My codes

Installing packages in Latex

2009-04-21T07:49:00.000-07:00

I am giving you a manual installation procedure for advanced packages in Latex for Windows. Installing it in Ubuntu is easier and I won't discuss here. Usually MikTex or other Latex editor softwares install packages automatically or give you the option to install it from the internet. But this does not work always. I am witting two procedure to install a missing package which worked for me. Remember after installation, you have to refresh the latex as instructed in red color.

1. Sometimes, installing a package is simple. I just type the package name in google ('package.sty') then copy the whole code in a ASCII editor, (e.g. vi or the latex editor itself) and save it with the extension '.sty'. (If you are using documentclass then the extension is '.cls'). This file now has to be placed in a correct directory which you can do in two ways. First, you can create a folder naming 'package' and put your 'package.sty' file in it. Now copy this folder to the location where you have your texmf folder into its subdiretory '...\texmf\tex\latex\'. Second, you can put your 'package.sty' in '...\texmf\tex\latex\misc'. See which one works. Run 'Refresh Now' from 'Start -> MikTeX -> MikTeX Option -> General -> Refresh Now' or in Vista I see its in 'Start -> MikTeX -> settings'. If you are not using MikTeX, find out the way to refresh your latex compiler.

2. (i) Download the package from CTAN (look in contrib or others wherever it is) or just search in google (e.g. install 'package' latex CTAN). After unzipping, you will find a folder with the same name. If that folder contains the appropriate 'package.sty' file you are all set otherwise it should contain a installation file 'package.ins'. Once yourun it, the required 'package.sty' should be created in the same folder. Now copy this folder into '...\texmf\tex\latex\'. Refresh your compiler now as written in red color before.

(ii) Some people suggest that you have to run the 'package.ins' file in this directory '...\texmf\source\latex\'. If the previous trial does not work, then copy your 'package' folder to this directory and then hit 'package.ins' and copy the folder to '...\texmf\tex\latex\'. Finally Refresh as given in red color before.

(iii) Again somewhere I find that you have to perform step 2(i) in '...\localtexmf\tex\latex'. See which one works.

3. Sometimes the package you find from internet contains the folder 'package' inside several other directories. Don't bother other folders or anything, just copy your needed folder 'package' wherever you find it and then paste into '...\texmf\tex\latex\'. And Refresh.

You may still find difficulties, in that case try to permute all the procedures I mentioned above and get google's help.

Even if you are not using MikTeX, the procedure should be same in principle, but the location of the directories might be different and you should be able to find the appropriate locations using analogy.

Lastly I hope you did not miss this advanced manual for latex 'The Not so short introduction to Latex 2'. Just google it. Thanks to Baris for letting me know that.

Bibliography sorting (Matlab Code)

2008-10-11T07:14:00.000-07:00

Those who write papers, especially longer one, they know how difficult and irritating it is to sort the bibliography every time you change the text. I made this little code to sort the bibliography as they appear in the text using '\cite{}'. Some journal does not allow to sort the bibliography as it appear in the figure caption. I have not given any special care to it for simplicity. The code appears below in a very misaligned fashion. It should work pretty well.

