Update pumping test notebooks (#60)

* Adding files with completed notebooks for tracking (Testing, some fixes still needs to be done) * Adding README, first version * Correcting English and adding extra images to the unconfined notes + rerunning the code in the leaky notes * Corrected English in notebooks and minor change in aquifer.py to avoid bug in leaky2_hardixveld * Reruning the outputs and correcting english * adding pumpingtest folders * merged change in pumping test notebook (dont know why it dind merge before) * removing unwanted files * revert all files in docs directory * last files to remove * Update confined1_oude_korendijk.ipynb Update using import ttim as ttm and change all ttim commands Fix pandas error for use of append - still gives deprecation warning Set default figure size and remove setting figure size Add grid to all graphs Remove next notebook cell at end * remove fitm fitm is part of ttim * modified confined pumpingtest notebooks according to #58 (comment) * move updated pumping test noteboks * update tutorials * move elements to concepts (from howto section) * move elements to concepts (from howto section) * delete old pumping test notebooks * remove url visited date from bib file * ruff formatting * organize examples in docs * ruff format notebooks * display inline math in notebooks in docs --------- Co-authored-by: vcantarella <vcantarella@gmail.com> Co-authored-by: Mark Bakker <markbak@gmail.com>
mbakker7 · Feb 13, 2024 · e81b27c · e81b27c
1 parent c6e4772
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diff --git a/docs/00tutorials/index.rst b/docs/00tutorials/index.rst
@@ -5,5 +5,6 @@ TTim tutorials.
 
 .. toctree::
     :maxdepth: 3
-    :hidden:
     :glob:
+
+    models.rst
diff --git a/docs/01howto/getting_started/models.rst → docs/00tutorials/models.rst b/docs/01howto/getting_started/models.rst → docs/00tutorials/models.rst
diff --git a/docs/01howto/getting_started/index.rst b/docs/01howto/getting_started/index.rst
diff --git a/docs/01howto/howto_pumpingtest.ipynb b/docs/01howto/howto_pumpingtest.ipynb
@@ -21,9 +21,10 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "import ttim as ttm\n",
+    "\n",
     "#\n",
-    "plt.rcParams['figure.figsize'] = (4, 3) # set default figure size\n",
-    "plt.rcParams['font.size'] = 8 # set default font size"
+    "plt.rcParams[\"figure.figsize\"] = (4, 3)  # set default figure size\n",
+    "plt.rcParams[\"font.size\"] = 8  # set default font size"
    ]
   },
   {
@@ -65,22 +66,26 @@
     }
    ],
    "source": [
-    "data = np.loadtxt('data/oudekorendijk_h30.dat')\n",
+    "data = np.loadtxt(\"data/oudekorendijk_h30.dat\")\n",
     "to1 = data[:, 0] / 60 / 24\n",
     "ho1 = -data[:, 1]\n",
     "ro1 = 30\n",
-    "print(f'first measurement time: {np.min(to1):.2e}, last measurement time: {np.max(to1):.2e} d')\n",
+    "print(\n",
+    "    f\"first measurement time: {np.min(to1):.2e}, last measurement time: {np.max(to1):.2e} d\"\n",
+    ")\n",
     "\n",
-    "drawdown = np.loadtxt('data/oudekorendijk_h90.dat')\n",
+    "drawdown = np.loadtxt(\"data/oudekorendijk_h90.dat\")\n",
     "to2 = drawdown[:, 0] / 60 / 24\n",
     "ho2 = -drawdown[:, 1]\n",
     "ro2 = 90\n",
-    "print(f'first measurement time: {np.min(to2):.2e}, last measurement time: {np.max(to2):.2e} d')\n",
