4.6. 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.

Given the complex nature of MD simulations where many operations can only be performed when suitable “real” simulation environment has been set up, not all tests will be unit tests in the strict definition of the term. They are rather executed on a more abstract level by issuing LAMMPS script commands and then inspecting the changes to the internal data. For some classes of tests, generic test programs have been written that can be applied to parts of LAMMPS that use the same interface (via polymorphism) and those are driven by input files, so tests can be added by simply adding more of those input files. Those tests should be seen more as a hybrid between unit and regression tests.

When adding tests it is recommended to also enable support for code coverage reporting, and study the coverage reports so that it is possible to monitor which parts of the code of a given file are executed during the tests and which tests would need to be added to increase the coverage.

The tests are grouped into categories and corresponding folders. The following sections describe how the tests are implemented and executed in those categories with increasing complexity of tests and implementation.

4.6.1. Tests for utility functions

These tests are driven by programs in the unittest/utils folder and most closely resemble conventional unit tests. There is one test program for each namespace or group of classes or file. The naming convention for the sources and executables is that they start with with test_. The following sources and groups of tests are currently available:

File name:

Test name:

Description:

test_fmtlib.cpp

FmtLib

Tests for fmtlib:: functions used by LAMMPS

test_math_eigen_impl.cpp

MathEigen

Tests for MathEigen:: classes and functions

test_mempool.cpp

MemPool

Tests for MyPage and MyPoolChunk

test_tokenizer.cpp

Tokenizer

Tests for Tokenizer and ValueTokenizer

test_utils.cpp

Utils

Tests for utils:: functions

To add tests either an existing source file needs to be modified or a new source file needs to be added to the distribution and enabled for testing. To add a new file suitable CMake script code needs to be added to the CMakeLists.txt file in the unittest/utils folder. Example:

add_executable(test_tokenizer test_tokenizer.cpp)
target_link_libraries(test_tokenizer PRIVATE lammps GTest::GMockMain GTest::GMock GTest::GTest)
add_test(Tokenizer test_tokenizer)

This adds instructions to build the test_tokenizer executable from test_tokenizer.cpp and links it with the GoogleTest libraries and the LAMMPS library as well as it uses the main() function from the GoogleMock library of GoogleTest. The third line registers the executable as a test program to be run from ctest under the name Tokenizer.

The test executable itself will execute multiple individual tests through the GoogleTest framework. In this case each test consists of creating a tokenizer class instance with a given string and explicit or default separator choice, and then executing member functions of the class and comparing their results with expected values. A few examples:

TEST(Tokenizer, empty_string)
{
    Tokenizer t("", " ");
    ASSERT_EQ(t.count(), 0);
}

TEST(Tokenizer, two_words)
{
    Tokenizer t("test word", " ");
    ASSERT_EQ(t.count(), 2);
}

TEST(Tokenizer, default_separators)
{
    Tokenizer t(" \r\n test \t word \f");
    ASSERT_THAT(t.next(), Eq("test"));
    ASSERT_THAT(t.next(), Eq("word"));
    ASSERT_EQ(t.count(), 2);
}

Each of these TEST functions will become an individual test run by the test program. When using the ctest command as a front end to run the tests, their output will be suppressed and only a summary printed, but adding the ‘-V’ option will then produce output from the tests above like the following:

[...]
1: [ RUN      ] Tokenizer.empty_string
1: [       OK ] Tokenizer.empty_string (0 ms)
1: [ RUN      ] Tokenizer.two_words
1: [       OK ] Tokenizer.two_words (0 ms)
1: [ RUN      ] Tokenizer.default_separators
1: [       OK ] Tokenizer.default_separators (0 ms)
[...]

The MathEigen test collection has been adapted from a standalone test and does not use the GoogleTest framework and thus not representative. The other test sources, however, can serve as guiding examples for additional tests.

