def gen_model():
# Create the model container object
mdl = smodel.Model()
# Create the chemical species
X = smodel.Spec('X', mdl)
Y = smodel.Spec('Y', mdl)
# Create separate volume systems for compartments A and B
vsysA = smodel.Volsys('vsysA', mdl)
vsysB = smodel.Volsys('vsysB', mdl)
# Describe diffusion of molecules in compartments A and B
# NOTE: diffusion is not defined for species X in compartment B
diff_X_A = smodel.Diff('diff_X_A', vsysA, X)
diff_X_A.dcst = 0.1e-9
diff_X_B = smodel.Diff('diff_X_B', vsysB, X)
diff_X_B.dcst = 0.1e-9
diff_Y_A = smodel.Diff('diff_Y_A', vsysA, Y)
diff_Y_A.dcst = 0.1e-9
diff_Y_B = smodel.Diff('diff_Y_B', vsysB, Y)
diff_Y_B.dcst = 0.1e-9
# Return the container object
return mdl
def setUp(self):
KCST = 10000.0
DCST = 0.08e-12
self.model = smodel.Model()
A = smodel.Spec('A', self.model)
B = smodel.Spec('B', self.model)
C = smodel.Spec('C', self.model)
D = smodel.Spec('D', self.model)
E = smodel.Spec('E', self.model)
F = smodel.Spec('F', self.model)
self.vsys1 = smodel.Volsys('vsys1', self.model)
self.vsys2 = smodel.Volsys('vsys2', self.model)
self.reac1 = smodel.Reac('reac1',
self.vsys1,
lhs=[A, B],
rhs=[C],
kcst=KCST)
self.reac2 = smodel.Reac('reac2',
self.vsys2,
lhs=[D, E],
rhs=[F],
kcst=KCST)
self.geom = sgeom.Geom()
self.comp1 = sgeom.Comp('comp1', self.geom, 1e-18)
self.comp1.addVolsys('vsys1')
self.comp2 = sgeom.Comp('comp2', self.geom, 1e-18)
self.comp2.addVolsys('vsys2')
if __name__ == "__main__":
self.mesh = meshio.importAbaqus('meshes/brick_40_4_4_1400tets.inp',
1e-6)[0]
else:
self.mesh = meshio.importAbaqus(
'multi_sys_test/meshes/brick_40_4_4_1400tets.inp', 1e-6)[0]
comp1_tets = []
comp2_tets = []
for t in range(self.mesh.ntets):
cord = self.mesh.getTetBarycenter(t)
if cord[0] < 0.0:
comp1_tets.append(t)
else:
comp2_tets.append(t)
self.tmcomp1 = sgeom.TmComp('comp1', self.mesh, comp1_tets)
self.tmcomp1.addVolsys('vsys1')
self.tmcomp2 = sgeom.TmComp('comp2', self.mesh, comp2_tets)
self.tmcomp2.addVolsys('vsys2')
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
def setUp(self):
self.model = smodel.Model()
A = smodel.Spec("A", self.model)
B = smodel.Spec("B", self.model)
C = smodel.Spec("C", self.model)
D = smodel.Spec("D", self.model)
E = smodel.Spec("E", self.model)
self.vsys1 = smodel.Volsys('vsys1', self.model)
self.vsys2 = smodel.Volsys('vsys2', self.model)
self.ssys1 = smodel.Surfsys('ssys1', self.model)
self.reac1 = smodel.Reac('reac1', self.vsys1, lhs = [A], rhs = [A], kcst = 1e5)
self.reac2 = smodel.Reac('reac2', self.vsys2, lhs = [E], rhs = [E], kcst = 1e4)
self.sreac = smodel.SReac('sreac', self.ssys1, slhs = [B], srhs = [B], kcst = 1e3)
if __name__ == "__main__":
self.mesh = meshio.loadMesh('meshes/cyl_len10_diam1')[0]
else:
self.mesh = meshio.loadMesh('getROIArea_bugfix_test/meshes/cyl_len10_diam1')[0]
ntets = self.mesh.countTets()
comp1Tets, comp2Tets = [], []
comp1Tris, comp2Tris = set(), set()
for i in range(ntets):
if self.mesh.getTetBarycenter(i)[0] > 0:
comp1Tets.append(i)
comp1Tris |= set(self.mesh.getTetTriNeighb(i))
else:
comp2Tets.append(i)
comp2Tris |= set(self.mesh.getTetTriNeighb(i))
patch1Tris = list(comp1Tris & comp2Tris)
self.comp1 = sgeom.TmComp('comp1', self.mesh, comp1Tets)
self.comp2 = sgeom.TmComp('comp2', self.mesh, comp2Tets)
self.comp1.addVolsys('vsys1')
self.comp2.addVolsys('vsys2')
self.patch1 = sgeom.TmPatch('patch1', self.mesh, patch1Tris, self.comp1, self.comp2)
self.patch1.addSurfsys('ssys1')
self.ROI1 = self.mesh.addROI('ROI1', sgeom.ELEM_TET, comp1Tets)
self.ROI2 = self.mesh.addROI('ROI2', sgeom.ELEM_TET, comp2Tets)
self.ROI3 = self.mesh.addROI('ROI3', sgeom.ELEM_TRI, patch1Tris)
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
tet_hosts = gd.linearPartition(self.mesh, [steps.mpi.nhosts, 1, 1])
tri_hosts = gd.partitionTris(self.mesh, tet_hosts, patch1Tris)
self.solver = solv.TetOpSplit(self.model, self.mesh, self.rng, solv.EF_NONE, tet_hosts, tri_hosts)
def setUp(self):
DCST = 0.08e-10
self.model = smodel.Model()
A = smodel.Spec('A', self.model)
self.vsys = smodel.Volsys('vsys', self.model)
self.ssys = smodel.Surfsys('ssys', self.model)
self.diff = smodel.Diff("diff", self.vsys, A, DCST)
self.sdiff = smodel.Diff("diff", self.ssys, A, DCST)
if __name__ == "__main__":
self.mesh = meshio.importAbaqus('meshes/test_mesh.inp', 1e-7)[0]
else:
self.mesh = meshio.importAbaqus(
'parallel_diff_sel_test/meshes/test_mesh.inp', 1e-7)[0]
self.tmcomp = sgeom.TmComp('comp', self.mesh, range(self.mesh.ntets))
self.tmcomp.addVolsys('vsys')
self.surf_tris = self.mesh.getSurfTris()
self.tmpatch = sgeom.TmPatch('patch',
self.mesh,
self.surf_tris,
icomp=self.tmcomp)
self.tmpatch.addSurfsys('ssys')
