From 3e2ee9995d469ef7527f4a239a913f14774a0ddd Mon Sep 17 00:00:00 2001 From: Rudolf Weeber Date: Thu, 31 Oct 2019 10:49:13 +0100 Subject: [PATCH 1/2] LB Boundary force: fix unit conversion and tests Reference solutions for forces on shear planes and for stokes drag need dynamic viscosity, but LB uses kinetmatic viscosity. This switches the tests to dynamic viscosity and removes a 1/rho from the unit conversion in the script interface. Also, a force balance test is added, which does not depend on the density. --- .../lbboundaries/LBBoundary.hpp | 4 +- testsuite/python/CMakeLists.txt | 3 +- testsuite/python/lb_boundary_volume_force.py | 116 ++++++++++++++++++ testsuite/python/lb_shear.py | 14 ++- testsuite/python/lb_stokes_sphere.py | 11 +- 5 files changed, 134 insertions(+), 14 deletions(-) create mode 100644 testsuite/python/lb_boundary_volume_force.py diff --git a/src/script_interface/lbboundaries/LBBoundary.hpp b/src/script_interface/lbboundaries/LBBoundary.hpp index cfa46fc75a5..55bd59b6198 100644 --- a/src/script_interface/lbboundaries/LBBoundary.hpp +++ b/src/script_interface/lbboundaries/LBBoundary.hpp @@ -67,11 +67,9 @@ class LBBoundary : public AutoParameters { if (name == "get_force") { // The get force method uses mpi callbacks on lb cpu if (this_node == 0) { - const auto rho = lb_lbfluid_get_density(); const auto agrid = lb_lbfluid_get_agrid(); const auto tau = lb_lbfluid_get_tau(); - const double unit_conversion = - agrid * agrid * agrid * agrid / rho / tau / tau; + const double unit_conversion = agrid / tau / tau; return m_lbboundary->get_force() * unit_conversion; } return none; diff --git a/testsuite/python/CMakeLists.txt b/testsuite/python/CMakeLists.txt index a06b5e8bf59..1c02b277167 100644 --- a/testsuite/python/CMakeLists.txt +++ b/testsuite/python/CMakeLists.txt @@ -121,7 +121,7 @@ python_test(FILE reaction_ensemble.py MAX_NUM_PROC 4) python_test(FILE widom_insertion.py MAX_NUM_PROC 1) python_test(FILE constant_pH.py MAX_NUM_PROC 4) python_test(FILE writevtf.py MAX_NUM_PROC 4) -python_test(FILE lb_stokes_sphere.py MAX_NUM_PROC 2 LABELS gpu long) +python_test(FILE lb_stokes_sphere.py MAX_NUM_PROC 4 LABELS gpu long) python_test(FILE ek_fluctuations.py MAX_NUM_PROC 1 LABELS gpu) python_test(FILE ek_charged_plate.py MAX_NUM_PROC 1 LABELS gpu) python_test(FILE ek_eof_one_species_x.py MAX_NUM_PROC 1 LABELS gpu) @@ -179,6 +179,7 @@ python_test(FILE thermalized_bond.py MAX_NUM_PROC 4) python_test(FILE thole.py MAX_NUM_PROC 4) python_test(FILE lb_switch.py MAX_NUM_PROC 1 LABELS gpu) python_test(FILE lb_boundary_velocity.py MAX_NUM_PROC 1) +python_test(FILE lb_boundary_volume_force.py MAX_NUM_PROC 4) python_test(FILE lb_thermo_virtual.py MAX_NUM_PROC 2 LABELS gpu) python_test(FILE lb_poiseuille.py MAX_NUM_PROC 4 LABELS gpu) python_test(FILE lb_poiseuille_cylinder.py MAX_NUM_PROC 2 LABELS gpu) diff --git a/testsuite/python/lb_boundary_volume_force.py b/testsuite/python/lb_boundary_volume_force.py new file mode 100644 index 00000000000..d23ca756d79 --- /dev/null +++ b/testsuite/python/lb_boundary_volume_force.py @@ -0,0 +1,116 @@ +# Copyright (C) 2010-2019 