load scene when both client and webpage are ready

examples/md.ipynb

@@ -0,0 +1,105 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Molecular Dynamics Simulation\n",
+    "\n",
+    "In this example we will run an MD simulation using ASE and visualise it using ZnDraw."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from zndraw import ZnDraw\n",
+    "\n",
+    "from ase.lattice.cubic import FaceCenteredCubic\n",
+    "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n",
+    "from ase.md.verlet import VelocityVerlet\n",
+    "from ase import units\n",
+    "\n",
+    "from ase.calculators.emt import EMT\n",
+    "size = 2\n",
+    "\n",
+    "# Set up a crystal\n",
+    "atoms = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],\n",
+    "                          symbol=\"Cu\",\n",
+    "                          size=(size, size, size),\n",
+    "                          pbc=True)\n",
+    "\n",
+    "# Describe the interatomic interactions with the Effective Medium Theory\n",
+    "atoms.calc = EMT()\n",
+    "\n",
+    "# Set the momenta corresponding to T=300K\n",
+    "MaxwellBoltzmannDistribution(atoms, temperature_K=300)\n",
+    "\n",
+    "# We want to run MD with constant energy using the VelocityVerlet algorithm.\n",
+    "dyn = VelocityVerlet(atoms, 5 * units.fs)  # 5 fs time step.\n",
+    "\n",
+    "\n",
+    "def printenergy(a=atoms):  # store a reference to atoms in the definition.\n",
+    "    \"\"\"Function to print the potential, kinetic and total energy.\"\"\"\n",
+    "    epot = a.get_potential_energy() / len(a)\n",
+    "    ekin = a.get_kinetic_energy() / len(a)\n",
+    "    print('Energy per atom: Epot = %.3feV  Ekin = %.3feV (T=%3.0fK)  '\n",
+    "          'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vis = ZnDraw(url=\"http://localhost:1234\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Now run the dynamics\n",
+    "\n",
+    "# dyn.attach(printenergy, interval=1)\n",
+    "dyn.attach(lambda: vis.append(atoms), interval=1)\n",
+    "printenergy()\n",
+    "dyn.run(200)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "zndraw",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.11"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

zndraw/app.py

@@ -56,9 +56,12 @@ def on_join(data):
     """Join a room."""
     try:
         join_room(session["uuid"])
+        print(f"Client for webpage joined room {session['uuid']}")
     except KeyError:
         session["uuid"] = data["uuid"]
         join_room(session["uuid"])
+        print(f"Client from 'zndraw.ZnDraw' joined room {session['uuid']}")
+    emit("join", {}, include_self=False, to=session["uuid"])
 
 
 @app.route("/exit")
@@ -186,12 +189,6 @@ class Scene(BaseModel):
     return schema
 
 
-@io.on("atoms:request")
-def atoms_request(url):
-    """Return the atoms."""
-    emit("atoms:request", url, include_self=False, to=session["uuid"])
-
-
 @io.on("modifier:run")
 def modifier_run(data):
     emit("modifier:run", data, include_self=False, to=session["uuid"])

zndraw/static/main.js

@@ -28,23 +28,15 @@ function main() {
 
   // creata a function displayIncomingAtoms that calls cache.get_length(), if larger 1 call world.setStep(0), else setTimerout(displayIncomingAtoms, 1000)
 
-  const displayIncomingAtoms = () => {
-    cache.get_length();
-    if (cache.get_length() > 0) {
-      world.setStep(0);
-      document.getElementById("atom-spinner").style.display = "none";
-    } else {
-      setTimeout(displayIncomingAtoms, 100);
-    }
-  };
-
-  socket.emit("atoms:request", window.location.href, () => {
-    displayIncomingAtoms();
+  socket.on("join", () => {
+    socket.emit("join", {}); // we send an ACK to the server, so that it can send us the atoms
   });
 
   socket.on("message:log", (msg) => {
     console.log(msg);
   });
+
+  document.getElementById("atom-spinner").style.display = "none";
 }
 
 main();

zndraw/zndraw.py

@@ -45,7 +45,7 @@ def on_answer(data):
 
 @dataclasses.dataclass
 class FileIO:
-    name: str
+    name: str = None
     start: int = 0
     stop: int = None
     step: int = 1
@@ -59,7 +59,7 @@ class ZnDraw(collections.abc.MutableSequence):
     bonds_calculator: ASEComputeBonds = dataclasses.field(
         default_factory=ASEComputeBonds
     )
-    file: FileIO = None
+    file: FileIO = dataclasses.field(default_factory=FileIO)
     wait: bool = False
     token: str = "default"
 
@@ -99,8 +99,8 @@ def __post_init__(self):
             )
 
             self.socket.on(
-                "atoms:request",
-                lambda url: self.read(
+                "join",
+                lambda *args: self.read(
                     self.file.name, self.file.start, self.file.stop, self.file.step
                 ),
             )