def main():
λx = 40
λy = 50
λz = 20
Tx = 3.797
Ty = 11.312
Tz = 2.045
n = 100
points = numpy.empty((n, 3))
points[:, 0] = 2. * numpy.sin(numpy.arange(n) * 2 * math.pi / λx)
points[:, 1] = 2. * numpy.sin(numpy.arange(n) * 2 * math.pi / λy)
points[:, 2] = 2. * numpy.sin(numpy.arange(n) * 2 * math.pi / λz)
basepoints = points.copy()
curve = vis.curve(pos=points, color=vis.color.red, radius=0.1)
fps = 30
t = 0.
while True:
points = basepoints * numpy.array([
numpy.cos(2 * math.pi * t / Tx),
numpy.cos(2 * math.pi * t / Ty),
numpy.cos(2 * math.pi * t / Tz)
])
curve.points = points
vis.rate(30)
t += 1. / fps
def main():
l = 0.5
verts = numpy.array( [ [-l, 0, -l], [ l, 0, -l], [-l, 0, l],
[-l, 0, l], [ l, 0, -l], [ l, 0, l],
[-l, 0, l], [ 0, 1.5*l, 0 ], [-l, 0, -l],
[ l, 0, l], [ 0, 1.5*l, 0 ], [-l, 0, l],
[ l, 0, -l], [ 0, 1.5*l, 0 ], [ l, 0, l],
[-l, 0, -l], [ 0, 1.5*l, 0 ], [ l, 0, -l] ] )
pyr = vis.faces(verts, color=vis.color.red)
while (True):
vis.rate(30)
def main():
file_name = str(sys.argv[1])
read_txt_file(file_name)
translation_vec = np.array([0., 0., 0.])
for atom in atom_builder.all_atoms:
translation_vec += atom.pos
translation_vec /= len(atom_builder.all_atoms)
for atom in atom_builder.all_atoms:
atom.pos -= translation_vec
for vis_atom in visual.all_visual_atoms:
vis_atom.visual.pos = vis_atom.atom_object.pos
for bond in visual.all_visual_bonds:
bond.visual.pos = bond.bond_object.atom1.pos
bond.visual.axis = bond.bond_object.atom2.pos - bond.bond_object.atom1.pos
for atom in atom_builder.all_atoms:
if atom.atom_type == 'NH1':
amine_nitrogen = atom
if atom.atom_type == 'CT1':
central_carbon = atom
for bond in bond_builder.all_bonds:
if bond.atom1.atom_type or bond.atom2.atom_type == 'C':
if bond.atom1.atom_type == 'O':
carbonyl_carbon = bond.atom2
if bond.atom2.atom_type == 'O':
carbonyl_carbon = bond.atom1
vis.label(text = 'N', pos = amine_nitrogen.pos, height = 3, font = 'serif', color = [1., 0., 0.], box = False,
units = "centidisplay", yoffset = 5, xoffset = 2)
vis.label(text = 'C', pos = central_carbon.pos, height = 3, font = 'serif', color = [0., 1., 0.], box = False,
units = "centidisplay", yoffset = 5, xoffset = 2)
vis.label(text = 'C', pos = carbonyl_carbon.pos, height = 3, font = 'serif', color = [0., 0., 1.], box = False,
units = "centidisplay", yoffset = 5, xoffset = 2)
display = True
disp = vis.scene()
disp.foreground = [1,1,1]
while display == True:
vis.rate(30)
def main():
file_name = str(sys.argv[1])
read_txt_file(file_name)
display = True
disp = vis.scene()
disp.foreground = [1, 1, 1]
while display == True:
vis.rate(30)
def main():
spheres = []
for i in range(2000):
spheres.append(
physvis.sphere(pos=(random.random() * 5 - 2.5,
random.random() * 5 - 2.5,
random.random() * 5 - 2.5),
radius=0.05,
color=(random.random(), random.random(),
random.random())))
while True:
physvis.rate(30)
def main():
fps = 30.
endt = 3
box = vis.box()
t = 0
while True:
newtime = time.perf_counter()
try:
dtime = newtime - lasttime
sys.stderr.write("fps: {}\n".format(1./dtime))
except(NameError):
pass
lasttime = newtime
vis.rate(fps)
t += 1./fps
if t >= endt:
return
def main():
Time_Unit = ((1.66054E-27 * 1E-20) / (1.60218E-19))**(1 / 2)
Epsilon = ((1.60218E-19)**2 * (Time_Unit)**2) / ((1E-10)**3 *
(1.66054E-27))
print('Time Units (seconds): {} and Epsilon: {}'.format(
Time_Unit, Epsilon))
s70 = math.sin(70 / 180 * math.pi)
c70 = math.cos(70 / 180 * math.pi)
s120 = math.sin(120 / 180 * math.pi)
c120 = math.cos(120 / 180 * math.pi)
s20 = math.sin(20 / 180 * math.pi)
c20 = math.cos(20 / 180 * math.pi)
l0 = 1.530
l1 = 1.111
h_bond = l1 * (1 / 2)**(1 / 2)
h1pos = np.array([-l1 * c70, -l1 * s70, 0.])
