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):
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)
surfsys = smodel.Surfsys('ssys', self.model)
D_a = smodel.Diff('D_a', surfsys, 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")
comp1 = sgeom.TmComp("comp1", self.mesh, v1_tets)
patch1 = sgeom.TmPatch("patch", self.mesh, boundary_tris, comp1)
patch1.addSurfsys("ssys")
self.neigh_tris = self.mesh.getROIData("neigh_tri")
self.focus_tri = self.mesh.getROIData("focus_tri")[0]
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
self.solver = solv.Tetexact(self.model, self.mesh, self.rng)
def setup_module():
global rng, NITER, DT, INT, CONC, DCST, SAMPLE, MESHFILE, tolerance
global tetidxs, tetrads
rng = srng.create('r123', 512)
rng.initialize(1000) # The max unsigned long
NITER = 10
DT = 0.01
INT = 0.05
CONC = 50.0e-6 # the number of initial molecules
DCST = 0.1e-9
SAMPLE = 12033
MESHFILE = 'cyl_diam0_4__len10_12Ktets'
# <1% fail with a tolerance of 5%
tolerance = 5.0 / 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)
def setup_module():
global rng, NITER, DT, INT
rng = srng.create('r123', 512)
rng.initialize(1000) # The max unsigned long
NITER = 10
DT = 0.01
INT = 0.11
global NINJECT, DCST, tolerance, SAMPLE, MESHFILE, tetidxs, tetrads
# The number of initial molecules:
NINJECT = 10000
DCST = 0.2e-9
# In tests, with good code, <1% fail with a tolerance of 5%
tolerance = 5.0 / 100
# The number of tets to sample at random:
SAMPLE = 1060
MESHFILE = 'cyl_diam2__len10_1060tets'
# 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)
def setUp(self):
mdl = smodel.Model()
S1 = smodel.Spec('S1', mdl)
ssys = smodel.Surfsys('ssys', mdl)
smodel.SReac('SR01', ssys, slhs=[S1], srhs=[S1], kcst=1)
if __name__ == "__main__":
mesh = meshio.importAbaqus('meshes/test.inp', 1e-7)[0]
else:
mesh = meshio.importAbaqus(
'tetODE_setPatchSReacK_bugfix_test/meshes/test.inp', 1e-7)[0]
comp1 = sgeom.TmComp('comp1', mesh, range(mesh.countTets()))
patch1 = sgeom.TmPatch('patch1', mesh, mesh.getSurfTris(), comp1)
patch1.addSurfsys('ssys')
rng = srng.create('mt19937', 512)
rng.initialize(1234)
self.sim = ssolver.TetODE(mdl, mesh, rng)
self.sim.setTolerances(1.0e-3, 1.0e-3)
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 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):
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 runSBMLmod(sbmlFile, time_end, time_dt, iter_n = 1, solver = 'Wmdirect', specs_plot = {}, vol_units = 1.0e-3, vol_def = False):
iSbml = ssbml.Interface(sbmlFile, volunits_def = vol_units, volume_def = vol_def)
mdl = iSbml.getModel()
mesh = iSbml.getGeom()
comp_specs = {}
if not specs_plot: got_sp = False
else: got_sp = True
for comp in mesh.getAllComps():
comp_specs[comp.getID()] = []
volsys_strings = comp.getVolsys()
for vsys_str in volsys_strings:
vsys = mdl.getVolsys(vsys_str)
specs = vsys.getAllSpecs()
for spec in specs:
comp_specs[comp.getID()].append(spec.getID())
if (got_sp == False): specs_plot.update({spec.getID():''})
comp_specs_n = 0
for comp in comp_specs:
comp_specs[comp].sort()
comp_specs_n += len(comp_specs[comp])
time_pnts = numpy.arange(0.0, time_end, time_dt)
points_n = int(round(time_end/time_dt))
if (len(time_pnts) == (points_n + 1)): time_pnts = numpy.delete(time_pnts, len(time_pnts)-1)
res = numpy.zeros([iter_n, points_n, comp_specs_n])
r = srng.create('mt19937', 256)
r.initialize(7233)
if (solver == 'Wmdirect'):
sim = ssolver.Wmdirect(mdl, mesh, r)
elif (solver == 'Wmrk4'):
sim = ssolver.Wmrk4(mdl, mesh, r)
sim.setDT(0.0001)
else:
raise NameError("Unsupported solver. SBML importer accepts well-mixed solvers 'Wmrk4' and 'Wmdirect'")
for it in range (0, iter_n):
