def gen_geom():
# import the tetrahedral mesh
mesh = meshio.importAbaqus('astrocyte.inp', 1e-6)[0]
# create a compartment comprising all mesh tetrahedrons
ntets = mesh.countTets()
# create cytosolic compartment
cyto = stetmesh.TmComp('cyto', mesh, range(ntets))
# add volume system to cytosol
cyto.addVolsys('vsys')
# create ER compartment
er = stetmesh.Comp('er', mesh)
# Assign volume to ER
er.setVol(0.00314e-19)
# add volume system to ER
cyto.addVolsys('er_vsys')
# Define surfaces
# "cylinder_mesh.txt" describes Cyto & ER surfaces to import
input = open("cylinder_mesh.txt", 'r')
ASTRO_TRIS = pickle.load(input)
ER_TRIS = pickle.load(input)
input.close()
# create the patch for ER membrane
er_patch = stetmesh.TmPatch('er_patch', mesh, ER_TRIS, cyto)
er_patch.addSurfsys('ssys')
# create the patch for astrocyte plasma membrane
cyto_patch = stetmesh.TmPatch('cyto_patch', mesh, ASTRO_TRIS, icomp=cyto)
cyto_patch.addSurfsys('mb_surf')
# return geometry container object
return mesh, ASTRO_TRIS, ER_TRIS
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 build_geometry(mesh_path, file_format="xml", scale=1.):
scale = float(scale)
if file_format == "xml":
mesh = meshio.loadMesh(mesh_path)[0]
elif file_format == "msh":
mesh = meshio.importGmsh(mesh_path + ".msh", scale)[0]
elif file_format == "inp":
mesh = meshio.importAbaqus(mesh_path + ".inp", scale)[0]
else:
raise TypeError("File format " + str(file_format) +
" not available: choose among xml, msh, inp")
cyto = sgeom.TmComp('cyto', mesh, range(mesh.ntets))
(zmin_tris, zmin_vset, zmax_tris, zmax_vset) = zminmax_tris(mesh)
memb_tris = list(mesh.getSurfTris())
for tri in zmin_tris:
memb_tris.remove(tri)
for tri in zmax_tris:
memb_tris.remove(tri)
memb = sgeom.TmPatch('memb', mesh, memb_tris, cyto)
membrane = sgeom.Memb('membrane', mesh, [memb])
mesh.addROI('v_zmin', sgeom.ELEM_VERTEX, zmin_vset)
mesh.addROI('v_zmin_sample', sgeom.ELEM_VERTEX,
radial_extrema(mesh, zmin_vset))
mesh.addROI('v_zmax_sample', sgeom.ELEM_VERTEX,
radial_extrema(mesh, zmax_vset))
return mesh
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 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):
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)
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 gen_geom():
mesh = smeshio.loadMesh('validation_rd/meshes/' + MESHFILE)[0]
ntets = mesh.countTets()
comp = stetmesh.TmComp('cyto', mesh, range(ntets))
alltris = mesh.getSurfTris()
patch_tris = []
for t in alltris:
baryc = mesh.getTriBarycenter(t)
rad = np.sqrt(np.power(baryc[0], 2) + np.power(baryc[1], 2))
# By checking the cubit mesh the outer tris fall in the following bound
if rad > 0.000009955 and rad < 0.00001001: patch_tris.append(t)
patch = stetmesh.TmPatch('patch', mesh, patch_tris, icomp=comp)
patch.addSurfsys('ssys')
area = 0
for t in patch_tris:
area += mesh.getTriArea(t)
inject_tris = []
for p in patch_tris:
# X should be maximum (10) for the inject region
if mesh.getTriBarycenter(p)[0] > 9.999e-6:
inject_tris.append(p)
patch_tris_n = len(patch_tris)
# Now find the distances along the edge for all tris
tridists = np.zeros(patch_tris_n)
triareas = np.zeros(patch_tris_n)
for i in range(patch_tris_n):
baryc = mesh.getTriBarycenter(patch_tris[i])
rad = np.sqrt(np.power(baryc[0], 2) + np.power(baryc[1], 2))
theta = np.arctan2(baryc[1], baryc[0])
tridists[i] = (theta * rad * 1e6)
triareas[i] = mesh.getTriArea(patch_tris[i])
# Triangles will be separated into those to the 'high' side (positive y) with positive L
# and those on the low side (negative y) with negative L
return mesh, patch_tris, patch_tris_n, inject_tris, tridists, triareas
def gen_geom():
mesh = smeshio.loadMesh('meshes/coin_10r_1h_13861')[0]
ntets = mesh.countTets()
comp = stetmesh.TmComp('cyto', mesh, range(ntets))
alltris = mesh.getSurfTris()
# Sort patch triangles as those of positive z
patch_tris = []
for t in alltris:
vert0, vert1, vert2 = mesh.getTri(t)
if (mesh.getVertex(vert0)[2] > 0.0 \
and mesh.getVertex(vert1)[2] > 0.0 \
and mesh.getVertex(vert2)[2] > 0.0):
patch_tris.append(t)
# Create the patch
patch = stetmesh.TmPatch('patch', mesh, patch_tris, icomp=comp)
patch.addSurfsys('ssys')
patch_tris_n = len(patch_tris)
trirads = pylab.zeros(patch_tris_n)
triareas = pylab.zeros(patch_tris_n)
# Find the central tri
ctetidx = mesh.findTetByPoint([0.0, 0.0, 0.5e-6])
ctet_trineighbs = mesh.getTetTriNeighb(ctetidx)
ctri_idx = -1
for t in ctet_trineighbs:
if t in patch_tris:
ctri_idx = t
# Now find the distance of the centre of each tri to the central tri
cbaryc = mesh.getTriBarycenter(ctri_idx)
for i in range(patch_tris_n):
baryc = mesh.getTriBarycenter(patch_tris[i])
r2 = math.pow((baryc[0]-cbaryc[0]),2) + \
math.pow((baryc[1]-cbaryc[1]),2) + \
math.pow((baryc[2]-cbaryc[2]),2)
r = math.sqrt(r2)
# Convert to microns
trirads[i] = r * 1.0e6
triareas[i] = mesh.getTriArea(patch_tris[i]) * 1.0e12
return mesh, patch_tris, patch_tris_n, ctri_idx, trirads, triareas
def boundTrisAsPatch(mesh, patch_name, icomp=None, ocomp=None, scale=1e-6):
"""
Create a patch in the STEPS Tetmesh object using triangles bound in selected volumes.
Parameters:
* mesh Associated Tetmesh object created in STEPS
* comp_name Name of the compartment
* scale LENGTH scale from the CUBIT gemoetry to real geometry.
e.g. a radius of 10 in CUBIT to a radius of 1 micron in STEPS, scale is 1e-7.
By default the scale is 1e-6, i.e. 1 unit in CUBIT equals 1 micron in STEPS.
Return:
steps.geom.TmComp object
"""
steps_ids = getTrisBoundInSelectedVols(mesh, scale)
patch = sgeom.TmPatch(patch_name, mesh, steps_ids, icomp, ocomp)
return patch
def SelectedTrisAsPatch(mesh, tri_proxy, patch_name, icomp=None, ocomp=None):
"""
Create a patch in the STEPS Tetmesh object using selected triangles.
