Re: [QE-users] compilation errors @ QE 6.8 version

2021-08-03 Thread Takahiro Chiba 
Dear Venkatesh,

I am sorry, but I am not able to tell you more. Your make.inc is still
messed up, possibly because you "sed"ed after "./configure".

---Sender---
Takahiro Chiba
1st-year student at grad. school of chem. sci. and eng., Hokkaido Univ.
Expected graduation date: Mar. 2023
takahiro_ch...@eis.hokudai.ac.jp
-
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[QE-users] No plane waves found: running on too many processors?

2021-08-03 Thread SYED ZAIN MEHMOOD 
I was vc-relaxing a bulk structure of a Rare Earth element "Gd" and it was
taking so long for *48 processors*. Now when i tried to run *pw.x* on *240
processors* there occurred an error as follows

" from n_plane_waves : error # 1
 No plane waves found: running on too many processors?   "

I have searched through the mail archives and found a 10 years old thread
about it,  a useful discussion between Payam Norouzzadeh and *Paolo
Giannozzi. *Though it was suggested to reduce the number of processors, the
issue was gone.
 I want to ask the reason for the error in the first place. Is Quantum
ESPRESSO limited to some specific maximum number of processors that it can
use ? If it is so, how many maximum processors can be used ?
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Re: [QE-users] [SUSPECT ATTACHMENT REMOVED] [QE-GPU] OpenMP is not working with my compilation

2021-08-03 Thread Takahiro Chiba 
Dear Spiga,

Thank you for the reply. I will ask admin how to do that.

---Sender---
Takahiro Chiba
1st-year student at grad. school of chem. sci. and eng., Hokkaido Univ.
Expected graduation date: Mar. 2023
takahiro_ch...@eis.hokudai.ac.jp
-

2021年8月3日(火) 17:55 Filippo Spiga :
>
> Dear Takahiro,
>
> if the cluster supports containers, you could try to deploy the Quantum 
> ESPRESSO on the NVIDIA GPU Cloud (NCG). See here: 
> https://ngc.nvidia.com/catalog/containers/hpc:quantum_espresso (latest 
> version uploaded is v6.7)
>
> Make sure you run the calculation only on the socket where the GPU is 
> attached. Consult your HPC centre User Support team to understand how to do 
> it.
>
> --
> Filippo SPIGA ~ http://fspiga.github.io ~ skype: filippo.spiga
>
>
> On Mon, 2 Aug 2021 at 00:01, Takahiro Chiba 
>  wrote:
>>
>> Dear experienced users,
>>
>> I have trouble in utilizing OpenMP with my compilation. From the
>> output file, pw.x 6.8 recognizes "OMP_NUM_THREADS=2", but it took same
>> time as "OMP_NUM_THREADS=1", and according to PBS batch queue, only
>> 100% (not 200%) of CPU is used. Therefore, QE 6.8 with GPU is not as
>> fast as expected.
>>
>> I used nvidia HPC SDK 20.9, cuda 10.1, and Intel MKL 2021.2. The node
>> has two Xeon Gold 6248, one Tesla V100 32GB, and 768GB of RAM.
>> Benchmark results and make.inc are attached as tarball.
>>
>> Could you please point out my mistake?
>>
>> ---Sender---
>> Takahiro Chiba
>> 1st-year student at grad. school of chem. sci. and eng., Hokkaido Univ.
>> Expected graduation date: Mar. 2023
>> takahiro_ch...@eis.hokudai.ac.jp
>> -
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>
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Re: [QE-users] Atomic velocities units

2021-08-03 Thread Lorenzo Paulatto 
It is a trivial fix, but I'm away from my pc for a couple of weeks. It is
fixed in my gitlab fork

https://gitlab.com/paulatz/q-e/-/commit/2c1e1d3d8b5c47639ba1af3842d187d5903115c5

-- 
Lorenzo Paulatto

On Mon, Aug 2, 2021, 17:18 valeria arteaga muñiz 
wrote:

> Thank you both for your replies.
> Okay, I will take that into consideration. Actually I wanted to use the
> atomic velocities together with the svr thermostat, do you suggest any
> other method since that one doesn't work well with the atomic velocities?
>
> Best,
> Valeria
>
> Valeria
>
> --
> *From:* users  on behalf of
> Paolo Giannozzi 
> *Sent:* Monday, August 2, 2021 8:47:07 AM
> *To:* Quantum ESPRESSO users Forum 
> *Subject:* Re: [QE-users] Atomic velocities units
>
> From a quick look at the code, it seems to me that the documentation is
> correct for both pw.x and cp.x. For cp.x,  the velocities are given with
> the same logic as for the atomic positions (in A, Bohr, units of lattice
> parameter, crystal units) divided by time in hartree a.u. (2.4189*10^-17 s)
> ; for pw.x, the velocities are always given in Bohr divided by Rydberg a.u.
> for time (4.8378*10^-17 s). I am rather puzzled by the cp.x logic, but this
> is how it works right now
>
> Paolo
>
> On Fri, Jul 30, 2021 at 3:07 PM Lorenzo Paulatto 
> wrote:
>
> I'm not sure, actually the time conversion I gave you is for pw.x, as cp.x
> use Hartree units instead of Rydberg for the energy there is a possible
> factor 2 difference (the base to find out this conversion is keep in mind
> that [ħ]=J·s=1 in atomic units.
>
> The input manual says that pw.x velocities are just "atomic units", no
> conversion is done in the code as far as I could see.
>
> Also keep in mind that ATOMIC_VELOCITIES is a seldom used feature, and may
> have bugs (i.e. I recently found out that it does not work with svr
> thermostat because of a little bug)
>
> hth
>
> --
> Lorenzo Paulatto - Paris
> On Jul 29 2021, at 8:17 pm, valeria arteaga muñiz 
> wrote:
>
>
> Hello Lorenzo,
>
> Thanks for your reply. This is also for the pw.x code, right?
>
>
>
> Best,
>
> Valeria
>
>
>
> *From: *Lorenzo Paulatto
> 
> *Sent: *Thursday, July 29, 2021 11:18 AM
> *To: *Quantum ESPRESSO users Forum
> 
> *Cc: *users@lists.quantum-espresso.org
> 
> *Subject: *Re: [QE-users] Atomic velocities units
>
>
> It depends on which units you have specified for atomic positions.
> Regarding time,
> 1 a.u.=4.8378 * 10^-17 s
>
>
> kind regards
>
>
> --
> Lorenzo Paulatto - Paris
> On Jul 29 2021, at 5:20 am, valeria arteaga muñiz 
> wrote:
>
>   Hello everyone. I am trying to perform a MD run using the pw.x code. I'd
> like to use the atomic positions and also velocities from another run in
> Angstroms and Å/picoseconds to the QE input, but I am not sure about the
> units I need to use. In the documentation, there says it should be atomic
> units, and when I read the co.c documentation it was the same, but in the
> description they mentioned we needed to use the units as they're in the
> atomic positions card and time in a.u. does anyone have an idea of what
> convertion should I use?
> Thanks for your time
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
>
> ___
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>
> [image: Sent from Mailspring]
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>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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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] Problem running relax and vc-relax after soft mode phase transition theory

2021-08-03 Thread Shahar Zuri 
Dear Users,

I am trying to recreate the phase transition of Fe4N P2/m at 10GPa.
I am trying to run the following .in file to get the new atomic positions:


  calculation = 'relax'
  etot_conv_thr =   5.00d-05
  forc_conv_thr =   1.00d-04
  outdir = './out/'
  pseudo_dir = './pseudo/'
  tprnfor = .true.
  tstress = .true.
  verbosity = 'high'
/

