[QE-users] Molecular Orbital Isovalue/Grid Value meaning?

[Jeremy Richard]

Hello,

I'm working on plotting many molecular orbitals for a system and just have
a question about the isovalues. What exactly do they represent? Like on
some orbitals I can do +/- 0.05, on others it's as low as +/- 0.0005, and
some there is essentially 0 for one sign and on the order of 0.01 for the
other sign.

Just for the purposes of comparing orbitals to each other it would be good
to know exactly yeah the isovalues represent.

Thank you,

Jeremy RIchard
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Re: [QE-users] Atomic velocities units

[valeria arteaga muñiz]

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 
mailto:paul...@gmail.com>> 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 
mailto:valitze...@hotmail.com>> 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 
mailto:valitze...@hotmail.com>> 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
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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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Re: [QE-users] Atomic velocities units

[Paolo Giannozzi]

>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
>
>
>
>
> ___
> 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
>
> [image: Sent from Mailspring]
> ___
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> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users



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

[Paolo Giannozzi]

I don't think there is any mistake: when GPU's are used, OpenMP has the
rather marginal role of speeding up some calculations that are not
GPU-accelerated

Paolo

On Mon, Aug 2, 2021 at 1:01 AM 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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> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users



-- 
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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Re: [QE-users] Electron-phonon with Hubbard U is not supported

[Iurii TIMROV via users]

Dear Dr. Grant,


Thank you for the references! We are pleased that you find our recent paper on 
arXiv about e-ph+U in CoO interesting! These advanced studies were possible 
thanks to the development of DFPT+U by Andrea Floris, Matteo Cococcioni, and 
coworkers (PRB 84, 161102(R) (2011) and PRB 101, 064305 (2020)). Let us stay in 
touch for further discussions about e-ph+U based on DFPT+U.


Best regards,

Iurii


--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: W2AGZ 
Sent: Saturday, July 31, 2021 7:06:52 AM
To: Iurii TIMROV; 'Quantum ESPRESSO users Forum'
Subject: RE: [QE-users] Electron-phonon with Hubbard U is not supported

Dear Iurii,
Paul Grant here. Not sure if we’ve met during my many planetary travels over my 
long careers at IBM and EPRI.  Please go to www.w2agz.com 
.  I was taught “molecular structure computational methods” by two of its 
pioneers Frank Herman and Enrico Clementi while I was at IBM.  When I became a 
manager, I hired John Hubbard into my group (John and I filed two “trade 
secrets” which I’m not allowed to disclose yet!).
To the point, I enjoyed reading your arxiv paper.  I’m one of the “founders” of 
the structure of the copper oxide perovskites which IBM internationally 
patented back in April, 1987.  I immediately began calculations  of the 
electron-phonon pair coupling which I continued for two decades, especially 
using Quantum-Espresso, in the hope of being able to predict magnon-spin 
pairing in the CuO perovskites.  However, as you point out QE to date cannot 
accommodate spin and lattice interactions at the same time to incorporate into 
a BCS model.  The best I’ve been able to do was published in 2008 here 
http://w2agz.com/Publications/Science%20&%20Technology/W2AGZ/06%20(2008)%20Electronic%20Properties%20of%20Cubic%20Rocksalt%20CuO,%20IOP-CS%20129,%20012042%20(2008).pdf
 .  Overall summaries can be found at 
http://w2agz.com/Publications/Science%20&%20Technology/W2AGZ/11%20(2017)%20Superconducting%20Flucturations%20in%20One-dimensional%20Quasi-periodic%20%20Metallic%20Chains,%20(6-30-2017%20Submitted)%20QSMF-S-17-00033.pdf
 and the article following by Gulian, et al. 
https://doi.org/10.1007/40509-017-0125-y .
Best and Keep in Touch,

Paul Michael Grant, PhD
Physicist and Science Writer
Senior Life Fellow, American Physical Society
Fellow, Institute of Physics, United Kingdom
Senior Member, IEEE
Member, MRS (1977-Present)
APS Distinguished Lecturer on Applications of Physics (2014-15)
Staff Associate, Jet Propulsion Laboratory, NASA (2011-18)
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member/Manager Emeritus
Principal, W2AGZ Technologies
w2...@w2agz.com
http://www.w2agz.com

From: users [mailto:users-boun...@lists.quantum-espresso.org] On Behalf Of 
Iurii TIMROV via users
Sent: Friday, July 30, 2021 12:49 AM
To: 526587466; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Electron-phonon with Hubbard U is not supported


Also, have a look at this paper: https://arxiv.org/pdf/2102.06840.pdf


Iurii



--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users  on behalf of 526587466 
via users 
Sent: Friday, July 30, 2021 9:29:06 AM
To: QEforum
Subject: [QE-users] Electron-phonon with Hubbard U is not supported

Dear Sir,

When performing the electron-phonon coupling calculations by the GGA+U methods, 
it prints the error "Electron-phonon with Hubbard U is not supported".  So,  
the QE6.6 does not support the DFT+U calculations for the electron-phonon 
coupling calculations, right?

Thanks.

