[Pw_forum] Langevin dynamics
Dear Paolo Giannozzi sir,
Thank you sir for your kind reply and sorry for delaying reply. I felt same
thing while reading previous threads in pw_forum archives. According to
suggestions given by Ari Paavo Seitsonen sir, I made all corrections and
tried my level best. All trials lead to collapse of structure during
Langevin dynamics.
Best,
Venkataramana
PhD student
IIT Bombay
Langevin dynamics was implemented many years ago in QE, but I have never
heard of anybody using it, nor seen any evidence that it works (or that it
doesn't).
Paolo
On Mon, Aug 10, 2015 at 1:10 PM, Venkataramana Imandi
http://pwscf.org/mailman/listinfo/pw_forum>> wrote:
Dear Sir/ Madam,
I am using quantum espresso (version:5.1.2) for doing Langevin dynamics on
Ethene molecules were kept top and bottom of silver oxide surface (total
atoms: 37) running on Red Hat machine with serial and parallel process. In
the output file, the coordinates of some of the atoms getting starred(***).
In order to understand more about results, I tried with simple systems
containing 2 Si atoms, the results shows that Langevin dynamics is working
fine but the distance between two Si atoms goes on increasing (at the end
of 100 md steps, the distance is 560 Angstroms). Moreover, herein Langevin
dynamics is over-damped and the parameter of gamma (friction coefficient)
is not mentioned anywhere in the input file description of pw.x related
manual. Hence, I request you kindly suggest me how to perform Langevin
calculations on my original system. Input file and starred(**) coordinates
of my original system (output file) were attached.
&control
calculation='md',
prefix='ag_eth',
dt=20.D0,
nstep=50,
etot_conv_thr=1.0D-6,
forc_conv_thr=1.0D-5,
pseudo_dir = '/home/venkat/ORR1/PPS1'
/
&system
ibrav=0,
nat=37,
ntyp=4,
ecutwfc = 30.0,
nosym=.true.,
occupations='smearing',
smearing='m-p',
degauss=0.03,
tot_charge=1.0
/
&electrons
electron_maxstep=2000,
diagonalization='david',
mixing_beta = 0.3,
conv_thr = 1.0D-6,
scf_must_converge=.false.
/
&ions
pot_extrapolation = 'second_order',
wfc_extrapolation = 'second_order',
ion_dynamics='langevin',
tempw=300.D0,
nraise=1
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
H 1.00794 H.pbe-rrkjus.UPF
O 15.9994 O.pbe-rrkjus.UPF
Ag 107.8682 Ag.pbe-d-rrkjus.UPF
CELL_PARAMETERS {angstrom}
7.898000 0.00 0.00
0.00 7.898000 0.00
0.00 0.00 9.747900
ATOMIC_POSITIONS {angstrom}
C 3.674759 2.942993-3.493103
H 4.121990 3.816735-4.007690
H 4.121990 2.069251-4.007690
C 2.211227 2.942993-3.493103
H 1.763996 3.816735-4.007690
H 1.763996 2.069251-4.007690
O 0.00 0.00-2.719012
Ag 4.448147 4.449893-1.919012
Ag 4.448147 1.436093-1.919012
Ag 1.437838 4.449893-1.919012
Ag 1.437838 1.436093-1.919012
Ag 2.942993 2.942993 0.00
Ag 2.942993 0.00 0.00
Ag 0.00 2.942993 0.00
Ag 0.00 0.00 0.00
Ag 1.437838 1.436093 1.919012
Ag 1.437838 4.449893 1.919012
Ag 4.448147 1.436093 1.919012
Ag 4.448147 4.449893 1.919012
O 0.00 0.00 2.719012