+    "print(\n",
+    "    f\"first measurement time: {np.min(to2):.2e}, last measurement time: {np.max(to2):.2e} d\"\n",
+    ")\n",
     "\n",
-    "plt.plot(to1, ho1, 'C0.', label='r=30 m')\n",
-    "plt.plot(to2, ho2, 'C1.', label='r=90 m')\n",
-    "plt.xlabel('time (d)')\n",
-    "plt.ylabel('head (m)')\n",
+    "plt.plot(to1, ho1, \"C0.\", label=\"r=30 m\")\n",
+    "plt.plot(to2, ho2, \"C1.\", label=\"r=90 m\")\n",
+    "plt.xlabel(\"time (d)\")\n",
+    "plt.ylabel(\"head (m)\")\n",
     "plt.legend()\n",
     "plt.grid()"
    ]
@@ -121,17 +126,8 @@
     }
    ],
    "source": [
-    "ml = ttm.ModelMaq(kaq=60, \n",
-    "              z=(-18, -25), \n",
-    "              Saq=1e-4, \n",
-    "              tmin=1e-5, \n",
-    "              tmax=1)\n",
-    "w = ttm.Well(model=ml, \n",
-    "         xw=0, \n",
-    "         yw=0, \n",
-    "         rw=0.1, \n",
-    "         tsandQ=[(0, 788)], \n",
-    "         layers=0)\n",
+    "ml = ttm.ModelMaq(kaq=60, z=(-18, -25), Saq=1e-4, tmin=1e-5, tmax=1)\n",
+    "w = ttm.Well(model=ml, xw=0, yw=0, rw=0.1, tsandQ=[(0, 788)], layers=0)\n",
     "ml.solve()"
    ]
   },
@@ -154,12 +150,12 @@
    "source": [
     "hm1 = ml.head(ro1, 0, to1)\n",
     "hm2 = ml.head(ro2, 0, to2)\n",
-    "plt.plot(to1, ho1, 'C0.', label='r=30 m')\n",
-    "plt.plot(to1, hm1[0], 'C0')\n",
-    "plt.plot(to2, ho2, 'C1.', label='r=90 m')\n",
-    "plt.plot(to2, hm2[0], 'C1')\n",
-    "plt.xlabel('time (d)')\n",
-    "plt.ylabel('head (m)')\n",
+    "plt.plot(to1, ho1, \"C0.\", label=\"r=30 m\")\n",
+    "plt.plot(to1, hm1[0], \"C0\")\n",
+    "plt.plot(to2, ho2, \"C1.\", label=\"r=90 m\")\n",
+    "plt.plot(to2, hm2[0], \"C1\")\n",
+    "plt.xlabel(\"time (d)\")\n",
+    "plt.ylabel(\"head (m)\")\n",
     "plt.legend()\n",
     "plt.grid()"
    ]
@@ -191,16 +187,17 @@
     }
    ],
    "source": [
-    "cal = ttm.Calibrate(model=ml) # create Calibration object\n",
-    "cal.set_parameter(name='kaq0', initial=20) # \n",
-    "cal.set_parameter(name='Saq0', initial=1e-4)\n",
-    "cal.series(name='obs1', # user specified name\n",
-    "           x=ro1, # x=location of observation well\n",
-    "           y=0, # y-location of obsevation well\n",
-    "           layer=0, # layer number\n",
-    "           t=to1, # observation times\n",
-    "           h=ho1 # observed heads\n",
-    "          )\n",
+    "cal = ttm.Calibrate(model=ml)  # create Calibration object\n",
+    "cal.set_parameter(name=\"kaq0\", initial=20)  #\n",
+    "cal.set_parameter(name=\"Saq0\", initial=1e-4)\n",
+    "cal.series(\n",
+    "    name=\"obs1\",  # user specified name\n",
+    "    x=ro1,  # x=location of observation well\n",
+    "    y=0,  # y-location of obsevation well\n",
+    "    layer=0,  # layer number\n",
+    "    t=to1,  # observation times\n",
+    "    h=ho1,  # observed heads\n",
+    ")\n",
     "cal.fit(report=False)"
    ]
   },
@@ -311,8 +308,8 @@
     }
    ],
    "source": [
-    "print('k of model: ', ml.aq.kaq)\n",
-    "print('Ss of model: ', ml.aq.Saq)"
+    "print(\"k of model: \", ml.aq.kaq)\n",
+    "print(\"Ss of model: \", ml.aq.Saq)"
    ]
   },
   {
@@ -340,10 +337,10 @@
    ],
    "source": [
     "hm1 = ml.head(ro1, 0, to1)\n",
