extended LAMMPS commands support

.clang-format

@@ -7,3 +7,6 @@ BinPackParameters: true
 IndentWidth: 4
 SpacesInParentheses: true
 BreakConstructorInitializersBeforeComma: true
+PointerAlignment: Right
+AlwaysBreakAfterReturnType: None
+KeepEmptyLinesAtTheStartOfBlocks: false

.github/workflows/format.yml

@@ -9,4 +9,4 @@ jobs:
     - name: Run clang-format style check
       uses: jidicula/[email protected]
       with:
-        clang-format-version: '10'
+        clang-format-version: '14'

.gitignore

@@ -2,3 +2,9 @@
 build
 .cproject
 .project
+*.jpg
+*.pvtu
+*.vtu
+
+cabanaMD.err
+cabanaMD.out

bin/main.cpp

@@ -58,7 +58,6 @@
 // This main file is simply a driver
 int main( int argc, char *argv[] )
 {
-
     MPI_Init( &argc, &argv );
 
     {

cmake/FindCLANG_FORMAT.cmake

@@ -18,17 +18,7 @@
 
 find_program(CLANG_FORMAT_EXECUTABLE
              NAMES clang-format
-                   clang-format-7
-                   clang-format-6.0
-                   clang-format-5.0
-                   clang-format-4.0
-                   clang-format-3.9
-                   clang-format-3.8
-                   clang-format-3.7
-                   clang-format-3.6
-                   clang-format-3.5
-                   clang-format-3.4
-                   clang-format-3.3
+                   clang-format-14
              DOC "clang-format executable")
 mark_as_advanced(CLANG_FORMAT_EXECUTABLE)
 
@@ -38,11 +28,11 @@ if(CLANG_FORMAT_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-  if(clang_format_version MATCHES "^clang-format version .*")
+  if(clang_format_version MATCHES "^.*clang-format version .*")
     # clang_format_version sample: "clang-format version 3.9.1-4ubuntu3~16.04.1
     # (tags/RELEASE_391/rc2)"
     string(REGEX
-           REPLACE "clang-format version ([.0-9]+).*"
+           REPLACE "^.*clang-format version ([.0-9]+).*"
                    "\\1"
                    CLANG_FORMAT_VERSION
                    "${clang_format_version}")

input/in.lb

@@ -0,0 +1,41 @@
+# Example for exercising load balancing (not intended to be physical)
+
+units		lj
+atom_style	atomic
+
+newton off
+
+lattice		fcc 0.8442
+region		lo-box block 0 10 0 10 0 10
+region		mid-box block 5 10 5 10 5 10
+region		hi-box block 0 5 15 20 15 20
+region		hj-box block 15 20 15 20 0 5
+create_box	4 box
+
+mass		1 2.0
+mass		2 8.0
+mass		3 9.0
+mass		4 1.0
+
+create_atoms	1 region lo-box
+create_atoms	2 region mid-box
+create_atoms	3 region hi-box
+create_atoms	4 region hj-box
+
+velocity	1 create 10.4 87287 loop geom
+velocity	2 create 41.6 87287 loop geom
+velocity	3 create 20.8 87287 loop geom
+velocity	4 create 10.4 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	every 20 one 50
+comm_modify	cutoff * 20
+fix		1 all nve
+thermo 10
+
+dump dmpvtk all vtk 10 dump%_*.vtu
+
+run		100

src/cabanamd.h

@@ -96,6 +96,11 @@ class CbnMD : public CabanaMD
 
     void dump_binary( int ) override;
     void check_correctness( int ) override;
+
+  private:
+    void print_summary( std::ofstream &out, int step, T_V_FLOAT T, T_F_FLOAT PE,
+                        T_V_FLOAT KE, double time, double rate,
+                        T_INT exchanged = -1 );
 };
 
 #include <cabanamd_impl.h>

src/cabanamd_impl.h

@@ -244,27 +244,8 @@ void CbnMD<t_System, t_Neighbor>::init( InputCL commandline )
         auto T = temp.compute( system );
         auto PE = pote.compute( system, force, neighbor ) / system->N;
         auto KE = kine.compute( system ) / system->N;
-        if ( !_print_lammps )
-        {
-#ifdef CabanaMD_ENABLE_LB
-            log( out, "\n", std::fixed, std::setprecision( 6 ),
-                 "#Timestep Temperature PotE ETot Time Atomsteps/s "
-                 "LBImbalance\n",
-                 step, " ", T, " ", PE, " ", PE + KE, " ",
-                 std::setprecision( 2 ), 0.0, " ", std::scientific, 0.0, " ",
-                 std::setprecision( 2 ), 0.0 );
-#else
-            log( out, "\n", std::fixed, std::setprecision( 6 ),
-                 "#Timestep Temperature PotE ETot Time Atomsteps/s\n", step,
-                 " ", T, " ", PE, " ", PE + KE, " ", std::setprecision( 2 ),
-                 0.0, " ", std::scientific, 0.0 );
-#endif
-        }
-        else
-        {
-            log( out, "\nStep Temp E_pair TotEng CPU\n", step, " ", T, " ", PE,
-                 " ", PE + KE, " ", 0.0 );
-        }
+
+        print_summary( out, step, T, PE, KE, 0.0, 0.0 );
     }
 
     if ( input->dumpbinaryflag )
@@ -313,6 +294,7 @@ void CbnMD<t_System, t_Neighbor>::run()
         integrate_timer.reset();
         integrator->initial_integrate( system );
         integrate_time += integrate_timer.seconds();
+        T_INT exchanged = -1;
 
         if ( step % input->comm_exchange_rate == 0 && step > 0 )
         {
@@ -328,7 +310,7 @@ void CbnMD<t_System, t_Neighbor>::run()
 
