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libmultiscale/test/python/test_cadd.py
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test_cadd.py
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#!/usr/bin/python3
import pylibmultiscale as lm
import pytest
import numpy as np
import barnett as barnett_helper
lm.loadModules()
Dim = 3
lm.spatial_dimension.fset(Dim)
# lm.print_trace.fset(True)
comm = lm.Communicator.getCommunicator()
cube = lm.Cube(Dim, 'md_geom')
cube.init()
gManager = lm.GeometryManager.getManager()
gManager.addGeometry(cube)
all_group = lm.Communicator.getGroup('all')
@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()
@pytest.fixture
def lammps_domain(managers):
dom = lm.DomainLammpsDynamic3('md', all_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'
A = 4.047971240341177
dom.params.lattice_size = A
dom.params.domain_geometry = "md_geom"
L = 5
dom.params.replica = [-L, L, -L, L, -L, L]
dom.params.lattice_origin = [.1, .1, .1]
cube.params.bbox = [-L*A, L*A, -L*A, L*A, -L*A, L*A]
cube.init()
dom.init()
lm.DomainMultiScale.getManager().addObject(dom)
return dom
test_ctrl = """
numXdoms = 1
numYdoms = 1
numZdoms = 1
numXcells = 4
numYcells = 4
numZcells = 4
#maxstep = 500
#remeshRule = 2
minSeg = 4.00000e+00
maxSeg = 4.00000e+02
timestepIntegrator = "trapezoidtimestep"
rTol = 5.000000e+00
rc = 20.41241
Ecore = 5.502262e+10
shearModulus = 2.600000e+10
pois = 3.000e-01
burgMag = 2.85671e-10
TempK = 2.000000e+01
MobScrew = 1.000000e+01
MobEdge = 1.000000e+01
MobClimb = 1.000000e-04
mobilityLaw = "FCC_0"
Rijmfile = "Rijm.cube.out"
RijmPBCfile = "RijmPBC.cube.out"
loadType = 0
#edotdir = [
# 1.949730e-05
# 2.755186e-06
# 1.000000e+00
# ]
#eRate = 1.000000e+04
#appliedStress = [
# 0.000000e+00
# 0.000000e+00
# 5.000000e+08
# 0.000000e+00
# 0.000000e+00
# 0.000000e+00
# ]
"""
test_data = """
dataFileVersion = 4
numFileSegments = 1
minCoordinates = [
-17500.0
-17500.0
-17500.0
]
maxCoordinates = [
17500.0
17500.0
17500.0
]
nodeCount = 29
dataDecompType = 1
dataDecompGeometry = [
1
1
1
]
#
# END OF DATA FILE PARAMETERS
#
domainDecomposition =
-17500.0
-17500.0
-17500.0
17500.0
17500.0
17500.0
nodalData =
# Primary lines: node_tag, x, y, z, num_arms, constraint
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz
0,0 5.00000e+01 -5.00000e+01 0.00000e+00 2 7
0,1 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,28 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,1 4.76621e+01 -2.85030e+01 0.00000e+00 2 7
0,0 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,2 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,2 4.07575e+01 -8.01109e+00 0.00000e+00 2 7
0,1 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,3 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,3 2.96093e+01 1.05174e+01 0.00000e+00 2 7
0,2 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,4 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,4 1.47386e+01 2.62162e+01 0.00000e+00 2 7
0,3 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,5 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,5 -3.15916e+00 3.83512e+01 0.00000e+00 2 7
0,4 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,6 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,6 -2.32472e+01 4.63550e+01 0.00000e+00 2 7
0,5 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,7 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,7 -4.45861e+01 4.98533e+01 0.00000e+00 2 7
0,6 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,8 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,8 -6.61782e+01 4.86827e+01 0.00000e+00 2 7
0,7 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,9 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,9 -8.70138e+01 4.28977e+01 0.00000e+00 2 7
0,8 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,10 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,10 -1.06119e+02 3.27689e+01 0.00000e+00 2 7
0,9 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,11 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,11 -1.22600e+02 1.87699e+01 0.00000e+00 2 7
0,10 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,12 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,12 -1.35686e+02 1.55539e+00 0.00000e+00 2 7
0,11 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,13 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,13 -1.44765e+02 -1.80698e+01 0.00000e+00 2 7
0,12 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,14 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,14 -1.49414e+02 -3.91881e+01 0.00000e+00 2 7
0,13 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,15 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,15 -1.49414e+02 -6.08119e+01 0.00000e+00 2 7
0,14 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,16 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,16 -1.44765e+02 -8.19302e+01 0.00000e+00 2 7
0,15 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,17 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,17 -1.35686e+02 -1.01555e+02 0.00000e+00 2 7
