more IWYU cleanup in packages

src/KIM/kim_init.cpp

@@ -57,24 +57,19 @@
 ------------------------------------------------------------------------- */
 
 #include "kim_init.h"
-#include "fix_store_kim.h"
-#include "kim_units.h"
-#include <cstring>
-#include <string>
-#include <sstream>
-#include <iomanip>
-#include "error.h"
-#include "atom.h"
+
+#include "citeme.h"
 #include "comm.h"
 #include "domain.h"
-#include "modify.h"
-#include "update.h"
-#include "universe.h"
+#include "error.h"
+#include "fix_store_kim.h"
 #include "input.h"
+#include "kim_units.h"
+#include "modify.h"
+#include "universe.h"
 #include "variable.h"
-#include "citeme.h"
-#include "utils.h"
-#include "fmt/format.h"
+
+#include <cstring>
 
 extern "C" {
 #include "KIM_SimulatorHeaders.h"

src/KIM/kim_interactions.cpp

@@ -57,23 +57,18 @@
 ------------------------------------------------------------------------- */
 
 #include "kim_interactions.h"
-#include <cstring>
-#include <cstdio>
-#include <string>
-#include <sstream>
-#include <vector>
-#include "error.h"
+
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
+#include "error.h"
+#include "fix_store_kim.h"
+#include "input.h"
 #include "modify.h"
 #include "update.h"
-#include "universe.h"
-#include "input.h"
-#include "variable.h"
-#include "utils.h"
-#include "fix_store_kim.h"
-#include "fmt/format.h"
+
+#include <cstring>
+#include <vector>
 
 extern "C" {
 #include "KIM_SimulatorHeaders.h"

src/KIM/kim_param.cpp

@@ -56,19 +56,18 @@
 ------------------------------------------------------------------------- */
 
 #include "kim_param.h"
-#include "fix_store_kim.h"
-#include "pair_kim.h"
-#include <mpi.h>
-#include <cstring>
-#include <string>
-#include <sstream>
+
 #include "comm.h"
 #include "error.h"
+#include "fix_store_kim.h"
+#include "force.h"
 #include "input.h"
 #include "modify.h"
+#include "pair_kim.h"
 #include "variable.h"
-#include "force.h"
-#include "fmt/format.h"
+
+#include <cstring>
+#include <sstream>
 
 extern "C"
 {

src/KIM/kim_property.cpp

@@ -53,21 +53,18 @@
    Designed for use with the kim-api-2.1.0 (and newer) package
 ------------------------------------------------------------------------- */
 
-#if LMP_PYTHON
-#define PY_SSIZE_T_CLEAN
-#include <Python.h>
-#endif
-
 #include "kim_property.h"
 
 #include "comm.h"
-#include "input.h"
-#include "variable.h"
-#include "utils.h"
 #include "error.h"
+#include "input.h"
 #include "lmppython.h"
+#include "variable.h"
 
-#include <string>
+#if LMP_PYTHON
+#define PY_SSIZE_T_CLEAN
+#include <Python.h>             // IWYU pragma: export
+#endif
 
 using namespace LAMMPS_NS;
 

src/KIM/kim_query.cpp

@@ -56,24 +56,22 @@
 ------------------------------------------------------------------------- */
 
 #include "kim_query.h"
-#include "fix_store_kim.h"
-#include <mpi.h>
-#include <cstring>
-#include <string>
-#include <sstream>
+
 #include "comm.h"
 #include "error.h"
+#include "fix_store_kim.h"
+#include "info.h"
 #include "input.h"
 #include "modify.h"
 #include "variable.h"
 #include "version.h"
-#include "info.h"
-#include "fmt/format.h"
+
+#include <cstring>
+#include <sstream>
 
 #if defined(LMP_KIM_CURL)
 #include <sys/types.h>
 #include <curl/curl.h>
-#include <cstdlib>
 #endif
 
 using namespace LAMMPS_NS;

src/KIM/kim_units.cpp

@@ -57,6 +57,8 @@
 #include <math.h>
 #include <string>
 #include <map>
+#include <utility>
+
 using namespace std;
 
 namespace

src/KIM/pair_kim.h

@@ -66,7 +66,6 @@ PairStyle(kim,PairKIM)
 class KIM_API_model;
 #include "pair.h"
 
-
 extern "C" {
 #include "KIM_SimulatorHeaders.h"
 }

src/MLIAP/mliap_descriptor_snap.cpp

@@ -12,20 +12,17 @@
 ------------------------------------------------------------------------- */
 
 #include "mliap_descriptor_snap.h"
-#include "pair_mliap.h"
-#include "mliap_data.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
+
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "utils.h"
-#include "sna.h"
-#include "memory.h"
 #include "error.h"
-#include "fmt/format.h"
+#include "memory.h"
+#include "mliap_data.h"
+#include "pair_mliap.h"
+#include "sna.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/MLIAP/mliap_model.cpp

@@ -12,17 +12,13 @@
 ------------------------------------------------------------------------- */
 
 #include "mliap_model.h"
-#include "pair_mliap.h"
-#include <cstring>
-#include <cmath>
+
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "utils.h"
-#include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
-#include "fmt/format.h"
+#include "memory.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/MLIAP/mliap_model_linear.h

@@ -20,7 +20,7 @@ namespace LAMMPS_NS {
 
 class MLIAPModelLinear : public MLIAPModel {
 public:
-  MLIAPModelLinear(LAMMPS*, char* = NULL);
+  MLIAPModelLinear(LAMMPS*, char* = nullptr);
   ~MLIAPModelLinear();
   virtual int get_nparams();
   virtual int get_gamma_nnz(class MLIAPData*);

src/MLIAP/pair_mliap.cpp

@@ -11,22 +11,22 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "pair_mliap.h"
 
-#include <cmath>
-
-#include <cstring>
 #include "mliap_data.h"
 #include "mliap_model_linear.h"
 #include "mliap_model_quadratic.h"
 #include "mliap_descriptor_snap.h"
-#include "pair_mliap.h"
+
 #include "atom.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "memory.h"
 #include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/MOLECULE/atom_vec_template.cpp

