PWSCF First examples

Transcription

1 PWSCF First examples (much more in espresso 3.1.1/examples directory!) Guido Fratesi (Università di Milano) Urbana, August 2006

2 A pw.x input file &CONTROL / &SYSTEM / &ELECTRONS title calculation restart_mode outdir pseudo_dir prefix 'Silicon bulk', 'scf', 'from_scratch', 'your directory for temporary files/', 'your directory containing pseudopotentials/', 'silicon', ibrav celldm(1) nat ntyp ecutwfc 2, 10.20, 2, 1, 18.0, conv_thr mixing_mode mixing_beta diagonalization 1.0d 8, 'plain', 0.7, 'david', Described in detail in the file ESPRESSO/Doc/INPUT_PW / ATOMIC_SPECIES Si Si.vbc.UPF ATOMIC_POSITIONS Si Si K_POINTS tpiba

3 Graphical User Interface 1) Download stand alone application (http//www k3.ijs.si/kokalj/pwgui/download.html) wget www k3.ijs.si/kokalj/pwgui/download/pwgui linux x86.zip 2) Unzip / untar file unzip pwgui linux x86.zip 3) Execute./pwgui 4) Open / create new input file 5) Save the input file 6) Run the calculation pw.x < input > output

4 GUI in practice Open file si.scf.in (File Open Open Pw.x Input si.scf.in) Set your directories outdir (containing temporary files) pseudo_dir (containing pseudopotentials) Save (File Save) Copy to computing machine Run calculation

5 And now the output file Scroll the output file (type less si.scf.out) informations on the system Version // Title... bravais lattice index 2 lattice parameter (a_0) a.u. unit cell volume (a.u.)^3 number of atoms/cell 2 number of atomic types 1 kinetic energy cutoff Ry charge density cutoff Ry convergence threshold 1.0E 08 beta number of iterations used 8 plain mixing Exchange correlation SLA PZ NOGX NOGC (1100) celldm(1) celldm(2) celldm(3) celldm(4) celldm(5) celldm(6) crystal axes (cart. coord. in units of a(1) ( a(2) ( a(3) ( reciprocal axes b(1) b(2) b(3) a_0) ) ) ) (cart. coord. in units 2 pi/a_0) ( ) ( ) ( )

6 And now the output file Scroll the output file informations on atoms and pseudopotentials PSEUDO 1 is Si (in numerical form atomic species Si zval 4.0 lmax grid points, xmin valence 4.00 mass lloc , dx ) pseudopotential Si( 1.00) 48 Sym.Ops. (with inversion) Cartesian axes site n. 1 2 atom Si Si tau( tau( 1) ( 2) ( positions (a_0 units) ) )

7 And now the output file Scroll the output file informations on K points and FFT number of k points 10 cart. coord. in units 2pi/a_0 1) ( ), 2) ( ), 3) ( ), 4) ( ), 5) ( ), 6) ( ), 7) ( ), 8) ( ), 9) ( ), 10) ( ), G cutoff nbndx nelec nbnd 8.00 nkb ( 2733 G vectors) 4 8 natomwfc ngl FFT grid ( 20, 20, 20) 8 65 npwx 350

8 And now the output file Scroll the output file the self consistent field loop starts Initial potential from superposition of free atoms starting charge , renormalised to Starting wfc are atomic total cpu time spent up to now is secs Self consistent Calculation iteration # 1 ecut ryd Davidson diagonalization with overlap ethr 1.00E 02, avg # of iterations beta Threshold (ethr) on eigenvalues was too large Diagonalizing with lowered threshold Davidson diagonalization with overlap ethr 7.75E 03, avg # of iterations total cpu time spent up to now is total energy estimated scf accuracy < secs ryd ryd

9 And now the output file Scroll the output file the self consistent field loop converges total energy estimated scf accuracy < ryd ryd iteration # 6 ecut ryd Davidson diagonalization with overlap ethr 7.18E 10, avg # of iterations total cpu time spent up to now is beta secs End of self consistent calculation k ( PWs) bands (ev)

10 And now the output file Scroll the output file summary of energy, forces, and stress tensor! total energy estimated scf accuracy band energy sum one electron contribution hartree contribution xc contribution ewald contribution < ryd 8.8E 10 ryd ryd ryd ryd ryd ryd convergence has been achieved Forces acting on atoms (Ry/au) atom atom 1 type 2 type Total force 1 1 force force Total SCF correction entering subroutine stress... total stress (ryd/bohr**3) (kbar) P

11 And now the output file Scroll the output file saving data file (restart, post processing,...) and timing informations Writing output data file silicon.save PWSCF 2.00s time init_run electrons forces stress 0.34s 1.52s 0.01s 0.07s electrons c_bands sum_band v_of_rho mix_rho 1.52s 1.21s 0.25s 0.03s 0.00s c_bands init_us_2 cegterg 1.21s ( 0.05s ( 1.17s ( 7 calls, 170 calls, 70 calls, s avg) s avg) s avg) sum_band 0.25s ( 7 calls, s avg) ( ( ( ( calls, calls, calls, calls, s s s s avg) avg) avg) avg)

12 Postprocessing charge density Let us plot the charge density of Si along the (110) plane. 1) Prepare input file si.pp.in with PWgui (see next slides) 2) execute pp.x pp.x < si.pp.in > si.pp.out (out of the many output formats available, let us choose the plotrho format) 3) execute plotrho.x plotrho.x Input file > silicon.charge110.dat r tau tau read 2 atomic positions output file > silicon.charge110.ps Read 29 * 41 grid Logarithmic scale (y/n)? > n Bounds min, max, # of levels > ) Visualize postscript file gv silicon.charge110.ps For advanced and 3D graphics, use XCrySDen ( or other formats

13 Postprocessing charge density Run PWgui and 0) Create a new PP.X input file Be consistent with the SCF run 1) prefix must be the same 2) outdir must be the same 3) Data will be saved in filplot in a raw format 4) Select quantity to plot (several choices) 5) Specify options

14 Postprocessing charge density 6) Select the raw data files to plot (here, filplot as given before) 7) Select the output file, the kind of plot, the output format (here plotrho) 8) Specify the region of the plot (here, the 110 plane)

15 A metal Cu bulk Change number of atoms, coordinates, pseudopotentials, K points, cutoffs, plus... Set additional variables by using PWgui or directly editing the input file &SYSTEM / ecutrho 300.0, occupations 'smearing', degauss 0.02, smearing 'marzari vanderbilt',

16 PWscf and XCrySDen Atomic structure, forces, charge densities, dynamics,... can be visualized by XCrySDen Download from http// e.g. (choose the version for your machine) wget http// latest linuxpc static.tar.gz Untar tar xzvf xc latest linuxpc static.tar.gz Install cd [xcrysden directory]./xcconfigure Source your profile (or open a new terminal) Visualize pw.x input/output files... xcrysden pwi si.scf.in xcrysden pwo si.scf.out...files generated by pp.x (output_format 3, 5)... xcrysden xsf file.xsf...animated files (NEB,...) xcrysden axsf prefix.axsf