apply include file conventions

src/AMOEBA/amoeba_charge_transfer.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -12,10 +13,12 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_amoeba.h"
-#include <cmath>
+
 #include "atom.h"
-#include "neigh_list.h"
 #include "memory.h"
+#include "neigh_list.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/AMOEBA/amoeba_convolution.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -12,14 +13,15 @@
 ------------------------------------------------------------------------- */
 
 #include "amoeba_convolution.h"
-#include "domain.h"
+
 #include "comm.h"
-#include "update.h"
-#include "neighbor.h"
+#include "domain.h"
 #include "fft3d_wrap.h"
-#include "remap_wrap.h"
 #include "gridcomm.h"
 #include "memory.h"
+#include "neighbor.h"
+#include "remap_wrap.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 

src/AMOEBA/amoeba_convolution.h

@@ -81,7 +81,5 @@ class AmoebaConvolution : protected Pointers {
   void debug_scalar(int, const char *);
   void debug_file(int, const char *);
 };
-
 }    // namespace LAMMPS_NS
-
 #endif

src/AMOEBA/amoeba_dispersion.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -17,11 +18,11 @@
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "neigh_list.h"
 #include "fft3d_wrap.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
+#include "neigh_list.h"
 
 #include <cmath>
 

src/AMOEBA/amoeba_file.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel ator
    https://www.lammps.org/ Sandia National Laboratories
@@ -12,16 +13,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_amoeba.h"
-#include <mpi.h>
+
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "utils.h"
+
 #include <cmath>
 #include <cstring>
 #include <cctype>
-#include "domain.h"
-#include "comm.h"
-#include "force.h"
-#include "memory.h"
-#include "error.h"
-#include "utils.h"
 
 using namespace LAMMPS_NS;
 

src/AMOEBA/amoeba_hal.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -12,10 +13,12 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_amoeba.h"
-#include <cmath>
+
 #include "atom.h"
-#include "neigh_list.h"
 #include "error.h"
+#include "neigh_list.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/AMOEBA/amoeba_induce.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -15,15 +16,15 @@
 
 #include "amoeba_convolution.h"
 #include "atom.h"
-#include "domain.h"
 #include "comm.h"
-#include "fix_store.h"
-#include "neigh_list.h"
+#include "domain.h"
+#include "error.h"
 #include "fft3d_wrap.h"
-#include "my_page.h"
+#include "fix_store.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 #include <cmath>
 #include <cstring>

src/AMOEBA/amoeba_kspace.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -12,12 +13,14 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_amoeba.h"
-#include <cmath>
+
 #include "atom.h"
 #include "domain.h"
 #include "math_const.h"
 #include "memory.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/AMOEBA/amoeba_multipole.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -15,12 +16,12 @@
 
 #include "amoeba_convolution.h"
 #include "atom.h"
-#include "domain.h"
 #include "comm.h"
-#include "neigh_list.h"
+#include "domain.h"
 #include "fft3d_wrap.h"
 #include "math_const.h"
 #include "memory.h"
+#include "neigh_list.h"
 
 #include <cmath>
 #include <cstring>

src/AMOEBA/amoeba_polar.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -12,15 +13,15 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_amoeba.h"
-#include "amoeba_convolution.h"
 
+#include "amoeba_convolution.h"
 #include "atom.h"
-#include "domain.h"
 #include "comm.h"
-#include "neigh_list.h"
+#include "domain.h"
 #include "fft3d_wrap.h"
 #include "math_const.h"
 #include "memory.h"
+#include "neigh_list.h"
 
 #include <cmath>
 #include <cstring>

src/AMOEBA/amoeba_repulsion.cpp

@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
@@ -12,11 +13,13 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_amoeba.h"
-#include <cmath>
+
 #include "atom.h"
 #include "comm.h"
-#include "neigh_list.h"
 #include "memory.h"
+#include "neigh_list.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/AMOEBA/amoeba_utils.cpp

@@ -12,13 +12,15 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_amoeba.h"
-#include <cmath>
+
 #include "atom.h"
-#include "domain.h"
 #include "comm.h"
-#include "neigh_list.h"
-#include "fix_store.h"
+#include "domain.h"
 #include "error.h"
+#include "fix_store.h"
+#include "neigh_list.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/AMOEBA/angle_amoeba.cpp

