def run2():
print(os.getcwd())
os.chdir('data')
print(os.getcwd())
print(dir(md))
dt = 0.002
ucells = 2
sigma = 1
N = ucells * ucells
dens = 0.1
nu = 0.5
L = math.sqrt(N / dens)
print(L)
T = 2.0
v0 = math.sqrt(2.0 * T)
eps = np.array([1.0])
rc = sigma * math.pow(2, 1.0 / 6.0)
rcut = np.array([rc])
shift = np.array([1.0])
E = 200
k = 50
pdb.set_trace()
box = np.array([L, L])
md.system_init(box)
#nodes = np.loadtxt("diskR1Vertices1.txt");
#cells = np.loadtxt("diskR1Triangles1.txt") - 1;
nodes, cells = mdmesh.uniform_mesh_on_unit_circle(.3)
L, R = fm.add_clusters(md, nodes, cells, 1.0, ucells, nu, 'sc')
box = md.system_get_box()
print("box", box)
md.system_set_boundary_conditions(0)
md.system_set_velocities(v0)
md.system_set_zero_center_of_mass_vel()
md.system_set_dt(dt)
md.system_set_avg_steps(100)
md.system_set_potential(eps, rcut, shift)
md.system_set_youngs_modulus(E)
#md.system_set_swelling_energy_constants(100,50,0)
#md.system_set_friction(.1)
#md.system_set_bond_spring_constant(k)
md.system_init_neighbor_list()
pos = md.system_get_positions()
vel = md.system_get_velocities()
upos = md.system_get_unfolded_positions()
tet = md.system_get_tetras()
bonds = md.system_get_bonds()
#plt.scatter(pos[:,0],pos[:,1])
#plt.show()
#plt.triplot(pos[:,0], pos[:,1], tet, 'go-', lw=1.0)
bonds = md.system_get_bonds()
refVol, currVol = md.system_get_elements_volumes()
I1, I2 = md.system_get_elements_invariants()
print("Volume check: ", refVol.shape[0], currVol.shape[0], np.sum(refVol),
np.sum(currVol))
pdb.set_trace()
sigmas = md.system_get_particle_sizes()
sigmas *= sigma
R = R - 0.5 + sigma / 2
#xyzfile = fm.Saver(0,"test_test",pos)
#vtkfile = fm.Saver(1,"test_test",upos,vel=vel,cells=tet)
#vtffile = fm.Saver(2,"test_test",upos,bonds=bonds,box=[box[0],box[1]])
#vtffile.append(0);
plot = Plotter.Plotter(pos, vel, tet, box[0], box[1], 'tri', I1,
sigma) # 2 is the radius
plot.update(0)
#plt.show()
for i in range(1000):
md.system_run(100)
avgs = md.system_get_avgs()
print(avgs)
#xyzfile.append(avgs[0])
#vtkfile.append(avgs[0])
#vtffile.append(avgs[0])
#md.system_unfold_positions()
if i % 1 == 0: plot.update(avgs[0])
print("finished")
plt.show()
def run0():
#Create a data directory for all data produced by the program
print(os.getcwd())
data_dir = 'data'
if not os.path.exists(data_dir):
os.makedirs(data_dir)
os.chdir(data_dir)
print(os.getcwd())
print(dir(md))
# define some variables
# delta time, time increment
dt = 0.005
# number of cells, will be used to assign the initial position of
# particles and for size of system
ucells = 10
# diameter of particles
sigma = 1
# Number of particles, we have one particle per cell
N = ucells * ucells
# Density, N/V, V volume
dens = 0.1
# packing fraction N*sigme*3/V
nu = 0.3
# size of of square
L = math.sqrt(N / dens)
print(L)
# Initial temperature
T = 2.0
# Initial average velocity of particles
v0 = math.sqrt(2.0 * T)
# lennard jones potential epsilon, strenght of potential
# it has to be declared using a list in case we have more type of particles
eps = np.array([1.0])
# Cut for the potetial,
rc = sigma * math.pow(2, 1.0 / 6.0)
rc = 2.5
rcut = np.array([rc])
# potential zero reference
shift = np.array([0.0])
