Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface
Dear Ari,
I misunderstood your message.
I ask you whether you got stable O_ad position at a bridge site.
With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.
On Tue, Apr 10, 2018 at 3:50 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:
> Dear Ari,
>
> What shall i do now. The wrong in the input file coordinates or system
> description.
> Can you give more hints. Even increasing system size (present 24 atoms to
> 48 Pt atoms), the results remain same.
>
> With best regards
> Venkataramana Imandi
> Postdoctoral fellow
> IIT Madras, India.
>
>
> On Tue, Apr 10, 2018 at 3:08 PM, Venkataramana Imandi <
> venkataramana.ima...@gmail.com> wrote:
>
>> Dear Ari,
>>
>> Sorry, I didn't mention that I also tried by fixing coordinate of O_ad at
>> a bridge position.
>> It resulted the Pt atoms moving, in such way that O_ad becomes three-fold
>> site(either fcc or hcp).
>>
>> With best regards
>> Venkataramana Imandi
>> Postdoctoral fellow
>> IIT Madras, India.
>>
>>
>> On Tue, Apr 10, 2018 at 2:44 PM, Venkataramana Imandi <
>> venkataramana.ima...@gmail.com> wrote:
>>
>>>
>>> Dear QE community,
>>>
>>> I am a new user of Quantum espresso simulation package. I installed
>>> 6.2.1 Quantum espresso in the Linux-X86_64-INTEL-MPI. I want to find out
>>> the binding energy of O_ad at various sites(top,bridge,hcp and fcc) on
>>> Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried on
>>> Pt-surface, and I got O_ad at top, hcp and fcc sites on Pt-surface,
>>> however, i couldn't find O_ad at bridge position.
>>> I have tried all possible ways of getting O_ad at the bridge
>>> position(between Pt-Pt). None of them were given succussful results, and
>>> the resulted O_ad comes to either fcc or hcp position. All possible ways:
>>> using with and without spin-polarization, davidson diagonalization anc cg,
>>> option (nosym = .TRUE. and .FALSE.), mixing mode(plain, local-TF and TF),
>>> changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative charge(-2) and
>>> different simulation setup (present 24 atoms to 48 Pt atoms). The last
>>> option, i used different pseudopotential(Pt.pw91-n-van.UPF and
>>> O.pw91-van_ak.UPF), herein, i got error as follows (Error in
>>> scalartorealdp Too few elements found). Now i stopped trials.
>>> I ask you can anyone do calculation in your simulation setup with the
>>> given input file, tell me the where the problem is.
>>>
>>> I really thanks to you in advance for any suggestions regarding this.
>>> For information, i used VASP in the last year, therein, i obtained O_ad
>>> at all sites on Pt-surface.
>>>
>>>
>>> calculation='relax'
>>> restart_mode='from_scratch',
>>> pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
>>> prefix='pt'
>>> tprnfor = .true.,
>>> nstep = 200
>>> /
>>>
>>> ibrav=0,
>>> nat=25,
>>> ntyp=2,
>>> ! nspin = 2,
>>> ! starting_magnetization(1)=0.7,
>>> ecutwfc = 32.0,
>>> ecutrho = 320.0,
>>> occupations='smearing',
>>> smearing='methfessel-paxton',
>>> degauss=0.02
>>>! tot_charge = -2,
>>> nosym = .TRUE.
>>> /
>>>
>>> diagonalization='cg'
>>> conv_thr = 1.0e-6
>>> mixing_beta = 0.3
>>>electron_maxstep = 1000
>>> /
>>>
>>> ion_dynamics='bfgs',
>>> /
>>> ATOMIC_SPECIES
>>> Pt 195.084 Pt.pbe-nd-rrkjus.UPF
>>> O15.999 O.pbe-rrkjus.UPF
>>>
>>> ATOMIC_POSITIONS {angstrom}
>>> O 3.45091550 1.17466050 13.69732100 1 1 1
>>> Pt4.84778787 1.20016667 12.44963917 1 1 1
>>> Pt3.46185858 3.60066659 12.44963917 1 1 1
>>> Pt2.07592929 1.20016667 12.44963917 1 1 1
>>> Pt0.6900 3.60066659 12.44963917 1 1 1
>>> Pt3.46185858 0.4000 10.18642611 1 1 1
>>> Pt4.84778787 2.80049996 10.18642611 1 1 1
>>> Pt0.6900 0.4000 10.18642611 1 1 1
>>> Pt2.07592929 2.80049996 10.18642611 1 1 1
>>> Pt3.46185858 2.0000 7.92321305 1 1 1
>>> Pt4.84778787 4.40083326 7.92321305 1
Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface
Dear Ari,
What shall i do now. The wrong in the input file coordinates or system
description.
Can you give more hints. Even increasing system size (present 24 atoms to
48 Pt atoms), the results remain same.
With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.
On Tue, Apr 10, 2018 at 3:08 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:
> Dear Ari,
>
> Sorry, I didn't mention that I also tried by fixing coordinate of O_ad at
> a bridge position.
> It resulted the Pt atoms moving, in such way that O_ad becomes three-fold
> site(either fcc or hcp).
>
> With best regards
> Venkataramana Imandi
> Postdoctoral fellow
> IIT Madras, India.
>
>
> On Tue, Apr 10, 2018 at 2:44 PM, Venkataramana Imandi <
> venkataramana.ima...@gmail.com> wrote:
>
>>
>> Dear QE community,
>>
>> I am a new user of Quantum espresso simulation package. I installed 6.2.1
>> Quantum espresso in the Linux-X86_64-INTEL-MPI. I want to find out the
>> binding energy of O_ad at various sites(top,bridge,hcp and fcc) on
>> Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried on
>> Pt-surface, and I got O_ad at top, hcp and fcc sites on Pt-surface,
>> however, i couldn't find O_ad at bridge position.
>> I have tried all possible ways of getting O_ad at the bridge
>> position(between Pt-Pt). None of them were given succussful results, and
>> the resulted O_ad comes to either fcc or hcp position. All possible ways:
>> using with and without spin-polarization, davidson diagonalization anc cg,
>> option (nosym = .TRUE. and .FALSE.), mixing mode(plain, local-TF and TF),
>> changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative charge(-2) and
>> different simulation setup (present 24 atoms to 48 Pt atoms). The last
>> option, i used different pseudopotential(Pt.pw91-n-van.UPF and
>> O.pw91-van_ak.UPF), herein, i got error as follows (Error in
>> scalartorealdp Too few elements found). Now i stopped trials.
>> I ask you can anyone do calculation in your simulation setup with the
>> given input file, tell me the where the problem is.
>>
>> I really thanks to you in advance for any suggestions regarding this.
>> For information, i used VASP in the last year, therein, i obtained O_ad
>> at all sites on Pt-surface.
>>
>>
>> calculation='relax'
>> restart_mode='from_scratch',
>> pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
>> prefix='pt'
>> tprnfor = .true.,
>> nstep = 200
>> /
>>
>> ibrav=0,
>> nat=25,
>> ntyp=2,
>> ! nspin = 2,
>> ! starting_magnetization(1)=0.7,
>> ecutwfc = 32.0,
>> ecutrho = 320.0,
>> occupations='smearing',
>> smearing='methfessel-paxton',
>> degauss=0.02
>>! tot_charge = -2,
>> nosym = .TRUE.
>> /
>>
>> diagonalization='cg'
>> conv_thr = 1.0e-6
>> mixing_beta = 0.3
>>electron_maxstep = 1000
>> /
>>
>> ion_dynamics='bfgs',
>> /
>> ATOMIC_SPECIES
>> Pt 195.084 Pt.pbe-nd-rrkjus.UPF
>> O15.999 O.pbe-rrkjus.UPF
>>
>> ATOMIC_POSITIONS {angstrom}
>> O 3.45091550 1.17466050 13.69732100 1 1 1
>> Pt4.84778787 1.20016667 12.44963917 1 1 1
>> Pt3.46185858 3.60066659 12.44963917 1 1 1
>> Pt2.07592929 1.20016667 12.44963917 1 1 1
>> Pt0.6900 3.60066659 12.44963917 1 1 1
>> Pt3.46185858 0.4000 10.18642611 1 1 1
>> Pt4.84778787 2.80049996 10.18642611 1 1 1
>> Pt0.6900 0.4000 10.18642611 1 1 1
>> Pt2.07592929 2.80049996 10.18642611 1 1 1
>> Pt3.46185858 2.0000 7.92321305 1 1 1
>> Pt4.84778787 4.40083326 7.92321305 1 1 1
>> Pt0.6900 2.0000 7.92321305 1 1 1
>> Pt2.07592929 4.40083326 7.92321305 1 1 1
>> Pt4.84778787 1.20016667 5.6600 1 1 1
>> Pt3.46185858 3.60066659 5.6600 1 1 1
>> Pt2.07592929 1.20016667 5.6600 1 1 1
>> Pt0.6900 3.60066659 5.6600 1 1 1
>> Pt3.46185858 0.4000 3.39678694 0 0 0
>> Pt4.84778787 2.80049996 3.39678694 0 0 0
>> Pt0.6900 0.4000 3.39678694 0 0 0
>> Pt2.07592929 2.80049996
Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface
Dear Ari,
Sorry, I didn't mention that I also tried by fixing coordinate of O_ad at a
bridge position.