4.6.2. Tests for individual LAMMPS commands

The tests unittest/commands are a bit more complex as they require to first create a LAMMPS class instance and then use the C++ API to pass individual commands to that LAMMPS instance. For that reason these tests use a GoogleTest “test fixture”, i.e. a class derived from testing::Test that will create (and delete) the required LAMMPS class instance for each set of tests in a TEST_F() function. Please see the individual source files for different examples of setting up suitable test fixtures. Here is an example for implementing a test using a fixture by first checking the default value and then issuing LAMMPS commands and checking whether they have the desired effect:

TEST_F(SimpleCommandsTest, ResetTimestep)
{
    ASSERT_EQ(lmp->update->ntimestep, 0);

    if (!verbose) ::testing::internal::CaptureStdout();
    lmp->input->one("reset_timestep 10");
    if (!verbose) ::testing::internal::GetCapturedStdout();
    ASSERT_EQ(lmp->update->ntimestep, 10);

    if (!verbose) ::testing::internal::CaptureStdout();
    lmp->input->one("reset_timestep 0");
    if (!verbose) ::testing::internal::GetCapturedStdout();
    ASSERT_EQ(lmp->update->ntimestep, 0);
}

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.

Another complexity of these tests stems from the need to capture situations where LAMMPS will stop with an error, i.e. handle so-called “death tests”. Here the LAMMPS code will operate differently depending on whether it was configured to throw C++ exceptions on errors or call either exit() or MPI_Abort(). In the latter case, the test code also needs to detect whether LAMMPS was compiled with the OpenMPI library, as OpenMPI is only compatible the death test options of the GoogleTest library when C++ exceptions are enabled; otherwise those “death tests” must be skipped to avoid reporting bogus failures. The specifics of this step are implemented in the TEST_FAILURE() macro. These tests operate by capturing the screen output when executing the failing command and then comparing that with a provided regular expression string pattern. Example:

TEST_F(SimpleCommandsTest, UnknownCommand)
{
    TEST_FAILURE(".*ERROR: Unknown command.*", lmp->input->one("XXX one two"););
}

The following test programs are currently available:

File name:

Test name:

Description:

test_simple_commands.cpp

SimpleCommands

Tests for LAMMPS commands that do not require a box

test_lattice_region.cpp

LatticeRegion

Tests to validate the lattice and region commands

test_kim_commands.cpp

KimCommands

Tests for several commands from the KIM package

test_reset_ids.cpp

ResetIDs

Tests to validate the reset_atom_ids and reset_mol_ids commands

4.6.3. Tests for the C-style library interface

Tests for validating the LAMMPS C-style library interface are in the unittest/c-library folder. They are implemented in either way used for utility functions and for LAMMPS commands, but use the functions implemented in the src/library.cpp file as much as possible. There may be some overlap with other tests, but only in as much as is required to test the C-style library API. The tests are distributed over multiple test programs which tries to match the grouping of the functions in the source code and in the manual.

This group of tests also includes tests invoking LAMMPS in parallel through the library interface, provided that LAMMPS was compiled with MPI support. These include tests where LAMMPS is run in multi-partition mode or only on a subset of the MPI world communicator. The CMake script code for adding this kind of test looks like this:

if (BUILD_MPI)
  add_executable(test_library_mpi test_library_mpi.cpp)
  target_link_libraries(test_library_mpi PRIVATE lammps GTest::GTest GTest::GMock)
  target_compile_definitions(test_library_mpi PRIVATE ${TEST_CONFIG_DEFS})
  add_mpi_test(NAME LibraryMPI NUM_PROCS 4 COMMAND $<TARGET_FILE:test_library_mpi>)
endif()

Note the custom function add_mpi_test() which adapts how ctest will execute the test so it is launched in parallel (with 4 MPI ranks).

4.6.4. Tests for the Python module and package

The unittest/python folder contains primarily tests for classes and functions in the LAMMPS python module but also for commands in the PYTHON package. These tests are only enabled, if the necessary prerequisites are detected or enabled during configuration and compilation of LAMMPS (shared library build enabled, Python interpreter found, Python development files found).

The Python tests are implemented using the unittest standard Python module and split into multiple files with similar categories as the tests for the C-style library interface.