Parameters:
* mesh Associated Tetmesh object created in STEPS
* tri_proxy Triangle element proxy generated by STEPS mesh importing function
* patch_name Name of the patch
* icomp Inner TmComp compartment object (not name), None by default
* ocomp Outer TmComp compartment object (not name), None by default
Return:
steps.geom.TmPatch object
"""
steps_ids = getSelectedTris(tri_proxy)[0]
patch = sgeom.TmPatch(patch_name, mesh, steps_ids, icomp, ocomp)
return patch
def gen_geom():
mesh = smeshio.loadMesh('validation_rd/meshes/' + MESHFILE)[0]
ctetidx = mesh.findTetByPoint([0.0, 0.0, 0.5e-6])
ntets = mesh.countTets()
comp = stetmesh.TmComp('cyto', mesh, range(ntets))
alltris = mesh.getSurfTris()
patch_tris = []
for t in alltris:
vert0, vert1, vert2 = mesh.getTri(t)
if (mesh.getVertex(vert0)[2] > 0.0 and mesh.getVertex(vert1)[2] > 0.0
and mesh.getVertex(vert2)[2] > 0.0):
patch_tris.append(t)
patch_tris_n = len(patch_tris)
patch = stetmesh.TmPatch('patch', mesh, patch_tris, icomp=comp)
patch.addSurfsys('ssys')
trirads = numpy.zeros(patch_tris_n)
triareas = numpy.zeros(patch_tris_n)
# TRy to find the central tri
ctet_trineighbs = mesh.getTetTriNeighb(ctetidx)
ctri_idx = -1
for t in ctet_trineighbs:
if t in patch_tris:
ctri_idx = t
# Now find the distance of the center of the tets to the center of the center tet (at 0,0,0)
cbaryc = mesh.getTriBarycenter(ctri_idx)
for i in range(patch_tris_n):
baryc = mesh.getTriBarycenter(patch_tris[i])
r2 = math.pow((baryc[0] - cbaryc[0]), 2) + math.pow(
(baryc[1] - cbaryc[1]), 2) + math.pow((baryc[2] - cbaryc[2]), 2)
r = math.sqrt(r2)
# Conver to microns
trirads[i] = r * 1.0e6
triareas[i] = mesh.getTriArea(patch_tris[i])
return mesh, patch_tris, patch_tris_n, ctri_idx, trirads, triareas
def build_geometry(mesh_path):
mesh = meshio.loadMesh(mesh_path)[0]
cyto = sgeom.TmComp('cyto', mesh, range(mesh.ntets))
(zmin_tris,zmin_vset,zmax_tris,zmax_vset) = zminmax_tris(mesh)
memb_tris = list(mesh.getSurfTris())
for tri in zmin_tris: memb_tris.remove(tri)
for tri in zmax_tris: memb_tris.remove(tri)
memb = sgeom.TmPatch('memb', mesh, memb_tris, cyto)
membrane = sgeom.Memb('membrane', mesh, [memb] )
#mesh.addROI('v_zmin',sgeom.ELEM_VERTEX,ROIset(zmin_vset))
#mesh.addROI('v_zmin_sample',sgeom.ELEM_VERTEX,ROIset(radial_extrema(mesh,zmin_vset)))
#mesh.addROI('v_zmax_sample',sgeom.ELEM_VERTEX,ROIset(radial_extrema(mesh,zmax_vset)))
mesh.addROI('v_zmin',sgeom.ELEM_VERTEX,zmin_vset)
mesh.addROI('v_zmin_sample',sgeom.ELEM_VERTEX,radial_extrema(mesh,zmin_vset))
mesh.addROI('v_zmax_sample',sgeom.ELEM_VERTEX,radial_extrema(mesh,zmax_vset))
return mesh
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 = 3.0 / 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 = 1000 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_soAA = 2.0 / 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 = 10.0e-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 = 3.0 / 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
NITER_so2d = 1000 # The number of iterations
# In tests fewer than 0.1% fail with tolerance of 2%
tolerance_so2d = 1.0 / 100
############################ Common parameters ########################
global VOL
DT = 0.1 # Sampling time-step
INT = 1.1 # Sim endtime
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)
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.Tetexact(mdl, mesh, 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
def setUp(self):
KCST = 1e6
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.ssys1 = smodel.Surfsys('ssys1', self.model)
self.ssys2 = smodel.Surfsys('ssys2', self.model)
self.sreac1 = smodel.SReac('sreac1',
self.ssys1,
slhs=[A, B],
srhs=[C],
kcst=KCST)
self.sreac2 = smodel.SReac('sreac2',
self.ssys2,
slhs=[D, E],
srhs=[F],
kcst=KCST)
self.geom = sgeom.Geom()
self.comp = sgeom.Comp('comp', self.geom, 1e-18)
self.patch1 = sgeom.Patch('patch1', self.geom, self.comp, None, 1e-12)
self.patch1.addSurfsys('ssys1')
self.patch2 = sgeom.Patch('patch2', self.geom, self.comp, None, 1e-12)
self.patch2.addSurfsys('ssys2')
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.tmcomp = sgeom.TmComp('comp', self.mesh, range(self.mesh.ntets))
surf_tris = self.mesh.getSurfTris()
patch_tris1 = []
patch_tris2 = []
for tri in surf_tris:
tet_neighs = self.mesh.getTriTetNeighb(tri)
for tet in tet_neighs:
if tet in comp1_tets:
patch_tris1.append(tri)
break
elif tet in comp2_tets:
patch_tris2.append(tri)
break
self.tmpatch1 = sgeom.TmPatch('patch1', self.mesh, patch_tris1,
self.tmcomp)
self.tmpatch1.addSurfsys('ssys1')
self.tmpatch2 = sgeom.TmPatch('patch2', self.mesh, patch_tris2,
self.tmcomp)
self.tmpatch2.addSurfsys('ssys2')
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
def loadMesh(pathname):
"""
Load a mesh in STEPS from the XML (and ASCII) file. This will
work with just the XML file, but this is akin to creating the mesh in STEPS
from scratch and really negates the use of storing the mesh infomation at all.
For maximum benefit the XML file should be accompanied by the ASCII file, which
contains all the internal information.
PARAMETERS:
* pathname: the root of the path where the file(s) are stored.
e.g. with 'meshes/spine1' this function will look for files /meshes/spine1.xml
and /meshes/spine1.txt
RETURNS: A tuple (mesh, comps, patches)
* mesh
The STEPS Tetmesh object (steps.geom.Tetmesh)
* comps
A list of any compartment objects (steps.geom.TmComp) from XML file
* patches
A list of any patches objects (steps.geom.TmPatch) from XML file
"""
# Try to open the XML file. An error will be thrown if it doesn't exist
xmlfile = open(pathname+'.xml', 'r')
# Try to open the text file. A warning will be shown and a flag set if it doesn't exist
havetxt = True
try :
textfile = open(pathname+'.txt', 'r')
except:
havetxt = False
if (havetxt == False) : print("WARNING: text file not found. Will construct mesh from information in XML file only.")
