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Grzegorz Kowal 2019-11-22 18:14:28 -03:00
commit 150146871e
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23
.gitlab-ci.yml Normal file
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image: debian
stages:
- build
build:
stage: build
before_script:
- apt-get -q update
- apt-get -q -y install gawk make gfortran libhdf5-dev libopenmpi-dev
script:
- cd ./build/
- cp -al make.default make.config
- cp -al ./hosts/default ./hosts/$HOSTNAME
- export HDF5DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial
- make MPI=N NDIMS=2
- make clean
- make MPI=N NDIMS=3
- make clean
- make MPI=Y NDIMS=2
- make clean
- make MPI=Y NDIMS=3

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CHANGELOG.md Normal file
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# 2019-10-04 No version yet. ##
----
- support for rectangular adaptive domain in 2D and 3D;
- support for hydrodynamical (HYDRO) and magnetohydrodynamical (MHD) equations, both in classical and relativistic formulations;
- support for adiabatic (ADI) and isothermal (ISO) equation of state;
- support for viscosity and resistivity source terms;
- support for passive scalars;
- time integration using Euler and 2nd order Runge-Kutta methods or up to 4th order Stron Stability Preserving Runge-Kutta;
- a number of spatial interpolation using 2nd order TVD methods, up to 9th order Monotonicity-Preserving;
- HLL-family of approximate Riemann solvers (HLL, HLLC, and HLLD);
- GLM scheme for the induction equation;
- MPI parallelization;

63
README.md
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@ -1,12 +1,11 @@
--------------------------------------------------------------------------------
# **The AMUN Code** # **The AMUN Code**
## Copyright (C) 2008-2019 Grzegorz Kowal ## ## Copyright (C) 2008-2019 Grzegorz Kowal
--------------------------------------------------------------------------------
AMUN is a parallel code to perform numerical simulations in fluid approximation AMUN is a parallel code to perform numerical simulations in fluid approximation
on uniform or non-uniform (adaptive) meshes. The goal in developing this code is on uniform or non-uniform (adaptive) meshes. The goal in developing this code is
to create a solid framework for simulations with support for number of numerical to create a solid framework for simulations with support for number of numerical
methods which can be selected in an easy way through the parameter file. The methods which can be selected in an easy way through a parameter file. The
following features are already implemented: following features are already implemented:
* hydrodynamic and magnetohydrodynamic set of equations (HD and MHD), * hydrodynamic and magnetohydrodynamic set of equations (HD and MHD),
@ -18,11 +17,13 @@ following features are already implemented:
* 2nd order TVD interpolation with number of limiters and higher order * 2nd order TVD interpolation with number of limiters and higher order
reconstructions, reconstructions,
* Riemann solvers of Roe- and HLL-types (HLL, HLLC, and HLLD), * Riemann solvers of Roe- and HLL-types (HLL, HLLC, and HLLD),
* periodic and open boundary conditions, * standard boundary conditions: periodic, open, reflective, hydrostatic, etc.
* viscous and resistive source terms, * viscous and resistive source terms,
* suppor for passive scalars (up to 100),
* data stored in the HDF5 format, * data stored in the HDF5 format,
* MPI parallelization, * MPI parallelization,
* completely written in Fortran 2003. * completely written in Fortran 2003,
* Python interface to read data.
This program is free software: you can redistribute it and/or modify it under This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software the terms of the GNU General Public License as published by the Free Software
@ -46,12 +47,16 @@ Developers
Requirements Requirements
============ ============
* Fortran 2003 compiler (tested compilers include * Fortran 2003 compiler, tested compilers include:
[GNU Fortran](http://gcc.gnu.org/fortran/) version 4.5 or newer, - [GNU Fortran](https://gcc.gnu.org/fortran/) version 4.5 or newer,
[Intel Fortran](https://software.intel.com/en-us/fortran-compilers) compiler - [PGI Community Edition](https://www.pgroup.com/products/community.htm),
version 9.0 or newer) version 18.10 or newer,
* [HDF5 libraries](http://www.hdfgroup.org/HDF5/) version 1.8 or newer. - [Intel Fortran](https://software.intel.com/en-us/fortran-compilers)
* [OpenMPI](https://www.open-mpi.org/) version 1.8 or newer for parallel runs. compiler version 9.0 or newer.
* [HDF5 libraries](https://www.hdfgroup.org/solutions/hdf5/), tested with
version 1.8 or newer.