#Now we create the simulation system
# initialize the system with a box size of [L,L]
md.system_init(np.array([L, L]))
# set the particles on a square lattice
fm.init_particles_simple_cubic(md, ucells, L)
lbox = md.system_get_box()
print("box", lbox)
#set boundary condiations
# we use the following construct in C++ enum PBCTYPE {NOPBC, XPBC, XYPBC, XYZPBC};
# 0, is no periadic boundary conditions, all hard walls
# 1 is boundary conditions in the x direction
# 2 is boundary conditions in both x and y direction
md.system_set_boundary_conditions(2)
#set the initial veloctities random with average v0
md.system_set_velocities(v0)
#substract the center of mass velocity
md.system_set_zero_center_of_mass_vel()
# set delta_t for the system
md.system_set_dt(dt)
# number of steps to average
md.system_set_avg_steps(100)
# set the potential using the varialbles eps, rcut and shift defined before
md.system_set_potential(eps, rcut, shift)
# initialize verlet list
md.system_init_neighbor_list()
# Get a pointer to array with position and velocities for later work
pos = md.system_get_positions1()
vel = md.system_get_velocities()
# we can save the position using any of these formats, uncomment the wa
#xyzfile = fm.Saver(0,"test_test",pos)
#vtkfile = fm.Saver(1,"test_test",pos,vel=vel,cells=tet)
#vtffile = fm.Saver(2,"test_test",upos,bonds=bonds,box=[lbox[0],lbox[1]])
#vtffile.append(0);
# If you want to plot the particles along with the simulation,
#uncomment these lines
#plot = Plotter.Plotter(pos,vel,None,lbox[0],lbox[1],'pts',sigma) # 2 is the radius
#plot.update(0)
for i in range(1000):
md.system_run(100)
avgs = md.system_get_avgs()
print(avgs)
#xyzfile.append(avgs[0])
#vtkfile.append(avgs[0])
#vtffile.append(avgs[0])
#md.system_unfold_positions()
#plot.update(avgs[0])
print("finished")
def run0():
# Switch to data directory
print(os.getcwd())
data_dir = 'data'
if not os.path.exists(data_dir):
os.makedirs(data_dir)
os.chdir(data_dir)
print(os.getcwd())
print(dir(md))
# set delta t for time evolution
dt = 0.002
# number of cell
ucells = 2
# size of particles
sigma = 1
# total number of elastormes 4, in this case
N = ucells*ucells
# set the density and packing fraction, will be modified later
# density
dens = 0.1
# packing fraction
nu = 0.5
# size of the box
L = math.sqrt(N / dens)
print(L)
# temperature and initial average velocity
T = 2.0
v0 = math.sqrt(2.0 * T )
# potetial parameters
eps=np.array([1.0])
rc = sigma*math.pow(2,1.0/6.0)
rcut=np.array([rc])
shift=np.array([1.0])
# young's modulus
E=200
# set the box size and initialize the system
box = np.array([L,L])
md.system_init(box)
# The elastomers and structure as a mesh with nodes and cells (triangle)
# you can read the nodes and triangles from a file or you can
# use the function mdmesh to produce the shape, in this example we
# use mdmesh, it returs the nodes and cells as an array of vector positions and
# another array of index of vertices for triangles, the .3 controls how
# fine we want the mesh, lower numbers will give you more triangles
# in this case the mesh is a disk of diameter 1
#nodes = np.loadtxt("diskR1Vertices1.txt");
#cells = np.loadtxt("diskR1Triangles1.txt") - 1;
