SALMON TUTORIAL, TSUKUBA, 2018 (modified for SALMON-v.1.2.0)

How to Use SALMON:
Geometry Optimization andMolecular Dynamics (MD)Exercise 4-3

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

1

Available Functions(Trial version now, only for periodic system) Geometry Optimization(Conjugated Gradient method)(MPI parallelization is not supported (single node only)) Molecular Dynamics (MD) Type of MD• Adiabatic ground-state MD• Nonadiabatic Ehrenfest MD (mean-field approximation)(surface-hopping, excited state MD are not available)

 Ensemble• NVT (Nose-Hoover thermostat, Velocity scaling)• NVE

Note that these functions are currently available only for periodic systems
and trial version
Scalable Ab-initio Light-Matter simulator for Optics and Nanosciences
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 20182

Menu of Exercise
Menu of the exercise
Calculations of single water molecule(with periodic boundary condition at gamma-point) :1. Geometry Optimization
 Input Files ---- in exercise4-3_md/1_H2O_opt/(H2O_opt.inp, O_rps.dat, H_rps.dat, k1x1x1.dat)

2. Ehrenfest MD simulation
 Input Files ---- in exercise4-3_md/2_H2O_md/(H2O_md.inp, O_rps.dat, H_rps.dat, k1x1x1.dat)

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

1. Geometry Optimization(Job Submission)
This example performs geometrical optimization of single water molecule(periodic boundary condition with gamma-point ; just test system)

Prepare files Submit job %> ls
H2O_opt.inp

H_rps.dat%> (job submit command)

k1x1x1.dat

O_rps.dat

Check following input files in the same directory H2O_opt.inp (input file) H_rps.dat, O_rps.dat (PS potential data)
 k1x1x1.dat (read-in k-point data (Γ-point))

Scalable Ab-initio Light-Matter simulator for Optics and Nanosciences
SALMON TUTORIAL, TSUKUBA, 2018
http://salmon-tddft.jp/4Calculation of Geometrical Optimization（Input File）
Important input keywords for optimization in Example input file&calculation
calc_mode = 'GS'
use_geometry_opt = 'y'/

Optimization option incombination with GS mode&opt
convrg_opt_fmax = 1d-3/

Convergence threshold ofoptimization (Maximum Force) [a.u.]&atomic_coor'H' 3.5 2.5'H' 2.5 3.5'O' 2.5 2.5/

2.5
2.5
2.5

1 y
1 y
2 y

Put “y” for the atoms to be optimized.
(but in the current version, all atoms must have ‘y’)Note:
• Algorism to find the structure with force=0 is used (not energy minimization algorism)• If you choose a functional of inaccurate force calculation, the optimization will not converge.
• option to read the pre-calculated ground state orbitals (gs_wfn_k/) as initial guess is available using read_gs_wfn_k='y'• The threshold of ground state SCF in the optimization iteration is from &scf block. If this is tight, the optimization calculation takes
long time. Additional threshold of ground state SCF is available specifying in &opt block.

Scalable Ab-initio Light-Matter simulator for Optics and Nanosciences
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20185

Calculation of Geometrical Optimization（Output File, Check of Result, Restart）
Important Output Files•out.log•H2O_trj.xyz --- atomic coordinates at each optimization step [Å]--- standard log (Here, just example name: the file name given in the job script file)

Checks of Output Files
Maximum Force %> grep Fmax out.log%> grep Fmax out.log
Convergence threshold of Fmax
= 1.0000000E-03
step=(perp= 0, line= 0) Fmax= 0.2361E+00 Fave= 0.2135E+00
step=(perp= 1, line= 1) Fmax= 0.2228E-01 Fave= 0.2206E-01
step=(perp= 2, line= 1) Fmax= 0.4918E-02 Fave= 0.4593E-02
step=(perp= 3, line= 1) Fmax= 0.8861E-03 Fave= 0.8109E-03

converged maximum force

Convergence

E= -0.16761049E+02
E= -0.16797253E+02
E= -0.16822598E+02
E= -0.16822264E+02

dE-perp= 0.0000E+00
dE-perp= -0.3620E-01
dE-perp= -0.2535E-01
dE-perp= 0.3347E-03

