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fix indent
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@chrisjonesBSU
chrisjonesBSU committed Aug 19, 2024
1 parent b69ae27 commit 99b590c
Showing 1 changed file with 50 additions and 25 deletions.
75 changes: 50 additions & 25 deletions tutorials/4-flowerMD-welding.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,9 @@
"metadata": {},
"outputs": [],
"source": [
" import warnings\n",
"warnings.filterwarnings('ignore')"
"import warnings\n",
"\n",
"warnings.filterwarnings(\"ignore\")"
]
},
{
Expand Down Expand Up @@ -97,9 +98,15 @@
"\n",
"system = Pack(\n",
" molecules=molecule,\n",
" density=1.1 * u.g/u.cm**3,\n",
" density=1.1 * u.g / u.cm**3,\n",
")\n",
"system.apply_forcefield(r_cut=2.5, force_field=OPLS_AA(), auto_scale=True,remove_charges=True, remove_hydrogens=True)"
"system.apply_forcefield(\n",
" r_cut=2.5,\n",
" force_field=OPLS_AA(),\n",
" auto_scale=True,\n",
" remove_charges=True,\n",
" remove_hydrogens=True,\n",
")"
]
},
{
Expand Down Expand Up @@ -134,7 +141,7 @@
"source": [
"sim = SlabSimulation.from_system(\n",
" system=system,\n",
" interface_axis=(1,0,0),\n",
" interface_axis=(1, 0, 0),\n",
" gsd_file_name=\"slab_x_interface.gsd\",\n",
")"
]
Expand Down Expand Up @@ -232,9 +239,13 @@
}
],
"source": [
"target_box = flowermd.utils.get_target_box_mass_density(density=1.2*u.g/u.cm**3, mass=sim.mass.to(\"g\"))\n",
"target_box = flowermd.utils.get_target_box_mass_density(\n",
" density=1.2 * u.g / u.cm**3, mass=sim.mass.to(\"g\")\n",
")\n",
"\n",
"sim.run_update_volume(final_box_lengths=target_box, n_steps=5e4, kT=5.0, period=100, tau_kt=0.001)"
"sim.run_update_volume(\n",
" final_box_lengths=target_box, n_steps=5e4, kT=5.0, period=100, tau_kt=0.001\n",
")"
]
},
{
Expand Down Expand Up @@ -294,7 +305,7 @@
}
],
"source": [
"sim.remove_walls(wall_axis=(1,0,0))\n",
"sim.remove_walls(wall_axis=(1, 0, 0))\n",
"sim.pickle_forcefield()\n",
"sim.flush_writers()"
]
Expand Down Expand Up @@ -328,7 +339,9 @@
}
],
"source": [
"sim_viewer = FresnelGSD(gsd_file=\"slab_x_interface.gsd\", view_axis=(0, 1, 0), frame=-1)\n",
"sim_viewer = FresnelGSD(\n",
" gsd_file=\"slab_x_interface.gsd\", view_axis=(0, 1, 0), frame=-1\n",
")\n",
"sim_viewer.view()"
]
},
Expand Down Expand Up @@ -392,7 +405,7 @@
}
],
"source": [
"sim_viewer.view_axis = (1,0,0)\n",
"sim_viewer.view_axis = (1, 0, 0)\n",
"sim_viewer.view()"
]
},
Expand Down Expand Up @@ -428,7 +441,9 @@
}
],
"source": [
"interface = Interface(gsd_files=[\"slab_x_interface.gsd\"], interface_axis=(1, 0, 0), gap=0.05)\n",
"interface = Interface(\n",
" gsd_files=[\"slab_x_interface.gsd\"], interface_axis=(1, 0, 0), gap=0.05\n",
")\n",
"\n",
"print(type(interface.hoomd_snapshot))\n",
"print(\"Slab number of particles:\", system.n_particles)\n",
Expand Down Expand Up @@ -512,7 +527,7 @@
" gsd_file_name=\"weld.gsd\",\n",
" log_file_name=\"weld_log.txt\",\n",
" log_write_freq=500,\n",
" dt=0.0003\n",
" dt=0.0003,\n",
")"
]
},
Expand Down Expand Up @@ -616,7 +631,9 @@
],
"source": [
"weld_sim.run_NVT(kT=10.0, n_steps=7e4, tau_kt=0.001)\n",
"cooling_ramp = weld_sim.temperature_ramp(n_steps=2e4, kT_start=10.0, kT_final=2.0)\n",
"cooling_ramp = weld_sim.temperature_ramp(\n",
" n_steps=2e4, kT_start=10.0, kT_final=2.0\n",
")\n",
