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LaMEM with FastScapeFortranLib #29

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LaMEM with FastScapeFortranLib #29

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0b3d47f
LaMEM with FastScapeFortranLib
liyy1125 Nov 4, 2024
ff19be0
correct some bugs and add some part
liyy1125 Nov 15, 2024
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58 changes: 49 additions & 9 deletions src/LaMEMLib.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,9 @@
#include "phase_transition.h"
#include "passive_tracer.h"

// surface process
#include "fastscape.h"

//---------------------------------------------------------------------------
PetscErrorCode LaMEMLibMain(void *param,PetscLogStage stages[4])
{
Expand Down Expand Up @@ -504,6 +507,12 @@ PetscErrorCode LaMEMLibSetLinks(LaMEMLib *lm)
lm->fs.scal = &lm->scal;
// FreeSurf
lm->surf.jr = &lm->jr;
lm->surf.FSLib = &lm->FSLib;
// FastScape
lm->FSLib.surf = &lm->surf;
lm->FSLib.pvsurf= &lm->pvsurf;
lm->FSLib.jr = &lm->jr;
lm->FSLib.dbm = &lm->dbm;
// BCCtx
lm->bc.scal = &lm->scal;
lm->bc.ts = &lm->ts;
Expand Down Expand Up @@ -566,8 +575,6 @@ PetscErrorCode LaMEMLibSaveOutput(LaMEMLib *lm)
step = ts->istep;
bgPhase = lm->actx.bgPhase;



// create directory (encode current time & step number)
asprintf(&dirName, "Timestep_%1.8lld_%1.8e", (LLD)step, time);

Expand Down Expand Up @@ -652,7 +659,6 @@ PetscErrorCode LaMEMLibSolve(LaMEMLib *lm, void *param, PetscLogStage stages[4])

// initialize boundary constraint vectors
ierr = BCApply(&lm->bc); CHKERRQ(ierr);


// initialize temperature
ierr = JacResInitTemp(&lm->jr); CHKERRQ(ierr);
Expand Down Expand Up @@ -702,7 +708,8 @@ PetscErrorCode LaMEMLibSolve(LaMEMLib *lm, void *param, PetscLogStage stages[4])
// restart if fixed time step is larger than CFLMAX
if(restart) continue;

// advect free surface
// advect free surface // change the topography, controled by the surf_max_angle, when equal to 0.0,
// don't using the process
ierr = FreeSurfAdvect(&lm->surf); CHKERRQ(ierr);

// advect markers
Expand All @@ -719,18 +726,51 @@ PetscErrorCode LaMEMLibSolve(LaMEMLib *lm, void *param, PetscLogStage stages[4])

PetscCall(PetscLogStagePop()); /* Stop profiling stage*/

// apply erosion to the free surface
ierr = FreeSurfAppErosion(&lm->surf); CHKERRQ(ierr);
int SurfaceMode;
SurfaceMode = SURFACE; // SURFACE, default value = 1

FreeSurf *surfmode;
surfmode = &lm->surf;

// apply sedimentation to the free surface
ierr = FreeSurfAppSedimentation(&lm->surf); CHKERRQ(ierr);
if( 1 == SurfaceMode) // compile without FastScape
{
// PetscPrintf(PETSC_COMM_WORLD, "\nCalculating surface process through LaMEM code \n");
// apply erosion to the free surface
ierr = FreeSurfAppErosion(&lm->surf); CHKERRQ(ierr);

// apply sedimentation to the free surface
ierr = FreeSurfAppSedimentation(&lm->surf); CHKERRQ(ierr);
}

if ( 2 == SurfaceMode) // compile with FastScape
{
if( 1 == surfmode->SurfMode )
// using LaMEM original code to calculate topography
{
// PetscPrintf(PETSC_COMM_WORLD, "\nCalculating surface process through LaMEM code \n");
// apply erosion to the free surface
ierr = FreeSurfAppErosion(&lm->surf); CHKERRQ(ierr);

