def set_points_and_lines(self):
self.sim_as = simulation()
self.sim_ac = simulation()
self.points = flex.vec3_double(self.sim_as.sites_cart_moved_F01)
self.points.extend(flex.vec3_double(self.sim_ac.sites_cart_moved_F01))
self.points.extend(flex.vec3_double(self.sim_as.sites_cart_wells_F01))
def add_line(i, j, color):
line = (i,j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
self.labels = []
n = len(self.sim_as.sites_cart_F1)
offs = 0
for prefix,color in [("S",(1,0,0)),("C",(0,0,1)),("W",(0,1,0))]:
for i in range(n):
add_line(offs+i, offs+(i+1)%n, color)
self.labels.append(prefix+str(i))
offs += n
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(
center=mcs.center(), radius=mcs.radius()*1.3)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 8
print("Press and hold Tab key to run the simulation.")
print("Press Shift-Tab to increase speed.")
print("Press Ctrl-Tab to decrease speed.")
def set_points_and_lines(self):
self.sim_as = simulation()
self.sim_ac = simulation()
self.points = flex.vec3_double(self.sim_as.sites_cart_moved_F01)
self.points.extend(flex.vec3_double(self.sim_ac.sites_cart_moved_F01))
self.points.extend(flex.vec3_double(self.sim_as.sites_cart_wells_F01))
def add_line(i, j, color):
line = (i,j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
self.labels = []
n = len(self.sim_as.sites_cart_F1)
offs = 0
for prefix,color in [("S",(1,0,0)),("C",(0,0,1)),("W",(0,1,0))]:
for i in xrange(n):
add_line(offs+i, offs+(i+1)%n, color)
self.labels.append(prefix+str(i))
offs += n
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(
center=mcs.center(), radius=mcs.radius()*1.3)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 8
print "Press and hold Tab key to run the simulation."
print "Press Shift-Tab to increase speed."
print "Press Ctrl-Tab to decrease speed."
def exercise_featherstone_FDab(out):
def check():
model = featherstone_system_model(
m=sim.m, I=sim.I_F1, J=six_dof_joint_euler_params_featherstone(qE=sim.J1.qE, qr=sim.J1.qr)
)
q = [None] # already stored in J1 as qE and qr
qd = [sim.qd]
tau = None
f_ext = [matrix.col((sim.nc_F1, sim.f_F1)).resolve_partitions()]
grav_accn = [0, 0, 0]
qdd = featherstone.FDab(model, q, qd, tau, f_ext, grav_accn)
if i_step % 10 == 0:
print >> out, "ang acc 3D:", sim.wd_F1.elems
print >> out, " 6D:", qdd[0].elems[:3]
print >> out
print >> out, "lin acc 3D:", sim.as_F1.elems
print >> out, " 6D:", qdd[0].elems[3:]
print >> out
assert approx_equal(qdd[0].elems[:3], sim.wd_F1)
assert approx_equal(qdd[0].elems[3:], sim.as_F1)
sim = fmri.simulation()
for i_step in xrange(100):
check()
sim.dynamics_step(delta_t=0.1) # large time step to sample
check() # diverse configurations
def exercise_reference_impl_long(n_dynamics_steps, out):
sim = fmri.simulation()
e_tots = flex.double([sim.e_tot])
print >> out, "i_step, [e_pot, e_kin_ang, e_kin_lin, e_kin, e_tot]"
def show(i_step):
print >> out, i_step, [sim.e_pot, sim.e_kin_ang, sim.e_kin_lin, sim.e_kin, sim.e_tot]
out.flush()
n_show = max(1, n_dynamics_steps // 10)
for i_step in xrange(n_dynamics_steps):
sim.dynamics_step(delta_t=0.001)
e_tots.append(sim.e_tot)
if i_step % n_show == 0:
show(i_step)
show(n_dynamics_steps)
print >> out
print >> out, "number of dynamics steps:", n_dynamics_steps
print >> out, "e_tot start:", e_tots[0]
print >> out, " final:", e_tots[-1]
print >> out, " min:", flex.min(e_tots)
print >> out, " max:", flex.max(e_tots)
print >> out, " max-min:", flex.max(e_tots) - flex.min(e_tots)
print >> out
out.flush()
def exercise_featherstone_FDab(out):
def check():
model = featherstone_system_model(
m=sim.m,
I=sim.I_F1,
J=six_dof_joint_euler_params_featherstone(qE=sim.J1.qE,
qr=sim.J1.qr))
