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nguyed99
molecular-simulation
Commits
3adf22f7
Commit
3adf22f7
authored
Apr 27, 2023
by
ziskaj00
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Add sheet 1 and 2
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a4547658
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3adf22f7
import
math
import
numpy
as
np
from
matplotlib
import
pyplot
as
plt
from
scipy.integrate
import
RK45
def
verlet
(
F
,
x0
,
p0
,
m
,
dt
,
N
):
if
isinstance
(
p0
,
float
):
x
=
np
.
zeros
(
N
)
p
=
np
.
zeros
(
N
)
else
:
x
=
np
.
zeros
((
N
,
*
x0
.
shape
))
p
=
np
.
zeros
((
N
,
*
p0
.
shape
))
x
[
0
]
=
x0
p
[
0
]
=
p0
for
i
in
range
(
1
,
N
):
p
[
i
]
=
p
[
i
-
1
]
+
1
/
2
*
F
(
x
[
i
-
1
])
*
dt
x
[
i
]
=
x
[
i
-
1
]
+
1
/
m
*
p
[
i
]
*
dt
p
[
i
]
=
p
[
i
]
+
1
/
2
*
F
(
x
[
i
])
*
dt
return
x
,
p
def
verlet_inv
(
F
,
x0
,
p0
,
m
,
dt
,
N
):
if
isinstance
(
p0
,
float
):
x
=
np
.
zeros
(
N
)
p
=
np
.
zeros
(
N
)
else
:
x
=
np
.
zeros
((
N
,
*
x0
.
shape
))
p
=
np
.
zeros
((
N
,
*
p0
.
shape
))
x
[
0
]
=
x0
p
[
0
]
=
p0
for
i
in
range
(
1
,
N
):
p
[
i
]
=
p
[
i
-
1
]
-
1
/
2
*
F
(
x
[
i
-
1
])
*
dt
x
[
i
]
=
x
[
i
-
1
]
-
1
/
m
*
p
[
i
]
*
dt
p
[
i
]
=
p
[
i
]
-
1
/
2
*
F
(
x
[
i
])
*
dt
return
x
,
p
def
heun
(
F
,
r0
,
p0
,
m
,
dt
,
N
):
p
=
np
.
zeros
(
N
)
p
[
0
]
=
p0
r
=
np
.
zeros
(
N
)
r
[
0
]
=
r0
for
i
in
range
(
1
,
N
):
rp
=
r
[
i
-
1
]
+
1
/
2
*
p
[
i
-
1
]
*
dt
/
m
# predictor step
r
[
i
]
=
rp
+
1
/
m
*
(
p
[
i
-
1
]
/
2
+
F
(
r
[
i
-
1
])
*
dt
/
2
)
*
dt
p
[
i
]
=
p
[
i
-
1
]
+
F
(
rp
)
*
dt
return
r
,
p
def
heun_inv
(
F
,
r0
,
p0
,
m
,
dt
,
N
):
p
=
np
.
zeros
(
N
)
p
[
0
]
=
p0
r
=
np
.
zeros
(
N
)
r
[
0
]
=
r0
for
i
in
range
(
1
,
N
):
rp
=
r
[
i
-
1
]
-
1
/
2
*
p
[
i
-
1
]
*
dt
/
m
# predictor step
r
[
i
]
=
rp
-
1
/
m
*
(
p
[
i
-
1
]
/
2
-
F
(
r
[
i
-
1
])
*
dt
/
2
)
*
dt
p
[
i
]
=
p
[
i
-
1
]
-
F
(
rp
)
*
dt
return
r
,
p
# Problem 1.1
# a)
dt
=
1e-3
# s
t
=
np
.
arange
(
0
,
10
,
dt
)
# s
x0
=
0
# m
p0
=
1e-3
# kg m / s
m
=
1e-3
# kg
k
=
0.1
# N / m
f
=
lambda
x
:
-
k
*
x
#r1, p1 = verlet_inv(f, x0, p0, m, dt, len(t))
r2
,
p2
=
heun_inv
(
f
,
x0
,
p0
,
m
,
dt
,
len
(
t
))
#plt.plot(r1, p1, label="Verlet")
plt
.
plot
(
r2
,
p2
,
label
=
"
Heun
"
)
plt
.
legend
()
plt
.
xlabel
(
r
"
$x(t)$
"
)
plt
.
ylabel
(
r
"
$p(t)$
"
)
plt
.
savefig
(
"
problem1.1c.png
"
)
plt
.
