Common routines

Overview

zcom.h is a C header file for common routines needed in simulations. These routines include

• util: convenience routines
• rng random numbers
• cfg configuration files
• argopt command-line arguments handling
• ss string manipulation
• bits bitwise operations
• blkmem blocked memory allocation
• osys operation-system-related routines
• rv2 real 2D vectors and matrices
• rv3 real 3D vectors and matrices
• rvn n-dimensional real vectors and matrices
• eig eigenvalues and eigenvectors
• lu LU decomposition
• svd single-value decomposition
• specfunc special functions
• savgol Savitzky-Golay filter
• hist histogram
• md molecular dynamics routines
• hmc hybrid MC routines
• pdb handling protein databank (.pdb) files
• ising Ising model
• potts Potts model
• lj Lennard-Jones liquid
• abpro AB beads protein model
• cago C_α Go protein model

The name stands for zipped common routines.

Usage

The quickest usage is the following. where we used the function fexists() to check if there is a file ex1.c. Download the code ex1.c.

  #include "zcom.h"

  int main(void) {
    return fexists("ex1.c");
  }

A recommended usage is demonstrated below, where we used the function sysrun() defined in the module osys. The program calls the system command ls and captures the output (for Windows, change ls to dir). The advantage of defining ZCOM_PICK before #include "zcom.h" is that we can select needed modules, and avoids possible name conflicts. Usually, there is no need to worry about the internal dependence among modules. Download the code ex2.c.

  #define ZCOM_PICK
  #define ZCOM_OSYS
  #include "zcom.h"

  int main(void) {
    char *out = sysrun("ls", NULL, 0);
    puts(out);
    return 0;
  }

Downloads

Program	Description	Language
zcom.h	A self-contained C header file for inclusion. A user only needs this.	C
zcom.zip	Individual modules in zcom.h (for developers), zcom.h is assembled by a python script. It needs Python 2.7 (probably works with 2.5 and 2.6 too). Linux environment is recommended since symbolic links are extensively used.	C, Python