Gnome 3 on Freebsd (self documentation)

install it using

#pkg install gnome3
/etc/fstab 
proc           /proc       procfs  rw  0   0
/etc/rc.conf
gdm_enable=“YES”
gnome_enable="YES"
The menu is missing
install Parallel Tools
#cd /usr/ports/emulators/parallels-tools/ && make install clean
but it need kernel source. 
Install via svn
#pkg install devel/subversion
# svnlite checkout http://svn0.eu.freebsd.org/base/releng/10.0/ /usr/src
run it again
#cd /usr/ports/emulators/parallels-tools/ && make install clean

Playing with FreeBSD

Got boot-only iso and managed to install it on my Parallel Desktop on my Macbook Air with Yosemite. 
Of course it just CLI.
Strange, the root shell have tab completion feature, but the normal users didn’t.
(DuckDuckGo-ing)
The answer come from 2003 and 2005 Mailing-List, 🙂
To enable tab completion
 
$chsh -s /bin/tcsh

 
(it didn’t enable tab completion actually , it change shell with tab completion feature 🙂 )
We could so use
 

$chsh -s /bin/csh 

 
tcsh shell support tab completion too.

 
Another thing is, normal user can’t use sudo command (because it’s not installed, 😛 )
So,  install sudo first (I used pkg command instead of pkg_add)

 
#pkg install sudo 
 
 
edit /usr/local/etc/sudoers as root and visudo command (don’t edit it using regular vi editor, or ANY editor)

%visudo

add this

username ALL=(ALL) ALL

 
and life become more easier...


 
 

Compare Native Loop Time in Python with “homemade” Fortran Module

This code print d and e as result of two matrix addition, e’s using python native code, d’s using fortran module compiled with F2PY

The code

import numpy as np
import aravir as ar
import time

n = 1000

u = np.ones((n,n))
v = np.ones((n,n))
e = np.ones((n,n))

t = time.clock()
d = ar.add3(u,v)
tfortran= time.clock()-t

t = time.clock()
for i in range (n):
for j in range (n):
e[i,j] = u[i,j]+v[i,j]
tnative = time.clock()-t

print 'fortran ', d
print 'native', e
print 'tfortran = ', tfortran, ', tnative = ', tnative

The fortran module I imported to python

        subroutine add3(a, b, c, n)
double precision a(n,n)
double precision b(n,n)
double precision c(n,n)

integer n
cf2py intent(in) :: a,b
cf2py intent(out) :: c,d
cf2py intent(hide) :: n
do 1700 i=1, n
do 1600 j=1, n
c(i,j) = a(i,j)
$ +b(i,j)

1600 continue
1700 continue
end

save it as aravir.f and compile using

$ f2py -c aravir.f -m aravir

And here the result

$ python cobamodul.py 
fortran [[ 2. 2. 2. ..., 2. 2. 2.]
[ 2. 2. 2. ..., 2. 2. 2.]
[ 2. 2. 2. ..., 2. 2. 2.]
...,
[ 2. 2. 2. ..., 2. 2. 2.]
[ 2. 2. 2. ..., 2. 2. 2.]
[ 2. 2. 2. ..., 2. 2. 2.]]
native [[ 2. 2. 2. ..., 2. 2. 2.]
[ 2. 2. 2. ..., 2. 2. 2.]
[ 2. 2. 2. ..., 2. 2. 2.]
...,
[ 2. 2. 2. ..., 2. 2. 2.]
[ 2. 2. 2. ..., 2. 2. 2.]
[ 2. 2. 2. ..., 2. 2. 2.]]
tfortran = 0.069974 , tnative = 1.202547

The Desktop, 🙂

Using ‘Home-Made’ Fortran Binary as Python module

Python is easy to use, but it’s slow, especially for loop computation. So I compute it using fortran like this

        subroutine subs(a, b, n)
double precision a(n)
double precision b(n)
integer n
cf2py intent(in) :: a
cf2py intent(out) :: b
cf2py intent(hide) :: n
! b(1) = a(1)
do 100 i=2, n
b(i) = a(i)-1
100 continue
end

save it as aravir.py and do the following command

$ f2py -c aravir.f -m aravir

To use the module on the python I use the code below

import numpy as np
import aravir as ar

a = np.linspace(0,1,100)

b = ar.subs(a)

print a
print b

🙂

3D Waterwave Simulation using Python

I used Numpy  Matplotlib with Animation and 3d Plot module on my OS X Yosemite.

