Updating to master
This commit is contained in:
Joel Clemmer
47
.github/workflows/codeql-analysis.yml
vendored
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47
.github/workflows/codeql-analysis.yml
vendored
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@ -0,0 +1,47 @@
|
||||
# GitHub action to run static code analysis on C++ and Python code
|
||||
name: "CodeQL Code Analysis"
|
||||
|
||||
on:
|
||||
push:
|
||||
branches: [master]
|
||||
|
||||
jobs:
|
||||
analyze:
|
||||
name: Analyze
|
||||
if: ${{ github.repository == 'lammps/lammps' }}
|
||||
runs-on: ubuntu-latest
|
||||
|
||||
strategy:
|
||||
fail-fast: false
|
||||
matrix:
|
||||
language: ['cpp', 'python']
|
||||
|
||||
steps:
|
||||
- name: Checkout repository
|
||||
uses: actions/checkout@v2
|
||||
with:
|
||||
fetch-depth: 2
|
||||
|
||||
- name: Setup Python
|
||||
uses: actions/setup-python@v2
|
||||
with:
|
||||
python-version: '3.x'
|
||||
|
||||
- name: Initialize CodeQL
|
||||
uses: github/codeql-action/init@v1
|
||||
with:
|
||||
languages: ${{ matrix.language }}
|
||||
|
||||
- name: Create Build Environment
|
||||
run: cmake -E make_directory ${{github.workspace}}/build
|
||||
|
||||
- name: Building LAMMPS via CMake
|
||||
if: ${{ matrix.language == 'cpp' }}
|
||||
shell: bash
|
||||
working-directory: ${{github.workspace}}/build
|
||||
run: |
|
||||
cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
|
||||
cmake --build . --parallel 2
|
||||
|
||||
- name: Perform CodeQL Analysis
|
||||
uses: github/codeql-action/analyze@v1
|
||||
34
.github/workflows/unittest-macos.yml
vendored
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34
.github/workflows/unittest-macos.yml
vendored
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@ -0,0 +1,34 @@
|
||||
# GitHub action to build LAMMPS on MacOS and run unit tests
|
||||
name: "Unittest for MacOS"
|
||||
|
||||
on:
|
||||
push:
|
||||
branches: [master]
|
||||
|
||||
jobs:
|
||||
build:
|
||||
name: MacOS Unit Test
|
||||
if: ${{ github.repository == 'lammps/lammps' }}
|
||||
runs-on: macos-latest
|
||||
|
||||
steps:
|
||||
- name: Checkout repository
|
||||
uses: actions/checkout@v2
|
||||
with:
|
||||
fetch-depth: 2
|
||||
|
||||
- name: Create Build Environment
|
||||
run: cmake -E make_directory ${{github.workspace}}/build
|
||||
|
||||
- name: Building LAMMPS via CMake
|
||||
shell: bash
|
||||
working-directory: ${{github.workspace}}/build
|
||||
run: |
|
||||
cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \
|
||||
-DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
|
||||
cmake --build . --parallel 2
|
||||
|
||||
- name: Run Tests
|
||||
working-directory: ${{github.workspace}}/build
|
||||
shell: bash
|
||||
run: ctest -V
|
||||
@ -107,13 +107,15 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
|
||||
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
|
||||
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
|
||||
QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
|
||||
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
|
||||
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
|
||||
USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
|
||||
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
|
||||
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
|
||||
USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
|
||||
set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
|
||||
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
|
||||
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
|
||||
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
|
||||
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
|
||||
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
|
||||
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF)
|
||||
|
||||
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
|
||||
|
||||
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
|
||||
option(PKG_${PKG} "Build ${PKG} Package" OFF)
|
||||
endforeach()
|
||||
|
||||
@ -2,6 +2,7 @@ set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
|
||||
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
|
||||
${GPU_SOURCES_DIR}/fix_gpu.h
|
||||
${GPU_SOURCES_DIR}/fix_gpu.cpp)
|
||||
target_compile_definitions(lammps PRIVATE -DLMP_GPU)
|
||||
|
||||
set(GPU_API "opencl" CACHE STRING "API used by GPU package")
|
||||
set(GPU_API_VALUES opencl cuda hip)
|
||||
|
||||
@ -1,4 +1,7 @@
|
||||
########################################################################
|
||||
# As of version 3.3.0 Kokkos requires C++14
|
||||
set(CMAKE_CXX_STANDARD 14)
|
||||
########################################################################
|
||||
# consistency checks and Kokkos options/settings required by LAMMPS
|
||||
if(Kokkos_ENABLE_CUDA)
|
||||
message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
|
||||
@ -35,8 +38,8 @@ if(DOWNLOAD_KOKKOS)
|
||||
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
|
||||
include(ExternalProject)
|
||||
ExternalProject_Add(kokkos_build
|
||||
URL https://github.com/kokkos/kokkos/archive/3.2.01.tar.gz
|
||||
URL_MD5 ba72440e285ccde05b403694ea0c92e5
|
||||
URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz
|
||||
URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
|
||||
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
|
||||
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
|
||||
)
|
||||
@ -50,7 +53,7 @@ if(DOWNLOAD_KOKKOS)
|
||||
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
|
||||
add_dependencies(LAMMPS::KOKKOS kokkos_build)
|
||||
elseif(EXTERNAL_KOKKOS)
|
||||
find_package(Kokkos 3.2.01 REQUIRED CONFIG)
|
||||
find_package(Kokkos 3.3.01 REQUIRED CONFIG)
|
||||
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
|
||||
else()
|
||||
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
||||
|
||||
@ -94,7 +94,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
|
||||
-e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
|
||||
-e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
|
||||
|
||||
html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
|
||||
html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
|
||||
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
|
||||
@$(MAKE) $(MFLAGS) -C graphviz all
|
||||
@(\
|
||||
@ -118,7 +118,7 @@ html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
|
||||
@rm -rf html/PDF/.[sg]*
|
||||
@echo "Build finished. The HTML pages are in doc/html."
|
||||
|
||||
spelling: xmlgen $(VENV) $(SPHINXCONFIG)/false_positives.txt
|
||||
spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
|
||||
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
|
||||
@(\
|
||||
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
|
||||
|
||||
@ -424,6 +424,8 @@ INPUT = @LAMMPS_SOURCE_DIR@/utils.cpp \
|
||||
@LAMMPS_SOURCE_DIR@/input.h \
|
||||
@LAMMPS_SOURCE_DIR@/tokenizer.cpp \
|
||||
@LAMMPS_SOURCE_DIR@/tokenizer.h \
|
||||
@LAMMPS_SOURCE_DIR@/arg_info.cpp \
|
||||
@LAMMPS_SOURCE_DIR@/arg_info.h \
|
||||
@LAMMPS_SOURCE_DIR@/text_file_reader.cpp \
|
||||
@LAMMPS_SOURCE_DIR@/text_file_reader.h \
|
||||
@LAMMPS_SOURCE_DIR@/potential_file_reader.cpp \
|
||||
|
||||
@ -521,11 +521,14 @@ They must be specified in uppercase.
|
||||
* - VEGA906
|
||||
- GPU
|
||||
- AMD GPU MI50/MI60 GFX906
|
||||
* - VEGA908
|
||||
- GPU
|
||||
- AMD GPU GFX908
|
||||
* - INTEL_GEN
|
||||
- GPU
|
||||
- Intel GPUs Gen9+
|
||||
|
||||
This list was last updated for version 3.2 of the Kokkos library.
|
||||
This list was last updated for version 3.3 of the Kokkos library.
|
||||
|
||||
.. tabs::
|
||||
|
||||
|
||||
@ -96,6 +96,7 @@ OPT.
|
||||
* :doc:`eam/cd <pair_eam>`
|
||||
* :doc:`eam/cd/old <pair_eam>`
|
||||
* :doc:`eam/fs (gikot) <pair_eam>`
|
||||
* :doc:`eam/he <pair_eam>`
|
||||
* :doc:`edip (o) <pair_edip>`
|
||||
* :doc:`edip/multi <pair_edip>`
|
||||
* :doc:`edpd <pair_mesodpd>`
|
||||
@ -262,6 +263,7 @@ OPT.
|
||||
* :doc:`ufm (got) <pair_ufm>`
|
||||
* :doc:`vashishta (gko) <pair_vashishta>`
|
||||
* :doc:`vashishta/table (o) <pair_vashishta>`
|
||||
* :doc:`wf/cut <pair_wf_cut>`
|
||||
* :doc:`yukawa (gko) <pair_yukawa>`
|
||||
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
|
||||
* :doc:`zbl (gko) <pair_zbl>`
|
||||
|
||||
@ -162,3 +162,26 @@ LAMMPS:
|
||||
triple quotes can be nested in the usual manner. See the doc pages
|
||||
for those commands for examples. Only one of level of nesting is
|
||||
allowed, but that should be sufficient for most use cases.
|
||||
|
||||
.. admonition:: ASCII versus UTF-8
|
||||
:class: note
|
||||
|
||||
LAMMPS expects and processes 7-bit ASCII format text internally.
|
||||
Many modern environments use UTF-8 encoding, which is a superset
|
||||
of the 7-bit ASCII character table and thus mostly compatible.
|
||||
However, there are several non-ASCII characters that can look
|
||||
very similar to their ASCII equivalents or are invisible (so they
|
||||
look like a blank), but are encoded differently. Web browsers,
|
||||
PDF viewers, document editors are known to sometimes replace one
|
||||
with the other for a better looking output. However, that can
|
||||
lead to problems, for instance, when using cut-n-paste of input
|
||||
file examples from web pages, or when using a document editor
|
||||
(not a dedicated plain text editor) for writing LAMMPS inputs.
|
||||
LAMMPS will try to detect this and substitute the non-ASCII
|
||||
characters with their ASCII equivalents where known. There also
|
||||
is going to be a warning printed, if this occurs. It is
|
||||
recommended to avoid such characters altogether in LAMMPS input,
|
||||
data and potential files. The replacement tables are likely
|
||||
incomplete and dependent on users reporting problems processing
|
||||
correctly looking input containing UTF-8 encoded non-ASCII
|
||||
characters.
|
||||
|
||||
@ -1,68 +1,75 @@
|
||||
Source files
|
||||
------------
|
||||
|
||||
The source files of the LAMMPS code are found in two
|
||||
directories of the distribution: ``src`` and ``lib``.
|
||||
Most of the code is C++ but there are small numbers of files
|
||||
in several other languages.
|
||||
The source files of the LAMMPS code are found in two directories of the
|
||||
distribution: ``src`` and ``lib``. Most of the code is written in C++
|
||||
but there are small a number of files in several other languages like C,
|
||||
Fortran, Shell script, or Python.
|
||||
|
||||
The core of the code is located in the
|
||||
``src`` folder and its sub-directories.
|
||||
A sizable number of these files are in the ``src`` directory
|
||||
itself, but there are plenty of :doc:`packages <Packages>`, which can be
|
||||
included or excluded when LAMMPS is built. See the :doc:`Include
|
||||
packages in build <Build_package>` section of the manual for more
|
||||
information about that part of the build process. LAMMPS currently
|
||||
supports building with :doc:`conventional makefiles <Build_make>` and
|
||||
through :doc:`CMake <Build_cmake>` which differ in how packages are
|
||||
enabled or disabled for a LAMMPS binary. The source files for each
|
||||
The core of the code is located in the ``src`` folder and its
|
||||
sub-directories. A sizable number of these files are in the ``src``
|
||||
directory itself, but there are plenty of :doc:`packages <Packages>`,
|
||||
which can be included or excluded when LAMMPS is built. See the
|
||||
:doc:`Include packages in build <Build_package>` section of the manual
|
||||
for more information about that part of the build process. LAMMPS
|
||||
currently supports building with :doc:`conventional makefiles
|
||||
<Build_make>` and through :doc:`CMake <Build_cmake>`. Those procedures
|
||||
differ in how packages are enabled or disabled for inclusion into a
|
||||
LAMMPS binary so they cannot be mixed. The source files for each
|
||||
package are in all-uppercase sub-directories of the ``src`` folder, for
|
||||
example ``src/MOLECULE`` or ``src/USER-MISC``. The ``src/STUBS``
|
||||
sub-directory is not a package but contains a dummy MPI library, that is
|
||||
used when building a serial version of the code. The ``src/MAKE``
|
||||
directory contains makefiles with settings and flags for a variety of
|
||||
configuration and machines for the build process with traditional
|
||||
makefiles.
|
||||
directory and its sub-directories contain makefiles with settings and
|
||||
flags for a variety of configuration and machines for the build process
|
||||
with traditional makefiles.
|
||||
|
||||
The ``lib`` directory contains the source code for several supporting
|
||||
libraries or files with configuration settings to use globally installed
|
||||
libraries, that are required by some of the optional packages.
|
||||
Each sub-directory, like ``lib/poems`` or ``lib/gpu``, contains the
|
||||
source files, some of which are in different languages such as Fortran
|
||||
or CUDA. These libraries are linked to during a LAMMPS build, if the
|
||||
corresponding package is installed.
|
||||
libraries, that are required by some of the optional packages. They may
|
||||
include python scripts that can transparently download additional source
|
||||
code on request. Each sub-directory, like ``lib/poems`` or ``lib/gpu``,
|
||||
contains the source files, some of which are in different languages such
|
||||
as Fortran or CUDA. These libraries included in the LAMMPS build,
|
||||
if the corresponding package is installed.
|
||||
|
||||
LAMMPS C++ source files almost always come in pairs, such as
|
||||
``src/run.cpp`` (implementation file) and ``src/run.h`` (header file).
|
||||
Each pair of files defines a C++
|
||||
class, for example the :cpp:class:`LAMMPS_NS::Run` class which contains
|
||||
the code invoked by the :doc:`run <run>` command in a LAMMPS input script.
|
||||
As this example illustrates, source file and class names often have a
|
||||
one-to-one correspondence with a command used in a LAMMPS input script.
|
||||
Some source files and classes do not have a corresponding input script
|
||||
Each pair of files defines a C++ class, for example the
|
||||
:cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the
|
||||
:doc:`run <run>` command in a LAMMPS input script. As this example
|
||||
illustrates, source file and class names often have a one-to-one
|
||||
correspondence with a command used in a LAMMPS input script. Some
|
||||
source files and classes do not have a corresponding input script
|
||||
command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
|
||||
class. They are discussed in the next section.
|
||||
|
||||
A small number of C++ classes and utility functions are implemented with
|
||||
only a ``.h`` file. Examples are the Pointer class or the MathVec functions.
|
||||
The names of all source files are in lower case and may use the
|
||||
underscore character '_' to separate words. Outside of bundled libraries
|
||||
which may have different conventions, all C and C++ header files have a
|
||||
``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
|
||||
``.c`` extension. A small number of C++ classes and utility functions
|
||||
are implemented with only a ``.h`` file. Examples are the Pointer class
|
||||
or the MathVec functions.
|
||||
|
||||
Class topology
|
||||
--------------
|
||||
|
||||
Though LAMMPS has a lot of source files and classes, its class topology
|
||||
is relative flat, as outlined in the :ref:`class-topology` figure. Each
|
||||
name refers to a class and has a pair of associated source files in the
|
||||
``src`` folder, for example the class :cpp:class:`LAMMPS_NS::Memory`
|
||||
corresponds to the files ``memory.cpp`` and ``memory.h``, or the class
|
||||
:cpp:class:`LAMMPS_NS::AtomVec` corresponds to the files
|
||||
``atom_vec.cpp`` and ``atom_vec.h``. Full lines in the figure represent
|
||||
compositing: that is the class to the left holds a pointer to an
|
||||
instance of the class to the right. Dashed lines instead represent
|
||||
inheritance: the class to the right is derived from the class on the
|
||||
left. Classes with a red boundary are not instantiated directly, but
|
||||
they represent the base classes for "styles". Those "styles" make up
|
||||
the bulk of the LAMMPS code and only a few typical examples are included
|
||||
in the figure for demonstration purposes.
|
||||
is not very deep, which can be seen from the :ref:`class-topology`
|
||||
figure. In that figure, each name refers to a class and has a pair of
|
||||
associated source files in the ``src`` folder, for example the class
|
||||
:cpp:class:`LAMMPS_NS::Memory` corresponds to the files ``memory.cpp``
|
||||
and ``memory.h``, or the class :cpp:class:`LAMMPS_NS::AtomVec`
|
||||
corresponds to the files ``atom_vec.cpp`` and ``atom_vec.h``. Full
|
||||
lines in the figure represent compositing: that is the class at the base
|
||||
of the arrow holds a pointer to an instance of the class at the tip.
|
||||
Dashed lines instead represent inheritance: the class to the tip of the
|
||||
arrow is derived from the class at the base. Classes with a red boundary
|
||||
are not instantiated directly, but they represent the base classes for
|
||||
"styles". Those "styles" make up the bulk of the LAMMPS code and only
|
||||
a few representative examples are included in the figure so it remains
|
||||
readable.
|
||||
|
||||
.. _class-topology:
|
||||
.. figure:: JPG/lammps-classes.png
|
||||
@ -82,8 +89,8 @@ in the figure for demonstration purposes.
|
||||
derived classes, which may also hold instances of other classes.
|
||||
|
||||
The :cpp:class:`LAMMPS_NS::LAMMPS` class is the topmost class and
|
||||
represents what is referred to an "instance" of LAMMPS. It is a
|
||||
composite holding references to instances of other core classes
|
||||
represents what is generally referred to an "instance" of LAMMPS. It is
|
||||
a composite holding pointers to instances of other core classes
|
||||
providing the core functionality of the MD engine in LAMMPS and through
|
||||
them abstractions of the required operations. The constructor of the
|
||||
LAMMPS class will instantiate those instances, process the command line
|
||||
@ -91,60 +98,67 @@ flags, initialize MPI (if not already done) and set up file pointers for
|
||||
input and output. The destructor will shut everything down and free all
|
||||
associated memory. Thus code for the standalone LAMMPS executable in
|
||||
``main.cpp`` simply initializes MPI, instantiates a single instance of
|
||||
LAMMPS, and passes it the command line flags and input script. It
|
||||
LAMMPS while passing it the command line flags and input script. It
|
||||
deletes the LAMMPS instance after the method reading the input returns
|
||||
and shuts down the MPI environment before it exits the executable.
|
||||
|
||||
The :cpp:class:`LAMMPS_NS::Pointers` is not shown in the
|
||||
:ref:`class-topology` figure, it holds references to members of the
|
||||
`LAMMPS_NS::LAMMPS`, so that all classes derived from
|
||||
:cpp:class:`LAMMPS_NS::Pointers` have direct access to those reference.
|
||||
From the class topology all classes with blue boundary are referenced in
|
||||
this class and all classes in the second and third columns, that are not
|
||||
listed as derived classes are instead derived from
|
||||
:cpp:class:`LAMMPS_NS::Pointers`.
|
||||
:ref:`class-topology` figure for clarity. It holds references to many
|
||||
of the members of the `LAMMPS_NS::LAMMPS`, so that all classes derived
|
||||
from :cpp:class:`LAMMPS_NS::Pointers` have direct access to those
|
||||
reference. From the class topology all classes with blue boundary are
|
||||
referenced in the Pointers class and all classes in the second and third
|
||||
columns, that are not listed as derived classes are instead derived from
|
||||
:cpp:class:`LAMMPS_NS::Pointers`. To initialize the pointer references
|
||||
in Pointers, a pointer to the LAMMPS class instance needs to be passed
|
||||
to the constructor and thus all constructors for classes derived from it
|
||||
must do so and pass this pointer to the constructor for Pointers.
|
||||
|
||||
Since all storage is encapsulated, the LAMMPS class can also be
|
||||
instantiated multiple times by a calling code, and that can be either
|
||||
simultaneously or consecutively. When running in parallel with MPI,
|
||||
care has to be taken, that suitable communicators are used to not
|
||||
create conflicts between different instances.
|
||||
Since all storage is supposed to be encapsulated (there are a few
|
||||
exceptions), the LAMMPS class can also be instantiated multiple times by
|
||||
a calling code. Outside of the aforementioned exceptions, those LAMMPS
|
||||
instances can be used alternately. As of the time of this writing
|
||||
(early 2021) LAMMPS is not yet sufficiently thread-safe for concurrent
|
||||
execution. When running in parallel with MPI, care has to be taken,
|
||||
that suitable copies of communicators are used to not create conflicts
|
||||
between different instances.
|
||||
|
||||
The LAMMPS class currently holds instances of 19 classes representing
|
||||
different core functionalities There are a handful of virtual parent
|
||||
classes in LAMMPS that define what LAMMPS calls ``styles``. They are
|
||||
shaded red in the :ref:`class-topology` figure. Each of these are
|
||||
The LAMMPS class currently (early 2021) holds instances of 19 classes
|
||||
representing the core functionality. There are a handful of virtual
|
||||
parent classes in LAMMPS that define what LAMMPS calls ``styles``. They
|
||||
are shaded red in the :ref:`class-topology` figure. Each of these are
|
||||
parents of a number of child classes that implement the interface
|
||||
defined by the parent class. There are two main categories of these
|
||||
``styles``: some may only have one instance active at a time (e.g. atom,
|
||||
pair, bond, angle, dihedral, improper, kspace, comm) and there is a
|
||||
dedicated pointer variable in the composite class that manages them.
|
||||
dedicated pointer variable for each of them in the composite class.
|
||||
Setups that require a mix of different such styles have to use a
|
||||
*hybrid* class that manages and forwards calls to the corresponding
|
||||
sub-styles for the designated subset of atoms or data. or the composite
|
||||
class may have lists of class instances, e.g. Modify handles lists of
|
||||
compute and fix styles, while Output handles dumps class instances.
|
||||
*hybrid* class that takes the place of the one allowed instance and then
|
||||
manages and forwards calls to the corresponding sub-styles for the
|
||||
designated subset of atoms or data. The composite class may also have
|
||||
lists of class instances, e.g. Modify handles lists of compute and fix
|
||||
styles, while Output handles a list of dump class instances.
|
||||
|
||||
The exception to this scheme are the ``command`` style classes. These
|
||||
implement specific commands that can be invoked before, after, or between
|
||||
runs or are commands which launch a simulation. For these an instance
|
||||
of the class is created, its command() method called and then, after
|
||||
completion, the class instance deleted. Examples for this are the
|
||||
create_box, create_atoms, minimize, run, or velocity command styles.
|
||||
implement specific commands that can be invoked before, after, or in
|
||||
between runs. For these an instance of the class is created, its
|
||||
command() method called and then, after completion, the class instance
|
||||
deleted. Examples for this are the create_box, create_atoms, minimize,
|
||||
run, or velocity command styles.
|
||||
|
||||
For all those ``styles`` certain naming conventions are employed: for
|
||||
the fix nve command the class is called FixNVE and the files are
|
||||
the fix nve command the class is called FixNVE and the source files are
|
||||
``fix_nve.h`` and ``fix_nve.cpp``. Similarly for fix ave/time we have
|
||||
FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``. Style names
|
||||
are lower case and without spaces or special characters. A suffix or
|
||||
multiple appended with a forward slash '/' denotes a variant of the
|
||||
corresponding class without the suffix. To connect the style name and
|
||||
the class name, LAMMPS uses macros like the following ATOM\_CLASS,
|
||||
PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS, FIX\_CLASS, COMPUTE\_CLASS,
|
||||
or DUMP\_CLASS in the corresponding header file. During compilation
|
||||
files with the pattern ``style_name.h`` are created that contain include
|
||||
statements including all headers of all styles of a given type that
|
||||
are currently active (or "installed).
|
||||
words are appended with a forward slash '/' which denotes a variant of
|
||||
the corresponding class without the suffix. To connect the style name
|
||||
and the class name, LAMMPS uses macros like: ``AtomStyle()``,
|
||||
``PairStyle()``, ``BondStyle()``, ``RegionStyle()``, and so on in the
|
||||
corresponding header file. During configuration or compilation files
|
||||
with the pattern ``style_<name>.h`` are created that consist of a list
|
||||
of include statements including all headers of all styles of a given
|
||||
type that are currently active (or "installed).
|
||||
|
||||
|
||||
More details on individual classes in the :ref:`class-topology` are as
|
||||
@ -152,11 +166,11 @@ follows:
|
||||
|
||||
- The Memory class handles allocation of all large vectors and arrays.
|
||||
|
||||
- The Error class prints all error and warning messages.
|
||||
- The Error class prints all (terminal) error and warning messages.
|
||||
|
||||
- The Universe class sets up partitions of processors so that multiple
|
||||
simulations can be run, each on a subset of the processors allocated
|
||||
for a run, e.g. by the mpirun command.
|
||||
- The Universe class sets up one or more partitions of processors so
|
||||
that one or multiple simulations can be run, on the processors
|
||||
allocated for a run, e.g. by the mpirun command.
|
||||
|
||||
- The Input class reads and processes input input strings and files,
|
||||
stores variables, and invokes :doc:`commands <Commands_all>`.
|
||||
@ -241,7 +255,8 @@ follows:
|
||||
.. TODO section on "Spatial decomposition and parallel operations"
|
||||
.. diagram of 3d processor grid, brick vs. tiled. local vs. ghost
|
||||
.. atoms, 6-way communication with pack/unpack functions,
|
||||
.. PBC as part of the communication
|
||||
.. PBC as part of the communication, forward and reverse communication
|
||||
.. rendezvous communication, ring communication.
|
||||
|
||||
.. TODO section on "Fixes, Computes, and Variables"
|
||||
.. how and when data is computed and provided and how it is
|
||||
|
||||
@ -71,12 +71,21 @@ and parsing files or arguments.
|
||||
|
||||
----------
|
||||
|
||||
.. doxygenfunction:: strdup
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: trim
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: trim_comment
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: has_utf8
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: utf8_subst
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: count_words(const char *text)
|
||||
:project: progguide
|
||||
|
||||
@ -286,6 +295,50 @@ This code example should produce the following output:
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Argument parsing classes
|
||||
---------------------------
|
||||
|
||||
The purpose of argument parsing classes it to simplify and unify how
|
||||
arguments of commands in LAMMPS are parsed and to make abstractions of
|
||||
repetitive tasks.
|
||||
|
||||
The :cpp:class:`LAMMPS_NS::ArgInfo` class provides an abstraction
|
||||
for parsing references to compute or fix styles or variables. These
|
||||
would start with a "c\_", "f\_", "v\_" followed by the ID or name of
|
||||
than instance and may be postfixed with one or two array indices
|
||||
"[<number>]" with numbers > 0.
|
||||
|
||||
A typical code segment would look like this:
|
||||
|
||||
.. code-block:: C++
|
||||
:caption: Usage example for ArgInfo class
|
||||
|
||||
int nvalues = 0;
|
||||
for (iarg = 0; iarg < nargnew; iarg++) {
|
||||
ArgInfo argi(arg[iarg]);
|
||||
|
||||
which[nvalues] = argi.get_type();
|
||||
argindex[nvalues] = argi.get_index1();
|
||||
ids[nvalues] = argi.copy_name();
|
||||
|
||||
if ((which[nvalues] == ArgInfo::UNKNOWN)
|
||||
|| (which[nvalues] == ArgInfo::NONE)
|
||||
|| (argi.get_dim() > 1))
|
||||
error->all(FLERR,"Illegal compute XXX command");
|
||||
|
||||
nvalues++;
|
||||
}
|
||||
|
||||
----------
|
||||
|
||||
.. doxygenclass:: LAMMPS_NS::ArgInfo
|
||||
:project: progguide
|
||||
:members:
|
||||
|
||||
|
||||
----------
|
||||
|
||||
File reader classes
|
||||
-------------------
|
||||
|
||||
|
||||
BIN
doc/src/JPG/WF_LJ.jpg
Normal file
BIN
doc/src/JPG/WF_LJ.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 292 KiB |
@ -14,6 +14,7 @@ This section documents the following functions:
|
||||
- :cpp:func:`lammps_config_has_package`
|
||||
- :cpp:func:`lammps_config_package_count`
|
||||
- :cpp:func:`lammps_config_package_name`
|
||||
- :cpp:func:`lammps_config_accelerator`
|
||||
- :cpp:func:`lammps_has_style`
|
||||
- :cpp:func:`lammps_style_count`
|
||||
- :cpp:func:`lammps_style_name`
|
||||
@ -126,6 +127,11 @@ approach.
|
||||
|
||||
-----------------------
|
||||
|
||||
.. doxygenfunction:: lammps_config_accelerator
|
||||
:project: progguide
|
||||
|
||||
-----------------------
|
||||
|
||||
.. doxygenfunction:: lammps_has_style
|
||||
:project: progguide
|
||||
|
||||
|
||||
@ -39,7 +39,9 @@ about compile time settings and included packages and styles.
|
||||
* :py:attr:`lammps.has_jpeg_support <lammps.lammps.has_jpeg_support>`
|
||||
* :py:attr:`lammps.has_ffmpeg_support <lammps.lammps.has_ffmpeg_support>`
|
||||
|
||||
* :py:attr:`lammps.installed_packages <lammps.lammps.installed_pages>`
|
||||
* :py:attr:`lammps.installed_packages <lammps.lammps.installed_packages>`
|
||||
|
||||
* :py:meth:`lammps.get_accelerator_config <lammps.lammps.accelerator_config>`
|
||||
|
||||
* :py:meth:`lammps.has_style() <lammps.lammps.has_style()>`
|
||||
* :py:meth:`lammps.available_styles() <lammps.lammps.available_styles()>`
|
||||
|
||||
@ -69,7 +69,7 @@ this.
|
||||
cd build
|
||||
|
||||
# configure LAMMPS compilation
|
||||
cmake -C cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
|
||||
cmake -C ../cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
|
||||
-D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
|
||||
|
||||
# compile LAMMPS
|
||||
@ -97,10 +97,12 @@ this.
|
||||
|
||||
For a system-wide installation you need to set
|
||||
``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
|
||||
``/usr/local``). The installation step (**not** the
|
||||
``/usr/local``); the default is ``${HOME}/.local``. The
|
||||
installation step for a system folder installation (**not** the
|
||||
configuration/compilation) needs to be done with superuser
|
||||
privilege, e.g. by using ``sudo cmake --install .``. The
|
||||
installation folders will then by changed to:
|
||||
installation folders will then be changed to (assuming ``/usr`` as
|
||||
prefix):
|
||||
|
||||
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
|
||||
| File | Location | Notes |
|
||||
|
||||
@ -26,6 +26,15 @@ task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
|
||||
GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
|
||||
produce an executable compatible with a specific hardware.
|
||||
|
||||
.. admonition:: C++14 support
|
||||
:class: note
|
||||
|
||||
Kokkos requires using a compiler that supports the c++14 standard. For
|
||||
some compilers, it may be necessary to add a flag to enable c++14 support.
|
||||
For example, the GNU compiler uses the -std=c++14 flag. For a list of
|
||||
compilers that have been tested with the Kokkos library, see the Kokkos
|
||||
`README <https://github.com/kokkos/kokkos/blob/master/README.md>`_.
|
||||
|
||||
.. admonition:: NVIDIA CUDA support
|
||||
:class: note
|
||||
|
||||
|
||||
@ -620,4 +620,4 @@ reset_mol_ids = yes, custom_charges = no, molecule = off
|
||||
|
||||
.. _Gissinger2020:
|
||||
|
||||
**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953–9961 (2020).
|
||||
**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
|
||||
|
||||
@ -120,22 +120,28 @@ increase in computational resources cost.
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
This fix writes the original coordinates of tethered atoms to :doc:`binary restart files <restart>`, so that the spring effect will be the
|
||||
same in a restarted simulation. See the :doc:`read restart <read_restart>` command for info on how to re-specify a fix
|
||||
in an input script that reads a restart file, so that the operation of
|
||||
the fix continues in an uninterrupted fashion.
|
||||
This fix writes the original coordinates of tethered atoms to
|
||||
:doc:`binary restart files <restart>`, so that the spring effect will
|
||||
be the same in a restarted simulation. See the :doc:`read restart
|
||||
<read_restart>` command for info on how to re-specify a fix in an
|
||||
input script that reads a restart file, so that the operation of the
|
||||
fix continues in an uninterrupted fashion.
|
||||
|
||||
The :doc:`fix modify <fix_modify>` *energy* option is supported by this
|
||||
fix to add the energy stored in the per-atom springs to the system's
|
||||
potential energy as part of :doc:`thermodynamic output <thermo_style>`.
|
||||
The :doc:`fix modify <fix_modify>` *energy* option is supported by
|
||||
this fix to add the energy stored in the per-atom springs to the
|
||||
system's potential energy as part of :doc:`thermodynamic output
|
||||
<thermo_style>`.
|
||||
|
||||
This fix computes a global scalar and a global vector quantities which
|
||||
can be accessed by various :doc:`output commands <Howto_output>`. The
|
||||
scalar is an energy which is the sum of the spring energy for each
|
||||
atom, where the per-atom energy is 0.5 \* k \* r\^2. The vector has 2
|
||||
positions, the first one is the coupling parameter lambda and the
|
||||
second one is the time derivative of lambda. The scalar and vector
|
||||
values calculated by this fix are "extensive".
|
||||
atom, where the per-atom energy is 0.5 \* k \* r\^2. The vector stores
|
||||
2 values. The first value is the coupling parameter lambda. The
|
||||
second value is the derivative of lambda with respect to the integer
|
||||
timestep *s*, i.e. d lambda / ds. In order to obtain d lambda / dt,
|
||||
where t is simulation time, this 2nd value needs to be divided by the
|
||||
timestep size (e.g. 0.5 fs). The scalar and vector values calculated
|
||||
by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -10,7 +10,7 @@ Syntax
|
||||
|
||||
info args
|
||||
|
||||
* args = one or more of the following keywords: *out*\ , *all*\ , *system*\ , *memory*\ , *communication*\ , *computes*\ , *dumps*\ , *fixes*\ , *groups*\ , *regions*\ , *variables*\ , *coeffs*\ , *styles*\ , *time*\ , or *configuration*
|
||||
* args = one or more of the following keywords: *out*\ , *all*\ , *system*\ , *memory*\ , *communication*\ , *computes*\ , *dumps*\ , *fixes*\ , *groups*\ , *regions*\ , *variables*\ , *coeffs*\ , *styles*\ , *time*\ , *accelerator*\ , or *configuration*
|
||||
* *out* values = *screen*\ , *log*\ , *append* filename, *overwrite* filename
|
||||
* *styles* values = *all*\ , *angle*\ , *atom*\ , *bond*\ , *compute*\ , *command*\ , *dump*\ , *dihedral*\ , *fix*\ , *improper*\ , *integrate*\ , *kspace*\ , *minimize*\ , *pair*\ , *region*
|
||||
|
||||
@ -88,6 +88,10 @@ The *coeffs* category prints a list for each defined force style
|
||||
corresponding coefficients have been set. This can be very helpful
|
||||
to debug error messages like "All pair coeffs are not set".
|
||||
|
||||
The *accelerator* category prints out information about compile time
|
||||
settings of included accelerator support for the GPU, KOKKOS, USER-INTEL,
|
||||
and USER-OMP packages.
|
||||
|
||||
The *styles* category prints the list of styles available in the
|
||||
current LAMMPS binary. It supports one of the following options
|
||||
to control which category of styles is printed out:
|
||||
|
||||
@ -18,6 +18,7 @@
|
||||
.. index:: pair_style eam/fs/kk
|
||||
.. index:: pair_style eam/fs/omp
|
||||
.. index:: pair_style eam/fs/opt
|
||||
.. index:: pair_style eam/he
|
||||
|
||||
pair_style eam command
|
||||
======================
|
||||
@ -38,6 +39,9 @@ pair_style eam/cd/old command
|
||||
pair_style eam/fs command
|
||||
=========================
|
||||
|
||||
pair_style eam/he command
|
||||
=========================
|
||||
|
||||
Accelerator Variants: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt*
|
||||
|
||||
Syntax
|
||||
@ -47,7 +51,7 @@ Syntax
|
||||
|
||||
pair_style style
|
||||
|
||||
* style = *eam* or *eam/alloy* or *eam/cd* or *eam/cd/old* or *eam/fs*
|
||||
* style = *eam* or *eam/alloy* or *eam/cd* or *eam/cd/old* or *eam/fs* or *eam/he*
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -67,6 +71,9 @@ Examples
|
||||
pair_style eam/fs
|
||||
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
|
||||
|
||||
pair_style eam/he
|
||||
pair_coeff * * PdHHe.eam.he Pd H He
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
@ -104,8 +111,8 @@ are parameterized in terms of LAMMPS :doc:`metal units <units>`.
|
||||
potentials, the same way that DYNAMO does. Alternatively, a single
|
||||
DYNAMO *setfl* file or Finnis/Sinclair EAM file can be used by LAMMPS
|
||||
to model alloy systems by invoking the *eam/alloy* or *eam/cd* or
|
||||
*eam/fs* styles as described below. These files require no mixing
|
||||
since they specify alloy interactions explicitly.
|
||||
*eam/fs* or *eam/he* styles as described below. These files require no
|
||||
mixing since they specify alloy interactions explicitly.
|
||||
|
||||
.. note::
|
||||
|
||||
@ -143,10 +150,6 @@ DYNAMO single-element *funcfl* format. If the DYNAMO file was created
|
||||
by a Fortran program, it cannot have "D" values in it for exponents.
|
||||
C only recognizes "e" or "E" for scientific notation.
|
||||
|
||||
Note that unlike for other potentials, cutoffs for EAM potentials are
|
||||
not set in the pair_style or pair_coeff command; they are specified in
|
||||
the EAM potential files themselves.
|
||||
|
||||
For style *eam* a potential file must be assigned to each I,I pair of
|
||||
atom types by using one or more pair_coeff commands, each with a
|
||||
single argument:
|
||||
@ -336,8 +339,11 @@ distribution have a ".cdeam" suffix.
|
||||
|
||||
Style *eam/fs* computes pairwise interactions for metals and metal
|
||||
alloys using a generalized form of EAM potentials due to Finnis and
|
||||
Sinclair :ref:`(Finnis) <Finnis1>`. The total energy Ei of an atom I is
|
||||
given by
|
||||
Sinclair :ref:`(Finnis) <Finnis1>`. Style *eam/he* is similar to
|
||||
*eam/fs* except that it allows for negative electron density in
|
||||
order to capture the behavior of helium in metals :ref:`(Zhou6) <Zhou6>`.
|
||||
|
||||
The total energy Ei of an atom I is given by
|
||||
|
||||
.. math::
|
||||
|
||||
@ -355,36 +361,36 @@ electron density at an atomic site depending on the identity of the
|
||||
element at that atomic site.
|
||||
|
||||
The associated :doc:`pair_coeff <pair_coeff>` command for style *eam/fs*
|
||||
reads a DYNAMO *setfl* file that has been extended to include
|
||||
additional rho_alpha_beta arrays of tabulated values. A discussion of
|
||||
how FS EAM differs from conventional EAM alloy potentials is given in
|
||||
:ref:`(Ackland1) <Ackland1>`. An example of such a potential is the same
|
||||
author's Fe-P FS potential :ref:`(Ackland2) <Ackland2>`. Note that while FS
|
||||
potentials always specify the embedding energy with a square root
|
||||
or *eam/he* reads a DYNAMO *setfl* file that has been extended to include
|
||||
additional :math:`\rho_{\alpha\beta}` arrays of tabulated values. A
|
||||
discussion of how FS EAM differs from conventional EAM alloy potentials is
|
||||
given in :ref:`(Ackland1) <Ackland1>`. An example of such a potential is the
|
||||
same author's Fe-P FS potential :ref:`(Ackland2) <Ackland2>`. Note that while
|
||||
FS potentials always specify the embedding energy with a square root
|
||||
dependence on the total density, the implementation in LAMMPS does not
|
||||
require that; the user can tabulate any functional form desired in the
|
||||
FS potential files.
|
||||
|
||||
For style *eam/fs*\ , the form of the pair_coeff command is exactly the
|
||||
same as for style *eam/alloy*\ , e.g.
|
||||
For style *eam/fs* and *eam/he* the form of the pair_coeff command is exactly
|
||||
the same as for style *eam/alloy*\ , e.g.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
|
||||
|
||||
where there are N additional arguments after the filename, where N is
|
||||
with N additional arguments after the filename, where N is
|
||||
the number of LAMMPS atom types. See the :doc:`pair_coeff <pair_coeff>`
|
||||
doc page for alternate ways to specify the path for the potential
|
||||
file. The N values determine the mapping of LAMMPS atom types to EAM
|
||||
elements in the file, as described above for style *eam/alloy*\ . As
|
||||
with *eam/alloy*\ , if a mapping value is NULL, the mapping is not
|
||||
performed. This can be used when an *eam/fs* potential is used as
|
||||
part of the *hybrid* pair style. The NULL values are used as
|
||||
performed. This can be used when an *eam/fs* or *eam/he* potential is
|
||||
used as part of a *hybrid* pair style. The NULL values are used as
|
||||
placeholders for atom types that will be used with other potentials.
|
||||
|
||||
FS EAM files include more information than the DYNAMO *setfl* format
|
||||
files read by *eam/alloy*\ , in that i,j density functionals for all
|
||||
pairs of elements are included as needed by the Finnis/Sinclair
|
||||
FS EAM and HE EAM files include more information than the DYNAMO *setfl*
|
||||
format files read by *eam/alloy*\ , in that i,j density functionals for
|
||||
all pairs of elements are included as needed by the Finnis/Sinclair
|
||||
formulation of the EAM.
|
||||
|
||||
FS EAM files in the *potentials* directory of the LAMMPS distribution
|
||||
@ -417,6 +423,25 @@ eV-Angstroms) as in EAM *setfl* files. Note that in Finnis/Sinclair,
|
||||
the phi(r) arrays are still symmetric, so only phi arrays for i >= j
|
||||
are listed.
|
||||
|
||||
HE EAM files in the *potentials* directory of the LAMMPS distribution
|
||||
have an ".eam.he" suffix. They are formatted as follows:
|
||||
|
||||
* lines 1,2,3 = comments (ignored)
|
||||
* line 4: Nelements Element1 Element2 ... ElementN
|
||||
* line 5: Nrho, drho, Nr, dr, cutoff, rhomax
|
||||
|
||||
The 5-line header section is identical to an FS EAM file
|
||||
except that line 5 lists an additional value, rhomax. Unlike in FS EAM
|
||||
files where embedding energies F(rho) are always defined between rho = 0
|
||||
and rho = (Nrho -1)drho, F(rho) in HE EAM files are defined between
|
||||
rho = rhomin and rho = rhomax. Since drho = (rhomax - rhomin)/(Nrho - 1),
|
||||
rhomin = rhomax - (Nrho - 1)drho. The embedding energies F(rho) are
|
||||
listed for rho = rhomin, rhomin + drho, rhomin + 2drho, ..., rhomax.
|
||||
This gives users additional flexibility to define a negative rhomin and
|
||||
therefore an embedding energy function that works for both positive and
|
||||
negative electron densities. The format and units of these sections are
|
||||
identical to the FS EAM files (see above).
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
@ -480,6 +505,10 @@ Daw, Baskes, Phys Rev B, 29, 6443 (1984).
|
||||
|
||||
**(Finnis)** Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
|
||||
|
||||
.. _Zhou6:
|
||||
|
||||
**(Zhou6)** Zhou, Bartelt, Sills, Physical Review B, 103, 014108 (2021).
|
||||
|
||||
.. _Stukowski:
|
||||
|
||||
**(Stukowski)** Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
|
||||
|
||||
@ -159,6 +159,7 @@ accelerated styles exist.
|
||||
* :doc:`eam/cd <pair_eam>` - concentration-dependent EAM
|
||||
* :doc:`eam/cd/old <pair_eam>` - older two-site model for concentration-dependent EAM
|
||||
* :doc:`eam/fs <pair_eam>` - Finnis-Sinclair EAM
|
||||
* :doc:`eam/he <pair_eam>` - Finnis-Sinclair EAM modified for Helium in metals
|
||||
* :doc:`edip <pair_edip>` - three-body EDIP potential
|
||||
* :doc:`edip/multi <pair_edip>` - multi-element EDIP potential
|
||||
* :doc:`edpd <pair_mesodpd>` - eDPD particle interactions
|
||||
@ -326,6 +327,7 @@ accelerated styles exist.
|
||||
* :doc:`ufm <pair_ufm>` -
|
||||
* :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential
|
||||
* :doc:`vashishta/table <pair_vashishta>` -
|
||||
* :doc:`wf/cut <pair_wf_cut>` - Wang-Frenkel Potential for short-ranged interactions
|
||||
* :doc:`yukawa <pair_yukawa>` - Yukawa potential
|
||||
* :doc:`yukawa/colloid <pair_yukawa_colloid>` - screened Yukawa potential for finite-size particles
|
||||
* :doc:`zbl <pair_zbl>` - Ziegler-Biersack-Littmark potential
|
||||
|
||||
@ -16,14 +16,23 @@ pair_style tersoff/table command
|
||||
|
||||
Accelerator Variants: *tersoff/table/omp*
|
||||
|
||||
pair_style tersoff/shift command
|
||||
================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style style
|
||||
pair_style style keywords values
|
||||
|
||||
* style = *tersoff* or *tersoff/table* or *tersoff/gpu* or *tersoff/omp* or *tersoff/table/omp*
|
||||
* keyword = *shift*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*shift* value = delta
|
||||
delta = negative shift in equilibrium bond length
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -37,6 +46,9 @@ Examples
|
||||
pair_style tersoff/table
|
||||
pair_coeff * * SiCGe.tersoff Si(D)
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * Si.tersoff Si
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
@ -46,7 +58,7 @@ The *tersoff* style computes a 3-body Tersoff potential
|
||||
.. math::
|
||||
|
||||
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
|
||||
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
|
||||
V_{ij} & = f_C(r_{ij} + \delta) \left[ f_R(r_{ij} + \delta) + b_{ij} f_A(r_{ij} + \delta) \right] \\
|
||||
f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
|
||||
1 & r < R - D \\
|
||||
\frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) &
|
||||
@ -56,14 +68,15 @@ The *tersoff* style computes a 3-body Tersoff potential
|
||||
f_R(r) & = A \exp (-\lambda_1 r) \\
|
||||
f_A(r) & = -B \exp (-\lambda_2 r) \\
|
||||
b_{ij} & = \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
|
||||
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
|
||||
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik} + \delta) g \left[ \theta_{ijk}(r_{ij}, r_{ik}) \right]
|
||||
\exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
|
||||
g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
|
||||
\frac{c^2}{\left[ d^2 + (\cos \theta - \cos \theta_0)^2\right]} \right)
|
||||
|
||||
where :math:`f_R` is a two-body term and :math:`f_A` includes three-body
|
||||
interactions. The summations in the formula are over all neighbors
|
||||
J and K of atom I within a cutoff distance = R + D.
|
||||
J and K of atom I within a cutoff distance = R + D. :math:`\delta` is
|
||||
an optional negative shift of the equilibrium bond length, as described below.
|
||||
|
||||
The *tersoff/table* style uses tabulated forms for the two-body,
|
||||
environment and angular functions. Linear interpolation is performed
|
||||
@ -167,6 +180,18 @@ Note that the twobody parameters in entries such as SiCC and CSiSi
|
||||
are often the same, due to the common use of symmetric mixing rules,
|
||||
but this is not always the case. For example, the beta and n parameters in
|
||||
Tersoff_2 :ref:`(Tersoff_2) <Tersoff_21>` are not symmetric.
|
||||
Similarly, the threebody parameters in entries such as SiCSi and SiSiC
|
||||
are often the same, but this is not always the case, particularly
|
||||
the value of R, which is sometimes typed on the
|
||||
first and second elements, sometimes on the first and third elements.
|
||||
Hence the need to specify R and D explicitly for all element triples.
|
||||
For example, while Tersoff's notation
|
||||
in Tersoff_2 :ref:`(Tersoff_2) <Tersoff_21>` is ambiguous on this point,
|
||||
and properties of the zincblende lattice are the same for either choice,
|
||||
Tersoff's results for rocksalt are consistent with typing on the first
|
||||
and third elements. :ref:`Albe et al. <Albe>` adopts the same convention.
|
||||
Conversely, the potential for B/N/C from the Cagin group
|
||||
uses the opposite convention, typing on the first and second elements.
|
||||
|
||||
We chose the above form so as to enable users to define all commonly
|
||||
used variants of the Tersoff potential. In particular, our form
|
||||
@ -212,6 +237,37 @@ Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
|
||||
for helping clarify how Tersoff parameters for alloys have been
|
||||
defined in various papers.
|
||||
|
||||
The *shift* keyword computes the energy E of a system of atoms, whose
|
||||
formula is the same as the Tersoff potential. The only modification is
|
||||
that the original equilibrium bond length ( :math:`r_0`) of the system
|
||||
is shifted to :math:`r_0-\delta`. The minus sign arises because each
|
||||
radial distance :math:`r` is replaced by :math:`r+\delta`.
|
||||
|
||||
The *shift* keyword is designed for simulations of closely matched van
|
||||
der Waals heterostructures. For instance, consider the case of a system
|
||||
with few-layers graphene atop a thick hexagonal boron nitride (h-BN)
|
||||
substrate simulated using periodic boundary conditions. The experimental
|
||||
lattice mismatch of ~1.8% between graphene and h-BN is not well captured
|
||||
by the equilibrium lattice constants of available potentials, thus a
|
||||
small in-plane strain will be introduced in the system when building a
|
||||
periodic supercell. To minimize the effect of strain on simulation
|
||||
results, the *shift* keyword allows adjusting the equilibrium bond
|
||||
length of one of the two materials (e.g., h-BN). Validation, benchmark
|
||||
tests, and applications of the *shift* keyword can be found in
|
||||
:ref:`(Mandelli_1) <Mandelli1>` and :ref:`(Ouyang_1) <Ouyang5>`.
|
||||
|
||||
For the specific case discussed above, the force field can be defined as
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay rebo tersoff shift -0.00407 ilp/graphene/hbn 16.0 coul/shield 16.0
|
||||
pair_coeff * * rebo CH.rebo NULL NULL C
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.695
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
@ -228,9 +284,10 @@ described above from values in the potential file.
|
||||
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||
shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
|
||||
need to re-specify the pair_style and pair_coeff commands in an input
|
||||
script that reads a restart file.
|
||||
This pair style does not write its information to :doc:`binary restart
|
||||
files <restart>`, since it is stored in potential files. Thus, you need
|
||||
to re-specify the pair_style and pair_coeff commands in an input script
|
||||
that reads a restart file.
|
||||
|
||||
This pair style can only be used via the *pair* keyword of the
|
||||
:doc:`run_style respa <run_style>` command. It does not support the
|
||||
@ -241,17 +298,24 @@ This pair style can only be used via the *pair* keyword of the
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This pair style is part of the MANYBODY package. It is only enabled
|
||||
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
This pair style is part of the MANYBODY package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
This pair style requires the :doc:`newton <newton>` setting to be "on"
|
||||
for pair interactions.
|
||||
|
||||
The *shift* keyword is not supported by the *tersoff/gpu*,
|
||||
*tersoff/intel*, *tersoff/kk*, *tersoff/table* or *tersoff/table/omp*
|
||||
variants.
|
||||
|
||||
The Tersoff potential files provided with LAMMPS (see the potentials
|
||||
directory) are parameterized for metal :doc:`units <units>`. You can
|
||||
use the Tersoff potential with any LAMMPS units, but you would need to
|
||||
directory) are parameterized for :doc:`"metal" units <units>`. In addition
|
||||
the pair style supports converting potential parameters on-the-fly between
|
||||
"metal" and "real" units. You can use the *tersoff* pair style variants
|
||||
with any LAMMPS units setting, but you would need to
|
||||
create your own Tersoff potential file with coefficients listed in the
|
||||
appropriate units if your simulation does not use "metal" units.
|
||||
appropriate units if your simulation does not use "metal" or "real" units.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
@ -261,7 +325,7 @@ Related commands
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
shift delta = 0.0
|
||||
|
||||
----------
|
||||
|
||||
@ -277,3 +341,11 @@ Condens. Matter, 15, 5649(2003).
|
||||
.. _Tersoff_21:
|
||||
|
||||
**(Tersoff_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
|
||||
|
||||
.. _Mandelli1:
|
||||
|
||||
**(Mandelli_1)** D. Mandelli, W. Ouyang, M. Urbakh, and O. Hod, ACS Nano 13(7), 7603-7609 (2019).
|
||||
|
||||
.. _Ouyang5:
|
||||
|
||||
**(Ouyang_1)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
|
||||
|
||||
@ -20,9 +20,15 @@ Syntax
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_style style keywords values
|
||||
|
||||
pair_style tersoff/mod/c
|
||||
* style = *tersoff/mod* or *tersoff/mod/c*
|
||||
* keyword = *shift*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*shift* value = delta
|
||||
delta = negative shift in equilibrium bond length
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -47,7 +53,7 @@ E of a system of atoms as
|
||||
.. math::
|
||||
|
||||
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
|
||||
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
|
||||
V_{ij} & = f_C(r_{ij} + \delta) \left[ f_R(r_{ij} + \delta) + b_{ij} f_A(r_{ij} + \delta) \right] \\
|
||||
f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
|
||||
1 & r < R - D \\
|
||||
\frac{1}{2} - \frac{9}{16} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) - \frac{1}{16} \sin \left( \frac{3\pi}{2} \frac{r-R}{D} \right) &
|
||||
@ -57,13 +63,16 @@ E of a system of atoms as
|
||||
f_R(r) & = A \exp (-\lambda_1 r) \\
|
||||
f_A(r) & = -B \exp (-\lambda_2 r) \\
|
||||
b_{ij} & = \left( 1 + {\zeta_{ij}}^\eta \right)^{-\frac{1}{2n}} \\
|
||||
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
|
||||
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik} + \delta) g(\theta_{ijk})
|
||||
\exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\
|
||||
g(\theta) & = c_1 + g_o(\theta) g_a(\theta) \\
|
||||
g_o(\theta) & = \frac{c_2 (h - \cos \theta)^2}{c_3 + (h - \cos \theta)^2} \\
|
||||
g_a(\theta) & = 1 + c_4 \exp \left[ -c_5 (h - \cos \theta)^2 \right] \\
|
||||
|
||||
where :math:`f_R` is a two-body term and :math:`f_A` includes three-body interactions.
|
||||
:math:`\delta` is an optional negative shift of the
|
||||
equilibrium bond length, as described below.
|
||||
|
||||
The summations in the formula are over all neighbors J and K of atom I
|
||||
within a cutoff distance = R + D.
|
||||
The *tersoff/mod/c* style differs from *tersoff/mod* only in the
|
||||
@ -71,7 +80,7 @@ formulation of the V_ij term, where it contains an additional c0 term.
|
||||
|
||||
.. math::
|
||||
|
||||
V_{ij} = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
|
||||
V_{ij} = f_C(r_{ij} + \delta) \left[ f_R(r_{ij} + \delta) + b_{ij} f_A(r_{ij} + \delta) + c_0 \right] \\
|
||||
|
||||
The modified cutoff function :math:`f_C` proposed by :ref:`(Murty) <Murty>` and
|
||||
having a continuous second-order differential is employed. The
|
||||
@ -156,6 +165,12 @@ the center atom in a three-body interaction and it is bonded to the
|
||||
second atom and the bond is influenced by the third atom. Thus an entry
|
||||
for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
|
||||
|
||||
The *shift* keyword computes the energy E of a system of atoms, whose formula
|
||||
is the same as the Tersoff potential. The only modification is that the original
|
||||
equilibrium bond length ( :math:`r_0`) of the system is shifted to :math:`r_0-\delta`.
|
||||
The minus sign arises because each radial distance :math:`r` is replaced by :math:`r+\delta`.
|
||||
More information on this option is given on the main :doc:`pair_tersoff <pair_tersoff>` page.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
@ -187,9 +202,13 @@ if LAMMPS was built with that package. See the :doc:`Build package <Build_packa
|
||||
This pair style requires the :doc:`newton <newton>` setting to be "on"
|
||||
for pair interactions.
|
||||
|
||||
The Tersoff/MOD potential files provided with LAMMPS (see the potentials
|
||||
The *shift* keyword is not supported by the *tersoff/gpu*,
|
||||
*tersoff/intel*, *tersoff/kk*, *tersoff/table* or *tersoff/table/omp*
|
||||
variants.
|
||||
|
||||
The *tersoff/mod* potential files provided with LAMMPS (see the potentials
|
||||
directory) are parameterized for metal :doc:`units <units>`. You can
|
||||
use the Tersoff/MOD potential with any LAMMPS units, but you would need to
|
||||
use the *tersoff/mod* pair style with any LAMMPS units, but you would need to
|
||||
create your own Tersoff/MOD potential file with coefficients listed in the
|
||||
appropriate units if your simulation does not use "metal" units.
|
||||
|
||||
|
||||
@ -13,7 +13,14 @@ Syntax
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style tersoff/zbl
|
||||
pair_style tersoff/zbl keywords values
|
||||
|
||||
* keyword = *shift*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*shift* value = delta
|
||||
delta = negative shift in equilibrium bond length
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -35,16 +42,17 @@ system of atoms as
|
||||
.. math::
|
||||
|
||||
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
|
||||
V_{ij} & = (1 - f_F(r_{ij})) V^{ZBL}_{ij} + f_F(r_{ij}) V^{Tersoff}_{ij} \\
|
||||
f_F(r_{ij}) & = \frac{1}{1 + e^{-A_F(r_{ij} - r_C)}}\\
|
||||
V_{ij} & = (1 - f_F(r_{ij} + \delta)) V^{ZBL}(r_{ij} + \delta)
|
||||
+ f_F(r_{ij} + \delta) V^{Tersoff}(r_{ij} + \delta) \\
|
||||
f_F(r) & = \frac{1}{1 + e^{-A_F(r - r_C)}}\\
|
||||
\\
|
||||
\\
|
||||
V^{ZBL}_{ij} & = \frac{1}{4\pi\epsilon_0} \frac{Z_1 Z_2 \,e^2}{r_{ij}} \phi(r_{ij}/a) \\
|
||||
V^{ZBL}(r) & = \frac{1}{4\pi\epsilon_0} \frac{Z_1 Z_2 \,e^2}{r} \phi(r/a) \\
|
||||
a & = \frac{0.8854\,a_0}{Z_{1}^{0.23} + Z_{2}^{0.23}}\\
|
||||
\phi(x) & = 0.1818e^{-3.2x} + 0.5099e^{-0.9423x} + 0.2802e^{-0.4029x} + 0.02817e^{-0.2016x}\\
|
||||
\\
|
||||
\\
|
||||
V^{Tersoff}_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
|
||||
V^{Tersoff}(r) & = f_C(r) \left[ f_R(r) + b_{ij} f_A(r) \right] \\
|
||||
f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
|
||||
1 & r < R - D \\
|
||||
\frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) &
|
||||
@ -54,7 +62,7 @@ system of atoms as
|
||||
f_R(r) & = A \exp (-\lambda_1 r) \\
|
||||
f_A(r) & = -B \exp (-\lambda_2 r) \\
|
||||
b_{ij} & = \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
|
||||
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
|
||||
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik} + \delta) g(\theta_{ijk})
|
||||
\exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
|
||||
g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
|
||||
\frac{c^2}{\left[ d^2 + (\cos \theta - \cos \theta_0)^2\right]} \right)
|
||||
@ -81,6 +89,9 @@ includes
|
||||
three-body interactions. The summations in the formula are over all
|
||||
neighbors J and K of atom I within a cutoff distance = R + D.
|
||||
|
||||
:math:`\delta` is an optional negative shift of the
|
||||
equilibrium bond length, as described below.
|
||||
|
||||
Only a single pair_coeff command is used with the *tersoff/zbl* style
|
||||
which specifies a Tersoff/ZBL potential file with parameters for all
|
||||
needed elements. These are mapped to LAMMPS atom types by specifying
|
||||
@ -228,6 +239,14 @@ for helping clarify how Tersoff parameters for alloys have been
|
||||
defined in various papers. Also thanks to Ram Devanathan for
|
||||
providing the base ZBL implementation.
|
||||
|
||||
The *shift* keyword computes the energy E of a system of atoms, whose
|
||||
formula is the same as the Tersoff potential. The only modification is
|
||||
that the original equilibrium bond length ( :math:`r_0`) of the system
|
||||
is shifted to :math:`r_0-\delta`. The minus sign arises because each
|
||||
radial distance :math:`r` is replaced by :math:`r+\delta`. More
|
||||
information on this option is given on the main :doc:`pair_tersoff
|
||||
<pair_tersoff>` page.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
@ -244,9 +263,10 @@ described above from values in the potential file.
|
||||
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||
shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
|
||||
need to re-specify the pair_style and pair_coeff commands in an input
|
||||
script that reads a restart file.
|
||||
This pair style does not write its information to :doc:`binary restart
|
||||
files <restart>`, since it is stored in potential files. Thus, you need
|
||||
to re-specify the pair_style and pair_coeff commands in an input script
|
||||
that reads a restart file.
|
||||
|
||||
This pair style can only be used via the *pair* keyword of the
|
||||
:doc:`run_style respa <run_style>` command. It does not support the
|
||||
@ -257,18 +277,23 @@ This pair style can only be used via the *pair* keyword of the
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This pair style is part of the MANYBODY package. It is only enabled
|
||||
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
This pair style is part of the MANYBODY package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
This pair style requires the :doc:`newton <newton>` setting to be "on"
|
||||
for pair interactions.
|
||||
|
||||
The Tersoff/ZBL potential files provided with LAMMPS (see the
|
||||
potentials directory) are parameterized for metal :doc:`units <units>`.
|
||||
You can use the Tersoff potential with any LAMMPS units, but you would
|
||||
need to create your own Tersoff potential file with coefficients
|
||||
listed in the appropriate units if your simulation does not use "metal"
|
||||
units.
|
||||
The *shift* keyword is currently not supported for the *tersoff/gpu* and
|
||||
*tersoff/kk* variants of this pair style.
|
||||
|
||||
The tersoff/zbl potential files provided with LAMMPS (see the potentials
|
||||
directory) are parameterized for :doc:`"metal" units <units>`. Also the
|
||||
pair style supports converting potential file parameters on-the-fly
|
||||
between "metal" and "real" units. You can use the tersoff/zbl pair
|
||||
style with any LAMMPS units, but you would need to create your own
|
||||
tersoff/zbl potential file with coefficients listed in the appropriate
|
||||
units if your simulation does not use "metal" or "real" units.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
117
doc/src/pair_wf_cut.rst
Normal file
117
doc/src/pair_wf_cut.rst
Normal file
@ -0,0 +1,117 @@
|
||||
.. index:: pair_style wf/cut
|
||||
|
||||
pair_style wf/cut command
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style wf/cut cutoff
|
||||
|
||||
* cutoff = cutoff for wf interactions (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style wf/cut 2.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 2.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *wf/cut* (Wang-Frenkel) style computes LJ-like potentials as
|
||||
described in :ref:`Wang2020 <Wang2020>`. This potential is by
|
||||
construction finite ranged and it vanishes quadratically at the cutoff
|
||||
distance, avoiding truncation, shifting, interpolation and other typical
|
||||
procedures with the LJ potential. The *wf/cut* can be used when a
|
||||
typical short-ranged potential with attraction is required. The
|
||||
potential is given by which is given by:
|
||||
|
||||
.. math::
|
||||
\phi(r)= \epsilon \alpha \left(\left[{\sigma\over r}\right]^{2\mu} -1 \right)\left(\left[{r_c\over r}\right]^{2\mu}-1\right)^{2\nu}
|
||||
|
||||
with
|
||||
|
||||
.. math::
|
||||
\alpha=2\nu\left(\frac{r_c}{\sigma}\right)^{2\mu}\left[\frac{1+2\nu}{2\nu\left[(r_c/\sigma)^{2\mu}-1\right]}\right]^{2\nu+1}
|
||||
|
||||
and
|
||||
|
||||
.. math::
|
||||
r_{min}=r_c\left[\frac{1+2\nu}{1+2\nu(r_c/\sigma)^{2\nu}}\right]^{1/{2\nu}}
|
||||
|
||||
:math:`r_c` is the cutoff.
|
||||
|
||||
Comparison of the non-truncated Lennard-Jones 12-6 potential (red curve),
|
||||
and the WF potentials with :math:`\mu=1` and :math:`\nu=1` are shown in
|
||||
the figure below. The blue curve has :math:`r_c =2.0` and the green
|
||||
curve has :math:`r_c =1.2` and can be used to describe colloidal
|
||||
interactions.
|
||||
|
||||
.. image:: JPG/WF_LJ.jpg
|
||||
:align: center
|
||||
:scale: 33%
|
||||
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the example
|
||||
above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands:
|
||||
|
||||
* :math:`\epsilon` (energy units)
|
||||
* :math:`\sigma` (distance units)
|
||||
* :math:`\nu`
|
||||
* :math:`\mu`
|
||||
* :math:`r_c` (distance units)
|
||||
|
||||
The last coefficient is optional. If not specified, the global cutoff
|
||||
given in the pair_style command is used. The exponents :math:`\nu` and
|
||||
:math:`\mu` are positive integers, usually set to 1. There is usually
|
||||
little to be gained by choosing other values of :math:`\nu` and
|
||||
:math:`\mu` (See discussion in :ref:`Wang2020 <Wang2020>`)
|
||||
|
||||
----------
|
||||
|
||||
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
|
||||
|
||||
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||
mixing and table options.
|
||||
|
||||
The :doc:`pair_modify <pair_modify>` tail option is not relevant
|
||||
for this pair style as it goes to zero at the cut-off radius.
|
||||
|
||||
This pair style writes its information to :doc:`binary restart files
|
||||
<restart>`, so pair_style and pair_coeff commands do not need to be
|
||||
specified in an input script that reads a restart file.
|
||||
|
||||
This pair style does not support the use of the *inner*\ , *middle*\ ,
|
||||
and *outer* keywords of the :doc:`run_style respa <run_style>` command.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
This pair style can only be used if LAMMPS was built with the
|
||||
USER-MISC package. See the :doc:`Build package <Build_package>` doc
|
||||
page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
.. _Wang2020:
|
||||
|
||||
**(Wang2020)** X. Wang, S. Ramirez-Hinestrosa, J. Dobnikar, and D. Frenkel, Phys. Chem. Chem. Phys. 22, 10624 (2020).
|
||||
@ -96,9 +96,11 @@ always include a divide by the number of atoms in the variable formula
|
||||
if this is not the case.
|
||||
|
||||
The *flush* keyword invokes a flush operation after thermodynamic info
|
||||
is written to the log file. This insures the output in that file is
|
||||
current (no buffering by the OS), even if LAMMPS halts before the
|
||||
simulation completes.
|
||||
is written to the screen and log file. This insures the output is
|
||||
updated and not buffered (by the application) even if LAMMPS halts
|
||||
before the simulation completes. Please note that this does not
|
||||
affect buffering by the OS or devices, so you may still lose data
|
||||
in case the simulation stops due to a hardware failure.
|
||||
|
||||
The *line* keyword determines whether thermodynamics will be output as
|
||||
a series of numeric values on one line or in a multi-line format with
|
||||
|
||||
@ -200,6 +200,7 @@ barostatted
|
||||
barostatting
|
||||
Barostatting
|
||||
Barrat
|
||||
Bartelt
|
||||
Bartels
|
||||
barycenter
|
||||
barye
|
||||
@ -329,6 +330,7 @@ Buyl
|
||||
Bybee
|
||||
bz
|
||||
cadetblue
|
||||
Cagin
|
||||
calc
|
||||
calibre
|
||||
caltech
|
||||
@ -690,6 +692,7 @@ dmi
|
||||
dnf
|
||||
DNi
|
||||
Dobson
|
||||
Dobnikar
|
||||
Dodds
|
||||
docenv
|
||||
dodgerblue
|
||||
@ -1218,6 +1221,7 @@ Herrmann
|
||||
Hertizian
|
||||
hertzian
|
||||
Hertzsch
|
||||
heterostructures
|
||||
hexahedrons
|
||||
hexatic
|
||||
hexorder
|
||||
@ -1229,6 +1233,7 @@ Hibbs
|
||||
Higdon
|
||||
Hijazi
|
||||
Hilger
|
||||
Hinestrosa
|
||||
histo
|
||||
histogrammed
|
||||
histogramming
|
||||
@ -2473,6 +2478,9 @@ Poresag
|
||||
pos
|
||||
Poschel
|
||||
posix
|
||||
postfix
|
||||
postfixed
|
||||
postfixes
|
||||
Postma
|
||||
Potapkin
|
||||
potin
|
||||
@ -2678,6 +2686,8 @@ rhodo
|
||||
Rhodo
|
||||
rhodopsin
|
||||
rhok
|
||||
rhomax
|
||||
rhomin
|
||||
rhorho
|
||||
rhosum
|
||||
ri
|
||||
@ -2726,6 +2736,7 @@ rNEMD
|
||||
ro
|
||||
Rochus
|
||||
Rockett
|
||||
rocksalt
|
||||
Rodrigues
|
||||
Rohart
|
||||
Ronchetti
|
||||
@ -3400,6 +3411,7 @@ WeinanE
|
||||
Wennberg
|
||||
Westmere
|
||||
Westview
|
||||
wf
|
||||
wget
|
||||
Whelan
|
||||
whitesmoke
|
||||
@ -3545,6 +3557,7 @@ zz
|
||||
Zm
|
||||
PowerShell
|
||||
filesystems
|
||||
zincblende
|
||||
Zstandard
|
||||
Zstd
|
||||
zstd
|
||||
|
||||
@ -112,7 +112,8 @@ steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
|
||||
streitz: Streitz-Mintmire potential for Al2O3
|
||||
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
|
||||
template: examples for using atom_style template and comparing to atom style molecular
|
||||
threebody: regression test input for a variety of manybody potentials
|
||||
tersoff: regression test input for Tersoff variants
|
||||
threebody: regression test input for a variety of threebody potentials
|
||||
vashishta: models using the Vashishta potential
|
||||
voronoi: Voronoi tesselation via compute voronoi/atom command
|
||||
wall: use of reflective walls with different stochastic models
|
||||
|
||||
92
examples/USER/misc/agni/log.20Jan21.adatom.g++.1
Normal file
92
examples/USER/misc/agni/log.20Jan21.adatom.g++.1
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
processors * * 1
|
||||
units metal
|
||||
boundary p p f
|
||||
read_data adatom.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (17.121441 14.827603 39.319732)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
181 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_jpc.agni Al
|
||||
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
|
||||
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 500 12345
|
||||
fix 1 all nvt temp 250 250 0.2
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15, bins = 5 4 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair agni, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.072 | 3.072 | 3.072 Mbytes
|
||||
Step KinEng Temp
|
||||
0 11.633413 500
|
||||
100 4.6059941 197.96401
|
||||
200 7.3700156 316.76068
|
||||
300 6.0443915 259.78582
|
||||
400 6.163119 264.88869
|
||||
500 6.2647284 269.25582
|
||||
600 5.2732533 226.64257
|
||||
700 5.651448 242.89725
|
||||
800 6.5572404 281.82788
|
||||
900 6.0576743 260.35671
|
||||
1000 6.5622234 282.04205
|
||||
Loop time of 16.4158 on 1 procs for 1000 steps with 181 atoms
|
||||
|
||||
Performance: 2.632 ns/day, 9.120 hours/ns, 60.917 timesteps/s
|
||||
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.395 | 16.395 | 16.395 | 0.0 | 99.88
|
||||
Neigh | 0.013275 | 0.013275 | 0.013275 | 0.0 | 0.08
|
||||
Comm | 0.0023484 | 0.0023484 | 0.0023484 | 0.0 | 0.01
|
||||
Output | 0.00014842 | 0.00014842 | 0.00014842 | 0.0 | 0.00
|
||||
Modify | 0.0035522 | 0.0035522 | 0.0035522 | 0.0 | 0.02
|
||||
Other | | 0.001173 | | | 0.01
|
||||
|
||||
Nlocal: 181.000 ave 181 max 181 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 563.000 ave 563 max 563 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 19484.0 ave 19484 max 19484 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19484
|
||||
Ave neighs/atom = 107.64641
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:16
|
||||
92
examples/USER/misc/agni/log.20Jan21.adatom.g++.4
Normal file
92
examples/USER/misc/agni/log.20Jan21.adatom.g++.4
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
processors * * 1
|
||||
units metal
|
||||
boundary p p f
|
||||
read_data adatom.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (17.121441 14.827603 39.319732)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
181 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_jpc.agni Al
|
||||
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
|
||||
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 500 12345
|
||||
fix 1 all nvt temp 250 250 0.2
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15, bins = 5 4 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair agni, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.063 | 3.063 | 3.063 Mbytes
|
||||
Step KinEng Temp
|
||||
0 11.633413 500
|
||||
100 4.6059939 197.964
|
||||
200 7.3700154 316.76067
|
||||
300 6.0443914 259.78582
|
||||
400 6.1631193 264.8887
|
||||
500 6.2647281 269.25581
|
||||
600 5.273254 226.6426
|
||||
700 5.6514484 242.89726
|
||||
800 6.5572409 281.82791
|
||||
900 6.0576737 260.35668
|
||||
1000 6.5622233 282.04205
|
||||
Loop time of 4.67437 on 4 procs for 1000 steps with 181 atoms
|
||||
|
||||
Performance: 9.242 ns/day, 2.597 hours/ns, 213.933 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.0668 | 4.2058 | 4.4078 | 7.1 | 89.98
|
||||
Neigh | 0.0033048 | 0.0033794 | 0.0034381 | 0.1 | 0.07
|
||||
Comm | 0.2547 | 0.45656 | 0.59576 | 21.5 | 9.77
|
||||
Output | 9.8817e-05 | 0.00035464 | 0.001121 | 0.0 | 0.01
|
||||
Modify | 0.0059429 | 0.0060754 | 0.0061966 | 0.2 | 0.13
|
||||
Other | | 0.002172 | | | 0.05
|
||||
|
||||
Nlocal: 45.2500 ave 52 max 40 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 376.500 ave 382 max 366 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4871.00 ave 5578 max 4374 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19484
|
||||
Ave neighs/atom = 107.64641
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:04
|
||||
92
examples/USER/misc/agni/log.20Jan21.vacancy.g++.1
Normal file
92
examples/USER/misc/agni/log.20Jan21.vacancy.g++.1
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vacancy.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (8.0711250 8.0711250 8.0711250)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
31 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_jpc.agni Al
|
||||
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
|
||||
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 1000 12345
|
||||
fix 1 all nvt temp 900 900 200
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke etotal temp
|
||||
|
||||
dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair agni, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.241 | 4.241 | 4.241 Mbytes
|
||||
Step KinEng TotEng Temp
|
||||
0 3.8778043 3.8778043 1000
|
||||
100 2.9986261 2.9986261 773.27936
|
||||
200 3.6860313 3.6860313 950.54598
|
||||
300 3.8133153 3.8133153 983.3697
|
||||
400 3.7330285 3.7330285 962.6655
|
||||
500 3.5875467 3.5875467 925.14897
|
||||
600 3.533152 3.533152 911.12178
|
||||
700 2.6509457 2.6509457 683.62028
|
||||
800 3.376349 3.376349 870.68576
|
||||
900 3.9036736 3.9036736 1006.6711
|
||||
1000 3.0884833 3.0884833 796.45156
|
||||
Loop time of 2.92678 on 1 procs for 1000 steps with 31 atoms
|
||||
|
||||
Performance: 14.760 ns/day, 1.626 hours/ns, 341.673 timesteps/s
|
||||
97.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.9144 | 2.9144 | 2.9144 | 0.0 | 99.58
|
||||
Neigh | 0.0068263 | 0.0068263 | 0.0068263 | 0.0 | 0.23
|
||||
Comm | 0.0029868 | 0.0029868 | 0.0029868 | 0.0 | 0.10
|
||||
Output | 0.00050202 | 0.00050202 | 0.00050202 | 0.0 | 0.02
|
||||
Modify | 0.0013382 | 0.0013382 | 0.0013382 | 0.0 | 0.05
|
||||
Other | | 0.0007672 | | | 0.03
|
||||
|
||||
Nlocal: 31.0000 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 869.000 ave 869 max 869 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4360.00 ave 4360 max 4360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4360
|
||||
Ave neighs/atom = 140.64516
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
92
examples/USER/misc/agni/log.20Jan21.vacancy.g++.4
Normal file
92
examples/USER/misc/agni/log.20Jan21.vacancy.g++.4
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vacancy.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (8.0711250 8.0711250 8.0711250)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
31 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_jpc.agni Al
|
||||
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
|
||||
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 1000 12345
|
||||
fix 1 all nvt temp 900 900 200
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke etotal temp
|
||||
|
||||
dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair agni, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.227 | 4.227 | 4.227 Mbytes
|
||||
Step KinEng TotEng Temp
|
||||
0 3.8778043 3.8778043 1000
|
||||
100 2.9986264 2.9986264 773.27944
|
||||
200 3.6860316 3.6860316 950.54606
|
||||
300 3.8133152 3.8133152 983.36966
|
||||
400 3.7330288 3.7330288 962.66559
|
||||
500 3.5875468 3.5875468 925.149
|
||||
600 3.5331519 3.5331519 911.12176
|
||||
700 2.6509452 2.6509452 683.62015
|
||||
800 3.3763492 3.3763492 870.68579
|
||||
900 3.9036736 3.9036736 1006.6711
|
||||
1000 3.0884821 3.0884821 796.45125
|
||||
Loop time of 0.91769 on 4 procs for 1000 steps with 31 atoms
|
||||
|
||||
Performance: 47.075 ns/day, 0.510 hours/ns, 1089.693 timesteps/s
|
||||
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.67405 | 0.76047 | 0.81748 | 6.1 | 82.87
|
||||
Neigh | 0.0015411 | 0.001691 | 0.001774 | 0.2 | 0.18
|
||||
Comm | 0.091364 | 0.14959 | 0.23513 | 13.8 | 16.30
|
||||
Output | 0.00027996 | 0.00040391 | 0.00075917 | 0.0 | 0.04
|
||||
Modify | 0.0028397 | 0.0039247 | 0.0050072 | 1.7 | 0.43
|
||||
Other | | 0.001611 | | | 0.18
|
||||
|
||||
Nlocal: 7.75000 ave 8 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 617.250 ave 621 max 612 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1090.00 ave 1131 max 993 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 4360
|
||||
Ave neighs/atom = 140.64516
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,87 +0,0 @@
|
||||
LAMMPS (21 Feb 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
processors * * 1
|
||||
units metal
|
||||
boundary p p f
|
||||
read_data adatom.data
|
||||
orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
181 atoms
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_jpc.agni Al
|
||||
Reading potential file Al_jpc.agni with DATE: 2017-02-24
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 500 12345
|
||||
fix 1 all nvt temp 250 250 0.2
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15, bins = 5 4 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair agni, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Memory usage per processor = 2.69795 Mbytes
|
||||
Step KinEng Temp
|
||||
0 11.633413 500
|
||||
100 4.6059939 197.964
|
||||
200 7.3700149 316.76065
|
||||
300 6.0443913 259.78581
|
||||
400 6.1631189 264.88868
|
||||
500 6.2647272 269.25577
|
||||
600 5.2732539 226.6426
|
||||
700 5.6514471 242.89721
|
||||
800 6.5572407 281.8279
|
||||
900 6.0576738 260.35669
|
||||
1000 6.5622233 282.04205
|
||||
Loop time of 51.9308 on 1 procs for 1000 steps with 181 atoms
|
||||
|
||||
Performance: 0.832 ns/day, 28.850 hours/ns, 19.256 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 51.89 | 51.89 | 51.89 | 0.0 | 99.92
|
||||
Neigh | 0.023158 | 0.023158 | 0.023158 | 0.0 | 0.04
|
||||
Comm | 0.0049036 | 0.0049036 | 0.0049036 | 0.0 | 0.01
|
||||
Output | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.00
|
||||
Modify | 0.010244 | 0.010244 | 0.010244 | 0.0 | 0.02
|
||||
Other | | 0.002483 | | | 0.00
|
||||
|
||||
Nlocal: 181 ave 181 max 181 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 563 ave 563 max 563 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 19484 ave 19484 max 19484 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19484
|
||||
Ave neighs/atom = 107.646
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:52
|
||||
@ -1,87 +0,0 @@
|
||||
LAMMPS (21 Feb 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
processors * * 1
|
||||
units metal
|
||||
boundary p p f
|
||||
read_data adatom.data
|
||||
orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
181 atoms
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_jpc.agni Al
|
||||
Reading potential file Al_jpc.agni with DATE: 2017-02-24
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 500 12345
|
||||
fix 1 all nvt temp 250 250 0.2
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15, bins = 5 4 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair agni, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Memory usage per processor = 3.06041 Mbytes
|
||||
Step KinEng Temp
|
||||
0 11.633413 500
|
||||
100 4.6059941 197.96401
|
||||
200 7.3700154 316.76067
|
||||
300 6.0443913 259.78581
|
||||
400 6.1631193 264.8887
|
||||
500 6.2647281 269.25581
|
||||
600 5.2732537 226.64259
|
||||
700 5.651448 242.89725
|
||||
800 6.5572405 281.82789
|
||||
900 6.0576741 260.3567
|
||||
1000 6.562224 282.04208
|
||||
Loop time of 14.5263 on 4 procs for 1000 steps with 181 atoms
|
||||
|
||||
Performance: 2.974 ns/day, 8.070 hours/ns, 68.841 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 12.858 | 13.227 | 13.574 | 8.0 | 91.06
|
||||
Neigh | 0.0056965 | 0.0058173 | 0.0060787 | 0.2 | 0.04
|
||||
Comm | 0.92934 | 1.276 | 1.6455 | 25.7 | 8.78
|
||||
Output | 0.00013971 | 0.00017625 | 0.00025463 | 0.0 | 0.00
|
||||
Modify | 0.012693 | 0.012756 | 0.012911 | 0.1 | 0.09
|
||||
Other | | 0.004066 | | | 0.03
|
||||
|
||||
Nlocal: 45.25 ave 52 max 40 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 376.5 ave 382 max 366 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4871 ave 5578 max 4374 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19484
|
||||
Ave neighs/atom = 107.646
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:14
|
||||
@ -1,87 +0,0 @@
|
||||
LAMMPS (21 Feb 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vacancy.data
|
||||
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
31 atoms
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_jpc.agni Al
|
||||
Reading potential file Al_jpc.agni with DATE: 2017-02-24
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 1000 12345
|
||||
fix 1 all nvt temp 900 900 200
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke etotal temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair agni, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Memory usage per processor = 2.73416 Mbytes
|
||||
Step KinEng TotEng Temp
|
||||
0 3.8778043 3.8778043 1000
|
||||
100 2.9986261 2.9986261 773.27937
|
||||
200 3.6860314 3.6860314 950.54599
|
||||
300 3.813315 3.813315 983.36961
|
||||
400 3.7330285 3.7330285 962.6655
|
||||
500 3.5875467 3.5875467 925.14896
|
||||
600 3.5331529 3.5331529 911.12202
|
||||
700 2.6509449 2.6509449 683.62008
|
||||
800 3.3763492 3.3763492 870.68582
|
||||
900 3.903673 3.903673 1006.6709
|
||||
1000 3.0884824 3.0884824 796.45133
|
||||
Loop time of 9.02712 on 1 procs for 1000 steps with 31 atoms
|
||||
|
||||
Performance: 4.786 ns/day, 5.015 hours/ns, 110.777 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.0039 | 9.0039 | 9.0039 | 0.0 | 99.74
|
||||
Neigh | 0.011892 | 0.011892 | 0.011892 | 0.0 | 0.13
|
||||
Comm | 0.0061693 | 0.0061693 | 0.0061693 | 0.0 | 0.07
|
||||
Output | 0.00014615 | 0.00014615 | 0.00014615 | 0.0 | 0.00
|
||||
Modify | 0.0035009 | 0.0035009 | 0.0035009 | 0.0 | 0.04
|
||||
Other | | 0.001521 | | | 0.02
|
||||
|
||||
Nlocal: 31 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 869 ave 869 max 869 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4360 ave 4360 max 4360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4360
|
||||
Ave neighs/atom = 140.645
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:09
|
||||
@ -1,87 +0,0 @@
|
||||
LAMMPS (21 Feb 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vacancy.data
|
||||
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
31 atoms
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_jpc.agni Al
|
||||
Reading potential file Al_jpc.agni with DATE: 2017-02-24
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 1000 12345
|
||||
fix 1 all nvt temp 900 900 200
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke etotal temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair agni, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Memory usage per processor = 2.72175 Mbytes
|
||||
Step KinEng TotEng Temp
|
||||
0 3.8778044 3.8778044 1000
|
||||
100 2.9986263 2.9986263 773.27942
|
||||
200 3.6860315 3.6860315 950.54602
|
||||
300 3.8133145 3.8133145 983.3695
|
||||
400 3.7330282 3.7330282 962.66543
|
||||
500 3.5875466 3.5875466 925.14895
|
||||
600 3.5331523 3.5331523 911.12186
|
||||
700 2.6509448 2.6509448 683.62005
|
||||
800 3.3763493 3.3763493 870.68584
|
||||
900 3.9036733 3.9036733 1006.671
|
||||
1000 3.0884818 3.0884818 796.45116
|
||||
Loop time of 2.46785 on 4 procs for 1000 steps with 31 atoms
|
||||
|
||||
Performance: 17.505 ns/day, 1.371 hours/ns, 405.212 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0737 | 2.299 | 2.3902 | 8.7 | 93.16
|
||||
Neigh | 0.0025222 | 0.0027327 | 0.0028174 | 0.2 | 0.11
|
||||
Comm | 0.059817 | 0.15141 | 0.37684 | 33.8 | 6.14
|
||||
Output | 0.0001502 | 0.00016767 | 0.00021219 | 0.0 | 0.01
|
||||
Modify | 0.0098755 | 0.010248 | 0.010664 | 0.3 | 0.42
|
||||
Other | | 0.004321 | | | 0.18
|
||||
|
||||
Nlocal: 7.75 ave 8 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 617.25 ave 621 max 612 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1090 ave 1131 max 993 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 4360
|
||||
Ave neighs/atom = 140.645
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
892
examples/hBN-momolayer-5nm.data
Normal file
892
examples/hBN-momolayer-5nm.data
Normal file
@ -0,0 +1,892 @@
|
||||
Makeup graphene nanoribbon on hBN
|
||||
|
||||
880 atoms
|
||||
|
||||
2 atom types
|
||||
|
||||
0.000000000000000 46.152979739999999 xlo xhi
|
||||
0.000000000000000 48.443364211584992 ylo yhi
|
||||
0.000000000000000 100.000000000000000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.420 0.000000000000000 0.000000000000000 0.000000000000000
|
||||
2 2 -0.420 0.698900000000000 1.210530287683010 0.000000000000000
|
||||
3 1 0.420 2.096700000000000 1.210530287683010 0.000000000000000
|
||||
4 2 -0.420 2.795600000000000 0.000000000000000 0.000000000000000
|
||||
5 1 0.420 4.193400000000000 0.000000000000000 0.000000000000000
|
||||
6 2 -0.420 4.892300000000000 1.210530287683010 0.000000000000000
|
||||
7 1 0.420 6.290100000000000 1.210530287683010 0.000000000000000
|
||||
8 2 -0.420 6.989000000000000 0.000000000000000 0.000000000000000
|
||||
9 1 0.420 8.386799999999999 0.000000000000000 0.000000000000000
|
||||
10 2 -0.420 9.085699999999999 1.210530287683010 0.000000000000000
|
||||
11 1 0.420 10.483499999999999 1.210530287683010 0.000000000000000
|
||||
12 2 -0.420 11.182399999999999 0.000000000000000 0.000000000000000
|
||||
13 1 0.420 12.580200000000000 0.000000000000000 0.000000000000000
|
||||
14 2 -0.420 13.279100000000000 1.210530287683010 0.000000000000000
|
||||
15 1 0.420 14.676900000000000 1.210530287683010 0.000000000000000
|
||||
16 2 -0.420 15.375800000000000 0.000000000000000 0.000000000000000
|
||||
17 1 0.420 16.773599999999998 0.000000000000000 0.000000000000000
|
||||
18 2 -0.420 17.472500000000000 1.210530287683010 0.000000000000000
|
||||
19 1 0.420 18.870300000000000 1.210530287683010 0.000000000000000
|
||||
20 2 -0.420 19.569199999999999 0.000000000000000 0.000000000000000
|
||||
21 1 0.420 20.966999999999999 0.000000000000000 0.000000000000000
|
||||
22 2 -0.420 21.665900000000001 1.210530287683010 0.000000000000000
|
||||
23 1 0.420 23.063699999999997 1.210530287683010 0.000000000000000
|
||||
24 2 -0.420 23.762599999999999 0.000000000000000 0.000000000000000
|
||||
25 1 0.420 25.160399999999999 0.000000000000000 0.000000000000000
|
||||
26 2 -0.420 25.859299999999998 1.210530287683010 0.000000000000000
|
||||
27 1 0.420 27.257099999999998 1.210530287683010 0.000000000000000
|
||||
28 2 -0.420 27.956000000000000 0.000000000000000 0.000000000000000
|
||||
29 1 0.420 29.353800000000000 0.000000000000000 0.000000000000000
|
||||
30 2 -0.420 30.052699999999998 1.210530287683010 0.000000000000000
|
||||
31 1 0.420 31.450499999999998 1.210530287683010 0.000000000000000
|
||||
32 2 -0.420 32.149400000000000 0.000000000000000 0.000000000000000
|
||||
33 1 0.420 33.547199999999997 0.000000000000000 0.000000000000000
|
||||
34 2 -0.420 34.246099999999998 1.210530287683010 0.000000000000000
|
||||
35 1 0.420 35.643899999999995 1.210530287683010 0.000000000000000
|
||||
36 2 -0.420 36.342799999999997 0.000000000000000 0.000000000000000
|
||||
37 1 0.420 37.740600000000001 0.000000000000000 0.000000000000000
|
||||
38 2 -0.420 38.439499999999995 1.210530287683010 0.000000000000000
|
||||
39 1 0.420 39.837299999999999 1.210530287683010 0.000000000000000
|
||||
40 2 -0.420 40.536200000000001 0.000000000000000 0.000000000000000
|
||||
41 1 0.420 41.933999999999997 0.000000000000000 0.000000000000000
|
||||
42 2 -0.420 42.632899999999999 1.210530287683010 0.000000000000000
|
||||
43 1 0.420 44.030699999999996 1.210530287683010 0.000000000000000
|
||||
44 2 -0.420 44.729599999999998 0.000000000000000 0.000000000000000
|
||||
45 1 0.420 0.000000000000000 2.421060575366020 0.000000000000000
|
||||
46 2 -0.420 0.698900000000000 3.631590863049030 0.000000000000000
|
||||
47 1 0.420 2.096700000000000 3.631590863049030 0.000000000000000
|
||||
48 2 -0.420 2.795600000000000 2.421060575366020 0.000000000000000
|
||||
49 1 0.420 4.193400000000000 2.421060575366020 0.000000000000000
|
||||
50 2 -0.420 4.892300000000000 3.631590863049030 0.000000000000000
|
||||
51 1 0.420 6.290100000000000 3.631590863049030 0.000000000000000
|
||||
52 2 -0.420 6.989000000000000 2.421060575366020 0.000000000000000
|
||||
53 1 0.420 8.386799999999999 2.421060575366020 0.000000000000000
|
||||
54 2 -0.420 9.085699999999999 3.631590863049030 0.000000000000000
|
||||
55 1 0.420 10.483499999999999 3.631590863049030 0.000000000000000
|
||||
56 2 -0.420 11.182399999999999 2.421060575366020 0.000000000000000
|
||||
57 1 0.420 12.580200000000000 2.421060575366020 0.000000000000000
|
||||
58 2 -0.420 13.279100000000000 3.631590863049030 0.000000000000000
|
||||
59 1 0.420 14.676900000000000 3.631590863049030 0.000000000000000
|
||||
60 2 -0.420 15.375800000000000 2.421060575366020 0.000000000000000
|
||||
61 1 0.420 16.773599999999998 2.421060575366020 0.000000000000000
|
||||
62 2 -0.420 17.472500000000000 3.631590863049030 0.000000000000000
|
||||
63 1 0.420 18.870300000000000 3.631590863049030 0.000000000000000
|
||||
64 2 -0.420 19.569199999999999 2.421060575366020 0.000000000000000
|
||||
65 1 0.420 20.966999999999999 2.421060575366020 0.000000000000000
|
||||
66 2 -0.420 21.665900000000001 3.631590863049030 0.000000000000000
|
||||
67 1 0.420 23.063699999999997 3.631590863049030 0.000000000000000
|
||||
68 2 -0.420 23.762599999999999 2.421060575366020 0.000000000000000
|
||||
69 1 0.420 25.160399999999999 2.421060575366020 0.000000000000000
|
||||
70 2 -0.420 25.859299999999998 3.631590863049030 0.000000000000000
|
||||
71 1 0.420 27.257099999999998 3.631590863049030 0.000000000000000
|
||||
72 2 -0.420 27.956000000000000 2.421060575366020 0.000000000000000
|
||||
73 1 0.420 29.353800000000000 2.421060575366020 0.000000000000000
|
||||
74 2 -0.420 30.052699999999998 3.631590863049030 0.000000000000000
|
||||
75 1 0.420 31.450499999999998 3.631590863049030 0.000000000000000
|
||||
76 2 -0.420 32.149400000000000 2.421060575366020 0.000000000000000
|
||||
77 1 0.420 33.547199999999997 2.421060575366020 0.000000000000000
|
||||
78 2 -0.420 34.246099999999998 3.631590863049030 0.000000000000000
|
||||
79 1 0.420 35.643899999999995 3.631590863049030 0.000000000000000
|
||||
80 2 -0.420 36.342799999999997 2.421060575366020 0.000000000000000
|
||||
81 1 0.420 37.740600000000001 2.421060575366020 0.000000000000000
|
||||
82 2 -0.420 38.439499999999995 3.631590863049030 0.000000000000000
|
||||
83 1 0.420 39.837299999999999 3.631590863049030 0.000000000000000
|
||||
84 2 -0.420 40.536200000000001 2.421060575366020 0.000000000000000
|
||||
85 1 0.420 41.933999999999997 2.421060575366020 0.000000000000000
|
||||
86 2 -0.420 42.632899999999999 3.631590863049030 0.000000000000000
|
||||
87 1 0.420 44.030699999999996 3.631590863049030 0.000000000000000
|
||||
88 2 -0.420 44.729599999999998 2.421060575366020 0.000000000000000
|
||||
89 1 0.420 0.000000000000000 4.842121150732040 0.000000000000000
|
||||
90 2 -0.420 0.698900000000000 6.052651438415050 0.000000000000000
|
||||
91 1 0.420 2.096700000000000 6.052651438415050 0.000000000000000
|
||||
92 2 -0.420 2.795600000000000 4.842121150732040 0.000000000000000
|
||||
93 1 0.420 4.193400000000000 4.842121150732040 0.000000000000000
|
||||
94 2 -0.420 4.892300000000000 6.052651438415050 0.000000000000000
|
||||
95 1 0.420 6.290100000000000 6.052651438415050 0.000000000000000
|
||||
96 2 -0.420 6.989000000000000 4.842121150732040 0.000000000000000
|
||||
97 1 0.420 8.386799999999999 4.842121150732040 0.000000000000000
|
||||
98 2 -0.420 9.085699999999999 6.052651438415050 0.000000000000000
|
||||
99 1 0.420 10.483499999999999 6.052651438415050 0.000000000000000
|
||||
100 2 -0.420 11.182399999999999 4.842121150732040 0.000000000000000
|
||||
101 1 0.420 12.580200000000000 4.842121150732040 0.000000000000000
|
||||
102 2 -0.420 13.279100000000000 6.052651438415050 0.000000000000000
|
||||
103 1 0.420 14.676900000000000 6.052651438415050 0.000000000000000
|
||||
104 2 -0.420 15.375800000000000 4.842121150732040 0.000000000000000
|
||||
105 1 0.420 16.773599999999998 4.842121150732040 0.000000000000000
|
||||
106 2 -0.420 17.472500000000000 6.052651438415050 0.000000000000000
|
||||
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|
||||
851 1 0.420 14.676900000000000 47.210681219637387 0.000000000000000
|
||||
852 2 -0.420 15.375800000000000 46.000150931954380 0.000000000000000
|
||||
853 1 0.420 16.773599999999998 46.000150931954380 0.000000000000000
|
||||
854 2 -0.420 17.472500000000000 47.210681219637387 0.000000000000000
|
||||
855 1 0.420 18.870300000000000 47.210681219637387 0.000000000000000
|
||||
856 2 -0.420 19.569199999999999 46.000150931954380 0.000000000000000
|
||||
857 1 0.420 20.966999999999999 46.000150931954380 0.000000000000000
|
||||
858 2 -0.420 21.665900000000001 47.210681219637387 0.000000000000000
|
||||
859 1 0.420 23.063699999999997 47.210681219637387 0.000000000000000
|
||||
860 2 -0.420 23.762599999999999 46.000150931954380 0.000000000000000
|
||||
861 1 0.420 25.160399999999999 46.000150931954380 0.000000000000000
|
||||
862 2 -0.420 25.859299999999998 47.210681219637387 0.000000000000000
|
||||
863 1 0.420 27.257099999999998 47.210681219637387 0.000000000000000
|
||||
864 2 -0.420 27.956000000000000 46.000150931954380 0.000000000000000
|
||||
865 1 0.420 29.353800000000000 46.000150931954380 0.000000000000000
|
||||
866 2 -0.420 30.052699999999998 47.210681219637387 0.000000000000000
|
||||
867 1 0.420 31.450499999999998 47.210681219637387 0.000000000000000
|
||||
868 2 -0.420 32.149400000000000 46.000150931954380 0.000000000000000
|
||||
869 1 0.420 33.547199999999997 46.000150931954380 0.000000000000000
|
||||
870 2 -0.420 34.246099999999998 47.210681219637387 0.000000000000000
|
||||
871 1 0.420 35.643899999999995 47.210681219637387 0.000000000000000
|
||||
872 2 -0.420 36.342799999999997 46.000150931954380 0.000000000000000
|
||||
873 1 0.420 37.740600000000001 46.000150931954380 0.000000000000000
|
||||
874 2 -0.420 38.439499999999995 47.210681219637387 0.000000000000000
|
||||
875 1 0.420 39.837299999999999 47.210681219637387 0.000000000000000
|
||||
876 2 -0.420 40.536200000000001 46.000150931954380 0.000000000000000
|
||||
877 1 0.420 41.933999999999997 46.000150931954380 0.000000000000000
|
||||
878 2 -0.420 42.632899999999999 47.210681219637387 0.000000000000000
|
||||
879 1 0.420 44.030699999999996 47.210681219637387 0.000000000000000
|
||||
880 2 -0.420 44.729599999999998 46.000150931954380 0.000000000000000
|
||||
37
examples/in.hBN_shift
Normal file
37
examples/in.hBN_shift
Normal file
@ -0,0 +1,37 @@
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN-momolayer-5nm.data
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff B N
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix thermostat all nve
|
||||
|
||||
############# Output ###############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp
|
||||
#thermo_modify lost warn
|
||||
thermo_modify line one format float %20.16g lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
1
examples/tersoff/BNC.tersoff
Symbolic link
1
examples/tersoff/BNC.tersoff
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/BNC.tersoff
|
||||
1
examples/tersoff/Si.tersoff
Symbolic link
1
examples/tersoff/Si.tersoff
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/Si.tersoff
|
||||
892
examples/tersoff/hBN-monolayer-5nm.data
Normal file
892
examples/tersoff/hBN-monolayer-5nm.data
Normal file
@ -0,0 +1,892 @@
|
||||
Makeup graphene nanoribbon on hBN
|
||||
|
||||
880 atoms
|
||||
|
||||
2 atom types
|
||||
|
||||
0.000000000000000 46.152979739999999 xlo xhi
|
||||
0.000000000000000 48.443364211584992 ylo yhi
|
||||
0.000000000000000 100.000000000000000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.420 0.000000000000000 0.000000000000000 0.000000000000000
|
||||
2 2 -0.420 0.698900000000000 1.210530287683010 0.000000000000000
|
||||
3 1 0.420 2.096700000000000 1.210530287683010 0.000000000000000
|
||||
4 2 -0.420 2.795600000000000 0.000000000000000 0.000000000000000
|
||||
5 1 0.420 4.193400000000000 0.000000000000000 0.000000000000000
|
||||
6 2 -0.420 4.892300000000000 1.210530287683010 0.000000000000000
|
||||
7 1 0.420 6.290100000000000 1.210530287683010 0.000000000000000
|
||||
8 2 -0.420 6.989000000000000 0.000000000000000 0.000000000000000
|
||||
9 1 0.420 8.386799999999999 0.000000000000000 0.000000000000000
|
||||
10 2 -0.420 9.085699999999999 1.210530287683010 0.000000000000000
|
||||
11 1 0.420 10.483499999999999 1.210530287683010 0.000000000000000
|
||||
12 2 -0.420 11.182399999999999 0.000000000000000 0.000000000000000
|
||||
13 1 0.420 12.580200000000000 0.000000000000000 0.000000000000000
|
||||
14 2 -0.420 13.279100000000000 1.210530287683010 0.000000000000000
|
||||
15 1 0.420 14.676900000000000 1.210530287683010 0.000000000000000
|
||||
16 2 -0.420 15.375800000000000 0.000000000000000 0.000000000000000
|
||||
17 1 0.420 16.773599999999998 0.000000000000000 0.000000000000000
|
||||
18 2 -0.420 17.472500000000000 1.210530287683010 0.000000000000000
|
||||
19 1 0.420 18.870300000000000 1.210530287683010 0.000000000000000
|
||||
20 2 -0.420 19.569199999999999 0.000000000000000 0.000000000000000
|
||||
21 1 0.420 20.966999999999999 0.000000000000000 0.000000000000000
|
||||
22 2 -0.420 21.665900000000001 1.210530287683010 0.000000000000000
|
||||
23 1 0.420 23.063699999999997 1.210530287683010 0.000000000000000
|
||||
24 2 -0.420 23.762599999999999 0.000000000000000 0.000000000000000
|
||||
25 1 0.420 25.160399999999999 0.000000000000000 0.000000000000000
|
||||
26 2 -0.420 25.859299999999998 1.210530287683010 0.000000000000000
|
||||
27 1 0.420 27.257099999999998 1.210530287683010 0.000000000000000
|
||||
28 2 -0.420 27.956000000000000 0.000000000000000 0.000000000000000
|
||||
29 1 0.420 29.353800000000000 0.000000000000000 0.000000000000000
|
||||
30 2 -0.420 30.052699999999998 1.210530287683010 0.000000000000000
|
||||
31 1 0.420 31.450499999999998 1.210530287683010 0.000000000000000
|
||||
32 2 -0.420 32.149400000000000 0.000000000000000 0.000000000000000
|
||||
33 1 0.420 33.547199999999997 0.000000000000000 0.000000000000000
|
||||
34 2 -0.420 34.246099999999998 1.210530287683010 0.000000000000000
|
||||
35 1 0.420 35.643899999999995 1.210530287683010 0.000000000000000
|
||||
36 2 -0.420 36.342799999999997 0.000000000000000 0.000000000000000
|
||||
37 1 0.420 37.740600000000001 0.000000000000000 0.000000000000000
|
||||
38 2 -0.420 38.439499999999995 1.210530287683010 0.000000000000000
|
||||
39 1 0.420 39.837299999999999 1.210530287683010 0.000000000000000
|
||||
40 2 -0.420 40.536200000000001 0.000000000000000 0.000000000000000
|
||||
41 1 0.420 41.933999999999997 0.000000000000000 0.000000000000000
|
||||
42 2 -0.420 42.632899999999999 1.210530287683010 0.000000000000000
|
||||
43 1 0.420 44.030699999999996 1.210530287683010 0.000000000000000
|
||||
44 2 -0.420 44.729599999999998 0.000000000000000 0.000000000000000
|
||||
45 1 0.420 0.000000000000000 2.421060575366020 0.000000000000000
|
||||
46 2 -0.420 0.698900000000000 3.631590863049030 0.000000000000000
|
||||
47 1 0.420 2.096700000000000 3.631590863049030 0.000000000000000
|
||||
48 2 -0.420 2.795600000000000 2.421060575366020 0.000000000000000
|
||||
49 1 0.420 4.193400000000000 2.421060575366020 0.000000000000000
|
||||
50 2 -0.420 4.892300000000000 3.631590863049030 0.000000000000000
|
||||
51 1 0.420 6.290100000000000 3.631590863049030 0.000000000000000
|
||||
52 2 -0.420 6.989000000000000 2.421060575366020 0.000000000000000
|
||||
53 1 0.420 8.386799999999999 2.421060575366020 0.000000000000000
|
||||
54 2 -0.420 9.085699999999999 3.631590863049030 0.000000000000000
|
||||
55 1 0.420 10.483499999999999 3.631590863049030 0.000000000000000
|
||||
56 2 -0.420 11.182399999999999 2.421060575366020 0.000000000000000
|
||||
57 1 0.420 12.580200000000000 2.421060575366020 0.000000000000000
|
||||
58 2 -0.420 13.279100000000000 3.631590863049030 0.000000000000000
|
||||
59 1 0.420 14.676900000000000 3.631590863049030 0.000000000000000
|
||||
60 2 -0.420 15.375800000000000 2.421060575366020 0.000000000000000
|
||||
61 1 0.420 16.773599999999998 2.421060575366020 0.000000000000000
|
||||
62 2 -0.420 17.472500000000000 3.631590863049030 0.000000000000000
|
||||
63 1 0.420 18.870300000000000 3.631590863049030 0.000000000000000
|
||||
64 2 -0.420 19.569199999999999 2.421060575366020 0.000000000000000
|
||||
65 1 0.420 20.966999999999999 2.421060575366020 0.000000000000000
|
||||
66 2 -0.420 21.665900000000001 3.631590863049030 0.000000000000000
|
||||
67 1 0.420 23.063699999999997 3.631590863049030 0.000000000000000
|
||||
68 2 -0.420 23.762599999999999 2.421060575366020 0.000000000000000
|
||||
69 1 0.420 25.160399999999999 2.421060575366020 0.000000000000000
|
||||
70 2 -0.420 25.859299999999998 3.631590863049030 0.000000000000000
|
||||
71 1 0.420 27.257099999999998 3.631590863049030 0.000000000000000
|
||||
72 2 -0.420 27.956000000000000 2.421060575366020 0.000000000000000
|
||||
73 1 0.420 29.353800000000000 2.421060575366020 0.000000000000000
|
||||
74 2 -0.420 30.052699999999998 3.631590863049030 0.000000000000000
|
||||
75 1 0.420 31.450499999999998 3.631590863049030 0.000000000000000
|
||||
76 2 -0.420 32.149400000000000 2.421060575366020 0.000000000000000
|
||||
77 1 0.420 33.547199999999997 2.421060575366020 0.000000000000000
|
||||
78 2 -0.420 34.246099999999998 3.631590863049030 0.000000000000000
|
||||
79 1 0.420 35.643899999999995 3.631590863049030 0.000000000000000
|
||||
80 2 -0.420 36.342799999999997 2.421060575366020 0.000000000000000
|
||||
81 1 0.420 37.740600000000001 2.421060575366020 0.000000000000000
|
||||
82 2 -0.420 38.439499999999995 3.631590863049030 0.000000000000000
|
||||
83 1 0.420 39.837299999999999 3.631590863049030 0.000000000000000
|
||||
84 2 -0.420 40.536200000000001 2.421060575366020 0.000000000000000
|
||||
85 1 0.420 41.933999999999997 2.421060575366020 0.000000000000000
|
||||
86 2 -0.420 42.632899999999999 3.631590863049030 0.000000000000000
|
||||
87 1 0.420 44.030699999999996 3.631590863049030 0.000000000000000
|
||||
88 2 -0.420 44.729599999999998 2.421060575366020 0.000000000000000
|
||||
89 1 0.420 0.000000000000000 4.842121150732040 0.000000000000000
|
||||
90 2 -0.420 0.698900000000000 6.052651438415050 0.000000000000000
|
||||
91 1 0.420 2.096700000000000 6.052651438415050 0.000000000000000
|
||||
92 2 -0.420 2.795600000000000 4.842121150732040 0.000000000000000
|
||||
93 1 0.420 4.193400000000000 4.842121150732040 0.000000000000000
|
||||
94 2 -0.420 4.892300000000000 6.052651438415050 0.000000000000000
|
||||
95 1 0.420 6.290100000000000 6.052651438415050 0.000000000000000
|
||||
96 2 -0.420 6.989000000000000 4.842121150732040 0.000000000000000
|
||||
97 1 0.420 8.386799999999999 4.842121150732040 0.000000000000000
|
||||
98 2 -0.420 9.085699999999999 6.052651438415050 0.000000000000000
|
||||
99 1 0.420 10.483499999999999 6.052651438415050 0.000000000000000
|
||||
100 2 -0.420 11.182399999999999 4.842121150732040 0.000000000000000
|
||||
101 1 0.420 12.580200000000000 4.842121150732040 0.000000000000000
|
||||
102 2 -0.420 13.279100000000000 6.052651438415050 0.000000000000000
|
||||
103 1 0.420 14.676900000000000 6.052651438415050 0.000000000000000
|
||||
104 2 -0.420 15.375800000000000 4.842121150732040 0.000000000000000
|
||||
105 1 0.420 16.773599999999998 4.842121150732040 0.000000000000000
|
||||
106 2 -0.420 17.472500000000000 6.052651438415050 0.000000000000000
|
||||
107 1 0.420 18.870300000000000 6.052651438415050 0.000000000000000
|
||||
108 2 -0.420 19.569199999999999 4.842121150732040 0.000000000000000
|
||||
109 1 0.420 20.966999999999999 4.842121150732040 0.000000000000000
|
||||
110 2 -0.420 21.665900000000001 6.052651438415050 0.000000000000000
|
||||
111 1 0.420 23.063699999999997 6.052651438415050 0.000000000000000
|
||||
112 2 -0.420 23.762599999999999 4.842121150732040 0.000000000000000
|
||||
113 1 0.420 25.160399999999999 4.842121150732040 0.000000000000000
|
||||
114 2 -0.420 25.859299999999998 6.052651438415050 0.000000000000000
|
||||
115 1 0.420 27.257099999999998 6.052651438415050 0.000000000000000
|
||||
116 2 -0.420 27.956000000000000 4.842121150732040 0.000000000000000
|
||||
117 1 0.420 29.353800000000000 4.842121150732040 0.000000000000000
|
||||
118 2 -0.420 30.052699999999998 6.052651438415050 0.000000000000000
|
||||
119 1 0.420 31.450499999999998 6.052651438415050 0.000000000000000
|
||||
120 2 -0.420 32.149400000000000 4.842121150732040 0.000000000000000
|
||||
121 1 0.420 33.547199999999997 4.842121150732040 0.000000000000000
|
||||
122 2 -0.420 34.246099999999998 6.052651438415050 0.000000000000000
|
||||
123 1 0.420 35.643899999999995 6.052651438415050 0.000000000000000
|
||||
124 2 -0.420 36.342799999999997 4.842121150732040 0.000000000000000
|
||||
125 1 0.420 37.740600000000001 4.842121150732040 0.000000000000000
|
||||
126 2 -0.420 38.439499999999995 6.052651438415050 0.000000000000000
|
||||
127 1 0.420 39.837299999999999 6.052651438415050 0.000000000000000
|
||||
128 2 -0.420 40.536200000000001 4.842121150732040 0.000000000000000
|
||||
129 1 0.420 41.933999999999997 4.842121150732040 0.000000000000000
|
||||
130 2 -0.420 42.632899999999999 6.052651438415050 0.000000000000000
|
||||
131 1 0.420 44.030699999999996 6.052651438415050 0.000000000000000
|
||||
132 2 -0.420 44.729599999999998 4.842121150732040 0.000000000000000
|
||||
133 1 0.420 0.000000000000000 7.263181726098059 0.000000000000000
|
||||
134 2 -0.420 0.698900000000000 8.473712013781070 0.000000000000000
|
||||
135 1 0.420 2.096700000000000 8.473712013781070 0.000000000000000
|
||||
136 2 -0.420 2.795600000000000 7.263181726098059 0.000000000000000
|
||||
137 1 0.420 4.193400000000000 7.263181726098059 0.000000000000000
|
||||
138 2 -0.420 4.892300000000000 8.473712013781070 0.000000000000000
|
||||
139 1 0.420 6.290100000000000 8.473712013781070 0.000000000000000
|
||||
140 2 -0.420 6.989000000000000 7.263181726098059 0.000000000000000
|
||||
141 1 0.420 8.386799999999999 7.263181726098059 0.000000000000000
|
||||
142 2 -0.420 9.085699999999999 8.473712013781070 0.000000000000000
|
||||
143 1 0.420 10.483499999999999 8.473712013781070 0.000000000000000
|
||||
144 2 -0.420 11.182399999999999 7.263181726098059 0.000000000000000
|
||||
145 1 0.420 12.580200000000000 7.263181726098059 0.000000000000000
|
||||
146 2 -0.420 13.279100000000000 8.473712013781070 0.000000000000000
|
||||
147 1 0.420 14.676900000000000 8.473712013781070 0.000000000000000
|
||||
148 2 -0.420 15.375800000000000 7.263181726098059 0.000000000000000
|
||||
149 1 0.420 16.773599999999998 7.263181726098059 0.000000000000000
|
||||
150 2 -0.420 17.472500000000000 8.473712013781070 0.000000000000000
|
||||
151 1 0.420 18.870300000000000 8.473712013781070 0.000000000000000
|
||||
152 2 -0.420 19.569199999999999 7.263181726098059 0.000000000000000
|
||||
153 1 0.420 20.966999999999999 7.263181726098059 0.000000000000000
|
||||
154 2 -0.420 21.665900000000001 8.473712013781070 0.000000000000000
|
||||
155 1 0.420 23.063699999999997 8.473712013781070 0.000000000000000
|
||||
156 2 -0.420 23.762599999999999 7.263181726098059 0.000000000000000
|
||||
157 1 0.420 25.160399999999999 7.263181726098059 0.000000000000000
|
||||
158 2 -0.420 25.859299999999998 8.473712013781070 0.000000000000000
|
||||
159 1 0.420 27.257099999999998 8.473712013781070 0.000000000000000
|
||||
160 2 -0.420 27.956000000000000 7.263181726098059 0.000000000000000
|
||||
161 1 0.420 29.353800000000000 7.263181726098059 0.000000000000000
|
||||
162 2 -0.420 30.052699999999998 8.473712013781070 0.000000000000000
|
||||
163 1 0.420 31.450499999999998 8.473712013781070 0.000000000000000
|
||||
164 2 -0.420 32.149400000000000 7.263181726098059 0.000000000000000
|
||||
165 1 0.420 33.547199999999997 7.263181726098059 0.000000000000000
|
||||
166 2 -0.420 34.246099999999998 8.473712013781070 0.000000000000000
|
||||
167 1 0.420 35.643899999999995 8.473712013781070 0.000000000000000
|
||||
168 2 -0.420 36.342799999999997 7.263181726098059 0.000000000000000
|
||||
169 1 0.420 37.740600000000001 7.263181726098059 0.000000000000000
|
||||
170 2 -0.420 38.439499999999995 8.473712013781070 0.000000000000000
|
||||
171 1 0.420 39.837299999999999 8.473712013781070 0.000000000000000
|
||||
172 2 -0.420 40.536200000000001 7.263181726098059 0.000000000000000
|
||||
173 1 0.420 41.933999999999997 7.263181726098059 0.000000000000000
|
||||
174 2 -0.420 42.632899999999999 8.473712013781070 0.000000000000000
|
||||
175 1 0.420 44.030699999999996 8.473712013781070 0.000000000000000
|
||||
176 2 -0.420 44.729599999999998 7.263181726098059 0.000000000000000
|
||||
177 1 0.420 0.000000000000000 9.684242301464080 0.000000000000000
|
||||
178 2 -0.420 0.698900000000000 10.894772589147090 0.000000000000000
|
||||
179 1 0.420 2.096700000000000 10.894772589147090 0.000000000000000
|
||||
180 2 -0.420 2.795600000000000 9.684242301464080 0.000000000000000
|
||||
181 1 0.420 4.193400000000000 9.684242301464080 0.000000000000000
|
||||
182 2 -0.420 4.892300000000000 10.894772589147090 0.000000000000000
|
||||
183 1 0.420 6.290100000000000 10.894772589147090 0.000000000000000
|
||||
184 2 -0.420 6.989000000000000 9.684242301464080 0.000000000000000
|
||||
185 1 0.420 8.386799999999999 9.684242301464080 0.000000000000000
|
||||
186 2 -0.420 9.085699999999999 10.894772589147090 0.000000000000000
|
||||
187 1 0.420 10.483499999999999 10.894772589147090 0.000000000000000
|
||||
188 2 -0.420 11.182399999999999 9.684242301464080 0.000000000000000
|
||||
189 1 0.420 12.580200000000000 9.684242301464080 0.000000000000000
|
||||
190 2 -0.420 13.279100000000000 10.894772589147090 0.000000000000000
|
||||
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|
||||
690 2 -0.420 30.052699999999998 37.526438918173312 0.000000000000000
|
||||
691 1 0.420 31.450499999999998 37.526438918173312 0.000000000000000
|
||||
692 2 -0.420 32.149400000000000 36.315908630490298 0.000000000000000
|
||||
693 1 0.420 33.547199999999997 36.315908630490298 0.000000000000000
|
||||
694 2 -0.420 34.246099999999998 37.526438918173312 0.000000000000000
|
||||
695 1 0.420 35.643899999999995 37.526438918173312 0.000000000000000
|
||||
696 2 -0.420 36.342799999999997 36.315908630490298 0.000000000000000
|
||||
697 1 0.420 37.740600000000001 36.315908630490298 0.000000000000000
|
||||
698 2 -0.420 38.439499999999995 37.526438918173312 0.000000000000000
|
||||
699 1 0.420 39.837299999999999 37.526438918173312 0.000000000000000
|
||||
700 2 -0.420 40.536200000000001 36.315908630490298 0.000000000000000
|
||||
701 1 0.420 41.933999999999997 36.315908630490298 0.000000000000000
|
||||
702 2 -0.420 42.632899999999999 37.526438918173312 0.000000000000000
|
||||
703 1 0.420 44.030699999999996 37.526438918173312 0.000000000000000
|
||||
704 2 -0.420 44.729599999999998 36.315908630490298 0.000000000000000
|
||||
705 1 0.420 0.000000000000000 38.736969205856319 0.000000000000000
|
||||
706 2 -0.420 0.698900000000000 39.947499493539325 0.000000000000000
|
||||
707 1 0.420 2.096700000000000 39.947499493539325 0.000000000000000
|
||||
708 2 -0.420 2.795600000000000 38.736969205856319 0.000000000000000
|
||||
709 1 0.420 4.193400000000000 38.736969205856319 0.000000000000000
|
||||
710 2 -0.420 4.892300000000000 39.947499493539325 0.000000000000000
|
||||
711 1 0.420 6.290100000000000 39.947499493539325 0.000000000000000
|
||||
712 2 -0.420 6.989000000000000 38.736969205856319 0.000000000000000
|
||||
713 1 0.420 8.386799999999999 38.736969205856319 0.000000000000000
|
||||
714 2 -0.420 9.085699999999999 39.947499493539325 0.000000000000000
|
||||
715 1 0.420 10.483499999999999 39.947499493539325 0.000000000000000
|
||||
716 2 -0.420 11.182399999999999 38.736969205856319 0.000000000000000
|
||||
717 1 0.420 12.580200000000000 38.736969205856319 0.000000000000000
|
||||
718 2 -0.420 13.279100000000000 39.947499493539325 0.000000000000000
|
||||
719 1 0.420 14.676900000000000 39.947499493539325 0.000000000000000
|
||||
720 2 -0.420 15.375800000000000 38.736969205856319 0.000000000000000
|
||||
721 1 0.420 16.773599999999998 38.736969205856319 0.000000000000000
|
||||
722 2 -0.420 17.472500000000000 39.947499493539325 0.000000000000000
|
||||
723 1 0.420 18.870300000000000 39.947499493539325 0.000000000000000
|
||||
724 2 -0.420 19.569199999999999 38.736969205856319 0.000000000000000
|
||||
725 1 0.420 20.966999999999999 38.736969205856319 0.000000000000000
|
||||
726 2 -0.420 21.665900000000001 39.947499493539325 0.000000000000000
|
||||
727 1 0.420 23.063699999999997 39.947499493539325 0.000000000000000
|
||||
728 2 -0.420 23.762599999999999 38.736969205856319 0.000000000000000
|
||||
729 1 0.420 25.160399999999999 38.736969205856319 0.000000000000000
|
||||
730 2 -0.420 25.859299999999998 39.947499493539325 0.000000000000000
|
||||
731 1 0.420 27.257099999999998 39.947499493539325 0.000000000000000
|
||||
732 2 -0.420 27.956000000000000 38.736969205856319 0.000000000000000
|
||||
733 1 0.420 29.353800000000000 38.736969205856319 0.000000000000000
|
||||
734 2 -0.420 30.052699999999998 39.947499493539325 0.000000000000000
|
||||
735 1 0.420 31.450499999999998 39.947499493539325 0.000000000000000
|
||||
736 2 -0.420 32.149400000000000 38.736969205856319 0.000000000000000
|
||||
737 1 0.420 33.547199999999997 38.736969205856319 0.000000000000000
|
||||
738 2 -0.420 34.246099999999998 39.947499493539325 0.000000000000000
|
||||
739 1 0.420 35.643899999999995 39.947499493539325 0.000000000000000
|
||||
740 2 -0.420 36.342799999999997 38.736969205856319 0.000000000000000
|
||||
741 1 0.420 37.740600000000001 38.736969205856319 0.000000000000000
|
||||
742 2 -0.420 38.439499999999995 39.947499493539325 0.000000000000000
|
||||
743 1 0.420 39.837299999999999 39.947499493539325 0.000000000000000
|
||||
744 2 -0.420 40.536200000000001 38.736969205856319 0.000000000000000
|
||||
745 1 0.420 41.933999999999997 38.736969205856319 0.000000000000000
|
||||
746 2 -0.420 42.632899999999999 39.947499493539325 0.000000000000000
|
||||
747 1 0.420 44.030699999999996 39.947499493539325 0.000000000000000
|
||||
748 2 -0.420 44.729599999999998 38.736969205856319 0.000000000000000
|
||||
749 1 0.420 0.000000000000000 41.158029781222339 0.000000000000000
|
||||
750 2 -0.420 0.698900000000000 42.368560068905346 0.000000000000000
|
||||
751 1 0.420 2.096700000000000 42.368560068905346 0.000000000000000
|
||||
752 2 -0.420 2.795600000000000 41.158029781222339 0.000000000000000
|
||||
753 1 0.420 4.193400000000000 41.158029781222339 0.000000000000000
|
||||
754 2 -0.420 4.892300000000000 42.368560068905346 0.000000000000000
|
||||
755 1 0.420 6.290100000000000 42.368560068905346 0.000000000000000
|
||||
756 2 -0.420 6.989000000000000 41.158029781222339 0.000000000000000
|
||||
757 1 0.420 8.386799999999999 41.158029781222339 0.000000000000000
|
||||
758 2 -0.420 9.085699999999999 42.368560068905346 0.000000000000000
|
||||
759 1 0.420 10.483499999999999 42.368560068905346 0.000000000000000
|
||||
760 2 -0.420 11.182399999999999 41.158029781222339 0.000000000000000
|
||||
761 1 0.420 12.580200000000000 41.158029781222339 0.000000000000000
|
||||
762 2 -0.420 13.279100000000000 42.368560068905346 0.000000000000000
|
||||
763 1 0.420 14.676900000000000 42.368560068905346 0.000000000000000
|
||||
764 2 -0.420 15.375800000000000 41.158029781222339 0.000000000000000
|
||||
765 1 0.420 16.773599999999998 41.158029781222339 0.000000000000000
|
||||
766 2 -0.420 17.472500000000000 42.368560068905346 0.000000000000000
|
||||
767 1 0.420 18.870300000000000 42.368560068905346 0.000000000000000
|
||||
768 2 -0.420 19.569199999999999 41.158029781222339 0.000000000000000
|
||||
769 1 0.420 20.966999999999999 41.158029781222339 0.000000000000000
|
||||
770 2 -0.420 21.665900000000001 42.368560068905346 0.000000000000000
|
||||
771 1 0.420 23.063699999999997 42.368560068905346 0.000000000000000
|
||||
772 2 -0.420 23.762599999999999 41.158029781222339 0.000000000000000
|
||||
773 1 0.420 25.160399999999999 41.158029781222339 0.000000000000000
|
||||
774 2 -0.420 25.859299999999998 42.368560068905346 0.000000000000000
|
||||
775 1 0.420 27.257099999999998 42.368560068905346 0.000000000000000
|
||||
776 2 -0.420 27.956000000000000 41.158029781222339 0.000000000000000
|
||||
777 1 0.420 29.353800000000000 41.158029781222339 0.000000000000000
|
||||
778 2 -0.420 30.052699999999998 42.368560068905346 0.000000000000000
|
||||
779 1 0.420 31.450499999999998 42.368560068905346 0.000000000000000
|
||||
780 2 -0.420 32.149400000000000 41.158029781222339 0.000000000000000
|
||||
781 1 0.420 33.547199999999997 41.158029781222339 0.000000000000000
|
||||
782 2 -0.420 34.246099999999998 42.368560068905346 0.000000000000000
|
||||
783 1 0.420 35.643899999999995 42.368560068905346 0.000000000000000
|
||||
784 2 -0.420 36.342799999999997 41.158029781222339 0.000000000000000
|
||||
785 1 0.420 37.740600000000001 41.158029781222339 0.000000000000000
|
||||
786 2 -0.420 38.439499999999995 42.368560068905346 0.000000000000000
|
||||
787 1 0.420 39.837299999999999 42.368560068905346 0.000000000000000
|
||||
788 2 -0.420 40.536200000000001 41.158029781222339 0.000000000000000
|
||||
789 1 0.420 41.933999999999997 41.158029781222339 0.000000000000000
|
||||
790 2 -0.420 42.632899999999999 42.368560068905346 0.000000000000000
|
||||
791 1 0.420 44.030699999999996 42.368560068905346 0.000000000000000
|
||||
792 2 -0.420 44.729599999999998 41.158029781222339 0.000000000000000
|
||||
793 1 0.420 0.000000000000000 43.579090356588360 0.000000000000000
|
||||
794 2 -0.420 0.698900000000000 44.789620644271366 0.000000000000000
|
||||
795 1 0.420 2.096700000000000 44.789620644271366 0.000000000000000
|
||||
796 2 -0.420 2.795600000000000 43.579090356588360 0.000000000000000
|
||||
797 1 0.420 4.193400000000000 43.579090356588360 0.000000000000000
|
||||
798 2 -0.420 4.892300000000000 44.789620644271366 0.000000000000000
|
||||
799 1 0.420 6.290100000000000 44.789620644271366 0.000000000000000
|
||||
800 2 -0.420 6.989000000000000 43.579090356588360 0.000000000000000
|
||||
801 1 0.420 8.386799999999999 43.579090356588360 0.000000000000000
|
||||
802 2 -0.420 9.085699999999999 44.789620644271366 0.000000000000000
|
||||
803 1 0.420 10.483499999999999 44.789620644271366 0.000000000000000
|
||||
804 2 -0.420 11.182399999999999 43.579090356588360 0.000000000000000
|
||||
805 1 0.420 12.580200000000000 43.579090356588360 0.000000000000000
|
||||
806 2 -0.420 13.279100000000000 44.789620644271366 0.000000000000000
|
||||
807 1 0.420 14.676900000000000 44.789620644271366 0.000000000000000
|
||||
808 2 -0.420 15.375800000000000 43.579090356588360 0.000000000000000
|
||||
809 1 0.420 16.773599999999998 43.579090356588360 0.000000000000000
|
||||
810 2 -0.420 17.472500000000000 44.789620644271366 0.000000000000000
|
||||
811 1 0.420 18.870300000000000 44.789620644271366 0.000000000000000
|
||||
812 2 -0.420 19.569199999999999 43.579090356588360 0.000000000000000
|
||||
813 1 0.420 20.966999999999999 43.579090356588360 0.000000000000000
|
||||
814 2 -0.420 21.665900000000001 44.789620644271366 0.000000000000000
|
||||
815 1 0.420 23.063699999999997 44.789620644271366 0.000000000000000
|
||||
816 2 -0.420 23.762599999999999 43.579090356588360 0.000000000000000
|
||||
817 1 0.420 25.160399999999999 43.579090356588360 0.000000000000000
|
||||
818 2 -0.420 25.859299999999998 44.789620644271366 0.000000000000000
|
||||
819 1 0.420 27.257099999999998 44.789620644271366 0.000000000000000
|
||||
820 2 -0.420 27.956000000000000 43.579090356588360 0.000000000000000
|
||||
821 1 0.420 29.353800000000000 43.579090356588360 0.000000000000000
|
||||
822 2 -0.420 30.052699999999998 44.789620644271366 0.000000000000000
|
||||
823 1 0.420 31.450499999999998 44.789620644271366 0.000000000000000
|
||||
824 2 -0.420 32.149400000000000 43.579090356588360 0.000000000000000
|
||||
825 1 0.420 33.547199999999997 43.579090356588360 0.000000000000000
|
||||
826 2 -0.420 34.246099999999998 44.789620644271366 0.000000000000000
|
||||
827 1 0.420 35.643899999999995 44.789620644271366 0.000000000000000
|
||||
828 2 -0.420 36.342799999999997 43.579090356588360 0.000000000000000
|
||||
829 1 0.420 37.740600000000001 43.579090356588360 0.000000000000000
|
||||
830 2 -0.420 38.439499999999995 44.789620644271366 0.000000000000000
|
||||
831 1 0.420 39.837299999999999 44.789620644271366 0.000000000000000
|
||||
832 2 -0.420 40.536200000000001 43.579090356588360 0.000000000000000
|
||||
833 1 0.420 41.933999999999997 43.579090356588360 0.000000000000000
|
||||
834 2 -0.420 42.632899999999999 44.789620644271366 0.000000000000000
|
||||
835 1 0.420 44.030699999999996 44.789620644271366 0.000000000000000
|
||||
836 2 -0.420 44.729599999999998 43.579090356588360 0.000000000000000
|
||||
837 1 0.420 0.000000000000000 46.000150931954380 0.000000000000000
|
||||
838 2 -0.420 0.698900000000000 47.210681219637387 0.000000000000000
|
||||
839 1 0.420 2.096700000000000 47.210681219637387 0.000000000000000
|
||||
840 2 -0.420 2.795600000000000 46.000150931954380 0.000000000000000
|
||||
841 1 0.420 4.193400000000000 46.000150931954380 0.000000000000000
|
||||
842 2 -0.420 4.892300000000000 47.210681219637387 0.000000000000000
|
||||
843 1 0.420 6.290100000000000 47.210681219637387 0.000000000000000
|
||||
844 2 -0.420 6.989000000000000 46.000150931954380 0.000000000000000
|
||||
845 1 0.420 8.386799999999999 46.000150931954380 0.000000000000000
|
||||
846 2 -0.420 9.085699999999999 47.210681219637387 0.000000000000000
|
||||
847 1 0.420 10.483499999999999 47.210681219637387 0.000000000000000
|
||||
848 2 -0.420 11.182399999999999 46.000150931954380 0.000000000000000
|
||||
849 1 0.420 12.580200000000000 46.000150931954380 0.000000000000000
|
||||
850 2 -0.420 13.279100000000000 47.210681219637387 0.000000000000000
|
||||
851 1 0.420 14.676900000000000 47.210681219637387 0.000000000000000
|
||||
852 2 -0.420 15.375800000000000 46.000150931954380 0.000000000000000
|
||||
853 1 0.420 16.773599999999998 46.000150931954380 0.000000000000000
|
||||
854 2 -0.420 17.472500000000000 47.210681219637387 0.000000000000000
|
||||
855 1 0.420 18.870300000000000 47.210681219637387 0.000000000000000
|
||||
856 2 -0.420 19.569199999999999 46.000150931954380 0.000000000000000
|
||||
857 1 0.420 20.966999999999999 46.000150931954380 0.000000000000000
|
||||
858 2 -0.420 21.665900000000001 47.210681219637387 0.000000000000000
|
||||
859 1 0.420 23.063699999999997 47.210681219637387 0.000000000000000
|
||||
860 2 -0.420 23.762599999999999 46.000150931954380 0.000000000000000
|
||||
861 1 0.420 25.160399999999999 46.000150931954380 0.000000000000000
|
||||
862 2 -0.420 25.859299999999998 47.210681219637387 0.000000000000000
|
||||
863 1 0.420 27.257099999999998 47.210681219637387 0.000000000000000
|
||||
864 2 -0.420 27.956000000000000 46.000150931954380 0.000000000000000
|
||||
865 1 0.420 29.353800000000000 46.000150931954380 0.000000000000000
|
||||
866 2 -0.420 30.052699999999998 47.210681219637387 0.000000000000000
|
||||
867 1 0.420 31.450499999999998 47.210681219637387 0.000000000000000
|
||||
868 2 -0.420 32.149400000000000 46.000150931954380 0.000000000000000
|
||||
869 1 0.420 33.547199999999997 46.000150931954380 0.000000000000000
|
||||
870 2 -0.420 34.246099999999998 47.210681219637387 0.000000000000000
|
||||
871 1 0.420 35.643899999999995 47.210681219637387 0.000000000000000
|
||||
872 2 -0.420 36.342799999999997 46.000150931954380 0.000000000000000
|
||||
873 1 0.420 37.740600000000001 46.000150931954380 0.000000000000000
|
||||
874 2 -0.420 38.439499999999995 47.210681219637387 0.000000000000000
|
||||
875 1 0.420 39.837299999999999 47.210681219637387 0.000000000000000
|
||||
876 2 -0.420 40.536200000000001 46.000150931954380 0.000000000000000
|
||||
877 1 0.420 41.933999999999997 46.000150931954380 0.000000000000000
|
||||
878 2 -0.420 42.632899999999999 47.210681219637387 0.000000000000000
|
||||
879 1 0.420 44.030699999999996 47.210681219637387 0.000000000000000
|
||||
880 2 -0.420 44.729599999999998 46.000150931954380 0.000000000000000
|
||||
37
examples/tersoff/in.hBN_shift
Normal file
37
examples/tersoff/in.hBN_shift
Normal file
@ -0,0 +1,37 @@
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN-monolayer-5nm.data
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff B N
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix thermostat all nve
|
||||
|
||||
############# Output ###############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp
|
||||
#thermo_modify lost warn
|
||||
thermo_modify line one format float %20.16g lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
135
examples/tersoff/in.tersoff
Normal file
135
examples/tersoff/in.tersoff
Normal file
@ -0,0 +1,135 @@
|
||||
# Simple regression tests for Tersoff potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
|
||||
create_box 8 myreg
|
||||
create_atoms 1 region myreg &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 3 &
|
||||
basis 4 4 &
|
||||
basis 5 5 &
|
||||
basis 6 6 &
|
||||
basis 7 7 &
|
||||
basis 8 8
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
|
||||
# Equilibrate using Tersoff model for silicon
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
write_restart restart.equil
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
101
examples/tersoff/log.13Jan21.hBN_shift.g++.1
Normal file
101
examples/tersoff/log.13Jan21.hBN_shift.g++.1
Normal file
@ -0,0 +1,101 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN-monolayer-5nm.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
880 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff B N
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix thermostat all nve
|
||||
|
||||
############# Output ###############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp
|
||||
#thermo_modify lost warn
|
||||
thermo_modify line one format float %20.16g lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.1
|
||||
ghost atom cutoff = 4.1
|
||||
binsize = 2.05, bins = 23 24 49
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.545 | 3.545 | 3.545 Mbytes
|
||||
Step TotEng PotEng KinEng Temp
|
||||
0 -6570.525999324201 -6604.6118995607 34.0859002365 300
|
||||
100 -6570.310828576855 -6584.788128201216 14.47729962436115 127.4189579026448
|
||||
200 -6570.372315727984 -6587.98140230295 17.60908657496611 154.9827329140911
|
||||
300 -6570.341402414283 -6587.005611017601 16.66420860331832 146.6665849019345
|
||||
400 -6570.373381655075 -6587.812074340169 17.43869268509366 153.48304633967
|
||||
500 -6570.357279692746 -6587.139105628337 16.78182593559217 147.7017695218898
|
||||
600 -6570.364533408486 -6588.199043380888 17.83450997240158 156.9667503160497
|
||||
700 -6570.362000654088 -6587.514376495223 17.15237584113499 150.9630878644169
|
||||
800 -6570.358394689025 -6587.200486866491 16.84209217746576 148.2321903832028
|
||||
900 -6570.372035122432 -6588.096861613308 17.72482649087559 156.0013938422734
|
||||
1000 -6570.355748883583 -6587.399428461676 17.04367957809225 150.0064201899072
|
||||
Loop time of 0.998048 on 1 procs for 1000 steps with 880 atoms
|
||||
|
||||
Performance: 86.569 ns/day, 0.277 hours/ns, 1001.956 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.98001 | 0.98001 | 0.98001 | 0.0 | 98.19
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.006538 | 0.006538 | 0.006538 | 0.0 | 0.66
|
||||
Output | 0.000224 | 0.000224 | 0.000224 | 0.0 | 0.02
|
||||
Modify | 0.00781 | 0.00781 | 0.00781 | 0.0 | 0.78
|
||||
Other | | 0.003467 | | | 0.35
|
||||
|
||||
Nlocal: 880.000 ave 880 max 880 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1518.00 ave 1518 max 1518 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 15840.0 ave 15840 max 15840 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 15840
|
||||
Ave neighs/atom = 18.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
101
examples/tersoff/log.13Jan21.hBN_shift.g++.4
Normal file
101
examples/tersoff/log.13Jan21.hBN_shift.g++.4
Normal file
@ -0,0 +1,101 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN-monolayer-5nm.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
880 atoms
|
||||
read_data CPU = 0.010 seconds
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff B N
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix thermostat all nve
|
||||
|
||||
############# Output ###############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp
|
||||
#thermo_modify lost warn
|
||||
thermo_modify line one format float %20.16g lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.1
|
||||
ghost atom cutoff = 4.1
|
||||
binsize = 2.05, bins = 23 24 49
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.297 | 3.297 | 3.297 Mbytes
|
||||
Step TotEng PotEng KinEng Temp
|
||||
0 -6570.525999324095 -6604.611899560595 34.08590023650001 300.0000000000001
|
||||
100 -6570.310828576847 -6584.788128201208 14.47729962436078 127.4189579026416
|
||||
200 -6570.372315727983 -6587.981402302948 17.60908657496569 154.9827329140874
|
||||
300 -6570.341402414288 -6587.005611017607 16.66420860331862 146.6665849019371
|
||||
400 -6570.373381655087 -6587.81207434018 17.43869268509319 153.4830463396659
|
||||
500 -6570.357279692746 -6587.139105628339 16.78182593559348 147.7017695219013
|
||||
600 -6570.364533408483 -6588.199043380885 17.83450997240217 156.9667503160549
|
||||
700 -6570.362000654081 -6587.514376495217 17.15237584113621 150.9630878644276
|
||||
800 -6570.358394689017 -6587.200486866481 16.84209217746396 148.2321903831871
|
||||
900 -6570.372035122433 -6588.096861613309 17.72482649087623 156.001393842279
|
||||
1000 -6570.355748883587 -6587.399428461678 17.0436795780913 150.0064201898988
|
||||
Loop time of 0.32051 on 4 procs for 1000 steps with 880 atoms
|
||||
|
||||
Performance: 269.571 ns/day, 0.089 hours/ns, 3120.030 timesteps/s
|
||||
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24483 | 0.26461 | 0.28741 | 2.9 | 82.56
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.026425 | 0.049039 | 0.068616 | 6.8 | 15.30
|
||||
Output | 0.000126 | 0.00016475 | 0.000248 | 0.0 | 0.05
|
||||
Modify | 0.002472 | 0.002794 | 0.002933 | 0.4 | 0.87
|
||||
Other | | 0.003905 | | | 1.22
|
||||
|
||||
Nlocal: 220.000 ave 241 max 199 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 563.000 ave 583 max 543 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3960.00 ave 4338 max 3582 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 15840
|
||||
Ave neighs/atom = 18.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
472
examples/tersoff/log.13Jan21.tersoff.g++.1
Normal file
472
examples/tersoff/log.13Jan21.tersoff.g++.1
Normal file
@ -0,0 +1,472 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for Tersoff potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Tersoff model for silicon
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.2
|
||||
ghost atom cutoff = 4.2
|
||||
binsize = 2.1, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2370.771 0 -2251.8775 12511.419
|
||||
10 1144.7447 -2327.3227 0 -2251.7759 21852.599
|
||||
20 770.19243 -2302.1547 0 -2251.7633 22286.587
|
||||
30 1059.4324 -2320.1988 0 -2251.8159 6242.222
|
||||
40 1000.972 -2314.6531 0 -2251.796 -3069.9273
|
||||
50 803.91758 -2300.1702 0 -2251.7834 -7154.1383
|
||||
60 761.38639 -2296.1731 0 -2251.7928 -14520.921
|
||||
70 750.57677 -2294.3086 0 -2251.7965 -21400.198
|
||||
80 676.66672 -2288.2634 0 -2251.7899 -23480.201
|
||||
90 640.24103 -2284.6678 0 -2251.7848 -20659.983
|
||||
100 742.67188 -2290.0616 0 -2251.7855 -16211.799
|
||||
Loop time of 0.107338 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 80.493 ns/day, 0.298 hours/ns, 931.637 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10455 | 0.10455 | 0.10455 | 0.0 | 97.40
|
||||
Neigh | 0.001115 | 0.001115 | 0.001115 | 0.0 | 1.04
|
||||
Comm | 0.000482 | 0.000482 | 0.000482 | 0.0 | 0.45
|
||||
Output | 0.000194 | 0.000194 | 0.000194 | 0.0 | 0.18
|
||||
Modify | 0.000787 | 0.000787 | 0.000787 | 0.0 | 0.73
|
||||
Other | | 0.000209 | | | 0.19
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 857.000 ave 857 max 857 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8404.00 ave 8404 max 8404 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8404
|
||||
Ave neighs/atom = 16.414062
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.006 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2210.6446 0 -2172.3685 -6444.2163
|
||||
110 1135.5853 -2234.6974 0 -2172.3908 113.80404
|
||||
120 1462.8415 -2253.8186 0 -2172.3853 10922.229
|
||||
130 1755.9617 -2270.5152 0 -2172.3964 18780.707
|
||||
140 1895.1939 -2277.1484 0 -2172.3965 22357.106
|
||||
150 1869.5375 -2273.2734 0 -2172.3851 22616.492
|
||||
160 1824.0448 -2268.4342 0 -2172.393 19254.299
|
||||
170 1637.9038 -2254.5219 0 -2172.3815 15904.928
|
||||
180 1451.9871 -2240.7199 0 -2172.3771 12064.754
|
||||
190 1362.8248 -2233.1942 0 -2172.3789 7970.534
|
||||
200 1341.1467 -2229.8951 0 -2172.3717 6244.8542
|
||||
Loop time of 0.128972 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 66.991 ns/day, 0.358 hours/ns, 775.362 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12498 | 0.12498 | 0.12498 | 0.0 | 96.91
|
||||
Neigh | 0.002322 | 0.002322 | 0.002322 | 0.0 | 1.80
|
||||
Comm | 0.000537 | 0.000537 | 0.000537 | 0.0 | 0.42
|
||||
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.14
|
||||
Modify | 0.000761 | 0.000761 | 0.000761 | 0.0 | 0.59
|
||||
Other | | 0.000192 | | | 0.15
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 960.000 ave 960 max 960 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 9244.00 ave 9244 max 9244 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9244
|
||||
Ave neighs/atom = 18.054688
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.205694
|
||||
ghost atom cutoff = 4.205694
|
||||
binsize = 2.102847, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.976 | 2.976 | 2.976 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2221.9308 0 -2183.6547 -11721.269
|
||||
110 1106.895 -2244.1196 0 -2183.6843 -2359.7819
|
||||
120 1327.6674 -2256.3155 0 -2183.6767 7904.6604
|
||||
130 1487.0219 -2264.3656 0 -2183.6707 14660.783
|
||||
140 1709.1746 -2276.4761 0 -2183.6886 19298.791
|
||||
150 1710.6528 -2274.1129 0 -2183.6764 22026.559
|
||||
160 1651.0659 -2267.9877 0 -2183.6699 20916.722
|
||||
170 1632.7705 -2264.7081 0 -2183.6777 17339.031
|
||||
180 1477.693 -2252.4683 0 -2183.6706 12563.594
|
||||
190 1310.8768 -2239.5419 0 -2183.6581 9591.0484
|
||||
200 1356.7172 -2240.5315 0 -2183.668 5584.6734
|
||||
Loop time of 0.133106 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 64.911 ns/day, 0.370 hours/ns, 751.281 timesteps/s
|
||||
96.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1291 | 0.1291 | 0.1291 | 0.0 | 96.99
|
||||
Neigh | 0.002343 | 0.002343 | 0.002343 | 0.0 | 1.76
|
||||
Comm | 0.0005 | 0.0005 | 0.0005 | 0.0 | 0.38
|
||||
Output | 0.000186 | 0.000186 | 0.000186 | 0.0 | 0.14
|
||||
Modify | 0.000786 | 0.000786 | 0.000786 | 0.0 | 0.59
|
||||
Other | | 0.000191 | | | 0.14
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 903.000 ave 903 max 903 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8414.00 ave 8414 max 8414 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8414
|
||||
Ave neighs/atom = 16.433594
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2973.8527 0 -2935.5766 3438975.9
|
||||
110 4061.1085 -3183.2489 0 -2930.1208 2211712.7
|
||||
120 4120.3231 -3187.0108 0 -2928.3047 2166764.3
|
||||
130 3602.7602 -3158.5939 0 -2926.6167 2244475.7
|
||||
140 3222.7773 -3141.7275 0 -2925.5369 2161607
|
||||
150 3487.4703 -3163.7495 0 -2921.2462 2222150.2
|
||||
160 3436.3009 -3169.4234 0 -2920.8775 2144368.7
|
||||
170 3308.1796 -3170.3773 0 -2920.8967 2223612.9
|
||||
180 3304.3776 -3178.7805 0 -2920.102 2072546.6
|
||||
190 3217.3561 -3180.7963 0 -2918.4548 2118776.2
|
||||
200 3041.6832 -3176.1794 0 -2916.5787 2130124.6
|
||||
Loop time of 0.134621 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 64.180 ns/day, 0.374 hours/ns, 742.826 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12837 | 0.12837 | 0.12837 | 0.0 | 95.35
|
||||
Neigh | 0.004553 | 0.004553 | 0.004553 | 0.0 | 3.38
|
||||
Comm | 0.000601 | 0.000601 | 0.000601 | 0.0 | 0.45
|
||||
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.13
|
||||
Modify | 0.000742 | 0.000742 | 0.000742 | 0.0 | 0.55
|
||||
Other | | 0.000181 | | | 0.13
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1051.00 ave 1051 max 1051 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14760.0 ave 14760 max 14760 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14760
|
||||
Ave neighs/atom = 28.828125
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -3294.0266 0 -3255.7505 1615779.4
|
||||
110 2870.7114 -3432.8485 0 -3257.629 1053310.6
|
||||
120 2898.0798 -3431.4968 0 -3256.6851 1223402.3
|
||||
130 2708.4483 -3419.0142 0 -3256.436 1105893.8
|
||||
140 2307.8661 -3394.1268 0 -3256.1686 1148075.8
|
||||
150 2215.3423 -3390.1427 0 -3255.8733 1138540
|
||||
160 2515.488 -3412.6704 0 -3255.1731 1122902.8
|
||||
170 2485.7109 -3415.0402 0 -3255.3787 1097748.5
|
||||
180 2327.476 -3408.2463 0 -3254.6537 1061602.6
|
||||
190 2339.5966 -3413.3961 0 -3254.7496 1088059
|
||||
200 2260.5961 -3411.477 0 -3254.0771 1104581.5
|
||||
Loop time of 0.120764 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 71.545 ns/day, 0.335 hours/ns, 828.061 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11521 | 0.11521 | 0.11521 | 0.0 | 95.40
|
||||
Neigh | 0.003874 | 0.003874 | 0.003874 | 0.0 | 3.21
|
||||
Comm | 0.000542 | 0.000542 | 0.000542 | 0.0 | 0.45
|
||||
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.15
|
||||
Modify | 0.000774 | 0.000774 | 0.000774 | 0.0 | 0.64
|
||||
Other | | 0.00019 | | | 0.16
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1037.00 ave 1037 max 1037 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14676.0 ave 14676 max 14676 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14676
|
||||
Ave neighs/atom = 28.664062
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
472
examples/tersoff/log.13Jan21.tersoff.g++.4
Normal file
472
examples/tersoff/log.13Jan21.tersoff.g++.4
Normal file
@ -0,0 +1,472 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for Tersoff potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Tersoff model for silicon
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.2
|
||||
ghost atom cutoff = 4.2
|
||||
binsize = 2.1, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2370.771 0 -2251.8775 12511.419
|
||||
10 1144.7447 -2327.3227 0 -2251.7759 21852.599
|
||||
20 770.19243 -2302.1547 0 -2251.7633 22286.587
|
||||
30 1059.4324 -2320.1988 0 -2251.8159 6242.222
|
||||
40 1000.972 -2314.6531 0 -2251.796 -3069.9273
|
||||
50 803.91758 -2300.1702 0 -2251.7834 -7154.1383
|
||||
60 761.38639 -2296.1731 0 -2251.7928 -14520.921
|
||||
70 750.57677 -2294.3086 0 -2251.7965 -21400.198
|
||||
80 676.66672 -2288.2634 0 -2251.7899 -23480.201
|
||||
90 640.24103 -2284.6678 0 -2251.7848 -20659.983
|
||||
100 742.67188 -2290.0616 0 -2251.7855 -16211.799
|
||||
Loop time of 0.0321762 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 268.521 ns/day, 0.089 hours/ns, 3107.882 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.026599 | 0.02712 | 0.027602 | 0.2 | 84.28
|
||||
Neigh | 0.000285 | 0.00028875 | 0.000294 | 0.0 | 0.90
|
||||
Comm | 0.003471 | 0.0039375 | 0.004446 | 0.6 | 12.24
|
||||
Output | 0.000112 | 0.00013675 | 0.000203 | 0.0 | 0.43
|
||||
Modify | 0.000443 | 0.0004555 | 0.000471 | 0.0 | 1.42
|
||||
Other | | 0.000238 | | | 0.74
|
||||
|
||||
Nlocal: 128.000 ave 131 max 126 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 447.750 ave 453 max 440 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2101.00 ave 2152 max 2032 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 8404
|
||||
Ave neighs/atom = 16.414062
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.002 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.949 | 2.950 | 2.950 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2210.6446 0 -2172.3685 -6444.2163
|
||||
110 1135.5853 -2234.6974 0 -2172.3908 113.80404
|
||||
120 1462.8415 -2253.8186 0 -2172.3853 10922.229
|
||||
130 1755.9617 -2270.5152 0 -2172.3964 18780.707
|
||||
140 1895.1939 -2277.1484 0 -2172.3965 22357.106
|
||||
150 1869.5375 -2273.2734 0 -2172.3851 22616.492
|
||||
160 1824.0448 -2268.4342 0 -2172.393 19254.299
|
||||
170 1637.9038 -2254.5219 0 -2172.3815 15904.928
|
||||
180 1451.9871 -2240.7199 0 -2172.3771 12064.754
|
||||
190 1362.8248 -2233.1942 0 -2172.3789 7970.534
|
||||
200 1341.1467 -2229.8951 0 -2172.3717 6244.8542
|
||||
Loop time of 0.0389003 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 222.107 ns/day, 0.108 hours/ns, 2570.678 timesteps/s
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.031362 | 0.032656 | 0.033605 | 0.5 | 83.95
|
||||
Neigh | 0.000575 | 0.000599 | 0.000613 | 0.0 | 1.54
|
||||
Comm | 0.003768 | 0.004733 | 0.006014 | 1.2 | 12.17
|
||||
Output | 0.000207 | 0.00022525 | 0.000276 | 0.0 | 0.58
|
||||
Modify | 0.000445 | 0.00047975 | 0.0005 | 0.0 | 1.23
|
||||
Other | | 0.0002077 | | | 0.53
|
||||
|
||||
Nlocal: 128.000 ave 135 max 123 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 491.500 ave 499 max 486 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2311.00 ave 2457 max 2192 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9244
|
||||
Ave neighs/atom = 18.054688
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.205694
|
||||
ghost atom cutoff = 4.205694
|
||||
binsize = 2.102847, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.949 | 2.949 | 2.949 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2221.9308 0 -2183.6547 -11721.269
|
||||
110 1106.895 -2244.1196 0 -2183.6843 -2359.7819
|
||||
120 1327.6674 -2256.3155 0 -2183.6767 7904.6604
|
||||
130 1487.0219 -2264.3656 0 -2183.6707 14660.783
|
||||
140 1709.1746 -2276.4761 0 -2183.6886 19298.791
|
||||
150 1710.6528 -2274.1129 0 -2183.6764 22026.559
|
||||
160 1651.0659 -2267.9877 0 -2183.6699 20916.722
|
||||
170 1632.7705 -2264.7081 0 -2183.6777 17339.031
|
||||
180 1477.693 -2252.4683 0 -2183.6706 12563.594
|
||||
190 1310.8768 -2239.5419 0 -2183.6581 9591.0484
|
||||
200 1356.7172 -2240.5315 0 -2183.668 5584.6734
|
||||
Loop time of 0.039244 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 220.161 ns/day, 0.109 hours/ns, 2548.160 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.03126 | 0.032782 | 0.033915 | 0.5 | 83.53
|
||||
Neigh | 0.000599 | 0.000707 | 0.000821 | 0.0 | 1.80
|
||||
Comm | 0.00363 | 0.004893 | 0.006493 | 1.5 | 12.47
|
||||
Output | 0.000122 | 0.0001425 | 0.000192 | 0.0 | 0.36
|
||||
Modify | 0.000497 | 0.00050925 | 0.000522 | 0.0 | 1.30
|
||||
Other | | 0.0002105 | | | 0.54
|
||||
|
||||
Nlocal: 128.000 ave 133 max 124 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Nghost: 459.000 ave 470 max 452 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2103.50 ave 2204 max 2014 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 8414
|
||||
Ave neighs/atom = 16.433594
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.952 | 2.952 | 2.952 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2973.8527 0 -2935.5766 3438975.9
|
||||
110 4061.1085 -3183.2489 0 -2930.1208 2211712.7
|
||||
120 4120.3231 -3187.0108 0 -2928.3047 2166764.3
|
||||
130 3602.7602 -3158.5939 0 -2926.6167 2244475.7
|
||||
140 3222.7773 -3141.7275 0 -2925.5369 2161607
|
||||
150 3487.4703 -3163.7495 0 -2921.2462 2222150.2
|
||||
160 3436.3009 -3169.4234 0 -2920.8775 2144368.7
|
||||
170 3308.1796 -3170.3773 0 -2920.8967 2223612.9
|
||||
180 3304.3776 -3178.7805 0 -2920.102 2072546.6
|
||||
190 3217.3561 -3180.7963 0 -2918.4548 2118776.2
|
||||
200 3041.6832 -3176.1794 0 -2916.5787 2130124.6
|
||||
Loop time of 0.0488862 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 176.737 ns/day, 0.136 hours/ns, 2045.565 timesteps/s
|
||||
93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.037364 | 0.039346 | 0.041066 | 0.8 | 80.49
|
||||
Neigh | 0.001207 | 0.0012568 | 0.00136 | 0.2 | 2.57
|
||||
Comm | 0.005218 | 0.007064 | 0.009117 | 1.9 | 14.45
|
||||
Output | 0.000173 | 0.00020325 | 0.000277 | 0.0 | 0.42
|
||||
Modify | 0.000709 | 0.000715 | 0.000723 | 0.0 | 1.46
|
||||
Other | | 0.0003008 | | | 0.62
|
||||
|
||||
Nlocal: 128.000 ave 132 max 123 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 543.000 ave 548 max 535 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3690.00 ave 3811 max 3529 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 14760
|
||||
Ave neighs/atom = 28.828125
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.952 | 2.952 | 2.952 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -3294.0266 0 -3255.7505 1615779.4
|
||||
110 2870.7114 -3432.8485 0 -3257.629 1053310.6
|
||||
120 2898.0798 -3431.4968 0 -3256.6851 1223402.3
|
||||
130 2708.4483 -3419.0142 0 -3256.436 1105893.8
|
||||
140 2307.8661 -3394.1268 0 -3256.1686 1148075.8
|
||||
150 2215.3423 -3390.1427 0 -3255.8733 1138540
|
||||
160 2515.488 -3412.6704 0 -3255.1731 1122902.8
|
||||
170 2485.7109 -3415.0402 0 -3255.3787 1097748.5
|
||||
180 2327.476 -3408.2463 0 -3254.6537 1061602.6
|
||||
190 2339.5966 -3413.3961 0 -3254.7496 1088059
|
||||
200 2260.5961 -3411.477 0 -3254.0771 1104581.5
|
||||
Loop time of 0.0409132 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 211.179 ns/day, 0.114 hours/ns, 2444.196 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.03285 | 0.033327 | 0.03406 | 0.3 | 81.46
|
||||
Neigh | 0.000975 | 0.0010677 | 0.001184 | 0.2 | 2.61
|
||||
Comm | 0.004915 | 0.005528 | 0.006044 | 0.7 | 13.51
|
||||
Output | 0.000129 | 0.0001535 | 0.000226 | 0.0 | 0.38
|
||||
Modify | 0.000564 | 0.0005885 | 0.000604 | 0.0 | 1.44
|
||||
Other | | 0.0002483 | | | 0.61
|
||||
|
||||
Nlocal: 128.000 ave 133 max 123 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Nghost: 535.250 ave 542 max 531 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3669.00 ave 3822 max 3522 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 14676
|
||||
Ave neighs/atom = 28.664062
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -46,7 +46,7 @@ create_atoms 1 region myreg &
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create $t 5287287 loop geom
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
@ -114,35 +114,3 @@ neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
|
||||
547
examples/threebody/log.13Jan21.threebody.g++.1
Normal file
547
examples/threebody/log.13Jan21.threebody.g++.1
Normal file
@ -0,0 +1,547 @@
|
||||
LAMMPS (30 Nov 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for threebody potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
binsize = 2.38559, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2220.3392 0 -2101.4457 12358.626
|
||||
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
|
||||
20 588.26396 -2139.7132 0 -2101.3117 11295.566
|
||||
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
|
||||
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
|
||||
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
|
||||
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
|
||||
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
|
||||
80 800.80221 -2146.1371 0 -2101.313 11995.66
|
||||
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
|
||||
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
|
||||
Loop time of 0.092666 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 93.238 ns/day, 0.257 hours/ns, 1079.144 timesteps/s
|
||||
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.089633 | 0.089633 | 0.089633 | 0.0 | 96.73
|
||||
Neigh | 0.001474 | 0.001474 | 0.001474 | 0.0 | 1.59
|
||||
Comm | 0.00041 | 0.00041 | 0.00041 | 0.0 | 0.44
|
||||
Output | 0.000153 | 0.000153 | 0.000153 | 0.0 | 0.17
|
||||
Modify | 0.000782 | 0.000782 | 0.000782 | 0.0 | 0.84
|
||||
Other | | 0.000214 | | | 0.23
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017.00 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13988.0 ave 13988 max 13988 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13988
|
||||
Ave neighs/atom = 27.320312
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.002 seconds
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.6320004
|
||||
ghost atom cutoff = 5.6320004
|
||||
binsize = 2.8160002, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -625.76163 0 -564.38354 462129.66
|
||||
110 1502.8461 -649.55768 0 -564.45814 463413.45
|
||||
120 1926.4523 -674.71265 0 -564.53612 486338.88
|
||||
130 1152.6663 -621.47264 0 -564.37203 514892.2
|
||||
140 1762.244 -659.86941 0 -564.4985 488159.88
|
||||
150 1767.8665 -657.67178 0 -564.48386 466721.31
|
||||
160 1075.2874 -610.12809 0 -564.36709 470151.9
|
||||
170 1697.9313 -649.3684 0 -564.47207 467953.71
|
||||
180 1856.1197 -657.14338 0 -564.48754 488372.27
|
||||
190 1346.1107 -621.42431 0 -564.38065 511750.04
|
||||
200 1919.5266 -657.26587 0 -564.47797 488684.56
|
||||
Loop time of 0.289193 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 29.876 ns/day, 0.803 hours/ns, 345.790 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.28463 | 0.28463 | 0.28463 | 0.0 | 98.42
|
||||
Neigh | 0.002821 | 0.002821 | 0.002821 | 0.0 | 0.98
|
||||
Comm | 0.000605 | 0.000605 | 0.000605 | 0.0 | 0.21
|
||||
Output | 0.000176 | 0.000176 | 0.000176 | 0.0 | 0.06
|
||||
Modify | 0.000769 | 0.000769 | 0.000769 | 0.0 | 0.27
|
||||
Other | | 0.000188 | | | 0.07
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1428.00 ave 1428 max 1428 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 17344.0 ave 17344 max 17344 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 17344
|
||||
Ave neighs/atom = 33.875000
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Vashishta model for In/P
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7
|
||||
ghost atom cutoff = 7
|
||||
binsize = 3.5, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair vashishta, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
|
||||
110 1250.545 -1504.5795 0 -1435.9786 345188.52
|
||||
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
|
||||
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
|
||||
140 1481.0477 -1513.0511 0 -1435.988 308725.1
|
||||
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
|
||||
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
|
||||
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
|
||||
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
|
||||
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
|
||||
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
|
||||
Loop time of 0.126684 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 68.201 ns/day, 0.352 hours/ns, 789.366 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11981 | 0.11981 | 0.11981 | 0.0 | 94.57
|
||||
Neigh | 0.004903 | 0.004903 | 0.004903 | 0.0 | 3.87
|
||||
Comm | 0.000846 | 0.000846 | 0.000846 | 0.0 | 0.67
|
||||
Output | 0.000145 | 0.000145 | 0.000145 | 0.0 | 0.11
|
||||
Modify | 0.000772 | 0.000772 | 0.000772 | 0.0 | 0.61
|
||||
Other | | 0.000207 | | | 0.16
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1838.00 ave 1838 max 1838 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 36482.0 ave 36482 max 36482 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 36482
|
||||
Ave neighs/atom = 71.253906
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
|
||||
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
|
||||
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
|
||||
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
|
||||
140 1486.0361 -3274.951 0 -3197.776 1871927.6
|
||||
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
|
||||
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
|
||||
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
|
||||
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
|
||||
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
|
||||
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
|
||||
Loop time of 0.114312 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 75.583 ns/day, 0.318 hours/ns, 874.799 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1121 | 0.1121 | 0.1121 | 0.0 | 98.06
|
||||
Neigh | 0.000773 | 0.000773 | 0.000773 | 0.0 | 0.68
|
||||
Comm | 0.000415 | 0.000415 | 0.000415 | 0.0 | 0.36
|
||||
Output | 0.000136 | 0.000136 | 0.000136 | 0.0 | 0.12
|
||||
Modify | 0.000703 | 0.000703 | 0.000703 | 0.0 | 0.61
|
||||
Other | | 0.000186 | | | 0.16
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1028.00 ave 1028 max 1028 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14604.0 ave 14604 max 14604 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14604
|
||||
Ave neighs/atom = 28.523438
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.986 | 2.986 | 2.986 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
|
||||
110 835.77436 -2289.6119 0 -2248.1918 19964.211
|
||||
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
|
||||
130 957.60664 -2293.7047 0 -2248.2139 14850.338
|
||||
140 865.12471 -2285.7774 0 -2248.1971 17101.553
|
||||
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
|
||||
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
|
||||
170 843.8591 -2277.9713 0 -2248.1911 18966.532
|
||||
180 1008.7412 -2286.922 0 -2248.2075 17275.649
|
||||
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
|
||||
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
|
||||
Loop time of 0.12412 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 69.610 ns/day, 0.345 hours/ns, 805.672 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12079 | 0.12079 | 0.12079 | 0.0 | 97.32
|
||||
Neigh | 0.001821 | 0.001821 | 0.001821 | 0.0 | 1.47
|
||||
Comm | 0.000407 | 0.000407 | 0.000407 | 0.0 | 0.33
|
||||
Output | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.13
|
||||
Modify | 0.000736 | 0.000736 | 0.000736 | 0.0 | 0.59
|
||||
Other | | 0.000203 | | | 0.16
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1007.00 ave 1007 max 1007 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8884.00 ave 8884 max 8884 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8884
|
||||
Ave neighs/atom = 17.351562
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.205694
|
||||
ghost atom cutoff = 4.205694
|
||||
binsize = 2.102847, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.980 | 2.980 | 2.980 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -2309.1331 0 -2247.755 20346.718
|
||||
110 831.93715 -2288.8853 0 -2247.7187 21758.195
|
||||
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
|
||||
130 972.43247 -2294.1847 0 -2247.7467 16614.835
|
||||
140 815.76148 -2282.0495 0 -2247.7194 18310.116
|
||||
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
|
||||
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
|
||||
170 787.17244 -2273.8946 0 -2247.7175 18586.606
|
||||
180 932.5662 -2281.6828 0 -2247.7315 18154.167
|
||||
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
|
||||
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
|
||||
Loop time of 0.12973 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 66.600 ns/day, 0.360 hours/ns, 770.832 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12643 | 0.12643 | 0.12643 | 0.0 | 97.45
|
||||
Neigh | 0.001798 | 0.001798 | 0.001798 | 0.0 | 1.39
|
||||
Comm | 0.000421 | 0.000421 | 0.000421 | 0.0 | 0.32
|
||||
Output | 0.00016 | 0.00016 | 0.00016 | 0.0 | 0.12
|
||||
Modify | 0.000733 | 0.000733 | 0.000733 | 0.0 | 0.57
|
||||
Other | | 0.000192 | | | 0.15
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 958.000 ave 958 max 958 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8416.00 ave 8416 max 8416 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8416
|
||||
Ave neighs/atom = 16.437500
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
547
examples/threebody/log.13Jan21.threebody.g++.4
Normal file
547
examples/threebody/log.13Jan21.threebody.g++.4
Normal file
@ -0,0 +1,547 @@
|
||||
LAMMPS (30 Nov 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for threebody potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
binsize = 2.38559, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2220.3392 0 -2101.4457 12358.626
|
||||
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
|
||||
20 588.26396 -2139.7132 0 -2101.3117 11295.566
|
||||
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
|
||||
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
|
||||
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
|
||||
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
|
||||
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
|
||||
80 800.80221 -2146.1371 0 -2101.313 11995.66
|
||||
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
|
||||
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
|
||||
Loop time of 0.0284905 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 303.259 ns/day, 0.079 hours/ns, 3509.942 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.022257 | 0.023383 | 0.025192 | 0.7 | 82.07
|
||||
Neigh | 0.00036 | 0.00037475 | 0.000387 | 0.0 | 1.32
|
||||
Comm | 0.002084 | 0.0039075 | 0.005034 | 1.8 | 13.72
|
||||
Output | 9.9e-05 | 0.00011525 | 0.00016 | 0.0 | 0.40
|
||||
Modify | 0.000428 | 0.00043675 | 0.000443 | 0.0 | 1.53
|
||||
Other | | 0.0002728 | | | 0.96
|
||||
|
||||
Nlocal: 128.000 ave 132 max 125 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 525.000 ave 528 max 521 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3497.00 ave 3619 max 3397 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 13988
|
||||
Ave neighs/atom = 27.320312
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.6320004
|
||||
ghost atom cutoff = 5.6320004
|
||||
binsize = 2.8160002, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.967 | 2.967 | 2.968 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -625.76163 0 -564.38354 462129.66
|
||||
110 1502.8461 -649.55768 0 -564.45814 463413.45
|
||||
120 1926.4523 -674.71265 0 -564.53613 486338.88
|
||||
130 1152.6663 -621.47265 0 -564.37203 514892.19
|
||||
140 1762.244 -659.86941 0 -564.4985 488159.88
|
||||
150 1767.8665 -657.67179 0 -564.48386 466721.31
|
||||
160 1075.2874 -610.1281 0 -564.36709 470151.9
|
||||
170 1697.9313 -649.3684 0 -564.47208 467953.7
|
||||
180 1856.1197 -657.14338 0 -564.48754 488372.26
|
||||
190 1346.1107 -621.42432 0 -564.38065 511750.03
|
||||
200 1919.5266 -657.26587 0 -564.47797 488684.56
|
||||
Loop time of 0.084576 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 102.157 ns/day, 0.235 hours/ns, 1182.369 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.072089 | 0.074912 | 0.076672 | 0.7 | 88.57
|
||||
Neigh | 0.000745 | 0.0008125 | 0.000883 | 0.0 | 0.96
|
||||
Comm | 0.006054 | 0.0077975 | 0.010598 | 2.1 | 9.22
|
||||
Output | 0.000129 | 0.00015525 | 0.000219 | 0.0 | 0.18
|
||||
Modify | 0.000523 | 0.000578 | 0.000641 | 0.0 | 0.68
|
||||
Other | | 0.0003213 | | | 0.38
|
||||
|
||||
Nlocal: 128.000 ave 135 max 122 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 759.750 ave 770 max 751 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4336.00 ave 4563 max 4128 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 17344
|
||||
Ave neighs/atom = 33.875000
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Vashishta model for In/P
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7
|
||||
ghost atom cutoff = 7
|
||||
binsize = 3.5, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair vashishta, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.988 | 2.988 | 2.988 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
|
||||
110 1250.545 -1504.5795 0 -1435.9786 345188.52
|
||||
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
|
||||
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
|
||||
140 1481.0477 -1513.0511 0 -1435.988 308725.1
|
||||
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
|
||||
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
|
||||
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
|
||||
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
|
||||
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
|
||||
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
|
||||
Loop time of 0.0404882 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 213.395 ns/day, 0.112 hours/ns, 2469.852 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.032713 | 0.033094 | 0.033544 | 0.2 | 81.74
|
||||
Neigh | 0.001251 | 0.0012875 | 0.001308 | 0.1 | 3.18
|
||||
Comm | 0.004788 | 0.005204 | 0.00557 | 0.4 | 12.85
|
||||
Output | 0.000123 | 0.0001385 | 0.000182 | 0.0 | 0.34
|
||||
Modify | 0.000492 | 0.00050725 | 0.000533 | 0.0 | 1.25
|
||||
Other | | 0.0002565 | | | 0.63
|
||||
|
||||
Nlocal: 128.000 ave 131 max 124 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 1013.25 ave 1025 max 1002 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 9120.50 ave 9356 max 8868 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 36482
|
||||
Ave neighs/atom = 71.253906
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.948 | 2.948 | 2.948 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
|
||||
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
|
||||
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
|
||||
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
|
||||
140 1486.0361 -3274.951 0 -3197.776 1871927.6
|
||||
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
|
||||
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
|
||||
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
|
||||
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
|
||||
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
|
||||
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
|
||||
Loop time of 0.03452 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 250.290 ns/day, 0.096 hours/ns, 2896.871 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.029269 | 0.029729 | 0.030688 | 0.3 | 86.12
|
||||
Neigh | 0.000203 | 0.00023375 | 0.000271 | 0.0 | 0.68
|
||||
Comm | 0.00275 | 0.0036492 | 0.004132 | 0.9 | 10.57
|
||||
Output | 0.000104 | 0.000121 | 0.000165 | 0.0 | 0.35
|
||||
Modify | 0.000456 | 0.0004605 | 0.000463 | 0.0 | 1.33
|
||||
Other | | 0.000326 | | | 0.94
|
||||
|
||||
Nlocal: 128.000 ave 132 max 123 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 529.500 ave 533 max 524 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3651.00 ave 3783 max 3494 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 14604
|
||||
Ave neighs/atom = 28.523438
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
|
||||
110 835.77436 -2289.6119 0 -2248.1918 19964.211
|
||||
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
|
||||
130 957.60664 -2293.7047 0 -2248.2139 14850.338
|
||||
140 865.12471 -2285.7774 0 -2248.1971 17101.553
|
||||
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
|
||||
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
|
||||
170 843.8591 -2277.9713 0 -2248.1911 18966.532
|
||||
180 1008.7412 -2286.922 0 -2248.2075 17275.649
|
||||
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
|
||||
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
|
||||
Loop time of 0.043388 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 199.133 ns/day, 0.121 hours/ns, 2304.785 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.033874 | 0.036197 | 0.037433 | 0.7 | 83.43
|
||||
Neigh | 0.000538 | 0.00055575 | 0.000575 | 0.0 | 1.28
|
||||
Comm | 0.004381 | 0.0055505 | 0.007783 | 1.8 | 12.79
|
||||
Output | 0.000141 | 0.0001635 | 0.000228 | 0.0 | 0.38
|
||||
Modify | 0.000532 | 0.000615 | 0.000692 | 0.0 | 1.42
|
||||
Other | | 0.000306 | | | 0.71
|
||||
|
||||
Nlocal: 128.000 ave 135 max 121 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 515.000 ave 518 max 508 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2221.00 ave 2328 max 2103 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 8884
|
||||
Ave neighs/atom = 17.351562
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.205694
|
||||
ghost atom cutoff = 4.205694
|
||||
binsize = 2.102847, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -2309.1331 0 -2247.755 20346.718
|
||||
110 831.93715 -2288.8853 0 -2247.7187 21758.195
|
||||
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
|
||||
130 972.43247 -2294.1847 0 -2247.7467 16614.835
|
||||
140 815.76148 -2282.0495 0 -2247.7194 18310.116
|
||||
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
|
||||
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
|
||||
170 787.17244 -2273.8946 0 -2247.7175 18586.606
|
||||
180 932.5662 -2281.6828 0 -2247.7315 18154.167
|
||||
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
|
||||
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
|
||||
Loop time of 0.0526065 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 164.238 ns/day, 0.146 hours/ns, 1900.906 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.044962 | 0.045875 | 0.046737 | 0.3 | 87.20
|
||||
Neigh | 0.000603 | 0.00062075 | 0.000646 | 0.0 | 1.18
|
||||
Comm | 0.003882 | 0.0047085 | 0.005598 | 1.0 | 8.95
|
||||
Output | 0.000159 | 0.0001995 | 0.000321 | 0.0 | 0.38
|
||||
Modify | 0.000767 | 0.0007775 | 0.000792 | 0.0 | 1.48
|
||||
Other | | 0.0004255 | | | 0.81
|
||||
|
||||
Nlocal: 128.000 ave 131 max 122 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 483.000 ave 485 max 479 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2104.00 ave 2169 max 2008 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 8416
|
||||
Ave neighs/atom = 16.437500
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,524 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for threebody potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
Time spent = 0.000483751 secs
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
Reading potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
binsize = 2.38559, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2220.3392 0 -2101.4457 12358.626
|
||||
10 993.48824 -2166.8749 0 -2101.3265 14121.853
|
||||
20 587.90768 -2139.6876 0 -2101.3093 11864.886
|
||||
30 1030.8616 -2167.8446 0 -2101.3947 6649.2566
|
||||
40 724.62874 -2145.9637 0 -2101.3436 5859.6447
|
||||
50 490.9053 -2129.5491 0 -2101.3077 6326.5434
|
||||
60 960.24533 -2159.427 0 -2101.3794 5733.9889
|
||||
70 906.76518 -2154.3675 0 -2101.3496 8380.4834
|
||||
80 800.7253 -2146.0714 0 -2101.3113 11515.737
|
||||
90 1249.2719 -2173.9445 0 -2101.3818 11593.728
|
||||
100 1080.3797 -2160.6174 0 -2101.3445 12414.602
|
||||
Loop time of 0.129171 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 66.888 ns/day, 0.359 hours/ns, 774.165 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12468 | 0.12468 | 0.12468 | 0.0 | 96.52
|
||||
Neigh | 0.0017159 | 0.0017159 | 0.0017159 | 0.0 | 1.33
|
||||
Comm | 0.00088573 | 0.00088573 | 0.00088573 | 0.0 | 0.69
|
||||
Output | 0.00011206 | 0.00011206 | 0.00011206 | 0.0 | 0.09
|
||||
Modify | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 1.11
|
||||
Other | | 0.0003417 | | | 0.26
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14044 ave 14044 max 14044 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14044
|
||||
Ave neighs/atom = 27.4297
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
|
||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.632
|
||||
ghost atom cutoff = 5.632
|
||||
binsize = 2.816, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.758 | 2.758 | 2.758 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1080.3797 -621.93681 0 -562.66385 464005.01
|
||||
110 1512.4547 -648.51133 0 -562.74194 463733.24
|
||||
120 1959.7565 -675.18668 0 -562.8255 486580.33
|
||||
130 1138.5498 -618.80419 0 -562.6427 515406.41
|
||||
140 1827.3403 -662.43867 0 -562.78985 485719
|
||||
150 1822.9803 -659.56725 0 -562.76627 465652.59
|
||||
160 1128.3444 -611.92808 0 -562.65512 469836.33
|
||||
170 1699.6402 -647.82381 0 -562.75353 467977.54
|
||||
180 1840.047 -654.5552 0 -562.77005 488397.41
|
||||
190 1312.0974 -617.70228 0 -562.6629 510856.48
|
||||
200 1809.8409 -648.6173 0 -562.75377 490822.97
|
||||
Loop time of 0.399255 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 21.640 ns/day, 1.109 hours/ns, 250.467 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.38979 | 0.38979 | 0.38979 | 0.0 | 97.63
|
||||
Neigh | 0.0061283 | 0.0061283 | 0.0061283 | 0.0 | 1.53
|
||||
Comm | 0.0013483 | 0.0013483 | 0.0013483 | 0.0 | 0.34
|
||||
Output | 0.00016642 | 0.00016642 | 0.00016642 | 0.0 | 0.04
|
||||
Modify | 0.0014937 | 0.0014937 | 0.0014937 | 0.0 | 0.37
|
||||
Other | | 0.0003231 | | | 0.08
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1386 ave 1386 max 1386 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 17388 ave 17388 max 17388 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 17388
|
||||
Ave neighs/atom = 33.9609
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Vashishta model for In/P
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
Reading potential file InP.vashishta with DATE: 2015-10-14
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7
|
||||
ghost atom cutoff = 7
|
||||
binsize = 3.5, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair vashishta, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.783 | 2.783 | 2.783 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1080.3797 -1491.8652 0 -1432.5922 358930.65
|
||||
110 1299.3069 -1504.494 0 -1432.6803 347566.41
|
||||
120 1396.3035 -1508.3817 0 -1432.672 336798.42
|
||||
130 1055.9254 -1483.8342 0 -1432.5849 341035.18
|
||||
140 1543.9033 -1513.8559 0 -1432.6931 314268.54
|
||||
150 1242.5383 -1491.417 0 -1432.6036 311068.53
|
||||
160 1240.1733 -1489.2495 0 -1432.6033 295776.98
|
||||
170 1559.5037 -1507.824 0 -1432.6417 266170.25
|
||||
180 1379.0358 -1493.4092 0 -1432.5869 251410.63
|
||||
190 1465.8073 -1496.8564 0 -1432.6105 226461.31
|
||||
200 1456.6383 -1493.8133 0 -1432.5852 208188.34
|
||||
Loop time of 0.198058 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 43.624 ns/day, 0.550 hours/ns, 504.903 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.18746 | 0.18746 | 0.18746 | 0.0 | 94.65
|
||||
Neigh | 0.00688 | 0.00688 | 0.00688 | 0.0 | 3.47
|
||||
Comm | 0.001718 | 0.001718 | 0.001718 | 0.0 | 0.87
|
||||
Output | 0.00013351 | 0.00013351 | 0.00013351 | 0.0 | 0.07
|
||||
Modify | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.76
|
||||
Other | | 0.0003531 | | | 0.18
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1810 ave 1810 max 1810 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 36480 ave 36480 max 36480 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 36480
|
||||
Ave neighs/atom = 71.25
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724)
|
||||
orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724)
|
||||
orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.74 | 2.74 | 2.74 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1080.3797 -3249.8451 0 -3190.5722 1925371.8
|
||||
110 1878.2843 -3300.7205 0 -3191.0964 1893058.6
|
||||
120 1153.8494 -3250.2114 0 -3190.5436 1932141.4
|
||||
130 1363.8664 -3261.6889 0 -3190.6116 1902268.1
|
||||
140 1565.5505 -3273.0405 0 -3190.6982 1878817
|
||||
150 1416.9458 -3261.1805 0 -3190.865 1916554.4
|
||||
160 1288.6997 -3249.8279 0 -3190.4141 1933227.4
|
||||
170 1768.3043 -3279.2164 0 -3190.4535 1898123.4
|
||||
180 1375.1942 -3251.0929 0 -3190.3781 1896205.1
|
||||
190 1527.0671 -3258.7679 0 -3190.4344 1900673.6
|
||||
200 1586.8691 -3260.4713 0 -3190.434 1912454.8
|
||||
Loop time of 0.210082 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 41.127 ns/day, 0.584 hours/ns, 476.006 timesteps/s
|
||||
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20628 | 0.20628 | 0.20628 | 0.0 | 98.19
|
||||
Neigh | 0.00099182 | 0.00099182 | 0.00099182 | 0.0 | 0.47
|
||||
Comm | 0.00085139 | 0.00085139 | 0.00085139 | 0.0 | 0.41
|
||||
Output | 0.00013494 | 0.00013494 | 0.00013494 | 0.0 | 0.06
|
||||
Modify | 0.0014665 | 0.0014665 | 0.0014665 | 0.0 | 0.70
|
||||
Other | | 0.0003612 | | | 0.17
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1027 ave 1027 max 1027 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14602 ave 14602 max 14602 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14602
|
||||
Ave neighs/atom = 28.5195
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.744 | 2.744 | 2.744 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1080.3797 -2307.5808 0 -2248.3078 18624.75
|
||||
110 851.21757 -2290.7529 0 -2248.2817 21041.97
|
||||
120 1074.6349 -2303.6437 0 -2248.321 15244.809
|
||||
130 1006.5662 -2296.9866 0 -2248.3057 15954.09
|
||||
140 855.64354 -2285.1581 0 -2248.2781 19346.662
|
||||
150 1111.1546 -2300.024 0 -2248.314 14698.998
|
||||
160 1114.7933 -2297.8629 0 -2248.3098 14414.14
|
||||
170 853.9568 -2278.6047 0 -2248.2716 20120.632
|
||||
180 1031.0925 -2288.3481 0 -2248.2949 18332.008
|
||||
190 1230.3458 -2298.9946 0 -2248.3111 15520.302
|
||||
200 1053.8799 -2284.8931 0 -2248.2816 20033.536
|
||||
Loop time of 0.158428 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 54.536 ns/day, 0.440 hours/ns, 631.200 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.15318 | 0.15318 | 0.15318 | 0.0 | 96.69
|
||||
Neigh | 0.0022631 | 0.0022631 | 0.0022631 | 0.0 | 1.43
|
||||
Comm | 0.00093651 | 0.00093651 | 0.00093651 | 0.0 | 0.59
|
||||
Output | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.12
|
||||
Modify | 0.0015035 | 0.0015035 | 0.0015035 | 0.0 | 0.95
|
||||
Other | | 0.0003462 | | | 0.22
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1001 ave 1001 max 1001 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8872 ave 8872 max 8872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8872
|
||||
Ave neighs/atom = 17.3281
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.20569
|
||||
ghost atom cutoff = 4.20569
|
||||
binsize = 2.10285, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1080.3797 -2307.5509 0 -2248.2779 21368.36
|
||||
110 846.70637 -2290.4239 0 -2248.2488 22856.37
|
||||
120 1083.0906 -2304.1686 0 -2248.2895 17530.457
|
||||
130 1008.7015 -2297.0835 0 -2248.2781 17698.498
|
||||
140 811.71413 -2282.2528 0 -2248.2417 19986.737
|
||||
150 1094.4969 -2298.9718 0 -2248.2836 15822.967
|
||||
160 1100.1109 -2296.9461 0 -2248.2804 15213.75
|
||||
170 801.20165 -2275.2175 0 -2248.2372 20153.957
|
||||
180 994.63485 -2286.1145 0 -2248.2621 19167.021
|
||||
190 1215.6425 -2298.2082 0 -2248.284 15895.654
|
||||
200 992.20385 -2281.0372 0 -2248.2425 19643.792
|
||||
Loop time of 0.282035 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 30.634 ns/day, 0.783 hours/ns, 354.565 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.27701 | 0.27701 | 0.27701 | 0.0 | 98.22
|
||||
Neigh | 0.0021927 | 0.0021927 | 0.0021927 | 0.0 | 0.78
|
||||
Comm | 0.00089169 | 0.00089169 | 0.00089169 | 0.0 | 0.32
|
||||
Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.05
|
||||
Modify | 0.0014682 | 0.0014682 | 0.0014682 | 0.0 | 0.52
|
||||
Other | | 0.0003295 | | | 0.12
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 972 ave 972 max 972 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8390 ave 8390 max 8390 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8390
|
||||
Ave neighs/atom = 16.3867
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,524 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for threebody potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
Time spent = 0.000348091 secs
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
Reading potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
binsize = 2.38559, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.957 | 2.957 | 2.957 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2220.3392 0 -2101.4457 12358.626
|
||||
10 979.93888 -2165.9769 0 -2101.3242 14172.134
|
||||
20 579.6159 -2139.1412 0 -2101.3085 11866.038
|
||||
30 1027.5223 -2167.6187 0 -2101.3942 6885.6751
|
||||
40 711.03138 -2145.0665 0 -2101.3405 6357.0866
|
||||
50 497.18304 -2129.9748 0 -2101.3052 7137.6093
|
||||
60 1008.411 -2162.5834 0 -2101.3804 6745.1775
|
||||
70 947.58674 -2156.9872 0 -2101.3508 9678.1622
|
||||
80 798.43683 -2145.8382 0 -2101.3074 12728.694
|
||||
90 1259.2065 -2174.5324 0 -2101.3799 12033.395
|
||||
100 1100.5203 -2161.8599 0 -2101.3468 12356.137
|
||||
Loop time of 0.0414283 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 208.553 ns/day, 0.115 hours/ns, 2413.811 timesteps/s
|
||||
95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.030011 | 0.032047 | 0.034036 | 0.8 | 77.36
|
||||
Neigh | 0.00043392 | 0.00045151 | 0.0004642 | 0.0 | 1.09
|
||||
Comm | 0.0050831 | 0.0067263 | 0.0091536 | 1.8 | 16.24
|
||||
Output | 0.00018191 | 0.00018775 | 0.00020432 | 0.0 | 0.45
|
||||
Modify | 0.00068116 | 0.0010136 | 0.001817 | 1.5 | 2.45
|
||||
Other | | 0.001002 | | | 2.42
|
||||
|
||||
Nlocal: 128 ave 132 max 126 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 525 ave 527 max 521 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3507 ave 3596 max 3470 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 14028
|
||||
Ave neighs/atom = 27.3984
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
|
||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.632
|
||||
ghost atom cutoff = 5.632
|
||||
binsize = 2.816, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.718 | 2.718 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1100.5203 -621.61663 0 -561.10352 462716.2
|
||||
110 1478.2708 -644.61282 0 -561.16927 464567.29
|
||||
120 1989.4577 -675.5312 0 -561.25985 486476.63
|
||||
130 1185.4652 -620.23829 0 -561.09359 514103.86
|
||||
140 1726.9774 -654.21952 0 -561.20676 488915.22
|
||||
150 1863.2061 -660.66167 0 -561.21416 466985.15
|
||||
160 1119.0313 -609.68409 0 -561.08624 471511.61
|
||||
170 1708.2653 -646.79823 0 -561.18829 468697.42
|
||||
180 1891.8451 -656.32585 0 -561.2042 489912.65
|
||||
190 1345.7703 -618.29258 0 -561.09909 512364.68
|
||||
200 1865.9507 -650.72167 0 -561.19281 491531.23
|
||||
Loop time of 0.117532 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 73.512 ns/day, 0.326 hours/ns, 850.834 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.096347 | 0.10005 | 0.10244 | 0.8 | 85.13
|
||||
Neigh | 0.000947 | 0.0010053 | 0.0011535 | 0.3 | 0.86
|
||||
Comm | 0.0098422 | 0.012949 | 0.016335 | 2.2 | 11.02
|
||||
Output | 0.00017452 | 0.00022596 | 0.00037885 | 0.0 | 0.19
|
||||
Modify | 0.00078702 | 0.0013881 | 0.0021975 | 1.6 | 1.18
|
||||
Other | | 0.001909 | | | 1.62
|
||||
|
||||
Nlocal: 128 ave 133 max 125 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 754.5 ave 759 max 748 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4353 ave 4512 max 4252 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 17412
|
||||
Ave neighs/atom = 34.0078
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Vashishta model for In/P
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
Reading potential file InP.vashishta with DATE: 2015-10-14
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7
|
||||
ghost atom cutoff = 7
|
||||
binsize = 3.5, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair vashishta, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1100.5203 -1495.2135 0 -1434.7004 357102.51
|
||||
110 1238.7371 -1502.5372 0 -1434.7528 348870.19
|
||||
120 1409.575 -1511.3137 0 -1434.7612 336831.6
|
||||
130 1081.541 -1487.5554 0 -1434.6881 339244.71
|
||||
140 1484.7455 -1512.0076 0 -1434.7646 313026.51
|
||||
150 1263.0321 -1494.834 0 -1434.7018 306496.02
|
||||
160 1253.4363 -1492.1804 0 -1434.7025 290683.01
|
||||
170 1536.7348 -1508.3735 0 -1434.7312 261755.69
|
||||
180 1342.0478 -1493.0615 0 -1434.6754 248519.54
|
||||
190 1457.921 -1498.4355 0 -1434.6991 223607.39
|
||||
200 1499.5384 -1498.7005 0 -1434.6898 204647.17
|
||||
Loop time of 0.060006 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 143.986 ns/day, 0.167 hours/ns, 1666.501 timesteps/s
|
||||
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.043862 | 0.047754 | 0.04964 | 1.0 | 79.58
|
||||
Neigh | 0.0018079 | 0.0018883 | 0.0019724 | 0.1 | 3.15
|
||||
Comm | 0.0067413 | 0.0083464 | 0.011978 | 2.3 | 13.91
|
||||
Output | 0.00018859 | 0.00029892 | 0.00062919 | 0.0 | 0.50
|
||||
Modify | 0.00088429 | 0.0011829 | 0.0014911 | 0.8 | 1.97
|
||||
Other | | 0.0005357 | | | 0.89
|
||||
|
||||
Nlocal: 128 ave 129 max 127 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 992.75 ave 1001 max 987 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 9116 ave 9213 max 9051 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 36464
|
||||
Ave neighs/atom = 71.2188
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724)
|
||||
orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724)
|
||||
orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.699 | 2.699 | 2.699 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1100.5203 -3252.8699 0 -3192.3567 1930742.5
|
||||
110 1858.7735 -3301.1227 0 -3192.8403 1901753.1
|
||||
120 1107.7693 -3248.8236 0 -3192.2522 1953649.4
|
||||
130 1315.4397 -3260.1471 0 -3192.2616 1898713.9
|
||||
140 1541.4371 -3273.1832 0 -3192.41 1887352.3
|
||||
150 1424.7104 -3262.9648 0 -3192.216 1960688.1
|
||||
160 1291.2932 -3251.5548 0 -3192.0201 1914541.2
|
||||
170 1719.1133 -3277.7936 0 -3192.33 1893926
|
||||
180 1312.8066 -3248.6914 0 -3192.1477 1921417.4
|
||||
190 1481.3472 -3257.1585 0 -3191.8991 1927045.6
|
||||
200 1615.282 -3263.8377 0 -3192.055 1920616.3
|
||||
Loop time of 0.0635643 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 135.925 ns/day, 0.177 hours/ns, 1573.210 timesteps/s
|
||||
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.051391 | 0.053262 | 0.05459 | 0.6 | 83.79
|
||||
Neigh | 0.00052404 | 0.00052798 | 0.00053144 | 0.0 | 0.83
|
||||
Comm | 0.0063059 | 0.0079132 | 0.0095143 | 1.5 | 12.45
|
||||
Output | 0.00017905 | 0.00029147 | 0.00062609 | 0.0 | 0.46
|
||||
Modify | 0.00064421 | 0.00096625 | 0.0012674 | 0.0 | 1.52
|
||||
Other | | 0.0006039 | | | 0.95
|
||||
|
||||
Nlocal: 128 ave 131 max 125 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 526.75 ave 532 max 523 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3646.5 ave 3722 max 3567 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 14586
|
||||
Ave neighs/atom = 28.4883
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.701 | 2.701 | 2.701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1100.5203 -2308.936 0 -2248.4229 18087.231
|
||||
110 821.82813 -2288.8477 0 -2248.3856 21245.995
|
||||
120 1082.3774 -2304.2287 0 -2248.4366 15467.483
|
||||
130 995.26561 -2296.2957 0 -2248.4145 16341.517
|
||||
140 826.97009 -2283.3692 0 -2248.3897 19123.5
|
||||
150 1048.4178 -2296.0496 0 -2248.4172 15060.312
|
||||
160 1101.7884 -2297.2417 0 -2248.426 15070.879
|
||||
170 859.48562 -2279.1747 0 -2248.383 21416.479
|
||||
180 1041.679 -2289.2303 0 -2248.4038 19572.707
|
||||
190 1278.0514 -2302.2822 0 -2248.4257 16006.173
|
||||
200 1097.0682 -2287.8121 0 -2248.3929 20906.774
|
||||
Loop time of 0.046846 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 184.434 ns/day, 0.130 hours/ns, 2134.653 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.037434 | 0.039142 | 0.041109 | 0.7 | 83.55
|
||||
Neigh | 0.0005877 | 0.00059921 | 0.00061464 | 0.0 | 1.28
|
||||
Comm | 0.0036416 | 0.0055436 | 0.0073476 | 1.8 | 11.83
|
||||
Output | 0.00016212 | 0.00027066 | 0.00059533 | 0.0 | 0.58
|
||||
Modify | 0.00063038 | 0.00065678 | 0.00067234 | 0.0 | 1.40
|
||||
Other | | 0.0006335 | | | 1.35
|
||||
|
||||
Nlocal: 128 ave 131 max 126 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 518 ave 525 max 513 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2202 ave 2257 max 2175 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 8808
|
||||
Ave neighs/atom = 17.2031
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.20569
|
||||
ghost atom cutoff = 4.20569
|
||||
binsize = 2.10285, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.701 | 2.701 | 2.701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1100.5203 -2308.5955 0 -2248.0824 20775.991
|
||||
110 813.33618 -2287.9469 0 -2248.04 22564.16
|
||||
120 1100.0902 -2305.051 0 -2248.092 17540.971
|
||||
130 1022.9471 -2297.7384 0 -2248.0801 17985.336
|
||||
140 761.99242 -2278.7251 0 -2248.0345 20462.975
|
||||
150 1053.3973 -2296.1039 0 -2248.081 16130.559
|
||||
160 1089.2622 -2296.1059 0 -2248.0833 15434.234
|
||||
170 776.25788 -2273.4496 0 -2248.0321 20642.702
|
||||
180 1016.1885 -2287.4305 0 -2248.0641 19276.936
|
||||
190 1266.3943 -2301.3675 0 -2248.0865 16199.281
|
||||
200 1012.4185 -2282.134 0 -2248.0423 20795.113
|
||||
Loop time of 0.0840016 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 102.855 ns/day, 0.233 hours/ns, 1190.454 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.068133 | 0.071658 | 0.075315 | 1.0 | 85.31
|
||||
Neigh | 0.00057864 | 0.00058872 | 0.00060058 | 0.0 | 0.70
|
||||
Comm | 0.0049844 | 0.008617 | 0.012086 | 2.8 | 10.26
|
||||
Output | 0.0001626 | 0.00027418 | 0.00060463 | 0.0 | 0.33
|
||||
Modify | 0.00070477 | 0.0011689 | 0.0022428 | 1.8 | 1.39
|
||||
Other | | 0.001694 | | | 2.02
|
||||
|
||||
Nlocal: 128 ave 129 max 127 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 489.75 ave 501 max 481 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2094.5 ave 2121 max 2060 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 8378
|
||||
Ave neighs/atom = 16.3633
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
149
lib/gpu/Makefile.cuda
Normal file
149
lib/gpu/Makefile.cuda
Normal file
@ -0,0 +1,149 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Linux Makefile for CUDA
|
||||
# - change CUDA_ARCH for your GPU
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
ifeq ($(CUDA_HOME),)
|
||||
CUDA_HOME = /usr/local/cuda
|
||||
endif
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
# precision for GPU calculations
|
||||
# -D_SINGLE_SINGLE # Single precision for all calculations
|
||||
# -D_DOUBLE_DOUBLE # Double precision for all calculations
|
||||
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
|
||||
|
||||
CUDA_PRECISION = -D_SINGLE_DOUBLE
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
|
||||
|
||||
# device code compiler and settings
|
||||
|
||||
NVCC = nvcc
|
||||
|
||||
CUDA_ARCH = -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] \
|
||||
-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] \
|
||||
-gencode arch=compute_70,code=[sm_70,compute_70] -gencode arch=compute_75,code=[sm_75,compute_75]
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||
CUDA_LINK = $(CUDA_LIB) -lcudart
|
||||
CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \
|
||||
$(CUDA_PRECISION)
|
||||
|
||||
BIN2C = $(CUDA_HOME)/bin/bin2c
|
||||
|
||||
# host code compiler and settings
|
||||
|
||||
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
|
||||
CUDR_OPTS = -O2 $(LMP_INC)
|
||||
CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \
|
||||
$(CUDPP_OPT)
|
||||
|
||||
# Headers for Geryon
|
||||
UCL_H = $(wildcard ./geryon/ucl*.h)
|
||||
NVD_H = $(wildcard ./geryon/nvd*.h) $(UCL_H) lal_preprocessor.h
|
||||
ALL_H = $(NVD_H) $(wildcard ./lal_*.h)
|
||||
|
||||
# Source files
|
||||
SRCS := $(wildcard ./lal_*.cpp)
|
||||
OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
|
||||
CUS := $(wildcard lal_*.cu)
|
||||
CUHS := $(filter-out pppm_cubin.h, $(CUS:lal_%.cu=%_cubin.h)) pppm_f_cubin.h pppm_d_cubin.h
|
||||
CUHS := $(addprefix $(OBJ_DIR)/, $(CUHS))
|
||||
|
||||
ifdef CUDPP_OPT
|
||||
CUDPP = $(OBJ_DIR)/cudpp.o $(OBJ_DIR)/cudpp_plan.o \
|
||||
$(OBJ_DIR)/cudpp_maximal_launch.o $(OBJ_DIR)/cudpp_plan_manager.o \
|
||||
$(OBJ_DIR)/radixsort_app.cu_o $(OBJ_DIR)/scan_app.cu_o
|
||||
endif
|
||||
|
||||
# targets
|
||||
|
||||
GPU_LIB = $(LIB_DIR)/libgpu.a
|
||||
|
||||
EXECS = $(BIN_DIR)/nvc_get_devices
|
||||
|
||||
all: $(OBJ_DIR) $(CUHS) $(GPU_LIB) $(EXECS)
|
||||
|
||||
$(OBJ_DIR):
|
||||
mkdir -p $@
|
||||
|
||||
# device code compilation
|
||||
|
||||
$(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=float -Dgrdtyp4=float4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_f_cubin.h: $(OBJ_DIR)/pppm_f.cubin
|
||||
$(BIN2C) -c -n pppm_f $(OBJ_DIR)/pppm_f.cubin > $(OBJ_DIR)/pppm_f_cubin.h
|
||||
|
||||
$(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=double -Dgrdtyp4=double4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin
|
||||
$(BIN2C) -c -n pppm_d $(OBJ_DIR)/pppm_d.cubin > $(OBJ_DIR)/pppm_d_cubin.h
|
||||
|
||||
$(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H)
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu
|
||||
$(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@
|
||||
@rm $(OBJ_DIR)/$*.cubin
|
||||
|
||||
# host code compilation
|
||||
|
||||
$(OBJ_DIR)/lal_%.o: lal_%.cpp $(CUHS) $(ALL_H)
|
||||
$(CUDR) -o $@ -c $< -I$(OBJ_DIR)
|
||||
|
||||
#ifdef CUDPP_OPT
|
||||
$(OBJ_DIR)/cudpp.o: cudpp_mini/cudpp.cpp
|
||||
$(CUDR) -o $@ -c cudpp_mini/cudpp.cpp -Icudpp_mini
|
||||
|
||||
$(OBJ_DIR)/cudpp_plan.o: cudpp_mini/cudpp_plan.cpp
|
||||
$(CUDR) -o $@ -c cudpp_mini/cudpp_plan.cpp -Icudpp_mini
|
||||
|
||||
$(OBJ_DIR)/cudpp_maximal_launch.o: cudpp_mini/cudpp_maximal_launch.cpp
|
||||
$(CUDR) -o $@ -c cudpp_mini/cudpp_maximal_launch.cpp -Icudpp_mini
|
||||
|
||||
$(OBJ_DIR)/cudpp_plan_manager.o: cudpp_mini/cudpp_plan_manager.cpp
|
||||
$(CUDR) -o $@ -c cudpp_mini/cudpp_plan_manager.cpp -Icudpp_mini
|
||||
|
||||
$(OBJ_DIR)/radixsort_app.cu_o: cudpp_mini/radixsort_app.cu
|
||||
$(CUDA) -o $@ -c cudpp_mini/radixsort_app.cu
|
||||
|
||||
$(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
|
||||
$(CUDA) -o $@ -c cudpp_mini/scan_app.cu
|
||||
#endif
|
||||
|
||||
# build libgpu.a
|
||||
|
||||
$(GPU_LIB): $(OBJS) $(CUDPP)
|
||||
$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# test app for querying device info
|
||||
|
||||
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
|
||||
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
|
||||
|
||||
clean:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo
|
||||
|
||||
veryclean: clean
|
||||
-rm -rf *~ *.linkinfo
|
||||
|
||||
cleanlib:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUHS) *.linkinfo
|
||||
|
||||
@ -1,72 +0,0 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Linux Makefile for CUDA
|
||||
# - Change CUDA_ARCH for your GPU
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
ifeq ($(CUDA_HOME),)
|
||||
CUDA_HOME = /usr/local/cuda
|
||||
endif
|
||||
|
||||
NVCC = nvcc
|
||||
|
||||
# obsolete hardware. not supported by current drivers anymore.
|
||||
#CUDA_ARCH = -arch=sm_13
|
||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||
|
||||
# Fermi hardware
|
||||
#CUDA_ARCH = -arch=sm_20
|
||||
#CUDA_ARCH = -arch=sm_21
|
||||
|
||||
# Kepler hardware
|
||||
#CUDA_ARCH = -arch=sm_30
|
||||
#CUDA_ARCH = -arch=sm_32
|
||||
#CUDA_ARCH = -arch=sm_35
|
||||
#CUDA_ARCH = -arch=sm_37
|
||||
|
||||
# Maxwell hardware
|
||||
CUDA_ARCH = -arch=sm_50
|
||||
#CUDA_ARCH = -arch=sm_52
|
||||
|
||||
# Pascal hardware
|
||||
#CUDA_ARCH = -arch=sm_60
|
||||
#CUDA_ARCH = -arch=sm_61
|
||||
|
||||
# Volta hardware
|
||||
#CUDA_ARCH = -arch=sm_70
|
||||
|
||||
# Turing hardware
|
||||
#CUDA_ARCH = -arch=sm_75
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
# precision for GPU calculations
|
||||
# -D_SINGLE_SINGLE # Single precision for all calculations
|
||||
# -D_DOUBLE_DOUBLE # Double precision for all calculations
|
||||
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
|
||||
|
||||
CUDA_PRECISION = -D_DOUBLE_DOUBLE
|
||||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||
|
||||
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC -std=c++11
|
||||
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
|
||||
|
||||
include Nvidia.makefile
|
||||
|
||||
@ -1,73 +0,0 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Linux Makefile for CUDA
|
||||
# - Change CUDA_ARCH for your GPU
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
ifeq ($(CUDA_HOME),)
|
||||
CUDA_HOME = /usr/local/cuda
|
||||
endif
|
||||
|
||||
NVCC = nvcc
|
||||
|
||||
# obsolete hardware. not supported by current drivers anymore.
|
||||
#CUDA_ARCH = -arch=sm_13
|
||||
# older CUDA
|
||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||
|
||||
# Fermi hardware
|
||||
#CUDA_ARCH = -arch=sm_20
|
||||
#CUDA_ARCH = -arch=sm_21
|
||||
|
||||
# Kepler hardware
|
||||
#CUDA_ARCH = -arch=sm_30
|
||||
#CUDA_ARCH = -arch=sm_32
|
||||
#CUDA_ARCH = -arch=sm_35
|
||||
#CUDA_ARCH = -arch=sm_37
|
||||
|
||||
# Maxwell hardware
|
||||
CUDA_ARCH = -arch=sm_50
|
||||
#CUDA_ARCH = -arch=sm_52
|
||||
|
||||
# Pascal hardware
|
||||
#CUDA_ARCH = -arch=sm_60
|
||||
#CUDA_ARCH = -arch=sm_61
|
||||
|
||||
# Volta hardware
|
||||
#CUDA_ARCH = -arch=sm_70
|
||||
|
||||
# Turing hardware
|
||||
#CUDA_ARCH = -arch=sm_75
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
# precision for GPU calculations
|
||||
# -D_SINGLE_SINGLE # Single precision for all calculations
|
||||
# -D_DOUBLE_DOUBLE # Double precision for all calculations
|
||||
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
|
||||
|
||||
CUDA_PRECISION = -D_SINGLE_DOUBLE
|
||||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||
|
||||
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC -std=c++11
|
||||
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
|
||||
|
||||
include Nvidia.makefile
|
||||
|
||||
@ -1,72 +0,0 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Linux Makefile for CUDA
|
||||
# - Change CUDA_ARCH for your GPU
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
ifeq ($(CUDA_HOME),)