It resulted the Pt atoms moving, in such way that O_ad becomes three-fold
site(either fcc or hcp).
With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.
On Tue, Apr 10, 2018 at 2:44 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:
>
> Dear QE community,
>
> I am a new user of Quantum espresso simulation package. I installed 6.2.1
> Quantum espresso in the Linux-X86_64-INTEL-MPI. I want to find out the
> binding energy of O_ad at various sites(top,bridge,hcp and fcc) on
> Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried on
> Pt-surface, and I got O_ad at top, hcp and fcc sites on Pt-surface,
> however, i couldn't find O_ad at bridge position.
> I have tried all possible ways of getting O_ad at the bridge
> position(between Pt-Pt). None of them were given succussful results, and
> the resulted O_ad comes to either fcc or hcp position. All possible ways:
> using with and without spin-polarization, davidson diagonalization anc cg,
> option (nosym = .TRUE. and .FALSE.), mixing mode(plain, local-TF and TF),
> changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative charge(-2) and
> different simulation setup (present 24 atoms to 48 Pt atoms). The last
> option, i used different pseudopotential(Pt.pw91-n-van.UPF and
> O.pw91-van_ak.UPF), herein, i got error as follows (Error in
> scalartorealdp Too few elements found). Now i stopped trials.
> I ask you can anyone do calculation in your simulation setup with the
> given input file, tell me the where the problem is.
>
> I really thanks to you in advance for any suggestions regarding this.
> For information, i used VASP in the last year, therein, i obtained O_ad at
> all sites on Pt-surface.
>
>
> calculation='relax'
> restart_mode='from_scratch',
> pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
> prefix='pt'
> tprnfor = .true.,
> nstep = 200
> /
>
> ibrav=0,
> nat=25,
> ntyp=2,
> ! nspin = 2,
> ! starting_magnetization(1)=0.7,
> ecutwfc = 32.0,
> ecutrho = 320.0,
> occupations='smearing',
> smearing='methfessel-paxton',
> degauss=0.02
>! tot_charge = -2,
> nosym = .TRUE.
> /
>
> diagonalization='cg'
> conv_thr = 1.0e-6
> mixing_beta = 0.3
>electron_maxstep = 1000
> /
>
> ion_dynamics='bfgs',
> /
> ATOMIC_SPECIES
> Pt 195.084 Pt.pbe-nd-rrkjus.UPF
> O15.999 O.pbe-rrkjus.UPF
>
> ATOMIC_POSITIONS {angstrom}
> O 3.45091550 1.17466050 13.69732100 1 1 1
> Pt4.84778787 1.20016667 12.44963917 1 1 1
> Pt3.46185858 3.60066659 12.44963917 1 1 1
> Pt2.07592929 1.20016667 12.44963917 1 1 1
> Pt0.6900 3.60066659 12.44963917 1 1 1
> Pt3.46185858 0.4000 10.18642611 1 1 1
> Pt4.84778787 2.80049996 10.18642611 1 1 1
> Pt0.6900 0.4000 10.18642611 1 1 1
> Pt2.07592929 2.80049996 10.18642611 1 1 1
> Pt3.46185858 2.0000 7.92321305 1 1 1
> Pt4.84778787 4.40083326 7.92321305 1 1 1
> Pt0.6900 2.0000 7.92321305 1 1 1
> Pt2.07592929 4.40083326 7.92321305 1 1 1
> Pt4.84778787 1.20016667 5.6600 1 1 1
> Pt3.46185858 3.60066659 5.6600 1 1 1
> Pt2.07592929 1.20016667 5.6600 1 1 1
> Pt0.6900 3.60066659 5.6600 1 1 1
> Pt3.46185858 0.4000 3.39678694 0 0 0
> Pt4.84778787 2.80049996 3.39678694 0 0 0
> Pt0.6900 0.4000 3.39678694 0 0 0
> Pt2.07592929 2.80049996 3.39678694 0 0 0
> Pt3.46185858 2.0000 1.13357388 0 0 0
> Pt4.84778787 4.40083326 1.13357388 0 0 0
> Pt0.6900 2.0000 1.13357388 0 0 0
> Pt2.07592929 4.40083326 1.13357388 0 0 0
>
> K_POINTS {automatic}
> 3 3 1 0 0 0
> CELL_PARAMETERS {angstrom}
> 5.5437171600 0.00 0.00
> 0.00 4.800000 0.00
> 0.00 0.0025.5792783300
>
>
> With best regards
> Venkataramana Imandi
> Postdoctoral fellow
> IIT Madras, India.
>
>
>
>
>
>
>
--
venkataramana
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[QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface
Dear QE community,
I am a new user of Quantum espresso simulation package. I installed 6.2.1
Quantum espresso in the Linux-X86_64-INTEL-MPI. I want to find out the
binding energy of O_ad at various sites(top,bridge,hcp and fcc) on
Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried on
Pt-surface, and I got O_ad at top, hcp and fcc sites on Pt-surface,
however, i couldn't find O_ad at bridge position.
I have tried all possible ways of getting O_ad at the bridge
position(between Pt-Pt). None of them were given succussful results, and
the resulted O_ad comes to either fcc or hcp position. All possible ways:
using with and without spin-polarization, davidson diagonalization anc cg,
option (nosym = .TRUE. and .FALSE.), mixing mode(plain, local-TF and TF),
changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative charge(-2) and
different simulation setup (present 24 atoms to 48 Pt atoms). The last
option, i used different pseudopotential(Pt.pw91-n-van.UPF and
O.pw91-van_ak.UPF), herein, i got error as follows (Error in
scalartorealdp Too few elements found). Now i stopped trials.
I ask you can anyone do calculation in your simulation setup with the given
input file, tell me the where the problem is.
I really thanks to you in advance for any suggestions regarding this.
For information, i used VASP in the last year, therein, i obtained O_ad at
all sites on Pt-surface.
calculation='relax'
restart_mode='from_scratch',
pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
prefix='pt'
tprnfor = .true.,
nstep = 200
/
ibrav=0,
nat=25,
ntyp=2,
! nspin = 2,
! starting_magnetization(1)=0.7,
ecutwfc = 32.0,
ecutrho = 320.0,
occupations='smearing',
smearing='methfessel-paxton',
degauss=0.02
! tot_charge = -2,
nosym = .TRUE.
/
diagonalization='cg'
conv_thr = 1.0e-6
mixing_beta = 0.3
electron_maxstep = 1000
/
ion_dynamics='bfgs',
/
ATOMIC_SPECIES
Pt 195.084 Pt.pbe-nd-rrkjus.UPF
O15.999 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
O 3.45091550 1.17466050 13.69732100 1 1 1
Pt4.84778787 1.20016667 12.44963917 1 1 1
Pt3.46185858 3.60066659 12.44963917 1 1 1
Pt2.07592929 1.20016667 12.44963917 1 1 1
Pt0.6900 3.60066659 12.44963917 1 1 1
Pt3.46185858 0.4000 10.18642611 1 1 1
Pt4.84778787 2.80049996 10.18642611 1 1 1
Pt0.6900 0.4000 10.18642611 1 1 1
Pt2.07592929 2.80049996 10.18642611 1 1 1
Pt3.46185858 2.0000 7.92321305 1 1 1
Pt4.84778787 4.40083326 7.92321305 1 1 1
Pt0.6900 2.0000 7.92321305 1 1 1
Pt2.07592929 4.40083326 7.92321305 1 1 1
Pt4.84778787 1.20016667 5.6600 1 1 1
Pt3.46185858 3.60066659 5.6600 1 1 1
Pt2.07592929 1.20016667 5.6600 1 1 1
Pt0.6900 3.60066659 5.6600 1 1 1
Pt3.46185858 0.4000 3.39678694 0 0 0
Pt4.84778787 2.80049996 3.39678694 0 0 0
Pt0.6900 0.4000 3.39678694 0 0 0
Pt2.07592929 2.80049996 3.39678694 0 0 0
Pt3.46185858 2.0000 1.13357388 0 0 0
Pt4.84778787 4.40083326 1.13357388 0 0 0
Pt0.6900 2.0000 1.13357388 0 0 0
Pt2.07592929 4.40083326 1.13357388 0 0 0
K_POINTS {automatic}
3 3 1 0 0 0
CELL_PARAMETERS {angstrom}
5.5437171600 0.00 0.00
0.00 4.800000 0.00
0.00 0.0025.5792783300
With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.
