Adding MESA v15140 to AMUSE (#731)

Major thanks to @rjfarmer for this.

examples/textbook/helium_star.py

@@ -17,11 +17,15 @@ def main():
 
     star =  Particle()
     star.mass = 12.0 | units.MSun
-    stop_radius = 100 | units.RSun
+    stop_radius = 90 | units.RSun # Avoid the model going through a blue loop
 
     stellar_evolution = MESA()
     se_star = stellar_evolution.particles.add_particle(star)
 
+    # This method is only really useful if you need a helium star from an exisiting model
+    # With the new interface you can do: stellar_evolution.pure_he_stars.add_particles(star)
+    # Which is much faster
+
     print("Evolving a", star.mass, "star with",
           stellar_evolution.__class__.__name__, end=' ') 
     print("until its radius exceeds", stop_radius)

examples/textbook/stellar_massloss_response.py

@@ -38,6 +38,7 @@ def main(Mstar, z, dmdt):
     stellar.parameters.metallicity = z
     bodies = Particles(mass=Mstar)
     stellar.particles.add_particles(bodies)
+    stellar = turnon_massloss(stellar)
     channel_to_framework = stellar.particles.new_channel_to(bodies)
     copy_argument = ["age", "mass", "radius", "stellar_type"]
     while stellar.particles[0].stellar_type < Second_Asymptotic_Giant_Branch:
@@ -49,6 +50,19 @@ def main(Mstar, z, dmdt):
               bodies[0].radius, dmdt, bodies[0].stellar_type)
     stellar.stop()
 ###BOOKLISTSTOP2###
+
+def turnon_massloss(stellar):
+    if stellar.mesa_version == '2208':
+        return stellar # Mass loss defaults to on in this version
+    else:
+        for particle in stellar.particles:
+            particle.set_control('cool_wind_RGB_scheme','Reimers')
+            particle.set_control('Reimers_scaling_factor',0.1)
+            particle.set_control('cool_wind_AGB_scheme','Blocker')
+            particle.set_control('Blocker_scaling_factor',0.5)
+            particle.set_control('RGB_to_AGB_wind_switch',10**-4)
+    return stellar
+
 