-    "plt.plot(to1, ho1, 'k.', label='r=30 m')\n",
-    "plt.plot(to1, hm1[0], 'C0', label='fit')\n",
-    "plt.xlabel('time (d)')\n",
-    "plt.ylabel('head (m)')\n",
+    "plt.plot(to1, ho1, \"k.\", label=\"r=30 m\")\n",
+    "plt.plot(to1, hm1[0], \"C0\", label=\"fit\")\n",
+    "plt.xlabel(\"time (d)\")\n",
+    "plt.ylabel(\"head (m)\")\n",
     "plt.legend()\n",
     "plt.grid()"
    ]
@@ -452,33 +449,31 @@
     }
    ],
    "source": [
-    "ml2 = ttm.ModelMaq(kaq=60, \n",
-    "              z=(-17, -18, -25), \n",
-    "              Saq=1e-4, \n",
-    "              c=[1000],\n",
-    "              Sll=0,\n",
-    "              topboundary='semi',\n",
-    "              tmin=1e-5, \n",
-    "              tmax=1)\n",
-    "w = ttm.Well(model=ml2, \n",
-    "         xw=0, \n",
-    "         yw=0, \n",
-    "         rw=0.1, \n",
-    "         tsandQ=[(0, 788)], \n",
-    "         layers=0)\n",
+    "ml2 = ttm.ModelMaq(\n",
+    "    kaq=60,\n",
+    "    z=(-17, -18, -25),\n",
+    "    Saq=1e-4,\n",
+    "    c=[1000],\n",
+    "    Sll=0,\n",
+    "    topboundary=\"semi\",\n",
+    "    tmin=1e-5,\n",
+    "    tmax=1,\n",
+    ")\n",
+    "w = ttm.Well(model=ml2, xw=0, yw=0, rw=0.1, tsandQ=[(0, 788)], layers=0)\n",
     "ml2.solve()\n",
     "#\n",
-    "cal2 = ttm.Calibrate(model=ml2) # create Calibration object\n",
-    "cal2.set_parameter(name='kaq0', initial=20) # \n",
-    "cal2.set_parameter(name='Saq0', initial=1e-4)\n",
-    "cal2.set_parameter(name='c0', initial=1000)\n",
-    "cal2.series(name='obs1', # user specified name\n",
-    "           x=ro1, # x=location of observation well\n",
-    "           y=0, # y-location of obsevation well\n",
-    "           layer=0, # layer number\n",
-    "           t=to1, # observation times\n",
-    "           h=ho1 # observed heads\n",
-    "          )\n",
+    "cal2 = ttm.Calibrate(model=ml2)  # create Calibration object\n",
+    "cal2.set_parameter(name=\"kaq0\", initial=20)  #\n",
+    "cal2.set_parameter(name=\"Saq0\", initial=1e-4)\n",
+    "cal2.set_parameter(name=\"c0\", initial=1000)\n",
+    "cal2.series(\n",
+    "    name=\"obs1\",  # user specified name\n",
+    "    x=ro1,  # x=location of observation well\n",
+    "    y=0,  # y-location of obsevation well\n",
+    "    layer=0,  # layer number\n",
+    "    t=to1,  # observation times\n",
+    "    h=ho1,  # observed heads\n",
+    ")\n",
     "cal2.fit(report=False)\n",
     "display(cal2.parameters)"
    ]
@@ -509,11 +504,11 @@
    "source": [
     "hm1 = ml.head(ro1, 0, to1)\n",
     "hm2 = ml2.head(ro1, 0, to1)\n",
-    "plt.plot(to1, ho1, 'k.', label='r=30 m')\n",
-    "plt.plot(to1, hm1[0], label='fit 2 params')\n",
-    "plt.plot(to1, hm2[0], label='fit 3 params')\n",
-    "plt.xlabel('time (d)')\n",
-    "plt.ylabel('head (m)')\n",
+    "plt.plot(to1, ho1, \"k.\", label=\"r=30 m\")\n",
+    "plt.plot(to1, hm1[0], label=\"fit 2 params\")\n",
+    "plt.plot(to1, hm2[0], label=\"fit 3 params\")\n",
+    "plt.xlabel(\"time (d)\")\n",
+    "plt.ylabel(\"head (m)\")\n",
     "plt.legend()\n",
     "plt.grid()"
    ]
@@ -540,8 +535,8 @@
     }
    ],
    "source": [
-    "print(f'rmse 2 params: {cal.rmse():.3f} m')\n",
-    "print(f'rmse 3 params: {cal2.rmse():.3f} m')"
+    "print(f\"rmse 2 params: {cal.rmse():.3f} m\")\n",