* [OpenMPI](https://www.open-mpi.org/) for parallel runs, tested with version
1.8 or newer.
Environment Variables Environment Variables
@ -65,11 +70,15 @@ the HDF5 libraries have been installed.
Compilation Compilation
=========== ===========
1. Clone the AMUN source code: `git clone https://bitbucket.org/amunteam/amun-code.git`, 1. Clone the AMUN source code:
or unpack the archive downloaded from page - from Bitbucket:
`git clone https://grzegorz_kowal@bitbucket.org/amunteam/amun-code.git`,
- from GitLab:
`git clone https://gitlab.com/gkowal/amun-code.git`
- or unpack the archive downloaded from page
[Downloads](https://bitbucket.org/amunteam/amun-code/downloads/). [Downloads](https://bitbucket.org/amunteam/amun-code/downloads/).
2. Go to directory **build/hosts/** and copy file **default** to a new file named 2. Go to directory **build/hosts/** and copy file **default** to a new file named
exactly as your host name (name returned by command `hostname`). exactly as your host name, i.e. `cp default $HOSTNAME`.
3. Customize your compiler and compilation options in your new host file. 3. Customize your compiler and compilation options in your new host file.
4. Go up to directory **build/** and copy file **make.default** to **make.config**. 4. Go up to directory **build/** and copy file **make.default** to **make.config**.
5. Customize compilation time options in **make.config**. 5. Customize compilation time options in **make.config**.
@ -80,16 +89,18 @@ Compilation
Usage Usage
===== =====
In order to run some test problems you can simply copy corresponding parameter In order to run some test problems you can simply copy the problem parameter
from directory **problems/** to the location when you wish to run your test. file from directory **problems/** to the location where you wish to run your
Copy the executable file **amun.x** compiled earlier to the same directory. If test. Copy the executable file **amun.x** from the **build/** directory compiled
you provide option _-i <parameter_file>_, the code will know that the parameters earlier. If you provide option _-i <parameter_file>_, the code will know that
have to be read from file _<parameter_file>_. If you don't provide this option, parameters have to be read from file _<parameter_file>_. If you don't provide
the code will assume that the parameters are stored in file **params.in** in the this option, the code assumes that the parameters are stored in file
same director. **params.in** in the same director.
In order to run serial version, type in your terminal: `amun.x -i params.in`. In order to run serial version, just type in your terminal:
`./amun.x -i ./params.in`.
In order to run the parallel version (after compiling the code with MPI In order to run parallel version (after compiling the code with MPI support),
version), type in your terminal: `mpirun -n N ./amun.x -i params.in`, where N is type in your terminal:
the number of processors. `mpirun -n N ./amun.x -i ./params.in`,
where N is the number of processors to use.

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bitbucket-pipelines.yml Normal file
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# This is a sample build configuration for Other.
# Check our guides at https://confluence.atlassian.com/x/5Q4SMw for more examples.
# Only use spaces to indent your .yml configuration.
# -----
# You can specify a custom docker image from Docker Hub as your build environment.
image: atlassian/default-image:2
pipelines:
default:
- step:
name: Build
script:
- apt-get -q update
- apt-get -q -y install gawk make gfortran libhdf5-dev libopenmpi-dev
- cd ./build
- cp -al make.default make.config
- cp -al ./hosts/default ./hosts/$HOSTNAME
- export HDF5DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial
- make MPI=N NDIMS=2
- make clean
- make MPI=N NDIMS=3
- make clean
- make MPI=Y NDIMS=2
- make clean
- make MPI=Y NDIMS=3

347
python/amun.py
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@ -37,6 +37,7 @@ import numpy as np
import os.path as op import os.path as op
import sys import sys
def amun_compatible(fname): def amun_compatible(fname):
''' '''
Subroutine checks if the HDF5 file is AMUN compatible. Subroutine checks if the HDF5 file is AMUN compatible.