 def new_option_parser():
     from amuse.units.optparse import OptionParser

src/amuse/codes.py

@@ -29,4 +29,4 @@ def _import_modules():
                 pass
 
 _import_modules()
-
+

src/amuse/community/mesa_r15140/.gitignore

@@ -0,0 +1,5 @@
+src/
+
+*.mod
+*.o
+*.smod

src/amuse/community/mesa_r15140/Makefile

@@ -0,0 +1,187 @@
+# standard amuse configuration include
+# config.mk will be made after ./configure has run
+ifeq ($(origin AMUSE_DIR), undefined)
+  AMUSE_DIR := $(shell amusifier --get-amuse-dir)
+endif
+-include ${AMUSE_DIR}/config.mk
+
+
+GFORTRAN_VERSION?=$(shell $(FC) -v 2>&1 | grep gcc\ version | cut -d\  -f3)
+GFORTRAN_MAJOR_MINOR=$(shell echo $(GFORTRAN_VERSION) | cut -s -d'.' -f1,2)
+#IFORT_VERSION?=$(shell $(FC) -v 2>&1 | cut -d\  -f2)
+#IFORT_MAJOR_MINOR=$(shell echo $(IFORT_VERSION) | cut -s -d'.' -f1,2)
+MPIF90 ?= mpif90
+MPICC ?= mpicc
+FORTRAN ?= gfortran
+PYTHON ?= python
+FC      ?= $(FORTRAN)
+export CC		?= gcc
+MPIFC+= $(FCFLAGS)
+MPICC+= $(CFLAGS)
+
+LAPACK_LIBS ?= -llapack
+BLAS_LIBS ?= -lblas
+
+export FC MPIFC MPICC LAPACK_LIBS BLAS_LIBS
+
+
+SRC_DIR := $(realpath ./src)
+
+MESA_MAKE_DIR=./mesa_reqs
+INCLUDE_DIR=./src/mesa/star/make
+export MESA_DIR = $(realpath ./src/mesa-r15140)
+MESA_LIB=$(MESA_DIR)/lib/libstar.a
+WORK_SRC_DIR=./
+
+export OPENMP_FCFLAGS=$(OPENMP_FCFLAG)
+
+CODE_GENERATOR ?= $(AMUSE_DIR)/build.py
+DOWNLOAD_FROM_WEB = $(PYTHON) ./download.py
+BUILD_DEP = $(PYTHON) ./build-dep.py
+PATCHES_DIR=./patches
+
+include $(PATCHES_DIR)/makefile_header_non_mesasdk
+
+all:	mesa_worker 
+
+ifdef DOWNLOAD_CODES
+$(MESA_DIR)/install:
+	make -C . download
+else
+$(MESA_DIR)/install:
+		@echo ""
+		@echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+		@echo ""
+		@echo "DOWNLOAD_CODES is not set. MESA will not be downloaded and built."
+		@echo "If you do want MESA, set DOWNLOAD_CODES to 1."
+		@echo "bash> export DOWNLOAD_CODES=1"
+		@echo "csh> setenv DOWNLOAD_CODES 1"
+		@echo "Note: MESA is quite large (2.5 GB downloaded, 19 GB built) and"
+		@echo "requires gfortran (version >= 9.0.0)."
+		@echo ""
+		@echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+		@echo ""
+		@make -s --no-print-directory -C . raise_error
+endif
+
+download:
+	$(RM) -Rf src
+	-mkdir src
+	$(DOWNLOAD_FROM_WEB)
+	make -C . patch
+	make -C . skip_tests
+	make -C . build_hdf5
+	make -C . build_ndiff
+	make -C . build_makedepf90
+	make -C . build_crmath
+	make -C . build_crlibm
+	make -C . build_fpx3_deps
+	make -C . build_fpx3
+	make -C . build_lapack95
+	make -C . install_deps
+
+build_ndiff:
+	cd $(MESA_DIR)/utils;\
+	rm -rf ndiff-2.00;\
+	tar xvf ndiff-2.00.tar.gz;\
+	cd ndiff-2.00;\
+	./configure;\
+	make;\
+
+build_makedepf90:
+	cd $(MESA_DIR)/utils;\
