Merge pull request #45 from chowland/pf-direct-force

Add direct forcing of velocity to zero inside solid phase

Makefile

@@ -8,7 +8,7 @@ FLAVOUR=GNU
 # 	Intel: 2022 intel/2022a FFTW/3.3.10-GCC-11.3.0 HDF5/1.12.2-iimpi-2021a
 # IRENE (Intel): flavor/hdf5/parallel hdf5 fftw3/gnu
 # MARENOSTRUM (Intel): fabric intel mkl impi hdf5 fftw szip
-# SUPERMUC (Intel): fftw hdf5
+# SUPERMUC (Intel): spack/23.1.0 intel-toolkit/2023.1.0 fftw hdf5
 # DISCOVERER:
 #	GNU: hdf5/1/1.14/latest-gcc-openmpi fftw/3/latest-gcc-openmpi lapack
 #	Intel: hdf5/1/1.14/latest-intel-openmpi fftw/3/latest-gcc-openmpi mkl
@@ -65,7 +65,7 @@ ifeq ($(MACHINE),MARENOSTRUM)
 	LDFLAGS = $(FFTW_LIBS) -mkl=sequential
 endif
 ifeq ($(MACHINE),SUPERMUC)
-	FC = mpif90 -fpp -r8 -O3 $(HDF5_INC)
+	FC = mpiifort -r8 -O3 $(HDF5_INC)
 	LDFLAGS = $(FFTW_LIB) $(HDF5_F90_SHLIB) $(HDF5_SHLIB) -qmkl=sequential
 endif
 
@@ -144,49 +144,49 @@ $(PROGRAM): $(MOBJS) $(OBJS)
 #  Dependencies 
 #============================================================================
 $(OBJDIR)/param.o: src/flow_solver/param.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/AuxiliaryRoutines.o: src/flow_solver/AuxiliaryRoutines.F90 
-	$(FC) -c -o $@ $< $(LDFLAGS) 
+	$(FC) -c -o $@ $<
 $(OBJDIR)/decomp_2d.o: src/flow_solver/2decomp/decomp_2d.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/decomp_2d_fft.o: src/flow_solver/2decomp/decomp_2d_fft.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/ibm_param.o: src/ibm/ibm_param.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/grid.o: src/grid.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/pressure.o: src/pressure.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/HermiteInterpolations.o: src/multires/HermiteInterpolations.F90 obj/ibm_param.o
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/h5_tools.o: src/h5tools/h5_tools.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/means.o: src/h5tools/means.F90 obj/ibm_param.o
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/IBMTools.o: src/ibm/IBMTools.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/salinity.o: src/salinity.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/phasefield.o: src/phasefield.F90 obj/salinity.o
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/moisture.o: src/moisture.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/time_averaging.o: src/time_averaging.F90
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/spectra.o: src/spectra.F90 obj/time_averaging.o obj/pressure.o
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/%.o: src/%.F90 $(MOBJS)
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/%.o: src/flow_solver/%.F90 $(MOBJS)
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/%.o: src/h5tools/%.F90 $(MOBJS)
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/%.o: src/multires/%.F90 $(MOBJS)
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/%.o: src/multires/IC_interpolation/%.F90 $(MOBJS)
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 $(OBJDIR)/%.o: src/ibm/%.F90 $(MOBJS)
-	$(FC) -c -o $@ $< $(LDFLAGS)
+	$(FC) -c -o $@ $<
 
 #============================================================================
 #  Clean up 

docs/index.md

@@ -21,7 +21,7 @@ Differences with [van der Poel et al (2015)](https://doi.org/10.1016/j.compfluid
 Differences with [Ostilla-Monico et al (2015)](https://doi.org/10.1016/j.jcp.2015.08.031):
 
 - Since the current code is modified from AFiD, it is pencil-parallelized in the periodic directions. This contrasts with the previous multi-resolution code, which was slab-parallelized in the wall-normal direction.
-- For reasons linked to this change in parallelization, the only terms calculated implicitly are the diffusive terms with derivatives in the wall-normal direction (e.g. $`\nu \partial_{xx}u`$). All other terms are computed explicitly.
+- For reasons linked to this change in parallelization, the only terms calculated implicitly are the diffusive terms with derivatives in the wall-normal direction (e.g. $\nu \partial_{xx}u$). All other terms are computed explicitly.
 - The multiple resolution strategy in time from [Ostilla-Monico et al (2015)](https://doi.org/10.1016/j.jcp.2015.08.031) is not yet implemented in the code. For now, we only rely on a CFL condition.
 
 ## Prerequisites

docs/inputs.md

@@ -115,4 +115,4 @@ The input parameter `ibm` can be used to specify different shapes of solid objec
 - `ibm = 4` produces a hexagonal lattice of spheres
 
 Of these options, only 1 and 4 have been reliably tested.
-Perform your own validation casses before using.
+Perform your own validation cases before using.

docs/prerequisites.md

@@ -17,7 +17,7 @@ These instructions also work for machines running Ubuntu in the Windows Subsyste
 
 ## Single-line prerequisite installation
 ```
-sudo apt install build-essential gfortran libblas-dev liblapack-dev libhdf5-mpich-dev libfftw3-dev
+sudo apt install build-essential gfortran libblas-dev liblapack-dev libhdf5-openmpi-dev libfftw3-dev
 ```
 
 ## Using a new HPC?

examples/2DAxisymMelting/bou.in

@@ -36,7 +36,7 @@ RAYT    PRAT    RAYS    PRAS    FFscaleS
 
 Time stepping parameters
 IDTV    DT      RESID   CFLMAX  DTMIN   DTMAX
-1       1e-3    1.e-3   1.0     1e-8    1e-2
+0       1e-2    1.e-3   1.0     1e-8    1e-2
 
 Dirichlet/Neumann BC flag on upper(N) and lower(S) walls
 inslwS  inslwN  TfixS   TfixN   SfixS   SfixN

examples/2DMeltingRBC/bou.in

@@ -12,15 +12,15 @@ FLAGSAL     FLAGPF
 
 Read flow / Reset logs
 NREAD       IRESET
-1           0
+0           0
 
 Time steps / time limit (wall/flow) 
 NTST        WALLTIMEMAX     TMAX
-1000000     120             100.0
+1000000     3500            100.0
 
 Time interval for saving stats/movie frames
 TOUT    TFRAME  SAVE_3D
-0.01    0.01     10.0
+0.1     1.0     10.0
 
 Domain size (keep ALX3 = 1.0)
 ALX3   YLEN   ZLEN
@@ -36,7 +36,7 @@ RAYT    PRAT    RAYS    PRAS    FFscaleS
 
 Time stepping parameters
 IDTV    DT      RESID   CFLMAX  DTMIN   DTMAX
-1       1e-3    1.e-3   1.0     1e-8    5e-3
+1       1e-3    1.e-3   1.0     1e-8    1e-3
 
 Dirichlet/Neumann BC flag on upper(N) and lower(S) walls
 inslwS  inslwN  TfixS   TfixN   SfixS   SfixN