C 3.674759 2.942993 3.493103
H 4.121990 3.816735 4.007690
H 4.121990 2.069251 4.007690
C 2.211227 2.942993 3.493103
H 1.763996 3.816735 4.007690
H 1.763996 2.069251 4.007690
O 0.00 5.885983-2.719012
Ag 2.942993 5.885983 0.00
Ag 0.00 5.885983 0.00
O 0.00 5.885983 2.719012
O 5.885983 0.00-2.719012
Ag 5.885983 2.942993 0.00
Ag 5.885983 0.00 0.00
O 5.885983 0.00 2.719012
O 5.885983 5.885983-2.719012
Ag 5.885983 5.885983 0.00
O 5.885983 5.885983 2.719012
K_POINTS {gamma}
A BIT of OUTPUT FILE
ATOMIC_POSITIONS (angstrom)
C 23.936881089 5.854758432 2.384283563
H5.319738992 3.101932011 -2.806230409
H5.032723666 3.366896985 -3.263624443
C -19.193958442 -0.839672619 -8.633281572
H2.840673809 3.320817821 -3.598829264
H2.259010092 3.506469010 -4.024573435
O3.200827481 3.891444136 -5.674056522
Ag -2.799093034 8.698187934 0.392246441
Ag 6.216802688 0.615454519 -1.827886947
Ag -1.094861601 5.714
[Pw_forum] Reply to all
Dear Paolo Giannozzi and Ari Paavo Seitsonen
Thank you sir for your kind reply and sorry for delaying reply. I felt same
thing while reading previous threads in pw_forum archives. According to
suggestions given by Ari Paavo Seitsonen sir, I made all corrections and
tried my level best. All trials lead to collapse of structure during
Langevin dynamics.
Best,
Venkataramana
PhD student
IIT Bombay
Langevin dynamics was implemented many years ago in QE, but I have never
heard of anybody using it, nor seen any evidence that it works (or that it
doesn't).
Paolo
On Mon, Aug 10, 2015 at 1:10 PM, Venkataramana Imandi
http://pwscf.org/mailman/listinfo/pw_forum>> wrote:
Dear Sir/ Madam,
I am using quantum espresso (version:5.1.2) for doing Langevin dynamics on
Ethene molecules were kept top and bottom of silver oxide surface (total
atoms: 37) running on Red Hat machine with serial and parallel process. In
the output file, the coordinates of some of the atoms getting starred(***).
In order to understand more about results, I tried with simple systems
containing 2 Si atoms, the results shows that Langevin dynamics is working
fine but the distance between two Si atoms goes on increasing (at the end
of 100 md steps, the distance is 560 Angstroms). Moreover, herein Langevin
dynamics is over-damped and the parameter of gamma (friction coefficient)
is not mentioned anywhere in the input file description of pw.x related
manual. Hence, I request you kindly suggest me how to perform Langevin
calculations on my original system. Input file and starred(**) coordinates
of my original system (output file) were attached.
&control
calculation='md',
prefix='ag_eth',
dt=20.D0,
nstep=50,
etot_conv_thr=1.0D-6,
forc_conv_thr=1.0D-5,
pseudo_dir = '/home/venkat/ORR1/PPS1'
/
&system
ibrav=0,
nat=37,
ntyp=4,
ecutwfc = 30.0,
nosym=.true.,
occupations='smearing',
smearing='m-p',
degauss=0.03,
tot_charge=1.0
/
&electrons
electron_maxstep=2000,
diagonalization='david',
mixing_beta = 0.3,
conv_thr = 1.0D-6,
scf_must_converge=.false.
