<div dir="ltr"><div><div>Dear all,<br><br></div>I am working on transport properties using wannier package. I have performed its example of BaTiO3 successfully. But when I move onto my material, scf and nscf run easily in which i have taken 4 4 4 k-point grid in scf and the k points generated in scf output i put then in nscf input. the same k points i put in xxx.win input and when i use wannie90.x -pp it says non-syemmetric k-points neighbors. Can anyone help me a solution for this.<br><br></div>Thanks in advance<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Aug 20, 2015 at 3:30 PM, <span dir="ltr"><<a href="mailto:pw_forum-request@pwscf.org" target="_blank">pw_forum-request@pwscf.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Pw_forum mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Error in compiling QE with libxc (Piyush Kumar)<br>
2. Re: Error in compiling QE with libxc (Ari P Seitsonen)<br>
3. Re: Error in compiling QE with libxc (Piyush Kumar)<br>
4. Re: Error in compiling QE with libxc (Ari P Seitsonen)<br>
5. Re: Error in compiling QE with libxc (Piyush Kumar)<br>
6. S matrix not positive definite (chaitanya varma)<br>
7. Re: Wrong k-string? in nscf+lelfield (Mojtaba Mirseraji)<br>
8. Reply to all (Venkataramana Imandi)<br>
9. Langevin dynamics (Venkataramana Imandi)<br>
10. Re: relax of 216 atoms (cubic structure) (Yevgen Melikhov)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 19 Aug 2015 18:00:26 +0530<br>
From: Piyush Kumar <<a href="mailto:piyushkr1990@gmail.com">piyushkr1990@gmail.com</a>><br>
Subject: [Pw_forum] Error in compiling QE with libxc<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAP1_1k+x9JNaV3j+KE=<a href="mailto:YePf%2BO4VJq20zobvSwRmg76BKfad9fw@mail.gmail.com">YePf+O4VJq20zobvSwRmg76BKfad9fw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all,<br>
I am trying to use MGGA functional 'TB09' in quantum espresso 5.1.2. When I<br>
tried to do calculation with input_dft='tb09', I got following error<br>
Error in routine tb09 (1):<br>
need libxc<br>
<br>
I compiled quantum espresso again by linking it with libxc.f90 in<br>
espresso-5.1.2/Modules, by manually editing the make files:<br>
<br>
In make.sys:<br>
<br>
DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA *-D__LIBXC*<br>
$(MANUAL_DFLAGS)<br>
<br>
In PW/src/Makefile<br>
<br>
MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules *-L../../Modules<br>
-lxcf90 -lxc*<br>
<br>
In Modules/Makefile<br>
<br>
MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../ELPA/src $(MOD_FLAG).* -L.<br>
-lxcf90 -lxc*<br>
<br>
In flib/Makefile<br>
<br>
MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../Modules $(MOD_FLAG).*<br>
-L../Modules -lxcf90 -lxc*<br>
<br>
After making above changes, I did "make pw", and I got following errors<br>
<br>
../../flib/flib.a(functionals.o): In function `slater':<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:31: undefined reference to<br>
`xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:32: undefined reference to<br>
`xc_f90_lda_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:33: undefined reference to<br>
`xc_f90_func_end_'<br>
../../flib/flib.a(functionals.o): In function `pz':<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:169: undefined reference<br>
to `xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:170: undefined reference<br>
to `xc_f90_lda_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:171: undefined reference<br>
to `xc_f90_func_end_'<br>
../../flib/flib.a(functionals.o): In function `pw':<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference<br>
to `xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference<br>
to `xc_f90_lda_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference<br>
to `xc_f90_func_end_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference<br>
to `xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference<br>
to `xc_f90_lda_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference<br>
to `xc_f90_func_end_'<br>
../../flib/flib.a(functionals.o): In function `pbex':<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1011: undefined reference<br>
to `xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1012: undefined reference<br>
to `xc_f90_gga_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1013: undefined reference<br>
to `xc_f90_func_end_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1016: undefined reference<br>
to `xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1017: undefined reference<br>
to `xc_f90_lda_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1018: undefined reference<br>
to `xc_f90_func_end_'<br>
../../flib/flib.a(functionals.o): In function `pbec':<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1222: undefined reference<br>
to `xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1223: undefined reference<br>
to `xc_f90_gga_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1224: undefined reference<br>
to `xc_f90_func_end_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1226: undefined reference<br>
to `xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1227: undefined reference<br>
to `xc_f90_lda_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/functionals.f90:1228: undefined reference<br>
to `xc_f90_func_end_'<br>
../../flib/flib.a(metagga.o): In function `tpsscxc':<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:57: undefined reference to<br>
`xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:58: undefined reference to<br>
`xc_f90_mgga_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:60: undefined reference to<br>
`xc_f90_func_end_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:68: undefined reference to<br>
`xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:69: undefined reference to<br>
`xc_f90_mgga_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:71: undefined reference to<br>
`xc_f90_func_end_'<br>
../../flib/flib.a(metagga.o): In function `tb09cxc':<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:1415: undefined reference to<br>
`xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:1416: undefined reference to<br>
`xc_f90_mgga_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:1418: undefined reference to<br>
`xc_f90_func_end_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:1428: undefined reference to<br>
`xc_f90_func_init_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:1429: undefined reference to<br>
`xc_f90_mgga_exc_vxc_'<br>
/home/piyukr/espresso-5.1.2/flib/metagga.f90:1431: undefined reference to<br>
`xc_f90_func_end_'<br>
make[2]: *** [pw.x] Error 1<br>
make[2]: Leaving directory `/home/piyukr/espresso-5.1.2/PW/src'<br>
make[1]: *** [pw] Error 1<br>
make[1]: Leaving directory `/home/piyukr/espresso-5.1.2/PW'<br>
make: *** [pw] Error 1<br>
<br>
I am using intel compilers.<br>
<br>
Can anyone please tell me what is correct way to link libxc?<br>
Thanking You.<br>
<br>
Piyush Kumar,<br>
M.Tech. Student<br>
Indian Institute of Technology (IIT), Kanpur,<br>
India<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 19 Aug 2015 14:48:37 +0200 (CEST)<br>
From: Ari P Seitsonen <<a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a>><br>
Subject: Re: [Pw_forum] Error in compiling QE with libxc<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:alpine.LSU.2.03.1508191443200.13289@chem.uzh.ch">alpine.LSU.2.03.1508191443200.13289@chem.uzh.ch</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
