SALMON TUTORIAL, CMD35

How to Use SALMON-Isolated Systems
Exercise-2

Takashi Takeuchi
Center for Computational Sciences, University of Tsukuba
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/

1Demonstration for C2H2
• Linear response calculation:• Ground state calculation → C2H2_gs.inp• Real-time TDDFT → C2H2_rt_response.inp• Pulse response calculation:• Ground state calculation → C2H2_gs.inp• Real-time TDDFT → C2H2_rt_pulse.inp

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20182

Demonstration for C2H2
• Linear response calculation:• Ground state calculation → C2H2_gs.inp• Real-time TDDFT → C2H2_rt_response.inp• Pulse response calculation:• Ground state calculation → C2H2_gs.inp• Real-time TDDFT → C2H2_rt_pulse.inp

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20183

Input keywords in C2H2_gs.inp
Basic rules for an input file• &units /• &calculation /• &control /• &system /• &pseudo /• &rgrid /• &scf /• &functional /• &atomic_coor /&category
keyword = xxx/
・ The input file consists of categories and keywords
with an input value and equal sign( = ).
・ A character input value requires
single quotation marks ( ‘ ’ ).
・ A real number input value can be written
in Fortran style. → e.g. 1.0d-5
・ “ ! ” is used as commented out.
・ Space free.
・ “&atomic_coor” / “&atomic_red_coor”
has to be put at the last part in the input.
・ All keywords are described in the SALMON manual.

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 2018

4

Input keywords in C2H2_gs.inp• &units /• &calculation /unit_system = ‘A_eV_fs’→ Unit system byÅ, eV, and fs.
(Default is atomic unit system.)• &control /• &system /• &pseudo /• &rgrid /• &scf /• &functional /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20185

Input keywords in C2H2_gs.inp• &units /• &calculation /• &control /calc_mode = ‘GS'
→ Ground state calculation.

• &system /• &pseudo /• &rgrid /• &scf /• &functional /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 2018

6

Input keywords in C2H2_gs.inp• &units /• &calculation /• &control /• &system /sysname = 'C2H2'→ Session name of output files.
→ This is used for a prefix of output files.

• &pseudo /• &rgrid /• &scf /• &functional /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20187

Input keywords in C2H2_gs.inp• &units /• &calculation /• &control /iperiodic = 0→ Number of directions to apply
periodic boundary condition.
→ 0 is for isolated systems.
al = 16d0, 16d0, 16d0
→ Side lengths (x,y,z) of system domain.

• &system /• &pseudo /nstate = 5→ Number of orbitals.

• &rgrid /• &scf /nelem = 2
→ Number of atomic elements (species).

• &functional /• &atomic_coor /natom = 4
→ Number of atoms.
nelec = 10
→ Number of valence electrons.

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20188

Input keywords in C2H2_gs.inp• &units /izatom(1) = 6, izatom(2) = 1→ Atomic number of each atomic element.

• &calculation /• &control /pseudo_file(1) = 'C.cpi', pseudo_file(2) = 'H.cpi'→ Name of pseudopotential files.

• &system /lmax_ps(1) = 1, lmax_ps(2) = 0→ Maximum angular momentum of
pseudopotential projectors.

• &pseudo /• &rgrid /• &scf /• &functional /lloc_ps (1) = 1, lloc_ps(2) = 0→ Angular momentum of pseudopotentialthat will be treated as local.
𝑃𝑆𝑃𝑆• &atomic_coor /|𝜓𝑙𝑚𝑣𝑙 ⟩⟨𝑣𝑙 𝜓𝑙𝑚 |• 𝑉𝑖𝑜𝑛 = 𝑉𝑙𝑜𝑐𝑎𝑙 + σ𝑙𝑚

𝑃𝑆𝑃𝑆⟨𝜓𝑙𝑚
𝑣𝑙 𝜓𝑙𝑚⟩𝑉𝑙𝑜𝑐𝑎𝑙 : local part of pseudopotential
𝑣𝑙 : non-local part of pseudopotential
𝑃𝑆
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience𝜓𝑙𝑚: pseudowavefunction
http://salmon-tddft.jp/

SALMON TUTORIAL, TSUKUBA, 2018

9

Input keywords in C2H2_gs.inp• &units /• &calculation /• &control /• &system /• &pseudo /dl = 0.25d0, 0.25d0, 0.25d0→ Spacing of real-space grids.

• &rgrid /• &scf /• &functional /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201810

Input keywords in C2H2_gs.inp• &units /• &calculation /• &control /• &system /ncg = 4
→ Number of iteration of Conjugate-Gradient method
for each scf-cycle.
(Default is 5.)
nscf = 1000
→ Number of maximum scf cycle.

• &pseudo /convergence = 'norm_rho_dng‘→ Convergence is checked by||rho_iter(ix)-rho_iter-1(ix)||2 / (number of grids).
(Default is rho_dne)(Difference of electron density / 1 electron)• &rgrid /• &scf /• &functional /• &atomic_coor /threshold_norm_rho = 1.d-15→ Threshold for convergence.
(Default is 1d-17.)

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201811

Input keywords in C2H2_gs.inp• &units /• &calculation /• &control /• &system /• &pseudo /• &rgrid /• &scf /• &functional /• &atomic_coor /xc = ‘PZ’→ Functional.
→ 'PZ': Perdew-Zunger LDA :Phys. Rev. B 23, 5048 (1981).