@@ -12,15 +12,10 @@
 ------------------------------------------------------------------------- */
 
 #include "atom_vec_template.h"
-#include "atom.h"
-#include "molecule.h"
-#include "comm.h"
-#include "domain.h"
-#include "modify.h"
-#include "fix.h"
-#include "memory.h"
-#include "error.h"
 
+#include "atom.h"
+#include "error.h"
+#include "molecule.h"
 
 using namespace LAMMPS_NS;
 

src/MPIIO/dump_cfg_mpiio.cpp

@@ -17,15 +17,16 @@
 
 #include "omp_compat.h"
 #include "dump_cfg_mpiio.h"
-#include <cmath>
 
-#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "update.h"
 #include "memory.h"
 #include "error.h"
 
+#include <cmath>
+#include <cstring>
+
 #ifdef LMP_USER_IO_TIMER
 #include <sys/times.h>
 #include <hwi/include/bqc/A2_inlines.h>

src/MPIIO/restart_mpiio.cpp

@@ -16,8 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "restart_mpiio.h"
-#include <mpi.h>
-#include <climits>
+
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/PERI/atom_vec_peri.cpp

@@ -16,13 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "atom_vec_peri.h"
-#include <cfloat>
-#include <cstring>
+
 #include "atom.h"
 #include "citeme.h"
-#include "memory.h"
 #include "error.h"
 
+#include <cfloat>
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 static const char cite_peri_package[] =

src/PERI/pair_peri_eps.cpp

@@ -17,24 +17,22 @@
 
 #include "pair_peri_eps.h"
 
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "fix_peri_neigh.h"
+#include "force.h"
+#include "lattice.h"
+#include "math_const.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+
 #include <cmath>
 #include <cstring>
 
-#include "atom.h"
-#include "domain.h"
-#include "lattice.h"
-#include "force.h"
-#include "modify.h"
-#include "fix.h"
-#include "fix_peri_neigh.h"
-#include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "math_const.h"
-#include "error.h"
-
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/PERI/pair_peri_lps.cpp

@@ -17,23 +17,20 @@
 
 #include "pair_peri_lps.h"
 
-#include <cmath>
-#include <cstring>
-
 #include "atom.h"
-#include "domain.h"
-#include "lattice.h"
-#include "force.h"
-#include "modify.h"
-#include "fix.h"
-#include "fix_peri_neigh.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
+#include "domain.h"
 #include "error.h"
-
+#include "fix_peri_neigh.h"
+#include "force.h"
+#include "lattice.h"
 #include "math_const.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/PERI/pair_peri_pmb.cpp

@@ -17,23 +17,20 @@
 
 #include "pair_peri_pmb.h"
 
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "fix_peri_neigh.h"
+#include "force.h"
+#include "lattice.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+
 #include <cmath>
 #include <cfloat>
-#include <cstring>
-
-#include "atom.h"
-#include "domain.h"
-#include "lattice.h"
-#include "force.h"
-#include "modify.h"
-#include "fix.h"
-#include "fix_peri_neigh.h"
-#include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-
 
 using namespace LAMMPS_NS;
 

src/PERI/pair_peri_ves.cpp

@@ -17,24 +17,21 @@
 
 #include "pair_peri_ves.h"
 
-#include <cmath>
-#include <cstring>
-
 #include "atom.h"
-#include "domain.h"
-#include "lattice.h"
-#include "force.h"
-#include "modify.h"
-#include "fix.h"
-#include "fix_peri_neigh.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
+#include "domain.h"
 #include "error.h"
-
+#include "fix_peri_neigh.h"
+#include "force.h"
+#include "lattice.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neighbor.h"
 #include "update.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */

src/PYTHON/fix_python_invoke.cpp

@@ -16,13 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_python_invoke.h"
-#include <Python.h>   // IWYU pragma: keep
-#include <cstring>
-#include "force.h"
-#include "update.h"
+
 #include "error.h"
 #include "lmppython.h"
 #include "python_compat.h"
+#include "update.h"
+
+#include <cstring>
+#include <Python.h>   // IWYU pragma: export
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/PYTHON/fix_python_move.cpp

@@ -16,12 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_python_move.h"
-#include <Python.h>   // IWYU pragma: keep
-#include <cstring>
-#include "lmppython.h"
+
 #include "error.h"
+#include "lmppython.h"
 #include "python_compat.h"
 
+#include <cstring>
+#include <Python.h>   // IWYU pragma: export
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/PYTHON/pair_python.cpp

@@ -16,17 +16,18 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_python.h"
-#include <Python.h>  // IWYU pragma: keep
+
+#include "atom.h"
+#include "error.h"
+#include "force.h"
+#include "lmppython.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "python_compat.h"
+#include "update.h"
 
 #include <cstring>
-#include "atom.h"
-#include "force.h"
-#include "memory.h"
-#include "update.h"
-#include "neigh_list.h"
-#include "lmppython.h"
-#include "error.h"
-#include "python_compat.h"
+#include <Python.h>  // IWYU pragma: export
 
 using namespace LAMMPS_NS;
 

src/PYTHON/python_compat.h

@@ -14,6 +14,8 @@
 #ifndef LMP_PYTHON_COMPAT_H
 #define LMP_PYTHON_COMPAT_H
 
+#include <Python.h>
+
 // Wrap API changes between Python 2 and 3 using macros
 #if PY_MAJOR_VERSION == 2
 #define PY_INT_FROM_LONG(X) PyInt_FromLong(X)

src/PYTHON/python_impl.cpp

@@ -12,19 +12,19 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing author: Richard Berger and Axel Kohlmeyer (Temple U)
+   Contributing authors: Richard Berger and Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
 #include "python_impl.h"
-#include <cstdlib>
-#include <cstring>
-#include <Python.h>  // IWYU pragma: keep
-#include "force.h"
-#include "input.h"
-#include "variable.h"
-#include "memory.h"
+
 #include "error.h"
+#include "input.h"
+#include "memory.h"
 #include "python_compat.h"
+#include "variable.h"
+
+#include <cstring>
+#include <Python.h>  // IWYU pragma: export
 
 using namespace LAMMPS_NS;
 

src/REPLICA/compute_event_displace.cpp

@@ -17,15 +17,15 @@
 
 #include "compute_event_displace.h"
 
