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Add ZnDraw in tutorials #4975

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Aug 23, 2024
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Add ZnDraw in tutorials #4975

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cfa136a
Add Zndraw in tutorials
RebeccaStephan Aug 12, 2024
efacee2
Edit and format tutorials
jngrad Aug 23, 2024
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44 changes: 41 additions & 3 deletions doc/tutorials/constant_pH/constant_pH.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
]
},
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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)"
Expand Down
67 changes: 53 additions & 14 deletions doc/tutorials/electrodes/electrodes_part2.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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\"])"
]
},
Expand Down Expand Up @@ -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:"
]
},
{
Expand All @@ -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",
Expand All @@ -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",
Expand Down
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