0,16 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,18 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,18 -1.22600e+02 -1.18770e+02 0.00000e+00 2 7
0,17 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,19 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,19 -1.06119e+02 -1.32769e+02 0.00000e+00 2 7
0,18 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,20 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,20 -8.70138e+01 -1.42898e+02 0.00000e+00 2 7
0,19 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,21 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,21 -6.61782e+01 -1.48683e+02 0.00000e+00 2 7
0,20 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,22 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,22 -4.45861e+01 -1.49853e+02 0.00000e+00 2 7
0,21 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,23 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,23 -2.32472e+01 -1.46355e+02 0.00000e+00 2 7
0,22 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,24 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,24 -3.15916e+00 -1.38351e+02 0.00000e+00 2 7
0,23 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,25 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,25 1.47386e+01 -1.26216e+02 0.00000e+00 2 7
0,24 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,26 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,26 2.96093e+01 -1.10517e+02 0.00000e+00 2 7
0,25 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,27 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,27 4.07575e+01 -9.19889e+01 0.00000e+00 2 7
0,26 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,28 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,28 4.76621e+01 -7.14970e+01 0.00000e+00 2 7
0,27 -2.85671e+00 -0.00000e+00 -0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
0,0 2.85671e+00 0.00000e+00 0.00000e+00
0.00000e+00 1.00000e+00 0.00000e+00
"""
@pytest.fixture
def paradis_domain(managers):
dom = lm.DomainParaDiS('paradis', all_group)
dom.params.numdlbsteps = 0
dom.params.controlfile = 'test.ctrl'
dom.params.datafile = 'test.data'
dom.params.timestep = 1e-7
open('test.data', 'w').write(test_data)
open('test.ctrl', 'w').write(test_ctrl)
print('init paradis domain')
dom.init()
return dom
def grid_point():
pts = np.array([2, 2, 2])
sz = 110
minCoords = sz*np.array([0., 0., -.1])
maxCoords = sz*np.array([1., 1., .1])
delta = (maxCoords-minCoords)/(pts-1)
pos = np.zeros((pts[0]*pts[1]*pts[2], 3))
p = 0
for i in range(pts[0]):
for j in range(pts[1]):
for k in range(pts[2]):
pos[p, :] = minCoords + delta*[i, j, k]
pos[p, 2] += .5
p += 1
return pos
def test_compute_python():
toto = lm.ComputePython('toto')
try:
toto.init()
toto.build()
raise RuntimeError('should raise an exception')
except lm.LibMultiScaleException:
pass
def test_barnett(paradis_domain):
dom_dd = paradis_domain
pset = lm.ComputePointSet('pset')
grid_points = grid_point()
pset.params.input = grid_points
pset.init()
pset.build()
barnett = lm.ComputeBarnett('computed_disp')
barnett.inputs.segments = dom_dd
barnett.inputs.points = pset
barnett.params.slip_plane = [0., 1., 0.]
barnett.init()
barnett.build()
computed_disp = barnett.getArray().to_array()
dd_nodes = lm.ComputeExtract('dd_nodes')
dd_nodes.inputs.input = dom_dd
dd_nodes.params.field = lm.position
dd_nodes.init()
dd_nodes.build()
node_positions = dd_nodes.getArray().to_array()
a = 4.04
r0 = a*np.sqrt(2)/2.
burg = np.array([1., 0., 0.])*r0
slip = np.array([0., 1., 0.])
# create segments from node positions knowing it is a loop
elems = np.zeros((node_positions.shape[0], 2), dtype=int)
elems[:, 0] = np.arange(0, node_positions.shape[0], dtype=int)
elems[:, 1] = np.arange(1, node_positions.shape[0]+1, dtype=int)
elems[-1, 1] = 0
python_computed_disp = barnett_helper.computeDisloDisplacements(
node_positions, elems, grid_points, burg, slip_plane=slip)
error = np.linalg.norm(computed_disp - python_computed_disp)
if error > 1e-5:
raise RuntimeError("barnett field was not well computed: {0}".format(
error))
# @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.getArray('toto').to_array() == v).all()
# assert (check.getArray('toto').to_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.getArray('toto').to_array() == v).all()
# assert (check.getArray('toto').to_array().shape == (1, 3))
#
#
# def test_compute_python3(managers):
# data = lm.ComputePython('data')
# code = """
# import numpy as np
# v = np.array([[1, 2, 3]])
#
# def toto(units=None, **kwargs):
# # print(units)
# print(kwargs)
# return v
# """
# f = open('tmp.py', 'w')
# f.write(code)
# f.close()
#
# data.params.filename = 'tmp'
# data.init()
# data.compute()
# v = np.array([[1, 2, 3]])
#
# assert (data.getArray('toto').to_array() == v).all()
# assert (data.getArray('toto').to_array().shape == (1, 3))
#
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