import mechanica as m
import threading
m.init(windowless=True, window_size=[1024, 1024])
print(m.system.gl_info())
class Na(m.Particle):
radius = 0.4
style = {"color": "orange"}
class Cl(m.Particle):
radius = 0.25
style = {"color": "spablue"}
uc = m.lattice.bcc(0.9, [Na, Cl])
m.lattice.create_lattice(uc, [10, 10, 10])
def threaded_steps(steps):
print('thread start')
print("thread, calling context_has_current()")
m.Simulator.context_has_current()\
print("thread, calling context_make_current())")
import mechanica as m
m.init()
class A(m.Particle):
radius = 0.2
uc = m.lattice.hex(1, A)
print(uc)
m.lattice.create_lattice(uc, [6, 4, 6])
m.show()
import mechanica as m
m.init(dt=0.1, dim=[15, 5, 5], cutoff = 3,
bc={'x':('periodic','reset')})
class A(m.Particle):
species = ['S1', 'S2', 'S3']
style = {"colormap" : {"species" : "S1",
"map" : "rainbow",
"range" : "auto"}}
a1 = A(m.universe.center - [0, 1, 0])
a2 = A(m.universe.center + [-5, 1, 0], velocity=[0.5, 0, 0])
pressure = m.forces.ConstantForce([0.1, 0, 0])
m.bind(pressure, A, "S1")
a1.species.S1 = 0
a2.species.S1 = 0.1
m.run()
import mechanica as m
import numpy as np
# dimensions of universe
dim=np.array([30., 30., 30.])
dist = 3.9
offset = 6
m.init(dim=dim,
cutoff=7,
cells=[3,3,3],
integrator=m.FORWARD_EULER,
dt=0.01,
bc={'z':'potential', 'x' : 'potential', 'y' : 'potential'})
class A(m.Particle):
radius=1
dynamics = m.Newtonian
mass=2.5
style={"color":"MediumSeaGreen"}
class Sphere(m.Particle):
radius=3
frozen = True
style={"color":"orange"}
class Test(m.Particle):
import mechanica as m
import numpy as np
# potential cutoff distance
cutoff = 8
receptor_count = 500
# dimensions of universe
dim = np.array([20., 20., 20.])
center = dim / 2
# new simulator
m.init(dim=dim, cutoff=cutoff, cells=[4, 4, 4], integrator=m.RUNGE_KUTTA_4)
class Big(m.Particle):
mass = 500000
radius = 3
class Receptor(m.Particle):
mass = 0.1
radius = 0.1
target_temperature = 1
dynamics = m.Overdamped
class Virus(m.Particle):
mass = 1
radius = 0.5
import mechanica as m
import numpy as np
# dimensions of universe
dim=np.array([30., 30., 30.])
m.init(dim=dim,
cutoff=10,
integrator=m.FORWARD_EULER,
cells=[3, 3, 3],
dt=0.001)
class A(m.Particle):
radius=1
dynamics = m.Newtonian
mass=20
style={"color":"MediumSeaGreen"}
p = m.Potential.glj(e=50, m=6, max=3)
cp = m.Potential.coulomb(q=5000, min=0.05, max=10)
m.bind(p, A, m.Cuboid)
m.bind(cp, A, A)
rforce = m.forces.friction(0.01, 0, 100)
# bind it just like any other force
m.bind(rforce, A)
c = m.Cuboid(m.Universe.center + [0, 0, 0], size=[25, 31, 5])
import mechanica as m
import numpy as np
m.init(dim=[20., 20., 20.], cutoff=8, bc=m.BOUNDARY_NONE)
class Bead(m.Particle):
mass = 1
radius = 0.1
dynamics = m.Overdamped
# simple harmonic potential to pull particles
pot = m.Potential.harmonic(k=1, r0=0.1, max=3)
# make a ring of of 50 particles
pts = m.points(m.Ring, 50) * 5 + m.Universe.center
# constuct a particle for each position, make
# a list of particles
beads = [Bead(p) for p in pts]
