Please Make A Note

OriginLab Settings for High Quality Graphs

2009-06-25T15:07:00.005-05:00

This is a well overdue post. I know that some readers have been waiting for this. I apologize for the delay. I hope you'll find this talk useful.

Flashget Script Error/Flashget Recommends bar

2009-06-24T21:17:00.001-05:00

In Flashget, go to:

View/Recommendation

and uncheck it.

Obviously, the ads displayed by flashget are generating an internet explorer script error. I never liked that recommend bar anyway.

hyperref and pdfdraftcopy

2009-06-04T14:02:00.001-05:00

There seems to be a problem when these two packages are used together. Try adding the following to your preamble – it worked well on my end

\makeatletter
    \def\@DRAFTdimen{% copied from pdfdraftcopy.sty
    \setlength\LLY{\paperheight}
    \addtolength\LLY{-\textheight}
    \addtolength\LLY{-\headheight}
    \addtolength\LLY{-\headsep}
    \addtolength\LLY{-1in}
    \addtolength\LLY{-3pt}
    \setlength\LLX{1in}
    \ifodd\value{page}% was \thepage
    \addtolength\LLX{\oddsidemargin}\else
    \addtolength\LLX{\evensidemargin}\fi
    \setlength\URX{\textwidth}
    \setlength\URY{\textheight}
}
\makeatother

Voila!

Make Nomenclature in WinEdt

2009-06-03T13:38:00.001-05:00

First, you need to download this file

http://www.winedt.org/Macros/LaTeX/MakeNomencl.php

Save it in the “Exec/MiKTeX” folder under your WinEdt path, e.g.

C:\Program Files\Winedt Team\WinEdt\Exec\MiKTeX

in WinEdt, do the following

Right click on the Menu bar

Select “Menu Steup”

Double click on any of the menus where you would like your make nomenclature command to go (Accessories would be a good candidate)

On your upper left, choose Insert->Macro

Name the new command (Make Nomenclature)

Under Macro, type the following: Exe('%b\Exec\MiKTeX\MakeNomencl.edt');

Voila!

7zip Batch Zip

2009-05-29T16:15:00.001-05:00

First, make sure that the 7zip directory is in your path. Usually, it is located at

C:\Program Files\7-Zip

Next, write the following in batch file

Zip all files in a directory

for /f %%A in ('dir /b') do 7z a -tbzip2 "%%A.bz2" "%%A"

Zip files with a specific extension in a directory (download batch file)

for /f %%A in ('dir /b *.txt *.dat') do 7z a -tbzip2 "%%A.bz2" "%%A"

Save and run in the directory where you want to zip the files.

Here, I am compressing using bzip2 (notice the switch: –tbzip2). You can change that to

-tzip for zip

-tgz for gz

-t7z for 7z

some more examples here.

Restart Windows in Remote Desktop

2009-05-29T15:58:00.001-05:00

press:

Alt + F4

Voila!

How to Add a Watermark in Latex

2009-05-21T22:21:00.001-05:00

More often than not, I like to place a “DRAFT” watermark on my documents. This can be easily and automatically done by just including a specific package (one for PS and one for PDF).

Here’s how

\usepackage[draftcopy] % for PS and DVI

\usepackage[pdfdraftcopy] % for PDF

Voila!

For the documentation of draftcopy check here.

For the documentation of pdfdraftcopy check here.

Wolfram Alpha

2009-05-19T01:56:00.001-05:00

It has been finally released!

http://www.wolframalpha.com/

I’m too sleepy now to experiment with it.

In the meantime, you can check the walking randomly blog.

How to Cite a Blog & Automatically Generate Citations for your Blog

2009-05-15T18:17:00.009-05:00

The MLA format for citing a blog is:

Last Name, First. "Title of Entry." Weblog Entry. Title of Weblog. Date Posted. Date Accessed (URL).

You can find more information on studenthacks and on the Purdue website.

Now comes the fun part. If you’re familiar with the Wolfram mathworld website, there is a “CITE THIS AS” section at the bottom of every page (example). I wanted to reproduce something similar for my blog. As you may have already noticed, there is a “Cite as” box at the bottom of every post. Of course, I didn’t go over every post to add a cite-as box. I used the google blogger API to automatically add this to every post. Here’s how you can reproduce it for your own blog

Go to the “Edit HTML” section for your template

Enable the “Expand Widget Templates” check box

Scroll down (or search: Ctrl + f) for
<data:post.body/>
This may require some tweaking as your template may be different. The idea is to locate the “post body” section – right after the body text of your post.
Copy the following HTML code:
 
 
 
 
Cite as: 
 
LAST NAME, FIRST NAME &quot;<data:post.title/>. 
&quot; Weblog entry from <a href='http://LINK-TO-YOUR-BLOG> <data:blog.title/></a>. 
<a expr:href='data:post.url'><data:post.url/></a> 
 

 
<!-- END CITE AS CODE –> 
Save your template

Voila! Don’t forget to put your name and the link to your blog. You can easily modify the above script with little HTML and CSS knowledge.

