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Update rebound interface to Rebound release version 4.0.1 #1019

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Update rebound interface to Rebound release version 4.0.1 #1019

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301fdfa
Update rebound interface to Rebound release version 4.0.1
rieder Dec 11, 2023
377585a
fix interface bug, update tests a bit
rieder Dec 12, 2023
9c28f75
rewrite and update rebound test
rieder Dec 14, 2023
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59 changes: 32 additions & 27 deletions src/amuse/community/rebound/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -20,15 +20,37 @@ OBJS = interface.o

CODELIB = src/librebound.a
CODEDIR = src/rebound
LIB_OBJ = $(CODEDIR)/src/rebound.o $(CODEDIR)/src/tree.o $(CODEDIR)/src/particle.o $(CODEDIR)/src/gravity.o \
$(CODEDIR)/src/integrator.o $(CODEDIR)/src/integrator_whfast.o $(CODEDIR)/src/integrator_whfasthelio.o \
$(CODEDIR)/src/integrator_ias15.o $(CODEDIR)/src/integrator_sei.o $(CODEDIR)/src/integrator_leapfrog.o \
$(CODEDIR)/src/integrator_hermes.o $(CODEDIR)/src/boundary.o \
$(CODEDIR)/src/collision.o $(CODEDIR)/src/tools.o \
$(CODEDIR)/src/communication_mpi.o $(CODEDIR)/src/display.o $(CODEDIR)/src/derivatives.o \
$(CODEDIR)/src/glad.o $(CODEDIR)/src/integrator_janus.o $(CODEDIR)/src/transformations.o \
$(CODEDIR)/src/simulationarchive.o $(CODEDIR)/src/output.o \
$(CODEDIR)/src/input.o \
LIB_OBJ = \
$(CODEDIR)/src/rebound.o \
$(CODEDIR)/src/tree.o \
$(CODEDIR)/src/particle.o \
$(CODEDIR)/src/gravity.o \
$(CODEDIR)/src/integrator.o \
$(CODEDIR)/src/integrator_whfast.o \
$(CODEDIR)/src/integrator_whfast512.o \
$(CODEDIR)/src/integrator_saba.o \
$(CODEDIR)/src/integrator_ias15.o \
$(CODEDIR)/src/integrator_sei.o \
$(CODEDIR)/src/integrator_bs.o \
$(CODEDIR)/src/integrator_leapfrog.o \
$(CODEDIR)/src/integrator_mercurius.o \
$(CODEDIR)/src/integrator_eos.o \
$(CODEDIR)/src/boundary.o \
$(CODEDIR)/src/input.o \
$(CODEDIR)/src/binarydiff.o \
$(CODEDIR)/src/output.o \
$(CODEDIR)/src/collision.o \
$(CODEDIR)/src/communication_mpi.o \
$(CODEDIR)/src/display.o \
$(CODEDIR)/src/tools.o \
$(CODEDIR)/src/rotations.o \
$(CODEDIR)/src/derivatives.o \
$(CODEDIR)/src/simulationarchive.o \
$(CODEDIR)/src/glad.o \
$(CODEDIR)/src/integrator_janus.o \
$(CODEDIR)/src/transformations.o \
$(CODEDIR)/src/fmemopen.o \
$(CODEDIR)/src/server.o

DOWNLOAD_FROM_WEB = $(PYTHON) ./download.py
PATCH_FILES = $(PYTHON) ./patch_files.py
Expand All @@ -39,25 +61,8 @@ AM_CFLAGS = -I$(AMUSE_DIR)/lib/amuse_mpi

all: rebound_worker

DOWNLOAD_CODES?=1

ifdef DOWNLOAD_CODES
$(CODEDIR)/Makefile:
make -C . download
else
$(CODEDIR)/Makefile:
@echo ""
@echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
@echo ""
@echo "DOWNLOAD_CODES is not set. Rebound will not be downloaded and built."
@echo "If you do want Rebound, set DOWNLOAD_CODES to 1."
@echo "bash> export DOWNLOAD_CODES=1"
@echo "csh> setenv DOWNLOAD_CODES 1"
@echo ""
@echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
@echo ""
@make -s --no-print-directory -C . raise_error
endif

download:
$(RM) -Rf .pc
Expand Down Expand Up @@ -85,7 +90,7 @@ distclean:
$(RM) -Rf .pc

$(CODELIB): $(CODEDIR)/Makefile
make -C $(CODEDIR) all CC=$(CC)
make -C $(CODEDIR) librebound CC=$(CC)
ar rv $(CODELIB) $(LIB_OBJ)
ranlib $(CODELIB)

Expand Down
80 changes: 48 additions & 32 deletions src/amuse/community/rebound/download.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,75 +2,91 @@

import subprocess
import os
import sys
import time
import argparse
import urllib.request
import urllib.parse
import urllib.error
from optparse import OptionParser
from shutil import which


class GetCodeFromHttp(object):
url_template = "https://github.com/hannorein/rebound/archive/{version}.tar.gz"
class GetCodeFromHttp:
filename_template = "{version}.tar.gz"
version = ""
name = ["rebound"]
url_template = [
"https://github.com/hannorein/rebound/archive/{version}.tar.gz"
]
version = [
"",
]

