Manual:Examples:Hello world
From OctopusWiki
As a first example, we will take a sodium atom. With your favourite text editor, create the file inp.
CalculationMode = gs
%Coordinates
'Na' | 0.0 | 0.0 | 0.0
%
This input file should be essentially self-explanatory.
Note that when a specie is not especified in the Species block, octopus reads the information of pseudopotentials from the defaults file (located under PREFIX/share/octopus/PP/. This file also contains default values for Mesh and Spacing.
Then run octopus – for example, do
$ octopus > out
so that the output is stored in out file. If everything goes OK, out should look like:
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
___
.-' `'.
/ \
| ;
| | ___.--,
_.._ |0) ~ (0) | _.---'`__.-( (_.
__.--'`_.. '.__.\ '--. \_.-' ,.--'` `""`
( ,.--'` ',__ /./; ;, '.__.'` __
_`) ) .---.__.' / | |\ \__..--"" """--.,_
`---' .'.''-._.-'`_./ /\ '. \ _.-~~~````~~~-._`-.__.'
| | .' _.-' | | \ \ '. `~---`
\ \/ .' \ \ '. '-._)
\/ / \ \ `=.__`~-.
jgs / /\ `) ) / / `"".`\
, _.-'.'\ \ / / ( ( / /
`--~` ) ) .-'.' '.'. | (
(/` ( (` ) ) '-;
` '-; (-'
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2, or (at your option)
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Running octopus, version 2.1pre1
build time - Wed Jun 28 18:15:19 CEST 2006
svn revision: 2252 [td_write.F90 2006-06-28]
Compiler: ifort
Compiler flags: -u -zero -fpp1 -nbs -pc80 -pad -align -unroll -O3 -ip -tpp7 -xN
The octopus is swimming in ddraig (Linux)
Calculation started on 2006/06/29 at 14:21:08
************************** Calculation Mode **************************
Input: [CalculationMode = gs]
**********************************************************************
****************************** Species *******************************
Reading pseudopotential from file:
'/home/xavier/share/octopus/PP/TM2/Na.ascii'
Calculating atomic pseudo-eigenfunctions for specie Na....
Done.
Info: l = 0 component used as local potential
**********************************************************************
Info: Using default spacing(1) [b] = 0.567
Info: Using default spacing(2) [b] = 0.567
Info: Using default spacing(3) [b] = 0.567
Input: [SpinComponents = unpolarized]
Input: [CurvMethod = curv_uniform]
Input: [DerivativesSpace = real_space]
Input: [DerivativesStencil = stencil_star]
************************** Parallelization ***************************
Octopus will run in *serial*
**********************************************************************
******************************** Grid ********************************
Simulation Box:
Type = around nuclei
Radius [b] = -1.000
The octopus will run in 3 dimension(s).
The octopus will treat the system as periodic in 0 dimension(s).
Main mesh:
Spacing [b] = ( 0.567, 0.567, 0.567) volume/point [b^3] = 0.18221
# inner mesh = 52971
# total mesh = 103523
Grid Cutoff [H] = 15.354
**********************************************************************
****************************** Hartree *******************************
Input: [PoissonSolver = fft]
Info: FFT allocated with size ( 105, 105, 105) in slot 1
Info: Poisson Cutoff Radius [b] = 29.763198
**********************************************************************
************************ Exchange-Correlation ************************
Exchange and correlation:
Exchange
Slater exchange (LDA)
Correlation
Perdew & Zunger (LDA)
[1] Perdew and Zunger, Phys. Rev. B 23, 5048 (1981)
Input: [SICCorrection = sic_none]
**********************************************************************
Input: [RelativisticCorrection = non_relativistic]
Input: [TDGauge = length]
Input: [AbsorbingBoundaries = no_absorbing]
Input: [RestartFileFormat = restart_plain]
******************** Loading restart information *********************
** Warning:
** Could not load wave-functions from 'tmp/restart_gs'
** Starting from scratch!
Info: Unnormalized total charge = 0.999665
Info: Renormalized total charge = 1.000000
Info: Setting up Hamiltonian.
Input: [LCAOStart = lcao_full]
Info: Performing initial LCAO calculation with 2 orbitals.
Eigenvalues [H]
#st Spin Eigenvalue Occupation
1 -- -0.103077 1.000000
Info: SCF using real wavefunctions.
