[gmx-developers] Doxygen commenting
Matthew Chan
talcite at gmail.com
Sun Dec 28 10:11:06 CET 2008
Hi Everyone,
I have good news! I managed to have everything building in eclipse, so
my productivity should increase a bit now, which hopefully will
translate into patches for GROMACS.
I've also given a shot at commenting a file according to Doxygen syntax.
I've attached a patch for submission along with the doxygen config if
you'd like to take a look. Make sure to change the compile directories
for the doxygen config. It's for the include/random.h header.
The descriptions are a bit crude, I manually traced the execution of the
functions and tried to guess what each variable was used for. Also, I
had no idea what the L parameter was in calc_cm(). Also, I'm trying to
pick up the latex mathematical syntax, so if you have any formulaic
representation of functions,in random.h or anywhere else, I can add them
into the descriptions for functions like I did in make_seed().
Please don't hesitate to write back with any comments or suggestions on
improving the quality of documentation.
I'll give a few more of these a shot and see if I can get the hang of
it. I find the hardest part is understanding what each parameter and
return value is for.
Happy Holidays,
Matt
-------------- next part --------------
### Eclipse Workspace Patch 1.0
#P gmx
Index: include/random.h
===================================================================
RCS file: /home/gmx/cvs/gmx/include/random.h,v
retrieving revision 1.17
diff -u -r1.17 random.h
--- include/random.h 5 Aug 2008 14:41:51 -0000 1.17
+++ include/random.h 28 Dec 2008 08:38:57 -0000
@@ -34,6 +34,11 @@
* Gromacs Runs On Most of All Computer Systems
*/
+/**
+ * @file random.h
+ * A random number generator.
+ */
+
#ifndef _random_h
#define _random_h
@@ -43,24 +48,56 @@
#include <typedefs.h>
+/**
+ * Seeds the random number generator.
+ * generates seeds according to the formula \f$(time + pid) \bmod 1000000\f$.
+ * @return the seed.
+ */
extern int make_seed(void);
-/* Make a random seed: (time+getpid) % 1000000 */
+/**
+* Generates a random number.
+* Number generated is between 0 and 1.
+* @param *seed a pointer for the function to store the random number.
+* @return the seed stored in *seed.
+*/
extern real rando(int *seed);
-/* Generate a random number 0 <= r < 1. seed is the (address of) the
- * random seed variable.
- */
+/**
+* Generates a velocity according to maxwellian distribution.
+* @param tempi scaled initial generated temperature. Used to initialize low_mspeed.
+* @param seed a seed used to initialize the gmx random number generator in gmx_rng_init. Auto generated if seed is -1.
+* @param *mtop molecule topology. See gmx_mtop_t for more information.
+* @param v[] the velocities (natoms)
+*/
extern void maxwell_speed(real tempi,int seed,
gmx_mtop_t *mtop, rvec v[]);
-/* Generate velocites according to a maxwellian distribution */
+/**
+* Calculates the centre of mass position, velocity, acceleration and the moment of Inertia.
+* @param *log the file to log if DEBUG is defined.
+* @param natoms number of elements in mass[], x[] and v[].
+* @param mass[] mass of atoms corresponding to x[] and v[].
+* @param x[] co-ordinates of atoms corresponding to mass[] and v[].
+* @param v[] velocities of atoms corresponding to mass[] and x[].
+* @param xcm c.o.m. position.
+* @param vcm c.o.m. velocity.
+* @param acm rotational velocity around c.o.m.
+* @param L L does something.
+* @return the total mass.
+*/
extern real calc_cm(FILE *log,int natoms,real mass[],rvec x[],rvec v[],
rvec xcm,rvec vcm,rvec acm,matrix L);
-/* Calculate the c.o.m. position, velocity, acceleration and the
- * moment of Inertia. Returns the total mass.
- */
+/**
+* Stops the centre of mass motion.
+* Subtracts the velocity from v[] using calc_cm.
+* @param *log the file to log if DEBUG is defined.
+* @param natoms number of elements in mass[], x[] and v[].
+* @param mass[] mass of atoms corresponding to x[] and v[].
+* @param x[] co-ordinates of atoms corresponding to mass[] and v[].
+* @param v[] velocities of atoms corresponding to mass[] and x[].
+*/
extern void stop_cm(FILE *log,int natoms,real mass[],rvec x[],rvec v[]);
#endif /* _random_h */
-------------- next part --------------
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