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
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]
comp = sgeom.TmComp("comp", self.mesh, range(self.mesh.ntets))
comp.addVolsys("vsys")
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
self.solver = solv.Tetexact(self.model, self.mesh, self.rng)
boundary_tris = self.mesh.getROIData("boundary")
boundary_tets1 = self.mesh.getROIData("boundary_tets_1")
boundary_tets2 = self.mesh.getROIData("boundary_tets_2")
self.pairing = {}
for tri in boundary_tris:
neigh_tets = self.mesh.getTriTetNeighb(tri)
if neigh_tets[0] in boundary_tets1:
self.pairing[tri] = (neigh_tets[0], neigh_tets[1])
else:
self.pairing[tri] = (neigh_tets[1], neigh_tets[0])
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 setUp(self):
self.model = smodel.Model()
self.vsys1 = smodel.Volsys('vsys1', self.model)
self.ssys1 = smodel.Surfsys('ssys1', self.model)
if __name__ == "__main__":
self.mesh = meshio.loadMesh('meshes/cyl_len10_diam1')[0]
else:
self.mesh = meshio.loadMesh(
'getROIArea_bugfix_test/meshes/cyl_len10_diam1')[0]
ntets = self.mesh.countTets()
comp1Tets, comp2Tets = [], []
comp1Tris, comp2Tris = set(), set()
for i in range(ntets):
if self.mesh.getTetBarycenter(i)[0] > 0:
comp1Tets.append(i)
comp1Tris |= set(self.mesh.getTetTriNeighb(i))
else:
comp2Tets.append(i)
comp2Tris |= set(self.mesh.getTetTriNeighb(i))
patch1Tris = list(comp1Tris & comp2Tris)
self.comp1 = sgeom.TmComp('comp1', self.mesh, comp1Tets)
self.comp2 = sgeom.TmComp('comp2', self.mesh, comp2Tets)
self.comp1.addVolsys('vsys1')
self.comp2.addVolsys('vsys1')
self.patch1 = sgeom.TmPatch('patch1', self.mesh, patch1Tris,
self.comp1, self.comp2)
self.patch1.addSurfsys('ssys1')
self.ROI1 = self.mesh.addROI('ROI1', sgeom.ELEM_TRI, patch1Tris)
def get_model():
mdl = smod.Model()
A = smod.Spec('A', mdl)
volsys = smod.Volsys('vsys',mdl)
R1 = smod.Reac('R1', volsys, lhs = [], rhs = [A])
R1.setKcst(1e-3)
return mdl
def gen_model():
mdl = smodel.Model()
A = smodel.Spec('A', mdl)
vsys = smodel.Volsys('cytosolv', mdl)
diff_A = smodel.Diff('diff_A', vsys, A)
diff_A.setDcst(DCST)
return mdl
def setUp(self):
# model setup
mdl = smodel.Model()
spc = smodel.Spec('A', mdl)
vsys = smodel.Volsys('A', mdl)
diff = smodel.Diff('diff_A', vsys, spc)
diff.setDcst(0.0)
# mesh
vertCoos = [0.0, 0.0, 0.0, \
1.0e-6, 0.0, 0.0, \
0.0, 1.0e-6, 0.0, \
0.0, 0.0, 1.0e-6, \
1.0e-6, 1.0e-6, 1.0e-6 ]
vertIds = [0, 1, 2, 3, \
1, 2, 3, 4 ]
# geom setup
msh = sgeom.Tetmesh(vertCoos, vertIds)
ntets = msh.countTets()
comp = sgeom.TmComp('comp', msh, range(ntets))
comp.addVolsys('A')
# init sim
rng = srng.create('mt19937', 512)
rng.initialize(2903)
tet_hosts = sgd.linearPartition(msh, [1, 1, smpi.nhosts])
self.sim = spsolver.TetOpSplit(mdl, msh, rng, spsolver.EF_NONE, tet_hosts)
def setUp(self):
DCST = 0.08e-10
self.model = smodel.Model()
A = smodel.Spec('A', self.model)
self.vsys = smodel.Volsys('vsys', self.model)
self.ssys = smodel.Surfsys('ssys', self.model)
self.diff = smodel.Diff("diff", self.vsys, A, DCST)
self.sdiff = smodel.Diff("diff", self.ssys, A, DCST)
if __name__ == "__main__":
self.mesh = meshio.importAbaqus('meshes/test_mesh.inp', 1e-7)[0]
else:
self.mesh = meshio.importAbaqus(
'parallel_std_string_bugfix_test/meshes/test_mesh.inp',
1e-7)[0]
self.tmcomp = sgeom.TmComp('comp', self.mesh, range(self.mesh.ntets))
self.tmcomp.addVolsys('vsys')
self.surf_tris = self.mesh.getSurfTris()
self.tmpatch = sgeom.TmPatch('patch',
self.mesh,
self.surf_tris,
icomp=self.tmcomp)
self.tmpatch.addSurfsys('ssys')
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
tet_hosts = gd.binTetsByAxis(self.mesh, steps.mpi.nhosts)
tri_hosts = gd.partitionTris(self.mesh, tet_hosts, self.surf_tris)
self.solver = solv.TetOpSplit(self.model, self.mesh, self.rng,
solv.EF_NONE, tet_hosts, tri_hosts)
self.solver.reset()
def gen_model():
mdl = smodel.Model()
X = smodel.Spec('X', mdl)
cytosolv = smodel.Volsys('cytosolv', mdl)
dif_X = smodel.Diff('diffX', cytosolv, X)
dif_X.setDcst(DCST)
return mdl
def test_masteq():
mdl = smod.Model()
A = smod.Spec('A', mdl)
volsys = smod.Volsys('vsys', mdl)
# Production
R1 = smod.Reac('R1', volsys, lhs=[], rhs=[A], kcst=KCST_f)
R2 = smod.Reac('R2', volsys, lhs=[A], rhs=[], kcst=KCST_b)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
comp1.addVolsys('vsys')
rng = srng.create('mt19937', 1000)
rng.initialize(int(time.time() % 4294967295))
sim = ssolv.Wmdirect(mdl, geom, rng)
sim.reset()
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res = numpy.zeros([ntpnts])
sim.restore('./validation_cp/cp/masteq')
for t in range(0, ntpnts):
sim.run(tpnts[t])
res[t] = sim.getCompCount('comp1', 'A')
def fact(x):
return (1 if x == 0 else x * fact(x - 1))
