From f83d98d66f681a82c62a9311cff33799ab7c8443 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= Date: Wed, 4 Dec 2024 21:28:29 +0100 Subject: [PATCH 1/2] Fix SimplePore distance function --- src/shapes/src/SimplePore.cpp | 40 ++++--- testsuite/python/simple_pore.py | 203 ++++++++++++++++++++++++++++++-- 2 files changed, 212 insertions(+), 31 deletions(-) diff --git a/src/shapes/src/SimplePore.cpp b/src/shapes/src/SimplePore.cpp index 5fc0531297e..a941735674a 100644 --- a/src/shapes/src/SimplePore.cpp +++ b/src/shapes/src/SimplePore.cpp @@ -20,6 +20,7 @@ #include #include +#include #include #include @@ -39,28 +40,33 @@ std::pair SimplePore::dist_half_pore(double r, double z) const { assert(r >= 0.0); /* - * We have to find the line that splits area 1 (r determines distance) from - * area 2 (z determines distance) inside pore. In area 3 we have to consider - * z and r to determine the distance. + * We have to find the line that splits area (1), where r determines + * the distance, from area (2), where z determines the distance. + * In area (3) we have to consider z and r to determine the distance. + * The line that separates area (1) from area (2) has parametric equation + * @f$ r = c_z + c_r - z @f$. * - * | x - * | 2 x - * | x - * _|_ x 1 - * \| ^ r - * 3 |-------| - * | z <- + * | . ^ r + * | (2) . | + * | . | + * ........|.. (1) | + * ^ \ : | + * | \_________| + * c_r | (3) : | + * | :<------>| + * v : c_z | + * z <-----------------+ */ if ((z <= c_z) && (r <= (c_z + c_r - z))) { - /* Cylinder section, inner */ + /* Cylinder section, inner, area (1) */ return {m_rad - r, 0}; } if (((z >= c_z) && (r >= c_r)) || ((z <= c_z) && (r > (c_z + c_r - z)))) { - /* Wall section and outer cylinder */ + /* Wall section and outer cylinder, area (2) */ return {0, m_half_length - z}; } - /* Smoothing area */ + /* Smoothing area (3) */ /* Vector to center of torus segment */ auto const dr = c_r - r; auto const dz = c_z - z; @@ -76,7 +82,7 @@ void SimplePore::calculate_dist(const Utils::Vector3d &pos, double &dist, Utils::Vector3d &vec) const { /* Coordinate transform to cylinder coords with origin at m_center. */ - Utils::Vector3d const c_dist = pos - m_center; + auto const c_dist = pos - m_center; auto const z = e_z * c_dist; auto const r_vec = c_dist - z * e_z; auto const r = r_vec.norm(); @@ -97,10 +103,8 @@ void SimplePore::calculate_dist(const Utils::Vector3d &pos, double &dist, } else { // smoothing area if (std::abs(z) >= c_z) { - auto const angle = std::asin((std::abs(z) - c_z) / m_smoothing_rad); - auto const dist_offset = - m_smoothing_rad - (std::cos(angle) * m_smoothing_rad); - if (m_half_length < std::abs(z) || r <= (m_rad + dist_offset)) { + auto const d_sq = Utils::sqr(r - c_r) + Utils::sqr(z - c_z); + if (d_sq > Utils::sqr(m_smoothing_rad)) { side = 1; } } diff --git a/testsuite/python/simple_pore.py b/testsuite/python/simple_pore.py index 9d036265de7..145a1dbf4e8 100644 --- a/testsuite/python/simple_pore.py +++ b/testsuite/python/simple_pore.py @@ -19,20 +19,24 @@ import unittest as ut import unittest_decorators as utx +import numpy as np import espressomd import espressomd.shapes -# Integration test for simple pore -# The rationale is to hit the pore everywhere with particles -# and check that it does not blow up. The cylinder is needed -# because the pore is tilted with respect to the box, without -# it particles could enter the constraint over the periodic boundaries, -# leading to force jumps. - -@utx.skipIfMissingFeatures(["LENNARD_JONES"]) class SimplePoreConstraint(ut.TestCase): + box_yz = 15. + box_x = 20. + system = espressomd.System(box_l=[box_x, box_yz, box_yz]) + system.time_step = 0.01 + system.cell_system.skin = 0.4 + + def tearDown(self): + self.system.constraints.clear() + self.system.part.clear() + self.system.non_bonded_inter.reset() + def test_orientation(self): pore = espressomd.shapes.SimplePore(axis=[1., 0., 0.], radius=2., smoothing_radius=.1, length=2., center=[5., 5., 5.]) @@ -43,13 +47,186 @@ def test_orientation(self): d, _ = pore.calc_distance(position=[5., 