Add ZnDraw in tutorials (#4975)

Partial fix for #4961

Description of changes:
- add ZnDraw visualizer in most tutorials
- reduce dependency on ffmpeg

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)"

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",