# Do cumulative count, but not comparing them all.
# Don't get over 50 (I hope)
steps_n_res = numpy.zeros(50)
for r in res:
steps_n_res[int(r)] += 1
for s in range(50):
steps_n_res[s] = steps_n_res[s] / ntpnts
passed = True
max_err = 0.0
k1 = KCST_b
k2 = KCST_f * (6.022e23 * 1.0e-15)
# Compare 5 to 15
for m in range(5, 16):
analy = (1.0 / fact(m)) * math.pow((k2 / k1), m) * math.exp(-(k2 / k1))
assert (tol_funcs.tolerable(steps_n_res[m], analy, tolerance))
def gen_model():
mdl = smodel.Model()
X = smodel.Spec('X', mdl)
A = smodel.Spec('A', mdl)
# Vol/surface systems
cytosolv = smodel.Volsys('cytosolv', mdl)
dif_X = smodel.Diff('diffX', cytosolv, X)
dif_X.setDcst(DCST)
reac_X = smodel.Reac('reacX', cytosolv, lhs=[A], rhs=[A, X])
return mdl
def test_forev():
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], rhs=[B], kcst=KCST_f)
R2 = smod.Reac('R2', volsys, lhs=[B], rhs=[A], kcst=KCST_b)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
comp1.addVolsys('vsys')
rng = srng.create('mt19937', 512)
rng.initialize(int(time.time() % 4294967295))
sim = ssolv.Wmdirect(mdl, geom, rng)
sim.reset()
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res_m = numpy.zeros([NITER, ntpnts, 2])
for i in range(0, NITER):
sim.restore('./validation_cp/cp/first_order_rev')
for t in range(0, ntpnts):
sim.run(tpnts[t])
res_m[i, t, 0] = sim.getCompConc('comp1', 'A') * 1e6
res_m[i, t, 1] = sim.getCompConc('comp1', 'B') * 1e6
mean_res = numpy.mean(res_m, 0)
Aeq = COUNT * (KCST_b /
KCST_f) / (1 +
(KCST_b / KCST_f)) / (VOL * 6.0221415e26) * 1e6
Beq = (COUNT / (VOL * 6.0221415e26)) * 1e6 - Aeq
max_err = 0.0
passed = True
for i in range(ntpnts):
if i < 7: continue
assert (tol_funcs.tolerable(mean_res[i, 0], Aeq, tolerance))
assert (tol_funcs.tolerable(mean_res[i, 1], Beq, tolerance))
def cbsa2steps(cbsa_model):
import steps.geom as swm
import steps.model as smodel
import steps.rng as srng
import steps.solver as ssolver
mdl = smodel.Model()
vsys = smodel.Volsys('vsys', mdl)
mols = [smodel.Spec('M'+str(i), mdl) for i in range(1,cbsa_model.exp_n_molecules)]
reactions = []
for i in range(1,cbsa_model.exp_n_reactions):
reactants = list(np.where(cbsa_model.expS[:,i] < 0)[0])
reactants_sto = list(cbsa_model.expS[:,i][reactants]*-1)
modifiers = list(np.where(cbsa_model.expR[:,i] > 0)[0])
modifiers_sto = list(cbsa_model.expR[:,i][modifiers])
products = list(np.where(cbsa_model.expS[:,i] > 0)[0])
products_sto = list(cbsa_model.expS[:,i][products])
reactants += modifiers
reactants_sto += modifiers_sto
products += modifiers
products_sto += modifiers_sto
reactants_objs = [[mols[reactants[j]-1] for k in range(reactants_sto[j])] for j in range(len(reactants))]
reactants_objs = [item for sublist in reactants_objs for item in sublist]
products_objs = [[mols[products[j]-1] for k in range(products_sto[j])] for j in range(len(products))]
products_objs = [item for sublist in products_objs for item in sublist]
reactions.append(smodel.Reac("R"+str(i), vsys, lhs=reactants_objs, rhs=products_objs, kcst=cbsa_model.exp_k[i]))
wmgeom = swm.Geom()
comp = swm.Comp('comp', wmgeom)
comp.addVolsys('vsys')
comp.setVol(1.6667e-21)
r = srng.create('mt19937', 256)
r.initialize(int(timer()))
sim = ssolver.Wmdirect(mdl, wmgeom, r)
sim.reset()
for i in range(1,cbsa_model.exp_n_molecules):
sim.setCompConc('comp', 'M'+str(i), cbsa_model.exp_x0[i]*1e-6)
return sim
def test_foirev():
mdl = smod.Model()
A = smod.Spec('A', mdl)
volsys = smod.Volsys('vsys', mdl)
R1 = smod.Reac('R1', volsys, lhs=[A], rhs=[], kcst=KCST)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
comp1.addVolsys('vsys')
rng = srng.create('mt19937', 1000)
rng.initialize(int(time.time() % 4294967295))
sim = ssolv.Wmdirect(mdl, geom, rng)
sim.reset()
tpnts = np.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res_m = np.zeros([NITER, ntpnts, 1])
res_std1 = np.zeros([ntpnts, 1])
res_std2 = np.zeros([ntpnts, 1])
for i in range(0, NITER):
sim.restore('./validation_cp/cp/first_order_irev')
for t in range(0, ntpnts):
sim.run(tpnts[t])
res_m[i, t, 0] = sim.getCompCount('comp1', 'A')
mean_res = np.mean(res_m, 0)
std_res = np.std(res_m, 0)
m_tol = 0
s_tol = 0
passed = True
for i in range(ntpnts):
if i == 0: continue
analy = N * np.exp(-KCST * tpnts[i])
std = np.power((N * (np.exp(-KCST * tpnts[i])) *
(1 - (np.exp(-KCST * tpnts[i])))), 0.5)
if not tol_funcs.tolerable(analy, mean_res[i], tolerance):
passed = False
assert (tol_funcs.tolerable(std, std_res[i], tolerance))
def gen_model():
mdl = smod.Model()
# The chemical species
A = smod.Spec('A', mdl)
B = smod.Spec('B', mdl)
C = smod.Spec('C', mdl)
D = smod.Spec('D', mdl)
E = smod.Spec('E', mdl)
F = smod.Spec('F', mdl)
G = smod.Spec('G', mdl)
H = smod.Spec('H', mdl)
I = smod.Spec('I', mdl)
J = smod.Spec('J', mdl)
volsys = smod.Volsys('vsys',mdl)
R1 = smod.Reac('R1', volsys, lhs = [A, B], rhs = [C], kcst = 1000.0e6)
R2 = smod.Reac('R2', volsys, lhs = [C], rhs = [A,B], kcst = 100)
R3 = smod.Reac('R3', volsys, lhs = [C, D], rhs = [E], kcst = 100e6)
R4 = smod.Reac('R4', volsys, lhs = [E], rhs = [C,D], kcst = 10)
R5 = smod.Reac('R5', volsys, lhs = [F, G], rhs = [H], kcst = 10e6)
R6 = smod.Reac('R6', volsys, lhs = [H], rhs = [F,G], kcst = 1)
R7 = smod.Reac('R7', volsys, lhs = [H, I], rhs = [J], kcst = 1e6)
R8 = smod.Reac('R8', volsys, lhs = [J], rhs = [H,I], kcst = 0.1*10)
# The diffusion rules
D1 = smod.Diff('D1', volsys, A, 100e-12)
D2 = smod.Diff('D2', volsys, B, 90e-12)
D3 = smod.Diff('D3', volsys, C, 80e-12)
D4 = smod.Diff('D4', volsys, D, 70e-12)
D5 = smod.Diff('D5', volsys, E, 60e-12)
D6 = smod.Diff('D6', volsys, F, 50e-12)
D7 = smod.Diff('D7', volsys, G, 40e-12)
D8 = smod.Diff('D8', volsys, H, 30e-12)
D9 = smod.Diff('D9', volsys, I, 20e-12)
D10 = smod.Diff('D10', volsys, J, 10e-12)
return mdl
def setUp(self):
mdl = smodel.Model()
self.v1 = 1e-20
self.v2 = 2e-20
self.a1 = 3e-14
self.kreac = 200.0
self.ksreac = 100.0
S1 = smodel.Spec('S1', mdl)
S2 = smodel.Spec('S2', mdl)
S1S2 = smodel.Spec('S1S2', mdl)
vsys = smodel.Volsys('vsys', mdl)
ssys = smodel.Surfsys('ssys', mdl)
smodel.Reac('reac', vsys, lhs=[S1, S2], rhs=[S2, S2], kcst=self.kreac)
smodel.SReac('sreac', ssys, ilhs=[S1], slhs=[S2], srhs=[S1S2], kcst=self.ksreac)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom)
comp1.setVol(self.v1)
comp1.addVolsys('vsys')
comp2 = sgeom.Comp('comp2', geom)
comp2.setVol(self.v2)
comp1.addVolsys('vsys')
patch = sgeom.Patch('patch', geom, comp1, comp2)
patch.addSurfsys('ssys')
patch.setArea(self.a1)
self.mdl, self.geom, self.rng = mdl, geom, srng.create('mt19937',512)
self.rng.initialize(1234)
def test_masteq():
"Reaction - Production and degradation (Wmdirect)"
########################################################################
KCST_f = 100 / (6.022e23 * 1.0e-15) # The reaction constant, production
KCST_b = 10 # The reaction constant, degradation
VOL = 1.0e-18
DT = 0.1 # Sampling time-step
INT = 200000.1 # Sim endtime
# Tolerance for the comparison:
# In tests with good code <1% fail with tolerance of 1.5%
tolerance = 1.5 / 100
########################################################################
mdl = smod.Model()
A = smod.Spec('A', mdl)
volsys = smod.Volsys('vsys', mdl)
# Production
R1 = smod.Reac('R1', volsys, lhs=[], rhs=[A], kcst=KCST_f)
R2 = smod.Reac('R2', volsys, lhs=[A], rhs=[], kcst=KCST_b)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
comp1.addVolsys('vsys')
rng = srng.create('r123', 1000)
rng.initialize(1000)
sim = ssolv.Wmdirect(mdl, geom, rng)
sim.reset()
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res = numpy.zeros([ntpnts])
sim.reset()
sim.setCompCount('comp1', 'A', 0)
for t in range(0, ntpnts):
sim.run(tpnts[t])
res[t] = sim.getCompCount('comp1', 'A')
def fact(x):
return (1 if x == 0 else x * fact(x - 1))