show
()
# b)
E_kin1
=
p1
**
2
/
(
2
*
m
)
E_pot1
=
1
/
2
*
k
*
r1
**
2
E1
=
E_pot1
+
E_kin1
dE1
=
E1
-
E1
[
0
]
E_kin2
=
p2
**
2
/
(
2
*
m
)
E_pot2
=
1
/
2
*
k
*
r2
**
2
E2
=
E_pot2
+
E_kin2
dE2
=
E2
-
E2
[
0
]
plt
.
plot
(
t
,
E1
,
label
=
"
Verlet
"
)
plt
.
plot
(
t
,
E2
,
label
=
"
Heun
"
)
plt
.
legend
()
plt
.
title
(
r
"
$E$
"
)
plt
.
xlabel
(
r
"
$t$
"
)
plt
.
ylabel
(
r
"
$E$
"
)
plt
.
show
()
plt
.
plot
(
t
,
dE1
,
label
=
"
Verlet
"
)
plt
.
plot
(
t
,
dE2
,
label
=
"
Heun
"
)
plt
.
xlabel
(
r
"
$t$
"
)
plt
.
ylabel
(
r
"
$E$
"
)
plt
.
title
(
r
"
$\Delta E$
"
)
plt
.
legend
()
plt
.
show
()
plt
.
plot
(
t
,
dE1
/
dt
,
label
=
"
Verlet
"
)
plt
.
plot
(
t
,
dE2
/
dt
,
label
=
"
Heun
"
)
plt
.
xlabel
(
r
"
$t$
"
)
plt
.
ylabel
(
r
"
$E$
"
)
plt
.
title
(
r
"
$\Delta E / \Delta t$
"
)
plt
.
legend
()
plt
.
show
()
plt
.
plot
(
t
,
dE1
/
dt
**
2
,
label
=
"
Verlet
"
)
plt
.
plot
(
t
,
dE2
/
dt
**
2
,
label
=
"
Heun
"
)
plt
.
xlabel
(
r
"
$t$
"
)
plt
.
ylabel
(
r
"
$E$
"
)
plt
.
title
(
r
"
$\Delta E / (\Delta t)^2$
"
)
plt
.
legend
()
plt
.
show
()
# Problem 1.2
# a)
R_c
=
1
# AU
R_L
=
2.57e-3
*
R_c
m_s
=
1
# solar mass
m_c
=
3.00e-6
*
m_s
m_L
=
3.69e-8
*
m_s
T_c
=
1
# yr
T_L
=
27.3
/
365.3
*
T_c
G
=
4
*
np
.
pi
**
2
# AU^3 / m / yr^2
m0
=
m_s
m1
=
m_c
m2
=
m_L
x0
=
np
.
array
([
R_c
,
0
,
R_c
+
R_L
,
0
,
0
,
m_c
*
R_c
*
2
*
np
.
pi
/
T_c
,
0
,
m_L
/
m_c
*
m_c
*
R_c
*
2
*
np
.
pi
/
T_c
+
m_L
*
R_L
*
2
*
np
.
pi
/
T_L
,
])
def
f
(
t
,
x
):
r1
=
x
[:
2
]
r2
=
x
[
2
:
4
]
p1
=
x
[
4
:
6
]
p2
=
x
[
6
:]
return
np
.
array
([
p1
/
m1
,
p2
/
m2
,
-
G
*
m1
*
(
m0
*
r1
/
np
.
linalg
.
norm
(
r1
)
**
3
+
m2
*
(
r1
-
r2
)
/
np
.
linalg
.
norm
(
r1
-
r2
)
**
3
),
-
G
*
m2
*
(
m0
*
r2
/
np
.
linalg
.
norm
(
r2
)
**
3
+
m1
*
(
r2
-
r1
)
/
np
.
linalg
.
norm
(
r2
-
r1
)
**
3
),
]).
flatten
()
n
=
5
T
=
0.3
# yr
dt
=
4
**
(
-
n
)
# yr
N
=
int
(
T
/
dt
)
t
=
np
.
arange
(
N
)
*
dt
rk
=
RK45
(
f
,
0
,
x0
,
T
,
first_step
=
dt
,
max_step
=
dt
,
atol
=
1e3
,
rtol
=
1e3
)
x
=
np
.
zeros
((
N
,
len
(
x0
)))
x
[
0
]
=
x0
for
i
in
range
(
1
,
N
):
rk
.
step
()
x
[
i
]
=
rk
.