h2pos = np.array([-l1 * c70, -l1 * s70 * c120, l1 * s70 * s120])
h3pos = np.array([-l1 * c70, -l1 * s70 * c120, -l1 * s70 * s120])
crotang = math.cos(20. / 180. * math.pi)
srotang = math.sin(20. / 180. * math.pi)
rotmat = np.array([[1., 0., 0.], [
0.,
crotang,
-srotang,
], [0., srotang, crotang]])
h1pos = np.matmul(rotmat, h1pos)
h2pos = np.matmul(rotmat, h2pos)
h3pos = np.matmul(rotmat, h3pos)
global vals
c_1 = atom(element='carbon',
element_type='CC32A',
atom_number=1,
y0=l0 / 2)
c_2 = atom(element='carbon',
element_type='CC32A',
atom_number=2,
y0=l0 * s20,
x0=l0 * c20)
c_3 = atom(element='carbon',
element_type='CC32A',
atom_number=3,
y0=-l0 * s20,
x0=l0 * c20)
c_4 = atom(element='carbon',
element_type='CC32A',
atom_number=4,
y0=-l0 / 2)
c_5 = atom(element='carbon',
element_type='CC32A',
atom_number=5,
y0=-l0 * s20,
x0=-l0 * c20)
c_6 = atom(element='carbon',
element_type='CC32A',
atom_number=6,
y0=l0 * s20,
x0=-l0 * c20)
h_1 = atom(atom_number=7,
element='hydrogen',
element_type='HCA2A',
x0=c_1.pos[0] - h_bond - 0.01,
y0=c_1.pos[1] + h_bond,
z0=.5)
h_2 = atom(atom_number=8,
element='hydrogen',
element_type='HCA2A',
x0=c_1.pos[0] + h_bond,
y0=c_1.pos[1] + h_bond,
z0=-0.5)
h_3 = atom(atom_number=9,
element='hydrogen',
element_type='HCA2A',
x0=c_2.pos[0] + h_bond,
y0=c_2.pos[1] + h_bond)
h_4 = atom(atom_number=10,
element='hydrogen',
element_type='HCA2A',
x0=c_2.pos[0] + l1,
y0=c_2.pos[1])
h_5 = atom(atom_number=11,
element='hydrogen',
element_type='HCA2A',
x0=c_3.pos[0] + l1,
y0=c_3.pos[1])
h_6 = atom(atom_number=12,
element='hydrogen',
element_type='HCA2A',
x0=c_3.pos[0] + h_bond,
y0=c_3.pos[1] - h_bond)
h_7 = atom(atom_number=13,
element='hydrogen',
element_type='HCA2A',
x0=c_4.pos[0] + h_bond,
y0=c_4.pos[1] - h_bond)
h_8 = atom(atom_number=14,
element='hydrogen',
element_type='HCA2A',
x0=c_4.pos[0] - h_bond,
y0=c_4.pos[1] - h_bond)
h_9 = atom(atom_number=15,
element='hydrogen',
element_type='HCA2A',
x0=c_5.pos[0] - l1,
y0=c_5.pos[1])
h_10 = atom(atom_number=16,
element='hydrogen',
element_type='HCA2A',
x0=c_5.pos[0] - h_bond,
y0=c_5.pos[1] - h_bond)
h_11 = atom(atom_number=17,
element='hydrogen',
element_type='HCA2A',
x0=c_6.pos[0] - h_bond,
y0=c_6.pos[1] + h_bond)
h_12 = atom(atom_number=18,
element='hydrogen',
element_type='HCA2A',
x0=c_6.pos[0] - l1,
y0=c_6.pos[1])
cyclohexane_1 = molecule()
cyclohexane_1.add_atom(h_1)
cyclohexane_1.add_atom(h_2)
cyclohexane_1.add_atom(h_3)
cyclohexane_1.add_atom(h_4)
cyclohexane_1.add_atom(h_5)
cyclohexane_1.add_atom(h_6)
cyclohexane_1.add_atom(h_7)
cyclohexane_1.add_atom(h_8)
cyclohexane_1.add_atom(h_9)
cyclohexane_1.add_atom(h_10)
cyclohexane_1.add_atom(h_11)
cyclohexane_1.add_atom(h_12)
cyclohexane_1.add_atom(c_1)
cyclohexane_1.add_atom(c_2)
cyclohexane_1.add_atom(c_3)
cyclohexane_1.add_atom(c_4)
cyclohexane_1.add_atom(c_5)
cyclohexane_1.add_atom(c_6)
cyclohexane_1.bond_atoms(h_1, c_1)
cyclohexane_1.bond_atoms(h_2, c_1)
cyclohexane_1.bond_atoms(h_3, c_2)
cyclohexane_1.bond_atoms(h_4, c_2)
cyclohexane_1.bond_atoms(h_5, c_3)
cyclohexane_1.bond_atoms(h_6, c_3)
cyclohexane_1.bond_atoms(h_7, c_4)
cyclohexane_1.bond_atoms(h_8, c_4)
cyclohexane_1.bond_atoms(h_9, c_5)
cyclohexane_1.bond_atoms(h_10, c_5)
cyclohexane_1.bond_atoms(h_11, c_6)
cyclohexane_1.bond_atoms(h_12, c_6)
cyclohexane_1.bond_atoms(c_1, c_2)
cyclohexane_1.bond_atoms(c_2, c_3)
cyclohexane_1.bond_atoms(c_3, c_4)
cyclohexane_1.bond_atoms(c_4, c_5)
cyclohexane_1.bond_atoms(c_5, c_6)
cyclohexane_1.bond_atoms(c_6, c_1)
for dangle in cyclohexane_1.dihedrals:
print(dangle.first_atom.atom_number, '-',
dangle.second_atom.atom_number, '-',
dangle.third_atom.atom_number, '-',
dangle.fourth_atom.atom_number)
print('\n', len(cyclohexane_1.dihedrals))