# Perform a basic check to see if we have the expected kind of file which has not been altered.
info = xmlfile.readline()
if(xmlfile.readline().rstrip() != '<tetmesh>'):
print('XML file is not a recognised STEPS mesh file')
return
# Collect basic node information and perform some checks on the data read from XML file
nodeinfo = xmlfile.readline().strip()
assert(nodeinfo.__len__() > 17)
assert(nodeinfo[-2:] == '">')
nnodes = int(nodeinfo[15:-2])
if (havetxt): assert (nnodes == int(textfile.readline()))
nodes_out = [0.0]*(nnodes*3)
for i in range(nnodes):
idxtemp = xmlfile.readline().strip()
assert(int(idxtemp[13:-2]) == i)
coordtemp = xmlfile.readline().strip()
assert(coordtemp[:8] == '<coords>' and coordtemp[-9:] == '</coords>')
coordtemp = coordtemp[8:-9].split(', ')
nodes_out[i*3], nodes_out[(i*3)+1], nodes_out[(i*3)+2] = float(coordtemp[0]), float(coordtemp[1]), float(coordtemp[2])
assert(xmlfile.readline().strip() == '</node>')
assert(xmlfile.readline().strip() == '</nodes>')
# Now read triangle information from xml file and text file if we have it
triinfo = xmlfile.readline().strip()
assert(triinfo.__len__() > 21)
assert(triinfo[-2:] == '">')
ntris = int(triinfo[19:-2])
if (havetxt) :
textfile.readline()
assert (ntris == int(textfile.readline()))
tris_out = [0]*(ntris*3) # numpy.zeros(ntris*3, dtype = 'int')
if (havetxt) :
triareas_out = [0.0]*ntris # numpy.zeros(ntris)
trinorms_out = [0.0]*(ntris*3) # numpy.zeros(ntris*3)
tritetns_out = [0]*(ntris*2) # numpy.zeros(ntris*2, dtype = 'int')
for i in range(ntris):
idxtemp = xmlfile.readline().strip()
assert(int(idxtemp[12:-2]) == i)
nodetemp = xmlfile.readline().strip()
assert (nodetemp[:7] == '<nodes>' and nodetemp[-8:] == '</nodes>')
nodetemp = nodetemp[7:-8].split(', ')
tris_out[i*3], tris_out[(i*3)+1], tris_out[(i*3)+2] = int(nodetemp[0]), int(nodetemp[1]), int(nodetemp[2])
assert(xmlfile.readline().strip() == '</tri>')
# Now read the text file, if it exists, and get the extra information
if (havetxt):
line = textfile.readline().rstrip().split(" ")
assert(line.__len__() == 6)
triareas_out[i], trinorms_out[i*3], trinorms_out[(i*3)+1], trinorms_out[(i*3)+2] = float(line[0]), float(line[1]), float(line[2]), float(line[3])
tritetns_out[i*2], tritetns_out[(i*2)+1] = int(line[4]), int(line[5])
assert(xmlfile.readline().strip() == '</triangles>')
# Now read tet information from xml file and text file if we have it
tetinfo = xmlfile.readline().strip()
assert(tetinfo.__len__() > 24)
assert(tetinfo[-2:] == '">')
ntets = int(tetinfo[22:-2])
if (havetxt) :
textfile.readline()
assert(ntets == int(textfile.readline()))
tets_out = [0]*(ntets*4) # numpy.zeros(ntets*4, dtype = 'int')
if (havetxt):
tetvols_out = [0.0]*ntets # numpy.zeros(ntets)
tetbarycs_out = [0.0]*(ntets*3) # numpy.zeros(ntets*3)
tettrins_out = [0]*(ntets*4) # numpy.zeros(ntets*4, dtype = 'int')
tettetns_out = [0]*(ntets*4) # numpy.zeros(ntets*4, dtype = 'int')
for i in range(ntets):
idxtemp = xmlfile.readline().strip()
assert(int(idxtemp[12:-2]) == i)
nodetemp = xmlfile.readline().strip()
assert (nodetemp[:7] == '<nodes>' and nodetemp[-8:] == '</nodes>')
nodetemp = nodetemp[7:-8].split(', ')
tets_out[i*4], tets_out[(i*4)+1], tets_out[(i*4)+2], tets_out[(i*4)+3] = int(nodetemp[0]), int(nodetemp[1]), int(nodetemp[2]), int(nodetemp[3])
assert(xmlfile.readline().strip() == '</tet>')
# Read the text file if we have it and get further information
if (havetxt):
line = textfile.readline().rstrip().split(" ")
assert (line.__len__() == 12)
tetvols_out[i], tetbarycs_out[i*3], tetbarycs_out[(i*3)+1], tetbarycs_out[(i*3)+2] = float(line[0]), float(line[1]), float(line[2]), float(line[3])
tettrins_out[i*4], tettrins_out[(i*4)+1], tettrins_out[(i*4)+2], tettrins_out[(i*4)+3] = int(line[4]), int(line[5]), int(line[6]), int(line[7])
tettetns_out[i*4], tettetns_out[(i*4)+1], tettetns_out[(i*4)+2], tettetns_out[(i*4)+3] = int(line[8]), int(line[9]), int(line[10]), int(line[11])
assert(xmlfile.readline().strip() == '</tetrahedrons>')
# We have all the information now. Time to make the Tetmesh object. New constructor keeps the order, which is:
# nodes, tris, tri areas, tri normals, tri tet neighbours, tets, tet volumes, tet barycenters, tet tri neighbs, tet tet neighbs.
mesh = stetmesh.Tetmesh(nodes_out, tris_out, triareas_out, trinorms_out, tritetns_out, tets_out, tetvols_out, tetbarycs_out, tettrins_out, tettetns_out)
# Now fetch any comp and patch information from XML file
compinfo = xmlfile.readline().strip()
assert(compinfo.__len__() > 24)
assert(compinfo[-2:] == '">')
ncomps = int(compinfo[22:-2])
comps_out = []
for i in range(ncomps):
idxtemp = xmlfile.readline().strip()
assert(int(idxtemp[13:-2]) == i)
idtemp = xmlfile.readline().strip()
assert(idtemp[:4] == '<id>' and idtemp[-5:] == '</id>')
idtemp = idtemp[4:-5]
volsystemp = xmlfile.readline().strip()
assert(volsystemp[:8] == '<volsys>' and volsystemp[-9:] == '</volsys>')
volsystemp = volsystemp[8:-9].split(',')
if (volsystemp[0] == '') : volsystemp = []
tettemp = xmlfile.readline().strip()
assert(tettemp[:6] == '<tets>' and tettemp[-7:] == '</tets>')
tettemp = tettemp[6:-7].split(',')
nctets = tettemp.__len__()
ctets = [0]*nctets # numpy.zeros(nctets, dtype = 'int')
for ct in range(nctets): ctets[ct] = int(tettemp[ct])
c_out = stetmesh.TmComp(idtemp, mesh, ctets)
for v in volsystemp: c_out.addVolsys(v)
comps_out.append(c_out)
assert(xmlfile.readline().strip() == '</comp>')
assert(xmlfile.readline().strip() == '</compartments>')
# Retrieve patch info
patchinfo = xmlfile.readline().strip()
assert(patchinfo.__len__() > 19)
assert(patchinfo[-2:] == '">')
npatches = int(patchinfo[17:-2])
patches_out = []
for i in range(npatches):
idxtemp = xmlfile.readline().strip()
assert(int(idxtemp[14:-2]) == i)
idtemp = xmlfile.readline().strip()
assert(idtemp[:4] == '<id>' and idtemp[-5:] == '</id>')
idtemp = idtemp[4:-5]
surfsystemp = xmlfile.readline().strip()
assert(surfsystemp[:9] == '<surfsys>' and surfsystemp[-10:] == '</surfsys>')
surfsystemp = surfsystemp[9:-10].split(',')
if (surfsystemp[0] == '') : surfsystemp = []
icomptemp = xmlfile.readline().strip()
assert(icomptemp[:7] == '<icomp>' and icomptemp[-8:] == '</icomp>')
icomptemp = icomptemp[7:-8]
ocomptemp = xmlfile.readline().strip()
assert(ocomptemp[:7] == '<ocomp>' and ocomptemp[-8:] == '</ocomp>')
ocomptemp = ocomptemp[7:-8]
tritemp = xmlfile.readline().strip()
assert(tritemp[:6] == '<tris>' and tritemp[-7:] == '</tris>')
tritemp = tritemp[6:-7].split(',')
nptris = tritemp.__len__()
ptris = [0]*nptris # numpy.zeros(nptris, dtype='int')
for pt in range(nptris): ptris[pt] = int(tritemp[pt])
if (ocomptemp != 'null'): p_out = stetmesh.TmPatch(idtemp, mesh, ptris, mesh.getComp(icomptemp), mesh.getComp(ocomptemp))
else : p_out = stetmesh.TmPatch(idtemp, mesh, ptris, mesh.getComp(icomptemp))
for s in surfsystemp: p_out.addSurfsys(s)
patches_out.append(p_out)
assert(xmlfile.readline().strip() == '</patch>')
assert(xmlfile.readline().strip() == '</patches>')
return (mesh,comps_out,patches_out)
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()
model = smodel.Model()
A = smodel.Spec('A', model)
surfsys = smodel.Surfsys('ssys', model)
D_a = smodel.Diff('D_a', surfsys, A)
DCST = 0.2e-9
D_a.setDcst(DCST)
mesh = meshio.importAbaqus2("mesh_tet.inp", "mesh_tri.inp", 1e-6,
"mesh_conf")[0]
boundary_tris = mesh.getROIData("boundary")
v1_tets = mesh.getROIData("v1_tets")
comp1 = sgeom.TmComp("comp1", mesh, v1_tets)
patch1 = sgeom.TmPatch("patch", mesh, boundary_tris, comp1)
patch1.addSurfsys("ssys")
neigh_tris = mesh.getROIData("neigh_tri")
focus_tri = mesh.getROIData("focus_tri")[0]
rng = srng.create('mt19937', 512)
rng.initialize(int(time.time() % 4294967295))
solver = solv.Tetexact(model, mesh, rng)
print "Set dcst from focus_tri to all neighbor tris to 0..."
