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Comment: + quantum espresso v7.1

Moduli

Quantum Espresso je preveden s Intel 2019 i MVAPICH2 2.2 i parametrima:.

Dostupne verzije su:

VerzijaModul
5.4.0quantum-espresso/5.4.0
6.3

quantum-espresso/6.3

6.3

quantum-espresso/6.3-nfilemax50

6.6quantum-espresso/6.6
6.7quantum-espresso/6.7
6.8 *quantum-espresso/6.8
7.1 *quantum-espresso/7.1

* modul uključuje i thermo_pw paket.

Note

U modulu quantum-espresso/6.3-nfilemax50 napravljena je izmjena u kodu gdje se parametar nfilemax povećao na 50.

PP/src/chdens_module.f90: INTEGER, PARAMETER :: nfilemax = 50

Korištenje

Izračun optičkog spektra benzena koristeći vremensko-ovisni pristup teorije funkcionala gustoće (Time-Dependent Density Functional Theory, TDDFT).

Prije samog izračuna potrebno je skinuti knjižnicu pseudopotencijala (za potrebe ovog izračuna potrebni su C i H pseudopotencijali) odabirući sljedeće parametre (NC SR(ONCVPSP v0.4), PBE, stringent, upf) s web stranice http://www.pseudo-dojo.org/index.html. U svim input datotekama zadati put do direktorija u kojem se knjižnica nalazi.

Posljednja geometrija u output datoteci predstavlja početnu geometriju u idućoj input datoteci.

Primjer skripte za opis poslova:

Code Block
titlerun.sge
linenumberstrue
#!/bin/bash

#$ -N qe
#$ -cwd
#$ -pe p28-mpi 2
#$ -j y

module load quantum-espresso/6.7

mpirun -np 2 /apps/qe/6.7
Code Block
export LIBMPI=-lmpich
export CC=icc
export CXX=icc
export FC=ifort
export MPIF90=mpif90
export FCFLAGS='-I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw'
export CFLAGS='-I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw'
export FFLAGS='-I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw'
export MPI_LIBS='-L/usr/lib64/mvapich2-intel-2.2/lib -lmpich'
export BLAS_LIBS='-L/opt/intel/mkl/lib/intel64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl'
export LAPACK_LIBS='/opt/intel/mkl/lib/intel64/libmkl_blas95_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_lapack95_ilp64.a -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl'
export FFT_LIBS='/opt/intel/mkl/lib/intel64/libmkl_blas95_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_lapack95_ilp64.a -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl'
export SCALAPACK_LIBS='/opt/intel/mkl/lib/intel64/libmkl_blas95_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_lapack95_ilp64.a -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl'
./configure --enable-parallel --with-scalapack=intel

Dostupne verzije su:

...

quantum-espresso/6.3

Primjer korištenja:

...

/bin/turbo_lanczos.x -inp benzene_tl.in > benzene_tl.out

Primjer pw.x input datoteke:

Code Block
titlepw.x
linenumberstrue
 &CONTROL
    calculation = 'vc-relax'
  prefix = 'benzene'
    outdir = './outdir'
    pseudo_dir = '/home/user/nc-sr-04_pbe_stringent_upf'
    etot_conv_thr = 1e-5
    forc_conv_thr = 1e-4
 /
 &SYSTEM
    ibrav = 6,
    celldm(1) = 32.0,
    celldm(3) = 0.83,
    nat = 12,
    ntyp = 2,
    ecutwfc = 30,
 /
 &ELECTRONS
    conv_thr =  1.0d-8
 /
 &IONS
 /
 &CELL
 /

ATOMIC_SPECIES
 C  12.0107  C.upf
 H  1.00784  H.upf

ATOMIC_POSITIONS angstrom
C   5.633200899   6.320861303   5.000000000 1 1 0
H   6.847051545   8.422621957   5.000000000 1 1 0

K_POINTS gamma

1. Izračun relaksacije molekule s ciljem ispravljanja neprirodne i/ili nepogodne geometrije poput nepravilnih duljina veza i vrijednosti kutova

Code Block
linenumberstrue
pw.x -inp benzene_relax.in > benzene_relax.out

2. Izračun konvergencije, odnosno stanja sustava gdje su sile unutar sustava esencijalno jednake 0

Code Block
pw.x -inp benzene_scf.in > benzene_scf.out

Primjer turbo_lanczos.x input datoteke:

Code Block
linenumberstrue
&LR_INPUT
prefix = 'benzene'
  outdir = './outdir'
/

&LR_CONTROL
  itermax = 500
  ipol = 4
/

3. Izračun vrijednosti β, γ i z rekurzijskih koeficijenata polarizabilnosti pomoću Lanczos-ovog algoritma

Code Block
linenumberstrue
turbo_lanczos.x -inp benzene_tl.in > bezneze_tl.out

4. Izračun polarizabilnosti apsorpcijskog spektra na temelju koeficijentata izračunatih u prethodnom koraku

Code Block
linenumberstrue
turbo_spectrum.x -inp benzene_ts.in > benzene_ts.out

Primjer gnuplot skripte:

Code Block
linenumberstrue
set   autoscale                       # scale axes automatically

unset log                               # remove any log-scaling

unset label                            # remove any previous labels

set xtic auto                          # set xtics automatically

set ytic auto                          # set ytics automatically

set title "title"

set xlabel "energy/eV"

set ylabel "absorption"

plot 'benzene.dat' u 1:2 title 'light absorption: benzene' with linespoints

pause -1 "Hit any key to continue\n"    #the code doesn't exit automatically

5. Grafički prikaz spektra sustava

Code Block
gnuplot benzene.gnu

Image Added

Više informacija dostupno na web stranici: https://www.quantum-espresso.org/documentation/

...

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