# create an explicit bond for each pair in the
# list of particles. The bind_pairwise method
# searches for all possible pairs within a cutoff
# distance and connects them with a bond.
m.bind_pairwise(pot, beads, 1)
# run the model
m.run()
import mechanica as m
import numpy as np
m.init(dt=0.1, dim=[15, 12, 10],
bc={'x':'no_slip',
'y':'periodic',
'bottom':'no_slip',
'top':{'velocity':[-0.4, 0, 0]}},
perfcounter_period=100)
# lattice spacing
a = 0.3
#m.universe.boundary_conditions.left.restore = 0.5
class A (m.Particle):
radius = 0.2
style={"color":"seagreen"}
dynamics = m.Newtonian
mass=10
dpd = m.Potential.dpd(alpha=0.3, gamma=1, sigma=1, cutoff=0.6)
dpd_wall = m.Potential.dpd(alpha=0.5, gamma=10, sigma=1, cutoff=0.1)
dpd_left = m.Potential.dpd(alpha=1, gamma=100, sigma=0, cutoff=0.5)
m.bind(dpd, A, A)
m.bind(dpd_wall, A, m.Universe.boundary_conditions.top)
m.bind(dpd_left, A, m.Universe.boundary_conditions.left)
uc = m.lattice.sc(a, A)
import mechanica as m
import numpy as np
# potential cutoff distance
cutoff = 3
# dimensions of universe
dim = [10., 10., 10.]
# new simulator
m.init(dim=dim, window_size=[900, 900], perfcounter_period=100)
# create a potential representing a 12-6 Lennard-Jones potential
# A The first parameter of the Lennard-Jones potential.
# B The second parameter of the Lennard-Jones potential.
# cutoff
pot = m.Potential.lennard_jones_12_6(0.275, cutoff, 9.5075e-06, 6.1545e-03,
1.0e-3)
# create a particle type
# all new Particle derived types are automatically
# registered with the universe
class Argon(m.Particle):
radius = 0.1
mass = 39.4
# bind the potential with the *TYPES* of the particles
m.Universe.bind(pot, Argon, Argon)
import mechanica as m
import numpy as np
# potential cutoff distance
cutoff = 8
count = 3000
# dimensions of universe
dim=np.array([20., 20., 20.])
center = dim / 2
# new simulator
m.init(dim=dim, cutoff=cutoff, bc=m.BOUNDARY_NONE)
class Yolk(m.Particle):
mass = 500000
radius = 3
class Cell(m.Particle):
mass = 5
radius = 0.2
target_temperature=0
dynamics = m.Overdamped
pot_bs = m.Potential.soft_sphere(kappa=5, epsilon=20, r0=2.9, \
eta=3, tol = 0.1, min=0, max=9)
pot_ss = m.Potential.soft_sphere(kappa=10, epsilon=0.000000001, r0=0.2, \
eta=2, tol = 0.05, min=0, max=3)
# bind the potential with the *TYPES* of the particles
import mechanica as m
import numpy as np
# dimensions of universe
dim = np.array([30., 30., 30.])
center = dim / 2
m.init(dim=dim, cutoff=10, integrator=m.FORWARD_EULER, dt=0.0005)
class C(m.Cluster):
radius = 3
class A(m.Particle):
radius = 0.5
dynamics = m.Overdamped
mass = 10
style = {"color": "MediumSeaGreen"}
class B(m.Particle):
radius = 0.5
dynamics = m.Overdamped
mass = 10
style = {"color": "skyblue"}
c1 = C(position=center - (3, 0, 0))
c2 = C(position=center + (7, 0, 0))
c1.A(2000)
c2.B(2000)
import mechanica as m
import numpy as np
m.init(dim=[25., 25., 25.], dt=0.0005, cutoff=3, bc=m.BOUNDARY_NONE)
class Green(m.Particle):
mass = 1
radius = 0.1
dynamics = m.Overdamped
style = {'color': 'mediumseagreen'}
class Big(m.Particle):
mass = 10
radius = 8
frozen = True
style = {'color': 'orange'}
# simple harmonic potential to pull particles
pot = m.Potential.harmonic(k=1, r0=0.1, max=3)
# potentials between green and big objects.
pot_yc = m.Potential.glj(e=1, r0=1, m=3, min=0.01)
pot_cc = m.Potential.glj(e=0.0001, r0=0.1, m=3, min=0.005, max=2)
# random points on surface of a sphere
pts = m.random_points(m.Sphere,
10000) * (Green.radius + Big.radius) + m.Universe.center
import numpy as np
# total number of cells
A_count = 5000
B_count = 5000
# potential cutoff distance
cutoff = 3
# dimensions of universe
dim = np.array([20., 20., 20.])