<br>
Dear Piyush Kuma,<br>
<br>
A bit unfortunate choice in the code: Here the external library 'libxc'<br>
is meant [ <a href="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" rel="noreferrer" target="_blank">http://www.tddft.org/programs/octopus/wiki/index.php/Libxc</a> ].<br>
You need to compile that and insert the path and libraries into the<br>
variables in 'make.sys' (not explicitly in any 'Makefile').<br>
<br>
There seems to be a related paper on this: DOI:10.1016/j.cpc.2013.02.020<br>
<br>
Greetings from Sunny Montrouge,<br>
<br>
apsi<br>
<br>
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-<br>
Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris<br>
Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935<br>
<br>
<br>
On Wed, 19 Aug 2015, Piyush Kumar wrote:<br>
<br>
> Dear all,I am trying to use MGGA functional 'TB09' in quantum espresso<br>
> 5.1.2. When I tried to do calculation with input_dft='tb09', I got following<br>
> error<br>
> ?Error in routine tb09 (1):<br>
> ? ? ?need libxc<br>
><br>
> I compiled quantum espresso again by linking it with libxc.f90 in<br>
> espresso-5.1.2/Modules, by manually editing the make files:<br>
><br>
> In make.sys: ?<br>
><br>
> DFLAGS ? ? ? ? = ?-D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC<br>
> $(MANUAL_DFLAGS)<br>
><br>
> In PW/src/Makefile<br>
><br>
> MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules -L../../Modules<br>
> -lxcf90 -lxc<br>
><br>
> In Modules/Makefile<br>
><br>
> MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../ELPA/src $(MOD_FLAG). -L.<br>
> -lxcf90 -lxc<br>
><br>
> In flib/Makefile<br>
><br>
> MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../Modules $(MOD_FLAG).<br>
> -L../Modules -lxcf90 -lxc<br>
><br>
> After making above changes, I did "make pw", and I got following errors<br>
><br>
> ../../flib/flib.a(functionals.o): In function `slater':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:31: undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:32: undefined reference to<br>
> `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:33: undefined reference to<br>
> `xc_f90_func_end_'<br>
> ../../flib/flib.a(functionals.o): In function `pz':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:169: undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:170: undefined reference to<br>
> `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:171: undefined reference to<br>
> `xc_f90_func_end_'<br>
> ../../flib/flib.a(functionals.o): In function `pw':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference to<br>
> `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference to<br>
> `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference to<br>
> `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference to<br>
> `xc_f90_func_end_'<br>
> ../../flib/flib.a(functionals.o): In function `pbex':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1011: undefined reference<br>
> to `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1012: undefined reference<br>
> to `xc_f90_gga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1013: undefined reference<br>
> to `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1016: undefined reference<br>
> to `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1017: undefined reference<br>
> to `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1018: undefined reference<br>
> to `xc_f90_func_end_'<br>
> ../../flib/flib.a(functionals.o): In function `pbec':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1222: undefined reference<br>
> to `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1223: undefined reference<br>
> to `xc_f90_gga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1224: undefined reference<br>
> to `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1226: undefined reference<br>
> to `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1227: undefined reference<br>
> to `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1228: undefined reference<br>
> to `xc_f90_func_end_'<br>
> ../../flib/flib.a(metagga.o): In function `tpsscxc':<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:57: undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:58: undefined reference to<br>
> `xc_f90_mgga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:60: undefined reference to<br>
> `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:68: undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:69: undefined reference to<br>
> `xc_f90_mgga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:71: undefined reference to<br>
> `xc_f90_func_end_'<br>
> ../../flib/flib.a(metagga.o): In function `tb09cxc':<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1415: undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1416: undefined reference to<br>
> `xc_f90_mgga_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1418: undefined reference to<br>
> `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1428: undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1429: undefined reference to<br>
> `xc_f90_mgga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1431: undefined reference to<br>
> `xc_f90_func_end_'<br>
> make[2]: *** [pw.x] Error 1<br>
> make[2]: Leaving directory `/home/piyukr/espresso-5.1.2/PW/src'<br>
> make[1]: *** [pw] Error 1<br>
> make[1]: Leaving directory `/home/piyukr/espresso-5.1.2/PW'<br>
> make: *** [pw] Error 1<br>
><br>
> I am using intel compilers.<br>
><br>
> Can anyone please tell me what is correct way to link libxc?<br>
> Thanking You.<br>
><br>
> Piyush Kumar,<br>
> M.Tech. Student<br>
> Indian Institute of Technology (IIT), Kanpur,<br>
> India<br>
><br>
><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 19 Aug 2015 19:27:48 +0530<br>
From: Piyush Kumar <<a href="mailto:piyushkr1990@gmail.com">piyushkr1990@gmail.com</a>><br>
Subject: Re: [Pw_forum] Error in compiling QE with libxc<br>
To: Ari Paavo Seitsonen <<a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a>>, PWSCF Forum<br>
<<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAP1_1k+ARnPyjS2L61maB9f0U=<a href="mailto:3stj3%2BW4Ave4pfXB3vHsj3xA@mail.gmail.com">3stj3+W4Ave4pfXB3vHsj3xA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Apsi,<br>
Thanks for the reply. I installed libxc-2.1.2 and again compiled QE, with<br>
the following changes in make.sys<br>
<br>
MANUAL_DFLAGS =<br>
DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA *-D__LIBXC*<br>
$(MANUAL_DFLAGS)<br>
FDFLAGS = $(DFLAGS) $(MANUAL_DFLAGS)<br>
MODFLAGS = -L/home/piyukr/Software/libxc-2.1.2/lib -lxcf90 -lxc<br>
(This line has been added)<br>
<br>
where /home/piyukr/Software/libxc-2.1.2 is the installation directory<br>
<br>
I am still getting the same error. Can you please tell me which variable I<br>
need to edit or add and with what values?<br>
<br>
Thanking you,<br>
Piyush<br>
<br>
<br>
On Wed, Aug 19, 2015 at 6:18 PM, Ari P Seitsonen <<a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a>><br>
wrote:<br>
<br>
><br>
> Dear Piyush Kuma,<br>
><br>
> A bit unfortunate choice in the code: Here the external library 'libxc'<br>
> is meant [ <a href="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" rel="noreferrer" target="_blank">http://www.tddft.org/programs/octopus/wiki/index.php/Libxc</a> ].<br>
> You need to compile that and insert the path and libraries into the<br>
