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04_cmdline_example_NaCl

README.md

Example 4: command line (NaCl)

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-format table input is a plain-text table-formatted file, column headers are used as keys
-k flux use the columns with header flux as the main (energy) flux
-j 'vcm[1] use the columns with header vcm[1] as the convective (mass) flux
-C heat the flux is a heat current
-u metal use LAMMPS metal units
-t 5.0 set the timestep to 5.0fs
--VOLUME 65013.301261 set the volume of the system
--param-from-input-file-column Temp TEMPERATURE use the column with header Temp as the temperature of the system
-w 0.1 set the width of the moving average filter to 0.1THz, that is used only to visualize the spectrum
--FSTAR 14.0 set the $f^*$ cutoff frequency to 14.0THz
-r resample the time-series according to the value of $f^*$ specified with --FSTAR

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.*".