diff --git a/build/README.md b/build/README.md
index f19cbc7826a56952be3e239407e6f26e9c8f4a4c..01d8f651732368753e65a697064164fd789ae3ac 100644
--- a/build/README.md
+++ b/build/README.md
@@ -13,15 +13,15 @@ This section describes the use of the pre-existing programs, once the binaries h
### cluster
1. cd to the `build/cluster` folder.
-2. Run `edfb`:
+2. Run `edfb_clu`:
- > ./edfb
+ > ./edfb_clu
3. Run `clu`:
> ./clu
-*NOTE:* both `edfb` and `clu` expect an input which is assumed to be in a folder named `../../test_data/cluster/` (i.e. two levels above the current execution path)
+*NOTE:* both `edfb_clu` and `clu` expect an input which is assumed to be in a folder named `../../test_data/cluster/` (i.e. two levels above the current execution path)
4. Run `np_cluster`:
@@ -31,22 +31,22 @@ This section describes the use of the pre-existing programs, once the binaries h
5. Check the consistency between the output files (the default output file for the *FORTRAN* code is named `OCLU`, while the corresponding *C++* output has the default name of `c_OCLU`).
-The default behaviour of `np_cluster` is to take the same input files as `edfb` and `clu` and to write the output in the current folder. If needed, different input and output paths can be given as command-line arguments:
+The default behaviour of `np_cluster` is to take the same input files as `edfb_clu` and `clu` and to write the output in the current folder. If needed, different input and output paths can be given as command-line arguments:
> ./np_cluster PATH_TO_DEDFB PATH_TO_DCLU OUTPUT_PATH
### sphere
1. cd to the `build/sphere` folder.
-2. Run `edfb`:
+2. Run `edfb_sph`:
- > ./edfb
+ > ./edfb_sph
3. Run `sph`:
> ./sph
-*NOTE:* both `edfb` and `sph` expect an input which is assumed to be in a folder named `../../test_data/sphere/` (i.e. two levels above the current execution path)
+*NOTE:* both `edfb_sph` and `sph` expect an input which is assumed to be in a folder named `../../test_data/sphere/` (i.e. two levels above the current execution path)
4. Run `np_sphere`:
@@ -56,7 +56,7 @@ The default behaviour of `np_cluster` is to take the same input files as `edfb`
5. Check the consistency between the output files (the default output file for the *FORTRAN* code is named `OSPH`, while the corresponding *C++* output has the default name of `c_OSPH`).
-The default behaviour of `np_sphere` is to take the same input files as `edfb` and `sph` and to write the output in the current folder. If needed, different input and output paths can be given as command-line arguments:
+The default behaviour of `np_sphere` is to take the same input files as `edfb_sph` and `sph` and to write the output in the current folder. If needed, different input and output paths can be given as command-line arguments:
> ./np_sphere PATH_TO_DEDFB PATH_TO_DSPH OUTPUT_PATH
diff --git a/containers/docker/Dockerfile b/containers/docker/Dockerfile
index 1157a744c5910567ff42c67b99881ed582cc4d6e..013c483ca45052c15956e6e50409a698bd260c0a 100644
--- a/containers/docker/Dockerfile
+++ b/containers/docker/Dockerfile
@@ -40,7 +40,7 @@ FROM debian:bookworm-slim AS np-tmcode-run-minimal
WORKDIR /root