-#include <cstring>
 #include "atom.h"
 #include "domain.h"
-#include "modify.h"
-#include "fix_event.h"
 #include "error.h"
-#include "force.h"
+#include "fix_event.h"
+#include "modify.h"
 #include "update.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 #define INVOKED_SCALAR 1

src/REPLICA/fix_event_hyper.cpp

@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_event_hyper.h"
+
 #include "comm.h"
 #include "error.h"
 #include "update.h"

src/REPLICA/fix_neb.cpp

@@ -18,21 +18,20 @@
 
 #include "fix_neb.h"
 
-#include <cmath>
-#include <cstring>
-
+#include "atom.h"
+#include "comm.h"
+#include "compute.h"
+#include "domain.h"
+#include "error.h"
+#include "group.h"
+#include "math_const.h"
+#include "memory.h"
+#include "modify.h"
 #include "universe.h"
 #include "update.h"
-#include "atom.h"
-#include "domain.h"
-#include "comm.h"
-#include "modify.h"
-#include "compute.h"
-#include "group.h"
-#include "memory.h"
-#include "error.h"
-#include "force.h"
-#include "math_const.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/REPLICA/hyper.cpp

@@ -12,28 +12,25 @@
 ------------------------------------------------------------------------- */
 
 #include "hyper.h"
-#include <mpi.h>
-#include <cstring>
-#include <string>
-#include "update.h"
-#include "domain.h"
-#include "region.h"
-#include "integrate.h"
-#include "min.h"
-#include "force.h"
-#include "neighbor.h"
-#include "modify.h"
+
 #include "compute_event_displace.h"
-#include "fix_hyper.h"
-#include "fix_event_hyper.h"
-#include "output.h"
+#include "domain.h"
 #include "dump.h"
-#include "finish.h"
-#include "timer.h"
-#include "memory.h"
 #include "error.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "finish.h"
+#include "fix_event_hyper.h"
+#include "fix_hyper.h"
+#include "integrate.h"
+#include "memory.h"
+#include "min.h"
+#include "modify.h"
+#include "neighbor.h"
+#include "output.h"
+#include "region.h"
+#include "timer.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/REPLICA/neb.cpp

@@ -12,28 +12,26 @@
 ------------------------------------------------------------------------- */
 
 #include "neb.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
-#include "universe.h"
+
 #include "atom.h"
-#include "update.h"
-#include "domain.h"
 #include "comm.h"
-#include "min.h"
-#include "modify.h"
+#include "domain.h"
+#include "error.h"
+#include "finish.h"
 #include "fix.h"
 #include "fix_neb.h"
+#include "math_const.h"
+#include "memory.h"
+#include "min.h"
+#include "modify.h"
 #include "output.h"
 #include "thermo.h"
-#include "finish.h"
 #include "timer.h"
-#include "memory.h"
-#include "error.h"
-#include "force.h"
-#include "math_const.h"
-#include "utils.h"
+#include "universe.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/REPLICA/prd.cpp

@@ -16,32 +16,29 @@
 ------------------------------------------------------------------------- */
 
 #include "prd.h"
-#include <mpi.h>
-#include <cstring>
-#include <string>
+
+#include "atom.h"
+#include "comm.h"
+#include "compute.h"
+#include "domain.h"
+#include "error.h"
+#include "finish.h"
+#include "fix_event_prd.h"
+#include "integrate.h"
+#include "memory.h"
+#include "min.h"
+#include "modify.h"
+#include "neighbor.h"
+#include "output.h"
+#include "random_mars.h"
+#include "random_park.h"
+#include "region.h"
+#include "timer.h"
 #include "universe.h"
 #include "update.h"
-#include "atom.h"
-#include "domain.h"
-#include "region.h"
-#include "comm.h"
 #include "velocity.h"
-#include "integrate.h"
-#include "min.h"
-#include "neighbor.h"
-#include "modify.h"
-#include "compute.h"
-#include "fix.h"
-#include "fix_event_prd.h"
-#include "force.h"
-#include "random_park.h"
-#include "random_mars.h"
-#include "output.h"
-#include "finish.h"
-#include "timer.h"
-#include "memory.h"
-#include "error.h"
-#include "utils.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/REPLICA/tad.cpp

@@ -16,28 +16,28 @@
 ------------------------------------------------------------------------- */
 
 #include "tad.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
-#include "universe.h"
-#include "update.h"
+
 #include "atom.h"
-#include "domain.h"
-#include "integrate.h"
-#include "min.h"
-#include "neighbor.h"
-#include "modify.h"
-#include "neb.h"
 #include "compute.h"
+#include "domain.h"
+#include "error.h"
+#include "finish.h"
 #include "fix_event_tad.h"
 #include "fix_store.h"
 #include "force.h"
-#include "output.h"
-#include "finish.h"
-#include "timer.h"
+#include "integrate.h"
 #include "memory.h"
-#include "error.h"
-#include "utils.h"
+#include "min.h"
+#include "modify.h"
+#include "neb.h"
+#include "neighbor.h"
+#include "output.h"
+#include "timer.h"
+#include "universe.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/REPLICA/temper.cpp

@@ -16,22 +16,23 @@
 ------------------------------------------------------------------------- */
 
 #include "temper.h"
-#include <cmath>
-#include <cstring>
-#include "universe.h"
-#include "domain.h"
+
 #include "atom.h"
-#include "update.h"
+#include "compute.h"
+#include "domain.h"
+#include "error.h"
+#include "finish.h"
+#include "fix.h"
+#include "force.h"
 #include "integrate.h"
 #include "modify.h"
-#include "compute.h"
-#include "force.h"
-#include "fix.h"
 #include "random_park.h"
-#include "finish.h"
 #include "timer.h"
-#include "error.h"
-#include "utils.h"
+#include "universe.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/USER-CGDNA/bond_oxrna2_fene.cpp

