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Merge pull request #4041 from akohlmey/test-fix-numdiff 

Add fix numdiff based tests for bonded interactions
This commit is contained in:
Axel Kohlmeyer 2024-02-06 14:15:28 -05:00 committed by GitHub
parent 98876e0e2f e95d52780c
commit d3784154bf
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GPG Key ID: B5690EEEBB952194
18 changed files with 286 additions and 40 deletions
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78
doc/src/Build_development.rst
View File

@ -122,32 +122,39 @@ Code Coverage and Unit Testing (CMake only)
-------------------------------------------
The LAMMPS code is subject to multiple levels of automated testing
during development: integration testing (i.e. whether the code compiles
on various platforms and with a variety of settings), unit testing
(i.e. whether certain individual parts of the code produce the expected
results for given inputs), run testing (whether selected complete input
decks run without crashing for multiple configurations), and regression
testing (i.e. whether selected input examples reproduce the same
results over a given number of steps and operations within a given
error margin). The status of this automated testing can be viewed on
`https://ci.lammps.org <https://ci.lammps.org>`_.
during development:
- Integration testing (i.e. whether the code compiles
on various platforms and with a variety of compilers and settings),
- Unit testing (i.e. whether certain functions or classes of the code
produce the expected results for given inputs),
- Run testing (i.e. whether selected input decks can run to completion
without crashing for multiple configurations),
- Regression testing (i.e. whether selected input examples reproduce the
same results over a given number of steps and operations within a
given error margin).
The status of this automated testing can be viewed on `https://ci.lammps.org
<https://ci.lammps.org>`_.
The scripts and inputs for integration, run, and regression testing
are maintained in a
`separate repository <https://github.com/lammps/lammps-testing>`_
of the LAMMPS project on GitHub.
of the LAMMPS project on GitHub. A few tests are also run as GitHub
Actions and their configuration files are in the ``.github/workflows/``
folder of the LAMMPS git tree.
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
The unit testing facility is integrated into the CMake build process of
the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <https://pyyaml.org/>`_ library and development
headers (if those are not found locally a recent version will be
downloaded and compiled along with LAMMPS and the test program) to
compile and will download and compile a specific recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.
It requires the `YAML <https://pyyaml.org/>`_ library and matching
development headers to compile (if those are not found locally a recent
version of that library will be downloaded and compiled along with
LAMMPS and the test programs) and will download and compile a specific
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
test framework that is used to implement the tests.
.. admonition:: Software version requirements for testing
.. admonition:: Software version and LAMMPS configuration requirements
:class: note
The compiler and library version requirements for the testing
@ -155,7 +162,7 @@ for implementing the tests.
example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
(version 4.8.x) are not sufficient. The CMake configuration will try
to detect incompatible versions and either skip incompatible tests or
stop with an error. Also the number of tests will depend on
stop with an error. Also the number of available tests will depend on
installed LAMMPS packages, development environment, operating system,
and configuration settings.
@ -234,12 +241,31 @@ will be skipped if prerequisite features are not available in LAMMPS.
time. Preference is given to parts of the code base that are easy to
test or commonly used.
Tests for styles of the same kind of style (e.g. pair styles or bond
styles) are performed with the same test executable using different
input files in YAML format. So to add a test for another style of the
same kind it may be sufficient to add a suitable YAML file.
:doc:`Detailed instructions for adding tests <Developer_unittest>` are
provided in the Programmer Guide part of the manual.
Tests as shown by the ``ctest`` program are command lines defined in the
``CMakeLists.txt`` files in the ``unittest`` directory tree. A few
tests simply execute LAMMPS with specific command line flags and check
the output to the screen for expected content. A large number of unit
tests are special tests programs using the `GoogleTest framework
<https://github.com/google/googletest/>`_ and linked to the LAMMPS
library that test individual functions or create a LAMMPS class
instance, execute one or more commands and check data inside the LAMMPS
class hierarchy. There are also tests for the C-library, Fortran, and
Python module interfaces to LAMMPS. The Python tests use the Python
"unittest" module in a similar fashion than the others use `GoogleTest`.
These special test programs are structured to perform multiple
individual tests internally and each of those contains several checks
(aka assertions) for internal data being changed as expected.
Tests for force computing or modifying styles (e.g. styles for non-bonded
and bonded interactions and selected fixes) are run by using a more generic
test program that reads its input from files in YAML format. The YAML file
provides the information on how to customized the test program to test
a specific style and - if needed - with specific settings.
To add a test for another, similar style (e.g. a new pair style) it is
usually sufficient to add a suitable YAML file. :doc:`Detailed
instructions for adding tests <Developer_unittest>` are provided in the
Programmer Guide part of the manual. A description of what happens
during the tests is given below.
Unit tests for force styles
^^^^^^^^^^^^^^^^^^^^^^^^^^^