             // Exchange atoms across MPI ranks
             comm_timer.reset();
-            comm->exchange();
+            exchanged = comm->exchange();
             comm_time += comm_timer.seconds();
 
             // Sort atoms
@@ -389,31 +371,14 @@ void CbnMD<t_System, t_Neighbor>::run()
             auto T = temp.compute( system );
             auto PE = pote.compute( system, force, neighbor ) / system->N;
             auto KE = kine.compute( system ) / system->N;
+            double time = timer.seconds();
+            double rate =
+                1.0 * system->N * input->thermo_rate / ( time - last_time );
+
+            print_summary( out, step, T, PE, KE, time, rate, exchanged );
+
+            last_time = time;
 
-            if ( !_print_lammps )
-            {
-                double time = timer.seconds();
-                double rate =
-                    1.0 * system->N * input->thermo_rate / ( time - last_time );
-#ifdef CabanaMD_ENABLE_LB
-                log( out, std::fixed, std::setprecision( 6 ), step, " ", T, " ",
-                     PE, " ", PE + KE, " ", std::setprecision( 2 ), time, " ",
-                     std::scientific, rate, " ", std::setprecision( 2 ),
-                     lb->getImbalance() );
-#else
-                log( out, std::fixed, std::setprecision( 6 ), step, " ", T, " ",
-                     PE, " ", PE + KE, " ", std::setprecision( 2 ), time, " ",
-                     std::scientific, rate );
-#endif
-                last_time = time;
-            }
-            else
-            {
-                double time = timer.seconds();
-                log( out, std::fixed, std::setprecision( 6 ), "     ", step,
-                     " ", T, " ", PE, " ", PE + KE, " ", time );
-                last_time = time;
-            }
 #ifdef CabanaMD_ENABLE_LB
             double work = system->N_local + system->N_ghost;
             std::array<double, 6> vertices;
@@ -681,3 +646,37 @@ void CbnMD<t_System, t_Neighbor>::check_correctness( int step )
     }
     err.close();
 }
+
+template <class t_System, class t_Neighbor>
+void CbnMD<t_System, t_Neighbor>::print_summary( std::ofstream &out, int step,
+                                                 T_V_FLOAT T, T_F_FLOAT PE,
+                                                 T_V_FLOAT KE, double time,
+                                                 double rate, T_INT exchanged )
+{
+    if ( !_print_lammps )
+    {
+        if ( step == 0 )
+        {
+            log( out, "\n#Timestep Temperature PotE ETot Time Atomsteps/s "
+#ifdef CabanaMD_ENABLE_LB
+                      "LB-Imbalance MPI-Exchanged"
+#endif
+            );
+        }
+
+        log( out, step, "\t", std::fixed, std::setprecision( 6 ), T, "\t", PE,
+             "\t", PE + KE, "\t", std::setprecision( 2 ), time, "\t",
+             std::scientific, rate
+#ifdef CabanaMD_ENABLE_LB
+             ,
+             "\t", std::setprecision( 2 ), lb->getImbalance(), "\t",
+             ( exchanged != -1 ) ? std::to_string( exchanged ) : "-"
+#endif
+        );
+    }
+    else
+    {
+        log( out, "\nStep Temp E_pair TotEng CPU\n", step, " ", T, " ", PE, " ",
+             PE + KE, " ", time );
+    }
+}

src/comm_mpi.h

@@ -125,7 +125,7 @@ class Comm
     Comm( t_System *s, T_X_FLOAT comm_depth_ );
     void init();
     void create_domain_decomposition();
-    void exchange();
+    T_INT exchange();
     void exchange_halo();
     void update_halo();
     void update_force();
@@ -323,7 +323,6 @@ class Comm
     KOKKOS_INLINE_FUNCTION
     void operator()( const TagHaloPBC, const T_INT &i ) const
     {
-
         switch ( phase )
         {
         case 0:

src/comm_mpi_impl.h

@@ -48,7 +48,7 @@
 
 #include <mpi.h>
 
-#include <algorithm>
+#include <output.h>
 
 template <class t_System>
 Comm<t_System>::Comm( t_System *s, T_X_FLOAT comm_depth_ )
@@ -189,9 +189,8 @@ void Comm<t_System>::reduce_min_float( T_FLOAT *vals, T_INT count )
 }
 
 template <class t_System>
-void Comm<t_System>::exchange()
+T_INT Comm<t_System>::exchange()
 {
-
     Kokkos::Profiling::pushRegion( "Comm::exchange" );
 
     N_local = system->N_local;
@@ -271,13 +270,16 @@ void Comm<t_System>::exchange()
     system->N_local = N_local;
     system->N_ghost = 0;
 
+    T_INT global_send = N_total_send;
+    reduce_int( &global_send, 1 );
+
     Kokkos::Profiling::popRegion();
+    return global_send;
 }
 
 template <class t_System>
 void Comm<t_System>::exchange_halo()
 {
-
     Kokkos::Profiling::pushRegion( "Comm::exchange_halo" );
 
     N_local = system->N_local;
@@ -367,7 +369,6 @@ void Comm<t_System>::exchange_halo()
 template <class t_System>
 void Comm<t_System>::update_halo()
 {
-
     Kokkos::Profiling::pushRegion( "Comm::update_halo" );
 
     N_local = system->N_local;
@@ -409,7 +410,6 @@ void Comm<t_System>::update_halo()
 template <class t_System>
 void Comm<t_System>::update_force()
 {
-
     Kokkos::Profiling::pushRegion( "Comm::update_force" );
 
     N_local = system->N_local;