function bibsort(fname,bibfile,outfile)
%
% 'bibsort' sorts the bibliography of the main latex file
% as the references appear in the text.
%
% bibsort('paper.tex','bibliography.tex',''outputfile.tex')
% will find the citation from file 'paper.tex' and find the
% bibliography from file 'bibliography.tex' and the sorted bibliograpy
% will be written in 'outputfile.tex'. Default biblography file is the
% main file and the default outputfile is 'bib.tex'.
%
% This program will identify a reference as written in '\cite{reference}'
% in the main file and then search for that reference in the bibliograpy
% as written in '\bibitem{refererence}'. More reference as seperated
% by , inside one '\cite{}' is incorporated. Again, one '\cite{}' as
% splitted into two lines are also taken care of.
%
% Tanmoy Das.
% Feb 12 2008.
%
if nargin<1;error('Specify your input latex file');end;
if nargin ==1;bibfile=fname;outfile = 'bib.tex';end;
if nargin ==2;outfile = 'bib.tex';end;
%
fid = fopen(fname,'rt');
if fid<0;error(sprintf('%s%s%s','Input file [',fname,'] NOT found'));end
bfid = fopen(bibfile,'rt');
if bfid<0;error(sprintf('%s%s%s','Bibliography file [',bibname,'] NOT found'));end
ofid = fopen(outfile,'w');
%
% Identify all the references and save in variable 'd'
b = 'cite{';
ii = 1; % No of references as identified
while feof(fid) == 0;
tline = fgetl(fid); %read one line
len = length(tline);
if len>=1&tline(1)=='%';continue;end
% find the indices where refereces are located
indi = findstr(tline, b);
%num = length(indi);
if length(indi) > 0
len1= length(indi);
ik = 1; % index for the length of a reference
ij = 1; % index for the no of reference in one line
while (ij<=len1)
%tline(indi(ij)-1)
if (indi(ij)>2)&(tline(indi(ij)-2)=='%');ij=ij+1;continue;end;
il = indi(ij)+5;
while(il<=len)
c = tline(il); % store one character of the line
%} is found then the ref(s) in \cite{} is identified
if c=='}' ;ii= ii+1; ik=1; break; end;
% if , in \cite{} is found then one ref if identified
if c==','; ik=1; ii=ii+1; il = il+1; end;
d(ii,ik)=tline(il); % Store one character of a ref.
ik = ik+1; % increases the character length of a ref
% check if the line is finished before identifying one full
% ref.
if il==len;
tlinen = fgetl(fid); % go to net line
while length(tlinen)>=1&tlinen(1)=='%';
tlinen = fgetl(fid); % go to net line
end
tline = [tline tlinen]; % add the new line to old one
len = length(tline); % modify the new line length
% look for aditional '\cite{' in the new line
indi = findstr(tline, b);
% modify the new no of '\cite{' in the total line
len1=length(indi);
end
il = il+1; % go to the next character in the line
end %while: all ref found under one '\cite'
ij = ij+1; % go to the next '\cite'
end %while
end % if
end % while
%%%%%%%%%%%%%%%%%%%%%
% Now remove the same reference and store all independent references in
% 'f', as they are in order
%%%%%%%%%%%%%%%%%%%%%
ii = 1;
f(ii,:) = d(ii,:);
for ij = 2:size(d,1)
flag = 0;
for ik = ij-1:-1:1
if d(ij,:)==d(ik,:);flag = 1;break;end;
end
if (flag==0)
ii = ii+1;
f(ii,:) = d(ij,:);
else
continue
end
end
fclose(fid);
%
% Now look for the references fron 'The bibliograpy'
%
bfid = fopen(bibfile,'rt');
while feof(bfid) == 0;
tline = fgetl(bfid);
%if length(tline)>=1&tline(1)=='%';continue;end
indi = findstr(tline, sprintf('%s%s%s','\begin{thebibliography'));
num = length(indi);
if num > 0
fprintf(ofid,'%s\n',tline);
break;
end
end
fclose(bfid);
%
for ii = 1:size(f,1)
bfid = fopen(bibfile,'rt');
while feof(bfid) == 0;
tline = fgetl(bfid);
%if length(tline)>=1&tline(1)=='%';continue;end
indi = findstr(tline, sprintf('%s%s%s','\bibitem{',f(ii,:),'}'));
num = length(indi);
if num > 0
if (indi(1)>1)&(tline(indi(1)-1)=='%');continue;end;
fprintf(ofid,'%s\n',tline);
num2 = 0;
while (num2==0)
tline1 = fgetl(bfid);
%while length(tline1)>=1;%&tline1(1)=='%';
% tline1 = fgetl(fid);
%end
ind1 = findstr(tline1, '\end{thebibliography');
num1 = length(ind1);
if num1 >0;break;end;
ind2 = findstr(tline1, '\bibitem{');
num2 = length(ind2);
if num2==0;
%tline = [tline; tline1];
fprintf(ofid,'%s\n',tline1);
end;
end
% fprintf(ofid,'%s\n',tline);
break
end
end
fclose(bfid);
if(num<=0)error(sprintf('%s%s%s','Reference[',f(ii,:),']not found'));end;
end
%
bfid = fopen(bibfile,'rt');
while feof(bfid) == 0;
tline = fgetl(bfid);
%if length(tline)>=1&tline(1)=='%';continue;end
indi = findstr(tline, sprintf('%s%s%s','\end{thebibliography'));
num = length(indi);
if num > 0
fprintf(ofid,'%s\n',tline);
end
end
fclose(bfid);
fclose(ofid);

return

spline interpolation function for advanced fortran

2008-10-11T07:11:00.000-07:00

This subroutine will help you to spline the whole dimension of a vector. This can be easily modified to multi-dimensional matrix calculation.