Total energy at each main optimization step%> tail out.log===================================================

Restart

Optimization Converged
Iteration step=3
Force(maximum)= 0.8860836326E-03 [a.u.]
Force(average)= 0.8108601090E-03 [a.u.]
Total Energy = -0.1682226358E+02 [a.u.]===================================================

Copy the atomic coordinate at the last step printed in H2O_trj.xyz
and paste into &atomic_coor in the next input file, and run
Scalable Ab-initio Light-Matter simulator for Optics and Nanosciences
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2. Ehrenfest Molecular Dynamics(Job Submission)
This example performs Ehrenfest molecular dynamics simulation of single water moleculeusing the optimized structure in the previous step
(but in this tutorial, the optimized coordinates are already given in the input file by a shortcut.)
The room temperature is given as initial condition.
The electric field is not applied now, but of course external field is available!

Prepare files 

Submit job %> ls
H2O_md.inp

H_rps.dat%> (job submit command)

k1x1x1.dat

O_rps.dat

Check following input files in the same directory H2O_md.inp (input file) H_rps.dat, O_rps.dat (PS potential data)
 k1x1x1.dat (read-in k-point data (Γ-point))

Scalable Ab-initio Light-Matter simulator for Optics and Nanosciences
SALMON TUTORIAL, TSUKUBA, 2018
http://salmon-tddft.jp/7Calculation of Ehrenfest MD（Input File）
Important input keywords for Ehrenfest MD in Example input file&calculation
calc_mode = ‘GS_RT'use_ehrenfest_md = 'y'/Ehrenfest MD option incombination with RT mode&md
ensemble = "NVE"
set_ini_velocity='y'temperature0_ion = 300.0d0
step_update_ps=50
step_update_ps2= 200/

&atomic_coor'H' 3.6867868204'H' 2.3313961246'O' 2.5139878343/

Ensemble: NVE is corresponding to energy conservation condition,
without temperature controller
Set initial velocity (give temperature at t=0)2.3313961921
3.6867870709
2.5139878474

Setting temperature [K].
temperature at t=0 as initial velocity in this caseTime step interval to update pseudopotential:
step_update_ps  interval of fully updating
step_update_ps2  interval of update without re-allocation(Note: calculation gets slower if the interval is small)

2.4999999893 1
2.4999999912 1
2.5000000182 2

Atomic coordinate. Usually in MD calculation, optimized
structure is used.

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

Calculation of Ehrenfest MD（Output File, Check of Results, Restart）
Important Output Files••H2O_trj.xyz --- Atomic coordinates [Å], velocity [a.u.] and force [a.u.] at each time step
H2O_rt.data•

H2O_rt_energy.data

Checks of Output Files Animation:
animation can be made by using visualization software such as VMD reading H2O_trj.xyz(but not in the tutorial menu) Plot of temperature.
%> gnuplot(Smaller grid spacing is necessary
to get appropriate results.)

gnuplot> p “H2O_rt_energy.data” u 1:5 w l Plot of kinetic, potential(electrons), and total energies.

Temperature(t)gnuplot> p “H2O_rt_energy.data” u 1:4 w l, “” u 1:6 w l, “” u 1:($4+$6) w l

RestartT(t)(1) use “write_rt_wfn_k=‘y’” in the first run,(2) copy or link the printed directory “rt_wfn_k” from the first to next directories.
(3) use “read_rt_wfn_k=‘y’” in the next run
Scalable Ab-initio Light-Matter simulator for Optics and Nanosciences
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 2018

E(t)
V(t)

9Example of adiabatic GS-MD
Input keywords (example)&calculation
calc_mode=‘GS’
use_adiabatic_md=‘y’/&mdensemble=‘NVT’
thermostat=‘nose-hoover’
thermostat_tau=100
temperature0_ion = 298.15
Equilibration process by adiabatic ground-state MD (Δt=0.5fs)
set_ini_velocity=‘r’
T0=298.15K
NVE
Temperature T0=250K
file_ini_velocity=“ini_vel.dat”
T0=200K
stop_system_momt =‘y’
T0=150K/
T0=100K
T0=50K

restartStart from optimized structure

Scalable Ab-initio Light-Matter simulator for Optics and Nanosciences
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 201810