write time as int64 instead of uint64 and change int64 FILL_VALUE to np.iinfo(np.int64).min to fix #2180

Author: reint-fischer

docs/examples/tutorial_Argofloats.ipynb

@@ -41,11 +41,9 @@
     "\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",
+    "        p.dz += vertical_speed * dt\n",
+    "        p.cycle_phase = np.where(p.z + p.dz >= driftdepth, 1, p.cycle_phase)\n",
+    "        p.dz = np.where(p.z + p.dz >= driftdepth, driftdepth - p.z, p.dz)\n",
     "\n",
     "    SinkingPhase(particles[particles.cycle_phase == 0])\n",
     "\n",
@@ -67,11 +65,9 @@
     "\n",
     "    def SecondSinkingPhase(p):\n",
     "        \"\"\"Phase 2: Sinking further to maxdepth\"\"\"\n",
-    "        p.ddepth += vertical_speed * dt\n",
-    "        p.cycle_phase = np.where(p.depth + p.ddepth >= maxdepth, 3, p.cycle_phase)\n",
-    "        p.ddepth = np.where(\n",
-    "            p.depth + p.ddepth >= maxdepth, maxdepth - p.depth, p.ddepth\n",
-    "        )\n",
+    "        p.dz += vertical_speed * dt\n",
+    "        p.cycle_phase = np.where(p.z + p.dz >= maxdepth, 3, p.cycle_phase)\n",
+    "        p.dz = np.where(p.z + p.dz >= maxdepth, maxdepth - p.z, p.dz)\n",
     "\n",
     "    SecondSinkingPhase(particles[particles.cycle_phase == 2])\n",
     "\n",
@@ -81,15 +77,13 @@
     "\n",
     "    def RisingPhase(p):\n",
     "        \"\"\"Phase 3: Rising with vertical_speed until at surface\"\"\"\n",
-    "        p.ddepth -= vertical_speed * dt\n",
-    "        p.temp = fieldset.thetao[p.time, p.depth, p.lat, p.lon]\n",
-    "        p.cycle_phase = np.where(\n",
-    "            p.depth + p.ddepth <= fieldset.mindepth, 4, p.cycle_phase\n",
-    "        )\n",
-    "        p.ddepth = np.where(\n",
-    "            p.depth + p.ddepth <= fieldset.mindepth,\n",
-    "            fieldset.mindepth - p.depth,\n",
-    "            p.ddepth,\n",
+    "        p.dz -= vertical_speed * dt\n",
+    "        p.temp = fieldset.thetao[p.time, p.z, p.lat, p.lon]\n",
+    "        p.cycle_phase = np.where(p.z + p.dz <= fieldset.mindepth, 4, p.cycle_phase)\n",
+    "        p.dz = np.where(\n",
+    "            p.z + p.dz <= fieldset.mindepth,\n",
+    "            fieldset.mindepth - p.z,\n",
+    "            p.dz,\n",
     "        )\n",
     "\n",
     "    RisingPhase(particles[particles.cycle_phase == 3])\n",
@@ -163,7 +157,7 @@
     "    pclass=ArgoParticle,\n",
     "    lon=[32],\n",
     "    lat=[-31],\n",
-    "    depth=[fieldset.mindepth],\n",
+    "    z=[fieldset.mindepth],\n",
     ")\n",
     "\n",
     "# combine Argo vertical movement kernel with built-in Advection kernel\n",
@@ -209,9 +203,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds_out = xr.open_zarr(\n",
-    "    output_file.store, decode_times=False\n",
-    ")  # TODO fix without using decode_times=False\n",
+    "ds_out = xr.open_zarr(output_file.store)\n",
     "x = ds_out[\"lon\"][:].squeeze()\n",
     "y = ds_out[\"lat\"][:].squeeze()\n",
     "z = ds_out[\"z\"][:].squeeze()\n",

docs/examples/tutorial_sampling.ipynb

@@ -96,7 +96,7 @@
     "time = np.repeat(\n",
     "    ds.time.values[0], npart\n",
     ")  # release all particles at the start time of the fieldset\n",
-    "depth = np.repeat(ds.depth.values[0], npart)\n",
+    "z = np.repeat(ds.depth.values[0], npart)\n",
     "\n",
     "# Plot temperature field and initial particle locations\n",
     "plt.figure()\n",
@@ -135,7 +135,7 @@
     "\n",
     "def SampleT(particles, fieldset):\n",
     "    particles.temperature = fieldset.thetao[\n",
-    "        particles.time, particles.depth, particles.lat, particles.lon\n",
+    "        particles.time, particles.z, particles.lat, particles.lon\n",
     "    ]"
    ]
   },
@@ -154,7 +154,7 @@
    "outputs": [],
    "source": [
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=SampleParticle, lon=lon, lat=lat, time=time, depth=depth\n",
+    "    fieldset=fieldset, pclass=SampleParticle, lon=lon, lat=lat, time=time, z=z\n",
     ")\n",
     "\n",
     "output_file = parcels.ParticleFile(\"SampleTemp.zarr\", outputdt=timedelta(hours=1))\n",
@@ -181,7 +181,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Particle_data = xr.open_zarr(\"SampleTemp.zarr\", decode_times=False)\n",
+    "Particle_data = xr.open_zarr(\"SampleTemp.zarr\")\n",
     "\n",
     "plt.figure()\n",
     "ax = plt.axes()\n",
@@ -228,7 +228,7 @@
     "\n",
     "\n",
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.Particle, lon=lon, lat=lat, time=time, depth=depth\n",
+    "    fieldset=fieldset, pclass=parcels.Particle, lon=lon, lat=lat, time=time, z=z\n",
     ")\n",
     "\n",
     "pset.execute(\n",
@@ -257,7 +257,7 @@
     "\n",
     "\n",
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.Particle, lon=lon, lat=lat, time=time, depth=depth\n",
+    "    fieldset=fieldset, pclass=parcels.Particle, lon=lon, lat=lat, time=time, z=z\n",
     ")\n",
     "\n",
     "pset.execute(SampleVel_correct, runtime=timedelta(hours=30), dt=timedelta(minutes=5))"
@@ -331,7 +331,7 @@
     "    lon=lon,\n",
     "    lat=lat,\n",
     "    time=time,\n",
-    "    depth=depth,\n",
+    "    z=z,\n",
     ")"
    ]
   },
@@ -406,7 +406,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.11.0"
   },
   "pycharm": {
    "stem_cell": {

src/parcels/_core/particlefile.py

@@ -32,7 +32,7 @@
     np.dtype(np.int8): np.iinfo(np.int8).max,
     np.dtype(np.int16): np.iinfo(np.int16).max,
     np.dtype(np.int32): np.iinfo(np.int32).max,
-    np.dtype(np.int64): np.iinfo(np.int64).max,
+    np.dtype(np.int64): np.iinfo(np.int64).min,
     np.dtype(np.uint8): np.iinfo(np.uint8).max,
     np.dtype(np.uint16): np.iinfo(np.uint16).max,
     np.dtype(np.uint32): np.iinfo(np.uint32).max,
@@ -335,7 +335,7 @@ def _maybe_convert_time_dtype(dtype: np.dtype | _SAME_AS_FIELDSET_TIME_INTERVAL)
     """Convert the dtype of time to float64 if it is not already."""
     if dtype is _SAME_AS_FIELDSET_TIME_INTERVAL.VALUE:
         return np.dtype(
-            np.uint64
+            np.int64
         )  #! We need to have here some proper mechanism for converting particle data to the data that is to be output to zarr (namely the time needs to be converted to float seconds by subtracting the time_interval.left)
     return dtype