for tri in neigh_tris:
solver.setTriDiffD(focus_tri, "D_a", 0, tri)
print solver.getTriDiffD(focus_tri, "D_a", tri)
solver.setTriCount(focus_tri, "A", 10)
submemb_tets_surftris = dict()
for m in submemb_tets:
tris = mesh_stoch.getTetTriNeighb(m)
for t in tris:
if t in memb_tris:
submemb_tets_surftris[m] = t
break
assert (len(submemb_tets_surftris.values()) == len(submemb_tets))
########## Create a membrane as a surface mesh
# Stochastic sim:
memb_stoch = sgeom.TmPatch('memb_stoch', mesh_stoch, memb_tris, cyto_stoch)
memb_stoch.addSurfsys('ssys_stoch')
# Determinsitic sim:
memb_det = sgeom.TmPatch('memb_det', mesh_det, memb_tris, cyto_det)
memb_det.addSurfsys('ssys_det')
# For EField calculation
print "Creating membrane.."
membrane = sgeom.Memb('membrane', mesh_stoch, [memb_stoch])
print "Membrane created."
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # SIMULATION # # # # # # # # # # # # # # # # # # # # # #
r = srng.create_mt19937(512)
pot_tet = numpy.zeros(pot_n, dtype='uint')
i = 0
for p in pot_pos:
# Axis is aligned with z-axis
pot_tet[i] = mesh.findTetByPoint([0.0, 0.0, pot_pos[i]])
i = i + 1
# # # # # # # # # # # # # # # GEOMETRY OBJECTS # # # # # # # # # # # # # # # # #
# Create cytosol compartment
cyto = sgeom.TmComp('cyto', mesh, range(mesh.ntets))
# Create the patch and associate with surface system 'ssys'
patch = sgeom.TmPatch('patch', mesh, memb_tris, cyto)
patch.addSurfsys('ssys')
# Create the membrane across which the potential will be solved
membrane = sgeom.Memb('membrane', mesh, [patch], opt_method=1)
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Create the random number generator
r = srng.create('mt19937', 512)
r.initialize(int(time.time() % 10000))
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# # # # # # # # # # # # # # # # # SIMULATION # # # # # # # # # # # # # # # # # #
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
and mesh.getVertex(vert2)[2] > 0.0):
if mesh.getTriBarycenter(t)[0] > 0.0:
patchA_tris.append(t)
bar = mesh.getTriBars(t)
patchA_bars.add(bar[0])
patchA_bars.add(bar[1])
patchA_bars.add(bar[2])
else:
patchB_tris.append(t)
bar = mesh.getTriBars(t)
patchB_bars.add(bar[0])
patchB_bars.add(bar[1])
patchB_bars.add(bar[2])
# Create the patch
patchA = stetmesh.TmPatch('patchA', mesh, patchA_tris, icomp = comp)
patchA.addSurfsys('ssys')
patchB = stetmesh.TmPatch('patchB', mesh, patchB_tris, icomp = comp)
patchB.addSurfsys('ssys')
# Find the set of bars that connect the two patches as the intersecting bars
barsDB = patchA_bars.intersection(patchB_bars)
barsDB=list(barsDB)
# Create the surface diffusion boundary
diffb = stetmesh.SDiffBoundary('sdiffb', mesh, barsDB, [patchA, patchB])
# Find the central tri
ctetidx = mesh.findTetByPoint([0.0, 0.0, 0.5e-6])
ctet_trineighbs = mesh.getTetTriNeighb(ctetidx)
ctri_idx=-1
def setUp(self):
self.DCST = 0.08e-12
self.model = smodel.Model()
A = smodel.Spec('A', self.model)
X = smodel.Spec('X', self.model)
self.ssys1 = smodel.Surfsys('ssys1', self.model)
self.ssys2 = smodel.Surfsys('ssys2', self.model)
self.sreac = smodel.SReac('sreac', self.ssys1, slhs = [A], srhs = [A], kcst = 1e5)
self.diff1 = smodel.Diff('diffX1', self.ssys1, X, self.DCST)
self.diff2 = smodel.Diff('diffX2', self.ssys2, X, self.DCST)
if __name__ == "__main__":
self.mesh = meshio.loadMesh('meshes/coin_10r_1h_13861')[0]
else:
self.mesh = meshio.loadMesh('sdiff_bugfix_test/meshes/coin_10r_1h_13861')[0]
ntets = self.mesh.countTets()
self.comp = sgeom.TmComp('cyto', self.mesh, range(ntets))
alltris = self.mesh.getSurfTris()
patchA_tris = []
patchB_tris = []
patchA_bars = set()
patchB_bars = set()
for t in alltris:
vert0, vert1, vert2 = self.mesh.getTri(t)
if (self.mesh.getVertex(vert0)[2] > 0.0 \
and self.mesh.getVertex(vert1)[2] > 0.0 \
and self.mesh.getVertex(vert2)[2] > 0.0):
if self.mesh.getTriBarycenter(t)[0] > 0.0:
patchA_tris.append(t)
bar = self.mesh.getTriBars(t)
patchA_bars.add(bar[0])
patchA_bars.add(bar[1])
patchA_bars.add(bar[2])
else:
patchB_tris.append(t)
bar = self.mesh.getTriBars(t)
patchB_bars.add(bar[0])
patchB_bars.add(bar[1])
patchB_bars.add(bar[2])
self.patchA = sgeom.TmPatch('patchA', self.mesh, patchA_tris, icomp = self.comp)
self.patchA.addSurfsys('ssys1')
self.patchB = sgeom.TmPatch('patchB', self.mesh, patchB_tris, icomp = self.comp)
self.patchB.addSurfsys('ssys2')
# Find the set of bars that connect the two patches as the intersecting bars
barsDB = patchA_bars.intersection(patchB_bars)
barsDB=list(barsDB)
# Create the surface diffusion boundary
self.diffb = sgeom.SDiffBoundary('sdiffb', self.mesh, barsDB, [self.patchA, self.patchB])
ctetidx = self.mesh.findTetByPoint([0.0, 0.0, 0.5e-6])
ctet_trineighbs = self.mesh.getTetTriNeighb(ctetidx)
self.ctri_idx=-1
for t in ctet_trineighbs:
if t in patchA_tris+patchB_tris:
self.ctri_idx = t
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