@@ -14,8 +14,6 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-
 #include "bond_oxrna2_fene.h"
 
 using namespace LAMMPS_NS;

src/USER-CGDNA/fix_nve_dotc_langevin.cpp

@@ -16,16 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_nve_dotc_langevin.h"
-#include <cmath>
-#include <cstring>
-#include "math_extra.h"
+
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "force.h"
-#include "update.h"
 #include "comm.h"
-#include "random_mars.h"
 #include "error.h"
+#include "math_extra.h"
+#include "random_mars.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-CGDNA/pair_oxdna2_coaxstk.cpp

@@ -16,20 +16,19 @@
 
 #include "pair_oxdna2_coaxstk.h"
 
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_const.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "mf_oxdna.h"
+#include "neigh_list.h"
+
 #include <cmath>
 #include <cstring>
-#include "mf_oxdna.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-
-#include "atom_vec_ellipsoid.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/USER-CGDNA/pair_oxdna2_dh.cpp

@@ -16,18 +16,17 @@
 
 #include "pair_oxdna2_dh.h"
 
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+
 #include <cmath>
 #include <cstring>
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-
-#include "atom_vec_ellipsoid.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 

src/USER-CGDNA/pair_oxdna_coaxstk.cpp

@@ -16,20 +16,19 @@
 
 #include "pair_oxdna_coaxstk.h"
 
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_const.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "mf_oxdna.h"
+#include "neigh_list.h"
+
 #include <cmath>
 #include <cstring>
-#include "mf_oxdna.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-
-#include "atom_vec_ellipsoid.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/USER-CGDNA/pair_oxdna_excv.cpp

@@ -16,19 +16,18 @@
 
 #include "pair_oxdna_excv.h"
 
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "mf_oxdna.h"
+#include "neigh_list.h"
+
 #include <cmath>
 #include <cstring>
-#include "mf_oxdna.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-
-#include "atom_vec_ellipsoid.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace MFOxdna;

src/USER-CGDNA/pair_oxdna_hbond.cpp

@@ -16,19 +16,18 @@
 
 #include "pair_oxdna_hbond.h"
 
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "mf_oxdna.h"
+#include "neigh_list.h"
+
 #include <cmath>
 #include <cstring>
-#include "mf_oxdna.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-
-#include "atom_vec_ellipsoid.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace MFOxdna;

src/USER-CGDNA/pair_oxdna_xstk.cpp

@@ -16,20 +16,19 @@
 
 #include "pair_oxdna_xstk.h"
 
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_const.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "mf_oxdna.h"
+#include "neigh_list.h"
+
 #include <cmath>
 #include <cstring>
-#include "mf_oxdna.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-
-#include "atom_vec_ellipsoid.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/USER-CGDNA/pair_oxrna2_excv.cpp

@@ -14,11 +14,9 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
+#include "pair_oxrna2_excv.h"
 
 #include <cstring>
-#include "pair_oxrna2_excv.h"
 
 using namespace LAMMPS_NS;
 

src/USER-CGDNA/pair_oxrna2_stk.cpp

@@ -14,26 +14,22 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-
-#include <cstring>
 #include "pair_oxrna2_stk.h"
-#include "mf_oxdna.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
 
+#include "atom.h"
 #include "atom_vec_ellipsoid.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_const.h"
 #include "math_extra.h"
+#include "memory.h"
+#include "mf_oxdna.h"
+#include "neighbor.h"
+
+#include <cmath>
+#include <cstring>
+#include <utility>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/USER-CGDNA/pair_oxrna2_xstk.cpp

@@ -16,20 +16,19 @@
 
 #include "pair_oxrna2_xstk.h"
 
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_const.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "mf_oxdna.h"
+#include "neigh_list.h"
+
 #include <cmath>
 #include <cstring>
-#include "mf_oxdna.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-
-#include "atom_vec_ellipsoid.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/USER-CGSDK/pair_lj_sdk.h

@@ -27,7 +27,6 @@ PairStyle(lj/sdk,PairLJSDK)
 #include "pair.h"
 
 namespace LAMMPS_NS {
-class LAMMPS;
 
 class PairLJSDK : public Pair {
  public:

src/USER-MEAMC/meam_dens_init.cpp

@@ -1,7 +1,9 @@
 #include "meam.h"
-#include <cmath>
-#include "memory.h"
+
 #include "math_special.h"
+#include "memory.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/USER-MEAMC/meam_force.cpp

@@ -1,10 +1,11 @@
 #include "meam.h"
-#include <cmath>
-#include <algorithm>
+
 #include "math_special.h"
 
-using namespace LAMMPS_NS;
+#include <cmath>
+#include <algorithm>
 
+using namespace LAMMPS_NS;
 
 void
 MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl,

src/USER-MEAMC/meam_funcs.cpp

@@ -16,7 +16,9 @@
 ------------------------------------------------------------------------- */
 
 #include "meam.h"
+
 #include "math_special.h"
+
 #include <cmath>
 
 using namespace LAMMPS_NS;

src/USER-MEAMC/meam_impl.cpp

@@ -16,9 +16,11 @@
 ------------------------------------------------------------------------- */
 
 #include "meam.h"
-#include <cstddef>
+
 #include "memory.h"
 
+#include <cstddef>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */

src/USER-MEAMC/meam_setup_done.cpp

@@ -1,9 +1,11 @@
 #include "meam.h"
+
+#include "math_special.h"
+#include "memory.h"
+
 #include <cmath>
 #include <cstddef>
 #include <algorithm>
-#include "math_special.h"
-#include "memory.h"
 
 using namespace LAMMPS_NS;
 

src/USER-MEAMC/meam_setup_global.cpp

@@ -1,5 +1,7 @@
 #include "meam.h"
+
 #include <cmath>
+
 using namespace LAMMPS_NS;
 
 template <typename TYPE, int maxi, int maxj>

src/USER-MEAMC/meam_setup_param.cpp

@@ -1,5 +1,10 @@
+
 #include "meam.h"
+
+#include "math_const.h"
 #include <algorithm>
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/USER-MISC/bond_special.cpp