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Re: [Pw_forum] compilation error
Many many thanks sir for your kind reply, I will tell to our hpc system administrator to change or install to latest gfortran compiler. Thanks. On Fri, Oct 23, 2015 at 10:25 PM, Venkataramana Imandi < venkataramana.ima...@gmail.com> wrote: > > Dear QE users, > > I am compiling QE (version:5.1.2) in the high performance computing (hpc) > using gfortran compiler. In the beginning, I did "./configure", the output > is showing like as follows. > > checking build system type... x86_64-unknown-linux-gnu > detected architecture... x86_64 > checking for ifort... no > checking for pgf90... no > checking for pathf95... no > checking for sunf95... no > checking for openf95... no > checking for gfortran... gfortran > configure: WARNING: using cross tools not prefixed with host triplet > checking for Fortran compiler default output file name... a.out > checking whether the Fortran compiler works... yes > checking whether we are cross compiling... yes > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU Fortran compiler... yes > checking whether gfortran accepts -g... yes > checking for Fortran flag to compile .f90 files... none > checking for mpif90... mpif90 > checking whether we are using the GNU Fortran compiler... yes > checking whether mpif90 accepts -g... yes > checking version of mpif90... gfortran 4.1.2 > setting F90... gfortran > setting MPIF90... mpif90 > checking for cc... cc > checking whether we are using the GNU C compiler... yes > checking whether cc accepts -g... yes > checking for cc option to accept ISO C89... none needed > setting CC... cc > checking how to run the C preprocessor... cc -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking size of int *... 8 > checking malloc.h usability... yes > checking malloc.h presence... yes > checking for malloc.h... yes > checking for struct mallinfo.arena... yes > checking for gfortran... gfortran > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether gfortran accepts -g... yes > setting F77... gfortran > using F90... gfortran > setting FFLAGS... -O3 -g > setting F90FLAGS... $(FFLAGS) -x f95-cpp-input > setting FFLAGS_NOOPT... -O0 -g > setting CFLAGS... -O3 > setting CPP... cpp > setting CPPFLAGS... -P -C -traditional > setting LD... mpif90 > setting LDFLAGS... -g -pthread > setting AR... ar > setting ARFLAGS... ruv > checking whether make sets $(MAKE)... yes > checking whether Fortran files must be preprocessed... no > checking how to get verbose linking output from gfortran... -v > checking for Fortran 77 libraries of gfortran... > -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 > -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/lib/../lib64 > -L/usr/lib/../lib64 -lgfortranbegin -lgfortran -lm > checking for dummy main to link with Fortran 77 libraries... none > checking for Fortran 77 name-mangling scheme... lower case, underscore, no > extra underscore > checking for library containing dgemm... no > MKL not found > in /opt/intel/composer*/mkl/lib/intel64: checking for library containing > dgemm... no > MKL not found > in /opt/intel/Compiler/11.1/073/mkl/lib/em64t: checking for library > containing dgemm... -lmkl_gf_lp64 > checking for library containing dspev... none required > setting BLAS_LIBS... -L/opt/intel/Compiler/11.1/073/mkl/lib/em64t > -lmkl_gf_lp64 -lmkl_sequential -lmkl_core > setting LAPACK_LIBS... > checking for library containing dfftw_execute_dft... -lfftw3 > setting FFT_LIBS... -lfftw3 > setting MASS_LIBS... > checking for library containing mpi_init... none required > setting MPI_LIBS... > checking for library containing mpi_init... (cached) none required > checking for library containing pdgemr2d... no > checking for library containing pdgemr2d... -lmkl_scalapack_lp64 > setting SCALAPACK_LIBS... -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 > setting DFLAGS... -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__MPI -D__PARA > -D__SCALAPACK > setting IFLAGS... -I../include > setting FDFLAGS... $(DFLAGS) > checking for ranlib... ranlib > setting RANLIB... ranlib > checking for wget... wget -O > setting WGET... wget -O > configure: creating ./config.status > config.status: cre
[Pw_forum] compilation error
Dear QE users, I am compiling QE (version:5.1.2) in the high performance computing (hpc) using gfortran compiler. In the beginning, I did "./configure", the output is showing like as follows. checking build system type... x86_64-unknown-linux-gnu detected architecture... x86_64 checking for ifort... no checking for pgf90... no checking for pathf95... no checking for sunf95... no checking for openf95... no checking for gfortran... gfortran configure: WARNING: using cross tools not prefixed with host triplet checking for Fortran compiler default output file name... a.out checking whether the Fortran compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking for Fortran flag to compile .f90 files... none checking for mpif90... mpif90 checking whether we are using the GNU Fortran compiler... yes checking whether mpif90 accepts -g... yes checking version of mpif90... gfortran 4.1.2 setting F90... gfortran setting MPIF90... mpif90 checking for cc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed setting CC... cc checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of int *... 8 checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for struct mallinfo.arena... yes checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes setting F77... gfortran using F90... gfortran setting FFLAGS... -O3 -g setting F90FLAGS... $(FFLAGS) -x f95-cpp-input setting FFLAGS_NOOPT... -O0 -g setting CFLAGS... -O3 setting CPP... cpp setting CPPFLAGS... -P -C -traditional setting LD... mpif90 setting LDFLAGS... -g -pthread setting AR... ar setting ARFLAGS... ruv checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... no checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -lgfortranbegin -lgfortran -lm checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for library containing dgemm... no MKL not found in /opt/intel/composer*/mkl/lib/intel64: checking for library containing dgemm... no MKL not found in /opt/intel/Compiler/11.1/073/mkl/lib/em64t: checking for library containing dgemm... -lmkl_gf_lp64 checking for library containing dspev... none required setting BLAS_LIBS... -L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -lmkl_gf_lp64 -lmkl_sequential -lmkl_core setting LAPACK_LIBS... checking for library containing dfftw_execute_dft... -lfftw3 setting FFT_LIBS... -lfftw3 setting MASS_LIBS... checking for library containing mpi_init... none required setting MPI_LIBS... checking for library containing mpi_init... (cached) none required checking for library containing pdgemr2d... no checking for library containing pdgemr2d... -lmkl_scalapack_lp64 setting SCALAPACK_LIBS... -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 setting DFLAGS... -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK setting IFLAGS... -I../include setting FDFLAGS... $(DFLAGS) checking for ranlib... ranlib setting RANLIB... ranlib checking for wget... wget -O setting WGET... wget -O configure: creating ./config.status config.status: creating include/fft_defs.h config.status: creating make.sys config.status: creating configure.msg config.status: creating install/make_wannier90.sys config.status: creating install/make_blas.inc config.status: creating install/make_lapack.inc config.status: creating include/c_defs.h config.status: include/c_defs.h is unchanged ESPRESSO can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. If a required library is not found, the local copy will be compiled. The following libraries have been found: BLAS_LIBS=-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -lmkl_gf_lp64 -lmkl_sequential -lmkl_core LAPACK_LIBS=
[Pw_forum] MD with manual velocities and printing of updated velocities
Dear QE users, I checked entire manual and keywords list of pw.x, there is nowhere information about manual entering of atomic velocities in the input file, If necessary sometimes. Moreover, I have seen dynamics_module.f90 file, it is shown that velocities are initialized from Maxwell-Boltzmann distribution or random number distribution or zero velocities. So, please make me understand, how to give manually velocities at a particular time step. In the input file, I am giving atomic coordinates in the angstrom units. If there is an option to give velocities in the input file, please tell me keywords information and what type of units I have to give for velocities (e.g. angstroms/rydberg, Bohrs/rydberg). In addition, in the output file, there is only updated atomic coordinates and no updated velocities at each time step. Can you please give a comment of the bit of code along with where to insert those bit of code in the dynamics_module.f90 file or wherever in the code, by that I can improve to add or doing something on the code to print updated velocities at each time step. Please, any suggestions are necessary to me. I don't have much command on the code, at-least I can try my level best. I anticipated thanks for suitable answers from well-wishers. venkataramana PhD student IIT Bombay ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Huge dispersion energy