> variables in 'make.sys' (not explicitly in any 'Makefile').<br>
><br>
> There seems to be a related paper on this: DOI:10.1016/j.cpc.2013.02.020<br>
><br>
> Greetings from Sunny Montrouge,<br>
><br>
> apsi<br>
><br>
><br>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-<br>
> Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
> Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris<br>
> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935<br>
><br>
><br>
> On Wed, 19 Aug 2015, Piyush Kumar wrote:<br>
><br>
> Dear all,I am trying to use MGGA functional 'TB09' in quantum espresso<br>
>><br>
>> 5.1.2. When I tried to do calculation with input_dft='tb09', I got<br>
>> following<br>
>> error<br>
>> Error in routine tb09 (1):<br>
>> need libxc<br>
>><br>
>> I compiled quantum espresso again by linking it with libxc.f90 in<br>
>> espresso-5.1.2/Modules, by manually editing the make files:<br>
>><br>
>> In make.sys:<br>
>><br>
>> DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC<br>
>> $(MANUAL_DFLAGS)<br>
>><br>
>> In PW/src/Makefile<br>
>><br>
>> MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules<br>
>> -L../../Modules<br>
>> -lxcf90 -lxc<br>
>><br>
>> In Modules/Makefile<br>
>><br>
>> MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../ELPA/src $(MOD_FLAG). -L.<br>
>> -lxcf90 -lxc<br>
>><br>
>> In flib/Makefile<br>
>><br>
>> MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../Modules $(MOD_FLAG).<br>
>> -L../Modules -lxcf90 -lxc<br>
>><br>
>> After making above changes, I did "make pw", and I got following errors<br>
>><br>
>> ../../flib/flib.a(functionals.o): In function `slater':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:31: undefined reference<br>
>> to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:32: undefined reference<br>
>> to<br>
>> `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:33: undefined reference<br>
>> to<br>
>> `xc_f90_func_end_'<br>
>> ../../flib/flib.a(functionals.o): In function `pz':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:169: undefined reference<br>
>> to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:170: undefined reference<br>
>> to<br>
>> `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:171: undefined reference<br>
>> to<br>
>> `xc_f90_func_end_'<br>
>> ../../flib/flib.a(functionals.o): In function `pw':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference<br>
>> to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference<br>
>> to<br>
>> `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference<br>
>> to<br>
>> `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference<br>
>> to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference<br>
>> to<br>
>> `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference<br>
>> to<br>
>> `xc_f90_func_end_'<br>
>> ../../flib/flib.a(functionals.o): In function `pbex':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1011: undefined reference<br>
>> to `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1012: undefined reference<br>
>> to `xc_f90_gga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1013: undefined reference<br>
>> to `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1016: undefined reference<br>
>> to `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1017: undefined reference<br>
>> to `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1018: undefined reference<br>
>> to `xc_f90_func_end_'<br>
>> ../../flib/flib.a(functionals.o): In function `pbec':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1222: undefined reference<br>
>> to `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1223: undefined reference<br>
>> to `xc_f90_gga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1224: undefined reference<br>
>> to `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1226: undefined reference<br>
>> to `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1227: undefined reference<br>
>> to `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1228: undefined reference<br>
>> to `xc_f90_func_end_'<br>
>> ../../flib/flib.a(metagga.o): In function `tpsscxc':<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:57: undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:58: undefined reference to<br>
>> `xc_f90_mgga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:60: undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:68: undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:69: undefined reference to<br>
>> `xc_f90_mgga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:71: undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> ../../flib/flib.a(metagga.o): In function `tb09cxc':<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1415: undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1416: undefined reference to<br>
>> `xc_f90_mgga_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1418: undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1428: undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1429: undefined reference to<br>
>> `xc_f90_mgga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1431: undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> make[2]: *** [pw.x] Error 1<br>
>> make[2]: Leaving directory `/home/piyukr/espresso-5.1.2/PW/src'<br>
>> make[1]: *** [pw] Error 1<br>
>> make[1]: Leaving directory `/home/piyukr/espresso-5.1.2/PW'<br>
>> make: *** [pw] Error 1<br>
>><br>
>> I am using intel compilers.<br>
>><br>
>> Can anyone please tell me what is correct way to link libxc?<br>
>> Thanking You.<br>
>><br>
>> Piyush Kumar,<br>
>> M.Tech. Student<br>
>> Indian Institute of Technology (IIT), Kanpur,<br>
>> India<br>
>><br>
>><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
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------------------------------<br>
<br>
Message: 4<br>
Date: Wed, 19 Aug 2015 16:22:27 +0200 (CEST)<br>
From: Ari P Seitsonen <<a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a>><br>
Subject: Re: [Pw_forum] Error in compiling QE with libxc<br>
To: Piyush Kumar <<a href="mailto:piyushkr1990@gmail.com">piyushkr1990@gmail.com</a>><br>
Cc: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:alpine.LSU.2.03.1508191620000.18755@chem.uzh.ch">alpine.LSU.2.03.1508191620000.18755@chem.uzh.ch</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
<br>
Dear Piyush Kumar,<br>
<br>
Why do you try to modify 'MODFLAGS', not 'LD_LIBS'? These are external<br>
routines, 'Modules/libxc.f90' only provides interfaces to them, if I see<br>
correctly.<br>
<br>
Greetings,<br>
<br>
apsi<br>
<br>
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-<br>
Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris<br>
Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935<br>
<br>
<br>
On Wed, 19 Aug 2015, Piyush Kumar wrote:<br>
<br>
> Dear Apsi,Thanks for the reply. I installed libxc-2.1.2 and again compiled<br>
> QE, with the following changes in make.sys<br>
><br>
> MANUAL_DFLAGS ?=<br>
> DFLAGS ? ? ? ? = ?-D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC<br>
> $(MANUAL_DFLAGS)<br>
> FDFLAGS ? ? ? ?= $(DFLAGS) $(MANUAL_DFLAGS)<br>
> MODFLAGS ? ? ? = -L/home/piyukr/Software/libxc-2.1.2/lib -lxcf90 -lxc ? ? ?<br>
> (This line has been added)<br>
><br>
> where /home/piyukr/Software/libxc-2.1.2 is the installation directory<br>
> ?<br>
> I am still getting the same error. Can you please tell me which variable I<br>