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201812

Input keywords in C2H2_gs.inp• &units /• &calculation /• &control /• &system /• &pseudo /• &rgrid /• &scf /• &functional /• &atomic_coor /

zxy
↓
↓
↓
'C' 0.000000 0.000000 0.599672 1'H' 0.000000 0.000000 1.662257 2'C' 0.000000 0.000000 -0.599672 1'H' 0.000000 0.000000 -1.662257 2→ Cartesian coordinates of atoms andindex number of atomic element.

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
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SALMON TUTORIAL, TSUKUBA, 201813

Output files by C2H2_gs.inp• variables.log→ All input variables and values used in the calculation.
• out_gs.log→ Standard output file.
• C2H2_info.data→ System information including number of states, electrons, and energy, etc..
• C2H2_gs.bin→ "Ground state data in binary format (for RT calculation).
• C2H2_eigen.data→ Orbital energies.

• PS_C_KY_n.dat & PS_H_KY_n.dat→ Pseudo potential and wave function for radial direction.

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 201814

out_gs.log
Press "q" for quit

• less out_gs .log

iteration count----------------------------------------------iter =54
Total Energy =-339.58127310

1-18.4138

5-7.3403

2-13.9736

310.00000000000000

Vh iteration =1-12.4006

4-7.3403

Orbital energies

iter and ||rho_i(ix)-rho_i-1(ix)||**2/(# of grids) =Ne=

Iteration count for Vh

Number of electros

54 0.67366858E-15

Convergence check

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201815

Visualization by ParaView
Electron density

Electron localization function

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201816

Demonstration for C2H2
• Linear response calculation:• Ground state calculation → C2H2_gs.inp• Real-time TDDFT → C2H2_rt_response.inp• Pulse response calculation:• Ground state calculation → C2H2_gs.inp• Real-time TDDFT → C2H2_rt_pulse.inp

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201817

Input keywords in C2H2_rt_response.inp• &units /• &calculation /• &control /• &system /• &pseudo /• &functional /• &tgrid /• &emfield /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201818

Input keywords in C2H2_rt_response.inp• &units /• &calculation /• &control /calc_mode = ‘RT'→ Real-time TDDFT calculation.

• &system /• &pseudo /• &functional /• &tgrid /• &emfield /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201819

Input keywords in C2H2_rt_response.inp• &units /• &calculation /• &control /• &system /• &pseudo /dt = 1.25d-3→ Time step size.

• &functional /• &tgrid /nt = 5000→ Number of total time steps.

• &emfield /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201820

Input keywords in C2H2_rt_response.inp• &units /• &calculation /• &control /• &system /• &pseudo /• &tgrid /ae_shape1 = 'impulse'→ Impulsive fields.

• &functional /• &emfield /• &atomic_coor /epdir_re1 = 0.d0,0.d0,1.d0→ Real part of polarization vector of the pulse field.

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 201821

Output files by C2H2_rt_response.inp• out_rt.log (less out_rt.log)→ Standard output file.
timesteptime[fs]

Press q for quit

Dipole moment(xyz)[A]

electrons

Total energy[eV]iterVh------------------------------------------------------10.00125000

0.16755557E-10 -0.23698286E-09

0.27416845E-02

10.00000000-339.56762344

97• C2H2_p.data→ Dipole moment at each time step.

• C2H2_lr.data→ The dipole moment in frequency domain and Oscillator strength.

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 2018

22

Oscillator strength by C2H2_rt_response.inp• gnuplot

Oscillator strength [1/eV]• plot 'C2H2_lr.data' u 1:10 w l lw 2To finish gnuplot → exit

Energy [eV]Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201823

Demonstration for C2H2
• Linear response calculation:• Ground state calculation → C2H2_gs.inp• Real-time TDDFT → C2H2_rt_response.inp• Pulse response calculation:• Ground state calculation → C2H2_gs.inp• Real-time TDDFT → C2H2_rt_pulse.inp

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201824

Real-time calculation by C2H2_rt_pulse.inp• &units /• &calculation /• &control /• &system /• &pseudo /• &functional /• &tgrid /• &emfield /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201825

Input keywords in C2H2_rt_pulse.inp• &units /• &calculation /• &control /• &system /• &pseudo /dt = 1.25d-3→ Time step size.

• &functional /• &tgrid /nt = 4800→ Number of total time steps.

• &emfield /• &atomic_coor /Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201826

Input keywords in C2H2_rt_pulse.inp• &units /• &calculation /• &control /ae_shape1 = 'Ecos2'→ Envelope of pulse field: cos2 type.
epdir_re1 = 0.d0,0.d0,1.d0→ Real part of polarization vector of the pulse field.

• &system /rlaser_int_wcm2_1 = 1.d8
→ Pulse intensity at peak(W/cm2).

• &pseudo /• &functional /omega1 = 9.28d0→ (Mean) pulse frequency (or photon energy).

• &tgrid /• &emfield /• &atomic_coor /pulse_tw1 = 6.d0
→ Duration of the pulse.
phi_cep1 = 0.75d0→ Carrier envelope phase of the pulse.

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
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SALMON TUTORIAL, TSUKUBA, 201827

Dipole moment by C2H2_rt_pulse.inp• gnuplot

C2H2_ps.data→ The dipole moment in frequency domain and the power spectrum.

To finish gnuplot → exit

dipole moment [Å]• plot 'C2H2_p.data' u 1:4 w l lw 2Time [fs]Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
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SALMON TUTORIAL, TSUKUBA, 201828

Visualization by ParaView
Change in electron density from GS

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201829