y
r1
=
x
[:,
0
:
2
]
r2
=
x
[:,
2
:
4
]
p1
=
x
[:,
4
:
6
]
p2
=
x
[:,
6
:
8
]
plt
.
plot
(
r1
[:,
0
],
r1
[:,
1
])
plt
.
title
(
r
"
$r_1$, Runge-Kutta
"
)
plt
.
xlabel
(
r
"
$x / \mathrm{AU}$
"
)
plt
.
ylabel
(
r
"
$y / \mathrm{AU}$
"
)
plt
.
savefig
(
f
"
problem1.2a-r_1-n=
{
n
}
.png
"
)
plt
.
show
()
plt
.
plot
(
r2
[:,
0
]
-
r1
[:,
0
],
r2
[:,
1
]
-
r1
[:,
1
])
plt
.
title
(
r
"
$r_2 - r_1$, Runge-Kutta
"
)
plt
.
xlabel
(
r
"
$x / \mathrm{AU}$
"
)
plt
.
ylabel
(
r
"
$y / \mathrm{AU}$
"
)
plt
.
savefig
(
f
"
problem1.2a-r_2-r_1-n=
{
n
}
.png
"
)
plt
.
show
()
H
=
np
.
linalg
.
norm
(
p1
,
axis
=
1
)
**
2
/
(
2
*
m1
)
+
np
.
linalg
.
norm
(
p2
,
axis
=
1
)
**
2
/
(
2
*
m2
)
+
\
-
G
*
m0
*
m1
/
np
.
linalg
.
norm
(
r1
,
axis
=
1
)
-
G
*
m0
*
m2
/
np
.
linalg
.
norm
(
r2
,
axis
=
1
)
+
\
-
G
*
m1
*
m2
/
np
.
linalg
.
norm
(
r2
-
r1
,
axis
=
1
)
L
=
np
.
abs
(
np
.
cross
(
r1
,
p1
,
axis
=
1
)
+
np
.
cross
(
r2
,
p2
,
axis
=
1
))
plt
.
plot
(
t
,
H
)
plt
.
title
(
r
"
$H(t)$
"
)
plt
.
xlabel
(
r
"
$t / \mathrm{yr}$
"
)
plt
.
ylabel
(
r
"
$L / \frac{m_\odot \mathrm{AU}^2}{\mathrm{yr}^2}$
"
)
plt
.
savefig
(
f
"
problem1.2a-Hn=
{
n
}
.png
"
)
plt
.
show
()
plt
.
plot
(
t
,
L
)
plt
.
title
(
r
"
$L(t)$
"
)
plt
.
xlabel
(
r
"
$t / \mathrm{yr}$
"
)
plt
.
ylabel
(
r
"
$L / \frac{m_\odot \mathrm{AU}^2}{\mathrm{yr}}$
"
)
plt
.
savefig
(
f
"
problem1.2a-L-n=
{
n
}
.png
"
)
plt
.
show
()
plt
.
plot
(
t
,
H
-
H
[
0
])
plt
.
title
(
r
"
$H(t) - H(0)$
"
)
plt
.
xlabel
(
r
"
$t / \mathrm{yr}$
"
)
plt
.
ylabel
(
r
"
$L / \frac{m_\odot \mathrm{AU}^2}{\mathrm{yr}^2}$
"
)
plt
.
savefig
(
f
"
problem1.2a-H-H0-n=
{
n
}
.png
"
)
plt
.
show
()
plt
.
plot
(
t
,
L
-
L
[
0
])
plt
.
title
(
r
"
$L(t) - L(0)$
"
)
plt
.
xlabel
(
r
"
$t / \mathrm{yr}$
"
)
plt
.
ylabel
(
r
"
$L / \frac{m_\odot \mathrm{AU}^2}{\mathrm{yr}}$
"
)
plt
.
savefig
(
f
"
problem1.2a-L-L0-n=
{
n
}
.png
"
)
plt
.
show
()
# b)
n_v
=
5
dt_v
=
4
**
(
-
n_v
)
# yr
def
F
(
x
):
r1
=
x
[
0
:
2
]
r2
=
x
[
2
:
4
]
return
np
.
array
([
-
G
*
m1
*
(
m0
*
r1
/
np
.
linalg
.
norm
(
r1
)
**
3
+
m2
*
(
r1
-
r2
)
/
np
.
linalg
.
norm
(
r1
-
r2
)
**
3
),
-
G
*
m2
*
(
m0
*
r2
/
np
.
linalg
.
norm
(
r2
)
**
3
+
m1
*
(
r2
-
r1
)
/
np
.
linalg
.