  degauss =   1.4699723600d-02
  ecutrho =   600
  ecutwfc =   100
  ibrav = 0
  nat = 7
  nspin = 2
  ntyp = 2
  occupations = 'smearing'
  smearing = 'cold'
  starting_magnetization(1) =   3.125000d-01
  starting_magnetization(2) =   1.00d-01
/

  conv_thr =   1.00d-09
  electron_maxstep = 80
  mixing_beta =   4.00d-01
/

  ion_dynamics='bfgs',
/
ATOMIC_SPECIES
Fe 55.845 Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
N  14.0067 N.pbe-n-radius_5.UPF
ATOMIC_POSITIONS crystal
Fe   0.50   0.50   0.00
Fe   0.729400   0.00   0.729300
Fe   0.764050   0.00   0.235870
Fe   0.00   0.50   0.00
Fe   0.00   0.50   0.50
Fe   0.50   0.50   0.50
N0.748940   0.50   0.748930
K_POINTS automatic
9 9 9 0 0 0
CELL_PARAMETERS angstrom
  5.247800   0.00   0.00
  0.00   3.719800   0.00
  0.00   0.00   5.247800

I got this information from the following paper:
Spontaneous magnetization-induced phonons stability in c0-Fe4N crystalline
alloys and high-pressure new phase

However, my process is killed before starting self consistancy iterations.
How can I solve this issue?

The original structure at 0GPa was calculated and optimized by the
following scf calculation:



  calculation = 'scf'

  etot_conv_thr =   5.00d-05

  forc_conv_thr =   1.00d-04

  outdir = './out/'

  prefix = 'aiida'

  pseudo_dir = './pseudo/'

  tprnfor = .true.

  tstress = .true.

  verbosity = 'high'

/



  degauss =   1.4699723600d-02

  ecutrho =   600

  ecutwfc =   100

  ibrav = 0

  nat = 5

  nosym = .false.

  nspin = 2

  ntyp = 2

  occupations = 'smearing'

  smearing = 'cold'

  starting_magnetization(1) =   3.125000d-01

  starting_magnetization(2) =   1.00d-01

/



  conv_thr =   1.00d-09

  electron_maxstep = 80

  mixing_beta =   4.00d-01

/

ATOMIC_SPECIES

Fe 55.845 Fe.pbe-spn-kjpaw_psl.0.2.1.UPF

N  14.0067 N.pbe-n-radius_5.UPF

ATOMIC_POSITIONS crystal

Fe   0.00   0.50   0.50

Fe   0.50   0.50   0.00

Fe   0.50   0.00   0.50

Fe   0.00   0.00   0.00

N0.50   0.50   0.50

K_POINTS automatic

9 9 9 0 0 0

CELL_PARAMETERS angstrom

  3.7727505860   0.00   0.00

  0.00   3.7727505860   0.00

  0.00   0.00   3.7727505860

Best wishes,
*Shahar Zuri | PhD student*
*Lifshitz research group*
Technion institute of technology
Schulich chemistry faculty, Solid-State institute, Hellen-Diller quantum
center
M +972-52-2769169 | shaharz...@gmail.com, shaharz...@campus.technion.ac.il
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[QE-users] Can not compile on MAC

2021-08-03 Thread Ola Starkolis 
Hi guys,

I have a problem compiling QE on my mac computer.
Here it is
Darwin MacBook-Air.local 20.6.0 Darwin Kernel Version 20.6.0: Wed Jun 23
00:26:31 PDT 2021; root:xnu-7195.141.2~5/RELEASE_X86_64 x86_64

./configure runs just fine, here is the output

The following libraries have been found:
  BLAS_LIBS= -lblas
  LAPACK_LIBS=-L/usr/local/lib -llapack  -lblas
  FFT_LIBS=-L/usr/local/lib -lfftw3

I've change CPP = cpp to CPP  = gcc -E in make.inc file
Running make all gives me another mistake:

   41 |
  |  1
Fatal Error: fftw3.f03: No such file or directory
compilation terminated.
make[1]: *** [fft_scalar.FFTW3.o] Error 1
make: *** [libfft] Error 1

Any help guys? Thank you so much in advance.
Big thank to all who can give some solutions
to the problem.

