Add ZnDraw in tutorials (#4975)

Partial fix for #4961 Description of changes: - add ZnDraw visualizer in most tutorials - reduce dependency on ffmpeg
espressomd · Aug 23, 2024 · 8db11b0 · 8db11b0
2 parents 3d5ca31 + efacee2
commit 8db11b0
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diff --git a/doc/tutorials/constant_pH/constant_pH.ipynb b/doc/tutorials/constant_pH/constant_pH.ipynb
@@ -153,6 +153,7 @@
     "import espressomd.electrostatics\n",
     "import espressomd.reaction_methods\n",
     "import espressomd.polymer\n",
+    "import espressomd.zn\n",
     "from espressomd.interactions import HarmonicBond"
    ]
   },
@@ -569,7 +570,7 @@
     "\n",
     "# add thermostat and short integration to let the system relax further\n",
     "system.thermostat.set_langevin(kT=KT_REDUCED, gamma=1.0, seed=7)\n",
-    "system.integrator.run(steps=1000)\n",
+    "system.integrator.run(1000)\n",
     "\n",
     "if USE_ELECTROSTATICS:\n",
     "    COULOMB_PREFACTOR=BJERRUM_LENGTH_REDUCED * KT_REDUCED\n",
@@ -739,6 +740,40 @@
    "outputs": [],
    "source": []
   },
+  {
+   "cell_type": "markdown",
+   "id": "cd417295-bab3-46a5-a574-fc60d06371a5",
+   "metadata": {},
+   "source": [
+    "We will initialize ZnDraw to visualize the simulation for increasing pH values:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "04dd303c",
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "color = {TYPES[\"HA\"]: \"#7fc454\", #green\n",
+    "         TYPES[\"A\"]: \"#225204\", #dark green\n",
+    "         TYPES[\"B\"]: \"#fca000\", #orange\n",
+    "         TYPES[\"Na\"]: \"#ff0000\", #red\n",
+    "         TYPES[\"Cl\"]: \"#030ffc\" #blue\n",
+    "        }\n",
+    "radii = {TYPES[\"HA\"]: 2,\n",
+    "         TYPES[\"A\"]: 2,\n",
+    "         TYPES[\"B\"]: 2,\n",
+    "         TYPES[\"Na\"]: 2,\n",
+    "         TYPES[\"Cl\"]: 2\n",
+    "        }\n",
+    "\n",
+    "vis = espressomd.zn.Visualizer(system, colors=color, radii=radii)\n",
+    "vis.update()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "07daa583",
@@ -778,11 +813,14 @@
    "outputs": [],
    "source": [
     "# SOLUTION CELL\n",
-    "def perform_sampling(type_A, num_samples, num_As:np.ndarray, reaction_steps, \n",
+    "def perform_sampling(type_A, num_samples, num_As:np.ndarray, reaction_steps,\n",
     "                     prob_integration=0.5, integration_steps=1000):\n",
     "    for i in range(num_samples):\n",
     "        if USE_WCA and np.random.random() < prob_integration:\n",
-    "            system.integrator.run(integration_steps)\n",
+    "            for _ in range(integration_steps):\n",
+    "                system.integrator.run(1)\n",
+    "            global vis\n",
+    "            vis.update()\n",
     "        # we should do at least one reaction attempt per reactive particle\n",
     "        RE.reaction(steps=reaction_steps)\n",
     "        num_As[i] = system.number_of_particles(type=type_A)"

diff --git a/doc/tutorials/electrodes/electrodes_part2.ipynb b/doc/tutorials/electrodes/electrodes_part2.ipynb
@@ -214,6 +214,7 @@
     "import espressomd.observables\n",
     "import espressomd.accumulators\n",
     "import espressomd.shapes\n",
+    "import espressomd.zn\n",
     "\n",
     "espressomd.assert_features(['WCA', 'ELECTROSTATICS'])\n",
     "rng = np.random.default_rng(42)\n",
@@ -476,20 +477,20 @@
    "source": [
     "# SOLUTION CELL\n",
     "offset = LJ_SIGMA # avoid unfavorable overlap at close distance to the walls\n",
-    "init_part_btw_z1 = offset \n",
+    "init_part_btw_z1 = offset\n",
     "init_part_btw_z2 = box_l_z - offset\n",
-    "ion_pos = np.empty((3), dtype=float)\n",
+    "ion_pos = np.empty((3,), dtype=float)\n",
     "\n",
-    "for i in range (N_IONPAIRS):\n",