@@ -13,19 +13,15 @@
    Contributing Author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-
-#include <cstring>
 #include "bond_special.h"
-#include "atom.h"
-#include "neighbor.h"
-#include "domain.h"
-#include "comm.h"
-#include "force.h"
-#include "pair.h"
-#include "memory.h"
-#include "error.h"
 
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neighbor.h"
+#include "pair.h"
 
 using namespace LAMMPS_NS;
 

src/USER-MISC/bond_special.h

@@ -22,7 +22,6 @@ BondStyle(special,BondSpecial)
 #ifndef LMP_BOND_SPECIAL_H
 #define LMP_BOND_SPECIAL_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {

src/USER-MISC/compute_hma.cpp

@@ -43,33 +43,30 @@ properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015
 https://doi.org/10.1103/PhysRevE.92.043303
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-
 #include "compute_hma.h"
-#include "atom.h"
-#include "update.h"
-#include "force.h"
-#include "pair.h"
-#include "bond.h"
+
 #include "angle.h"
+#include "atom.h"
+#include "bond.h"
+#include "comm.h"
 #include "dihedral.h"
-#include "improper.h"
-#include "kspace.h"
-#include "group.h"
 #include "domain.h"
-#include "modify.h"
+#include "error.h"
 #include "fix.h"
 #include "fix_store.h"
+#include "force.h"
+#include "group.h"
+#include "improper.h"
+#include "kspace.h"
 #include "memory.h"
-#include "error.h"
-#include "comm.h"
-#include "neighbor.h"
-#include "neigh_request.h"
+#include "modify.h"
 #include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
 
-#include <vector>
-
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/USER-MISC/compute_viscosity_cos.cpp

@@ -15,17 +15,18 @@
    Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com)
 ------------------------------------------------------------------------- */
 
-
 #include "compute_viscosity_cos.h"
+
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "domain.h"
-#include "comm.h"
 #include "group.h"
 #include "error.h"
 #include "math_const.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/USER-MISC/dihedral_spherical.cpp

@@ -19,20 +19,19 @@
 
 #include "dihedral_spherical.h"
 
-#include <cmath>
-#include <cassert>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "domain.h"
+#include "error.h"
 #include "force.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
 
+#include <cmath>
+#include <cassert>
 
-using namespace std;
 using namespace LAMMPS_NS;
 using namespace MathConst;
 using namespace MathExtra;

src/USER-MISC/dihedral_table.cpp

@@ -17,33 +17,24 @@
                           the "tridiag.c" written by Gerard Jungman for GSL
 ------------------------------------------------------------------------- */
 
-
-#include <cctype>
-#include <cmath>
-
-#include <cstring>
-
-#include <sstream>  // IWYU pragma: keep
-#include <fstream>  // IWYU pragma: keep
+#include "dihedral_table.h"
 
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "domain.h"
-#include "force.h"
-#include "memory.h"
 #include "error.h"
-
-#include "dihedral_table.h"
-
-#include "tokenizer.h"
-#include "table_file_reader.h"
-
-
+#include "force.h"
 #include "math_const.h"
 #include "math_extra.h"
+#include "memory.h"
+#include "neighbor.h"
+#include "table_file_reader.h"
+#include "tokenizer.h"
+
+#include <cmath>
+#include <cstring>
+#include <fstream>  // IWYU pragma: keep
 
-using namespace std;
 using namespace LAMMPS_NS;
 using namespace MathConst;
 using namespace MathExtra;
@@ -829,28 +820,20 @@ void DihedralTable::coeff(int narg, char **arg)
   // ---  and resolve issues with periodicity  ---
 
   if (tb->ninput < 2) {
-    string err_msg;
-    err_msg = string("Invalid dihedral table length (")
-      + string(arg[2]) + string(").");
-    error->one(FLERR,err_msg);
-  }
-  else if ((tb->ninput == 2) && (tabstyle == SPLINE)) {
-    string err_msg;
-    err_msg = string("Invalid dihedral spline table length. (Try linear)\n (")
-      + string(arg[2]) + string(").");
-    error->one(FLERR,err_msg);
+    error->one(FLERR,fmt::format("Invalid dihedral table length ({}).",
+                                 arg[2]));
+  } else if ((tb->ninput == 2) && (tabstyle == SPLINE)) {
+    error->one(FLERR,fmt::format("Invalid dihedral spline table length. "
+                                 "(Try linear)\n ({}).",arg[2]));
   }
 
   // check for monotonicity
   for (int i=0; i < tb->ninput-1; i++) {
     if (tb->phifile[i] >= tb->phifile[i+1]) {
-      stringstream i_str;
-      i_str << i+1;
-      string err_msg =
-        string("Dihedral table values are not increasing (") +
-        string(arg[2]) + string(", ")+i_str.str()+string("th entry)");
+      auto err_msg = fmt::format("Dihedral table values are not increasing "
+                                 "({}, {}th entry)",arg[2],i+1);
       if (i==0)
-        err_msg += string("\n(This is probably a mistake with your table format.)\n");
+        err_msg += std::string("\n(This is probably a mistake with your table format.)\n");
       error->all(FLERR,err_msg);
     }
   }
@@ -859,20 +842,13 @@ void DihedralTable::coeff(int narg, char **arg)
   double philo = tb->phifile[0];
   double phihi = tb->phifile[tb->ninput-1];
   if (tb->use_degrees) {
-    if ((phihi - philo) >= 360) {
-      string err_msg;
-      err_msg = string("Dihedral table angle range must be < 360 degrees (")
-        +string(arg[2]) + string(").");
-      error->all(FLERR,err_msg);
-    }
-  }
-  else {
-    if ((phihi - philo) >= MY_2PI) {
-      string err_msg;
-      err_msg = string("Dihedral table angle range must be < 2*PI radians (")
-        + string(arg[2]) + string(").");
-      error->all(FLERR,err_msg);
-    }
+    if ((phihi - philo) >= 360)
+      error->all(FLERR,fmt::format("Dihedral table angle range must be < 360 "
+                                   "degrees ({}).",arg[2]));
+  } else {
+    if ((phihi - philo) >= MY_2PI)
+      error->all(FLERR,fmt::format("Dihedral table angle range must be < 2*PI "
+                                   "radians ({}).",arg[2]));
   }
 
