diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
index 3421c45d6..fe5ab4adc 100644
--- a/docs/Doxyfile.in
+++ b/docs/Doxyfile.in
@@ -130,7 +130,7 @@ INLINE_INHERITED_MEMB  = YES
 # shortest path that makes the file name unique will be used
 # The default value is: YES.
 
-FULL_PATH_NAMES        = NO
+FULL_PATH_NAMES        = YES
 
 # The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
 # Stripping is only done if one of the specified strings matches the left-hand
diff --git a/sorc/fre-nctools.fd/shared_lib/affinity.c b/sorc/fre-nctools.fd/shared_lib/affinity.c
index ed2360b0d..4f8eb32d7 100644
--- a/sorc/fre-nctools.fd/shared_lib/affinity.c
+++ b/sorc/fre-nctools.fd/shared_lib/affinity.c
@@ -1,4 +1,6 @@
-/** @file */
+/** @file 
+    @brief Set or get CPU affinity.
+*/
 #define _GNU_SOURCE
 
 #include <stdio.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/constant.h b/sorc/fre-nctools.fd/shared_lib/constant.h
index 10c98f6d9..3a3bf74d7 100644
--- a/sorc/fre-nctools.fd/shared_lib/constant.h
+++ b/sorc/fre-nctools.fd/shared_lib/constant.h
@@ -1,3 +1,5 @@
-/** @file */
+/** @file 
+    @brief Set some global constants.
+*/
 #define RADIUS        (6371000.)
 #define STRING        255
diff --git a/sorc/fre-nctools.fd/shared_lib/create_xgrid.c b/sorc/fre-nctools.fd/shared_lib/create_xgrid.c
index 0b850ba40..858c5b5c4 100644
--- a/sorc/fre-nctools.fd/shared_lib/create_xgrid.c
+++ b/sorc/fre-nctools.fd/shared_lib/create_xgrid.c
@@ -1,4 +1,6 @@
-/** @file */
+/** @file
+    @brief Utility routines to create and process exchange grids.
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <math.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/create_xgrid.h b/sorc/fre-nctools.fd/shared_lib/create_xgrid.h
index 585100474..5264eb0c4 100644
--- a/sorc/fre-nctools.fd/shared_lib/create_xgrid.h
+++ b/sorc/fre-nctools.fd/shared_lib/create_xgrid.h
@@ -1,4 +1,6 @@
-/** @file */
+/** @file
+    @brief Function declarations for create_xgrid.c.
+*/
 #ifndef CREATE_XGRID_H_
 #define CREATE_XGRID_H_
 #ifndef MAXXGRID
diff --git a/sorc/fre-nctools.fd/shared_lib/gradient.F90 b/sorc/fre-nctools.fd/shared_lib/gradient.F90
index d41af3035..6fc93f390 100644
--- a/sorc/fre-nctools.fd/shared_lib/gradient.F90
+++ b/sorc/fre-nctools.fd/shared_lib/gradient.F90
@@ -1,3 +1,8 @@
+!> @file
+!!
+!! @brief Utility routines to calculate gradient.
+!!
+!! @author Zhi.Liang@noaa.gov
 module gradient_mod
 ! <CONTACT EMAIL="Zhi.Liang@noaa.gov">
 !   Zhi Liang
diff --git a/sorc/fre-nctools.fd/shared_lib/gradient_c2l.c b/sorc/fre-nctools.fd/shared_lib/gradient_c2l.c
index 95544a67b..31f683edd 100644
--- a/sorc/fre-nctools.fd/shared_lib/gradient_c2l.c
+++ b/sorc/fre-nctools.fd/shared_lib/gradient_c2l.c
@@ -1,4 +1,6 @@
-/** @file */
+/** @file
+    @brief Compute gradient terms.
+*/
 #include <math.h>
 #include <stdlib.h>
 #include "constant.h"
diff --git a/sorc/fre-nctools.fd/shared_lib/gradient_c2l.h b/sorc/fre-nctools.fd/shared_lib/gradient_c2l.h
index 93264c01d..6a9132602 100644
--- a/sorc/fre-nctools.fd/shared_lib/gradient_c2l.h
+++ b/sorc/fre-nctools.fd/shared_lib/gradient_c2l.h
@@ -1,4 +1,6 @@
-/** @file */
+/** @file 
+    @brief Function declarations for gradient_c2l.c
+*/
 #ifndef GRADIENT_H_
 #define GRADIENT_H_
 void grad_c2l(const int *nlon, const int *nlat, const double *pin, const double *dx, const double *dy, const double *area,
diff --git a/sorc/fre-nctools.fd/shared_lib/grid.F90 b/sorc/fre-nctools.fd/shared_lib/grid.F90
index 262efd14a..9bf45deba 100644
--- a/sorc/fre-nctools.fd/shared_lib/grid.F90
+++ b/sorc/fre-nctools.fd/shared_lib/grid.F90
@@ -1,3 +1,6 @@
+!> @file
+!! @brief Utility routines to compute grid parameters such as size and area.
+!!
 module grid_mod
 
 use mpp_mod, only : mpp_root_pe
diff --git a/sorc/fre-nctools.fd/shared_lib/interp.c b/sorc/fre-nctools.fd/shared_lib/interp.c
index 0bcd190e0..1e4381cb7 100644
--- a/sorc/fre-nctools.fd/shared_lib/interp.c
+++ b/sorc/fre-nctools.fd/shared_lib/interp.c
@@ -1,8 +1,5 @@
-/** @file */
-/*
-  Copyright 2011 NOAA Geophysical Fluid Dynamics Lab, Princeton, NJ
-  This program is distributed under the terms of the GNU General Public
-  License. See the file COPYING contained in this directory
+/** @file 
+    @brief Interpolation utilities.
 */
 #include <stdio.h>
 #include <stdlib.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/interp.h b/sorc/fre-nctools.fd/shared_lib/interp.h
index 139928291..8abb2639f 100644
--- a/sorc/fre-nctools.fd/shared_lib/interp.h
+++ b/sorc/fre-nctools.fd/shared_lib/interp.h
@@ -1,16 +1,9 @@
-/** @file */
-/*
-  Copyright 2011 NOAA Geophysical Fluid Dynamics Lab, Princeton, NJ
-  This program is distributed under the terms of the GNU General Public
-  License. See the file COPYING contained in this directory
+/** @file
+    @brief Function declarations for interp.c
+    @author Zhi.Liang@noaa.gov
 */
 #ifndef INTERP_H_
 #define INTERP_H_
-/*********************************************************************
-                     interp.h
-   This header files contains defition of some interpolation routine  (1-D or 2-D).
-   contact: Zhi.Liang@noaa.gov
-*********************************************************************/
 void cubic_spline_sp(int size1, int size2, const double *grid1, const double *grid2, const double *data1,
                   double *data2 );
 void cubic_spline(int size1, int size2, const double *grid1, const double *grid2, const double *data1,
diff --git a/sorc/fre-nctools.fd/shared_lib/mosaic.F90 b/sorc/fre-nctools.fd/shared_lib/mosaic.F90
index 794c8219a..820c5a4b6 100644
--- a/sorc/fre-nctools.fd/shared_lib/mosaic.F90
+++ b/sorc/fre-nctools.fd/shared_lib/mosaic.F90
@@ -1,3 +1,7 @@
+!> @file
+!! @brief Read information from the mosaic file.
+!! @author Zhi.Liang@noaa.gov
+!!
 module mosaic_mod
 
 ! <CONTACT EMAIL="Zhi.Liang@noaa.gov">
diff --git a/sorc/fre-nctools.fd/shared_lib/mosaic_util.c b/sorc/fre-nctools.fd/shared_lib/mosaic_util.c
index 61a5d85db..99868ba71 100644
--- a/sorc/fre-nctools.fd/shared_lib/mosaic_util.c
+++ b/sorc/fre-nctools.fd/shared_lib/mosaic_util.c
@@ -1,4 +1,6 @@
-/** @file */
+/** @file 
+    @brief Compute various grid statistics. 
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <math.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/mosaic_util.h b/sorc/fre-nctools.fd/shared_lib/mosaic_util.h
index 7ea07bda9..052243aa7 100644
--- a/sorc/fre-nctools.fd/shared_lib/mosaic_util.h
+++ b/sorc/fre-nctools.fd/shared_lib/mosaic_util.h
@@ -1,10 +1,7 @@
-/** @file */
-/***********************************************************************
-                      mosaic_util.h
-    This header file provide some utilities routine that will be used in many tools.
-    
-    contact: Zhi.Liang@noaa.gov
-***********************************************************************/
+/** @file
+    @brief Function declarations for mosaic_util.c.
+    @author Zhi.Liang@noaa.gov
+*/
 #ifndef MOSAIC_UTIL_H_
 #define MOSAIC_UTIL_H_
 
diff --git a/sorc/fre-nctools.fd/shared_lib/mpp.c b/sorc/fre-nctools.fd/shared_lib/mpp.c
index 49fdf614a..87e143850 100644
--- a/sorc/fre-nctools.fd/shared_lib/mpp.c
+++ b/sorc/fre-nctools.fd/shared_lib/mpp.c
@@ -1,4 +1,6 @@
-/** @file */
+/** @file
+    @brief MPI utility routines 
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/mpp.h b/sorc/fre-nctools.fd/shared_lib/mpp.h
index 01df53e0c..fae05d05f 100644
--- a/sorc/fre-nctools.fd/shared_lib/mpp.h
+++ b/sorc/fre-nctools.fd/shared_lib/mpp.h
@@ -1,11 +1,10 @@
-/** @file */
+/** @file
 
-/*********************************************************************
-                    mpp.h
-  This header contains subroutine for parallel programming.
-  only MPI parallel is implemented. 
-  Contact: Zhi.Liang@noaa.gov
- ********************************************************************/
+  @brief Function declarations for parallel programming. Only
+  MPI parallel is implemented. 
+
+  @author Zhi.Liang@noaa.gov
+*/
 #ifndef MPP_H_
 #define MPP_H_
 
diff --git a/sorc/fre-nctools.fd/shared_lib/mpp_domain.c b/sorc/fre-nctools.fd/shared_lib/mpp_domain.c
index 482701754..722951907 100644
--- a/sorc/fre-nctools.fd/shared_lib/mpp_domain.c
+++ b/sorc/fre-nctools.fd/shared_lib/mpp_domain.c
@@ -1,10 +1,8 @@
-/** @file */
-/*
-      **** MppDomain.cpp ****
-      MppDomain package
-      NOTE: only mpi is implemented here. if needed, shmem version
-      will be added on in the future.
-      Contact: Zhi.Liang@noaa.gov
+/** @file
+    @brief MppDomain package
+    @note Only mpi is implemented here. If needed, shmem version
+    will be added on in the future.
+    @author Zhi.Liang@noaa.gov
 */
 #include <stdlib.h>
 #include <math.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/mpp_domain.h b/sorc/fre-nctools.fd/shared_lib/mpp_domain.h
index d6d18b202..3b95661aa 100644
--- a/sorc/fre-nctools.fd/shared_lib/mpp_domain.h
+++ b/sorc/fre-nctools.fd/shared_lib/mpp_domain.h
@@ -1,14 +1,15 @@
-/** @file */
-/****************************************************************
-                        mpp_domain.h 
-   This headers define interface to define domain layout, 
-   define domain decomposition and global field to root pe, 
-   some utilities routine to return domain decomposition.
-   Currently it only used in tools and assume only one domain is created. 
-   If more domains are needed, we may define a struct to hold domain informaiton.
-   contact: Zhi.Liang@noaa.gov
+/** @file
+  
+    @brief Headers that define interface, domain layout, 
+    domain decomposition and global field to root pe.
+    Some routines return domain decomposition.
 
-****************************************************************/
+    @note Currently it only used in tools and assumes only one domain is created. 
+    If more domains are needed, we may define a struct to hold domain informaiton.
+
+    @author Zhi.Liang@noaa.gov
+
+*/
 #ifndef MPP_DOMAIN_H_
 #define MPP_DOMAIN_H_
 #define max(a,b) (a>b ? a:b)
diff --git a/sorc/fre-nctools.fd/shared_lib/mpp_io.c b/sorc/fre-nctools.fd/shared_lib/mpp_io.c
index 08067caab..a226343d7 100644
--- a/sorc/fre-nctools.fd/shared_lib/mpp_io.c
+++ b/sorc/fre-nctools.fd/shared_lib/mpp_io.c
@@ -1,4 +1,7 @@
-/** @file */
+/** @file
+    @brief Utility routines to read/write netcdf.
+    @author Zhi.Liang@noaa.gov
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/mpp_io.h b/sorc/fre-nctools.fd/shared_lib/mpp_io.h
index 9905588c7..ae08654b9 100644
--- a/sorc/fre-nctools.fd/shared_lib/mpp_io.h
+++ b/sorc/fre-nctools.fd/shared_lib/mpp_io.h
@@ -1,12 +1,7 @@
-/** @file */
-/****************************************************************
-                    mpp_io.h
-   This headers defines interface to read and write netcdf file. All the data
-will be written out from root pe. 
-
-   contact: Zhi.Liang@noaa.gov
-
-****************************************************************/
+/** @file 
+    @brief Define constants and function declarations for mpp_io.c
+    @author Zhi.Liang@noaa.gov
+*/
 #ifndef MPP_IO_H_
 #define MPP_IO_H_
 #include <netcdf.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/read_mosaic.c b/sorc/fre-nctools.fd/shared_lib/read_mosaic.c
index 10db07643..582110af1 100644
--- a/sorc/fre-nctools.fd/shared_lib/read_mosaic.c
+++ b/sorc/fre-nctools.fd/shared_lib/read_mosaic.c
@@ -1,4 +1,6 @@
-/** @file */
+/** @file 
+    @brief Utilities to read the mosaic file.
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <math.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/read_mosaic.h b/sorc/fre-nctools.fd/shared_lib/read_mosaic.h
index 1f6934e9c..11abbcbba 100644
--- a/sorc/fre-nctools.fd/shared_lib/read_mosaic.h
+++ b/sorc/fre-nctools.fd/shared_lib/read_mosaic.h
@@ -1,4 +1,6 @@
-/** @file */
+/** @file
+    @brief Function declarations for read_mosaic.c 
+*/
 #ifndef READ_MOSAIC_H_
 #define READ_MOSAIC_H_
 
diff --git a/sorc/fre-nctools.fd/shared_lib/tool_util.c b/sorc/fre-nctools.fd/shared_lib/tool_util.c
index c68469717..dbe120cd5 100644
--- a/sorc/fre-nctools.fd/shared_lib/tool_util.c
+++ b/sorc/fre-nctools.fd/shared_lib/tool_util.c
@@ -1,4 +1,7 @@
-/** @file */
+/** @file
+    @brief Utility routines used by many tools.
+    @author Zhi.Liang@noaa.gov
+*/
 #include <stdlib.h> 
 #include <stdio.h>
 #include <string.h>
diff --git a/sorc/fre-nctools.fd/shared_lib/tool_util.h b/sorc/fre-nctools.fd/shared_lib/tool_util.h
index 288e29501..873bc5ae7 100644
--- a/sorc/fre-nctools.fd/shared_lib/tool_util.h
+++ b/sorc/fre-nctools.fd/shared_lib/tool_util.h
@@ -1,6 +1,5 @@
 /** @file 
-    This header file provide some utilities routine that will be used in many tools.
-    
+    @brief Function declarations for tool_util.c
     @author Zhi.Liang@noaa.gov
 */
 #ifndef TOOL_UTIL_H_
diff --git a/sorc/fre-nctools.fd/tools/fregrid/bilinear_interp.c b/sorc/fre-nctools.fd/tools/fregrid/bilinear_interp.c
index 4767dc1f1..745bb03ab 100644
--- a/sorc/fre-nctools.fd/tools/fregrid/bilinear_interp.c
+++ b/sorc/fre-nctools.fd/tools/fregrid/bilinear_interp.c
@@ -1,3 +1,6 @@
+/** @file
+    @brief Routines to perform bilinear interpolation.
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <math.h>
diff --git a/sorc/fre-nctools.fd/tools/fregrid/bilinear_interp.h b/sorc/fre-nctools.fd/tools/fregrid/bilinear_interp.h
index faead206a..8c4cc3b8e 100644
--- a/sorc/fre-nctools.fd/tools/fregrid/bilinear_interp.h
+++ b/sorc/fre-nctools.fd/tools/fregrid/bilinear_interp.h
@@ -1,3 +1,6 @@
+/** @file 
+    @brief Function declarations for bilinear interpolation module.
+*/
 #ifndef BILINEAR_INTERP_H_
 #define BILINEAR_INTERP_H_
 void setup_bilinear_interp(int ntiles_in, const Grid_config *grid_in, int ntiles_out, const Grid_config *grid_out, 
diff --git a/sorc/fre-nctools.fd/tools/fregrid/conserve_interp.c b/sorc/fre-nctools.fd/tools/fregrid/conserve_interp.c
index 78c766b16..3ce31af13 100644
--- a/sorc/fre-nctools.fd/tools/fregrid/conserve_interp.c
+++ b/sorc/fre-nctools.fd/tools/fregrid/conserve_interp.c
@@ -1,3 +1,6 @@
+/** @file 
+    @brief Routines to perform conservative interpolation.
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
diff --git a/sorc/fre-nctools.fd/tools/fregrid/conserve_interp.h b/sorc/fre-nctools.fd/tools/fregrid/conserve_interp.h
index 18d7bbd8e..3489c6da9 100644
--- a/sorc/fre-nctools.fd/tools/fregrid/conserve_interp.h
+++ b/sorc/fre-nctools.fd/tools/fregrid/conserve_interp.h
@@ -1,3 +1,6 @@
+/** @file 
+    @brief Function declarations for conservative interpolation module.
+*/
 #ifndef CONSERVE_INTERP_H_
 #define CONSERVE_INTERP_H_
 #include "globals.h"
diff --git a/sorc/fre-nctools.fd/tools/fregrid/fregrid.c b/sorc/fre-nctools.fd/tools/fregrid/fregrid.c
index 151813f6b..80f1df331 100644
--- a/sorc/fre-nctools.fd/tools/fregrid/fregrid.c
+++ b/sorc/fre-nctools.fd/tools/fregrid/fregrid.c
@@ -1,24 +1,10 @@
-/*
-  This program remaps (scalar or vector) data from the input grid
+/** @file
+  
+  @brief This program remaps (scalar or vector) data from the input grid
   to the output grid
 
- AUTHOR: Zhi Liang (Zhi.Liang@noaa.gov)
+  @author Zhi Liang (Zhi.Liang@noaa.gov)
           NOAA Geophysical Fluid Dynamics Lab, Princeton, NJ
- 
-  This program is free software; you can redistribute it and/or modify
-  it under the terms of the GNU General Public License as published by
-  the Free Software Foundation; either version 2 of the License, or
-  (at your option) any later version.
- 
-  This program is distributed in the hope that it will be useful,
-  but WITHOUT ANY WARRANTY; without even the implied warranty of
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  GNU General Public License for more details.
- 
-  For the full text of the GNU General Public License,
-  write to: Free Software Foundation, Inc.,
-            675 Mass Ave, Cambridge, MA 02139, USA.  
------------------------------------------------------------------------
 */
 #include <stdlib.h>
 #include <stdio.h>
diff --git a/sorc/fre-nctools.fd/tools/fregrid/fregrid_util.c b/sorc/fre-nctools.fd/tools/fregrid/fregrid_util.c
index 199529c55..13434216a 100644
--- a/sorc/fre-nctools.fd/tools/fregrid/fregrid_util.c
+++ b/sorc/fre-nctools.fd/tools/fregrid/fregrid_util.c
@@ -1,3 +1,6 @@
+/** @file 
+    @brief Utilities for the fregrid program.
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <math.h>
diff --git a/sorc/fre-nctools.fd/tools/fregrid/fregrid_util.h b/sorc/fre-nctools.fd/tools/fregrid/fregrid_util.h
index dfd27b07b..42bbf13ba 100644
--- a/sorc/fre-nctools.fd/tools/fregrid/fregrid_util.h
+++ b/sorc/fre-nctools.fd/tools/fregrid/fregrid_util.h
@@ -1,3 +1,6 @@
+/** @file
+    @brief Function declarations for the fregrid utility module.
+*/
 #ifndef FREGRID_UTIL_H_
 #define FREGRID_UTIL_H_
 #include "globals.h"
diff --git a/sorc/fre-nctools.fd/tools/fregrid/globals.h b/sorc/fre-nctools.fd/tools/fregrid/globals.h
index 5ed598d83..a4ed1cb88 100644
--- a/sorc/fre-nctools.fd/tools/fregrid/globals.h
+++ b/sorc/fre-nctools.fd/tools/fregrid/globals.h
@@ -1,3 +1,6 @@
+/** @file
+    @brief Define global constants and type definitions.
+*/
 #ifndef GLOBALS_H_
 #define GLOBALS_H_
 #include <netcdf.h>
diff --git a/sorc/fre-nctools.fd/tools/make_hgrid/create_conformal_cubic_grid.c b/sorc/fre-nctools.fd/tools/make_hgrid/create_conformal_cubic_grid.c
index 4e9c9dea9..364cf2d62 100644
--- a/sorc/fre-nctools.fd/tools/make_hgrid/create_conformal_cubic_grid.c
+++ b/sorc/fre-nctools.fd/tools/make_hgrid/create_conformal_cubic_grid.c
@@ -1,3 +1,6 @@
+/** @file
+    @brief Create conformal cubic grids.
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <complex.h>
diff --git a/sorc/fre-nctools.fd/tools/make_hgrid/create_gnomonic_cubic_grid.c b/sorc/fre-nctools.fd/tools/make_hgrid/create_gnomonic_cubic_grid.c
index 9d4b68b70..078e7f257 100644
--- a/sorc/fre-nctools.fd/tools/make_hgrid/create_gnomonic_cubic_grid.c
+++ b/sorc/fre-nctools.fd/tools/make_hgrid/create_gnomonic_cubic_grid.c
@@ -1,3 +1,6 @@
+/** @file
+    @brief Create gnomonic cubic grids.
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
diff --git a/sorc/fre-nctools.fd/tools/make_hgrid/create_grid_from_file.c b/sorc/fre-nctools.fd/tools/make_hgrid/create_grid_from_file.c
index 9d08aac9d..7ff06e218 100644
--- a/sorc/fre-nctools.fd/tools/make_hgrid/create_grid_from_file.c
+++ b/sorc/fre-nctools.fd/tools/make_hgrid/create_grid_from_file.c
@@ -1,7 +1,5 @@
-/*
-  Copyright 2011 NOAA Geophysical Fluid Dynamics Lab, Princeton, NJ
-  This program is distributed under the terms of the GNU General Public
-  License. See the file COPYING contained in this directory
+/** @file
+    @brief Create grid from a file.
 */
 #include <stdlib.h>
 #include <stdio.h>
diff --git a/sorc/fre-nctools.fd/tools/make_hgrid/create_hgrid.h b/sorc/fre-nctools.fd/tools/make_hgrid/create_hgrid.h
index 599fc1aab..2b807b3f1 100644
--- a/sorc/fre-nctools.fd/tools/make_hgrid/create_hgrid.h
+++ b/sorc/fre-nctools.fd/tools/make_hgrid/create_hgrid.h
@@ -1,12 +1,12 @@
-/*******************************************************************************
-                             create_hgrid.h
+/** @file
+  
   This header file provide interface to create different types of horizontal 
-  grid. geographical grid location, cell length, cell area and rotation
+  grid. Geographical grid location, cell length, cell area and rotation
   angle are returned. All the returned data are on supergrid.
 
-  contact: Zhi.Liang@noaa.gov
+  @author Zhi.Liang@noaa.gov
 
-*******************************************************************************/
+*/
 #ifndef CREATE_HGRID_H_
 #define CREATE_HGRID_H_
 void create_regular_lonlat_grid( int *nxbnds, int *nybnds, double *xbnds, double *ybnds,
diff --git a/sorc/fre-nctools.fd/tools/make_hgrid/create_lonlat_grid.c b/sorc/fre-nctools.fd/tools/make_hgrid/create_lonlat_grid.c
index 6b7a0a1aa..665cf5d94 100644
--- a/sorc/fre-nctools.fd/tools/make_hgrid/create_lonlat_grid.c
+++ b/sorc/fre-nctools.fd/tools/make_hgrid/create_lonlat_grid.c
@@ -1,3 +1,7 @@
+/** @file 
+    @brief Routines to create regular lat/lon, spectral, tripolar
+    and f-plane grids.
+*/ 
 #include <stdlib.h>
 #include <stdio.h>
 #include <complex.h>
diff --git a/sorc/fre-nctools.fd/tools/make_hgrid/make_hgrid.c b/sorc/fre-nctools.fd/tools/make_hgrid/make_hgrid.c
index ccce0aec9..7543ba14b 100644
--- a/sorc/fre-nctools.fd/tools/make_hgrid/make_hgrid.c
+++ b/sorc/fre-nctools.fd/tools/make_hgrid/make_hgrid.c
@@ -1,11 +1,8 @@
-/*
-  Copyright 2011 NOAA Geophysical Fluid Dynamics Lab, Princeton, NJ
-  This program is distributed under the terms of the GNU General Public
-  License. See the file COPYING contained in this directory
+/** @file
 
-  This program generates various types of horizontal grids in netCDF file format
+  @brief This program generates various types of horizontal grids in netCDF file format
 
- AUTHOR: Zhi Liang (Zhi.Liang@noaa.gov)
+  @author Zhi Liang (Zhi.Liang@noaa.gov)
           NOAA Geophysical Fluid Dynamics Lab, Princeton, NJ
 */
 #include <stdlib.h>
diff --git a/sorc/fre-nctools.fd/tools/make_solo_mosaic/get_contact.c b/sorc/fre-nctools.fd/tools/make_solo_mosaic/get_contact.c
index 2923b7180..1850e2e7d 100644
--- a/sorc/fre-nctools.fd/tools/make_solo_mosaic/get_contact.c
+++ b/sorc/fre-nctools.fd/tools/make_solo_mosaic/get_contact.c
@@ -1,3 +1,6 @@
+/** @file
+    @brief Determine contacts between tiles.
+*/
 #include <stdlib.h>
 #include <math.h>
 #include "mosaic_util.h"
diff --git a/sorc/fre-nctools.fd/tools/make_solo_mosaic/get_contact.h b/sorc/fre-nctools.fd/tools/make_solo_mosaic/get_contact.h
index 120d24634..3ae5f6917 100644
--- a/sorc/fre-nctools.fd/tools/make_solo_mosaic/get_contact.h
+++ b/sorc/fre-nctools.fd/tools/make_solo_mosaic/get_contact.h
@@ -1,3 +1,6 @@
+/** @file
+    @brief Function declarations for computing contacts between tiles.
+*/
 #ifndef GET_CONTACT_
 #define GET_CONTACT_
 /**********************************************************************
diff --git a/sorc/fre-nctools.fd/tools/make_solo_mosaic/make_solo_mosaic.c b/sorc/fre-nctools.fd/tools/make_solo_mosaic/make_solo_mosaic.c
index f78ec54a5..2321e0546 100644
--- a/sorc/fre-nctools.fd/tools/make_solo_mosaic/make_solo_mosaic.c
+++ b/sorc/fre-nctools.fd/tools/make_solo_mosaic/make_solo_mosaic.c
@@ -1,3 +1,6 @@
+/** @file
+    @brief Generate mosaic information between tiles.
+*/
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
diff --git a/sorc/orog_mask_tools.fd/orog.fd/CMakeLists.txt b/sorc/orog_mask_tools.fd/orog.fd/CMakeLists.txt
index 5e38c7a35..9ed6f78cc 100644
--- a/sorc/orog_mask_tools.fd/orog.fd/CMakeLists.txt
+++ b/sorc/orog_mask_tools.fd/orog.fd/CMakeLists.txt
@@ -1,4 +1,5 @@
 set(fortran_src
+    machine.f90
     mtnlm7_oclsm.f
     netcdf_io.F90)
 
diff --git a/sorc/orog_mask_tools.fd/orog.fd/machine.f90 b/sorc/orog_mask_tools.fd/orog.fd/machine.f90
new file mode 100644
index 000000000..134331577
--- /dev/null
+++ b/sorc/orog_mask_tools.fd/orog.fd/machine.f90
@@ -0,0 +1,14 @@
+!> @file
+!! @brief Machine dependant constants
+ module machine
+!
+ integer    kind_io2,kind_io4,kind_io8
+ integer    kind_evod
+!
+ parameter (kind_io2 =2)
+ parameter (kind_io4 =4)
+ parameter (kind_io8 =8)
+ parameter (kind_evod=8)
+ real(kind=kind_evod) mprec !< machine precision to restrict dep
+ parameter(mprec  = 1.e-12 )
+ end module machine
diff --git a/sorc/orog_mask_tools.fd/orog.fd/machine.h b/sorc/orog_mask_tools.fd/orog.fd/machine.h
deleted file mode 100644
index a9316ed4b..000000000
--- a/sorc/orog_mask_tools.fd/orog.fd/machine.h
+++ /dev/null
@@ -1,11 +0,0 @@
-cc    Machine dependant constants (*j*) added io2 20051101
-cc
-      integer    kind_io2,kind_io4,kind_io8
-      integer    kind_evod
-cc
-      parameter (kind_io2 =2)
-      parameter (kind_io4 =4)
-      parameter (kind_io8 =8)
-      parameter (kind_evod=8)
-      real(kind=kind_evod) mprec ! machine precision to restrict dep
-      parameter(mprec  = 1.e-12 )
diff --git a/sorc/orog_mask_tools.fd/orog.fd/mtnlm7_oclsm.f b/sorc/orog_mask_tools.fd/orog.fd/mtnlm7_oclsm.f
index 2f6da24ca..98a0df836 100644
--- a/sorc/orog_mask_tools.fd/orog.fd/mtnlm7_oclsm.f
+++ b/sorc/orog_mask_tools.fd/orog.fd/mtnlm7_oclsm.f
@@ -163,8 +163,8 @@
       SUBROUTINE TERSUB(IMN,JMN,IM,JM,NM,NR,NF0,NF1,NW,EFAC,BLAT,
      &     OUTGRID,INPUTOROG)
 !jaa      use ipfort
+      use machine
       implicit none
-      include 'machine.h'
       include 'netcdf.inc'
 C
       integer                      :: IMN,JMN,IM,JM,NW
@@ -3895,10 +3895,8 @@ subroutine read_g(glob,ITOPO)
 ! --- tiles in the output working dir.  The glob array can not be 
 ! --- acted on with grads, but the tiles can be if lat/lon are reduced slightly
 cc
+      use machine
       implicit none
-cc
-      include 'machine.h'
-      include 'resevod.h'
 cc
       integer*2    glob(360*120,180*120)
 cc
diff --git a/sorc/orog_mask_tools.fd/orog.fd/netcdf_io.F90 b/sorc/orog_mask_tools.fd/orog.fd/netcdf_io.F90
index aecc63dc2..f3c188434 100644
--- a/sorc/orog_mask_tools.fd/orog.fd/netcdf_io.F90
+++ b/sorc/orog_mask_tools.fd/orog.fd/netcdf_io.F90
@@ -1,6 +1,6 @@
 !> @file
-!-------------------------------------------------------------------------------
-! write out data in netcdf format
+!! @brief Write out data in netcdf format
+!!
   subroutine write_netcdf(im, jm, slm, land_frac, oro, orf, hprime, ntiles, tile, geolon, geolat, lon, lat)
     implicit none
     integer, intent(in):: im, jm, ntiles, tile
diff --git a/sorc/orog_mask_tools.fd/orog.fd/resevod.h b/sorc/orog_mask_tools.fd/orog.fd/resevod.h
deleted file mode 100644
index 5943e28be..000000000
--- a/sorc/orog_mask_tools.fd/orog.fd/resevod.h
+++ /dev/null
@@ -1,7 +0,0 @@
-      integer              latg,latg2
-      integer              lonf
-      real(kind=kind_evod) rerth
-cc
-      parameter ( lonf   = 192 )
-      parameter ( latg   = 94 )
-      parameter ( latg2  = latg/2 )