Ola.
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Re: [QE-users] compilation errors @ QE 6.8 version

2021-08-03 Thread venky ch 
Dear Takahiro Chiba,

Thanks for your email. I have removed the libxc path. But as my MKL doesn't
have a fftw library, I have to use fftw libraries from my local
fftw_folder.

Although, it seems that the errors before are eliminated, another error
came out after the compilation as shown below. I have attached the
"make.inc" for your reference.


==

make[1]: Entering directory `/home/proj/21/isuch/soft/QE/q-e-qe-6.8/upflib'
mpiifort -O2 -assume byterecl -g -traceback -openmp -nomodule -fpp -D__FFTW
-D__MPI -D__SCALAPACK   -I/home/proj/21/isuch/soft/QE/q-e-qe-6.8/include
-I/home/proj/21/isuch/soft/QE/q-e-qe-6.8/FoX/finclude
-I/home/proj/21/isuch/soft/fftw/include
-I/opt/intel/composer_xe_2013.1.117/mkl/include
-I/home/proj/21/isuch/soft/QE/q-e-qe-6.8/Modules
-I/home/proj/21/isuch/soft/QE/q-e-qe-6.8/FoX/finclude -I../UtilXlib
-I../external/devxlib/src -c init_us_2_base_gpu.f90
init_us_2_base_gpu.f90(24): error #7002: Error in opening the compiled
module file.  Check INCLUDE paths.   [DEVICE_FBUFF_M]
  USE device_fbuff_m,   ONLY : dev_buf
--^
init_us_2_base_gpu.f90(95): error #6406: Conflicting attributes or multiple
declaration of name.   [DEV_BUF]
  CALL dev_buf%lock_buffer(vkb1_d, (/ npw_, nhm /), istat(1) )

.
.
.
.
.

init_us_2_base_gpu.f90(24): error #6580: Name in only-list does not exist.
  [DEV_BUF]
  USE device_fbuff_m,   ONLY : dev_buf
---^
compilation aborted for init_us_2_base_gpu.f90 (code 1)
make[1]: *** [init_us_2_base_gpu.o] Error 1
make[1]: Leaving directory `/home/proj/21/isuch/soft/QE/q-e-qe-6.8/upflib'
make: *** [libupf] Error 1

=

thanks



On Mon, Aug 2, 2021 at 1:52 PM Takahiro Chiba <
takahiro_ch...@eis.hokudai.ac.jp> wrote:

> Dear Venkatesh,
>
> First of all, I am not a professor, just a graduate school student.
>
> According to errors, I think it is related to libxc. I cannot advise
> you on this because I don't know much. I recommend that you should
> firstly compile with minimal dependencies, which means, how about with
> neither libxc nor fftw3? As far as I know, you don't need to link
> FFTW3 because MKL offers FFT(-D__DFTI).
>
> P.S.
> Please disclose your academic affiliation. Here, almost everyone does.
>
> ---Sender---
> Takahiro Chiba
> 1st-year student at grad. school of chem. sci. and eng., Hokkaido Univ.
> Expected graduation date: Mar. 2023
> takahiro_ch...@eis.hokudai.ac.jp
> -
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> users mailing list users@lists.quantum-espresso.org
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>


-- 
Venkatesh
Postdoctoral Fellow,
Department of Instrumentation and Applied Physics
IISc Bangalore, India


make.inc
Description: Binary data
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[QE-users] Forces are oscillating for P

2021-08-03 Thread Dr. K. C. Bhamu 
Dear QE Users,
I am trying to run phosphorus  with QE_6.4 but the forces are
oscillating between two values as shown below:
scf.in.out: Total force = 0.008737 Total SCF correction =
0.02
scf.in.out: Total force = 0.014135 Total SCF correction =
0.02
scf.in.out: Total force = 0.008737 Total SCF correction =
0.02
scf.in.out: Total force = 0.014135 Total SCF correction =
0.02