   // convert phi from degrees to radians
@@ -940,10 +916,9 @@ void DihedralTable::coeff(int narg, char **arg)
   // Optional: allow the user to print out the interpolated spline tables
 
   if (me == 0) {
-    if (!checkU_fname.empty())
-    {
-      ofstream checkU_file;
-      checkU_file.open(checkU_fname, ios::out);
+    if (!checkU_fname.empty()) {
+      std::ofstream checkU_file;
+      checkU_file.open(checkU_fname, std::ios::out);
       for (int i=0; i < tablength; i++) {
         double phi = i*MY_2PI/tablength;
         double u = tb->e[i];
@@ -953,12 +928,10 @@ void DihedralTable::coeff(int narg, char **arg)
       }
       checkU_file.close();
     }
-    if (!checkF_fname.empty())
-    {
-      ofstream checkF_file;
-      checkF_file.open(checkF_fname, ios::out);
-      for (int i=0; i < tablength; i++)
-      {
+    if (!checkF_fname.empty()) {
+      std::ofstream checkF_file;
+      checkF_file.open(checkF_fname, std::ios::out);
+      for (int i=0; i < tablength; i++) {
         double phi = i*MY_2PI/tablength;
         double f;
         if ((tabstyle == SPLINE) && (tb->f_unspecified)) {
@@ -973,8 +946,7 @@ void DihedralTable::coeff(int narg, char **arg)
             //  To be nice and report something, I do the same thing here.)
             cyc_splintD(tb->phi, tb->e, tb->e2, tablength, MY_2PI,phi);
           f = -dU_dphi;
-        }
-        else
+        } else
           // Otherwise we calculated the tb->f[] array.  Report its contents.
           f = tb->f[i];
         if (tb->use_degrees) {
@@ -991,8 +963,7 @@ void DihedralTable::coeff(int narg, char **arg)
 
   // store ptr to table in tabindex
   int count = 0;
-  for (int i = ilo; i <= ihi; i++)
-  {
+  for (int i = ilo; i <= ihi; i++) {
     tabindex[i] = ntables;
     //phi0[i] = tb->phi0; <- equilibrium dihedral angles not supported
     setflag[i] = 1;
@@ -1213,7 +1184,7 @@ void DihedralTable::spline_table(Table *tb)
     } // for (int i=0; i<tb->ninput; i++)
 
     if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) {
-      string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n");
+      std::string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n");
       error->all(FLERR, msg);
     }
 
@@ -1319,7 +1290,7 @@ void DihedralTable::param_extract(Table *tb, char *line)
     ValueTokenizer values(line);
 
     while (values.has_next()) {
-      std::string word = values.next_string();
+      auto word = values.next_string();
       if (word == "N") {
         tb->ninput = values.next_int();
       }
@@ -1342,10 +1313,8 @@ void DihedralTable::param_extract(Table *tb, char *line)
       //else if (word == "EQ") {
       //  tb->theta0 = values.next_double();
       //}
-      else {
-        string err_msg = fmt::format("Invalid keyword in dihedral angle table parameters ({})", word);
-        error->one(FLERR,err_msg);
-      }
+      else error->one(FLERR,fmt::format("Invalid keyword in dihedral angle "
+                                        "table parameters ({})", word));
     }
   } catch (TokenizerException & e) {
     error->one(FLERR, e.what());

src/USER-MISC/fix_accelerate_cos.cpp

@@ -16,15 +16,9 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_accelerate_cos.h"
+
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "domain.h"
-#include "region.h"
-#include "respa.h"
-#include "input.h"
-#include "variable.h"
-#include "memory.h"
 #include "error.h"
 #include "force.h"
 #include "math_const.h"

src/USER-MISC/fix_ave_correlate_long.cpp

@@ -23,19 +23,18 @@
 
 #include "fix_ave_correlate_long.h"
 
-#include <cmath>
+#include "citeme.h"
+#include "compute.h"
+#include "error.h"
+#include "input.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+#include "variable.h"
 
+#include <cmath>
 #include <cstring>
 #include <unistd.h>
-#include "update.h"
-#include "modify.h"
-#include "compute.h"
-#include "input.h"
-#include "variable.h"
-#include "citeme.h"
-#include "memory.h"
-#include "error.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_electron_stopping.cpp

@@ -17,21 +17,22 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_electron_stopping.h"
-#include <cmath>
-#include <cstring>
-#include "mpi.h"
+
 #include "atom.h"
-#include "update.h"
-#include "domain.h"
-#include "region.h"
-#include "force.h"
-#include "fix.h"
-#include "memory.h"
 #include "comm.h"
+#include "domain.h"
 #include "error.h"
-#include "neighbor.h"
+#include "fix.h"
+#include "force.h"
+#include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
+#include "neighbor.h"
+#include "region.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_flow_gauss.cpp

@@ -18,15 +18,15 @@
 
 #include "fix_flow_gauss.h"
 
-#include <cstring>
 #include "atom.h"
-#include "force.h"
-#include "group.h"
-#include "update.h"
+#include "citeme.h"
 #include "domain.h"
 #include "error.h"
-#include "citeme.h"
+#include "group.h"
 #include "respa.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_imd.cpp

@@ -48,16 +48,15 @@ negotiate an appropriate license for such distribution."
 ------------------------------------------------------------------------- */
 