sim.reset()
iSbml.reset()
iSbml.setupSim(sim)
for tp in range(0, points_n):
sim.run(time_pnts[tp])
i = 0
for comp in comp_specs:
for spec in comp_specs[comp]:
res[it, tp, i] = sim.getCompConc(comp, spec)
i+=1
iSbml.updateSim(sim, time_dt)
mean_res = numpy.mean(res, 0)
i=0
for comp in comp_specs:
for spec in comp_specs[comp]:
if (spec in specs_plot):
if (specs_plot[spec]): plot(time_pnts, mean_res[:,i], label = spec+ ", "+ comp, color = specs_plot[spec])
else: plot(time_pnts, mean_res[:,i], label = spec+ ", "+ comp)
i+=1
legend(loc = 'best', numpoints=1)
xlabel('Time (s)')
ylabel('Conc (M)')
show()
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 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 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 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 init_sim(model, mesh, seed, param):
# previous setup
# rng = srng.create('r123', 512)
# rng.initialize(seed)
# sim = ssolver.Tetexact(model, mesh, rng, True)
# Create the solver objects
if param['SSA_solver'] == 'TetODE':
sim = ssolver.TetODE(model,
mesh,
calcMembPot=sim_parameters['EF_solver'])
sim.setTolerances(1.0e-6, 1e-6)
elif param['SSA_solver'] == 'Tetexact':
rng = srng.create('mt19937', 512)
rng.initialize(seed)
sim = ssolver.Tetexact(model,
mesh,
rng,
calcMembPot=sim_parameters['EF_solver'])
sim.reset()
sim.setEfieldDT(param['EF_dt'])
else:
raise ValueError('SSA solver ' + param['SSA_solver'] + 'not available')
print('Running Rallpack1 test with ' + param['SSA_solver'])
# Correction factor for deviation between mesh and model cylinder:
area_cylinder = np.pi * param['diameter'] * param['length']
area_mesh_factor = sim.getPatchArea('memb') / area_cylinder
# Set initial conditions
memb = sgeom.castToTmPatch(mesh.getPatch('memb'))
for t in memb.tris:
sim.setTriCount(t, 'Leak', 1)
sim.setMembPotential('membrane', param['E_M'])
sim.setMembVolRes('membrane', param['R_A'])
sim.setMembCapac('membrane', param['C_M'] / area_mesh_factor)
v_zmin = mesh.getROIData('v_zmin')
I = param['Iinj'] / len(v_zmin)
for v in v_zmin:
sim.setVertIClamp(v, I)
return sim
def get_solver(solver_type, mdl, geom):
r = srng.create('r123', 1000)
if solver_type == "Wmrk4":
solver = ssolv.Wmrk4(mdl, geom)
solver.setDT(1e-5)
return solver
elif solver_type == "Wmdirect":
solver = ssolv.Wmdirect(mdl, geom, r)
return solver
if solver_type == "Wmrssa":
solver = ssolv.Wmrssa(mdl, geom, r)
return solver
elif solver_type == "Tetexact":
solver = ssolv.Tetexact(mdl, geom, r)
return solver
else:
assert (False)
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 setup_module():
global rng, DT, INT, NINJECT, DCST, tolerance, MESHFILE
rng = srng.create('r123', 1024)
rng.initialize(1000) # The max unsigned long
# plotting dt; sim endtime:
DT = 0.02
INT = 3.02
# Number of molecules injected in centre; diff constant
NINJECT = 1000
DCST = 0.01e-9
# Error from non-zero injection width etc should be less than 1%
tolerance = 1.0 / 100
########################################################################
MESHFILE = 'ring2_or10_ir9_injx0width2_60084tets.inp'
def setup_module():
global rng, NITER, DT, INT, NINJECT, DCST, tolerance, MESHFILE
rng = srng.create('r123', 1024)
rng.initialize(1000) # The max 32bit unsigned long
# Number of iterations; plotting dt; sim endtime:
NITER = 100
DT = 0.02
INT = 3.02
# Number of molecules injected in centre; diff constant
NINJECT = 5000
DCST = 0.01e-9
# In tests <1% fail with tolerance of 5%
tolerance = 5.0 / 100
########################################################################
MESHFILE = 'ring2_or10_ir9_injx0width2_640tets.inp'
def setup_module():
global rng
rng = srng.create('r123', 1024)