subroutine spline(n,x,y,yp1,ypn,no,xo,yo)
cccccccccccccccccccccccccccccccccccccccccccccccccccc
c This subroutine will calculate the cubic-spline intepolated value of
c given any function for single variable of any dimension
c
c inputs/output:
c n : (input) [scalar] dimension of input array
c x : (input) [vector of length 'n'], independent variable of dimension 'n'
c y : (input)[vector of length 'n']' the function of x (an array of dimension 'n'
c yp1 : (input) [scalar] =1.e+30 :: the routine is signaled to set
c the corresponding boundary condition
c for a natural spline, with zero
c second derivative on that boundary
c ypn : (input) same to yp1 = 1.e+30
c no : (input) [scalar] dimension output array
c xo : (input) [vector of length 'no'], 'x' values at which you want to spline
c yo : (output) [vector of length 'no'], splined value
c
c Note: This works properly in any inter fortran compiler and f90-compiler
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
c
c Tanmoy Das.
c
c Feb 13, 2008.
c
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
integer::n,no,io
real,dimension(1:n)::x,y,y2,u
real,dimension(1:no)::xo,yo
c
if (yp1.gt.0.99e30) then
y2(1)=0.
u(1)=0.
else
y2(1)=-0.5
u(1)=(3./(x(2)-x(1)))*((y(2)-y(1))/(x(2)-x(1))-yp1)
endif
do 11 i=2,n-1
sig=(x(i)-x(i-1))/(x(i+1)-x(i-1))
p=sig*y2(i-1)+2.
y2(i)=(sig-1.)/p
u(i)=(6.*((y(i+1)-y(i))/(x(i+1)-x(i))-(y(i)-y(i-1))
& /(x(i)-x(i-1)))/(x(i+1)-x(i-1))-sig*u(i-1))/p
11 continue
if (ypn.gt.0.99e30) then
qn=0.
un=0.
else
qn=0.5
un=(3./(x(n)-x(n-1)))*(ypn-(y(n)-y(n-1))/(x(n)-x(n-1)))
endif
y2(n)=(un-qn*u(n-1))/(qn*y2(n-1)+1.)
do 12 k=n-1,1,-1
y2(k)=y2(k)*y2(k+1)+u(k)
12 continue
cccccccccccccccccccccccccccccccccccccccccccccc
c now for any arbitrary x
cccccccccccccccccccccccccccccccccccccccccccccc
do io = 1,no
klo=1
khi=n
1 if (khi-klo.gt.1) then
k=(khi+klo)/2.
if (x(k).gt.xo(io)) then
khi=k
else
klo=k
endif
goto 1
endif
h=x(khi)-x(klo)
if (h.eq.0.) pause 'bad XA input'
a=(x(khi)-xo(io))/h
b=(xo(io)-x(klo))/h
yo(io)=a*y(klo)+b*y(khi)+
& (a*(a*a-1.)*y2(klo)+b*(b*b-1.)*y2(khi))*h*h/6.

enddo
c
return
end

The main code to use mpi_distrbt

2008-10-11T07:07:00.000-07:00

This is the example of the script you can insert in your main program to use mpi_istrbt.

max_ipara=bzq ! the maximum array dimension to be parallelized
if(MPImyid.eq.0)then ! do the distribution in main node only
write(6,*)' Master process #',MPImyid,' starting'
c
call mpi_distrbt(max_ipara,nummpiprocsm,
& MPInumprocs,ipara_ini_fin)
endif ! master processor selection
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
c
c THIS IS EXECUTED BY ALL (MASTER+SLAVE) PROCESSORS
c
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
write(6,*)' Slave process #',MPImyid,' starting'
c blocking receive of integer data
icount=2*MPInumprocs
iroot=0
call MPI_BCAST(ipara_ini_fin, icount, MPI_INTEGER, iroot,
& MPI_COMM_WORLD, ierr)

c call the serial version
ipara_ini=ipara_ini_fin(1,MPImyid)
ipara_fin=ipara_ini_fin(2,MPImyid)

write(6,*)'Slave #',MPImyid,
& ' computing from ipara ',ipara_ini,' to ',ipara_fin

