Merge branch 'master' into refactor-reaxff-parser

# Conflicts:
#	doc/src/fix_qeq_reax.rst
#	src/OPENMP/reaxc_bond_orders_omp.h
#	src/OPENMP/reaxc_bonds_omp.h
#	src/OPENMP/reaxc_forces_omp.h
#	src/OPENMP/reaxc_hydrogen_bonds_omp.h
#	src/OPENMP/reaxc_init_md_omp.cpp
#	src/OPENMP/reaxc_init_md_omp.h
#	src/OPENMP/reaxc_multi_body_omp.h
#	src/OPENMP/reaxc_nonbonded_omp.h
#	src/OPENMP/reaxc_torsion_angles_omp.h
#	src/OPENMP/reaxc_valence_angles_omp.h
#	src/OPENMP/reaxff_omp.h
#	src/Purge.list
#	src/QEQ/fix_qeq.cpp
#	src/QEQ/fix_qeq.h
#	src/QEQ/fix_qeq_dynamic.cpp
#	src/QEQ/fix_qeq_fire.cpp
#	src/REAXFF/fix_qeq_reax.cpp
#	src/REAXFF/reaxc_allocate.h
#	src/REAXFF/reaxc_bond_orders.h
#	src/REAXFF/reaxc_bonds.h
#	src/REAXFF/reaxc_control.h
#	src/REAXFF/reaxc_defs.h
#	src/REAXFF/reaxc_ffield.h
#	src/REAXFF/reaxc_forces.h
#	src/REAXFF/reaxc_hydrogen_bonds.h
#	src/REAXFF/reaxc_init_md.cpp
#	src/REAXFF/reaxc_init_md.h
#	src/REAXFF/reaxc_io_tools.cpp
#	src/REAXFF/reaxc_io_tools.h
#	src/REAXFF/reaxc_list.h
#	src/REAXFF/reaxc_lookup.h
#	src/REAXFF/reaxc_multi_body.h
#	src/REAXFF/reaxc_nonbonded.h
#	src/REAXFF/reaxc_reset_tools.h
#	src/REAXFF/reaxc_system_props.cpp
#	src/REAXFF/reaxc_system_props.h
#	src/REAXFF/reaxc_tool_box.h
#	src/REAXFF/reaxc_torsion_angles.h
#	src/REAXFF/reaxc_traj.cpp
#	src/REAXFF/reaxc_traj.h
#	src/REAXFF/reaxc_types.h
#	src/REAXFF/reaxc_valence_angles.h
#	src/REAXFF/reaxc_vector.cpp
#	src/REAXFF/reaxc_vector.h
#	src/REAXFF/reaxff_api.h
#	src/REAXFF/reaxff_defs.h
#	src/REAXFF/reaxff_inline.h
#	src/REAXFF/reaxff_types.h
#	src/text_file_reader.cpp
#	src/text_file_reader.h
#	unittest/force-styles/tests/atomic-pair-reax_c.yaml
#	unittest/force-styles/tests/atomic-pair-reax_c_lgvdw.yaml
#	unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml

unittest/commands/CMakeLists.txt

@@ -1,6 +1,6 @@
 
 # build LAMMPS plugins, but not on Windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" AND PKG_PLUGIN)
+if((NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows")) AND PKG_PLUGIN)
   ExternalProject_Add(plugins
                       SOURCE_DIR      "${LAMMPS_DIR}/examples/plugins"
                       BINARY_DIR      ${CMAKE_BINARY_DIR}/build-plugins
@@ -56,3 +56,10 @@ add_executable(test_reset_ids test_reset_ids.cpp)
 target_compile_definitions(test_reset_ids PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
 target_link_libraries(test_reset_ids PRIVATE lammps GTest::GMock GTest::GTest)
 add_test(NAME ResetIDs COMMAND test_reset_ids WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+
+if(BUILD_MPI)
+  add_executable(test_mpi_load_balancing test_mpi_load_balancing.cpp)
+  target_link_libraries(test_mpi_load_balancing PRIVATE lammps GTest::GTest GTest::GMock)
+  target_compile_definitions(test_mpi_load_balancing PRIVATE ${TEST_CONFIG_DEFS})
+  add_mpi_test(NAME MPILoadBalancing NUM_PROCS 4 COMMAND $<TARGET_FILE:test_mpi_load_balancing>)
+endif()