|
||||
CUDA_HOME = /usr/local/cuda
|
||||
endif
|
||||
|
||||
NVCC = nvcc
|
||||
|
||||
# obsolete hardware. not supported by current drivers anymore.
|
||||
#CUDA_ARCH = -arch=sm_13
|
||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||
|
||||
# Fermi hardware
|
||||
#CUDA_ARCH = -arch=sm_20
|
||||
#CUDA_ARCH = -arch=sm_21
|
||||
|
||||
# Kepler hardware
|
||||
#CUDA_ARCH = -arch=sm_30
|
||||
#CUDA_ARCH = -arch=sm_32
|
||||
#CUDA_ARCH = -arch=sm_35
|
||||
#CUDA_ARCH = -arch=sm_37
|
||||
|
||||
# Maxwell hardware
|
||||
CUDA_ARCH = -arch=sm_50
|
||||
#CUDA_ARCH = -arch=sm_52
|
||||
|
||||
# Pascal hardware
|
||||
#CUDA_ARCH = -arch=sm_60
|
||||
#CUDA_ARCH = -arch=sm_61
|
||||
|
||||
# Volta hardware
|
||||
#CUDA_ARCH = -arch=sm_70
|
||||
|
||||
# Turing hardware
|
||||
#CUDA_ARCH = -arch=sm_75
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
# precision for GPU calculations
|
||||
# -D_SINGLE_SINGLE # Single precision for all calculations
|
||||
# -D_DOUBLE_DOUBLE # Double precision for all calculations
|
||||
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
|
||||
|
||||
CUDA_PRECISION = -D_SINGLE_SINGLE
|
||||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||
|
||||
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC -std=c++11
|
||||
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
|
||||
|
||||
include Nvidia.makefile
|
||||
|
||||
@ -1 +0,0 @@
|
||||
Makefile.linux
|
||||
92
lib/gpu/Makefile.opencl
Normal file
92
lib/gpu/Makefile.opencl
Normal file
@ -0,0 +1,92 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Linux Makefile for OpenCL
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.opencl
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
# precision for GPU calculations
|
||||
# -D_SINGLE_SINGLE # Single precision for all calculations
|
||||
# -D_DOUBLE_DOUBLE # Double precision for all calculations
|
||||
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
|
||||
|
||||
OCL_PREC = -D_SINGLE_DOUBLE
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
# Compiler and linker settings
|
||||
|
||||
# OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi
|
||||
# OCL_TUNE = -DKEPLER_OCL # -- Uncomment for NVIDIA Kepler
|
||||
# OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress
|
||||
OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device
|
||||
|
||||
OCL_INC = -I/usr/local/cuda/include # Path to CL directory
|
||||
OCL_CPP = mpic++ $(DEFAULT_DEVICE) -g -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC)
|
||||
OCL_LINK = -lOpenCL
|
||||
OCL = $(OCL_CPP) $(OCL_PREC) $(OCL_TUNE) -DUSE_OPENCL
|
||||
|
||||
# Headers for Geryon
|
||||
UCL_H = $(wildcard ./geryon/ucl*.h)
|
||||
OCL_H = $(wildcard ./geryon/ocl*.h) $(UCL_H) lal_preprocessor.h
|
||||
PRE1_H = lal_preprocessor.h lal_aux_fun1.h
|
||||
ALL_H = $(OCL_H) $(wildcard ./lal_*.h)
|
||||
|
||||
# Source files
|
||||
SRCS := $(wildcard ./lal_*.cpp)
|
||||
OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
|
||||
CUS := $(wildcard lal_*.cu)
|
||||
KERS := $(subst ./,$(OBJ_DIR)/,$(CUS:lal_%.cu=%_cl.h))
|
||||
KERS := $(addprefix $(OBJ_DIR)/, $(KERS))
|
||||
|
||||
# targets
|
||||
|
||||
GPU_LIB = $(LIB_DIR)/libgpu.a
|
||||
|
||||
EXECS = $(BIN_DIR)/ocl_get_devices
|
||||
|
||||
all: $(OBJ_DIR) $(KERS) $(GPU_LIB) $(EXECS)
|
||||
|
||||
$(OBJ_DIR):
|
||||
mkdir -p $@
|
||||
|
||||
# device code compilation
|
||||
|
||||
$(OBJ_DIR)/%_cl.h: lal_%.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh $* $(PRE1_H) $< $@;
|
||||
|
||||
# host code compilation
|
||||
|
||||
$(OBJ_DIR)/lal_%.o: lal_%.cpp $(KERS)
|
||||
$(OCL) -o $@ -c $< -I$(OBJ_DIR)
|
||||
|
||||
# build libgpu.a
|
||||
|
||||
$(GPU_LIB): $(OBJS)
|
||||
$(AR) -crusv $(GPU_LIB) $(OBJS)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# test app for querying device info
|
||||
|
||||
$(BIN_DIR)/ocl_get_devices: ./geryon/ucl_get_devices.cpp $(OCL_H)
|
||||
$(OCL) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_OPENCL $(OCL_LINK)
|
||||
|
||||
clean:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(KERS) *.linkinfo
|
||||
|
||||
veryclean: clean
|
||||
-rm -rf *~ *.linkinfo
|
||||
|
||||
cleanlib:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(KERS) *.linkinfo
|
||||
|
||||
@ -1,24 +0,0 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Makefile for OpenCL for use with MPI STUBS library
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
OCL_HOME = $(HOME)/intelocl
|
||||
OCL_CPP = g++ -O3 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS -I$(OCL_HOME)/include/
|
||||
# available tuned parameter sets: FERMI_OCL, CYPRESS_OCL
|
||||
#OCL_TUNE = -DFERMI_OCL
|
||||
OCL_TUNE = -DCYPRESS_OCL
|
||||
OCL_LINK = -lOpenCL -L../../src/STUBS -lmpi
|
||||
OCL_PREC = -D_SINGLE_DOUBLE
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
include Opencl.makefile
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
NVCC = $(CUDA_HOME)/bin/nvcc
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
CUDA_ARCH = -arch=sm_35
|
||||
CUDA_ARCH = -arch=sm_75
|
||||
CUDA_PRECISION = -D_SINGLE_DOUBLE
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64 -lcudart
|
||||
@ -1,32 +0,0 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Makefile for Cray XK7 Architecture supporting Hyper-Q with Proxy
|
||||
# - Uses PrgEnv-gnu
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
CUDA_HOME = $(CRAY_CUDATOOLKIT_DIR)
|
||||
NVCC = nvcc
|
||||
|
||||
CUDA_ARCH = -arch=sm_35
|
||||
|
||||
CUDA_PRECISION = -D_SINGLE_DOUBLE
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math
|
||||
|
||||
CUDR_CPP = CC -DCUDA_PROXY -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||
CUDR_OPTS = -O2 -march=bdver1 -ftree-vectorize
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
CUDPP_OPT = # -DUSE_CUDPP -Icudpp_mini
|
||||
|
||||
include Nvidia.makefile
|
||||
|
||||
@ -1,157 +1,67 @@
|
||||
CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \
|
||||
$(CUDA_PRECISION)
|
||||
CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \
|
||||
$(CUDPP_OPT)
|
||||
CUDA_LINK = $(CUDA_LIB) -lcudart
|
||||
BIN2C = $(CUDA_HOME)/bin/bin2c
|
||||
|
||||
GPU_LIB = $(LIB_DIR)/libgpu.a
|
||||
|
||||
# Headers for Geryon
|
||||
UCL_H = $(wildcard ./geryon/ucl*.h)
|
||||
NVC_H = $(wildcard ./geryon/nvc*.h) $(UCL_H)
|
||||
NVD_H = $(wildcard ./geryon/nvd*.h) $(UCL_H) lal_preprocessor.h
|
||||
# Headers for Pair Stuff
|
||||
PAIR_H = lal_atom.h lal_answer.h lal_neighbor_shared.h \
|
||||
lal_neighbor.h lal_precision.h lal_device.h \
|
||||
lal_balance.h lal_pppm.h
|
||||
ALL_H = $(NVD_H) $(wildcard ./lal_*.h)
|
||||
|
||||
ALL_H = $(NVD_H) $(PAIR_H)
|
||||
# Source files
|
||||
SRCS := $(wildcard ./lal_*.cpp)
|
||||
OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
|
||||
CUS := $(wildcard lal_*.cu)
|
||||
CUHS := $(filter-out pppm_cubin.h, $(CUS:lal_%.cu=%_cubin.h)) pppm_f_cubin.h pppm_d_cubin.h
|
||||
CUHS := $(addprefix $(OBJ_DIR)/, $(CUHS))
|
||||
|
||||
EXECS = $(BIN_DIR)/nvc_get_devices
|
||||
ifdef CUDPP_OPT
|
||||
CUDPP = $(OBJ_DIR)/cudpp.o $(OBJ_DIR)/cudpp_plan.o \
|
||||
$(OBJ_DIR)/cudpp_maximal_launch.o $(OBJ_DIR)/cudpp_plan_manager.o \
|
||||
$(OBJ_DIR)/radixsort_app.cu_o $(OBJ_DIR)/scan_app.cu_o
|
||||
endif
|
||||
OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
|
||||
$(OBJ_DIR)/lal_neighbor.o $(OBJ_DIR)/lal_neighbor_shared.o \
|
||||
$(OBJ_DIR)/lal_device.o $(OBJ_DIR)/lal_base_atomic.o \
|
||||
$(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_base_ellipsoid.o \
|
||||
$(OBJ_DIR)/lal_base_dipole.o $(OBJ_DIR)/lal_base_three.o \
|
||||
$(OBJ_DIR)/lal_base_dpd.o \
|
||||
$(OBJ_DIR)/lal_pppm.o $(OBJ_DIR)/lal_pppm_ext.o \
|
||||
$(OBJ_DIR)/lal_gayberne.o $(OBJ_DIR)/lal_gayberne_ext.o \
|
||||
$(OBJ_DIR)/lal_re_squared.o $(OBJ_DIR)/lal_re_squared_ext.o \
|
||||
$(OBJ_DIR)/lal_lj.o $(OBJ_DIR)/lal_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_lj96.o $(OBJ_DIR)/lal_lj96_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_expand.o $(OBJ_DIR)/lal_lj_expand_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul.o $(OBJ_DIR)/lal_lj_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_long.o $(OBJ_DIR)/lal_lj_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_dsf.o $(OBJ_DIR)/lal_lj_dsf_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_class2_long.o $(OBJ_DIR)/lal_lj_class2_long_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_long.o $(OBJ_DIR)/lal_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_morse.o $(OBJ_DIR)/lal_morse_ext.o \
|
||||
$(OBJ_DIR)/lal_charmm_long.o $(OBJ_DIR)/lal_charmm_long_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_sdk.o $(OBJ_DIR)/lal_lj_sdk_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_sdk_long.o $(OBJ_DIR)/lal_lj_sdk_long_ext.o \
|
||||
$(OBJ_DIR)/lal_eam.o $(OBJ_DIR)/lal_eam_ext.o \
|
||||
$(OBJ_DIR)/lal_eam_fs_ext.o $(OBJ_DIR)/lal_eam_alloy_ext.o \
|
||||
$(OBJ_DIR)/lal_buck.o $(OBJ_DIR)/lal_buck_ext.o \
|
||||
$(OBJ_DIR)/lal_buck_coul.o $(OBJ_DIR)/lal_buck_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_buck_coul_long.o $(OBJ_DIR)/lal_buck_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_table.o $(OBJ_DIR)/lal_table_ext.o \
|
||||
$(OBJ_DIR)/lal_yukawa.o $(OBJ_DIR)/lal_yukawa_ext.o \
|
||||
$(OBJ_DIR)/lal_born.o $(OBJ_DIR)/lal_born_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_wolf.o $(OBJ_DIR)/lal_born_coul_wolf_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_long.o $(OBJ_DIR)/lal_born_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_lj.o $(OBJ_DIR)/lal_dipole_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf.o $(OBJ_DIR)/lal_dipole_lj_sf_ext.o \
|
||||
$(OBJ_DIR)/lal_colloid.o $(OBJ_DIR)/lal_colloid_ext.o \
|
||||
$(OBJ_DIR)/lal_gauss.o $(OBJ_DIR)/lal_gauss_ext.o \
|
||||
$(OBJ_DIR)/lal_yukawa_colloid.o $(OBJ_DIR)/lal_yukawa_colloid_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \
|
||||
$(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \
|
||||
$(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \
|
||||
$(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \
|
||||
$(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \
|
||||
$(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_msm.o $(OBJ_DIR)/lal_lj_coul_msm_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_gromacs.o $(OBJ_DIR)/lal_lj_gromacs_ext.o \
|
||||
$(OBJ_DIR)/lal_dpd.o $(OBJ_DIR)/lal_dpd_ext.o $(OBJ_DIR)/lal_dpd_tstat_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff.o $(OBJ_DIR)/lal_tersoff_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff_zbl.o $(OBJ_DIR)/lal_tersoff_zbl_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff_mod.o $(OBJ_DIR)/lal_tersoff_mod_ext.o \
|
||||
$(OBJ_DIR)/lal_coul.o $(OBJ_DIR)/lal_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \
|
||||
$(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \
|
||||
$(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
|
||||
|
||||
CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
|
||||
$(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \
|
||||
$(OBJ_DIR)/neighbor_cpu.cubin $(OBJ_DIR)/neighbor_cpu_cubin.h \
|
||||
$(OBJ_DIR)/neighbor_gpu.cubin $(OBJ_DIR)/neighbor_gpu_cubin.h \
|
||||
$(OBJ_DIR)/pppm_f.cubin $(OBJ_DIR)/pppm_f_cubin.h \
|
||||
$(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/pppm_d_cubin.h \
|
||||
$(OBJ_DIR)/ellipsoid_nbor.cubin $(OBJ_DIR)/ellipsoid_nbor_cubin.h \
|
||||
$(OBJ_DIR)/gayberne.cubin $(OBJ_DIR)/gayberne_lj.cubin \
|
||||
$(OBJ_DIR)/gayberne_cubin.h $(OBJ_DIR)/gayberne_lj_cubin.h \
|
||||
$(OBJ_DIR)/re_squared.cubin $(OBJ_DIR)/re_squared_lj.cubin \
|
||||
$(OBJ_DIR)/re_squared_cubin.h $(OBJ_DIR)/re_squared_lj_cubin.h \
|
||||
$(OBJ_DIR)/lj.cubin $(OBJ_DIR)/lj_cubin.h \
|
||||
$(OBJ_DIR)/lj96.cubin $(OBJ_DIR)/lj96_cubin.h \
|
||||
$(OBJ_DIR)/lj_expand.cubin $(OBJ_DIR)/lj_expand_cubin.h \
|
||||
$(OBJ_DIR)/lj_coul.cubin $(OBJ_DIR)/lj_coul_cubin.h \
|
||||
$(OBJ_DIR)/lj_coul_long.cubin $(OBJ_DIR)/lj_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/lj_dsf.cubin $(OBJ_DIR)/lj_dsf_cubin.h \
|
||||
$(OBJ_DIR)/lj_class2_long.cubin $(OBJ_DIR)/lj_class2_long_cubin.h \
|
||||
$(OBJ_DIR)/coul_long.cubin $(OBJ_DIR)/coul_long_cubin.h \
|
||||
$(OBJ_DIR)/morse.cubin $(OBJ_DIR)/morse_cubin.h \
|
||||
$(OBJ_DIR)/charmm_long.cubin $(OBJ_DIR)/charmm_long_cubin.h \
|
||||
$(OBJ_DIR)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk_cubin.h \
|
||||
$(OBJ_DIR)/lj_sdk_long.cubin $(OBJ_DIR)/lj_sdk_long_cubin.h \
|
||||
$(OBJ_DIR)/eam.cubin $(OBJ_DIR)/eam_cubin.h \
|
||||
$(OBJ_DIR)/buck.cubin $(OBJ_DIR)/buck_cubin.h \
|
||||
$(OBJ_DIR)/buck_coul_long.cubin $(OBJ_DIR)/buck_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/buck_coul.cubin $(OBJ_DIR)/buck_coul_cubin.h \
|
||||
$(OBJ_DIR)/table.cubin $(OBJ_DIR)/table_cubin.h \
|
||||
$(OBJ_DIR)/yukawa.cubin $(OBJ_DIR)/yukawa_cubin.h \
|
||||
$(OBJ_DIR)/born.cubin $(OBJ_DIR)/born_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_wolf.cubin $(OBJ_DIR)/born_coul_wolf_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_long.cubin $(OBJ_DIR)/born_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/dipole_lj.cubin $(OBJ_DIR)/dipole_lj_cubin.h \
|
||||
$(OBJ_DIR)/dipole_lj_sf.cubin $(OBJ_DIR)/dipole_lj_sf_cubin.h \
|
||||
$(OBJ_DIR)/colloid.cubin $(OBJ_DIR)/colloid_cubin.h \
|
||||
$(OBJ_DIR)/gauss.cubin $(OBJ_DIR)/gauss_cubin.h \
|
||||
$(OBJ_DIR)/yukawa_colloid.cubin $(OBJ_DIR)/yukawa_colloid_cubin.h \
|
||||
$(OBJ_DIR)/lj_coul_debye.cubin $(OBJ_DIR)/lj_coul_debye_cubin.h \
|
||||
$(OBJ_DIR)/coul_dsf.cubin $(OBJ_DIR)/coul_dsf_cubin.h \
|
||||
$(OBJ_DIR)/sw.cubin $(OBJ_DIR)/sw_cubin.h \
|
||||
$(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta_cubin.h \
|
||||
$(OBJ_DIR)/beck.cubin $(OBJ_DIR)/beck_cubin.h \
|
||||
$(OBJ_DIR)/mie.cubin $(OBJ_DIR)/mie_cubin.h \
|
||||
$(OBJ_DIR)/soft.cubin $(OBJ_DIR)/soft_cubin.h \
|
||||
$(OBJ_DIR)/lj_coul_msm.cubin $(OBJ_DIR)/lj_coul_msm_cubin.h \
|
||||
$(OBJ_DIR)/lj_gromacs.cubin $(OBJ_DIR)/lj_gromacs_cubin.h \
|
||||
$(OBJ_DIR)/dpd.cubin $(OBJ_DIR)/dpd_cubin.h \
|
||||
$(OBJ_DIR)/tersoff.cubin $(OBJ_DIR)/tersoff_cubin.h \
|
||||
$(OBJ_DIR)/tersoff_zbl.cubin $(OBJ_DIR)/tersoff_zbl_cubin.h \
|
||||
$(OBJ_DIR)/tersoff_mod.cubin $(OBJ_DIR)/tersoff_mod_cubin.h \
|
||||
$(OBJ_DIR)/coul.cubin $(OBJ_DIR)/coul_cubin.h \
|
||||
$(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye_cubin.h \
|
||||
$(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl_cubin.h \
|
||||
$(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \
|
||||
$(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \
|
||||
$(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \
|
||||
$(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h \
|
||||
$(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long_cubin.h
|
||||
# targets
|
||||
|
||||
all: $(OBJ_DIR) $(GPU_LIB) $(EXECS)
|
||||
GPU_LIB = $(LIB_DIR)/libgpu.a
|
||||
|
||||
EXECS = $(BIN_DIR)/nvc_get_devices
|
||||
|
||||
all: $(OBJ_DIR) $(CUHS) $(GPU_LIB) $(EXECS)
|
||||
|
||||
$(OBJ_DIR):
|
||||
mkdir -p $@
|
||||
|
||||
# Compilers and linkers
|
||||
|
||||
CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \
|
||||
$(CUDA_PRECISION)
|
||||
CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \
|
||||
$(CUDPP_OPT)
|
||||
CUDA_LINK = $(CUDA_LIB) -lcudart
|
||||
|
||||
BIN2C = $(CUDA_HOME)/bin/bin2c
|
||||
|
||||
# device code compilation
|
||||
|
||||
$(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=float -Dgrdtyp4=float4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_f_cubin.h: $(OBJ_DIR)/pppm_f.cubin
|
||||
$(BIN2C) -c -n pppm_f $(OBJ_DIR)/pppm_f.cubin > $(OBJ_DIR)/pppm_f_cubin.h
|
||||
|
||||
$(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=double -Dgrdtyp4=double4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin
|
||||
$(BIN2C) -c -n pppm_d $(OBJ_DIR)/pppm_d.cubin > $(OBJ_DIR)/pppm_d_cubin.h
|
||||
|
||||
$(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H)
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu
|
||||
$(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@
|
||||
@rm $(OBJ_DIR)/$*.cubin
|
||||
|
||||
# host code compilation
|
||||
|
||||
$(OBJ_DIR)/lal_%.o: lal_%.cpp $(CUHS) $(ALL_H)
|
||||
$(CUDR) -o $@ -c $< -I$(OBJ_DIR)
|
||||
|
||||
#ifdef CUDPP_OPT
|
||||
$(OBJ_DIR)/cudpp.o: cudpp_mini/cudpp.cpp
|
||||
$(CUDR) -o $@ -c cudpp_mini/cudpp.cpp -Icudpp_mini
|
||||
|
||||
@ -169,745 +79,24 @@ $(OBJ_DIR)/radixsort_app.cu_o: cudpp_mini/radixsort_app.cu
|
||||
|
||||
$(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
|
||||
$(CUDA) -o $@ -c cudpp_mini/scan_app.cu
|
||||
#endif
|
||||
|
||||
$(OBJ_DIR)/atom.cubin: lal_atom.cu lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_atom.cu
|
||||
|
||||
$(OBJ_DIR)/atom_cubin.h: $(OBJ_DIR)/atom.cubin
|
||||
$(BIN2C) -c -n atom $(OBJ_DIR)/atom.cubin > $(OBJ_DIR)/atom_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_atom.o: lal_atom.cpp lal_atom.h $(NVD_H) $(OBJ_DIR)/atom_cubin.h
|
||||
$(CUDR) -o $@ -c lal_atom.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_ans.o: lal_answer.cpp lal_answer.h $(NVD_H)
|
||||
$(CUDR) -o $@ -c lal_answer.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/neighbor_cpu.cubin: lal_neighbor_cpu.cu lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_neighbor_cpu.cu
|
||||
|
||||
$(OBJ_DIR)/neighbor_cpu_cubin.h: $(OBJ_DIR)/neighbor_cpu.cubin
|
||||
$(BIN2C) -c -n neighbor_cpu $(OBJ_DIR)/neighbor_cpu.cubin > $(OBJ_DIR)/neighbor_cpu_cubin.h
|
||||
|
||||
$(OBJ_DIR)/neighbor_gpu.cubin: lal_neighbor_gpu.cu lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_neighbor_gpu.cu
|
||||
|
||||
$(OBJ_DIR)/neighbor_gpu_cubin.h: $(OBJ_DIR)/neighbor_gpu.cubin
|
||||
$(BIN2C) -c -n neighbor_gpu $(OBJ_DIR)/neighbor_gpu.cubin > $(OBJ_DIR)/neighbor_gpu_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_neighbor_shared.o: lal_neighbor_shared.cpp lal_neighbor_shared.h $(OBJ_DIR)/neighbor_cpu_cubin.h $(OBJ_DIR)/neighbor_gpu_cubin.h $(NVD_H)
|
||||
$(CUDR) -o $@ -c lal_neighbor_shared.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_neighbor.o: lal_neighbor.cpp lal_neighbor.h lal_neighbor_shared.h $(NVD_H)
|
||||
$(CUDR) -o $@ -c lal_neighbor.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/device.cubin: lal_device.cu lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_device.cu
|
||||
|
||||
$(OBJ_DIR)/device_cubin.h: $(OBJ_DIR)/device.cubin
|
||||
$(BIN2C) -c -n device $(OBJ_DIR)/device.cubin > $(OBJ_DIR)/device_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_device.o: lal_device.cpp lal_device.h $(ALL_H) $(OBJ_DIR)/device_cubin.h
|
||||
$(CUDR) -o $@ -c lal_device.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_base_atomic.o: $(ALL_H) lal_base_atomic.h lal_base_atomic.cpp
|
||||
$(CUDR) -o $@ -c lal_base_atomic.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_charge.o: $(ALL_H) lal_base_charge.h lal_base_charge.cpp
|
||||
$(CUDR) -o $@ -c lal_base_charge.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_ellipsoid.o: $(ALL_H) lal_base_ellipsoid.h lal_base_ellipsoid.cpp $(OBJ_DIR)/ellipsoid_nbor_cubin.h
|
||||
$(CUDR) -o $@ -c lal_base_ellipsoid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_base_dipole.o: $(ALL_H) lal_base_dipole.h lal_base_dipole.cpp
|
||||
$(CUDR) -o $@ -c lal_base_dipole.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_three.o: $(ALL_H) lal_base_three.h lal_base_three.cpp
|
||||
$(CUDR) -o $@ -c lal_base_three.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_dpd.o: $(ALL_H) lal_base_dpd.h lal_base_dpd.cpp
|
||||
$(CUDR) -o $@ -c lal_base_dpd.cpp
|
||||
|
||||
$(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -Dgrdtyp=float -Dgrdtyp4=float4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_f_cubin.h: $(OBJ_DIR)/pppm_f.cubin
|
||||
$(BIN2C) -c -n pppm_f $(OBJ_DIR)/pppm_f.cubin > $(OBJ_DIR)/pppm_f_cubin.h
|
||||
|
||||
$(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -Dgrdtyp=double -Dgrdtyp4=double4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin
|
||||
$(BIN2C) -c -n pppm_d $(OBJ_DIR)/pppm_d.cubin > $(OBJ_DIR)/pppm_d_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_pppm.o: $(ALL_H) lal_pppm.h lal_pppm.cpp $(OBJ_DIR)/pppm_f_cubin.h $(OBJ_DIR)/pppm_d_cubin.h
|
||||
$(CUDR) -o $@ -c lal_pppm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_pppm_ext.o: $(ALL_H) lal_pppm.h lal_pppm_ext.cpp
|
||||
$(CUDR) -o $@ -c lal_pppm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/ellipsoid_nbor.cubin: lal_ellipsoid_nbor.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_ellipsoid_nbor.cu
|
||||
|
||||
$(OBJ_DIR)/ellipsoid_nbor_cubin.h: $(OBJ_DIR)/ellipsoid_nbor.cubin
|
||||
$(BIN2C) -c -n ellipsoid_nbor $(OBJ_DIR)/ellipsoid_nbor.cubin > $(OBJ_DIR)/ellipsoid_nbor_cubin.h
|
||||
|
||||
$(OBJ_DIR)/gayberne.cubin: lal_gayberne.cu lal_precision.h lal_ellipsoid_extra.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_gayberne.cu
|
||||
|
||||
$(OBJ_DIR)/gayberne_lj.cubin: lal_gayberne_lj.cu lal_precision.h lal_ellipsoid_extra.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_gayberne_lj.cu
|
||||
|
||||
$(OBJ_DIR)/gayberne_cubin.h: $(OBJ_DIR)/gayberne.cubin
|
||||
$(BIN2C) -c -n gayberne $(OBJ_DIR)/gayberne.cubin > $(OBJ_DIR)/gayberne_cubin.h
|
||||
|
||||
$(OBJ_DIR)/gayberne_lj_cubin.h: $(OBJ_DIR)/gayberne_lj.cubin
|
||||
$(BIN2C) -c -n gayberne_lj $(OBJ_DIR)/gayberne_lj.cubin > $(OBJ_DIR)/gayberne_lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_gayberne.o: $(ALL_H) lal_gayberne.h lal_gayberne.cpp $(OBJ_DIR)/gayberne_cubin.h $(OBJ_DIR)/gayberne_lj_cubin.h $(OBJ_DIR)/lal_base_ellipsoid.o
|
||||
$(CUDR) -o $@ -c lal_gayberne.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_gayberne_ext.o: $(ALL_H) $(OBJ_DIR)/lal_gayberne.o lal_gayberne_ext.cpp
|
||||
$(CUDR) -o $@ -c lal_gayberne_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/re_squared.cubin: lal_re_squared.cu lal_precision.h lal_ellipsoid_extra.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_re_squared.cu
|
||||
|
||||
$(OBJ_DIR)/re_squared_lj.cubin: lal_re_squared_lj.cu lal_precision.h lal_ellipsoid_extra.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_re_squared_lj.cu
|
||||
|
||||
$(OBJ_DIR)/re_squared_cubin.h: $(OBJ_DIR)/re_squared.cubin
|
||||
$(BIN2C) -c -n re_squared $(OBJ_DIR)/re_squared.cubin > $(OBJ_DIR)/re_squared_cubin.h
|
||||
|
||||
$(OBJ_DIR)/re_squared_lj_cubin.h: $(OBJ_DIR)/re_squared_lj.cubin
|
||||
$(BIN2C) -c -n re_squared_lj $(OBJ_DIR)/re_squared_lj.cubin > $(OBJ_DIR)/re_squared_lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_re_squared.o: $(ALL_H) lal_re_squared.h lal_re_squared.cpp $(OBJ_DIR)/re_squared_cubin.h $(OBJ_DIR)/re_squared_lj_cubin.h $(OBJ_DIR)/lal_base_ellipsoid.o
|
||||
$(CUDR) -o $@ -c lal_re_squared.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_re_squared_ext.o: $(ALL_H) $(OBJ_DIR)/lal_re_squared.o lal_re_squared_ext.cpp
|
||||
$(CUDR) -o $@ -c lal_re_squared_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj.cubin: lal_lj.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj.cu
|
||||
|
||||
$(OBJ_DIR)/lj_cubin.h: $(OBJ_DIR)/lj.cubin $(OBJ_DIR)/lj.cubin
|
||||
$(BIN2C) -c -n lj $(OBJ_DIR)/lj.cubin > $(OBJ_DIR)/lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp $(OBJ_DIR)/lj_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_tip4p_long.cubin: lal_lj_tip4p_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_tip4p_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_tip4p_long_cubin.h: $(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long.cubin
|
||||
$(BIN2C) -c -n lj_tip4p_long $(OBJ_DIR)/lj_tip4p_long.cubin > $(OBJ_DIR)/lj_tip4p_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp $(OBJ_DIR)/lj_tip4p_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul.cubin: lal_lj_coul.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_coul.cu
|
||||
|
||||
$(OBJ_DIR)/lj_coul_cubin.h: $(OBJ_DIR)/lj_coul.cubin $(OBJ_DIR)/lj_coul.cubin
|
||||
$(BIN2C) -c -n lj_coul $(OBJ_DIR)/lj_coul.cubin > $(OBJ_DIR)/lj_coul_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul.o: $(ALL_H) lal_lj_coul.h lal_lj_coul.cpp $(OBJ_DIR)/lj_coul_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_ext.o: $(ALL_H) lal_lj_coul.h lal_lj_coul_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_class2_long.cubin: lal_lj_class2_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_class2_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_class2_long_cubin.h: $(OBJ_DIR)/lj_class2_long.cubin $(OBJ_DIR)/lj_class2_long.cubin
|
||||
$(BIN2C) -c -n lj_class2_long $(OBJ_DIR)/lj_class2_long.cubin > $(OBJ_DIR)/lj_class2_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_class2_long.o: $(ALL_H) lal_lj_class2_long.h lal_lj_class2_long.cpp $(OBJ_DIR)/lj_class2_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_class2_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_class2_long_ext.o: $(ALL_H) lal_lj_class2_long.h lal_lj_class2_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_class2_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_long.cubin: lal_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/coul_long_cubin.h: $(OBJ_DIR)/coul_long.cubin $(OBJ_DIR)/coul_long.cubin
|
||||
$(BIN2C) -c -n coul_long $(OBJ_DIR)/coul_long.cubin > $(OBJ_DIR)/coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long.o: $(ALL_H) lal_coul_long.h lal_coul_long.cpp $(OBJ_DIR)/coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_ext.o: $(ALL_H) lal_coul_long.h lal_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_long.cubin: lal_lj_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_coul_long_cubin.h: $(OBJ_DIR)/lj_coul_long.cubin $(OBJ_DIR)/lj_coul_long.cubin
|
||||
$(BIN2C) -c -n lj_coul_long $(OBJ_DIR)/lj_coul_long.cubin > $(OBJ_DIR)/lj_coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_long.o: $(ALL_H) lal_lj_coul_long.h lal_lj_coul_long.cpp $(OBJ_DIR)/lj_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_long_ext.o: $(ALL_H) lal_lj_coul_long.h lal_lj_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_dsf.cubin: lal_lj_dsf.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_dsf.cu
|
||||
|
||||
$(OBJ_DIR)/lj_dsf_cubin.h: $(OBJ_DIR)/lj_dsf.cubin $(OBJ_DIR)/lj_dsf.cubin
|
||||
$(BIN2C) -c -n lj_dsf $(OBJ_DIR)/lj_dsf.cubin > $(OBJ_DIR)/lj_dsf_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_dsf.o: $(ALL_H) lal_lj_dsf.h lal_lj_dsf.cpp $(OBJ_DIR)/lj_dsf_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_dsf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_dsf_ext.o: $(ALL_H) lal_lj_dsf.h lal_lj_dsf_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_dsf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/morse.cubin: lal_morse.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_morse.cu
|
||||
|
||||
$(OBJ_DIR)/morse_cubin.h: $(OBJ_DIR)/morse.cubin $(OBJ_DIR)/morse.cubin
|
||||
$(BIN2C) -c -n morse $(OBJ_DIR)/morse.cubin > $(OBJ_DIR)/morse_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_morse.o: $(ALL_H) lal_morse.h lal_morse.cpp $(OBJ_DIR)/morse_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_morse.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_morse_ext.o: $(ALL_H) lal_morse.h lal_morse_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_morse_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/charmm_long.cubin: lal_charmm_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_charmm_long.cu
|
||||
|
||||
$(OBJ_DIR)/charmm_long_cubin.h: $(OBJ_DIR)/charmm_long.cubin $(OBJ_DIR)/charmm_long.cubin
|
||||
$(BIN2C) -c -n charmm_long $(OBJ_DIR)/charmm_long.cubin > $(OBJ_DIR)/charmm_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_charmm_long.o: $(ALL_H) lal_charmm_long.h lal_charmm_long.cpp $(OBJ_DIR)/charmm_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_charmm_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_charmm_long_ext.o: $(ALL_H) lal_charmm_long.h lal_charmm_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_charmm_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj96.cubin: lal_lj96.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj96.cu
|
||||
|
||||
$(OBJ_DIR)/lj96_cubin.h: $(OBJ_DIR)/lj96.cubin $(OBJ_DIR)/lj96.cubin
|
||||
$(BIN2C) -c -n lj96 $(OBJ_DIR)/lj96.cubin > $(OBJ_DIR)/lj96_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj96.o: $(ALL_H) lal_lj96.h lal_lj96.cpp $(OBJ_DIR)/lj96_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj96.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj96_ext.o: $(ALL_H) lal_lj96.h lal_lj96_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj96_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_expand.cubin: lal_lj_expand.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_expand.cu
|
||||
|
||||
$(OBJ_DIR)/lj_expand_cubin.h: $(OBJ_DIR)/lj_expand.cubin $(OBJ_DIR)/lj_expand.cubin
|
||||
$(BIN2C) -c -n lj_expand $(OBJ_DIR)/lj_expand.cubin > $(OBJ_DIR)/lj_expand_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand.o: $(ALL_H) lal_lj_expand.h lal_lj_expand.cpp $(OBJ_DIR)/lj_expand_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_expand.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_ext.o: $(ALL_H) lal_lj_expand.h lal_lj_expand_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_expand_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_sdk.cubin: lal_lj_sdk.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_sdk.cu
|
||||
|
||||
$(OBJ_DIR)/lj_sdk_cubin.h: $(OBJ_DIR)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk.cubin
|
||||
$(BIN2C) -c -n lj_sdk $(OBJ_DIR)/lj_sdk.cubin > $(OBJ_DIR)/lj_sdk_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk.cpp $(OBJ_DIR)/lj_sdk_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_sdk.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_ext.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_sdk_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_sdk_long.cubin: lal_lj_sdk_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_sdk_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_sdk_long_cubin.h: $(OBJ_DIR)/lj_sdk_long.cubin $(OBJ_DIR)/lj_sdk_long.cubin
|
||||
$(BIN2C) -c -n lj_sdk_long $(OBJ_DIR)/lj_sdk_long.cubin > $(OBJ_DIR)/lj_sdk_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_long.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long.cpp $(OBJ_DIR)/lj_sdk_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_sdk_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_long_ext.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_sdk_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/eam.cubin: lal_eam.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_eam.cu
|
||||
|
||||
$(OBJ_DIR)/eam_cubin.h: $(OBJ_DIR)/eam.cubin $(OBJ_DIR)/eam.cubin
|
||||
$(BIN2C) -c -n eam $(OBJ_DIR)/eam.cubin > $(OBJ_DIR)/eam_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_eam.o: $(ALL_H) lal_eam.h lal_eam.cpp $(OBJ_DIR)/eam_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_eam.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_ext.o: $(ALL_H) lal_eam.h lal_eam_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_eam_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_fs_ext.o: $(ALL_H) lal_eam.h lal_eam_fs_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_eam_fs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_alloy_ext.o: $(ALL_H) lal_eam.h lal_eam_alloy_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_eam_alloy_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck.cubin: lal_buck.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_buck.cu
|
||||
|
||||
$(OBJ_DIR)/buck_cubin.h: $(OBJ_DIR)/buck.cubin $(OBJ_DIR)/buck.cubin
|
||||
$(BIN2C) -c -n buck $(OBJ_DIR)/buck.cubin > $(OBJ_DIR)/buck_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_buck.o: $(ALL_H) lal_buck.h lal_buck.cpp $(OBJ_DIR)/buck_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_buck.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_ext.o: $(ALL_H) lal_buck.h lal_buck_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_buck_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck_coul.cubin: lal_buck_coul.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_buck_coul.cu
|
||||
|
||||
$(OBJ_DIR)/buck_coul_cubin.h: $(OBJ_DIR)/buck_coul.cubin $(OBJ_DIR)/buck_coul.cubin
|
||||
$(BIN2C) -c -n buck_coul $(OBJ_DIR)/buck_coul.cubin > $(OBJ_DIR)/buck_coul_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul.o: $(ALL_H) lal_buck_coul.h lal_buck_coul.cpp $(OBJ_DIR)/buck_coul_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_buck_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_ext.o: $(ALL_H) lal_buck_coul.h lal_buck_coul_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_buck_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck_coul_long.cubin: lal_buck_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_buck_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/buck_coul_long_cubin.h: $(OBJ_DIR)/buck_coul_long.cubin $(OBJ_DIR)/buck_coul_long.cubin
|
||||
$(BIN2C) -c -n buck_coul_long $(OBJ_DIR)/buck_coul_long.cubin > $(OBJ_DIR)/buck_coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_long.o: $(ALL_H) lal_buck_coul_long.h lal_buck_coul_long.cpp $(OBJ_DIR)/buck_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_buck_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_long_ext.o: $(ALL_H) lal_buck_coul_long.h lal_buck_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_buck_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/table.cubin: lal_table.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_table.cu
|
||||
|
||||
$(OBJ_DIR)/table_cubin.h: $(OBJ_DIR)/table.cubin $(OBJ_DIR)/table.cubin
|
||||
$(BIN2C) -c -n table $(OBJ_DIR)/table.cubin > $(OBJ_DIR)/table_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_table.o: $(ALL_H) lal_table.h lal_table.cpp $(OBJ_DIR)/table_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_table.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_table_ext.o: $(ALL_H) lal_table.h lal_table_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_table_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/yukawa.cubin: lal_yukawa.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_yukawa.cu
|
||||
|
||||
$(OBJ_DIR)/yukawa_cubin.h: $(OBJ_DIR)/yukawa.cubin $(OBJ_DIR)/yukawa.cubin
|
||||
$(BIN2C) -c -n yukawa $(OBJ_DIR)/yukawa.cubin > $(OBJ_DIR)/yukawa_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa.o: $(ALL_H) lal_yukawa.h lal_yukawa.cpp $(OBJ_DIR)/yukawa_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_yukawa.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_ext.o: $(ALL_H) lal_yukawa.h lal_yukawa_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_yukawa_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born.cubin: lal_born.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_born.cu
|
||||
|
||||
$(OBJ_DIR)/born_cubin.h: $(OBJ_DIR)/born.cubin $(OBJ_DIR)/born.cubin
|
||||
$(BIN2C) -c -n born $(OBJ_DIR)/born.cubin > $(OBJ_DIR)/born_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born.o: $(ALL_H) lal_born.h lal_born.cpp $(OBJ_DIR)/born_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_born.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_ext.o: $(ALL_H) lal_born.h lal_born_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_born_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf.cubin: lal_born_coul_wolf.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_born_coul_wolf.cu
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf_cubin.h: $(OBJ_DIR)/born_coul_wolf.cubin $(OBJ_DIR)/born_coul_wolf.cubin
|
||||
$(BIN2C) -c -n born_coul_wolf $(OBJ_DIR)/born_coul_wolf.cubin > $(OBJ_DIR)/born_coul_wolf_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf.o: $(ALL_H) lal_born_coul_wolf.h lal_born_coul_wolf.cpp $(OBJ_DIR)/born_coul_wolf_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_born_coul_wolf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_ext.o: $(ALL_H) lal_born_coul_wolf.h lal_born_coul_wolf_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_born_coul_wolf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_long.cubin: lal_born_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_born_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/born_coul_long_cubin.h: $(OBJ_DIR)/born_coul_long.cubin $(OBJ_DIR)/born_coul_long.cubin
|
||||
$(BIN2C) -c -n born_coul_long $(OBJ_DIR)/born_coul_long.cubin > $(OBJ_DIR)/born_coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long.o: $(ALL_H) lal_born_coul_long.h lal_born_coul_long.cpp $(OBJ_DIR)/born_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_born_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_ext.o: $(ALL_H) lal_born_coul_long.h lal_born_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_born_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_lj.cubin: lal_dipole_lj.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_dipole_lj.cu
|
||||
|
||||
$(OBJ_DIR)/dipole_lj_cubin.h: $(OBJ_DIR)/dipole_lj.cubin $(OBJ_DIR)/dipole_lj.cubin
|
||||
$(BIN2C) -c -n dipole_lj $(OBJ_DIR)/dipole_lj.cubin > $(OBJ_DIR)/dipole_lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj.o: $(ALL_H) lal_dipole_lj.h lal_dipole_lj.cpp $(OBJ_DIR)/dipole_lj_cubin.h $(OBJ_DIR)/lal_base_dipole.o
|
||||
$(CUDR) -o $@ -c lal_dipole_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_ext.o: $(ALL_H) lal_dipole_lj.h lal_dipole_lj_ext.cpp lal_base_dipole.h
|
||||
$(CUDR) -o $@ -c lal_dipole_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_lj_sf.cubin: lal_dipole_lj_sf.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_dipole_lj_sf.cu
|
||||
|
||||
$(OBJ_DIR)/dipole_lj_sf_cubin.h: $(OBJ_DIR)/dipole_lj_sf.cubin $(OBJ_DIR)/dipole_lj_sf.cubin
|
||||
$(BIN2C) -c -n dipole_lj_sf $(OBJ_DIR)/dipole_lj_sf.cubin > $(OBJ_DIR)/dipole_lj_sf_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf.o: $(ALL_H) lal_dipole_lj_sf.h lal_dipole_lj_sf.cpp $(OBJ_DIR)/dipole_lj_sf_cubin.h $(OBJ_DIR)/lal_base_dipole.o
|
||||
$(CUDR) -o $@ -c lal_dipole_lj_sf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf_ext.o: $(ALL_H) lal_dipole_lj_sf.h lal_dipole_lj_sf_ext.cpp lal_base_dipole.h
|
||||
$(CUDR) -o $@ -c lal_dipole_lj_sf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/colloid.cubin: lal_colloid.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_colloid.cu
|
||||
|
||||
$(OBJ_DIR)/colloid_cubin.h: $(OBJ_DIR)/colloid.cubin $(OBJ_DIR)/colloid.cubin
|
||||
$(BIN2C) -c -n colloid $(OBJ_DIR)/colloid.cubin > $(OBJ_DIR)/colloid_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_colloid.o: $(ALL_H) lal_colloid.h lal_colloid.cpp $(OBJ_DIR)/colloid_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_colloid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_colloid_ext.o: $(ALL_H) lal_colloid.h lal_colloid_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_colloid_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/gauss.cubin: lal_gauss.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_gauss.cu
|
||||
|
||||
$(OBJ_DIR)/gauss_cubin.h: $(OBJ_DIR)/gauss.cubin $(OBJ_DIR)/gauss.cubin
|
||||
$(BIN2C) -c -n gauss $(OBJ_DIR)/gauss.cubin > $(OBJ_DIR)/gauss_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_gauss.o: $(ALL_H) lal_gauss.h lal_gauss.cpp $(OBJ_DIR)/gauss_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_gauss.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_gauss_ext.o: $(ALL_H) lal_gauss.h lal_gauss_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_gauss_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/yukawa_colloid.cubin: lal_yukawa_colloid.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_yukawa_colloid.cu
|
||||
|
||||
$(OBJ_DIR)/yukawa_colloid_cubin.h: $(OBJ_DIR)/yukawa_colloid.cubin $(OBJ_DIR)/yukawa_colloid.cubin
|
||||
$(BIN2C) -c -n yukawa_colloid $(OBJ_DIR)/yukawa_colloid.cubin > $(OBJ_DIR)/yukawa_colloid_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_colloid.o: $(ALL_H) lal_yukawa_colloid.h lal_yukawa_colloid.cpp $(OBJ_DIR)/yukawa_colloid_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_yukawa_colloid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_colloid_ext.o: $(ALL_H) lal_yukawa_colloid.h lal_yukawa_colloid_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_yukawa_colloid_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_debye.cubin: lal_lj_coul_debye.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_coul_debye.cu
|
||||
|
||||
$(OBJ_DIR)/lj_coul_debye_cubin.h: $(OBJ_DIR)/lj_coul_debye.cubin $(OBJ_DIR)/lj_coul_debye.cubin
|
||||
$(BIN2C) -c -n lj_coul_debye $(OBJ_DIR)/lj_coul_debye.cubin > $(OBJ_DIR)/lj_coul_debye_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_debye.o: $(ALL_H) lal_lj_coul_debye.h lal_lj_coul_debye.cpp $(OBJ_DIR)/lj_coul_debye_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_coul_debye.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_debye_ext.o: $(ALL_H) lal_lj_coul_debye.h lal_lj_coul_debye_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_coul_debye_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_dsf.cubin: lal_coul_dsf.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_coul_dsf.cu
|
||||
|
||||
$(OBJ_DIR)/coul_dsf_cubin.h: $(OBJ_DIR)/coul_dsf.cubin $(OBJ_DIR)/coul_dsf.cubin
|
||||
$(BIN2C) -c -n coul_dsf $(OBJ_DIR)/coul_dsf.cubin > $(OBJ_DIR)/coul_dsf_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul_dsf.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf.cpp $(OBJ_DIR)/coul_dsf_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_coul_dsf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_dsf_ext.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_coul_dsf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/vashishta.cubin: lal_vashishta.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_vashishta.cu
|
||||
|
||||
$(OBJ_DIR)/vashishta_cubin.h: $(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta.cubin
|
||||
$(BIN2C) -c -n vashishta $(OBJ_DIR)/vashishta.cubin > $(OBJ_DIR)/vashishta_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_vashishta.o: $(ALL_H) lal_vashishta.h lal_vashishta.cpp $(OBJ_DIR)/vashishta_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_vashishta.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_vashishta_ext.o: $(ALL_H) lal_vashishta.h lal_vashishta_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_vashishta_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/sw.cubin: lal_sw.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_sw.cu
|
||||
|
||||
$(OBJ_DIR)/sw_cubin.h: $(OBJ_DIR)/sw.cubin $(OBJ_DIR)/sw.cubin
|
||||
$(BIN2C) -c -n sw $(OBJ_DIR)/sw.cubin > $(OBJ_DIR)/sw_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_sw.o: $(ALL_H) lal_sw.h lal_sw.cpp $(OBJ_DIR)/sw_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_sw.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_sw_ext.o: $(ALL_H) lal_sw.h lal_sw_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_sw_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/beck.cubin: lal_beck.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_beck.cu
|
||||
|
||||
$(OBJ_DIR)/beck_cubin.h: $(OBJ_DIR)/beck.cubin $(OBJ_DIR)/beck.cubin
|
||||
$(BIN2C) -c -n beck $(OBJ_DIR)/beck.cubin > $(OBJ_DIR)/beck_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_beck.o: $(ALL_H) lal_beck.h lal_beck.cpp $(OBJ_DIR)/beck_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_beck.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_beck_ext.o: $(ALL_H) lal_beck.h lal_beck_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_beck_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/mie.cubin: lal_mie.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_mie.cu
|
||||
|
||||
$(OBJ_DIR)/mie_cubin.h: $(OBJ_DIR)/mie.cubin $(OBJ_DIR)/mie.cubin
|
||||
$(BIN2C) -c -n mie $(OBJ_DIR)/mie.cubin > $(OBJ_DIR)/mie_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_mie.o: $(ALL_H) lal_mie.h lal_mie.cpp $(OBJ_DIR)/mie_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_mie.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_mie_ext.o: $(ALL_H) lal_mie.h lal_mie_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_mie_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/soft.cubin: lal_soft.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_soft.cu
|
||||
|
||||
$(OBJ_DIR)/soft_cubin.h: $(OBJ_DIR)/soft.cubin $(OBJ_DIR)/soft.cubin
|
||||
$(BIN2C) -c -n soft $(OBJ_DIR)/soft.cubin > $(OBJ_DIR)/soft_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_soft.o: $(ALL_H) lal_soft.h lal_soft.cpp $(OBJ_DIR)/soft_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_soft.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_soft_ext.o: $(ALL_H) lal_soft.h lal_soft_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_soft_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_msm.cubin: lal_lj_coul_msm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_coul_msm.cu
|
||||
|
||||
$(OBJ_DIR)/lj_coul_msm_cubin.h: $(OBJ_DIR)/lj_coul_msm.cubin $(OBJ_DIR)/lj_coul_msm.cubin
|
||||
$(BIN2C) -c -n lj_coul_msm $(OBJ_DIR)/lj_coul_msm.cubin > $(OBJ_DIR)/lj_coul_msm_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_msm.o: $(ALL_H) lal_lj_coul_msm.h lal_lj_coul_msm.cpp $(OBJ_DIR)/lj_coul_msm_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_coul_msm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_msm_ext.o: $(ALL_H) lal_lj_coul_msm.h lal_lj_coul_msm_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_coul_msm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_gromacs.cubin: lal_lj_gromacs.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_gromacs.cu
|
||||
|
||||
$(OBJ_DIR)/lj_gromacs_cubin.h: $(OBJ_DIR)/lj_gromacs.cubin $(OBJ_DIR)/lj_gromacs.cubin
|
||||
$(BIN2C) -c -n lj_gromacs $(OBJ_DIR)/lj_gromacs.cubin > $(OBJ_DIR)/lj_gromacs_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_gromacs.o: $(ALL_H) lal_lj_gromacs.h lal_lj_gromacs.cpp $(OBJ_DIR)/lj_gromacs_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_gromacs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_gromacs_ext.o: $(ALL_H) lal_lj_gromacs.h lal_lj_gromacs_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_gromacs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dpd.cubin: lal_dpd.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_dpd.cu
|
||||
|
||||
$(OBJ_DIR)/dpd_cubin.h: $(OBJ_DIR)/dpd.cubin $(OBJ_DIR)/dpd.cubin
|
||||
$(BIN2C) -c -n dpd $(OBJ_DIR)/dpd.cubin > $(OBJ_DIR)/dpd_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_dpd.o: $(ALL_H) lal_dpd.h lal_dpd.cpp $(OBJ_DIR)/dpd_cubin.h $(OBJ_DIR)/lal_base_dpd.o
|
||||
$(CUDR) -o $@ -c lal_dpd.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dpd_ext.o: $(ALL_H) lal_dpd.h lal_dpd_ext.cpp lal_base_dpd.h
|
||||
$(CUDR) -o $@ -c lal_dpd_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dpd_tstat_ext.o: $(ALL_H) lal_dpd.h lal_dpd_tstat_ext.cpp lal_base_dpd.h
|
||||
$(CUDR) -o $@ -c lal_dpd_tstat_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/ufm.cubin: lal_ufm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_ufm.cu
|
||||
|
||||
$(OBJ_DIR)/ufm_cubin.h: $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm.cubin
|
||||
$(BIN2C) -c -n ufm $(OBJ_DIR)/ufm.cubin > $(OBJ_DIR)/ufm_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_ufm.o: $(ALL_H) lal_ufm.h lal_ufm.cpp $(OBJ_DIR)/ufm_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_ufm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_ufm_ext.o: $(ALL_H) lal_ufm.h lal_ufm_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_ufm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff.cubin: lal_tersoff.cu lal_precision.h lal_tersoff_extra.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_tersoff.cu
|
||||
|
||||
$(OBJ_DIR)/tersoff_cubin.h: $(OBJ_DIR)/tersoff.cubin $(OBJ_DIR)/tersoff.cubin
|
||||
$(BIN2C) -c -n tersoff $(OBJ_DIR)/tersoff.cubin > $(OBJ_DIR)/tersoff_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff.o: $(ALL_H) lal_tersoff.h lal_tersoff.cpp $(OBJ_DIR)/tersoff_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_tersoff.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_ext.o: $(ALL_H) lal_tersoff.h lal_tersoff_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_tersoff_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff_zbl.cubin: lal_tersoff_zbl.cu lal_precision.h lal_tersoff_zbl_extra.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_tersoff_zbl.cu
|
||||
|
||||
$(OBJ_DIR)/tersoff_zbl_cubin.h: $(OBJ_DIR)/tersoff_zbl.cubin $(OBJ_DIR)/tersoff_zbl.cubin
|
||||
$(BIN2C) -c -n tersoff_zbl $(OBJ_DIR)/tersoff_zbl.cubin > $(OBJ_DIR)/tersoff_zbl_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_zbl.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl.cpp $(OBJ_DIR)/tersoff_zbl_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_tersoff_zbl.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_zbl_ext.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_tersoff_zbl_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff_mod.cubin: lal_tersoff_mod.cu lal_precision.h lal_tersoff_mod_extra.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_tersoff_mod.cu
|
||||
|
||||
$(OBJ_DIR)/tersoff_mod_cubin.h: $(OBJ_DIR)/tersoff_mod.cubin $(OBJ_DIR)/tersoff_mod.cubin
|
||||
$(BIN2C) -c -n tersoff_mod $(OBJ_DIR)/tersoff_mod.cubin > $(OBJ_DIR)/tersoff_mod_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_mod.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod.cpp $(OBJ_DIR)/tersoff_mod_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_tersoff_mod.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_mod_ext.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_tersoff_mod_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul.cubin: lal_coul.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_coul.cu
|
||||
|
||||
$(OBJ_DIR)/coul_cubin.h: $(OBJ_DIR)/coul.cubin $(OBJ_DIR)/coul.cubin
|
||||
$(BIN2C) -c -n coul $(OBJ_DIR)/coul.cubin > $(OBJ_DIR)/coul_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul.o: $(ALL_H) lal_coul.h lal_coul.cpp $(OBJ_DIR)/coul_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_ext.o: $(ALL_H) lal_coul.h lal_coul_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_debye.cubin: lal_coul_debye.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_coul_debye.cu
|
||||
|
||||
$(OBJ_DIR)/coul_debye_cubin.h: $(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye.cubin
|
||||
$(BIN2C) -c -n coul_debye $(OBJ_DIR)/coul_debye.cubin > $(OBJ_DIR)/coul_debye_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul_debye.o: $(ALL_H) lal_coul_debye.h lal_coul_debye.cpp $(OBJ_DIR)/coul_debye_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_coul_debye.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_debye_ext.o: $(ALL_H) lal_coul_debye.h lal_coul_debye_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_coul_debye_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/zbl.cubin: lal_zbl.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_zbl.cu
|
||||
|
||||
$(OBJ_DIR)/zbl_cubin.h: $(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl.cubin
|
||||
$(BIN2C) -c -n zbl $(OBJ_DIR)/zbl.cubin > $(OBJ_DIR)/zbl_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_zbl.o: $(ALL_H) lal_zbl.h lal_zbl.cpp $(OBJ_DIR)/zbl_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_zbl.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_zbl_ext.o: $(ALL_H) lal_zbl.h lal_zbl_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_zbl_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_cubic.cubin: lal_lj_cubic.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_cubic.cu
|
||||
|
||||
$(OBJ_DIR)/lj_cubic_cubin.h: $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic.cubin
|
||||
$(BIN2C) -c -n lj_cubic $(OBJ_DIR)/lj_cubic.cubin > $(OBJ_DIR)/lj_cubic_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_cubic.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic.cpp $(OBJ_DIR)/lj_cubic_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_cubic.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_cubic_ext.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_cubic_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_long_lj.cubin: lal_dipole_long_lj.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_dipole_long_lj.cu
|
||||
|
||||
$(OBJ_DIR)/dipole_long_lj_cubin.h: $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj.cubin
|
||||
$(BIN2C) -c -n dipole_long_lj $(OBJ_DIR)/dipole_long_lj.cubin > $(OBJ_DIR)/dipole_long_lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_long_lj.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj.cpp $(OBJ_DIR)/dipole_long_lj_cubin.h $(OBJ_DIR)/lal_base_dipole.o
|
||||
$(CUDR) -o $@ -c lal_dipole_long_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_long_lj_ext.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj_ext.cpp lal_base_dipole.h
|
||||
$(CUDR) -o $@ -c lal_dipole_long_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_expand_coul_long.cubin: lal_lj_expand_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_expand_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_expand_coul_long_cubin.h: $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long.cubin
|
||||
$(BIN2C) -c -n lj_expand_coul_long $(OBJ_DIR)/lj_expand_coul_long.cubin > $(OBJ_DIR)/lj_expand_coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long.cpp $(OBJ_DIR)/lj_expand_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_expand_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_coul_long_cs.cu
|
||||
|
||||
$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin
|
||||
$(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o
|
||||
$(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h
|
||||
$(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu
|
||||
|
||||
$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin
|
||||
$(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o
|
||||
$(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h
|
||||
$(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin
|
||||
$(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o
|
||||
$(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h
|
||||
$(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
|
||||
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
|
||||
# build libgpu.a
|
||||
|
||||
$(GPU_LIB): $(OBJS) $(CUDPP)
|
||||
$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# test app for querying device info
|
||||
|
||||
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
|
||||
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
|
||||
|
||||
clean:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CBNS) *.linkinfo
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo
|
||||
|
||||
veryclean: clean
|
||||
-rm -rf *~ *.linkinfo
|
||||
|
||||
cleanlib:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CBNS) *.linkinfo
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUHS) *.linkinfo
|
||||
|
||||
@ -1,157 +1,67 @@
|
||||
CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \
|
||||
$(CUDA_PRECISION)
|
||||
CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \
|
||||
$(CUDPP_OPT)
|
||||
CUDA_LINK = $(CUDA_LIB) -lcudart
|
||||
BIN2C = $(CUDA_HOME)/bin/bin2c
|
||||
|
||||
GPU_LIB = $(LIB_DIR)/libgpu.a
|
||||
|
||||
# Headers for Geryon
|
||||
UCL_H = $(wildcard ./geryon/ucl*.h)
|
||||
NVC_H = $(wildcard ./geryon/nvc*.h) $(UCL_H)
|
||||
NVD_H = $(wildcard ./geryon/nvd*.h) $(UCL_H) lal_preprocessor.h
|
||||
# Headers for Pair Stuff
|
||||
PAIR_H = lal_atom.h lal_answer.h lal_neighbor_shared.h \
|
||||
lal_neighbor.h lal_precision.h lal_device.h \
|
||||
lal_balance.h lal_pppm.h
|
||||
ALL_H = $(NVD_H) $(wildcard ./lal_*.h)
|
||||
|
||||
ALL_H = $(NVD_H) $(PAIR_H)
|
||||
# Source files
|
||||
SRCS := $(wildcard ./lal_*.cpp)
|
||||
OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
|
||||
CUS := $(wildcard lal_*.cu)
|
||||
CUHS := $(filter-out pppm_cubin.h, $(CUS:lal_%.cu=%_cubin.h)) pppm_f_cubin.h pppm_d_cubin.h
|
||||
CUHS := $(addprefix $(OBJ_DIR)/, $(CUHS))
|
||||
|
||||
EXECS = $(BIN_DIR)/nvc_get_devices
|
||||
ifdef CUDPP_OPT
|
||||
CUDPP = $(OBJ_DIR)/cudpp.o $(OBJ_DIR)/cudpp_plan.o \
|
||||
$(OBJ_DIR)/cudpp_maximal_launch.o $(OBJ_DIR)/cudpp_plan_manager.o \
|
||||
$(OBJ_DIR)/radixsort_app.cu_o $(OBJ_DIR)/scan_app.cu_o
|
||||
endif
|
||||
OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
|
||||
$(OBJ_DIR)/lal_neighbor.o $(OBJ_DIR)/lal_neighbor_shared.o \
|
||||
$(OBJ_DIR)/lal_device.o $(OBJ_DIR)/lal_base_atomic.o \
|
||||
$(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_base_ellipsoid.o \
|
||||
$(OBJ_DIR)/lal_base_dipole.o $(OBJ_DIR)/lal_base_three.o \
|
||||
$(OBJ_DIR)/lal_base_dpd.o \
|
||||
$(OBJ_DIR)/lal_pppm.o $(OBJ_DIR)/lal_pppm_ext.o \
|
||||
$(OBJ_DIR)/lal_gayberne.o $(OBJ_DIR)/lal_gayberne_ext.o \
|
||||
$(OBJ_DIR)/lal_re_squared.o $(OBJ_DIR)/lal_re_squared_ext.o \
|
||||
$(OBJ_DIR)/lal_lj.o $(OBJ_DIR)/lal_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_lj96.o $(OBJ_DIR)/lal_lj96_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_expand.o $(OBJ_DIR)/lal_lj_expand_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul.o $(OBJ_DIR)/lal_lj_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_long.o $(OBJ_DIR)/lal_lj_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_dsf.o $(OBJ_DIR)/lal_lj_dsf_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_class2_long.o $(OBJ_DIR)/lal_lj_class2_long_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_long.o $(OBJ_DIR)/lal_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_morse.o $(OBJ_DIR)/lal_morse_ext.o \
|
||||
$(OBJ_DIR)/lal_charmm_long.o $(OBJ_DIR)/lal_charmm_long_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_sdk.o $(OBJ_DIR)/lal_lj_sdk_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_sdk_long.o $(OBJ_DIR)/lal_lj_sdk_long_ext.o \
|
||||
$(OBJ_DIR)/lal_eam.o $(OBJ_DIR)/lal_eam_ext.o \
|
||||
$(OBJ_DIR)/lal_eam_fs_ext.o $(OBJ_DIR)/lal_eam_alloy_ext.o \
|
||||
$(OBJ_DIR)/lal_buck.o $(OBJ_DIR)/lal_buck_ext.o \
|
||||
$(OBJ_DIR)/lal_buck_coul.o $(OBJ_DIR)/lal_buck_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_buck_coul_long.o $(OBJ_DIR)/lal_buck_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_table.o $(OBJ_DIR)/lal_table_ext.o \
|
||||
$(OBJ_DIR)/lal_yukawa.o $(OBJ_DIR)/lal_yukawa_ext.o \
|
||||
$(OBJ_DIR)/lal_born.o $(OBJ_DIR)/lal_born_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_wolf.o $(OBJ_DIR)/lal_born_coul_wolf_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_long.o $(OBJ_DIR)/lal_born_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_lj.o $(OBJ_DIR)/lal_dipole_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf.o $(OBJ_DIR)/lal_dipole_lj_sf_ext.o \
|
||||
$(OBJ_DIR)/lal_colloid.o $(OBJ_DIR)/lal_colloid_ext.o \
|
||||
$(OBJ_DIR)/lal_gauss.o $(OBJ_DIR)/lal_gauss_ext.o \
|
||||
$(OBJ_DIR)/lal_yukawa_colloid.o $(OBJ_DIR)/lal_yukawa_colloid_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \
|
||||
$(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \
|
||||
$(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \
|
||||
$(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \
|
||||
$(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \
|
||||
$(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_msm.o $(OBJ_DIR)/lal_lj_coul_msm_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_gromacs.o $(OBJ_DIR)/lal_lj_gromacs_ext.o \
|
||||
$(OBJ_DIR)/lal_dpd.o $(OBJ_DIR)/lal_dpd_ext.o $(OBJ_DIR)/lal_dpd_tstat_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff.o $(OBJ_DIR)/lal_tersoff_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff_zbl.o $(OBJ_DIR)/lal_tersoff_zbl_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff_mod.o $(OBJ_DIR)/lal_tersoff_mod_ext.o \
|
||||
$(OBJ_DIR)/lal_coul.o $(OBJ_DIR)/lal_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \
|
||||
$(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \
|
||||
$(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
|
||||
|
||||
CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
|
||||
$(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \
|
||||
$(OBJ_DIR)/neighbor_cpu.cubin $(OBJ_DIR)/neighbor_cpu_cubin.h \
|
||||
$(OBJ_DIR)/neighbor_gpu.cubin $(OBJ_DIR)/neighbor_gpu_cubin.h \
|
||||
$(OBJ_DIR)/pppm_f.cubin $(OBJ_DIR)/pppm_f_cubin.h \
|
||||
$(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/pppm_d_cubin.h \
|
||||
$(OBJ_DIR)/ellipsoid_nbor.cubin $(OBJ_DIR)/ellipsoid_nbor_cubin.h \
|
||||
$(OBJ_DIR)/gayberne.cubin $(OBJ_DIR)/gayberne_lj.cubin \
|
||||
$(OBJ_DIR)/gayberne_cubin.h $(OBJ_DIR)/gayberne_lj_cubin.h \
|
||||
$(OBJ_DIR)/re_squared.cubin $(OBJ_DIR)/re_squared_lj.cubin \
|
||||
$(OBJ_DIR)/re_squared_cubin.h $(OBJ_DIR)/re_squared_lj_cubin.h \
|
||||
$(OBJ_DIR)/lj.cubin $(OBJ_DIR)/lj_cubin.h \
|
||||
$(OBJ_DIR)/lj96.cubin $(OBJ_DIR)/lj96_cubin.h \
|
||||
$(OBJ_DIR)/lj_expand.cubin $(OBJ_DIR)/lj_expand_cubin.h \
|
||||
$(OBJ_DIR)/lj_coul.cubin $(OBJ_DIR)/lj_coul_cubin.h \
|
||||
$(OBJ_DIR)/lj_coul_long.cubin $(OBJ_DIR)/lj_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/lj_dsf.cubin $(OBJ_DIR)/lj_dsf_cubin.h \
|
||||
$(OBJ_DIR)/lj_class2_long.cubin $(OBJ_DIR)/lj_class2_long_cubin.h \
|
||||
$(OBJ_DIR)/coul_long.cubin $(OBJ_DIR)/coul_long_cubin.h \
|
||||
$(OBJ_DIR)/morse.cubin $(OBJ_DIR)/morse_cubin.h \
|
||||
$(OBJ_DIR)/charmm_long.cubin $(OBJ_DIR)/charmm_long_cubin.h \
|
||||
$(OBJ_DIR)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk_cubin.h \
|
||||
$(OBJ_DIR)/lj_sdk_long.cubin $(OBJ_DIR)/lj_sdk_long_cubin.h \
|
||||
$(OBJ_DIR)/eam.cubin $(OBJ_DIR)/eam_cubin.h \
|
||||
$(OBJ_DIR)/buck.cubin $(OBJ_DIR)/buck_cubin.h \
|
||||
$(OBJ_DIR)/buck_coul_long.cubin $(OBJ_DIR)/buck_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/buck_coul.cubin $(OBJ_DIR)/buck_coul_cubin.h \
|
||||
$(OBJ_DIR)/table.cubin $(OBJ_DIR)/table_cubin.h \
|
||||
$(OBJ_DIR)/yukawa.cubin $(OBJ_DIR)/yukawa_cubin.h \
|
||||
$(OBJ_DIR)/born.cubin $(OBJ_DIR)/born_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_wolf.cubin $(OBJ_DIR)/born_coul_wolf_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_long.cubin $(OBJ_DIR)/born_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/dipole_lj.cubin $(OBJ_DIR)/dipole_lj_cubin.h \
|
||||
$(OBJ_DIR)/dipole_lj_sf.cubin $(OBJ_DIR)/dipole_lj_sf_cubin.h \
|
||||
$(OBJ_DIR)/colloid.cubin $(OBJ_DIR)/colloid_cubin.h \
|
||||
$(OBJ_DIR)/gauss.cubin $(OBJ_DIR)/gauss_cubin.h \
|
||||
$(OBJ_DIR)/yukawa_colloid.cubin $(OBJ_DIR)/yukawa_colloid_cubin.h \
|
||||
$(OBJ_DIR)/lj_coul_debye.cubin $(OBJ_DIR)/lj_coul_debye_cubin.h \
|
||||
$(OBJ_DIR)/coul_dsf.cubin $(OBJ_DIR)/coul_dsf_cubin.h \
|
||||
$(OBJ_DIR)/sw.cubin $(OBJ_DIR)/sw_cubin.h \
|
||||
$(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta_cubin.h \
|
||||
$(OBJ_DIR)/beck.cubin $(OBJ_DIR)/beck_cubin.h \
|
||||
$(OBJ_DIR)/mie.cubin $(OBJ_DIR)/mie_cubin.h \
|
||||
$(OBJ_DIR)/soft.cubin $(OBJ_DIR)/soft_cubin.h \
|
||||
$(OBJ_DIR)/lj_coul_msm.cubin $(OBJ_DIR)/lj_coul_msm_cubin.h \
|
||||
$(OBJ_DIR)/lj_gromacs.cubin $(OBJ_DIR)/lj_gromacs_cubin.h \
|
||||
$(OBJ_DIR)/dpd.cubin $(OBJ_DIR)/dpd_cubin.h \
|
||||
$(OBJ_DIR)/tersoff.cubin $(OBJ_DIR)/tersoff_cubin.h \
|
||||
$(OBJ_DIR)/tersoff_zbl.cubin $(OBJ_DIR)/tersoff_zbl_cubin.h \
|
||||
$(OBJ_DIR)/tersoff_mod.cubin $(OBJ_DIR)/tersoff_mod_cubin.h \
|
||||
$(OBJ_DIR)/coul.cubin $(OBJ_DIR)/coul_cubin.h \
|
||||
$(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye_cubin.h \
|
||||
$(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl_cubin.h \
|
||||
$(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \
|
||||
$(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \
|
||||
$(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \
|
||||
$(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h \
|
||||
$(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long_cubin.h
|
||||
# targets
|
||||
|
||||
all: $(OBJ_DIR) $(GPU_LIB) $(EXECS)
|
||||
GPU_LIB = $(LIB_DIR)/libgpu.a
|
||||
|
||||
EXECS = $(BIN_DIR)/nvc_get_devices
|
||||
|
||||
all: $(OBJ_DIR) $(CUHS) $(GPU_LIB) $(EXECS)
|
||||
|
||||
$(OBJ_DIR):
|
||||
mkdir -p $@
|
||||
|
||||
# Compilers and linkers
|
||||
|
||||
CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \
|
||||
$(CUDA_PRECISION)
|
||||
CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \
|
||||
$(CUDPP_OPT)
|
||||
CUDA_LINK = $(CUDA_LIB) -lcudart
|
||||
|
||||
BIN2C = $(CUDA_HOME)/bin/bin2c
|
||||
|
||||
# device code compilation
|
||||
|
||||
$(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=float -Dgrdtyp4=float4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_f_cubin.h: $(OBJ_DIR)/pppm_f.cubin
|
||||
$(BIN2C) -c -n pppm_f $(OBJ_DIR)/pppm_f.cubin > $(OBJ_DIR)/pppm_f_cubin.h
|
||||
|
||||
$(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=double -Dgrdtyp4=double4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin
|
||||
$(BIN2C) -c -n pppm_d $(OBJ_DIR)/pppm_d.cubin > $(OBJ_DIR)/pppm_d_cubin.h
|
||||
|
||||
$(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H)
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu
|
||||
$(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@
|
||||
@rm $(OBJ_DIR)/$*.cubin
|
||||
|
||||
# host code compilation
|
||||
|
||||
$(OBJ_DIR)/lal_%.o: lal_%.cpp $(CUHS) $(ALL_H)
|
||||
$(CUDR) -o $@ -c $< -I$(OBJ_DIR)
|
||||
|
||||
#ifdef CUDPP_OPT
|
||||
$(OBJ_DIR)/cudpp.o: cudpp_mini/cudpp.cpp
|
||||
$(CUDR) -o $@ -c cudpp_mini/cudpp.cpp -Icudpp_mini
|
||||
|
||||
@ -169,745 +79,24 @@ $(OBJ_DIR)/radixsort_app.cu_o: cudpp_mini/radixsort_app.cu
|
||||
|
||||
$(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
|
||||
$(CUDA) -o $@ -c cudpp_mini/scan_app.cu
|
||||
#endif
|
||||
|
||||
$(OBJ_DIR)/atom.cubin: lal_atom.cu lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_atom.cu
|
||||
|
||||
$(OBJ_DIR)/atom_cubin.h: $(OBJ_DIR)/atom.cubin
|
||||
$(BIN2C) -c -n atom $(OBJ_DIR)/atom.cubin > $(OBJ_DIR)/atom_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_atom.o: lal_atom.cpp lal_atom.h $(NVD_H) $(OBJ_DIR)/atom_cubin.h
|
||||
$(CUDR) -o $@ -c lal_atom.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_ans.o: lal_answer.cpp lal_answer.h $(NVD_H)
|
||||
$(CUDR) -o $@ -c lal_answer.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/neighbor_cpu.cubin: lal_neighbor_cpu.cu lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_neighbor_cpu.cu
|
||||
|
||||
$(OBJ_DIR)/neighbor_cpu_cubin.h: $(OBJ_DIR)/neighbor_cpu.cubin
|
||||
$(BIN2C) -c -n neighbor_cpu $(OBJ_DIR)/neighbor_cpu.cubin > $(OBJ_DIR)/neighbor_cpu_cubin.h
|
||||
|
||||
$(OBJ_DIR)/neighbor_gpu.cubin: lal_neighbor_gpu.cu lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_neighbor_gpu.cu
|
||||
|
||||
$(OBJ_DIR)/neighbor_gpu_cubin.h: $(OBJ_DIR)/neighbor_gpu.cubin
|
||||
$(BIN2C) -c -n neighbor_gpu $(OBJ_DIR)/neighbor_gpu.cubin > $(OBJ_DIR)/neighbor_gpu_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_neighbor_shared.o: lal_neighbor_shared.cpp lal_neighbor_shared.h $(OBJ_DIR)/neighbor_cpu_cubin.h $(OBJ_DIR)/neighbor_gpu_cubin.h $(NVD_H)
|
||||
$(CUDR) -o $@ -c lal_neighbor_shared.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_neighbor.o: lal_neighbor.cpp lal_neighbor.h lal_neighbor_shared.h $(NVD_H)
|
||||
$(CUDR) -o $@ -c lal_neighbor.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/device.cubin: lal_device.cu lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_device.cu
|
||||
|
||||
$(OBJ_DIR)/device_cubin.h: $(OBJ_DIR)/device.cubin
|
||||
$(BIN2C) -c -n device $(OBJ_DIR)/device.cubin > $(OBJ_DIR)/device_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_device.o: lal_device.cpp lal_device.h $(ALL_H) $(OBJ_DIR)/device_cubin.h
|
||||
$(CUDR) -o $@ -c lal_device.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_base_atomic.o: $(ALL_H) lal_base_atomic.h lal_base_atomic.cpp
|
||||
$(CUDR) -o $@ -c lal_base_atomic.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_charge.o: $(ALL_H) lal_base_charge.h lal_base_charge.cpp
|
||||
$(CUDR) -o $@ -c lal_base_charge.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_ellipsoid.o: $(ALL_H) lal_base_ellipsoid.h lal_base_ellipsoid.cpp $(OBJ_DIR)/ellipsoid_nbor_cubin.h
|
||||
$(CUDR) -o $@ -c lal_base_ellipsoid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_base_dipole.o: $(ALL_H) lal_base_dipole.h lal_base_dipole.cpp
|
||||
$(CUDR) -o $@ -c lal_base_dipole.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_three.o: $(ALL_H) lal_base_three.h lal_base_three.cpp
|
||||
$(CUDR) -o $@ -c lal_base_three.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_dpd.o: $(ALL_H) lal_base_dpd.h lal_base_dpd.cpp
|
||||
$(CUDR) -o $@ -c lal_base_dpd.cpp
|
||||
|
||||
$(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=float -Dgrdtyp4=float4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_f_cubin.h: $(OBJ_DIR)/pppm_f.cubin
|
||||
$(BIN2C) -c -n pppm_f $(OBJ_DIR)/pppm_f.cubin > $(OBJ_DIR)/pppm_f_cubin.h
|
||||
|
||||
$(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=double -Dgrdtyp4=double4 -o $@ lal_pppm.cu
|
||||
|
||||
$(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin
|
||||
$(BIN2C) -c -n pppm_d $(OBJ_DIR)/pppm_d.cubin > $(OBJ_DIR)/pppm_d_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_pppm.o: $(ALL_H) lal_pppm.h lal_pppm.cpp $(OBJ_DIR)/pppm_f_cubin.h $(OBJ_DIR)/pppm_d_cubin.h
|
||||
$(CUDR) -o $@ -c lal_pppm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_pppm_ext.o: $(ALL_H) lal_pppm.h lal_pppm_ext.cpp
|
||||
$(CUDR) -o $@ -c lal_pppm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/ellipsoid_nbor.cubin: lal_ellipsoid_nbor.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_ellipsoid_nbor.cu
|
||||
|
||||
$(OBJ_DIR)/ellipsoid_nbor_cubin.h: $(OBJ_DIR)/ellipsoid_nbor.cubin
|
||||
$(BIN2C) -c -n ellipsoid_nbor $(OBJ_DIR)/ellipsoid_nbor.cubin > $(OBJ_DIR)/ellipsoid_nbor_cubin.h
|
||||
|
||||
$(OBJ_DIR)/gayberne.cubin: lal_gayberne.cu lal_precision.h lal_ellipsoid_extra.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_gayberne.cu
|
||||
|
||||
$(OBJ_DIR)/gayberne_lj.cubin: lal_gayberne_lj.cu lal_precision.h lal_ellipsoid_extra.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_gayberne_lj.cu
|
||||
|
||||
$(OBJ_DIR)/gayberne_cubin.h: $(OBJ_DIR)/gayberne.cubin
|
||||
$(BIN2C) -c -n gayberne $(OBJ_DIR)/gayberne.cubin > $(OBJ_DIR)/gayberne_cubin.h
|
||||
|
||||
$(OBJ_DIR)/gayberne_lj_cubin.h: $(OBJ_DIR)/gayberne_lj.cubin
|
||||
$(BIN2C) -c -n gayberne_lj $(OBJ_DIR)/gayberne_lj.cubin > $(OBJ_DIR)/gayberne_lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_gayberne.o: $(ALL_H) lal_gayberne.h lal_gayberne.cpp $(OBJ_DIR)/gayberne_cubin.h $(OBJ_DIR)/gayberne_lj_cubin.h $(OBJ_DIR)/lal_base_ellipsoid.o
|
||||
$(CUDR) -o $@ -c lal_gayberne.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_gayberne_ext.o: $(ALL_H) $(OBJ_DIR)/lal_gayberne.o lal_gayberne_ext.cpp
|
||||
$(CUDR) -o $@ -c lal_gayberne_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/re_squared.cubin: lal_re_squared.cu lal_precision.h lal_ellipsoid_extra.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_re_squared.cu
|
||||
|
||||
$(OBJ_DIR)/re_squared_lj.cubin: lal_re_squared_lj.cu lal_precision.h lal_ellipsoid_extra.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_re_squared_lj.cu
|
||||
|
||||
$(OBJ_DIR)/re_squared_cubin.h: $(OBJ_DIR)/re_squared.cubin
|
||||
$(BIN2C) -c -n re_squared $(OBJ_DIR)/re_squared.cubin > $(OBJ_DIR)/re_squared_cubin.h
|
||||
|
||||
$(OBJ_DIR)/re_squared_lj_cubin.h: $(OBJ_DIR)/re_squared_lj.cubin
|
||||
$(BIN2C) -c -n re_squared_lj $(OBJ_DIR)/re_squared_lj.cubin > $(OBJ_DIR)/re_squared_lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_re_squared.o: $(ALL_H) lal_re_squared.h lal_re_squared.cpp $(OBJ_DIR)/re_squared_cubin.h $(OBJ_DIR)/re_squared_lj_cubin.h $(OBJ_DIR)/lal_base_ellipsoid.o
|
||||
$(CUDR) -o $@ -c lal_re_squared.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_re_squared_ext.o: $(ALL_H) $(OBJ_DIR)/lal_re_squared.o lal_re_squared_ext.cpp
|
||||
$(CUDR) -o $@ -c lal_re_squared_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj.cubin: lal_lj.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj.cu
|
||||
|
||||
$(OBJ_DIR)/lj_cubin.h: $(OBJ_DIR)/lj.cubin $(OBJ_DIR)/lj.cubin
|
||||
$(BIN2C) -c -n lj $(OBJ_DIR)/lj.cubin > $(OBJ_DIR)/lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp $(OBJ_DIR)/lj_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_tip4p_long.cubin: lal_lj_tip4p_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_tip4p_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_tip4p_long_cubin.h: $(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long.cubin
|
||||
$(BIN2C) -c -n lj_tip4p_long $(OBJ_DIR)/lj_tip4p_long.cubin > $(OBJ_DIR)/lj_tip4p_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp $(OBJ_DIR)/lj_tip4p_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul.cubin: lal_lj_coul.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_coul.cu
|
||||
|
||||
$(OBJ_DIR)/lj_coul_cubin.h: $(OBJ_DIR)/lj_coul.cubin $(OBJ_DIR)/lj_coul.cubin
|
||||
$(BIN2C) -c -n lj_coul $(OBJ_DIR)/lj_coul.cubin > $(OBJ_DIR)/lj_coul_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul.o: $(ALL_H) lal_lj_coul.h lal_lj_coul.cpp $(OBJ_DIR)/lj_coul_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_ext.o: $(ALL_H) lal_lj_coul.h lal_lj_coul_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_class2_long.cubin: lal_lj_class2_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_class2_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_class2_long_cubin.h: $(OBJ_DIR)/lj_class2_long.cubin $(OBJ_DIR)/lj_class2_long.cubin
|
||||
$(BIN2C) -c -n lj_class2_long $(OBJ_DIR)/lj_class2_long.cubin > $(OBJ_DIR)/lj_class2_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_class2_long.o: $(ALL_H) lal_lj_class2_long.h lal_lj_class2_long.cpp $(OBJ_DIR)/lj_class2_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_class2_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_class2_long_ext.o: $(ALL_H) lal_lj_class2_long.h lal_lj_class2_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_class2_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_long.cubin: lal_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/coul_long_cubin.h: $(OBJ_DIR)/coul_long.cubin $(OBJ_DIR)/coul_long.cubin
|
||||
$(BIN2C) -c -n coul_long $(OBJ_DIR)/coul_long.cubin > $(OBJ_DIR)/coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long.o: $(ALL_H) lal_coul_long.h lal_coul_long.cpp $(OBJ_DIR)/coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_ext.o: $(ALL_H) lal_coul_long.h lal_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_long.cubin: lal_lj_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_coul_long_cubin.h: $(OBJ_DIR)/lj_coul_long.cubin $(OBJ_DIR)/lj_coul_long.cubin
|
||||
$(BIN2C) -c -n lj_coul_long $(OBJ_DIR)/lj_coul_long.cubin > $(OBJ_DIR)/lj_coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_long.o: $(ALL_H) lal_lj_coul_long.h lal_lj_coul_long.cpp $(OBJ_DIR)/lj_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_long_ext.o: $(ALL_H) lal_lj_coul_long.h lal_lj_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_dsf.cubin: lal_lj_dsf.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_dsf.cu
|
||||
|
||||
$(OBJ_DIR)/lj_dsf_cubin.h: $(OBJ_DIR)/lj_dsf.cubin $(OBJ_DIR)/lj_dsf.cubin
|
||||
$(BIN2C) -c -n lj_dsf $(OBJ_DIR)/lj_dsf.cubin > $(OBJ_DIR)/lj_dsf_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_dsf.o: $(ALL_H) lal_lj_dsf.h lal_lj_dsf.cpp $(OBJ_DIR)/lj_dsf_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_dsf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_dsf_ext.o: $(ALL_H) lal_lj_dsf.h lal_lj_dsf_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_dsf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/morse.cubin: lal_morse.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_morse.cu
|
||||
|
||||
$(OBJ_DIR)/morse_cubin.h: $(OBJ_DIR)/morse.cubin $(OBJ_DIR)/morse.cubin
|
||||
$(BIN2C) -c -n morse $(OBJ_DIR)/morse.cubin > $(OBJ_DIR)/morse_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_morse.o: $(ALL_H) lal_morse.h lal_morse.cpp $(OBJ_DIR)/morse_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_morse.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_morse_ext.o: $(ALL_H) lal_morse.h lal_morse_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_morse_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/charmm_long.cubin: lal_charmm_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_charmm_long.cu
|
||||
|
||||
$(OBJ_DIR)/charmm_long_cubin.h: $(OBJ_DIR)/charmm_long.cubin $(OBJ_DIR)/charmm_long.cubin
|
||||
$(BIN2C) -c -n charmm_long $(OBJ_DIR)/charmm_long.cubin > $(OBJ_DIR)/charmm_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_charmm_long.o: $(ALL_H) lal_charmm_long.h lal_charmm_long.cpp $(OBJ_DIR)/charmm_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_charmm_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_charmm_long_ext.o: $(ALL_H) lal_charmm_long.h lal_charmm_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_charmm_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj96.cubin: lal_lj96.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj96.cu
|
||||
|
||||
$(OBJ_DIR)/lj96_cubin.h: $(OBJ_DIR)/lj96.cubin $(OBJ_DIR)/lj96.cubin
|
||||
$(BIN2C) -c -n lj96 $(OBJ_DIR)/lj96.cubin > $(OBJ_DIR)/lj96_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj96.o: $(ALL_H) lal_lj96.h lal_lj96.cpp $(OBJ_DIR)/lj96_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj96.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj96_ext.o: $(ALL_H) lal_lj96.h lal_lj96_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj96_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_expand.cubin: lal_lj_expand.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_expand.cu
|
||||
|
||||
$(OBJ_DIR)/lj_expand_cubin.h: $(OBJ_DIR)/lj_expand.cubin $(OBJ_DIR)/lj_expand.cubin
|
||||
$(BIN2C) -c -n lj_expand $(OBJ_DIR)/lj_expand.cubin > $(OBJ_DIR)/lj_expand_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand.o: $(ALL_H) lal_lj_expand.h lal_lj_expand.cpp $(OBJ_DIR)/lj_expand_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_expand.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_ext.o: $(ALL_H) lal_lj_expand.h lal_lj_expand_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_expand_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_sdk.cubin: lal_lj_sdk.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_sdk.cu
|
||||
|
||||
$(OBJ_DIR)/lj_sdk_cubin.h: $(OBJ_DIR)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk.cubin
|
||||
$(BIN2C) -c -n lj_sdk $(OBJ_DIR)/lj_sdk.cubin > $(OBJ_DIR)/lj_sdk_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk.cpp $(OBJ_DIR)/lj_sdk_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_sdk.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_ext.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_sdk_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_sdk_long.cubin: lal_lj_sdk_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_sdk_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_sdk_long_cubin.h: $(OBJ_DIR)/lj_sdk_long.cubin $(OBJ_DIR)/lj_sdk_long.cubin
|
||||
$(BIN2C) -c -n lj_sdk_long $(OBJ_DIR)/lj_sdk_long.cubin > $(OBJ_DIR)/lj_sdk_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_long.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long.cpp $(OBJ_DIR)/lj_sdk_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_sdk_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_long_ext.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_sdk_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/eam.cubin: lal_eam.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_eam.cu
|
||||
|
||||
$(OBJ_DIR)/eam_cubin.h: $(OBJ_DIR)/eam.cubin $(OBJ_DIR)/eam.cubin
|
||||
$(BIN2C) -c -n eam $(OBJ_DIR)/eam.cubin > $(OBJ_DIR)/eam_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_eam.o: $(ALL_H) lal_eam.h lal_eam.cpp $(OBJ_DIR)/eam_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_eam.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_ext.o: $(ALL_H) lal_eam.h lal_eam_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_eam_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_fs_ext.o: $(ALL_H) lal_eam.h lal_eam_fs_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_eam_fs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_alloy_ext.o: $(ALL_H) lal_eam.h lal_eam_alloy_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_eam_alloy_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck.cubin: lal_buck.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_buck.cu
|
||||
|
||||
$(OBJ_DIR)/buck_cubin.h: $(OBJ_DIR)/buck.cubin $(OBJ_DIR)/buck.cubin
|
||||
$(BIN2C) -c -n buck $(OBJ_DIR)/buck.cubin > $(OBJ_DIR)/buck_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_buck.o: $(ALL_H) lal_buck.h lal_buck.cpp $(OBJ_DIR)/buck_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_buck.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_ext.o: $(ALL_H) lal_buck.h lal_buck_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_buck_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck_coul.cubin: lal_buck_coul.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_buck_coul.cu
|
||||
|
||||
$(OBJ_DIR)/buck_coul_cubin.h: $(OBJ_DIR)/buck_coul.cubin $(OBJ_DIR)/buck_coul.cubin
|
||||
$(BIN2C) -c -n buck_coul $(OBJ_DIR)/buck_coul.cubin > $(OBJ_DIR)/buck_coul_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul.o: $(ALL_H) lal_buck_coul.h lal_buck_coul.cpp $(OBJ_DIR)/buck_coul_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_buck_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_ext.o: $(ALL_H) lal_buck_coul.h lal_buck_coul_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_buck_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck_coul_long.cubin: lal_buck_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_buck_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/buck_coul_long_cubin.h: $(OBJ_DIR)/buck_coul_long.cubin $(OBJ_DIR)/buck_coul_long.cubin
|
||||
$(BIN2C) -c -n buck_coul_long $(OBJ_DIR)/buck_coul_long.cubin > $(OBJ_DIR)/buck_coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_long.o: $(ALL_H) lal_buck_coul_long.h lal_buck_coul_long.cpp $(OBJ_DIR)/buck_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_buck_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_long_ext.o: $(ALL_H) lal_buck_coul_long.h lal_buck_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_buck_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/table.cubin: lal_table.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_table.cu
|
||||
|
||||
$(OBJ_DIR)/table_cubin.h: $(OBJ_DIR)/table.cubin $(OBJ_DIR)/table.cubin
|
||||
$(BIN2C) -c -n table $(OBJ_DIR)/table.cubin > $(OBJ_DIR)/table_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_table.o: $(ALL_H) lal_table.h lal_table.cpp $(OBJ_DIR)/table_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_table.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_table_ext.o: $(ALL_H) lal_table.h lal_table_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_table_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/yukawa.cubin: lal_yukawa.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_yukawa.cu
|
||||
|
||||
$(OBJ_DIR)/yukawa_cubin.h: $(OBJ_DIR)/yukawa.cubin $(OBJ_DIR)/yukawa.cubin
|
||||
$(BIN2C) -c -n yukawa $(OBJ_DIR)/yukawa.cubin > $(OBJ_DIR)/yukawa_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa.o: $(ALL_H) lal_yukawa.h lal_yukawa.cpp $(OBJ_DIR)/yukawa_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_yukawa.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_ext.o: $(ALL_H) lal_yukawa.h lal_yukawa_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_yukawa_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born.cubin: lal_born.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born.cu
|
||||
|
||||
$(OBJ_DIR)/born_cubin.h: $(OBJ_DIR)/born.cubin $(OBJ_DIR)/born.cubin
|
||||
$(BIN2C) -c -n born $(OBJ_DIR)/born.cubin > $(OBJ_DIR)/born_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born.o: $(ALL_H) lal_born.h lal_born.cpp $(OBJ_DIR)/born_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_born.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_ext.o: $(ALL_H) lal_born.h lal_born_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_born_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf.cubin: lal_born_coul_wolf.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_wolf.cu
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf_cubin.h: $(OBJ_DIR)/born_coul_wolf.cubin $(OBJ_DIR)/born_coul_wolf.cubin
|
||||
$(BIN2C) -c -n born_coul_wolf $(OBJ_DIR)/born_coul_wolf.cubin > $(OBJ_DIR)/born_coul_wolf_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf.o: $(ALL_H) lal_born_coul_wolf.h lal_born_coul_wolf.cpp $(OBJ_DIR)/born_coul_wolf_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_born_coul_wolf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_ext.o: $(ALL_H) lal_born_coul_wolf.h lal_born_coul_wolf_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_born_coul_wolf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_long.cubin: lal_born_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/born_coul_long_cubin.h: $(OBJ_DIR)/born_coul_long.cubin $(OBJ_DIR)/born_coul_long.cubin
|
||||
$(BIN2C) -c -n born_coul_long $(OBJ_DIR)/born_coul_long.cubin > $(OBJ_DIR)/born_coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long.o: $(ALL_H) lal_born_coul_long.h lal_born_coul_long.cpp $(OBJ_DIR)/born_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_born_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_ext.o: $(ALL_H) lal_born_coul_long.h lal_born_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_born_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_lj.cubin: lal_dipole_lj.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_dipole_lj.cu
|
||||
|
||||
$(OBJ_DIR)/dipole_lj_cubin.h: $(OBJ_DIR)/dipole_lj.cubin $(OBJ_DIR)/dipole_lj.cubin
|
||||
$(BIN2C) -c -n dipole_lj $(OBJ_DIR)/dipole_lj.cubin > $(OBJ_DIR)/dipole_lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj.o: $(ALL_H) lal_dipole_lj.h lal_dipole_lj.cpp $(OBJ_DIR)/dipole_lj_cubin.h $(OBJ_DIR)/lal_base_dipole.o
|
||||
$(CUDR) -o $@ -c lal_dipole_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_ext.o: $(ALL_H) lal_dipole_lj.h lal_dipole_lj_ext.cpp lal_base_dipole.h
|
||||
$(CUDR) -o $@ -c lal_dipole_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_lj_sf.cubin: lal_dipole_lj_sf.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_dipole_lj_sf.cu
|
||||
|
||||
$(OBJ_DIR)/dipole_lj_sf_cubin.h: $(OBJ_DIR)/dipole_lj_sf.cubin $(OBJ_DIR)/dipole_lj_sf.cubin
|
||||
$(BIN2C) -c -n dipole_lj_sf $(OBJ_DIR)/dipole_lj_sf.cubin > $(OBJ_DIR)/dipole_lj_sf_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf.o: $(ALL_H) lal_dipole_lj_sf.h lal_dipole_lj_sf.cpp $(OBJ_DIR)/dipole_lj_sf_cubin.h $(OBJ_DIR)/lal_base_dipole.o
|
||||
$(CUDR) -o $@ -c lal_dipole_lj_sf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf_ext.o: $(ALL_H) lal_dipole_lj_sf.h lal_dipole_lj_sf_ext.cpp lal_base_dipole.h
|
||||
$(CUDR) -o $@ -c lal_dipole_lj_sf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/colloid.cubin: lal_colloid.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_colloid.cu
|
||||
|
||||
$(OBJ_DIR)/colloid_cubin.h: $(OBJ_DIR)/colloid.cubin $(OBJ_DIR)/colloid.cubin
|
||||
$(BIN2C) -c -n colloid $(OBJ_DIR)/colloid.cubin > $(OBJ_DIR)/colloid_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_colloid.o: $(ALL_H) lal_colloid.h lal_colloid.cpp $(OBJ_DIR)/colloid_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_colloid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_colloid_ext.o: $(ALL_H) lal_colloid.h lal_colloid_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_colloid_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/gauss.cubin: lal_gauss.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_gauss.cu
|
||||
|
||||
$(OBJ_DIR)/gauss_cubin.h: $(OBJ_DIR)/gauss.cubin $(OBJ_DIR)/gauss.cubin
|
||||
$(BIN2C) -c -n gauss $(OBJ_DIR)/gauss.cubin > $(OBJ_DIR)/gauss_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_gauss.o: $(ALL_H) lal_gauss.h lal_gauss.cpp $(OBJ_DIR)/gauss_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_gauss.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_gauss_ext.o: $(ALL_H) lal_gauss.h lal_gauss_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_gauss_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/yukawa_colloid.cubin: lal_yukawa_colloid.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_yukawa_colloid.cu
|
||||
|
||||
$(OBJ_DIR)/yukawa_colloid_cubin.h: $(OBJ_DIR)/yukawa_colloid.cubin $(OBJ_DIR)/yukawa_colloid.cubin
|
||||
$(BIN2C) -c -n yukawa_colloid $(OBJ_DIR)/yukawa_colloid.cubin > $(OBJ_DIR)/yukawa_colloid_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_colloid.o: $(ALL_H) lal_yukawa_colloid.h lal_yukawa_colloid.cpp $(OBJ_DIR)/yukawa_colloid_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_yukawa_colloid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_colloid_ext.o: $(ALL_H) lal_yukawa_colloid.h lal_yukawa_colloid_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_yukawa_colloid_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_debye.cubin: lal_lj_coul_debye.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_coul_debye.cu
|
||||
|
||||
$(OBJ_DIR)/lj_coul_debye_cubin.h: $(OBJ_DIR)/lj_coul_debye.cubin $(OBJ_DIR)/lj_coul_debye.cubin
|
||||
$(BIN2C) -c -n lj_coul_debye $(OBJ_DIR)/lj_coul_debye.cubin > $(OBJ_DIR)/lj_coul_debye_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_debye.o: $(ALL_H) lal_lj_coul_debye.h lal_lj_coul_debye.cpp $(OBJ_DIR)/lj_coul_debye_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_coul_debye.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_debye_ext.o: $(ALL_H) lal_lj_coul_debye.h lal_lj_coul_debye_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_coul_debye_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_dsf.cubin: lal_coul_dsf.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_dsf.cu
|
||||
|
||||
$(OBJ_DIR)/coul_dsf_cubin.h: $(OBJ_DIR)/coul_dsf.cubin $(OBJ_DIR)/coul_dsf.cubin
|
||||
$(BIN2C) -c -n coul_dsf $(OBJ_DIR)/coul_dsf.cubin > $(OBJ_DIR)/coul_dsf_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul_dsf.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf.cpp $(OBJ_DIR)/coul_dsf_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_coul_dsf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_dsf_ext.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_coul_dsf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/vashishta.cubin: lal_vashishta.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_vashishta.cu
|
||||
|
||||
$(OBJ_DIR)/vashishta_cubin.h: $(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta.cubin
|
||||
$(BIN2C) -c -n vashishta $(OBJ_DIR)/vashishta.cubin > $(OBJ_DIR)/vashishta_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_vashishta.o: $(ALL_H) lal_vashishta.h lal_vashishta.cpp $(OBJ_DIR)/vashishta_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_vashishta.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_vashishta_ext.o: $(ALL_H) lal_vashishta.h lal_vashishta_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_vashishta_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/sw.cubin: lal_sw.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_sw.cu
|
||||
|
||||
$(OBJ_DIR)/sw_cubin.h: $(OBJ_DIR)/sw.cubin $(OBJ_DIR)/sw.cubin
|
||||
$(BIN2C) -c -n sw $(OBJ_DIR)/sw.cubin > $(OBJ_DIR)/sw_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_sw.o: $(ALL_H) lal_sw.h lal_sw.cpp $(OBJ_DIR)/sw_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_sw.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_sw_ext.o: $(ALL_H) lal_sw.h lal_sw_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_sw_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/beck.cubin: lal_beck.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_beck.cu
|
||||
|
||||
$(OBJ_DIR)/beck_cubin.h: $(OBJ_DIR)/beck.cubin $(OBJ_DIR)/beck.cubin
|
||||
$(BIN2C) -c -n beck $(OBJ_DIR)/beck.cubin > $(OBJ_DIR)/beck_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_beck.o: $(ALL_H) lal_beck.h lal_beck.cpp $(OBJ_DIR)/beck_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_beck.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_beck_ext.o: $(ALL_H) lal_beck.h lal_beck_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_beck_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/mie.cubin: lal_mie.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_mie.cu
|
||||
|
||||
$(OBJ_DIR)/mie_cubin.h: $(OBJ_DIR)/mie.cubin $(OBJ_DIR)/mie.cubin
|
||||
$(BIN2C) -c -n mie $(OBJ_DIR)/mie.cubin > $(OBJ_DIR)/mie_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_mie.o: $(ALL_H) lal_mie.h lal_mie.cpp $(OBJ_DIR)/mie_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_mie.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_mie_ext.o: $(ALL_H) lal_mie.h lal_mie_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_mie_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/soft.cubin: lal_soft.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_soft.cu
|
||||
|
||||
$(OBJ_DIR)/soft_cubin.h: $(OBJ_DIR)/soft.cubin $(OBJ_DIR)/soft.cubin
|
||||
$(BIN2C) -c -n soft $(OBJ_DIR)/soft.cubin > $(OBJ_DIR)/soft_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_soft.o: $(ALL_H) lal_soft.h lal_soft.cpp $(OBJ_DIR)/soft_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_soft.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_soft_ext.o: $(ALL_H) lal_soft.h lal_soft_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_soft_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_msm.cubin: lal_lj_coul_msm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_coul_msm.cu
|
||||
|
||||
$(OBJ_DIR)/lj_coul_msm_cubin.h: $(OBJ_DIR)/lj_coul_msm.cubin $(OBJ_DIR)/lj_coul_msm.cubin
|
||||
$(BIN2C) -c -n lj_coul_msm $(OBJ_DIR)/lj_coul_msm.cubin > $(OBJ_DIR)/lj_coul_msm_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_msm.o: $(ALL_H) lal_lj_coul_msm.h lal_lj_coul_msm.cpp $(OBJ_DIR)/lj_coul_msm_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_coul_msm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_msm_ext.o: $(ALL_H) lal_lj_coul_msm.h lal_lj_coul_msm_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_coul_msm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_gromacs.cubin: lal_lj_gromacs.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_gromacs.cu
|
||||
|
||||
$(OBJ_DIR)/lj_gromacs_cubin.h: $(OBJ_DIR)/lj_gromacs.cubin $(OBJ_DIR)/lj_gromacs.cubin
|
||||
$(BIN2C) -c -n lj_gromacs $(OBJ_DIR)/lj_gromacs.cubin > $(OBJ_DIR)/lj_gromacs_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_gromacs.o: $(ALL_H) lal_lj_gromacs.h lal_lj_gromacs.cpp $(OBJ_DIR)/lj_gromacs_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_gromacs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_gromacs_ext.o: $(ALL_H) lal_lj_gromacs.h lal_lj_gromacs_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_gromacs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dpd.cubin: lal_dpd.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_dpd.cu
|
||||
|
||||
$(OBJ_DIR)/dpd_cubin.h: $(OBJ_DIR)/dpd.cubin $(OBJ_DIR)/dpd.cubin
|
||||
$(BIN2C) -c -n dpd $(OBJ_DIR)/dpd.cubin > $(OBJ_DIR)/dpd_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_dpd.o: $(ALL_H) lal_dpd.h lal_dpd.cpp $(OBJ_DIR)/dpd_cubin.h $(OBJ_DIR)/lal_base_dpd.o
|
||||
$(CUDR) -o $@ -c lal_dpd.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dpd_ext.o: $(ALL_H) lal_dpd.h lal_dpd_ext.cpp lal_base_dpd.h
|
||||
$(CUDR) -o $@ -c lal_dpd_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dpd_tstat_ext.o: $(ALL_H) lal_dpd.h lal_dpd_tstat_ext.cpp lal_base_dpd.h
|
||||
$(CUDR) -o $@ -c lal_dpd_tstat_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/ufm.cubin: lal_ufm.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_ufm.cu
|
||||
|
||||
$(OBJ_DIR)/ufm_cubin.h: $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm.cubin
|
||||
$(BIN2C) -c -n ufm $(OBJ_DIR)/ufm.cubin > $(OBJ_DIR)/ufm_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_ufm.o: $(ALL_H) lal_ufm.h lal_ufm.cpp $(OBJ_DIR)/ufm_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_ufm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_ufm_ext.o: $(ALL_H) lal_ufm.h lal_ufm_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_ufm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff.cubin: lal_tersoff.cu lal_precision.h lal_tersoff_extra.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_tersoff.cu
|
||||
|
||||
$(OBJ_DIR)/tersoff_cubin.h: $(OBJ_DIR)/tersoff.cubin $(OBJ_DIR)/tersoff.cubin
|
||||
$(BIN2C) -c -n tersoff $(OBJ_DIR)/tersoff.cubin > $(OBJ_DIR)/tersoff_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff.o: $(ALL_H) lal_tersoff.h lal_tersoff.cpp $(OBJ_DIR)/tersoff_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_tersoff.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_ext.o: $(ALL_H) lal_tersoff.h lal_tersoff_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_tersoff_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff_zbl.cubin: lal_tersoff_zbl.cu lal_precision.h lal_tersoff_zbl_extra.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_tersoff_zbl.cu
|
||||
|
||||
$(OBJ_DIR)/tersoff_zbl_cubin.h: $(OBJ_DIR)/tersoff_zbl.cubin $(OBJ_DIR)/tersoff_zbl.cubin
|
||||
$(BIN2C) -c -n tersoff_zbl $(OBJ_DIR)/tersoff_zbl.cubin > $(OBJ_DIR)/tersoff_zbl_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_zbl.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl.cpp $(OBJ_DIR)/tersoff_zbl_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_tersoff_zbl.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_zbl_ext.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_tersoff_zbl_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff_mod.cubin: lal_tersoff_mod.cu lal_precision.h lal_tersoff_mod_extra.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_tersoff_mod.cu
|
||||
|
||||
$(OBJ_DIR)/tersoff_mod_cubin.h: $(OBJ_DIR)/tersoff_mod.cubin $(OBJ_DIR)/tersoff_mod.cubin
|
||||
$(BIN2C) -c -n tersoff_mod $(OBJ_DIR)/tersoff_mod.cubin > $(OBJ_DIR)/tersoff_mod_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_mod.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod.cpp $(OBJ_DIR)/tersoff_mod_cubin.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(CUDR) -o $@ -c lal_tersoff_mod.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_mod_ext.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod_ext.cpp lal_base_three.h
|
||||
$(CUDR) -o $@ -c lal_tersoff_mod_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul.cubin: lal_coul.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul.cu
|
||||
|
||||
$(OBJ_DIR)/coul_cubin.h: $(OBJ_DIR)/coul.cubin $(OBJ_DIR)/coul.cubin
|
||||
$(BIN2C) -c -n coul $(OBJ_DIR)/coul.cubin > $(OBJ_DIR)/coul_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul.o: $(ALL_H) lal_coul.h lal_coul.cpp $(OBJ_DIR)/coul_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_ext.o: $(ALL_H) lal_coul.h lal_coul_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_debye.cubin: lal_coul_debye.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_debye.cu
|
||||
|
||||
$(OBJ_DIR)/coul_debye_cubin.h: $(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye.cubin
|
||||
$(BIN2C) -c -n coul_debye $(OBJ_DIR)/coul_debye.cubin > $(OBJ_DIR)/coul_debye_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul_debye.o: $(ALL_H) lal_coul_debye.h lal_coul_debye.cpp $(OBJ_DIR)/coul_debye_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_coul_debye.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_debye_ext.o: $(ALL_H) lal_coul_debye.h lal_coul_debye_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_coul_debye_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/zbl.cubin: lal_zbl.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_zbl.cu
|
||||
|
||||
$(OBJ_DIR)/zbl_cubin.h: $(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl.cubin
|
||||
$(BIN2C) -c -n zbl $(OBJ_DIR)/zbl.cubin > $(OBJ_DIR)/zbl_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_zbl.o: $(ALL_H) lal_zbl.h lal_zbl.cpp $(OBJ_DIR)/zbl_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_zbl.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_zbl_ext.o: $(ALL_H) lal_zbl.h lal_zbl_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_zbl_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_cubic.cubin: lal_lj_cubic.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_cubic.cu
|
||||
|
||||
$(OBJ_DIR)/lj_cubic_cubin.h: $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic.cubin
|
||||
$(BIN2C) -c -n lj_cubic $(OBJ_DIR)/lj_cubic.cubin > $(OBJ_DIR)/lj_cubic_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_cubic.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic.cpp $(OBJ_DIR)/lj_cubic_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_cubic.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_cubic_ext.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_cubic_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_long_lj.cubin: lal_dipole_long_lj.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_dipole_long_lj.cu
|
||||
|
||||
$(OBJ_DIR)/dipole_long_lj_cubin.h: $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj.cubin
|
||||
$(BIN2C) -c -n dipole_long_lj $(OBJ_DIR)/dipole_long_lj.cubin > $(OBJ_DIR)/dipole_long_lj_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_long_lj.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj.cpp $(OBJ_DIR)/dipole_long_lj_cubin.h $(OBJ_DIR)/lal_base_dipole.o
|
||||
$(CUDR) -o $@ -c lal_dipole_long_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_long_lj_ext.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj_ext.cpp lal_base_dipole.h
|
||||
$(CUDR) -o $@ -c lal_dipole_long_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_expand_coul_long.cubin: lal_lj_expand_coul_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_expand_coul_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_expand_coul_long_cubin.h: $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long.cubin
|
||||
$(BIN2C) -c -n lj_expand_coul_long $(OBJ_DIR)/lj_expand_coul_long.cubin > $(OBJ_DIR)/lj_expand_coul_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long.cpp $(OBJ_DIR)/lj_expand_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(CUDR) -o $@ -c lal_lj_expand_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h
|
||||
$(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_long_cs.cu
|
||||
|
||||
$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin
|
||||
$(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o
|
||||
$(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h
|
||||
$(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu
|
||||
|
||||
$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin
|
||||
$(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o
|
||||
$(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h
|
||||
$(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin
|
||||
$(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o
|
||||
$(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h
|
||||
$(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
|
||||
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
|
||||
# build libgpu.a
|
||||
|
||||
$(GPU_LIB): $(OBJS) $(CUDPP)
|
||||
$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# test app for querying device info
|
||||
|
||||
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
|
||||
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
|
||||
|
||||
clean:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CBNS) *.linkinfo
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo
|
||||
|
||||
veryclean: clean
|
||||
-rm -rf *~ *.linkinfo
|
||||
|
||||
cleanlib:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CBNS) *.linkinfo
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUHS) *.linkinfo
|
||||
|
||||
@ -1,671 +1,54 @@
|
||||
OCL = $(OCL_CPP) $(OCL_PREC) $(OCL_TUNE) -DUSE_OPENCL
|
||||
OCL_LIB = $(LIB_DIR)/libgpu.a
|
||||
# Headers for Geryon
|
||||
UCL_H = $(wildcard ./geryon/ucl*.h)
|
||||
OCL_H = $(wildcard ./geryon/ocl*.h) $(UCL_H)
|
||||
# Headers for Pair Stuff
|
||||
PAIR_H = lal_atom.h lal_answer.h lal_neighbor_shared.h \
|
||||
lal_neighbor.h lal_precision.h lal_device.h \
|
||||
lal_balance.h lal_pppm.h
|
||||
# Headers for Preprocessor/Auxiliary Functions
|
||||
OCL_H = $(wildcard ./geryon/ocl*.h) $(UCL_H) lal_preprocessor.h
|
||||
PRE1_H = lal_preprocessor.h lal_aux_fun1.h
|
||||
ALL_H = $(OCL_H) $(wildcard ./lal_*.h)
|
||||
|
||||
ALL_H = $(OCL_H) $(PAIR_H)
|
||||
# Source files
|
||||
SRCS := $(wildcard ./lal_*.cpp)
|
||||
OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
|
||||
CUS := $(wildcard lal_*.cu)
|
||||
KERS := $(subst ./,$(OBJ_DIR)/,$(CUS:lal_%.cu=%_cl.h))
|
||||
KERS := $(addprefix $(OBJ_DIR)/, $(KERS))
|
||||
|
||||
# targets
|
||||
|
||||
GPU_LIB = $(LIB_DIR)/libgpu.a
|
||||
|
||||
EXECS = $(BIN_DIR)/ocl_get_devices
|
||||
OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \
|
||||
$(OBJ_DIR)/lal_neighbor_shared.o $(OBJ_DIR)/lal_neighbor.o \
|
||||
$(OBJ_DIR)/lal_device.o $(OBJ_DIR)/lal_base_atomic.o \
|
||||
$(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_base_ellipsoid.o \
|
||||
$(OBJ_DIR)/lal_base_dipole.o $(OBJ_DIR)/lal_base_three.o \
|
||||
$(OBJ_DIR)/lal_base_dpd.o \
|
||||
$(OBJ_DIR)/lal_pppm.o $(OBJ_DIR)/lal_pppm_ext.o \
|
||||
$(OBJ_DIR)/lal_gayberne.o $(OBJ_DIR)/lal_gayberne_ext.o \
|
||||
$(OBJ_DIR)/lal_re_squared.o $(OBJ_DIR)/lal_re_squared_ext.o \
|
||||
$(OBJ_DIR)/lal_lj.o $(OBJ_DIR)/lal_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_lj96.o $(OBJ_DIR)/lal_lj96_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_expand.o $(OBJ_DIR)/lal_lj_expand_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul.o $(OBJ_DIR)/lal_lj_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_long.o $(OBJ_DIR)/lal_lj_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_dsf.o $(OBJ_DIR)/lal_lj_dsf_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_class2_long.o $(OBJ_DIR)/lal_lj_class2_long_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_long.o $(OBJ_DIR)/lal_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_morse.o $(OBJ_DIR)/lal_morse_ext.o \
|
||||
$(OBJ_DIR)/lal_charmm_long.o $(OBJ_DIR)/lal_charmm_long_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_sdk.o $(OBJ_DIR)/lal_lj_sdk_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_sdk_long.o $(OBJ_DIR)/lal_lj_sdk_long_ext.o \
|
||||
$(OBJ_DIR)/lal_eam.o $(OBJ_DIR)/lal_eam_ext.o \
|
||||
$(OBJ_DIR)/lal_eam_fs_ext.o $(OBJ_DIR)/lal_eam_alloy_ext.o \
|
||||
$(OBJ_DIR)/lal_buck.o $(OBJ_DIR)/lal_buck_ext.o \
|
||||
$(OBJ_DIR)/lal_buck_coul.o $(OBJ_DIR)/lal_buck_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_buck_coul_long.o $(OBJ_DIR)/lal_buck_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_table.o $(OBJ_DIR)/lal_table_ext.o \
|
||||
$(OBJ_DIR)/lal_yukawa.o $(OBJ_DIR)/lal_yukawa_ext.o \
|
||||
$(OBJ_DIR)/lal_born.o $(OBJ_DIR)/lal_born_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_wolf.o $(OBJ_DIR)/lal_born_coul_wolf_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_long.o $(OBJ_DIR)/lal_born_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_lj.o $(OBJ_DIR)/lal_dipole_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf.o $(OBJ_DIR)/lal_dipole_lj_sf_ext.o \
|
||||
$(OBJ_DIR)/lal_colloid.o $(OBJ_DIR)/lal_colloid_ext.o \
|
||||
$(OBJ_DIR)/lal_gauss.o $(OBJ_DIR)/lal_gauss_ext.o \
|
||||
$(OBJ_DIR)/lal_yukawa_colloid.o $(OBJ_DIR)/lal_yukawa_colloid_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \
|
||||
$(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \
|
||||
$(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \
|
||||
$(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \
|
||||
$(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \
|
||||
$(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_coul_msm.o $(OBJ_DIR)/lal_lj_coul_msm_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_gromacs.o $(OBJ_DIR)/lal_lj_gromacs_ext.o \
|
||||
$(OBJ_DIR)/lal_dpd.o $(OBJ_DIR)/lal_dpd_ext.o $(OBJ_DIR)/lal_dpd_tstat_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff.o $(OBJ_DIR)/lal_tersoff_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff_zbl.o $(OBJ_DIR)/lal_tersoff_zbl_ext.o \
|
||||
$(OBJ_DIR)/lal_tersoff_mod.o $(OBJ_DIR)/lal_tersoff_mod_ext.o \
|
||||
$(OBJ_DIR)/lal_coul.o $(OBJ_DIR)/lal_coul_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \
|
||||
$(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \
|
||||
$(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \
|
||||
$(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
|
||||
|
||||
KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
|
||||
$(OBJ_DIR)/neighbor_cpu_cl.h $(OBJ_DIR)/pppm_cl.h \
|
||||
$(OBJ_DIR)/ellipsoid_nbor_cl.h $(OBJ_DIR)/gayberne_cl.h \
|
||||
$(OBJ_DIR)/gayberne_lj_cl.h $(OBJ_DIR)/re_squared_cl.h \
|
||||
$(OBJ_DIR)/re_squared_lj_cl.h $(OBJ_DIR)/lj_cl.h $(OBJ_DIR)/lj96_cl.h \
|
||||
$(OBJ_DIR)/lj_expand_cl.h $(OBJ_DIR)/lj_coul_cl.h \
|
||||
$(OBJ_DIR)/lj_coul_long_cl.h $(OBJ_DIR)/lj_dsf_cl.h \
|
||||
$(OBJ_DIR)/lj_class2_long_cl.h \
|
||||
$(OBJ_DIR)/coul_long_cl.h $(OBJ_DIR)/morse_cl.h \
|
||||
$(OBJ_DIR)/charmm_long_cl.h $(OBJ_DIR)/lj_sdk_cl.h \
|
||||
$(OBJ_DIR)/lj_sdk_long_cl.h $(OBJ_DIR)/neighbor_gpu_cl.h \
|
||||
$(OBJ_DIR)/eam_cl.h $(OBJ_DIR)/buck_cl.h \
|
||||
$(OBJ_DIR)/buck_coul_cl.h $(OBJ_DIR)/buck_coul_long_cl.h \
|
||||
$(OBJ_DIR)/table_cl.h $(OBJ_DIR)/yukawa_cl.h \
|
||||
$(OBJ_DIR)/born_cl.h $(OBJ_DIR)/born_coul_wolf_cl.h \
|
||||
$(OBJ_DIR)/born_coul_long_cl.h $(OBJ_DIR)/dipole_lj_cl.h \
|
||||
$(OBJ_DIR)/dipole_lj_sf_cl.h $(OBJ_DIR)/colloid_cl.h \
|
||||
$(OBJ_DIR)/gauss_cl.h $(OBJ_DIR)/yukawa_colloid_cl.h \
|
||||
$(OBJ_DIR)/lj_coul_debye_cl.h $(OBJ_DIR)/coul_dsf_cl.h \
|
||||
$(OBJ_DIR)/sw_cl.h $(OBJ_DIR)/beck_cl.h $(OBJ_DIR)/mie_cl.h \
|
||||
$(OBJ_DIR)/soft_cl.h $(OBJ_DIR)/lj_coul_msm_cl.h \
|
||||
$(OBJ_DIR)/lj_gromacs_cl.h $(OBJ_DIR)/dpd_cl.h \
|
||||
$(OBJ_DIR)/lj_gauss_cl.h $(OBJ_DIR)/dzugutov_cl.h \
|
||||
$(OBJ_DIR)/tersoff_cl.h $(OBJ_DIR)/tersoff_zbl_cl.h \
|
||||
$(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/coul_cl.h \
|
||||
$(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/zbl_cl.h \
|
||||
$(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h \
|
||||
$(OBJ_DIR)/ufm_cl.h $(OBJ_DIR)/dipole_long_lj_cl.h \
|
||||
$(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/coul_long_cs_cl.h \
|
||||
$(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h \
|
||||
$(OBJ_DIR)/lj_tip4p_long_cl.h
|
||||
|
||||
|
||||
OCL_EXECS = $(BIN_DIR)/ocl_get_devices
|
||||
|
||||
all: $(OBJ_DIR) $(OCL_LIB) $(EXECS)
|
||||
all: $(OBJ_DIR) $(KERS) $(GPU_LIB) $(EXECS)
|
||||
|
||||
$(OBJ_DIR):
|
||||
mkdir -p $@
|
||||
|
||||
$(OBJ_DIR)/atom_cl.h: lal_atom.cu lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh atom lal_preprocessor.h lal_atom.cu $(OBJ_DIR)/atom_cl.h
|
||||
# Compiler and linker
|
||||
|
||||
$(OBJ_DIR)/lal_atom.o: lal_atom.cpp lal_atom.h $(OCL_H) $(OBJ_DIR)/atom_cl.h
|
||||
$(OCL) -o $@ -c lal_atom.cpp -I$(OBJ_DIR)
|
||||
OCL = $(OCL_CPP) $(OCL_PREC) $(OCL_TUNE) -DUSE_OPENCL
|
||||
|
||||
$(OBJ_DIR)/lal_answer.o: lal_answer.cpp lal_answer.h $(OCL_H)
|
||||
$(OCL) -o $@ -c lal_answer.cpp -I$(OBJ_DIR)
|
||||
# device code compilation
|
||||
|
||||
$(OBJ_DIR)/neighbor_cpu_cl.h: lal_neighbor_cpu.cu lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh neighbor_cpu lal_preprocessor.h lal_neighbor_cpu.cu $(OBJ_DIR)/neighbor_cpu_cl.h
|
||||
$(OBJ_DIR)/%_cl.h: lal_%.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh $* $(PRE1_H) $< $@;
|
||||
|
||||
$(OBJ_DIR)/neighbor_gpu_cl.h: lal_neighbor_gpu.cu lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh neighbor_gpu lal_preprocessor.h lal_neighbor_gpu.cu $(OBJ_DIR)/neighbor_gpu_cl.h
|
||||
# host code compilation
|
||||
|
||||
$(OBJ_DIR)/lal_neighbor_shared.o: lal_neighbor_shared.cpp lal_neighbor_shared.h $(OCL_H) $(OBJ_DIR)/neighbor_cpu_cl.h $(OBJ_DIR)/neighbor_gpu_cl.h
|
||||
$(OCL) -o $@ -c lal_neighbor_shared.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_neighbor.o: lal_neighbor.cpp lal_neighbor.h $(OCL_H) lal_neighbor_shared.h
|
||||
$(OCL) -o $@ -c lal_neighbor.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/device_cl.h: lal_device.cu lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh device lal_preprocessor.h lal_device.cu $(OBJ_DIR)/device_cl.h
|
||||
|
||||
$(OBJ_DIR)/lal_device.o: lal_device.cpp lal_device.h $(ALL_H) $(OBJ_DIR)/device_cl.h
|
||||
$(OCL) -o $@ -c lal_device.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_base_atomic.o: $(OCL_H) lal_base_atomic.h lal_base_atomic.cpp
|
||||
$(OCL) -o $@ -c lal_base_atomic.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_charge.o: $(OCL_H) lal_base_charge.h lal_base_charge.cpp
|
||||
$(OCL) -o $@ -c lal_base_charge.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_ellipsoid.o: $(OCL_H) lal_base_ellipsoid.h lal_base_ellipsoid.cpp $(OBJ_DIR)/ellipsoid_nbor_cl.h
|
||||
$(OCL) -o $@ -c lal_base_ellipsoid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_base_dipole.o: $(OCL_H) lal_base_dipole.h lal_base_dipole.cpp
|
||||
$(OCL) -o $@ -c lal_base_dipole.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_base_three.o: $(OCL_H) lal_base_three.h lal_base_three.cpp
|
||||
$(OCL) -o $@ -c lal_base_three.cpp
|
||||
|
||||
$(OBJ_DIR)/lal_base_dpd.o: $(OCL_H) lal_base_dpd.h lal_base_dpd.cpp
|
||||
$(OCL) -o $@ -c lal_base_dpd.cpp
|
||||
|
||||
$(OBJ_DIR)/pppm_cl.h: lal_pppm.cu lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh pppm lal_preprocessor.h lal_pppm.cu $(OBJ_DIR)/pppm_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_pppm.o: $(ALL_H) lal_pppm.h lal_pppm.cpp $(OBJ_DIR)/pppm_cl.h $(OBJ_DIR)/pppm_cl.h
|
||||
$(OCL) -o $@ -c lal_pppm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_pppm_ext.o: $(ALL_H) lal_pppm.h lal_pppm_ext.cpp
|
||||
$(OCL) -o $@ -c lal_pppm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/ellipsoid_nbor_cl.h: lal_ellipsoid_nbor.cu lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh ellipsoid_nbor lal_preprocessor.h lal_ellipsoid_nbor.cu $(OBJ_DIR)/ellipsoid_nbor_cl.h
|
||||
|
||||
$(OBJ_DIR)/gayberne_cl.h: lal_gayberne.cu lal_ellipsoid_extra.h lal_aux_fun1.h lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh gayberne lal_preprocessor.h lal_aux_fun1.h lal_ellipsoid_extra.h lal_gayberne.cu $(OBJ_DIR)/gayberne_cl.h;
|
||||
|
||||
$(OBJ_DIR)/gayberne_lj_cl.h: lal_gayberne_lj.cu lal_ellipsoid_extra.h lal_aux_fun1.h lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh gayberne_lj lal_preprocessor.h lal_aux_fun1.h lal_ellipsoid_extra.h lal_gayberne_lj.cu $(OBJ_DIR)/gayberne_lj_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_gayberne.o: $(ALL_H) lal_gayberne.h lal_gayberne.cpp $(OBJ_DIR)/gayberne_cl.h $(OBJ_DIR)/gayberne_lj_cl.h $(OBJ_DIR)/lal_base_ellipsoid.o
|
||||
$(OCL) -o $@ -c lal_gayberne.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_gayberne_ext.o: $(ALL_H) $(OBJ_DIR)/lal_gayberne.o lal_gayberne_ext.cpp
|
||||
$(OCL) -o $@ -c lal_gayberne_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/re_squared_cl.h: lal_re_squared.cu lal_ellipsoid_extra.h lal_aux_fun1.h lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh re_squared lal_preprocessor.h lal_aux_fun1.h lal_ellipsoid_extra.h lal_re_squared.cu $(OBJ_DIR)/re_squared_cl.h;
|
||||
|
||||
$(OBJ_DIR)/re_squared_lj_cl.h: lal_re_squared_lj.cu lal_ellipsoid_extra.h lal_aux_fun1.h lal_preprocessor.h
|
||||
$(BSH) ./geryon/file_to_cstr.sh re_squared_lj lal_preprocessor.h lal_aux_fun1.h lal_ellipsoid_extra.h lal_re_squared_lj.cu $(OBJ_DIR)/re_squared_lj_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_re_squared.o: $(ALL_H) lal_re_squared.h lal_re_squared.cpp $(OBJ_DIR)/re_squared_cl.h $(OBJ_DIR)/re_squared_lj_cl.h $(OBJ_DIR)/lal_base_ellipsoid.o
|
||||
$(OCL) -o $@ -c lal_re_squared.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_re_squared_ext.o: $(ALL_H) $(OBJ_DIR)/lal_re_squared.o lal_re_squared_ext.cpp
|
||||