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)
def unpack_downloaded_file(self, filename, name, version):
print(f"unpacking {filename}")
arguments = ["tar", "-xf"]
arguments.append(filename)
subprocess.call(arguments, cwd=os.path.join(self.src_directory()))
subprocess.call(
["mv", "rebound-{version}".format(version=self.version), "rebound"],
["mv", f"{name}-{version}", name],
cwd=os.path.join(self.src_directory()),
)
print("done")

def start(self):
if os.path.exists("src"):
counter = 0
while os.path.exists("src.{0}".format(counter)):
while os.path.exists(f"src.{counter}"):
counter += 1
if counter > 100:
print("too many backup directories")
break
os.rename("src", "src.{0}".format(counter))
os.rename("src", f"src.{counter}")

os.mkdir("src")

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)
for i, url_template in enumerate(self.url_template):
url = url_template.format(version=self.version[i])
filename = self.filename_template.format(version=self.version[i])
filepath = os.path.join(self.src_directory(), filename)
print(f"downloading version {self.version[i]} from {url} to {filename}")
if which("wget") is not None:
arguments = ["wget", url]
subprocess.call(arguments, cwd=os.path.join(self.src_directory()))
elif which("curl") is not None:
arguments = ["curl", "-L", "-O", url]
subprocess.call(arguments, cwd=os.path.join(self.src_directory()))
else:
urllib.request.urlretrieve(url, filepath)
print("downloading finished")
self.unpack_downloaded_file(filename, self.name[i], self.version[i])


def new_argument_parser():
result = argparse.ArgumentParser()
result.add_argument(
"--rebound-version",
default="111bcd50de54e4cc70e1d4915918226a4adbe188",
# default="4df2b4603058e7d767aee9c26b586b55a5f4de65",
dest="rebound_version",
help="Rebound commit hash to download",
type=str,
)
return result


def main(version=""):
arguments = new_argument_parser().parse_args()
version = [
arguments.rebound_version,
]
instance = GetCodeFromHttp()
instance.version = version
instance.start()


def new_option_parser():
result = OptionParser()
result.add_option(
"--version",
default="31d117bdc92182073d0941c331f76e95f515bfc6",
dest="version",
help="version number to download",
type="string",
)
return result


if __name__ == "__main__":
options, arguments = new_option_parser().parse_args()
main(**options.__dict__)
main()
59 changes: 38 additions & 21 deletions src/amuse/community/rebound/interface.cc
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ static inline particle_location get_particle_from_identity(int index_of_the_part
for( ReboundSimulationVector::iterator i = codes.begin(); i != codes.end(); i++) {
code_state cs = *i;
particle.code = cs.code;
particle.p = reb_get_particle_by_hash(particle.code, index_of_the_particle);
particle.p = reb_simulation_particle_by_hash(particle.code, index_of_the_particle);
if (particle.p != NULL) break;
//*i = cs;
}
Expand Down Expand Up @@ -124,7 +124,7 @@ int set_mass(int index_of_the_particle, double mass){

if(p->m==0){
if(mass>0){
int index_old=reb_get_particle_index(p);
int index_old=reb_simulation_particle_index(p);
if(index_old!=code->N_active){
struct reb_particle tmp = code->particles[index_old];
for(int j=index_old; j>code->N_active; j--){
Expand All @@ -137,7 +137,7 @@ int set_mass(int index_of_the_particle, double mass){
}
else {
if(mass==0){
int index_old=reb_get_particle_index(p);
int index_old=reb_simulation_particle_index(p);
code->N_active--;

if(index_old!=code->N_active){
Expand Down Expand Up @@ -178,7 +178,7 @@ int new_particle(int * index_of_the_particle, double mass, double x,
pt.m = mass;
pt.r = radius;
pt.hash = new_hash;
reb_add(codes[code_index].code, pt);
reb_simulation_add(codes[code_index].code, pt);
//std::cout<<"new particle :"<<pt.id<< " << "<<code_index<<" << "<<pt.x<<std::endl;
*index_of_the_particle = new_hash;

Expand Down Expand Up @@ -275,10 +275,10 @@ int _evolve_code(double _tmax, code_state * cs){
return(1);
}

reb_step(code); // 0 to not do timing within step
reb_simulation_step(code); // 0 to not do timing within step

if ((code->t+code->dt)*dtsign>=tmax*dtsign && exact_finish_time==1){
reb_integrator_synchronize(code);
reb_simulation_synchronize(code);
code->dt = tmax-code->t;
last_step++;
}else{
Expand Down Expand Up @@ -383,7 +383,7 @@ int _evolve_code(double _tmax, code_state * cs){
}
}
}
reb_integrator_synchronize(code);
reb_simulation_synchronize(code);
code->dt = code->dt_last_done;
get_kinetic_energy(cs->subset, &ke1);
//printf("Code time: %d , %f -> %f (%f,%f)\n",cs->subset , code->t, tmax, ke1, (ke1-ke)/ke);
Expand Down Expand Up @@ -437,7 +437,7 @@ int _delete_particle(int index_of_the_particle, int code_index){
if(code_index < 0 || code_index >= (signed) codes.size()){
return -10;
}
reb_remove_by_hash(codes[code_index].code, index_of_the_particle, keepSorted);
reb_simulation_remove_particle_by_hash(codes[code_index].code, index_of_the_particle, keepSorted);
return 0;
}