q = [None] # already stored in J1 as qE and qr
qd = [sim.qd]
tau = None
f_ext = [matrix.col((sim.nc_F1, sim.f_F1)).resolve_partitions()]
grav_accn = [0, 0, 0]
qdd = featherstone.FDab(model, q, qd, tau, f_ext, grav_accn)
if (i_step % 10 == 0):
print("ang acc 3D:", sim.wd_F1.elems, file=out)
print(" 6D:", qdd[0].elems[:3], file=out)
print(file=out)
print("lin acc 3D:", sim.as_F1.elems, file=out)
print(" 6D:", qdd[0].elems[3:], file=out)
print(file=out)
assert approx_equal(qdd[0].elems[:3], sim.wd_F1)
assert approx_equal(qdd[0].elems[3:], sim.as_F1)
sim = fmri.simulation()
for i_step in range(100):
check()
sim.dynamics_step(delta_t=0.1) # large time step to sample
check() # diverse configurations
def exercise_reference_impl_long(n_dynamics_steps, out):
sim = fmri.simulation()
e_tots = flex.double([sim.e_tot])
print("i_step, [e_pot, e_kin_ang, e_kin_lin, e_kin, e_tot]", file=out)
def show(i_step):
print(i_step,
[sim.e_pot, sim.e_kin_ang, sim.e_kin_lin, sim.e_kin, sim.e_tot],
file=out)
out.flush()
n_show = max(1, n_dynamics_steps // 10)
for i_step in range(n_dynamics_steps):
sim.dynamics_step(delta_t=0.001)
e_tots.append(sim.e_tot)
if (i_step % n_show == 0):
show(i_step)
show(n_dynamics_steps)
print(file=out)
print("number of dynamics steps:", n_dynamics_steps, file=out)
print("e_tot start:", e_tots[0], file=out)
print(" final:", e_tots[-1], file=out)
print(" min:", flex.min(e_tots), file=out)
print(" max:", flex.max(e_tots), file=out)
print(" max-min:", flex.max(e_tots) - flex.min(e_tots), file=out)
print(file=out)
out.flush()
def exercise_reference_impl_quick():
sites_cart = fmri.create_triangle_with_center_of_mass_at_origin()
assert approx_equal(flex.vec3_double(sites_cart).mean(), (0, 0, 0))
inertia1 = fmri.body_inertia(sites_cart=sites_cart)
inertia2 = matrix.sym(sym_mat3=scitbx.math.inertia_tensor(
points=flex.vec3_double(sites_cart), pivot=(0, 0, 0)))
assert approx_equal(inertia1, inertia2)
#
for use_classical_accel in [False, True]:
sim = fmri.simulation()
assert approx_equal(
[sim.e_pot, sim.e_kin_ang, sim.e_kin_lin, sim.e_kin, sim.e_tot], [
0.64030878777041611, 0.012310594130384761, 0.02835,
0.04066059413038476, 0.68096938190080092
])
for i in range(100):
sim.dynamics_step(delta_t=0.01,
use_classical_accel=use_classical_accel)
expected = [[
0.028505221929112364, 0.091503230553568404, 0.56329655444242244,
0.65479978499599079, 0.6833050069251031
],
[
0.053276067541032097, 0.091503230553568404,
0.53805622991666513, 0.62955946047023348,
0.68283552801126557
]][int(use_classical_accel)]
assert approx_equal(
[sim.e_pot, sim.e_kin_ang, sim.e_kin_lin, sim.e_kin, sim.e_tot],
expected)
def exercise_reference_impl_quick():
sites_cart = fmri.create_triangle_with_center_of_mass_at_origin()
assert approx_equal(flex.vec3_double(sites_cart).mean(), (0, 0, 0))
inertia1 = fmri.body_inertia(sites_cart=sites_cart)
inertia2 = matrix.sym(sym_mat3=scitbx.math.inertia_tensor(points=flex.vec3_double(sites_cart), pivot=(0, 0, 0)))
assert approx_equal(inertia1, inertia2)
#
for use_classical_accel in [False, True]:
sim = fmri.simulation()
assert approx_equal(
[sim.e_pot, sim.e_kin_ang, sim.e_kin_lin, sim.e_kin, sim.e_tot],
[0.64030878777041611, 0.012310594130384761, 0.02835, 0.04066059413038476, 0.68096938190080092],
)
for i in xrange(100):
sim.dynamics_step(delta_t=0.01, use_classical_accel=use_classical_accel)
expected = [
[0.028505221929112364, 0.091503230553568404, 0.56329655444242244, 0.65479978499599079, 0.6833050069251031],
[0.053276067541032097, 0.091503230553568404, 0.53805622991666513, 0.62955946047023348, 0.68283552801126557],
][int(use_classical_accel)]
assert approx_equal([sim.e_pot, sim.e_kin_ang, sim.e_kin_lin, sim.e_kin, sim.e_tot], expected)