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -3797,6 +3797,7 @@ unimodal
uninstall
unitarg
unitless
unittest
Universite
unix
unmaintained

54
unittest/force-styles/test_angle_style.cpp
View File

@ -27,6 +27,7 @@
#include "atom.h"
#include "compute.h"
#include "exceptions.h"
#include "fix.h"
#include "fmt/format.h"
#include "force.h"
#include "info.h"
@ -528,6 +529,59 @@ TEST(AngleStyle, omp)
if (!verbose) ::testing::internal::GetCapturedStdout();
};
TEST(AngleStyle, numdiff)
{
if (!LAMMPS::is_installed_pkg("EXTRA-FIX")) GTEST_SKIP();
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
LAMMPS::argv args = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite"};
::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(args, test_config, true);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
}
EXPECT_THAT(output, StartsWith("LAMMPS ("));
EXPECT_THAT(output, HasSubstr("Loop time"));
// abort if running in parallel and not all atoms are local
const int nlocal = lmp->atom->nlocal;
ASSERT_EQ(lmp->atom->natoms, nlocal);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("fix diff all numdiff 2 6.05504e-6");
lmp->input->one("run 2 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
Fix *ifix = lmp->modify->get_fix_by_id("diff");
if (ifix) {
double epsilon = test_config.epsilon * 5.0e8;
ErrorStats stats;
double **f1 = lmp->atom->f;
double **f2 = ifix->array_atom;
SCOPED_TRACE("EXPECT FORCES: numdiff");
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f1[i][0], f2[i][0], epsilon);
EXPECT_FP_LE_WITH_EPS(f1[i][1], f2[i][1], epsilon);
EXPECT_FP_LE_WITH_EPS(f1[i][2], f2[i][2], epsilon);
}
if (print_stats)
std::cerr << "numdiff stats: " << stats << " epsilon: " << epsilon << std::endl;
}
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
}
TEST(AngleStyle, single)
{
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();

55
unittest/force-styles/test_bond_style.cpp
View File

@ -27,6 +27,7 @@
#include "bond.h"
#include "compute.h"
#include "exceptions.h"
#include "fix.h"
#include "fmt/format.h"
#include "force.h"
#include "info.h"
@ -530,6 +531,60 @@ TEST(BondStyle, omp)
if (!verbose) ::testing::internal::GetCapturedStdout();
};
TEST(BondStyle, numdiff)
{
if (!LAMMPS::is_installed_pkg("EXTRA-FIX")) GTEST_SKIP();
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
LAMMPS::argv args = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"};
::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(args, test_config, true);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
}
EXPECT_THAT(output, StartsWith("LAMMPS ("));
EXPECT_THAT(output, HasSubstr("Loop time"));
// abort if running in parallel and not all atoms are local
const int nlocal = lmp->atom->nlocal;
ASSERT_EQ(lmp->atom->natoms, nlocal);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("fix diff all numdiff 2 6.05504e-6");
lmp->input->one("run 2 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
Fix *ifix = lmp->modify->get_fix_by_id("diff");
if (ifix) {
double epsilon = test_config.epsilon * 5.0e8;
ErrorStats stats;
double **f1 = lmp->atom->f;
double **f2 = ifix->array_atom;
SCOPED_TRACE("EXPECT FORCES: numdiff");
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f1[i][0], f2[i][0], epsilon);
EXPECT_FP_LE_WITH_EPS(f1[i][1], f2[i][1], epsilon);
EXPECT_FP_LE_WITH_EPS(f1[i][2], f2[i][2], epsilon);
}
if (print_stats)
std::cerr << "numdiff stats: " << stats << " epsilon: " << epsilon << std::endl;
}
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
}
TEST(BondStyle, single)
{
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();

