Example 4: command line (NaCl)ΒΆ
In this example we perform the same analysis that is performed in the correspondent example notebook, but using the command-line interface.
Simply run, after installing the package, the following command (see run_example.sh):
sportran-analysis ../data/NaCl/NaCl.dat --input-format table -k flux -j 'vcm[1]' -C heat -u metal -t 5.0 --VOLUME 65013.301261 --param-from-input-file-column Temp TEMPERATURE -w 0.1 --FSTAR 14.0 -r
The options have the following meaning:
command |
explanation |
|---|---|
|
input is a plain-text table-formatted file, column headers are used as keys |
|
use the columns with header |
|
use the columns with header |
|
the flux is a heat current |
|
use LAMMPS metal units |
|
set the timestep to 5.0fs |
|
set the volume of the system |
|
use the column with header |
|
set the width of the moving average filter to 0.1THz, that is used only to visualize the spectrum |
|
set the \(f^*\) cutoff frequency to 14.0THz |
|
resample the time-series according to the value of \(f^*\) specified with |
The output of the program in the terminal is:
Input file (table): ../data/NaCl/NaCl.dat
Units: metal
Time step: 5.0 fs
# Molten NaCl - Fumi-Tosi potential
# https://journals.aps.org/prl/supplemental/10.1103/PhysRevLett.122.255901/Bertossa_et_al_Supplemental_Material.pdf
# 1728 atoms, T~1400K
# NVE, dt = 1.0 fs, 100 ps, print_step = 5.0 fs
# Volume = 65013.301261 A^3
# LAMMPS metal units
Temp c_flux[1] c_flux[2] c_flux[3] c_vcm[1][1] c_vcm[1][2] c_vcm[1][3]
#####################################
all_ckeys = [('Temp', [0]), ('flux', array([1, 2, 3])), ('vcm[1]', array([4, 5, 6]))]
#####################################
Data length = 20000
ckey = [('Temp', [0]), ('flux', array([1, 2, 3])), ('vcm[1]', array([4, 5, 6]))]
( 20000 ) steps read.
DONE. Elapsed time: 0.19688773155212402seconds
VOLUME (input): 65013.301261
Mean TEMPERATURE (computed): 1399.3477811999999 +/- 19.318785820942594
Time step (input): 5.0 fs
currents shape is (2, 20000, 3)
snippet:
[[[ 2.5086549e+02 2.0619423e+01 2.0011500e+02]
[ 1.9622265e+02 8.2667342e+01 2.8433250e+02]
[ 1.2639441e+02 1.6075472e+02 3.4036769e+02]
...
[ 1.7991856e+02 1.8612706e+01 -1.3265623e+02]
[ 2.0471193e+02 -4.6643315e-01 -2.0401650e+02]
[ 2.4123318e+02 -1.8295461e+01 -2.5246475e+02]]
[[-1.5991832e-01 -7.1370426e-02 2.0687917e-02]
[-1.3755206e-01 -7.1002931e-02 -1.1279876e-02]
[-1.0615044e-01 -6.2381243e-02 -4.1568120e-02]
...
[-9.1939899e-02 -8.4778292e-02 6.0011385e-02]
[-1.3384949e-01 -1.1474530e-01 8.9323546e-02]
[-1.8385053e-01 -1.3693430e-01 1.1434060e-01]]]
Using multicomponent code.
Number of currents = 2
Number of equivalent components = 3
KAPPA_SCALE = 1.4604390788939313e-07
Nyquist_f = 100.0 THz
Using multicomponent code.
-----------------------------------------------------
RESAMPLE TIME SERIES
-----------------------------------------------------
Original Nyquist freq f_Ny = 100.00000 THz
Resampling freq f* = 14.28571 THz
Sampling time TSKIP = 7 steps
= 35.000 fs
Original n. of frequencies = 10001
Resampled n. of frequencies = 1429
PSD @cutoff (pre-filter&sample) ~ 443152.37265
(post-filter&sample) ~ 564877.86516
log(PSD) @cutoff (pre-filter&sample) ~ 12.89638
(post-filter&sample) ~ 13.05597
min(PSD) (pre-filter&sample) = 0.31536
min(PSD) (post-filter&sample) = 22166.11934
% of original PSD Power f<f* (pre-filter&sample) = 96.679 %
-----------------------------------------------------
-----------------------------------------------------
CEPSTRAL ANALYSIS
-----------------------------------------------------
cutoffK = (P*-1) = 3 (auto, AIC_Kmin = 3, corr_factor = 1.0)
L_0* = 15.158757 +/- 0.056227
S_0* = 6824108.702608 +/- 383697.095268
-----------------------------------------------------
kappa* = 0.498310 +/- 0.028018 W/m/K
-----------------------------------------------------
The program outputs raw data and some PDF plots.
In this example the output files are called "output.*".