Checked (and updated) example notebooks

ydluo · Mar 22, 2024 · a76fa79 · a76fa79
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diff --git a/examples/notebooks/3D_mesh_builder.ipynb b/examples/notebooks/3D_mesh_builder.ipynb
diff --git a/examples/notebooks/CNS_spring-block.ipynb b/examples/notebooks/CNS_spring-block.ipynb
diff --git a/examples/notebooks/RSF_spring-block.ipynb b/examples/notebooks/RSF_spring-block.ipynb
diff --git a/examples/notebooks/compute_events.ipynb b/examples/notebooks/compute_events.ipynb
@@ -9,6 +9,27 @@
     "This notebook shows the workflow to compute the seismic events of a simulation using the python function `extract_events`. For usage details of this function, check the source code in `qdyn/utils/postprocessing/extract_events`"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "7f4eb619",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib widget\n",
+    "\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "import os\n",
+    "import sys\n",
+    "import pickle\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "# Import QDYN wrapper\n",
+    "from qdyn import qdyn\n",
+    "from qdyn.utils import post_processing"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 11,
@@ -25,19 +46,7 @@
     }
    ],
    "source": [
-    "# reload modules automatically\n",
-    "%load_ext autoreload\n",
-    "%autoreload 2\n",
     "\n",
-    "\"\"\"\n",
-    "INITIAL PARAMETERS\n",
-    "\"\"\"\n",
-    "import numpy as np\n",
-    "import pandas as pd\n",
-    "import os\n",
-    "import sys\n",
-    "import pickle\n",
-    "import matplotlib.pyplot as plt\n",
     "\n",
     "# Add QDYN source directory to PATH\n",
     "# Go up in the directory tree\n",
@@ -683,7 +692,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/double_asperity.ipynb b/examples/notebooks/double_asperity.ipynb
diff --git a/examples/notebooks/intersecting_faults.ipynb b/examples/notebooks/intersecting_faults.ipynb
diff --git a/examples/notebooks/restart_simulation.ipynb b/examples/notebooks/restart_simulation.ipynb
diff --git a/examples/notebooks/single_asperity.ipynb b/examples/notebooks/single_asperity.ipynb
diff --git a/examples/notebooks/single_asperity_3D.ipynb b/examples/notebooks/single_asperity_3D.ipynb
diff --git a/qdyn/pyqdyn.py b/qdyn/pyqdyn.py
@@ -791,7 +791,7 @@ def read_output(self, mirror=False, path_output=None, read_ot=True, filename_ot=
 
                 df = read_csv(
                     filename_iot, header=None, skiprows=nheaders_ot,
-                    names=quants_ot, delim_whitespace=True
+                    names=quants_ot, sep="\s+"
                 )
 
                 # Sanitise output (check for near-infinite numbers, etc.)
@@ -807,7 +807,7 @@ def read_output(self, mirror=False, path_output=None, read_ot=True, filename_ot=
 
             self.ot_vmax = read_csv(
                 filename_vmax, header=None, skiprows=nheaders_vmax,
-                names=quants_vmax, delim_whitespace=True
+                names=quants_vmax, sep="\s+"
             )
             # Discard duplicate rows from duplicate time-steps
             self.ot_vmax = self.ot_vmax.drop_duplicates(subset=["step"], keep="first") 
@@ -825,7 +825,7 @@ def read_output(self, mirror=False, path_output=None, read_ot=True, filename_ot=
             if path_output!= None:
                 filename_ox= path_output + filename_ox
 
-            data_ox = read_csv(filename_ox, header=None, names=quants_ox, delim_whitespace=True, comment="#")
+            data_ox = read_csv(filename_ox, header=None, names=quants_ox, sep="\s+", comment="#")
 
             # Store snapshot data in self.ox
             self.ox = data_ox
@@ -852,7 +852,7 @@ def read_output(self, mirror=False, path_output=None, read_ot=True, filename_ot=
             if path_output!= None:
                 filename_ox_last = path_output + filename_ox_last
 
-            data_ox_last = read_csv(filename_ox_last, header=None, names=quants_ox, delim_whitespace=True, comment="#")
+            data_ox_last = read_csv(filename_ox_last, header=None, names=quants_ox, sep="\s+", comment="#")
 
             # Store snapshot data in self.ox
             self.ox_last = data_ox_last
@@ -892,7 +892,7 @@ def read_output(self, mirror=False, path_output=None, read_ot=True, filename_ot=
                 # Read pre-rupture file
                 data_ox_dyn_pre[i] = read_csv(
                     ox_dyn_files_pre[i], header=None, names=quants_ox,
-                    delim_whitespace=True, comment="#"
+                    sep="\s+", comment="#"
                 )
                 # Sanitise output (check for near-infinite numbers, etc.)
                 data_ox_dyn_pre[i] = data_ox_dyn_pre[i].apply(pd.to_numeric, errors="coerce")
@@ -903,7 +903,7 @@ def read_output(self, mirror=False, path_output=None, read_ot=True, filename_ot=
                 # Read pre-rupture file
                 data_ox_dyn_post[i] = read_csv(
                     ox_dyn_files_post[i], header=None, names=quants_ox,
-                    delim_whitespace=True, comment="#"
+                    sep="\s+", comment="#"
                 )
                 # Sanitise output (check for near-infinite numbers, etc.)
                 data_ox_dyn_post[i] = data_ox_dyn_post[i].apply(pd.to_numeric, errors="coerce")
@@ -914,7 +914,7 @@ def read_output(self, mirror=False, path_output=None, read_ot=True, filename_ot=
                 # Rupture stats file
                 data_ox_dyn_rup[i] = read_csv(
                     ox_dyn_files_rup[i], header=None, names=quants_rup,
-                    delim_whitespace=True, comment="#"
+                    sep="\s+", comment="#"
                 )
                 # Sanitise output (check for near-infinite numbers, etc.)
                 data_ox_dyn_rup[i] = data_ox_dyn_rup[i].apply(pd.to_numeric, errors="coerce")
@@ -957,7 +957,7 @@ def read_output(self, mirror=False, path_output=None, read_ot=True, filename_ot=
                 # Read output file
                 self.fault[n] = read_csv(
                 filename_fault, header=None, skiprows=nheaders_fault, usecols=col_list,
-                names=quants_fault, delim_whitespace=True
+                names=quants_fault, sep="\s+"
                 )
 
                 # Discard duplicate rows from duplicate time-steps

diff --git a/qdyn/utils/post_processing/plot_functions.py b/qdyn/utils/post_processing/plot_functions.py
@@ -69,8 +69,6 @@ def slip_profile(ox, warm_up=0, orientation="horizontal"):
 
     ind_warmup = np.where(t_vals >= warm_up)[0][0]
 
-    print(ind_warmup)
-
     Nx = len(x_unique)
     Nt = len(t_vals) - 1