From d16eb3760522efc97eba7ca4578b5d6df636c932 Mon Sep 17 00:00:00 2001
From: Davide Tisi <47503434+DavideTisi@users.noreply.github.com>
Date: Fri, 8 Dec 2023 16:21:50 +0100
Subject: [PATCH] notebook works added test

---
 .../06_example_cepstrum_viscosity_h2o.ipynb   | 72 ++++++++++++++++---
 tests/test_notebooks.py                       |  7 ++
 2 files changed, 71 insertions(+), 8 deletions(-)

diff --git a/examples/06_example_cepstrum_viscosity_h2o.ipynb b/examples/06_example_cepstrum_viscosity_h2o.ipynb
index 960c8a0..59afda5 100644
--- a/examples/06_example_cepstrum_viscosity_h2o.ipynb
+++ b/examples/06_example_cepstrum_viscosity_h2o.ipynb
@@ -60,7 +60,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Temp\ts_xy\t_xz\ts_yz \n"
+      "Temp\ts_xy\ts_xz\ts_yz \n"
      ]
     }
    ],
@@ -74,9 +74,63 @@
    "metadata": {
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Temp\ts_xy\ts_xz\ts_yz \n",
+      " #####################################\n",
+      "  all_ckeys =  [('Temp', [0]), ('s_xy', [1]), ('s_xz', [2]), ('s_yz', [3])]\n",
+      " #####################################\n",
+      "Data length =  100000\n",
+      "  ckey =  [('Temp', [0]), ('s_xy', [1]), ('s_xz', [2]), ('s_yz', [3])]\n",
+      "    step =    100000 - 100.00% completed\n",
+      "  ( 100000 ) steps read.\n",
+      "DONE.  Elapsed time:  1.4065170288085938 seconds\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "{'Temp': array([[408.14857],\n",
+       "        [404.83967],\n",
+       "        [400.74475],\n",
+       "        ...,\n",
+       "        [375.49635],\n",
+       "        [374.86153],\n",
+       "        [373.89371]]),\n",
+       " 's_xy': array([[788.37874],\n",
+       "        [636.10743],\n",
+       "        [478.48531],\n",
+       "        ...,\n",
+       "        [501.14159],\n",
+       "        [552.52985],\n",
+       "        [564.72988]]),\n",
+       " 's_xz': array([[  14.137608],\n",
+       "        [ -89.647884],\n",
+       "        [-201.87593 ],\n",
+       "        ...,\n",
+       "        [-251.91173 ],\n",
+       "        [-302.26323 ],\n",
+       "        [-333.25187 ]]),\n",
+       " 's_yz': array([[-171.66794],\n",
+       "        [-178.72951],\n",
+       "        [-164.36904],\n",
+       "        ...,\n",
+       "        [ 633.03153],\n",
+       "        [ 419.70789],\n",
+       "        [ 191.02963]])}"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "data = np.loadtxt('data/h2o/h2o.dat', skiprows = 1)"
+    "jfile = st.i_o.TableFile('./data/h2o/h2o.dat')\n",
+    "jfile.read_datalines()"
    ]
   },
   {
@@ -106,11 +160,12 @@
    ],
    "source": [
     "DT_FS = 1                                  # time step [fs]\n",
-    "TEMPERATURE = np.mean(data[:,0])           # temperature [K] (983.173 K)\n",
+    "TEMPERATURE = np.mean(jfile.data['Temp'])  # temperature [K] (983.173 K)\n",
     "VOLUME = 1918.4149658                      # volume [A^3]\n",
     "print(DT_FS, TEMPERATURE, VOLUME)\n",
     "\n",
-    "j = st.StressCurrent(data[:,1:], UNITS='real', DT_FS=DT_FS, TEMPERATURE=TEMPERATURE, VOLUME=VOLUME)"
+    "j = st.StressCurrent(np.column_stack([jfile.data['s_xy'], jfile.data['s_xz'], jfile.data['s_yz']]),\n",
+    "                     UNITS='real', DT_FS=DT_FS, TEMPERATURE=TEMPERATURE, VOLUME=VOLUME)"
    ]
   },
   {
@@ -629,15 +684,16 @@
     "tgap = 10    # see Allen-Tildelsey's book for better understanding\n",
     "tcor = 10000  # maximum value of time (in timesteps) at which we want to compute the ACF \n",
     "acf_ = []\n",
-    "n = len(data[:,1:])//segments\n",
+    "data = np.column_stack([jfile.data['s_xy'], jfile.data['s_xz'], jfile.data['s_yz']])\n",
+    "n = len(data[:,1])//segments\n",
     "print(n)\n",
     "for i in range(segments):\n",
+    "    tmp , norm = ACF(data[(i*n):(i*n+n),0],tcor,n-tcor,tgap=tgap)\n",
+    "    acf_.append(tmp)\n",
     "    tmp , norm = ACF(data[(i*n):(i*n+n),1],tcor,n-tcor,tgap=tgap)\n",
     "    acf_.append(tmp)\n",
     "    tmp , norm = ACF(data[(i*n):(i*n+n),2],tcor,n-tcor,tgap=tgap)\n",
     "    acf_.append(tmp)\n",
-    "    tmp , norm = ACF(data[(i*n):(i*n+n),3],tcor,n-tcor,tgap=tgap)\n",
-    "    acf_.append(tmp)\n",
     "    \n",
     "\n",
     "acf = np.column_stack(acf_)\n",
diff --git a/tests/test_notebooks.py b/tests/test_notebooks.py
index 3c3cc7b..633b27b 100644
--- a/tests/test_notebooks.py
+++ b/tests/test_notebooks.py
@@ -33,6 +33,13 @@ def test_doublecomp_NaCl(tb, file_regression):
 def test_singlecomp_silica(tb, file_regression):
     res = tb.cell_output_text('results_cell')
     file_regression.check(res, basename='final_result2')
+    
+@local_dir
+@testbook(test_folder_path + '/../examples/06_example_cepstrum_viscosity_h2o.ipynb', execute=True)
+def test_singlecomp_silica(tb, file_regression):
+    res = tb.cell_output_text('results_cell')
+    file_regression.check(res, basename='final_result6')
+    
 
 
 @local_dir