norm
(
r2
-
r1
)
**
3
),
]).
flatten
()
rv
,
pv
=
verlet
(
F
,
x0
[:
4
],
x0
[
4
:],
np
.
array
([
m1
,
m1
,
m2
,
m2
]),
dt_v
,
math
.
ceil
(
T
/
dt_v
))
rv1
=
rv
[:,:
2
]
rv2
=
rv
[:,
2
:]
pv1
=
pv
[:,:
2
]
pv2
=
pv
[:,
2
:]
plt
.
plot
(
r1
[:,
0
],
r1
[:,
1
],
label
=
"
Runge-Kutta
"
)
plt
.
plot
(
rv1
[:,
0
],
rv1
[:,
1
],
label
=
"
Verlet
"
)
plt
.
legend
()
plt
.
title
(
r
"
$r_1$, Verlet
"
)
plt
.
xlabel
(
r
"
$x / \mathrm{AU}$
"
)
plt
.
ylabel
(
r
"
$y / \mathrm{AU}$
"
)
plt
.
savefig
(
f
"
problem1.2b-r_v1-n=
{
n_v
}
.png
"
)
plt
.
show
()
plt
.
plot
(
r2
[:,
0
]
-
r1
[:,
0
],
r2
[:,
1
]
-
r1
[:,
1
],
label
=
"
Runge-Kutta
"
)
plt
.
plot
(
rv2
[:,
0
]
-
rv1
[:,
0
],
rv2
[:,
1
]
-
rv1
[:,
1
],
label
=
"
Verlet
"
)
plt
.
legend
()
plt
.
title
(
r
"
$r_2 - r_1$, Verlet
"
)
plt
.
xlabel
(
r
"
$x / \mathrm{AU}$
"
)
plt
.
ylabel
(
r
"
$y / \mathrm{AU}$
"
)
plt
.
savefig
(
f
"
problem1.2b-r_v2-r_v1-n=
{
n_v
}
.png
"
)
plt
.
show
()
# c)
xT
=
np
.
array
([
r1
[
-
1
],
r2
[
-
1
],
-
p1
[
-
1
],
-
p2
[
-
1
],
]).
flatten
()
n
=
5
T
=
0.3
# yr
dt
=
4
**
(
-
n
)
# yr
N
=
int
(
T
/
dt
)
t
=
np
.
arange
(
N
)
*
dt
rk
=
RK45
(
f
,
0
,
xT
,
T
,
first_step
=
dt
,
max_step
=
dt
,
atol
=
1e3
,
rtol
=
1e3
)
x
=
np
.
zeros
((
N
,
len
(
x0
)))
x
[
0
]
=
xT
for
i
in
range
(
1
,
N
):
rk
.
step
()
x
[
i
]
=
rk
.
y
rb1
=
x
[:,
0
:
2
]
rb2
=
x
[:,
2
:
4
]
pb1
=
x
[:,
4
:
6
]
pb2
=
x
[:,
6
:
8
]
plt
.
plot
(
r1
[:,
0
],
r1
[:,
1
],
label
=
"
Forwards
"
)
plt
.
plot
(
rb1
[:,
0
],
rb1
[:,
1
],
label
=
"
Backwards
"
)
plt
.
legend
()
plt
.
title
(
r
"
$r_1$, Runge-Kutta
"
)
plt
.
xlabel
(
r
"
$x / \mathrm{AU}$
"
)
plt
.
ylabel
(
r
"
$y / \mathrm{AU}$
"
)
plt
.
savefig
(
f
"
problem1.2c-r_1.png
"
)
plt
.
show
()
plt
.
plot
(
r2
[:,
0
]
-
r1
[:,
0
],
r2
[:,
1
]
-
r1
[:,
1
],
label
=
"
Forwards
"
)
plt
.
plot
(
rb2
[:,
0
]
-
rb1
[:,
0
],
rb2
[:,
1
]
-
rb1
[:,
1
],
label
=
"
Backwards
"
)
plt
.
legend
()
plt
.
title
(
r
"
$r_2 - r_1$, Runge-Kutta
"
)
plt
.
xlabel
(
r
"
$x / \mathrm{AU}$
"
)
plt
.
ylabel
(
r
"
$y / \mathrm{AU}$
"
)
plt
.
savefig
(
f
"
problem1.2c-r_2-r_1.png
"
)
plt
.
show
()
rvb
,
pvb
=
verlet
(
F
,
xT
[:
4
],
xT
[
4
:],
np
.