rng.initialize(1000) # The max unsigned long
global NITER, DT, INT, NINJECT, DCST, tolerance
# Number of iterations; plotting dt; sim endtime:
NITER = 10
DT = 0.01
INT = 0.21
# Number of molecules injected in centre; diff constant; number of tets sampled:
NINJECT = 100000
DCST = 0.02e-9
# With good code <1% fail with a tolerance of 5%
tolerance = 5.0 / 100
########################################################################
global SAMPLE, MESHFILE
SAMPLE = 32552 # all tets
MESHFILE = 'sphere_rad10_33Ktets_adaptive'
# create the array of tet indices to be found at random
global tetidxs
tetidxs = np.zeros(SAMPLE, dtype='int')
for i in range(SAMPLE):
tetidxs[i] = i
# further create the array of tet barycentre distance to centre
global tetrads, tetvols
tetrads = np.zeros(SAMPLE)
tetvols = np.zeros(SAMPLE)
def setup_module():
global rng, NITER, DT, INT, NINJECT, DCST, tolerance, MESHFILE
rng = srng.create('r123', 1024)
rng.initialize(1000) # The max unsigned long
# Number of iterations; plotting dt; sim endtime:
NITER = 100
DT = 0.01
INT = 0.21
# Number of molecules injected in center; diff constant; number of tets sampled:
NINJECT = 1000
DCST = 0.02e-9
# With good code <1% fail with a tolerance of 6%
tolerance = 6.0 / 100
########################################################################
MESHFILE = 'coin_10r_1h_13861.inp'
def setup_module():
global rng, DT, INT, DCST, FLUX, SAMPLE, MESHFILE, tetidxs, tetrads, tolerance
rng = srng.create('r123', 512)
rng.initialize(1000) # The max unsigned long
DT = 0.001
INT = 0.025
DCST = 0.05e-9
FLUX = 300000.0 # The flux at the boundaries,
SAMPLE = 12033 # All tets
MESHFILE = 'cyl_diam0_4__len10_12Ktets_STEPS'
# create the array of tet indices to be found at random
tetidxs = np.zeros(SAMPLE, dtype='int')
# further create the array of tet barycentre distance to centre
tetrads = np.zeros(SAMPLE)
# Small expected error from non plane source
tolerance = 3.0 / 100
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 init_sim(model, mesh, seed, param):
rng = srng.create('r123', 512)
# previous setup
# rng.initialize(seed)
rng.initialize(steps.mpi.rank + 1000)
memb = sgeom.castToTmPatch(mesh.getPatch('memb'))
# partition geometry across hosts
(tet_hosts, tri_hosts) = host_assignment_by_axis(mesh, memb.tris)
# sim = ssolver.TetOpSplit(model, mesh, rng, True, tet_hosts, tri_hosts)
sim = ssolver.TetOpSplit(model, mesh, rng, param['EF_solver'], tet_hosts,
tri_hosts)
# Correction factor for deviation between mesh and model cylinder:
area_cylinder = np.pi * param['diameter'] * param['length']
area_mesh_factor = sim.getPatchArea('memb') / area_cylinder
# Set initial conditions
sim.reset()
for t in memb.tris:
sim.setTriCount(t, 'Leak', 1)
sim.setEfieldDT(param['EF_dt'])
sim.setMembPotential('membrane', param['E_M'])
sim.setMembVolRes('membrane', param['R_A'])
sim.setMembCapac('membrane', param['C_M'] / area_mesh_factor)
v_zmin = mesh.getROIData('v_zmin')
I = param['Iinj'] / len(v_zmin)
for v in v_zmin:
sim.setVertIClamp(v, I)
return sim
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
#R1 = smod.Reac('R1', volsys, lhs = [A,B], rhs = [C])
#R1.setKcst(RCST)
D_a = smod.Diff('D_a', volsys, A, dcst = DCSTA)
#D_b = smod.Diff('D_b', volsys, B, dcst = DCSTB)
#D_c = smod.Diff('D_c', volsys, C, dcst = DCSTB)
mesh, nodeproxy, tetproxy, triproxy = smeshio.importAbaqus('brick_40_4_4_2_comp.inp', scale)
ntets = mesh.ntets
tet_groups = tetproxy.blocksToGroups()
Atets = tet_groups['EB1']
nATets = len(Atets)
Btets = tet_groups['EB2']
nBTets = len(Btets)
comp1 = sgeom.TmComp('comp1', mesh, xrange(mesh.ntets))
comp1.addVolsys('vsys')
rng = srng.create('mt19937', 16384)
rng.initialize(1)
