculations i.e. taking nspin=1 .Please suggest the necessary.
> 
> 
> Thank you
> Amita
> Dept of Chemistry
> Indian Institute of Technology Gandhinagar


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est la conservation des droits naturels et 
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   ResearcherID: F-6308-2012

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Re: [Pw_forum] Regarding energy calculation in solvent medium

[Oliviero Andreussi]

Dear Rameswar,

QE has access to implicit solvent models through the Environ module 
www.quantum-environ.org. The module needs to be 
downloaded separately, e.g. from 
here, please take care of 
downloading the right version for the version of QE that you are using: QE 
versions 5.3, 5.4 and 6.0 all require Environ-0.2.tgz, previous versions of QE 
require specific Environ-0.2 packages and may have less features enabled.

Once untarred, the Environ/ directory should be placed inside the main QE 
directory and the module should be installed following the steps reported in 
the Environ/README file or online in the Documentation page. The procedure 
involves a few steps, but it does not require any special 
library/compiler/linker and it should be easy to follow if you already managed 
to have the bare QE installed.

To use the module you can refer to the examples in the Environ/examples 
directory, to the online Documentation page and its FAQ section, to the 
previous discussions on the PWForum, to the keyword description in the 
INPUT_ENVIRON file 
(here
 or in the Environ/Doc directory), and eventually you can contact me (directly 
or via PWForum) if you have any problem with the module.

Best regards,

P.S. please remember to sign with your affiliation when asking questions to the 
forum.

Oliviero Andreussi
--
Senior Postdoctoral Researcher
École Polytechnique Fédérale de Lausanne (EPFL) and
Università della Svizzera Italiana (USI) of Lugano
USI Campus, Via G. Buffi 17, 6904 Lugano, Switzerland
Emails: oliviero.andreussi @ epfl.ch -or- usi.ch
Tel: +41-(0)58-666-4810 / Skype: olivieroandreussi
Web: https://sites.google.com/site/olivieroandreussi


From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of 
Rameswar Bhattacharjee [bhattacharjeerames...@gmail.com]
Sent: Thursday, October 27, 2016 6:20 PM
To: pw_forum@pwscf.org
Subject: [Pw_forum] Regarding energy calculation in solvent medium

Dear QE users,

I want to estimate the binding energy of a complex in water (solvent) medium. 
Can anybody tell me how to use a implicit solvent model in QE to obtain the 
solvation energy? Thank you


--
best wishes
Rameswar Bhattacharjee

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Re: [Pw_forum] LSDA calculation with Hybrid functional

[Rita Maji]

Hi Lorenzo,
I am doing LSDA calculation for a 5x5 doped graphene calculation, to see
the change in magnetic property for hybrid functional I am trying to do
with PBE0, it is taking long time and also not printing total energy at
each scf steps so that I can see whether it is converging properly or not,
and also not showing any error during running. First time I am using Hybrid
functional so I have used all default parameters as of now, Here I have
attached the input file, any suggestion will be very much helpful.

Thanks,
Rita

On Fri, Oct 28, 2016 at 2:31 PM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

> Dear Rita,
> please provide more details.
>
> kind regards
>
> On Friday, October 28, 2016 11:01:09 AM CEST Rita Maji wrote:
> > Dear all,
> > during LSDA calcultion with hybrid functional (PBE0) it is not writing
> > total and absolute magnetization and also all the contribution to total
> > energy, can anybody help me .
> >
> >
> > Thanking You,
> > Rita Maji
> > NISER, Bhubaneswar
>
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
>
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>


scf0.in
Description: Binary data
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Re: [Pw_forum] LSDA calculation with Hybrid functional

[Lorenzo Paulatto]

Hi Rita,
my guess is that the calculation is just much slower than you expect! Exact 
exchange is slow in general.

Try to do a test run with:
- only one k-point
- a much lower cutoff

This will give you an idea of the time it will take to reach convergence, than 
you can start to crank it up.

Note that the time should increase with cutoff to power 3/2 and with the square 
of the number of k-points ! 