# Do cumulative count, but not comparing them all.
# Don't get over 50 (I hope)
steps_n_res = numpy.zeros(50)
for r in res:
steps_n_res[int(r)] += 1
for s in range(50):
steps_n_res[s] = steps_n_res[s] / ntpnts
passed = True
max_err = 0.0
k1 = KCST_b
k2 = KCST_f * (6.022e23 * 1.0e-15)
# Compare 5 to 15
for m in range(5, 16):
analy = (1.0 / fact(m)) * math.pow((k2 / k1), m) * math.exp(-(k2 / k1))
assert tol_funcs.tolerable(steps_n_res[m], analy, tolerance)
VOL = 1.0e-18
NITER = 100000 # The number of iterations
DT = 0.1 # Sampling time-step
INT = 1.1 # Sim endtime
# Tolerance for the comparison:
# In test runs, with good code, < 1% will fail with a 1.5% tolerance
tolerance = 2.0 / 100
########################################################################
mdl = smod.Model()
A = smod.Spec('A', mdl)
volsys = smod.Volsys('vsys', mdl)
R1 = smod.Reac('R1', volsys, lhs=[A], rhs=[], kcst=KCST)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
comp1.addVolsys('vsys')
rng = srng.create('mt19937', 1000)
rng.initialize(int(time.time() % 4294967295))
sim = ssolv.Wmdirect(mdl, geom, rng)
sim.reset()
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
def run_sim():
# Set up and run the simulations once, before the tests
# analyze the results.
##################### First order irreversible #########################
global KCST_foi, N_foi, tolerance_foi
KCST_foi = 5 # The reaction constant
N_foi = 50 # Can set count or conc
NITER_foi = 1 # The number of iterations
# Tolerance for the comparison:
tolerance_foi = 1.0e-4 / 100
####################### First order reversible #########################
global KCST_f_for, KCST_b_for, COUNT_for, tolerance_for
KCST_f_for = 20.0 # The reaction constant
KCST_b_for = 5.0
COUNT_for = 100000 # Can set count or conc
NITER_for = 1 # The number of iterations
tolerance_for = 1.0e-4 / 100
####################### Second order irreversible A2 ###################
global KCST_soA2, CONCA_soA2, tolerance_soA2
KCST_soA2 = 10.0e6 # The reaction constant
CONCA_soA2 = 10.0e-6
NITER_soA2 = 1 # The number of iterations
tolerance_soA2 = 1.0e-4 / 100
####################### Second order irreversible AA ###################
global KCST_soAA, CONCA_soAA, CONCB_soAA, tolerance_soAA
KCST_soAA = 5.0e6 # The reaction constant
CONCA_soAA = 20.0e-6
CONCB_soAA = CONCA_soAA
NITER_soAA = 1 # The number of iterations
tolerance_soAA = 1.0e-4 / 100
####################### Second order irreversible AB ###################
global KCST_soAB, CONCA_soAB, CONCB_soAB, tolerance_soAB
KCST_soAB = 5.0e6 # The reaction constant
CONCA_soAB = 1.0e-6
n_soAB = 2
CONCB_soAB = CONCA_soAB / n_soAB
NITER_soAB = 1 # The number of iterations
tolerance_soAB = 1.0e-4 / 100
####################### Third order irreversible A3 ###################
global KCST_toA3, CONCA_toA3, tolerance_toA3
KCST_toA3 = 1.0e12 # The reaction constant
CONCA_toA3 = 10.0e-6
NITER_toA3 = 1 # The number of iterations
tolerance_toA3 = 1.0e-4 / 100
####################### Third order irreversible A2B ###################
global KCST_toA2B, CONCA_toA2B, CONCB_toA2B, tolerance_toA2B
KCST_toA2B = 0.1e12 # The reaction constant
CONCA_toA2B = 30.0e-6
CONCB_toA2B = 20.0e-6
NITER_toA2B = 1 # The number of iterations
tolerance_toA2B = 1.0e-4 / 100
####################### Second order irreversible 2D ###################
global COUNTA_so2d, COUNTB_so2d, CCST_so2d, tolerance_so2d
COUNTA_so2d = 100.0
n_so2d = 2.0
COUNTB_so2d = COUNTA_so2d / n_so2d
KCST_so2d = 10.0e10 # The reaction constant
AREA_so2d = 10.0e-12
NITER_so2d = 1 # The number of iterations
tolerance_so2d = 1.0e-4 / 100
############################ Common parameters ########################
global VOL
DT = 0.1 # Sampling time-step
INT = 1.1 # Sim endtime
NITER_max = 1
########################################################################
mdl = smod.Model()
volsys = smod.Volsys('vsys', mdl)
surfsys = smod.Surfsys('ssys', mdl)
# First order irreversible
A_foi = smod.Spec('A_foi', mdl)
A_foi_diff = smod.Diff('A_foi_diff', volsys, A_foi, 0.01e-12)
R1_foi = smod.Reac('R1_foi', volsys, lhs=[A_foi], rhs=[], kcst=KCST_foi)
# First order reversible
A_for = smod.Spec('A_for', mdl)
B_for = smod.Spec('B_for', mdl)
A_for_diff = smod.Diff('A_for_diff', volsys, A_for, 0.01e-12)
B_for_diff = smod.Diff('B_for_diff', volsys, B_for, 0.01e-12)
R1_for = smod.Reac('R1_for',
volsys,
lhs=[A_for],
rhs=[B_for],
kcst=KCST_f_for)
R2_for = smod.Reac('R2_for',
volsys,
lhs=[B_for],
rhs=[A_for],
kcst=KCST_b_for)
# Second order irreversible A2
A_soA2 = smod.Spec('A_soA2', mdl)
C_soA2 = smod.Spec('C_soA2', mdl)
A_soA2_diff = smod.Diff('A_soA2_diff', volsys, A_soA2, 1e-12)
R1_soA2 = smod.Reac('R1_soA2',
volsys,
lhs=[A_soA2, A_soA2],
rhs=[C_soA2],
kcst=KCST_soA2)
# Second order irreversible AA
A_soAA = smod.Spec('A_soAA', mdl)
B_soAA = smod.Spec('B_soAA', mdl)
C_soAA = smod.Spec('C_soAA', mdl)
A_soAA_diff = smod.Diff('A_soAA_diff', volsys, A_soAA, 0.2e-12)
B_soAA_diff = smod.Diff('B_soAA_diff', volsys, B_soAA, 0.2e-12)
