Computational Physics

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9 Νοε 2013 (πριν από 3 χρόνια και 8 μήνες)

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Computational Physics

Dr. Guy Tel
-
Zur

2011A

Sunny Yellow
Flower. Picture
by
Sharee
Basinger
, publicdomainpictures.net

About me...

1988

1991

1996

1996
+

2001
+

2003
-
2004

2005
+

Survey


Please answer the survey at:

http://
spreadsheets.google.com/gform?key=t
3
T
cOcxehKAzYyhm
6
WukzeA#invite


The Course Vision

“The crucial need for today's students and
readers is to move forward from the

older
"formula
-
based"
emphasis toward a
solution
-
based

course. Solving problems

is the heart of modern engineering mathematics
and scientific computing. “


Gilbert
Strang



Computational Science and Engineering, page
7
, SIAM (
2007
).

What is Computational Physics

Reference:
Resource
Letter

CP
-
2
:
Computational

Physics

Rubin H. Landau, Am. J. Phys.
76 4
&
5
, April/May
2008

A broader view



Computational Science

X

Math

CS

Computational


X

X=Physics, Biology, Chemistry, …

Reference:
Resource
Letter

CP
-
2
:
Computational

Physics

Rubin H. Landau, Am. J. Phys.
76 4
&
5
, April/May
2008

3
Pillars

Theory

Computational

Physics

Experiment

4
Pillars?

Theory

Computational

Physics

Data Mining

Experiment

2
Computational Pillars

See next slide, from Communications of
the ACM,
http://cacm.acm.org/magazines/
2010
/
9
/
98038
-
science
-
has
-
only
-
two
-
legs/fulltext


September
2010
issue

NVIDIA CEO at the GTC
2010
, Sept.
2010

The
3
rd

Pillar of Science is HPC !!!


HPC = High


Performance Computing

What is Computational Physics?

Computational
Physics combines physics, computer
science and applied mathematics in order to provide
scientific solutions to realistic and often complex
problems. Areas of application include the nature of
elementary particles, the study and design of
materials,


the study of complex structures (like
proteins) in biological physics, environmental
modeling, and medical imaging. A computational
physicist understands not only the workings of
computers and the relevant science and mathematics,
but also how computer algorithms and simulations
connect the two.


Source: http://www.sru.edu/academics/colleges/ches/physics/Pages/ComputationalPhysics%
28
BS%
29
.aspx

Computational Physics is an active field

Journals and Magazines…

APS, EPS, IPS…

No CP division


Scientific Papers On
-
line at
arXiv.org

http://arxiv.org/list/physics.comp
-
ph/recent

Career Opportunities for
Computational Physicists


A graduate degree in physics in areas such as biophysics, condensed matter
physics, particle physics, astrophysics to name a few.


A
career in High
-
performance and scientific computing, in the energy and
aerospace sectors, with chemical and pharmaceutical companies, with
environmental management agencies.


Employment
in firms that develop scientific software, as well as computer
games.


A
research career in an academic, industrial, or national
laboratory


A
teaching career in physics


A
job in Wall Street. Even Wall Street employers are interested in people
with a background in computational physics.

Source: http://www.sru.edu/academics/colleges/ches/physics/Pages/ComputationalPhysics%
28
BS%
29
.aspx

Physics Engine in Computer Games

Course Building Blocks

Tools

Methods

Case Studies

Practice

Parallel and distributed
computing

Rubin Landau et al, “A Survey of Computational Physics”

Rubin Landau et al, “A Survey of Computational Physics”

Scheme on previous slide refers to at least
2
quarters (
20
weeks) course

Scientific Discovery through
Advanced Computing (
SciDAC
)

DOE Office of Science

http
://www.scidac.gov/

When will be such a national initiative in Israel…?


Source: http://www.princeton.edu/as/LNL/presentations/spring
2010
/LnL
031010
TangFusionSimulation.pdf

What V&V Means?

The
problem
of quantifying
uncertainty:

Validation
"Solving the right equations"

Verification
"Solving the equations right"

T
ools


Programming Languages


C/C++


Fortran


Python


N
umerical

T
ools


CERN
paw/root
/
Matlab
/Octave/
Scilab


V
isualization


VTK

-

grace


-

Paraview

-
VisIt

-
Mayavi


V
python

-

GNUplot

-
DX


W
orkflow


K
epler
(?)


+
OpenMP

+MPI

+Condor

Full Scientific Research Study


“Workflow”

Raw Data

Number
Crunching/Data
Analysis

Reduced Data

Visualization

“Batch”

“Data Base”

Specific Format ,
e.g.
NetCDF

Interactive
mode

Prototyping
(
Matlab
)

P
arallelism

AMD


6
cores microprocessor

My Goal: Introducing Parallelism whenever
possible is going to be my own “twist” to the
course

Power
7
: IBM’s Next
-
Generation Server Processor with
8
cores.