The code is still messy and clearly not efficient (there’s slow loop here and there) but it works, 🙂
Here The Result
The Code

import numpy as np

n = 8;
g = 9.8;
dt = 0.02;
dx = 1.0;
dy = 1.0;

h = np.ones((n+2,n+2))
u = np.zeros((n+2,n+2))
v = np.zeros((n+2,n+2))

hx = np.zeros((n+1,n+1))
ux = np.zeros((n+1,n+1))
vx = np.zeros((n+1,n+1))

hy = np.zeros((n+1,n+1))
uy = np.zeros((n+1,n+1))
vy = np.zeros((n+1,n+1))

nsteps = 0
h[1,1] = .5;

def reflective():
h[:,0] = h[:,1]
h[:,n+1] = h[:,n]
h[0,:] = h[1,:]
h[n+1,:] = h[n,:]
u[:,0] = u[:,1]
u[:,n+1] = u[:,n]
u[0,:] = -u[1,:]
u[n+1,:] = -u[n,:]
v[:,0] = -v[:,1]
v[:,n+1] = -v[:,n]
v[0,:] = v[1,:]
v[n+1,:] = v[n,:]

def proses():
#hx = (h[1:,:]+h[:-1,:])/2-dt/(2*dx)*(u[1:,:]-u[:-1,:])
for i in range (n+1):
for j in range(n):
hx[i,j] = (h[i+1,j+1]+h[i,j+1])/2 - dt/(2*dx)*(u[i+1,j+1]-u[i,j+1])
ux[i,j] = (u[i+1,j+1]+u[i,j+1])/2- dt/(2*dx)*((pow(u[i+1,j+1],2)/h[i+1,j+1]+ g/2*pow(h[i+1,j+1],2))- (pow(u[i,j+1],2)/h[i,j+1]+ g/2*pow(h[i,j+1],2)))
vx[i,j] = (v[i+1,j+1]+v[i,j+1])/2 - dt/(2*dx)*((u[i+1,j+1]*v[i+1,j+1]/h[i+1,j+1]) - (u[i,j+1]*v[i,j+1]/h[i,j+1]))

for i in range (n):
for j in range(n+1):
hy[i,j] = (h[i+1,j+1]+h[i+1,j])/2 - dt/(2*dy)*(v[i+1,j+1]-v[i+1,j])
uy[i,j] = (u[i+1,j+1]+u[i+1,j])/2 - dt/(2*dy)*((v[i+1,j+1]*u[i+1,j+1]/h[i+1,j+1]) - (v[i+1,j]*u[i+1,j]/h[i+1,j]))
vy[i,j] = (v[i+1,j+1]+v[i+1,j])/2 - dt/(2*dy)*((pow(v[i+1,j+1],2)/h[i+1,j+1] + g/2*pow(h[i+1,j+1],2)) - (pow(v[i+1,j],2)/h[i+1,j] + g/2*pow(h[i+1,j],2)))

for i in range (1,n+1):
for j in range(1,n+1):
h[i,j] = h[i,j] - (dt/dx)*(ux[i,j-1]-ux[i-1,j-1]) - (dt/dy)*(vy[i-1,j]-vy[i-1,j-1])
u[i,j] = u[i,j] - (dt/dx)*((pow(ux[i,j-1],2)/hx[i,j-1] + g/2*pow(hx[i,j-1],2)) - (pow(ux[i-1,j-1],2)/hx[i-1,j-1] + g/2*pow(hx[i-1,j-1],2))) - (dt/dy)*((vy[i-1,j]*uy[i-1,j]/hy[i-1,j]) - (vy[i-1,j-1]*uy[i-1,j-1]/hy[i-1,j-1]))
v[i,j] = v[i,j] - (dt/dx)*((ux[i,j-1]*vx[i,j-1]/hx[i,j-1]) - (ux[i-1,j-1]*vx[i-1,j-1]/hx[i-1,j-1])) - (dt/dy)*((pow(vy[i-1,j],2)/hy[i-1,j] + g/2*pow(hy[i-1,j],2)) - (pow(vy[i-1,j-1],2)/hy[i-1,j-1] + g/2*pow(hy[i-1,j-1],2)))

#dh = dt/dt*(ux[1:,:]-ux[:-1,:])+ dt/dy*(vy[:,1:]-vy[:,:-1])
reflective()
return h,u,v
'''
for i in range (17):
#print h
proses(1)
'''

import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
from mpl_toolkits.mplot3d import Axes3D
a = n
x = np.arange(n+2)
y = np.arange(n+2)
x,y = np.meshgrid(x,y)

fig = plt.figure()

ax = fig.add_subplot(111, projection='3d')

def plotset():
ax.set_xlim3d(0, a)
ax.set_ylim3d(0, a)
ax.set_zlim3d(0.5,1.5)
ax.set_autoscalez_on(False)
ax.zaxis.set_major_locator(LinearLocator(10))
ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
cset = ax.contour(x, y, h, zdir='x', offset=0 , cmap=cm.coolwarm)
cset = ax.contour(x, y, h, zdir='y', offset=n , cmap=cm.coolwarm)
cset = ax.contour(x, y, h, zdir='z', offset=.5, cmap=cm.coolwarm)

plotset()

