add CMake language specs; various quality-of-life improvements

.gitignore

@@ -0,0 +1,55 @@
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# build output
+build/
+
+# IDE
+.idea
+
+# vim
+*.sw*
+
+# sym-links added by cmake
+CMakePresets.json
+IgnoreWarning.h
+.pre-commit-config.yaml
+.clang-format
+.clang-tidy
+
+# python cache
+__pycache__/
+
+# saved output files
+*.npy
+*.gif

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "cmake"]
 	path = cmake
-	url = git@github.com:pmontalb/CmakeUtilities.git
+	url = git@github.com:chronopoulos/cmake-utils-turing-patterns.git
 [submodule "PdeFiniteDifferenceSolver"]
 	path = PdeFiniteDifferenceSolver
 	url = git@github.com:pmontalb/PdeFiniteDifferenceSolver.git

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.14)
-project(TuringPatterns)
+project(TuringPatterns CXX C CUDA)
 
 include(cmake/All.cmake)
 set(LANGUAGES_USE_CUDA ON CACHE BOOL "" FORCE)

README.md

@@ -31,3 +31,28 @@ I made a python script that calls the C++ executable and gather the numerical re
   <img src="https://raw.githubusercontent.com/pmontalb/TuringPatterns/master/lines_compressed.gif">
   <img src="https://raw.githubusercontent.com/pmontalb/TuringPatterns/master/schnakenberg_compressed.gif">
 </p>
+
+## Dependencies
+
+This code requires CUDA version 11. Download it here:
+
+https://developer.nvidia.com/cuda-11.0-download-archive
+
+
+## Building
+
+```
+git submodule update --init --recursive
+mkdir build
+cd build/
+cmake ..
+make
+```
+
+# Running
+
+From the top level:
+
+```
+python3 patternRunner.py
+```

patternRunner.py

@@ -14,8 +14,8 @@
     X_GRID_FILE = "{}\\x_grid.npy".format(CWD)
     Y_GRID_FILE = "{}\\y_grid.npy".format(CWD)
 else:
-    debugBin = "{}/cmake-build-gcc-debug/TuringPatterns".format(CWD)
-    releaseBin = "{}/cmake-build-gcc-release/TuringPatterns".format(CWD)
+    debugBin = "{}/build/bin/TuringPatterns".format(CWD)
+    releaseBin = "{}/build/bin/TuringPatterns".format(CWD)
 
     GRID_FILE = "{}/grid.npy".format(CWD)
     INITIAL_CONDITION_FILE = "{}/ic.npy".format(CWD)
@@ -175,7 +175,7 @@ def run_gray_scott_coral3(run=True, save=False):
                   ["-bc", "Periodic"] +
                   ["-xd", str(N_x)] +
                   ["-yd", str(N_x)] +
-                  ["-nIter", "100"] +
+                  ["-nIter", str(N)] +
                   ["-nIterPerRound", "100"] +
                   ["-dt", ".5"] +
                   ["-wns", ".05"] +
@@ -207,7 +207,7 @@ def run_gray_scott_lines(run=True, save=False):
                   ["-bc", "Periodic"] +
                   ["-xd", str(N_x)] +
                   ["-yd", str(N_x)] +
-                  ["-nIter", "100"] +
+                  ["-nIter", str(N)] +
                   ["-nIterPerRound", "100"] +
                   ["-dt", "1"] +
                   ["-wns", ".05"] +
@@ -399,7 +399,7 @@ def run_fitz_hugh_nagumo_low_beta(run=True, save=False):
                   ["-bc", "ZeroFlux"] +
                   ["-xd", str(N_x)] +
                   ["-yd", str(N_x)] +
-                  ["-nIter", "100"] +
+                  ["-nIter", str(N)] +
                   ["-nIterPerRound", "1000"] +
                   ["-dt", "0.001"] +
                   ["-wns", ".05"] +
@@ -431,7 +431,7 @@ def run_fitz_hugh_nagumo_spatial(run=True, save=False):
                   ["-bc", "ZeroFlux"] +
                   ["-xd", str(N_x)] +
                   ["-yd", str(N_x)] +
-                  ["-nIter", "100"] +
+                  ["-nIter", str(N)] +
                   ["-nIterPerRound", "1000"] +
                   ["-dt", "0.001"] +
                   ["-wns", ".05"] +
@@ -454,6 +454,7 @@ def run_fitz_hugh_nagumo_spatial(run=True, save=False):
 
 
 if __name__ == "__main__":
+
     run_gray_scott_bacteria(run=True, save=False)
     # run_gray_scott_bacteria2(run=True, save=False)
     # run_gray_scott_coral(run=True, save=False)
@@ -464,4 +465,5 @@ def run_fitz_hugh_nagumo_spatial(run=True, save=False):
     # run_brussellator_dots(run=True, save=False)
     # run_schnakenberg(run=True, save=False)
     # run_thomas(run=True, save=False)
-    # run_fitz_hugh_nagumo(run=True, save=False)
+    # run_fitz_hugh_nagumo(run=True, save=False)
+