Merge branch 'quasimc'

MintonGroup · Jun 14, 2024 · 471b490 · 471b490
2 parents 12d15c3 + e846d0b
commit 471b490
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Showing 47 changed files with 564 additions and 1,489 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,7 +7,10 @@
 !distclean.cmake
 !README.md
 !version.txt
+!ctem/
 !ctem/**.py
 !cmake/Modules/*.cmake
+!*.bash
+
 !pyproject.toml
 !LICENSE
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -11,11 +11,12 @@
 ##################################################
 # Define the project and the depencies that it has
 ##################################################
-CMAKE_MINIMUM_REQUIRED(VERSION 3.6.0...3.27.1)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.24.0...3.27.1)
+SET(SKBUILD_PROJECT_NAME "ctem" CACHE STRING "Name of project set by scikit-build")
 
 # Get version stored in text file
 FILE(READ "version.txt" VERSION)
-PROJECT(CTEM LANGUAGES C Fortran VERSION ${VERSION})
+PROJECT(${SKBUILD_PROJECT_NAME} LANGUAGES C Fortran VERSION ${VERSION})
 
 IF (CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
     SET(COMPILER_OPTIONS "Intel" CACHE STRING "Compiler identified as Intel")
@@ -26,7 +27,6 @@ ELSE ()
 ENDIF ()
 
 # Set some options the user may choose
-OPTION(USE_COARRAY "Use Coarray Fortran for parallelization of test particles" OFF)
 OPTION(USE_OPENMP "Use OpenMP for parallelization" ON)
 OPTION(USE_SIMD "Use SIMD vectorization" ON)
 OPTION(BUILD_SHARED_LIBS "Build using shared libraries" ON)
@@ -39,30 +39,40 @@ ENDIF()
 # Ensure scikit-build modules
 FIND_PACKAGE(Python COMPONENTS Interpreter Development.Module REQUIRED)
 
-# Add our local modules to the module path
-FILE(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules" LOCAL_MODULE_PATH)
-LIST(APPEND CMAKE_MODULE_PATH ${LOCAL_MODULE_PATH})
-
 # Define some directories that are important to the build
 SET(SRC "${CMAKE_SOURCE_DIR}/src")
-SET(LIB "${CMAKE_SOURCE_DIR}/lib")
-SET(BIN "${CMAKE_SOURCE_DIR}/bin")
-SET(MOD "${CMAKE_SOURCE_DIR}/include")
 SET(PY "${CMAKE_SOURCE_DIR}/ctem")
 
 # Make sure paths are correct for Unix or Windows style
 FILE(TO_CMAKE_PATH ${SRC} SRC)
-FILE(TO_CMAKE_PATH ${LIB} LIB)
-FILE(TO_CMAKE_PATH ${BIN} BIN)
-FILE(TO_CMAKE_PATH ${MOD} MOD)
 FILE(TO_CMAKE_PATH ${PY} PY)
 
-set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${LIB})
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${LIB})
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${BIN})
+INCLUDE(GNUInstallDirs)
+IF (SKBUILD)
+    SET(INSTALL_BINDIR ${SKBUILD_SCRIPTS_DIR})
+    SET(INSTALL_LIBDIR ${SKBUILD_DATA_DIR}/lib) 
+    SET(INSTALL_INCLUDEDIR ${SKBUILD_HEADERS_DIR}) 
+    SET(INSTALL_PYPROJ ${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}) 
+    IF (APPLE)
+        SET(CMAKE_INSTALL_RPATH "@loader_path;${CMAKE_BINARY_DIR}/bin")
+    ELSEIF (LINUX)
+        SET(CMAKE_INSTALL_RPATH "@ORIGIN;${CMAKE_BINARY_DIR}/bin")
+    ENDIF ()
+ELSE ()
+    SET(INSTALL_PYPROJ ${PY})
+    SET(INSTALL_BINDIR ${CMAKE_INSTALL_BINDIR})
+    SET(INSTALL_LIBDIR ${CMAKE_INSTALL_LIBDIR})
+    SET(INSTALL_INCLUDEDIR ${CMAKE_INSTALL_INCLUDEDIR})
+ENDIF ()
+
+SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 # Have the .mod files placed in the lib folder
-SET(CMAKE_Fortran_MODULE_DIRECTORY ${MOD})
+SET(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
+
+# Add our local modules to the module path
+FILE(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules" LOCAL_MODULE_PATH)
+LIST(APPEND CMAKE_MODULE_PATH ${LOCAL_MODULE_PATH})
 
