Separating each Argo phase into its own Kernel

This fixes the issue that the cycle_phase is not updated correctly

Author: erikvansebille

docs/examples/tutorial_Argofloats.ipynb

@@ -24,33 +24,45 @@
    "source": [
     "import numpy as np\n",
     "\n",
+    "# Define the new Kernels that mimic Argo vertical movement\n",
+    "driftdepth = 1000  # maximum depth in m\n",
+    "maxdepth = 2000  # maximum depth in m\n",
+    "vertical_speed = 0.10  # sink and rise speed in m/s\n",
+    "cycletime = (\n",
+    "    10 * 86400\n",
+    ")  # total time of cycle in seconds  # TODO update to \"timedelta64[s]\"\n",
+    "drifttime = 9 * 86400  # time of deep drift in seconds\n",
     "\n",
-    "# Define the new Kernel that mimics Argo vertical movement\n",
-    "def ArgoVerticalMovement(particles, fieldset):\n",
-    "    driftdepth = 1000  # maximum depth in m\n",
-    "    maxdepth = 2000  # maximum depth in m\n",
-    "    vertical_speed = 0.10  # sink and rise speed in m/s\n",
-    "    cycletime = (\n",
-    "        10 * 86400\n",
-    "    )  # total time of cycle in seconds  # TODO update to \"timedelta64[s]\"\n",
-    "    drifttime = 9 * 86400  # time of deep drift in seconds\n",
     "\n",
+    "def ArgoPhase1(particles, fieldset):\n",
     "    dt = particles.dt / np.timedelta64(1, \"s\")  # convert dt to seconds\n",
     "\n",
-    "    def SinkPhase(p):\n",
+    "    def SinkingPhase(p):\n",
     "        \"\"\"Phase 0: Sinking with vertical_speed until depth is driftdepth\"\"\"\n",
     "        p.ddepth += vertical_speed * dt\n",
     "        p.cycle_phase = np.where(p.depth + p.ddepth >= driftdepth, 1, p.cycle_phase)\n",
     "        p.ddepth = np.where(\n",
     "            p.depth + p.ddepth >= driftdepth, driftdepth - p.depth, p.ddepth\n",
     "        )\n",
     "\n",
+    "    SinkingPhase(particles[particles.cycle_phase == 0])\n",
+    "\n",
+    "\n",
+    "def ArgoPhase2(particles, fieldset):\n",
+    "    dt = particles.dt / np.timedelta64(1, \"s\")  # convert dt to seconds\n",
+    "\n",
     "    def DriftingPhase(p):\n",
     "        \"\"\"Phase 1: Drifting at depth for drifttime seconds\"\"\"\n",
     "        p.drift_age += dt\n",
     "        p.cycle_phase = np.where(p.drift_age >= drifttime, 2, p.cycle_phase)\n",
     "        p.drift_age = np.where(p.drift_age >= drifttime, 0, p.drift_age)\n",
     "\n",
+    "    DriftingPhase(particles[particles.cycle_phase == 1])\n",
+    "\n",
+    "\n",
+    "def ArgoPhase3(particles, fieldset):\n",
+    "    dt = particles.dt / np.timedelta64(1, \"s\")  # convert dt to seconds\n",
+    "\n",
     "    def SecondSinkingPhase(p):\n",
     "        \"\"\"Phase 2: Sinking further to maxdepth\"\"\"\n",
     "        p.ddepth += vertical_speed * dt\n",
@@ -59,6 +71,12 @@
     "            p.depth + p.ddepth >= maxdepth, maxdepth - p.depth, p.ddepth\n",
     "        )\n",
     "\n",
+    "    SecondSinkingPhase(particles[particles.cycle_phase == 2])\n",
+    "\n",
+    "\n",
+    "def ArgoPhase4(particles, fieldset):\n",
+    "    dt = particles.dt / np.timedelta64(1, \"s\")  # convert dt to seconds\n",
+    "\n",
     "    def RisingPhase(p):\n",
     "        \"\"\"Phase 3: Rising with vertical_speed until at surface\"\"\"\n",
     "        p.ddepth -= vertical_speed * dt\n",
@@ -67,17 +85,20 @@
     "            p.depth + p.ddepth <= fieldset.mindepth, 4, p.cycle_phase\n",
     "        )\n",
     "\n",
-    "    def TransmitPhase(p):\n",
+    "    RisingPhase(particles[particles.cycle_phase == 3])\n",
+    "\n",
+    "\n",
+    "def ArgoPhase5(particles, fieldset):\n",
+    "    def TransmittingPhase(p):\n",
     "        \"\"\"Phase 4: Transmitting at surface until cycletime is reached\"\"\"\n",
     "        p.cycle_phase = np.where(p.cycle_age >= cycletime, 0, p.cycle_phase)\n",
     "        p.cycle_age = np.where(p.cycle_age >= cycletime, 0, p.cycle_age)\n",
     "\n",
-    "    SinkPhase(particles[particles.cycle_phase == 0])\n",
-    "    DriftingPhase(particles[particles.cycle_phase == 1])\n",
-    "    SecondSinkingPhase(particles[particles.cycle_phase == 2])\n",
-    "    RisingPhase(particles[particles.cycle_phase == 3])\n",
-    "    TransmitPhase(particles[particles.cycle_phase == 4])\n",
+    "    TransmittingPhase(particles[particles.cycle_phase == 4])\n",
+    "\n",
     "\n",
+    "def ArgoPhase6(particles, fieldset):\n",
+    "    dt = particles.dt / np.timedelta64(1, \"s\")  # convert dt to seconds\n",
     "    particles.cycle_age += dt  # update cycle_age"
    ]
   },
@@ -162,7 +183,15 @@
     ")\n",
     "\n",
     "# combine Argo vertical movement kernel with built-in Advection kernel\n",
-    "kernels = [ArgoVerticalMovement, parcels.AdvectionRK4]\n",
+    "kernels = [\n",
+    "    ArgoPhase1,\n",
+    "    ArgoPhase2,\n",
+    "    ArgoPhase3,\n",
+    "    ArgoPhase4,\n",
+    "    ArgoPhase5,\n",
+    "    ArgoPhase6,\n",
+    "    parcels.AdvectionRK4,\n",
+    "]\n",
     "\n",
     "# Create a ParticleFile object to store the output\n",
     "output_file = parcels.ParticleFile(\n",