diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index d08217a590..2f7a09924c 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -21,12 +21,13 @@ Examples .. code-block:: LAMMPS + units real compute cos all viscosity/cos variable V equal c_cos[7] - variable A equal 0.02E-5 + variable A equal 0.02E-5 # A/fs^2 variable density equal density variable lz equal lz - variable reciprocalViscosity equal v_V/${A}/v_density*39.4784/v_lz/v_lz*100 + variable reciprocalViscosity equal v_V/${A}/v_density*39.4784/v_lz/v_lz*100 # 1/(Pa*s) Description """"""""""" diff --git a/doc/src/fix_accelerate_cos.rst b/doc/src/fix_accelerate_cos.rst index 46e08e68b4..904e853ad8 100644 --- a/doc/src/fix_accelerate_cos.rst +++ b/doc/src/fix_accelerate_cos.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * accelerate/cos = style name of this fix command -* value = amplitude of acceleration (in unit of force/mass) +* value = amplitude of acceleration (in unit of velocity/time) Examples diff --git a/src/ADIOS/Install.sh b/src/ADIOS/Install.sh index ddca8c6efe..bd0acb1414 100644 --- a/src/ADIOS/Install.sh +++ b/src/ADIOS/Install.sh @@ -31,17 +31,17 @@ done if (test $1 = 1) then CONFIGSCRIPT=none - if ( test `which adios2-config 2>> /dev/null` ) then + if ( type adios2-config > /dev/null 2>&1 ) then CONFIGSCRIPT=adios2-config elif ( ! test -z "$ADIOS2_DIR" ) then - if ( test `which $ADIOS2_DIR/bin/adios2-config` ) then + if ( type $ADIOS2_DIR/bin/adios2-config > /dev/null 2>&1 ) then CONFIGSCRIPT=$ADIOS2_DIR/bin/adios2-config else echo "ERROR: ADIOS2_DIR environment variable is set but" \ "\$ADIOS2_DIR/bin/adios2-config does not exist" fi elif ( ! test -z "$ADIOS_DIR" ) then - if ( test `which $ADIOS_DIR/bin/adios2-config` ) then + if ( type $ADIOS_DIR/bin/adios2-config > /dev/null 2>&1 ) then CONFIGSCRIPT=$ADIOS_DIR/bin/adios2-config else echo "ERROR: ADIOS_DIR environment variable is set but" \ diff --git a/src/ML-IAP/Install.sh b/src/ML-IAP/Install.sh index 753dfae358..3a1a7493aa 100755 --- a/src/ML-IAP/Install.sh +++ b/src/ML-IAP/Install.sh @@ -46,7 +46,7 @@ action mliap_model_python_couple.pyx python_impl.cpp # edit 2 Makefile.package files to include/exclude package info if (test $1 = 1) then - if (test "$(type cythonize 2> /dev/null)" != "" && test -e ../python_impl.cpp) then + if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then if (test -e ../Makefile.package) then sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package fi @@ -69,7 +69,7 @@ elif (test $1 = 0) then sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings elif (test $1 = 2) then - if (type cythonize 2>&1 > /dev/null && test -e ../python_impl.cpp) then + if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then if (test -e ../Makefile.package) then sed -i -e 's/[^ \t]*-DMLIAP_PYTHON[^ \t]* //g' ../Makefile.package fi diff --git a/src/input.cpp b/src/input.cpp index 6c4fc56776..a28bd48296 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1195,11 +1195,9 @@ void Input::shell() if (me == 0) { for (int i = 1; i < narg; i++) { rv = (platform::mkdir(arg[i]) < 0) ? errno : 0; - MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world); - errno = err; - if (err != 0) - error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'", - arg[i],utils::getsyserror()); + if (rv != 0) + error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'", arg[i], + utils::getsyserror()); } } } else if (strcmp(arg[0],"mv") == 0) { diff --git a/src/utils.h b/src/utils.h index f7f269a97d..6726240d0d 100644 --- a/src/utils.h +++ b/src/utils.h @@ -56,8 +56,7 @@ namespace utils { * \param cmd name of the failing command * \param error pointer to Error class instance (for abort) or nullptr */ - [[noreturn]] void missing_cmd_args(const std::string &file, int line, const std::string &cmd, - Error *error); + void missing_cmd_args(const std::string &file, int line, const std::string &cmd, Error *error); /* Internal function handling the argument list for logmesg(). */ diff --git a/tools/singularity/fedora36_mingw.def b/tools/singularity/fedora36_mingw.def new file mode 100644 index 0000000000..79213e9e92 --- /dev/null +++ b/tools/singularity/fedora36_mingw.def @@ -0,0 +1,125 @@ +BootStrap: docker +From: fedora:36 + +%post + dnf -y update + dnf -y install vim-enhanced git file make cmake patch which file Lmod \ + ninja-build clang clang-tools-extra libomp-devel libubsan libasan libtsan \ + diffutils dos2unix findutils rsync