5., .0]) self.assertLess(d, 0.) + def test_distance_calculation(self): + """ + Check the distance calculation function for all 3 sections of + a simple pore. The test works in cylindrical coordinates. + """ + twopi = 2. * np.pi + shape = espressomd.shapes.SimplePore( + axis=[0., 0., 1.], radius=3., smoothing_radius=.1, length=6., + center=self.system.box_l / 2.) + + def calc_cartesian_coord(body, pos): + """ + Convert cylindrical coordinates in the body frame + to Cartesian coordinates in the lab frame. + """ + origin = body.center + r, phi, z = pos + x = r * np.cos(phi) + origin[0] + y = r * np.sin(phi) + origin[1] + z = z + origin[2] + return [x, y, z] + + def calc_distance(shape, pos): + """Compute the distance vector from a shape surface.""" + return shape.calc_distance( + position=calc_cartesian_coord(shape, pos)) + + def angledist(val, ref): + """Compute the absolute distance between two angles.""" + twopi = 2. * np.pi + d1 = np.abs((ref - val) % twopi) + d2 = np.abs((ref - val) % twopi - twopi) + return min(d1, d2) + + tols = {"atol": 1e-10, "rtol": 1e-7} + + # scan points along the cylinder main axis + for h in np.linspace(-1., 1., 21): + z = h * (shape.length / 2. - shape.smoothing_radius) + for phi in np.linspace(0., twopi, 31): + dist, vec = calc_distance(shape, (0., phi, z)) + np.testing.assert_allclose(dist, shape.radius, **tols) + np.testing.assert_allclose(vec[0], -shape.radius, **tols) + np.testing.assert_allclose(vec[2], 0., **tols) + + # scan cylinder section + for ref_dist in np.linspace(-0.99, 0.99, 21) * shape.smoothing_radius: + r = shape.radius - ref_dist + for h in np.linspace(-0.99, 0.99, 21): + z = h * (shape.length / 2. - shape.smoothing_radius) + for phi in np.linspace(0., twopi, 31): + pos = calc_cartesian_coord(shape, (r, phi, z)) + dist, vec = shape.calc_distance(position=pos) + is_inside = shape.is_inside(position=pos) + cur_r = np.linalg.norm(vec[:2]) + np.testing.assert_allclose(dist, ref_dist, **tols) + np.testing.assert_allclose(cur_r, np.abs(ref_dist), **tols) + np.testing.assert_allclose(vec[2], 0., **tols) + if np.abs(ref_dist) > 1e-4: + ref_phi = phi if ref_dist < 0. else phi + np.pi + cur_phi = np.arctan2(vec[1], vec[0]) + angle_diff = angledist(cur_phi, ref_phi) + np.testing.assert_allclose(angle_diff, 0., **tols) + self.assertEqual(is_inside, ref_dist < 0.) + + # scan wall section + for r in np.linspace(2.01, 3.01, 21) + shape.radius: + for ref_dist in np.linspace(-2.0, 2.0, 21): + for sgn in [+1, -1]: + z = ref_dist + shape.length / 2. + for phi in np.linspace(0., twopi, 31): + pos = calc_cartesian_coord(shape, (r, phi, sgn * z)) + dist, vec = shape.calc_distance(position=pos) + is_inside = shape.is_inside(position=pos) + ref_z = sgn * ref_dist + np.testing.assert_allclose(dist, ref_dist, **tols) + np.testing.assert_allclose(vec[0], 0., **tols) + np.testing.assert_allclose(vec[1], 0., **tols) + np.testing.assert_allclose(vec[2], ref_z, **tols) + if np.abs(ref_dist) > 1e-4: + self.assertEqual(is_inside, ref_dist < 0.) + + # scan torus section + for phi in np.linspace(0., twopi, 21): + r = shape.radius + shape.smoothing_radius + z = shape.length / 2. - shape.smoothing_radius + origin = np.array(calc_cartesian_coord(shape, (r, phi, z))) + for rho in np.linspace(0.01, 2.01, 21) * shape.smoothing_radius: + ref_dist = rho - shape.smoothing_radius + for theta in np.linspace(np.pi / 2. + 0.01, np.pi - 0.01, 31): + dr = rho * np.cos(theta) + dz = rho * np.sin(theta) + rdr = ref_dist * np.cos(theta) + rdz = ref_dist * np.sin(theta) + pos_cyl = (r + dr, phi, z + dz) + normal = (r + rdr, phi, z + rdz) + pos = calc_cartesian_coord(shape, pos_cyl) + dist, vec = shape.calc_distance(position=pos) + is_inside = shape.is_inside(position=pos) + ref_vec = calc_cartesian_coord(shape, normal) - origin + np.testing.assert_allclose(dist, ref_dist, **tols) + np.testing.assert_allclose(np.copy(vec), ref_vec, **tols) + if np.abs(ref_dist) > 1e-4: + self.assertEqual(is_inside, ref_dist < 0.) + + @utx.skipIfMissingFeatures(["LENNARD_JONES"]) + def