def setUp(self):
self.model = smodel.Model()
A = smodel.Spec('A', self.model)
volsys = smodel.Volsys('vsys', self.model)
D_a = smodel.Diff('D_a', volsys, A)
self.DCST = 0.2e-9
D_a.setDcst(self.DCST)
self.mesh = meshio.importAbaqus2("directional_dcst_test/mesh_tet.inp",
"directional_dcst_test/mesh_tri.inp",
1e-6,
"directional_dcst_test/mesh_conf")[0]
boundary_tris = self.mesh.getROIData("boundary")
v1_tets = self.mesh.getROIData("v1_tets")
v2_tets = self.mesh.getROIData("v2_tets")
comp1 = sgeom.TmComp("comp1", self.mesh, v1_tets)
comp2 = sgeom.TmComp("comp2", self.mesh, v2_tets)
comp1.addVolsys("vsys")
comp2.addVolsys("vsys")
db = sgeom.DiffBoundary("boundary", self.mesh, boundary_tris)
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
self.solver = solv.Tetexact(self.model, self.mesh, self.rng)
def gen_geom():
mesh = meshio.loadMesh('meshes/cyl_len10_diam1')[0]
ntets = mesh.countTets()
tets_compA = []
tets_compB = []
tris_compA = set()
tris_compB = set()
z_max = mesh.getBoundMax()[2]
z_min = mesh.getBoundMin()[2]
z_mid = z_min + (z_max - z_min) / 2.0
for t in range(ntets):
# Fetch the z coordinate of the barycenter
barycz = mesh.getTetBarycenter(t)[2]
# Fetch the triangle indices of the tetrahedron, a tuple of length 4:
tris = mesh.getTetTriNeighb(t)
if barycz < z_mid:
tets_compA.append(t)
tris_compA.add(tris[0])
tris_compA.add(tris[1])
tris_compA.add(tris[2])
tris_compA.add(tris[3])
else:
tets_compB.append(t)
tris_compB.add(tris[0])
tris_compB.add(tris[1])
tris_compB.add(tris[2])
tris_compB.add(tris[3])
# Create the mesh compartments
compA = sgeom.TmComp('compA', mesh, tets_compA)
compB = sgeom.TmComp('compB', mesh, tets_compB)
compA.addVolsys('vsysA')
compB.addVolsys('vsysB')
# Make the diff boundary tris with the intersection and convert to list
tris_DB = tris_compA.intersection(tris_compB)
tris_DB = list(tris_DB)
# Create the diffusion boundary between compA and compB
diffb = sgeom.DiffBoundary('diffb', mesh, tris_DB)
return mesh, tets_compA, tets_compB
else:
bcomptets.append(t)
compbtris.add(tris[0])
compbtris.add(tris[1])
compbtris.add(tris[2])
compbtris.add(tris[3])
dbset = compatris.intersection(compbtris)
dbtris = list(dbset)
compa = sgeom.TmComp('compa', mesh, acomptets)
compb = sgeom.TmComp('compb', mesh, bcomptets)
compa.addVolsys('vsys')
compb.addVolsys('vsys')
diffb = sgeom.DiffBoundary('diffb', mesh, dbtris)
# Now fill the array holding the tet indices to sample at random
assert(SAMPLE <= ntets)
numfilled = 0
while (numfilled < SAMPLE):
tetidxs[numfilled] = numfilled
numfilled +=1
# Now find the distance of the center of the tets to the Z lower face
for i in range(SAMPLE):
baryc = mesh.getTetBarycenter(int(tetidxs[i]))
r = baryc[0]
tetrads[i] = r*1.0e6
def test_kisilevich():
"Reaction-diffusion - Degradation-diffusion (Parallel TetOpSplit)"
NITER = 50 # The number of iterations
DT = 0.1 # Sampling time-step
INT = 0.3 # Sim endtime
DCSTA = 400 * 1e-12
DCSTB = DCSTA