$(OCL) -o $@ -c lal_re_squared_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_cl.h: lal_lj.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj $(PRE1_H) lal_lj.cu $(OBJ_DIR)/lj_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp $(OBJ_DIR)/lj_cl.h $(OBJ_DIR)/lj_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_tip4p_long_cl.h: lal_lj_tip4p_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_tip4p_long $(PRE1_H) lal_lj_tip4p_long.cu $(OBJ_DIR)/lj_tip4p_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp $(OBJ_DIR)/lj_tip4p_long_cl.h $(OBJ_DIR)/lj_tip4p_long_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_cl.h: lal_lj_coul.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_coul $(PRE1_H) lal_lj_coul.cu $(OBJ_DIR)/lj_coul_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul.o: $(ALL_H) lal_lj_coul.h lal_lj_coul.cpp $(OBJ_DIR)/lj_coul_cl.h $(OBJ_DIR)/lj_coul_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_lj_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_ext.o: $(ALL_H) lal_lj_coul.h lal_lj_coul_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_lj_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_long_cl.h: lal_lj_coul_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_coul_long $(PRE1_H) lal_lj_coul_long.cu $(OBJ_DIR)/lj_coul_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_long.o: $(ALL_H) lal_lj_coul_long.h lal_lj_coul_long.cpp $(OBJ_DIR)/lj_coul_long_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_lj_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_long_ext.o: $(ALL_H) lal_lj_coul_long.h lal_lj_coul_long_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_lj_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_dsf_cl.h: lal_lj_dsf.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_dsf $(PRE1_H) lal_lj_dsf.cu $(OBJ_DIR)/lj_dsf_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_dsf.o: $(ALL_H) lal_lj_dsf.h lal_lj_dsf.cpp $(OBJ_DIR)/lj_dsf_cl.h $(OBJ_DIR)/lj_dsf_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_lj_dsf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_dsf_ext.o: $(ALL_H) lal_lj_dsf.h lal_lj_dsf_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_lj_dsf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_class2_long_cl.h: lal_lj_class2_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_class2_long $(PRE1_H) lal_lj_class2_long.cu $(OBJ_DIR)/lj_class2_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_class2_long.o: $(ALL_H) lal_lj_class2_long.h lal_lj_class2_long.cpp $(OBJ_DIR)/lj_class2_long_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_lj_class2_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_class2_long_ext.o: $(ALL_H) lal_lj_class2_long.h lal_lj_class2_long_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_lj_class2_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_long_cl.h: lal_coul_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh coul_long $(PRE1_H) lal_coul_long.cu $(OBJ_DIR)/coul_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long.o: $(ALL_H) lal_coul_long.h lal_coul_long.cpp $(OBJ_DIR)/coul_long_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_ext.o: $(ALL_H) lal_coul_long.h lal_coul_long_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/morse_cl.h: lal_morse.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh morse $(PRE1_H) lal_morse.cu $(OBJ_DIR)/morse_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_morse.o: $(ALL_H) lal_morse.h lal_morse.cpp $(OBJ_DIR)/morse_cl.h $(OBJ_DIR)/morse_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_morse.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_morse_ext.o: $(ALL_H) lal_morse.h lal_morse_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_morse_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/charmm_long_cl.h: lal_charmm_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh charmm_long $(PRE1_H) lal_charmm_long.cu $(OBJ_DIR)/charmm_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_charmm_long.o: $(ALL_H) lal_charmm_long.h lal_charmm_long.cpp $(OBJ_DIR)/charmm_long_cl.h $(OBJ_DIR)/charmm_long_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_charmm_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_charmm_long_ext.o: $(ALL_H) lal_charmm_long.h lal_charmm_long_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_charmm_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj96_cl.h: lal_lj96.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj96 $(PRE1_H) lal_lj96.cu $(OBJ_DIR)/lj96_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj96.o: $(ALL_H) lal_lj96.h lal_lj96.cpp $(OBJ_DIR)/lj96_cl.h $(OBJ_DIR)/lj96_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj96.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj96_ext.o: $(ALL_H) lal_lj96.h lal_lj96_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj96_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_expand_cl.h: lal_lj_expand.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_expand $(PRE1_H) lal_lj_expand.cu $(OBJ_DIR)/lj_expand_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand.o: $(ALL_H) lal_lj_expand.h lal_lj_expand.cpp $(OBJ_DIR)/lj_expand_cl.h $(OBJ_DIR)/lj_expand_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj_expand.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_ext.o: $(ALL_H) lal_lj_expand.h lal_lj_expand_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj_expand_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_sdk_cl.h: lal_lj_sdk.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_sdk $(PRE1_H) lal_lj_sdk.cu $(OBJ_DIR)/lj_sdk_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk.cpp $(OBJ_DIR)/lj_sdk_cl.h $(OBJ_DIR)/lj_sdk_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj_sdk.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_ext.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj_sdk_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_sdk_long_cl.h: lal_lj_sdk_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_sdk_long $(PRE1_H) lal_lj_sdk_long.cu $(OBJ_DIR)/lj_sdk_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_long.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long.cpp $(OBJ_DIR)/lj_sdk_long_cl.h $(OBJ_DIR)/lj_sdk_long_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj_sdk_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_sdk_long_ext.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_lj_sdk_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/eam_cl.h: lal_eam.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh eam $(PRE1_H) lal_eam.cu $(OBJ_DIR)/eam_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_eam.o: $(ALL_H) lal_eam.h lal_eam.cpp $(OBJ_DIR)/eam_cl.h $(OBJ_DIR)/eam_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_eam.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_ext.o: $(ALL_H) lal_eam.h lal_eam_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_eam_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_fs_ext.o: $(ALL_H) lal_eam.h lal_eam_fs_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_eam_fs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_eam_alloy_ext.o: $(ALL_H) lal_eam.h lal_eam_alloy_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_eam_alloy_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck_cl.h: lal_buck.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh buck $(PRE1_H) lal_buck.cu $(OBJ_DIR)/buck_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_buck.o: $(ALL_H) lal_buck.h lal_buck.cpp $(OBJ_DIR)/buck_cl.h $(OBJ_DIR)/buck_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_buck.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_ext.o: $(ALL_H) lal_buck.h lal_buck_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_buck_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck_coul_cl.h: lal_buck_coul.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh buck_coul $(PRE1_H) lal_buck_coul.cu $(OBJ_DIR)/buck_coul_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul.o: $(ALL_H) lal_buck_coul.h lal_buck_coul.cpp $(OBJ_DIR)/buck_coul_cl.h $(OBJ_DIR)/buck_coul_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_buck_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_ext.o: $(ALL_H) lal_buck_coul.h lal_buck_coul_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_buck_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/buck_coul_long_cl.h: lal_buck_coul_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh buck_coul_long $(PRE1_H) lal_buck_coul_long.cu $(OBJ_DIR)/buck_coul_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_long.o: $(ALL_H) lal_buck_coul_long.h lal_buck_coul_long.cpp $(OBJ_DIR)/buck_coul_long_cl.h $(OBJ_DIR)/buck_coul_long_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_buck_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_buck_coul_long_ext.o: $(ALL_H) lal_buck_coul_long.h lal_buck_coul_long_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_buck_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/table_cl.h: lal_table.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh table $(PRE1_H) lal_table.cu $(OBJ_DIR)/table_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_table.o: $(ALL_H) lal_table.h lal_table.cpp $(OBJ_DIR)/table_cl.h $(OBJ_DIR)/table_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_table.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_table_ext.o: $(ALL_H) lal_table.h lal_table_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_table_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/yukawa_cl.h: lal_yukawa.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh yukawa $(PRE1_H) lal_yukawa.cu $(OBJ_DIR)/yukawa_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa.o: $(ALL_H) lal_yukawa.h lal_yukawa.cpp $(OBJ_DIR)/yukawa_cl.h $(OBJ_DIR)/yukawa_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_yukawa.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_ext.o: $(ALL_H) lal_yukawa.h lal_yukawa_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_yukawa_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_cl.h: lal_born.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh born $(PRE1_H) lal_born.cu $(OBJ_DIR)/born_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_born.o: $(ALL_H) lal_born.h lal_born.cpp $(OBJ_DIR)/born_cl.h $(OBJ_DIR)/born_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_born.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_ext.o: $(ALL_H) lal_born.h lal_born_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_born_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf_cl.h: lal_born_coul_wolf.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh born_coul_wolf $(PRE1_H) lal_born_coul_wolf.cu $(OBJ_DIR)/born_coul_wolf_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf.o: $(ALL_H) lal_born_coul_wolf.h lal_born_coul_wolf.cpp $(OBJ_DIR)/born_coul_wolf_cl.h $(OBJ_DIR)/born_coul_wolf_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_born_coul_wolf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_ext.o: $(ALL_H) lal_born_coul_wolf.h lal_born_coul_wolf_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_born_coul_wolf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_long_cl.h: lal_born_coul_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh born_coul_long $(PRE1_H) lal_born_coul_long.cu $(OBJ_DIR)/born_coul_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long.o: $(ALL_H) lal_born_coul_long.h lal_born_coul_long.cpp $(OBJ_DIR)/born_coul_long_cl.h $(OBJ_DIR)/born_coul_long_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_born_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_ext.o: $(ALL_H) lal_born_coul_long.h lal_born_coul_long_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_born_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_lj_cl.h: lal_dipole_lj.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh dipole_lj $(PRE1_H) lal_dipole_lj.cu $(OBJ_DIR)/dipole_lj_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj.o: $(ALL_H) lal_dipole_lj.h lal_dipole_lj.cpp $(OBJ_DIR)/dipole_lj_cl.h $(OBJ_DIR)/dipole_lj_cl.h $(OBJ_DIR)/lal_base_dipole.o
|
||||
$(OCL) -o $@ -c lal_dipole_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_ext.o: $(ALL_H) lal_dipole_lj.h lal_dipole_lj_ext.cpp lal_base_dipole.h
|
||||
$(OCL) -o $@ -c lal_dipole_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_lj_sf_cl.h: lal_dipole_lj_sf.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh dipole_lj_sf $(PRE1_H) lal_dipole_lj_sf.cu $(OBJ_DIR)/dipole_lj_sf_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf.o: $(ALL_H) lal_dipole_lj_sf.h lal_dipole_lj_sf.cpp $(OBJ_DIR)/dipole_lj_sf_cl.h $(OBJ_DIR)/dipole_lj_sf_cl.h $(OBJ_DIR)/lal_base_dipole.o
|
||||
$(OCL) -o $@ -c lal_dipole_lj_sf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_lj_sf_ext.o: $(ALL_H) lal_dipole_lj_sf.h lal_dipole_lj_sf_ext.cpp lal_base_dipole.h
|
||||
$(OCL) -o $@ -c lal_dipole_lj_sf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/colloid_cl.h: lal_colloid.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh colloid $(PRE1_H) lal_colloid.cu $(OBJ_DIR)/colloid_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_colloid.o: $(ALL_H) lal_colloid.h lal_colloid.cpp $(OBJ_DIR)/colloid_cl.h $(OBJ_DIR)/colloid_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_colloid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_colloid_ext.o: $(ALL_H) lal_colloid.h lal_colloid_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_colloid_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/gauss_cl.h: lal_gauss.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh gauss $(PRE1_H) lal_gauss.cu $(OBJ_DIR)/gauss_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_gauss.o: $(ALL_H) lal_gauss.h lal_gauss.cpp $(OBJ_DIR)/gauss_cl.h $(OBJ_DIR)/gauss_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_gauss.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_gauss_ext.o: $(ALL_H) lal_gauss.h lal_gauss_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_gauss_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/yukawa_colloid_cl.h: lal_yukawa_colloid.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh yukawa_colloid $(PRE1_H) lal_yukawa_colloid.cu $(OBJ_DIR)/yukawa_colloid_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_colloid.o: $(ALL_H) lal_yukawa_colloid.h lal_yukawa_colloid.cpp $(OBJ_DIR)/yukawa_colloid_cl.h $(OBJ_DIR)/yukawa_colloid_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_yukawa_colloid.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_yukawa_colloid_ext.o: $(ALL_H) lal_yukawa_colloid.h lal_yukawa_colloid_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_yukawa_colloid_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_debye_cl.h: lal_lj_coul_debye.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_coul_debye $(PRE1_H) lal_lj_coul_debye.cu $(OBJ_DIR)/lj_coul_debye_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_debye.o: $(ALL_H) lal_lj_coul_debye.h lal_lj_coul_debye.cpp $(OBJ_DIR)/lj_coul_debye_cl.h $(OBJ_DIR)/lj_coul_debye_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_lj_coul_debye.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_debye_ext.o: $(ALL_H) lal_lj_coul_debye.h lal_lj_coul_debye_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_lj_coul_debye_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_dsf_cl.h: lal_coul_dsf.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh coul_dsf $(PRE1_H) lal_coul_dsf.cu $(OBJ_DIR)/coul_dsf_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_coul_dsf.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf.cpp $(OBJ_DIR)/coul_dsf_cl.h $(OBJ_DIR)/coul_dsf_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_coul_dsf.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_dsf_ext.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_coul_dsf_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/sw_cl.h: lal_sw.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh sw $(PRE1_H) lal_sw.cu $(OBJ_DIR)/sw_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_sw.o: $(ALL_H) lal_sw.h lal_sw.cpp $(OBJ_DIR)/sw_cl.h $(OBJ_DIR)/sw_cl.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(OCL) -o $@ -c lal_sw.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_sw_ext.o: $(ALL_H) lal_sw.h lal_sw_ext.cpp lal_base_three.h
|
||||
$(OCL) -o $@ -c lal_sw_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/vashishta_cl.h: lal_vashishta.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh vashishta $(PRE1_H) lal_vashishta.cu $(OBJ_DIR)/vashishta_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_vashishta.o: $(ALL_H) lal_vashishta.h lal_vashishta.cpp $(OBJ_DIR)/vashishta_cl.h $(OBJ_DIR)/vashishta_cl.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(OCL) -o $@ -c lal_vashishta.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_vashishta_ext.o: $(ALL_H) lal_vashishta.h lal_vashishta_ext.cpp lal_base_three.h
|
||||
$(OCL) -o $@ -c lal_vashishta_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/beck_cl.h: lal_beck.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh beck $(PRE1_H) lal_beck.cu $(OBJ_DIR)/beck_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_beck.o: $(ALL_H) lal_beck.h lal_beck.cpp $(OBJ_DIR)/beck_cl.h $(OBJ_DIR)/beck_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_beck.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_beck_ext.o: $(ALL_H) lal_beck.h lal_beck_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_beck_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/mie_cl.h: lal_mie.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh mie $(PRE1_H) lal_mie.cu $(OBJ_DIR)/mie_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_mie.o: $(ALL_H) lal_mie.h lal_mie.cpp $(OBJ_DIR)/mie_cl.h $(OBJ_DIR)/mie_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_mie.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_mie_ext.o: $(ALL_H) lal_mie.h lal_mie_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_mie_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/soft_cl.h: lal_soft.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh soft $(PRE1_H) lal_soft.cu $(OBJ_DIR)/soft_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_soft.o: $(ALL_H) lal_soft.h lal_soft.cpp $(OBJ_DIR)/soft_cl.h $(OBJ_DIR)/soft_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_soft.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_soft_ext.o: $(ALL_H) lal_soft.h lal_soft_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_soft_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_msm_cl.h: lal_lj_coul_msm.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_coul_msm $(PRE1_H) lal_lj_coul_msm.cu $(OBJ_DIR)/lj_coul_msm_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_msm.o: $(ALL_H) lal_lj_coul_msm.h lal_lj_coul_msm.cpp $(OBJ_DIR)/lj_coul_msm_cl.h $(OBJ_DIR)/lj_coul_msm_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_lj_coul_msm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_coul_msm_ext.o: $(ALL_H) lal_lj_coul_msm.h lal_lj_coul_msm_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_lj_coul_msm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_gromacs_cl.h: lal_lj_gromacs.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_gromacs $(PRE1_H) lal_lj_gromacs.cu $(OBJ_DIR)/lj_gromacs_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_gromacs.o: $(ALL_H) lal_lj_gromacs.h lal_lj_gromacs.cpp $(OBJ_DIR)/lj_gromacs_cl.h $(OBJ_DIR)/lj_gromacs_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj_gromacs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_gromacs_ext.o: $(ALL_H) lal_lj_gromacs.h lal_lj_gromacs_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj_gromacs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dpd_cl.h: lal_dpd.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh dpd $(PRE1_H) lal_dpd.cu $(OBJ_DIR)/dpd_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_dpd.o: $(ALL_H) lal_dpd.h lal_dpd.cpp $(OBJ_DIR)/dpd_cl.h $(OBJ_DIR)/dpd_cl.h $(OBJ_DIR)/lal_base_dpd.o
|
||||
$(OCL) -o $@ -c lal_dpd.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dpd_ext.o: $(ALL_H) lal_dpd.h lal_dpd_ext.cpp lal_base_dpd.h
|
||||
$(OCL) -o $@ -c lal_dpd_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dpd_tstat_ext.o: $(ALL_H) lal_dpd.h lal_dpd_tstat_ext.cpp lal_base_dpd.h
|
||||
$(OCL) -o $@ -c lal_dpd_tstat_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff_cl.h: lal_tersoff.cu lal_tersoff_extra.h $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh tersoff $(PRE1_H) lal_tersoff_extra.h lal_tersoff.cu $(OBJ_DIR)/tersoff_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff.o: $(ALL_H) lal_tersoff.h lal_tersoff.cpp $(OBJ_DIR)/tersoff_cl.h $(OBJ_DIR)/tersoff_cl.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(OCL) -o $@ -c lal_tersoff.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_ext.o: $(ALL_H) lal_tersoff.h lal_tersoff_ext.cpp lal_base_three.h
|
||||
$(OCL) -o $@ -c lal_tersoff_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff_zbl_cl.h: lal_tersoff_zbl.cu lal_tersoff_zbl_extra.h $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh tersoff_zbl $(PRE1_H) lal_tersoff_zbl_extra.h lal_tersoff_zbl.cu $(OBJ_DIR)/tersoff_zbl_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_zbl.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl.cpp $(OBJ_DIR)/tersoff_zbl_cl.h $(OBJ_DIR)/tersoff_zbl_cl.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(OCL) -o $@ -c lal_tersoff_zbl.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_zbl_ext.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl_ext.cpp lal_base_three.h
|
||||
$(OCL) -o $@ -c lal_tersoff_zbl_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/tersoff_mod_cl.h: lal_tersoff_mod.cu lal_tersoff_mod_extra.h $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh tersoff_mod $(PRE1_H) lal_tersoff_mod_extra.h lal_tersoff_mod.cu $(OBJ_DIR)/tersoff_mod_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_mod.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod.cpp $(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/lal_base_three.o
|
||||
$(OCL) -o $@ -c lal_tersoff_mod.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_tersoff_mod_ext.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod_ext.cpp lal_base_three.h
|
||||
$(OCL) -o $@ -c lal_tersoff_mod_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_cl.h: lal_coul.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh coul $(PRE1_H) lal_coul.cu $(OBJ_DIR)/coul_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_coul.o: $(ALL_H) lal_coul.h lal_coul.cpp $(OBJ_DIR)/coul_cl.h $(OBJ_DIR)/coul_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_coul.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_ext.o: $(ALL_H) lal_coul.h lal_coul_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_coul_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_debye_cl.h: lal_coul_debye.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh coul_debye $(PRE1_H) lal_coul_debye.cu $(OBJ_DIR)/coul_debye_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_coul_debye.o: $(ALL_H) lal_coul_debye.h lal_coul_debye.cpp $(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_coul_debye.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_debye_ext.o: $(ALL_H) lal_coul_debye.h lal_coul_debye_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_coul_debye_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/zbl_cl.h: lal_zbl.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh zbl $(PRE1_H) lal_zbl.cu $(OBJ_DIR)/zbl_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_zbl.o: $(ALL_H) lal_zbl.h lal_zbl.cpp $(OBJ_DIR)/zbl_cl.h $(OBJ_DIR)/zbl_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_zbl.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_zbl_ext.o: $(ALL_H) lal_zbl.h lal_zbl_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_zbl_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_cubic_cl.h: lal_lj_cubic.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_cubic $(PRE1_H) lal_lj_cubic.cu $(OBJ_DIR)/lj_cubic_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_cubic.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic.cpp $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj_cubic.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_cubic_ext.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj_cubic_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/ufm_cl.h: lal_ufm.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh ufm $(PRE1_H) lal_ufm.cu $(OBJ_DIR)/ufm_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_ufm.o: $(ALL_H) lal_ufm.h lal_ufm.cpp $(OBJ_DIR)/ufm_cl.h $(OBJ_DIR)/ufm_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_ufm.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_ufm_ext.o: $(ALL_H) lal_ufm.h lal_ufm_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_ufm_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/dipole_long_lj_cl.h: lal_dipole_long_lj.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh dipole_long_lj $(PRE1_H) lal_dipole_long_lj.cu $(OBJ_DIR)/dipole_long_lj_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_long_lj.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj.cpp $(OBJ_DIR)/dipole_long_lj_cl.h $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_dipole_long_lj.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_dipole_long_lj_ext.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj_ext.cpp lal_base_dipole.h
|
||||
$(OCL) -o $@ -c lal_dipole_long_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_expand_coul_long_cl.h: lal_lj_expand_coul_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_expand_coul_long $(PRE1_H) lal_lj_expand_coul_long.cu $(OBJ_DIR)/lj_expand_coul_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long.cpp $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/lal_base_charge.o
|
||||
$(OCL) -o $@ -c lal_lj_expand_coul_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h
|
||||
$(OCL) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/coul_long_cs_cl.h: lal_coul_long_cs.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh coul_long_cs $(PRE1_H) lal_coul_long_cs.cu $(OBJ_DIR)/coul_long_cs_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cl.h $(OBJ_DIR)/coul_long_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o
|
||||
$(OCL) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h
|
||||
$(OCL) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_long_cs_cl.h: lal_born_coul_long_cs.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh born_coul_long_cs $(PRE1_H) lal_born_coul_long_cs.cu $(OBJ_DIR)/born_coul_long_cs_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o
|
||||
$(OCL) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h
|
||||
$(OCL) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/born_coul_wolf_cs_cl.h: lal_born_coul_wolf_cs.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh born_coul_wolf_cs $(PRE1_H) lal_born_coul_wolf_cs.cu $(OBJ_DIR)/born_coul_wolf_cs_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o
|
||||
$(OCL) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h
|
||||
$(OCL) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR)
|
||||
$(OBJ_DIR)/lal_%.o: lal_%.cpp $(KERS)
|
||||
$(OCL) -o $@ -c $< -I$(OBJ_DIR)
|
||||
|
||||
$(BIN_DIR)/ocl_get_devices: ./geryon/ucl_get_devices.cpp $(OCL_H)
|
||||
$(OCL) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_OPENCL $(OCL_LINK)
|
||||
|
||||
$(OCL_LIB): $(OBJS) $(PTXS)
|
||||
$(AR) -crusv $(OCL_LIB) $(OBJS)
|
||||
$(GPU_LIB): $(OBJS)
|
||||
$(AR) -crusv $(GPU_LIB) $(OBJS)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
opencl: $(OCL_EXECS)
|
||||
|
||||
clean:
|
||||
-rm -rf $(EXECS) $(OCL_EXECS) $(OCL_LIB) $(OBJS) $(KERS) *.linkinfo
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(KERS) *.linkinfo
|
||||
|
||||
veryclean: clean
|
||||
-rm -rf *~ *.linkinfo
|
||||
|
||||
cleanlib:
|
||||
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(KERS) *.linkinfo
|
||||
|
||||
|
||||
@ -783,3 +783,39 @@ double lmp_gpu_forces(double **f, double **tor, double *eatom,
|
||||
double **vatom, double *virial, double &ecoul) {
|
||||
return global_device.fix_gpu(f,tor,eatom,vatom,virial,ecoul);
|
||||
}
|
||||
|
||||
bool lmp_gpu_config(const std::string &category, const std::string &setting)
|
||||
{
|
||||
if (category == "api") {
|
||||
#if defined(USE_OPENCL)
|
||||
return setting == "opencl";
|
||||
#elif defined(USE_HIP)
|
||||
return setting == "hip";
|
||||
#elif defined(USE_CUDA)
|
||||
return setting == "cuda";
|
||||
#endif
|
||||
return false;
|
||||
}
|
||||
if (category == "precision") {
|
||||
if (setting == "single") {
|
||||
#if defined(_SINGLE_SINGLE)
|
||||
return true;
|
||||
#else
|
||||
return false;
|
||||
#endif
|
||||
} else if (setting == "mixed") {
|
||||
#if defined(_SINGLE_DOUBLE)
|
||||
return true;
|
||||
#else
|
||||
return false;
|
||||
#endif
|
||||
} else if (setting == "double") {
|
||||
#if defined(_DOUBLE_DOUBLE)
|
||||
return true;
|
||||
#else
|
||||
return false;
|
||||
#endif
|
||||
} else return false;
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
@ -65,10 +65,15 @@ which activates the OpenMP backend. All of the options controlling device backen
|
||||
|
||||
## Spack
|
||||
An alternative to manually building with the CMake is to use the Spack package manager.
|
||||
To do so, download the `kokkos-spack` git repo and add to the package list:
|
||||
Make sure you have downloaded [Spack](https://github.com/spack/spack).
|
||||
The easiest way to configure the Spack environment is:
|
||||
````bash
|
||||
> spack repo add $path-to-kokkos-spack
|
||||
> source spack/share/spack/setup-env.sh
|
||||
````
|
||||
with other scripts available for other shells.
|
||||
You can display information about how to install packages with:
|
||||
````bash
|
||||
> spack info kokkos
|
||||
A basic installation would be done as:
|
||||
````bash
|
||||
> spack install kokkos
|
||||
@ -178,8 +183,8 @@ Options can be enabled by specifying `-DKokkos_ENABLE_X`.
|
||||
|
||||
## Other Options
|
||||
* Kokkos_CXX_STANDARD
|
||||
* The C++ standard for Kokkos to use: c++11, c++14, c++17, or c++20. This should be given in CMake style as 11, 14, 17, or 20.
|
||||
* STRING Default: 11
|
||||
* The C++ standard for Kokkos to use: c++14, c++17, or c++20. This should be given in CMake style as 14, 17, or 20.
|
||||
* STRING Default: 14
|
||||
|
||||
## Third-party Libraries (TPLs)
|
||||
The following options control enabling TPLs:
|
||||
|
||||
@ -1,5 +1,111 @@
|
||||
# Change Log
|
||||
|
||||
## [3.3.01](https://github.com/kokkos/kokkos/tree/3.3.01) (2021-01-06)
|
||||
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.3.00...3.3.01)
|
||||
|
||||
**Bug Fixes:**
|
||||
- Fix severe performance bug in DualView which added memcpys for sync and modify [\#3693](https://github.com/kokkos/kokkos/issues/#3693)
|
||||
- Fix performance bug in CUDA backend, where the cuda Cache config was not set correct.
|
||||
|
||||
## [3.3.00](https://github.com/kokkos/kokkos/tree/3.3.00) (2020-12-16)
|
||||
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.2.01...3.3.00)
|
||||
|
||||
**Features:**
|
||||
- Require C++14 as minimum C++ standard. C++17 and C++20 are supported too.
|
||||
- HIP backend is nearly feature complete. Kokkos Dynamic Task Graphs are missing.
|
||||
- Major update for OpenMPTarget: many capabilities now work. For details contact us.
|
||||
- Added DPC++/SYCL backend: primary capabilites are working.
|
||||
- Added Kokkos Graph API analogous to CUDA Graphs.
|
||||
- Added parallel_scan support with TeamThreadRange [\#3536](https://github.com/kokkos/kokkos/pull/#3536)
|
||||
- Added Logical Memory Spaces [\#3546](https://github.com/kokkos/kokkos/pull/#3546)
|
||||
- Added initial half precision support [\#3439](https://github.com/kokkos/kokkos/pull/#3439)
|
||||
- Experimental feature: control cuda occupancy [\#3379](https://github.com/kokkos/kokkos/pull/#3379)
|
||||
|
||||
**Implemented enhancements Backends and Archs:**
|
||||
- Add a64fx and fujitsu Compiler support [\#3614](https://github.com/kokkos/kokkos/pull/#3614)
|
||||
- Adding support for AMD gfx908 archictecture [\#3375](https://github.com/kokkos/kokkos/pull/#3375)
|
||||
- SYCL parallel\_for MDRangePolicy [\#3583](https://github.com/kokkos/kokkos/pull/#3583)
|
||||
- SYCL add parallel\_scan [\#3577](https://github.com/kokkos/kokkos/pull/#3577)
|
||||
- SYCL custom reductions [\#3544](https://github.com/kokkos/kokkos/pull/#3544)
|
||||
- SYCL Enable container unit tests [\#3550](https://github.com/kokkos/kokkos/pull/#3550)
|
||||
- SYCL feature level 5 [\#3480](https://github.com/kokkos/kokkos/pull/#3480)
|
||||
- SYCL Feature level 4 (parallel\_for) [\#3474](https://github.com/kokkos/kokkos/pull/#3474)
|
||||
- SYCL feature level 3 [\#3451](https://github.com/kokkos/kokkos/pull/#3451)
|
||||
- SYCL feature level 2 [\#3447](https://github.com/kokkos/kokkos/pull/#3447)
|
||||
- OpenMPTarget: Hierarchial reduction for + operator on scalars [\#3504](https://github.com/kokkos/kokkos/pull/#3504)
|
||||
- OpenMPTarget hierarchical [\#3411](https://github.com/kokkos/kokkos/pull/#3411)
|
||||
- HIP Add Impl::atomic\_[store,load] [\#3440](https://github.com/kokkos/kokkos/pull/#3440)
|
||||
- HIP enable global lock arrays [\#3418](https://github.com/kokkos/kokkos/pull/#3418)
|
||||
- HIP Implement multiple occupancy paths for various HIP kernel launchers [\#3366](https://github.com/kokkos/kokkos/pull/#3366)
|
||||
|
||||
**Implemented enhancements Policies:**
|
||||
- MDRangePolicy: Let it be semiregular [\#3494](https://github.com/kokkos/kokkos/pull/#3494)
|
||||
- MDRangePolicy: Check narrowing conversion in construction [\#3527](https://github.com/kokkos/kokkos/pull/#3527)
|
||||
- MDRangePolicy: CombinedReducers support [\#3395](https://github.com/kokkos/kokkos/pull/#3395)
|
||||
- Kokkos Graph: Interface and Default Implementation [\#3362](https://github.com/kokkos/kokkos/pull/#3362)
|
||||
- Kokkos Graph: add Cuda Graph implementation [\#3369](https://github.com/kokkos/kokkos/pull/#3369)
|
||||
- TeamPolicy: implemented autotuning of team sizes and vector lengths [\#3206](https://github.com/kokkos/kokkos/pull/#3206)
|
||||
- RangePolicy: Initialize all data members in default constructor [\#3509](https://github.com/kokkos/kokkos/pull/#3509)
|
||||
|
||||
**Implemented enhancements BuildSystem:**
|
||||
- Auto-generate core test files for all backends [\#3488](https://github.com/kokkos/kokkos/pull/#3488)
|
||||
- Avoid rewriting test files when calling cmake [\#3548](https://github.com/kokkos/kokkos/pull/#3548)
|
||||
- RULE\_LAUNCH\_COMPILE and RULE\_LAUNCH\_LINK system for nvcc\_wrapper [\#3136](https://github.com/kokkos/kokkos/pull/#3136)
|
||||
- Adding -include as a known argument to nvcc\_wrapper [\#3434](https://github.com/kokkos/kokkos/pull/#3434)
|
||||
- Install hpcbind script [\#3402](https://github.com/kokkos/kokkos/pull/#3402)
|
||||
- cmake/kokkos\_tribits.cmake: add parsing for args [\#3457](https://github.com/kokkos/kokkos/pull/#3457)
|
||||
|
||||
**Implemented enhancements Tools:**
|
||||
- Changed namespacing of Kokkos::Tools::Impl::Impl::tune\_policy [\#3455](https://github.com/kokkos/kokkos/pull/#3455)
|
||||
- Delegate to an impl allocate/deallocate method to allow specifying a SpaceHandle for MemorySpaces [\#3530](https://github.com/kokkos/kokkos/pull/#3530)
|
||||
- Use the Kokkos Profiling interface rather than the Impl interface [\#3518](https://github.com/kokkos/kokkos/pull/#3518)
|
||||
- Runtime option for tuning [\#3459](https://github.com/kokkos/kokkos/pull/#3459)
|
||||
- Dual View Tool Events [\#3326](https://github.com/kokkos/kokkos/pull/#3326)
|
||||
|
||||
**Implemented enhancements Other:**
|
||||
- Abort on errors instead of just printing [\#3528](https://github.com/kokkos/kokkos/pull/#3528)
|
||||
- Enable C++14 macros unconditionally [\#3449](https://github.com/kokkos/kokkos/pull/#3449)
|
||||
- Make ViewMapping trivially copyable [\#3436](https://github.com/kokkos/kokkos/pull/#3436)
|
||||
- Rename struct ViewMapping to class [\#3435](https://github.com/kokkos/kokkos/pull/#3435)
|
||||
- Replace enums in Kokkos\_ViewMapping.hpp (removes -Wextra) [\#3422](https://github.com/kokkos/kokkos/pull/#3422)
|
||||
- Use bool for enums representing bools [\#3416](https://github.com/kokkos/kokkos/pull/#3416)
|
||||
- Fence active instead of default execution space instances [\#3388](https://github.com/kokkos/kokkos/pull/#3388)
|
||||
- Refactor parallel\_reduce fence usage [\#3359](https://github.com/kokkos/kokkos/pull/#3359)
|
||||
- Moved Space EBO helpers to Kokkos\_EBO [\#3357](https://github.com/kokkos/kokkos/pull/#3357)
|
||||
- Add remove\_cvref type trait [\#3340](https://github.com/kokkos/kokkos/pull/#3340)
|
||||
- Adding identity type traits and update definition of identity\_t alias [\#3339](https://github.com/kokkos/kokkos/pull/#3339)
|
||||
- Add is\_specialization\_of type trait [\#3338](https://github.com/kokkos/kokkos/pull/#3338)
|
||||
- Make ScratchMemorySpace semi-regular [\#3309](https://github.com/kokkos/kokkos/pull/#3309)
|
||||
- Optimize min/max atomics with early exit on no-op case [\#3265](https://github.com/kokkos/kokkos/pull/#3265)
|
||||
- Refactor Backend Development [\#2941](https://github.com/kokkos/kokkos/pull/#2941)
|
||||
|
||||
**Fixed bugs:**
|
||||
- Fixup MDRangePolicy construction from Kokkos arrays [\#3591](https://github.com/kokkos/kokkos/pull/#3591)
|
||||
- Add atomic functions for unsigned long long using gcc built-in [\#3588](https://github.com/kokkos/kokkos/pull/#3588)
|
||||
- Fixup silent pointless comparison with zero in checked\_narrow\_cast (compiler workaround) [\#3566](https://github.com/kokkos/kokkos/pull/#3566)
|
||||
- Fixes for ROCm 3.9 [\#3565](https://github.com/kokkos/kokkos/pull/#3565)
|
||||
- Fix windows build issues which crept in for the CUDA build [\#3532](https://github.com/kokkos/kokkos/pull/#3532)
|
||||
- HIP Fix atomics of large data types and clean up lock arrays [\#3529](https://github.com/kokkos/kokkos/pull/#3529)
|
||||
- Pthreads fix exception resulting from 0 grain size [\#3510](https://github.com/kokkos/kokkos/pull/#3510)
|
||||
- Fixup do not require atomic operation to be default constructible [\#3503](https://github.com/kokkos/kokkos/pull/#3503)
|
||||
- Fix race condition in HIP backend [\#3467](https://github.com/kokkos/kokkos/pull/#3467)
|
||||
- Replace KOKKOS\_DEBUG with KOKKOS\_ENABLE\_DEBUG [\#3458](https://github.com/kokkos/kokkos/pull/#3458)
|
||||
- Fix multi-stream team scratch space definition for HIP [\#3398](https://github.com/kokkos/kokkos/pull/#3398)
|
||||
- HIP fix template deduction [\#3393](https://github.com/kokkos/kokkos/pull/#3393)
|
||||
- Fix compiling with HIP and C++17 [\#3390](https://github.com/kokkos/kokkos/pull/#3390)
|
||||
- Fix sigFPE in HIP blocksize deduction [\#3378](https://github.com/kokkos/kokkos/pull/#3378)
|
||||
- Type alias change: replace CS with CTS to avoid conflicts with NVSHMEM [\#3348](https://github.com/kokkos/kokkos/pull/#3348)
|
||||
- Clang compilation of CUDA backend on Windows [\#3345](https://github.com/kokkos/kokkos/pull/#3345)
|
||||
- Fix HBW support [\#3343](https://github.com/kokkos/kokkos/pull/#3343)
|
||||
- Added missing fences to unique token [\#3260](https://github.com/kokkos/kokkos/pull/#3260)
|
||||
|
||||
**Incompatibilities:**
|
||||
- Remove unused utilities (forward, move, and expand\_variadic) from Kokkos::Impl [\#3535](https://github.com/kokkos/kokkos/pull/#3535)
|
||||
- Remove unused traits [\#3534](https://github.com/kokkos/kokkos/pull/#3534)
|
||||
- HIP: Remove old HCC code [\#3301](https://github.com/kokkos/kokkos/pull/#3301)
|
||||
- Prepare for deprecation of ViewAllocateWithoutInitializing [\#3264](https://github.com/kokkos/kokkos/pull/#3264)
|
||||
- Remove ROCm backend [\#3148](https://github.com/kokkos/kokkos/pull/#3148)
|
||||
|
||||
## [3.2.01](https://github.com/kokkos/kokkos/tree/3.2.01) (2020-11-17)
|
||||
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.2.00...3.2.01)
|
||||
|
||||
@ -36,37 +142,31 @@
|
||||
- Windows Cuda support [\#3018](https://github.com/kokkos/kokkos/issues/3018)
|
||||
- Pass `-Wext-lambda-captures-this` to NVCC when support for `__host__ __device__` lambda is enabled from CUDA 11 [\#3241](https://github.com/kokkos/kokkos/issues/3241)
|
||||
- Use explicit staging buffer for constant memory kernel launches and cleanup host/device synchronization [\#3234](https://github.com/kokkos/kokkos/issues/3234)
|
||||
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 1: [\#3202](https://github.com/kokkos/kokkos/issues/3202)
|
||||
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 2: [\#3203](https://github.com/kokkos/kokkos/issues/3203)
|
||||
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 3: [\#3196](https://github.com/kokkos/kokkos/issues/3196)
|
||||
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable: [\#3202](https://github.com/kokkos/kokkos/issues/3202) , [\#3203](https://github.com/kokkos/kokkos/issues/3203) , [\#3196](https://github.com/kokkos/kokkos/issues/3196)
|
||||
- Annotations for `DefaultExectutionSpace` and `DefaultHostExectutionSpace` to use in static analysis [\#3189](https://github.com/kokkos/kokkos/issues/3189)
|
||||
- Add documentation on using Spack to install Kokkos and developing packages that depend on Kokkos [\#3187](https://github.com/kokkos/kokkos/issues/3187)
|
||||
- Improve support for nvcc\_wrapper with exotic host compiler [\#3186](https://github.com/kokkos/kokkos/issues/3186)
|
||||
- Add OpenMPTarget backend flags for NVC++ compiler [\#3185](https://github.com/kokkos/kokkos/issues/3185)
|
||||
- Move deep\_copy/create\_mirror\_view on Experimental::OffsetView into Kokkos:: namespace [\#3166](https://github.com/kokkos/kokkos/issues/3166)
|
||||
- Allow for larger block size in HIP [\#3165](https://github.com/kokkos/kokkos/issues/3165)
|
||||
- View: Added names of Views to the different View initialize/free kernels [\#3159](https://github.com/kokkos/kokkos/issues/3159)
|
||||
- Cuda: Caching cudaFunctorAttributes and whether L1/Shmem prefer was set [\#3151](https://github.com/kokkos/kokkos/issues/3151)
|
||||
- BuildSystem: Provide an explicit default CMAKE\_BUILD\_TYPE [\#3131](https://github.com/kokkos/kokkos/issues/3131)
|
||||
- BuildSystem: Improved performance in default configuration by defaulting to Release build [\#3131](https://github.com/kokkos/kokkos/issues/3131)
|
||||
- Cuda: Update CUDA occupancy calculation [\#3124](https://github.com/kokkos/kokkos/issues/3124)
|
||||
- Vector: Adding data() to Vector [\#3123](https://github.com/kokkos/kokkos/issues/3123)
|
||||
- BuildSystem: Add CUDA Ampere configuration support [\#3122](https://github.com/kokkos/kokkos/issues/3122)
|
||||
- General: Apply [[noreturn]] to Kokkos::abort when applicable [\#3106](https://github.com/kokkos/kokkos/issues/3106)
|
||||
- TeamPolicy: Validate storage level argument passed to TeamPolicy::set\_scratch\_size() [\#3098](https://github.com/kokkos/kokkos/issues/3098)
|
||||
- nvcc\_wrapper: send --cudart to nvcc instead of host compiler [\#3092](https://github.com/kokkos/kokkos/issues/3092)
|
||||
- BuildSystem: Make kokkos\_has\_string() function in Makefile.kokkos case insensitive [\#3091](https://github.com/kokkos/kokkos/issues/3091)
|
||||
- Modify KOKKOS\_FUNCTION macro for clang-tidy analysis [\#3087](https://github.com/kokkos/kokkos/issues/3087)
|
||||
- Move allocation profiling to allocate/deallocate calls [\#3084](https://github.com/kokkos/kokkos/issues/3084)
|
||||
- BuildSystem: FATAL\_ERROR when attempting in-source build [\#3082](https://github.com/kokkos/kokkos/issues/3082)
|
||||
- Change enums in ScatterView to types [\#3076](https://github.com/kokkos/kokkos/issues/3076)
|
||||
- HIP: Changes for new compiler/runtime [\#3067](https://github.com/kokkos/kokkos/issues/3067)
|
||||
- Extract and use get\_gpu [\#3061](https://github.com/kokkos/kokkos/issues/3061)
|
||||
- Extract and use get\_gpu [\#3048](https://github.com/kokkos/kokkos/issues/3048)
|
||||
- Extract and use get\_gpu [\#3061](https://github.com/kokkos/kokkos/issues/3061) , [\#3048](https://github.com/kokkos/kokkos/issues/3048)
|
||||
- Add is\_allocated to View-like containers [\#3059](https://github.com/kokkos/kokkos/issues/3059)
|
||||
- Combined reducers for scalar references [\#3052](https://github.com/kokkos/kokkos/issues/3052)
|
||||
- Add configurable capacity for UniqueToken [\#3051](https://github.com/kokkos/kokkos/issues/3051)
|
||||
- Add installation testing [\#3034](https://github.com/kokkos/kokkos/issues/3034)
|
||||
- BuildSystem: Add -expt-relaxed-constexpr flag to nvcc\_wrapper [\#3021](https://github.com/kokkos/kokkos/issues/3021)
|
||||
- HIP: Add UniqueToken [\#3020](https://github.com/kokkos/kokkos/issues/3020)
|
||||
- Autodetect number of devices [\#3013](https://github.com/kokkos/kokkos/issues/3013)
|
||||
|
||||
@ -82,11 +182,13 @@
|
||||
- ScatterView: fix for OpenmpTarget remove inheritance from reducers [\#3162](https://github.com/kokkos/kokkos/issues/3162)
|
||||
- BuildSystem: Set OpenMP flags according to host compiler [\#3127](https://github.com/kokkos/kokkos/issues/3127)
|
||||
- OpenMP: Fix logic for nested omp in partition\_master bug [\#3101](https://github.com/kokkos/kokkos/issues/3101)
|
||||
- nvcc\_wrapper: send --cudart to nvcc instead of host compiler [\#3092](https://github.com/kokkos/kokkos/issues/3092)
|
||||
- BuildSystem: Fixes for Cuda/11 and c++17 [\#3085](https://github.com/kokkos/kokkos/issues/3085)
|
||||
- HIP: Fix print\_configuration [\#3080](https://github.com/kokkos/kokkos/issues/3080)
|
||||
- Conditionally define get\_gpu [\#3072](https://github.com/kokkos/kokkos/issues/3072)
|
||||
- Fix bounds for ranges in random number generator [\#3069](https://github.com/kokkos/kokkos/issues/3069)
|
||||
- Fix Cuda minor arch check [\#3035](https://github.com/kokkos/kokkos/issues/3035)
|
||||
- BuildSystem: Add -expt-relaxed-constexpr flag to nvcc\_wrapper [\#3021](https://github.com/kokkos/kokkos/issues/3021)
|
||||
|
||||
**Incompatibilities:**
|
||||
|
||||
|
||||
@ -111,7 +111,7 @@ ENDIF()
|
||||
|
||||
|
||||
set(Kokkos_VERSION_MAJOR 3)
|
||||
set(Kokkos_VERSION_MINOR 2)
|
||||
set(Kokkos_VERSION_MINOR 3)
|
||||
set(Kokkos_VERSION_PATCH 1)
|
||||
set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}")
|
||||
math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}")
|
||||
@ -139,13 +139,15 @@ ENDIF()
|
||||
# I really wish these were regular variables
|
||||
# but scoping issues can make it difficult
|
||||
GLOBAL_SET(KOKKOS_COMPILE_OPTIONS)
|
||||
GLOBAL_SET(KOKKOS_LINK_OPTIONS)
|
||||
GLOBAL_SET(KOKKOS_LINK_OPTIONS -DKOKKOS_DEPENDENCE)
|
||||
GLOBAL_SET(KOKKOS_CUDA_OPTIONS)
|
||||
GLOBAL_SET(KOKKOS_CUDAFE_OPTIONS)
|
||||
GLOBAL_SET(KOKKOS_XCOMPILER_OPTIONS)
|
||||
# We need to append text here for making sure TPLs
|
||||
# we import are available for an installed Kokkos
|
||||
GLOBAL_SET(KOKKOS_TPL_EXPORTS)
|
||||
# this could probably be scoped to project
|
||||
GLOBAL_SET(KOKKOS_COMPILE_DEFINITIONS KOKKOS_DEPENDENCE)
|
||||
|
||||
# Include a set of Kokkos-specific wrapper functions that
|
||||
# will either call raw CMake or TriBITS
|
||||
@ -191,8 +193,6 @@ ELSE()
|
||||
SET(KOKKOS_IS_SUBDIRECTORY FALSE)
|
||||
ENDIF()
|
||||
|
||||
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
#
|
||||
# A) Forward declare the package so that certain options are also defined for
|
||||
@ -253,9 +253,7 @@ KOKKOS_PROCESS_SUBPACKAGES()
|
||||
KOKKOS_PACKAGE_DEF()
|
||||
KOKKOS_EXCLUDE_AUTOTOOLS_FILES()
|
||||
KOKKOS_PACKAGE_POSTPROCESS()
|
||||
|
||||
#We are ready to configure the header
|
||||
CONFIGURE_FILE(cmake/KokkosCore_config.h.in KokkosCore_config.h @ONLY)
|
||||
KOKKOS_CONFIGURE_CORE()
|
||||
|
||||
IF (NOT KOKKOS_HAS_TRILINOS AND NOT Kokkos_INSTALL_TESTING)
|
||||
ADD_LIBRARY(kokkos INTERFACE)
|
||||
@ -272,7 +270,10 @@ INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_install.cmake)
|
||||
# executables also need nvcc_wrapper. Thus, we need to install it.
|
||||
# If the argument of DESTINATION is a relative path, CMake computes it
|
||||
# as relative to ${CMAKE_INSTALL_PATH}.
|
||||
INSTALL(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
# KOKKOS_INSTALL_ADDITIONAL_FILES will install nvcc wrapper and other generated
|
||||
# files
|
||||
KOKKOS_INSTALL_ADDITIONAL_FILES()
|
||||
|
||||
|
||||
# Finally - if we are a subproject - make sure the enabled devices are visible
|
||||
IF (HAS_PARENT)
|
||||
|
||||
@ -11,27 +11,27 @@ CXXFLAGS += $(SHFLAGS)
|
||||
endif
|
||||
|
||||
KOKKOS_VERSION_MAJOR = 3
|
||||
KOKKOS_VERSION_MINOR = 2
|
||||
KOKKOS_VERSION_MINOR = 3
|
||||
KOKKOS_VERSION_PATCH = 1
|
||||
KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc)
|
||||
|
||||
# Options: Cuda,HIP,ROCm,OpenMP,Pthread,Serial
|
||||
# Options: Cuda,HIP,OpenMP,Pthread,Serial
|
||||
KOKKOS_DEVICES ?= "OpenMP"
|
||||
#KOKKOS_DEVICES ?= "Pthread"
|
||||
# Options:
|
||||
# Intel: KNC,KNL,SNB,HSW,BDW,SKX
|
||||
# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80
|
||||
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2
|
||||
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX
|
||||
# IBM: BGQ,Power7,Power8,Power9
|
||||
# AMD-GPUS: Vega900,Vega906
|
||||
# AMD-GPUS: Vega900,Vega906,Vega908
|
||||
# AMD-CPUS: AMDAVX,Zen,Zen2
|
||||
KOKKOS_ARCH ?= ""
|
||||
# Options: yes,no
|
||||
KOKKOS_DEBUG ?= "no"
|
||||
# Options: hwloc,librt,experimental_memkind
|
||||
KOKKOS_USE_TPLS ?= ""
|
||||
# Options: c++11,c++14,c++1y,c++17,c++1z,c++2a
|
||||
KOKKOS_CXX_STANDARD ?= "c++11"
|
||||
# Options: c++14,c++1y,c++17,c++1z,c++2a
|
||||
KOKKOS_CXX_STANDARD ?= "c++14"
|
||||
# Options: aggressive_vectorization,disable_profiling,enable_large_mem_tests,disable_complex_align
|
||||
KOKKOS_OPTIONS ?= ""
|
||||
KOKKOS_CMAKE ?= "no"
|
||||
@ -66,7 +66,6 @@ kokkos_path_exists=$(if $(wildcard $1),1,0)
|
||||
# Check for general settings
|
||||
|
||||
KOKKOS_INTERNAL_ENABLE_DEBUG := $(call kokkos_has_string,$(KOKKOS_DEBUG),yes)
|
||||
KOKKOS_INTERNAL_ENABLE_CXX11 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++11)
|
||||
KOKKOS_INTERNAL_ENABLE_CXX14 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++14)
|
||||
KOKKOS_INTERNAL_ENABLE_CXX1Y := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++1y)
|
||||
KOKKOS_INTERNAL_ENABLE_CXX17 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++17)
|
||||
@ -279,14 +278,12 @@ else
|
||||
endif
|
||||
endif
|
||||
|
||||
# Set C++11 flags.
|
||||
# Set C++ version flags.
|
||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
||||
KOKKOS_INTERNAL_CXX11_FLAG := --c++11
|
||||
KOKKOS_INTERNAL_CXX14_FLAG := --c++14
|
||||
KOKKOS_INTERNAL_CXX17_FLAG := --c++17
|
||||
else
|
||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1)
|
||||
KOKKOS_INTERNAL_CXX11_FLAG := -std=c++11
|
||||
KOKKOS_INTERNAL_CXX14_FLAG := -std=c++14
|
||||
KOKKOS_INTERNAL_CXX1Y_FLAG := -std=c++1y
|
||||
#KOKKOS_INTERNAL_CXX17_FLAG := -std=c++17
|
||||
@ -294,17 +291,12 @@ else
|
||||
#KOKKOS_INTERNAL_CXX2A_FLAG := -std=c++2a
|
||||
else
|
||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
||||
KOKKOS_INTERNAL_CXX11_FLAG := -hstd=c++11
|
||||
KOKKOS_INTERNAL_CXX14_FLAG := -hstd=c++14
|
||||
#KOKKOS_INTERNAL_CXX1Y_FLAG := -hstd=c++1y
|
||||
#KOKKOS_INTERNAL_CXX17_FLAG := -hstd=c++17
|
||||
#KOKKOS_INTERNAL_CXX1Z_FLAG := -hstd=c++1z
|
||||
#KOKKOS_INTERNAL_CXX2A_FLAG := -hstd=c++2a
|
||||
else
|
||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_HCC), 1)
|
||||
KOKKOS_INTERNAL_CXX11_FLAG :=
|
||||
else
|
||||
KOKKOS_INTERNAL_CXX11_FLAG := --std=c++11
|
||||
KOKKOS_INTERNAL_CXX14_FLAG := --std=c++14
|
||||
KOKKOS_INTERNAL_CXX1Y_FLAG := --std=c++1y
|
||||
KOKKOS_INTERNAL_CXX17_FLAG := --std=c++17
|
||||
@ -312,7 +304,6 @@ else
|
||||
KOKKOS_INTERNAL_CXX2A_FLAG := --std=c++2a
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
|
||||
# Check for Kokkos Architecture settings.
|
||||
@ -377,7 +368,8 @@ KOKKOS_INTERNAL_USE_ARCH_ARMV80 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8
|
||||
KOKKOS_INTERNAL_USE_ARCH_ARMV81 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv81)
|
||||
KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-ThunderX)
|
||||
KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-TX2)
|
||||
KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2) | bc))
|
||||
KOKKOS_INTERNAL_USE_ARCH_A64FX := $(call kokkos_has_string,$(KOKKOS_ARCH),A64FX)
|
||||
KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2)+$(KOKKOS_INTERNAL_USE_ARCH_A64FX) | bc))
|
||||
|
||||
# IBM based.
|
||||
KOKKOS_INTERNAL_USE_ARCH_BGQ := $(call kokkos_has_string,$(KOKKOS_ARCH),BGQ)
|
||||
@ -392,6 +384,7 @@ KOKKOS_INTERNAL_USE_ARCH_ZEN2 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen2)
|
||||
KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen)
|
||||
KOKKOS_INTERNAL_USE_ARCH_VEGA900 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega900)
|
||||
KOKKOS_INTERNAL_USE_ARCH_VEGA906 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega906)
|
||||
KOKKOS_INTERNAL_USE_ARCH_VEGA908 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega908)
|
||||
|
||||
# Any AVX?
|
||||
KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM))
|
||||
@ -459,7 +452,6 @@ H := \#
|
||||
# Do not append first line
|
||||
tmp := $(shell echo "/* ---------------------------------------------" > KokkosCore_config.tmp)
|
||||
tmp := $(call kokkos_append_header,"Makefile constructed configuration:")
|
||||
tmp := $(call kokkos_append_header,"$(shell date)")
|
||||
tmp := $(call kokkos_append_header,"----------------------------------------------*/")
|
||||
|
||||
tmp := $(call kokkos_append_header,'$H''if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H)')
|
||||
@ -479,10 +471,6 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
||||
tmp := $(call kokkos_append_header,"$H""define KOKKOS_COMPILER_CUDA_VERSION $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION)")
|
||||
endif
|
||||
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
|
||||
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_ROCM')
|
||||
tmp := $(call kokkos_append_header,'$H''define KOKKOS_IMPL_ROCM_CLANG_WORKAROUND 1')
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
||||
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_HIP')
|
||||
endif
|
||||
@ -542,12 +530,6 @@ endif
|
||||
|
||||
#only add the c++ standard flags if this is not CMake
|
||||
tmp := $(call kokkos_append_header,"/* General Settings */")
|
||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX11), 1)
|
||||
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
|
||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX11_FLAG)
|
||||
endif
|
||||
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX11")
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX14), 1)
|
||||
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
|
||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX14_FLAG)
|
||||
@ -765,6 +747,13 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV81), 1)
|
||||
endif
|
||||
endif
|
||||
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_A64FX), 1)
|
||||
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_A64FX")
|
||||
|
||||
KOKKOS_CXXFLAGS += -march=armv8.2-a+sve
|
||||
KOKKOS_LDFLAGS += -march=armv8.2-a+sve
|
||||
endif
|
||||
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN), 1)
|
||||
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_ZEN")
|
||||
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_AVX2")
|
||||
@ -1143,6 +1132,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
||||
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA906")
|
||||
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx906
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA908), 1)
|
||||
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_HIP 908")
|
||||
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA908")
|
||||
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx908
|
||||
endif
|
||||
|
||||
|
||||
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.cpp)
|
||||
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.hpp)
|
||||
@ -1173,6 +1168,55 @@ ifneq ($(KOKKOS_INTERNAL_NEW_CONFIG), 0)
|
||||
tmp := $(shell cp KokkosCore_config.tmp KokkosCore_config.h)
|
||||
endif
|
||||
|
||||
# Functions for generating config header file
|
||||
kokkos_start_config_header = $(shell sed 's~@INCLUDE_NEXT_FILE@~~g' $(KOKKOS_PATH)/cmake/KokkosCore_Config_HeaderSet.in > $1)
|
||||
kokkos_update_config_header = $(shell sed 's~@HEADER_GUARD_TAG@~$1~g' $2 > $3)
|
||||
kokkos_append_config_header = $(shell echo $1 >> $2))
|
||||
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_FwdBackend.tmp")
|
||||
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_SetupBackend.tmp")
|
||||
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_DeclareBackend.tmp")
|
||||
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_PostInclude.tmp")
|
||||
tmp := $(call kokkos_update_config_header, KOKKOS_FWD_HPP_, "KokkosCore_Config_FwdBackend.tmp", "KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config_SetupBackend.tmp", "KokkosCore_Config_SetupBackend.hpp")
|
||||
tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp")
|
||||
tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp")
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
||||
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_CUDA.hpp>","KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_CUDA.hpp>","KokkosCore_Config_DeclareBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <setup/Kokkos_Setup_Cuda.hpp>","KokkosCore_Config_SetupBackend.hpp")
|
||||
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1)
|
||||
else
|
||||
endif
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
|
||||
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_OPENMPTARGET.hpp>","KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_OPENMPTARGET.hpp>","KokkosCore_Config_DeclareBackend.hpp")
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
||||
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_HIP.hpp>","KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_HIP.hpp>","KokkosCore_Config_DeclareBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <setup/Kokkos_Setup_HIP.hpp>","KokkosCore_Config_SetupBackend.hpp")
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
|
||||
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_OPENMP.hpp>","KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_OPENMP.hpp>","KokkosCore_Config_DeclareBackend.hpp")
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
||||
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_THREADS.hpp>","KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_THREADS.hpp>","KokkosCore_Config_DeclareBackend.hpp")
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
|
||||
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_HPX.hpp>","KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_HPX.hpp>","KokkosCore_Config_DeclareBackend.hpp")
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
||||
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_SERIAL.hpp>","KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_SERIAL.hpp>","KokkosCore_Config_DeclareBackend.hpp")
|
||||
endif
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1)
|
||||
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_HBWSpace.hpp>","KokkosCore_Config_FwdBackend.hpp")
|
||||
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_HBWSpace.hpp>","KokkosCore_Config_DeclareBackend.hpp")
|
||||
endif
|
||||
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/*.hpp)
|
||||
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/impl/*.hpp)
|
||||
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/containers/src/*.hpp)
|
||||
@ -1290,7 +1334,7 @@ ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
||||
endif
|
||||
|
||||
# With Cygwin functions such as fdopen and fileno are not defined
|
||||
# when strict ansi is enabled. strict ansi gets enabled with --std=c++11
|
||||
# when strict ansi is enabled. strict ansi gets enabled with --std=c++14
|
||||
# though. So we hard undefine it here. Not sure if that has any bad side effects
|
||||
# This is needed for gtest actually, not for Kokkos itself!
|
||||
ifeq ($(KOKKOS_INTERNAL_OS_CYGWIN), 1)
|
||||
@ -1313,7 +1357,9 @@ KOKKOS_OBJ_LINK = $(notdir $(KOKKOS_OBJ))
|
||||
include $(KOKKOS_PATH)/Makefile.targets
|
||||
|
||||
kokkos-clean:
|
||||
rm -f $(KOKKOS_OBJ_LINK) KokkosCore_config.h KokkosCore_config.tmp libkokkos.a
|
||||
rm -f $(KOKKOS_OBJ_LINK) KokkosCore_config.h KokkosCore_config.tmp libkokkos.a KokkosCore_Config_SetupBackend.hpp \
|
||||
KokkosCore_Config_FwdBackend.hpp KokkosCore_Config_DeclareBackend.hpp KokkosCore_Config_DeclareBackend.tmp \
|
||||
KokkosCore_Config_FwdBackend.tmp KokkosCore_Config_PostInclude.hpp KokkosCore_Config_PostInclude.tmp KokkosCore_Config_SetupBackend.tmp
|
||||
|
||||
libkokkos.a: $(KOKKOS_OBJ_LINK) $(KOKKOS_SRC) $(KOKKOS_HEADERS)
|
||||
ar cr libkokkos.a $(KOKKOS_OBJ_LINK)
|
||||
|
||||
@ -53,23 +53,10 @@ Kokkos_HIP_Space.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Space.cpp
|
||||
Kokkos_HIP_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Instance.cpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Instance.cpp
|
||||
Kokkos_HIP_KernelLaunch.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_KernelLaunch.cpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_KernelLaunch.cpp
|
||||
Kokkos_HIP_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Locks.cpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Locks.cpp
|
||||
endif
|
||||
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
|
||||
Kokkos_ROCm_Exec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Exec.cpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Exec.cpp
|
||||
Kokkos_ROCm_Space.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Space.cpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Space.cpp
|
||||
Kokkos_ROCm_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Task.cpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Task.cpp
|
||||
Kokkos_ROCm_Impl.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp
|
||||
endif
|
||||
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
||||
Kokkos_ThreadsExec_base.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec_base.cpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec_base.cpp
|
||||
|
||||
@ -54,24 +54,16 @@ For specifics see the LICENSE file contained in the repository or distribution.
