[QE-users] [EXT] Re: QE 6.3-backports + ENVIRON-1.0 installation
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Mon Feb 4 17:09:02 CET 2019
Dear Oliviero
Thank you, it seems to work now (with 6.3-backports). Let me only add
(because it may be useful to developers) that I've also tried with the
current develop branch (snapshot downloaded yesterday), and even if
Environ was successfully installed, the results were wrong (very high
forces on ions, completely different from those obtained with the
regular version).
Best
Giuseppe
"Andreussi, Oliviero" <Oliviero.Andreussi at unt.edu> ha scritto:
> Dear Giuseppe,
>
> The error you are reporting is due to Environ being too picky. After
> several people encountering this issue I realized that the check
> that Environ does on the integral of the electronic density is too
> tight. You can fix this by changing by hand the tolerance of this
> test (is in the file src/environ_types.f90 subroutine
> update_environ_electrons) you can change tol to 1.D-8 or you can
> just comment out the last part of the subroutine where it performs
> this check.
>
> Thanks for reporting the issue. Hope this helps.
>
> Best
>
> Oliviero
>
> Oliviero Andreussi
> --
> Assistant Professor
> Department of Physics
> University of North Texas
> Email: oliviero.andreussi at unt.edu<mailto:oliviero.andreussi at unt.edu>
> Phone: +1-(940)-369-5316
> Skype: olivieroandreussi
> Web: https://sites.google.com/site/olivieroandreussi
>
> On Feb 2, 2019, at 12:10 PM, Giuseppe Mattioli
> <giuseppe.mattioli at ism.cnr.it<mailto:giuseppe.mattioli at ism.cnr.it>>
> wrote:
>
>
> Dear Francesco
> I've downloaded and installed the 6.3-tailored version of
> environ-1.0 without problems, but when I try to use it with pw.x it
> fails at the first scf step
>
> Environ Module
> ==============
>
> Plese cite
> O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136,
> 064102 (2012)
> in publications or presentations arising from this work.
>
> compensation onset threshold = 0.1000E-01
> static permittivity = 78.30
> epsilon calculation mode = electronic
> surface tension in input (dyn/cm) = 50.00
> surface tension in internal units = 0.6423E-04
> external pressure in input (GPa) = -0.35
> external pressure in inter. units = -0.2379E-04
>
> Electrostatic Setup
> -------------------
> electrostatic problem to solve = generalized
> numerical solver adopted = cg
> type of auxiliary density adopted = none
> type of core tool for poisson = fft
> type of core tool for s(r) deriv = analytic
>
> ...
>
> number of k points= 1 gaussian smearing, width (Ry)= 0.0100
> cart. coord. in units 2pi/alat
> k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 1.0000000
>
> Dense grid: 1130075 G-vectors FFT dimensions: ( 180, 180, 180)
>
> Estimated max dynamical RAM per process > 138.27 MB
>
> Estimated total dynamical RAM > 9.18 GB
> Generating pointlists ...
> new r_m : 0.0461 (alat units) 1.3823 (a.u.) for type 1
> new r_m : 0.0250 (alat units) 0.7492 (a.u.) for type 2
> new r_m : 0.0250 (alat units) 0.7492 (a.u.) for type 3
>
> Initial potential from superposition of free atoms
>
> starting charge 291.99815, renormalised to 292.00000
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine update_environ_electrons (1):
> Missmatch in integrated electronic charge
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> stopping ...
>
> QE 6.2.1 version instead runs the very same pw.x input (and the same
> environ.in file) without any problem.
>
> I can provide input files and PPs, if needed.
> Thank you again
> Giuseppe
>
>
> Quoting Francesco Nattino
> <francesco.nattino at epfl.ch<mailto:francesco.nattino at epfl.ch>>:
>
> Dear Giuseppe,
>
> The following Environ version should work with QE 6.3 (the original
> 1.0 version works with QE 6.2.X):
>
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2Folivieroandreussi%2FEnviron%2Ftree%2Fv1.0-QE-6.3&data=02%7C01%7Coliviero.andreussi%40unt.edu%7Cf9c5ee828e0140ee992f08d68939d326%7C70de199207c6480fa318a1afcba03983%7C0%7C0%7C636847278815353356&sdata=pUwmud8XU3p27mB%2B9qOva90xMUCCCoIrceosXVJmD%2FQ%3D&reserved=0
>
> Best,
>
> Francesco Nattino
>
> EPFL
>
>
> On 2/1/19 17:09, Giuseppe Mattioli wrote:
>
> Dear users and developers
> I'm trying to patch the 6.3-backports version with environ 1.0. I'm
> not using 6.3-backports out of caprice: there was an issue with
> neb.x used with lda_plus_u a few months ago, that was fixed in such
> version, so I can possibly update to the current unstable release,
> if needed. Now I need to perform NEB simulations with my system
> embedded in an implicit solvation environment, and I need therefore
> to install the ENVIRON plug-in. However, all I obtain if I follow
> the instructions and recompile the code (on marconi at cineca) is
>
> mpiifort -O2 -assume byterecl -g -traceback -nomodule -fpp -D__DFTI
> -D__MPI -D__FFTW -D__ENVIRON
> -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//include
> -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//FoX/finclude
> -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//S3DE/iotk/include/ -I/cineca/prod/opt/compilers/intel/pe-xe-2017/binary/mkl/include -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//iotk/src -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//Modules -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//FFTXlib -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//LAXlib -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//UtilXlib -I/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports//FoX/finclude -I../ELPA/src -c
> tools_generate_functions.f90
> tools_generate_functions.f90(44): error #6580: Name in only-list
> does not exist. [NL]
> USE gvect, ONLY : nl, nlm, ngm, gg, gstart
> -------------------------------^
> tools_generate_functions.f90(44): error #6580: Name in only-list
> does not exist. [NLM]
> USE gvect, ONLY : nl, nlm, ngm, gg, gstart
> -----------------------------------^
> tools_generate_functions.f90(59): error #6404: This name does not
> have a type, and must have an explicit type. [NL]
> auxg(nl(1:ngm)) = auxr(nl(1:ngm))
> ---------^
> tools_generate_functions.f90(59): error #6514: Substring or array
> slice notation requires CHARACTER type or array. [NL]
> auxg(nl(1:ngm)) = auxr(nl(1:ngm))
> ---------^
> tools_generate_functions.f90(59): error #7973: A numeric or LOGICAL
> data type is required in this context. [NL]
> auxg(nl(1:ngm)) = auxr(nl(1:ngm))
> ---------^
> tools_generate_functions.f90(59): error #6514: Substring or array
> slice notation requires CHARACTER type or array. [NL]
> auxg(nl(1:ngm)) = auxr(nl(1:ngm))
> ---------------------------^
> tools_generate_functions.f90(59): error #7973: A numeric or LOGICAL
> data type is required in this context. [NL]
> auxg(nl(1:ngm)) = auxr(nl(1:ngm))
> ---------------------------^
> tools_generate_functions.f90(64): error #6514: Substring or array
> slice notation requires CHARACTER type or array. [NL]
> auxg(nl(1:ngm)) = auxg(nl(1:ngm)) * auxr(nl(1:ngm))
> ---------^
> tools_generate_functions.f90(64): error #7973: A numeric or LOGICAL
> data type is required in this context. [NL]
> auxg(nl(1:ngm)) = auxg(nl(1:ngm)) * auxr(nl(1:ngm))