Dear Ari Paavo Seitsonen You are exactly correct, I am extracting dispersion energy. I calculated binding or adsorption energy, it was 16.6 kJ/mol, which is close to physisorption well (I think that the depth of physisorption well is the binding or adsorption energy). The energy of physisorption well has a depth of 4-12 kJ/mol from experiments. If the depth of physisorption well is not binding energy, then there is no exact experimental information of binding energy of methane on top of Ir(111) surface. However, one Ir10 cluster calculations (J.Catal, 185, 12-22, 1999) has reported that binding energy was 13.5 kJ/mol. Anyway, you mentioned that dispersion energy is not defined with vdW-DF, then what is specialty of vdW-DF functionals than grimme-d2 or DFT-D of semiempirical corrections. This is just I would like to know more about these functionals. Thanks for response. On Sat, Oct 10, 2015 at 6:36 PM, Venkataramana Imandi < venkataramana.ima...@gmail.com> wrote: > Dear QE users, > > The geometry of methane molecule on the top of Iridium slab is relaxed. > In that relaxed geometry, methane molecule is sitting 4.32 angstroms on > the top of Iridium atom, which is exactly same as Henkelman results (prl, > 86,664-667,2001). > The total energy of relaxed geometry is -5861698.6 kJ/mol. (val1) > I took that relaxed geometry coordinates and then I applied dispersion > interactions of that configuration only. (input file is attached, > Dispersion interactions with non-local functional) > The total energy with dispersion interactions is -5893444.5 kJ/mol. (val2) > The difference of val2 and val1 is -31745.9 kJ/mol. > Moreover, I used grimme-d2 dispersion interactions (commenting out > input_dft='vdw-df') , then total energy is -5876733.8 kJ/mol. (val3) > The difference of val3 and val1 is -15035.2 kJ/mol. > > I want to reproduce the results of Henkelman. In these results the total > energy difference between with dispersion and without dispersion is roughly > 10 kJ/mol. > > I am unable to find out where the mistake is. are input parameters correct > in the input file (input file is attached). > Thanks in advance for any suggestions and help. > > > calculation='scf', > prefix='ir_ch', > nstep=5000, >etot_conv_thr=1.0D-5, >forc_conv_thr=1.0D-4, >pseudo_dir = '/home/venkat/ORR1/PPS1' > / > >ibrav=0, >nat=77, > ntyp=3, > ecutwfc = 35.D0, > ecutrho=350.D0, > nosym=.true., > occupations='smearing', > smearing='m-p', > degauss=0.07D0, > input_dft='vdw-df' > ! vdw_corr='grimme-d2', > ! london_s6=1.07 > / > >electron_maxstep=2000, > diagonalization='david', >mixing_beta = 0.7D0, > conv_thr = 1.0D-8, >scf_must_converge=.true. > mixing_mode = 'local-TF' , >startingpot = 'atomic' , >startingwfc = 'atomic' , > / > ATOMIC_SPECIES > C12.0107 C.pw91-n-rrkjus_psl.0.1.UPF > H1.00794 H.pw91-rrkjus_psl.0.1.UPF > Ir 192.217 Ir.pw91-n-rrkjus_psl.0.2.3.UPF > > CELL_PARAMETERS angstrom > 8.14374880.0. > 0.0009.403591120. > 0.0000. 23.29868610 > > ATOMIC_POSITIONS angstrom > C 2.503115327 3.097048163 11.006076080 > H 2.559820746 3.082197974 12.098882130 > H 3.514431623 3.102156372 10.587895658 > H 1.968544691 2.208651619 10.655809495 > H 1.969648626 3.995188986 10.679852435 > Ir 6.786984985 5.377327249 6.690210403 > Ir 5.429761742 7.728578222 6.689802926 > Ir 5.429746349 4.650752045 4.467294416 > Ir 6.787041667 7.001529230 4.467393130 > Ir 5.429722714 6.240972848 2.221357938 > Ir 6.787038463 8.591738181 2.221368427 > Ir 4.072711710 5.377961700 6.689813188 > Ir 2.715081868 7.728500982 6.690023074 > Ir 2.715156078 4.650646584 4.467806211 > Ir 4.072348477 7.001642794 4.467556443 > Ir 2.715176306 6.240724087 2.221365994 > Ir 4.072433521 8.591776168 2.221423434 > Ir 1.357573198 5.378108129 6.689576660 > Ir 0.000492878 7.728616956 6.689942506 > Ir 0.000525907 4.650701814 4.467367485 > Ir 1.357873390 7.001703168 4.467414495 > Ir 0.000608784 6.240914105 2.221325333 > Ir 1.357921734 8.591831421 2.221404032 > Ir 6.786998124 0.675884041 6.690188874 > Ir 5.429896882 3.027018594 6.689570921 > Ir 5.429772024 -0.051058629 4.467515860 > Ir 6.787070082 2.299704238 4.467484822 > Ir 5.429712380 1.539122018 2.221560696 > Ir 6.787043197 3.8899075
[Pw_forum] Huge dispersion energy
Dear QE users, The geometry of methane molecule on the top of Iridium slab is relaxed. In that relaxed geometry, methane molecule is sitting 4.32 angstroms on the top of Iridium atom, which is exactly same as Henkelman results (prl, 86,664-667,2001). The total energy of relaxed geometry is -5861698.6 kJ/mol. (val1) I took that relaxed geometry coordinates and then I applied dispersion interactions of that configuration only. (input file is attached, Dispersion interactions with non-local functional) The total energy with dispersion interactions is -5893444.5 kJ/mol. (val2) The difference of val2 and val1 is -31745.9 kJ/mol. Moreover, I used grimme-d2 dispersion interactions (commenting out input_dft='vdw-df') , then total energy is -5876733.8 kJ/mol. (val3) The difference of val3 and val1 is -15035.2 kJ/mol. I want to reproduce the results of Henkelman. In these results the total energy difference between with dispersion and without dispersion is roughly 10 kJ/mol. I am unable to find out where the mistake is. are input parameters correct in the input file (input file is attached). Thanks in advance for any suggestions and help. calculation='scf', prefix='ir_ch', nstep=5000, etot_conv_thr=1.0D-5, forc_conv_thr=1.0D-4, pseudo_dir = '/home/venkat/ORR1/PPS1' / ibrav=0, nat=77, ntyp=3, ecutwfc = 35.D0, ecutrho=350.D0, nosym=.true., occupations='smearing', smearing='m-p', degauss=0.07D0, input_dft='vdw-df' ! vdw_corr='grimme-d2', ! london_s6=1.07 / electron_maxstep=2000, diagonalization='david', mixing_beta = 0.7D0, conv_thr = 1.0D-8, scf_must_converge=.true. mixing_mode = 'local-TF' , startingpot = 'atomic' , startingwfc = 'atomic' , / ATOMIC_SPECIES C12.0107 C.pw91-n-rrkjus_psl.0.1.UPF H1.00794 H.pw91-rrkjus_psl.0.1.UPF Ir 192.217 Ir.pw91-n-rrkjus_psl.0.2.3.UPF CELL_PARAMETERS angstrom 8.14374880.0. 0.0009.403591120. 0.0000. 23.29868610 ATOMIC_POSITIONS angstrom C 2.503115327 3.097048163 11.006076080 H 2.559820746 3.082197974 12.098882130 H 3.514431623 3.102156372 10.587895658 H 1.968544691 2.208651619 10.655809495 H 1.969648626 3.995188986 10.679852435 Ir 6.786984985 5.377327249 6.690210403 Ir 5.429761742 7.728578222 6.689802926 Ir 5.429746349 4.650752045 4.467294416 Ir 6.787041667 7.001529230 4.467393130 Ir 5.429722714 6.240972848 2.221357938 Ir 6.787038463 8.591738181 2.221368427 Ir 4.072711710 5.377961700 6.689813188 Ir 2.715081868 7.728500982 6.690023074 Ir 2.715156078 4.650646584 4.467806211 Ir 4.072348477 7.001642794 4.467556443 Ir 2.715176306 6.240724087 2.221365994 Ir 4.072433521 8.591776168 2.221423434 Ir 1.357573198 5.378108129 6.689576660 Ir 0.000492878 7.728616956 6.689942506 Ir 0.000525907 4.650701814 4.467367485 Ir 1.357873390 7.001703168 4.467414495 Ir 0.000608784 6.240914105 2.221325333 Ir 1.357921734 8.591831421 2.221404032 Ir 6.786998124 0.675884041 6.690188874 Ir 5.429896882 3.027018594 6.689570921 Ir 5.429772024 -0.051058629 4.467515860 Ir 6.787070082 2.299704238 4.467484822 Ir 5.429712380 1.539122018 2.221560696 Ir 6.787043197 3.889907517 2.221290932 Ir 4.072528886 0.675690271 6.689950314 Ir 2.715144414 3.026427071 6.690591842 Ir 2.715184457 -0.051003432 4.467559212 Ir 4.072256200 2.299934774 4.467754385 Ir 2.715207159 1.539060724 2.221195718 Ir 4.072485784 3.889991322 2.221325430 Ir 1.357730275 0.675696976 6.689663193 Ir 0.000402805 3.026907165 6.689722063 Ir 0.000465563 -0.051073916 4.467501695 Ir 1.358021383 2.299936261 4.467561579 Ir 0.000648125 1.539099393 2.221473282 Ir 1.357895673 3.890022499 2.221300840 Ir 6.787097597 5.514587239 -0.053952363 Ir 5.429839890 7.865526352 -0.054013090 Ir 5.429858365 4.753810264 -2.300201608 Ir 6.787129254 7.104615003 -2.300285157 Ir 5.429861628 6.377672836 -4.522696367 Ir 6.787164952 8.728667505 -4.522668683 Ir 4.072555282 5.514603378 -0.054059495 Ir 2.715247652 7.865432797 -0.054052327 Ir 2.715268974 4.753802500 -2.300196550 Ir 4.072605680 7.104724090 -2.300233141 Ir 2.715285443 6.377796366 -4.522582334 Ir 4.072611873 8.728652635 -4.522585040 Ir 1.357905576 5.514612078 -0.054088067 Ir 0.000614738 7.865518063 -0.054021354 Ir 0.000674468 4.753790149 -2.300199617 Ir 1.357948399 7.104749029 -2.300179393 Ir 0.000728657 6.377731702 -4.522632394 Ir 1.357977623 8.728636821
[Pw_forum] How to set occupations numbers under OCCUPATIONS card
