Tully Model-II (RPSH)

This tutorial demonstrates how to run RPSH simulation in parallel mode. The number of parallel runs is controlled by the value of ncore  n specified in the param.in file.

Follow the steps below to perform the simulation:

Prepare param.in

Set ncore  n (where 4 is the number of desired parallel runs).

#tully model-II input parameters
model        tully2
nParticle    1
nbeads       4
approx       CA
nmode        matrix
iseed        12345
ncore        4
tstep        1.0
nsteps       3000
ntraj        1000
pinit        15.0
rsamp        gaussian
vsamp        fixed
rundtail     Yes
iprint       10
finish

Run Simulation

Run the simulation using the provided job script in utility/ directory (e.g., job-script-hpc.sh for an HPC cluster, or job-script-local.sh for local execution).

Based on ncore  4, the job script will:

  • Create 4 run* directories.

  • Distribute the trajectories evenly across the runs.

  • Execute the simulations in parallel.

  • After all parallel simulations are complete, the script automatically averages the results from the 4 run* and produces the final population output.

    Note

    To get average result from parallel runs, must to specify fname, and df inside the write_average_input() fucntion in job_script_hcp.sh or job_script_local.sh as:

    # ==== FUNCTION TO CREATE AVERAGE INPUT ====
write_average_input() {
#fname :: File name of specific population data for averaging
#df    :: No. of data column(s)(except first column)

fname="pop_diabat3.out"
df=2
.
.

    Note

    To compute a standalone average of a specific output file after completing the parallel simulation, one can use job_script_avg.sh script provided in utility/ directory.

    Warning

    Pay attention to modifying the variables fname (output filename) and df (number of data columns, excluding the first column) inside the write_average_input() function of job_script_avg.sh.

    .
.
# ==== FUNCTION TO CREATE AVERAGE INPUT ====
write_average_input() {
#fname :: File name of specific population data for averaging
#df    :: No. of data column(s)(except first column)

fname="pop_diabat2.out"
df=4
.
.

Plot Results

Finally, use any visualization tool (e.g., gnuplot or matplotlib) to plot the population dynamics from the output files and analyze the results.

#!/usr/bin/gnuplot

set xlabel "Time (a.u.)"
set ylabel "Population"
set title "Tully2 Diabatic Populations"
plot "pop_diabat3_ave.out" u 1:2 w l lw 2 title "Diabatic State 1", \
     "pop_diabat3_ave.out" u 1:3 w l lw 2 title "Diabatic State 2"