-    "    ion_pos[0] = rng.random(1) * system.box_l[0]\n",
-    "    ion_pos[1] = rng.random(1) * system.box_l[1]\n",
-    "    ion_pos[2] = rng.random(1) * (init_part_btw_z2 - init_part_btw_z1) + init_part_btw_z1\n",
+    "for i in range(N_IONPAIRS):\n",
+    "    ion_pos[0] = rng.random(1)[0] * system.box_l[0]\n",
+    "    ion_pos[1] = rng.random(1)[0] * system.box_l[1]\n",
+    "    ion_pos[2] = rng.random(1)[0] * (init_part_btw_z2 - init_part_btw_z1) + init_part_btw_z1\n",
     "    system.part.add(pos=ion_pos, type=types[\"Cation\"], q=charges[\"Cation\"])\n",
-    "    \n",
-    "for i in range (N_IONPAIRS):\n",
-    "    ion_pos[0] = rng.random(1) * system.box_l[0]\n",
-    "    ion_pos[1] = rng.random(1) * system.box_l[1]\n",
-    "    ion_pos[2] = rng.random(1) * (init_part_btw_z2 - init_part_btw_z1) + init_part_btw_z1\n",
+    "\n",
+    "for i in range(N_IONPAIRS):\n",
+    "    ion_pos[0] = rng.random(1)[0] * system.box_l[0]\n",
+    "    ion_pos[1] = rng.random(1)[0] * system.box_l[1]\n",
+    "    ion_pos[2] = rng.random(1)[0] * (init_part_btw_z2 - init_part_btw_z1) + init_part_btw_z1\n",
     "    system.part.add(pos=ion_pos, type=types[\"Anion\"], q=charges[\"Anion\"])"
    ]
   },
@@ -1008,7 +1009,41 @@
     "\n",
     "With the above knowledge, we can now assess the \n",
     "differential capacitance of the system, by changing the applied voltage\n",
-    "difference and determining the corresponding surface charge density."
+    "difference and determining the corresponding surface charge density.\n",
+    "We will use ZnDraw to visualize our system:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ef5d908f-a7f0-4845-9555-34822128c141",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "color = {\n",
+    "    types[\"Cation\"]: \"#ff0000\", #red\n",
+    "    types[\"Anion\"]: \"#030ffc\" #blue\n",
+    "    }\n",
+    "    \n",
+    "radii = {\n",
+    "    types[\"Cation\"]: LJ_SIGMA,\n",
+    "    types[\"Anion\"]: LJ_SIGMA\n",
+    "    }\n",
+    "\n",
+    "vis = espressomd.zn.Visualizer(system, colors=color, radii=radii)\n",
+    "#vis.draw_constraints([floor, ceiling])\n",
+    "\n",
+    "# note: you may need to zoom out since the ELC gap region takes a significant portion of\n",
+    "# the box along the non-periodic direction. The particles are only in the smaller subsystem.\n",
+    "# note: The particles are shown bigger for visualization purpose."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "21da58e8-e666-4d06-8538-a8d6af521148",
+   "metadata": {},
+   "source": [
+    "Do the sampling from high to low potential:"
    ]
   },
   {
@@ -1029,7 +1064,9 @@
     "for potential_diff in tqdm.tqdm(np.linspace(MIN_PHI, MAX_PHI, N_PHI)[::-1]):\n",
     "    system.auto_update_accumulators.clear()\n",
     "    system.electrostatics.solver = setup_electrostatic_solver(potential_diff)\n",
-    "    system.integrator.run(N_SAMPLES_EQUIL_CAP * STEPS_PER_SAMPLE)\n",
+    "    for i in range(N_SAMPLES_EQUIL_CAP * STEPS_PER_SAMPLE//50):\n",
+    "        system.integrator.run(50)\n",
+    "        vis.update()\n",
     "    sigmas = []\n",
     "\n",
     "    for tm in range(N_SAMPLES_CAP):\n",
@@ -1039,7 +1076,9 @@
     "        system.auto_update_accumulators.clear()\n",
     "        system.auto_update_accumulators.add(density_accumulator_cation)\n",
     "        system.auto_update_accumulators.add(density_accumulator_anion)\n",
-    "        system.integrator.run(STEPS_PER_SAMPLE)\n",
+    "        for j in range(int(STEPS_PER_SAMPLE/50)):\n",
+    "            system.integrator.run(50)\n",
+    "            vis.update()\n",
     "\n",
     "        cation_profile_mean = density_accumulator_cation.mean()[0, 0, :]\n",
     "        anion_profile_mean = density_accumulator_anion.mean()[0, 0, :]\n",