Dear QE users, I want to do total energy of isolated Iridium atom. In case of occupations='from_input', how to give occupations numbers under OCCUPATIONS card for Isolated Iridium atom (electronic configuration: [Xe].4f^14.5d^7.6s^2) with considering nspin=2 option. I am new to QE calculations. Many many thanks in advance. venkataramana PhD student IIT Bombay Mumbai ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Good values for Dispersion interactions parameters
Dear all How to take good values of london_s6 and london_rcut for bulk Iridium (total atoms:72). Similarly, how to determine landon_s6 and london_rcut values for Iridium using any mathematical formula instead of taking default values from the QE keywords list. Any suggestions are valuable to me. I am anticipatively thanks. venkataramana PhD student, IIT Bombay Mumbai ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Cohesive energy of bulk Iridium
4.70179556 -2.21644769 Ir 4.07187440 7.05269336 -2.21644769 Ir 2.71458293 6.26906075 -4.43289537 Ir 4.07187440 8.61995854 -4.43289537 Ir 1.35729146 5.48542817 0. Ir 0. 7.83632593 0. Ir 0. 4.70179556 -2.21644769 Ir 1.35729146 7.05269336 -2.21644769 Ir 0. 6.26906075 -4.43289537 Ir 1.35729146 8.61995854 -4.43289537 Ir 6.78645733 0.78363261 0. Ir 5.42916587 3.13453037 0. Ir 5.42916587 0. -2.21644769 Ir 6.78645733 2.35089780 -2.21644769 Ir 5.42916587 1.56726519 -4.43289537 Ir 6.78645733 3.91816298 -4.43289537 Ir 4.07187440 0.78363261 0. Ir 2.71458293 3.13453037 0. Ir 2.71458293 0. -2.21644769 Ir 4.07187440 2.35089780 -2.21644769 Ir 2.71458293 1.56726519 -4.43289537 Ir 4.07187440 3.91816298 -4.43289537 Ir 1.35729146 0.78363261 0. Ir 0. 3.13453037 0. Ir 0. 0. -2.21644769 Ir 1.35729146 2.35089780 -2.21644769 Ir 0. 1.56726519 -4.43289537 Ir 1.35729146 3.91816298 -4.43289537 K_POINTS gamma Venkataramana PhD student IIT Bombay Mumbai On Mon, Oct 5, 2015 at 9:20 AM, Venkataramana Imandi < venkataramana.ima...@gmail.com> wrote: > Dear prof. Stefano, > Thank you very much for kind your help. > I will check results. > > On Sat, Oct 3, 2015 at 2:59 PM, Venkataramana Imandi < > venkataramana.ima...@gmail.com> wrote: > >> Dear prof. *STEFANO DE GIRONCOLI* >> >> Many thanks for spontaneous reply. On the basis of your answer, If I >> understood correctly, I can use nspin=2 for atomic Iridium and bulk Iridium >> (since Iridium is paramagnetic from literature data). However, I have to >> specify starting_magnetization in the input file in the both atomic Iridium >> and bulk Iridium >> input files. The keywords list information says that values range between >> -1 (all spins down for the valence electrons of atom type 'i') to 1 (all >> spins up). Iridium has three unpaired electrons in the spin up. >> 1. It indicates can I use starting_magnetization(1)=1 along with nspin=2. >> 2. If not that value, what value I have to use, I don't know, please >> suggest me. >> 3. I am not using full relativistic pseudopotential for Iridium, so, I >> can skip nspin=4, am I correct ?. >> >> Please verify my assumptions. >> The reply of previous thread of clean stop of running job, now I got >> clean stop during running job. >> >> >> On Sat, Oct 3, 2015 at 12:52 PM, Venkataramana Imandi < >> venkataramana.ima...@gmail.com> wrote: >> >>> >>> Dear all >>> >>> I want to calculate ground state total energy of single Iridium neutral >>> gaseous atom. >>> The electronic configuration of Iridium atom is [Xe].4f^14.5d^7.6s^2 and >>> in the 5d orbital, three unpaired electrons are there. >>> So, the resultant spin multiplicity is 4. Hence, in keywords list, >>> nspin=4 or noncolin=.true. is essential. >>> I am asking that whether nspin means spin multiplicity or not ?. >>> Am i correct for determining total energy of Iridium with nspin=4 or >>> noncolin=.true. ? >>> In case of bulk Iridium (total atoms=72), then can I skip nspin=4 or >>> noncolin=.true. ? >>> In case of bulk Iridium electrons can get paired or not ? >>> >>> Finally I want to calculate cohesive energy of bulk Iridium. >>> >>> I am extremely say sorry, if questions are fundamental and trivial. >>> >>> Any suggestions are appreciated and thanks in anticipated. >>> >>> >>> venkataramana >>> PhD student >>> IIT Bombay >>> Mumbai >>> >> >> >> >> -- >> venkataramana >> > > > > -- > venkataramana > -- venkataramana ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Cohesive energy of bulk Iridium
Dear prof. Stefano, Thank you very much for kind your help. I will check results. On Sat, Oct 3, 2015 at 2:59 PM, Venkataramana Imandi < venkataramana.ima...@gmail.com> wrote: > Dear prof. *STEFANO DE GIRONCOLI* > > Many thanks for spontaneous reply. On the basis of your answer, If I > understood correctly, I can use nspin=2 for atomic Iridium and bulk Iridium > (since Iridium is paramagnetic from literature data). However, I have to > specify starting_magnetization in the input file in the both atomic Iridium > and bulk Iridium > input files. The keywords list information says that values range between > -1 (all spins down for the valence electrons of atom type 'i') to 1 (all > spins up). Iridium has three unpaired electrons in the spin up. > 1. It indicates can I use starting_magnetization(1)=1 along with nspin=2. > 2. If not that value, what value I have to use, I don't know, please > suggest me. > 3. I am not using full relativistic pseudopotential for Iridium, so, I can > skip nspin=4, am I correct ?. > > Please verify my assumptions. > The reply of previous thread of clean stop of running job, now I got > clean stop during running job. > > > On Sat, Oct 3, 2015 at 12:52 PM, Venkataramana Imandi < > venkataramana.ima...@gmail.com> wrote: > >> >> Dear all >> >> I want to calculate ground state total energy of single Iridium neutral >> gaseous atom. >> The electronic configuration of Iridium atom is [Xe].4f^14.5d^7.6s^2 and >> in the 5d orbital, three unpaired electrons are there. >> So, the resultant spin multiplicity is 4. Hence, in keywords list, >> nspin=4 or noncolin=.true. is essential. >> I am asking that whether nspin means spin multiplicity or not ?. >> Am i correct for determining total energy of Iridium with nspin=4 or >> noncolin=.true. ? >> In case of bulk Iridium (total atoms=72), then can I skip nspin=4 or >> noncolin=.true. ? >> In case of bulk Iridium electrons can get paired or not ? >> >> Finally I want to calculate cohesive energy of bulk Iridium. >> >> I am extremely say sorry, if questions are fundamental and trivial. >> >> Any suggestions are appreciated and thanks in anticipated. >> >> >> venkataramana >> PhD student >> IIT Bombay >> Mumbai >> > > > > -- > venkataramana > -- venkataramana ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Cohesive energy of bulk Iridium
Dear prof. *STEFANO DE GIRONCOLI* Many thanks for spontaneous reply. On the basis of your answer, If I understood correctly, I can use nspin=2 for atomic Iridium and bulk Iridium (since Iridium is paramagnetic from literature data). However, I have to specify starting_magnetization in the input file in the both atomic Iridium and bulk Iridium input files. The keywords list information says that values range between -1 (all spins down for the valence electrons of atom type 'i') to 1 (all spins up). Iridium has three unpaired electrons in the spin up. 1. It indicates can I use starting_magnetization(1)=1 along with nspin=2. 2. If not that value, what value I have to use, I don't know, please suggest me. 3. I am not using full relativistic pseudopotential for Iridium, so, I can skip nspin=4, am I correct ?. Please verify my assumptions. The reply of previous thread of clean stop of running job, now I got clean stop during running job. On Sat, Oct 3, 2015 at 12:52 PM, Venkataramana Imandi < venkataramana.ima...@gmail.com> wrote: > > Dear all > > I want to calculate ground state total energy of single Iridium neutral > gaseous atom. > The electronic configuration of Iridium atom is [Xe].4f^14.5d^7.6s^2 and > in the 5d orbital, three unpaired electrons are there. > So, the resultant spin multiplicity is 4. Hence, in keywords list, nspin=4 > or noncolin=.true. is essential. > I am asking that whether nspin means spin multiplicity or not ?. > Am i correct for determining total energy of Iridium with nspin=4 or > noncolin=.true. ? > In case of bulk Iridium (total atoms=72), then can I skip nspin=4 or > noncolin=.true. ? > In case of bulk Iridium electrons can get paired or not ? > > Finally I want to calculate cohesive energy of bulk Iridium. > > I am extremely say sorry, if questions are fundamental and trivial. > > Any suggestions are appreciated and thanks in anticipated. > > > venkataramana > PhD student > IIT Bombay > Mumbai > -- venkataramana ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] How to do clean stop during running job
Dear Dr. Lorenzo Paulatto,
According to your suggestions, I got clean stop during running job.