self.solver = solv.Tetexact(self.model, self.mesh, self.rng)
def test_rallpack3():
print("Rallpack 3 with TetODE")
#meshfile ='axon_cube_L1000um_D866m_600tets'
meshfile = 'axon_cube_L1000um_D866m_1135tets'
#meshfile = 'axon_cube_L1000um_D866nm_1978tets'
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Potassium conductance, Siemens/m^2
K_G = 360
# Sodium conductance, Siemens/m^2
Na_G = 1200
# Leak conductance, Siemens/m^2
L_G = 0.25
# Potassium reversal potential, V
K_rev = -77e-3
# Sodium reversal potential, V
Na_rev = 50e-3
# Leak reveral potential, V
leak_rev = -65.0e-3
# Potassium channel density
K_ro = 18.0e12
# Sodium channel density
Na_ro = 60.0e12
# Total leak conductance for ideal cylinder:
surfarea_cyl = 1.0 * np.pi * 1000 * 1e-12
L_G_tot = L_G * surfarea_cyl
# A table of potassium density factors at -65mV, found in getpops. n0, n1, n2, n3, n4
K_FACS = [0.216750577045, 0.40366011853, 0.281904943772, \
0.0874997924409, 0.0101845682113 ]
# A table of sodium density factors. m0h1, m1h1, m2h1, m3h1, m0h0, m1h0, m2h0, m3h0
NA_FACS = [0.343079175644, 0.0575250437508, 0.00321512825945, 5.98988373918e-05, \
0.506380603793, 0.0849062503811, 0.00474548939393, 8.84099403236e-05]
# Ohm.m
Ra = 1.0
# # # # # # # # # # # # # # # # SIMULATION CONTROLS # # # # # # # # # # # # # #
# The simulation dt (seconds); for TetODE this is equivalent to EField dt
SIM_DT = 5.0e-6
# Sim end time (seconds)
SIM_END = 0.1
# The number of sim 'time points'; * SIM_DT = sim end time
SIM_NTPNTS = int(SIM_END / SIM_DT) + 1
# The current injection in amps
Iinj = 0.1e-9
# # # # # # # # # # # # # DATA COLLECTION # # # # # # # # # # # # # # # # # #
# record potential at the two extremes along (z) axis
POT_POS = np.array([0.0, 1.0e-03])
POT_N = len(POT_POS)
# Length of the mesh, in m
LENGTH = 1000.0e-6
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
mdl = smodel.Model()
ssys = smodel.Surfsys('ssys', mdl)
# K channel
K = smodel.Chan('K', mdl)
K_n0 = smodel.ChanState('K_n0', mdl, K)
K_n1 = smodel.ChanState('K_n1', mdl, K)
K_n2 = smodel.ChanState('K_n2', mdl, K)
K_n3 = smodel.ChanState('K_n3', mdl, K)
K_n4 = smodel.ChanState('K_n4', mdl, K)
# Na channel
Na = smodel.Chan('Na', mdl)
Na_m0h1 = smodel.ChanState('Na_m0h1', mdl, Na)
Na_m1h1 = smodel.ChanState('Na_m1h1', mdl, Na)
Na_m2h1 = smodel.ChanState('Na_m2h1', mdl, Na)
Na_m3h1 = smodel.ChanState('Na_m3h1', mdl, Na)
Na_m0h0 = smodel.ChanState('Na_m0h0', mdl, Na)
Na_m1h0 = smodel.ChanState('Na_m1h0', mdl, Na)
Na_m2h0 = smodel.ChanState('Na_m2h0', mdl, Na)
Na_m3h0 = smodel.ChanState('Na_m3h0', mdl, Na)
# Leak
L = smodel.Chan('L', mdl)
Leak = smodel.ChanState('Leak', mdl, L)
# Gating kinetics
_a_m = lambda mV: ((((0.1 * (25 - (mV + 65.)) / (np.exp(
(25 - (mV + 65.)) / 10.) - 1)))))
_b_m = lambda mV: ((((4. * np.exp(-((mV + 65.) / 18.))))))
_a_h = lambda mV: ((((0.07 * np.exp((-(mV + 65.) / 20.))))))
_b_h = lambda mV: ((((1. / (np.exp((30 - (mV + 65.)) / 10.) + 1)))))
_a_n = lambda mV: ((((0.01 * (10 - (mV + 65.)) / (np.exp(
(10 - (mV + 65.)) / 10.) - 1)))))
_b_n = lambda mV: ((((0.125 * np.exp(-(mV + 65.) / 80.)))))
Kn0n1 = smodel.VDepSReac('Kn0n1',
ssys,
slhs=[K_n0],
srhs=[K_n1],
k=lambda V: 1.0e3 * 4. * _a_n(V * 1.0e3))
Kn1n2 = smodel.VDepSReac('Kn1n2',
ssys,
slhs=[K_n1],
srhs=[K_n2],
k=lambda V: 1.0e3 * 3. * _a_n(V * 1.0e3))
Kn2n3 = smodel.VDepSReac('Kn2n3',
ssys,
slhs=[K_n2],
srhs=[K_n3],
k=lambda V: 1.0e3 * 2. * _a_n(V * 1.0e3))
Kn3n4 = smodel.VDepSReac('Kn3n4',
ssys,
slhs=[K_n3],
srhs=[K_n4],
k=lambda V: 1.0e3 * 1. * _a_n(V * 1.0e3))
Kn4n3 = smodel.VDepSReac('Kn4n3',
ssys,
slhs=[K_n4],
srhs=[K_n3],
k=lambda V: 1.0e3 * 4. * _b_n(V * 1.0e3))
Kn3n2 = smodel.VDepSReac('Kn3n2',
ssys,
slhs=[K_n3],
srhs=[K_n2],
k=lambda V: 1.0e3 * 3. * _b_n(V * 1.0e3))
Kn2n1 = smodel.VDepSReac('Kn2n1',
ssys,
slhs=[K_n2],
srhs=[K_n1],
k=lambda V: 1.0e3 * 2. * _b_n(V * 1.0e3))
Kn1n0 = smodel.VDepSReac('Kn1n0',
ssys,
slhs=[K_n1],
srhs=[K_n0],
k=lambda V: 1.0e3 * 1. * _b_n(V * 1.0e3))
Na_m0h1_m1h1 = smodel.VDepSReac('Na_m0h1_m1h1',
ssys,
slhs=[Na_m0h1],
srhs=[Na_m1h1],
k=lambda V: 1.0e3 * 3. * _a_m(V * 1.0e3))
Na_m1h1_m2h1 = smodel.VDepSReac('Na_m1h1_m2h1',
ssys,
slhs=[Na_m1h1],
srhs=[Na_m2h1],
k=lambda V: 1.0e3 * 2. * _a_m(V * 1.0e3))
Na_m2h1_m3h1 = smodel.VDepSReac('Na_m2h1_m3h1',
ssys,
slhs=[Na_m2h1],
srhs=[Na_m3h1],
k=lambda V: 1.0e3 * 1. * _a_m(V * 1.0e3))
Na_m3h1_m2h1 = smodel.VDepSReac('Na_m3h1_m2h1',
ssys,
slhs=[Na_m3h1],
srhs=[Na_m2h1],
k=lambda V: 1.0e3 * 3. * _b_m(V * 1.0e3))
Na_m2h1_m1h1 = smodel.VDepSReac('Na_m2h1_m1h1',
ssys,
slhs=[Na_m2h1],
srhs=[Na_m1h1],
k=lambda V: 1.0e3 * 2. * _b_m(V * 1.0e3))
Na_m1h1_m0h1 = smodel.VDepSReac('Na_m1h1_m0h1',
ssys,
slhs=[Na_m1h1],
srhs=[Na_m0h1],
k=lambda V: 1.0e3 * 1. * _b_m(V * 1.0e3))
Na_m0h0_m1h0 = smodel.VDepSReac('Na_m0h0_m1h0',
ssys,
slhs=[Na_m0h0],
srhs=[Na_m1h0],
k=lambda V: 1.0e3 * 3. * _a_m(V * 1.0e3))