R1_soAA = smod.Reac('R1_soAA',
volsys,
lhs=[A_soAA, B_soAA],
rhs=[C_soAA],
kcst=KCST_soAA)
# Second order irreversible AB
A_soAB = smod.Spec('A_soAB', mdl)
B_soAB = smod.Spec('B_soAB', mdl)
C_soAB = smod.Spec('C_soAB', mdl)
A_soAB_diff = smod.Diff('A_soAB_diff', volsys, A_soAB, 0.1e-12)
B_soAB_diff = smod.Diff('B_soAB_diff', volsys, B_soAB, 0.1e-12)
R1_soAB = smod.Reac('R1_soAB',
volsys,
lhs=[A_soAB, B_soAB],
rhs=[C_soAB],
kcst=KCST_soAB)
# Third order irreversible A3
A_toA3 = smod.Spec('A_toA3', mdl)
C_toA3 = smod.Spec('C_toA3', mdl)
A_soA3_diff = smod.Diff('A_soA3_diff', volsys, A_toA3, 0.2e-12)
R1_toA3 = smod.Reac('R1_toA3',
volsys,
lhs=[A_toA3, A_toA3, A_toA3],
rhs=[C_toA3],
kcst=KCST_toA3)
# Third order irreversible A2B
A_toA2B = smod.Spec('A_toA2B', mdl)
B_toA2B = smod.Spec('B_toA2B', mdl)
C_toA2B = smod.Spec('C_toA2B', mdl)
A_soA2B_diff = smod.Diff('A_soA2B_diff', volsys, A_toA2B, 0.1e-12)
B_soA2B_diff = smod.Diff('B_soA2B_diff', volsys, B_toA2B, 0.1e-12)
R1_toA3 = smod.Reac('R1_toA2B',
volsys,
lhs=[A_toA2B, A_toA2B, B_toA2B],
rhs=[C_toA2B],
kcst=KCST_toA2B)
# Second order irreversible 2D
A_so2d = smod.Spec('A_so2d', mdl)
B_so2d = smod.Spec('B_so2d', mdl)
C_so2d = smod.Spec('C_so2d', mdl)
A_so2d_diff = smod.Diff('A_so2d_diff', surfsys, A_so2d, 1.0e-12)
B_so2d_diff = smod.Diff('B_so2d_diff', surfsys, B_so2d, 1.0e-12)
SR1_so2d = smod.SReac('SR1_so2d',
surfsys,
slhs=[A_so2d, B_so2d],
srhs=[C_so2d],
kcst=KCST_so2d)
mesh = smeshio.importAbaqus('validation_rd/meshes/sphere_rad1_37tets.inp',
1e-6)[0]
VOL = mesh.getMeshVolume()
comp1 = sgeom.TmComp('comp1', mesh, range(mesh.ntets))
comp1.addVolsys('vsys')
patch1 = sgeom.TmPatch('patch1', mesh, mesh.getSurfTris(), comp1)
patch1.addSurfsys('ssys')
CCST_so2d = KCST_so2d / (6.02214179e23 * patch1.getArea())
rng = srng.create('r123', 512)
rng.initialize(1000)
sim = ssolv.TetODE(mdl, mesh, rng)
sim.setTolerances(1e-9, 1e-7)
global tpnts, ntpnts
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res_m_foi = numpy.zeros([NITER_foi, ntpnts, 1])
res_m_for = numpy.zeros([NITER_for, ntpnts, 2])
res_m_soA2 = numpy.zeros([NITER_soA2, ntpnts, 2])
res_m_soAA = numpy.zeros([NITER_soAA, ntpnts, 3])
res_m_soAB = numpy.zeros([NITER_soAB, ntpnts, 3])
res_m_toA3 = numpy.zeros([NITER_toA3, ntpnts, 2])
res_m_toA2B = numpy.zeros([NITER_toA2B, ntpnts, 3])
res_m_so2d = numpy.zeros([NITER_so2d, ntpnts, 3])
for i in range(0, NITER_max):
if i < NITER_foi:
sim.setCompCount('comp1', 'A_foi', N_foi)
if i < NITER_for:
sim.setCompCount('comp1', 'A_for', COUNT_for)
sim.setCompCount('comp1', 'B_for', 0.0)
if i < NITER_soA2:
sim.setCompConc('comp1', 'A_soA2', CONCA_soA2)
if i < NITER_soAA:
sim.setCompConc('comp1', 'A_soAA', CONCA_soAA)
sim.setCompConc('comp1', 'B_soAA', CONCB_soAA)
if i < NITER_soAB:
sim.setCompConc('comp1', 'A_soAB', CONCA_soAB)
sim.setCompConc('comp1', 'B_soAB', CONCB_soAB)
if i < NITER_toA3:
sim.setCompConc('comp1', 'A_toA3', CONCA_toA3)
if i < NITER_toA2B:
sim.setCompConc('comp1', 'A_toA2B', CONCA_toA2B)
sim.setCompConc('comp1', 'B_toA2B', CONCB_toA2B)
if i < NITER_so2d:
sim.setPatchCount('patch1', 'A_so2d', COUNTA_so2d)
sim.setPatchCount('patch1', 'B_so2d', COUNTB_so2d)
for t in range(0, ntpnts):
sim.run(tpnts[t])
if i < NITER_foi:
res_m_foi[i, t, 0] = sim.getCompCount('comp1', 'A_foi')
if i < NITER_for:
res_m_for[i, t, 0] = sim.getCompConc('comp1', 'A_for') * 1e6
res_m_for[i, t, 1] = sim.getCompConc('comp1', 'B_for') * 1e6
if i < NITER_soA2:
res_m_soA2[i, t, 0] = sim.getCompConc('comp1', 'A_soA2')
if i < NITER_soAA:
res_m_soAA[i, t, 0] = sim.getCompConc('comp1', 'A_soAA')
res_m_soAA[i, t, 1] = sim.getCompConc('comp1', 'B_soAA')
if i < NITER_soAB:
res_m_soAB[i, t, 0] = sim.getCompConc('comp1', 'A_soAB')
res_m_soAB[i, t, 1] = sim.getCompConc('comp1', 'B_soAB')
if i < NITER_toA3:
res_m_toA3[i, t, 0] = sim.getCompConc('comp1', 'A_toA3')
if i < NITER_toA2B:
res_m_toA2B[i, t, 0] = sim.getCompConc('comp1', 'A_toA2B')
res_m_toA2B[i, t, 1] = sim.getCompConc('comp1', 'B_toA2B')
res_m_toA2B[i, t, 2] = sim.getCompConc('comp1', 'C_toA2B')
if i < NITER_so2d:
res_m_so2d[i, t, 0] = sim.getPatchCount('patch1', 'A_so2d')
res_m_so2d[i, t, 1] = sim.getPatchCount('patch1', 'B_so2d')
global mean_res_foi
mean_res_foi = numpy.mean(res_m_foi, 0)
global mean_res_for
mean_res_for = numpy.mean(res_m_for, 0)
global mean_res_soA2
mean_res_soA2 = numpy.mean(res_m_soA2, 0)
global mean_res_soAA
mean_res_soAA = numpy.mean(res_m_soAA, 0)
global mean_res_soAB
mean_res_soAB = numpy.mean(res_m_soAB, 0)
global mean_res_toA3
mean_res_toA3 = numpy.mean(res_m_toA3, 0)
global mean_res_toA2B
mean_res_toA2B = numpy.mean(res_m_toA2B, 0)
global mean_res_so2d
mean_res_so2d = numpy.mean(res_m_so2d, 0)
global ran_sim
ran_sim = True
import steps.model as smodel
#import package steps.model that contains all the definitions of
#the objects and functions you need to describe the physics and
#chemistory.
mdl = smodel.Model()
#mdl variable for discribing model.