/
&ions
pot_extrapolation = 'second_order',
wfc_extrapolation = 'second_order',
ion_dynamics='langevin',
tempw=300.D0,
nraise=1
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
H 1.00794 H.pbe-rrkjus.UPF
O 15.9994 O.pbe-rrkjus.UPF
Ag 107.8682 Ag.pbe-d-rrkjus.UPF
CELL_PARAMETERS {angstrom}
7.898000 0.00 0.00
0.00 7.898000 0.00
0.00 0.00 9.747900
ATOMIC_POSITIONS {angstrom}
C 3.674759 2.942993-3.493103
H 4.121990 3.816735-4.007690
H 4.121990 2.069251-4.007690
C 2.211227 2.942993-3.493103
H 1.763996 3.816735-4.007690
H 1.763996 2.069251-4.007690
O 0.00 0.00-2.719012
Ag 4.448147 4.449893-1.919012
Ag 4.448147 1.436093-1.919012
Ag 1.437838 4.449893-1.919012
Ag 1.437838 1.436093-1.919012
Ag 2.942993 2.942993 0.00
Ag 2.942993 0.00 0.00
Ag 0.00 2.942993 0.00
Ag 0.00 0.00 0.00
Ag 1.437838 1.436093 1.919012
Ag 1.437838 4.449893 1.919012
Ag 4.448147 1.436093 1.919012
Ag 4.448147 4.449893 1.919012
O 0.00 0.00 2.719012
C 3.674759 2.942993 3.493103
H 4.121990 3.816735 4.007690
H 4.121990 2.069251 4.007690
C 2.211227 2.942993 3.493103
H 1.763996 3.816735 4.007690
H 1.763996 2.069251 4.007690
O 0.00 5.885983-2.719012
Ag 2.942993 5.885983 0.00
Ag 0.00 5.885983 0.00
O 0.00 5.885983 2.719012
O 5.885983 0.00-2.719012
Ag 5.885983 2.942993 0.00
Ag 5.885983 0.00 0.00
O 5.885983 0.00 2.719012
O 5.885983 5.885983-2.719012
Ag 5.885983 5.885983 0.00
O 5.885983 5.885983 2.719012
K_POINTS {gamma}
A BIT of OUTPUT FILE
ATOMIC_POSITIONS (angstrom)
C 23.936881089 5.854758432 2.384283563
H5.319738992 3.101932011 -2.806230409
H5.032723666 3.366896985 -3.263624443
C -19.193958442 -0.839672619 -8.633281572
H2.840673809 3.320817821 -3.598829264
H2.259010092 3.506469010 -4.024573435
O3.200827481 3.891444136 -5.674056522
Ag -2.799093034 8.698187934 0.392246441
Ag 6.216802688 0.615454519 -1.827886947
Ag -
Re: [Pw_forum] Wrong k-string? in nscf+lelfield
Dear All
I have this error when I run this nscf input:
&CONTROL
calculation = 'nscf' ,
restart_mode = 'from_scratch' ,
prefix= 'E',
tstress = .true. ,
tprnfor = .true. ,
outdir='?',
etot_conv_thr = 1.0E-6 ,
forc_conv_thr = 1.0D-6 ,
pseudo_dir = '?',
lelfield= .true. ,
lberry= .true. ,
gdir= 3 ,
nppstr= 25 ,
/
&SYSTEM
ibrav = 0,
celldm(1)= ?,
nat = 5,
ntyp = 3,
ecutwfc = 80.0 ,
ecutrho = 800.0 ,
occupations = 'fixed' ,
/
&ELECTRONS
conv_thr = 1.D-6 ,
diago_full_acc = .TRUE.,
efield_cart(1) = 0.0D0 ,
efield_cart(2) = 0.0D0 ,
efield_cart(3) = 0.1D0 ,
/
ATOMIC_SPECIES
O 15.9994 ?.UPF
Ti47.867 ?.UPF
Ba137.327?.UPF
CELL_PARAMETERS {cubic}
1. 0.0.000
0. 1.0.000
0. 0.1.0135088
ATOMIC_POSITIONS {alat}
O0.0 0.5 0.497977245
O0.5 0.0 0.497977245
O0.5 0.5 -0.016512609
Ti 0.5 0.5 0.525300320
Ba 0.0 0.0 0.005257800
K_POINTS {automatic}
2 2 2 1 1 1
I have changed all numbers of this input file but this error appeared !
Thanks
Mojtaba
On 8/8/15, David Foster wrote:
> please provide your input file
> Regards
>
> David Foster
>
> Ph.D. Student of Chemistry
>
>
> On Fri, 8/7/15, Mojtaba Mirseraji wrote:
>
> Subject: [Pw_forum] Wrong k-string? in nscf+lelfield
> To: Pw_forum@pwscf.org
> Date: Friday, August 7, 2015, 9:47 AM
>
> Dear Users
>
> I perform lelfield=.true. option in PWSCF (only in nscf) for
> berry
> calculations of polarization but unfortunately
> " Wrong k-string? "
> error is showed.