Na_m1h0_m2h0 = smodel.VDepSReac('Na_m1h0_m2h0',
ssys,
slhs=[Na_m1h0],
srhs=[Na_m2h0],
k=lambda V: 1.0e3 * 2. * _a_m(V * 1.0e3))
Na_m2h0_m3h0 = smodel.VDepSReac('Na_m2h0_m3h0',
ssys,
slhs=[Na_m2h0],
srhs=[Na_m3h0],
k=lambda V: 1.0e3 * 1. * _a_m(V * 1.0e3))
Na_m3h0_m2h0 = smodel.VDepSReac('Na_m3h0_m2h0',
ssys,
slhs=[Na_m3h0],
srhs=[Na_m2h0],
k=lambda V: 1.0e3 * 3. * _b_m(V * 1.0e3))
Na_m2h0_m1h0 = smodel.VDepSReac('Na_m2h0_m1h0',
ssys,
slhs=[Na_m2h0],
srhs=[Na_m1h0],
k=lambda V: 1.0e3 * 2. * _b_m(V * 1.0e3))
Na_m1h0_m0h0 = smodel.VDepSReac('Na_m1h0_m0h0',
ssys,
slhs=[Na_m1h0],
srhs=[Na_m0h0],
k=lambda V: 1.0e3 * 1. * _b_m(V * 1.0e3))
Na_m0h1_m0h0 = smodel.VDepSReac('Na_m0h1_m0h0',
ssys,
slhs=[Na_m0h1],
srhs=[Na_m0h0],
k=lambda V: 1.0e3 * _a_h(V * 1.0e3))
Na_m1h1_m1h0 = smodel.VDepSReac('Na_m1h1_m1h0',
ssys,
slhs=[Na_m1h1],
srhs=[Na_m1h0],
k=lambda V: 1.0e3 * _a_h(V * 1.0e3))
Na_m2h1_m2h0 = smodel.VDepSReac('Na_m2h1_m2h0',
ssys,
slhs=[Na_m2h1],
srhs=[Na_m2h0],
k=lambda V: 1.0e3 * _a_h(V * 1.0e3))
Na_m3h1_m3h0 = smodel.VDepSReac('Na_m3h1_m3h0',
ssys,
slhs=[Na_m3h1],
srhs=[Na_m3h0],
k=lambda V: 1.0e3 * _a_h(V * 1.0e3))
Na_m0h0_m0h1 = smodel.VDepSReac('Na_m0h0_m0h1',
ssys,
slhs=[Na_m0h0],
srhs=[Na_m0h1],
k=lambda V: 1.0e3 * _b_h(V * 1.0e3))
Na_m1h0_m1h1 = smodel.VDepSReac('Na_m1h0_m1h1',
ssys,
slhs=[Na_m1h0],
srhs=[Na_m1h1],
k=lambda V: 1.0e3 * _b_h(V * 1.0e3))
Na_m2h0_m2h1 = smodel.VDepSReac('Na_m2h0_m2h1',
ssys,
slhs=[Na_m2h0],
srhs=[Na_m2h1],
k=lambda V: 1.0e3 * _b_h(V * 1.0e3))
Na_m3h0_m3h1 = smodel.VDepSReac('Na_m3h0_m3h1',
ssys,
slhs=[Na_m3h0],
srhs=[Na_m3h1],
k=lambda V: 1.0e3 * _b_h(V * 1.0e3))
OC_K = smodel.OhmicCurr('OC_K',
ssys,
chanstate=K_n4,
erev=K_rev,
g=K_G / K_ro)
OC_Na = smodel.OhmicCurr('OC_Na',
ssys,
chanstate=Na_m3h0,
erev=Na_rev,
g=Na_G / Na_ro)
# Mesh geometry
mesh = meshio.loadMesh('validation_efield/meshes/' + meshfile)[0]
cyto = sgeom.TmComp('cyto', mesh, range(mesh.ntets))
# The tetrahedrons from which to record potential
POT_TET = np.zeros(POT_N, dtype='uint')
i = 0
for p in POT_POS:
# Assuming axiz aligned with z-axis
POT_TET[i] = mesh.findTetByPoint([0.0, 0.0, POT_POS[i]])
i = i + 1
# Find the tets connected to the bottom face
# First find all the tets with ONE face on a boundary
boundtets = []
#store the 0to3 index of the surface triangle for each of these boundary tets
bt_srftriidx = []
for i in range(mesh.ntets):
tettemp = mesh.getTetTetNeighb(i)
if (tettemp[0] == -1 or tettemp[1] == -1 or tettemp[2] == -1
or tettemp[3] == -1):
boundtets.append(i)
templist = []
if (tettemp[0] == -1):
templist.append(0)
if (tettemp[1] == -1):
templist.append(1)
if (tettemp[2] == -1):
templist.append(2)
if (tettemp[3] == -1):
templist.append(3)
bt_srftriidx.append(templist)
assert (boundtets.__len__() == bt_srftriidx.__len__())
# Find the tets on the z=0 and z=1000um boundaries, and the triangles
minztets = []
minztris = []
maxztris = []
minzverts = set([])
boundminz = mesh.getBoundMin()[2] + LENGTH / mesh.ntets
boundmaxz = mesh.getBoundMax()[2] - LENGTH / mesh.ntets
for i in range(boundtets.__len__()):
# get the boundary triangle
for btriidx in bt_srftriidx[i]:
zminboundtri = True
tribidx = mesh.getTetTriNeighb(boundtets[i])[btriidx]
tritemp = mesh.getTri(tribidx)
trizs = [0.0, 0.0, 0.0]
trizs[0] = mesh.getVertex(tritemp[0])[2]
trizs[1] = mesh.getVertex(tritemp[1])[2]
trizs[2] = mesh.getVertex(tritemp[2])[2]
for j in range(3):
if (trizs[j] > boundminz): zminboundtri = False
if (zminboundtri):
minztets.append(boundtets[i])
minztris.append(tribidx)
minzverts.add(tritemp[0])
minzverts.add(tritemp[1])
minzverts.add(tritemp[2])
continue
zmaxboundtri = True
for j in range(3):
if (trizs[j] < boundmaxz): zmaxboundtri = False
if (zmaxboundtri):
maxztris.append(tribidx)
n_minztris = len(minztris)
assert (n_minztris > 0)
minzverts = list(minzverts)
n_minzverts = len(minzverts)
assert (n_minzverts > 0)
memb_tris = list(mesh.getSurfTris())
# Doing this now, so will inject into first little z section
for t in minztris:
memb_tris.remove(t)
for t in maxztris:
memb_tris.remove(t)
# Create the membrane with the tris removed at faces
memb = sgeom.TmPatch('memb', mesh, memb_tris, cyto)
memb.addSurfsys('ssys')
membrane = sgeom.Memb('membrane',
mesh, [memb],
opt_method=2,
search_percent=100.0)
# Set the single-channel conductance:
g_leak_sc = L_G_tot / len(memb_tris)
OC_L = smodel.OhmicCurr('OC_L',
ssys,
chanstate=Leak,
erev=leak_rev,
g=g_leak_sc)
# Create the solver objects
sim = ssolver.TetODE(mdl, mesh, calcMembPot=True)
sim.setTolerances(1.0e-6, 1e-6)
surfarea_mesh = sim.getPatchArea('memb')
surfarea_cyl = 1.0 * np.pi * 1000 * 1e-12
corr_fac_area = surfarea_mesh / surfarea_cyl
vol_cyl = np.pi * 0.5 * 0.5 * 1000 * 1e-18
vol_mesh = sim.getCompVol('cyto')
corr_fac_vol = vol_mesh / vol_cyl
RES_POT = np.zeros((SIM_NTPNTS, POT_N))
for t in memb_tris:
sim.setTriCount(t, 'Leak', 1)