 # Set the name of the ctem library
 SET(CTEM_LIBRARY ctem)

diff --git a/cmake/Modules/SetFortranFlags.cmake b/cmake/Modules/SetFortranFlags.cmake
@@ -533,10 +533,10 @@ IF (CMAKE_BUILD_TYPE STREQUAL "RELEASE" OR CMAKE_BUILD_TYPE STREQUAL "PROFILE")
             )
 
             # Tells the compiler to link to certain libraries in the Intel oneAPI Math Kernel Library (oneMKL). 
-            SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE}"
-                Fortran "/Qmkl:cluster" # Intel Windows
-                        "/Qmkl"     # Intel Windows
-            ) 
+            # SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE}"
+            #     Fortran "/Qmkl:cluster" # Intel Windows
+            #             "/Qmkl"     # Intel Windows
+            # ) 
 
             # Enables additional interprocedural optimizations for a single file compilation
             SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE}"
@@ -574,10 +574,10 @@ IF (CMAKE_BUILD_TYPE STREQUAL "RELEASE" OR CMAKE_BUILD_TYPE STREQUAL "PROFILE")
             )
 
             # Tells the compiler to link to certain libraries in the Intel oneAPI Math Kernel Library (oneMKL). 
-            SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE}"
-                Fortran "-qmkl=cluster" # Intel
-                        "-qmkl"     # Intel
-            ) 
+            # SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE}"
+            #     Fortran "-qmkl=cluster" # Intel
+            #             "-qmkl"     # Intel
+            # ) 
 
             # Enables additional interprocedural optimizations for a single file compilation
             SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE}"
@@ -671,11 +671,11 @@ IF (CMAKE_BUILD_TYPE STREQUAL "PROFILE")
     # Enables the optimization reports to be generated
         IF (WINOPT)
             SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_PROFILE "${CMAKE_Fortran_FLAGS_RELEASE}"
-                Fortran "/O2 /Qopt-report:5 /traceback /Z7"    # Intel Windows
+                Fortran "/O2 /Qopt-report:3 /traceback /Z7"    # Intel Windows
             )
         ELSE ()
             SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_PROFILE "${CMAKE_Fortran_FLAGS_RELEASE}"
-                Fortran "-O2 -pg -qopt-report=5 -traceback -p -g3" # Intel
+                Fortran "-O2 -pg -qopt-report=3 -traceback -p -g3" # Intel
             )
         ENDIF ()
     ELSEIF (COMPILER_OPTIONS STREQUAL "GNU")

diff --git a/cmake/Modules/SetParallelizationLibrary.cmake b/cmake/Modules/SetParallelizationLibrary.cmake
@@ -17,20 +17,11 @@ IF (USE_OPENMP)
     ENDIF (NOT OpenMP_Fortran_FLAGS)
 ENDIF (USE_OPENMP)
 
-IF (USE_COARRAY)
-    IF (NOT Coarray_Fortran_FLAGS)
-        FIND_PACKAGE (Coarray_Fortran)
-        IF (NOT Coarray_Fortran_FLAGS)
-            MESSAGE (FATAL_ERROR "Fortran compiler does not support Coarrays")
-        ENDIF (NOT Coarray_Fortran_FLAGS)
-    ENDIF (NOT Coarray_Fortran_FLAGS)
-ENDIF (USE_COARRAY)
 