The chip is
567
mm
2
and contains
1.2
billion transistors

Recommended Reading:
http://www.computer.org/cms/Computer.org/ComputingNow
/homepage/
2010
/
0710
/W_MI_Power
7
.pdf

NVIDIA CEO at GTC
2010

GPGPU increase presence at the Top
500
Supercomputers

Serial vs
. Parallel
-

demo

Execute: C
:
\
FlexPDE
5
student
\
samples_student
\
steady_state
\
fluids
\
swirl

Low
cpu

utilization

Uses only one core

Some highlights of the course


Next slides

We will have:


1.
Standard “Classical” text PLUS

2.
Several “Mini
-
Courses”


My add
-
ons

1.
Parallel Computing


MPI,
OpenMP

2.
Batch/Grid Computing


Condor

3.
Visualization (next slide)

4.
Cluster Computing

Parallel Visualization

A visit to the parallel visualization lab at the
Mechanical Engineering building

How to build a parallel computing
cluster


hands on demo

A report from SC
10

The Latest Innovations

Course Web Site

http://physics.bgu.ac.il/~gtelzur/teaching/comphy/
2011
A/

םינויצו סרוקה תובוח


לכ תשגה תבוח תמייק
4

תיבה יליגרת
(
השעי דועתה
ב
-

LaTeX

כ שגויו
-

PDF

אודה תועצמאב
"
הצרמל ל
.


ןויצ םהילע ןתנייו םיליגרת וקדבי ימגדמ ןפואב
(
דע
לכמ תחא הדובע תוחפה לכל קדבית רטסמסה ףוס
טנדוטס
)


לקשמ
:
20%


רועישה ימוכיס


לע רמאמ טמרופב םכוסי רועיש לכ
-
לע ןתנייו רחא טנדוטס ידי
-
ןויצ ךכ
.
ב השעי םוכיסה
-

LaTeX
.
לקשמ
:
10%
)*(
יפוס אל
-

רפסמב יולת
םיטנדוטסה


רטסמסה ףוסב


רמג יטקיורפ
.
םיקלח ינש טקיורפל
:
םכסמ חודו תגצמ
70%


ךשמהב םיפסונ םיטרפ ואר
.

סרוקב יופצה סמועה יבגל יתלאשנ

Keys to success
Right motivation, working diligently, effectively and efficiently is the key to
success.

If you work regularly and allocate enough time each day to practice and complete

the assignments on time and keep up with the course, you will get the most out of

the course both intellectually and grade
-
wise.

You should invest about
6
-
9
hours per week outside of class to succeed in this

course
. This is consistent with university guidelines (i.e. two to three hours of

outside preparation time for every credit hour).
Students with little or no

programming experience (or those who love the subject and wish to do extremely

well in it) may want to put in more hours. Please, let me know as soon as possible

if you have difficulties and may need extra help.

You are recommended to start you assignments well before the last night when

your assignments are due. It is a general experience that a computer program

usually does not work correctly (if works at all) at the beginning. A search for a

problem, or a computer bug, may take more time that you expect.

The following is from:
Old Dominion University Physics
420
/
520
Spring
2010


תופסונ תורעה
:



עב
"
לע פ
-
הצרמה ידי

תיבה יליגרת


Approximately
4
sets of homework problems will be assigned.


The
students will write
computer programs
based on computational algorithms discussed in
class.


These
assignments constitute
a very
important part of the course, since the thinking involved
in scientific programming can
only be
developed through practical work.


The
assignments must be returned by their stated due dates
, unless
an extension is granted
by the instructor. For late return of assignments, a
10
%
point deduction
will be applied for
each late day.


Programs
should be written in Fortran
90
/
95
or in C/C++ or in Python.


The
programs as well as a short report discussing the results should be handed in to
the
instructor
by the stated due date. The solution programs should be sent as an attachment in
an e
-
mail
to the address
gtelzur@bgu.ac.il.
The report (hardcopy required)
should
be handed
to
the instructor
in class
before
the deadline
.


Every
student is expected to work independently on the assignments. However, discussions
with fellow
students are allowed, indeed encouraged, as long as they are kept on a general
level
and do
not amount to direct copying of ideas or programming solutions.


Although
discussions and some degree of cooperation between students is allowed,
The
material
turned in must be independently written.

Inspired from: http://physics.bu.edu/~py
502
/syllabus.pdf

רמגה יטקיורפ


סרוקה לע ןויצב יראה קלחה תא םיווהמ
.


הבר תובישח םהל סחיימ
.


ולש טקייורפה אשונ תא התיכה ינפב גיצי טנדוטס לכ


ימעטמ םיאשונ תמישר ךשמהב םסרפא ינא


םכלשמ םיאשונ עיצהל םינמזומ םתא
.