Could you please advise me on how can I handle this?
Below is my input file.


  calculation = 'vc-relax'
   etot_conv_thr = 0.0001
   forc_conv_thr = 0.001
  outdir = './tmp'
  prefix = 'pwscf'
  pseudo_dir = './PPs'
  tprnfor = .true.
  tstress = .true.
/

  degauss =   1.4699723600d-02
  ecutrho =   4.50d+02
  ecutwfc =   4.50d+01
  ibrav = 0
  nat = 24
  nosym = .false.
  ntyp = 1
  occupations = 'smearing'
  smearing = 'cold'

/

  conv_thr =   1.00d-010
  electron_maxstep = 100
  mixing_beta =   3.00d-01
/

ion_dynamics = 'bfgs'
 /

/
ATOMIC_SPECIES
  P 30.973800d0 P.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
P0.072058   0.002225   0.186819
P0.927942   0.997775   0.813181
P0.850467   0.952993   0.312077
P0.149533   0.047007   0.687923
P0.006843   0.134953   0.309157
P0.993157   0.865047   0.690843
P0.221928   0.011505   0.366927
P0.778072   0.988495   0.633073
P0.763585   0.368292   0.057523
P0.236415   0.631708   0.942477
P0.592584   0.186137   0.034895
P0.407416   0.813863   0.965105
P0.513831   0.305591   0.165930
P0.486169   0.694409   0.834070
P0.396884   0.320114   0.985814
P0.603116   0.679886   0.014186
P0.296883   0.682883   0.463448
P0.703117   0.317117   0.536552
P0.947588   0.627152   0.367824
P0.052412   0.372848   0.632176
P0.201284   0.515294   0.359954
P0.798716   0.484706   0.640046
P0.236519   0.676026   0.277493
P0.763481   0.323974   0.722507
K_POINTS automatic
6 3 3 0 0 0
CELL_PARAMETERS angstrom
  6.024789   0.00   0.00
 -2.0978219998  11.6760139950   0.00
 -1.8239009989  -1.2036659990  11.818676


Regards
Bhamu
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Re: [QE-users] [SUSPECT ATTACHMENT REMOVED] [QE-GPU] OpenMP is not working with my compilation

2021-08-03 Thread Filippo Spiga 
Dear Takahiro,

if the cluster supports containers, you could try to deploy the Quantum
ESPRESSO on the NVIDIA GPU Cloud (NCG). See here:
https://ngc.nvidia.com/catalog/containers/hpc:quantum_espresso (latest
version uploaded is v6.7)

Make sure you run the calculation *only* on the socket where the GPU is
attached. Consult your HPC centre User Support team to understand how to do
it.

--
Filippo SPIGA ~ http://fspiga.github.io ~ skype: filippo.spiga


On Mon, 2 Aug 2021 at 00:01, Takahiro Chiba <
takahiro_ch...@eis.hokudai.ac.jp> wrote:

> Dear experienced users,
>
> I have trouble in utilizing OpenMP with my compilation. From the
> output file, pw.x 6.8 recognizes "OMP_NUM_THREADS=2", but it took same
> time as "OMP_NUM_THREADS=1", and according to PBS batch queue, only
> 100% (not 200%) of CPU is used. Therefore, QE 6.8 with GPU is not as
> fast as expected.
>
> I used nvidia HPC SDK 20.9, cuda 10.1, and Intel MKL 2021.2. The node
> has two Xeon Gold 6248, one Tesla V100 32GB, and 768GB of RAM.
> Benchmark results and make.inc are attached as tarball.
>
> Could you please point out my mistake?
>
> ---Sender---
> Takahiro Chiba
> 1st-year student at grad. school of chem. sci. and eng., Hokkaido Univ.
> Expected graduation date: Mar. 2023
> takahiro_ch...@eis.hokudai.ac.jp
> -
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