# install the strictly needed runtime libraries needed to run the executables
# and the python check scripts
-RUN DEBIAN_FRONTEND=noninteractive apt update && DEBIAN_FRONTEND=noninteractive apt upgrade && DEBIAN_FRONTEND=noninteractive apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 python3 python-is-python3 python3-regex && rm -rf /var/lib/apt/lists/*
+RUN DEBIAN_FRONTEND=noninteractive apt update && DEBIAN_FRONTEND=noninteractive apt upgrade && DEBIAN_FRONTEND=noninteractive apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 python3 python-is-python3 python3-regex hdf5-tools && rm -rf /var/lib/apt/lists/*
COPY --from=np-tmcode-run-dev /root /root
# remove everything which is not needed to run the codes
RUN cd /root/np-tmcode && find build -name "*.o" -exec rm -v \{\} \; && find build -name "*.gcno" -exec rm -v \{\} \; && cd src && rm -rvf cluster libnptm trapping include sphere Makefile make.inc README.md && cd .. && rm -rvf containers && cd doc && rm -rvf src && cd build/latex && rm -rvf *.tex *.out *.sty *.ind *.log *.toc *.ilg *.idx *.aux *.eps Makefile class*.pdf
diff --git a/containers/singularity/np-tmcode-run.def b/containers/singularity/np-tmcode-run.def
index 924baadc0e5baf4792c8755834997056271380ba..da7025e0dd6899c8bf0698ec4615cb923bcc01ad 100644
--- a/containers/singularity/np-tmcode-run.def
+++ b/containers/singularity/np-tmcode-run.def
@@ -32,7 +32,7 @@ Stage: np-tmcode-run-minimal
%post
apt update
apt -y upgrade
- apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 python3 python-is-python3 python3-regex
+ apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 python3 python-is-python3 python3-regex hdf5-tools
rm -rf /var/lib/apt/lists/*
cd /usr/local/np-tmcode
find build -name "*.o" -exec rm -v \{\} \;
@@ -45,7 +45,7 @@ Stage: np-tmcode-run-minimal
rm -rvf src/cluster /src/include /src/libntpm /src/sphere /src/trapping /src/Makefile /src/make.inc
cd build/latex
rm -rvf *.tex *.out *.sty *.ind *.log *.toc *.ilg *.idx *.aux *.eps Makefile class*.pdf
- cp -a /usr/bin/ld.so /usr/bin/sh /usr/bin/dash /usr/bin/mkdir /usr/bin/rm /usr/bin/cp /usr/bin/python* /usr/local/bin/
+ cp -a /usr/bin/ld.so /usr/bin/sh /usr/bin/dash /usr/bin/mkdir /usr/bin/rm /usr/bin/cp /usr/bin/python* /usr/bin/h5* /usr/local/bin/
rm -rvf /bin/* /usr/bin/* /sbin /usr/sbin /usr/games /usr/local/games
/usr/local/bin/mkdir -p /bin
/usr/local/bin/cp -av /usr/local/bin/* /bin/
diff --git a/containers/singularity/np-tmcode-run.sif b/containers/singularity/np-tmcode-run.sif
index 26b865aa590a022035d0b3bb2b2bb7f4d384ab41..ef165c012d75f3722d7921179f09c9aea22ef58f 100755
Binary files a/containers/singularity/np-tmcode-run.sif and b/containers/singularity/np-tmcode-run.sif differ
diff --git a/src/cluster/Makefile b/src/cluster/Makefile
index 37c271251f2eff079354ab9610d1c6e4adc9fcc8..49e2fe59d5bc48d6fadbaac1a30415c218474b19 100644
--- a/src/cluster/Makefile
+++ b/src/cluster/Makefile
@@ -3,13 +3,13 @@ BUILDDIR=../../build/cluster
include ../make.inc
-all: clu edfb np_cluster
+all: clu edfb_clu np_cluster
clu: clu.o
$(FC) $(FCFLAGS) -o $(BUILDDIR)/clu $(BUILDDIR)/clu.o $(LDFLAGS)
-edfb: edfb.o
- $(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb $(BUILDDIR)/edfb.o $(LDFLAGS)