center = dim / 2
# new simulator
m.init(dim=dim,
cutoff=cutoff,
clip_planes=[([8, 8, 8], [1, 1, 0]), ([11, 11, 11], [-1, -1, 0])])
class A(m.Particle):
mass = 40
radius = 0.4
dynamics = m.Overdamped
class B(m.Particle):
mass = 40
radius = 0.4
dynamics = m.Overdamped
import mechanica as m
import numpy as np
m.init(dim=[25., 25., 25.], cutoff=3, bc=m.BOUNDARY_NONE)
class Blue(m.Particle):
mass = 1
radius = 0.1
dynamics = m.Overdamped
style = {'color': 'dodgerblue'}
class Big(m.Particle):
mass = 1
radius = 8
frozen = True
style = {'color': 'orange'}
# simple harmonic potential to pull particles
pot = m.Potential.harmonic(k=1, r0=0.1, max=3)
# make big cell in the middle
Big(m.Universe.center)
#Big.style.visible = False
# create a uniform mesh of particles and bonds on the surface of a sphere
parts, bonds = m.bind_sphere(pot,
type=Blue,
# number of particles
count = 6000
# number of time points we avg things
avg_pts = 3
# dimensions of universe
dim=np.array([50., 50., 100.])
center = dim / 2
# new simulator
m.init(dim=dim,
cutoff=cutoff,
integrator=m.FORWARD_EULER,
bc=m.BOUNDARY_NONE,
dt=0.001,
max_distance=0.2,
threads=8,
cells=[5, 5, 5])
clump_radius = 8
class Yolk(m.Particle):
mass = 500000
radius = 20
frozen = True
class Cell(m.Particle):
mass = 10
radius = 1.2
target_temperature=0
import mechanica as m
import numpy as np
m.init(dt=0.1,
dim=[15, 12, 10],
bc={
'x': 'periodic',
'z': 'no_slip',
'y': 'periodic'
},
perfcounter_period=100)
# lattice spacing
a = 0.7
class A(m.Particle):
radius = 0.3
style = {"color": "seagreen"}
dynamics = m.Newtonian
mass = 10
dpd = m.Potential.dpd(sigma=1.5)
m.bind(dpd, A, A)
f = m.forces.ConstantForce([0.01, 0, 0])
m.bind(f, A)
import mechanica as m
import numpy as np
# dimensions of universe
dim = np.array([30., 30., 30.])
m.init(dim=dim,
cutoff=10,
integrator=m.FORWARD_EULER,
cells=[1, 1, 1],
dt=0.005)
class A(m.Particle):
radius = 0.5
dynamics = m.Newtonian
mass = 30
style = {"color": "MediumSeaGreen"}
class Sphere(m.Particle):
radius = 3
frozen = True
style = {"color": "orange"}
class Test(m.Particle):
radius = 0
frozen = True
style = {"color": "orange"}
import mechanica as m
import numpy as np
# potential cutoff distance
cutoff = 1
# new simulator
m.init(dim=[20., 20., 20.])
pot = m.Potential.soft_sphere(kappa=10,
epsilon=0.1,
r0=0.6,
eta=3,
tol=0.1,
min=0.05,
max=4)
class Cell(m.Particle):
mass = 20
target_temperature = 0
radius = 0.5
events = [
m.on_time(m.Particle.fission, period=1, distribution='exponential')
]
dynamics = m.Overdamped
m.Universe.bind(pot, Cell, Cell)
rforce = m.forces.random(0, 0.5)
import mechanica as m
import numpy as np
# potential cutoff distance
cutoff = 1
# dimensions of universe
dim=[10., 10., 10.]