> need to edit or add and with what values?<br>
><br>
> Thanking you,<br>
> Piyush<br>
><br>
><br>
> On Wed, Aug 19, 2015 at 6:18 PM, Ari P Seitsonen <<a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a>><br>
> wrote:<br>
><br>
> Dear Piyush Kuma,<br>
><br>
> ? A bit unfortunate choice in the code: Here the external<br>
> library 'libxc' is meant [<br>
> <a href="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" rel="noreferrer" target="_blank">http://www.tddft.org/programs/octopus/wiki/index.php/Libxc</a> ].<br>
> You need to compile that and insert the path and libraries into<br>
> the variables in 'make.sys' (not explicitly in any 'Makefile').<br>
><br>
> ? There seems to be a related paper on this:<br>
> DOI:10.1016/j.cpc.2013.02.020<br>
><br>
> ? ? Greetings from Sunny Montrouge,<br>
><br>
> ? ? ? ?apsi<br>
><br>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*<br>
> =-<br>
> ? Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a> /<br>
> <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
> ? Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris<br>
> ? Mobile (F) : +33 789 37 24 25? ? (CH) : +41 79 71 90 935<br>
><br>
><br>
> On Wed, 19 Aug 2015, Piyush Kumar wrote:<br>
><br>
> Dear all,I am trying to use MGGA functional 'TB09'<br>
> in quantum espresso<br>
> 5.1.2. When I tried to do calculation with<br>
> input_dft='tb09', I got following<br>
> error<br>
> ?Error in routine tb09 (1):<br>
> ? ? ?need libxc<br>
><br>
> I compiled quantum espresso again by linking it with<br>
> libxc.f90 in<br>
> espresso-5.1.2/Modules, by manually editing the make<br>
> files:<br>
><br>
> In make.sys: ?<br>
><br>
> DFLAGS ? ? ? ? = ?-D__INTEL -D__FFTW -D__MPI<br>
> -D__PARA -D__LIBXC<br>
> $(MANUAL_DFLAGS)<br>
><br>
> In PW/src/Makefile<br>
><br>
> MODFLAGS= $(MOD_FLAG)../../iotk/src<br>
> $(MOD_FLAG)../../Modules -L../../Modules<br>
> -lxcf90 -lxc<br>
><br>
> In Modules/Makefile<br>
><br>
> MODFLAGS= $(MOD_FLAG)../iotk/src<br>
> $(MOD_FLAG)../ELPA/src $(MOD_FLAG). -L.<br>
> -lxcf90 -lxc<br>
><br>
> In flib/Makefile<br>
><br>
> MODFLAGS= $(MOD_FLAG)../iotk/src<br>
> $(MOD_FLAG)../Modules $(MOD_FLAG).<br>
> -L../Modules -lxcf90 -lxc<br>
><br>
> After making above changes, I did "make pw", and I<br>
> got following errors<br>
><br>
> ../../flib/flib.a(functionals.o): In function<br>
> `slater':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:31:<br>
> undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:32:<br>
> undefined reference to<br>
> `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:33:<br>
> undefined reference to<br>
> `xc_f90_func_end_'<br>
> ../../flib/flib.a(functionals.o): In function `pz':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:169:<br>
> undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:170:<br>
> undefined reference to<br>
> `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:171:<br>
> undefined reference to<br>
> `xc_f90_func_end_'<br>
> ../../flib/flib.a(functionals.o): In function `pw':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374:<br>
> undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375:<br>
> undefined reference to<br>
> `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376:<br>
> undefined reference to<br>
> `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374:<br>
> undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375:<br>
> undefined reference to<br>
> `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376:<br>
> undefined reference to<br>
> `xc_f90_func_end_'<br>
> ../../flib/flib.a(functionals.o): In function<br>
> `pbex':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1011:<br>
> undefined reference<br>
> to `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1012:<br>
> undefined reference<br>
> to `xc_f90_gga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1013:<br>
> undefined reference<br>
> to `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1016:<br>
> undefined reference<br>
> to `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1017:<br>
> undefined reference<br>
> to `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1018:<br>
> undefined reference<br>
> to `xc_f90_func_end_'<br>
> ../../flib/flib.a(functionals.o): In function<br>
> `pbec':<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1222:<br>
> undefined reference<br>
> to `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1223:<br>
> undefined reference<br>
> to `xc_f90_gga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1224:<br>
> undefined reference<br>
> to `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1226:<br>
> undefined reference<br>
> to `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1227:<br>
> undefined reference<br>
> to `xc_f90_lda_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1228:<br>
> undefined reference<br>
> to `xc_f90_func_end_'<br>
> ../../flib/flib.a(metagga.o): In function `tpsscxc':<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:57:<br>
> undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:58:<br>
> undefined reference to<br>
> `xc_f90_mgga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:60:<br>
> undefined reference to<br>
> `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:68:<br>
> undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:69:<br>
> undefined reference to<br>
> `xc_f90_mgga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:71:<br>
> undefined reference to<br>
> `xc_f90_func_end_'<br>
> ../../flib/flib.a(metagga.o): In function `tb09cxc':<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1415:<br>
> undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1416:<br>
> undefined reference to<br>
> `xc_f90_mgga_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1418:<br>
> undefined reference to<br>
> `xc_f90_func_end_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1428:<br>
> undefined reference to<br>
> `xc_f90_func_init_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1429:<br>
> undefined reference to<br>
> `xc_f90_mgga_exc_vxc_'<br>
> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1431:<br>
> undefined reference to<br>
> `xc_f90_func_end_'<br>
> make[2]: *** [pw.x] Error 1<br>
> make[2]: Leaving directory<br>
> `/home/piyukr/espresso-5.1.2/PW/src'<br>
> make[1]: *** [pw] Error 1<br>
> make[1]: Leaving directory<br>
> `/home/piyukr/espresso-5.1.2/PW'<br>
> make: *** [pw] Error 1<br>
><br>
> I am using intel compilers.<br>
><br>
> Can anyone please tell me what is correct way to<br>
> link libxc?<br>
> Thanking You.<br>
><br>
> Piyush Kumar,<br>
> M.Tech. Student<br>
> Indian Institute of Technology (IIT), Kanpur,<br>
> India<br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
><br>
><br>
><br>
><br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Wed, 19 Aug 2015 20:42:11 +0530<br>
From: Piyush Kumar <<a href="mailto:piyushkr1990@gmail.com">piyushkr1990@gmail.com</a>><br>
Subject: Re: [Pw_forum] Error in compiling QE with libxc<br>
To: Ari Paavo Seitsonen <<a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a>><br>
Cc: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAP1_1k+S=<a href="mailto:dfZpwgpbgbXGmCFqQLDgBnNJzV3fgK9_VU4cq7cMQ@mail.gmail.com">dfZpwgpbgbXGmCFqQLDgBnNJzV3fgK9_VU4cq7cMQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Thanks a lot,<br>
I tried specifying the library in LD_LIBS as LD_LIBS =<br>
