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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| # | ||
| # Copyright (C) 2013-2019 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/>. | ||
| # | ||
|
|
||
| """ | ||
| Benchmark Lattice-Boltzmann fluid + Lennard-Jones particles | ||
| """ | ||
| import os | ||
| import sys | ||
| import numpy as np | ||
| from time import time | ||
| import argparse | ||
|
|
||
| parser = argparse.ArgumentParser(description="Benchmark LB simulations. " | ||
| "Save the results to a CSV file.") | ||
| parser.add_argument("--particles_per_core", metavar="N", action="store", | ||
| type=int, default=125, required=False, | ||
| help="Number of particles in the simulation box") | ||
| parser.add_argument("--lb_sites_per_particle", metavar="N_LB", action="store", | ||
| type=float, default=28, required=False, | ||
| help="Number of particles in the simulation box") | ||
| parser.add_argument("--volume_fraction", metavar="FRAC", action="store", | ||
| type=float, default=0.03, required=False, | ||
| help="Fraction of the simulation box volume occupied by " | ||
| "particles (range: [0.01-0.74], default: 0.50)") | ||
| group = parser.add_mutually_exclusive_group() | ||
| group.add_argument("--output", metavar="FILEPATH", action="store", | ||
| type=str, required=False, default="benchmarks.csv", | ||
| help="Output file (default: benchmarks.csv)") | ||
|
|
||
| args = parser.parse_args() | ||
|
|
||
| # process and check arguments | ||
| n_iterations = 30 | ||
| assert args.volume_fraction > 0, "volume_fraction must be a positive number" | ||
| assert args.volume_fraction < np.pi / (3 * np.sqrt(2)), \ | ||
| "volume_fraction exceeds the physical limit of sphere packing (~0.74)" | ||
|
|
||
|
|
||
| import espressomd | ||
| required_features = ["LENNARD_JONES"] | ||
| espressomd.assert_features(required_features) | ||
|
|
||
|
|
||
| # System | ||
| ############################################################# | ||
| system = espressomd.System(box_l=[1, 1, 1]) | ||
|
|
||
| # Interaction parameters (Lennard-Jones) | ||
| ############################################################# | ||
|
|
||
| lj_eps = 1.0 # LJ epsilon | ||
| lj_sig = 1.0 # particle diameter | ||
| lj_cut = lj_sig * 2**(1. / 6.) # cutoff distance | ||
|
|
||
| # System parameters | ||
| ############################################################# | ||
|
|
||
| n_proc = system.cell_system.get_state()['n_nodes'] | ||
| n_part = n_proc * args.particles_per_core | ||
| # volume of N spheres with radius r: N * (4/3*pi*r^3) | ||
| box_l = (n_part * 4. / 3. * np.pi * (lj_sig / 2.)**3 | ||
| / args.volume_fraction)**(1. / 3.) | ||
| lb_grid = int((round(n_part * args.lb_sites_per_particle)**(1. / 3))) | ||
| agrid = box_l / lb_grid | ||
| measurement_steps = int(max(120**3 / lb_grid**3, 50)) | ||
|
|
||
| # System | ||
| ############################################################# | ||
| system.box_l = 3 * (box_l,) | ||
|
|
||
| # PRNG seeds | ||
| ############################################################# | ||
| # np.random.seed(1) | ||
|
|
||
| # Integration parameters | ||
| ############################################################# | ||
| system.time_step = 0.01 | ||
| system.cell_system.skin = 0.5 | ||
| system.thermostat.turn_off() | ||
|
|
||
|
|
||
| ############################################################# | ||
| # Setup System # | ||
| ############################################################# | ||
|
|
||
| # Interaction setup | ||
| ############################################################# | ||
| system.non_bonded_inter[0, 0].lennard_jones.set_params( | ||
| epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, shift="auto") | ||
|
|
||
|
|
||
| # Particle setup | ||
| ############################################################# | ||
|
|
||
| # Warmup Integration # | ||
| ############################################################# | ||
|
|
||
| system.integrator.set_steepest_descent( | ||
| f_max=0, | ||
| gamma=0.001, | ||
| max_displacement=0.01) | ||
|
|
||
| # warmup | ||
| while system.analysis.energy()["total"] > 0.1 * n_part: | ||
| print("minimization: {:.1f}".format(system.analysis.energy()["total"])) | ||
| system.integrator.run(20) | ||
| print("minimization: {:.1f}".format(system.analysis.energy()["total"])) | ||
| print() | ||
| system.integrator.set_vv() | ||
|
|
||
| system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42) | ||
|
|
||
| # tuning and equilibration | ||
| print("Tune skin: {}".format(system.cell_system.tune_skin( | ||
| min_skin=0.2, max_skin=1, tol=0.05, int_steps=100))) | ||
| system.integrator.run(500) | ||
| print("Tune skin: {}".format(system.cell_system.tune_skin( | ||
| min_skin=0.2, max_skin=1, tol=0.05, int_steps=100))) | ||
| system.integrator.run(500) | ||
|
|
||
|
|
||
| system.thermostat.turn_off() | ||
| print("lb sites", lb_grid, "agrid", agrid) | ||
| if "LBFluid" in dir(espressomd.lb): | ||
| LBClass = espressomd.lb.LBFluid | ||
| elif "LBFluidWalberla" in dir(espressomd.lb): | ||
| LBClass = espressomd.lb.LBFluidWalberla | ||
| else: | ||
| raise Exception("LB not built in") | ||
|
|
||
| lbf = LBClass(agrid=agrid, dens=1, visc=1, tau=system.time_step, kT=1, seed=1) | ||
| system.actors.add(lbf) | ||
| print("lb shape", lbf.shape) | ||
| system.thermostat.set_lb(gamma=10, LB_fluid=lbf, seed=2) | ||
|
|
||
|
|
||
| # time integration loop | ||
| print("Timing every {} steps".format(measurement_steps)) | ||
| main_tick = time() | ||
| all_t = [] | ||
| for i in range(n_iterations): | ||
| tick = time() | ||
| system.integrator.run(measurement_steps) | ||
| tock = time() | ||
| t = (tock - tick) / measurement_steps | ||
| print("step {}, time = {:.2e}, verlet: {:.2f}, energy: {:.2e}" | ||
| .format(i, t, system.cell_system.get_state()["verlet_reuse"], | ||
| system.analysis.energy()["total"])) | ||
| all_t.append(t) | ||
| main_tock = time() | ||
| # average time | ||
| all_t = np.array(all_t) | ||
| avg = np.average(all_t) | ||
| ci = 1.96 * np.std(all_t) / np.sqrt(len(all_t) - 1) | ||
| print("average: {:.3e} +/- {:.3e} (95% C.I.)".format(avg, ci)) | ||
|
|
||
| cmd = " ".join(x for x in sys.argv[1:] if not x.startswith("--output")) | ||
| report = ('"{script}","{arguments}",{cores},{mean:.3e},' | ||
| '{ci:.3e},{n},{dur:.1f}\n'.format( | ||
| script=os.path.basename(sys.argv[0]), arguments=cmd, | ||
| cores=n_proc, dur=main_tock - main_tick, n=measurement_steps, | ||
| mean=avg, ci=ci)) | ||
| if not os.path.isfile(args.output): | ||
| report = ('"script","arguments","cores","mean","ci",' | ||
| '"nsteps","duration"\n' + report) | ||
| with open(args.output, "a") as f: | ||
| f.write(report) |
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