# Something is v wrong with my dihedral counter.
# It appears as though our worst fears have been confirmed ...
# the cyclic molecule is causing me to wayyyyy over count the
# number of dihedrals present. I am pretty sure that
# cyclohexane should not have 121 dihedrals in it. Jake,
# implement a method to fix this overcounting and you should
# also fix that ValueError that you are getting in the bond
# force function with the arcsin. When theta is 90 you are
# getting this error.
############################################################################################
index = 0
n_atoms = 0
for mol in molecule.all_molecules:
n_atoms += len(mol.atoms)
vals = np.empty(6 * n_atoms)
integrator = ode(ders)
integrator.set_integrator("vode")
for mol in molecule.all_molecules:
for at in mol.atoms:
at.move_data_to_buffers(
vals[index:index + 3],
vals[3 * n_atoms + index:3 * n_atoms + index + 3])
index += 3
t = 0
tf = 500
dt = 1E-1
t_stall = 5
integrator.set_initial_value(vals)
have_already_printed = False
while t < tf:
integrator.integrate(t + dt)
vals[:] = integrator.y
visual.update_visual()
while t <= t_stall:
t += dt
vels = [mag(atom.vel) for atom in cyclohexane_1.atoms]
maxvel = max(vels)
if not have_already_printed and maxvel <= 1E-5:
print(maxvel)
for bangle in cyclohexane_1.bond_angles:
r1 = bangle.end_atom.pos - bangle.middle_atom.pos
r2 = bangle.start_atom.pos - bangle.middle_atom.pos
the_angle_bruh = math.acos(
(r1 * r2).sum() / mag(r1) / mag(r2)) * 180. / math.pi
print("{:20s} : {:.2f}°".format(bangle.typedex,
the_angle_bruh))
have_already_printed = True
t += dt
vis.rate(30)
def main():
description = "Draw two growing curves"
epilog = "Try setting fps to various different values. If your graphics system syncs to the monitor's vblank (many of them do), this will limit how many calculation updates you can have per second to that rate. At least *some* systems can disable this synchronization by setting the environment variable vblank_mode to 0; your OS and graphics card driver may have different ways to do this. Try setting fps to different values (and using -g) and playing with this to see what you can effectively get."
parser = argparse.ArgumentParser(description=description, epilog=epilog)
parser.add_argument(
"-t",
"--endt",
type=float,
default=10.,
dest="endt",
help=
"Run until the simulation gets to this time in seconds (default: 10)")
parser.add_argument("-q",
"--qt",
action="store_true",
default=False,
dest="qt",
help="Use the Qt backend (default: GLUT)")
parser.add_argument(
"-f",
"--fps",
type=int,
default=60,
dest="fps",
help="Try to do this many updates per second (default: 60)")
parser.add_argument(
"-p",
"--printevery",
type=float,
default=2.,
dest="printevery",
help=
"Print updates per second every (roughtly) this many real seconds (default: 2)"
)
parser.add_argument("-g",
"--gfps",
action="store_true",
default=False,
dest="gfps",
help="Print graphics frames per second")
args = parser.parse_args()
fps = args.fps
endt = args.endt
useqt = args.qt
printevery = args.printevery
GrContext.print_fps = args.gfps
if useqt:
app = qt.QApplication([])
window = qt.QWidget()
vbox = qt.QVBoxLayout()
window.setLayout(vbox)
wid = qtgrcontext.QtGrContext()
vbox.addWidget(wid, 1)
window.show()
curver = TwoCurves(endt=endt, fps=fps, printevery=printevery)
if useqt:
mainlooptimer = qtcore.QTimer()
mainlooptimer.timeout.connect(lambda: curver.update(app))
mainlooptimer.start(1000. / fps)
app.exec_()
else:
while True:
curver.update(None)
vis.rate(fps)
