Rename examples, add silica cmdline example

sissaschool · Jun 27, 2022 · f42405e · f42405e
1 parent 51a4801
commit f42405e
Show file tree

Hide file tree

Showing 23 changed files with 58,557 additions and 36 deletions.
diff --git a/.../example_cepstrum_singlecomp_silica.ipynb → ..._example_cepstrum_singlecomp_silica.ipynb b/.../example_cepstrum_singlecomp_silica.ipynb → ..._example_cepstrum_singlecomp_silica.ipynb
diff --git a/...es/example_cepstrum_doublecomp_NaCl.ipynb → ...02_example_cepstrum_doublecomp_NaCl.ipynb b/...es/example_cepstrum_doublecomp_NaCl.ipynb → ...02_example_cepstrum_doublecomp_NaCl.ipynb
diff --git a/examples/03_cmdline_example_silica/README.md b/examples/03_cmdline_example_silica/README.md
@@ -0,0 +1,95 @@
+# Command line example
+
+In this example we perform the same analysis that is performed in the correspondent [example notebook](../02_example_cepstrum_doublecomp_NaCl.ipynb), but using the command-line interface.
+
+Simply run, after installing the package, the following command (see [`run_example.sh`](run_example.sh)):
+
+```bash
+sportran-analysis ../data/Silica/Silica.dat --input-format table -k flux1 -C heat -u metal -t 1.0 --VOLUME 3130.431110818 --param-from-input-file-column Temp TEMPERATURE -w 0.1 --FSTAR 28.0 -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 flux1` | use the columns with header `flux1` as the main (energy) flux |
+| `-C heat` | the flux is a heat current |
+| `-u metal` | use LAMMPS metal units |
+| `-t 1.0` | set the timestep to 1.0fs |
+| `--VOLUME 3130.431110818` | 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 28.0` | set the $f^*$ cutoff frequency to 28.0THz |
+| `-r` | resample the time-series according to the value of $f^*$ specified with `--FSTAR` |
+
+The [output](output_ref.log) of the program in the terminal is:
+
+```text
+ Input file (table):      ../data/Silica/Silica.dat
+ Units:      metal
+ Time step:      1.0 fs
+# Solid Silica - BKS potential, melted and quenched
+# 216 atoms, T~1000K, dens~2.295g/cm^3
+# NVE, dt = 1.0 fs, 100 ps, print_step = 1.0 fs
+# Temperature = 983.172635 K, Volume = 3130.431110818 A^3
+# LAMMPS metal units
+Temp c_flux1[1] c_flux1[2] c_flux1[3]
+ #####################################
+  all_ckeys = [('Temp', [0]), ('flux1', array([1, 2, 3]))]
+ #####################################
+Data length = 100001
+  ckey = [('Temp', [0]), ('flux1', array([1, 2, 3]))]
+    step =    100000 - 100.00% completed
+  ( 100000 ) steps read.
+DONE.  Elapsed time: 0.6583120822906494seconds
+VOLUME (input): 3130.431110818
+Mean TEMPERATURE (computed): 983.1726353043 +/- 39.36090003953625
+ Time step (input):  1.0 fs
+  currents shape is (1, 100000, 3)
+snippet:
+[[[ -265.30586   1520.6107      67.461829]
+  [ -168.68352   1377.4459     101.82146 ]
+  [  -93.688306  1180.375      117.20939 ]
+  ...
+  [ 1226.9778     212.0939   -1126.4643  ]
+  [ 1223.8753     186.93836   -881.39541 ]
+  [ 1232.7723     141.30647   -620.41895 ]]]
+Using single component code.
+ Number of currents = 1
+ Number of equivalent components = 3
+ KAPPA_SCALE = 6.144312221539281e-06
+ Nyquist_f   = 500.0  THz
+Using single component code.
+-----------------------------------------------------
+  RESAMPLE TIME SERIES
+-----------------------------------------------------
+ Original Nyquist freq  f_Ny =     500.00000 THz
+ Resampling freq          f* =      27.77778 THz
+ Sampling time         TSKIP =            18 steps
+                             =        18.000 fs
+ Original  n. of frequencies =         50001
+ Resampled n. of frequencies =          2778
+ PSD      @cutoff  (pre-filter&sample) ~ 2802468.65938
+                  (post-filter&sample) ~ 2455132.46201
+ log(PSD) @cutoff  (pre-filter&sample) ~     14.59530
+                  (post-filter&sample) ~     14.38333
+ min(PSD)          (pre-filter&sample) =      4.03008
+ min(PSD)         (post-filter&sample) =  60168.84968
+ % of original PSD Power f<f* (pre-filter&sample)  = 77.164 %
+-----------------------------------------------------
+