>
> I do not know how to solve it
>
> Regards
>
> Mojtaba Mirseraji
> Ph.D. Candidate
> Theoretical Condensed Matter Physics
> Arak Univ.
> IRAN
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[Pw_forum] S matrix not positive definite
Dear sir,I am trying to work on Ni-Zn ferrite regarding magnetic moment and band structure and DOS i used .cif file for writing atomic positions and wrote input filewhen i tried to run the code it is giving the following error Error in routine cdiaghg (348): S matrix not positive definite %% stopping ... i am attaching the input and output files for your kind reference. can anyone tell me where i did wrong?Thanks in advancewith kind regards Chaitanya Varma M Assistant professorDepartment of PhysicsGITGITAM UniversityVisakhapatnamIndia NiZn1.scf.out Description: Binary data NiZn1.scf.in Description: Binary data ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Error in compiling QE with libxc
Thanks a lot, I tried specifying the library in LD_LIBS as LD_LIBS = /home/piyukr/Software/libxc-2.1.2/lib/libxc.a and its working now. On Wed, Aug 19, 2015 at 7:52 PM, Ari P Seitsonen wrote: > > Dear Piyush Kumar, > > Why do you try to modify 'MODFLAGS', not 'LD_LIBS'? These are external > routines, 'Modules/libxc.f90' only provides interfaces to them, if I see > correctly. > > Greetings, > >apsi > > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ > Ecole Normale Supérieure (ENS), Département de Chimie, Paris > Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 > > > On Wed, 19 Aug 2015, Piyush Kumar wrote: > > Dear Apsi,Thanks for the reply. I installed libxc-2.1.2 and again compiled >> >> QE, with the following changes in make.sys >> >> MANUAL_DFLAGS = >> DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC >> $(MANUAL_DFLAGS) >> FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS) >> MODFLAGS = -L/home/piyukr/Software/libxc-2.1.2/lib -lxcf90 -lxc >> >> (This line has been added) >> >> where /home/piyukr/Software/libxc-2.1.2 is the installation directory >> >> I am still getting the same error. Can you please tell me which variable I >> need to edit or add and with what values? >> >> Thanking you, >> Piyush >> >> >> On Wed, Aug 19, 2015 at 6:18 PM, Ari P Seitsonen >> wrote: >> >> Dear Piyush Kuma, >> >> A bit unfortunate choice in the code: Here the external >> library 'libxc' is meant [ >> http://www.tddft.org/programs/octopus/wiki/index.php/Libxc ]. >> You need to compile that and insert the path and libraries into >> the variables in 'make.sys' (not explicitly in any 'Makefile'). >> >> There seems to be a related paper on this: >> DOI:10.1016/j.cpc.2013.02.020 >> >> Greetings from Sunny Montrouge, >> >> apsi >> >> >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=* >> =- >> Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / >> http://www.iki.fi/~apsi/ >> Ecole Normale Supérieure (ENS), Département de Chimie, Paris >> Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 >> >> >> On Wed, 19 Aug 2015, Piyush Kumar wrote: >> >> Dear all,I am trying to use MGGA functional 'TB09' >> in quantum espresso >> 5.1.2. When I tried to do calculation with >> input_dft='tb09', I got following >> error >> Error in routine tb09 (1): >> need libxc >> >> I compiled quantum espresso again by linking it with >> libxc.f90 in >> espresso-5.1.2/Modules, by manually editing the make >> files: >> >> In make.sys: >> >> DFLAGS = -D__INTEL -D__FFTW -D__MPI >> -D__PARA -D__LIBXC >> $(MANUAL_DFLAGS) >> >> In PW/src/Makefile >> >> MODFLAGS= $(MOD_FLAG)../../iotk/src >> $(MOD_FLAG)../../Modules -L../../Modules >> -lxcf90 -lxc >> >> In Modules/Makefile >> >> MODFLAGS= $(MOD_FLAG)../iotk/src >> $(MOD_FLAG)../ELPA/src $(MOD_FLAG). -L. >> -lxcf90 -lxc >> >> In flib/Makefile >> >> MODFLAGS= $(MOD_FLAG)../iotk/src >> $(MOD_FLAG)../Modules $(MOD_FLAG). >> -L../Modules -lxcf90 -lxc >> >> After making above changes, I did "make pw", and I >> got following errors >> >> ../../flib/flib.a(functionals.o): In