Expand Down Expand Up @@ -495,7 +495,7 @@ int get_state(int index_of_the_particle, double * mass, double * x,
#endif // COLLISIONS_NONE
for( ReboundSimulationVector::iterator i = codes.begin(); i != codes.end(); i++) {
code_state cs = *i;
p = reb_get_particle_by_hash(cs.code, index_of_the_particle);
p = reb_simulation_particle_by_hash(cs.code, index_of_the_particle);
if (p != NULL) {
*subset = cs.subset;
break;
Expand Down Expand Up @@ -608,7 +608,7 @@ int get_subset(int index_of_the_particle, int * subset){
struct reb_particle* p=NULL;
for( ReboundSimulationVector::iterator i = codes.begin(); i != codes.end(); i++) {
code_state cs = *i;
p = reb_get_particle_by_hash(cs.code, index_of_the_particle);
p = reb_simulation_particle_by_hash(cs.code, index_of_the_particle);
if (p != NULL) {
*subset = cs.subset;
break;
Expand Down Expand Up @@ -638,7 +638,7 @@ int set_subset(int index_of_the_particle, int subset){
struct reb_particle* p=NULL;
for( ReboundSimulationVector::iterator i = codes.begin(); i != codes.end(); i++) {
code_state cs = *i;
p = reb_get_particle_by_hash(cs.code, index_of_the_particle);
p = reb_simulation_particle_by_hash(cs.code, index_of_the_particle);
if (p != NULL) {
if(cs.subset != subset) {return -2;}
break;
Expand All @@ -653,8 +653,8 @@ int cleanup_code() {
for( ReboundSimulationVector::iterator i = codes.begin(); i != codes.end(); i++) {
code_state cs = *i;
if(cs.code){
reb_remove_all(cs.code);
reb_free_simulation(cs.code);
reb_simulation_remove_all_particles(cs.code);
reb_simulation_free(cs.code);
cs.code = 0;
*i = cs;
}
Expand All @@ -679,7 +679,7 @@ int initialize_code(){
int nt = omp_get_max_threads();
omp_set_num_threads(nt);
#endif
reb_simulation * code = reb_create_simulation();
reb_simulation * code = reb_simulation_create();
codes.push_back(code_state(code));
code->integrator = reb_simulation::REB_INTEGRATOR_IAS15;
code->N_active = 0;
Expand Down Expand Up @@ -789,8 +789,8 @@ int set_velocity(int index_of_the_particle, double vx, double vy,
}

int new_subset(int * index, double time_offset) {
reb_simulation * code = reb_create_simulation();
reb_integrator_reset(code);
reb_simulation * code = reb_simulation_create();
reb_simulation_reset_integrator(code);
code->dt = timestep;
if(time_offset < 0) {time_offset = _time;}
code->integrator = reb_simulation::REB_INTEGRATOR_IAS15;
Expand All @@ -811,8 +811,8 @@ int stop_subset(int code_index) {
code_state cs = codes[code_index];
if(cs.code) {
reb_simulation * code = cs.code;
reb_remove_all(code);
reb_free_simulation(code);
reb_simulation_remove_all_particles(code);
reb_simulation_free(code);
cs.code = 0;
codes[code_index] = cs;
}
Expand Down Expand Up @@ -845,17 +845,34 @@ int _set_integrator(int value, int code_index){
code->integrator = reb_simulation::REB_INTEGRATOR_LEAPFROG;
break;
case 5:
code->integrator = reb_simulation::REB_INTEGRATOR_HERMES;
// This integrator was removed
return -1;
break;
case 6:
code->integrator = reb_simulation::REB_INTEGRATOR_WHFASTHELIO;
// This integrator was removed
return -1;
break;
case 7:
code->integrator = reb_simulation::REB_INTEGRATOR_NONE;
break;
case 8:
code->integrator = reb_simulation::REB_INTEGRATOR_JANUS;
break;
case 9:
code->integrator = reb_simulation::REB_INTEGRATOR_WHFAST512;
break;
case 10:
code->integrator = reb_simulation::REB_INTEGRATOR_SABA;
break;
case 11:
code->integrator = reb_simulation::REB_INTEGRATOR_MERCURIUS;
break;
case 12:
code->integrator = reb_simulation::REB_INTEGRATOR_EOS;
break;
case 13:
code->integrator = reb_simulation::REB_INTEGRATOR_BS;
break;
default:
code->integrator = reb_simulation::REB_INTEGRATOR_NONE;
return -1;
Expand Down Expand Up @@ -1014,7 +1031,7 @@ int set_boundary_size(double boundary_size, int code_index){
return -11;
}
reb_simulation * code = codes[code_index].code;
reb_configure_box(code,boundary_size,1,1,1);
reb_simulation_configure_box(code,boundary_size,1,1,1);
return 0;
}