55
unittest/force-styles/test_dihedral_style.cpp
View File

@ -27,6 +27,7 @@
#include "compute.h"
#include "dihedral.h"
#include "exceptions.h"
#include "fix.h"
#include "fmt/format.h"
#include "force.h"
#include "info.h"
@ -531,3 +532,57 @@ TEST(DihedralStyle, omp)
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
};
TEST(DihedralStyle, numdiff)
{
if (!LAMMPS::is_installed_pkg("EXTRA-FIX")) GTEST_SKIP();
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
LAMMPS::argv args = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite"};
::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(args, test_config, true);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
}
EXPECT_THAT(output, StartsWith("LAMMPS ("));
EXPECT_THAT(output, HasSubstr("Loop time"));
// abort if running in parallel and not all atoms are local
const int nlocal = lmp->atom->nlocal;
ASSERT_EQ(lmp->atom->natoms, nlocal);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("fix diff all numdiff 2 6.05504e-6");
lmp->input->one("run 2 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
Fix *ifix = lmp->modify->get_fix_by_id("diff");
if (ifix) {
double epsilon = test_config.epsilon * 5.0e8;
ErrorStats stats;
double **f1 = lmp->atom->f;
double **f2 = ifix->array_atom;
SCOPED_TRACE("EXPECT FORCES: numdiff");
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f1[i][0], f2[i][0], epsilon);
EXPECT_FP_LE_WITH_EPS(f1[i][1], f2[i][1], epsilon);
EXPECT_FP_LE_WITH_EPS(f1[i][2], f2[i][2], epsilon);
}
if (print_stats)
std::cerr << "numdiff stats: " << stats << " epsilon: " << epsilon << std::endl;
}
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
}

54
unittest/force-styles/test_improper_style.cpp
View File

@ -26,6 +26,7 @@
#include "atom.h"
#include "compute.h"
#include "exceptions.h"
#include "fix.h"
#include "fmt/format.h"
#include "force.h"
#include "improper.h"
@ -524,3 +525,56 @@ TEST(ImproperStyle, omp)
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
};
TEST(ImproperStyle, numdiff)
{
if (!LAMMPS::is_installed_pkg("EXTRA-FIX")) GTEST_SKIP();
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
LAMMPS::argv args = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite"};
::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(args, test_config, true);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
}
EXPECT_THAT(output, StartsWith("LAMMPS ("));
EXPECT_THAT(output, HasSubstr("Loop time"));
// abort if running in parallel and not all atoms are local
const int nlocal = lmp->atom->nlocal;
ASSERT_EQ(lmp->atom->natoms, nlocal);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("fix diff all numdiff 2 6.05504e-6");
lmp->input->one("run 2 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
Fix *ifix = lmp->modify->get_fix_by_id("diff");
if (ifix) {
double epsilon = test_config.epsilon * 5.0e8;
ErrorStats stats;
double **f1 = lmp->atom->f;
double **f2 = ifix->array_atom;
SCOPED_TRACE("EXPECT FORCES: numdiff");
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f1[i][0], f2[i][0], epsilon);
EXPECT_FP_LE_WITH_EPS(f1[i][1], f2[i][1], epsilon);
EXPECT_FP_LE_WITH_EPS(f1[i][2], f2[i][2], epsilon);
}
if (print_stats)
std::cerr << "numdiff stats: " << stats << " epsilon: " << epsilon << std::endl;
}
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
}