RCST = 100000.0e6
#NA0 = 100000 # 1000000 # Initial number of A molecules
NA0 = 1000
NB0 = NA0 # Initial number of B molecules
SAMPLE = 1686
# <1% fail with a tolerance of 7.5%
tolerance = 7.5 / 100
# create the array of tet indices to be found at random
tetidxs = numpy.zeros(SAMPLE, dtype='int')
# further create the array of tet barycentre distance to centre
tetrads = numpy.zeros(SAMPLE)
mdl = smod.Model()
A = smod.Spec('A', mdl)
B = smod.Spec('B', mdl)
volsys = smod.Volsys('vsys', mdl)
R1 = smod.Reac('R1', volsys, lhs=[A, B], rhs=[])
R1.setKcst(RCST)
D_a = smod.Diff('D_a', volsys, A)
D_a.setDcst(DCSTA)
D_b = smod.Diff('D_b', volsys, B)
D_b.setDcst(DCSTB)
mesh = meshio.loadMesh('validation_rd_mpi/meshes/brick_40_4_4_1686tets')[0]
VOLA = mesh.getMeshVolume() / 2.0
VOLB = VOLA
ntets = mesh.countTets()
acomptets = []
bcomptets = []
max = mesh.getBoundMax()
min = mesh.getBoundMax()
midz = 0.0
compatris = set()
compbtris = set()
for t in range(ntets):
barycz = mesh.getTetBarycenter(t)[0]
tris = mesh.getTetTriNeighb(t)
if barycz < midz:
acomptets.append(t)
compatris.add(tris[0])
compatris.add(tris[1])
compatris.add(tris[2])
compatris.add(tris[3])
else:
bcomptets.append(t)
compbtris.add(tris[0])
compbtris.add(tris[1])
compbtris.add(tris[2])
compbtris.add(tris[3])
dbset = compatris.intersection(compbtris)
dbtris = list(dbset)
compa = sgeom.TmComp('compa', mesh, acomptets)
compb = sgeom.TmComp('compb', mesh, bcomptets)
compa.addVolsys('vsys')
compb.addVolsys('vsys')
diffb = sgeom.DiffBoundary('diffb', mesh, dbtris)
# Now fill the array holding the tet indices to sample at random
assert (SAMPLE <= ntets)
numfilled = 0
while (numfilled < SAMPLE):
tetidxs[numfilled] = numfilled
numfilled += 1
# Now find the distance of the centre of the tets to the Z lower face
for i in range(SAMPLE):
baryc = mesh.getTetBarycenter(int(tetidxs[i]))
r = baryc[0]
tetrads[i] = r * 1.0e6
Atets = acomptets
Btets = bcomptets
rng = srng.create('r123', 512)
rng.initialize(1000)
tet_hosts = gd.binTetsByAxis(mesh, steps.mpi.nhosts)
sim = solvmod.TetOpSplit(mdl, mesh, rng, False, tet_hosts)
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
resA = numpy.zeros((NITER, ntpnts, SAMPLE))
resB = numpy.zeros((NITER, ntpnts, SAMPLE))
for i in range(0, NITER):
sim.reset()
sim.setDiffBoundaryDiffusionActive('diffb', 'A', True)
sim.setDiffBoundaryDiffusionActive('diffb', 'B', True)
sim.setCompCount('compa', 'A', NA0)
sim.setCompCount('compb', 'B', NB0)
for t in range(0, ntpnts):
sim.run(tpnts[t])
for k in range(SAMPLE):
resA[i, t, k] = sim.getTetCount(int(tetidxs[k]), 'A')
resB[i, t, k] = sim.getTetCount(int(tetidxs[k]), 'B')
itermeansA = numpy.mean(resA, axis=0)
itermeansB = numpy.mean(resB, axis=0)
def getdetc(t, x):
N = 1000 # The number to represent infinity in the exponential calculation
L = 20e-6
concA = 0.0
for n in range(N):
concA += ((1.0 / (2 * n + 1)) * math.exp(
(-(DCSTA / (20.0e-6)) * math.pow(
(2 * n + 1), 2) * math.pow(math.pi, 2) * t) / (4 * L)) *