function >> `slater': >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:31: >> undefined reference to >> `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:32: >> undefined reference to >> `xc_f90_lda_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:33: >> undefined reference to >> `xc_f90_func_end_' >> ../../flib/flib.a(functionals.o): In function `pz': >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:169: >> undefined reference to >> `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:170: >> undefined reference to >> `xc_f90_lda_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:171: >> undefined reference to >> `xc_f90_func_end_' >> ../../flib/flib.a(functionals.o): In function `pw': >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: >> undefined reference to >> `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: >> undefined reference to >> `xc_f90_lda_exc_vxc_' >>
Re: [Pw_forum] Error in compiling QE with libxc
Dear Piyush Kumar, Why do you try to modify 'MODFLAGS', not 'LD_LIBS'? These are external routines, 'Modules/libxc.f90' only provides interfaces to them, if I see correctly. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Supérieure (ENS), Département de Chimie, Paris Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 On Wed, 19 Aug 2015, Piyush Kumar wrote: Dear Apsi,Thanks for the reply. I installed libxc-2.1.2 and again compiled QE, with the following changes in make.sys MANUAL_DFLAGS = DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC $(MANUAL_DFLAGS) FDFLAGS = $(DFLAGS) $(MANUAL_DFLAGS) MODFLAGS = -L/home/piyukr/Software/libxc-2.1.2/lib -lxcf90 -lxc (This line has been added) where /home/piyukr/Software/libxc-2.1.2 is the installation directory I am still getting the same error. Can you please tell me which variable I need to edit or add and with what values? Thanking you, Piyush On Wed, Aug 19, 2015 at 6:18 PM, Ari P Seitsonen wrote: Dear Piyush Kuma, A bit unfortunate choice in the code: Here the external library 'libxc' is meant [ http://www.tddft.org/programs/octopus/wiki/index.php/Libxc ]. You need to compile that and insert the path and libraries into the variables in 'make.sys' (not explicitly in any 'Makefile'). There seems to be a related paper on this: DOI:10.1016/j.cpc.2013.02.020 Greetings from Sunny Montrouge, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=* =- Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Supérieure (ENS), Département de Chimie, Paris Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 On Wed, 19 Aug 2015, Piyush Kumar wrote: Dear all,I am trying to use MGGA functional 'TB09' in quantum espresso 5.1.2. When I tried to do calculation with input_dft='tb09', I got following error Error in routine tb09 (1): need libxc I compiled quantum espresso again by linking it with libxc.f90 in espresso-5.1.2/Modules, by manually editing the make files: In make.sys: DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC $(MANUAL_DFLAGS) In PW/src/Makefile MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules -L../../Modules -lxcf90 -lxc In Modules/Makefile MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../ELPA/src $(MOD_FLAG). -L. -lxcf90 -lxc In flib/Makefile MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../Modules $(MOD_FLAG). -L../Modules -lxcf90 -lxc After making above changes, I did "make pw", and I got following errors ../../flib/flib.a(functionals.o): In function `slater': /home/piyukr/espresso-5.1.2/flib/functionals.f90:31: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:32: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:33: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pz': /home/piyukr/espresso-5.1.2/flib/functionals.f90:169: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:170: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:171: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pw': /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference to `xc_f90_func_end_' ..