test_scattering(self): + """ + Create a line of particles along the pore main axis with a velocity + vector pointing up. Particles inside the pore and outside the pore + will bounce up and down (force vector is perpendicular to main axis). + Particles at the pore mouth will scatter along the main axis due + to reflection by the torus. Two peaks will appear in the trajectory + of the particles x-position, which roughly follow a sine wave + (we'll use a polynomial fit). Since we don't use a thermostat, + the two peaks are perfectly symmetric. + """ + system = self.system + system.non_bonded_inter[0, 1].lennard_jones.set_params( + epsilon=1., sigma=1., cutoff=2**(1. / 6.), shift="auto") + xpos_init = np.arange(800) * (self.box_x / 800.) + + def get_diffusion(): + return np.copy(self.system.part.all().pos[:, 0]) - xpos_init + + def get_series(): + ydata = get_diffusion() + xdata = np.arange(250, 340) + xdata = xdata[np.nonzero(ydata[250:340])[0]] + ydata = ydata[xdata[0]:xdata[-1] + 1] + xdata = np.array(xdata, dtype=float) / system.box_l[0] + return (xdata, ydata) + + system.constraints.add( + particle_type=0, penetrable=False, only_positive=False, + shape=espressomd.shapes.SimplePore( + axis=[1., 0., 0.], radius=3., smoothing_radius=.1, length=5., + center=system.box_l / 2.)) + + for x0 in xpos_init: + rpos = [x0, 0.5 * self.box_yz, 0.5 * self.box_yz] + system.part.add(pos=rpos, type=1, v=[0., 1., 0.]) + + # integrate until particles interact with the simple pore + system.integrator.run(300) + system.time = 0. + xdata, ydata = get_series() + coefs_init = np.polyfit(xdata, ydata, 4)[::-1] + coefs_growth = np.array([5398.954, -1483.69746, 152.9315, + -7.0115546, 0.1207058]) + + # verify particles trajectory + for _ in range(10): + system.integrator.run(20) + # check symmetry + ydata = get_diffusion()[1:] + np.testing.assert_allclose(ydata, -ydata[::-1], rtol=0., atol=1e-9) + # check one peak + coefs = coefs_init + system.time * coefs_growth + xdata, ydata = get_series() + ydata_hat = np.sum([coefs[j] * xdata**j for j in range(5)], axis=0) + magnitude = -np.min(ydata_hat) + deviation = (ydata - ydata_hat)[2:-2] # remove outliers + rmsd = np.sqrt(np.mean(deviation**2)) + self.assertLess(rmsd / magnitude, 0.01) + + @utx.skipIfMissingFeatures(["LENNARD_JONES"]) def test_stability(self): - box_yz = 15. - box_x = 20. - system = espressomd.System(box_l=[box_x, box_yz, box_yz]) - system.time_step = 0.01 - system.cell_system.skin = 0.4 + """ + Stability test for a simple pore tilted along the box diagonal. + The rationale is to hit the pore everywhere with particles + and check that no singularity occurs. The cylinder is needed + because the pore is tilted with respect to the box, without + it particles could enter the constraint over the periodic + boundaries, leading to force jumps. + """ + box_yz = self.box_yz + box_x = self.box_x + system = self.system lj_eps = 1.0 lj_sig = 1.0 lj_cut = lj_sig * 2**(1. / 6.) From 310d9934507096badf3f65e85b874d84d918945b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= Date: Wed, 4 Dec 2024 21:29:35 +0100 Subject: [PATCH 2/2] CI: Drop flaky hdf5-mpi package from macOS --- .github/actions/build_and_check/action.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/actions/build_and_check/action.yml b/.github/actions/build_and_check/action.yml index 5e87f0e7ad0..9b647ec349b 100644 --- a/.github/actions/build_and_check/action.yml +++ b/.github/actions/build_and_check/action.yml @@ -5,12 +5,11 @@ runs: steps: - run: | brew install boost boost-mpi fftw - brew install hdf5-mpi - pip3 install -c requirements.txt "cython<3.0" numpy scipy h5py packaging + pip3 install -c requirements.txt "cython<3.0" numpy scipy packaging shell: bash if: runner.os == 'macOS' - run: | - export myconfig=maxset with_cuda=false with_gsl=false test_timeout=800 check_skip_long=true + export myconfig=maxset with_cuda=false with_gsl=false with_hdf5=false test_timeout=800 check_skip_long=true bash maintainer/CI/build_cmake.sh shell: bash # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4