Input: [What2Mix = density] (what to mix during SCF cycles)
Input: [TypeOfMixing = broyden]
Input: [EigenSolver = cg]
*********************** SCF CYCLE ITER # 1 ************************
etot = -1.84248567E-01 abs_ev = 3.88E-04 rel_ev = 3.75E-03
abs_dens = 1.17E-04 rel_dens = 1.17E-04
Matrix vector products: 27
Converged eigenvectors: 0
Eigenvalues [H]
#st Spin Eigenvalue Occupation Error
1 -- -0.103465 1.000000 (8.2E-04)
**********************************************************************
*********************** SCF CYCLE ITER # 2 ************************
etot = -1.84249567E-01 abs_ev = 7.64E-05 rel_ev = 7.39E-04
abs_dens = 1.40E-04 rel_dens = 1.40E-04
Matrix vector products: 27
Converged eigenvectors: 0
Eigenvalues [H]
#st Spin Eigenvalue Occupation Error
1 -- -0.103389 1.000000 (5.8E-05)
**********************************************************************
*********************** SCF CYCLE ITER # 3 ************************
etot = -1.84248966E-01 abs_ev = 1.15E-04 rel_ev = 1.12E-03
abs_dens = 2.06E-04 rel_dens = 2.06E-04
Matrix vector products: 23
Converged eigenvectors: 1
Eigenvalues [H]
#st Spin Eigenvalue Occupation Error
1 -- -0.103504 1.000000 (9.9E-07)
**********************************************************************
*********************** SCF CYCLE ITER # 4 ************************
etot = -1.84250323E-01 abs_ev = 3.85E-04 rel_ev = 3.73E-03
abs_dens = 1.53E-05 rel_dens = 1.53E-05
Matrix vector products: 27
Converged eigenvectors: 0
Eigenvalues [H]
#st Spin Eigenvalue Occupation Error
1 -- -0.103119 1.000000 (5.8E-06)
**********************************************************************
*********************** SCF CYCLE ITER # 5 ************************
etot = -1.84250321E-01 abs_ev = 4.65E-06 rel_ev = 4.51E-05
abs_dens = 1.93E-05 rel_dens = 1.93E-05
Matrix vector products: 16
Converged eigenvectors: 1
Eigenvalues [H]
#st Spin Eigenvalue Occupation Error
1 -- -0.103124 1.000000 (9.9E-07)
**********************************************************************
*********************** SCF CYCLE ITER # 6 ************************
etot = -1.84250325E-01 abs_ev = 9.85E-06 rel_ev = 9.55E-05
abs_dens = 5.28E-07 rel_dens = 5.28E-07
Matrix vector products: 25
Converged eigenvectors: 1
Eigenvalues [H]
#st Spin Eigenvalue Occupation Error
1 -- -0.103134 1.000000 (7.5E-07)
**********************************************************************
Info: SCF converged in 6 iterations
Info: FFT deallocated from slot 1
Calculation ended on 2006/06/29 at 14:21:22
Take now a look at the working directory. It should include the following files:
-rw-r--r-- 1 xavier xavier 84 2006-06-29 14:21 inp drwxr-xr-x 2 xavier xavier 4096 2006-06-29 14:21 static drwxr-xr-x 2 xavier xavier 4096 2006-06-29 14:21 status drwxr-xr-x 3 xavier xavier 4096 2006-06-29 14:21 tmp
Besides the initial file (inp) and the out file, three new directories appear. In static/, you will find the file info, with information about the static calculation (it should be hopefully self-explanatory, otherwise please complain to the authors). In tmp/, you will find the restart_gs directory that contains restart information about the ground-state, which is used if, for example, you want to start a time-dependent calculation afterwards. Finally, the status/ directory has information about the run of octopus, inside the out.oct contains all the input variables parsed by octopus.
[edit]
Exercises
- Study how the total energy and eigenvalue of the sodium atom improve with the mesh spacing.
- Calculate the static polarizability of the sodium atom (
CalculationMode= pol). A linear/polarizability will be created, this files contains the static polarizability tensor. - Calculate a few unoccupied states (
CalculationMode= unocc). The eigenspectrum will be in the file static/eigenvalues. Why don't we find a Rydberg series in the eigenspectrum? - Repeat the previous calculation with different exchange and correlation functionals like PBE, LB94, and exact exchange.
- Perform a time-dependent evolution (
CalculationMode= td), to calculate the optical spectrum of the Na atom. Use aTDDeltaStrength= 0.05, polarised in the x direction. The multipole moments of the density are output to the file td.general/multipoles. You can process this file with the utility oct-cross-section to obtain the optical spectrum. If you have computer time to waste, re-run the time-dependent simulation for some other xc choices.