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 . +import unittest as ut +import unittest_decorators as utx +import numpy as np + +import espressomd.lb +import espressomd.lbboundaries +import espressomd.shapes + + +""" +Checks force on lb boundaries for a fluid with a uniform volume force +""" + + +AGRID = 0.5 +EXT_FORCE = np.array([-.01, 0.02, 0.03]) +VISC = 3.5 +DENS = 1.5 +TIME_STEP = 0.05 +LB_PARAMS = {'agrid': AGRID, + 'dens': DENS, + 'visc': VISC, + 'tau': TIME_STEP, + 'ext_force_density': EXT_FORCE} + + +class LBBoundaryForceCommon: + + """Base class of the test that holds the test logic.""" + lbf = None + system = espressomd.System(box_l=np.array([12.0, 4.0, 4.0]) * AGRID) + system.time_step = TIME_STEP + system.cell_system.skin = 0.4 * AGRID + + def count_fluid_nodes(self): + # Count non-boundary nodes: + fluid_nodes = 0 + for n in self.lbf.nodes(): + if not n.boundary: + fluid_nodes += 1 + return fluid_nodes + + def test(self): + """ + Integrate the LB fluid until steady state is reached within a certain + accuracy. Then compare the foce balance between force exerted on fluid + and forces acting on the boundaries. + + """ + self.system.actors.clear() + self.system.lbboundaries.clear() + self.system.actors.add(self.lbf) + wall_shape1 = espressomd.shapes.Wall(normal=[1, 0, 0], dist=AGRID) + wall_shape2 = espressomd.shapes.Wall( + normal=[-1, 0, 0], dist=-(self.system.box_l[0] - AGRID)) + wall1 = espressomd.lbboundaries.LBBoundary(shape=wall_shape1) + wall2 = espressomd.lbboundaries.LBBoundary(shape=wall_shape2) + + self.system.lbboundaries.add(wall1) + self.system.lbboundaries.add(wall2) + fluid_nodes = self.count_fluid_nodes() + + self.system.integrator.run(20) + diff = float("inf") + old_val = float("inf") + while diff > 0.002: + self.system.integrator.run(10) + new_val = wall1.get_force()[0] + diff = abs(new_val - old_val) + old_val = new_val + + surface_area = self.system.box_l[1] * self.system.box_l[2] + expected_force = fluid_nodes * AGRID**3 * \ + np.copy(self.lbf.ext_force_density) + measured_force = np.array(wall1.get_force()) + \ + np.array(wall2.get_force()) + np.testing.assert_allclose(measured_force, expected_force, atol=2E-2) + + +@utx.skipIfMissingFeatures(['LB_BOUNDARIES', 'EXTERNAL_FORCES']) +class LBCPUBoundaryForce(ut.TestCase, LBBoundaryForceCommon): + + """Test for the CPU implementation of the LB.""" + + def setUp(self): + self.lbf = espressomd.lb.LBFluid(**LB_PARAMS) + + +@utx.skipIfMissingGPU() +@utx.skipIfMissingFeatures(['LB_BOUNDARIES_GPU', 'EXTERNAL_FORCES']) +class LBGPUBoundaryForce(ut.TestCase, LBBoundaryForceCommon): + + """Test for the GPU implementation of the LB.""" + + def setUp(self): + self.lbf = espressomd.lb.LBFluidGPU(**LB_PARAMS) + + +if __name__ == '__main__': + ut.main() diff --git a/testsuite/python/lb_shear.py b/testsuite/python/lb_shear.py index 2673252a5ec..9bc866768c8 100644 --- a/testsuite/python/lb_shear.py +++ b/testsuite/python/lb_shear.py @@ -83,7 +83,6 @@ def shear_flow(x, t, nu, v, h, k_max): class LBShearCommon: """Base class of the test that holds the test logic.""" - lbf = None system = espressomd.System(box_l=[H + 2. * AGRID, W, W]) @@ -98,9 +97,14 @@ def check_profile(self, shear_plane_normal, shear_direction): """ self.system.lbboundaries.clear() self.system.actors.clear() + try: + del self.lbf + except BaseException: + pass self.system.box_l = np.max( ((W, W, W), shear_plane_normal * (H + 2 * AGRID)), 0) + self.lbf = self.lb_class(**LB_PARAMS) self.system.actors.add(self.lbf) wall_shape1 = espressomd.shapes.Wall( @@ -164,8 +168,8 @@ def check_profile(self, shear_plane_normal, shear_direction): np.copy(wall1.get_force()), -np.copy(wall2.get_force()), atol=1E-4) - np.testing.assert_allclose(np.copy(wall1.get_force()), - shear_direction * SHEAR_VELOCITY / H * W**2 * VISC, atol=2E-4) + np.testing.assert_allclose(np.dot(np.copy(wall1.get_force()), shear_direction), + SHEAR_VELOCITY / H * W**2 * dynamic_viscosity, atol=2E-4) def test(self): x = np.array((1, 0, 0), dtype=float) @@ -185,7 +189,7 @@ class LBCPUShear(ut.TestCase, LBShearCommon): """Test for the CPU implementation of the LB.""" def setUp(self): - self.lbf = espressomd.lb.LBFluid(**LB_PARAMS) + self.lb_class = espressomd.lb.LBFluid @utx.skipIfMissingGPU() @@ -195,7 +199,7 @@ class LBGPUShear(ut.TestCase, LBShearCommon): """Test for the GPU implementation of the LB.""" def setUp(self): - self.lbf = espressomd.lb.LBFluidGPU(**LB_PARAMS) + self.lb_class = espressomd.lb.LBFluidGPU if __name__ == '__main__': diff --git a/testsuite/python/lb_stokes_sphere.py b/testsuite/python/lb_stokes_sphere.py index feb5b90c4e9..103a1d48b0f 100644 --- a/testsuite/python/lb_stokes_sphere.py +++ b/testsuite/python/lb_stokes_sphere.py @@ -42,10 +42,10 @@ 'visc': KVISC, 'tau': TIME_STEP} # System setup -radius = 8 * AGRID -box_width = 62 * AGRID +radius = 7 * AGRID +box_width = 52 * AGRID real_width = box_width + 2 * AGRID -box_length = 62 * AGRID +box_length = 54 * AGRID c_s = np.sqrt(1. / 3. * AGRID**2 / TIME_STEP**2) v = [0, 0, 0.2 * c_s] # The boundary slip @@ -91,10 +91,11 @@ def size(vector): return np.sqrt(tmp) last_force = -1000. - stokes_force = 6 * np.pi * KVISC * radius * size(v) + dynamic_viscosity = self.lbf.viscosity * self.lbf.density + stokes_force = 6 * np.pi * dynamic_viscosity * radius * size(v) self.system.integrator.run(35) while True: - self.system.integrator.run(10) + self.system.integrator.run(5) force = np.linalg.norm(sphere.get_force()) if np.abs(last_force - force) < 0.01 * stokes_force: break From 88730c86ec14efbfa7d2803e5a47d9e3d186bfec Mon Sep 17 00:00:00 2001 From: Rudolf Weeber Date: Thu, 31 Oct 2019 12:30:27 +0100 Subject: [PATCH 2/2] Remove leaked-in debug code --- testsuite/python/lb_shear.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/testsuite/python/lb_shear.py b/testsuite/python/lb_shear.py index 9bc866768c8..7778dd10e5e 100644 --- a/testsuite/python/lb_shear.py +++ b/testsuite/python/lb_shear.py @@ -97,10 +97,6 @@ def check_profile(self, shear_plane_normal, shear_direction): """ self.system.lbboundaries.clear() self.system.actors.clear() - try: - del self.lbf - except BaseException: - pass self.system.box_l = np.max( ((W, W, W), shear_plane_normal * (H + 2 * AGRID)), 0)