Index: trunk/psLib/src/sys/psAbort.h
===================================================================
--- trunk/psLib/src/sys/psAbort.h	(revision 11154)
+++ trunk/psLib/src/sys/psAbort.h	(revision 11248)
@@ -1,3 +1,2 @@
-
 /** @file  psAbort.h
  *
@@ -8,11 +7,8 @@
  *  needing to abort from program execution.
  *
- *  @ingroup ErrorHandling
- *
  *  @author Eric Van Alst, MHPCC
  *
- *  @version $Revision: 1.12 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2006-08-26 04:34:28 $
- *
+ *  $Revision: 1.13 $ $Name: not supported by cvs2svn $
+ *  $Date: 2007-01-23 22:47:23 $
  *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
  */
@@ -21,9 +17,6 @@
 #define PS_ABORT_H
 
-// Doxygen grouping tags
-
-/** @addtogroup ErrorHandling
- *  @{
- */
+/// @addtogroup SysUtils System Utilities
+/// @{
 
 /** Reports an abort message to logging facility
@@ -51,5 +44,4 @@
 #endif // __GNUC__
 
-/** @} */ // Doxygen - End of SystemGroup Functions
-
+/// @}
 #endif // #ifndef PS_ABORT_H
Index: trunk/psLib/src/sys/psAssert.h
===================================================================
--- trunk/psLib/src/sys/psAssert.h	(revision 11154)
+++ trunk/psLib/src/sys/psAssert.h	(revision 11248)
@@ -1,4 +1,7 @@
 #ifndef PS_ASSERT_H
 #define PS_ASSERT_H
+
+/// @addtogroup SysUtils System Utilities
+/// @{
 
 #include <assert.h>
@@ -263,3 +266,4 @@
 
 
+/// @}
 #endif
Index: trunk/psLib/src/sys/psConfigure.h
===================================================================
--- trunk/psLib/src/sys/psConfigure.h	(revision 11154)
+++ trunk/psLib/src/sys/psConfigure.h	(revision 11248)
@@ -1,6 +1,5 @@
 /** @file  psConfigure.h
  *
- *  @brief Contains the declarations for initialization, memory finalization,
- *   and configuration.
+ *  @brief Functions to init and cleanup psLib
  *
  *  These functions initalize psLib data before the beginning of a run and
@@ -8,11 +7,10 @@
  *  also provided to return the current psLib version.
  *
- *  @ingroup Configure
  *
  *  @author Ross Harman, MHPCC
  *  @author Robert DeSonia, MHPCC
  *
- *  @version $Revision: 1.9 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2006-11-29 21:33:09 $
+ *  @version $Revision: 1.10 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2007-01-23 22:47:23 $
  *
  *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
@@ -22,7 +20,6 @@
 #define PS_CONFIGURE_H
 
-/** @addtogroup Configure
- *  @{
- */
+/// @addtogroup SysUtils System Utilities
+/// @{
 
 /** Get current psLib version
@@ -70,5 +67,4 @@
 void p_psMemoryCheck(void);
 
-/** @} */
-
+/// @}
 #endif // #ifndef PS_CONFIGURE_H
Index: trunk/psLib/src/sys/psError.h
===================================================================
--- trunk/psLib/src/sys/psError.h	(revision 11154)
+++ trunk/psLib/src/sys/psError.h	(revision 11248)
@@ -1,5 +1,5 @@
 /** @file  psError.h
  *
- *  @brief Contains the declarations for the error reporting functions
+ *  @brief error reporting functions
  *
  *  Error reporting functions shall be used to create log entries in the
@@ -8,10 +8,9 @@
  *  of error detected.
  *
- *  @ingroup ErrorHandling
- *
+ *  @author RHL, Princeton
  *  @author Eric Van Alst, MHPCC
  *
- *  @version $Revision: 1.31 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2006-09-12 21:39:47 $
+ *  @version $Revision: 1.32 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2007-01-23 22:47:23 $
  *
  *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
@@ -20,4 +19,7 @@
 #ifndef PS_ERROR_H
 #define PS_ERROR_H
+
+/// @addtogroup SysUtils System Utilities
+/// @{
 