nodes, cells = mdmesh.uniform_mesh_on_unit_circle(.3)
# Now that we have the basic mesh for one elastomer we will replicate it 4 times
# in the box, we will also rescale the size of of the box and meshes so that ieach
# vertices contains a particle of diameter 1. Refore to function in add cluster
# to see how it is done
L,R = fm.add_clusters(md,nodes,cells,1.0,ucells,nu,'sc')
# get the new size of the box
box = md.system_get_box()
print("box",box)
# set boundary conditions, 0 for hard walls in all directions
md.system_set_boundary_conditions(0)
# set initial velocities
md.system_set_velocities(v0)
# substract center of mass
md.system_set_zero_center_of_mass_vel()
# set delta t for the sytem
md.system_set_dt(dt)
# set average steps
md.system_set_avg_steps(100)
# set the potential, interaction between particles
md.system_set_potential(eps,rcut,shift)
# set the youngs modulus for elactic interaction
md.system_set_youngs_modulus(E)
# if we wnat to initially swell the particles , uncomment this line
#md.system_set_swelling_energy_constants(100,50,0)
# if we want to get rid of thermal fluctiation, uncomment this line
#md.system_set_friction(.1)
#if we want to simulate a system with spring interactions instead, we use
# the line below, but we would need to set k, and set E = 0
#md.system_set_bond_spring_constant(k)
# initialize neighbor list
md.system_init_neighbor_list()
# get pointers to positions, velocities and unfolded positions
# also get a pointer ot the array of triangles
pos = md.system_get_positions()
vel = md.system_get_velocities()
upos = md.system_get_unfolded_positions()
tet = md.system_get_tetras()
# get pointers to arrays fo initial area (refVol), and
# current area, (currVol) of triangles
# also, array with the invariants of the triangles
refVol, currVol = md.system_get_elements_volumes()
I1,I2 = md.system_get_elements_invariants()
print("Volume check: ",refVol.shape[0], currVol.shape[0], np.sum(refVol), np.sum(currVol))
#pdb.set_trace()
# we rescale the particles at the vertices
sigmas = md.system_get_particle_sizes()
sigmas *= sigma
R = R - 0.5 + sigma/2
#if we want to save the configuration, we can use the formats below
#xyzfile = fm.Saver(0,"test_test",pos)
#vtkfile = fm.Saver(1,"test_test",upos,vel=vel,cells=tet)
#vtffile = fm.Saver(2,"test_test",upos,bonds=bonds,box=[box[0],box[1]])
#vtffile.append(0)
# lets create a plot for animation
plot = Plotter.Plotter(pos,vel,tet,box[0],box[1],'tri',I1,sigma) # 2 is the radius
plot.update(0)
# run the simulation
for i in range(1000):
md.system_run(100);
avgs = md.system_get_avgs()
print(avgs)
#xyzfile.append(avgs[0])
#vtkfile.append(avgs[0])
#vtffile.append(avgs[0])
#md.system_unfold_positions()
if i % 1 == 0: plot.update(avgs[0])
print("finished")
plt.show()
def run0():
print(os.getcwd())
os.chdir('data')
print(os.getcwd())
print(dir(md))
dt = 0.005
ucells = 10
sigma = 1
N = ucells * ucells
dens = 0.1
nu = 0.3
L = math.sqrt(N / dens)
print(L)
T = 2.0
v0 = math.sqrt(2.0 * T)
eps = np.array([1.0])
rc = sigma * math.pow(2, 1.0 / 6.0)
rc = 2.5
rcut = np.array([rc])
shift = np.array([0.0])
E = 200
k = 50
pdb.set_trace()
md.system_init(np.array([L, L]))
fm.init_particles_simple_cubic(md, ucells, L)