# new simulator
m.init(dim=dim)
# create a potential representing a 12-6 Lennard-Jones potential
# A The first parameter of the Lennard-Jones potential.
# B The second parameter of the Lennard-Jones potential.
# cutoff
#pot = m.Potential.lennard_jones_12_6(0.275 , cutoff, 9.5075e-06 , 6.1545e-03 , 1.0e-3 )
pot = m.Potential.glj(e=0.1, min=0.5, max=3)
# create a particle type
# all new Particle derived types are automatically
# registered with the universe
class Argon(m.Particle):
radius=0.19
mass = 39.4
# bind the potential with the *TYPES* of the particles
m.Universe.bind(pot, Argon, Argon)
# uniform random cube
import mechanica as m
m.init(windowless=True,
window_size=[1024, 1024],
clip_planes=[([2, 2, 2], [1, 1, 0]), ([5, 5, 5], [-1, -1, 0])])
print(m.system.gl_info())
class Na(m.Particle):
radius = 0.4
style = {"color": "orange"}
class Cl(m.Particle):
radius = 0.25
style = {"color": "spablue"}
uc = m.lattice.bcc(0.9, [Na, Cl])
m.lattice.create_lattice(uc, [10, 10, 10])
# m.system.image_data() is a jpg byte stream of the
# contents of the frame buffer.
with open('system.jpg', 'wb') as f:
f.write(m.system.image_data())
import mechanica as m
m.init(window_size=[1000, 1000])
class Na(m.Particle):
radius = 0.4
style = {"color": "orange"}
class Cl(m.Particle):
radius = 0.25
style = {"color": "spablue"}
uc = m.lattice.bcc(0.9, [Na, Cl])
m.lattice.create_lattice(uc, [10, 10, 10])
m.show()
import mechanica as m
m.init(dim=[6.5, 6.5, 6.5], bc=m.FREESLIP_FULL)
class A(m.Particle):
radius = 0.1
species = ['S1', 'S2', 'S3']
style = {"colormap": {"species": "S1", "map": "rainbow", "range": "auto"}}
class B(m.Particle):
radius = 0.1
species = ['S1', 'S2', 'S3']
style = {"colormap": {"species": "S1", "map": "rainbow", "range": "auto"}}
def spew(self, event):
print("spew...")
# reset the value of the species
# secrete consumes material...
self.species.S1 = 500
self.species.S1.secrete(250, distance=1)
m.flux(A, A, "S1", 5, 0.005)
uc = m.lattice.sc(0.25, A)
parts = m.lattice.create_lattice(uc, [25, 25, 25])
import mechanica as m
import numpy as np
m.init(dt=0.1, dim=[15, 12, 10]) #, bc=m.FREESLIP_FULL)
# lattice spacing
a = 0.65
class A(m.Particle):
radius = 0.3
style = {"color": "seagreen"}
dynamics = m.Overdamped
class B(m.Particle):
radius = 0.3
style = {"color": "red"}
dynamics = m.Overdamped
class Fixed(m.Particle):
radius = 0.3
style = {"color": "blue"}
frozen = True
repulse = m.Potential.coulomb(q=0.08, min=0.01, max=2 * a)
m.bind(repulse, A, A)
m.bind(repulse, A, B)
import mechanica as m
import numpy as np
# potential cutoff distance
cutoff = 8
receptor_count = 10000
# dimensions of universe
dim = np.array([20., 20., 20.])
center = dim / 2
# new simulator
m.init(dim=dim, cutoff=cutoff, cells=[4, 4, 4], threads=8)
class Nucleus(m.Particle):
mass = 500000
radius = 1
class Receptor(m.Particle):
mass = 0.2
radius = 0.05
target_temperature = 1
#dynamics = m.Overdamped
# locations of initial receptor positions
receptor_pts = m.random_points(m.SolidSphere, receptor_count) * 5 + center
import mechanica as m
import numpy as np
cutoff = 8
count = 3
# dimensions of universe
dim = np.array([20., 20., 20.])