/home/piyukr/Software/libxc-2.1.2/lib/libxc.a and its working now.<br>
<br>
<br>
<br>
On Wed, Aug 19, 2015 at 7:52 PM, Ari P Seitsonen <<a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a>><br>
wrote:<br>
<br>
><br>
> Dear Piyush Kumar,<br>
><br>
> Why do you try to modify 'MODFLAGS', not 'LD_LIBS'? These are external<br>
> routines, 'Modules/libxc.f90' only provides interfaces to them, if I see<br>
> correctly.<br>
><br>
> Greetings,<br>
><br>
> apsi<br>
><br>
><br>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-<br>
> Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
> Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris<br>
> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935<br>
><br>
><br>
> On Wed, 19 Aug 2015, Piyush Kumar wrote:<br>
><br>
> Dear Apsi,Thanks for the reply. I installed libxc-2.1.2 and again compiled<br>
>><br>
>> QE, with the following changes in make.sys<br>
>><br>
>> MANUAL_DFLAGS =<br>
>> DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC<br>
>> $(MANUAL_DFLAGS)<br>
>> FDFLAGS = $(DFLAGS) $(MANUAL_DFLAGS)<br>
>> MODFLAGS = -L/home/piyukr/Software/libxc-2.1.2/lib -lxcf90 -lxc<br>
>><br>
>> (This line has been added)<br>
>><br>
>> where /home/piyukr/Software/libxc-2.1.2 is the installation directory<br>
>><br>
>> I am still getting the same error. Can you please tell me which variable I<br>
>> need to edit or add and with what values?<br>
>><br>
>> Thanking you,<br>
>> Piyush<br>
>><br>
>><br>
>> On Wed, Aug 19, 2015 at 6:18 PM, Ari P Seitsonen <<a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a>><br>
>> wrote:<br>
>><br>
>> Dear Piyush Kuma,<br>
>><br>
>> A bit unfortunate choice in the code: Here the external<br>
>> library 'libxc' is meant [<br>
>> <a href="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" rel="noreferrer" target="_blank">http://www.tddft.org/programs/octopus/wiki/index.php/Libxc</a> ].<br>
>> You need to compile that and insert the path and libraries into<br>
>> the variables in 'make.sys' (not explicitly in any 'Makefile').<br>
>><br>
>> There seems to be a related paper on this:<br>
>> DOI:10.1016/j.cpc.2013.02.020<br>
>><br>
>> Greetings from Sunny Montrouge,<br>
>><br>
>> apsi<br>
>><br>
>><br>
>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*<br>
>> =-<br>
>> Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a> /<br>
>> <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
>> Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris<br>
>> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935<br>
>><br>
>><br>
>> On Wed, 19 Aug 2015, Piyush Kumar wrote:<br>
>><br>
>> Dear all,I am trying to use MGGA functional 'TB09'<br>
>> in quantum espresso<br>
>> 5.1.2. When I tried to do calculation with<br>
>> input_dft='tb09', I got following<br>
>> error<br>
>> Error in routine tb09 (1):<br>
>> need libxc<br>
>><br>
>> I compiled quantum espresso again by linking it with<br>
>> libxc.f90 in<br>
>> espresso-5.1.2/Modules, by manually editing the make<br>
>> files:<br>
>><br>
>> In make.sys:<br>
>><br>
>> DFLAGS = -D__INTEL -D__FFTW -D__MPI<br>
>> -D__PARA -D__LIBXC<br>
>> $(MANUAL_DFLAGS)<br>
>><br>
>> In PW/src/Makefile<br>
>><br>
>> MODFLAGS= $(MOD_FLAG)../../iotk/src<br>
>> $(MOD_FLAG)../../Modules -L../../Modules<br>
>> -lxcf90 -lxc<br>
>><br>
>> In Modules/Makefile<br>
>><br>
>> MODFLAGS= $(MOD_FLAG)../iotk/src<br>
>> $(MOD_FLAG)../ELPA/src $(MOD_FLAG). -L.<br>
>> -lxcf90 -lxc<br>
>><br>
>> In flib/Makefile<br>
>><br>
>> MODFLAGS= $(MOD_FLAG)../iotk/src<br>
>> $(MOD_FLAG)../Modules $(MOD_FLAG).<br>
>> -L../Modules -lxcf90 -lxc<br>
>><br>
>> After making above changes, I did "make pw", and I<br>
>> got following errors<br>
>><br>
>> ../../flib/flib.a(functionals.o): In function<br>
>> `slater':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:31:<br>
>> undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:32:<br>
>> undefined reference to<br>
>> `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:33:<br>
>> undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> ../../flib/flib.a(functionals.o): In function `pz':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:169:<br>
>> undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:170:<br>
>> undefined reference to<br>
>> `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:171:<br>
>> undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> ../../flib/flib.a(functionals.o): In function `pw':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374:<br>
>> undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375:<br>
>> undefined reference to<br>
>> `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376:<br>
>> undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374:<br>
>> undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375:<br>
>> undefined reference to<br>
>> `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376:<br>
>> undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> ../../flib/flib.a(functionals.o): In function<br>
>> `pbex':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1011:<br>
>> undefined reference<br>
>> to `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1012:<br>
>> undefined reference<br>
>> to `xc_f90_gga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1013:<br>
>> undefined reference<br>
>> to `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1016:<br>
>> undefined reference<br>
>> to `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1017:<br>
>> undefined reference<br>
>> to `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1018:<br>
>> undefined reference<br>
>> to `xc_f90_func_end_'<br>
>> ../../flib/flib.a(functionals.o): In function<br>
>> `pbec':<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1222:<br>
>> undefined reference<br>
>> to `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1223:<br>
>> undefined reference<br>
>> to `xc_f90_gga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1224:<br>
>> undefined reference<br>
>> to `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1226:<br>
>> undefined reference<br>
>> to `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1227:<br>
>> undefined reference<br>
>> to `xc_f90_lda_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1228:<br>
>> undefined reference<br>
>> to `xc_f90_func_end_'<br>
>> ../../flib/flib.a(metagga.o): In function `tpsscxc':<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:57:<br>
>> undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:58:<br>
>> undefined reference to<br>
>> `xc_f90_mgga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:60:<br>
>> undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:68:<br>
>> undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:69:<br>
>> undefined reference to<br>
>> `xc_f90_mgga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:71:<br>
>> undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> ../../flib/flib.a(metagga.o): In function `tb09cxc':<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1415:<br>
>> undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1416:<br>
>> undefined reference to<br>
>> `xc_f90_mgga_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1418:<br>
>> undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1428:<br>
>> undefined reference to<br>
>> `xc_f90_func_init_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1429:<br>
>> undefined reference to<br>
>> `xc_f90_mgga_exc_vxc_'<br>