Re: [Pw_forum] Error in compiling QE with libxc
Dear Apsi, Thanks for the reply. I installed libxc-2.1.2 and again compiled QE, with the following changes in make.sys MANUAL_DFLAGS = DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA *-D__LIBXC* $(MANUAL_DFLAGS) FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS) MODFLAGS = -L/home/piyukr/Software/libxc-2.1.2/lib -lxcf90 -lxc (This line has been added) where /home/piyukr/Software/libxc-2.1.2 is the installation directory I am still getting the same error. Can you please tell me which variable I need to edit or add and with what values? Thanking you, Piyush On Wed, Aug 19, 2015 at 6:18 PM, Ari P Seitsonen wrote: > > Dear Piyush Kuma, > > A bit unfortunate choice in the code: Here the external library 'libxc' > is meant [ http://www.tddft.org/programs/octopus/wiki/index.php/Libxc ]. > You need to compile that and insert the path and libraries into the > variables in 'make.sys' (not explicitly in any 'Makefile'). > > There seems to be a related paper on this: DOI:10.1016/j.cpc.2013.02.020 > > Greetings from Sunny Montrouge, > >apsi > > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ > Ecole Normale Supérieure (ENS), Département de Chimie, Paris > Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 > > > On Wed, 19 Aug 2015, Piyush Kumar wrote: > > Dear all,I am trying to use MGGA functional 'TB09' in quantum espresso >> >> 5.1.2. When I tried to do calculation with input_dft='tb09', I got >> following >> error >> Error in routine tb09 (1): >> need libxc >> >> I compiled quantum espresso again by linking it with libxc.f90 in >> espresso-5.1.2/Modules, by manually editing the make files: >> >> In make.sys: >> >> DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC >> $(MANUAL_DFLAGS) >> >> In PW/src/Makefile >> >> MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules >> -L../../Modules >> -lxcf90 -lxc >> >> In Modules/Makefile >> >> MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../ELPA/src $(MOD_FLAG). -L. >> -lxcf90 -lxc >> >> In flib/Makefile >> >> MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../Modules $(MOD_FLAG). >> -L../Modules -lxcf90 -lxc >> >> After making above changes, I did "make pw", and I got following errors >> >> ../../flib/flib.a(functionals.o): In function `slater': >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:31: undefined reference >> to >> `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:32: undefined reference >> to >> `xc_f90_lda_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:33: undefined reference >> to >> `xc_f90_func_end_' >> ../../flib/flib.a(functionals.o): In function `pz': >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:169: undefined reference >> to >> `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:170: undefined reference >> to >> `xc_f90_lda_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:171: undefined reference >> to >> `xc_f90_func_end_' >> ../../flib/flib.a(functionals.o): In function `pw': >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference >> to >> `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference >> to >> `xc_f90_lda_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference >> to >> `xc_f90_func_end_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference >> to >> `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference >> to >> `xc_f90_lda_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference >> to >> `xc_f90_func_end_' >> ../../flib/flib.a(functionals.o): In function `pbex': >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1011: undefined reference >> to `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1012: undefined reference >> to `xc_f90_gga_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1013: undefined reference >> to `xc_f90_func_end_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1016: undefined reference >> to `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1017: undefined reference >> to `xc_f90_lda_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1018: undefined reference >> to `xc_f90_func_end_' >> ../../flib/flib.a(functionals.o): In function `pbec': >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1222: undefined reference >> to `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1223: undefined reference >> to `xc_f90_gga_exc_vxc_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1224: undefined reference >> to `xc_f90_func_end_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1226: undefined reference >> to `xc_f90_func_init_' >> /home/piyukr/espresso-5.1.2/flib/functionals.f90:1227: undefined refere
Re: [Pw_forum] Error in compiling QE with libxc
Dear Piyush Kuma, A bit unfortunate choice in the code: Here the external library 'libxc' is meant [ http://www.tddft.org/programs/octopus/wiki/index.php/Libxc ]. You need to compile that and insert the path and libraries into the variables in 'make.sys' (not explicitly in any 'Makefile'). There seems to be a related paper on this: DOI:10.1016/j.cpc.2013.02.020 Greetings from Sunny Montrouge, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Supérieure (ENS), Département de Chimie, Paris Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 On Wed, 19 Aug 2015, Piyush Kumar wrote: Dear all,I am trying to use MGGA functional 'TB09' in quantum espresso 5.1.2. When I tried to do calculation with input_dft='tb09', I got following error Error in routine tb09 (1): need libxc I compiled quantum espresso again by linking it with libxc.f90 in espresso-5.1.2/Modules, by manually editing the make files: In make.sys: DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__LIBXC $(MANUAL_DFLAGS) In PW/src/Makefile MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules -L../../Modules -lxcf90 -lxc In Modules/Makefile MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../ELPA/src $(MOD_FLAG). -L. -lxcf90 -lxc In flib/Makefile MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../Modules $(MOD_FLAG). -L../Modules -lxcf90 -lxc After making above changes, I did "make