array
([
m1
,
m1
,
m2
,
m2
]),
dt_v
,
math
.
ceil
(
T
/
dt_v
))
rvb1
=
rvb
[:,:
2
]
rvb2
=
rvb
[:,
2
:]
pvb1
=
pvb
[:,:
2
]
pvb2
=
pvb
[:,
2
:]
plt
.
plot
(
rv1
[:,
0
],
rv1
[:,
1
],
label
=
"
Forwards
"
)
plt
.
plot
(
rvb1
[:,
0
],
rvb1
[:,
1
],
label
=
"
Backwards
"
)
plt
.
legend
()
plt
.
title
(
r
"
$r_1$, Verlet
"
)
plt
.
xlabel
(
r
"
$x$
"
)
plt
.
ylabel
(
r
"
$y$
"
)
plt
.
savefig
(
f
"
problem1.2c-r_v1.png
"
)
plt
.
show
()
plt
.
plot
(
rv2
[:,
0
]
-
rv1
[:,
0
],
rv2
[:,
1
]
-
rv1
[:,
1
],
label
=
"
Forwards
"
)
plt
.
plot
(
rvb2
[:,
0
]
-
rvb1
[:,
0
],
rvb2
[:,
1
]
-
rvb1
[:,
1
],
label
=
"
Backwards
"
)
plt
.
legend
()
plt
.
title
(
r
"
$r_2 - r_1$, Verlet
"
)
plt
.
xlabel
(
r
"
$x$
"
)
plt
.
ylabel
(
r
"
$y$
"
)
plt
.
savefig
(
f
"
problem1.2c-r_v2-r_v1.png
"
)
plt
.
show
()
This diff is collapsed.
Click to expand it.
Jaslo/sheet2.py
0 → 100644
+
267
−
0
View file @
3adf22f7
import
numpy
as
np
import
matplotlib.pyplot
as
plt
# Problem 2.1
# a)
def
verlet
(
force
,
x0
,
p0
,
m
,
dt
,
N
):
assert
(
x0
.
shape
==
p0
.
shape
)
x
=
np
.
zeros
((
N
,
*
x0
.
shape
))
p
=
np
.
zeros
((
N
,
*
p0
.
shape
))
x
[
0
]
=
x0
p
[
0
]
=
p0
for
i
in
range
(
1
,
N
):
p
[
i
]
=
p
[
i
-
1
]
+
1
/
2
*
force
(
x
[
i
-
1
])
*
dt
x
[
i
]
=
x
[
i
-
1
]
+
p
[
i
]
/
m
*
dt
p
[
i
]
=
p
[
i
]
+
1
/
2
*
force
(
x
[
i
])
*
dt
return
x
,
p
r1_0
=
np
.
array
([
1
/
3
,
0
,
0
])
r2_0
=
-
r1_0
x0
=
np
.
array
([
r1_0
,
r2_0
]).
flatten
()
p1_0
=
np
.
array
([
-
6
/
7
,
3
/
7
,
-
2
/
7
])
p2_0
=
-
p1_0
p0
=
np
.
array
([
p1_0
,
p2_0
]).
flatten
()
m
=
np
.
array
([
1
,
1
,
1
,
1
,
1
,
1
])
# ??
a
=
1
# ??
epsilon
=
1
# ??
k
=
1
# ??
dt
=
1e-2
# 1/omega_0
t_max
=
10
# 1/omeag_0
t
=
np
.
arange
(
0
,
t_max
,
dt
)
def
F_H
(
x
):
r1
=
x
[:
3
]
r2
=
x
[
3
:]
return
np
.
array
([
-
k
*
(
r1
-
r2
),
k
*
(
r1
-
r2
),
]).
flatten
()
x
,
p
=
verlet
(
F_H
,
x0
,
p0
,
m
,
dt
,
int
(
t_max
/
dt
))
r1
=
x
[:,:
3
]
r2
=
x
[:,
3
:]
p1
=
p
[:,:
3
]
p2
=
p
[:,
3
:]
plt
.
plot
(
r1
[:,
0
],
r1
[:,
1
],
label
=
"
Particle 1
"
,
lw
=
4
)
plt
.
plot
(
r2
[:,
0
],
r2
[:,
1
],
label
=
"
Particle 2
"
)
plt
.
xlabel
(
r
"
$x / a$
"
)
plt
.
ylabel
(
r
"
$y / a$
"
)
plt
.
title
(
"
Trajectories
"
)
plt
.
legend
()
plt
.
savefig
(
"
problem2.1a-trajectories.png
"
)
plt
.