"weld_sim.run_NVT(kT=cooling_ramp, n_steps=2e4, tau_kt=0.001)\n",
"weld_sim.save_restart_gsd(\"weld_restart.gsd\")\n",
"weld_sim.flush_writers()"
Expand Down Expand Up @@ -651,10 +668,12 @@
}
],
"source": [
"sim_viewer = FresnelGSD(gsd_file=\"weld.gsd\", view_axis=(0, 1, 0), frame=0, height=12)\n",
"sim_viewer = FresnelGSD(\n",
" gsd_file=\"weld.gsd\", view_axis=(0, 1, 0), frame=0, height=12\n",
")\n",
"weld_colors = np.zeros_like(sim_viewer.positions)\n",
"weld_colors[:weld_colors.shape[0]//2 + 1] = np.array([0.5, 0.25, 0.5])\n",
"weld_colors[weld_colors.shape[0]//2 + 1:] = np.array([0.5, 0.1, 0.1])\n",
"weld_colors[: weld_colors.shape[0] // 2 + 1] = np.array([0.5, 0.25, 0.5])\n",
"weld_colors[weld_colors.shape[0] // 2 + 1 :] = np.array([0.5, 0.1, 0.1])\n",
"sim_viewer.colors = weld_colors\n",
"sim_viewer.view(width=500, height=500)"
]
Expand Down Expand Up @@ -737,7 +756,9 @@
"sim_data = np.genfromtxt(\"weld_log.txt\", names=True)\n",
"lj_energy = sim_data[\"mdpairLJenergy\"]\n",
"time_step = sim_data[\"flowermdmodulesweldingWeldSimulationtimestep\"]\n",
"plt.plot(time_step, lj_energy/interface.hoomd_snapshot.particles.N, linewidth=3)\n",
"plt.plot(\n",
" time_step, lj_energy / interface.hoomd_snapshot.particles.N, linewidth=3\n",
")\n",
"plt.ylabel(\"$\\dfrac{\\epsilon}{N}$\", fontsize=15)\n",
"plt.xlabel(\"Time step\", fontsize=15)"
]
Expand Down Expand Up @@ -775,16 +796,16 @@
"# Open and load the forcefield picke file\n",
"with open(\"forcefield.pickle\", \"rb\") as f:\n",
" hoomd_forces = pickle.load(f)\n",
" \n",
"\n",
"tensile_sim = Tensile(\n",
" initial_state=\"weld_restart.gsd\",\n",
" forcefield=hoomd_forces,\n",
" tensile_axis=(1,0,0),\n",
" tensile_axis=(1, 0, 0),\n",
" gsd_file_name=\"tensile.gsd\",\n",
" gsd_write_freq=1000,\n",
" log_file_name=\"tensile_log.txt\",\n",
" log_write_freq=500,\n",
" fix_ratio=0.30\n",
" fix_ratio=0.30,\n",
")"
]
},
Expand Down Expand Up @@ -945,7 +966,9 @@
}
],
"source": [
"tensile_sim.run_tensile(n_steps=1e5, strain=0.30, period=500, kT=2.0, tau_kt=0.001)\n",
"tensile_sim.run_tensile(\n",
" n_steps=1e5, strain=0.30, period=500, kT=2.0, tau_kt=0.001\n",
")\n",
"tensile_sim.flush_writers()"
]
},
Expand Down Expand Up @@ -975,10 +998,12 @@
}
],
"source": [
"sim_viewer = FresnelGSD(gsd_file=\"tensile.gsd\", view_axis=(0, 1, 0), frame=0, height=12)\n",
"sim_viewer = FresnelGSD(\n",
" gsd_file=\"tensile.gsd\", view_axis=(0, 1, 0), frame=0, height=12\n",
")\n",
"weld_colors = np.zeros_like(sim_viewer.positions)\n",
"weld_colors[:weld_colors.shape[0]//2 + 1] = np.array([0.5, 0.25, 0.5])\n",
"weld_colors[weld_colors.shape[0]//2 + 1:] = np.array([0.5, 0.1, 0.1])\n",
"weld_colors[: weld_colors.shape[0] // 2 + 1] = np.array([0.5, 0.25, 0.5])\n",
"weld_colors[weld_colors.shape[0] // 2 + 1 :] = np.array([0.5, 0.1, 0.1])\n",
"sim_viewer.colors = weld_colors\n",
"sim_viewer.view(width=500, height=500)"
]
Expand Down Expand Up @@ -1059,7 +1084,7 @@
" new_x = snap.configuration.box[0]\n",
" strain = (new_x - initial_x_len) / initial_x_len\n",
" energy = snap.log[\"md/pair/LJ/energy\"]\n",
" plt.plot(strain, energy/snap.particles.N, \"ro\")\n",
" plt.plot(strain, energy / snap.particles.N, \"ro\")\n",
"\n",
"plt.show()"
]
Expand Down

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