+	rm -rf makedepf90-2.8.8;\
+	tar xvf makedepf90-2.8.8.tar.gz;\
+	cd 	makedepf90-2.8.8;\
+	./configure;\
+	make;\
+
+build_crmath:
+	cd $(SRC_DIR)/crmath-1.2;\
+	make;\
+
+build_crlibm:
+	cd $(SRC_DIR)/crlibm-1.0beta4;\
+	./configure --enable-static=yes;\
+	make;\
+	make install;\
+	ar cru libcrlibm.a *.o scs_lib/*.o
+
+build_fpx3:
+	mv $(SRC_DIR)/fpx3 $(SRC_DIR)/fpx3_folder;\
+	cp $(SRC_DIR)/fpx3_folder/fpx3 $(SRC_DIR)/fpx3
+
+build_lapack95:
+	cd $(SRC_DIR)/LAPACK95/SRC;\
+	mkdir ../lapack95_modules;\
+	make clean;\
+	make single_double_complex_dcomplex
+
+build_fpx3_deps:
+	chmod u+x $(SRC_DIR)/fpx3_deps
+
+build_hdf5:
+	cd $(SRC_DIR)/hdf5-1.12.0;\
+	./configure --enable-fortran --enable-fortran2003 --enable-parallel --prefix=$(MESA_DIR) --enable-shared=no;\
+	make;\
+	make install
+
+clean:
+	$(RM) -f *~ *.pyc *.mod *.smod *.o worker_code worker_code.f90 $(MESA_LIB)
+	$(RM) -f mesa_worker mesa_worker_sockets worker_code-sockets.f90
+	make -C $(MESA_MAKE_DIR) clean
+
+veryclean: clean
+	cd $(MESA_DIR); ./clean
+
+distclean: clean
+	$(RM) -Rf src
+	$(RM) -Rf src.*
+	$(RM) -Rf .pc
+
+mesa_worker:	worker_code.f90  mesa_interface.o interface.o run_star_extras.o
+	$(MPIF90) $(FCFLAGS) $(FFLAGS) $(LDFLAGS) $(FCopenmp) $(FS_FLAGS) $^ -o $@ \
+		$(LOAD_EXTRAS1) $(OTHER_INCLUDES) $(LOAD_MESA_STAR) $(LOAD_EXTRAS) $(FS_LIBS)  $(LIBS)
+
+mesa_interface.o: mesa_interface.f90 $(MESA_LIB) run_star_extras.o
+	$(WORK_COMPILE) -I$(MESA_DIR)/star/make -I./ $<
+
+
+run_star_extras.o: run_star_extras.f90 $(MESA_LIB)
+	$(WORK_COMPILE) $<
+
+
+worker_code.f90: interface.py
+	$(CODE_GENERATOR) --type=f90 interface.py MESAInterface -o $@
+
+
+$(MESA_LIB):  $(MESA_DIR)/install
+	mkdir -p $(MESA_DIR)/lib $(MESA_DIR)/include
+	cd $(MESA_DIR);\
+	env PATH=$(MESA_DIR)/../:$(PATH) ./install
+
+
+patch:
+	mkdir -p $(MESA_DIR)/lib $(MESA_DIR)/include
+	$(PYTHON) ./patch_files.py
+	cp $(PATCHES_DIR)/makefile_header_non_mesasdk $(MESA_DIR)/utils/makefile_header
+
+install_deps:
+	cp ./src/crmath-1.2/libcrmath.a $(MESA_DIR)/lib/.
+	cp ./src/crmath-1.2/*.mod $(MESA_DIR)/include/.
+	cp ./src/crmath-1.2/*.smod $(MESA_DIR)/include/.
+	cp ./src/crlibm-1.0beta4/libcrlibm.a $(MESA_DIR)/lib/.
+	cp ./src/LAPACK95/lapack95_modules/*.mod $(MESA_DIR)/include/.
+	cp ./src/LAPACK95/lapack95.a $(MESA_DIR)/lib/liblapack95.a
+	cp $(MESA_DIR)/utils/makedepf90-2.8.8/makedepf90 $(SRC_DIR)/.
+	cp $(MESA_DIR)/utils/ndiff-2.00/ndiff $(SRC_DIR)/.
+
+interface.o: interface.f90 $(MESA_LIB)
+	$(WORK_COMPILE) $<
+
+skip_tests:
+#This one should always be skipped
+	touch $(MESA_DIR)/adipls/skip_test
+# We cant guarentee bit-for-bit as we dont control the compiler used
+# So everyone has to skip the build tests
+	touch $(MESA_DIR)/skip_test

