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test_bridging.py
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Wed, Jan 15, 04:09

test_bridging.py
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#!/usr/bin/python3
import pylibmultiscale as lm
import pytest
import numpy as np
################################################################
# geometrical properties
################################################################
r0 = 1.23157195294235
nb_atoms = 1000
LMD = nb_atoms*r0
el_size = 8.1*r0
nb_el = 300
LFE = el_size*nb_el
bridging_size = el_size*10
rcut = 2.2*r0
################################################################
lm.loadModules()
Dim = 3
lm.print_trace.fset(True)
comm = lm.Communicator.getCommunicator()
nb_proc = comm.getNumberFreeProcs()
comm.addGroup('md', nb_proc)
md_group = lm.Communicator.getGroup('md')
fe_group = md_group
md_geom = lm.Ball(Dim, 'md_geom')
md_geom.params.center = [0]
md_geom.params.radii = [0, LMD+bridging_size]
md_geom.init()
fe_geom = lm.Ball(Dim, 'fe_geom')
fe_geom.params.center = [0]
fe_geom.params.radii = [LMD, LMD+LFE]
fe_geom.init()
# coupling geom
bridge_geom = lm.Ball(Dim, 'bridge_geom')
bridge_geom.params.center = [0]
bridge_geom.params.radii = [LMD, LMD+bridging_size-el_size]
bridge_geom.init()
gManager = lm.GeometryManager.getManager()
gManager.addGeometry(md_geom)
gManager.addGeometry(fe_geom)
gManager.addGeometry(bridge_geom)
@pytest.fixture
def managers():
lm.FilterManager.getManager(Dim)
lm.ActionManager.getManager(Dim)
lm.DomainMultiScale.getManager()
yield
lm.FilterManager.destroy()
lm.ActionManager.destroy()
lm.DomainMultiScale.destroy()
def test_create_domain(managers):
domMD = lm.DomainMD1D('md', md_group)
domMD.params.rcut = rcut
domMD.params.r0 = r0
domMD.params.mass = 39.95
domMD.params.timestep = 10
domMD.params.epsilon = 1.6567944e-21/6.94769e-21
domMD.params.sigma = 1.1
domMD.params.domain_geometry = "md_geom"
domMD.init()
lm.DomainMultiScale.getManager().addObject(domMD)
domFE = lm.DomainMeca1D('fe', fe_group)
domFE.params.elem_size = el_size
domFE.params.domain_geometry = "fe_geom"
domFE.params.mass = 39.95
domFE.params.r0 = r0
domFE.params.rcut = rcut
domFE.params.epsilon = 1.6567944e-21/6.94769e-21
domFE.params.sigma = 1.1
domFE.params.timestep = 10
domFE.init()
lm.DomainMultiScale.getManager().addObject(domFE)
return domMD, domFE
@pytest.fixture
def domains(managers):
return test_create_domain(managers)
def test_bridge_init(domains):
domMD, domFE = domains
assert domMD is not None
assert domFE is not None
bridge = lm.Bridging("test")
bridge.params.geometry = "bridge_geom"
bridge.init(domMD.getContainer(), domFE.getContainer())
return domMD, domFE, bridge
@pytest.fixture
def bridge_domain(domains):
return test_bridge_init(domains)
def test_bridge_constant_field_interpolation(bridge_domain):
domMD, domFE, bridge = bridge_domain
extract = lm.ComputeExtract('extractor')
extract.params.field = lm.position0
extract.compute(bridge.meshList)
pos0 = extract.evalArrayOutput().array()
set_field = lm.StimulationField('set')
set_field.params.field = lm.position
set_field.compute(dofs=bridge.meshList, field=np.ones_like(pos0))
out = lm.ContainerArrayReal(bridge.pointList.castContainer().size())
bridge.mesh2Point(lm.position, out)
assert (out.array() == np.ones_like(out.array())).all()
def test_bridge_linear_field_interpolation(bridge_domain):
domMD, domFE, bridge = bridge_domain
extract = lm.ComputeExtract('extractor')
extract.params.field = lm.position0
extract.compute(bridge.meshList)
pos0 = extract.evalArrayOutput().array()
set_field = lm.StimulationField('set')
set_field.params.field = lm.position
alpha = 1.45
beta = 4.546
linear_field = pos0 * alpha + beta
set_field.compute(dofs=bridge.meshList, field=linear_field)
out = lm.ContainerArrayReal(bridge.pointList.castContainer().size())
bridge.mesh2Point(lm.position, out)
extract.params.field = lm.position0
extract.compute(bridge.pointList)
pos0 = extract.evalArrayOutput().array()
assert out.array().shape == pos0.shape
assert (np.abs(out.array() - (pos0 * alpha + beta)) < 1e-12).all()

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