Merge pull request #114 from cz4rs/misc-fixes

General updates

.github/workflows/CI.yml

@@ -15,7 +15,7 @@ jobs:
         cxx: ['g++', 'clang++']
         backend: ['SERIAL', 'OPENMP']
         cmake_build_type: ['Debug', 'Release']
-        kokkos_ver: ['3.7.02']
+        kokkos_ver: ['4.3.01']
         arborx: ['ArborX', 'NoArborX']
         nnp: ['ON', 'OFF']
         layout: ['1']
@@ -27,7 +27,7 @@ jobs:
             cxx: 'g++'
             openmp: 'ON'
             cmake_build_type: 'Release'
-            kokkos_ver: '3.7.02'
+            kokkos_ver: '4.3.01'
             arborx: 'NoArborX'
             nnp: 'OFF'
             layout: '2'
@@ -38,7 +38,7 @@ jobs:
             cxx: 'g++'
             openmp: 'ON'
             cmake_build_type: 'Release'
-            kokkos_ver: '3.7.02'
+            kokkos_ver: '4.3.01'
             arborx: 'NoArborX'
             nnp: 'ON'
             layout: '6'
@@ -49,7 +49,7 @@ jobs:
             cxx: 'g++'
             openmp: 'ON'
             cmake_build_type: 'Release'
-            kokkos_ver: '3.7.02'
+            kokkos_ver: '4.3.01'
             arborx: 'NoArborX'
             nnp: 'OFF'
             layout: '6'

src/inputFile.h

@@ -58,6 +58,7 @@
 #include <system.h>
 #include <types.h>
 
+#include <array>
 #include <fstream>
 #include <vector>
 
@@ -149,52 +150,54 @@ template <class t_System>
 class InputFile
 {
   private:
-    bool timestepflag; // input timestep?
+    bool timestepflag = false; // input timestep?
   public:
     InputCL commandline;
     t_System *system;
 
     bool _print_rank;
-    int units_style;
-    int lattice_style;
-    double lattice_constant, lattice_offset_x, lattice_offset_y,
-        lattice_offset_z;
+
+    // defaults match ExaMiniMD LJ example
+    int units_style = UNITS_LJ;
+    int lattice_style = LATTICE_FCC;
+    double lattice_constant = 0.8442, lattice_offset_x = 0.0,
+           lattice_offset_y = 0.0, lattice_offset_z = 0.0;
     int lattice_nx, lattice_ny, lattice_nz;
-    int box[6];
+    std::array<int, 6> box = { 0, 40, 0, 40, 0, 40 };
 
     char *data_file;
     int data_file_type;
 
     std::string output_file;
     std::string error_file;
 
-    double temperature_target;
-    int temperature_seed;
+    double temperature_target = 1.4;
+    int temperature_seed = 87287;
 
-    int integrator_type;
-    int nsteps;
+    int integrator_type = INTEGRATOR_NVE;
+    int nsteps = 100;
 
-    int binning_type;
+    int binning_type = BINNING_LINKEDCELL;
 
-    int comm_type;
-    int comm_exchange_rate;
+    int comm_type = COMM_MPI;
+    int comm_exchange_rate = 20;
 
-    int force_type;
+    int force_type = FORCE_LJ;
     int force_iteration_type;
     int force_neigh_parallel_type;
 
-    T_F_FLOAT force_cutoff;
+    T_F_FLOAT force_cutoff = 2.5;
     std::vector<std::vector<std::string>> force_coeff_lines;
 
-    T_F_FLOAT neighbor_skin;
-    int neighbor_type;
-    T_INT max_neigh_guess;
+    T_F_FLOAT neighbor_skin = 0.0;
+    int neighbor_type = NEIGH_VERLET_2D;
+    T_INT max_neigh_guess = 50;
 
     int layout_type;
     int nnp_layout_type;
 
-    int thermo_rate, dumpbinary_rate, correctness_rate;
-    bool dumpbinaryflag, correctnessflag;
+    int thermo_rate = 10, dumpbinary_rate = 0, correctness_rate = 0;
+    bool dumpbinaryflag = false, correctnessflag = false;
     char *dumpbinary_path, *reference_path, *correctness_file;
     std::string input_data_file;
     std::string output_data_file;

src/inputFile_impl.h

@@ -49,7 +49,7 @@
 #include <inputFile.h>
 #include <property_temperature.h>
 
-#include <iostream>
+#include <algorithm>
 #include <regex>
 
 std::vector<std::string> split( const std::string &line )
@@ -71,56 +71,12 @@ InputFile<t_System>::InputFile( InputCL commandline_, t_System *system_ )
     : commandline( commandline_ )
     , system( system_ )
 {
-    comm_type = COMM_MPI;
-    integrator_type = INTEGRATOR_NVE;
-    neighbor_type = NEIGH_VERLET_2D;
-    force_type = FORCE_LJ;
-    binning_type = BINNING_LINKEDCELL;
-
     neighbor_type = commandline.neighbor_type;
     force_iteration_type = commandline.force_iteration_type;
     force_neigh_parallel_type = commandline.force_neigh_parallel_type;
 
     output_file = commandline.output_file;
     error_file = commandline.error_file;
-
-    // set defaults (matches ExaMiniMD LJ example)
-
-    nsteps = 0;
-
-    thermo_rate = 0;
-    dumpbinary_rate = 0;
-    correctness_rate = 0;
-    dumpbinaryflag = false;
-    correctnessflag = false;
-    timestepflag = false;
-
-    lattice_offset_x = 0.0;
-    lattice_offset_y = 0.0;
-    lattice_offset_z = 0.0;
-    box[0] = 0;
-    box[2] = 0;
-    box[4] = 0;
-    box[1] = 40;
-    box[3] = 40;
-    box[5] = 40;
-
-    units_style = UNITS_LJ;
-    lattice_style = LATTICE_FCC;
-    lattice_constant = 0.8442;
-
-    temperature_target = 1.4;
-    temperature_seed = 87287;
-
-    nsteps = 100;
-    thermo_rate = 10;
-
-    neighbor_skin = 0.3;
-    neighbor_skin = 0.0; // for metal and real units
-    max_neigh_guess = 50;
-    comm_exchange_rate = 20;
-
-    force_cutoff = 2.5;
 }
 
 template <class t_System>

src/integrator_nve_impl.h

@@ -64,10 +64,8 @@ void Integrator<t_System>::initial_integrate( t_System *system )
     f = system->f;
     type = system->type;
 
-    static int step = 1;
     Kokkos::parallel_for( "IntegratorNVE::initial_integrate",
                           t_policy_initial( 0, system->N_local ), *this );
-    step++;
 }
 
 template <class t_System>
@@ -80,10 +78,8 @@ void Integrator<t_System>::final_integrate( t_System *system )
     f = system->f;
     type = system->type;
 
-    static int step = 1;
     Kokkos::parallel_for( "IntegratorNVE::final_integrate",
                           t_policy_final( 0, system->N_local ), *this );
-    step++;
 }
 
 template <class t_System>