 #include "fix_imd.h"
+
 #include "atom.h"
 #include "comm.h"
-#include "update.h"
-#include "respa.h"
 #include "domain.h"
-#include "force.h"
 #include "error.h"
 #include "group.h"
 #include "memory.h"
-
+#include "respa.h"
+#include "update.h"
 
 #include <cstring>
 

src/USER-MISC/fix_momentum_chunk.cpp

@@ -13,18 +13,17 @@
 
 #include "fix_momentum_chunk.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "compute.h"
 #include "compute_chunk_atom.h"
 #include "compute_com_chunk.h"
 #include "domain.h"
-#include "group.h"
 #include "error.h"
-#include "force.h"
+#include "group.h"
 #include "modify.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_orient_eco.cpp

@@ -17,12 +17,9 @@
 
 #include "fix_orient_eco.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "citeme.h"
 #include "comm.h"
-#include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "math_const.h"
@@ -34,7 +31,8 @@
 #include "respa.h"
 #include "update.h"
 
-
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_pafi.cpp

@@ -20,24 +20,21 @@
 
 #include "fix_pafi.h"
 
-#include <cmath>
-#include <cstring>
-
-#include "math_extra.h"
 #include "atom.h"
-#include "force.h"
-#include "update.h"
-#include "modify.h"
-#include "domain.h"
-#include "respa.h"
+#include "citeme.h"
 #include "comm.h"
 #include "compute.h"
-#include "random_mars.h"
-#include "memory.h"
+#include "domain.h"
 #include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "random_mars.h"
+#include "respa.h"
+#include "update.h"
 
-#include "citeme.h"
-
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -61,7 +58,7 @@ using namespace FixConst;
 /* ---------------------------------------------------------------------- */
 
 FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg), random(NULL), computename(NULL),
+  Fix(lmp, narg, arg), computename(NULL), random(NULL),
       h(NULL), step_respa(NULL)
 {
   if (lmp->citeme) lmp->citeme->add(cite_fix_pafi_package);
@@ -215,7 +212,7 @@ void FixPAFI::min_setup(int vflag)
 }
 
 
-void FixPAFI::post_force(int vflag)
+void FixPAFI::post_force(int /*vflag*/)
 {
   double **x = atom->x;
   double **v = atom->v;
@@ -236,8 +233,6 @@ void FixPAFI::post_force(int vflag)
   PathCompute->compute_peratom();
   double **path = PathCompute->array_atom;
 
-  double xum=0.;
-
   // proj 0,1,2 = f.n, v.n, h.n
   // proj 3,4,5 = psi, f.n**2, f*(1-psi)
   // c_v 0,1,2 = fxcom, fycom, fzcom etc
@@ -252,8 +247,6 @@ void FixPAFI::post_force(int vflag)
 
   double deviation[3] = {0.,0.,0.};
 
-  double fn;
-
   force_flag=0;
   for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
@@ -378,13 +371,12 @@ void FixPAFI::post_force(int vflag)
 
 };
 
-void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop)
+void FixPAFI::post_force_respa(int vflag, int ilevel, int /*iloop*/)
 {
   // set force to desired value on requested level, 0.0 on other levels
 
   if (ilevel == ilevel_respa) post_force(vflag);
   else {
-    double **x = atom->x;
     double **f = atom->f;
     int *mask = atom->mask;
     int nlocal = atom->nlocal;
@@ -396,22 +388,17 @@ void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop)
   }
 };
 
-void FixPAFI::min_post_force(int vflag)
+void FixPAFI::min_post_force(int /*vflag*/)
 {
   double **x = atom->x;
   double **v = atom->v;
   double **f = atom->f;
-  double *rmass = atom->rmass;
-  double *mass = atom->mass;
-  int *type = atom->type;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
   PathCompute->compute_peratom();
   double **path = PathCompute->array_atom;
 
-  double xum=0.;
-
   // proj 0,1,2 = f.n, v.n, h.n
   // proj 3,4,5 = psi, f.n**2, f*(1-psi)
   // c_v 0,1,2 = fxcom, fycom, fzcom etc
@@ -426,8 +413,6 @@ void FixPAFI::min_post_force(int vflag)
 
   double deviation[3] = {0.,0.,0.};
 
-  double fn;
-
   force_flag=0;
   for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
@@ -519,7 +504,7 @@ double FixPAFI::compute_vector(int n)
 
 
 
-void FixPAFI::initial_integrate(int vflag)
+void FixPAFI::initial_integrate(int /*vflag*/)
 {
   double dtfm;
 
@@ -710,7 +695,7 @@ void FixPAFI::final_integrate()
 
 /* ---------------------------------------------------------------------- */
 
-void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
 {
   dtv = step_respa[ilevel];
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -724,7 +709,7 @@ void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop)
 
 /* ---------------------------------------------------------------------- */
 
-void FixPAFI::final_integrate_respa(int ilevel, int iloop)
+void FixPAFI::final_integrate_respa(int ilevel, int /*iloop*/)
 {
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
   final_integrate();

src/USER-MISC/fix_propel_self.cpp

@@ -19,25 +19,15 @@
 
 #include "fix_propel_self.h"
 
-#include <cstdio>
-#include <cstring>
-
-
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "citeme.h"
-#include "comm.h"
 #include "error.h"
-#include "force.h"
-#include "group.h"
 #include "math.h"
 #include "math_const.h"
 #include "math_extra.h"
-#include "math_vector.h"
-#include "modify.h"
-#include "random_mars.h"
-#include "respa.h"
-#include "update.h"
+
+#include <cctype>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_rhok.cpp

@@ -15,17 +15,16 @@
 
 #include "fix_rhok.h"
 
-#include <cstring>
-#include <cmath>
-
 #include "atom.h"
+#include "citeme.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
+#include "math_const.h"
 #include "respa.h"
 #include "update.h"
-#include "citeme.h"
-#include "math_const.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_smd.cpp

@@ -18,16 +18,16 @@
 
 #include "fix_smd.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "update.h"
-#include "respa.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
 #include "group.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_srp.cpp

