Updated some documentation.

espressomd · Feb 3, 2004 · 50eea71 · 50eea71
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diff --git a/binary_file.h b/binary_file.h
@@ -11,6 +11,9 @@
 /** \file binary_file.h
     This file defines a binary file format for the particle data.
 
+The functions in this file are no longer supported by the Espresso
+team. Use them at your own risk!
+
     <b>Responsible:</b>
     <a href="mailto:arnolda@mpip-mainz.mpg.de">Axel</a>
 

diff --git a/config.h b/config.h
@@ -6,12 +6,32 @@
 // if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
 // write to Max-Planck-Institute for Polymer Research, Theory Group, PO Box 3148, 55021 Mainz, Germany.
 // Copyright (c) 2002-2003; all rights reserved unless otherwise stated.
+
 /** \file config.h 
+ *
+ *  This file contains all Precompiler Flags deciding which features
+ *  of Espresso to turn on/off. It is recommended to turn everything
+ *  off which you do not need in order to optimize the performance of
+ *  Espresso for your problem. 
+ *
+ *  There are also quite a number of features which are turned off by
+ *  default since they are used only rarely.
+ *
+ *  You can get information on the compilation status of the code you
+ *  are working with by using the tcl command \ref tcl_code_info
+ *  "code_info" within your tcl_script. It is highly recommended to
+ *  store this information with your simulation data in order to
+ *  maintain the reproducibility of your results.
+ *
+ *  If you add a new compile flag you also have to add the
+ *  corresponding lines in the function \ref compilation_callback.
  *
  *  <b>Responsible:</b>
  *  <a href="mailto:arnolda@mpip-mainz.mpg.de">Axel</a>
 */
 
+
+
 /** if defined, the code will be slower, but with the \ref #periodic
     array you can choose which coordinates are bound to p.b.c and
     which are not. If not defined, all coordinates are bound to

diff --git a/constraint.h b/constraint.h
@@ -18,7 +18,7 @@
  *  see also \ref interaction_data.h
  *
  *  <b>Responsible:</b>
- *  <a href="mailto:limbach@mpip-mainz.mpg.de">Hanjo</a>
+ *  <a href="mailto:sayar@mpip-mainz.mpg.de">Mehmet</a>
  */
 
 #ifdef CONSTRAINTS

diff --git a/lj.h b/lj.h
@@ -18,6 +18,8 @@
  *  <a href="mailto:limbach@mpip-mainz.mpg.de">Hanjo</a>
 */
 
+/** Calculate lennard Jones force between particle p1 and p2 and add
+    it to their force. */
 MDINLINE void add_lj_pair_force(Particle *p1, Particle *p2, IA_parameters *ia_params,
 				double d[3], double dist)
 {
@@ -71,6 +73,7 @@ MDINLINE void add_lj_pair_force(Particle *p1, Particle *p2, IA_parameters *ia_pa
   }
 }
 
+/** calculate Lennard jones energy between particle p1 and p2. */
 MDINLINE double lj_pair_energy(Particle *p1, Particle *p2, IA_parameters *ia_params,
 				double d[3], double dist)
 {

diff --git a/polymer.h b/polymer.h
@@ -9,9 +9,11 @@
 #ifndef POLYMER_H
 #define POLYMER_H
 /** \file polymer.h
-    This file contains everything needed to create a start-up configuration
-    of (partially charged) polymer chains with counterions and salt molecules,
-    assigning velocities to the particles and crosslinking the polymers if necessary.
+
+    This file contains everything needed to create a start-up
+    configuration of (partially charged) polymer chains with
+    counterions and salt molecules, assigning velocities to the
+    particles and crosslinking the polymers if necessary.
  
     For more information on polymer, see \ref polymer.c "polymer.c"
   
@@ -20,12 +22,8 @@
 */
 
 #include <tcl.h>
-
 #include "particle_data.h"
 
-
-
-
 /************************************************************* 
  * Functions                                                 *
  * ---------                                                 *

diff --git a/pressure.h b/pressure.h
@@ -8,6 +8,9 @@
 // Copyright (c) 2002-2003; all rights reserved unless otherwise stated.
 #ifndef PRESSURE_H
 #define PRESSURE_H
+
+
+
 #include "config.h"
 #include "statistics.h"
 #include "thermostat.h"

diff --git a/random.h b/random.h
@@ -9,7 +9,10 @@
 #ifndef RANDOM_H
 #define RANDOM_H
 
-/** \file random.h a random generator
+/** \file random.h 
+
+    A random generator
+
     <b>Responsible:</b>
     <a href="mailto:muehlbac@mpip-mainz.mpg.de">Frank</a>
 */

diff --git a/statistics.h b/statistics.h
@@ -9,7 +9,7 @@
 #ifndef STATISTICS_H
 #define STATISTICS_H
 /** \file statistics.h
-    This file contains the code for simply statistics on the data.
+    This file contains the code for statistics on the data.
 
     <b>Responsible:</b>
     <a href="mailto:mann@mpip-mainz.mpg.de">BAM</a>

diff --git a/statistics_chain.h b/statistics_chain.h
@@ -8,6 +8,14 @@
 // Copyright (c) 2002-2003; all rights reserved unless otherwise stated.
 #ifndef STATISTICS_CHAIN_H
 #define STATISTICS_CHAIN_H
+/** \file statistics_chain.h 
+
+    This file contains the code for statistics on the data using the
+    molecule information set with analyse set chains.
+
+    <b>Responsible:</b>
+    <a href="mailto:mann@mpip-mainz.mpg.de">BAM</a>
+*/
 
 /** \name Exported Functions */
 /************************************************************/

diff --git a/thermostat.h b/thermostat.h
@@ -8,15 +8,15 @@
 // Copyright (c) 2002-2003; all rights reserved unless otherwise stated.
 #ifndef THERMOSTAT_H
 #define THERMOSTAT_H
-/** \file thermostat.h
-    Contains all thermostats. 
+/** \file thermostat.h 
+
+    Contains all thermostats. At the moment this is only a langevin
+    thermostat for translational (\ref friction_thermo) and rotational
+    (\ref friction_thermo_rotation) degrees of freedom.
 
     <b>Responsible:</b>
     <a href="mailto:muehlbac@mpip-mainz.mpg.de">Frank</a>
 
-
-    Currently there is only the
-    \ref friction_thermo.
 */
 #include <tcl.h>
 #include "particle_data.h"