4.6.5. Tests for the Fortran interface

Tests for using the Fortran module are in the unittest/fortran folder. Since they are also using the GoogleTest library, they require to also implement test wrappers in C++ that will call fortran functions which provide a C function interface through ISO_C_BINDINGS that will in turn call the functions in the LAMMPS Fortran module. This part of the unit tests is incomplete since the Fortran module it is based on is incomplete as well.

4.6.6. Tests for the C++-style library interface

The tests in the unittest/cplusplus folder are somewhat similar to the tests for the C-style library interface, but do not need to test the several convenience and utility functions that are only available through the C-style interface. Instead it can focus on the more generic features that are used internally. This part of the unit tests is currently still mostly in the planning stage.

4.6.7. Tests for reading and writing file formats

The unittest/formats folder contains test programs for reading and writing files like data files, restart files, potential files or dump files. This covers simple things like the file i/o convenience functions in the utils:: namespace to complex tests of atom styles where creating and deleting of atoms with different properties is tested in different ways and through script commands or reading and writing of data or restart files.

4.6.8. Tests for styles computing or modifying forces

These are tests common configurations for pair styles, bond styles, angle styles, kspace styles and certain fix styles. Those are tests driven by some test executables build from sources in the unittest/force-styles folder and use LAMMPS input template and data files as well as input files in YAML format from the unittest/force-styles/tests folder. The YAML file names have to follow some naming conventions so they get associated with the test programs and categorized and listed with canonical names in the list of tests as displayed by ctest -N. If you add a new YAML file, you need to re-run CMake to update the corresponding list of tests.

A minimal YAML file for a (molecular) pair style test will looks something like the following (see mol-pair-zero.yaml):

---
lammps_version: 24 Aug 2020
date_generated: Tue Sep 15 09:44:21 202
epsilon: 1e-14
prerequisites: ! |
  atom full
  pair zero
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
pair_style: zero 8.0
pair_coeff: ! |
  * *
extract: ! ""
natoms: 29
init_vdwl: 0
init_coul: 0

[...]

The following table describes the available keys and their purpose for testing pair styles:

Key:

Description:

lammps_version

LAMMPS version used to last update the reference data

date_generated

date when the file was last updated

epsilon

base value for the relative precision required for tests to pass

prerequisites

list of style kind / style name pairs required to run the test

pre_commands

LAMMPS commands to be executed before the input template file is read

post_commands

LAMMPS commands to be executed right before the actual tests

input_file

LAMMPS input file template based on pair style zero

pair_style

arguments to the pair_style command to be tested

pair_coeff

list of pair_coeff arguments to set parameters for the input template

extract

list of keywords supported by Pair::extract() and their dimension

natoms

number of atoms in the input file template

init_vdwl

non-Coulomb pair energy after “run 0”

init_coul

Coulomb pair energy after “run 0”

init_stress

stress tensor after “run 0”

init_forces

forces on atoms after “run 0”

run_vdwl

non-Coulomb pair energy after “run 4”

run_coul

Coulomb pair energy after “run 4”

run_stress

stress tensor after “run 4”

run_forces

forces on atoms after “run 4”

The test program will read all this data from the YAML file and then create a LAMMPS instance, apply the settings/commands from the YAML file as needed and then issue a “run 0” command, write out a restart file, a data file and a coeff file. The actual test will then compare computed energies, stresses, and forces with the reference data, issue a “run 4” command and compare to the second set of reference data. This will be run with both the newton_pair setting enabled and disabled and is expected to generate the same results (allowing for some numerical noise). Then it will restart from the previously generated restart and compare with the reference and also start from the data file. A final check will use multi-cutoff r-RESPA (if supported by the pair style) at a 1:1 split and compare to the Verlet results. These sets of tests are run with multiple test fixtures for accelerated styles (OPT, USER-OMP, USER-INTEL) and for the latter two with 4 OpenMP threads enabled. For these tests the relative error (epsilon) is lowered by a common factor due to the additional numerical noise, but the tests are still comparing to the same reference data.

Additional tests will check whether all listed extract keywords are supported and have the correct dimensionality and the final set of tests will set up a few pairs of atoms explicitly and in such a fashion that the forces on the atoms computed from Pair::compute() will match individually with the results from Pair::single(), if the pair style does support that functionality.