unittest/commands/test_groups.cpp

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract

unittest/commands/test_kim_commands.cpp

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract

unittest/commands/test_lattice_region.cpp

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract

unittest/commands/test_mpi_load_balancing.cpp

@@ -0,0 +1,257 @@
+// unit tests for checking LAMMPS MPI load balancing
+
+#define LAMMPS_LIB_MPI 1
+#include "lammps.h"
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "neighbor.h"
+#include "input.h"
+#include "timer.h"
+#include "info.h"
+#include <string>
+
+#include "gmock/gmock.h"
+#include "gtest/gtest.h"
+
+#include "../testing/test_mpi_main.h"
+
+using ::testing::ExitedWithCode;
+using ::testing::HasSubstr;
+using ::testing::StartsWith;
+using ::testing::StrEq;
+
+namespace LAMMPS_NS
+{
+
+class MPILoadBalanceTest : public ::testing::Test {
+public:
+    void command(const std::string &line) { lmp->input->one(line); }
+
+protected:
+    const char *testbinary = "LAMMPSTest";
+    LAMMPS *lmp;
+
+    void SetUp() override
+    {
+        const char *args[] = {testbinary, "-log", "none", "-echo", "screen", "-nocite"};
+        char **argv        = (char **)args;
+        int argc           = sizeof(args) / sizeof(char *);
+        if (!verbose) ::testing::internal::CaptureStdout();
+        lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
+        InitSystem();
+        if (!verbose) ::testing::internal::GetCapturedStdout();
+    }
+
+    virtual void InitSystem()
+    {
+        command("boundary        f f f");
+        command("units           lj");
+        command("atom_style      atomic");
+        command("atom_modify     map yes");
+
+        command("region          box block 0 20 0 20 0 20");
+        command("create_box      1 box");
+        command("mass            1 1.0");
+
+
+        command("pair_style      lj/cut 2.5");
+        command("pair_coeff      1 1 1.0 1.0 2.5");
+
+        command("neighbor        0.3 bin");
+        command("neigh_modify    every 20 delay 0 check no");
+    }
+
+    void TearDown() override
+    {
+        if (!verbose) ::testing::internal::CaptureStdout();
+        delete lmp;
+        lmp = nullptr;
+        if (!verbose) ::testing::internal::GetCapturedStdout();
+    }
+};
+
+TEST_F(MPILoadBalanceTest, grid_yz)
+{
+    command("create_atoms 1 single 0 0 0");
+    command("create_atoms 1 single 0 0 5");
+    command("create_atoms 1 single 0 5 0");
+    command("create_atoms 1 single 0 5 5");
+    command("create_atoms 1 single 5 0 0");
+    command("create_atoms 1 single 5 0 5");
+    command("create_atoms 1 single 5 5 0");
+    command("create_atoms 1 single 5 5 5");
+    ASSERT_EQ(lmp->atom->natoms, 8);
+    ASSERT_EQ(lmp->comm->nprocs, 4);
+
+    // initial state
+    switch(lmp->comm->me) {
+      case 0:
+        ASSERT_EQ(lmp->atom->nlocal, 8);
+        break;
+      case 1:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 2:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 3:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+    }
+
+    command("balance 1 x uniform y 0.125 z uniform");
+
+    // state after balance command
+    switch(lmp->comm->me) {
+      case 0:
+        ASSERT_EQ(lmp->atom->nlocal, 4);
+        break;
+      case 1:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 2:
+        ASSERT_EQ(lmp->atom->nlocal, 4);
+        break;
+      case 3:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+    }
+
+    command("balance 1 x uniform y 0.125 z 0.125");
+
+    // state after second balance command
+    switch(lmp->comm->me) {
+      case 0:
+        ASSERT_EQ(lmp->atom->nlocal, 2);
+        break;
+      case 1:
+        ASSERT_EQ(lmp->atom->nlocal, 2);
+        break;
+      case 2:
+        ASSERT_EQ(lmp->atom->nlocal, 2);
+        break;
+      case 3:
+        ASSERT_EQ(lmp->atom->nlocal, 2);
+        break;
+    }
+}
+
+TEST_F(MPILoadBalanceTest, rcb)
+{
+    command("comm_style tiled");
+    command("create_atoms 1 single 0 0 0");
+    command("create_atoms 1 single 0 0 5");
+    command("create_atoms 1 single 0 5 0");
+    command("create_atoms 1 single 0 5 5");
+    command("create_atoms 1 single 5 0 0");
+    command("create_atoms 1 single 5 0 5");
+    command("create_atoms 1 single 5 5 0");
+    command("create_atoms 1 single 5 5 5");
+
+    // initial state
+    switch(lmp->comm->me) {
+      case 0:
+        ASSERT_EQ(lmp->atom->nlocal, 8);
+        break;
+      case 1:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 2:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 3:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+    }
+
+    command("balance 1 rcb");
+
+    // state after balance command
+    switch(lmp->comm->me) {
+      case 0:
+        ASSERT_EQ(lmp->atom->nlocal, 2);
+        break;
+      case 1:
+        ASSERT_EQ(lmp->atom->nlocal, 2);
+        break;
+      case 2:
+        ASSERT_EQ(lmp->atom->nlocal, 2);
+        break;
+      case 3:
+        ASSERT_EQ(lmp->atom->nlocal, 2);
+        break;
+    }
+
+    // box dimensions should have minimal size
+    double dx = lmp->domain->subhi[0] - lmp->domain->sublo[0];
+    double dy = lmp->domain->subhi[1] - lmp->domain->sublo[1];
+    double dz = lmp->domain->subhi[2] - lmp->domain->sublo[2];
+
+    ASSERT_GT(dx, lmp->neighbor->skin);
+    ASSERT_GT(dy, lmp->neighbor->skin);
+    ASSERT_GT(dz, lmp->neighbor->skin);
+}
+
+TEST_F(MPILoadBalanceTest, rcb_min_size)
+{
+    GTEST_SKIP();
+    // TODO minimum domain size is not enforced right now
+    // skipping for now to allow other MPI tests to get merged
+    command("comm_style tiled");
+    command("create_atoms 1 single 0 0 0");
+    command("create_atoms 1 single 0 0 0.25");
+    command("create_atoms 1 single 0 0.25 0");
+    command("create_atoms 1 single 0 0.25 0.25");
+    command("create_atoms 1 single 0.25 0 0");
+    command("create_atoms 1 single 0.25 0 0.25");
+    command("create_atoms 1 single 0.25 0.25 0");
+    command("create_atoms 1 single 0.25 0.25 0.25");
+
+    // initial state
+    switch(lmp->comm->me) {
+      case 0:
+        ASSERT_EQ(lmp->atom->nlocal, 8);
+        break;
+      case 1:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 2:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 3:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+    }
+
+    // this should fail and not change the boxes
+    // or keep them at a minimum size
+    command("balance 1 rcb");
+
+    // state after balance command
+    switch(lmp->comm->me) {
+      case 0:
+        ASSERT_EQ(lmp->atom->nlocal, 8);
+        break;
+      case 1:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 2:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+      case 3:
+        ASSERT_EQ(lmp->atom->nlocal, 0);
+        break;
+    }
+
+    // box dimensions should have minimal size
+    double dx = lmp->domain->subhi[0] - lmp->domain->sublo[0];
+    double dy = lmp->domain->subhi[1] - lmp->domain->sublo[1];
+    double dz = lmp->domain->subhi[2] - lmp->domain->sublo[2];
+
+    ASSERT_GT(dx, lmp->neighbor->skin);
+    ASSERT_GT(dy, lmp->neighbor->skin);
+    ASSERT_GT(dz, lmp->neighbor->skin);
+}
+
+}