Thanks again for your kind help.
On Fri, Oct 2, 2015 at 10:56 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:
> Dear all,
>
> In the manual clean stop occurs as follows.
> 1. prefix.EXIT file is created in the execution directory.
> In my calculations, prefix.EXIT file is not created (prefix name given in
> the control namelist) during the calculations.
> If it is created in the execution directory, how to stop calculations
> (please suggest command prompt).
> 2. signal trapping
> add \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS} in the
> make.sys file for clean stop.
> But I don't know where and which position the above command add in the
> make.sys file (attached make.sys file) and please suggest me.
> I tried several ways with command as follows.
> qsig jobid
> qsig -s SIGTERM jobid
> qsig -s SIGTERM jobidname
>
> the above commands do not give clean stop, that means compilation is
> required with \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS}
> in the make.sys file.
> Please suggest, how to do clean stop in the QE calculations.
>
> make.sys file:
>
> # make.sys. Generated from make.sys.in by configure.
>
> # compilation rules
>
> .SUFFIXES :
> .SUFFIXES : .o .c .f .f90
>
> # most fortran compilers can directly preprocess c-like directives: use
> # $(MPIF90) $(F90FLAGS) -c $<
> # if explicit preprocessing by the C preprocessor is needed, use:
> # $(CPP) $(CPPFLAGS) $< -o $*.F90
> # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
> # remember the tabulator in the first column !!!
>
> .f90.o:
> $(MPIF90) $(F90FLAGS) -c $<
>
> # .f.o and .c.o: do not modify
>
> .f.o:
> $(F77) $(FFLAGS) -c $<
>
> .c.o:
> $(CC) $(CFLAGS) -c $<
>
>
>
> # topdir for linking espresso libs with plugins
> TOPDIR = /soft/espresso-5.1.2-gnu
>
> # DFLAGS = precompilation options (possible arguments to -D and -U)
> # used by the C compiler and preprocessor
> # FDFLAGS = as DFLAGS, for the f90 compiler
> # See include/defs.h.README for a list of options and their meaning
> # With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
> # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas
>
> # MANUAL_DFLAGS = additional precompilation option(s), if desired
> # You may use this instead of tweaking DFLAGS and FDFLAGS
> # BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
> MANUAL_DFLAGS =
> DFLAGS = -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA
> $(MANUAL_DFLAGS)
> FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS)
>
> # IFLAGS = how to locate directories where files to be included are
>
> # In most cases, IFLAGS = -I../include
>
> IFLAGS = -I../include
>
> # MOD_FLAGS = flag used by f90 compiler to locate modules
> # Each Makefile defines the list of needed modules in MODFLAGS
>
> MOD_FLAG = -I
>
> # Compilers: fortran-90, fortran-77, C
> # If a parallel compilation is desired, MPIF90 should be a fortran-90
> # compiler that produces executables for parallel execution using MPI
> # (such as for instance mpif90, mpf90, mpxlf90,...);
> # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
> # If you have a parallel machine but no suitable candidate for MPIF90,
> # try to specify the directory containing "mpif.h" in IFLAGS
> # and to specify the location of MPI libraries in MPI_LIBS
>
> MPIF90 = mpif90
> #F90 = gfortran
> CC = cc
> F77= gfortran
>
> # C preprocessor and preprocessing flags - for explicit preprocessing,
> # if needed (see the compilation rules above)
> # preprocessing flags must include DFLAGS and IFLAGS
>
> CPP= cpp
> CPPFLAGS = -P -C -traditional $(DFLAGS) $(IFLAGS)
>
> # compiler flags: C, F90, F77
> # C flags must include DFLAGS and IFLAGS
> # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate
> syntax
>
> CFLAGS = -O3 $(DFLAGS) $(IFLAGS)
> F90FLAGS = $(FFLAGS) -x f95-cpp-input $(FDFLAGS) $(IFLAGS)
> $(MODFLAGS)
> FFLAGS = -O3 -g
>
> # compiler flags without optimization for fortran-77
> # the latter is NEEDED to properly compile dlamch.f, used by lapack
>
> FFLAGS_NOOPT = -O0 -g
>
> # compiler flag needed by some compilers when the main is not fortran
> # Currently used for YamboFFLAGS_NOMAIN =
>
> # Linker, linker-specific flags (if any)
> # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty
>
> LD
[Pw_forum] Cohesive energy of bulk Iridium
Dear all I want to calculate ground state total energy of single Iridium neutral gaseous atom. The electronic configuration of Iridium atom is [Xe].4f^14.5d^7.6s^2 and in the 5d orbital, three unpaired electrons are there. So, the resultant spin multiplicity is 4. Hence, in keywords list, nspin=4 or noncolin=.true. is essential. I am asking that whether nspin means spin multiplicity or not ?. Am i correct for determining total energy of Iridium with nspin=4 or noncolin=.true. ? In case of bulk Iridium (total atoms=72), then can I skip nspin=4 or noncolin=.true. ? In case of bulk Iridium electrons can get paired or not ? Finally I want to calculate cohesive energy of bulk Iridium. I am extremely say sorry, if questions are fundamental and trivial. Any suggestions are appreciated and thanks in anticipated. venkataramana PhD student IIT Bombay Mumbai ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] How to do clean stop during running job
Dear all,
In the manual clean stop occurs as follows.
1. prefix.EXIT file is created in the execution directory.
In my calculations, prefix.EXIT file is not created (prefix name given in
the control namelist) during the calculations.
If it is created in the execution directory, how to stop calculations
(please suggest command prompt).
2. signal trapping
add \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS} in the
make.sys file for clean stop.
But I don't know where and which position the above command add in the
make.sys file (attached make.sys file) and please suggest me.
I tried several ways with command as follows.
qsig jobid
qsig -s SIGTERM jobid
qsig -s SIGTERM jobidname
the above commands do not give clean stop, that means compilation is
required with \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS}
in the make.sys file.
Please suggest, how to do clean stop in the QE calculations.
make.sys file:
# make.sys. Generated from make.sys.in by configure.
# compilation rules
.SUFFIXES :