#create a top-level container object for our model this top model
#container is required for all simulations in STEPS.
molX1bar = smodel.Spec('molX1bar', mdl)
molY1 = smodel.Spec('molY1', mdl)
#create 2 steps.model.Spec objects corresponding to 2 chamical
#spicies
vsys = smodel.Volsys('vsys', mdl)
#create a volume system
#volume systems art container objects that group a number of
#stoichimetric reaction rules.
c1reac_f = smodel.Reac('c1reac_f', vsys, lhs=[molX1bar], rhs=[molY1], kcst=0.2)
#create the reaction rules themselves
#what is cicst = 0.3e6?
import steps.geom as swm
#import the geometry module that contains the objects used to
#define the geometry, namely steps.geom.
wmgeom = swm.Geom()
#generate parent container object
# ip3r_model.py
#
# Katri Hituri
# IP3R model by Doi et al. 2005
###########
# Import packages
import steps.model as smodel
import steps.geom as sgeom
# *MODEL*
#
mdl = smodel.Model()
volsys = smodel.Volsys('vsys', mdl) # Volume system
surfsys = smodel.Surfsys('ssys', mdl) # Surface system
# CHEMICAL SPECIES
Ca = smodel.Spec('Ca', mdl) # Calcium
IP3 = smodel.Spec('IP3', mdl) # IP3
# IP3 receptor states
R = smodel.Spec('R', mdl) # IP3 receptor with no bound ligands
RIP3 = smodel.Spec('RIP3', mdl) # bound IP3
Ropen = smodel.Spec('Ropen', mdl) # bound IP3 and Ca (open)
RCa = smodel.Spec('RCa', mdl) # 1 bound Ca to inactivation site
RCa2 = smodel.Spec('RCa2', mdl) # 2 bound Ca to inactivation sites
RCa3 = smodel.Spec('RCa3', mdl) # 3 bound Ca to inactivation sites
RCa4 = smodel.Spec('RCa4', mdl) # 4 bound Ca to inactivation sites
def setUp(self):
mdl = smodel.Model()
S1 = smodel.Spec('S1', mdl)
vsys = smodel.Volsys('vsys', mdl)
ssys = smodel.Surfsys('ssys', mdl)
smodel.Reac('R01', vsys, lhs=[S1], rhs=[S1], kcst=1)
smodel.SReac('SR01', ssys, slhs=[S1], srhs=[S1], kcst=1)
vrange = [-200.0e-3, 50e-3, 1e-3]
vrate = lambda v: 2.0
Chan1 = smodel.Chan('Chan1', mdl)
chanop = smodel.ChanState('chanop', mdl, Chan1)
chancl = smodel.ChanState('chancl', mdl, Chan1)
smodel.VDepSReac('VDSR01',
ssys,
slhs=[chancl],
srhs=[chanop],
k=vrate,
vrange=vrange)
smodel.VDepSReac('VDSR02',
ssys,
srhs=[chancl],
slhs=[chanop],
k=vrate,
vrange=vrange)
Chan1_Ohm_I = smodel.OhmicCurr('Chan1_Ohm_I',
ssys,
chanstate=chanop,
g=20e-12,
erev=-77e-3)
if __name__ == "__main__":
self.mesh = meshio.importAbaqus('meshes/test.inp', 1e-7)[0]
else:
self.mesh = meshio.importAbaqus(
'missing_solver_methods_test/meshes/test.inp', 1e-7)[0]
comp1 = sgeom.TmComp('comp1', self.mesh, range(self.mesh.countTets()))
comp1.addVolsys('vsys')
patch1 = sgeom.TmPatch('patch1', self.mesh, self.mesh.getSurfTris(),
comp1)
patch1.addSurfsys('ssys')
self.c1ROIInds = range(10)
self.p1ROIInds = range(5)
self.mesh.addROI('comp1ROI', sgeom.ELEM_TET, self.c1ROIInds)
self.mesh.addROI('patch1ROI', sgeom.ELEM_TRI, self.p1ROIInds)
membrane = sgeom.Memb('membrane', self.mesh, [patch1], opt_method=1)
rng = srng.create('mt19937', 512)
rng.initialize(1234)
self.sim = ssolver.Tetexact(mdl, self.mesh, rng, True)
self.sim.setEfieldDT(1e-4)
self.sim.reset()
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # STEPS - STochastic Engine for Pathway Simulation # Copyright (C) 2007-2011 Okinawa Institute of Science and Technology, Japan. # Copyright (C) 2003-2006 University of Antwerp, Belgium. # # See the file AUTHORS for details. # # This file is part of STEPS. # # STEPS 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. # # STEPS 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 <http://www.gnu.org/licenses/>. # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # import steps.model as smod import steps.geom as sgeom import steps.rng as srng import steps.solver as ssolv import math import time import steps.utilities.meshio as smeshio
CBCaf = smodel.Spec('CBCaf', mdl_det)
# CBCaCa
CBCaCa = smodel.Spec('CBCaCa', mdl_det)
# PV
PV = smodel.Spec('PV', mdl_det)
# PVMg
PVMg = smodel.Spec('PVMg', mdl_det)
# PVCa
PVCa = smodel.Spec('PVCa', mdl_det)
# Mg
Mg = smodel.Spec('Mg', mdl_det)
# Vol/surface systems
vsys_stoch = smodel.Volsys('vsys_stoch', mdl_stoch)
ssys_stoch = smodel.Surfsys('ssys_stoch', mdl_stoch)
vsys_det = smodel.Volsys('vsys_det', mdl_det)
ssys_det = smodel.Surfsys('ssys_det', mdl_det)
# Diffusions
diff_Ca = smodel.Diff('diff_Ca', vsys_det, Ca_det)
diff_Ca.setDcst(DCST)
diff_CBsf = smodel.Diff('diff_CBsf', vsys_det, CBsf)
diff_CBsf.setDcst(DCB)
diff_CBsCa = smodel.Diff('diff_CBsCa', vsys_det, CBsCa)
diff_CBsCa.setDcst(DCB)
diff_CBCaf = smodel.Diff('diff_CBCaf', vsys_det, CBCaf)
diff_CBCaf.setDcst(DCB)
diff_CBCaCa = smodel.Diff('diff_CBCaCa', vsys_det, CBCaCa)
def test_masteqdiff():
SCALE = 1.0
KCST_f = 100e6 * SCALE # The reaction constant, degradation
KCST_b = (20.0e-10 * SCALE) # The reaction constant, production
DCST_A = 20e-12
DCST_B = 20e-12
B0 = 1 # The number of B moleucles
DT = 0.1 # Sampling time-step
INT = 50000.1 # Sim endtime
filename = 'cube_1_1_1_73tets.inp'
# A tolerance of 7.5% will fail <1% of the time
tolerance = 7.5 / 100
########################################################################
mdl = smod.Model()
A = smod.Spec('A', mdl)
B = smod.Spec('B', mdl)
volsys = smod.Volsys('vsys', mdl)
diffA = smod.Diff('diffA', volsys, A)
diffA.setDcst(DCST_A)
diffB = smod.Diff('diffB', volsys, B)
diffB.setDcst(DCST_B)
# Production
R1 = smod.Reac('R1', volsys, lhs=[A, B], rhs=[B], kcst=KCST_f)
R2 = smod.Reac('R2', volsys, lhs=[], rhs=[A], kcst=KCST_b)
geom = meshio.loadMesh('./validation_rd/meshes/' + filename)[0]
comp1 = sgeom.TmComp('comp1', geom, range(geom.ntets))
comp1.addVolsys('vsys')
rng = srng.create('mt19937', 512)
rng.initialize(int(time.time() % 4294967295))
sim = ssolv.Tetexact(mdl, geom, rng)
sim.reset()
tpnts = np.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res = np.zeros([ntpnts])
res_std1 = np.zeros([ntpnts])
res_std2 = np.zeros([ntpnts])
sim.restore('./validation_cp/cp/masteq_diff')
b_time = time.time()
for t in range(0, ntpnts):
sim.run(tpnts[t])
res[t] = sim.getCompCount('comp1', 'A')
def fact(x):
return (1 if x == 0 else x * fact(x - 1))