You may also want to set nqx1, nqx2, nqx3 to a divisor of the number of k-
points in the three directions (no luck with 7, I'm afraid!) which reduces the 
exchange integral to a subset of the k-points, at the expenses of some 
accuracy

cheers



On Friday, October 28, 2016 7:54:59 PM CEST Rita Maji wrote:
> Hi Lorenzo,
> I am doing LSDA calculation for a 5x5 doped graphene calculation, to see
> the change in magnetic property for hybrid functional I am trying to do
> with PBE0, it is taking long time and also not printing total energy at
> each scf steps so that I can see whether it is converging properly or not,
> and also not showing any error during running. First time I am using Hybrid
> functional so I have used all default parameters as of now, Here I have
> attached the input file, any suggestion will be very much helpful.
> 
> Thanks,
> Rita
> 
> On Fri, Oct 28, 2016 at 2:31 PM, Lorenzo Paulatto <
> 
> lorenzo.paula...@impmc.upmc.fr> wrote:
> > Dear Rita,
> > please provide more details.
> > 
> > kind regards
> > 
> > On Friday, October 28, 2016 11:01:09 AM CEST Rita Maji wrote:
> > > Dear all,
> > > during LSDA calcultion with hybrid functional (PBE0) it is not writing
> > > total and absolute magnetization and also all the contribution to total
> > > energy, can anybody help me .
> > > 
> > > 
> > > Thanking You,
> > > Rita Maji
> > > NISER, Bhubaneswar
> > 
> > --
> > Dr. Lorenzo Paulatto
> > IdR @ IMPMC -- CNRS & Université Paris 6
> > phone: +33 (0)1 44275 084 / skype: paulatz
> > www:   http://www-int.impmc.upmc.fr/~paulatto/
> > mail:  23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
> > 
> > ___
> > Pw_forum mailing list
> > Pw_forum@pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum


-- 
Dr. Lorenzo Paulatto 
IdR @ IMPMC -- CNRS & Université Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05

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[Pw_forum] Stability

[systec...@yahoo.com]

I am beginner, I am asking please witch test to do to prove the existence or 
stability of a new structure before losing time and reagents to 
synthesize.please link of tutorial in this case.

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Re: [Pw_forum] LSDA calculation with Hybrid functional

[Rita Maji]

Hi Lorenzo,
Thanks for your quick reply.

Thanks,
Rita

On Fri, Oct 28, 2016 at 8:17 PM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

> Hi Rita,
> my guess is that the calculation is just much slower than you expect! Exact
> exchange is slow in general.
>
> Try to do a test run with:
> - only one k-point
> - a much lower cutoff
>
> This will give you an idea of the time it will take to reach convergence,
> than
> you can start to crank it up.
>
> Note that the time should increase with cutoff to power 3/2 and with the
> square
> of the number of k-points !
>
> You may also want to set nqx1, nqx2, nqx3 to a divisor of the number of k-
> points in the three directions (no luck with 7, I'm afraid!) which reduces
> the
> exchange integral to a subset of the k-points, at the expenses of some
> accuracy
>
> cheers
>
>
>
> On Friday, October 28, 2016 7:54:59 PM CEST Rita Maji wrote:
> > Hi Lorenzo,
> > I am doing LSDA calculation for a 5x5 doped graphene calculation, to see
> > the change in magnetic property for hybrid functional I am trying to do
> > with PBE0, it is taking long time and also not printing total energy at
> > each scf steps so that I can see whether it is converging properly or
> not,
> > and also not showing any error during running. First time I am using
> Hybrid
> > functional so I have used all default parameters as of now, Here I have
> > attached the input file, any suggestion will be very much helpful.
> >
> > Thanks,
> > Rita
> >
> > On Fri, Oct 28, 2016 at 2:31 PM, Lorenzo Paulatto <
> >
> > lorenzo.paula...@impmc.upmc.fr> wrote:
> > > Dear Rita,
> > > please provide more details.
> > >
> > > kind regards
> > >
> > > On Friday, October 28, 2016 11:01:09 AM CEST Rita Maji wrote:
> > > > Dear all,
> > > > during LSDA calcultion with hybrid functional (PBE0) it is not
> writing
> > > > total and absolute magnetization and also all the contribution to
> total
> > > > energy, can anybody help me .
> > > >
> > > >
> > > > Thanking You,
> > > > Rita Maji
> > > > NISER, Bhubaneswar
> > >
> > > --
> > > Dr. Lorenzo Paulatto
> > > IdR @ IMPMC -- CNRS & Université Paris 6
> > > phone: +33 (0)1 44275 084 / skype: paulatz
> > > www:   http://www-int.impmc.upmc.fr/~paulatto/
> > > mail:  23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris
> Cédex 05
> > >
> > > ___
> > > Pw_forum mailing list
> > > Pw_forum@pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
>
> ___
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> http://pwscf.org/mailman/listinfo/pw_forum
>
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Re: [Pw_forum] [Non-DoD Source] Re: QE 6.0 intel compile 'open socket' error

[Downs, Andrew S CTR USARMY ARL (US)]

Hi Paolo,

Configure does seem to notice mkl and adds it on the  include line, but it 
doesn't do anything else.