.SUFFIXES : .o .c .f .f90
# most fortran compilers can directly preprocess c-like directives: use
# $(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
# $(CPP) $(CPPFLAGS) $< -o $*.F90
# $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!
.f90.o:
$(MPIF90) $(F90FLAGS) -c $<
# .f.o and .c.o: do not modify
.f.o:
$(F77) $(FFLAGS) -c $<
.c.o:
$(CC) $(CFLAGS) -c $<
# topdir for linking espresso libs with plugins
TOPDIR = /soft/espresso-5.1.2-gnu
# DFLAGS = precompilation options (possible arguments to -D and -U)
# used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas
# MANUAL_DFLAGS = additional precompilation option(s), if desired
# You may use this instead of tweaking DFLAGS and FDFLAGS
# BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
MANUAL_DFLAGS =
DFLAGS = -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA
$(MANUAL_DFLAGS)
FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS)
# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
IFLAGS = -I../include
# MOD_FLAGS = flag used by f90 compiler to locate modules
# Each Makefile defines the list of needed modules in MODFLAGS
MOD_FLAG = -I
# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90
# compiler that produces executables for parallel execution using MPI
# (such as for instance mpif90, mpf90, mpxlf90,...);
# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
# If you have a parallel machine but no suitable candidate for MPIF90,
# try to specify the directory containing "mpif.h" in IFLAGS
# and to specify the location of MPI libraries in MPI_LIBS
MPIF90 = mpif90
#F90 = gfortran
CC = cc
F77= gfortran
# C preprocessor and preprocessing flags - for explicit preprocessing,
# if needed (see the compilation rules above)
# preprocessing flags must include DFLAGS and IFLAGS
CPP= cpp
CPPFLAGS = -P -C -traditional $(DFLAGS) $(IFLAGS)
# compiler flags: C, F90, F77
# C flags must include DFLAGS and IFLAGS
# F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate
syntax
CFLAGS = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS = $(FFLAGS) -x f95-cpp-input $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS = -O3 -g
# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack
FFLAGS_NOOPT = -O0 -g
# compiler flag needed by some compilers when the main is not fortran
# Currently used for YamboFFLAGS_NOMAIN =
# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty
LD = mpif90
LDFLAGS= -g -pthread
LD_LIBS=
# External Libraries (if any) : blas, lapack, fft, MPI
# If you have nothing better, use the local copy :
# BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
# BLAS_LIBS_SWITCH = internal
BLAS_LIBS = -lblas
BLAS_LIBS_SWITCH = external
# If you have nothing better, use the local copy :
# LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order
LAPACK_LIBS= -llapack -lblas
LAPACK_LIBS_SWITCH = external
ELPA_LIBS_SWITCH = disabled
SCALAPACK_LIBS =
# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)
FFT_LIBS =
# For parallel execution, the correct path to MPI libraries
Re: [Pw_forum] Cell parameters representation for cubic fcc(111) Iridium structure
Dear Arles V. Gil Rebaza, What is significance of cos60 and sin60. I don't know much. Thanks in advance. Dear Venkataramana, if you have a FCC(111) surface, probabily you should have these lattice vectors (is a option representation) a0 0 b*cos60 b*sin60 0 00 c+h where a, b, and c are the distance that you are reporting, and "h" is the vacuum to simulate a surface. Best. Arles V. Gil Rebaza IFLP-Argentina On Fri, Sep 25, 2015 at 9:46 PM, Venkataramana Imandi < venkataramana.ima...@gmail.com> wrote: > Dear all, > > I generated cubic fcc(111) in the form of 3x2x2 type structure (6 layers > and each layer has 12 atoms) with Iridium (lattice constant:3.839 > angstroms). > In the generated coordinates file, crystal axes are 8.14374880, > 9.40359112, 13.29868610 (generated coordinate are attached). Can i represent > CELL_PARAMETERS angstrom in addition to ibrav=0 in the system namelist as > shown below (for whole Iridium structure). > 8.14374880 0.0.0 > 0. 9.403591120.0 > 0. 0.13.29868610 > > Is the above representation correct (maintains cubic fcc), if not, please > suggest me how to represent CELL_PARAMETERS for whole Iridium structure. > I am new user and please suggest me correct way of doing calculations. > > Again, I want to keep manually methane molecule on the top of Iridium (on > the top of z-axis, above 5 angstroms from the top atom in the z-axis), then > the resultant whole structure maintain fcc cubic. Please give some > suggestions. I am new to quantum espresso calculations. > > 72 72 72 72 > 8.14374880 9.4035911213.29868610 0. > 0. 0. MD time = 0.000E+00 ps > Ir 6.78645733 5.48542817 6.64934305 > Ir 5.42916587 7.83632593 6.64934305 > Ir 5.42916587 4.70179556 4.43289536 > Ir 6.78645733 7.05269336 4.43289536 > Ir 5.42916587 6.26906075 2.21644768 > Ir 6.78645733 8.61995854 2.21644768 > Ir 4.07187440 5.48542817 6.64934305 > Ir 2.71458293 7.83632593 6.64934305 > Ir 2.71458293 4.70179556 4.43289536 > Ir 4.07187440 7.05269336 4.43289536 > Ir 2.71458293 6.26906075 2.21644768 > Ir 4.07187440 8.61995854 2.21644768 > Ir 1.35729146 5.48542817 6.64934305 > Ir 0. 7.83632593 6.64934305 > Ir 0. 4.70179556 4.43289536 > Ir 1.35729146 7.05269336 4.43289536 > Ir 0. 6.26906075 2.21644768 > Ir 1.35729146 8.61995854 2.21644768 > Ir 6.78645733 0.78363261 6.64934305 > Ir 5.42916587 3.13453037 6.64934305 > Ir 5.42916587 0. 4.43289536 > Ir 6.78645733 2.35089780 4.43289536 > Ir 5.42916587 1.56726519 2.21644768 > Ir 6.78645733 3.91816298 2.21644768 > Ir 4.07187440 0.78363261 6.64934305 > Ir 2.71458293 3.13453037 6.64934305 > Ir 2.71458293 0. 4.43289536 > Ir 4.07187440 2.35089780 4.43289536 > Ir 2.71458293 1.56726519 2.21644768 > Ir 4.07187440 3.91816298 2.21644768 > Ir 1.35729146 0.78363261 6.64934305 > Ir 0. 3.13453037 6.64934305 > Ir 0. 0. 4.43289536 > Ir 1.35729146 2.35089780 4.43289536 > Ir 0. 1.56726519 2.21644768 > Ir 1.35729146 3.91816298 2.21644768 > Ir 6.78645733 5.48542817 0. > Ir 5.42916587 7.83632593 0. > Ir 5.42916587 4.70179556 -2.21644769 > Ir 6.78645733 7.05269336 -2.21644769 > Ir 5.42916587 6.26906075 -4.43289537 > Ir 6.78645733 8.61995854 -4.43289537 > Ir 4.07187440 5.48542817 0. > Ir 2.71458293 7.83632593 0. > Ir 2.71458293 4.70179556 -2.21644769 > Ir
Re: [Pw_forum] Cell parameters representation for cubic fcc(111) Iridium structure
Dear Arles V. Gil Rebaza, What is the significance of cos60 and sin60. I don't know much. Thanks in advance Venkat PhD student IIT Bombay Mumbai Dear Venkataramana, if you have a FCC(111) surface, probabily you should have these lattice vectors (is a option representation) a0 0 b*cos60 b*sin60 0 00 c+h where a, b, and c are the distance that you are reporting, and "h" is the vacuum to simulate a surface. Best. Arles V. Gil Rebaza IFLP-Argentina On Fri, Sep 25, 2015 at 9:46 PM, Venkataramana Imandi < venkataramana.ima...@gmail.com> wrote: > Dear all, > > I generated cubic fcc(111) in the form of 3x2x2 type structure (6 layers > and each layer has 12 atoms) with Iridium (lattice constant:3.839 > angstroms). > In the generated coordinates file, crystal axes are 8.14374880, > 9.40359112, 13.29868610 (generated coordinate are attached). Can i represent > CELL_PARAMETERS angstrom in addition to ibrav=0 in the system namelist as > shown below (for whole Iridium structure). > 8.14374880 0.0.0 > 0. 9.403591120.0 > 0. 0.13.29868610 > > Is the above representation correct (maintains cubic fcc), if not, please > suggest me how to represent CELL_PARAMETERS for whole Iridium structure. > I am new user and please suggest me correct way of doing calculations. > > Again, I want to keep manually methane molecule on the top of Iridium (on > the top of z-axis, above 5 angstroms from the top atom in the z-axis), then > the resultant whole structure maintain fcc cubic. Please give some > suggestions. I am new to quantum espresso calculations. > > 72 72 72 72 > 8.14374880 9.4035911213.29868610 0. > 0. 0. MD time = 0.000E+00 ps > Ir 6.78645733 5.48542817 6.64934305 > Ir 5.42916587 7.83632593 6.64934305 > Ir 5.42916587 4.70179556 4.43289536 > Ir 6.78645733 7.05269336 4.43289536 > Ir 5.42916587 6.26906075 2.21644768 > Ir 6.78645733 8.61995854 2.21644768 > Ir 4.07187440 5.48542817 6.64934305 > Ir 2.71458293 7.83632593 6.64934305 > Ir 2.71458293 4.70179556 4.43289536 > Ir 4.07187440 7.05269336 4.43289536 > Ir 2.71458293 6.26906075 2.21644768 > Ir 4.07187440 8.61995854 2.21644768 > Ir 1.35729146 5.48542817 6.64934305 > Ir 0. 7.83632593 6.64934305 > Ir 0. 4.70179556 4.43289536 > Ir 1.35729146 7.05269336 4.43289536 > Ir 0. 6.26906075 2.21644768 > Ir 1.35729146 8.61995854 2.21644768 > Ir 6.78645733 0.78363261 6.64934305 > Ir 5.42916587 3.13453037 6.64934305 > Ir 5.42916587 0. 4.43289536 > Ir 6.78645733 2.35089780 4.43289536 > Ir 5.42916587 1.56726519 2.21644768 > Ir 6.78645733 3.91816298 2.21644768 > Ir 4.07187440 0.78363261 6.64934305 > Ir 2.71458293 3.13453037 6.64934305 > Ir 2.71458293 0. 4.43289536 > Ir 4.07187440 2.35089780 4.43289536 > Ir 2.71458293 1.56726519 2.21644768 > Ir 4.07187440 3.91816298 2.21644768 > Ir 1.35729146 0.78363261 6.64934305 > Ir 0. 3.13453037 6.64934305 > Ir 0. 0. 4.43289536 > Ir 1.35729146 2.35089780 4.43289536 > Ir 0. 1.56726519 2.21644768 > Ir 1.35729146 3.91816298 2.21644768 > Ir 6.78645733 5.48542817 0. > Ir 5.42916587 7.83632593 0. > Ir 5.42916587 4.70179556 -2.21644769 > Ir 6.78645733 7.05269336 -2.21644769 > Ir 5.42916587 6.26906075 -4.43289537 > Ir 6.78645733 8.61995854 -4.43289537 > Ir 4.07187440 5.48542817 0. > Ir 2.71458293 7.83632593 0. > Ir 2.71458293 4.70179