show
()
p_tot
=
p1
+
p2
plt
.
plot
(
t
,
np
.
linalg
.
norm
(
p_tot
-
p_tot
[
0
],
axis
=
1
))
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$p / \sqrt{m \epsilon}$
"
)
plt
.
title
(
"
Momentum Deviations
"
)
plt
.
savefig
(
"
problem2.1a-dp.png
"
)
plt
.
show
()
J
=
np
.
cross
(
r1
,
p1
,
axis
=
1
)
+
np
.
cross
(
r2
,
p2
,
axis
=
1
)
plt
.
plot
(
t
,
np
.
linalg
.
norm
(
J
-
J
[
0
],
axis
=
1
))
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$J / a \sqrt{m \epsilon}$
"
)
plt
.
title
(
"
Angular Momentum Deviations
"
)
plt
.
savefig
(
"
problem2.1a-dJ.png
"
)
plt
.
show
()
plt
.
plot
(
t
,
1
-
np
.
inner
(
J
,
J
[
0
])
/
(
np
.
linalg
.
norm
(
J
,
axis
=
1
)
*
np
.
linalg
.
norm
(
J
[
0
])))
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$J / a \sqrt{m \epsilon}$
"
)
plt
.
title
(
"
Momentum Deviations function
"
)
plt
.
savefig
(
"
problem2.1a-J?.png
"
)
plt
.
show
()
E
=
1
/
2
*
np
.
linalg
.
norm
(
p1
,
axis
=
1
)
**
2
+
1
/
2
*
np
.
linalg
.
norm
(
p2
,
axis
=
1
)
**
2
+
1
/
2
*
k
*
np
.
linalg
.
norm
(
r1
-
r2
,
axis
=
1
)
**
2
plt
.
plot
(
t
,
E
-
E
[
0
])
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$E / \epsilon$
"
)
plt
.
title
(
"
Energy Deviations
"
)
plt
.
savefig
(
"
problem2.1a-dE.png
"
)
plt
.
show
()
print
(
f
"
Maximum energy deviation:
{
np
.
max
(
np
.
abs
((
E
-
E
[
0
])
/
E
[
0
]))
}
"
)
# b)
def
FENE
(
x
):
r1
=
x
[:
3
]
r2
=
x
[
3
:]
f1
=
-
epsilon
*
(
r1
-
r2
)
/
(
a
**
2
-
np
.
linalg
.
norm
(
r1
-
r2
)
**
2
)
f2
=
-
f1
return
np
.
array
([
f1
,
f2
,
]).
flatten
()
x_F
,
p_F
=
verlet
(
FENE
,
x0
,
p0
,
m
,
dt
,
int
(
t_max
/
dt
))
r1_F
=
x_F
[:,:
3
]
r2_F
=
x_F
[:,
3
:]
p1_F
=
p_F
[:,:
3
]
p2_F
=
p_F
[:,
3
:]
plt
.
plot
(
r1_F
[:,
0
],
r1_F
[:,
1
],
label
=
"
Particle 1
"
)
plt
.
plot
(
r2_F
[:,
0
],
r2_F
[:,
1
],
label
=
"
Particle 2
"
)
plt
.
xlabel
(
r
"
$x / a$
"
)
plt
.
ylabel
(
r
"
$y / a$
"
)
plt
.
title
(
"
Trajectories
"
)
plt
.
legend
()
plt
.
savefig
(
"
problem2.1b-trajectories.png
"
)
plt
.
show
()
p_totF
=
p1_F
+
p2_F
plt
.
plot
(
t
,
np
.
linalg
.
norm
(
p_totF
-
p_totF
[
0
],
axis
=
1
))
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$p / \sqrt{m \epsilon}$
"
)
plt
.
title
(
"
Momentum Deviations
"
)
plt
.
savefig
(
"
problem2.1b-dp.png
"
)
plt
.
show
()
J_F
=
np
.
cross
(
r1_F
,
p1_F
,
axis
=
1
)
+
np
.
cross
(
r2_F
,
p2_F
,
axis
=
1
)
plt
.
plot
(
t
,
np
.
linalg
.
norm
(
J_F
-
J_F
[
0
],
axis
=
1
))
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$J / a \sqrt{m \epsilon}$
"
)
plt
.
title
(
"
Angular Momentum Deviations
"
)
plt
.
savefig
(
"
problem2.1b-dJ.png
"
)
plt
.
show
()
plt
.
plot
(
t
,
1
-
np
.
inner
(
J
,
J
[
0
])
/
(
np
.