-IF (NOT USE_OPENMP AND NOT USE_COARRAY)
-    # Turn off both OpenMP and CAF
+IF (NOT USE_OPENMP)
+    # Turn off OpenMP 
     SET (OMP_NUM_PROCS 0 CACHE
          STRING "Number of processors OpenMP may use" FORCE)
     UNSET (OpenMP_Fortran_FLAGS CACHE)
-    UNSET (Coarray_Fortran_FLAGS CACHE)
     UNSET (GOMP_Fortran_LINK_FLAGS CACHE)
-ENDIF (NOT USE_OPENMP AND NOT USE_COARRAY)
+ENDIF ()
diff --git a/ctem/ctem/NPF.py → ctem/NPF.py b/ctem/ctem/NPF.py → ctem/NPF.py
diff --git a/ctem/__init__.py b/ctem/__init__.py
@@ -0,0 +1,2 @@
+from ctem.driver import *
+from ctem import util
diff --git a/ctem/ctem/craterproduction.py → ctem/craterproduction.py b/ctem/ctem/craterproduction.py → ctem/craterproduction.py
diff --git a/ctem/ctem/__init__.py b/ctem/ctem/__init__.py
diff --git a/ctem/ctem/driver.py → ctem/driver.py b/ctem/ctem/driver.py → ctem/driver.py
@@ -52,14 +52,10 @@ def __init__(self, param_file="ctem.in", isnew=True):
         }
 
         # Get the location of the CTEM executable
-        self.ctem_executable = Path(_pyfile).parent.parent.parent / "bin" / "CTEM"
-        if not self.ctem_executable.exists():
-            print(f"CTEM driver not found at {self.ctem_executable}. Trying current directory.")
-            self.ctem_executable = Path(currentdir) / "CTEM"
-            if not self.ctem_executable.exists():
-                warnings.warn(f"Cannot find the CTEM driver {str(self.ctem_executable)}", stacklevel=2)
-                self.ctem_executable = None
-
+        self.ctem_executable = shutil.which("CTEM")
+        if not self.ctem_executable:
+            warnings.warn(f"Cannot find the CTEM driver {str(self.ctem_executable)}", stacklevel=2)
+            self.ctem_executable = None
 
         self.user = util.read_user_input(self.user)
 
@@ -169,7 +165,10 @@ def __init__(self, param_file="ctem.in", isnew=True):
                     rclist[:,0] = np.exp(interp(np.log(rclist[:,0])))
 
                     #Convert age in Ga to "interval time"
-                    rclist[:,5] = (self.user['interval'] * self.user['numintervals']) - craterproduction.Tscale(rclist[:,5], 'NPF_Moon')
+                    if (self.user['runtype'].upper() == 'STATISTICAL'):
+                        rclist[:,5] = (self.user['interval']) - craterproduction.Tscale(rclist[:,5], 'NPF_Moon')
+                    else:
+                        rclist[:,5] = (self.user['interval'] * self.user['numintervals']) - craterproduction.Tscale(rclist[:,5], 'NPF_Moon')
                     rclist = rclist[rclist[:,5].argsort()]
 
                     #Export to dat file

diff --git a/ctem/setup.py b/ctem/setup.py
diff --git a/ctem/ctem/util.py → ctem/util.py b/ctem/ctem/util.py → ctem/util.py
@@ -136,7 +136,7 @@ def image_regolith(user, regolith):
     height = user['gridsize'] / dpi
     width = height
     fig = plt.figure(figsize=(width, height), dpi=dpi)
-    fig.figimage(regolith_scaled, cmap=cm.nipy_spectral, origin='lower')
+    fig.figimage(regolith_scaled, cmap=cm.magma, origin='lower')
     plt.savefig(filename)
     plt.close()
 

diff --git a/ctem/ctem/viewer3d.py → ctem/viewer3d.py b/ctem/ctem/viewer3d.py → ctem/viewer3d.py
diff --git a/debug_compile.bash b/debug_compile.bash
@@ -0,0 +1,3 @@
+cmake -P distclean.cmake
+cmake -B build -S . -DCMAKE_BUILD_TYPE=Debug
+cmake --build build
diff --git a/examples/global-lunar-bombardment/ctem.in b/examples/global-lunar-bombardment/ctem.in
@@ -2,21 +2,21 @@
 
