Overview

• This project collects commonly-used routines into a single header file zcom.h.

• Each individual module has a separate directory, except zcom.h, which is a combination of all frequently-used ones.

• Code should be concise and small, module names should be short.

• Use symbolic links to define inter-modular dependence, Use `_' to define the preceding module.

Files

File	Description
zcom.0.h:	template that creates zcom.h
zcom.h	generated from zcom.0.h, combined header, by assemble.py
assemble.py	the python script that assembles modules to a single header ./assemble.py -a
Makefile	Makefile for common tasks, such as usb', usball', etc
gen.mak	generic Makefile to be used for new modules
license.txt	GPL less license, version 2
zcompick.py	end-user tool to remove certain modules from zcom.h

Directories

Directory	Description
python	helper python scripts, such as add2d.py, rmdbg.py
programs	although the project is mainly a library, several useful programs are collected `programs' directory
cspacer.py	code beautifiers: cspacer.py, rstrip.py

Modules

Module	Description
util:	useful but unclassified routines
bits:	bit operations
blkmem:	block memory
ss:	smart string
endn:	handle endianness
bio:	macros for read/write binary files
osys:	operating system related
rng:	random number generator
rc:	real complex number
rv2:	real 2-vectors and 2x2 matrices
rv3:	real 3-vectors and 3x3 matrices
rvn:	real D-vectors and DxD matrices
eig:	eigenvalues and eigenvectors
cholesky:	Cholesky decomposition
lu:	LU decomposition
svd:	single value decomposition
savgol:	compute Savitzky-Golay coefficients
specfunc:	special functions
opt:	options
argopt:	command line arguments and options
cfg:	configuration file
log:	log file
av:	simple mean/deviation
hist:	simple histograms (1d/2d)
mds:	multidimensional scaling
pdb:	read/write pdb
md:	common molecular dynamics routines
hmc:	hybrid Monte Carlo/molecular dynamics
ising2:	two dimensional ising model
potts2:	two dimensional potts model
lj:	Lennard Jones system
abpro:	AB beads protein model
cago:	C-alpha Go model
glez:	common uses for GLUT

modules with a leading underscore are experimental, and not added to zcom.h

Notes:

• Try to apply cspacer.py/reindent.py under cspacer to check the source here from time to time

• zcom.h should not have a routine like zcom_finish() because in case of multiple inclusion, zcom_finish is defined in the first instance, it has no knowledge of modules included later.

TOOLS:

• Makefile common tasks make: call assemble.py to assemble zcom.h from modules make zcom.zip: make a package

• assemble.py -a assemble zcom.h from modules

• zcompick.py client tool to extract a few modules from zcom.h to a smaller version