> ---------^
> tools_generate_functions.f90(64): error #6514: Substring or array
> slice notation requires CHARACTER type or array. [NL]
> auxg(nl(1:ngm)) = auxg(nl(1:ngm)) * auxr(nl(1:ngm))
> ---------------------------^
> tools_generate_functions.f90(64): error #7973: A numeric or LOGICAL
> data type is required in this context. [NL]
> auxg(nl(1:ngm)) = auxg(nl(1:ngm)) * auxr(nl(1:ngm))
> ---------------------------^
> tools_generate_functions.f90(64): error #6514: Substring or array
> slice notation requires CHARACTER type or array. [NL]
> auxg(nl(1:ngm)) = auxg(nl(1:ngm)) * auxr(nl(1:ngm))
> ---------------------------------------------^
> tools_generate_functions.f90(64): error #7973: A numeric or LOGICAL
> data type is required in this context. [NL]
> auxg(nl(1:ngm)) = auxg(nl(1:ngm)) * auxr(nl(1:ngm))
> ---------------------------------------------^
> tools_generate_functions.f90(66): error #6404: This name does not
> have a type, and must have an explicit type. [NLM]
> IF ( gamma_only ) auxg(nlm(1:ngm)) = CMPLX( REAL(
> auxg(nl(1:ngm)) ), -AIMAG( auxg(nl(1:ngm)) ) ,kind=DP)
> ---------------------------^
> tools_generate_functions.f90(66): error #6514: Substring or array
> slice notation requires CHARACTER type or array. [NLM]
> IF ( gamma_only ) auxg(nlm(1:ngm)) = CMPLX( REAL(
> auxg(nl(1:ngm)) ), -AIMAG( auxg(nl(1:ngm)) ) ,kind=DP)
> ---------------------------^
> tools_generate_functions.f90(66): error #7973: A numeric or LOGICAL
> data type is required in this context. [NLM]
> IF ( gamma_only ) auxg(nlm(1:ngm)) = CMPLX( REAL(
> auxg(nl(1:ngm)) ), -AIMAG( auxg(nl(1:ngm)) ) ,kind=DP)
> ---------------------------^
> tools_generate_functions.f90(66): error #6514: Substring or array
> slice notation requires CHARACTER type or array. [NL]
> IF ( gamma_only ) auxg(nlm(1:ngm)) = CMPLX( REAL(
> auxg(nl(1:ngm)) ), -AIMAG( auxg(nl(1:ngm)) ) ,kind=DP)
> -----------------------------------------------------------^
> tools_generate_functions.f90(66): error #7973: A numeric or LOGICAL
> data type is required in this context. [NL]
> IF ( gamma_only ) auxg(nlm(1:ngm)) = CMPLX( REAL(
> auxg(nl(1:ngm)) ), -AIMAG( auxg(nl(1:ngm)) ) ,kind=DP)
> -----------------------------------------------------------^
> tools_generate_functions.f90(66): error #6514: Substring or array
> slice notation requires CHARACTER type or array. [NL]
> IF ( gamma_only ) auxg(nlm(1:ngm)) = CMPLX( REAL(
> auxg(nl(1:ngm)) ), -AIMAG( auxg(nl(1:ngm)) ) ,kind=DP)
> --------------------------------------------------------------------------------------^ tools_generate_functions.f90(66): error #7973: A numeric or LOGICAL data type is required in this context.
> [NL]
> IF ( gamma_only ) auxg(nlm(1:ngm)) = CMPLX( REAL(
> auxg(nl(1:ngm)) ), -AIMAG( auxg(nl(1:ngm)) ) ,kind=DP)
> --------------------------------------------------------------------------------------^ compilation aborted for tools_generate_functions.f90 (code
> 1)
> make[1]: *** [tools_generate_functions.o] Errore 1
> make[1]: Leaving directory
> `/marconi/home/userexternal/gmattiol/knl/QE/6.3-backports/Modules'
> make: *** [mods] Errore 1
>
> Can anybody suggest improvements?
> Thank you in advance
> Giuseppe
>
>
> 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: <giuseppe.mattioli at ism.cnr.it>
>
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>
>
> 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: <giuseppe.mattioli at ism.cnr.it<mailto:giuseppe.mattioli at ism.cnr.it>>
>
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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: <giuseppe.mattioli at ism.cnr.it>
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