+-----------------------------------------------------
+  CEPSTRAL ANALYSIS
+-----------------------------------------------------
+  cutoffK = (P*-1) = 33  (auto, AIC_Kmin = 33, corr_factor =  1.0)
+  L_0*   =          13.114928 +/-   0.097614
+  S_0*   =      717769.108506 +/- 70064.257396
+-----------------------------------------------------
+  kappa* =           2.205099 +/-   0.215248  W/m/K
+-----------------------------------------------------
+```
+
+The program outputs raw data and some [PDF plots](output_ref.plots.pdf).
+
+In this example the output files are called `"output.*"`.
diff --git a/examples/03_cmdline_example_silica/output_ref.cepstral.dat b/examples/03_cmdline_example_silica/output_ref.cepstral.dat
diff --git a/examples/03_cmdline_example_silica/output_ref.cepstrumfiltered_psd.dat b/examples/03_cmdline_example_silica/output_ref.cepstrumfiltered_psd.dat
diff --git a/examples/03_cmdline_example_silica/output_ref.log b/examples/03_cmdline_example_silica/output_ref.log
@@ -0,0 +1,66 @@
+Command:
+ /home/lercole/.virtualenvs/pydevelop/bin/sportran-analysis ../data/Silica/Silica.dat --input-format table -k flux1 -C heat -u metal -t 1.0 --VOLUME 3130.431110818 --param-from-input-file-column Temp TEMPERATURE -w 0.1 --FSTAR 28.0 -r
+
+
+ Input file (table):      ../data/Silica/Silica.dat
+ Units:      metal
+ Time step:      1.0 fs
+# Solid Silica - BKS potential, melted and quenched
+# 216 atoms, T~1000K, dens~2.295g/cm^3
+# NVE, dt = 1.0 fs, 100 ps, print_step = 1.0 fs
+# Temperature = 983.172635 K, Volume = 3130.431110818 A^3
+# LAMMPS metal units
+Temp c_flux1[1] c_flux1[2] c_flux1[3]
+ #####################################
+  all_ckeys = [('Temp', [0]), ('flux1', array([1, 2, 3]))]
+ #####################################
+Data length = 100001
+  ckey = [('Temp', [0]), ('flux1', array([1, 2, 3]))]
+    step =    100000 - 100.00% completed
+  ( 100000 ) steps read.
+DONE.  Elapsed time: 0.641770601272583seconds
+VOLUME (input): 3130.431110818
+Mean TEMPERATURE (computed): 983.1726353043 +/- 39.36090003953625
+ Time step (input):  1.0 fs
+  currents shape is (1, 100000, 3)
+snippet:
+[[[ -265.30586   1520.6107      67.461829]
+  [ -168.68352   1377.4459     101.82146 ]
+  [  -93.688306  1180.375      117.20939 ]
+  ...
+  [ 1226.9778     212.0939   -1126.4643  ]
+  [ 1223.8753     186.93836   -881.39541 ]
+  [ 1232.7723     141.30647   -620.41895 ]]]
+Using single component code.
+ Number of currents = 1
+ Number of equivalent components = 3
+ KAPPA_SCALE = 6.144312221539281e-06
+ Nyquist_f   = 500.0  THz
+Using single component code.
+-----------------------------------------------------
+  RESAMPLE TIME SERIES
+-----------------------------------------------------
+ Original Nyquist freq  f_Ny =     500.00000 THz
+ Resampling freq          f* =      27.77778 THz
+ Sampling time         TSKIP =            18 steps
+                             =        18.000 fs
+ Original  n. of frequencies =         50001
+ Resampled n. of frequencies =          2778
+ PSD      @cutoff  (pre-filter&sample) ~ 2802468.65938
+                  (post-filter&sample) ~ 2455132.46201
+ log(PSD) @cutoff  (pre-filter&sample) ~     14.59530
+                  (post-filter&sample) ~     14.38333
+ min(PSD)          (pre-filter&sample) =      4.03008
+ min(PSD)         (post-filter&sample) =  60168.84968
+ % of original PSD Power f<f* (pre-filter&sample)  = 77.164 %
+-----------------------------------------------------
+
+-----------------------------------------------------
+  CEPSTRAL ANALYSIS
+-----------------------------------------------------
+  cutoffK = (P*-1) = 33  (auto, AIC_Kmin = 33, corr_factor =  1.0)
+  L_0*   =          13.114928 +/-   0.097614
+  S_0*   =      717769.108506 +/- 70064.257396
+-----------------------------------------------------
+  kappa* =           2.205099 +/-   0.215248  W/m/K
+-----------------------------------------------------
diff --git a/examples/03_cmdline_example_silica/output_ref.plots.pdf b/examples/03_cmdline_example_silica/output_ref.plots.pdf