Configure automatically did this:

IFLAGS = -I$(TOPDIR)/include -I../include/ 
-I/opt/intel/compilers_and_libraries_2016.0.109/linux/mkl/include

And I think that's right.  However, on my BLAS_LIBS, it seems like no matter 
what I put there I get undefined reference errors.

(it's a pain to type in because of how outlook works, just pretend these are 
all complete lines, I'm just trying to show what files I'm linking against)

BLAS_LIBS  =  
/opt/intel/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64_lin/libmkl_core.a
 
libmkl_sequential.a
libmkl_gf_lp64.a
libmkl_intel_thread.a
libmkl_intel_lp64.a
libmkl_core.a

BLAS_LIBS_SWITCH = external

When I had it link against just 'libmkl_core.a' I got some undefined 
references, but very few.  For each undefined reference, I went to the library 
directory and did a search inside all files to find which files contained the 
function that caused the undefined reference, and then added that file to my 
link line.  Now I have so many undefined references I can't scroll all the way 
back in my shell history.

If anybody has managed to compile statically with a 2016 intel compiler, I 
would *love* to know what you linked against.

-Andrew


-Original Message-
From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf 
Of Paolo Giannozzi
Sent: Friday, October 28, 2016 1:46 AM
To: PWSCF Forum 
Subject: Re: [Pw_forum] [Non-DoD Source] Re: QE 6.0 intel compile 'open socket' 
error

All active links contained in this email were disabled. Please verify the 
identity of the sender, and confirm the authenticity of all links contained 
within the message prior to copying and pasting the address to a Web browser. 






"configure" recognizes mkl, if present and properly installed. The link to 
libraries should be in BLAS_LIBS, but you may also need to specify in IFLAGS 
the directory where files to be included can be found.


Paolo


On Thu, Oct 27, 2016 at 9:47 PM, Downs, Andrew S CTR USARMY ARL (US) 
mailto:andrew.s.downs3@mail.mil > > 
wrote:


Paolo,

Thank you.  On which line in the make.inc would I link them?  Is there 
an example for intel/MKL builds?

-Andrew Downs

-Original Message-
From: pw_forum-boun...@pwscf.org < 
Caution-mailto:pw_forum-boun...@pwscf.org >  
[Caution-mailto:pw_forum-boun...@pwscf.org < 
Caution-mailto:pw_forum-boun...@pwscf.org > ] On Behalf Of Paolo Giannozzi
Sent: Thursday, October 27, 2016 3:42 PM
To: PWSCF Forum mailto:pw_forum@pwscf.org 
> >
Subject: [Non-DoD Source] Re: [Pw_forum] QE 6.0 intel compile 'open 
socket' error

All active links contained in this email were disabled. Please verify 
the identity of the sender, and confirm the authenticity of all links contained 
within the message prior to copying and pasting the address to a Web browser.






Intel DFTI FFT's are contained in the Intel MKL libraries. You should 
link them if you have them installed


Paolo


On Thu, Oct 27, 2016 at 8:10 PM, Downs, Andrew S CTR USARMY ARL (US) 
mailto:andrew.s.downs3@mail.mil >  
< Caution-Caution-mailto:andrew.s.downs3@mail.mil < 
Caution-mailto:andrew.s.downs3@mail.mil >  > > wrote:


Hello again,

I did eventually get QE6.0 to build on our Cray XC-40 by 
setting the arch type to crayxt, and some other small changes, however, I can 
only get it to work with GCC.  I'd really like to compile it with Intel (we 
have Intel 16)  but for whatever reason, it seems like no matter what I change, 
I always get hung up on the same 'open socket' spot.