With this scheme a large fraction of the code of any tested pair style will be executed and consistent results are required for different settings and between different accelerated pair style variants and the base class, as well as for computing individual pairs through the Pair::single() where supported.

The test_pair_style tester is used with 4 categories of test inputs:

  • pair styles compatible with molecular systems using bonded interactions and exclusions. For pair styles requiring a KSpace style the KSpace computations are disabled. The YAML files match the pattern “mol-pair-*.yaml” and the tests are correspondingly labeled with “MolPairStyle:*”

  • pair styles not compatible with the previous input template. The YAML files match the pattern “atomic-pair-*.yaml” and the tests are correspondingly labeled with “AtomicPairStyle:*”

  • manybody pair styles. The YAML files match the pattern “atomic-pair-*.yaml” and the tests are correspondingly labeled with “AtomicPairStyle:*”

  • kspace styles. The YAML files match the pattern “kspace-*.yaml” and the tests are correspondingly labeled with “KSpaceStyle:*”. In these cases a compatible pair style is defined, but the computation of the pair style contributions is disabled.

The test_bond_style and test_angle_style are set up in a similar fashion and share support functions with the pair style tester. The final group of tests in this section is for fix styles that add/manipulate forces and velocities, e.g. for time integration, thermostats and more.

Adding a new test is easiest done by copying and modifying an existing test for a style that is similar to one to be tested. The file name should follow the naming conventions described above and after copying the file, the first step is to replace the style names where needed. The coefficient values do not have to be meaningful, just in a reasonable range for the given system. It does not matter if some forces are large, for as long as they do not diverge.

The template input files define a large number of index variables at the top that can be modified inside the YAML file to control the behavior. For example, if a pair style requires a “newton on” setting, the following can be used in as the “pre_commands” section:

pre_commands: ! |
  variable newton_pair delete
  variable newton_pair index on

And for a pair style requiring a kspace solver the following would be used as the “post_commands” section:

post_commands: ! |
  pair_modify table 0
  kspace_style pppm/tip4p 1.0e-6
  kspace_modify gewald 0.3
  kspace_modify compute no

Note that this disables computing the kspace contribution, but still will run the setup. The “gewald” parameter should be set explicitly to speed up the run. For styles with long-range electrostatics, typically two tests are added one using the (slower) analytic approximation of the erfc() function and the other using the tabulated coulomb, to test both code paths. The reference results in the YAML files then should be compared manually, if they agree well enough within the limits of those two approximations.

The test_pair_style and equivalent programs have special command line options to update the YAML files. Running a command like

$ test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml

will read the settings from the mol-pair-lennard_mdf.yaml file and then compute the reference data and write a new file with to new.yaml. If this step fails, there are likely some (LAMMPS or YAML) syntax issues in the YAML file that need to be resolved and then one can compare the two files to see if the output is as expected.

It is also possible to do an update in place with:

$ test_pair_style mol-pair-lennard_mdf.yaml -u

And one can finally run the full set of tests with:

$ test_pair_style mol-pair-lennard_mdf.yaml

This will just print a summary of the groups of tests. When using the “-v” flag the test will also keep any LAMMPS output and when using the “-s” flag, there will be some statistics reported on the relative errors for the individual checks which can help to figure out what would be a good choice of the epsilon parameter. It should be as small as possible to catch any unintended side effects from changes elsewhere, but large enough to accommodate the numerical noise due to the implementation of the potentials and differences in compilers.

Note

These kinds of tests can be very sensitive to compiler optimization and thus the expectation is that they pass with compiler optimization turned off. When compiler optimization is enabled, there may be some failures, but one has to carefully check whether those are acceptable due to the enhanced numerical noise from reordering floating-point math operations or due to the compiler mis-compiling the code. That is not always obvious.

4.6.9. Tests for programs in the tools folder

The unittest/tools folder contains tests for programs in the tools folder. This currently only contains tests for the LAMMPS shell, which are implemented as a python scripts using the unittest Python module and launching the tool commands through the subprocess Python module.