@@ -17,18 +17,18 @@
 
 #include "fix_srp.h"
 
+#include "atom.h"
+#include "atom_vec.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "neighbor.h"
+
 #include <cmath>
 #include <cstring>
-#include "atom.h"
-#include "force.h"
-#include "domain.h"
-#include "modify.h"
-#include "comm.h"
-#include "memory.h"
-#include "error.h"
-#include "neighbor.h"
-#include "atom_vec.h"
-#include "modify.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_ti_spring.cpp

@@ -20,15 +20,15 @@
 
 #include "fix_ti_spring.h"
 
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "domain.h"
-#include "respa.h"
-#include "memory.h"
-#include "error.h"
 #include "citeme.h"
-#include "force.h"
+#include "domain.h"
+#include "error.h"
+#include "memory.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_wall_ees.cpp

@@ -16,13 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_wall_ees.h"
-#include <cmath>
+
 #include "math_extra.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
 #include "error.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/USER-MISC/fix_wall_reflect_stochastic.cpp

@@ -17,19 +17,17 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_wall_reflect_stochastic.h"
-#include <cstring>
 
 #include "atom.h"
 #include "comm.h"
-#include "update.h"
-#include "modify.h"
 #include "domain.h"
+#include "error.h"
 #include "force.h"
 #include "lattice.h"
-#include "input.h"
-#include "variable.h"
 #include "random_mars.h"
-#include "error.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_wall_region_ees.cpp

@@ -17,17 +17,17 @@
 
 #include "fix_wall_region_ees.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
 #include "domain.h"
-#include "region.h"
-#include "force.h"
-#include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "math_extra.h"
+#include "region.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/pair_agni.cpp

@@ -17,21 +17,19 @@
 
 #include "pair_agni.h"
 
-#include <cmath>
-
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
-#include "comm.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "citeme.h"
-#include "math_special.h"
+#include "comm.h"
+#include "error.h"
 #include "math_const.h"
+#include "math_special.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;

src/USER-MISC/pair_cosine_squared.cpp

@@ -15,22 +15,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_cosine_squared.h"
-#include <cmath>
 
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/USER-MISC/pair_coul_slater_cut.cpp

@@ -15,18 +15,15 @@
  *     Contributing author:  Evangelos Voyiatzis (Royal DSM)
  * ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-
-#include <cstring>
 #include "pair_coul_slater_cut.h"
+
 #include "atom.h"
 #include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
+#include "force.h"
+#include "neigh_list.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/USER-MISC/pair_coul_slater_long.cpp

@@ -15,23 +15,19 @@
  *     Contributing author:  Evangelos Voyiatzis (Royal DSM)
  * ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-
-#include <cstring>
 #include "pair_coul_slater_long.h"
+
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "kspace.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neighbor.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/USER-MISC/pair_local_density.cpp

@@ -19,21 +19,17 @@
 
 #include "pair_local_density.h"
 
-#include <cmath>
-
-#include <cstring>
-
 #include "atom.h"
-#include "force.h"
-#include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "memory.h"
-#include "error.h"
-#include "domain.h"
 #include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/USER-MISC/temper_npt.cpp

@@ -18,22 +18,23 @@
 ------------------------------------------------------------------------- */
 
 #include "temper_npt.h"
-#include <cmath>
-#include <cstring>
-#include "universe.h"
-#include "domain.h"
+
 #include "atom.h"
-#include "update.h"
+#include "compute.h"
+#include "domain.h"
+#include "error.h"
+#include "finish.h"
+#include "fix.h"
+#include "force.h"
 #include "integrate.h"
 #include "modify.h"
-#include "compute.h"
-#include "force.h"
-#include "fix.h"
 #include "random_park.h"
-#include "finish.h"
 #include "timer.h"
-#include "error.h"
-#include "utils.h"
+#include "universe.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/USER-SMD/atom_vec_smd.cpp

@@ -23,9 +23,10 @@
  ------------------------------------------------------------------------- */
 
 #include "atom_vec_smd.h"
-#include <cstring>
+
 #include "atom.h"
-#include "error.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/USER-SMD/compute_smd_tlsph_defgrad.cpp

@@ -23,14 +23,16 @@
  ------------------------------------------------------------------------- */
 
 #include "compute_smd_tlsph_defgrad.h"
-#include <cstring>
-#include <Eigen/Eigen>
+
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "comm.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+
+#include <cstring>
+#include <Eigen/Eigen>          // IWYU pragma: export
 
 using namespace Eigen;
 using namespace std;

src/USER-SMD/compute_smd_tlsph_shape.cpp

@@ -23,16 +23,18 @@
  ------------------------------------------------------------------------- */
 
 #include "compute_smd_tlsph_shape.h"
-#include <cstring>
-#include <Eigen/Eigen>
+
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "error.h"
+#include "modify.h"
 #include "pair.h"
+#include "update.h"
+
+#include <cstring>
+#include <Eigen/Eigen>          // IWYU pragma: export
 
 using namespace Eigen;
 using namespace std;

src/USER-SMD/compute_smd_tlsph_strain.cpp

@@ -24,16 +24,18 @@
  ------------------------------------------------------------------------- */
 
 #include "compute_smd_tlsph_strain.h"
-#include <cstring>
-#include <Eigen/Eigen>
+
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "error.h"
+#include "modify.h"
 #include "pair.h"
+#include "update.h"
+
+#include <cstring>
+#include <Eigen/Eigen>          // IWYU pragma: export
 
 using namespace Eigen;
 using namespace std;

src/USER-SMD/compute_smd_tlsph_strain_rate.cpp

@@ -23,17 +23,19 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <Eigen/Eigen>
 #include "compute_smd_tlsph_strain_rate.h"
+
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "error.h"
+#include "modify.h"
 #include "pair.h"
+#include "update.h"
+
+#include <cstring>
+#include <Eigen/Eigen>          // IWYU pragma: export
 
 using namespace Eigen;
 using namespace LAMMPS_NS;