@@ -14,17 +14,18 @@
 
 #include "angle_amoeba.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
 #include "force.h"
-#include "pair.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
+#include "pair.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/AMOEBA/atom_vec_amoeba.cpp

@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "atom_vec_amoeba.h"
+
 #include "atom.h"
 
 using namespace LAMMPS_NS;

src/AMOEBA/fix_amoeba_bitorsion.cpp

@@ -14,19 +14,19 @@
 
 #include "fix_amoeba_bitorsion.h"
 
-#include <cmath>
-
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "respa.h"
-#include "domain.h"
-#include "force.h"
-#include "pair.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -40,22 +40,22 @@ using namespace MathConst;
 // spline weighting factors
 
 static constexpr double WT[16][16] = {
-{ 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
-{ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
-{-3.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 0.0,-2.0, 0.0, 0.0,-1.0, 0.0, 0.0, 0.0, 0.0},
-{ 2.0, 0.0, 0.0,-2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0},
-{ 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
-{ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0},
-{ 0.0, 0.0, 0.0, 0.0,-3.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 0.0,-2.0, 0.0, 0.0,-1.0},
-{ 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0,-2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0},
-{-3.0, 3.0, 0.0, 0.0,-2.0,-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
-{ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,-3.0, 3.0, 0.0, 0.0,-2.0,-1.0, 0.0, 0.0},
-{ 9.0,-9.0, 9.0,-9.0, 6.0, 3.0,-3.0,-6.0, 6.0,-6.0,-3.0, 3.0, 4.0, 2.0, 1.0, 2.0},
-{-6.0, 6.0,-6.0, 6.0,-4.0,-2.0, 2.0, 4.0,-3.0, 3.0, 3.0,-3.0,-2.0,-1.0,-1.0,-2.0},
-{ 2.0,-2.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
-{ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 2.0,-2.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0},
-{-6.0, 6.0,-6.0, 6.0,-3.0,-3.0, 3.0, 3.0,-4.0, 4.0, 2.0,-2.0,-2.0,-2.0,-1.0,-1.0},
-{ 4.0,-4.0, 4.0,-4.0, 2.0, 2.0,-2.0,-2.0, 2.0,-2.0,-2.0, 2.0, 1.0, 1.0, 1.0, 1.0}
+  { 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+  { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+  {-3.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 0.0,-2.0, 0.0, 0.0,-1.0, 0.0, 0.0, 0.0, 0.0},
+  { 2.0, 0.0, 0.0,-2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0},
+  { 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+  { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0},
+  { 0.0, 0.0, 0.0, 0.0,-3.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 0.0,-2.0, 0.0, 0.0,-1.0},
+  { 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0,-2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0},
+  {-3.0, 3.0, 0.0, 0.0,-2.0,-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+  { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,-3.0, 3.0, 0.0, 0.0,-2.0,-1.0, 0.0, 0.0},
+  { 9.0,-9.0, 9.0,-9.0, 6.0, 3.0,-3.0,-6.0, 6.0,-6.0,-3.0, 3.0, 4.0, 2.0, 1.0, 2.0},
+  {-6.0, 6.0,-6.0, 6.0,-4.0,-2.0, 2.0, 4.0,-3.0, 3.0, 3.0,-3.0,-2.0,-1.0,-1.0,-2.0},
+  { 2.0,-2.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
+  { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 2.0,-2.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0},
+  {-6.0, 6.0,-6.0, 6.0,-3.0,-3.0, 3.0, 3.0,-4.0, 4.0, 2.0,-2.0,-2.0,-2.0,-1.0,-1.0},
+  { 4.0,-4.0, 4.0,-4.0, 2.0, 2.0,-2.0,-2.0, 2.0,-2.0,-2.0, 2.0, 1.0, 1.0, 1.0, 1.0}
 };
 
 /* ---------------------------------------------------------------------- */

src/AMOEBA/fix_amoeba_pitorsion.cpp

@@ -14,19 +14,19 @@
 
 #include "fix_amoeba_pitorsion.h"
 
-#include <cmath>
-
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "respa.h"
-#include "domain.h"
-#include "force.h"
-#include "pair.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/AMOEBA/improper_amoeba.cpp

@@ -14,16 +14,17 @@
 
 #include "improper_amoeba.h"
 
-#include <cmath>
 #include "atom.h"
 #include "comm.h"
-#include "update.h"
-#include "neighbor.h"
+#include "error.h"
 #include "force.h"
-#include "pair.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;