src/amuse/community/mesa_r15140/download.py

@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+
+import subprocess
+import os
+import sys
+import time
+import urllib.request
+import urllib.parse
+import urllib.error
+from optparse import OptionParser
+import glob
+import shutil
+import stat
+
+class GetCodeFromHttp(object):
+    url_template = ''
+    filename_template = "mesa-r{version}.zip"
+    version = ""
+    zip=True
+    unpack=True
+
+    def directory(self):
+        return os.path.abspath(os.path.dirname(__file__))
+
+    def src_directory(self):
+        return os.path.join(self.directory(), 'src')
+
+    def unpack_downloaded_file(self, filename):
+        print("unpacking", filename)
+        if self.unpack:
+            if self.zip:
+                arguments = ['unzip']
+            else:
+                arguments = ['tar','xvf']
+            arguments.append(filename)
+            subprocess.call(
+                arguments,
+                cwd=os.path.join(self.src_directory())
+            )
+        print("done")
+
+    def start(self):
+        try:
+            os.mkdir('src')
+        except FileExistsError:
+            pass
+
+        url = self.url_template.format(version=self.version)
+        filename = self.filename_template.format(version=self.version)
+        filepath = os.path.join(self.src_directory(), filename)
+        print("downloading version", self.version, "from", url, "to", filename)
+        urllib.request.urlretrieve(url, filepath)
+        print("downloading finished")
+        self.unpack_downloaded_file(filename)
+
+
+def make_exectuable(filename):
+    st = os.stat(filename)
+    os.chmod(filename, st.st_mode | stat.S_IEXEC)
+
+def get_crmath():
+    instance = GetCodeFromHttp()
+    instance.url_template = 'https://github.com/rhdtownsend/crmath/archive/{version}.zip'
+    instance.filename_template='{version}.zip'
+    instance.version = 'v1.2'
+    instance.start()  
+
+
+def get_crlibm():
+    instance = GetCodeFromHttp()
+    instance.url_template = 'http://www.astro.wisc.edu/~townsend/resource/download/sdk2/src/crlibm-{version}.tar.gz'
+    instance.filename_template='crlibm-{version}.tar.gz'
+    instance.version = '1.0beta4'
+    instance.zip=False
+    instance.start()  
+
+def get_fpx3deps():
+    instance = GetCodeFromHttp()
+    instance.url_template = 'https://raw.githubusercontent.com/rhdtownsend/sdk2/master/profile/common/fpx3/fpx3_deps'
+    instance.filename_template='fpx3_deps'
+    instance.version = ''
+    instance.zip=False
+    instance.unpack=False
+    instance.start()  
+
+def get_fpx3():
+    instance = GetCodeFromHttp()
+    instance.url_template = 'http://www.astro.wisc.edu/~townsend/resource/download/sdk2/src/fpx3.tar.gz'
+    instance.filename_template='fpx3.tar.gz'
+    instance.version = ''
+    instance.zip=False
+    instance.start()  
+
+def get_lapack95():
+    instance = GetCodeFromHttp()
+    instance.url_template = 'http://www.astro.wisc.edu/~townsend/resource/download/sdk2/src/lapack95.tgz'
+    instance.filename_template='lapack95.tar.gz'
+    instance.version = ''
+    instance.zip=False
+    instance.start()      
+
+def get_mesa():
+    instance = GetCodeFromHttp()
+
+    if 'AMUSE_LOCAL_COPY_MESA' in os.environ:
+        instance.url_template = os.environ['AMUSE_LOCAL_COPY_MESA']
+    else:
+        instance.url_template = "https://zenodo.org/record/4311514/files/mesa-r{version}.zip"
+
+    instance.version='15140'
+    instance.start()   
+
+def get_hdf5():
+    instance = GetCodeFromHttp()
+    instance.url_template = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-{version}/src/hdf5-{version}.tar.bz2"
+    instance.filename_template='hdf-{version}.tar.bz2'
+    instance.version = '1.12.0'
+    instance.zip=False
+    instance.start()      
+
+
+def main():
+    get_lapack95()
+    get_crmath()
+    get_crlibm()
+    get_fpx3()
+    get_fpx3deps()
+    get_hdf5()
+    get_mesa()
+
+
+
+if __name__ == "__main__":
+    main()

src/amuse/community/mesa_r15140/examples/__init__.py

@@ -0,0 +1,8 @@
+"""
+The Astrophysical Multipurpose Software Environment
+
+AMUSE contains a lot of functionality to execute astrophysical experiments.
+Look into the interface packages for the interfacing to physical model simulation software.
+You can also use AMUSE to convert common data formats.
+
+"""