linalg
.
norm
(
J
,
axis
=
1
)
*
np
.
linalg
.
norm
(
J
[
0
])))
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$J / a \sqrt{m \epsilon}$
"
)
plt
.
title
(
"
Momentum Deviations function
"
)
plt
.
savefig
(
"
problem2.1a-J?.png
"
)
plt
.
show
()
E_F
=
1
/
2
*
np
.
linalg
.
norm
(
p1_F
,
axis
=
1
)
**
2
+
1
/
2
*
np
.
linalg
.
norm
(
p2_F
,
axis
=
1
)
**
2
+
1
/
2
*
k
*
np
.
linalg
.
norm
(
r1_F
-
r2_F
,
axis
=
1
)
**
2
plt
.
plot
(
t
,
E_F
-
E_F
[
0
])
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$E / \epsilon$
"
)
plt
.
title
(
"
Energy Deviations
"
)
plt
.
savefig
(
"
problem2.1b-dE.png
"
)
plt
.
show
()
print
(
f
"
Maximum energy deviation:
{
np
.
max
(
np
.
abs
((
E_F
-
E_F
[
0
])
/
E_F
[
0
]))
}
"
)
# c)
lambda_c
=
1
/
2
-
(
2
*
np
.
sqrt
(
326
)
+
36
)
**
(
1
/
3
)
/
12
+
1
/
(
6
*
(
2
*
np
.
sqrt
(
326
)
+
36
)
**
(
1
/
3
))
def
verlet_BABAB
(
force
,
x0
,
p0
,
m
,
dt
,
N
,
lambda_
):
assert
(
x0
.
shape
==
p0
.
shape
)
x
=
np
.
zeros
((
N
,
*
x0
.
shape
))
p
=
np
.
zeros
((
N
,
*
p0
.
shape
))
x
[
0
]
=
x0
p
[
0
]
=
p0
for
i
in
range
(
1
,
N
):
p
[
i
]
=
p
[
i
-
1
]
+
lambda_
*
force
(
x
[
i
-
1
])
*
dt
x
[
i
]
=
x
[
i
-
1
]
+
1
/
2
*
p
[
i
]
/
m
*
dt
p
[
i
]
=
p
[
i
]
+
(
1
-
2
*
lambda_
)
*
force
(
x
[
i
])
*
dt
x
[
i
]
=
x
[
i
]
+
1
/
2
*
p
[
i
]
/
m
*
dt
p
[
i
]
=
p
[
i
]
+
lambda_
*
force
(
x
[
i
])
*
dt
return
x
,
p
for
f
in
(
F_H
,
FENE
,):
for
n
in
range
(
1
,
5
):
for
j
in
range
(
1
,
6
):
dt
=
4
**
(
-
j
)
t
=
np
.
arange
(
0
,
t_max
,
dt
)
x
,
p
=
verlet_BABAB
(
f
,
x0
,
p0
,
m
,
dt
,
len
(
t
),
lambda_c
)
r1
=
x
[:,:
3
]
r2
=
x
[:,
3
:]
p1
=
p
[:,:
3
]
p2
=
p
[:,
3
:]
E
=
1
/
(
2
*
m
[
0
])
*
np
.
linalg
.
norm
(
p1
,
axis
=
1
)
**
2
+
1
/
(
2
*
m
[
3
])
*
np
.
linalg
.
norm
(
p2
,
axis
=
1
)
**
2
+
1
/
2
*
k
*
np
.
linalg
.
norm
(
r1
-
r2
,
axis
=
1
)
**
2
plt
.
plot
(
t
,
(
E
-
E
[
0
])
/
dt
**
n
,
label
=
"
$k =
"
+
str
(
j
)
+
"
$
"
)
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$\frac{E}{t^
"
+
str
(
n
)
+
r
"
} / \epsilon \omega_0^
"
+
str
(
n
)
+
r
"
$
"
)
plt
.
title
(
"
$n =
"
+
str
(
n
)
+
"
$
"
)
plt
.
legend
(
loc
=
"
lower left
"
)
plt
.
savefig
(
f
"
problem2.1c-dE-
{
f
.