python-devel libjpeg-devel libpng-devel \ + ccache gcc-c++ gcc-gfortran gdb valgrind eigen3-devel openblas-devel \ + openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \ + netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \ + readline-devel python3-pyyaml python3-Cython \ + mingw-filesystem-base mingw32-nsis mingw-binutils-generic \ + mingw32-filesystem mingw32-pkg-config \ + mingw64-filesystem mingw64-pkg-config \ + mingw32-crt mingw32-headers mingw32-binutils \ + mingw64-crt mingw64-headers mingw64-binutils \ + mingw32-cpp mingw32-gcc mingw32-gcc-gfortran mingw32-gcc-c++ \ + mingw64-cpp mingw64-gcc mingw64-gcc-gfortran mingw64-gcc-c++ \ + mingw32-libgomp mingw64-libgomp \ + mingw32-winpthreads mingw64-winpthreads \ + mingw32-eigen3 mingw64-eigen3 \ + mingw32-fftw mingw64-fftw \ + mingw32-libjpeg-turbo mingw64-libjpeg-turbo \ + mingw32-libpng mingw64-libpng \ + mingw32-python3 mingw64-python3 \ + mingw32-python3-numpy mingw64-python3-numpy \ + mingw32-python3-pyyaml mingw64-python3-pyyaml \ + mingw32-python3-setuptools mingw64-python3-setuptools \ + mingw32-readline mingw64-readline \ + mingw32-termcap mingw64-termcap \ + mingw32-zlib mingw64-zlib \ + mingw32-zstd mingw64-zstd \ + enchant python3-virtualenv doxygen latexmk \ + texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \ + texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \ + texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \ + texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \ + texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng texlive-xindy \ + blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel \ + zstd libzstd-devel yaml-cpp-devel + dnf clean all + + # enable Lmod and load MPI + source /usr/share/lmod/lmod/init/profile + module purge + module load mpi + + # manually install Plumed + mkdir plumed + cd plumed + version=2.7.4 + curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz + tar -xzf plumed.tar.gz + cd plumed-${version} + ./configure --disable-doc --prefix=/usr + make + make install + # fix up installation for CentOS and Fedora + mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/ + cd ../../ + rm -rvf plumed + + # create missing termcap pkgconfig files + cat > /usr/i686-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc < /usr/x86_64-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc <$CUSTOM_PROMPT_ENV <$CUSTOM_PROMPT_ENV < + +// whether to print verbose output (i.e. not capturing LAMMPS screen output). +bool verbose = false; + +namespace LAMMPS_NS { + +class Advanced_utils : public LAMMPSTest { +protected: + Error *error; + + void SetUp() override + { + testbinary = "AdvancedUtils"; + LAMMPSTest::SetUp(); + error = lmp->error; + } + + void atomic_system() + { + BEGIN_HIDE_OUTPUT(); + command("units real"); + command("lattice sc 1.0 origin 0.125 0.125 0.125"); + command("region box block -2 2 -2 2 -2 2"); + command("create_box 8 box"); + command("create_atoms 1 box"); + command("pair_style zero 3.5"); + command("pair_coeff * *"); + command("mass * 1.0"); + command("region left block -2.0 -1.0 INF INF INF INF"); + command("region right block 0.5 2.0 INF INF INF INF"); + command("region top block INF INF -2.0 -1.0 INF INF"); + command("set region left type 2"); + command("set region right type 3"); + END_HIDE_OUTPUT(); + } +}; + +TEST_F(Advanced_utils, missing_cmd_args) +{ + auto output = CAPTURE_OUTPUT([&] { + utils::missing_cmd_args(FLERR, "dummy", nullptr); + }); + EXPECT_EQ(output, ""); + + TEST_FAILURE("ERROR: Illegal dummy command: missing argument", + utils::missing_cmd_args(FLERR, "dummy", error);); +}; + +TEST_F(Advanced_utils, logmesg) +{ + auto output = CAPTURE_OUTPUT([&] { + utils::logmesg(lmp, "test message"); + }); + EXPECT_EQ(output, "test message"); + + output = CAPTURE_OUTPUT([&] { + utils::logmesg(lmp, "test message from test {}", testbinary); + }); + EXPECT_EQ(output, "test message from test " + testbinary); +}; + +// death tests only. the other cases are tested in the basic utils unit tester +TEST_F(Advanced_utils, bounds_int_fail) +{ + int nlo, nhi; + TEST_FAILURE("ERROR: Invalid range string: 1x ", + utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: -1 ", + utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: \\+1 ", + utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: 1:3 ", + utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: \\? ", + utils::bounds(FLERR, "?", -10, 5, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: 3\\*:2 ", + utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, error);); +} + +TEST_F(Advanced_utils, bounds_bigint_fail) +{ + bigint nlo, nhi; + TEST_FAILURE("ERROR: Invalid range string: 1x ", + utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: -1 ", + utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: \\+1 ", + utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: 1:3 ", + utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: \\? ", + utils::bounds(FLERR, "?", -10, 5, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: 3\\*:2 ", + utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, error);); +} + +TEST_F(Advanced_utils, expand_args) +{ + atomic_system(); + BEGIN_CAPTURE_OUTPUT(); + command("compute temp all temp"); + command("variable temp vector c_temp"); + command("variable step equal step"); + command("variable pe equal pe"); + command("variable pe equal pe"); + command("variable epair equal epair"); + command("compute gofr all rdf 20 1 1 1 2"); + command("fix 1 all ave/time 1 1 1 v_step v_pe v_epair"); + command("fix 2 all nve"); + command("run 1 post no"); + auto output = END_CAPTURE_OUTPUT(); + + char **args, **earg; + constexpr int oarg = 9; + args = new char *[oarg]; + args[0] = utils::strdup("v_step"); + args[1] = utils::strdup("c_temp"); + args[2] = utils::strdup("f_1[2*]"); + args[3] = utils::strdup("c_temp[2*4]"); + args[4] = utils::strdup("v_temp[*4]"); + args[5] = utils::strdup("c_rdf[*]"); + args[6] = utils::strdup("c_rdf[1][*]"); + args[7] = utils::strdup("c_rdf[*][2]"); + args[8] = utils::strdup("c_rdf[*][*]"); + + auto narg = utils::expand_args(FLERR, oarg, args, 0, earg, lmp); + EXPECT_EQ(narg, 12); + EXPECT_STREQ(earg[0], "v_step"); + EXPECT_STREQ(earg[1], "c_temp"); + EXPECT_STREQ(earg[2], "f_1[2]"); + EXPECT_STREQ(earg[3], "f_1[3]"); + EXPECT_STREQ(earg[4], "c_temp[2]"); + EXPECT_STREQ(earg[5], "c_temp[3]"); + EXPECT_STREQ(earg[6], "c_temp[4]"); + EXPECT_STREQ(earg[7], "v_temp[*4]"); + EXPECT_STREQ(earg[8], "c_rdf[*]"); + EXPECT_STREQ(earg[9], "c_rdf[1][*]"); + EXPECT_STREQ(earg[10], "c_rdf[*][2]"); + EXPECT_STREQ(earg[11], "c_rdf[*][*]"); + + for (int i = 0; i < narg; ++i) + delete[] earg[i]; + lmp->memory->sfree(earg); + + narg = utils::expand_args(FLERR, oarg, args, 1, earg, lmp); + EXPECT_EQ(narg, oarg); + EXPECT_NE(args, earg); + EXPECT_STREQ(earg[0], "v_step"); + EXPECT_STREQ(earg[1], "c_temp"); + EXPECT_STREQ(earg[2], "f_1[2*]"); + EXPECT_STREQ(earg[3], "c_temp[2*4]"); + EXPECT_STREQ(earg[4], "v_temp[*4]"); + EXPECT_STREQ(earg[5], "c_rdf[*]"); + EXPECT_STREQ(earg[6], "c_rdf[1][*]"); + EXPECT_STREQ(earg[7], "c_rdf[*][2]"); + EXPECT_STREQ(earg[8], "c_rdf[*][*]"); + + for (int i = 0; i < oarg; ++i) + delete[] args[i]; + delete[] args; + for (int i = 0; i < narg; ++i) + delete[] earg[i]; + lmp->memory->sfree(earg); +} + +} // namespace LAMMPS_NS + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (platform::mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) + std::cout << "Warning: using OpenMPI without exceptions. Death tests will be skipped\n"; + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} diff --git a/unittest/cplusplus/test_error_class.cpp b/unittest/cplusplus/test_error_class.cpp index 27318646be..a94e6a3e41 100644 --- a/unittest/cplusplus/test_error_class.cpp +++ b/unittest/cplusplus/test_error_class.cpp @@ -1,4 +1,4 @@ -// unit tests for issuing command to a LAMMPS instance through the Input class +// unit tests for public member functions of the Error class #include "error.h" #include "info.h" @@ -129,8 +129,7 @@ int main(int argc, char **argv) ::testing::InitGoogleMock(&argc, argv); if (platform::mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) - std::cout << "Warning: using OpenMPI without exceptions. " - "Death tests will be skipped\n"; + std::cout << "Warning: using OpenMPI without exceptions. Death tests will be skipped\n"; // handle arguments passed via environment variable if (const char *var = getenv("TEST_ARGS")) { diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 900ce6814c..5967ac087a 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -746,6 +746,12 @@ TEST(Utils, boundsbig_case3) ASSERT_EQ(nhi, -1); } +TEST(Utils, errorurl) +{ + auto errmesg = utils::errorurl(10); + ASSERT_THAT(errmesg, Eq("\nFor more information see https://docs.lammps.org/err0010")); +} + TEST(Utils, getsyserror) { #if defined(__linux__)