+    "print(f\"rmse 3 params: {cal2.rmse():.3f} m\")"
    ]
   },
   {
@@ -651,16 +646,16 @@
     }
    ],
    "source": [
-    "cal.series(name='obs2', # user specified name\n",
-    "           x=ro2, # x=location of observation well\n",
-    "           y=0, # y-location of obsevation well\n",
-    "           layer=0, # layer number\n",
-    "           t=to2, # observation times\n",
-    "           h=ho2 # observed heads\n",
-    "          )\n",
+    "cal.series(\n",
+    "    name=\"obs2\",  # user specified name\n",
+    "    x=ro2,  # x=location of observation well\n",
+    "    y=0,  # y-location of obsevation well\n",
+    "    layer=0,  # layer number\n",
+    "    t=to2,  # observation times\n",
+    "    h=ho2,  # observed heads\n",
+    ")\n",
     "cal.fit(report=False)\n",
-    "display(cal.parameters)\n",
-    "print"
+    "display(cal.parameters)"
    ]
   },
   {
@@ -758,13 +753,14 @@
     }
    ],
    "source": [
-    "cal2.series(name='obs2', # user specified name\n",
-    "           x=ro2, # x=location of observation well\n",
-    "           y=0, # y-location of obsevation well\n",
-    "           layer=0, # layer number\n",
-    "           t=to2, # observation times\n",
-    "           h=ho2 # observed heads\n",
-    "          )\n",
+    "cal2.series(\n",
+    "    name=\"obs2\",  # user specified name\n",
+    "    x=ro2,  # x=location of observation well\n",
+    "    y=0,  # y-location of obsevation well\n",
+    "    layer=0,  # layer number\n",
+    "    t=to2,  # observation times\n",
+    "    h=ho2,  # observed heads\n",
+    ")\n",
     "cal2.fit(report=False)\n",
     "display(cal2.parameters)"
    ]
@@ -784,8 +780,8 @@
     }
    ],
    "source": [
-    "print(f'rmse 2 params: {cal.rmse():.3f} m')\n",
-    "print(f'rmse 3 params: {cal2.rmse():.3f} m')"
+    "print(f\"rmse 2 params: {cal.rmse():.3f} m\")\n",
+    "print(f\"rmse 3 params: {cal2.rmse():.3f} m\")"
    ]
   },
   {
@@ -809,24 +805,24 @@
     "plt.subplot(121)\n",
     "hm1 = ml.head(ro1, 0, to1)\n",
     "hm2 = ml.head(ro2, 0, to2)\n",
-    "plt.plot(to1, ho1, 'C0.', label='r=30 m')\n",
-    "plt.plot(to2, ho2, 'C1.', label='r=90 m')\n",
-    "plt.plot(to1, hm1[0], 'C0', label='fit 2 params')\n",
-    "plt.plot(to2, hm2[0], 'C1', label='fit 2 params')\n",
-    "plt.xlabel('time (d)')\n",
-    "plt.ylabel('head (m)')\n",
+    "plt.plot(to1, ho1, \"C0.\", label=\"r=30 m\")\n",
+    "plt.plot(to2, ho2, \"C1.\", label=\"r=90 m\")\n",
+    "plt.plot(to1, hm1[0], \"C0\", label=\"fit 2 params\")\n",
+    "plt.plot(to2, hm2[0], \"C1\", label=\"fit 2 params\")\n",
+    "plt.xlabel(\"time (d)\")\n",
+    "plt.ylabel(\"head (m)\")\n",
     "plt.legend()\n",
     "plt.grid()\n",
     "#\n",
     "plt.subplot(122)\n",
     "hm1 = ml2.head(ro1, 0, to1)\n",
     "hm2 = ml2.head(ro2, 0, to2)\n",
-    "plt.plot(to1, ho1, 'C0.', label='r=30 m')\n",
-    "plt.plot(to2, ho2, 'C1.', label='r=90 m')\n",
-    "plt.plot(to1, hm1[0], 'C0', label='fit 3 params')\n",
-    "plt.plot(to2, hm2[0], 'C1', label='fit 3 params')\n",
-    "plt.xlabel('time (d)')\n",
-    "plt.ylabel('head (m)')\n",
+    "plt.plot(to1, ho1, \"C0.\", label=\"r=30 m\")\n",
+    "plt.plot(to2, ho2, \"C1.\", label=\"r=90 m\")\n",
+    "plt.plot(to1, hm1[0], \"C0\", label=\"fit 3 params\")\n",