surf = ax.plot_surface(x, y, h,rstride=1, cstride=1,cmap=cm.coolwarm,linewidth=0,antialiased=False, alpha=0.7)

fig.colorbar(surf, shrink=0.5, aspect=5)


from matplotlib import animation


def data(k,h,surf):
proses()
ax.clear()
plotset()
surf = ax.plot_surface(x, y, h,rstride=1, cstride=1,cmap=cm.coolwarm,linewidth=0,antialiased=False, alpha=0.7)
return surf,

ani = animation.FuncAnimation(fig, data, fargs=(h,surf), interval=10, blit=False)
#ani.save('air.mp4', bitrate=512)
plt.show()

and the snapshot

3D Surface Plot Animation using Matplotlib in Python

And here’s the animation

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from mpl_toolkits.mplot3d import Axes3D

def data(i, z, line):
z = np.sin(x+y+i)
ax.clear()
line = ax.plot_surface(x, y, z,color= 'b')
return line,

n = 2.*np.pi
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')

x = np.linspace(0,n,100)
y = np.linspace(0,n,100)
x,y = np.meshgrid(x,y)
z = np.sin(x+y)
line = ax.plot_surface(x, y, z,color= 'b')

ani = animation.FuncAnimation(fig, data, fargs=(z, line), interval=30, blit=False)

plt.show()

The result

The snapshot

3D Surface Plot using Matplotlib in Python

It’s slightly modified from before

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from mpl_toolkits.mplot3d import Axes3D

n = 2.*np.pi
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')

x = np.linspace(0,n,100)
y = np.linspace(0,n,100)
x,y = np.meshgrid(x,y)
z = np.sin(x+y)
line = ax.plot_surface(x, y, z,color= 'b')

plt.show()

the result


the snapshot

Matplotlib Animation in Python

Here is the update from before

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation

def simData():
t_max = n
dt = 1./8
k = 0.0
t = np.linspace(0,t_max,100)
while k < t_max:
x = np.sin(np.pi*t+np.pi*k)
k = k + dt
yield x, t

def simPoints(simData):
x, t = simData[0], simData[1]
line.set_data(t, x)
return line
n = 2.
fig = plt.figure()
ax = fig.add_subplot(111)
line, = ax.plot([], [], 'b')
ax.set_ylim(-1, 1)
ax.set_xlim(0, n)

ani = animation.FuncAnimation(fig, simPoints, simData, blit=False,
interval=100, repeat=True)
plt.show()

and the result

Playing with Matplotlib Animation in Python

Coding like this

import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation

fig = plt.figure()
n = 10
x = np.linspace(0,2*np.pi,100)



def init():
pass
def animate(k):
h = np.sin(x+np.pik)
plt.plot(x,h)


ax = plt.axes(xlim=(0, 2*np.pi), ylim=(-1.1, 1.1))

anim = animation.FuncAnimation(fig, animate,init_func=init,frames=360,interval=20,blit=False)

plt.show()

The result

Playing (again) with ‘Home Made’ Vector in Delphi

Here it is. I create a vector as new type, which is in itself is three dimension array.

Then I declared u as vector with three dimension;
u (h,i,j)

where h = 0, 1, 2  as physical component (eg: height, velocity, momentum)
i , j = 0, 1, 2, …, n as row n column

So if we read u[0,1,1], it means height value at coordinate (1,1); u[1,1,1] is the velocity value; [2,1,1] is the momentum value at the same coordinate.

Trying some of properties of it. I found out that we can initialize all component of vector-u with this one line code

u:=fu(h[i,j],i,j);

so the component u(h,i,j) will filled. Notice that the function has vector (or in this case array) return value.

The code below show how I fill the value of component u(0, i, j)

unit Unit1;

interface

uses
Windows, Messages, SysUtils, Variants, Classes, Graphics, Controls, Forms,
Dialogs, StdCtrls;
const n=3;
type vector=array[0..2,0..n,0..n]of real;

type
TForm1 = class(TForm)
Button1: TButton;
Memo1: TMemo;
function fu(a:real;i,j:integer):vector;
procedure FormCreate(Sender: TObject);
private
{ Private declarations }
public
{ Public declarations }
end;

var
Form1: TForm1;

implementation{$R *.dfm}

function tform1.fu(a:real;i,j:integer):vector;
begin
fu[0,i,j]:=a;
end;

procedure TForm1.FormCreate(Sender: TObject);
var i,j:integer;
h:array[0..n,0..n]of real;
u:vector;
begin
for i:=0 to n do begin
for j:=0 to n do begin
h[i,j]:=1;
u:=fu(h[i,j],i,j);
end;
end;
memo1.Text:='';
memo1.Lines.Append('h[1,1]='+floattostr(h[1,1]));
memo1.Lines.Append('u[0,1,1]='+floattostr(u[0,1,1]));
memo1.Lines.Append('u[0,2,1]='+floattostr(u[0,2,1]));
end;

end.

🙂