Modifying Mathematica Menus

2009-05-15T16:59:00.002-05:00

UPDATE - FRIDAY MAY 15, 2009
The same procedure applies for Mathematica 7.x - just look in the 7.0 directory. For convenience, I posted the Mathematica 7.0.1 modified menu file. Of course, there is no guarantee that this will work on your end, so by all means do backup your copy of the MenuSteup.tr file before using this one. You can download it from here.

UPDATE - MONDAY JUNE 02, 2008
As was kindly pointed out by an anonymous comment, Mathematica version 6.0.2 includes the "Evaluate Notebook" menu item. Also, removing the backup files from the MenuSetup directory is a must. - Thanks

In Mathematica 6.x, a couple of nice features are missing, namely, the "Evaluate Notebook" menu command and the placement of the "Quit Kernel" command. First, the "Evaluate Notebook" is completely missing form the "Evaluation" menu - and I don't see the reason for removing such a useful command from the new version. Regarding the "Quit Kernel", which is probably the most used command during a Mathematica session, is now located under Evaluation/Quit Kernel/Local. Instead of keeping that command one level higher (i.e. Evaluation/Quit Kernel), for some reason it was placed under a sub-menu.

Yesterday, I found out that one can modify the whole Mathematica menu, and in the process, add the "Evaluate Notebook" command and modify the location of the "Quit Kernel" command. Thanks to the Walking Randomly blog for sharing this information - you can find the original post here.

So here's what I have done on my end to make my Mathematica workspace fit to my needs.

Locate the file "MenuSetup.tr" - This is usually found somewhere within the "Wolfram Research" directory. A simple search would be enough to find that file. (try C:\Program Files\Wolfram Research\Mathematica\6.0\SystemFiles\FrontEnd\TextResources\Windows\)
Open "MenuSetup.str" with a text editor. In windows, I use wordpad to do that because it keeps the formatting correct and wraps the text quite nicely.
Scroll down to the end of the file and locate the last brace-then-bracket "}]" then add the following before that
Type a comma then go to a new line
Insert the following
Delimiter,
Item["Evaluate &Notebook", "EvaluateNotebook"],
Item["&Quit Local Kernel", "MenuListQuitEvaluators", MenuAnchor->True]

Voila!

You should be able to see two new menu items on the menu bar. Make sure also to backup your original MenuSetup.tr. If nothing shows up on the Mathematica menu, you might have to move the backup copy from the MenuSetup directory.

Calling Gnuplot from c Using Pipes... Again!

2009-05-15T00:08:00.006-05:00

Here's another way of calling gnuplot. I like this method because it provides a standalone function that plots your results. Here's the code:


#include <stdio.h>
#include <stdlib.h>
#include <math.h>
void plotResults(double* xData, double* yData, int dataSize);
int main() {
  int i = 0;
  int nIntervals = 100;
  double intervalSize = 1.0;
  double stepSize = intervalSize/nIntervals;
  double* xData = (double*) malloc((nIntervals+1)*sizeof(double));
  double* yData = (double*) malloc((nIntervals+1)*sizeof(double));
  xData[0] = 0.0;
  double x0 = 0.0;
  for (i = 0; i < nIntervals; i++) {
      x0 = xData[i];
      xData[i+1] = x0 + stepSize;
  }
  for (i = 0; i <= nIntervals; i++) {
      x0 = xData[i];
      yData[i] = sin(x0)*cos(10*x0);
  }
  plotResults(xData,yData,nIntervals);
  return 0;
}
void plotResults(double* xData, double* yData, int dataSize) {
  FILE *gnuplotPipe,*tempDataFile;
  char *tempDataFileName;
  double x,y;
  int i;
  tempDataFileName = "tempData";
  gnuplotPipe = popen("c:\\gnuplot\\bin\\pgnuplot -persist","w");
  if (gnuplotPipe) {
      fprintf(gnuplotPipe,"plot \"%s\" with lines\n",tempDataFileName);
      fflush(gnuplotPipe);
      tempDataFile = fopen(tempDataFileName,"w");
      for (i=0; i <= dataSize; i++) {
          x = xData[i];
          y = yData[i];            
          fprintf(tempDataFile,"%lf %lf\n",x,y);        
      }        
      fclose(tempDataFile);        
      printf("press enter to continue...");        
      getchar();        
      remove(tempDataFileName);        
      fprintf(gnuplotPipe,"exit \n");    
  } else {        
      printf("gnuplot not found...");    
  }
}

This code should run as is. Of course, feel free to take the plot function and use it in your own codes.