>> /home/piyukr/espresso-5.1.2/flib/metagga.f90:1431:<br>
>> undefined reference to<br>
>> `xc_f90_func_end_'<br>
>> make[2]: *** [pw.x] Error 1<br>
>> make[2]: Leaving directory<br>
>> `/home/piyukr/espresso-5.1.2/PW/src'<br>
>> make[1]: *** [pw] Error 1<br>
>> make[1]: Leaving directory<br>
>> `/home/piyukr/espresso-5.1.2/PW'<br>
>> make: *** [pw] Error 1<br>
>><br>
>> I am using intel compilers.<br>
>><br>
>> Can anyone please tell me what is correct way to<br>
>> link libxc?<br>
>> Thanking You.<br>
>><br>
>> Piyush Kumar,<br>
>> M.Tech. Student<br>
>> Indian Institute of Technology (IIT), Kanpur,<br>
>> India<br>
>><br>
>><br>
>> _______________________________________________<br>
>> Pw_forum mailing list<br>
>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
>><br>
>><br>
>><br>
>><br>
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------------------------------<br>
<br>
Message: 6<br>
Date: Wed, 19 Aug 2015 15:51:32 +0000 (UTC)<br>
From: chaitanya varma <<a href="mailto:chvar81@yahoo.co.in">chvar81@yahoo.co.in</a>><br>
Subject: [Pw_forum] S matrix not positive definite<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:1809178400.5466022.1439999492946.JavaMail.yahoo@mail.yahoo.com">1809178400.5466022.1439999492946.JavaMail.yahoo@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear sir,I am trying to work on Ni-Zn ferrite regarding magnetic moment and band structure and DOS<br>
i used .cif file for writing atomic positions and wrote input filewhen i tried to run the code it is giving the following error<br>
<br>
<br>
<br>
???? Error in routine cdiaghg (348):<br>
???? S matrix not positive definite<br>
?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
???? stopping ...<br>
i am attaching the input and output files for your kind reference.<br>
can anyone tell me where i did wrong?Thanks in advancewith kind regards<br>
<br>
Chaitanya Varma M ?Assistant professorDepartment of PhysicsGITGITAM UniversityVisakhapatnamIndia<br>
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------------------------------<br>
<br>
Message: 7<br>
Date: Wed, 19 Aug 2015 21:29:01 +0430<br>
From: Mojtaba Mirseraji <<a href="mailto:quantum.pwscf@gmail.com">quantum.pwscf@gmail.com</a>><br>
Subject: Re: [Pw_forum] Wrong k-string? in nscf+lelfield<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAPw9g86hTP02SvwDeWCtGZgk1ZQKmQse9avoo4iTeJ0%2Bw9cdBA@mail.gmail.com">CAPw9g86hTP02SvwDeWCtGZgk1ZQKmQse9avoo4iTeJ0+w9cdBA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=UTF-8<br>
<br>
Dear All<br>
<br>
I have this error when I run this nscf input:<br>
<br>
&CONTROL<br>
calculation = 'nscf' ,<br>
restart_mode = 'from_scratch' ,<br>
prefix= 'E',<br>
tstress = .true. ,<br>
tprnfor = .true. ,<br>
outdir='?',<br>
etot_conv_thr = 1.0E-6 ,<br>
forc_conv_thr = 1.0D-6 ,<br>
pseudo_dir = '?',<br>
lelfield= .true. ,<br>
lberry= .true. ,<br>
gdir= 3 ,<br>
nppstr= 25 ,<br>
/<br>
&SYSTEM<br>
ibrav = 0,<br>
celldm(1)= ?,<br>
nat = 5,<br>
ntyp = 3,<br>
ecutwfc = 80.0 ,<br>
ecutrho = 800.0 ,<br>
occupations = 'fixed' ,<br>
/<br>
&ELECTRONS<br>
conv_thr = 1.D-6 ,<br>
diago_full_acc = .TRUE.,<br>
efield_cart(1) = 0.0D0 ,<br>
efield_cart(2) = 0.0D0 ,<br>
efield_cart(3) = 0.00001D0 ,<br>
/<br>
ATOMIC_SPECIES<br>
O 15.9994 ?.UPF<br>
Ti 47.867 ?.UPF<br>
Ba 137.327 ?.UPF<br>
CELL_PARAMETERS {cubic}<br>
1.00000000 0.00000000 0.0000000<br>
0.00000000 1.00000000 0.0000000<br>
0.00000000 0.00000000 1.0135088<br>
ATOMIC_POSITIONS {alat}<br>
O 0.000000000 0.500000000 0.497977245<br>
O 0.500000000 0.000000000 0.497977245<br>
O 0.500000000 0.500000000 -0.016512609<br>
Ti 0.500000000 0.500000000 0.525300320<br>
Ba 0.000000000 0.000000000 0.005257800<br>
K_POINTS {automatic}<br>
2 2 2 1 1 1<br>
<br>
<br>
<br>
I have changed all numbers of this input file but this error appeared !!!!!<br>
<br>
Thanks<br>
<br>
Mojtaba<br>
<br>
On 8/8/15, David Foster <<a href="mailto:davidfoster751@yahoo.com">davidfoster751@yahoo.com</a>> wrote:<br>
> please provide your input file<br>
> Regards<br>
><br>
> David Foster<br>
><br>
> Ph.D. Student of Chemistry<br>
><br>
> --------------------------------------------<br>
> On Fri, 8/7/15, Mojtaba Mirseraji <<a href="mailto:quantum.pwscf@gmail.com">quantum.pwscf@gmail.com</a>> wrote:<br>
><br>
> Subject: [Pw_forum] Wrong k-string? in nscf+lelfield<br>
> To: <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> Date: Friday, August 7, 2015, 9:47 AM<br>
><br>
> Dear Users<br>
><br>
> I perform lelfield=.true. option in PWSCF (only in nscf) for<br>
> berry<br>
> calculations of polarization but unfortunately<br>
> " Wrong k-string? "<br>
> error is showed.<br>
><br>
> I do not know how to solve it<br>
><br>
> Regards<br>
><br>
> Mojtaba Mirseraji<br>
> Ph.D. Candidate<br>
> Theoretical Condensed Matter Physics<br>
> Arak Univ.<br>
> IRAN<br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
><br>
> _______________________________________________<br>
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><br>
<br>
<br>
------------------------------<br>
<br>
Message: 8<br>
Date: Thu, 20 Aug 2015 09:55:17 +0530<br>
From: Venkataramana Imandi <<a href="mailto:venkataramana.imandi@gmail.com">venkataramana.imandi@gmail.com</a>><br>
Subject: [Pw_forum] Reply to all<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Cc: <a href="mailto:Ari.P.Seitsonen@iki.fi">Ari.P.Seitsonen@iki.fi</a><br>
Message-ID:<br>
<<a href="mailto:CAEJJhnuu2GfD5K6ixYcuAfFRdnZfo_fBUFgy%2BYTsSB106kCY2A@mail.gmail.com">CAEJJhnuu2GfD5K6ixYcuAfFRdnZfo_fBUFgy+YTsSB106kCY2A@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Paolo Giannozzi and Ari Paavo Seitsonen<br>
<br>
<br>
<br>
Thank you sir for your kind reply and sorry for delaying reply. I felt same<br>
thing while reading previous threads in pw_forum archives. According to<br>
suggestions given by Ari Paavo Seitsonen sir, I made all corrections and<br>
tried my level best. All trials lead to collapse of structure during<br>
Langevin dynamics.<br>
<br>
Best,<br>
Venkataramana<br>
PhD student<br>
IIT Bombay<br>
<br>
Langevin dynamics was implemented many years ago in QE, but I have never<br>
heard of anybody using it, nor seen any evidence that it works (or that it<br>
doesn't).<br>
<br>
Paolo<br>
<br>
On Mon, Aug 10, 2015 at 1:10 PM, Venkataramana Imandi<br>
<venkataramana.imandi at <a href="http://gmail.com" rel="noreferrer" target="_blank">gmail.com</a><br>
<<a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a>>> wrote:<br>
<br>
<br>
<br>
Dear Sir/ Madam,<br>
<br>
I am using quantum espresso (version:5.1.2) for doing Langevin dynamics on<br>
Ethene molecules were kept top and bottom of silver oxide surface (total<br>
atoms: 37) running on Red Hat machine with serial and parallel process. In<br>
the output file, the coordinates of some of the atoms getting starred(***).<br>
In order to understand more about results, I tried with simple systems<br>
containing 2 Si atoms, the results shows that Langevin dynamics is working<br>
fine but the distance between two Si atoms goes on increasing (at the end<br>
of 100 md steps, the distance is 560 Angstroms). Moreover, herein Langevin<br>
dynamics is over-damped and the parameter of gamma (friction coefficient)<br>
is not mentioned anywhere in the input file description of pw.x related<br>
manual. Hence, I request you kindly suggest me how to perform Langevin<br>
calculations on my original system. Input file and starred(**) coordinates<br>