print "create sim"
sim = ssolv.Tetexact(mdl, mesh, rng)
print "reset"
sim.reset()
#set molecules
sim.setTetCount(0, "A", 1)
sim.run(1e-3)
math.pow((baryc[2]-cbaryc[2]),2))
# Store the radial distance (in microns):
tetrads[i] = r * 1.0e6
print "Tetrahedron samples found"
return mesh
########################################################################
model = gen_model()
tmgeom = gen_geom()
rng = srng.create('mt19937', 512)
rng.initialize(2903)
sim = solvmod.Tetexact(model, tmgeom, rng)
tpnts = numpy.arange(0.0, INT, DT)
# Find how many "time points" we have
ntpnts = tpnts.shape[0]
# Create the data structure: iterations x time points x tet samples
res = numpy.zeros((NITER, ntpnts, SAMPLE))
# Fetch the index of the tetrahedron at the centre of the mesh
ctetidx = tmgeom.findTetByPoint([0.0, 0.0, 0.0])
# Run NITER number of iterations:
# 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]
res_m = numpy.zeros([NITER, ntpnts, 1])
res_std1 = numpy.zeros([ntpnts, 1])
res_std2 = numpy.zeros([ntpnts, 1])
sim.reset()
sim.setCompCount('comp1', 'A', N)
sim.checkpoint('./validation_cp/cp/first_order_irev')
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)
volComp = volComp * pow(10,-3)
comp.vol = volComp
species = iSbml.getSpecies() #Dict specie --> concentration
molecules = iSbml.setMols(smodel, mdl, species) # Name Specie --> Mols in STEPS
reactions = iSbml.getReactions(molecules)
iSbml.instantiate_reaction(smodel, volsys, reactions)
############
r = srng.create('mt19937', 256)
r.initialize(7233)
tpnt = np.arange(0.0, ENDTIME, DT)
res_m = np.zeros([NITER, POINTS, len(species)])
legendDict = {}
print "Setting up the model"
sim = ssolver.Wmdirect(mdl, mesh, r)
print "before simulation"
for it in range (0, NITER):
sim.reset()
iSbml.set_initial_conditions(sim, species)
for t in xrange(0,POINTS):
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 the geometry module that contains the objects used to
#define the geometry, namely steps.geom.
wmgeom = swm.Geom()
#generate parent container object
comp = swm.Comp('comp', wmgeom)
comp.addVolsys('vsys')
comp.setVol(1.6667e-27)
#To this symple model, we only create one compartment and we
#store it in the variable called comp.
import steps.rng as srng
#import package with alias srng.
r = srng.create('mt19937', 256)
#we actually generate a random number generator we want.
#using the function steps.rng.create()
#STEPS currently only implements one pseudo RNG algorithm, 'mt19937'
r.initialize(23412)
#initialize the random number generator with a seed value
import steps.solver as ssolver
#to create the actual solver object, first of all we import the
#package in which all solvers have been implemented
sim = ssolver.Wmdirect(mdl, wmgeom, r)
sim.reset()
#reset the function on the solver project
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 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
math.pow((baryc[1]-cbaryc[1]),2) + \
math.pow((baryc[2]-cbaryc[2]),2))
# Store the radial distance (in microns):
tetrads[i] = r*1.0e6
print "Tetrahedron samples found"
return mesh
########################################################################
model = gen_model()
tmgeom = gen_geom()
rng = srng.create('mt19937', 512)
rng.initialize(2903) # The max unsigned long
sim = solvmod.Tetexact(model, tmgeom, rng)
tpnts = numpy.arange(0.0, INT, DT)
# Find how many "time points" we have
ntpnts = tpnts.shape[0]
# Create the data structure: iterations x time points x tet samples
res = numpy.zeros((NITER, ntpnts, SAMPLE))
# Fetch the index of the tetrahedron at the centre of the mesh
ctetidx = tmgeom.findTetByPoint([0.0, 0.0, 0.0])
# Run NITER number of iterations:
