Feature/floodfill from seed point

README.md

@@ -63,7 +63,19 @@ If you see error messages about missing software (for example, telling you that
 
 Run make install `make install`. This will create an executable file called cme in the CoastalME folder.
 
-Edit cme.ini to tell CoastalME which input file to read (for example, in/test_suite/minimal_wave_angle_230/minimal.dat). You'll need to make sure that the "Path for output" listed in cme.ini (for example, out/test_suite/minimal_wave_angle_230) exists. If it doesn't exist, then create it: `mkdir -p out/test_suite/minimal_wave_angle_230/`.
+CoastalME supports two configuration file formats: `.ini` (legacy) and `.yaml` (modern).
+
+**Using YAML format (recommended)**:
+Edit `cme.yaml` to specify input and output paths. Example:
+```yaml
+input_data_file: in/test_suite/minimal_wave_angle_230/minimal.yaml
+output_path: out/test_suite/minimal_wave_angle_230/
+```
+
+**Using legacy .ini format**:
+Edit `cme.ini` to tell CoastalME which input file to read (for example, in/test_suite/minimal_wave_angle_230/minimal.dat). You'll need to make sure that the "Path for output" listed in cme.ini (for example, out/test_suite/minimal_wave_angle_230) exists. If it doesn't exist, then create it: `mkdir -p out/test_suite/minimal_wave_angle_230/`.
+
+**Note**: CoastalME will automatically detect which format to use. If both `cme.yaml` and `cme.ini` exist, `cme.yaml` takes priority.
 
 Run cme `./cme`. Output will appear in the "Path for output" folder.
 

cme.yaml

@@ -0,0 +1,32 @@
+#======================================================================================================================
+#
+# CoastalME initialization file (YAML format)
+#
+# Copyright (C) 2024 David Favis-Mortlock and Andres Payo
+#
+#=====================================================================================================================
+#
+# 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 3 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.
+#
+# You should have received a copy of the GNU General Public License along with this program; if not, write to the Free
+# Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+#
+#======================================================================================================================
+
+# Path to the main input configuration file (.dat or .yaml)
+# Can be absolute or relative to the directory containing this file
+input_data_file: /home/wilfchun/CoastalME/CoastalME_data_local/Typology/Cliff/in/cliff.yaml
+
+# Path for output files
+# Can be absolute or relative to the directory containing this file
+# IMPORTANT: A trailing slash is required
+output_path: /home/wilfchun/CoastalME/CoastalME_data_local/Typology/Cliff/out/
+
+# Email address for notification messages (optional, Linux only)
+# Uncomment to enable email notifications
+# email_address: user@example.com

src/CMakeLists.txt

@@ -178,11 +178,22 @@ elseif(CMAKE_BUILD_TYPE_LC STREQUAL "relwithdebinfo")
   add_compile_options(
       -march=native
       -O3
+      -g3
+      -gdwarf-3
+      -fopenmp
+      # -foffload=nvidia-ptx
+      -ffast-math
+      -fno-omit-frame-pointer
       # -Wall
       -fno-delete-null-pointer-checks
       -fno-strict-overflow
       -fno-strict-aliasing
       -ftrivial-auto-var-init=zero
+      -flto=auto
+  )
+  add_link_options(
+      -flto=auto
+      -rdynamic
   )
   if(CMAKE_CXX_COMPILER_ID MATCHES "^(GNU|LCC|QCC)$")
     # Production build using gcc
@@ -239,6 +250,7 @@ elseif(CMAKE_BUILD_TYPE_LC STREQUAL "release")
       -fno-strict-overflow
       -fno-strict-aliasing
       -ftrivial-auto-var-init=zero
+      -flto
   )
   if(CMAKE_CXX_COMPILER_ID MATCHES "^(GNU|LCC|QCC)$")
     # Production build using gcc
@@ -251,9 +263,9 @@ endif()
 
 # Finally set some gcc-specific linker flags, for all build types
 if(UNIX)
-  add_link_options(-Wl)
+  # add_link_options(-Wl)
   if(LINUX)
-    add_link_options(--as-needed -Wl,--no-undefined)
+    # add_link_options(--as-needed -Wl,--no-undefined)
   elseif(APPLE)
   endif()
 endif()

src/cell.h

@@ -420,4 +420,9 @@ class CGeomCell
    void SetDownDriftZoneNumber(int const);
    int nGetDownDriftZoneNumber(void) const;
 };
+
+// Include inline implementations for CGeomRasterGrid::Cell() methods
+// Must be included here after CGeomCell is fully defined to avoid circular dependency
+#include "raster_grid_inline.h"
+
 #endif // CELL_H