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Merge branch 'master' into gran_attractive

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This commit is contained in:
Joel Clemmer
2021-04-06 13:11:37 -06:00
parent 80a65150c2 00e4bdb2b7
commit 6294a7c0dd
42 changed files with 522 additions and 148 deletions
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13
doc/src/Build_extras.rst
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@ -125,7 +125,7 @@ CMake build
# default is sm_50
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
# default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no
-D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs)
@ -169,17 +169,24 @@ desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
.. code:: bash
# AMDGPU target
# AMDGPU target (ROCm <= 4.0)
export HIP_PLATFORM=hcc
export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
.. code:: bash
# AMDGPU target (ROCm >= 4.1)
export HIP_PLATFORM=amd
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
.. code:: bash
# CUDA target (not recommended, use GPU_ARCH=cuda)

45
doc/src/Developer_unittest.rst
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@ -4,10 +4,10 @@ Adding tests for unit testing
This section discusses adding or expanding tests for the unit test
infrastructure included into the LAMMPS source code distribution.
Unlike example inputs, unit tests focus on testing the "local" behavior
of individual features, tend to run very fast, and should be set up to
cover as much of the added code as possible. When contributing code to
the distribution, the LAMMPS developers will appreciate if additions
to the integrated unit test facility are included.
of individual features, tend to run fast, and should be set up to cover
as much of the added code as possible. When contributing code to the
distribution, the LAMMPS developers will appreciate if additions to the
integrated unit test facility are included.
Given the complex nature of MD simulations where many operations can
only be performed when suitable "real" simulation environment has been
@ -50,6 +50,9 @@ available:
* - File name:
- Test name:
- Description:
* - ``test_argutils.cpp``
- ArgInfo
- Tests for ``ArgInfo`` class used by LAMMPS
* - ``test_fmtlib.cpp``
- FmtLib
- Tests for ``fmtlib::`` functions used by LAMMPS
@ -155,23 +158,27 @@ have the desired effect:
{
ASSERT_EQ(lmp->update->ntimestep, 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_timestep 10");
if (!verbose) ::testing::internal::GetCapturedStdout();
BEGIN_HIDE_OUTPUT();
command("reset_timestep 10");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_timestep 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
BEGIN_HIDE_OUTPUT();
command("reset_timestep 0");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 0);
TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10"););
TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
}
Please note the use of the (global) verbose variable to control whether
the LAMMPS command will be silent by capturing the output or not. In
the default case, verbose == false, the test output will be compact and
not mixed with LAMMPS output. However setting the verbose flag (via
setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
helpful to understand why tests fail unexpectedly.
Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
functions that will capture output from running LAMMPS. This is normally
discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
environment variable, ``TEST_ARGS=-v``) it can be printed and used to
understand why tests fail unexpectedly.
Another complexity of these tests stems from the need to capture
situations where LAMMPS will stop with an error, i.e. handle so-called
@ -210,6 +217,12 @@ The following test programs are currently available:
* - ``test_lattice_region.cpp``
- LatticeRegion
- Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands
* - ``test_groups.cpp``
- GroupTest
- Tests to validate the :doc:`group <group>` command
* - ``test_variables.cpp``
- VariableTest
- Tests to validate the :doc:`variable <variable>` command
* - ``test_kim_commands.cpp``
- KimCommands
- Tests for several commands from the :ref:`KIM package <PKG-KIM>`

2
doc/src/Packages_standard.rst
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@ -71,6 +71,8 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PLUGIN <PKG-PLUGIN>` | Plugin loader command | :doc:`plugin <plugin>` | plugins | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PYTHON <PKG-PYTHON>` | embed Python code in an input script | :doc:`python <python>` | python | sys |

9
doc/src/rerun.rst
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@ -15,7 +15,7 @@ Syntax
.. parsed-literal::
keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *dump*
keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *post* or *dump*
*first* args = Nfirst
Nfirst = dump timestep to start on
*last* args = Nlast
@ -28,6 +28,7 @@ Syntax
Nstart = timestep on which pseudo run will start
*stop* args = Nstop
Nstop = timestep to which pseudo run will end
*post* value = *yes* or *no*
*dump* args = same as :doc:`read_dump <read_dump>` command starting with its field arguments
Examples
@ -154,6 +155,10 @@ Also note that an error will occur if you read a snapshot from the
dump file with a timestep value larger than the *stop* setting you
have specified.
The *post* keyword can be used to minimize the output to the screen that
happens after a *rerun* command, similar to the post keyword of the
:doc:`run command <run>`. It is set to *no* by default.
The *dump* keyword is required and must be the last keyword specified.
Its arguments are passed internally to the :doc:`read_dump <read_dump>`
command. The first argument following the *dump* keyword should be
@ -226,4 +231,4 @@ Default
The option defaults are first = 0, last = a huge value (effectively
infinity), start = same as first, stop = same as last, every = 0, skip
= 1;
= 1, post = no;