# Do cumulative count, but not comparing them all.
# Don't get over 50 (I hope)
steps_n_res = np.zeros(50)
for r in res:
steps_n_res[int(r)] += 1
for s in range(50):
steps_n_res[s] = steps_n_res[s] / ntpnts
passed = True
max_err = 0.0
k1 = KCST_f / 6.022e23
k2 = KCST_b * 6.022e23
v = comp1.getVol() * 1.0e3 # litres
for m in range(5, 11):
analy = (1.0 / fact(m)) * np.power(
(k2 * v * v) / (B0 * k1), m) * np.exp(-((k2 * v * v) / (k1 * B0)))
assert (tol_funcs.tolerable(steps_n_res[m], analy, tolerance))
def run_sim():
# Set up and run the simulations once, before the tests
# analyze the results.
##################### First order irreversible #########################
global KCST_foi, N_foi, tolerance_foi
KCST_foi = 5 # The reaction constant
N_foi = 50 # Can set count or conc
NITER_foi = 100000 # The number of iterations
# Tolerance for the comparison:
# In test runs, with good code, < 1% will fail with a 1.5% tolerance
tolerance_foi = 2.0 / 100
####################### First order reversible #########################
global KCST_f_for, KCST_b_for, COUNT_for, tolerance_for
KCST_f_for = 10.0 # The reaction constant
KCST_b_for = 2.0
COUNT_for = 100000 # Can set count or conc
NITER_for = 10 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_for = 1.0 / 100
####################### Second order irreversible A2 ###################
global KCST_soA2, CONCA_soA2, tolerance_soA2
KCST_soA2 = 10.0e6 # The reaction constant
CONCA_soA2 = 10.0e-6
NITER_soA2 = 1000 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 2%
tolerance_soA2 = 1.0 / 100
####################### Second order irreversible AA ###################
global KCST_soAA, CONCA_soAA, CONCB_soAA, tolerance_soAA
KCST_soAA = 50.0e6 # The reaction constant
CONCA_soAA = 20.0e-6
CONCB_soAA = CONCA_soAA
NITER_soAA = 1000 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_soAA = 1.0 / 100
####################### Second order irreversible AB ###################
global KCST_soAB, CONCA_soAB, CONCB_soAB, tolerance_soAB
KCST_soAB = 5.0e6 # The reaction constant
CONCA_soAB = 1.0e-6
n_soAB = 2
CONCB_soAB = CONCA_soAB / n_soAB
NITER_soAB = 1000 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_soAB = 1.0 / 100
####################### Third order irreversible A3 ###################
global KCST_toA3, CONCA_toA3, tolerance_toA3
KCST_toA3 = 1.0e12 # The reaction constant
CONCA_toA3 = 100.0e-6
NITER_toA3 = 1000 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_toA3 = 1.0 / 100
####################### Third order irreversible A2B ###################
global KCST_toA2B, CONCA_toA2B, CONCB_toA2B, tolerance_toA2B
KCST_toA2B = 0.1e12 # The reaction constant
CONCA_toA2B = 30.0e-6
CONCB_toA2B = 20.0e-6
NITER_toA2B = 1000 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_toA2B = 1.0 / 100
####################### Second order irreversible 2D ###################
global COUNTA_so2d, COUNTB_so2d, CCST_so2d, tolerance_so2d
COUNTA_so2d = 100.0
n_so2d = 2.0
COUNTB_so2d = COUNTA_so2d / n_so2d
KCST_so2d = 10.0e10 # The reaction constant
AREA_so2d = 10.0e-12
CCST_so2d = KCST_so2d / (6.02214179e23 * AREA_so2d)
NITER_so2d = 1000 # The number of iterations
# In tests fewer than 0.1% fail with tolerance of 2%
tolerance_so2d = 2.0 / 100
############################ Common parameters ########################
global VOL
DT = 0.1 # Sampling time-step
INT = 1.1 # Sim endtime
VOL = 9.0e-18
NITER_max = 100000
########################################################################
mdl = smod.Model()
volsys = smod.Volsys('vsys', mdl)
surfsys = smod.Surfsys('ssys', mdl)
# First order irreversible
A_foi = smod.Spec('A_foi', mdl)
R1_foi = smod.Reac('R1_foi', volsys, lhs=[A_foi], rhs=[], kcst=KCST_foi)
# First order reversible
A_for = smod.Spec('A_for', mdl)
B_for = smod.Spec('B_for', mdl)
R1_for = smod.Reac('R1_for',
volsys,
lhs=[A_for],
rhs=[B_for],
kcst=KCST_f_for)
R2_for = smod.Reac('R2_for',
volsys,
lhs=[B_for],
rhs=[A_for],
kcst=KCST_b_for)
# Second order irreversible A2
A_soA2 = smod.Spec('A_soA2', mdl)
C_soA2 = smod.Spec('C_soA2', mdl)
R1_soA2 = smod.Reac('R1_soA2',
volsys,
lhs=[A_soA2, A_soA2],
rhs=[C_soA2],
kcst=KCST_soA2)
# Second order irreversible AA
A_soAA = smod.Spec('A_soAA', mdl)
B_soAA = smod.Spec('B_soAA', mdl)
C_soAA = smod.Spec('C_soAA', mdl)
R1_soAA = smod.Reac('R1_soAA',
volsys,
lhs=[A_soAA, B_soAA],
rhs=[C_soAA],
kcst=KCST_soAA)
# Second order irreversible AB
A_soAB = smod.Spec('A_soAB', mdl)
B_soAB = smod.Spec('B_soAB', mdl)
C_soAB = smod.Spec('C_soAB', mdl)
R1_soAB = smod.Reac('R1_soAB',
volsys,
lhs=[A_soAB, B_soAB],
rhs=[C_soAB],
kcst=KCST_soAB)
# Third order irreversible A3
A_toA3 = smod.Spec('A_toA3', mdl)
C_toA3 = smod.Spec('C_toA3', mdl)