unittest/commands/test_reset_ids.cpp

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract

unittest/commands/test_simple_commands.cpp

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
@@ -14,6 +14,7 @@
 #include "lammps.h"
 
 #include "citeme.h"
+#include "comm.h"
 #include "force.h"
 #include "info.h"
 #include "input.h"
@@ -25,6 +26,7 @@
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
 #include "../testing/core.h"
+#include "../testing/utils.h"
 
 #include <cstdio>
 #include <cstring>
@@ -174,6 +176,38 @@ TEST_F(SimpleCommandsTest, Partition)
     ASSERT_THAT(text, StrEq(""));
 }
 
+TEST_F(SimpleCommandsTest, Processors)
+{
+    // default setting is "*" for all dimensions
+    ASSERT_EQ(lmp->comm->user_procgrid[0], 0);
+    ASSERT_EQ(lmp->comm->user_procgrid[1], 0);
+    ASSERT_EQ(lmp->comm->user_procgrid[2], 0);
+
+    BEGIN_HIDE_OUTPUT();
+    command("processors 1 1 1");
+    END_HIDE_OUTPUT();
+    ASSERT_EQ(lmp->comm->user_procgrid[0], 1);
+    ASSERT_EQ(lmp->comm->user_procgrid[1], 1);
+    ASSERT_EQ(lmp->comm->user_procgrid[2], 1);
+
+    BEGIN_HIDE_OUTPUT();
+    command("processors * 1 *");
+    END_HIDE_OUTPUT();
+    ASSERT_EQ(lmp->comm->user_procgrid[0], 0);
+    ASSERT_EQ(lmp->comm->user_procgrid[1], 1);
+    ASSERT_EQ(lmp->comm->user_procgrid[2], 0);
+
+    BEGIN_HIDE_OUTPUT();
+    command("processors 0 0 0");
+    END_HIDE_OUTPUT();
+    ASSERT_EQ(lmp->comm->user_procgrid[0], 0);
+    ASSERT_EQ(lmp->comm->user_procgrid[1], 0);
+    ASSERT_EQ(lmp->comm->user_procgrid[2], 0);
+
+    TEST_FAILURE(".*ERROR: Illegal processors command .*", command("processors -1 0 0"););
+    TEST_FAILURE(".*ERROR: Specified processors != physical processors.*", command("processors 100 100 100"););
+}
+
 TEST_F(SimpleCommandsTest, Quit)
 {
     BEGIN_HIDE_OUTPUT();

unittest/commands/test_variables.cpp

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://lammps.sandia.gov/, Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
@@ -105,8 +105,8 @@ protected:
               "# comments only\n	five\n#END\n",
               fp);
         fclose(fp);
-        fp = fopen("test_variable.atomfile", "w");
 
+        fp = fopen("test_variable.atomfile", "w");
         fputs("# test file for atomfile style variable\n\n"
               "4  # four lines\n4 0.5   #with comment\n"
               "2 -0.5         \n3 1.5\n1 -1.5\n\n"