add poiseuille.py script for ESPResSo

ESPResSo/poiseuille.py

@@ -0,0 +1,107 @@
+#
+# Copyright (C) 2010-2022 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+"""
+Visualize the Poiseuille flow in a lattice-Boltzmann fluid with an
+external force applied. The CPU implementation runs best on 8 cores.
+The GPU implementation only needs 1 core.
+"""
+
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+import mpl_ascii
+import argparse
+import numpy as np
+import tqdm
+import espressomd
+import espressomd.lb
+import espressomd.lbboundaries
+import espressomd.shapes
+
+mpl_ascii.AXES_WIDTH=100
+mpl_ascii.AXES_HEIGHT=24
+mpl.use("module://mpl_ascii")
+
+parser = argparse.ArgumentParser(description="Poiseuille flow in a rectangular channel.")
+parser.add_argument("--gpu", default=False, action="store_true")
+args = parser.parse_args()
+
+required_features = ["LB_BOUNDARIES", "EXTERNAL_FORCES"]
+if args.gpu:
+    required_features += ["CUDA", "LB_BOUNDARIES_GPU"]
+espressomd.assert_features(required_features)
+
+BOX_L = 16.0
+TIME_STEP = 0.01
+AGRID = 0.5
+VISCOSITY = 2.0
+FORCE_DENSITY = [0.0, 0.001, 0.0]
+DENSITY = 1.5
+WALL_OFFSET = AGRID
+HEIGHT = BOX_L - 2.0 * AGRID
+
+def poiseuille_flow(x, force_density, dynamic_viscosity, height):
+    return force_density / (2 * dynamic_viscosity) * (height**2 / 4 - x**2)
+
+system = espressomd.System(box_l=[BOX_L] * 3)
+system.time_step = TIME_STEP
+system.cell_system.skin = 0.4
+
+if args.gpu:
+    LBFluid = espressomd.lb.LBFluidGPU
+else:
+    LBFluid = espressomd.lb.LBFluid
+lbf = LBFluid(agrid=AGRID, dens=DENSITY, visc=VISCOSITY,
+              tau=TIME_STEP, ext_force_density=FORCE_DENSITY)
+system.actors.add(lbf)
+top_wall = espressomd.shapes.Wall(normal=[1, 0, 0], dist=WALL_OFFSET)
+bottom_wall = espressomd.shapes.Wall(normal=[-1, 0, 0], dist=-(BOX_L - WALL_OFFSET))
+top_boundary = espressomd.lbboundaries.LBBoundary(shape=top_wall)
+bottom_boundary = espressomd.lbboundaries.LBBoundary(shape=bottom_wall)
+system.lbboundaries.add(top_boundary)
+system.lbboundaries.add(bottom_boundary)
+
+sim_xdata = (np.arange(lbf.shape[0]) + 0.5) * AGRID
+sim_ydata_list = []
+for i in tqdm.trange(30):
+    system.integrator.run(50)
+    if (i + 1) % 10 == 0:
+        fluid_velocities = (lbf[:,:,:].velocity)[:,:,:,1]
+        fluid_velocities = np.average(fluid_velocities, axis=(1,2))
+        sim_ydata_list.append((system.time, fluid_velocities))
+
+ref_xdata = np.linspace(0.0, BOX_L, lbf.shape[0])
+ref_ydata = poiseuille_flow(ref_xdata - (HEIGHT / 2 + AGRID), FORCE_DENSITY[1],
+                           VISCOSITY * DENSITY, HEIGHT)
+# velocity is zero inside the walls
+ref_ydata[np.nonzero(ref_xdata < WALL_OFFSET)] = 0.0
+ref_ydata[np.nonzero(ref_xdata > BOX_L - WALL_OFFSET)] = 0.0
+
+print("\n\n")
+
+fig, ax = plt.subplots()
+ax.scatter(ref_xdata, ref_ydata, label="Analytical solution")
+for sim_time, sim_ydata in sim_ydata_list[::-1]:
+    ax.scatter(sim_xdata, sim_ydata,  label=f"Simulation at t={sim_time:.0f}")
+
+ax.set_title("Poiseuille flow in a rectangular channel")
+ax.set_xlabel("Position on the x-axis")
+ax.set_ylabel("v")
+ax.legend(title=None)
+plt.show()

ESPResSo/run_plate.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+set -e
+
+if [[ $EESSI_CVMFS_REPO == "/cvmfs/software.eessi.io" ]] && [[ $EESSI_VERSION == "2023.06" ]]; then
+    module load ESPResSo/4.2.2-foss-2023a-CUDA-12.1.1
+    module load matplotlib/3.7.2-gfbf-2023a
+    module load tqdm/4.66.1-GCCcore-12.3.0
+    module load mpl-ascii/0.10.0-gfbf-2023a
+else echo "Don't know which ESPResSo module to load for ${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}" >&2; exit 1
+fi
+
+python poiseuille.py --gpu