Best regards,

Roc

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

[Takahiro Chiba]

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

[venky ch]

Dear Prof. takahiro,

Even though I followed your suggestions, the same erros are coming. I
have attached the make.inc file, made as per your suggestions.

thanks

venkatesh

===

mpif90 -openmp -o pw.x \
   pwscf.o  libpw.a ../../Modules/libqemod.a
../../KS_Solvers/libks_solvers.a ../../FFTXlib/libqefft.a
../../LAXlib/libqela.a ../../UtilXlib/libutil.a ../../dft-d3/libdftd3qe.a
/home/proj/21/isuch/soft/QE/q-e-qe-6.4/clib/clib.a
 /home/proj/21/isuch/soft/QE/q-e-qe-6.4/iotk/src/libiotk.a
 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
 -L/home/proj/21/isuch/soft/QE/q-e-qe-6.4/FoX/lib  -lFoX_dom -lFoX_sax
-lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys
 -L/home/proj/21/isuch/soft/fftw/lib -lfftw3 -lmkl_intel_lp64
 -lmkl_intel_thread -lmkl_core
-L/home/proj/21/isuch/soft/libxc_install/lib/ -lxc -lxcf90
../../Modules/libqemod.a(functionals.o): In function `slater':
/home/proj/21/isuch/soft/QE/q-e-qe-6.4/Modules/functionals.f90:31:
undefined reference to `xc_f90_func_init_'
/home/proj/21/isuch/soft/QE/q-e-qe-6.4/Modules/functionals.f90:32:
undefined reference to `xc_f90_lda_exc_vxc_'
/home/proj/21/isuch/soft/QE/q-e-qe-6.4/Modules/functionals.f90:33:
undefined reference to `xc_f90_func_end_'
../../Modules/libqemod.a(functionals.o): In function `pz':


===

On Mon, Aug 2, 2021 at 9:38 AM Takahiro Chiba <
takahiro_ch...@eis.hokudai.ac.jp> wrote:

> Dear venkatesh,
>
> There are so many weird things in your make.inc.
> 1. In DFLAGS line, both D__FFTW and D__DFTI are found. Usually, either
> of the two is found.
> 2. In IFLAGS line, ancient mkl and mpi are included. Why you manually
> add such things?
> 3. CUDA_F90FLAGS is set. In your case, it is expected to be empty.
> 4. -I is found in FFLAGS line.
> 5. Intel MKL is not used in BLAS and LAPACK line.
> etc... In short, your manual modification to make.inc is likely the
> cause of your issue.
>
> Just remove the directory, logout, re-login, untar again, cd to the
> directory, and then
> source
> /home/proj/21/isuch/intel/compilers_and_libraries_2018.0.128/linux/mpi/intel64/bin/mpivars.sh
> source
> /home/proj/21/isuch/intel/compilers_and_libraries_2018.0.128/linux/bin/compilervars.sh
> intel64
> ./configure --enable-openmp --with-scalapack=intel
> will generate an appropriate make.inc for you. This procedure will
> yield something similar to "expected_make.inc". Two "source" lines
> will apply appropriate environment variables to use intel MPI and
> intel compilers 2018.0. If you think this is similar to
> "expected_make.inc", you don't have to modify make.inc. Just "make all
> -j" will generate executables.
>
> I don't know much about libxc, but adding
> "--with-libxc-prefix=/home/proj/21/isuch/soft/libxc_install
> --with-libxc-include=/home/proj/21/isuch/soft/libxc_install/include"
> is good, I think.
>
> ---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2日(月) 11:23 venky ch :
>
> >
> >
> > Dear QE users,
> >
> > The update of the mpi compiler has solved the previous problem. But
> again there is an error while going on further compilation as shown below.
> The same type error came when I tried to compile the QE6.4 also . Kindly
> help me. I am attaching the "make.inc" for your reference.
> >
> > thanks in advance
> >
> > venkatesh
> >
> > ==
> >
> > make[2]: Entering directory
> `/home/proj/21/isuch/soft/QE/q-e-qe-6.8/PW/src'
> > if test -n "" ; then \
> > ( cd ../.. ; make  || exit 1 ) ; fi
> > mpif90 -O3 -g -I/opt/intel/composer_xe_2013.1.117/mkl/include/fftw -cpp
> -D__DFTI -D__MPI -D__SCALAPACK -D__LIBXC -D__FFTW
> -I/home/proj/21/isuch/soft/QE/q-e-qe-6.8//external/devxlib/src
> -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/libxc_install/include
> -I/home/proj/21/isuch/soft/fftw/include
> -I/opt/intel/composer_xe_2013.1.117/mkl/include
> -I/opt/intel/composer_xe_2013.1.117/mkl/include/intel64/lp64
> -I/home/proj/21/isuch/intel/compilers_and_libraries_2018.0.128/linux/mpi/intel64/include
> -I/usr/include -I/home/proj/21/isuch/soft/QE/q-e-qe-6.8//upflib
> -I/home/proj/21/isuch/soft/QE/q-e-qe-6.8//XClib
> -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//FFTXlib
> -I/home/proj/21/isuch/soft/QE/q-e-qe-6.8//LAXlib
> -I/home/proj/21/isuch/soft/QE/q-e-qe-6.8//UtilXlib
> -I/home/proj/21/isuch/soft/QE/q-e-qe-6.8//MBD
> -I/home/proj/21/isuch/soft/QE/q-e-qe-6.8//FoX/finclude -I../../dft-d3/ -c
> pwscf.f90
> > mpif90 -g -I/home/proj/21/isuch/soft/libxc_install/include -o pw.x \
> >pwscf.o  libpw.a ../../Modules/libqemod.a
> ../../KS_Solvers/libks_solvers.a ../../upflib/libupf.a ../../XClib/xc_lib.a
> ../../FFTXlib/libqefft.a ../../LAXlib/libqela.a ../../UtilXlib/libutil.a
> ../../dft-d3/libdftd3qe.a
>