math.sin(((2 * n + 1) * math.pi * x) / (2 * L)))
concA *= ((4 * NA0 / math.pi) / (VOLA * 6.022e26)) * 1.0e6
return concA
tpnt_compare = [1, 2]
passed = True
max_err = 0.0
for tidx in tpnt_compare:
NBINS = 10
radmax = 0.0
radmin = 10.0
for r in tetrads:
if (r > radmax): radmax = r
if (r < radmin): radmin = r
rsec = (radmax - radmin) / NBINS
binmins = numpy.zeros(NBINS + 1)
tetradsbinned = numpy.zeros(NBINS)
r = radmin
bin_vols = numpy.zeros(NBINS)
for b in range(NBINS + 1):
binmins[b] = r
if (b != NBINS): tetradsbinned[b] = r + rsec / 2.0
r += rsec
bin_countsA = [None] * NBINS
bin_countsB = [None] * NBINS
for i in range(NBINS):
bin_countsA[i] = []
bin_countsB[i] = []
filled = 0
for i in range(itermeansA[tidx].size):
irad = tetrads[i]
for b in range(NBINS):
if (irad >= binmins[b] and irad < binmins[b + 1]):
bin_countsA[b].append(itermeansA[tidx][i])
bin_vols[b] += sim.getTetVol(int(tetidxs[i]))
filled += 1.0
break
filled = 0
for i in range(itermeansB[tidx].size):
irad = tetrads[i]
for b in range(NBINS):
if (irad >= binmins[b] and irad < binmins[b + 1]):
bin_countsB[b].append(itermeansB[tidx][i])
filled += 1.0
break
bin_concsA = numpy.zeros(NBINS)
bin_concsB = numpy.zeros(NBINS)
for c in range(NBINS):
for d in range(bin_countsA[c].__len__()):
bin_concsA[c] += bin_countsA[c][d]
for d in range(bin_countsB[c].__len__()):
bin_concsB[c] += bin_countsB[c][d]
bin_concsA[c] /= (bin_vols[c])
bin_concsA[c] *= (1.0e-3 / 6.022e23) * 1.0e6
bin_concsB[c] /= (bin_vols[c])
bin_concsB[c] *= (1.0e-3 / 6.022e23) * 1.0e6
for i in range(NBINS):
rad = abs(tetradsbinned[i]) * 1.0e-6
if (tetradsbinned[i] < -5):
# compare A
det_conc = getdetc(tpnts[tidx], rad)
steps_conc = bin_concsA[i]
assert tol_funcs.tolerable(det_conc, steps_conc, tolerance)
if (tetradsbinned[i] > 5):
# compare B
det_conc = getdetc(tpnts[tidx], rad)
steps_conc = bin_concsB[i]
assert tol_funcs.tolerable(det_conc, steps_conc, tolerance)
D_a = smodel.Diff('D_a', volsys, A)
D_a.setDcst(DCST)
mesh = meshio.importAbaqus2("mesh_tet.inp", "mesh_tri.inp", 1e-6, "mesh_conf")[0]
boundary_tris = mesh.getROIData("boundary")
v1_tets = mesh.getROIData("v1_tets")
v2_tets = mesh.getROIData("v2_tets")
comp1 = sgeom.TmComp("comp1", mesh, v1_tets)
comp2 = sgeom.TmComp("comp2", mesh, v2_tets)
comp1.addVolsys("vsys")
comp2.addVolsys("vsys")
db = sgeom.DiffBoundary("boundary", mesh, boundary_tris)
rng = srng.create('mt19937', 512)
rng.initialize(int(time.time()%4294967295))
solver = solv.Tetexact(model, mesh, rng)
print "Set directonal dcst from comp1 to comp2, and from comp2 to comp1 to 0..."
solver.setCompCount("comp1", "A", 100)
solver.setCompCount("comp2", "A", 20)
solver.setDiffBoundaryDcst("boundary", "A", 0)
print "V1 Count: ", solver.getCompCount("comp1", "A")
print "V2 Count: ", solver.getCompCount("comp2", "A")
solver.run(1)
print "V1 Count: ", solver.getCompCount("comp1", "A")
print "V2 Count: ", solver.getCompCount("comp2", "A")