__name__
}
-n=
{
n
}
.png
"
)
plt
.
show
()
for
lambda_
in
(
1
/
3
,
0
,
1
/
2
):
dt
=
4
**
(
-
2
)
t
=
np
.
arange
(
0
,
t_max
,
dt
)
x
,
p
=
verlet_BABAB
(
f
,
x0
,
p0
,
m
,
dt
,
len
(
t
),
lambda_
)
r1
=
x
[:,:
3
]
r2
=
x
[:,
3
:]
p1
=
p
[:,:
3
]
p2
=
p
[:,
3
:]
E
=
1
/
(
2
*
m
[
0
])
*
np
.
linalg
.
norm
(
p1
,
axis
=
1
)
**
2
+
1
/
(
2
*
m
[
3
])
*
np
.
linalg
.
norm
(
p2
,
axis
=
1
)
**
2
+
1
/
2
*
k
*
np
.
linalg
.
norm
(
r1
-
r2
,
axis
=
1
)
**
2
print
(
f
"
Maximum energy deviation for
{
lambda_
}
:
{
np
.
max
(
np
.
abs
(
E
))
}
"
)
# d)
theta
=
0.08398315262876693
lambda_d
=
0.6822365335719091
rho
=
0.2539785108410595
mu
=
-
0.03230286765269967
def
verlet_d
(
force
,
x0
,
p0
,
m
,
dt
,
N
):
assert
(
x0
.
shape
==
p0
.
shape
)
x
=
np
.
zeros
((
N
,
*
x0
.
shape
))
p
=
np
.
zeros
((
N
,
*
p0
.
shape
))
x
[
0
]
=
x0
p
[
0
]
=
p0
for
i
in
range
(
1
,
N
):
p
[
i
]
=
p
[
i
-
1
]
+
theta
*
force
(
x
[
i
-
1
])
*
dt
x
[
i
]
=
x
[
i
-
1
]
+
rho
*
p
[
i
]
/
m
*
dt
p
[
i
]
=
p
[
i
]
+
lambda_d
*
force
(
x
[
i
])
*
dt
x
[
i
]
=
x
[
i
]
+
mu
*
p
[
i
]
/
m
*
dt
p
[
i
]
=
p
[
i
]
+
(
1
-
2
*
(
lambda_d
+
theta
))
/
2
*
force
(
x
[
i
])
*
dt
x
[
i
]
=
x
[
i
]
+
(
1
-
2
*
(
mu
+
rho
))
*
p
[
i
]
/
m
*
dt
p
[
i
]
=
p
[
i
]
+
(
1
-
2
*
(
lambda_d
+
theta
))
/
2
*
force
(
x
[
i
])
*
dt
x
[
i
]
=
x
[
i
]
+
mu
*
p
[
i
]
/
m
*
dt
p
[
i
]
=
p
[
i
]
+
lambda_d
*
force
(
x
[
i
])
*
dt
x
[
i
]
=
x
[
i
]
+
rho
*
p
[
i
]
/
m
*
dt
p
[
i
]
=
p
[
i
]
+
theta
*
force
(
x
[
i
])
*
dt
return
x
,
p
for
f
in
(
F_H
,
FENE
):
for
n
in
range
(
1
,
5
):
for
j
in
range
(
1
,
4
):
dt
=
5
*
2
**
(
-
j
)
t
=
np
.
arange
(
0
,
t_max
,
dt
)
x
,
p
=
verlet_d
(
f
,
x0
,
p0
,
m
,
dt
,
len
(
t
))
r1
=
x
[:,:
3
]
r2
=
x
[:,
3
:]
p1
=
p
[:,:
3
]
p2
=
p
[:,
3
:]
E
=
1
/
(
2
*
m
[
0
])
*
np
.
linalg
.
norm
(
p1
,
axis
=
1
)
**
2
+
1
/
(
2
*
m
[
3
])
*
np
.
linalg
.
norm
(
p2
,
axis
=
1
)
**
2
+
1
/
2
*
k
*
np
.
linalg
.
norm
(
r1
-
r2
,
axis
=
1
)
**
2
plt
.
plot
(
t
,
(
E
-
E
[
0
])
/
dt
**
n
,
label
=
"
$k =
"
+
str
(
j
)
+
"
$
"
)
plt
.
xlabel
(
r
"
$t / \omega_0^{-1}$
"
)
plt
.
ylabel
(
r
"
$\frac{E}{t^
"
+
str
(
n
)
+
r
"
} / \epsilon \omega_0^
"
+
str
(
n
)
+
r
"
$
"
)
plt
.
title
(
"
$n =
"
+
str
(
n
)
+
"
$
"
)
plt
.
legend
(
loc
=
"
lower left
"
)
plt
.
savefig
(
f
"
problem2.1d-dE-
{
f
.
__name__
}
-n=
{
n
}
.png
"
)
plt
.
show
()
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