 
 ! Testing input. These are used to perform non-Monte Carlo tests.
-testflag     F                                 ! Set to T to create a single crater with user-defined impactor properties
-testimp      100000       ! Diameter of test impactor (m)
+testflag     T                                 ! Set to T to create a single crater with user-defined impactor properties
+testimp      15000.0       ! Diameter of test impactor (m)
 testvel      18.3e3                            ! Velocity of test crater (m/s)
-testang      45.0                              ! Impact angle of test crater (deg) - Default 90.0
-testxoffset  0                            ! x-axis offset of crater center from grid center (m) - Default 0.0
-testyoffset  0                            ! y-axis offset of crater center from grid center (m) - Default 0.0
+testang      90.0                              ! Impact angle of test crater (deg) - Default 90.0
+testxoffset  0.0                             ! x-axis offset of crater center from grid center (m) - Default 0.0
+testyoffset  0.0                            ! y-axis offset of crater center from grid center (m) - Default 0.0
 tallyonly    F                                 ! Tally the craters without generating any craters
 testtally    F   
 quasimc      F                                 ! MC run constrained by non-MC 'real' craters given in a list
-realcraterlist    qmctest2.in                ! list of 'real' craters for Quasi-MC runs
+realcraterlist    craterlist.in                ! list of 'real' craters for Quasi-MC runs
 
 
 
 ! IDL driver in uts
-interval     10.0
+interval     1.0
 numintervals 1                                  ! Total number of intervals (total time = interval * numintervals) <--when runtype is 'single'
 restart      F                                  ! Restart a previous run
 impfile      NPFextrap.dat          ! Impactor SFD rate file (col 1: Dimp (m), col 2: ! impactors > D (m**(-2) y**(-1))
@@ -33,10 +33,10 @@ runtype      single                             ! Run type: options are normal /
                                                 !    statistical: surface is reset between intervals
 
 ! CTEM required inputs
-seed         765                    ! Random number generator seed
-gridsize     500                          ! Size of grid in pixels
+seed         1111                    ! Random number generator seed
+gridsize     1000                          ! Size of grid in pixels
 numlayers    10                                 ! Number of perched layers
-pix          12.32e3                          ! Pixel size (m)
+pix          6.16e3                           ! Pixel size (m)
 mat          rock                               ! Material (rock or ice)
 ! Bedrock scaling parameters
 mu_b         0.55e0                             ! Experimentally derived parameter for bedrock crater scaling law 
@@ -60,11 +60,11 @@ doseismic    F                                  ! Perform seismic shaking calcul
 
 ! Optional inputF These have internally set default values that work reasonable well. Comment them out with
 deplimit        9e99                            ! Depth limit for craters (m) - Default is to ignore.
-maxcrat         0.15                          ! Fraction of gridsize that maximum crater can be - Default 1.0 (0.15 for full MC; 3.15e-2 for Quasi-MC)
+maxcrat         3.15e-2                          ! Fraction of gridsize that maximum crater can be - Default 1.0 <--0.15 for full MC; 3.15e-2 for Quasi-MC
 killatmaxcrater F                               ! Stop the run if a crater larger than the maximum is produced - Default F      
-basinimp        35.0e3                          ! Size of impactor to switch to lunar basin scaling law - Default is to ignore
+basinimp        35.0e6                          ! Size of impactor to switch to lunar basin scaling law - Default is to ignore
 docollapse      T                               ! Do slope collapse - Default T
-dosoftening     T                               ! Do ejecta softening - Default T
+dosoftening     F                               ! Do ejecta softening - Default T
 doangle         T                               ! Vary the impact angle. Set to F to have only vertical impacts - Default T
 Kd1             0.0001
 psi             2.000
@@ -74,5 +74,5 @@ doregotrack T
 dorays  F 
 superdomain F
 dorealistic F
-domixing T
-dotopodiffusion F
+dotopodiffusion F
+domixing F
diff --git a/examples/global-lunar-bombardment/ctemdriver.py b/examples/global-lunar-bombardment/ctemdriver.py
diff --git a/examples/global-lunar-bombardment/temp.in b/examples/global-lunar-bombardment/temp.in
diff --git a/examples/quasimc-global/CTEM b/examples/quasimc-global/CTEM