@ -47,39 +48,28 @@ def amun_compatible(fname):
Return values: Return values:
ret - True or False; True or False;
Examples: Examples:
comp = amun_compatible('p000010_00000.h5') comp = amun_compatible('p000010_00000.h5')
''' '''
try: with h5.File(fname, 'r') as f:
f = h5.File(fname, 'r') if 'codes' in f.attrs:
if f.attrs['code'].astype(str) == "AMUN":
# check if the file is written in the AMUN format or at least contains return True
# necessary groups else:
# print("'%s' contains attribute 'code'," % fname, \
ret = True " but it is not 'AMUN'!")
if 'code' in f.attrs: return False
if f.attrs['code'].astype(str) != "AMUN": elif 'attributes' in f and 'coordinates' in f and \
print("'%s' contains attribute 'code'", \ 'variables' in f:
" but it is not set to 'AMUN'!" % fname) return True
ret = False else:
elif not 'attributes' in f or \ print("'%s' misses one of these groups:" % fname, \
not 'coordinates' in f or \ "'attributes', 'coordinates' or 'variables'!")
not 'variables' in f: return False
print("'%s' misses one of these groups: ", \
"'attributes', 'coordinates' or 'variables'!" % fname)
ret = False
f.close()
except:
print("It seems '%s' is not an HDF5 file!" % fname)
ret = False
return ret
def amun_attribute(fname, aname): def amun_attribute(fname, aname):
@ -93,7 +83,7 @@ def amun_attribute(fname, aname):
Return values: Return values:
ret - the value of the attribute; ret - the value of the attribute or None;
Examples: Examples:
@ -101,29 +91,19 @@ def amun_attribute(fname, aname):
''' '''
if not amun_compatible(fname): if not amun_compatible(fname):
return False return None
try: with h5.File(fname, 'r') as f:
f = h5.File(fname, 'r') if aname in f['attributes'].attrs:
g = f['attributes'] attr = f['attributes'].attrs[aname]
if aname in g.attrs:
attr = g.attrs[aname]
if attr.dtype.type is np.string_: if attr.dtype.type is np.string_:
ret = np.squeeze(attr).astype(str) ret = np.squeeze(attr).astype(str)
else: else:
ret = np.squeeze(attr) ret = np.squeeze(attr)
return ret
else: else:
print("Attribute '%s' cannot be retrieved from '%s'!" % (aname, fname)) print("Attribute '%s' cannot be found in '%s'!" % (aname, fname))
ret = False return None
f.close()
except:
print("Attribute '%s' cannot be retrieved from '%s'!" % (aname, fname))
ret = False
return ret
def amun_coordinate(fname, iname): def amun_coordinate(fname, iname):
@ -137,7 +117,7 @@ def amun_coordinate(fname, iname):
Return values: Return values:
ret - the values of the item; ret - the value of the item or None;
Examples: Examples:
@ -145,29 +125,14 @@ def amun_coordinate(fname, iname):
''' '''
if not amun_compatible(fname): if not amun_compatible(fname):
return False return None
try: with h5.File(fname, 'r') as f:
f = h5.File(fname, 'r') if iname in f['coordinates']:
g = f['coordinates'] return np.array(f['coordinates'][iname])
if iname in g:
item = g[iname]
if item.dtype.type is np.string_:
ret = np.squeeze(item).astype(str)
else:
ret = np.squeeze(item)
else: else:
print("Coordinate item '%s' cannot be retrieved from '%s'!" % (iname, fname)) print("Coordinate item '%s' not found in group 'coordinate' of '%s'!" % (iname, fname))
ret = False return None
f.close()
except:
print("Coordinate item '%s' cannot be retrieved from '%s'!" % (iname, fname))
ret = False
return ret
def amun_dataset(fname, vname, shrink = 1, progress = False): def amun_dataset(fname, vname, shrink = 1, progress = False):
@ -192,138 +157,138 @@ def amun_dataset(fname, vname, shrink = 1, progress = False):
''' '''
if not amun_compatible(fname): if not amun_compatible(fname):
return False return None
try: dname = op.dirname(fname)
dname = op.dirname(fname)
if progress: if progress:
sys.stdout.write("Data file path:\n '%s'\n" % (dname)) sys.stdout.write("Data file path:\n '%s'\n" % (dname))
# get attributes necessary to reconstruct the domain # get attributes necessary to reconstruct the domain
# #
eqsys = amun_attribute(fname, 'eqsys') eqsys = amun_attribute(fname, 'eqsys')
eos = amun_attribute(fname, 'eos') eos = amun_attribute(fname, 'eos')
nr = amun_attribute(fname, 'isnap') nr = amun_attribute(fname, 'isnap')