sim.setPatchCount('memb', 'Na_m0h1', (Na_ro * surfarea_cyl * NA_FACS[0]))
sim.setPatchCount('memb', 'Na_m1h1', (Na_ro * surfarea_cyl * NA_FACS[1]))
sim.setPatchCount('memb', 'Na_m2h1', (Na_ro * surfarea_cyl * NA_FACS[2]))
sim.setPatchCount('memb', 'Na_m3h1', (Na_ro * surfarea_cyl * NA_FACS[3]))
sim.setPatchCount('memb', 'Na_m0h0', (Na_ro * surfarea_cyl * NA_FACS[4]))
sim.setPatchCount('memb', 'Na_m1h0', (Na_ro * surfarea_cyl * NA_FACS[5]))
sim.setPatchCount('memb', 'Na_m2h0', (Na_ro * surfarea_cyl * NA_FACS[6]))
sim.setPatchCount('memb', 'Na_m3h0', (Na_ro * surfarea_cyl * NA_FACS[7]))
sim.setPatchCount('memb', 'K_n0', (K_ro * surfarea_cyl * K_FACS[0]))
sim.setPatchCount('memb', 'K_n1', (K_ro * surfarea_cyl * K_FACS[1]))
sim.setPatchCount('memb', 'K_n2', (K_ro * surfarea_cyl * K_FACS[2]))
sim.setPatchCount('memb', 'K_n3', (K_ro * surfarea_cyl * K_FACS[3]))
sim.setPatchCount('memb', 'K_n4', (K_ro * surfarea_cyl * K_FACS[4]))
sim.setMembPotential('membrane', -65e-3)
sim.setMembVolRes('membrane', Ra * corr_fac_vol)
sim.setMembCapac('membrane', 0.01 / corr_fac_area)
for v in minzverts:
sim.setVertIClamp(v, Iinj / n_minzverts)
for l in range(SIM_NTPNTS):
sim.run(SIM_DT * l)
for p in range(POT_N):
RES_POT[l, p] = sim.getTetV(int(POT_TET[p])) * 1.0e3
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Benchmark
# At 0um- the end of the mesh
ifile_benchmark_x0 = open(
'validation_efield/data/rallpack3_benchmark/rallpack3_0_0.001dt_1000seg',
'r')
# At 1000um- the end of the mesh
ifile_benchmark_x1000 = open(
'validation_efield/data/rallpack3_benchmark/rallpack3_1000_0.001dt_1000seg',
'r')
tpnt_benchmark = []
v_benchmark_x0 = []
v_benchmark_x1000 = []
lines_benchmark_x0 = ifile_benchmark_x0.readlines()[2:]
# Read in mv and ms
for line_benchmark_x0 in lines_benchmark_x0:
nums = line_benchmark_x0.split()
tpnt_benchmark.append(float(nums[0]))
v_benchmark_x0.append(float(nums[1]))
lines_benchmark_x1000 = ifile_benchmark_x1000.readlines()[2:]
for line_benchmark_x1000 in lines_benchmark_x1000:
nums = line_benchmark_x1000.split()
v_benchmark_x1000.append(float(nums[1]))
# Get rid of the last point which seems to be missing from STEPS
v_benchmark_x0 = v_benchmark_x0[:-1]
tpnt_benchmark = tpnt_benchmark[:-1]
v_benchmark_x1000 = v_benchmark_x1000[:-1]
rms0 = stats(v_benchmark_x0, RES_POT[:, 0])
assert (rms0 < 0.15)
rms1000 = stats(v_benchmark_x1000, RES_POT[:, 1])
assert (rms1000 < 1.1)
for j in range(4):
out_tris.add(tritemp[j])
in_tris = set()
for i in inner_tets:
tritemp = mesh.getTetTriNeighb(i)
for j in range(4):
in_tris.add(tritemp[j])
memb_tris = out_tris.intersection(in_tris)
memb_tris = list(memb_tris)
print len(memb_tris), " surface triangles."
########## Create a membrane as a surface mesh
memb = sgeom.TmPatch('memb', mesh, memb_tris, cyto)
memb.addSurfsys('ssys')
print "Area: ", memb.getArea()
print "Creating membrane.."
membrane = sgeom.Memb('membrane', mesh, [memb])
print "Membrane created."
# # # # # # # # # # # # # # # # # # # # # # # # SIMULATION # # # # # # # # # # # # # # # # # # # # # #
r = srng.create_mt19937(512)
r.initialize(7)
sim = ssolver.Tetexact(mdl, mesh, r, True)
DCST) # name, where, what, how fast
# diff_Ca_sens = smodel.Diff('diff_Ca_sens', surfsys2, Ca_sens, DCST) # name, where, what, how fast
# define compartments:
cyto_comp = stetmesh.TmComp('cyto_comp', mesh, CS_tet_IDs)
ER_comp = stetmesh.TmComp('ER_comp', mesh, ER_tet_IDs)
# get surf tris in comps:
CS_memb_tris = meshctrl.findSurfTrisInComp(mesh, cyto_comp)
ER_memb_tris = meshctrl.findOverlapTris(mesh, CS_tet_IDs, ER_tet_IDs)
# patches:
ER_surf = stetmesh.TmPatch('ER_surf',
mesh,
ER_memb_tris,
icomp=ER_comp,
ocomp=cyto_comp)
memb_surf = stetmesh.TmPatch('memb_surf',
mesh,
NotAzTris,
icomp=cyto_comp,
ocomp=None)
# AZ_surf = stetmesh.TmPatch('AZ_surf', mesh, az_tris, icomp = cyto_comp)
# $-----$-----$-----$-----$-----$-----$-----$-----$-----$-----$-----$-----
# Create the patch and associate with surface system 'ssys'
patch = stetmesh.TmPatch('patch', mesh, NotCaSensTris, icomp=cyto_comp)
# Create the membrane across which the potential will be solved
membrane = stetmesh.Memb('membrane', mesh, [patch], opt_method=1)
Compborder_tri_areas = [0.0]*len(Length)
for i in range(len(Length)):
Compborder_triIDs[i]=[]
for j in range(len(Comp_tetIDs[i])):
tritemp = mesh_stoch.getTetTriNeighb(Comp_tetIDs[i][j])
for tri in tritemp:
if tri in memb_tris:
Compborder_triIDs[i].append(tri)
Compborder_tri_areas[i] = Compborder_tri_areas[i] + mesh_stoch.getTriArea(tri)
break
########## Create a membrane as a surface mesh
# Stochastic sim:
memb_stoch = sgeom.TmPatch('memb_stoch', mesh_stoch, memb_tris, cyto_stoch)
memb_stoch.addSurfsys('ssys_stoch')
# For EField calculation
print "Creating membrane.."
membrane = sgeom.Memb('membrane', mesh_stoch, [memb_stoch], opt_file_name = './meshes/'+meshfile_ab+"_optimalidx")
print "Membrane created."