// apply sedimentation to the free surface
ierr = FreeSurfAppSedimentation(&lm->surf); CHKERRQ(ierr);
}

if( 2 == surfmode->SurfMode)
// Using FastScape to calculate topography
{
// PetscPrintf(PETSC_COMM_WORLD, "\n-------------------------------------------------------------------\n");
PetscPrintf(PETSC_COMM_WORLD, "Begin FastScape \n");
PetscPrintf(PETSC_COMM_WORLD, "--------------------------------------------------------------------------\n");
ierr = fastscape(&lm->FSLib); CHKERRQ(ierr);
}
}

// remap markers onto (stretched) grid
ierr = ADVRemap(&lm->actx); CHKERRQ(ierr);

// update phase ratios taking into account actual free surface position
ierr = FreeSurfGetAirPhaseRatio(&lm->surf); CHKERRQ(ierr);

//==================
// Save data to disk
//==================
Expand Down
6 changes: 5 additions & 1 deletion src/LaMEMLib.h
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Original file line number Diff line number Diff line change
Expand Up @@ -28,15 +28,17 @@ enum RunMode
};

//---------------------------------------------------------------------------
#include "fastscape.h"

struct LaMEMLib
{
Scaling scal; // scaling
TSSol ts; // time-stepping controls
DBMat dbm; // material database
DBPropDike dbdike; // dike database
DBPropDike dbdike; // dike database
FDSTAG fs; // staggered-grid layout
FreeSurf surf; // free-surface grid
FastScapeLib FSLib; // fastscape grid
BCCtx bc; // boundary condition context
AdvCtx actx; // advection context
JacRes jr; // Jacobian & residual context
Expand All @@ -48,6 +50,8 @@ struct LaMEMLib
PVPtr pvptr; // paraview out passive tracers
};



//---------------------------------------------------------------------------
// LAMEM LIBRARY FUNCTIONS
//---------------------------------------------------------------------------
Expand Down
60 changes: 51 additions & 9 deletions src/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,14 @@ include Makefile.in
# Environmental variables for PETSc installation directories:
# PETSC_DEB = /directory/where/petsc/debug/is/installed
# PETSC_OPT = /directory/where/petsc/optimized/is/installed
# FASTSCAPELIB = /directory/where/FastScapeLib/is/located
#
# LaMEM compilation command:
# make mode=deb all (compile debug version of LaMEM and put in /bin/deb)
# make mode=opt all (compile optimized version of LaMEM and put in /bin/opt)
# make all (compile optimized version of LaMEM and put in /bin/opt)
# make mode=optFS all surface=SURFACE=2 (compile optimized version of LaMEM with fastscape and put in /bin/optFS)
# surf_mode = 1; don't use fastscape; surf_mode = 2; use fastscape

ifeq ($(mode), deb)
ifeq (${PETSC_DEB},)
Expand All @@ -35,6 +38,15 @@ ifeq (${PETSC_OPT},)
$(error Environmental variable PETSC_OPT must be set to PETSc optimized installation directory)
endif
PETSC_DIR = ${PETSC_OPT}
else ifeq ($(mode), optFS)
# ifneq (, $(filter,${FASTSCAPE_LIB} ${PETSC_OPT}))
ifeq (${FASTSCAPE_LIB},)
${error Environmental variable PETSC_OPT and FASTSCAPE_LIB must be set to installation directory, respectively}
else ifeq (${PETSC_OPT},)
${error Environmental variable PETSC_OPT and FASTSCAPE_LIB must be set to installation directory, respectively}
endif
PETSC_DIR = ${PETSC_OPT}
FASTSCAPE_DIR = ${FASTSCAPE_LIB}
else
$(error Unknown compilation mode specified)
endif
Expand All @@ -45,19 +57,30 @@ include ${PETSC_DIR}/lib/petsc/conf/rules
# Define PETSc-based C++ compiler command
CCOMPILER = ${CXX} ${CXX_FLAGS} ${CXXFLAGS} ${CCPPFLAGS}

# Define FastScape-based fortran compiler command
GF = gfortran
# Define FastScapeFortranLib
FS_LIB = -L${FASTSCAPE_DIR} -lfastscapelib_fortran

#====================================================

# Define list of LaMEM library source files
# List files to be excluded after filter-out
CSRC = $(filter-out LaMEM.cpp, $(wildcard *.cpp))
FS = $(wildcard *.f90)