lbox = md.system_get_box()
print("box", lbox)
md.system_set_boundary_conditions(2)
md.system_set_velocities(v0)
md.system_set_zero_center_of_mass_vel()
md.system_set_dt(dt)
md.system_set_avg_steps(100)
md.system_set_potential(eps, rcut, shift)
md.system_init_neighbor_list()
pos = md.system_get_positions1()
vel = md.system_get_velocities()
#upos = md.system_get_unfolded_positions()
#tet = md.system_get_tetras()
#bonds = md.system_get_bonds()
#sigmas = md.system_get_particle_sizes()
#sigmas *= sigma
#R = R - 0.5 + sigma/2
#xyzfile = fm.Saver(0,"test_test",pos)
#vtkfile = fm.Saver(1,"test_test",pos,vel=vel,cells=tet)
#vtffile = fm.Saver(2,"test_test",upos,bonds=bonds,box=[lbox[0],lbox[1]])
#vtffile.append(0);
plot = Plotter.Plotter(pos, vel, None, lbox[0], lbox[1], 'pts',
sigma) # 2 is the radius
plot.update(0)
#r = 0.0
#md.system_set_walls_moving_rate(r,r)
#pdb.set_trace()
for i in range(1000):
md.system_run(100)
avgs = md.system_get_avgs()
print(avgs)
#xyzfile.append(avgs[0])
#vtkfile.append(avgs[0])
#vtffile.append(avgs[0])
#md.system_unfold_positions()
plot.update(avgs[0])
print("finished")
def run1():
print(os.getcwd())
os.chdir('c:\\tmp\\test1')
print(os.getcwd())
print(dir(md))
dt = 0.002
ucells = 2
sigma = 2
N = ucells * ucells
dens = 0.2
#nu = 0.5
nu = 0.3
dens = nu / np.pi
L = math.sqrt(N / dens)
print(L)
T = 1
#v0 = math.sqrt(2.0 * T * (1.0-1.0/N))
v0 = math.sqrt(2.0 * T)
eps = np.array([1.0])
rc = sigma * math.pow(2, 1.0 / 6.0)
rcut = np.array([rc])
shift = np.array([1.0])
E = 200
k = 200
pdb.set_trace()
box = np.array([L, L])
md.system_init(box)
#nodes = np.loadtxt("diskR1Vertices1.txt");
#cells = np.loadtxt("diskR1Triangles1.txt") - 1;
nodes, cells = mdmesh.uniform_mesh_on_unit_circle(.15)
#L,R = fm.add_clusters(md,nodes,cells,1.0,ucells,nu,'sc1')
L, R = fm.add_binary_clusters(md, nodes, cells, 1.0, 1.0, .15, ucells, nu,
'sc')
box = md.system_get_box()
md.system_set_boundary_conditions(0)
md.system_set_moving_walls(0)
md.system_set_velocities(v0)
md.system_set_zero_center_of_mass_vel()
md.system_set_dt(dt)
md.system_set_avg_steps(100)
md.system_set_potential(eps, rcut, shift)
md.system_set_youngs_modulus(E)
#md.system_set_swelling_energy_constants(100,250,0.0)
md.system_set_friction(.1)
#md.system_set_bond_spring_constant(k)
md.system_init_neighbor_list()
pos = md.system_get_positions()
vel = md.system_get_velocities()
upos = md.system_get_unfolded_positions()
tet = md.system_get_tetras()
#plt.scatter(pos[:,0],pos[:,1])
#plt.show()
#plt.triplot(pos[:,0], pos[:,1], tet, 'go-', lw=1.0)
bonds = md.system_get_bonds()
refVol, currVol = md.system_get_elements_volumes()
I1, I2 = md.system_get_elements_invariants()
print("Volume check: ", refVol.shape[0], currVol.shape[0], np.sum(refVol),
np.sum(currVol))
sigmas = md.system_get_particle_sizes()
sigmas *= sigma
R = R - 0.5 + sigma / 2
n1 = 0.79
L1 = np.sqrt(ucells**2 * np.pi * R**2 / n1)
nf = 0.95
Lf = np.sqrt(ucells**2 * np.pi * R**2 / nf)
print(L, Lf, R)
pdb.set_trace()
#xyzfile = fm.Saver(0,"test_test",pos)
vtkfile = fm.Saver(1, "test_test", pos, vel=vel, cells=tet, I2=I2)
#vtffile = fm.Saver(2,"test_test",upos,bonds=bonds,box=[Lx,Lx])
vtkfile.append(0)
