From 8a3c24e6db84cf5487405c61509ea1a4667de1a7 Mon Sep 17 00:00:00 2001 From: Jonas Landsgesell Date: Thu, 20 Dec 2018 02:45:34 +0100 Subject: [PATCH] Electrostatic pressure consistency (#2409) * add check * add check * patch * imports * up * Update p3m_electrostatic_pressure.py * format * Update p3m_electrostatic_pressure.py * apply patch * exchange assert code * docstring for test * apply patch * reformulate comparison * year * patch * revert to np testing * changed comparison to maximal 2 percent deviation * changed comparison to maximal 2 percent deviation * patch * empty * add tune skin * add warmup * patch * refactor pressure calculation in small python class * patch * new style class * add LJ to required features * patch --- testsuite/python/CMakeLists.txt | 1 + .../python/p3m_electrostatic_pressure.py | 142 ++++++++++++++++++ 2 files changed, 143 insertions(+) create mode 100644 testsuite/python/p3m_electrostatic_pressure.py diff --git a/testsuite/python/CMakeLists.txt b/testsuite/python/CMakeLists.txt index 17778e8dca6..ee682ae70fd 100644 --- a/testsuite/python/CMakeLists.txt +++ b/testsuite/python/CMakeLists.txt @@ -167,6 +167,7 @@ python_test(FILE lb_boundary.py MAX_NUM_PROC 2) python_test(FILE lb_streaming.py MAX_NUM_PROC 4) python_test(FILE lb_shear.py MAX_NUM_PROC 2) python_test(FILE lb_thermostat.py MAX_NUM_PROC 2) +python_test(FILE p3m_electrostatic_pressure.py MAX_NUM_PROC 2) if(PY_H5PY) python_test(FILE h5md.py MAX_NUM_PROC 2) diff --git a/testsuite/python/p3m_electrostatic_pressure.py b/testsuite/python/p3m_electrostatic_pressure.py new file mode 100644 index 00000000000..0f2b982a43a --- /dev/null +++ b/testsuite/python/p3m_electrostatic_pressure.py @@ -0,0 +1,142 @@ +# +# Copyright (C) 2013-2018 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 . +# +from __future__ import print_function +import unittest as ut +import numpy as np +import numpy.testing as npt + +import espressomd +from espressomd import electrostatics + + +class pressureViaVolumeScaling(object): + + def __init__(self, system, kbT): + self.system = system + self.kbT = kbT + self.old_box_lengths = np.copy(system.box_l) + self.old_volume = np.prod(self.old_box_lengths) + dV_div_old_volume = 0.001 + self.dV = -dV_div_old_volume * self.old_volume + self.new_volume = self.old_volume + self.dV + self.new_box_l = (self.new_volume)**(1. / 3.) + + self.list_of_previous_values = [] + + def measure_pressure_via_volume_scaling( + self): + # taken from "Efficient pressure estimation in molecular simulations without evaluating the virial" + # only works so far for isotropic volume changes, i.e. the isotropic + # pressure + energy = self.system.analysis.energy() + Epot_old = energy["total"] - energy["kinetic"] + self.system.change_volume_and_rescale_particles(self.new_box_l, "xyz") + self.system.integrator.run(0) + energy = self.system.analysis.energy() + Epot_new = energy["total"] - energy["kinetic"] + self.system.change_volume_and_rescale_particles( + self.old_box_lengths[0], "xyz") + self.system.integrator.run(0) + DeltaEpot = Epot_new - Epot_old + particle_number = len(self.system.part[:].id) + current_value = (self.new_volume / self.old_volume)**particle_number * \ + np.exp(-DeltaEpot / self.kbT) + self.list_of_previous_values.append(current_value) + + def get_result(self): + average_value = np.mean(self.list_of_previous_values) + + pressure = self.kbT / self.dV * np.log(average_value) + return pressure + + +@ut.skipIf(not espressomd.has_features(["ELECTROSTATICS, LENNARD_JONES"]), + "Features not available, skipping test!") +class VirialPressureConsistency(ut.TestCase): + + """Test the consistency of the core implementation of the virial pressure with an analytical relation which allows + for the calculation of the pressure as a volume derivative of a function of the potential energy change on infinitesimal volume changes. + The relation and its derivation can be found in the paper with the name "Efficient pressure estimation in molecular simulations without evaluating the virial" + by Harismiadis, V. I., J. Vorholz, and A. Z. Panagiotopoulos. 1996 + + """ + # Handle to espresso system + system = espressomd.System(box_l=[50, 50, 50]) + + def setUp(self): + np.random.seed(seed=1) + self.system.seed = range( + self.system.cell_system.get_state()["n_nodes"]) + self.system.time_step = 0.01 + self.kT = 0.5 + self.system.non_bonded_inter[0, 0].lennard_jones.set_params( + epsilon=1.0, sigma=1.0, cutoff=2**(1.0 / 6.0), shift="auto") + num_part = 40 + mass = 1 + + for i in range(num_part): + self.system.part.add(pos=np.random.random( + 3) * self.system.box_l, q=1, v=np.sqrt(self.kT / mass) * np.random.normal(loc=[0, 0, 0])) + self.system.part.add(pos=np.random.random( + 3) * self.system.box_l, q=-1, v=np.sqrt(self.kT / mass) * np.random.normal(loc=[0, 0, 0])) + + ############################################################# + # Warmup Integration # + ############################################################# + + self.system.integrator.set_steepest_descent( + f_max=0, + gamma=0.001, + max_displacement=0.01) + + # warmup + while self.system.analysis.energy()["total"] > 10 * num_part: + print("minimization: {:.1f}".format( + self.system.analysis.energy()["total"])) + self.system.integrator.run(10) + self.system.integrator.set_vv() + self.system.thermostat.set_langevin(kT=self.kT, gamma=1.0) + + def test_p3m_pressure(self): + pressures_via_virial = [] + pressures_via_volume_scaling = [] + print("Tune skin: {}".format(self.system.cell_system.tune_skin( + min_skin=1.0, max_skin=1.6, tol=0.05, int_steps=100))) + p3m = electrostatics.P3M(prefactor=2.0, accuracy=1e-3) + self.system.actors.add(p3m) + print("Tune skin: {}".format(self.system.cell_system.tune_skin( + min_skin=1.0, max_skin=1.6, tol=0.05, int_steps=100))) + num_samples = 100 + pressure_via_volume_scaling = pressureViaVolumeScaling( + self.system, self.kT) + for i in range(num_samples): + self.system.integrator.run(100) + pressures_via_virial.append( + self.system.analysis.pressure()['total']) + pressure_via_volume_scaling.measure_pressure_via_volume_scaling() + pressure_virial = np.mean(pressures_via_virial) + abs_deviation_in_percent = abs( + pressure_virial / pressure_via_volume_scaling.get_result() - 1.0) * 100.0 # should be 0% ideally + npt.assert_array_less( + abs_deviation_in_percent, + 5.0) # devation should be below 5% + + +if __name__ == "__main__": + ut.main()