Changing the meaning of the lower bound of the snapshots attribute

stammler · May 16, 2024 · 4ddb0c2 · 4ddb0c2
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diff --git a/examples/1_simple_integration.ipynb b/examples/1_simple_integration.ipynb
@@ -380,7 +380,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In addition to that, the integration variable needs to know about snapshots, i.e. points in space or time, when data should be written. Even you don't want to write data, you need to give at least one fineal value, because `simframe` needs to know when to stop the calculation. The snapshots have to be either a list or an array with the desired snapshots in increasing order."
+    "In addition to that, the integration variable needs to know about snapshots, i.e. points in space or time, when data should be written. Even you don't want to write data, you need to give at least one fineal value, because `simframe` needs to know when to stop the calculation. The snapshots have to be either a list or an array with the desired snapshots in increasing order. If you want `simframe` to write out the initial conditions, the snapshots need to contain the initial values of your integrations variable."
    ]
   },
   {
@@ -389,7 +389,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim.x.snapshots = np.linspace(1., 10., 10)"
+    "sim.x.snapshots = np.linspace(0., 10., 11)"
    ]
   },
   {
@@ -618,7 +618,7 @@
        "------------------------------------\n",
        "    Data directory : data\n",
        "    File names     : data/data0000.hdf5\n",
-       "    Overwrite      : False\n",
+       "    Overwrite      : \u001b[93mFalse\u001b[0m\n",
        "    Dumping        : True\n",
        "    Options        : {'com': 'lzf', 'comopts': None}\n",
        "    Verbosity      : 1"
@@ -677,7 +677,7 @@
        "------------------------------------\n",
        "    Data directory : 1_data\n",
        "    File names     : 1_data/data0000.hdf5\n",
-       "    Overwrite      : \u001b[93mTrue\u001b[0m\n",
+       "    Overwrite      : True\n",
        "    Dumping        : True\n",
        "    Options        : {'com': 'lzf', 'comopts': None}\n",
        "    Verbosity      : 1"
@@ -717,6 +717,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "Creating data directory 1_data.\n",
       "Writing file \u001b[94m1_data/data0000.hdf5\u001b[0m\n",
       "Writing dump file \u001b[94m1_data/frame.dmp\u001b[0m\n",
       "Writing file \u001b[94m1_data/data0001.hdf5\u001b[0m\n",
@@ -1094,7 +1095,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim_cont.x.snapshots = np.linspace(1., 20., 20)"
+    "sim_cont.x.snapshots = np.linspace(0., 20., 21)"
    ]
   },
   {

diff --git a/examples/2_advanced_integration.ipynb b/examples/2_advanced_integration.ipynb
@@ -460,14 +460,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim.t.snapshots = np.arange(snapwidth, tmax, snapwidth)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "**Note:** If the initial value of the integration variable is smaller the first snapshot, `simframe` automatically writes an output with initial conditions, if a writer is set."
+    "sim.t.snapshots = np.arange(0., tmax, snapwidth)"
    ]
   },
   {
@@ -996,7 +989,7 @@
       "Saving frame 0071\n",
       "Saving frame 0072\n",
       "Saving frame 0073\n",
-      "Execution time: \u001b[94m0:00:00\u001b[0m\n"
+      "Execution time: \u001b[94m0:00:01\u001b[0m\n"
      ]
     }
    ],
@@ -1167,7 +1160,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Execution time: \u001b[94m0:00:00\u001b[0m\n"
+      "Execution time: \u001b[94m0:00:02\u001b[0m\n"
      ]
     }
    ],

diff --git a/examples/3_updating.ipynb b/examples/3_updating.ipynb
@@ -186,7 +186,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim.t.snapshots = np.arange(snapwidth, tmax+1, snapwidth)"
+    "sim.t.snapshots = np.arange(0., tmax, snapwidth)"
    ]
   },
   {
@@ -435,7 +435,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Execution time: \u001b[94m0:00:00\u001b[0m\n"
+      "Execution time: \u001b[94m0:00:01\u001b[0m\n"
      ]
     }
    ],
@@ -1071,9 +1071,9 @@
        "Heartbeat\n",
        "---------\n",
        "\n",
-       "\u001b[91mSystole: \u001b[0m <function T_sys at 0x7f6f8bb1d9e0>\n",
-       "\u001b[91mUpdater: \u001b[0m <function T at 0x7f6f8a5aaf20>\n",
-       "\u001b[91mDiastole:\u001b[0m <function T_dia at 0x7f6f8bb1da80>\n",
+       "\u001b[91mSystole: \u001b[0m <function T_sys at 0x7f7dbd6de660>\n",
+       "\u001b[91mUpdater: \u001b[0m <function T at 0x7f7dbd087600>\n",
+       "\u001b[91mDiastole:\u001b[0m <function T_dia at 0x7f7dbd6de7a0>\n",
        "\n",
        "Docstrings\n",
        "----------\n",
@@ -1122,7 +1122,7 @@
        "    msg = \"{:6s}: T = {:5.1f} K\".format(\"Before\", sim.Earth.T)\n",
        "    print(msg)\n",
        "\n",
-       "\u001b[91mFile:\u001b[0m /tmp/ipykernel_23644/2382827243.py\n",
+       "\u001b[91mFile:\u001b[0m /tmp/ipykernel_11686/2382827243.py\n",
        "\u001b[91mType:\u001b[0m function"
       ]
      },
@@ -1152,7 +1152,7 @@
        "    \"\"\"Function computes the equilibrium temperature of the Earth\"\"\"\n",
        "    return frame.Sun.T * (frame.Sun.R**2 / (4.*frame.Earth.d**2))**0.25\n",
        "\n",
-       "\u001b[91mFile:\u001b[0m /tmp/ipykernel_23644/4057753429.py\n",
+       "\u001b[91mFile:\u001b[0m /tmp/ipykernel_11686/4057753429.py\n",
        "\u001b[91mType:\u001b[0m function"
       ]
      },