walls = md.system_get_walls_pos()
print("walls", walls)
walls = [walls[0][0], walls[1][0], walls[0][1], walls[1][1]]
print("walls", walls)
plot = Plotter.Plotter(pos, vel, tet, box[0], box[1], 'tripts1', I1,
sigma) # 2 is the radius
plot.update(0, walls, "")
#plt.show()
r = Lf / 800
r00 = np.array([1.01 * r, r])
r10 = np.array([-1.01 * r, r])
r0 = np.array([r, r])
r1 = np.array([-r, -r])
r02 = np.array([-r, r])
r12 = np.array([r, -r])
r_stop = np.array([0, 0])
data = []
totRefVol = np.sum(refVol)
totCurrVol = np.sum(currVol)
md.system_set_moving_walls(0)
md.system_set_walls_moving_rate(r0, r1)
pdb.set_trace()
shear = 0
Ws = 0
for Ws in np.arange(0, 0, 100):
md.system_run(100)
avgs = md.system_get_avgs()
print("\nstep %d" % avgs[0])
print(avgs)
title = "steps = %d" % (avgs[0])
#if Ws % 10 == 0:
#Ws += 10
md.system_set_swelling_energy_constants(100, Ws, 0.0)
plot.update(avgs[0], walls, title)
#vtkfile.append(avgs[0])
md.system_set_friction(1)
md.system_set_moving_walls(1)
md.system_set_walls_moving_rate(r0, r1)
for i in range(10000):
md.system_run(100)
avgs = md.system_get_avgs()
walls = md.system_get_walls_pos()
walls = [walls[0][0], walls[1][0], walls[0][1], walls[1][1]]
print("\nstep %d" % avgs[0])
print("walls", walls)
Lx = walls[1] - walls[0]
Ly = walls[3] - walls[2]
print("Box Vol = ", Lx * Ly)
if i == 20:
md.system_set_walls_moving_rate(r00, r10)
if Ly / Lx > 1.1 and shear == 0:
md.system_set_walls_moving_rate(r0, r1)
if totCurrVol / totRefVol < 1.5 and i > 20:
shear = 1
if shear == 1:
c = Lx / Ly
r02 = np.array([-c * r, r])
r12 = np.array([c * r, -r])
md.system_set_walls_moving_rate(r02, r12)
#md.system_set_walls_shear(1)
if Lx > L:
md.system_set_walls_moving_rate(r_stop, r_stop)
md.system_unfold_positions()
#xyzfile.append(avgs[0])
vtkfile.append(avgs[0])
#vtffile.append(avgs[0])
#if i % 1 == 0:
print(avgs)
wf = md.system_get_walls_forces()
#return Py_BuildValue("((dd)(dd))", f[0][0], f[0][1], f[1][0], f[1][1]);
wf = [wf[0][0], wf[0][1], wf[1][0], wf[1][1]]
print("force on walls :", wf)
totCurrVol = np.sum(currVol)
data.append([
dt * avgs[0], wf[0], wf[1], wf[2], wf[3], totCurrVol / totRefVol,
avgs[5]
])
print("Volumes: ", totRefVol, totCurrVol, totCurrVol / totRefVol * 100)
print("I1 max", I1.max())
title = "steps = %d Lini = %f Lx = %f Ly = %f nu = %f V/Vref= %f" % (
avgs[0], L, Lx, Ly, ucells**2 * np.pi * R**2 /
(Lx * Ly), totCurrVol / totRefVol)
if i % 10 == 0:
plot.update(avgs[0], walls, title)
wf = np.array(data)
np.savetxt("data.dat", wf)
vtkfile.append(avgs[0])
wf = np.array(data)
np.savetxt("data.dat", wf)
print("finished")
plt.show()
def run2():
print(os.getcwd())
os.chdir('c:\\tmp\\test1')
print(os.getcwd())
print(dir(md))
#md.system_c_main()
dt = 0.005
ucells = 2
sigma = 1
N = ucells * ucells
dens = 0.1
nu = 0.2
L = math.sqrt(N / dens)
print(L)
T = 2.0
v0 = math.sqrt(2.0 * T)
eps = np.array([1.0])
rc = sigma * math.pow(2, 1.0 / 6.0)
rcut = np.array([rc])
shift = np.array([1.0])
E = 200
k = 50
md.system_init(L, L)
#nodes = np.loadtxt("diskR1Vertices1.txt");
#cells = np.loadtxt("diskR1Triangles1.txt") - 1;
nodes, cells = mdmesh.uniform_mesh_on_unit_circle(.2)
L, R = fm.add_clusters(md, nodes, cells, 1.0, ucells, nu, 'sc')