of my original system (output file) were attached.<br>
<br>
&control<br>
calculation='md',<br>
prefix='ag_eth',<br>
dt=20.D0,<br>
nstep=50,<br>
etot_conv_thr=1.0D-6,<br>
forc_conv_thr=1.0D-5,<br>
pseudo_dir = '/home/venkat/ORR1/PPS1'<br>
/<br>
&system<br>
ibrav=0,<br>
nat=37,<br>
ntyp=4,<br>
ecutwfc = 30.0,<br>
nosym=.true.,<br>
occupations='smearing',<br>
smearing='m-p',<br>
degauss=0.03,<br>
tot_charge=1.0<br>
/<br>
&electrons<br>
electron_maxstep=2000,<br>
diagonalization='david',<br>
mixing_beta = 0.3,<br>
conv_thr = 1.0D-6,<br>
scf_must_converge=.false.<br>
/<br>
&ions<br>
pot_extrapolation = 'second_order',<br>
wfc_extrapolation = 'second_order',<br>
ion_dynamics='langevin',<br>
tempw=300.D0,<br>
nraise=1<br>
/<br>
ATOMIC_SPECIES<br>
C 12.0107 C.pbe-rrkjus.UPF<br>
H 1.00794 H.pbe-rrkjus.UPF<br>
O 15.9994 O.pbe-rrkjus.UPF<br>
Ag 107.8682 Ag.pbe-d-rrkjus.UPF<br>
<br>
CELL_PARAMETERS {angstrom}<br>
7.8980000000 0.0000000000 0.0000000000<br>
0.0000000000 7.8980000000 0.0000000000<br>
0.0000000000 0.0000000000 9.7479000000<br>
<br>
ATOMIC_POSITIONS {angstrom}<br>
<br>
C 3.674759 2.942993 -3.493103<br>
H 4.121990 3.816735 -4.007690<br>
H 4.121990 2.069251 -4.007690<br>
C 2.211227 2.942993 -3.493103<br>
H 1.763996 3.816735 -4.007690<br>
H 1.763996 2.069251 -4.007690<br>
O 0.000000 0.000000 -2.719012<br>
Ag 4.448147 4.449893 -1.919012<br>
Ag 4.448147 1.436093 -1.919012<br>
Ag 1.437838 4.449893 -1.919012<br>
Ag 1.437838 1.436093 -1.919012<br>
Ag 2.942993 2.942993 0.000000<br>
Ag 2.942993 0.000000 0.000000<br>
Ag 0.000000 2.942993 0.000000<br>
Ag 0.000000 0.000000 0.000000<br>
Ag 1.437838 1.436093 1.919012<br>
Ag 1.437838 4.449893 1.919012<br>
Ag 4.448147 1.436093 1.919012<br>
Ag 4.448147 4.449893 1.919012<br>
O 0.000000 0.000000 2.719012<br>
C 3.674759 2.942993 3.493103<br>
H 4.121990 3.816735 4.007690<br>
H 4.121990 2.069251 4.007690<br>
C 2.211227 2.942993 3.493103<br>
H 1.763996 3.816735 4.007690<br>
H 1.763996 2.069251 4.007690<br>
O 0.000000 5.885983 -2.719012<br>
Ag 2.942993 5.885983 0.000000<br>
Ag 0.000000 5.885983 0.000000<br>
O 0.000000 5.885983 2.719012<br>
O 5.885983 0.000000 -2.719012<br>
Ag 5.885983 2.942993 0.000000<br>
Ag 5.885983 0.000000 0.000000<br>
O 5.885983 0.000000 2.719012<br>
O 5.885983 5.885983 -2.719012<br>
Ag 5.885983 5.885983 0.000000<br>
O 5.885983 5.885983 2.719012<br>
<br>
K_POINTS {gamma}<br>
<br>
A BIT of OUTPUT FILE<br>
<br>
ATOMIC_POSITIONS (angstrom)<br>
C 23.936881089 5.854758432 2.384283563<br>
H 5.319738992 3.101932011 -2.806230409<br>
H 5.032723666 3.366896985 -3.263624443<br>
C -19.193958442 -0.839672619 -8.633281572<br>
H 2.840673809 3.320817821 -3.598829264<br>
H 2.259010092 3.506469010 -4.024573435<br>
O 3.200827481 3.891444136 -5.674056522<br>
Ag -2.799093034 8.698187934 0.392246441<br>
Ag 6.216802688 0.615454519 -1.827886947<br>
Ag -1.094861601 5.714331653 -3.826763750<br>
Ag -0.821908140 -7.523290040 -8.937996255<br>
Ag 7.394141127 8.391763262 7.199208896<br>
Ag 66.2293865871065.326804153 192.584344197<br>
Ag 4515.057117298 369.600932228 188.645687521<br>
Ag 395.079974228 976.555500510 23.641381229<br>
Ag -0.868373165 1.254442767 -0.725095564<br>
Ag 0.598543920 4.290748028 1.130598433<br>
Ag 3.451303546 0.003835176 -2.147641351<br>
Ag 4.967046204 4.664900169 1.274377193<br>
O 4.154896086 3.538399188 4.404896973<br>
C 399.041692489-175.281493613-563.071390643<br>
H 3.281002088 3.892508380 4.191590229<br>
H 5.590682748 1.083007852 4.528641700<br>
C -206.161786136-122.423501782 -55.021382542<br>
H 0.246549207 5.329189077 3.491183253<br>
H 1.659499381 1.418695757 3.087580955<br>
O -19.384256566 28.168644116 11.242605036<br>
Ag -75.320660159**************-197.570811974<br>
Ag 561.119359654-921.736664610 96.273929826<br>
O 0.652654857 4.794099697 2.674333108<br>
O 0.725736992 1.497121799 -3.145265492<br>
Ag ************** -53.851744674 435.559732159<br>
Ag -59.3881630261875.893021868 -68.801534006<br>
O 4.092070388 0.327775217 7.087480811<br>
O 1.475113672 4.942700103 -3.552674785<br>
Ag -847.347981606************** -58.746720826<br>
O 5.344579864 2.986191369 5.581658260<br>
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<br>
Message: 9<br>
Date: Thu, 20 Aug 2015 10:10:35 +0530<br>
From: Venkataramana Imandi <<a href="mailto:venkataramana.imandi@gmail.com">venkataramana.imandi@gmail.com</a>><br>
Subject: [Pw_forum] Langevin dynamics<br>
To: <a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a><br>
Cc: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<<a href="mailto:CAEJJhntF50S6PqPhMWkoSrm8N4nDUOkyTy22mMJSBWtDySU12A@mail.gmail.com">CAEJJhntF50S6PqPhMWkoSrm8N4nDUOkyTy22mMJSBWtDySU12A@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Paolo Giannozzi sir,<br>
<br>
<br>
<br>
Thank you sir for your kind reply and sorry for delaying reply. I felt same<br>
thing while reading previous threads in pw_forum archives. According to<br>
suggestions given by Ari Paavo Seitsonen sir, I made all corrections and<br>
tried my level best. All trials lead to collapse of structure during<br>
Langevin dynamics.<br>
<br>
Best,<br>
Venkataramana<br>
PhD student<br>
IIT Bombay<br>
<br>
Langevin dynamics was implemented many years ago in QE, but I have never<br>
heard of anybody using it, nor seen any evidence that it works (or that it<br>
doesn't).<br>
<br>
Paolo<br>
<br>
On Mon, Aug 10, 2015 at 1:10 PM, Venkataramana Imandi<br>
<venkataramana.imandi at <a href="http://gmail.com" rel="noreferrer" target="_blank">gmail.com</a><br>
<<a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a>>> wrote:<br>
<br>
<br>
<br>
Dear Sir/ Madam,<br>
<br>
I am using quantum espresso (version:5.1.2) for doing Langevin dynamics on<br>
Ethene molecules were kept top and bottom of silver oxide surface (total<br>
atoms: 37) running on Red Hat machine with serial and parallel process. In<br>
the output file, the coordinates of some of the atoms getting starred(***).<br>
In order to understand more about results, I tried with simple systems<br>
containing 2 Si atoms, the results shows that Langevin dynamics is working<br>
fine but the distance between two Si atoms goes on increasing (at the end<br>
of 100 md steps, the distance is 560 Angstroms). Moreover, herein Langevin<br>
dynamics is over-damped and the parameter of gamma (friction coefficient)<br>
is not mentioned anywhere in the input file description of pw.x related<br>
manual. Hence, I request you kindly suggest me how to perform Langevin<br>
calculations on my original system. Input file and starred(**) coordinates<br>
of my original system (output file) were attached.<br>
<br>
&control<br>
calculation='md',<br>
prefix='ag_eth',<br>
dt=20.D0,<br>
nstep=50,<br>
etot_conv_thr=1.0D-6,<br>
forc_conv_thr=1.0D-5,<br>
pseudo_dir = '/home/venkat/ORR1/PPS1'<br>
/<br>
&system<br>
ibrav=0,<br>
nat=37,<br>
ntyp=4,<br>
ecutwfc = 30.0,<br>
nosym=.true.,<br>
occupations='smearing',<br>
smearing='m-p',<br>
degauss=0.03,<br>
tot_charge=1.0<br>
/<br>
&electrons<br>
electron_maxstep=2000,<br>
diagonalization='david',<br>
mixing_beta = 0.3,<br>
conv_thr = 1.0D-6,<br>
scf_must_converge=.false.<br>
/<br>
&ions<br>
pot_extrapolation = 'second_order',<br>
wfc_extrapolation = 'second_order',<br>
ion_dynamics='langevin',<br>
tempw=300.D0,<br>
nraise=1<br>
/<br>
ATOMIC_SPECIES<br>
C 12.0107 C.pbe-rrkjus.UPF<br>
H 1.00794 H.pbe-rrkjus.UPF<br>
O 15.9994 O.pbe-rrkjus.UPF<br>
Ag 107.8682 Ag.pbe-d-rrkjus.UPF<br>
<br>
CELL_PARAMETERS {angstrom}<br>