+edfb_clu: edfb_clu.o
+ $(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb_clu $(BUILDDIR)/edfb_clu.o $(LDFLAGS)
np_cluster: $(BUILDDIR)/np_cluster.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/clu_subs.o $(BUILDDIR)/cluster.o
$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_cluster $(BUILDDIR)/np_cluster.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/clu_subs.o $(BUILDDIR)/cluster.o $(CXXLDFLAGS)
@@ -42,5 +42,5 @@ clean:
rm -f $(BUILDDIR)/*.o
wipe:
- rm -f $(BUILDDIR)/clu $(BUILDDIR)/edfb $(BUILDDIR)/*.o
+ rm -f $(BUILDDIR)/clu $(BUILDDIR)/edfb_clu $(BUILDDIR)/*.o
diff --git a/src/cluster/edfb.f b/src/cluster/edfb_clu.f
similarity index 100%
rename from src/cluster/edfb.f
rename to src/cluster/edfb_clu.f
diff --git a/src/make.inc b/src/make.inc
index ac95b212b05534d9318db6149ea347705b09c73c..4dd67a1420877749f14490f4463781f788be16aa 100644
--- a/src/make.inc
+++ b/src/make.inc
@@ -1,32 +1,43 @@
+# FC defines the fortran compiler to use. If undefined, GNU Make tries to use `f77`
ifndef FC
override FC=gfortran
endif
+# FCFLAGS defines the compilation options for the fortran compiler
ifndef FCFLAGS
override FCFLAGS=-std=legacy -O3
endif
+# LDFLAGS defines the default linker flags
ifndef LDFLAGS
override LDFLAGS=
endif
+# CXX defines the default C++ compiler to use. If undefined, GNU Make tries to use g++
ifndef CXX
override CXX=g++
endif
+# HDF5_INCLUDE defines the default path to the HDF5 include files to use
ifndef HDF5_INCLUDE
override HDF5_INCLUDE=/usr/include/hdf5/serial
endif
+# CXXFLAGS defines the default compilation options for the C++ compiler
ifndef CXXFLAGS
-override CXXFLAGS=-O3 -ggdb -pg -coverage -I$(HDF5_INCLUDE)
+#override CXXFLAGS=-O3 -ggdb -pg -coverage -I$(HDF5_INCLUDE)
+override CXXFLAGS=-O3 -I$(HDF5_INCLUDE)
endif
+# HDF5_LIB defines the default path to the HDF5 libraries to use
+# CXXLDFLAGS defines the default linker flags to use for C++ codes
ifndef CXXLDFLAGS
ifndef HDF5_LIB
override HDF5_LIB=/usr/lib/x86_64-linux-gnu/hdf5/serial
endif
override CXXLDFLAGS=-L/usr/lib64 -L$(HDF5_LIB) -lhdf5 $(LDFLAGS)
+#else
+#override CXXLDFLAGS=-L/usr/lib64 -L$(HDF5_LIB) -lhdf5 $(CXXLDFLAGS)
endif
%.o : %.f
diff --git a/src/sphere/Makefile b/src/sphere/Makefile
index 384a85b9ede135f920d78585c0f924495e9d13f9..c2e8b5c5fb609308557866c19ec08850b17b27ba 100644
--- a/src/sphere/Makefile
+++ b/src/sphere/Makefile
@@ -9,10 +9,10 @@ include ../make.inc
#CXXFLAGS=-O2 -ggdb -pg -coverage
#CXXLFLAGS=-L/usr/lib64 -lhdf5_hl -lhdf5
-all: edfb sph np_sphere
+all: edfb_sph sph np_sphere
-edfb: edfb.o
- $(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb $(BUILDDIR)/edfb.o $(LDFLAGS)
+edfb_sph: edfb_sph.o
+ $(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb_sph $(BUILDDIR)/edfb_sph.o $(LDFLAGS)
sph: sph.o
$(FC) $(FCFLAGS) -o $(BUILDDIR)/sph $(BUILDDIR)/sph.o $(LDFLAGS)
@@ -45,5 +45,5 @@ clean:
rm -f $(BUILDDIR)/*.o
wipe:
- rm -f $(BUILDDIR)/edfb $(BUILDDIR)/sph $(BUILDDIR)/*.o
+ rm -f $(BUILDDIR)/edfb_sph $(BUILDDIR)/sph $(BUILDDIR)/*.o
diff --git a/src/sphere/edfb.f b/src/sphere/edfb_sph.f
similarity index 100%
rename from src/sphere/edfb.f
rename to src/sphere/edfb_sph.f