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Description

AMUSE is the Astrophysical MUltipurpose Software Environment, with which you can simulate many types of astrophysical systems. Within NEMO we focus on Gravitational Dynamics, as this is the prime focus in NEMO.

The user interacts with AMUSE in python, for example you can set up an amuse profile in ipython that preloads some common imports

ipython --profile=amuse

Internally many components in AMUSE are legacy codes (C,C++,Fortran) running at fantastic speeds, but the user will interact via python interfaces.

An example is shown below, and within NEMO the script amuse_convert.py can be used to convert between different snapshot formats that AMUSE supports. See also unsio(3NEMO) for another approach to such snapshot conversion.

Examples

1. Here is an example snippet of AMUSE python code creating a Plummer sphere (see also mkplummer(1NEMO) ), in nbody units and writing the resulting snapshot as an ascii table:

from amuse.ic.plummer import new_plummer_model
from amuse.io import write_set_to_file

stars = new_plummer_model(10)
write_set_to_file(stars, ’plummer.txt’, format=’txt’)

This table has mass, radius, velocity and position, one star per row. Notice velocity comes before position! Thus the following NEMO command will convert it to a standard snapshot(5NEMO) file:

nbody=$(tabcols plummer.txt | wc -l)
tabcols plummer.txt |\
tabtos - plummer.snap block1=mass,skip,vx,vy,vz,x,y,z nbody=$nbody

(the current version of tabtos(1NEMO) is not smart enough to skip comment lines.

2. Here is a more NEMO like example, running from the commandline. If AMUSE is properly installed, the first example creates a Plummer model in memory, the second example creates an output text file, of which the first particle is displayed as the 3rd line in this table:

amuse_convert.py
amuse_convert.py -o plummer.txt
head -3 plummer.txt

#mass radius vx vy vz x y z #mass length length * time**-1 length * time**-1 length * time**-1 length length length 0.0078125 0.0 -0.256557735045 0.0863119421344 -0.0484937398944 -0.609540735858 -0.854122523728 0.736476012616

3. Here is an not-yet-working example of creating initial conditions in NEMO, using an integration method in AMUSE, and returning the data back to NEMO for further analysis:

mkplummer - 20 | snapprint - m,0.0,vx,vy,vz,x,y,z format=%16.13f csv=t > p20.csv
amuse_convert.py -i p20.csv -I csv -o p20.amuse -O amuse
amuse_integrate.py -i p20.amuse -o p20a.amuse -T 10 -t 1 -c hermite
amuse_convert.py -i p20a.amuse

Bugs

The follow round trip exercise on the txt format causes an error:

fmt=txt amuse_convert.py -o junk1 -O $fmt -n 100 amuse_convert.py -i junk1 -I $fmt -o junk2 -O $fmt amuse.io.base.IoException: IO exception: Number of values on line ’0.01 0.0 -0.319149817818 0.911387278048 0.00131274766207 -1.22528821614 -0.310636170602 0.0257190619401’ is 8, expected 0

formats like csv, amuse-txt, tsf, dyn all seem to work.

Install

Within NEMO the command

mknemo amuse

will get you started on the install. Note there is a user release that does not need NEMO, which can be a series of pip install:

pip install amuse-framework
pip install amuse-bhtree

A developer release is recommended with NEMO, the start of which will likely look as follows:

cd $NEMO/local/amuse
./setup develop amuse-framework
./setup develop bhtree
./setup test bhtree

The AMUSE bhtree code should be the same as the original program bhtree(1NEMO) in NEMO, allowing for a closer comparison was it not for some output timing bug. AMUSE will also install the BHTC program, which should be the same as our bhtree(1NEMO) .

Snapshot

As described in the help (-h) of amuse_convert.py, the following formats are supported by AMUSE: 
amuse        HDF5 file
amuse-txt    text files with AMUSE header format
csv        comma separated files
dyn        Starlab binary structured file
gadget        Gadget binary data file
hdf5        HDF5 file
nemo        NEMO structured file, binary version?
starlab        Starlab binary structured file
tsf        NEMO structured file, ascii version 
txt        text file containing a table of values separated by a predefined
vts        text file containing a table of values separated by a predefined character
vtu        text file containing a table of values separated by a predefined character

Programs

The following AMUSE scripts are available via NEMO:

amuse_convert.py
converts snapshots using AMUSE, optionally create a Plummer sphere if only output is requested.

amuse_integrate.py
integrates a snapshot using AMUSE. Only a few codes are supported: bhtree (default), hermite, smalln and brutus. For convenience it will generate a Plummer sphere if no input file (-i) is provided.

Files


$NEMO/src/scripts/mknemo.d/amuse - example install script (can be run via
mknemo)
$NEMO/usr/amuse - amuse_convert.py, amuse_integrate.py - also copied to $NEMOBIN
during install
$NEMO/usr/amuse/95-amuse.py - example ipython profile file for ~/.ipython/profile_amuse/startup/
$NEMO/local/amuse - root of AMUSE source code after install via mknemo (a.k.a.
$AMUSE_DIR to some)
95-amuse.py

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See Also

nemo(1NEMO) , zeno(1NEMO) , starlab(1NEMO) , bhtree(1NEMO) , tabtos(1NEMO) , unsio(3NEMO) 


https://www.amusecode.org/

History

Geneology: arguably AMUSE is derived from starlab, which in itself was an outcome of NEMO. 


25-may-2025    man page and amuse_convert.py written (MODEST25-SPZ)    PJT
27-mar-2025    overhauled AMUSE installation method        PJT
14-jun-2025    added scripts to $NEMO/usr/amuse    PJT

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