+    "plt.plot(to2, hm2[0], \"C1\", label=\"fit 3 params\")\n",
+    "plt.xlabel(\"time (d)\")\n",
+    "plt.ylabel(\"head (m)\")\n",
     "plt.legend()\n",
     "plt.grid()"
    ]
@@ -859,24 +855,24 @@
     "plt.subplot(121)\n",
     "hm1 = ml.head(ro1, 0, to1)\n",
     "hm2 = ml.head(ro2, 0, to2)\n",
-    "plt.semilogx(to1, ho1, 'C0.', label='r=30 m')\n",
-    "plt.semilogx(to2, ho2, 'C1.', label='r=90 m')\n",
-    "plt.semilogx(to1, hm1[0], 'C0', label='fit 2 params')\n",
-    "plt.semilogx(to2, hm2[0], 'C1', label='fit 2 params')\n",
-    "plt.xlabel('time (d)')\n",
-    "plt.ylabel('head (m)')\n",
+    "plt.semilogx(to1, ho1, \"C0.\", label=\"r=30 m\")\n",
+    "plt.semilogx(to2, ho2, \"C1.\", label=\"r=90 m\")\n",
+    "plt.semilogx(to1, hm1[0], \"C0\", label=\"fit 2 params\")\n",
+    "plt.semilogx(to2, hm2[0], \"C1\", label=\"fit 2 params\")\n",
+    "plt.xlabel(\"time (d)\")\n",
+    "plt.ylabel(\"head (m)\")\n",
     "plt.legend()\n",
     "plt.grid()\n",
     "#\n",
     "plt.subplot(122)\n",
     "hm1 = ml2.head(ro1, 0, to1)\n",
     "hm2 = ml2.head(ro2, 0, to2)\n",
-    "plt.semilogx(to1, ho1, 'C0.', label='r=30 m')\n",
-    "plt.semilogx(to2, ho2, 'C1.', label='r=90 m')\n",
-    "plt.semilogx(to1, hm1[0], 'C0', label='fit 3 params')\n",
-    "plt.semilogx(to2, hm2[0], 'C1', label='fit 3 params')\n",
-    "plt.xlabel('time (d)')\n",
-    "plt.ylabel('head (m)')\n",
+    "plt.semilogx(to1, ho1, \"C0.\", label=\"r=30 m\")\n",
+    "plt.semilogx(to2, ho2, \"C1.\", label=\"r=90 m\")\n",
+    "plt.semilogx(to1, hm1[0], \"C0\", label=\"fit 3 params\")\n",
+    "plt.semilogx(to2, hm2[0], \"C1\", label=\"fit 3 params\")\n",
+    "plt.xlabel(\"time (d)\")\n",
+    "plt.ylabel(\"head (m)\")\n",
     "plt.legend()\n",
     "plt.grid()"
    ]

diff --git a/docs/01howto/index.rst b/docs/01howto/index.rst
@@ -7,6 +7,4 @@ This section contains how to guides on building groundwater models with TTim.
 .. toctree::
     :maxdepth: 1
 
-    getting_started/index.rst
-    elements/index.rst
     howto_pumpingtest
diff --git a/docs/01howto/elements/areasinks.rst → docs/02concepts/elements/areasinks.rst b/docs/01howto/elements/areasinks.rst → docs/02concepts/elements/areasinks.rst
diff --git a/docs/01howto/elements/index.rst → docs/02concepts/elements/index.rst b/docs/01howto/elements/index.rst → docs/02concepts/elements/index.rst
diff --git a/docs/01howto/elements/linedoublets.rst → docs/02concepts/elements/linedoublets.rst b/docs/01howto/elements/linedoublets.rst → docs/02concepts/elements/linedoublets.rst
diff --git a/docs/01howto/elements/linesinks.rst → docs/02concepts/elements/linesinks.rst b/docs/01howto/elements/linesinks.rst → docs/02concepts/elements/linesinks.rst
diff --git a/docs/01howto/elements/wells.rst → docs/02concepts/elements/wells.rst b/docs/01howto/elements/wells.rst → docs/02concepts/elements/wells.rst
diff --git a/docs/02concepts/index.rst b/docs/02concepts/index.rst
@@ -7,4 +7,5 @@ This section contains explanations of some basic concepts that are used in TTim.
 .. toctree::
     :maxdepth: 3
 
-
+    elements/index.rst
+    pathlines.rst
diff --git a/docs/01howto/getting_started/pathlines.rst → docs/02concepts/pathlines.rst b/docs/01howto/getting_started/pathlines.rst → docs/02concepts/pathlines.rst