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # SIMULATION # # # # # # # # # # # # # # # # # # # # # #
r = srng.create_mt19937(512)
r.initialize(int(time.time()%1000))
# Random-number generator
r_dummy = srng.create_mt19937(512)
r_dummy.initialize(int(time.time()%1000))
def __init__(self, x):
if x.INT_DOMAIN == []:
DOMAIN_NAMES = [x.CYT_NAME, x.PSD_NAME]
else:
DOMAIN_NAMES = [x.CYT_NAME, x.SER_NAME, x.PSD_NAME]
print x.GeoFileName
print x.scale
print DOMAIN_NAMES
print 'importAbaqus ... \n'
mesh, nodeproxy, tetproxy, triproxy = smeshio.importAbaqus(
x.GeoFileName, x.scale, DOMAIN_NAMES)
print 'OK\n'
print 'Load Head, Neck, and Dend IDs\n'
Head_ID = np.loadtxt(x.HeadIDFileName) - 1
Neck_ID = np.loadtxt(x.NeckIDFileName) - 1
Dend_ID = np.loadtxt(x.DendIDFileName) - 1
Head_ID = Head_ID.astype(np.int)
Neck_ID = Neck_ID.astype(np.int)
Dend_ID = Dend_ID.astype(np.int)
print 'OK\n'
ntets = mesh.ntets
tet_groups = tetproxy.blocksToGroups()
Cyt_tets = tet_groups[x.CYT_NAME]
nCyt_tets = len(Cyt_tets)
if x.INT_DOMAIN != []:
SER_tets = tet_groups[x.SER_NAME]
nSER_tets = len(SER_tets)
print 'nGol_tets: ', nSER_tets
tri_groups = triproxy.blocksToGroups()
tri_PSD = tri_groups[x.PSD_NAME]
tri_nPSD = len(tri_PSD)
###
### Volume system
### Annotation of geometry
###
Cytosol = sgeom.TmComp('Cytosol', mesh, Cyt_tets)
Cytosol.addVolsys('vsys_Cyt')
# Golgi = sgeom.TmComp('Golgi', mesh, Gol_tets)
# Golgi.addVolsys('vsys_Gol')
####
#### Surface & PSD mesh preparation
####
## Obtain IDs of neighboring triangles from cytosolic tetrahedrons
tri_S = set(mesh.getSurfTris())
if x.INT_DOMAIN != []:
tri_SER = set()
for i in SER_tets:
tri = mesh.getTetTriNeighb(i)
tri_SER.add(tri[0])
tri_SER.add(tri[1])
tri_SER.add(tri[2])
tri_SER.add(tri[3])
tri_S.difference(tri_SER)
###
###
tri_S_PSD = tri_S.intersection(tri_PSD)
tri_Head = set()
for i in Head_ID:
tri = mesh.getTetTriNeighb(i)
tri_Head.add(tri[0])
tri_Head.add(tri[1])
tri_Head.add(tri[2])
tri_Head.add(tri[3])
tri_Neck = set()
for i in Neck_ID:
tri = mesh.getTetTriNeighb(i)
tri_Neck.add(tri[0])
tri_Neck.add(tri[1])
tri_Neck.add(tri[2])
tri_Neck.add(tri[3])
tri_Dend = set()
for i in Dend_ID:
tri = mesh.getTetTriNeighb(i)
tri_Dend.add(tri[0])
tri_Dend.add(tri[1])
tri_Dend.add(tri[2])
tri_Dend.add(tri[3])
tri_S_Head = tri_S.intersection(tri_Head)
tri_S_Neck = tri_S.intersection(tri_Neck)
tri_S_Dend = tri_S.intersection(tri_Dend)
tri_S_Head_PSD = tri_S_Head.intersection(tri_PSD)
tri_S_Neck_PSD = tri_S_Neck.intersection(tri_PSD)
tri_S_Head_noPSD = tri_S_Head.difference(tri_PSD)
tri_S_Neck_noPSD = tri_S_Neck.difference(tri_PSD)
##
## Make list from set
##
tri_S = list(tri_S)
tri_S_Dend = list(tri_S_Dend)
tri_S_Head_PSD = list(tri_S_Head_PSD)
tri_S_Neck_PSD = list(tri_S_Neck_PSD)
tri_S_Head_noPSD = list(tri_S_Head_noPSD)
tri_S_Neck_noPSD = list(tri_S_Neck_noPSD)
##
## Surface system
## Annotation of geometry
##
p_Dend = sgeom.TmPatch('Dend', mesh, tri_S_Dend, icomp=Cytosol)
p_Head_PSD = sgeom.TmPatch('Head_PSD',
mesh,
tri_S_Head_PSD,
icomp=Cytosol)
p_Neck_PSD = sgeom.TmPatch('Neck_PSD',
mesh,
tri_S_Neck_PSD,
icomp=Cytosol)
p_Head_noPSD = sgeom.TmPatch('Head_noPSD',
mesh,
tri_S_Head_noPSD,
icomp=Cytosol)
p_Neck_noPSD = sgeom.TmPatch('Neck_noPSD',
mesh,
tri_S_Neck_noPSD,
icomp=Cytosol)
p_Dend.addSurfsys('ssys')
p_Head_PSD.addSurfsys('ssys')
p_Neck_PSD.addSurfsys('ssys')
p_Head_noPSD.addSurfsys('ssys')
p_Neck_noPSD.addSurfsys('ssys')
self.mesh = mesh
self.ntets = ntets
self.Cyt_tets = Cyt_tets
self.nCyt_tets = nCyt_tets
self.Cytosol = Cytosol
self.tri_S = tri_S
self.tri_S_Dend = tri_S_Dend
self.tri_S_Head_PSD = tri_S_Head_PSD
self.tri_S_Neck_PSD = tri_S_Neck_PSD
self.tri_S_Head_noPSD = tri_S_Head_noPSD
self.tri_S_Neck_noPSD = tri_S_Neck_noPSD
self.p_Dend = p_Dend
self.p_Head_PSD = p_Head_PSD
self.p_Neck_PSD = p_Neck_PSD
self.p_Head_noPSD = p_Head_noPSD
self.p_Neck_noPSD = p_Neck_noPSD
##
## SER surf mesh
##
if x.INT_DOMAIN != []:
tris_Cyt = set()
for i in range(nCyt_tets):
tris = mesh.getTetTriNeighb(Cyt_tets[i])
tris_Cyt.add(tris[0])
tris_Cyt.add(tris[1])
tris_Cyt.add(tris[2])
tris_Cyt.add(tris[3])
tris_SER = set()
for i in range(nSER_tets):
tris = mesh.getTetTriNeighb(SER_tets[i])
tris_SER.add(tris[0])
tris_SER.add(tris[1])
tris_SER.add(tris[2])
tris_SER.add(tris[3])
tris_S_SER = tris_Cyt.intersection(tris_SER)
self.tris_S_SER = list(tris_S_SER)
else:
self.tris_S_SER = []
##
## Obtain IDs for fluxes
##
mesh.addROI('Head_ROI', sgeom.ELEM_TET, Head_ID)
mesh.addROI('Neck_ROI', sgeom.ELEM_TET, Neck_ID)
mesh.addROI('Dend_ROI', sgeom.ELEM_TET, Dend_ID)
print 'tri_S : ', len(tri_S)
print 'tri_S_Head_PSD : ', len(tri_S_Head_PSD)
print 'tri_S_Neck_PSD : ', len(tri_S_Neck_PSD)
print 'tri_S_Head_noPSD : ', len(tri_S_Head_noPSD)
print 'tri_S_Neck_noPSD : ', len(tri_S_Neck_noPSD)
print 'tri_S_Dend : ', len(tri_S_Dend)
tmp = len(tri_S_Head_PSD + tri_S_Neck_PSD + tri_S_Dend +
tri_S_Neck_noPSD + tri_S_Head_noPSD)
print 'Head_PSD + Neck_PSD + Dend + Neck_noPSD + Head_noPSD: ', tmp
# print mesh.getSurfSys()
print 'Gend_geom has been finished!\n'
def test_efield_vc():
mesh = make_tri_prism(3, 10, 1.0)
interior = sgeom.TmComp('interior', mesh, range(mesh.ntets))
model = smodel.Model()
# need at minimum one species
sA = smodel.Spec('A', model)
patch = sgeom.TmPatch('patch', mesh, mesh.getSurfTris(), interior)
memb = sgeom.Memb('membrane', mesh, [patch], opt_method=1)
rng = srng.create('r123', 512)
sim = ssolver.Tetexact(model, mesh, rng, True)
EF_dt = 1e-6 # 1 microsecond
sim.reset()
sim.setEfieldDT(EF_dt)
# initialise potential of mesh vertices to 0V
sim.setMembPotential('membrane', 0)
# membrane capacitance
sim.setMembCapac('membrane', 0)
# volume resistivity
sim.setMembVolRes('membrane', 1) # 1 ohm·m
# clamp top and bottom of prism
vtop = set(
(vi for tri in mesh.getROIData('top') for vi in mesh.getTri(tri)))
vbottom = set(
(vi for tri in mesh.getROIData('bottom') for vi in mesh.getTri(tri)))
for v in vtop:
sim.setVertV(v, 10.0)
sim.setVertVClamped(v, True)
for v in vbottom:
sim.setVertV(v, 0.0)
sim.setVertVClamped(v, True)
# get means across all horizontal slices
slices = dict((int(mo.group(1)), mesh.getROIData(s))
for s in mesh.getAllROINames()
for mo in [re.search('slice(\d+)', s)] if mo)
slice_keys = list(slices.keys())
slice_keys.sort()
N = 10
result = np.zeros((N, 1 + len(slice_keys)))
for k in range(N):
result[k, 0] = k
sim.advance(EF_dt)
j = 1
for s in slice_keys:
nv = 0
sumv = 0.0
for vi in slices[s]:
nv += 1
sumv += sim.getVertV(vi)
result[k, j] = sumv / nv
j += 1
for i in np.arange(1.0, 12.0):
for j in result[1:, int(i)]:
assert (abs(j - (i - 1)) < 1e-10)