Wolfram Alpha

2009-05-14T19:16:00.005-05:00

I can't wait for this to be released!

http://www.wolframalpha.com/index.html

In the meantime, check out this presentation by Stephen Wolfram himself

or this CNET demonstration

How to Call Gnuplot from c Using Pipes (Windows)

2009-05-14T11:53:00.007-05:00

Try this:

// Open a pipe to gnuplot
FILE *gnuplotPipe = popen("c:\\gnuplot\\bin\\pgnuplot -persist","w");
// If gnuplot is found
if (gnuplotPipe) {
  // using fprintf on the gnuplotPipe, we can directly issue commands in gnuplot
  fprintf(gnuplotPipe, "set style data lines\n");
  fprintf(gnuplotPipe, "cd 'C:\\gnuplot\\bin'\n");
  // assuming your data file is placed in the gnuplot bin directory
  fprintf(gnuplotPipe, "plot \"data-file.dat\" using 1:2\n");
  fflush(gnuplotPipe);
  fprintf(stderr,"Press enter to continue...");
  fflush(stderr);
  getchar();
  // exit gnuplot
  fprintf(gnuplotPipe,"exit \n");
  pclose(gnuplotPipe);
}

One year anniversary – Please Make a Note

2009-05-12T12:12:00.002-05:00

Today marks the one year anniversary of Please Make a Note! This idea that started as a mere way of keeping track of how I accomplished certain tasks so that I can refer to them later has had an unexpected (positive) outcome: the number of visitors to this blog. Although I had wished (as everybody who owns a blog does) to reach as many online users as possible, I had never expected the current results. I am also quite pleased with the several hits that PMAN received from some important bloggers and software companies (yes!!! PMAN was visited by Mathematica people!).

In any event, I would like to thank all those who have shown interest in this blog. I hope that you found some useful posts here.

This is the monthly visits report from statcounter (12 May 2008 – 12 May 2009).

(P.S. I have no idea what happened in march!)

	Page Loads	Unique Visitors	First Time Visitors	Returning Visitors
Total	41,947	27,326	23,797	3,529
Average/month	3,227	2,102	1,831	271

Voila!

How to Flatten or Embed Comments in a PDF using Acrobat©

2009-05-04T10:47:00.001-05:00

Most often than not, I implement all my comments to PDF files (such as manuscript proofs) using the many rich features of Adobe’s Acrobat Professional. However, I always prefer to “flatten” these comments that is, make them a permanent part of the PDF document. There are a few methods for doing this, but by far, the fastest and most clever is this one, found on PlanetPDF

In Acrobat professional, type “Ctrl + j” to invoke the java script dialog

In that dialog, type: this.flattenPages();

press “Ctrl + Enter”

Voila!

Don’t forget to save your document.

EndNote to JabRef to EndNote

2009-04-21T20:31:00.001-05:00

In Endnote, select the citations you want to export and go to “File / Export”

Select “RefMan (RIS) Export” in the Output Styles dropdown box
(in case it is not there, choose “Select Another Style…” and look for RefMan RIS Export)

After exporting the file, go to JabRef and import as RIS

Voila!

There are many ways of doing this. Here’s one on fellow blog Fundamental Thinking. Josh’s method is based on the JabRef Endnote Export Filter.

To go from JabRef to Endnote

In JabRef, select the citations you want to export and go to “File / Export”

Select “Endnote” from the dropdown box

In Endnote go to “File / Import”

Choose the data file that you just exported from JabRef

Under import option, choose “EndNote Import”

Voila!

How to Resolve or Link to a DOI

2009-04-15T00:55:00.002-05:00

Given a DOI number (for a journal manuscript for instance) one can link to this DOI in a word document for example or in an HTML page by invoking the following

http://dx.doi.org/YOUR-DOI-NMBER

Try this for example

http://dx.doi.org/10.1103/PhysRev.47.777

Voila!

The DOI, or Digital Object Identifier system, is a systematic way of identifying digital resources in a rather permanent way. It is a neat way for tracking and managing digital resources in an absolute reference manner. So, for example, if you want to link to a journal paper, you can either use the permalink for that specific paper or simply link to the DOI. In theory, no matter what happens, the DOI number will always locate that paper.

The Story with Euler…

2009-03-13T01:28:00.001-05:00

Recently, I have been deeply immersed in studying some of Euler’s original works (based on translations where applicable, of course). Here is my conclusion:

Whatever you think you have discovered… Euler may have beaten you to it!

and yes… please quote me for that one!

I made it a necessary condition in my research, and before publishing any manuscript, to check with Euler first. Many of his results and especially the intricate steps of his derivations are lost within the edifices of his collected works (or simply because later generations of mathematicians have superseded his proofs with modern versions). Yet, you will be surprised to find in one of those steps, the exact same thing that you may be currently discovering!