Build output:

ftn -openmp -o pw.x \
   pwscf.o  libpw.a ../../Modules/libqemod.a 
../../FFTXlib/libqefft.a ../../LAXlib/libqela.a 
/p/home/adowns/useraide/qe6/qe-6.0//clib/clib.a 
/p/home/adowns/useraide/qe6/qe-6.0//iotk/src/libiotk.a
/p/home/adowns/useraide/qe6/qe-6.0//clib/clib.a(sockets.o): In 
function `open_socket':
sockets.c:(.text+0x88): warning: Using 'getaddrinfo' in 
statically linked applications requires at runtime the shared libraries from 
the glibc version used for linking
../../FFTXlib/libqefft.a(fft_scalar.o): In function 
`fft_scalar_mp_cft_1z_':
fft_scalar.f90:(.text+0x38f): undefined reference to 
`dfti_compute_backward_zz'
fft_scalar.f90:(.text+0x74f): undefined reference to 
`dfti_compute_forward_zz'
../../FFTXlib/libqefft.a(fft_scalar.o): In function 
`fft_scalarcft_1z_mp_init_dfti_':
fft_scalar.f90:(

[Pw_forum] Gathering 3-d arrays across pools using QE's mp_sum

[Vahid Askarpour]

Dear QE Users,

I am working on some modifications to the QE-6.0 code using symmetry. When I 
try to combine a 3-D array scattered across nodes, I use the following:

output(3,nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=input(3,nbnds,1:k_pool)

Here, nbnds is the number of bands, k_pool is the number of k points/pool, and 
pool_id is the id of the pool. Here I am assuming the the number of k points is 
divisible by the number of pools.

Then I call mp_sum(output,inter_pool_comm) to put all the segments of input 
across the nodes  into one output file.

When I run the modified QE code in parallel, the output file is different from 
the serial run.

Does the QE's mp_sum allow the above operation for a three-D array?

Any hints or suggestions would be greatly appreciated.

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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Re: [Pw_forum] Gathering 3-d arrays across pools using QE's mp_sum

[Ye Luo]

In Fortran, whatever-D array is 1-D array. mp_sum should be fine.
I saw something strange in your code that you were not copying the right
things as you expected.
How about the following?
output(1:3,1:nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=
input(1:3,1:nbnds,1:k_pool)

Ye

===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2016-10-28 12:29 GMT-05:00 Vahid Askarpour :

> Dear QE Users,
>
> I am working on some modifications to the QE-6.0 code using symmetry. When
> I try to combine a 3-D array scattered across nodes, I use the following:
>
> output(3,nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=
> input(3,nbnds,1:k_pool)
>
> Here, nbnds is the number of bands, k_pool is the number of k points/pool,
> and pool_id is the id of the pool. Here I am assuming the the number of k
> points is divisible by the number of pools.
>
> Then I call mp_sum(output,inter_pool_comm) to put all the segments of
> input across the nodes  into one output file.
>
> When I run the modified QE code in parallel, the output file is different
> from the serial run.
>
> Does the QE's mp_sum allow the above operation for a three-D array?
>
> Any hints or suggestions would be greatly appreciated.
>
> Vahid
>
> Vahid Askarpour
> Department of Physics and Atmospheric Science
> Dalhousie University,
> Halifax, NS, Canada
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Re: [Pw_forum] Gathering 3-d arrays across pools using QE's mp_sum

[Vahid Askarpour]

Hi Ye,

Thank you for your suggestion. I tried it and when I ran the code, it 
seg-faulted. I put flags in the code to see where the segmentation faults 
occurs. It happens as the code calls mp_sum. It seems that mp_sum may not
be able to handle this reduction.

Cheers,
Vahid

On Oct 28, 2016, at 2:51 PM, Ye Luo 
mailto:xw111lu...@gmail.com>> wrote:

In Fortran, whatever-D array is 1-D array. mp_sum should be fine.
I saw something strange in your code that you were not copying the right things 
as you expected.
How about the following?
output(1:3,1:nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=input(1:3,1:nbnds,1:k_pool)

Ye

===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2016-10-28 12:29 GMT-05:00 Vahid Askarpour 
mailto:vh261...@dal.ca>>:
Dear QE Users,

I am working on some modifications to the QE-6.0 code using symmetry. When I 
try to combine a 3-D array scattered across nodes, I use the following:

output(3,nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=input(3,nbnds,1:k_pool)

Here, nbnds is the number of bands, k_pool is the number of k points/pool, and 
pool_id is the id of the pool. Here I am assuming the the number of k points is 
divisible by the number of pools.

Then I call mp_sum(output,inter_pool_comm) to put all the segments of input 
across the nodes  into one output file.

When I run the modified QE code in parallel, the output file is different from 
the serial run.

Does the QE's mp_sum allow the above operation for a three-D array?

Any hints or suggestions would be greatly appreciated.

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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[Pw_forum] structure stability

[systec...@yahoo.com]

  I am beginner on quantum espresso so, I am asking please witch test to do to 
prove the existence or stability of a new structure before losing time and 
reagents to synthesize.please link of tutorial in this case.

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