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120 changes: 120 additions & 0 deletions INSTALL
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// Copyright (c) 2018, Lawrence Livermore National Security, LLC.
// Produced at the Lawrence Livermore National Laboratory
// Written by M.R. Dorr, J.-L. Fattebert and M.E. Wickett
// LLNL-CODE-747500
// All rights reserved.
// This file is part of AMPE.
// For details, see https://github.com/LLNL/AMPE
// Please also read AMPE/LICENSE.
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
// - Redistributions of source code must retain the above copyright notice,
// this list of conditions and the disclaimer below.
// - Redistributions in binary form must reproduce the above copyright notice,
// this list of conditions and the disclaimer (as noted below) in the
// documentation and/or other materials provided with the distribution.
// - Neither the name of the LLNS/LLNL nor the names of its contributors may be
// used to endorse or promote products derived from this software without
// specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY,
// LLC, THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY
// DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
// OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
// HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
// STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
// IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
//
Step 0:
Run autoconf:

autoconf

This should generate the 'configure' file

Step 1: Configure for a specific combination of platform, compiler and
optimization level

After checking out from the repository, cd into the top level
directory and execute the configure script for the
platform-compiler-optimization you want to build. For example, to
configure for cab using the Intel C++ and Fortran compilers with
optimization, execute

scripts/doconfig_peloton_icpc_ifort_opt

If a script does not exist for the platform-compiler_optimization
combination you want, you'll have to create your own using one of the
existing scripts as an example. Note that all of the scripts
currently in the "scripts" subdirectory assume that they are being
executed from the top level directory (as indicated above), which is
the location of of the configure script the "doconfig" scripts depend
upon.

Step 2: Install the base (i.e., third-party) libraries for the
new platform-compiler-optimization combination

The configuration step just performed will create a subdirectory
"build" of the top level directory (if it didn't already exist) and a
subdirectory of the "build" directory labeled by the associated
platform-compiler-optimization combination. Underneath that
subdirectory are three more subdirectories: base, config, and objects.
In other words, for the current example, the following directory tree
is created if ruuning the script on cab:

(top level directory)
|
|
build
|
|
cab-mpiicpc-14.0.174-ifort-14.0.174-opt
| | |
| | |
base config objects

To install the base libraries, cd into the base subdirectory and
execute the doinstall script located there:

cd build/cab-mpiicpc-14.0.174-ifort-14.0.174-opt/base
doinstall

This will compile and install the base libraries, which currently
consist of Hypre, Sundials and SAMRAI. The SAMRAI build takes a while, so
patience is required.

Step 3: Build the AMPE code

Under the build/platform-compiler-optimization/objects directory
created by the configuration step performed in Step 1, you will find a
directory tree that mirrors all of the subdirectories of the top level
source directory that contain a "Makefile.in" file.

To build the AMPE code, just cd to the objects directory amd gmake:

cd build/cab-mpiicpc-14.0.174-ifort-14.0.174-opt/objects
gmake

The object files and executable are generated in the current
directory. You can run the code from there. Note that the input
files (which do not depend on the specific choice of
platform-compiler-optimization) will still be over in the common
source directory, so you will have to specify the path (or perhaps
make a link). For example,

srun -n32 -ppdebug ampe2d top-level-directory/ampe/trunk/examples/AuNi_2D/9grains_AuNi_initial.input


Miscellaneous notes:

1. The configuration performed in Step 1 generates the Makefile in
build/cab-mpiicpc-14.0.174-ifort-14.0.174-opt/objects from the template Makefile.in in
source. This includes the generation of the file Makefile.depend in
source, which describes the build dependencies. This means that if
any changes are made to the source code that could affect the
dependencies, the configuration step should be redone.
63 changes: 63 additions & 0 deletions LICENSE
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Copyright (c) 2006-2018, Lawrence Livermore National Security, LLC.

Produced at the Lawrence Livermore National Laboratory

Written by:

Milo R. Dorr ([email protected])
Jean-Luc Fattebert ([email protected])
Mike E. Wickett ([email protected])

LLNL-CODE-747500.

