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test_lammps.py
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Tue, Sep 10, 10:12

test_lammps.py
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#!/usr/bin/python3
import pylibmultiscale as lm
import pytest
import numpy as np
import os
lm.loadModules()
Dim = 3
comm = lm.Communicator.getCommunicator()
nb_proc = comm.getNumberFreeProcs()
comm.addGroup('md', nb_proc)
md_group = lm.Communicator.getGroup('md')
A = 4.047971240341177
L = 5
cube = lm.Cube(Dim, 'md_geom')
cube.params.bbox = [-L*A, L*A, -L*A, L*A, -L*A, L*A]
cube.init()
gManager = lm.GeometryManager.getManager()
gManager.reset()
gManager.addGeometry(cube)
@pytest.fixture
def managers():
yield
lm.FilterManager.destroy()
lm.ActionManager.destroy()
lm.DomainMultiScale.destroy()
def test_create_domain(managers):
dom = lm.DomainLammps3('md', md_group)
open("lammps.in", 'w').write("""
mass * 26.98153860
pair_style lj/cut 6.03863042319
pair_coeff * * 2.4621 2.596037
fix 2 all nve
""")
dom.params.lammps_file = "lammps.in"
dom.params.create_header = True
dom.params.boundary = ['p', 'p', 'p']
dom.params.lattice = 'fcc'
dom.params.lattice_size = A
dom.params.domain_geometry = "md_geom"
dom.params.replica = [-L, L, -L, L, -L, L]
dom.params.lattice_origin = [.1, .1, .1]
dom.params.timestep = 1.
dom.init()
lm.DomainMultiScale.getManager().addObject(dom)
return dom
@pytest.fixture
def lammps_domain(managers):
return test_create_domain(managers)
def test_stimulate_temperature(lammps_domain):
dom = lammps_domain
assert dom is not None
initial_temp = lm.StimulationTemperature('initial_temp')
initial_temp.params.input = 'md'
initial_temp.params.seed = 40
initial_temp.params.temp = 100
initial_temp.params.oneshot = True
initial_temp.init()
initial_temp.stimulate()
lm.ActionManager.getManager().addObject(initial_temp)
thermostat = lm.StimulationLangevin('thermostat')
thermostat.params.input = 'md'
thermostat.params.freq = 1
thermostat.params.damp = 10
thermostat.params.temp = 50
thermostat.params.seed = 40
thermostat.params.timestep = 1
thermostat.params.work = True
thermostat.init()
lm.ActionManager.getManager().addObject(thermostat)
ekin = lm.ComputeEKin('ekin')
ekin.params.input = 'md'
ekin.init()
temperature = ekin.evalOutput("Temperature")
print(temperature.size())
print(temperature.getDim())
array = ekin.evalOutput('EKin').array()
array = ekin.evalOutput('EKin_vector').array()
print(array.shape)
print(array)
assert np.abs(temperature.array() - 100) < 1e-10
dumper = lm.DumperParaview('dumper')
dumper.params.input = 'md'
dumper.init()
dumper.dump()
@pytest.fixture
def lammps_domain_100K(lammps_domain):
dom = lammps_domain
test_stimulate_temperature(dom)
return dom
def test_compute_python():
check = lm.ComputePython('check')
v = np.array([[1, 2, 3]])
def toto(units=None, **kwargs):
# print(units)
print(kwargs)
return v
check.params.func = {'toto': toto}
check.init()
check.compute()
assert (check.evalOutput('toto').array() == v).all()
assert (check.evalOutput('toto').array().shape == (1, 3))
def test_compute_python2(managers):
data = lm.ComputePython('data')
check = lm.ComputePython('check')
v = np.array([[1, 2, 3]])
def toto(units=None, **kwargs):
# print(units)
print(kwargs)
return v
data.params.func = {'toto': toto}
data.init()
lm.FilterManager.getManager().addObject(data)
check.params.input = 'data.toto'
check.params.func = {'toto': toto}
check.init()
check.compute()
assert (check.evalOutput('toto').array() == v).all()
assert (check.evalOutput('toto').array().shape == (1, 3))
def test_compute_python3(managers):
data = lm.ComputePython('data')
print(os.getcwd())
with open('tmp.py', 'w') as f:
code = """
import numpy as np
v = np.array([[1, 2, 3]])
def toto(units=None, **kwargs):
# print(units)
print(kwargs)
return v
"""
f.write(code)
import sys
print(os.getcwd())
sys.path.append(os.getcwd())
data.params.filename = 'tmp'
data.init()
data.compute()
v = np.array([[1, 2, 3]])
assert (data.evalOutput('toto').array() == v).all()
assert (data.evalOutput('toto').array().shape == (1, 3))

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