nc = amun_attribute(fname, 'nprocs') nc = amun_attribute(fname, 'nprocs')
nl = amun_attribute(fname, 'nleafs') nl = amun_attribute(fname, 'nleafs')
if eos == 'adi': if eos == 'adi':
gm = amun_attribute(fname, 'gamma') gm = amun_attribute(fname, 'gamma')
# prepare array to hold data # get block dimensions and the maximum level
# #
ndims = amun_attribute(fname, 'ndims') ndims = amun_attribute(fname, 'ndims')
nn = amun_attribute(fname, 'ncells') nn = amun_attribute(fname, 'ncells')
bm = np.array([nn, nn, nn]) bm = np.array([nn, nn, nn])
if ndims == 2: if ndims == 2:
bm[2] = 1 bm[2] = 1
ng = amun_attribute(fname, 'nghosts') ng = amun_attribute(fname, 'nghosts')
ml = amun_attribute(fname, 'maxlev') ml = amun_attribute(fname, 'maxlev')
f = h5.File(fname, 'r')
if 'rdims' in f['attributes'].attrs:
rm = amun_attribute(fname, 'rdims')
elif 'bdims' in f['attributes'].attrs:
rm = amun_attribute(fname, 'bdims')
else:
rm = amun_attribute(fname, 'domain_base_dims')
f.close()
# build the list of supported variables # get the base block dimensions
# #
variables = [] rm = amun_attribute(fname, 'bdims')
f = h5.File(fname, 'r') if rm is None:
rm = amun_attribute(fname, 'domain_base_dims')
if rm is None:
rm = amun_attribute(fname, 'rdims')
if rm is None:
return None
# build the list of supported variables
#
variables = []
with h5.File(fname, 'r') as f:
for var in f['variables'].keys(): for var in f['variables'].keys():
variables.append(var) variables.append(var)
f.close()
# add derived variables if possible # add derived variables if possible
# #
variables.append('level') variables.append('level')
if 'velx' in variables and 'vely' in variables and 'velz' in variables: if 'velx' in variables and 'vely' in variables and 'velz' in variables:
variables.append('velo') variables.append('velo')
variables.append('divv') variables.append('divv')
variables.append('vort') variables.append('vort')
if 'magx' in variables and 'magy' in variables and 'magz' in variables: if 'magx' in variables and 'magy' in variables and 'magz' in variables:
variables.append('magn') variables.append('magn')
variables.append('divb') variables.append('divb')
variables.append('curr') variables.append('curr')
if (eqsys == 'hd' or eqsys == 'mhd') and eos == 'adi' \ if (eqsys == 'hd' or eqsys == 'mhd') and eos == 'adi' \
and 'pres' in variables: and 'pres' in variables:
variables.append('eint') variables.append('eint')
if 'dens' in variables and 'pres' in variables: if 'dens' in variables and 'pres' in variables:
variables.append('temp') variables.append('temp')
if (eqsys == 'hd' or eqsys == 'mhd') \ if (eqsys == 'hd' or eqsys == 'mhd') \
and 'dens' in variables \ and 'dens' in variables \
and 'velx' in variables \ and 'velx' in variables \
and 'vely' in variables \ and 'vely' in variables \
and 'velz' in variables: and 'velz' in variables:
variables.append('ekin') variables.append('ekin')
if (eqsys == 'mhd' or eqsys == 'srmhd') \ if (eqsys == 'mhd' or eqsys == 'srmhd') \
and 'magx' in variables \ and 'magx' in variables \
and 'magy' in variables \ and 'magy' in variables \
and 'magz' in variables: and 'magz' in variables:
variables.append('emag') variables.append('emag')
if eqsys == 'hd' and 'ekin' in variables and 'eint' in variables: if eqsys == 'hd' and 'ekin' in variables and 'eint' in variables:
variables.append('etot') variables.append('etot')
if eqsys == 'mhd' and 'eint' in variables \ if eqsys == 'mhd' and 'eint' in variables \
and 'ekin' in variables \ and 'ekin' in variables \
and 'emag' in variables: and 'emag' in variables:
variables.append('etot') variables.append('etot')
if (eqsys == 'srhd' or eqsys == 'srmhd') and 'velo' in variables: if (eqsys == 'srhd' or eqsys == 'srmhd') and 'velo' in variables:
variables.append('lore') variables.append('lore')
# check if the requested variable is in the variable list # check if the requested variable is in the variable list
# #
if not vname in variables: if not vname in variables:
print('The requested variable cannot be extracted from the file datasets!') print('The requested variable cannot be extracted from the file datasets!')