אבה רושיקב תונויער לבקל רשפא
:
/projects.html
516
shaas/
/~
http://physics.usc.edu

רמגה יטקיורפ


תגצמ


התיכה ינפב גצוי טקיורפה
.
תא ראתל שי
הדובעה אשונ
,
ןתמל ךרדהו יבושיחה רגתאה
רגתאל הנעמ
.
תביתכ תשרדנ אל הזה בלשב
בשחמ תינכת


לקשמ
10%

יפוסה ןויצהמ


םכסמ חוד
:
תגצמה תוברל טקיורפה לכ תא םכסי
ורובע בתכתש בשחמה תינכתו
.
אלמ דועית ףרוצי
תונקסמו
(
הדובעה הנבמ טורפ


ךשמהב
.)
לקשמ
:
60%

יפוסה ןויצהמ


רמגה יטקיורפ לש תוגצמה


אשונ גיצי טנדוטס לכ


טמרופ
PPT
,
PDF
,
HTML


סרוקה לש םינורחאה םירועישה ינשב הנמייקתת תוגצמה


הפש
:
תירבע
/
תילגנא
(
רוביד
/
םיפקש
.)


תוצח דע הצרמה לא תגצמה תא ליימה תועצמאב חולשל שי
הצרמה בשחמל הלעות תגצמהש ךכ רועישה ינפלש הלילה
וא םיינוציח םינקתהמ תונקתה לש ןמז זובזב היהי אלו
רועישה ןמזב ןרקמל םיבשחמ רוביח


תבותכל חולשל שי תוגצמה תא
:
gtelzur@gmail.com

רמגה טקיורפ לש םכסמה חודה


סרוקה רתאל ךשמהב הנלעות תודובעה לכ וא קלח


הדובעה הנבמ
:
רעש
(
םש
,
ת
.
ז
.
,
תרתוכ
)
,
תיצמת
,
אובמ
,
הדובעה ףוג
,
תונקסמ
,
ןיכומיס תמישר
,
םיחפסנ
.


לולכל ץלמומ
םיפארג
,
םימישרת
,
תשחמהל תואלבט
תואצותה


טמרופ ץלמומ
LaTeX



ךשמהב ואר


דבלב תינורטקלא השגה


תבותכל
:
gtelzur@gmail.com

More tips about the Final Projects


Consult these links:

1.
http://www.odu.edu/~
agodunov/teaching/p
hys
420
_
10
/organize_comp_proj.pdf

2.
http://www.odu.edu/~
agodunov/teaching/p
hys
420
_
10
/Sample_Project.pdf

3.
http://www.odu.edu/~
agodunov/teaching/n
otes/Intr
02
_projects.pdf




Programming Languages


C/C++


Fortran
90
/
95


Python


More discussion on that in the next
presentation!

השחמה ילכ
-

Visualization Tools


Gnuplot



included in Python(
x,y
)


Xmgrace



2
D, Linux only


vPython



included in Python(
x,y
)


Qtiplot



Free for Linux OS (Origin clone)
http://soft.proindependent.com/qtiplot.html



Excel


CERN’s PAW/Root )if time will permit)

LaTeX


Learn
LaTex
, here are a few links to tutorials:


http://
www.cs.cornell.edu/Info/Misc/LaTeX
-
Tutorial/LaTeX
-
Home.html


http://www.pages.drexel.edu/~
pyo
22
/students/la
texRelated/latexTutorial.html


Getting Started With
LaTex
:
http://www.maths.tcd.ie/~
dwilkins/LaTeXPrimer/
GSWLaTeX.pdf


LaTeX

Recommended Environment

(install it on your laptops)


MikTeX
:
http://www.miktex.org
/


LaTeX

Editor
:
Led
-
http
://
www.latexeditor.org/index.html


Optional:
LyX

-

http://www.lyx.org
/

(less recommended)


Online check your
LaTeX

equations with
Texify
:
http://
www.texify.com/links.php



Linux Background

Check:
http://www.physics.udel.edu/~bnikolic/teaching/phys
660
/RUTE/rute/index.html

דוע המ
?


תופי תומגדהלו םיקחשמל ןמז אוצמל לדתשנ
!


Open
Source Physics
-

http://www.compadre.org/osp
/


ןיינעמ רמאמב םתלקתנ
?
טנרטניאב יטנוולר רושיק


ילא הז עדימ וחלשת םא םכל הדוא


רשק לע הרימש


ליימב ילא תונפל םילוכי םתא
:
gtelzur@gmail.com


רשא סרוקה לש טנרטניאה רתא ירחא בוקעל אנ
ףטוש ןפואב ןכדעתמ


Mailing lists?



לגוגב םיקהל רשפא


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...
?

Let’s get started!