Fortran paraller programming : job distributor to several processors

2008-02-25T17:01:00.001-08:00

subroutine mpi_distrbt(max_ipara,nummpiprocsm,
& MPInumprocs,ipara_ini_fin)
ccccccccccccccccccccccccccccccc
cc This subroutine helps to distribute your total no of array dimension into the total number of
cc avaiable processor.
cc max_ipara = array dimension
cc nummpiprocsm = maximum number of processor available in the cluster
cc MPInumprocs = Number of processors you are using
cc ipara_ini_fin = output: real, dimension (1:2,1:MPImyid), where MPImyid is the identification number for
cc the processor
cc
cc A typical code to demonstrate how to use this is given in the blog.
cc
cc ALL COPYRIGHT IS RESERVED by Tanmoy Das.
cc Created in 2006/2007.
cc
cc I thank Seppo Sharakorpi for creating the basic structure and the algorithm of this code.
cc
ccccccccccccccccccccccc
real :: dummy
integer :: nummpiprocsm,max_ipara
integer,dimension(0:nummpiprocsm) :: isendcounts
integer,dimension(1:2,0:nummpiprocsm) :: ipara_ini_fin
c
C THESE ARE THE START AND FINISH VALUES OF OLD LOOP, NOW PARALLELIZED
c
ipara_ini_tot=1
ipara_fin_tot=max_ipara
write(6,*)
write(6,*)' ipara ranging from ',
& ipara_ini_tot,' to ',ipara_fin_tot
write(6,*)

c broadcast tasks to slaves
nummpitask_tot=ipara_fin_tot-ipara_ini_tot+1
cc
write(6,*)'---------------------------------------------------'

write(6,*) 'MPI MASTER: Scattering total of ',nummpitask_tot,' tasks'
write(6,*)'---------------------------------------------------'
cc
if ( nummpitask_tot < style="color: rgb(255, 153, 255);">then
write(6,*)' SERIOUS ERROR:: nummpitask_tot <>'
write(6,*) ipara_ini_tot, ipara_fin_tot, MPInumprocs
endif
cc
dummy=nummpitask_tot/MPInumprocs
islavetasks=floor(dummy)+1
isendcounts(0)=nummpitask_tot-(MPInumprocs-1)*islavetasks
cc
if ( isendcounts(0) > 0 ) then
ipara_ini_fin(1,0)=ipara_ini_tot
ipara_ini_fin(2,0)=ipara_ini_tot+isendcounts(0)-1
cc
do ii=1,(MPInumprocs-1)
isendcounts(ii)=islavetasks
ipara_ini_fin(1,ii)=ipara_ini_fin(2,ii-1)+1
ipara_ini_fin(2,ii)=ipara_ini_fin(1,ii)+isendcounts(ii)-1
end do
cc
write(6,*) isendcounts(0),' tasks for the master'
write(6,*) isendcounts(1),' tasks for each of the ',
& (MPInumprocs-1),' slaves'
write(6,*)
else
c if number of tasks is only slightly larger than MPInumprocs
islavetasks=floor(dummy)
isendcounts(0)=islavetasks
ipara_ini_fin(1,0)=ipara_ini_tot
ipara_ini_fin(2,0)=ipara_ini_tot+isendcounts(0)-1
idummy=nummpitask_tot-(MPInumprocs)*islavetasks
cc
do ii=1,(MPInumprocs-1)
isendcounts(ii)=islavetasks
cc
if ( ii <= idummy ) then isendcounts(ii)=isendcounts(ii)+1 end if
cc
ipara_ini_fin(1,ii)=ipara_ini_fin(2,ii-1)+1
ipara_ini_fin(2,ii)=ipara_ini_fin(1,ii)+isendcounts(ii)-1
end do
cc
write(6,*) isendcounts(0),' tasks for the master,'
write(6,*)isendcounts(1),' tasks for each of the first',
& idummy,' slaves and'
write(6,*)isendcounts(idummy+1),
& ' tasks for each of the other',
& (MPInumprocs-1)-idummy,' slaves'
write(6,*)

end if
cc
return
end subroutine