#====================================================

ifeq ($(mode), optFS)
# Generate lists of library object files:
COBJ := $(addprefix ../lib/${mode}/, $(notdir $(CSRC:.cpp=.o)))
COBJ := $(addprefix ../lib/${mode}/, $(notdir $(CSRC:.cpp=.o) $(FS:.f90=.o)))

# Generate lists of library dependency files:
CDEP := $(addprefix ../dep/${mode}/, $(notdir $(CSRC:.cpp=.d) $(FS:.f90=.d)))

else
COBJ := $(addprefix ../lib/${mode}/, $(notdir $(CSRC:.cpp=.o)))
CDEP := $(addprefix ../dep/${mode}/, $(notdir $(CSRC:.cpp=.d)))
endif

# Get library and executable objects:
LaMEM = ../bin/${mode}/LaMEM
Expand All @@ -74,7 +97,7 @@ endif

# Target list

.PHONY: builddir buildlib lamemlib linkexe lamem print clean_all doc
.PHONY: builddir buildlib lamemlib linkexe lamem print clean_all doc

# Default target (build executable)

Expand Down Expand Up @@ -136,8 +159,11 @@ ${LaMEM_LIB} : ../dep/$(mode)/makefile.stat ${COBJ}

# Create a dynamic library
dylib: ${COBJ}
ifeq ($(mode), optFS)
$(CCOMPILER) -shared -fPIC -o ../lib/$(mode)/LaMEMLib.dylib ${COBJ} ${PETSC_LIB} ${FS_LIB}
else
$(CCOMPILER) -shared -fPIC -o ../lib/$(mode)/LaMEMLib.dylib ${COBJ} ${PETSC_LIB}

endif
#====================================================

# Link LaMEM executable
Expand All @@ -150,16 +176,28 @@ ${LaMEM} : ${LaMEM_LIB} ${LaMEM_OBJ}
@echo "............................................."
@echo "......... Linking LaMEM Executable .........."
@echo "............................................."
${CXXLINKER} ${LaMEM_OBJ} ${LaMEM_LIB} ${PETSC_LIB} ${CLIB_FLAGS} -o $@
ifeq ($(mode), optFS)
${CXXLINKER} ${LaMEM_OBJ} ${LaMEM_LIB} ${PETSC_LIB} ${CLIB_FLAGS} ${FS_LIB} -o $@
else
${CXXLINKER} ${LaMEM_OBJ} ${LaMEM_LIB} ${PETSC_LIB} ${CLIB_FLAGS} -o $@
endif

#====================================================

# Pattern rules for automatic generation of object & dependency files
# Insert full path to object files in dependency files with sed command
# NOTE: IBM XL compiler generates dependency as a by-product of compilation
ifeq ($(mode), optFS)
../lib/${mode}/%.o : %.f90
${GF} ${FS_LIB} -c $< -o $@
endif

# define SURFACE 1 in Cpp script when there isn't a value setting in bash
surface=SURFACE=1

../lib/${mode}/%.o : %.cpp
${CCOMPILER} ${LAMEM_FLAGS} -D$(surface) -c $< -o $@

../lib/${mode}/%.o : %.cpp
${CCOMPILER} ${LAMEM_FLAGS} -c $< -o $@
ifeq ($(PLATFORM), ppc64)
@mv -f ../lib/${mode}/$*.d ../dep/${mode}/$*.d.tmp
else
Expand Down Expand Up @@ -210,6 +248,11 @@ endif
@echo "............................................."
@echo "PETSC_LIB : " ${PETSC_LIB}
@echo "............................................."
ifeq ($(mode), optFS)
@echo "............................................."
@echo "FASTSCAPE_LIB : " ${FS_LIB}
@echo "............................................."
endif
@echo "CLIB_FLAGS : " ${CLIB_FLAGS}
@echo "............................................."

Expand All @@ -222,12 +265,11 @@ clean_all :
@rm -rf ../lib/$(mode)/*
@rm -rf ../bin/$(mode)/*
@rm -rf ../dep/$(mode)/*

#====================================================

# Create automatic documentation

doc:
PDFLATEX=$(PDFLATEX) BIBTEX=$(BIBTEX) ../doc/Manual/./CreateDevelDoc.sh

#====================================================
#====================================================
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