Difference between revisions of "Tutorial-v.1.0.0"

Revision as of 07:19, 9 November 2017

Getting Started

Welcome! In this tutorial, we explain the use of SALMON from the very beginning, taking a few examples that cover applications of SALMON in several directions. We assume that you are in the computational environment of UNIX/Linux OS. First you need to download and install SALMON in your computational environment. You may find detailed instruction in download-v.1.0.0 and install and Run-v.1.0.0.

As described in Install and Run-v.1.0.0, you are required to prepare at least input file and pseudopotential files to run SALMON. In the following, we present input files for several example calculations. We provide a brief explanation of the namelists that appear in the input files. Pseudopotential files of elements that appear in the example are also attached. We also present main output files and explain what they include.

You can run SALMON at your own environment just getting files from this page. You may also be able to modify the input file reading the explanation of the namelists.

We present 6 samples.

First 3 samples (Sample-1 ~ 3) are for an isolated molecule, acetylene C2H2. If you are interested in learning electron dynamics calculations in isolated systems, please look into these samples. In SALMON, we usually calculate the ground state DFT solution first. This is illustrated in Sample-1. After finishing the ground state calculations, two samples of electron dynamics calculations are prepared. Sample-2 illustrates the calculation of linear optical responses in real time, getting polarizability and photoabsorption of the molecule. [[#Sample-3: Electron dynamics in C2H2 molecule under a pulsed electric field|Sample-3] illustrates the calculation of electron dynamics in the molecule under a pulsed electric field.

Next 2 samples (Sample-4 ~ 5) are for a crystalline silicon. If you are interested in learning electron dynamics calculations in extended periodic systems, please look into these samples. Since the time evolution calculation is much more time consuming than the ground state calculation in extended systems, we recommend to calculate the ground and the time evolution calculations as a single job. Sample-4 illustrates the calculation of linear response properties of crystalline silicon, getting the dielectric function. Sample-5 illustrates the calculation of electron dynamics in the crystalline silicon induced by a pulsed electric field.

The final sample (Sample-6) is for a propagation of a pulsed light in a bulk medium, coupling Maxwell equations for the electromagnetic fields of pulsed light and the electron dynamics in unit cells. This calculation is quite time-consuming and is only possible using massively parallel supercomputers. Sample-6 illustrates the calculation of a pulsed, linearly polarized light irradiating normally on a surface of bulk silicon.

C2H2 (isolated molecules)

Sample-1: Ground state of C2H2 molecule

In this sample, we learn the preparation of the ground state solution of an isolated system such as molecules, taking acetylene (C2H2) molecule as an example. We assume that atomic positions of a molecule to be calculated are known (use the measured geometry, or prepare by other calculations). You can look at a sample input file, C2H2_gs.inp, or download the sample input file as well as pseudopotential files of Carbon and Hydrogen, File:C2H2 gs v1 0 0.zip). In the input file, namelists variables are specified. Most of them are mandatory to run the ground state calculation. You may find explanation of the namelist variables in [[Explanations for C2H2_gs input files-v.1.0.0].

• input file (C2H2_gs.inp, File:C2H2 gs v1 0 0.zip)
• pseudo potential files (C_rps.data, H_rps.data, File:Pseudopotentials C2H2.zip)
  • Explanations for C2H2_gs input files-v.1.0.0
• an output file (C2H2.info, File:C2H2 info v1 0 0.zip) and additional output files (File:C2H2 gs output v1 0 0.zip)
  • Explanations for C2H2_gs output files-v.1.0.0
• images generated by cube files (psi: highest occupied molecular orbital (HOMO), dns: electron density, ELF: electron localization function)

Sample-2: Polarizability and photoabsorption of C2H2 molecule

• input file (C2H2_rt_response.inp, File:C2H2 rt response v1 0 0.zip)
• pseudo potential files (C_rps.data, H_rps.data, File:Pseudopotentials C2H2.zip)
  • Explanations for C2H2_rt_response input files-v.1.0.0
• output files (C2H2-RT.data, C2H2-ALP.data, File:C2H2 response data v1 0 0.zip)
  • Explanations for C2H2_rt_response output files-v.1.0.0

Sample-3: Electron dynamics of C2H2 molecule under a pulsed electric field

• input file (C2H2_rt_pulse.inp, File:C2H2 rt pulse v1 0 0.zip)
• pseudo potential files (C_rps.data, H_rps.data, File:Pseudopotentials C2H2.zip)
  • Explanations for C2H2_rt_pulse input files-v.1.0.0
• output files (C2H2-RT.data, C2H2-ALP.data, File:C2H2 pulse data v1 0 0.zip)
  • Explanations for C2H2_rt_pulse output files-v.1.0.0

Crystalline silicon (periodic solids)

Sample-4: Ground state and dielectric function of crystalline silicon

• input file (Si_sc_response.inp)
• pseudo potential files ( Si_rps.dat)
  • Explanations for Si_response input files-v.1.0.0
• output files
  • Explanations for Si response output files-v.1.0.0

Sample-5: Ground state and electron dynamics in crystalline silicon under a pulsed electric field

• input file ( Si_sc_pulse.inp)
• pseudo potential files ( Si_rps.dat)
  • Explanations for Si_sc_pulse input files-v.1.0.0
• output files ( Si_sc_pulse.out, Si_sc_pulse_j_ac.out
  • Explanations for Si_sc_pulse output files-v.1.0.0

Light propagation in bulk silicon (Maxwell + TDDFT)

Sample-6: Coupled multiscale calculation of electrons and electromagnetic fields in crystalline silicon

• input file ( Si_ms_pulse.inp)
• pseudo potential files ( Si_rps.dat)
  • Explanations for Si_ms input files-v.1.0.0
• output files(Si_ms_pulse.out, Si_ms_pulse_Ac_000000.out)
  • Explanations for Si_ms output files-v.1.0.0