center = dim / 2
m.init(dim=dim, cutoff=cutoff)
class B(m.Particle):
mass = 1
dynamics = m.Overdamped
# make a glj potential, this automatically reads the
# particle radius to determine rest distance.
pot = m.Potential.glj(e=1)
m.bind(pot, B, B)
p1 = B(center + (-2, 0, 0))
p2 = B(center + (2, 0, 0))
p1.radius = 1
p2.radius = 2
m.Simulator.run()
import mechanica as m
import numpy as np
cutoff = 1
m.init(dim=[10., 10., 10.])
class Argon(m.Particle):
mass = 39.4
target_temperature = 100
# hook up the destroy method on the Argon type to the
# on_time event
m.on_time(Argon.destroy, period=2, distribution='exponential')
pot = m.Potential.lennard_jones_12_6(0.275, cutoff, 9.5075e-06, 6.1545e-03,
1.0e-3)
m.Universe.bind(pot, Argon, Argon)
tstat = m.forces.berenderson_tstat(10)
m.Universe.bind(tstat, Argon)
size = 100
# uniform random cube
positions = np.random.uniform(low=0, high=10, size=(size, 3))
velocities = np.random.normal(0, 0.2, size=(size, 3))
import mechanica as m
import numpy as np
# dimensions of universe
dim=np.array([30., 30., 30.])
center = dim / 2
m.init(dim=dim,
cutoff=3,
integrator=m.FORWARD_EULER,
dt=0.001)
class C(m.Cluster):
radius=2.3
class B(m.Particle):
radius=0.25
dynamics = m.Overdamped
mass=15
style={"color":"skyblue"}
def split(self, event):
print("C.split(" + str(self) + ", event: " + str(event) + ")")
axis = self.position - C.yolk_pos
print("axis: " + str(axis))
m.Cluster.split(self, axis=axis)
m.on_time(C.split, period=0.2, predicate="largest")
class Yolk(m.Particle):
import mechanica as m
import numpy as np
# dimensions of universe
dim = np.array([30., 30., 30.])
center = dim / 2
m.init(dim=dim,
cutoff=3,
integrator=m.FORWARD_EULER,
dt=0.001,
cells=[6, 6, 6])
class C(m.Cluster):
radius = 5
class B(m.Particle):
radius = 0.25
dynamics = m.Overdamped
mass = 15
style = {"color": "skyblue"}
def split(self, event):
print("splitting cluster, C.split(" + str(self) + ", event: " +
str(event) + ")")
axis = self.position - C.yolk_pos
print("axis: " + str(axis))
m.Cluster.split(self, axis=axis)
print("new cluster count: ", len(C.items()))
import mechanica as m
import numpy as np
m.init(dt=0.1,
dim=[15, 12, 10],
cells=[7, 6, 5],
cutoff=0.5,
bc={
'x': 'periodic',
'y': 'periodic',
'top': {
'velocity': [0, 0, 0]
},
'bottom': {
'velocity': [0, 0, 0]
}
})
# lattice spacing
a = 0.15
class A(m.Particle):
radius = 0.05
style = {"color": "seagreen"}
dynamics = m.Newtonian
mass = 10
dpd = m.Potential.dpd(alpha=10, sigma=1)
import mechanica as m
import numpy as np
# potential cutoff distance
cutoff = 3
# dimensions of universe
dim=[10., 10., 10.]
# new simulator
m.init(dim=dim,
window_size=[900,900],
perfcounter_period=100,
clip_planes = [([2, 2, 2], [1, 1, 0.5]), ([8, 8, 8], [-1, -1, 0.9])])
# create a potential representing a 12-6 Lennard-Jones potential
# A The first parameter of the Lennard-Jones potential.
# B The second parameter of the Lennard-Jones potential.
# cutoff
pot = m.Potential.lennard_jones_12_6(0.275 , cutoff, 9.5075e-06 , 6.1545e-03 , 1.0e-3 )
# create a particle type
# all new Particle derived types are automatically
# registered with the universe
class Argon(m.Particle):
radius=0.1
mass = 39.4
# bind the potential with the *TYPES* of the particles
m.Universe.bind(pot, Argon, Argon)