7.8980000000 0.0000000000 0.0000000000<br>
0.0000000000 7.8980000000 0.0000000000<br>
0.0000000000 0.0000000000 9.7479000000<br>
<br>
ATOMIC_POSITIONS {angstrom}<br>
<br>
C 3.674759 2.942993 -3.493103<br>
H 4.121990 3.816735 -4.007690<br>
H 4.121990 2.069251 -4.007690<br>
C 2.211227 2.942993 -3.493103<br>
H 1.763996 3.816735 -4.007690<br>
H 1.763996 2.069251 -4.007690<br>
O 0.000000 0.000000 -2.719012<br>
Ag 4.448147 4.449893 -1.919012<br>
Ag 4.448147 1.436093 -1.919012<br>
Ag 1.437838 4.449893 -1.919012<br>
Ag 1.437838 1.436093 -1.919012<br>
Ag 2.942993 2.942993 0.000000<br>
Ag 2.942993 0.000000 0.000000<br>
Ag 0.000000 2.942993 0.000000<br>
Ag 0.000000 0.000000 0.000000<br>
Ag 1.437838 1.436093 1.919012<br>
Ag 1.437838 4.449893 1.919012<br>
Ag 4.448147 1.436093 1.919012<br>
Ag 4.448147 4.449893 1.919012<br>
O 0.000000 0.000000 2.719012<br>
C 3.674759 2.942993 3.493103<br>
H 4.121990 3.816735 4.007690<br>
H 4.121990 2.069251 4.007690<br>
C 2.211227 2.942993 3.493103<br>
H 1.763996 3.816735 4.007690<br>
H 1.763996 2.069251 4.007690<br>
O 0.000000 5.885983 -2.719012<br>
Ag 2.942993 5.885983 0.000000<br>
Ag 0.000000 5.885983 0.000000<br>
O 0.000000 5.885983 2.719012<br>
O 5.885983 0.000000 -2.719012<br>
Ag 5.885983 2.942993 0.000000<br>
Ag 5.885983 0.000000 0.000000<br>
O 5.885983 0.000000 2.719012<br>
O 5.885983 5.885983 -2.719012<br>
Ag 5.885983 5.885983 0.000000<br>
O 5.885983 5.885983 2.719012<br>
<br>
K_POINTS {gamma}<br>
<br>
A BIT of OUTPUT FILE<br>
<br>
ATOMIC_POSITIONS (angstrom)<br>
C 23.936881089 5.854758432 2.384283563<br>
H 5.319738992 3.101932011 -2.806230409<br>
H 5.032723666 3.366896985 -3.263624443<br>
C -19.193958442 -0.839672619 -8.633281572<br>
H 2.840673809 3.320817821 -3.598829264<br>
H 2.259010092 3.506469010 -4.024573435<br>
O 3.200827481 3.891444136 -5.674056522<br>
Ag -2.799093034 8.698187934 0.392246441<br>
Ag 6.216802688 0.615454519 -1.827886947<br>
Ag -1.094861601 5.714331653 -3.826763750<br>
Ag -0.821908140 -7.523290040 -8.937996255<br>
Ag 7.394141127 8.391763262 7.199208896<br>
Ag 66.2293865871065.326804153 192.584344197<br>
Ag 4515.057117298 369.600932228 188.645687521<br>
Ag 395.079974228 976.555500510 23.641381229<br>
Ag -0.868373165 1.254442767 -0.725095564<br>
Ag 0.598543920 4.290748028 1.130598433<br>
Ag 3.451303546 0.003835176 -2.147641351<br>
Ag 4.967046204 4.664900169 1.274377193<br>
O 4.154896086 3.538399188 4.404896973<br>
C 399.041692489-175.281493613-563.071390643<br>
H 3.281002088 3.892508380 4.191590229<br>
H 5.590682748 1.083007852 4.528641700<br>
C -206.161786136-122.423501782 -55.021382542<br>
H 0.246549207 5.329189077 3.491183253<br>
H 1.659499381 1.418695757 3.087580955<br>
O -19.384256566 28.168644116 11.242605036<br>
Ag -75.320660159**************-197.570811974<br>
Ag 561.119359654-921.736664610 96.273929826<br>
O 0.652654857 4.794099697 2.674333108<br>
O 0.725736992 1.497121799 -3.145265492<br>
Ag ************** -53.851744674 435.559732159<br>
Ag -59.3881630261875.893021868 -68.801534006<br>
O 4.092070388 0.327775217 7.087480811<br>
O 1.475113672 4.942700103 -3.552674785<br>
Ag -847.347981606************** -58.746720826<br>
O 5.344579864 2.986191369 5.581658260<br>
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<br>
Message: 10<br>
Date: Thu, 20 Aug 2015 07:14:50 +0000 (UTC)<br>
From: Yevgen Melikhov <<a href="mailto:melikhovyy@yahoo.com">melikhovyy@yahoo.com</a>><br>
Subject: Re: [Pw_forum] relax of 216 atoms (cubic structure)<br>
To: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>>, PWSCF Forum<br>
<<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:2130001740.7981590.1440054890966.JavaMail.yahoo@mail.yahoo.com">2130001740.7981590.1440054890966.JavaMail.yahoo@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Thank you, Paolo!<br>
<br>
I am trying these things right now. Lets see how this will work out!<br>
At the same time, I decided to use PBEsol downloaded from <a href="http://theossrv1.epfl.ch/Main/PseudopotentialsIs" rel="noreferrer" target="_blank">http://theossrv1.epfl.ch/Main/PseudopotentialsIs</a> there a reason why PBEsol for Ga and As are available <a href="http://www.quantum-espresso.org/pseudopotentials/" rel="noreferrer" target="_blank">http://www.quantum-espresso.org/pseudopotentials/</a> but not for Mn?<br>
<br>
Best regards,Yevgen.<br>
<br>
<br>
<br>
From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>>Sent: Saturday, 15 August 2015, 10:21<br>
Increase smearing: 0.0005 is very small. Don't use diagonalization='cg' unless you have a good reason to.<br>
<br>
Paolo<br>
<br>
<br>
On Wed, Aug 5, 2015 at 2:42 PM, Yevgen Melikhov <<a href="mailto:melikhovyy@yahoo.com">melikhovyy@yahoo.com</a>> wrote:<br>
<br>
<br>
<br>
Dear all users of QE,?I am trying to relax GaAs doped with alittle bit of Mn and with some point defects and, of course, I have someproblems in doing that.?In order to construct my initial structureI took cubic cell GaAs with 8 atoms and translated it: (I) 3x2x2 to produce a structurewith 96 atoms and (II) 3x3x3 to produce a structure with 216 atoms. After thatI substitute Ga with Mn (where necessary) and introduce point defects (wherenecessary). ?The structure with 96 atoms (sometimes 94or 95 depending on the problem) with GAMMA point relaxes quite well (please seethe attached input file). ?However, I could not relax the structurewith 216 atoms (sometimes 214 or 215) (please see the attached input and output files). ?If I choose GAMMA point only (that is, ofcourse, what I wanted to speed up calculations), the error is:%%%%%%%%%%%%%%%%%%%%%%%Error in routine efermig (1):Internal error, cannot bracket Ef %%%%%%%%%%%%%%%%%%%%%%%which usually happens in the SCF iteration#2 of th<br>
e first BFGS cycle.After checking the forum and playing withthe parameters I decided to increase the number of k-point. ?If I choose more k-points (as in the attachedfile), the SCF cannot converge (usually this happens within the second orsometimes third BFGS cycle) for 70-100 cycles and, due to time limit on thecluster, the job is not finished. I tried to restart the job but the problem,in my opinion, is not in having not enough time to finish SCF calculations but ratherin oscillations of the scf accuracy (please see the extracted parts of the output file). The first BFGS cycle usually is convergedwithin 10-20 SCF cycles.?Is my assumption that I need to changeconv_thr to lager values correct: the number of atoms doubled (96 vs216), so is the energy (-10300 Ry vs -23000 Ry), and therefore, at least I needto double the conv_thr (currently it is at its default value 1.0D-6)? For sucha big system may I even increase it further 1.0D-4??Thank you in advance for anyhints/comments!<br>
?Yevgen Melikhov?Lab of X-ray and Electron MicroscopyResearc!<br>
hInstitu<br>
te of Physics, PASWarsaw, Poland<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><div style="font-family:arial;font-size:small">Amreen Bano</div><div style="font-family:arial;font-size:small">Department of Physics,</div><div style="font-family:arial;font-size:small">Barkatullah University,</div><div style="font-family:arial;font-size:small">Bhopal-462 026</div><div style="font-family:arial;font-size:small">INDIA</div><div style="font-family:arial;font-size:small">+91-7805081167</div><div style="font-family:arial;font-size:small"><a href="mailto:banoamreen.7@gmail.com" target="_blank">banoamreen.7@gmail.com</a></div></div></div>
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