8
unittest/force-styles/test_main.cpp
View File

@ -47,7 +47,7 @@ void EXPECT_STRESS(const std::string &name, double *stress, const stress_t &expe
EXPECT_FP_LE_WITH_EPS(stress[3], expected_stress.xy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], expected_stress.xz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], expected_stress.yz, epsilon);
if (print_stats) std::cerr << name << " stats" << stats << std::endl;
if (print_stats) std::cerr << name << " stats: " << stats << std::endl;
}
void EXPECT_FORCES(const std::string &name, Atom *atom, const std::vector<coord_t> &f_ref,
@ -64,7 +64,7 @@ void EXPECT_FORCES(const std::string &name, Atom *atom, const std::vector<coord_
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << name << " stats" << stats << std::endl;
if (print_stats) std::cerr << name << " stats: " << stats << std::endl;
}
void EXPECT_POSITIONS(const std::string &name, Atom *atom, const std::vector<coord_t> &x_ref,
@ -81,7 +81,7 @@ void EXPECT_POSITIONS(const std::string &name, Atom *atom, const std::vector<coo
EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << name << " stats" << stats << std::endl;
if (print_stats) std::cerr << name << " stats: " << stats << std::endl;
}
void EXPECT_VELOCITIES(const std::string &name, Atom *atom, const std::vector<coord_t> &v_ref,
@ -98,7 +98,7 @@ void EXPECT_VELOCITIES(const std::string &name, Atom *atom, const std::vector<co
EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << name << " stats" << stats << std::endl;
if (print_stats) std::cerr << name << " stats: " << stats << std::endl;
}
// common read_yaml_file function

2
unittest/force-styles/tests/angle-cosine_delta.yaml
View File

@ -2,7 +2,7 @@
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:51 2022
epsilon: 5e-13
skip_tests:
skip_tests: numdiff
prerequisites: ! |
atom full
angle cosine/delta

1
unittest/force-styles/tests/angle-fourier_simple.yaml
View File

@ -5,6 +5,7 @@ epsilon: 2.5e-13
prerequisites: ! |
atom full
angle fourier/simple
skip_tests: numdiff
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol

2
unittest/force-styles/tests/angle-mm3.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:52 2022
epsilon: 2.5e-13
epsilon: 2.5e-12
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/angle-table_linear.yaml
View File

@ -2,7 +2,7 @@
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:52 2022
epsilon: 5e-13
skip_tests:
skip_tests: numdiff
prerequisites: ! |
atom full
angle table

2
unittest/force-styles/tests/bond-table_linear.yaml
View File

@ -2,7 +2,7 @@
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:51 2022
epsilon: 2.5e-13
skip_tests:
skip_tests: numdiff
prerequisites: ! |
atom full
bond table

2
unittest/force-styles/tests/dihedral-charmm.yaml
View File

@ -2,7 +2,7 @@
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:01 2022
epsilon: 2.5e-13
skip_tests:
skip_tests: numdiff
prerequisites: ! |
atom full
dihedral charmm

2
unittest/force-styles/tests/dihedral-charmmfsw.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:02 2022
epsilon: 2.5e-13
epsilon: 5.0e-12
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/dihedral-table_cut_linear.yaml
View File

@ -3,7 +3,7 @@ lammps_version: 17 Feb 2022
tags: unstable
date_generated: Fri Mar 18 22:18:02 2022
epsilon: 1e-13
skip_tests:
skip_tests: numdiff
prerequisites: ! |
atom full
dihedral table/cut

2
unittest/force-styles/tests/dihedral-table_linear.yaml
View File

@ -3,7 +3,7 @@ lammps_version: 22 Dec 2022
tags: unstable
date_generated: Mon Dec 26 16:49:31 2022
epsilon: 7.5e-14
skip_tests:
skip_tests: numdiff
prerequisites: ! |
atom full
dihedral table

2
unittest/force-styles/tests/dihedral-table_spline.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 22 Dec 2022
date_generated: Mon Dec 26 16:49:37 2022
epsilon: 1e-13
epsilon: 1.0e-13
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/improper-cossq.yaml
View File

@ -2,7 +2,7 @@
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:02 2022
epsilon: 2.5e-13
skip_tests:
skip_tests: numdiff
prerequisites: ! |
atom full
improper cossq