return False return None
# check if the shrink parameter is correct (block dimensions should be # check if the shrink parameter is correct (block dimensions should be
# divisible by the shrink factor) # divisible by the shrink factor)
# #
shrink = max(1, int(shrink)) shrink = max(1, int(shrink))
if shrink > 1: if shrink > 1:
if (nn % shrink) != 0: if (nn % shrink) != 0:
print('The block dimension should be divisible by the shrink factor!') print('The block dimension should be divisible by the shrink factor!')
return False return None
sh = shrink sh = shrink
while(sh > 2 and sh % 2 == 0): while(sh > 2 and sh % 2 == 0):
sh = int(sh / 2) sh = int(sh / 2)
if (sh % 2) != 0: if (sh % 2) != 0:
print('The shrink factor should be a power of 2!') print('The shrink factor should be a power of 2!')
return False return None
# determine the actual maximum level from the blocks # determine the actual maximum level from the blocks
# #
ml = 0 levs = []
for n in range(nc): for n in range(nc):
fname = 'p%06d_%05d.h5' % (nr, n) fname = 'p%06d_%05d.h5' % (nr, n)
lname = op.join(dname, fname) lname = op.join(dname, fname)
dblocks = amun_attribute(lname, 'dblocks') dblocks = amun_attribute(lname, 'dblocks')
if dblocks > 0: if dblocks > 0:
levels = amun_coordinate(lname, 'levels') levs = np.append(levs, [amun_coordinate(lname, 'levels')])
ml = max(ml, levels.max()) ml = int(levs.max())
# prepare dimensions of the output array and allocate it # prepare dimensions of the output array and allocate it
# #
dm = np.array(rm[0:ndims] * bm[0:ndims] * 2**(ml - 1) / shrink, \ dm = np.array(rm[0:ndims] * bm[0:ndims] * 2**(ml - 1) / shrink, \
dtype = np.int32) dtype = np.int32)
ret = np.zeros(dm[::-1]) ret = np.zeros(dm[::-1])
# iterate over all subdomain files # iterate over all subdomain files
# #
nb = 0 nb = 0
for n in range(nc): for n in range(nc):
fname = 'p%06d_%05d.h5' % (nr, n) fname = 'p%06d_%05d.h5' % (nr, n)
lname = op.join(dname, fname) lname = op.join(dname, fname)
dblocks = amun_attribute(lname, 'dblocks') dblocks = amun_attribute(lname, 'dblocks')
if dblocks > 0: if dblocks > 0:
levels = amun_coordinate(lname, 'levels') levels = amun_coordinate(lname, 'levels')
coords = amun_coordinate(lname, 'coords') coords = amun_coordinate(lname, 'coords')
dx = amun_coordinate(lname, 'dx') dx = amun_coordinate(lname, 'dx')
dy = amun_coordinate(lname, 'dy') dy = amun_coordinate(lname, 'dy')
dz = amun_coordinate(lname, 'dz') dz = amun_coordinate(lname, 'dz')
f = h5.File(lname, 'r') with h5.File(lname, 'r') as f:
g = f['variables'] g = f['variables']
if vname == 'level': if vname == 'level':
dataset = np.zeros(g[variables[0]].shape) dataset = np.zeros(g[variables[0]].shape)
@ -451,8 +416,6 @@ def amun_dataset(fname, vname, shrink = 1, progress = False):
else: else:
dataset = g[vname][:,:,:,:] dataset = g[vname][:,:,:,:]
f.close()
# rescale all blocks to the effective resolution # rescale all blocks to the effective resolution
# #
for l in range(dblocks): for l in range(dblocks):
@ -479,13 +442,9 @@ def amun_dataset(fname, vname, shrink = 1, progress = False):
% (vname, fname, nb, nl)) % (vname, fname, nb, nl))
sys.stdout.flush() sys.stdout.flush()
if (progress): if (progress):
sys.stdout.write('\n') sys.stdout.write('\n')
sys.stdout.flush() sys.stdout.flush()
except:
print("Dataset '%s' cannot be retrieved from '%s'!" % (vname, fname))
ret = False
return ret return ret

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python/setup.py Normal file
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@ -0,0 +1,13 @@
from setuptools import setup
setup(
name='amun',
description='Python Interface fo AMUN snapshots',
version='0.1',
author='Grzegorz Kowal',
author_email='grzegorz@amuncode.org',
url='https://www.amuncode.org/',
license='GPLv3',
py_modules=['amun'],
install_requires=['h5py', 'numpy']
)