#fm.init_particles_simple_cubic(md,ucells,L)
Lx, Ly = md.system_get_box()
md.system_set_boundary_conditions(0)
md.system_set_velocities(v0)
md.system_set_zero_center_of_mass_vel()
md.system_set_dt(dt)
md.system_set_avg_steps(100)
md.system_set_potential(eps, rcut, shift)
md.system_set_youngs_modulus(E)
#md.system_set_swelling_energy_constants(100,50,0)
md.system_set_friction(.1)
#md.system_set_bond_spring_constant(k)
md.system_init_neighbor_list()
pos = md.system_get_positions()
vel = md.system_get_velocities()
#vel += 1
upos = md.system_get_unfolded_positions()
tet = md.system_get_tetras()
bonds = md.system_get_bonds()
sigmas = md.system_get_particle_sizes()
sigmas *= sigma
R = R - 0.5 + sigma / 2
xyzfile = fm.Saver(0, "test_test", pos)
vtkfile = fm.Saver(1, "test_test", upos, vel=vel, cells=tet)
vtffile = fm.Saver(2, "test_test", upos, bonds=bonds, box=[Lx, Lx])
vtffile.append(0)
plot = Plotter.Plotter(pos, vel, tet, Lx, Lx, 'tripts1',
sigma) # 2 is the radius
plot.update(0)
r = 0.01
md.system_set_walls_moving_rate(r, r)
#pdb.set_trace()
for i in range(1000):
md.system_run(100)
avgs = md.system_get_avgs()
print(avgs)
xyzfile.append(avgs[0])
vtkfile.append(avgs[0])
vtffile.append(avgs[0])
md.system_unfold_positions()
if i % 10 == 0: plot.update(avgs[0])
print("finished")
plt.show()
def run1():
print(os.getcwd())
os.chdir('c:\\tmp\\test1')
print(os.getcwd())
print(dir(md))
#md.system_c_main()
dt = 0.005
ucells = 2
sigma = 2
N = ucells * ucells
dens = 0.1
nu = 0.2
dens = nu / np.pi
L = math.sqrt(N / dens)
print(L)
T = 1.1
#v0 = math.sqrt(2.0 * T * (1.0-1.0/N))
v0 = math.sqrt(2.0 * T)
eps = np.array([1.0])
rc = sigma * math.pow(2, 1.0 / 6.0)
rcut = np.array([rc])
shift = np.array([1.0])
E = 200
k = 200
md.system_init(L, L)
#nodes = np.loadtxt("diskR1Vertices1.txt");
#cells = np.loadtxt("diskR1Triangles1.txt") - 1;
nodes, cells = mdmesh.uniform_mesh_on_unit_circle(.1)
L, R = fm.add_clusters(md, nodes, cells, 1.0, ucells, nu, 'sc1')
#init_particles_simple_cubic(ucells,L)
Lx, Ly = md.system_get_box()
md.system_set_boundary_conditions(0)
md.system_set_velocities(v0)
md.system_set_zero_center_of_mass_vel()
md.system_set_dt(dt)
md.system_set_avg_steps(100)
md.system_set_potential(eps, rcut, shift)
md.system_set_youngs_modulus(E)
md.system_set_swelling_energy_constants(100, 50, 0)
md.system_set_friction(1)
#md.system_set_bond_spring_constant(k)
md.system_init_neighbor_list()
pos = md.system_get_positions()
vel = md.system_get_velocities()
#vel += 1
upos = md.system_get_unfolded_positions()
tet = md.system_get_tetras()
bonds = md.system_get_bonds()
refVol, currVol = md.system_get_elements_volumes()
sigmas = md.system_get_particle_sizes()
sigmas *= sigma
R = R - 0.5 + sigma / 2
n1 = 0.79
L1 = np.sqrt(ucells**2 * np.pi * R**2 / n1)
nf = 0.95
Lf = np.sqrt(ucells**2 * np.pi * R**2 / nf)
print(L, Lf, R)
#xyzfile = fm.Saver(0,"test_test",pos)
vtkfile = fm.Saver(1, "test_test", upos, vel=vel, cells=tet)
#vtffile = fm.Saver(2,"test_test",upos,bonds=bonds,box=[Lx,Lx])
#vtffile.append(0);
plot = Plotter.Plotter(pos, vel, tet, Lx, Lx, 'tripts1',
sigma) # 2 is the radius
plot.update(0)
r = Lf / 800
md.system_set_walls_moving_rate(0, 0)