diff --git a/examples/5_adaptive_schemes.ipynb b/examples/5_adaptive_schemes.ipynb
@@ -192,7 +192,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "sim.x.snapshots = np.arange(dx, 15., dx)"
+    "sim.x.snapshots = np.arange(0., 15., dx)"
    ]
   },
   {

diff --git a/examples/6_implicit_integration.ipynb b/examples/6_implicit_integration.ipynb
@@ -122,7 +122,7 @@
     "def fdx(frame):\n",
     "    return dx\n",
     "sim_expl.x.updater = fdx\n",
-    "sim_expl.x.snapshots = [10.]"
+    "sim_expl.x.snapshots = [0., 10.]"
    ]
   },
   {

diff --git a/examples/C_changelog.ipynb b/examples/C_changelog.ipynb
@@ -34,7 +34,15 @@
     "\n",
     "#### Squeezing zero-dimensional Fields\n",
     "\n",
-    "When initializing field with scalar values, zero-dimensional arrays, or one-dimensional arrays of size one, the field will now be squeezed to shape `()`, since the previous behavior was inconsistent in these cases."
+    "When initializing field with scalar values, zero-dimensional arrays, or one-dimensional arrays of size one, the field will now be squeezed to shape `()`, since the previous behavior was inconsistent in these cases.\n",
+    "\n",
+    "#### Allowing for `Path` objects\n",
+    "\n",
+    "The `datadir` attribute of the `Writer` class can now also take `pathlib.Path` objects in addition to strings.\n",
+    "\n",
+    "#### Range of `snapshots`\n",
+    "\n",
+    "The `snapshots` attribute of the `Integrationvariable` class now also needs to contain the values of the initial conditions. Previously `simframe` was automatically writing the initial conditions if the integration variable was below the lower bound of the `snapshots` array. This was ambiguous if the simulation was interupted and restarted before it reached the first desired snapshot."
    ]
   },
   {

diff --git a/examples/example_compartmental_models.ipynb b/examples/example_compartmental_models.ipynb
@@ -438,7 +438,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim.t.snapshots = np.arange(1., 366., 1.)"
+    "sim.t.snapshots = np.arange(0., 366., 1.)"
    ]
   },
   {
@@ -633,7 +633,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Execution time: \u001b[94m0:00:01\u001b[0m\n"
+      "Execution time: \u001b[94m0:00:00\u001b[0m\n"
      ]
     }
    ],
@@ -903,7 +903,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Execution time: \u001b[94m0:00:01\u001b[0m\n"
+      "Execution time: \u001b[94m0:00:00\u001b[0m\n"
      ]
     }
    ],
@@ -1681,7 +1681,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim.t.snapshots = np.arange(1., 181., 1.)"
+    "sim.t.snapshots = np.arange(0., 181., 1.)"
    ]
   },
   {

diff --git a/examples/example_coupled_oscillators.ipynb b/examples/example_coupled_oscillators.ipynb
diff --git a/examples/example_double_pendulum.ipynb b/examples/example_double_pendulum.ipynb
diff --git a/examples/example_nbody.ipynb b/examples/example_nbody.ipynb
diff --git a/simframe/frame/frame.py b/simframe/frame/frame.py
@@ -136,8 +136,8 @@ def run(self):
         # Timekeeping
         tini = monotonic()
 
-        # Write initial conditions
-        if self.integrator.var < self.integrator.var.snapshots[0]:
+        # Write initial conditions if at first given snapshot
+        if self.integrator.var == self.integrator.var.snapshots[0]:
             self.writeoutput(0)
 
         # Staring index of snapshots
@@ -168,7 +168,7 @@ def run(self):
             if self.verbosity > 1:
                 self.progressbar._reset()
 
-            self.writeoutput(i + 1)
+            self.writeoutput(i)
 
         # Timekeeping
         tfin = monotonic()

diff --git a/tests/io/test_namespacewriter.py b/tests/io/test_namespacewriter.py
@@ -39,7 +39,7 @@ def dYdx(f, x, Y):
     def dx(f):
         return 1.
     f.x.updater = dx
-    f.x.snapshots = [1.]
+    f.x.snapshots = [0., 1.]
     f.integrator = Integrator(f.x)
     f.integrator.instructions = [Instruction(schemes.expl_1_euler, f.Y)]
     f.writer = writers.namespacewriter()

diff --git a/tests/io/test_reader.py b/tests/io/test_reader.py
@@ -63,7 +63,7 @@ def dYdx(f, x, Y):
     def dx(f):
         return 1.
     f.x.updater = dx
-    f.x.snapshots = [1.]
+    f.x.snapshots = [0., 1.]
     f.integrator = Integrator(f.x)
     f.integrator.instructions = [Instruction(schemes.expl_1_euler, f.Y)]
     f.writer = writers.hdf5writer()