|
||||
# Requirements
|
||||
|
||||
### Primary tested compilers on X86 are:
|
||||
* GCC 4.8.4
|
||||
* GCC 4.9.3
|
||||
* GCC 5.1.0
|
||||
* GCC 5.3.0
|
||||
* GCC 5.4.0
|
||||
* GCC 5.5.0
|
||||
* GCC 6.1.0
|
||||
* GCC 7.2.0
|
||||
* GCC 7.3.0
|
||||
* GCC 8.1.0
|
||||
* Intel 15.0.2
|
||||
* Intel 16.0.1
|
||||
* Intel 17.0.1
|
||||
* Intel 17.4.196
|
||||
* Intel 18.2.128
|
||||
* Clang 3.6.1
|
||||
* Clang 3.7.1
|
||||
* Clang 3.8.1
|
||||
* Clang 3.9.0
|
||||
* Clang 4.0.0
|
||||
* Clang 6.0.0 for CUDA (CUDA Toolkit 9.0)
|
||||
* Clang 7.0.0 for CUDA (CUDA Toolkit 9.1)
|
||||
@ -81,6 +73,7 @@ For specifics see the LICENSE file contained in the repository or distribution.
|
||||
* NVCC 9.2 for CUDA (with gcc 7.2.0)
|
||||
* NVCC 10.0 for CUDA (with gcc 7.4.0)
|
||||
* NVCC 10.1 for CUDA (with gcc 7.4.0)
|
||||
* NVCC 11.0 for CUDA (with gcc 8.4.0)
|
||||
|
||||
### Primary tested compilers on Power 8 are:
|
||||
* GCC 6.4.0 (OpenMP,Serial)
|
||||
@ -89,9 +82,8 @@ For specifics see the LICENSE file contained in the repository or distribution.
|
||||
* NVCC 9.2.88 for CUDA (with gcc 7.2.0 and XL 16.1.0)
|
||||
|
||||
### Primary tested compilers on Intel KNL are:
|
||||
* Intel 16.4.258 (with gcc 4.7.2)
|
||||
* Intel 17.2.174 (with gcc 4.9.3)
|
||||
* Intel 18.2.199 (with gcc 4.9.3)
|
||||
* Intel 17.2.174 (with gcc 6.2.0 and 6.4.0)
|
||||
* Intel 18.2.199 (with gcc 6.2.0 and 6.4.0)
|
||||
|
||||
### Primary tested compilers on ARM (Cavium ThunderX2)
|
||||
* GCC 7.2.0
|
||||
|
||||
@ -806,7 +806,7 @@ class Random_XorShift64 {
|
||||
const double V = 2.0 * drand() - 1.0;
|
||||
S = U * U + V * V;
|
||||
}
|
||||
return U * std::sqrt(-2.0 * log(S) / S);
|
||||
return U * std::sqrt(-2.0 * std::log(S) / S);
|
||||
}
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
@ -1042,7 +1042,7 @@ class Random_XorShift1024 {
|
||||
const double V = 2.0 * drand() - 1.0;
|
||||
S = U * U + V * V;
|
||||
}
|
||||
return U * std::sqrt(-2.0 * log(S) / S);
|
||||
return U * std::sqrt(-2.0 * std::log(S) / S);
|
||||
}
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
|
||||
@ -222,11 +222,11 @@ class BinSort {
|
||||
"Kokkos::SortImpl::BinSortFunctor::bin_count", bin_op.max_bins());
|
||||
bin_count_const = bin_count_atomic;
|
||||
bin_offsets =
|
||||
offset_type(ViewAllocateWithoutInitializing(
|
||||
offset_type(view_alloc(WithoutInitializing,
|
||||
"Kokkos::SortImpl::BinSortFunctor::bin_offsets"),
|
||||
bin_op.max_bins());
|
||||
sort_order =
|
||||
offset_type(ViewAllocateWithoutInitializing(
|
||||
offset_type(view_alloc(WithoutInitializing,
|
||||
"Kokkos::SortImpl::BinSortFunctor::sort_order"),
|
||||
range_end - range_begin);
|
||||
}
|
||||
@ -279,7 +279,7 @@ class BinSort {
|
||||
}
|
||||
|
||||
scratch_view_type sorted_values(
|
||||
ViewAllocateWithoutInitializing(
|
||||
view_alloc(WithoutInitializing,
|
||||
"Kokkos::SortImpl::BinSortFunctor::sorted_values"),
|
||||
values.rank_dynamic > 0 ? len : KOKKOS_IMPL_CTOR_DEFAULT_ARG,
|
||||
values.rank_dynamic > 1 ? values.extent(1)
|
||||
|
||||
@ -24,7 +24,7 @@ KOKKOS_ADD_TEST_LIBRARY(
|
||||
# avoid deprecation warnings from MSVC
|
||||
TARGET_COMPILE_DEFINITIONS(kokkosalgorithms_gtest PUBLIC GTEST_HAS_TR1_TUPLE=0 GTEST_HAS_PTHREAD=0)
|
||||
|
||||
IF(NOT (Kokkos_ENABLE_CUDA AND WIN32))
|
||||
IF((NOT (Kokkos_ENABLE_CUDA AND WIN32)) AND (NOT ("${KOKKOS_CXX_COMPILER_ID}" STREQUAL "Fujitsu")))
|
||||
TARGET_COMPILE_FEATURES(kokkosalgorithms_gtest PUBLIC cxx_std_11)
|
||||
ENDIF()
|
||||
|
||||
|
||||
@ -31,10 +31,10 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
||||
TEST_TARGETS += test-cuda
|
||||
endif
|
||||
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
|
||||
OBJ_ROCM = TestROCm.o UnitTestMain.o gtest-all.o
|
||||
TARGETS += KokkosAlgorithms_UnitTest_ROCm
|
||||
TEST_TARGETS += test-rocm
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
||||
OBJ_HIP = TestHIP.o UnitTestMain.o gtest-all.o
|
||||
TARGETS += KokkosAlgorithms_UnitTest_HIP
|
||||
TEST_TARGETS += test-hip
|
||||
endif
|
||||
|
||||
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
||||
@ -64,8 +64,8 @@ endif
|
||||
KokkosAlgorithms_UnitTest_Cuda: $(OBJ_CUDA) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(EXTRA_PATH) $(OBJ_CUDA) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Cuda
|
||||
|
||||
KokkosAlgorithms_UnitTest_ROCm: $(OBJ_ROCM) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(EXTRA_PATH) $(OBJ_ROCM) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_ROCm
|
||||
KokkosAlgorithms_UnitTest_HIP: $(OBJ_HIP) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(EXTRA_PATH) $(OBJ_HIP) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_HIP
|
||||
|
||||
KokkosAlgorithms_UnitTest_Threads: $(OBJ_THREADS) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(EXTRA_PATH) $(OBJ_THREADS) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Threads
|
||||
@ -82,8 +82,8 @@ KokkosAlgorithms_UnitTest_Serial: $(OBJ_SERIAL) $(KOKKOS_LINK_DEPENDS)
|
||||
test-cuda: KokkosAlgorithms_UnitTest_Cuda
|
||||
./KokkosAlgorithms_UnitTest_Cuda
|
||||
|
||||
test-rocm: KokkosAlgorithms_UnitTest_ROCm
|
||||
./KokkosAlgorithms_UnitTest_ROCm
|
||||
test-hip: KokkosAlgorithms_UnitTest_HIP
|
||||
./KokkosAlgorithms_UnitTest_HIP
|
||||
|
||||
test-threads: KokkosAlgorithms_UnitTest_Threads
|
||||
./KokkosAlgorithms_UnitTest_Threads
|
||||
|
||||
@ -1,31 +1,38 @@
|
||||
KOKKOS_PATH = ${HOME}/kokkos
|
||||
KOKKOS_DEVICES = "OpenMP"
|
||||
KOKKOS_ARCH = "SNB"
|
||||
EXE_NAME = "test"
|
||||
KOKKOS_DEVICES=Cuda
|
||||
KOKKOS_CUDA_OPTIONS=enable_lambda
|
||||
KOKKOS_ARCH = "SNB,Volta70"
|
||||
|
||||
SRC = $(wildcard *.cpp)
|
||||
|
||||
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
|
||||
|
||||
ifndef KOKKOS_PATH
|
||||
KOKKOS_PATH = $(MAKEFILE_PATH)../..
|
||||
endif
|
||||
|
||||
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
|
||||
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
|
||||
|
||||
vpath %.cpp $(sort $(dir $(SRC)))
|
||||
|
||||
default: build
|
||||
echo "Start Build"
|
||||
|
||||
|
||||
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
|
||||
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
|
||||
EXE = ${EXE_NAME}.cuda
|
||||
KOKKOS_CUDA_OPTIONS = "enable_lambda"
|
||||
EXE = atomic_perf.cuda
|
||||
else
|
||||
CXX = g++
|
||||
EXE = ${EXE_NAME}.host
|
||||
EXE = atomic_perf.exe
|
||||
endif
|
||||
|
||||
CXXFLAGS = -O3
|
||||
|
||||
LINK = ${CXX}
|
||||
LINKFLAGS = -O3
|
||||
CXXFLAGS ?= -O3 -g
|
||||
override CXXFLAGS += -I$(MAKEFILE_PATH)
|
||||
|
||||
DEPFLAGS = -M
|
||||
LINK = ${CXX}
|
||||
LINKFLAGS =
|
||||
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
OBJ = $(notdir $(SRC:.cpp=.o))
|
||||
LIB =
|
||||
|
||||
include $(KOKKOS_PATH)/Makefile.kokkos
|
||||
@ -36,9 +43,9 @@ $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
|
||||
|
||||
clean: kokkos-clean
|
||||
rm -f *.o *.cuda *.host
|
||||
rm -f *.o atomic_perf.cuda atomic_perf.exe
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp $(KOKKOS_CPP_DEPENDS)
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
|
||||
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)
|
||||
|
||||
@ -9,7 +9,7 @@ if [[ ${USE_CUDA} > 0 ]]; then
|
||||
BAF_EXE=bytes_and_flops.cuda
|
||||
TEAM_SIZE=256
|
||||
else
|
||||
BAF_EXE=bytes_and_flops.host
|
||||
BAF_EXE=bytes_and_flops.exe
|
||||
TEAM_SIZE=1
|
||||
fi
|
||||
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
KOKKOS_DEVICES=Cuda
|
||||
KOKKOS_CUDA_OPTIONS=enable_lambda
|
||||
KOKKOS_ARCH = "SNB,Kepler35"
|
||||
KOKKOS_ARCH = "SNB,Volta70"
|
||||
|
||||
|
||||
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
|
||||
@ -22,7 +22,7 @@ CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
|
||||
EXE = bytes_and_flops.cuda
|
||||
else
|
||||
CXX = g++
|
||||
EXE = bytes_and_flops.host
|
||||
EXE = bytes_and_flops.exe
|
||||
endif
|
||||
|
||||
CXXFLAGS ?= -O3 -g
|
||||
|
||||
@ -1,7 +1,18 @@
|
||||
KOKKOS_PATH = ${HOME}/kokkos
|
||||
SRC = $(wildcard *.cpp)
|
||||
KOKKOS_DEVICES=Cuda
|
||||
KOKKOS_CUDA_OPTIONS=enable_lambda
|
||||
KOKKOS_ARCH = "SNB,Volta70"
|
||||
|
||||
|
||||
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
|
||||
|
||||
ifndef KOKKOS_PATH
|
||||
KOKKOS_PATH = $(MAKEFILE_PATH)../..
|
||||
endif
|
||||
|
||||
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
|
||||
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
|
||||
|
||||
vpath %.cpp $(sort $(dir $(SRC)))
|
||||
|
||||
default: build
|
||||
echo "Start Build"
|
||||
@ -9,36 +20,32 @@ default: build
|
||||
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
|
||||
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
|
||||
EXE = gather.cuda
|
||||
KOKKOS_DEVICES = "Cuda,OpenMP"
|
||||
KOKKOS_ARCH = "SNB,Kepler35"
|
||||
else
|
||||
CXX = g++
|
||||
EXE = gather.host
|
||||
KOKKOS_DEVICES = "OpenMP"
|
||||
KOKKOS_ARCH = "SNB"
|
||||
EXE = gather.exe
|
||||
endif
|
||||
|
||||
CXXFLAGS = -O3 -g
|
||||
CXXFLAGS ?= -O3 -g
|
||||
override CXXFLAGS += -I$(MAKEFILE_PATH)
|
||||
|
||||
DEPFLAGS = -M
|
||||
LINK = ${CXX}
|
||||
LINKFLAGS =
|
||||
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
OBJ = $(notdir $(SRC:.cpp=.o))
|
||||
LIB =
|
||||
|
||||
include $(KOKKOS_PATH)/Makefile.kokkos
|
||||
|
||||
$(warning ${KOKKOS_CPPFLAGS})
|
||||
build: $(EXE)
|
||||
|
||||
$(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
|
||||
|
||||
clean: kokkos-clean
|
||||
rm -f *.o *.cuda *.host
|
||||
rm -f *.o gather.cuda gather.exe
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) gather_unroll.hpp gather.hpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
|
||||
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)
|
||||
|
||||
@ -1,28 +1,38 @@
|
||||
#Set your Kokkos path to something appropriate
|
||||
KOKKOS_PATH = ${HOME}/git/kokkos-github-repo
|
||||
KOKKOS_DEVICES = "Cuda"
|
||||
KOKKOS_ARCH = "Pascal60"
|
||||
KOKKOS_CUDA_OPTIONS = enable_lambda
|
||||
#KOKKOS_DEVICES = "OpenMP"
|
||||
#KOKKOS_ARCH = "Power8"
|
||||
KOKKOS_DEVICES=Cuda
|
||||
KOKKOS_CUDA_OPTIONS=enable_lambda
|
||||
KOKKOS_ARCH = "SNB,Volta70"
|
||||
|
||||
SRC = gups-kokkos.cc
|
||||
|
||||
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
|
||||
|
||||
ifndef KOKKOS_PATH
|
||||
KOKKOS_PATH = $(MAKEFILE_PATH)../..
|
||||
endif
|
||||
|
||||
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
|
||||
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
|
||||
|
||||
vpath %.cpp $(sort $(dir $(SRC)))
|
||||
|
||||
default: build
|
||||
echo "Start Build"
|
||||
|
||||
CXXFLAGS = -O3
|
||||
CXX = ${HOME}/git/kokkos-github-repo/bin/nvcc_wrapper
|
||||
#CXX = g++
|
||||
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
|
||||
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
|
||||
EXE = gups.cuda
|
||||
else
|
||||
CXX = g++
|
||||
EXE = gups.exe
|
||||
endif
|
||||
|
||||
LINK = ${CXX}
|
||||
|
||||
LINKFLAGS =
|
||||
EXE = gups-kokkos
|
||||
CXXFLAGS ?= -O3 -g
|
||||
override CXXFLAGS += -I$(MAKEFILE_PATH)
|
||||
|
||||
DEPFLAGS = -M
|
||||
LINK = ${CXX}
|
||||
LINKFLAGS =
|
||||
|
||||
OBJ = $(SRC:.cc=.o)
|
||||
OBJ = $(notdir $(SRC:.cpp=.o))
|
||||
LIB =
|
||||
|
||||
include $(KOKKOS_PATH)/Makefile.kokkos
|
||||
@ -33,9 +43,9 @@ $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
|
||||
|
||||
clean: kokkos-clean
|
||||
rm -f *.o $(EXE)
|
||||
rm -f *.o gups.cuda gups.exe
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cc $(KOKKOS_CPP_DEPENDS)
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
|
||||
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)
|
||||
|
||||
@ -1,31 +1,38 @@
|
||||
KOKKOS_PATH = ../..
|
||||
SRC = $(wildcard *.cpp)
|
||||
KOKKOS_DEVICES=Cuda
|
||||
KOKKOS_CUDA_OPTIONS=enable_lambda
|
||||
KOKKOS_ARCH = "SNB,Volta70"
|
||||
|
||||
|
||||
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
|
||||
|
||||
ifndef KOKKOS_PATH
|
||||
KOKKOS_PATH = $(MAKEFILE_PATH)../..
|
||||
endif
|
||||
|
||||
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
|
||||
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
|
||||
|
||||
vpath %.cpp $(sort $(dir $(SRC)))
|
||||
|
||||
default: build
|
||||
echo "Start Build"
|
||||
|
||||
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
|
||||
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
|
||||
CXXFLAGS = -O3 -g
|
||||
LINK = ${CXX}
|
||||
LINKFLAGS =
|
||||
EXE = policy_performance.cuda
|
||||
KOKKOS_DEVICES = "Cuda,OpenMP"
|
||||
KOKKOS_ARCH = "SNB,Kepler35"
|
||||
KOKKOS_CUDA_OPTIONS+=enable_lambda
|
||||
EXE = policy_perf.cuda
|
||||
else
|
||||
CXX = g++
|
||||
CXXFLAGS = -O3 -g -Wall -Werror
|
||||
LINK = ${CXX}
|
||||
LINKFLAGS =
|
||||
EXE = policy_performance.host
|
||||
KOKKOS_DEVICES = "OpenMP"
|
||||
KOKKOS_ARCH = "SNB"
|
||||
EXE = policy_perf.exe
|
||||
endif
|
||||
|
||||
DEPFLAGS = -M
|
||||
CXXFLAGS ?= -O3 -g
|
||||
override CXXFLAGS += -I$(MAKEFILE_PATH)
|
||||
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
DEPFLAGS = -M
|
||||
LINK = ${CXX}
|
||||
LINKFLAGS =
|
||||
|
||||
OBJ = $(notdir $(SRC:.cpp=.o))
|
||||
LIB =
|
||||
|
||||
include $(KOKKOS_PATH)/Makefile.kokkos
|
||||
@ -36,9 +43,9 @@ $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
|
||||
|
||||
clean: kokkos-clean
|
||||
rm -f *.o *.cuda *.host
|
||||
rm -f *.o policy_perf.cuda policy_perf.exe
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) main.cpp policy_perf_test.hpp
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
|
||||
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)
|
||||
|
||||
@ -146,11 +146,11 @@ int main(int argc, char* argv[]) {
|
||||
// Call a 'warmup' test with 1 repeat - this will initialize the corresponding
|
||||
// view appropriately for test and should obey first-touch etc Second call to
|
||||
// test is the one we actually care about and time
|
||||
view_type_1d v_1(Kokkos::ViewAllocateWithoutInitializing("v_1"),
|
||||
view_type_1d v_1(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_1"),
|
||||
team_range * team_size);
|
||||
view_type_2d v_2(Kokkos::ViewAllocateWithoutInitializing("v_2"),
|
||||
view_type_2d v_2(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_2"),
|
||||
team_range * team_size, thread_range);
|
||||
view_type_3d v_3(Kokkos::ViewAllocateWithoutInitializing("v_3"),
|
||||
view_type_3d v_3(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_3"),
|
||||
team_range * team_size, thread_range, vector_range);
|
||||
|
||||
double result_computed = 0.0;
|
||||
|
||||
@ -1,28 +1,38 @@
|
||||
#Set your Kokkos path to something appropriate
|
||||
KOKKOS_PATH = ${HOME}/git/kokkos-github-repo
|
||||
#KOKKOS_DEVICES = "Cuda"
|
||||
#KOKKOS_ARCH = "Pascal60"
|
||||
#KOKKOS_CUDA_OPTIONS = enable_lambda
|
||||
KOKKOS_DEVICES = "OpenMP"
|
||||
KOKKOS_ARCH = "Power8"
|
||||
KOKKOS_DEVICES=Cuda
|
||||
KOKKOS_CUDA_OPTIONS=enable_lambda
|
||||
KOKKOS_ARCH = "SNB,Volta70"
|
||||
|
||||
SRC = stream-kokkos.cc
|
||||
|
||||
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
|
||||
|
||||
ifndef KOKKOS_PATH
|
||||
KOKKOS_PATH = $(MAKEFILE_PATH)../..
|
||||
endif
|
||||
|
||||
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
|
||||
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
|
||||
|
||||
vpath %.cpp $(sort $(dir $(SRC)))
|
||||
|
||||
default: build
|
||||
echo "Start Build"
|
||||
|
||||
CXXFLAGS = -O3
|
||||
#CXX = ${HOME}/git/kokkos-github-repo/bin/nvcc_wrapper
|
||||
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
|
||||
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
|
||||
EXE = stream.cuda
|
||||
else
|
||||
CXX = g++
|
||||
EXE = stream.exe
|
||||
endif
|
||||
|
||||
LINK = ${CXX}
|
||||
|
||||
LINKFLAGS =
|
||||
EXE = stream-kokkos
|
||||
CXXFLAGS ?= -O3 -g
|
||||
override CXXFLAGS += -I$(MAKEFILE_PATH)
|
||||
|
||||
DEPFLAGS = -M
|
||||
LINK = ${CXX}
|
||||
LINKFLAGS =
|
||||
|
||||
OBJ = $(SRC:.cc=.o)
|
||||
OBJ = $(notdir $(SRC:.cpp=.o))
|
||||
LIB =
|
||||
|
||||
include $(KOKKOS_PATH)/Makefile.kokkos
|
||||
@ -33,9 +43,9 @@ $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
|
||||
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
|
||||
|
||||
clean: kokkos-clean
|
||||
rm -f *.o $(EXE)
|
||||
rm -f *.o stream.cuda stream.exe
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cc $(KOKKOS_CPP_DEPENDS)
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
|
||||
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
|
||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)
|
||||
|
||||
87
lib/kokkos/bin/kokkos_launch_compiler
Executable file
87
lib/kokkos/bin/kokkos_launch_compiler
Executable file
@ -0,0 +1,87 @@
|
||||
#!/bin/bash -e
|
||||
#
|
||||
# This script allows CMAKE_CXX_COMPILER to be a standard
|
||||
# C++ compiler and Kokkos sets RULE_LAUNCH_COMPILE and
|
||||
# RULE_LAUNCH_LINK in CMake so that all compiler and link
|
||||
# commands are prefixed with this script followed by the
|
||||
# C++ compiler. Thus if $1 == $2 then we know the command
|
||||
# was intended for the C++ compiler and we discard both
|
||||
# $1 and $2 and redirect the command to NVCC_WRAPPER.
|
||||
# If $1 != $2 then we know that the command was not intended
|
||||
# for the C++ compiler and we just discard $1 and launch
|
||||
# the original command. Examples of when $2 will not equal
|
||||
# $1 are 'ar', 'cmake', etc. during the linking phase
|
||||
#
|
||||
|
||||
# check the arguments for the KOKKOS_DEPENDENCE compiler definition
|
||||
KOKKOS_DEPENDENCE=0
|
||||
for i in ${@}
|
||||
do
|
||||
if [ -n "$(echo ${i} | grep 'KOKKOS_DEPENDENCE$')" ]; then
|
||||
KOKKOS_DEPENDENCE=1
|
||||
break
|
||||
fi
|
||||
done
|
||||
|
||||
# if C++ is not passed, someone is probably trying to invoke it directly
|
||||
if [ -z "${1}" ]; then
|
||||
echo -e "\n${BASH_SOURCE[0]} was invoked without the C++ compiler as the first argument."
|
||||
echo "This script is not indended to be directly invoked by any mechanism other"
|
||||
echo -e "than through a RULE_LAUNCH_COMPILE or RULE_LAUNCH_LINK property set in CMake\n"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# if there aren't two args, this isn't necessarily invalid, just a bit strange
|
||||
if [ -z "${2}" ]; then exit 0; fi
|
||||
|
||||
# store the expected C++ compiler
|
||||
CXX_COMPILER=${1}
|
||||
|
||||
# remove the expected C++ compiler from the arguments
|
||||
shift
|
||||
|
||||
# after the above shift, $1 is now the exe for the compile or link command, e.g.
|
||||
# kokkos_launch_compiler g++ gcc -c file.c -o file.o
|
||||
# becomes:
|
||||
# kokkos_launch_compiler gcc -c file.c -o file.o
|
||||
# Check to see if the executable is the C++ compiler and if it is not, then
|
||||
# just execute the command.
|
||||
#
|
||||
# Summary:
|
||||
# kokkos_launch_compiler g++ gcc -c file.c -o file.o
|
||||
# results in this command being executed:
|
||||
# gcc -c file.c -o file.o
|
||||
# and
|
||||
# kokkos_launch_compiler g++ g++ -c file.cpp -o file.o
|
||||
# results in this command being executed:
|
||||
# nvcc_wrapper -c file.cpp -o file.o
|
||||
if [[ "${KOKKOS_DEPENDENCE}" -eq "0" || "${CXX_COMPILER}" != "${1}" ]]; then
|
||||
# the command does not depend on Kokkos so just execute the command w/o re-directing to nvcc_wrapper
|
||||
eval $@
|
||||
else
|
||||
# the executable is the C++ compiler, so we need to re-direct to nvcc_wrapper
|
||||
|
||||
# find the nvcc_wrapper from the same build/install
|
||||
NVCC_WRAPPER="$(dirname ${BASH_SOURCE[0]})/nvcc_wrapper"
|
||||
|
||||
if [ -z "${NVCC_WRAPPER}" ]; then
|
||||
echo -e "\nError: nvcc_wrapper not found in $(dirname ${BASH_SOURCE[0]}).\n"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# set default nvcc wrapper compiler if not specified
|
||||
: ${NVCC_WRAPPER_DEFAULT_COMPILER:=${CXX_COMPILER}}
|
||||
export NVCC_WRAPPER_DEFAULT_COMPILER
|
||||
|
||||
# calling itself will cause an infinitely long build
|
||||
if [ "${NVCC_WRAPPER}" = "${NVCC_WRAPPER_DEFAULT_COMPILER}" ]; then
|
||||
echo -e "\nError: NVCC_WRAPPER == NVCC_WRAPPER_DEFAULT_COMPILER. Terminating to avoid infinite loop!\n"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# discard the compiler from the command
|
||||
shift
|
||||
|
||||
# execute nvcc_wrapper
|
||||
${NVCC_WRAPPER} $@
|
||||
fi
|
||||
@ -90,7 +90,12 @@ replace_pragma_ident=0
|
||||
# Mark first host compiler argument
|
||||
first_xcompiler_arg=1
|
||||
|
||||
temp_dir=${TMPDIR:-/tmp}
|
||||
# Allow for setting temp dir without setting TMPDIR in parent (see https://docs.olcf.ornl.gov/systems/summit_user_guide.html#setting-tmpdir-causes-jsm-jsrun-errors-job-state-flip-flop)
|
||||
if [[ ! -z ${NVCC_WRAPPER_TMPDIR+x} ]]; then
|
||||
temp_dir=${TMPDIR:-/tmp}
|
||||
else
|
||||
temp_dir=${NVCC_WRAPPER_TMPDIR+x}
|
||||
fi
|
||||
|
||||
# optimization flag added as a command-line argument
|
||||
optimization_flag=""
|
||||
@ -194,7 +199,7 @@ do
|
||||
cuda_args="$cuda_args $1"
|
||||
;;
|
||||
#Handle known nvcc args that have an argument
|
||||
-rdc|-maxrregcount|--default-stream|-Xnvlink|--fmad|-cudart|--cudart)
|
||||
-rdc|-maxrregcount|--default-stream|-Xnvlink|--fmad|-cudart|--cudart|-include)
|
||||
cuda_args="$cuda_args $1 $2"
|
||||
shift
|
||||
;;
|
||||
|
||||
@ -1,3 +1,9 @@
|
||||
# No need for policy push/pop. CMake also manages a new entry for scripts
|
||||
# loaded by include() and find_package() commands except when invoked with
|
||||
# the NO_POLICY_SCOPE option
|
||||
# CMP0057 + NEW -> IN_LIST operator in IF(...)
|
||||
CMAKE_POLICY(SET CMP0057 NEW)
|
||||
|
||||
# Compute paths
|
||||
@PACKAGE_INIT@
|
||||
|
||||
@ -12,3 +18,18 @@ GET_FILENAME_COMPONENT(Kokkos_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
|
||||
INCLUDE("${Kokkos_CMAKE_DIR}/KokkosTargets.cmake")
|
||||
INCLUDE("${Kokkos_CMAKE_DIR}/KokkosConfigCommon.cmake")
|
||||
UNSET(Kokkos_CMAKE_DIR)
|
||||
|
||||
# if CUDA was enabled and separable compilation was specified, e.g.
|
||||
# find_package(Kokkos COMPONENTS separable_compilation)
|
||||
# then we set the RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK
|
||||
IF(@Kokkos_ENABLE_CUDA@ AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS)
|
||||
# run test to see if CMAKE_CXX_COMPILER=nvcc_wrapper
|
||||
kokkos_compiler_is_nvcc(IS_NVCC ${CMAKE_CXX_COMPILER})
|
||||
# if not nvcc_wrapper, use RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK
|
||||
IF(NOT IS_NVCC AND NOT CMAKE_CXX_COMPILER_ID STREQUAL Clang AND
|
||||
(NOT DEFINED Kokkos_LAUNCH_COMPILER OR Kokkos_LAUNCH_COMPILER))
|
||||
MESSAGE(STATUS "kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to nvcc_wrapper")
|
||||
kokkos_compilation(GLOBAL)
|
||||
ENDIF()
|
||||
UNSET(IS_NVCC) # be mindful of the environment, pollution is bad
|
||||
ENDIF()
|
||||
|
||||
@ -89,3 +89,73 @@ function(kokkos_check)
|
||||
set(${KOKKOS_CHECK_RETURN_VALUE} ${KOKKOS_CHECK_SUCCESS} PARENT_SCOPE)
|
||||
endif()
|
||||
endfunction()
|
||||
|
||||
# this function is provided to easily select which files use nvcc_wrapper:
|
||||
#
|
||||
# GLOBAL --> all files
|
||||
# TARGET --> all files in a target
|
||||
# SOURCE --> specific source files
|
||||
# DIRECTORY --> all files in directory
|
||||
# PROJECT --> all files/targets in a project/subproject
|
||||
#
|
||||
FUNCTION(kokkos_compilation)
|
||||
CMAKE_PARSE_ARGUMENTS(COMP "GLOBAL;PROJECT" "" "DIRECTORY;TARGET;SOURCE" ${ARGN})
|
||||
|
||||
# search relative first and then absolute
|
||||
SET(_HINTS "${CMAKE_CURRENT_LIST_DIR}/../.." "@CMAKE_INSTALL_PREFIX@")
|
||||
|
||||
# find kokkos_launch_compiler
|
||||
FIND_PROGRAM(Kokkos_COMPILE_LAUNCHER
|
||||
NAMES kokkos_launch_compiler
|
||||
HINTS ${_HINTS}
|
||||
PATHS ${_HINTS}
|
||||
PATH_SUFFIXES bin)
|
||||
|
||||
IF(NOT Kokkos_COMPILE_LAUNCHER)
|
||||
MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'")
|
||||
ENDIF()
|
||||
|
||||
IF(COMP_GLOBAL)
|
||||
# if global, don't bother setting others
|
||||
SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
|
||||
SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
|
||||
ELSE()
|
||||
FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE)
|
||||
# make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...)
|
||||
IF("${_TYPE}" STREQUAL "PROJECT" AND COMP_${_TYPE})
|
||||
LIST(APPEND COMP_DIRECTORY ${PROJECT_SOURCE_DIR})
|
||||
UNSET(COMP_${_TYPE})
|
||||
ENDIF()
|
||||
# set the properties if defined
|
||||
IF(COMP_${_TYPE})
|
||||
# MESSAGE(STATUS "Using nvcc_wrapper :: ${_TYPE} :: ${COMP_${_TYPE}}")
|
||||
SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
|
||||
SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
|
||||
ENDIF()
|
||||
ENDFOREACH()
|
||||
ENDIF()
|
||||
ENDFUNCTION()
|
||||
|
||||
# A test to check whether a downstream project set the C++ compiler to NVCC or not
|
||||
# this is called only when Kokkos was installed with Kokkos_ENABLE_CUDA=ON
|
||||
FUNCTION(kokkos_compiler_is_nvcc VAR COMPILER)
|
||||
# Check if the compiler is nvcc (which really means nvcc_wrapper).
|
||||
EXECUTE_PROCESS(COMMAND ${COMPILER} ${ARGN} --version
|
||||
OUTPUT_VARIABLE INTERNAL_COMPILER_VERSION
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE
|
||||
RESULT_VARIABLE RET)
|
||||
# something went wrong
|
||||
IF(RET GREATER 0)
|
||||
SET(${VAR} false PARENT_SCOPE)
|
||||
ELSE()
|
||||
STRING(REPLACE "\n" " - " INTERNAL_COMPILER_VERSION_ONE_LINE ${INTERNAL_COMPILER_VERSION} )
|
||||
STRING(FIND ${INTERNAL_COMPILER_VERSION_ONE_LINE} "nvcc" INTERNAL_COMPILER_VERSION_CONTAINS_NVCC)
|
||||
STRING(REGEX REPLACE "^ +" "" INTERNAL_HAVE_COMPILER_NVCC "${INTERNAL_HAVE_COMPILER_NVCC}")
|
||||
IF(${INTERNAL_COMPILER_VERSION_CONTAINS_NVCC} GREATER -1)
|
||||
SET(${VAR} true PARENT_SCOPE)
|
||||
ELSE()
|
||||
SET(${VAR} false PARENT_SCOPE)
|
||||
ENDIF()
|
||||
ENDIF()
|
||||
ENDFUNCTION()
|
||||
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
|
||||
/*
|
||||
//@HEADER
|
||||
// ************************************************************************
|
||||
@ -42,6 +41,9 @@
|
||||
// ************************************************************************
|
||||
//@HEADER
|
||||
*/
|
||||
#ifndef @HEADER_GUARD_TAG@
|
||||
#define @HEADER_GUARD_TAG@
|
||||
|
||||
#include <cuda/TestCuda_Category.hpp>
|
||||
#include <TestComplex.hpp>
|
||||
@INCLUDE_NEXT_FILE@
|
||||
|
||||
#endif
|
||||
@ -21,6 +21,7 @@
|
||||
#cmakedefine KOKKOS_ENABLE_HPX
|
||||
#cmakedefine KOKKOS_ENABLE_MEMKIND
|
||||
#cmakedefine KOKKOS_ENABLE_LIBRT
|
||||
#cmakedefine KOKKOS_ENABLE_SYCL
|
||||
|
||||
#ifndef __CUDA_ARCH__
|
||||
#cmakedefine KOKKOS_ENABLE_TM
|
||||
@ -31,7 +32,6 @@
|
||||
#endif
|
||||
|
||||
/* General Settings */
|
||||
#cmakedefine KOKKOS_ENABLE_CXX11
|
||||
#cmakedefine KOKKOS_ENABLE_CXX14
|
||||
#cmakedefine KOKKOS_ENABLE_CXX17
|
||||
#cmakedefine KOKKOS_ENABLE_CXX20
|
||||
@ -58,7 +58,7 @@
|
||||
/* TPL Settings */
|
||||
#cmakedefine KOKKOS_ENABLE_HWLOC
|
||||
#cmakedefine KOKKOS_USE_LIBRT
|
||||
#cmakedefine KOKKOS_ENABLE_HWBSPACE
|
||||
#cmakedefine KOKKOS_ENABLE_HBWSPACE
|
||||
#cmakedefine KOKKOS_ENABLE_LIBDL
|
||||
#cmakedefine KOKKOS_IMPL_CUDA_CLANG_WORKAROUND
|
||||
|
||||
|
||||
@ -73,20 +73,20 @@ Compiler features are more fine-grained and require conflicting requests to be r
|
||||
Suppose I have
|
||||
````
|
||||
add_library(A a.cpp)
|
||||
target_compile_features(A PUBLIC cxx_std_11)
|
||||
target_compile_features(A PUBLIC cxx_std_14)
|
||||
````
|
||||
then another target
|
||||
````
|
||||
add_library(B b.cpp)
|
||||
target_compile_features(B PUBLIC cxx_std_14)
|
||||
target_compile_features(B PUBLIC cxx_std_17)
|
||||
target_link_libraries(A B)
|
||||
````
|
||||
I have requested two different features.
|
||||
CMake understands the requests and knows that `cxx_std_11` is a subset of `cxx_std_14`.
|
||||
CMake then picks C++14 for library `B`.
|
||||
CMake understands the requests and knows that `cxx_std_14` is a subset of `cxx_std_17`.
|
||||
CMake then picks C++17 for library `B`.
|
||||
CMake would not have been able to do feature resolution if we had directly done:
|
||||
````
|
||||
target_compile_options(A PUBLIC -std=c++11)
|
||||
target_compile_options(A PUBLIC -std=c++14)
|
||||
````
|
||||
|
||||
### Adding Kokkos Options
|
||||
|
||||
@ -1,14 +1,16 @@
|
||||
# @HEADER
|
||||
# ************************************************************************
|
||||
#
|
||||
# Trilinos: An Object-Oriented Solver Framework
|
||||
# Copyright (2001) Sandia Corporation
|
||||
# Kokkos v. 3.0
|
||||
# Copyright (2020) National Technology & Engineering
|
||||
# Solutions of Sandia, LLC (NTESS).
|
||||
#
|
||||
# Under the terms of Contract DE-NA0003525 with NTESS,
|
||||
# the U.S. Government retains certain rights in this software.
|
||||
#
|
||||
# Copyright (2001) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
|
||||
# work by or on behalf of the U.S. Government. Export of this program
|
||||
# may require a license from the United States Government.
|
||||
# Redistribution and use in source and binary forms, with or without
|
||||
# modification, are permitted provided that the following conditions are
|
||||
# met:
|
||||
#
|
||||
# 1. Redistributions of source code must retain the above copyright
|
||||
# notice, this list of conditions and the following disclaimer.
|
||||
@ -21,10 +23,10 @@
|
||||
# contributors may be used to endorse or promote products derived from
|
||||
# this software without specific prior written permission.
|
||||
#
|
||||
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
|
||||
# THIS SOFTWARE IS PROVIDED BY NTESS "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 SANDIA CORPORATION OR THE
|
||||
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
|
||||
# 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
|
||||
@ -33,22 +35,7 @@
|
||||
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
#
|
||||
# NOTICE: The United States Government is granted for itself and others
|
||||
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
|
||||
# license in this data to reproduce, prepare derivative works, and
|
||||
# perform publicly and display publicly. Beginning five (5) years from
|
||||
# July 25, 2001, the United States Government is granted for itself and
|
||||
# others acting on its behalf a paid-up, nonexclusive, irrevocable
|
||||
# worldwide license in this data to reproduce, prepare derivative works,
|
||||
# distribute copies to the public, perform publicly and display
|
||||
# publicly, and to permit others to do so.
|
||||
#
|
||||
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
|
||||
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
|
||||
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL 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.
|
||||
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
|
||||
#
|
||||
# ************************************************************************
|
||||
# @HEADER
|
||||
|
||||
@ -1,14 +1,16 @@
|
||||
# @HEADER
|
||||
# ************************************************************************
|
||||
#
|
||||
# Trilinos: An Object-Oriented Solver Framework
|
||||
# Copyright (2001) Sandia Corporation
|
||||
# Kokkos v. 3.0
|
||||
# Copyright (2020) National Technology & Engineering
|
||||
# Solutions of Sandia, LLC (NTESS).
|
||||
#
|
||||
# Under the terms of Contract DE-NA0003525 with NTESS,
|
||||
# the U.S. Government retains certain rights in this software.
|
||||
#
|
||||
# Copyright (2001) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
|
||||
# work by or on behalf of the U.S. Government. Export of this program
|
||||
# may require a license from the United States Government.
|
||||
# Redistribution and use in source and binary forms, with or without
|
||||
# modification, are permitted provided that the following conditions are
|
||||
# met:
|
||||
#
|
||||
# 1. Redistributions of source code must retain the above copyright
|
||||
# notice, this list of conditions and the following disclaimer.
|
||||
@ -21,10 +23,10 @@
|
||||
# contributors may be used to endorse or promote products derived from
|
||||
# this software without specific prior written permission.
|
||||
#
|
||||
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
|
||||
# THIS SOFTWARE IS PROVIDED BY NTESS "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 SANDIA CORPORATION OR THE
|
||||
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
|
||||
# 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
|
||||
@ -33,22 +35,7 @@
|
||||
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
#
|
||||
# NOTICE: The United States Government is granted for itself and others
|
||||
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
|
||||
# license in this data to reproduce, prepare derivative works, and
|
||||
# perform publicly and display publicly. Beginning five (5) years from
|
||||
# July 25, 2001, the United States Government is granted for itself and
|
||||
# others acting on its behalf a paid-up, nonexclusive, irrevocable
|
||||
# worldwide license in this data to reproduce, prepare derivative works,
|
||||
# distribute copies to the public, perform publicly and display
|
||||
# publicly, and to permit others to do so.
|
||||
#
|
||||
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
|
||||
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
|
||||
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL 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.
|
||||
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
|
||||
#
|
||||
# ************************************************************************
|
||||
# @HEADER
|
||||
|
||||
@ -1,14 +1,16 @@
|
||||
# @HEADER
|
||||
# ************************************************************************
|
||||
#
|
||||
# Trilinos: An Object-Oriented Solver Framework
|
||||
# Copyright (2001) Sandia Corporation
|
||||
# Kokkos v. 3.0
|
||||
# Copyright (2020) National Technology & Engineering
|
||||
# Solutions of Sandia, LLC (NTESS).
|
||||
#
|
||||
# Under the terms of Contract DE-NA0003525 with NTESS,
|
||||
# the U.S. Government retains certain rights in this software.
|
||||
#
|
||||
# Copyright (2001) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
|
||||
# work by or on behalf of the U.S. Government. Export of this program
|
||||
# may require a license from the United States Government.
|
||||
# Redistribution and use in source and binary forms, with or without
|
||||
# modification, are permitted provided that the following conditions are
|
||||
# met:
|
||||
#
|
||||
# 1. Redistributions of source code must retain the above copyright
|
||||
# notice, this list of conditions and the following disclaimer.
|
||||
@ -21,10 +23,10 @@
|
||||
# contributors may be used to endorse or promote products derived from
|
||||
# this software without specific prior written permission.
|
||||
#
|
||||
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
|
||||
# THIS SOFTWARE IS PROVIDED BY NTESS "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 SANDIA CORPORATION OR THE
|
||||
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
|
||||
# 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
|
||||
@ -33,22 +35,7 @@
|
||||
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
#
|
||||
# NOTICE: The United States Government is granted for itself and others
|
||||
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
|
||||
# license in this data to reproduce, prepare derivative works, and
|
||||
# perform publicly and display publicly. Beginning five (5) years from
|
||||
# July 25, 2001, the United States Government is granted for itself and
|
||||
# others acting on its behalf a paid-up, nonexclusive, irrevocable
|
||||
# worldwide license in this data to reproduce, prepare derivative works,
|
||||
# distribute copies to the public, perform publicly and display
|
||||
# publicly, and to permit others to do so.
|
||||
#
|
||||
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
|
||||
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
|
||||
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL 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.
|
||||
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
|
||||
#
|
||||
# ************************************************************************
|
||||
# @HEADER
|
||||
|
||||
@ -1,14 +1,16 @@
|
||||
# @HEADER
|
||||
# ************************************************************************
|
||||
#
|
||||
# Trilinos: An Object-Oriented Solver Framework
|
||||
# Copyright (2001) Sandia Corporation
|
||||
# Kokkos v. 3.0
|
||||
# Copyright (2020) National Technology & Engineering
|
||||
# Solutions of Sandia, LLC (NTESS).
|
||||
#
|
||||
# Under the terms of Contract DE-NA0003525 with NTESS,
|
||||
# the U.S. Government retains certain rights in this software.
|
||||
#
|
||||
# Copyright (2001) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
|
||||
# work by or on behalf of the U.S. Government. Export of this program
|
||||
# may require a license from the United States Government.
|
||||
# Redistribution and use in source and binary forms, with or without
|
||||
# modification, are permitted provided that the following conditions are
|
||||
# met:
|
||||
#
|
||||
# 1. Redistributions of source code must retain the above copyright
|
||||
# notice, this list of conditions and the following disclaimer.
|
||||
@ -21,10 +23,10 @@
|
||||
# contributors may be used to endorse or promote products derived from
|
||||
# this software without specific prior written permission.
|
||||
#
|
||||
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
|
||||
# THIS SOFTWARE IS PROVIDED BY NTESS "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 SANDIA CORPORATION OR THE
|
||||
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
|
||||
# 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
|
||||
@ -33,22 +35,7 @@
|
||||
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
#
|
||||
# NOTICE: The United States Government is granted for itself and others
|
||||
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
|
||||
# license in this data to reproduce, prepare derivative works, and
|
||||
# perform publicly and display publicly. Beginning five (5) years from
|
||||
# July 25, 2001, the United States Government is granted for itself and
|
||||
# others acting on its behalf a paid-up, nonexclusive, irrevocable
|
||||
# worldwide license in this data to reproduce, prepare derivative works,
|
||||
# distribute copies to the public, perform publicly and display
|
||||
# publicly, and to permit others to do so.
|
||||
#
|
||||
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
|
||||
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
|
||||
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL 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.
|
||||
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
|
||||
#
|
||||
# ************************************************************************
|
||||
# @HEADER
|
||||
|
||||
@ -38,12 +38,6 @@ MACRO(GLOBAL_SET VARNAME)
|
||||
SET(${VARNAME} ${ARGN} CACHE INTERNAL "" FORCE)
|
||||
ENDMACRO()
|
||||
|
||||
FUNCTION(VERIFY_EMPTY CONTEXT)
|
||||
if(${ARGN})
|
||||
MESSAGE(FATAL_ERROR "Kokkos does not support all of Tribits. Unhandled arguments in ${CONTEXT}:\n${ARGN}")
|
||||
endif()
|
||||
ENDFUNCTION()
|
||||
|
||||
MACRO(PREPEND_GLOBAL_SET VARNAME)
|
||||
ASSERT_DEFINED(${VARNAME})
|
||||
GLOBAL_SET(${VARNAME} ${ARGN} ${${VARNAME}})
|
||||
@ -89,7 +83,7 @@ FUNCTION(KOKKOS_ADD_TEST)
|
||||
CMAKE_PARSE_ARGUMENTS(TEST
|
||||
""
|
||||
"EXE;NAME;TOOL"
|
||||
""
|
||||
"ARGS"
|
||||
${ARGN})
|
||||
IF(TEST_EXE)
|
||||
SET(EXE_ROOT ${TEST_EXE})
|
||||
@ -102,6 +96,7 @@ FUNCTION(KOKKOS_ADD_TEST)
|
||||
NAME ${TEST_NAME}
|
||||
COMM serial mpi
|
||||
NUM_MPI_PROCS 1
|
||||
ARGS ${TEST_ARGS}
|
||||
${TEST_UNPARSED_ARGUMENTS}
|
||||
ADDED_TESTS_NAMES_OUT ALL_TESTS_ADDED
|
||||
)
|
||||
@ -110,18 +105,25 @@ FUNCTION(KOKKOS_ADD_TEST)
|
||||
SET(TEST_NAME ${PACKAGE_NAME}_${TEST_NAME})
|
||||
SET(EXE ${PACKAGE_NAME}_${EXE_ROOT})
|
||||
|
||||
# The function TRIBITS_ADD_TEST() has a CATEGORIES argument that defaults
|
||||
# to BASIC. If a project elects to only enable tests marked as PERFORMANCE,
|
||||
# the test won't actually be added and attempting to set a property on it below
|
||||
# will yield an error.
|
||||
if(TARGET ${EXE})
|
||||
if(TEST_TOOL)
|
||||
add_dependencies(${EXE} ${TEST_TOOL}) #make sure the exe has to build the tool
|
||||
foreach(TEST_ADDED ${ALL_TESTS_ADDED})
|
||||
set_property(TEST ${TEST_ADDED} APPEND PROPERTY ENVIRONMENT "KOKKOS_PROFILE_LIBRARY=$<TARGET_FILE:${TEST_TOOL}>")
|
||||
endforeach()
|
||||
endif()
|
||||
endif()
|
||||
else()
|
||||
CMAKE_PARSE_ARGUMENTS(TEST
|
||||
"WILL_FAIL"
|
||||
"FAIL_REGULAR_EXPRESSION;PASS_REGULAR_EXPRESSION;EXE;NAME;TOOL"
|
||||
"CATEGORIES;CMD_ARGS"
|
||||
"CATEGORIES;ARGS"
|
||||
${ARGN})
|
||||
SET(TESTS_ADDED)
|
||||
# To match Tribits, we should always be receiving
|
||||
# the root names of exes/libs
|
||||
IF(TEST_EXE)
|
||||
@ -133,11 +135,32 @@ FUNCTION(KOKKOS_ADD_TEST)
|
||||
# These should be the full target name
|
||||
SET(TEST_NAME ${PACKAGE_NAME}_${TEST_NAME})
|
||||
SET(EXE ${PACKAGE_NAME}_${EXE_ROOT})
|
||||
IF (TEST_ARGS)
|
||||
SET(TEST_NUMBER 0)
|
||||
FOREACH (ARG_STR ${TEST_ARGS})
|
||||
# This is passed as a single string blob to match TriBITS behavior
|
||||
# We need this to be turned into a list
|
||||
STRING(REPLACE " " ";" ARG_STR_LIST ${ARG_STR})
|
||||
IF(WIN32)
|
||||
ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX} ${TEST_CMD_ARGS})
|
||||
ADD_TEST(NAME ${TEST_NAME}${TEST_NUMBER} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH}
|
||||
COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX} ${ARG_STR_LIST})
|
||||
ELSE()
|
||||
ADD_TEST(NAME ${TEST_NAME} COMMAND ${EXE} ${TEST_CMD_ARGS})
|
||||
ADD_TEST(NAME ${TEST_NAME}${TEST_NUMBER} COMMAND ${EXE} ${ARG_STR_LIST})
|
||||
ENDIF()
|
||||
LIST(APPEND TESTS_ADDED "${TEST_NAME}${TEST_NUMBER}")
|
||||
MATH(EXPR TEST_NUMBER "${TEST_NUMBER} + 1")
|
||||
ENDFOREACH()
|
||||
ELSE()
|
||||
IF(WIN32)
|
||||
ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH}
|
||||
COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX})
|
||||
ELSE()
|
||||
ADD_TEST(NAME ${TEST_NAME} COMMAND ${EXE})
|
||||
ENDIF()
|
||||
LIST(APPEND TESTS_ADDED "${TEST_NAME}")
|
||||
ENDIF()
|
||||
|
||||
FOREACH(TEST_NAME ${TESTS_ADDED})
|
||||
IF(TEST_WILL_FAIL)
|
||||
SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES WILL_FAIL ${TEST_WILL_FAIL})
|
||||
ENDIF()
|
||||
@ -151,6 +174,7 @@ FUNCTION(KOKKOS_ADD_TEST)
|
||||
add_dependencies(${EXE} ${TEST_TOOL}) #make sure the exe has to build the tool
|
||||
set_property(TEST ${TEST_NAME} APPEND_STRING PROPERTY ENVIRONMENT "KOKKOS_PROFILE_LIBRARY=$<TARGET_FILE:${TEST_TOOL}>")
|
||||
endif()
|
||||
ENDFOREACH()
|
||||
VERIFY_EMPTY(KOKKOS_ADD_TEST ${TEST_UNPARSED_ARGUMENTS})
|
||||
endif()
|
||||
ENDFUNCTION()
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user