Discussing the Divine Comedy with Dante

2009-03-07T19:32:00.001-06:00

Check out this 2006 oil painting by Dai Dudu, Li Tiezi, and Zhang An.

Click on the image to see a larger version with an image map and wiki links for the people featured in the image. There are few inaccuracies in this version, but this version has more accurate data.

An Easy to Use Free IDE for C/C++

2009-03-07T11:39:00.001-06:00

I know that you’ve always wondered about what C/C++ compiler and IDE to use under windows. While Microsoft offers its version of the C/C++ compiler, many people still prefer to use the GNU suite of compilers. This, without mentioning the fact that you will need to install visual studio or, if not, manually compile your code, which should be a prehistoric task by now because there are things called IDEs that take care of that.

The other hassle about installing the GCC (GNU C Compiler) under windows, is that you have to first install MingW.

I recently found this excellent and easy to use free IDE that does everything for you. It is called Code::Blocks. This program is very easy to use, intuitive, and installs the GCC compiler and MingW for you.

Voila!

The Illusion of Knowledge

2009-02-28T19:44:00.001-06:00

Although not along the general theme of this blog, I am obligated to make this post so that I remember this, and hopefully, share it with many other fellow engineers and researchers.

I was deeply motivated and moved by a quote from Daniel J. Boorstin:

The greatest obstacle to discovery is not ignorance, it is the illusion of knowledge.

Indeed, often times we find ourselves locked within an bubble of knowledge, thinking that we know everything and that we have solutions for all, yet, we fail to realize that this only an imaginary crust beyond which lies the unknown.

8. Derivation of the Continuity Equation in Cylindrical Coordinates

2009-02-22T18:56:00.001-06:00

This is one of my favorite derivations. Although it would sound a bit intimidating at first, as none of the standard textbooks carry out the derivation in curvilinear coordinates; it is rather easy to obtain. And guess what? the math is quite rewarding!

So we first have to start by selecting a convenient control volume. The idea here is to pick a volume whose sides are parallel per say to the coordinates. For cylindrical coordinates, one may choose the following control volume

Again, as we did in the previous post, we need to account for all the fluid that is accumulating, and flowing through this control volume, namely:

Rate of Accumulation + Rate of Flow In = Rate of Flow Out

First, let’s get some basics laid out. The velocity field will be described as

I always prefer to use u, v, and w instead of ur, utheta, and uz to save on subscripts, although the latter nomenclature is a bit more descriptive… we’ll get used to it. Now, by construction, the volume of the differential control volume is

while the mass of fluid in the control volume is

The rate of change of mass or accumulation in the control volume is then

For the net flow through the control volume, we deal with it one face at a time. Starting with the r faces, the net inflow is

while the outflow in the r direction is

So that the net flow in the r direction is

Being O(dr^2), the last term in this equation can be dropped so that the net flow on the r faces is

The net flow in the theta direction is slightly easier to compute since the areas of the inflow and outflow faces are the same. At the outset, the net flow in the theta direction is

We now turn our attention to the z direction. This requires a little bit of extra work. The most essential ingredient of computing the flow in the z direction is to compute the face areas. As shown in the figure above, the z faces are essentially trapezoids (in the differential limit) and their area is equal to the average of the bases times the height, in other words

then, the inflow at the lower z face is

while the outflow at the upper z face is

Finally, the net flow in the z direction is

Now we can put things together to obtain the continuity equation

dividing by dV and rearranging the r components of the velocity

Voila!

7. Derivation of the Continuity Equation in Cartesian Coordinates

2009-02-21T01:55:00.002-06:00

[Previous Article: How Euler Derived the Continuity Equation]

The continuity equation is an expression of a fundamental conservation principle, namely, that of mass conservation. It is a statement that fluid mass is conserved: all fluid particles that flow into any fluid region must flow out. To obtain this equation, we consider a cubical control volume inside a fluid. Mass conservation requires that the the net flow through the control volume is zero. In other words, all fluid that is accumulated inside the control volume (due to compressibility for example) + all fluid that is flowing into the control volume must be equal to the amount of fluid flowing out of the control volume.

Accumulation + Flow In = Flow Out

The mass of the control volume at some time t is

The time rate of change of mass in the control volume is

Now we can compute the net flow through the control volume faces. Starting with the x direction, the net flow is

Similarly, the net flow through the y faces is

while that through the z faces is

Upon adding up the resulting net flow and diving by the volume of the fluid element (i.e. dxdydz), we get the continuity equation in Cartesian coordinates

Voila!

The Coming Revolutions in Theoretical Physics

2009-02-19T19:41:00.001-06:00

Check out this interesting talk by David Gross

Windows Defender Update Issues

2009-02-19T02:44:00.001-06:00

For some reason, windows defender starts messing up and is not able to detect the latest updates. You will then need to download and install these updates manually. Check this out

How to troubleshoot definition update issues for Windows Defender

I hope that works out for you.