 #include<stdio.h>
@@ -28,8 +30,4 @@
 
 #define _(string) string
-
-/** @addtogroup ErrorHandling
- *  @{
- */
 
 /** Error message object */
@@ -231,5 +229,4 @@
 );
 
-/* @} */// End of SysUtils Functions
-
+/// @}
 #endif
Index: trunk/psLib/src/sys/psErrorCodes.h.in
===================================================================
--- trunk/psLib/src/sys/psErrorCodes.h.in	(revision 11154)
+++ trunk/psLib/src/sys/psErrorCodes.h.in	(revision 11248)
@@ -3,10 +3,9 @@
  *  @brief Contains the error codes for the error classes
  *
- *  @ingroup ErrorHandling
- *
+ *  @author RHL, Princeton
  *  @author Robert DeSonia, MHPCC
  *
- *  @version $Revision: 1.3 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2006-07-25 00:30:31 $
+ *  @version $Revision: 1.4 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2007-01-23 22:47:23 $
  *
  *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
@@ -16,9 +15,8 @@
 #define PS_ERROR_CODES_H
 
+/// @addtogroup SysUtils System Utilities 
+/// @{
+
 #include "psType.h"
-
-/** @addtogroup ErrorHandling
- *  @{
- */
 
 /** enumeration of the static error code classes
@@ -84,4 +82,3 @@
 
 /// @}
-
 #endif // #ifndef PS_ERROR_CODES_H
Index: trunk/psLib/src/sys/psExit.h
===================================================================
--- trunk/psLib/src/sys/psExit.h	(revision 11154)
+++ trunk/psLib/src/sys/psExit.h	(revision 11248)
@@ -1,4 +1,7 @@
 #ifndef PS_EXIT_H
 #define PS_EXIT_H
+
+/// @addtogroup SysUtils System Utilities
+/// @{
 
 /// Exit status codes
@@ -15,3 +18,4 @@
 } psExit;
 
+/// @}
 #endif
Index: trunk/psLib/src/sys/psLine.h
===================================================================
--- trunk/psLib/src/sys/psLine.h	(revision 11154)
+++ trunk/psLib/src/sys/psLine.h	(revision 11248)
@@ -1,16 +1,14 @@
 /** @file  psLine.h
  *
- *
- *  @brief Contains the declarations of line utility functions
- *
- *  @ingroup SysUtils
+ *  @brief charater-string fixed-length line functions
  *
  *  The psLine functions allow manipulation of fixed-length lines.
  *
+ *  @author EAM, IFA
  *  @author Paul Price, IFA
  *  @author David Robbins, MHPCC
  *
- *  @version $Revision: 1.4 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2006-07-21 02:39:33 $
+ *  @version $Revision: 1.5 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2007-01-23 22:47:23 $
  *
  *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
@@ -20,9 +18,8 @@
 #define PS_LINE_H
 
+/// @addtogroup SysUtils System Utilities
+/// @{
+
 #include "psString.h"
-
-/** @addtogroup SysUtils
- *  @{
- */
 
 /** Structure to carry a dynamic string */
@@ -77,3 +74,4 @@
 );
 
+/// @}
 #endif /* PS_LINE_H */
Index: trunk/psLib/src/sys/psLogMsg.h
===================================================================
--- trunk/psLib/src/sys/psLogMsg.h	(revision 11154)
+++ trunk/psLib/src/sys/psLogMsg.h	(revision 11248)
@@ -1,28 +1,27 @@
 /** @file  psLogMsg.h
+ *
  *  @brief Procedures for logging messages.
- *  \ingroup LogTrace
  *
  *  This file will hold the prototypes for defining procedure which set
  *  message log levels, messahe log formats, message log destinations, and
  *  for generating the messages themselves.
- *  @ingroup LogTrace
  *
  *  @author Robert Lupton, Princeton University
  *  @author GLG, MHPCC
  *
- *  @version $Revision: 1.37 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2006-12-04 20:45:46 $
+ *  @version $Revision: 1.38 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2007-01-23 22:47:23 $
  *
  *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
  */
+
 #ifndef PS_LOG_MSG_H
 #define PS_LOG_MSG_H
+
+/// @addtogroup SysUtils System Utilities
+/// @{
+
 #include <stdarg.h>
-
 #include "psType.h"
-
-/** @addtogroup LogTrace
- *  @{
- */
 
 /** This procedure sets the destination for future log messages.
@@ -137,4 +136,3 @@
 
 /// @}
-
 #endif // #ifndef PS_LOG_MSG_H
Index: trunk/psLib/src/sys/psMemory.h
===================================================================
--- trunk/psLib/src/sys/psMemory.h	(revision 11154)
+++ trunk/psLib/src/sys/psMemory.h	(revision 11248)
@@ -1,19 +1,16 @@
-/** @file  psMemory.h
- *
- *  @brief Contains the definitions for the memory management system
- *
- *  This is the generic memory management system put inbetween the user's high level code and the OS-level
- *  memory allocation routines.  This system adds such features as callback routines for memory error events,
- *  tracing capabilities, and reference counting.
- *
- *  @author Robert DeSonia, MHPCC
- *  @author Robert Lupton, Princeton University
- *
- *  @ingroup MemoryManagement
- *
- *  @version $Revision: 1.61 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2006-10-13 21:13:48 $
- *
- *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
+/* @file  psMemory.h
+ *
+ * @brief Contains the definitions for the memory management system
+ *
+ * This is the generic memory management system put inbetween the user's high level code and the OS-level
+ * memory allocation routines.  This system adds such features as callback routines for memory error events,
+ * tracing capabilities, and reference counting.
+ *
+ * @author Robert Lupton, Princeton University
+ * @author Robert DeSonia, MHPCC
+ *
+ * $Revision: 1.62 $ $Name: not supported by cvs2svn $
+ * $Date: 2007-01-23 22:47:23 $
+ * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
  */
 
@@ -21,32 +18,12 @@
 #define PS_MEMORY_H
 
+/// @addtogroup SysUtils System Utilities
+/// @{
+
 #include <stdio.h>                     // needed for FILE
 #include <pthread.h>                   // we need a mutex to make this stuff thread safe.
-
 #include "psType.h"
 
-/** @addtogroup MemoryManagement
- *  @{
- */
-
 #define P_PS_MEMMAGIC (psPtr)0xdeadbeef   // Magic number in psMemBlock header
-
-/**
- *  @addtogroup memCallback Memory Callbacks
- *
- *  Routines dealing with the creating and setting of memory management callback functions.
- */
-
-/**
- *  @addtogroup memTracing Memory Tracing
- *
- *  Routines dealing with memory tracing and corruption checking.
- */
-
-/**
- *  @addtogroup memRefCount Reference Count
- *
- *  Routines dealing with the reference counting of allocated buffers.
- */
 
 /// typedef for memory identification numbers.  Guaranteed to be some variety of integer.
@@ -84,5 +61,4 @@
  *
  *  @see psMemAllocCallbackSet
- *  @ingroup memCallback
  */
 typedef psMemId(*psMemAllocCallback) (
@@ -93,5 +69,4 @@
  *
  *  @see psMemFreeCallbackSet
- *  @ingroup memCallback
  */
 typedef psMemId(*psMemFreeCallback) (
@@ -104,5 +79,4 @@
  *
  *  @see psMemProblemCallbackSet
- *  @ingroup memCallback
  */
 typedef void (*psMemProblemCallback) (
@@ -118,5 +92,4 @@
  *
  *  @see psMemExhaustedCallbackSet
- *  @ingroup memCallback
  */
 typedef psPtr (*psMemExhaustedCallback) (
@@ -303,5 +276,4 @@
  *              blocks above id0 that have not been freed.
  *  @see psAlloc, psFree, psgetMemId, psMemProblemCallbackSet
- *  @ingroup memTracing
  */
 int psMemCheckLeaks(
@@ -317,5 +289,4 @@
  *  @return int
  *
- *  @ingroup memTracing
  */
 int psMemCheckCorruption(
@@ -327,5 +298,4 @@
  *  @return psReferenceCount
  *
- *  @ingroup memRefCount
  */
 psReferenceCount psMemGetRefCounter(
@@ -337,5 +307,4 @@
  *  @return psPtr
  *
- *  @ingroup memRefCount
  */
 #ifdef DOXYGEN
@@ -358,5 +327,4 @@
 /** Decrement reference counter and return the pointer
  *
- *  @ingroup memRefCount
  *
  *  @return psPtr    the pointer deremented in refCount, or NULL if pointer is
@@ -381,6 +349,4 @@
 
 /** Set reference counter and return the pointer
- *
- *  @ingroup memRefCount
  *
  *  @return psPtr    the pointer with refCount set, or NULL if pointer is
@@ -411,6 +377,4 @@
  *  stack. If any of these checks discover that the memory stack is corrupted,
  *  the psMemProblemCallback is called.
- 
- *  @ingroup memCallback
  *
  *  @return psMemProblemCallback       old psMemProblemCallback function
@@ -431,6 +395,4 @@
  *  request and try again, limiting the size of the operating buffer.
  *
- *  @ingroup memCallback
- *
  *  @return psMemExhaustedCallback     old psMemExhaustedCallback function
  */
@@ -446,6 +408,4 @@
  *  just before memory is returned to the calling function.
  *
- *  @ingroup memCallback
- *
  *  @return psMemAllocCallback      old psMemAllocCallback function
  */
@@ -461,6 +421,4 @@
  *  before the memory block is freed.
  *
- *  @ingroup memCallback
- *
  *  @return psMemFreeCallback          old psMemFreeCallback function
  */
@@ -471,6 +429,4 @@
 /** get next memory ID
  *
- *  @ingroup memCallback
- *
  *  @return psMemId                 the next memory ID to be used
  */
@@ -478,6 +434,4 @@
 
 /** get the last memory ID used
- *
- *  @ingroup memCallback
  *
  *  @return psMemId                 the last memory ID used
@@ -492,6 +446,4 @@
  *  just before memory is returned to the calling function.
  *
- *  @ingroup memCallback
- *
  *  @return psMemId
  *
@@ -509,6 +461,4 @@
  *  before the memory block is freed.
  *
- *  @ingroup memCallback
- *
  *  @return psMemId                 the old p_psMemFreeID
  *
@@ -530,5 +480,5 @@
                   size_t *freelist); ///< memory that's waiting to be recycled
 
-//@} End of Memory Management Functions
+/// @} end of SysUtils
 
 #ifndef DOXYGEN
@@ -549,4 +499,3 @@
 
 #endif // #ifndef DOXYGEN
-
 #endif // #ifndef PS_MEMORY_H
Index: trunk/psLib/src/sys/psSlurp.h
===================================================================
--- trunk/psLib/src/sys/psSlurp.h	(revision 11154)
+++ trunk/psLib/src/sys/psSlurp.h	(revision 11248)
@@ -1,4 +1,15 @@
+/* @file  psSlurp.h
+ * @brief read complete files into strings
+ *
+ * @author JH
+ * @version $Revision: 1.5 $ $Name: not supported by cvs2svn $
+ * @date $Date: 2007-01-23 22:47:23 $
+ */
+
 #ifndef PS_SLURP_H
 #define PS_SLURP_H
+
+/// @addtogroup FileIO Input/Output
+/// @{
 
 // Read ("slurp") a file (specified by file descriptor)
@@ -12,4 +23,4 @@
                     );
 
-
+/// @}
 #endif
Index: trunk/psLib/src/sys/psString.h
===================================================================
--- trunk/psLib/src/sys/psString.h	(revision 11154)
+++ trunk/psLib/src/sys/psString.h	(revision 11248)
@@ -1,25 +1,24 @@
-/** @file  psString.h
- *
- * -*- mode: C; c-basic-indent: 4; tab-width: 8; indent-tabs-mode: nil -*-
- * vim: set cindent ts=8 sw=4 expandtab:
- *
- *  @brief Contains the declarations of string utility functions
- *
- *  @ingroup SysUtils
- *
- *  String utility functions defined shall provide basic string copying
- *  capabilities.
- *
- *  @author Eric Van Alst, MHPCC
- *  @author David Robbins, MHPCC
- *
- *  @version $Revision: 1.34 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2007-01-06 04:13:51 $
- *
- *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
+/* @file  psString.h
+ *
+ * @brief string utility functions
+ *
+ * String utility functions defined shall provide basic string copying
+ * capabilities.
+ *
+ * @author EAM, IfA
+ * @author Eric Van Alst, MHPCC
+ * @author David Robbins, MHPCC
+ *
+ * @version $Revision: 1.35 $ $Name: not supported by cvs2svn $
+ * @date $Date: 2007-01-23 22:47:23 $
+ *
+ * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
  */
 
 #ifndef PS_STRING_H
 #define PS_STRING_H
+
+/// @addtogroup SysUtils System Utilities
+/// @{
 
 #include <sys/types.h>
@@ -35,10 +34,4 @@
 const char *p_psFileLine(const char *file, int line);
 #define PS_FILE_LINE p_psFileLine(__FILE__,__LINE__)
-
-// Doxygen group tags
-
-/** @addtogroup SysUtils
- *  @{
- */
 
 /** Allocates a new psString.
@@ -230,5 +223,4 @@
 #endif // ifndef DOXYGEN
 
-/** @} */// Doxygen - End of SystemGroup Functions
-
+/// @}
 #endif // #ifndef PS_STRING_H
Index: trunk/psLib/src/sys/psTrace.h
===================================================================
--- trunk/psLib/src/sys/psTrace.h	(revision 11154)
+++ trunk/psLib/src/sys/psTrace.h	(revision 11248)
@@ -1,5 +1,5 @@
 /** @file psTrace.h
- *  \brief basic run-time trace facilities
- *  \ingroup LogTrace
+ *
+ *  @brief basic run-time trace facilities
  *
  *  This file will hold the prototypes for defining procedures to insert
@@ -9,11 +9,16 @@
  *  @author GLG, MHPCC
  *
- *  @version $Revision: 1.52 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2006-10-13 22:29:23 $
+ *  @version $Revision: 1.53 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2007-01-23 22:47:23 $
  *
  *  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
  */
-#if !defined(PS_TRACE_H)
+
+#ifndef PS_TRACE_H
 #define PS_TRACE_H 1
+
+/// @addtogroup SysUtils System Utilities
+/// @{
+
 #include <stdarg.h>
 
@@ -21,8 +26,4 @@
 #define PS_DEFAULT_TRACE_LEVEL -1
 #define PS_THE_OTHER_DEFAULT_TRACE_LEVEL 0
-
-/** \addtogroup LogTrace
- *  \{
- */
 
 enum {
@@ -171,8 +172,5 @@
 int psTraceGetDestination(void);
 
-/* \} */// End of SystemGroup Functions
-
+/// @}
 #endif /* PS_NO_TRACE */
-
 #endif /* PS_TRACE_H */
-
Index: trunk/psLib/src/sys/psType.h
===================================================================
--- trunk/psLib/src/sys/psType.h	(revision 11154)
+++ trunk/psLib/src/sys/psType.h	(revision 11248)
@@ -1,21 +1,22 @@
-/** @file  psType.h
-*
-*  @brief Contains support for basic types
-*
-*  This file defines common datatypes used throughout psLib.
-*
-*  @ingroup DataContainer
-*
-*  @author Robert DeSonia, MHPCC
-*  @author Ross Harman, MHPCC
-*
-*  @version $Revision: 1.52 $ $Name: not supported by cvs2svn $
-*  @date $Date: 2006-10-14 00:02:31 $
-*
-*  Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
-*/
+/* @file  psType.h
+ *
+ * @brief Contains support for basic types
+ *
+ * This file defines common datatypes used throughout psLib.
+ *
+ * @author Robert DeSonia, MHPCC
+ * @author Ross Harman, MHPCC
+ *
+ * @version $Revision: 1.53 $ $Name: not supported by cvs2svn $
+ * @date $Date: 2007-01-23 22:47:23 $
+ *
+ * Copyright 2004-2005 Maui High Performance Computing Center, University of Hawaii
+ */
 
 #ifndef PS_TYPE_H
 #define PS_TYPE_H
+
+/// @addtogroup DataContainer Data Containers
+/// @{
 
 #include <complex.h>
@@ -23,7 +24,4 @@
 #include <float.h>
 #include <stdbool.h>
-
-/// @addtogroup DataContainer
-/// @{
 
 /******************************************************************************/
@@ -301,4 +299,3 @@
 
 /// @}
-
 #endif // #ifndef PS_TYPE_H