data = []
totRefVol = np.sum(refVol)
md.system_set_walls_moving_rate(r, r)
for i in range(10):
md.system_run(100)
avgs = md.system_get_avgs()
walls = md.system_get_walls_pos()
#print(walls)
Lx = walls[1] - walls[0]
Ly = walls[3] - walls[2]
#if i == 20:
# md.system_set_walls_moving_rate(r,r)
if Ly < L1 and Ly > Lf:
md.system_set_walls_moving_rate(-r, r)
if Lx > L:
md.system_set_walls_moving_rate(0.0, 0.0)
md.system_unfold_positions()
#xyzfile.append(avgs[0])
#vtkfile.append(avgs[0])
#vtffile.append(avgs[0])
#if i % 1 == 0:
print(avgs)
wf = md.system_get_walls_forces()
print("force on walls :", wf)
data.append([dt * avgs[0], wf[0], wf[1], wf[2], wf[3]])
totCurrVol = np.sum(currVol)
print("Volumes: ", totRefVol, totCurrVol, totCurrVol / totRefVol * 100)
title = "steps = %d Lini = %f Lx = %f Ly = %f nu = %f" % (
avgs[0], L, Lx, Ly, ucells**2 * np.pi * R**2 / (Lx * Ly))
if i % 1 == 0: plot.update(avgs[0], walls, title)
wf = np.array(data)
np.savetxt("data.dat", wf)
print("finished")
def run3D():
print(os.getcwd())
os.chdir('c:\\tmp\\test1')
print(os.getcwd())
print(dir(md))
#md.system_c_main()
dt = 0.005
ucells = 1
sigma = 1
N = ucells**3
dens = 0.1
nu = 0.1
L = math.pow(N / dens,1/3.0)
print(L)
T = 2.0
v0 = math.sqrt(2.0 * T )
eps=np.array([1.0])
rc = sigma*math.pow(2,1.0/6.0)
#rc = 2.5
rcut=np.array([rc])
shift=np.array([1.0])
E=200
k=50
pdb.set_trace()
md.system_init(np.array([L,L,L]))
#nodes = np.loadtxt("diskR1Vertices1.txt");
#cells = np.loadtxt("diskR1Triangles1.txt") - 1;
nodes, cells = mdmesh.uniform_mesh_on_unit_ball(.2)
L,R = fm.add_3D_clusters(md,nodes,cells,1.0,ucells,nu,'sc1')
#fm.init_particles_simple_cubic3D(md,ucells,L)
lbox = md.system_get_box()
md.system_set_boundary_conditions(0)
md.system_set_velocities(v0)
md.system_set_zero_center_of_mass_vel()
md.system_set_dt(dt)
md.system_set_avg_steps(100)
md.system_set_potential(eps,rcut,shift)
md.system_set_youngs_modulus(E)
md.system_set_swelling_energy_constants(100,10,0)
md.system_set_friction(1)
#md.system_set_bond_spring_constant(k)
md.system_init_neighbor_list()
pos = md.system_get_positions()
print(pos)
vel = md.system_get_velocities()
#vel += 1
#upos = md.system_get_unfolded_positions()
#tet = md.system_get_tetras()
#bonds = md.system_get_bonds()
#sigmas = md.system_get_particle_sizes()
#sigmas *= sigma
#R = R - 0.5 + sigma/2
xyzfile = fm.Saver(0,"test_test",pos,dims=3)
vtkfile = fm.Saver(1,"test_test",pos,dims=3,vel=vel,cells=tet)
vtkfile.append(0)
'''
lx = lbox[0]
fig = plt.figure()
ax = a3.Axes3D(fig)
ax.set_aspect('equal')
ax.set_xlim(0,lx)
ax.set_ylim(0,lx)
ax.set_zlim(0,lx)
fig.set_size_inches(15, 15)
ax.scatter(pos[:,0],pos[:,1],pos[:,2])
ax.add_collection3d(tri)
plt.show()
'''
#vtffile = fm.Saver(2,"test_test",upos,bonds=bonds,box=[lbox[0],lbox[1]])
#vtffile.append(0);
#plot = Plotter.Plotter(pos,vel,tet,lbox[0],lbox[1],'pts',sigma) # 2 is the radius
#plot.update(0)
#r = 0.0
#md.system_set_walls_moving_rate(r,r)
#pdb.set_trace()
for i in range(1000):
md.system_run(100);
avgs = md.system_get_avgs()
print(avgs)
xyzfile.append(avgs[0])
vtkfile.append(avgs[0])
#vtffile.append(avgs[0])
#md.system_unfold_positions()
#plot.update(avgs[0])
print("finished")
plt.show()