All rights reserved.

This file is part of AMPE. For details, see https://github.com/LLNL/AMPE.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

- Redistributions of source code must retain the above copyright notice, this
list of conditions and the disclaimer below.

- Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the disclaimer (as noted below) in the
documentation and/or other materials provided with the distribution.

- Neither the name of the LLNS/LLNL nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY, LLC, THE
U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Additional BSD Notice

1. This notice is required to be provided under our contract with the U.S.
Department of Energy (DOE). This work was produced at Lawrence Livermore
National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE.

2. Neither the United States Government nor Lawrence Livermore National
Security, LLC nor any of their employees, makes any warranty, express or
implied, or assumes any liability or responsibility for the accuracy,
completeness, or usefulness of any information, apparatus, product, or process
disclosed, or represents that its use would not infringe privately-owned rights.

3. Also, reference herein to any specific commercial products, process, or
services by trade name, trademark, manufacturer or otherwise does not
necessarily constitute or imply its endorsement, recommendation, or favoring by
the United States Government or Lawrence Livermore National Security, LLC. The
views and opinions of authors expressed herein do not necessarily state or
reflect those of the United States Government or Lawrence Livermore National
Security, LLC, and shall not be used for advertising or product endorsement
purposes.

65 changes: 65 additions & 0 deletions README.md
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AMPE v2.0
=========

Adaptive Mesh Phase-field Evolution

Authors
-------

* Milo R. Dorr ([email protected])
* Jean-Luc Fattebert ([email protected])
* Mike E. Wickett ([email protected])

Dependencies
------------

* [Hypre] (https://github.com/LLNL/hypre)

* [SAMRAI] (https://github.com/LLNL/SAMRAI)

* [CPODES] (https://simtk.org/projects/cpodes)

* [Sundials] (https://github.com/LLNL/sundials)

* [HDF5] (https://support.hdfgroup.org/HDF5)

* [NetCDF] (https://www.unidata.ucar.edu/software/netcdf)

* [BOOST] (http://www.boost.org)

Since CPODES is currently not distributed with Sundials, and SAMRAI
does not supports the lastest SUNDIALS release, modifications to
these libraries had to be made. The modified libraries are distributed
with this code under the 'base' directory and need to be built before
building the main code.

References
----------

M. R. Dorr, J.-L. Fattebert, M. E. Wickett, J. F. Belak, P. E. A. Turchi,
"A Numerical Algorithm for the Solution of a Phase-Field Model of
Polycrystalline materials",
J. Comp. Phys. 229 (3), p. 626-641 (2010)

J.-L. Fattebert, M. E. Wickett, P. E. A. Turchi,
"Phase-field modeling of coring during solidification of Au-Ni alloy using
quaternions and CALPHAD input",
ACTA MATERIALIA, 62, (2014), 89-104

Release
-------

Copyright (c) 2018, Lawrence Livermore National Security, LLC.

Produced at the Lawrence Livermore National Laboratory.

All rights reserved.

Unlimited Open Source - BSD Distribution

For release details and restrictions, please read the LICENSE file.
It is also linked here:
- [LICENSE](./LICENSE)

`LLNL-CODE-747500` `OCEC-18-028`

29 changes: 29 additions & 0 deletions aclocal.m4
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# generated automatically by aclocal 1.9.2 -*- Autoconf -*-

# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004
# Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.

m4_include([config/arg-with-environment.m4])
m4_include([config/btng.m4])
m4_include([config/casc_cxx.m4])
m4_include([config/casc_libs_and_headers.m4])
m4_include([config/casc_misc.m4])
m4_include([config/casc_mpi.m4])
m4_include([config/compiler-id.m4])
m4_include([config/compiling-boolean.m4])
m4_include([config/compiling-namespace.m4])
m4_include([config/split-libs-string.m4])
m4_include([config/support-hdf5.m4])
m4_include([config/support-boost.m4])
m4_include([config/support-netcdf.m4])
m4_include([config/support-hypre.m4])
m4_include([config/support-restrict.m4])
m4_include([config/variable-header-filenames.m4])
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