[Pw_forum] Cell parameters representation for cubic fcc(111) Iridium structure
Dear all, I generated cubic fcc(111) in the form of 3x2x2 type structure (6 layers and each layer has 12 atoms) with Iridium (lattice constant:3.839 angstroms). In the generated coordinates file, crystal axes are 8.14374880, 9.40359112, 13.29868610 (generated coordinate are attached). Can i represent CELL_PARAMETERS angstrom in addition to ibrav=0 in the system namelist as shown below (for whole Iridium structure). 8.14374880 0.0.0 0. 9.403591120.0 0. 0.13.29868610 Is the above representation correct (maintains cubic fcc), if not, please suggest me how to represent CELL_PARAMETERS for whole Iridium structure. I am new user and please suggest me correct way of doing calculations. Again, I want to keep manually methane molecule on the top of Iridium (on the top of z-axis, above 5 angstroms from the top atom in the z-axis), then the resultant whole structure maintain fcc cubic. Please give some suggestions. I am new to quantum espresso calculations. 72 72 72 72 8.14374880 9.4035911213.29868610 0. 0. 0. MD time = 0.000E+00 ps Ir 6.78645733 5.48542817 6.64934305 Ir 5.42916587 7.83632593 6.64934305 Ir 5.42916587 4.70179556 4.43289536 Ir 6.78645733 7.05269336 4.43289536 Ir 5.42916587 6.26906075 2.21644768 Ir 6.78645733 8.61995854 2.21644768 Ir 4.07187440 5.48542817 6.64934305 Ir 2.71458293 7.83632593 6.64934305 Ir 2.71458293 4.70179556 4.43289536 Ir 4.07187440 7.05269336 4.43289536 Ir 2.71458293 6.26906075 2.21644768 Ir 4.07187440 8.61995854 2.21644768 Ir 1.35729146 5.48542817 6.64934305 Ir 0. 7.83632593 6.64934305 Ir 0. 4.70179556 4.43289536 Ir 1.35729146 7.05269336 4.43289536 Ir 0. 6.26906075 2.21644768 Ir 1.35729146 8.61995854 2.21644768 Ir 6.78645733 0.78363261 6.64934305 Ir 5.42916587 3.13453037 6.64934305 Ir 5.42916587 0. 4.43289536 Ir 6.78645733 2.35089780 4.43289536 Ir 5.42916587 1.56726519 2.21644768 Ir 6.78645733 3.91816298 2.21644768 Ir 4.07187440 0.78363261 6.64934305 Ir 2.71458293 3.13453037 6.64934305 Ir 2.71458293 0. 4.43289536 Ir 4.07187440 2.35089780 4.43289536 Ir 2.71458293 1.56726519 2.21644768 Ir 4.07187440 3.91816298 2.21644768 Ir 1.35729146 0.78363261 6.64934305 Ir 0. 3.13453037 6.64934305 Ir 0. 0. 4.43289536 Ir 1.35729146 2.35089780 4.43289536 Ir 0. 1.56726519 2.21644768 Ir 1.35729146 3.91816298 2.21644768 Ir 6.78645733 5.48542817 0. Ir 5.42916587 7.83632593 0. Ir 5.42916587 4.70179556 -2.21644769 Ir 6.78645733 7.05269336 -2.21644769 Ir 5.42916587 6.26906075 -4.43289537 Ir 6.78645733 8.61995854 -4.43289537 Ir 4.07187440 5.48542817 0. Ir 2.71458293 7.83632593 0. Ir 2.71458293 4.70179556 -2.21644769 Ir 4.07187440 7.05269336 -2.21644769 Ir 2.71458293 6.26906075 -4.43289537 Ir 4.07187440 8.61995854 -4.43289537 Ir 1.35729146 5.48542817 0. Ir 0. 7.83632593 0. Ir 0. 4.70179556 -2.21644769 Ir 1.35729146 7.05269336 -2.21644769 Ir 0. 6.26906075 -4.43289537 Ir 1.35729146 8.61995854 -4.43289537 Ir 6.78645733 0.78363261 0. Ir 5.42916587 3.13453037 0. Ir 5.42916587 0. -2.21644769 Ir 6.78645733 2.35089780 -2.21644769 Ir 5.42916587 1.56726519 -4.43289537 Ir 6.78645733 3.91816298
[Pw_forum] Langevin dynamics
Dear Dr. Xiaochuan Ge Thank you for intimating particularly about time step in the Langevin dynamics. I tried with 2.D0 (0.1 fs), however, system is exploding. I tried according to your suggestion 0.2D0 (0.01 fs), it is working. I am asking you is there any possibility to do Langevin dynamics at higher timestep e.g. 0.1 fs or 0.2 fs. If there such type of possibility, please inform me as soon as possible and what parameters i have to alter in the input file for doing Langevin dynamics at higher time step. Once again thanks for remembering me about Langevin dynamics is successful at small time step. Best Venkataramana Imandi PhD student IIT Bombay Dear Venkataramana, I have some experience using the Langevin code. ?Before we go further to understand your problem, I would suggest you to significantly lower the dt and try again. Please try dt=0.2 instead of 20. If it still does not work, please let me know. Best, === Dr. Xiaochuan Ge (Giovanni) Center for Functional Nanomaterials Brookhaven national laboratory === ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[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.
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'
/
ibrav=0,
nat=37,
ntyp=4,
ecutwfc = 30.0,
nosym=.true.,
occupations='smearing',
smearing='m-p',
degauss=0.03,
tot_charge=1.0
/
electron_maxstep=2000,
diagonalization='david',
mixing_beta = 0.3,
conv_thr = 1.0D-6,
scf_must_converge=.false.
/
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 5.714331653 -3.826763
[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.
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'
/
ibrav=0,
nat=37,
ntyp=4,
ecutwfc = 30.0,
nosym=.true.,
occupations='smearing',
smearing='m-p',
degauss=0.03,
tot_charge=1.0
/
electron_maxstep=2000,
diagonalization='david',
mixing_beta = 0.3,
conv_thr = 1.0D-6,
scf_must_converge=.false.
/
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] cell is blowing during Langevin dynamics
Dear all,
I am using quantum espresso (version:5.1.2) for doing Langevin dynamics on
silicon cluster (total atoms: 2) running on Red Hat machine with serial and
parallel process. If I don't use "nosym=.true." keyword in the input file,
the following error is observed, which is shown below. If I use
"nosym=.true." keyword, then super cell is blowing during Langevin
dynamics. Moreover, the coordinates of individual silicon atoms is merging
in the output file, which is shown below for one of the snapshot during
Langevin dynamics. The distance between two Silicon atoms is increasing and
at the end of 70 md steps the distance is 1152 angstroms. Kindly suggest me
what is region behind in the error. I am new user and not well aware of
Langevin dynamics in the quantum espresso software package. Input file and
coordinates of one of the snapshot are attached.
%%
Error in routine checkallsym (1):
some of the original symmetry operations not satisfied
%%
calculation='md',
dt=20.D0,
nstep=100,
etot_conv_thr=1.0D-5,
forc_conv_thr=1.0D-4,
prefix='si_lang' ,
pseudo_dir='/home/venkat/ORR1/PPS1'
/
ibrav= 2,
celldm(1)=10.18,
nat=2,
ntyp= 1,
ecutwfc = 8.0,
nosym=.true.
/
electron_maxstep=2000,
diagonalization='david',
conv_thr = 1.0e-5,
mixing_beta = 0.3,
scf_must_converge=.false.
/
pot_extrapolation = 'second_order',
wfc_extrapolation = 'second_order',
ion_dynamics='langevin',
refold_pos=.true.
tempw=300.D0,
nraise=2
/
ATOMIC_SPECIES
Si 28.086 Si.pz-vbc.UPF
ATOMIC_POSITIONS {alat}
Si -0.123 -0.123 -0.123
Si 0.123 0.123 0.123
K_POINTS {automatic}
1 1 1 0 0 0
one snapshot during Langevin dynamics
ATOMIC_POSITIONS (alat)
Si 210.463044756 215.584817447-144.659285586
Si-210.463044756-215.584817447 144.659285586
Best,
Venkataramana
PhD student
IIT Bombay
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[Pw_forum] Langevin dynamics
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.
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'
/
ibrav=0,
nat=37,
ntyp=4,
ecutwfc = 30.0,
nosym=.true.,
occupations='smearing',
smearing='m-p',
degauss=0.03,
tot_charge=1.0
/
electron_maxstep=2000,
diagonalization='david',
mixing_beta = 0.3,
conv_thr = 1.0D-6,
scf_must_converge=.false.
/
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 5.714331653 -3.826763750
Ag -0.821908140 -7.523290040 -8.937996255
Ag 7.394141127 8.391763262 7.199208896
Ag 66.2293865871065.326804153 192.584344197
Ag4515.057117298 369.600932228 188.645687521
Ag 395.079974228 976.00510 23.641381229
Ag -0.868373165 1.254442767 -0.725095564
Ag 0.598543920 4.290748028 1.130598433
Ag 3.451303546 0.003835176 -2.147641351
Ag 4.967046204 4.664900169 1.274377193
O4.154896086 3.538399188 4.404896973
C 399.041692489-175.281493613-563.071390643
H3.281002088 3.892508380 4.191590229
H5.590682748 1.083007852 4.528641700
C