R1_toA3 = smod.Reac('R1_toA3',
volsys,
lhs=[A_toA3, A_toA3, A_toA3],
rhs=[C_toA3],
kcst=KCST_toA3)
# Third order irreversible A2B
A_toA2B = smod.Spec('A_toA2B', mdl)
B_toA2B = smod.Spec('B_toA2B', mdl)
C_toA2B = smod.Spec('C_toA2B', mdl)
R1_toA3 = smod.Reac('R1_toA2B',
volsys,
lhs=[A_toA2B, A_toA2B, B_toA2B],
rhs=[C_toA2B],
kcst=KCST_toA2B)
# Second order irreversible 2D
A_so2d = smod.Spec('A_so2d', mdl)
B_so2d = smod.Spec('B_so2d', mdl)
C_so2d = smod.Spec('C_so2d', mdl)
SR1_so2d = smod.SReac('SR1_so2d',
surfsys,
slhs=[A_so2d, B_so2d],
srhs=[C_so2d],
kcst=KCST_so2d)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
comp1.addVolsys('vsys')
patch1 = sgeom.Patch('patch1', geom, comp1, area=AREA_so2d)
patch1.addSurfsys('ssys')
rng = srng.create('r123', 512)
rng.initialize(1000)
sim = ssolv.Wmdirect(mdl, geom, rng)
sim.reset()
global tpnts, ntpnts
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res_m_foi = numpy.zeros([NITER_foi, ntpnts, 1])
res_std1_foi = numpy.zeros([ntpnts, 1])
res_std2_foi = numpy.zeros([ntpnts, 1])
res_m_for = numpy.zeros([NITER_for, ntpnts, 2])
res_m_soA2 = numpy.zeros([NITER_soA2, ntpnts, 2])
res_m_soAA = numpy.zeros([NITER_soAA, ntpnts, 3])
res_m_soAB = numpy.zeros([NITER_soAB, ntpnts, 3])
res_m_toA3 = numpy.zeros([NITER_toA3, ntpnts, 2])
res_m_toA2B = numpy.zeros([NITER_toA2B, ntpnts, 3])
res_m_so2d = numpy.zeros([NITER_so2d, ntpnts, 3])
for i in range(0, NITER_max):
sim.reset()
if i < NITER_foi:
sim.setCompCount('comp1', 'A_foi', N_foi)
if i < NITER_for:
sim.setCompCount('comp1', 'A_for', COUNT_for)
sim.setCompCount('comp1', 'B_for', 0.0)
if i < NITER_soA2:
sim.setCompConc('comp1', 'A_soA2', CONCA_soA2)
if i < NITER_soAA:
sim.setCompConc('comp1', 'A_soAA', CONCA_soAA)
sim.setCompConc('comp1', 'B_soAA', CONCB_soAA)
if i < NITER_soAB:
sim.setCompConc('comp1', 'A_soAB', CONCA_soAB)
sim.setCompConc('comp1', 'B_soAB', CONCB_soAB)
if i < NITER_toA3:
sim.setCompConc('comp1', 'A_toA3', CONCA_toA3)
if i < NITER_toA2B:
sim.setCompConc('comp1', 'A_toA2B', CONCA_toA2B)
sim.setCompConc('comp1', 'B_toA2B', CONCB_toA2B)
if i < NITER_so2d:
sim.setPatchCount('patch1', 'A_so2d', COUNTA_so2d)
sim.setPatchCount('patch1', 'B_so2d', COUNTB_so2d)
for t in range(0, ntpnts):
sim.run(tpnts[t])
if i < NITER_foi:
res_m_foi[i, t, 0] = sim.getCompCount('comp1', 'A_foi')
if i < NITER_for:
res_m_for[i, t, 0] = sim.getCompConc('comp1', 'A_for') * 1e6
res_m_for[i, t, 1] = sim.getCompConc('comp1', 'B_for') * 1e6
if i < NITER_soA2:
res_m_soA2[i, t, 0] = sim.getCompConc('comp1', 'A_soA2')
if i < NITER_soAA:
res_m_soAA[i, t, 0] = sim.getCompConc('comp1', 'A_soAA')
res_m_soAA[i, t, 1] = sim.getCompConc('comp1', 'B_soAA')
if i < NITER_soAB:
res_m_soAB[i, t, 0] = sim.getCompConc('comp1', 'A_soAB')
res_m_soAB[i, t, 1] = sim.getCompConc('comp1', 'B_soAB')
if i < NITER_toA3:
res_m_toA3[i, t, 0] = sim.getCompConc('comp1', 'A_toA3')
if i < NITER_toA2B:
res_m_toA2B[i, t, 0] = sim.getCompConc('comp1', 'A_toA2B')
res_m_toA2B[i, t, 1] = sim.getCompConc('comp1', 'B_toA2B')
res_m_toA2B[i, t, 2] = sim.getCompConc('comp1', 'C_toA2B')
if i < NITER_so2d:
res_m_so2d[i, t, 0] = sim.getPatchCount('patch1', 'A_so2d')
res_m_so2d[i, t, 1] = sim.getPatchCount('patch1', 'B_so2d')
global mean_res_foi, std_res_foi
mean_res_foi = numpy.mean(res_m_foi, 0)
std_res_foi = numpy.std(res_m_foi, 0)
global mean_res_for
mean_res_for = numpy.mean(res_m_for, 0)
global mean_res_soA2
mean_res_soA2 = numpy.mean(res_m_soA2, 0)
global mean_res_soAA
mean_res_soAA = numpy.mean(res_m_soAA, 0)
global mean_res_soAB
mean_res_soAB = numpy.mean(res_m_soAB, 0)
global mean_res_toA3
mean_res_toA3 = numpy.mean(res_m_toA3, 0)
global mean_res_toA2B
mean_res_toA2B = numpy.mean(res_m_toA2B, 0)
global mean_res_so2d
mean_res_so2d = numpy.mean(res_m_so2d, 0)
global ran_sim
ran_sim = True
""" Example of tetrahedron directional dcst."""
import random
import steps.model as smodel
import steps.geom as sgeom
import steps.rng as srng
import steps.solver as solv
from steps.utilities import meshio
import time
DCST = 0.2e-9
# define model
model = smodel.Model()
A = smodel.Spec('A', model)
volsys = smodel.Volsys('vsys', model)
D_a = smodel.Diff('D_a', volsys, A)
D_a.setDcst(DCST)
# setup geometry
mesh = meshio.importAbaqus2("mesh_tet.inp", "mesh_tri.inp", 1e-6, "mesh_conf")[0]
comp = sgeom.TmComp("comp", mesh, range(mesh.ntets))
comp.addVolsys("vsys")
# boundary triangles splitting v1 and v2
boundary_tris = mesh.getROIData("boundary")
# tetrahedrons in v1 and adjancent to the boundary
boundary_tets1 = mesh.getROIData("boundary_tets_1")
# tetrahedrons in v2 and adjancent to the boundary
boundary_tets2 = mesh.getROIData("boundary_tets_2")