pw", and I got following errors ../../flib/flib.a(functionals.o): In function `slater': /home/piyukr/espresso-5.1.2/flib/functionals.f90:31: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:32: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:33: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pz': /home/piyukr/espresso-5.1.2/flib/functionals.f90:169: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:170: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:171: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pw': /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pbex': /home/piyukr/espresso-5.1.2/flib/functionals.f90:1011: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1012: undefined reference to `xc_f90_gga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1013: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1016: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1017: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1018: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pbec': /home/piyukr/espresso-5.1.2/flib/functionals.f90:1222: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1223: undefined reference to `xc_f90_gga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1224: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1226: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1227: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1228: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(metagga.o): In function `tpsscxc': /home/piyukr/espresso-5.1.2/flib/metagga.f90:57: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:58: undefined reference to `xc_f90_mgga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:60: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:68: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:69: undefined reference to `xc_f90_mgga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:71: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(metagga.o): In function `tb09cxc': /home/piyukr/espresso-5.1.2/flib/metagga.f90:1415: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:1416: unde
[Pw_forum] Error in compiling QE with libxc
Dear all, I am trying to use MGGA functional 'TB09' in quantum espresso 5.1.2. When I tried to do calculation with input_dft='tb09', I got following error Error in routine tb09 (1): need libxc I compiled quantum espresso again by linking it with libxc.f90 in espresso-5.1.2/Modules, by manually editing the make files: In make.sys: DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA *-D__LIBXC* $(MANUAL_DFLAGS) In PW/src/Makefile MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules *-L../../Modules -lxcf90 -lxc* In Modules/Makefile MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../ELPA/src $(MOD_FLAG).* -L. -lxcf90 -lxc* In flib/Makefile MODFLAGS= $(MOD_FLAG)../iotk/src $(MOD_FLAG)../Modules $(MOD_FLAG).* -L../Modules -lxcf90 -lxc* After making above changes, I did "make pw", and I got following errors ../../flib/flib.a(functionals.o): In function `slater': /home/piyukr/espresso-5.1.2/flib/functionals.f90:31: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:32: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:33: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pz': /home/piyukr/espresso-5.1.2/flib/functionals.f90:169: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:170: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:171: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pw': /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:374: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:375: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:376: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pbex': /home/piyukr/espresso-5.1.2/flib/functionals.f90:1011: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1012: undefined reference to `xc_f90_gga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1013: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1016: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1017: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1018: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(functionals.o): In function `pbec': /home/piyukr/espresso-5.1.2/flib/functionals.f90:1222: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1223: undefined reference to `xc_f90_gga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1224: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1226: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1227: undefined reference to `xc_f90_lda_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/functionals.f90:1228: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(metagga.o): In function `tpsscxc': /home/piyukr/espresso-5.1.2/flib/metagga.f90:57: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:58: undefined reference to `xc_f90_mgga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:60: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:68: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:69: undefined reference to `xc_f90_mgga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:71: undefined reference to `xc_f90_func_end_' ../../flib/flib.a(metagga.o): In function `tb09cxc': /home/piyukr/espresso-5.1.2/flib/metagga.f90:1415: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:1416: undefined reference to `xc_f90_mgga_vxc_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:1418: undefined reference to `xc_f90_func_end_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:1428: undefined reference to `xc_f90_func_init_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:1429: undefined reference to `xc_f90_mgga_exc_vxc_' /home/piyukr/espresso-5.1.2/flib/metagga.f90:1431: undefined reference to `xc_f90_func_end_' make[2]: *** [pw.x] Error 1 make[2]: Leaving directory `/home/piyukr/espresso-5.1.2/PW/src' make[1]: *** [pw] Error 1 make[1]: Leaving directory `/home/piyukr/espresso-5.1.2/PW' make: *** [pw] Error 1 I am using intel compilers. Can anyone please tell me what is correct way to link libxc? Thanking You. Piyush Kumar, M.T
