Solve #10, update command-line example

sissaschool · Nov 18, 2019 · 37fb881 · 37fb881
1 parent b5da08a
commit 37fb881
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -28,6 +28,11 @@
   - id: double-quote-string-fixer
   - id: end-of-file-fixer
   - id: trailing-whitespace
+    exclude: >
+      (?x)^(
+        docs/.*|
+        examples/.*|
+      )$
 
 #  # prospector: collection of linters
 #  - id: prospector

diff --git a/examples/example_commandline_NaCl/output_ref.cepstral.dat b/examples/example_commandline_NaCl/output_ref.cepstral.dat
diff --git a/examples/example_commandline_NaCl/output_ref.cepstrumfiltered_psd.dat b/examples/example_commandline_NaCl/output_ref.cepstrumfiltered_psd.dat
diff --git a/examples/example_commandline_NaCl/output_ref.cospectrum.dat b/examples/example_commandline_NaCl/output_ref.cospectrum.dat
diff --git a/examples/example_commandline_NaCl/output_ref.cospectrum.filt.dat b/examples/example_commandline_NaCl/output_ref.cospectrum.filt.dat
diff --git a/examples/example_commandline_NaCl/output_ref.log b/examples/example_commandline_NaCl/output_ref.log
@@ -0,0 +1,40 @@
+Command:
+ /home/lercole/.virtualenvs/thermotest3/bin/thermocepstrum-analysis ../data/NaCl.dat -k flux -j vcm[1] -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r
+
+ Input file (table):      ../data/NaCl.dat
+ Units:      metal
+ Time step:      5.0 fs
+ Mean Temperature (computed):  1399.3477811999999 K  +/-  19.318785820942594
+ Volume (input):  65013.301261 A^3
+ Time step (input):  5.0 fs
+  currents shape is (2, 20000, 3)
+ Number of currrents = 2
+ Number of components = 3
+ kappa_scale = 1.4604390788939313e-07
+ Nyquist_f   = 100.0  THz
+-----------------------------------------------------
+  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) = 443152.37265
+                  (post-filter) = 564877.86516
+ log(PSD) @cutoff  (pre-filter) =     12.89638
+                  (post-filter) =     13.05597
+ min(PSD)          (pre-filter) =      0.31536
+ min(PSD)         (post-filter) =  22166.11934
+ % of original PSD Power f<f* (pre-filter)  = 96.678574
+-----------------------------------------------------
+-----------------------------------------------------
+  CEPSTRAL ANALYSIS
+-----------------------------------------------------
+  AIC_Kmin  = 3  (P* = 4, corr_factor = 1.000000)
+  L_0*   =          15.158757 +/-   0.056227
+  S_0*   =     6824108.702608 +/- 383697.095268
+-----------------------------------------------------
+  kappa* =           0.498310 +/-   0.028018  W/mK
+-----------------------------------------------------
diff --git a/examples/example_commandline_NaCl/output_ref.plots.pdf b/examples/example_commandline_NaCl/output_ref.plots.pdf
diff --git a/examples/example_commandline_NaCl/output_ref.psd.dat b/examples/example_commandline_NaCl/output_ref.psd.dat
diff --git a/examples/example_commandline_NaCl/output_ref.resampled_psd.dat b/examples/example_commandline_NaCl/output_ref.resampled_psd.dat
diff --git a/thermocepstrum/analysis.py b/thermocepstrum/analysis.py
@@ -229,7 +229,7 @@ def main():
         jdata = jfile.data
         START_STEP = 0   # reset to zero, as later we will need to read all of jdata
     elif (input_format == 'dict'):
-        jdata = np.load(inputfile,allow_pickle=True).tolist()
+        jdata = np.load(inputfile, allow_pickle=True).tolist()
     elif (input_format == 'lammps'):
         jfile = tc.i_o.LAMMPSLogFile(inputfile, run_keyword=run_keyword)
         if temperature is None:
@@ -560,7 +560,7 @@ def plt_cepstral_conv(jf, pstar_max=None, k_SI_max=None, pstar_tick=None, kappa_
     if k_SI_max is None:
         k_SI_max = jf.dct.tau[jf.dct.aic_Kmin] * jf.kappa_scale
 
-    f, (ax2) = plt.subplots(1, 1, figsize=(3.8, 2.3))
+    f, ax2 = plt.subplots(1, 1, figsize=(3.8, 2.3))
     ax2.axvline(x=jf.dct.aic_Kmin + 1, ls='--', c='k', dashes=(1.4, 0.6), zorder=-3)
     ax2.fill_between(np.arange(jf.dct.logtau.shape[0]) + 1,\
                      (jf.dct.tau - jf.dct.tau_THEORY_std) * jf.kappa_scale * 0.5,\
@@ -607,8 +607,7 @@ def plt_other(jf, idx1, idx2, f_THz_max=None, k_SI_max=None, k_SI_min=None, k_ti
     if k_SI_min is None:
         k_SI_min = -k_SI_max
 
-    figure=plt.figure(figsize=(3.8, 2.3))
-    ax=figure.add_subplots()
+    figure, ax = plt.subplots(1, 1, figsize=(3.8, 2.3))
     ax.plot(jf.freqs_THz, np.real(jf.fcospectrum[idx1][idx2]) * jf.kappa_scale * 0.5, c=c[3], lw=1.0, zorder=1)
     ax.plot(jf.freqs_THz, np.imag(jf.fcospectrum[idx1][idx2]) * jf.kappa_scale * 0.5, c=c[2], lw=1.0, zorder=1)
 
@@ -653,8 +652,7 @@ def plt_psd(jf, j2=None, j2pl=None, f_THz_max=None, k_SI_max=None, k_tick=None,
         k_SI_max = np.max(
             jf.fpsd[:int(jf.freqs_THz.shape[0] * f_THz_max / jf.freqs_THz[-1])] * jf.kappa_scale * 0.5) * 1.3
 
-    figure=plt.figure(figsize=(3.8, 2.3))
-    ax=figure.add_subplot()
+    figure, ax = plt.subplots(1, 1, figsize=(3.8, 2.3))
     ax.plot(jf.freqs_THz, jf.psd * jf.kappa_scale * 0.5, lw=0.2, c='0.8', zorder=0)
     ax.plot(jf.freqs_THz, jf.fpsd * jf.kappa_scale * 0.5, c=c[0], zorder=2)
     if j2 is not None: