continuing include file handling cleanup

src/USER-MANIFOLD/fix_manifoldforce.cpp

@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "fix_manifoldforce.h"  // For stuff
+#include <mpi.h>
 #include <cstring>
-#include <cstdlib>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
@@ -21,7 +21,6 @@
 #include "force.h"
 
 #include "manifold.h"
-#include "fix_manifoldforce.h"  // For stuff
 #include "manifold_factory.h"   // For constructing manifold
 
 

src/USER-MANIFOLD/fix_manifoldforce.h

@@ -43,9 +43,9 @@ FixStyle(manifoldforce,FixManifoldForce)
 #define LMP_FIX_MANIFOLDFORCE_H
 
 #include "fix.h"
-#include "manifold.h"
 
 namespace LAMMPS_NS {
+namespace user_manifold { class manifold; }
 
 class FixManifoldForce : public Fix {
  public:

src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp

@@ -32,24 +32,18 @@
 ------------------------------------------------------------------------- */
 
 
-#include <cstdio>
-#include <cstdlib>
+#include "fix_nve_manifold_rattle.h"
+#include <mpi.h>
 #include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
-#include "group.h"
-#include <cmath>
 #include "input.h"
 #include "variable.h"
 #include "citeme.h"
-#include "memory.h"
 #include "comm.h"
 
-
-#include "fix_nve_manifold_rattle.h"
 #include "manifold_factory.h"
 #include "manifold.h"
 

src/USER-MANIFOLD/fix_nve_manifold_rattle.h

@@ -42,12 +42,10 @@ FixStyle(nve/manifold/rattle,FixNVEManifoldRattle)
 #define LMP_FIX_NVE_MANIFOLD_RATTLE_H
 
 #include "fix.h"
-#include "manifold.h"
-
 
 namespace LAMMPS_NS {
 
-// namespace user_manifold {
+namespace user_manifold { class manifold; }
 
   class FixNVEManifoldRattle : public Fix {
    public:
@@ -98,9 +96,7 @@ namespace LAMMPS_NS {
 
     user_manifold::manifold *ptr_m;
 
-
     void print_stats( const char * );
-
     int was_var( const char * );
 
     virtual void update_var_params();

src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp

@@ -32,25 +32,18 @@
 ------------------------------------------------------------------------- */
 
 
-#include <cstdio>
-#include <cstdlib>
+#include "fix_nvt_manifold_rattle.h"
 #include <cstring>
 #include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "group.h"
-#include "input.h"
-#include "variable.h"
 #include "citeme.h"
-#include "memory.h"
-#include "comm.h"
 #include "modify.h"
 #include "compute.h"
 
-#include "fix_nvt_manifold_rattle.h"
 #include "manifold.h"
 
 

src/USER-MANIFOLD/manifold_factory.h

@@ -35,8 +35,7 @@
 #ifndef LMP_MANIFOLD_FACTORY_H
 #define LMP_MANIFOLD_FACTORY_H
 
-
-#include "manifold.h"
+#include <cstddef>
 #include <cstring>
 
 /*
@@ -79,14 +78,16 @@ static FILE *screen = fopen("/dev/stdout","w");
 #define FLERR __FILE__,__LINE__    // Equivalent to definition in pointers.h
 #endif // USE_PHONY_LAMMPS
 
-
-
 /* Here the actual implementation of LAMMPS-related functions begins. */
 
 namespace LAMMPS_NS {
+class LAMMPS;
 
 namespace user_manifold {
 
+// forward declaration
+class manifold;
+
   // Templated, so needs to be in header.
   template <typename m_type>
   void make_manifold_if( manifold **man_ptr, const char *name,
@@ -103,8 +104,6 @@ namespace user_manifold {
                             int , char ** );
 
 } // namespace user_manifold
-
 } // namespace LAMMPS_NS
 
-
 #endif // LMP_MANIFOLD_FACTORY_H

src/USER-MANIFOLD/manifold_thylakoid.cpp

@@ -1,6 +1,6 @@
 #include "manifold_thylakoid.h"
 #include <cmath>
-
+#include "manifold_thylakoid_shared.h"
 #include "comm.h"
 #include "domain.h" // For some checks regarding the simulation box.
 #include "error.h"

src/USER-MANIFOLD/manifold_thylakoid.h

@@ -4,12 +4,10 @@
 #include "manifold.h"
 #include <vector>
 
-#include "manifold_thylakoid_shared.h"
-
 namespace LAMMPS_NS {
 
 namespace user_manifold {
-
+  struct thyla_part;
 
   class manifold_thylakoid : public manifold {
    public:

src/USER-MEAMC/meam.h

@@ -1,12 +1,12 @@
 #ifndef LMP_MEAM_H
 #define LMP_MEAM_H
 
-#include "memory.h"
 #include <cmath>
 
 #define maxelt 5
 
 namespace LAMMPS_NS {
+class Memory;
 
 typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t;
 

src/USER-MEAMC/meam_dens_final.cpp

@@ -1,5 +1,4 @@
 #include "meam.h"
-#include "math_special.h"
 
 using namespace LAMMPS_NS;
 

src/USER-MEAMC/meam_dens_init.cpp

@@ -1,4 +1,6 @@
 #include "meam.h"
+#include <cmath>
+#include "memory.h"
 #include "math_special.h"
 
 using namespace LAMMPS_NS;

src/USER-MEAMC/meam_force.cpp

@@ -1,6 +1,7 @@
 #include "meam.h"
-#include "math_special.h"
+#include <cmath>
 #include <algorithm>
+#include "math_special.h"
 
 using namespace LAMMPS_NS;
 

src/USER-MEAMC/meam_impl.cpp

@@ -16,6 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "meam.h"
+#include <cstddef>
 #include "memory.h"
 
 using namespace LAMMPS_NS;

src/USER-MEAMC/meam_setup_done.cpp

@@ -1,6 +1,10 @@
 #include "meam.h"
-#include "math_special.h"
+#include <cmath>
+#include <cstddef>
 #include <algorithm>
+#include "math_special.h"
+#include "memory.h"
+
 using namespace LAMMPS_NS;
 
 void

src/USER-MEAMC/pair_meamc.cpp

@@ -15,16 +15,14 @@
    Contributing author: Greg Wagner (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
+#include "pair_meamc.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
 #include "meam.h"
-#include "pair_meamc.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"

src/USER-MEAMC/pair_meamc.h

@@ -24,7 +24,6 @@ PairStyle(meam,PairMEAMC)
 #include "pair.h"
 
 namespace LAMMPS_NS {
-class MEAM;
 
 class PairMEAMC : public Pair {
  public:

src/USER-MGPT/mgpt_linalg.cpp

@@ -20,8 +20,6 @@
 
 #include <cstdio>
 #include <cstdlib>
-#include <cmath>
-#include <cassert>
 
 #define restrict __restrict__
 

src/USER-MGPT/mgpt_readpot.h

@@ -19,7 +19,9 @@
 #ifndef READPOT__
 #define READPOT__
 
-
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
 #include "mgpt_splinetab.h"
 
 struct potdata {

src/USER-MGPT/pair_mgpt.cpp

@@ -21,17 +21,16 @@
    (2011).  See LLNL copyright notice at bottom of this file.
 ------------------------------------------------------------------------- */
 
+#include "pair_mgpt.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <cassert>
 
-#include "pair_mgpt.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"

src/USER-MGPT/pair_mgpt.h

@@ -32,6 +32,7 @@ PairStyle(mgpt,PairMGPT)
 
 #include <new>
 #include <cmath>
+#include <cstdlib>
 #include <cassert>
 
 #include "pair.h"
@@ -77,29 +78,29 @@ public:
       Link(const K &k,Link *n) : next(n),key(k),hits(1) {}
 
       static void *operator new(std::size_t sz) {
-	const size_t align = 32;
-	size_t x = (size_t) (void *) ::operator new(sz+align);
-	size_t y = (x + align) - ((x+align)&(align-1));
-	assert(sizeof(void *) <= align);
-	assert((x & (sizeof(void *)-1)) == 0);
-	((void **) y)[-1] = (void *) x;
-	return (void *) y;
+        const size_t align = 32;
+        size_t x = (size_t) (void *) ::operator new(sz+align);
+        size_t y = (x + align) - ((x+align)&(align-1));
+        assert(sizeof(void *) <= align);
+        assert((x & (sizeof(void *)-1)) == 0);
+        ((void **) y)[-1] = (void *) x;
+        return (void *) y;
       }
       static void operator delete(void *ptr) {
-	::operator delete(((void **) ptr)[-1]);
+        ::operator delete(((void **) ptr)[-1]);
       }
     };
 
     int isprime(int x) {
       if(x%2 == 0)
-	return 0;
+        return 0;
       else {
-	int k = 3;
-	while(k*k <= x) {
-	  if(x%k == 0) return 0;
-	  k = k+2;
-	}
-	return 1;
+        int k = 3;
+        while(k*k <= x) {
+          if(x%k == 0) return 0;
+          k = k+2;
+        }
+        return 1;
     }
   }
 
@@ -117,25 +118,25 @@ public:
       Iterator(Hash &HH) : H(HH),idx(-1),p(0) { next(); }
       Iterator(Hash &HH,int iidx,Link *pp) : H(HH),idx(iidx),p(pp) {}
       void next() {
-	if(idx >= H.Size()) return;
-	if(p != 0) p = p->next;
-	if(p == 0) {
-	  do {
-	    idx = idx+1;
-	    if(idx >= H.Size()) return;
-	    p = H.table[idx];
-	  } while(p == 0);
-	}
+        if(idx >= H.Size()) return;
+        if(p != 0) p = p->next;
+        if(p == 0) {
+          do {
+            idx = idx+1;
+            if(idx >= H.Size()) return;
+            p = H.table[idx];
+          } while(p == 0);
+        }
       }
       K *key() { return &p->key; }
       T *data() { return &p->data; }
       Link *link() { return p; }
 
       int operator==(const Iterator &a) {
-	return idx==a.idx && p==a.p;
+        return idx==a.idx && p==a.p;
       }
       int operator!=(const Iterator &a) {
-	return !(*this == a);
+        return !(*this == a);
       }
     };
 
@@ -147,7 +148,7 @@ public:
 
       table = new Link *[size];
       for(int i = 0; i<size; i++)
-	table[i] = 0;
+        table[i] = 0;
 
       /* Counters for statistics */
       maxlength = 0;
@@ -157,12 +158,12 @@ public:
 
     ~Hash() {
       for(int i = 0; i<size; i++) {
-	Link *p = table[i];
-	while(p != 0) {
-	  Link *q = p->next;
-	delete p;
-	p = q;
-	}
+        Link *p = table[i];
+        while(p != 0) {
+          Link *q = p->next;
+        delete p;
+        p = q;
+        }
       }
       delete[] table;
     }
@@ -179,24 +180,24 @@ public:
       int idx = key.hash() % size;
       if(idx < 0) idx = idx + size;
       if(idx >= size || idx < 0) {
-	printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
-	exit(1);
+        printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+        exit(1);
       }
 
       used = used + 1;
       if(1) {
-	table[idx] = new Link(key,table[idx]);
-	return &table[idx]->data;
+        table[idx] = new Link(key,table[idx]);
+        return &table[idx]->data;
       } else { /* This is for threading... and incomplete */
-	typedef Link *LinkPtr;
-	LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0);
+        typedef Link *LinkPtr;
+        LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0);
 
-	while(ptr != 0) {
-	  last = ptr;
-	  ptr = ptr->next;
-	}
-	*((volatile LinkPtr *) &(last->next)) = dataptr;
-	return &(dataptr->data);
+        while(ptr != 0) {
+          last = ptr;
+          ptr = ptr->next;
+        }
+        *((volatile LinkPtr *) &(last->next)) = dataptr;
+        return &(dataptr->data);
       }
     }
     void Remove(const K &key) {
@@ -205,28 +206,28 @@ public:
       int count = 1;
       if(idx < 0) idx = idx + size;
       if(idx >= size || idx < 0) {
-	printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
-	exit(1);
+        printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+        exit(1);
       }
 
       p = table[idx];
       while(p != 0 && !(p->key == key)) {
-	last = p;
-	p = p->next;
-	count = count + 1;
+        last = p;
+        p = p->next;
+        count = count + 1;
       }
 
       if(p != 0) {
-	used = used - 1;
-	if(last == 0)
-	  table[idx] = p->next;
-	else
-	  last->next = p->next;
-	delete p;
+        used = used - 1;
+        if(last == 0)
+          table[idx] = p->next;
+        else
+          last->next = p->next;
+        delete p;
       }
 
       if(count > maxlength)
-	maxlength = count;
+        maxlength = count;
       nsearch = nsearch + 1;
       nstep = nstep + count;
     }
@@ -236,19 +237,19 @@ public:
       int count = 1;
       if(idx < 0) idx = idx + size;
       if(idx >= size || idx < 0) {
-	printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
-	exit(1);
+        printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+        exit(1);
       }
 
 
       p = table[idx];
       while(p != 0 && !(p->key == key)) {
-	p = p->next;
-	count = count + 1;
+        p = p->next;
+        count = count + 1;
       }
 
       if(count > maxlength)
-	maxlength = count;
+        maxlength = count;
       nsearch = nsearch + 1;
       nstep = nstep + count;
 
@@ -283,46 +284,46 @@ public:
     }
     void zero() {
       for(int i = 0; i<8; i++)
-	for(int j = 0; j<8; j++)
-	  m[i][j] = 0.0;
+        for(int j = 0; j<8; j++)
+          m[i][j] = 0.0;
     }
 
     void operator=(const Matrix &A) {
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  m[i][j] = A.m[i][j];
+        for(int j = 1; j<=sz; j++)
+          m[i][j] = A.m[i][j];
     }
     void operator=(double x) {
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  m[i][j] = x;
+        for(int j = 1; j<=sz; j++)
+          m[i][j] = x;
     }
     Matrix operator+(const Matrix &B) const {
       Matrix s;
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  s.m[i][j] = m[i][j] + B.m[i][j];
+        for(int j = 1; j<=sz; j++)
+          s.m[i][j] = m[i][j] + B.m[i][j];
       return s;
     }
     Matrix operator-(const Matrix &B) const {
       Matrix s;
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  s.m[i][j] = m[i][j] - B.m[i][j];
+        for(int j = 1; j<=sz; j++)
+          s.m[i][j] = m[i][j] - B.m[i][j];
       return s;
     }
     Matrix operator-() const {
       Matrix s;
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  s.m[i][j] =  -m[i][j];
+        for(int j = 1; j<=sz; j++)
+          s.m[i][j] =  -m[i][j];
       return s;
     }
     Matrix operator*(double x) const {
       Matrix P;
       for(int i = 1; i<=sz; i++)
-	for(int j = 0; j<=sz; j++)
-	  P.m[i][j] = m[i][j] * x;
+        for(int j = 0; j<=sz; j++)
+          P.m[i][j] = m[i][j] * x;
       return P;
     }
     Matrix operator/(double x) const {
@@ -331,8 +332,8 @@ public:
     Matrix transpose() const {
       Matrix T;
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  T.m[j][i] = m[i][j];
+        for(int j = 1; j<=sz; j++)
+          T.m[j][i] = m[i][j];
       return T;
     }
   };
@@ -374,13 +375,13 @@ public:
 
     int align_check() {
       return
-	(H1H2.align_check()  << 0) |
-	(H1xH2.align_check() << 1) |
-	(H1yH2.align_check() << 2) |
-	(H1zH2.align_check() << 3) |
-	(H1H2x.align_check() << 4) |
-	(H1H2y.align_check() << 5) |
-	(H1H2z.align_check() << 6) ;
+        (H1H2.align_check()  << 0) |
+        (H1xH2.align_check() << 1) |
+        (H1yH2.align_check() << 2) |
+        (H1zH2.align_check() << 3) |
+        (H1H2x.align_check() << 4) |
+        (H1H2y.align_check() << 5) |
+        (H1H2z.align_check() << 6) ;
     }
 
     void zero() {
@@ -396,18 +397,18 @@ public:
   void make_bond(const double xx[][3],int i,int j,bond_data *bptr);
   void make_triplet(bond_data *ij_bond,bond_data *ik_bond,triplet_data *triptr);
   triplet_data *get_triplet(const double xx[][3],int i,int j,int k,
-			    Hash<bond_data,Doublet> *bhash,triplet_data *twork,
-			    double *dvir_ij_p,double *dvir_ik_p);
+                            Hash<bond_data,Doublet> *bhash,triplet_data *twork,
+                            double *dvir_ij_p,double *dvir_ik_p);
 
   int c1_outside(const double a[3],
-		 int triclinic,const double alpha[3]) {
+                 int triclinic,const double alpha[3]) {
     const double stol = 1e-5;
 
     if(triclinic) {
       for(int p = 0; p<3; p++) {
-	double cog = a[p];
-	if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1;
-	if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1;
+        double cog = a[p];
+        if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1;
+        if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1;
       }
 
     } else {
@@ -415,63 +416,63 @@ public:
 
 
       for(int p = 0; p<3; p++) {
-	double cog = a[p];
-	if(cog < domain->sublo[p]-0.5*rmax-stol) return 1;
-	if(cog > domain->subhi[p]+0.5*rmax+stol) return 1;
+        double cog = a[p];
+        if(cog < domain->sublo[p]-0.5*rmax-stol) return 1;
+        if(cog > domain->subhi[p]+0.5*rmax+stol) return 1;
 
-	if(cog < domain->sublo[p]-stol) {
-	  double t = cog - (domain->sublo[p]-stol);
-	  rout = rout + t*t;
-	} else if(cog > domain->subhi[p]+stol) {
-	  double t = cog - (domain->subhi[p]+stol);
-	  rout = rout + t*t;
-	}
+        if(cog < domain->sublo[p]-stol) {
+          double t = cog - (domain->sublo[p]-stol);
+          rout = rout + t*t;
+        } else if(cog > domain->subhi[p]+stol) {
+          double t = cog - (domain->subhi[p]+stol);
+          rout = rout + t*t;
+        }
 
       }
 
       if(rout > 0.25*rmax*rmax)
-	return 1;
+        return 1;
     }
 
     return 0;
   }
   int c2_outside(const double a[3],const double b[3],
-		 int triclinic,const double alpha[3]) {
+                 int triclinic,const double alpha[3]) {
     const double stol = 1e-5;
 
     if(triclinic) {
       for(int p = 0; p<3; p++) {
-	double cog = 0.5*(a[p] + b[p]);
-	if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1;
-	if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1;
+        double cog = 0.5*(a[p] + b[p]);
+        if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1;
+        if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1;
       }
     } else {
       double rout = 0.0;
 
       for(int p = 0; p<3; p++) {
-	double cog = 0.5*(a[p] + b[p]);
-	if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1;
-	if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1;
+        double cog = 0.5*(a[p] + b[p]);
+        if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1;
+        if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1;
 
-	if(cog < domain->sublo[p]-stol) {
-	  double t = cog - (domain->sublo[p]-stol);
-	  rout = rout + t*t;
-	} else if(cog > domain->subhi[p]+stol) {
-	  double t = cog - (domain->subhi[p]+stol);
-	  rout = rout + t*t;
-	}
+        if(cog < domain->sublo[p]-stol) {
+          double t = cog - (domain->sublo[p]-stol);
+          rout = rout + t*t;
+        } else if(cog > domain->subhi[p]+stol) {
+          double t = cog - (domain->subhi[p]+stol);
+          rout = rout + t*t;
+        }
 
       }
 
       if(rout > 0.25*rcrit*rcrit)
-	return 1;
+        return 1;
     }
 
     return 0;
   }
   double get_weight(const int triclinic,
-		    const double a[3] = 0,const double b[3] = 0,
-		    const double c[3] = 0,const double d[3] = 0) {
+                    const double a[3] = 0,const double b[3] = 0,
+                    const double c[3] = 0,const double d[3] = 0) {
     const double
       *s0 = triclinic ? domain->sublo_lamda : domain->sublo,
       *s1 = triclinic ? domain->subhi_lamda : domain->subhi;
@@ -498,46 +499,46 @@ public:
   }
 
   void force_debug_3t(double xx[][3],
-		      int i0,int j0,int k0,
-		      int i ,int j ,int k ,
-		      double dfix,double dfiy,double dfiz,
-		      double dfjx,double dfjy,double dfjz,
-		      double dfkx,double dfky,double dfkz);
+                      int i0,int j0,int k0,
+                      int i ,int j ,int k ,
+                      double dfix,double dfiy,double dfiz,
+                      double dfjx,double dfjy,double dfjz,
+                      double dfkx,double dfky,double dfkz);
 
   void force_debug_3v(double xx[][3],
-		      int i0,int j0,int k0,
-		      int i ,int j ,int k ,
-		      double dfix,double dfiy,double dfiz,
-		      double dfjx,double dfjy,double dfjz,
-		      double dfkx,double dfky,double dfkz);
+                      int i0,int j0,int k0,
+                      int i ,int j ,int k ,
+                      double dfix,double dfiy,double dfiz,
+                      double dfjx,double dfjy,double dfjz,
+                      double dfkx,double dfky,double dfkz);
 
   void force_debug_4(double xx[][3],
-		     int i0,int j0,int k0,int m0,
-		     int i ,int j ,int k ,int m ,
-		     double dfix,double dfiy,double dfiz,
-		     double dfjx,double dfjy,double dfjz,
-		     double dfkx,double dfky,double dfkz,
-		     double dfmx,double dfmy,double dfmz);
+                     int i0,int j0,int k0,int m0,
+                     int i ,int j ,int k ,int m ,
+                     double dfix,double dfiy,double dfiz,
+                     double dfjx,double dfjy,double dfjz,
+                     double dfkx,double dfky,double dfkz,
+                     double dfmx,double dfmy,double dfmz);
 
   double numderiv3t(double xx[][3],int i,int j,int k,int p);
   double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert);
   double numderiv4(double xx[][3],int i,int j,int k,int m,int p);
   void compute_x(const int *nnei,const int * const *nlist,
-		 double *e_s,double *e_p,double *e_t,double *e_q,
-		 int evflag,int newton_pair);
+                 double *e_s,double *e_p,double *e_t,double *e_q,
+                 int evflag,int newton_pair);
 
   /* Reimplementation of bond matrix computation */
   void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat,
-		    double &fl_0,double &fl_x,double &fl_y,double &fl_z,
-		    double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al);
+                    double &fl_0,double &fl_x,double &fl_y,double &fl_z,
+                    double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al);
   void hamltn_5_raw(const double xin,const double yin,const double zin,
-		    double M [8][8],double Mx[8][8],
-		    double My[8][8],double Mz[8][8],
-		    double *fl_deriv_sum_p);
+                    double M [8][8],double Mx[8][8],
+                    double My[8][8],double Mz[8][8],
+                    double *fl_deriv_sum_p);
   void hamltn_7_raw(const double xin,const double yin,const double zin,
-		    double M [8][8],double Mx[8][8],
-		    double My[8][8],double Mz[8][8],
-		    double *fl_deriv_sum_p);
+                    double M [8][8],double Mx[8][8],
+                    double My[8][8],double Mz[8][8],
+                    double *fl_deriv_sum_p);
   /* * */
   // Old matrix routines, only used in force debug routines.
 
@@ -546,9 +547,9 @@ public:
     Matrix h;
     for(int l = 1; l <= lmax; l++) {
       for(int n = 1; n <= lmax; n++) {
-	h.m[l][n] = 0.0;
-	for(int m = 1; m <= lmax; m++)
-	  h.m[l][n] += ha.m[l][m] * hb.m[m][n];
+        h.m[l][n] = 0.0;
+        for(int m = 1; m <= lmax; m++)
+          h.m[l][n] += ha.m[l][m] * hb.m[m][n];
       }
     }
     return h;
@@ -560,7 +561,7 @@ public:
     for(int n = 1; n <= lmax; n++) {
       double cquan = 0.0;
       for(int m = 1; m <= lmax; m++)
-	cquan += ha.m[n][m] * hb.m[m][n];
+        cquan += ha.m[n][m] * hb.m[m][n];
       zquan += cquan;
     }
     return zquan;
@@ -572,32 +573,32 @@ public:
       int i,j,k;
 
       if(lmax == 5) {
-	const int n = 5;
-	for(i = 1; i<=n; i++)
-	  for(j = 1; j<=n; j++) {
-	    double s = 0.0;
-	    for(k = 1; k<=n; k++)
-	      s = s + a.m[i][k]*b.m[j][k];
-	    c.m[i][j] = s;
-	      }
+        const int n = 5;
+        for(i = 1; i<=n; i++)
+          for(j = 1; j<=n; j++) {
+            double s = 0.0;
+            for(k = 1; k<=n; k++)
+              s = s + a.m[i][k]*b.m[j][k];
+            c.m[i][j] = s;
+              }
       } else if(lmax == 7) {
-	const int n = 7;
-	for(i = 1; i<=n; i++)
-	  for(j = 1; j<=n; j++) {
-	    double s = 0.0;
-	    for(k = 1; k<=n; k++)
-	      s = s + a.m[i][k]*b.m[j][k];
-	    c.m[i][j] = s;
-	  }
+        const int n = 7;
+        for(i = 1; i<=n; i++)
+          for(j = 1; j<=n; j++) {
+            double s = 0.0;
+            for(k = 1; k<=n; k++)
+              s = s + a.m[i][k]*b.m[j][k];
+            c.m[i][j] = s;
+          }
       } else {
-	const int n = lmax;
-	for(i = 1; i<=n; i++)
-	  for(j = 1; j<=n; j++) {
-	    double s = 0.0;
-	    for(k = 1; k<=n; k++)
-	      s = s + a.m[i][k]*b.m[j][k];
-	    c.m[i][j] = s;
-	  }
+        const int n = lmax;
+        for(i = 1; i<=n; i++)
+          for(j = 1; j<=n; j++) {
+            double s = 0.0;
+            for(k = 1; k<=n; k++)
+              s = s + a.m[i][k]*b.m[j][k];
+            c.m[i][j] = s;
+          }
       }
     }
 
@@ -608,7 +609,7 @@ public:
 
     for(i = 0; i<n; i++)
       for(j = 1; j<=n; j++)
-	s = s + A[i][j]*B[i][j];
+        s = s + A[i][j]*B[i][j];
     return s;
   }
   inline double transtrace(const Matrix& a,const Matrix& b) const
@@ -617,25 +618,25 @@ public:
       double s = 0.0;
 
       if(linalg.single)
-	return transtrace_s((const float (*)[8]) &a.m[1][0],(const float (*)[8]) &b.m[1][0]);
+        return transtrace_s((const float (*)[8]) &a.m[1][0],(const float (*)[8]) &b.m[1][0]);
 
       //printf("Calling transtrace... That is shit\n");
 
       if(lmax == 5) {
-	const int n = 5;
-	for(i = 1; i<=n; i++)
-	  for(k = 1; k<=n; k++)
-	    s = s + a.m[i][k]*b.m[i][k];
+        const int n = 5;
+        for(i = 1; i<=n; i++)
+          for(k = 1; k<=n; k++)
+            s = s + a.m[i][k]*b.m[i][k];
       } else if(lmax == 7) {
-	const int n = 7;
-	for(i = 1; i<=n; i++)
-	  for(k = 1; k<=n; k++)
-	    s = s + a.m[i][k]*b.m[i][k];
+        const int n = 7;
+        for(i = 1; i<=n; i++)
+          for(k = 1; k<=n; k++)
+            s = s + a.m[i][k]*b.m[i][k];
       } else {
-	const int n = lmax;
-	for(i = 1; i<=n; i++)
-	  for(k = 1; k<=n; k++)
-	    s = s + a.m[i][k]*b.m[i][k];
+        const int n = lmax;
+        for(i = 1; i<=n; i++)
+          for(k = 1; k<=n; k++)
+            s = s + a.m[i][k]*b.m[i][k];
       }
       return s;
     }

src/USER-MISC/angle_cosine_shift.cpp

@@ -15,9 +15,9 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_shift.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/USER-MISC/angle_cosine_shift_exp.cpp

@@ -15,9 +15,9 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_shift_exp.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/USER-MISC/angle_dipole.cpp

@@ -15,9 +15,9 @@
    Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_dipole.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/USER-MISC/angle_fourier.cpp

@@ -16,9 +16,9 @@
    [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_fourier.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/USER-MISC/angle_fourier_simple.cpp

@@ -16,9 +16,9 @@
    [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_fourier_simple.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/USER-MISC/angle_quartic.cpp

@@ -16,9 +16,9 @@
    [ based on angle_harmonic.cpp]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_quartic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/USER-MISC/bond_harmonic_shift.cpp

@@ -15,12 +15,11 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_harmonic_shift.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/USER-MISC/bond_harmonic_shift_cut.cpp

@@ -15,12 +15,11 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_harmonic_shift_cut.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/USER-MISC/compute_cnp_atom.cpp

@@ -21,11 +21,10 @@
    branicio@usc.edu
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
-
 #include "compute_cnp_atom.h"
+#include <mpi.h>
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"

src/USER-MISC/compute_entropy_atom.cpp

@@ -15,10 +15,9 @@
    Contributing author: Pablo Piaggi (EPFL Lausanne)
 ------------------------------------------------------------------------- */
 
+#include "compute_entropy_atom.h"
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "compute_entropy_atom.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -28,13 +27,11 @@
 #include "force.h"
 #include "pair.h"
 #include "comm.h"
-#include "math_extra.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "domain.h"
 
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/USER-MISC/compute_pressure_cylinder.cpp

@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "compute_pressure_cylinder.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -22,7 +21,6 @@
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list.h"
-#include "group.h"
 #include "memory.h"
 #include "error.h"
 #include "citeme.h"

src/USER-MISC/compute_pressure_grem.cpp

@@ -11,17 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
-#include <cstdlib>
 #include "compute_pressure_grem.h"
-#include "atom.h"
+#include <cstring>
 #include "update.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
 #include "force.h"
-#include "pair.h"
 #include "kspace.h"
 #include "error.h"
 

src/USER-MISC/compute_stress_mop.cpp

@@ -15,18 +15,14 @@
   Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
   --------------------------------------------------------------------------*/
 
+#include "compute_stress_mop.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
 
-#include "compute_stress_mop.h"
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
-#include "group.h"
-#include "modify.h"
-#include "fix.h"
 #include "neighbor.h"
 #include "force.h"
 #include "pair.h"

src/USER-MISC/compute_stress_mop_profile.cpp

@@ -15,18 +15,14 @@
   Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
   --------------------------------------------------------------------------*/
 
+#include "compute_stress_mop_profile.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
 
-#include "compute_stress_mop_profile.h"
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
-#include "group.h"
-#include "modify.h"
-#include "fix.h"
 #include "neighbor.h"
 #include "force.h"
 #include "pair.h"

src/USER-MISC/compute_temp_rotate.cpp

@@ -15,16 +15,13 @@
    Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
 #include "compute_temp_rotate.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "group.h"
 #include "domain.h"
-#include "lattice.h"
 #include "error.h"
 #include "memory.h"
 

src/USER-MISC/dihedral_cosine_shift_exp.cpp

@@ -15,14 +15,12 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
+#include "dihedral_cosine_shift_exp.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "dihedral_cosine_shift_exp.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"

src/USER-MISC/dihedral_fourier.cpp

@@ -16,16 +16,13 @@
    [ based on dihedral_charmm.cpp Paul Crozier (SNL) ]
 ------------------------------------------------------------------------- */
 
+#include "dihedral_fourier.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "dihedral_fourier.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
-#include "pair.h"
 #include "update.h"
 #include "math_const.h"
 #include "memory.h"

src/USER-MISC/dihedral_nharmonic.cpp

@@ -16,12 +16,11 @@
    [ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "dihedral_nharmonic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "update.h"

src/USER-MISC/dihedral_quadratic.cpp

@@ -16,12 +16,11 @@
    [ based on dihedral_helix.cpp Paul Crozier (SNL) ]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "dihedral_quadratic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "update.h"

src/USER-MISC/dihedral_spherical.cpp

@@ -17,22 +17,19 @@
      and Paul Crozier (SNL) ]
 ------------------------------------------------------------------------- */
 
+#include "dihedral_spherical.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cassert>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "force.h"
-#include "pair.h"
-#include "update.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"
-#include "dihedral_spherical.h"
 
 using namespace std;
 using namespace LAMMPS_NS;

src/USER-MISC/dihedral_table.cpp

@@ -17,21 +17,20 @@
                           the "tridiag.c" written by Gerard Jungman for GSL
 ------------------------------------------------------------------------- */
 
+#include <mpi.h>
+#include <cctype>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include <cassert>
 #include <string>
-#include <fstream>
-#include <iostream>
-#include <sstream>
+#include <sstream>  // IWYU pragma: keep
+#include <fstream>  // IWYU pragma: keep
 
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "memory.h"
 #include "error.h"
 #include "dihedral_table.h"

src/USER-MISC/dihedral_table_cut.cpp

@@ -16,25 +16,23 @@
    Based on tabulated dihedral (dihedral_table.cpp) by Andrew Jewett
 ------------------------------------------------------------------------- */
 
+#include "dihedral_table_cut.h"
+#include <mpi.h>
+#include <cctype>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include <cassert>
 #include <string>
-#include <fstream>
-#include <iostream>
-#include <sstream>
+#include <fstream>  // IWYU pragma: keep
+#include <sstream>  // IWYU pragma: keep
 
-#include "dihedral_table_cut.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "update.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "citeme.h"
 #include "math_const.h"
-#include "math_extra.h"
 #include "memory.h"
 #include "error.h"
 #include "utils.h"
@@ -42,8 +40,6 @@
 using namespace LAMMPS_NS;
 using namespace MathConst;
 using namespace std;
-using namespace MathExtra;
-
 
 static const char cite_dihedral_tablecut[] =
   "dihedral_style  table/cut  command:\n\n"

src/USER-MISC/fix_addtorque.cpp

@@ -15,9 +15,9 @@
    Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_addtorque.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -25,7 +25,6 @@
 #include "respa.h"
 #include "input.h"
 #include "variable.h"
-#include "memory.h"
 #include "error.h"
 #include "group.h"
 #include "force.h"

src/USER-MISC/fix_ave_correlate_long.cpp

@@ -21,11 +21,12 @@
    see J. Chem. Phys. 133, 154103 (2010)
 ------------------------------------------------------------------------- */
 
+#include "fix_ave_correlate_long.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
 #include <unistd.h>
-#include "fix_ave_correlate_long.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"

src/USER-MISC/fix_bond_react.cpp

@@ -15,11 +15,10 @@ See the README file in the top-level LAMMPS directory.
 Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
 ------------------------------------------------------------------------- */
 
+#include "fix_bond_react.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_bond_react.h"
 #include "update.h"
 #include "modify.h"
 #include "respa.h"

src/USER-MISC/fix_electron_stopping.cpp

@@ -16,16 +16,14 @@
    Information: k.avchachov@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #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 "group.h"
 #include "force.h"
 #include "fix.h"
 #include "memory.h"

src/USER-MISC/fix_ffl.cpp

@@ -18,31 +18,21 @@
 
 /* ----------------------------------------------------------------------
    Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL),
-			 Michele Ceriotti (EPFL)
+                         Michele Ceriotti (EPFL)
 ------------------------------------------------------------------------- */
 
+#include "fix_ffl.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_ffl.h"
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "force.h"
 #include "update.h"
-#include "modify.h"
-#include "compute.h"
-#include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
-#include "input.h"
-#include "variable.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
-#include "group.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_filter_corotate.cpp

@@ -16,30 +16,25 @@
      some subroutines are from fix_shake.cpp
    ------------------------------------------------------------------------- */
 
+#include "fix_filter_corotate.h"
 #include <mpi.h>
+#include <cctype>
+#include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "fix_filter_corotate.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "bond.h"
+#include "comm.h"
+#include "domain.h"
 #include "angle.h"
+#include "bond.h"
 #include "math_const.h"
 #include "update.h"
 #include "modify.h"
-#include "domain.h"
-#include "region.h"
 #include "memory.h"
 #include "error.h"
 #include "force.h"
-#include "comm.h"
-#include "error.h"
-#include "memory.h"
-#include "domain.h"
-#include "integrate.h"
 #include "respa.h"
-#include "neighbor.h"
 #include "citeme.h"
 
 using namespace LAMMPS_NS;

src/USER-MISC/fix_flow_gauss.cpp

@@ -16,13 +16,12 @@
    Joel.Eaves@Colorado.edu
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_flow_gauss.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "group.h"
-#include "comm.h"
 #include "update.h"
 #include "domain.h"
 #include "error.h"

src/USER-MISC/fix_gle.cpp

@@ -16,28 +16,19 @@
                          Axel Kohylmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "fix_gle.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "fix_gle.h"
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "force.h"
 #include "update.h"
-#include "modify.h"
-#include "compute.h"
-#include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
-#include "input.h"
-#include "variable.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
-#include "group.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_grem.cpp

@@ -22,19 +22,14 @@
                          Tom Keyes (Boston University)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
-#include "comm.h"
 #include "fix_grem.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "modify.h"
 #include "domain.h"
-#include "input.h"
 #include "compute.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/USER-MISC/fix_ipi.cpp

@@ -15,15 +15,12 @@
    Contributing author: Michele Ceriotti (EPFL), Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdio>
-#include <cstring>
-#include <cstdlib>
 #include "fix_ipi.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "kspace.h"
 #include "modify.h"
@@ -32,8 +29,6 @@
 #include "neighbor.h"
 #include "irregular.h"
 #include "domain.h"
-#include "compute_pressure.h"
-#include <errno.h>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_nvk.cpp

@@ -15,18 +15,16 @@
      Contributing author: Efrem Braun (UC Berkeley)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nvk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "respa.h"
 #include "error.h"
-#include "compute.h"
 #include "math_extra.h"
-#include "domain.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_pimd.cpp

@@ -21,10 +21,11 @@
    Version      1.0
 ------------------------------------------------------------------------- */
 
+#include "fix_pimd.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "fix_pimd.h"
 #include "universe.h"
 #include "comm.h"
 #include "force.h"

src/USER-MISC/fix_rhok.cpp

@@ -13,12 +13,11 @@
    Contributing author: Ulf R. Pedersen, ulf@urp.dk
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
+#include "fix_rhok.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
 
-#include "fix_rhok.h"
 #include "atom.h"
 #include "domain.h"
 #include "error.h"

src/USER-MISC/fix_smd.cpp

@@ -16,10 +16,10 @@
    based on fix spring by: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_smd.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "update.h"

src/USER-MISC/fix_srp.cpp

@@ -15,9 +15,10 @@
    Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_srp.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
@@ -635,11 +636,11 @@ void FixSRP::restart(char *buf)
 int FixSRP::modify_param(int /*narg*/, char **arg)
 {
   if (strcmp(arg[0],"btype") == 0) {
-    btype = atoi(arg[1]);
+    btype = force->inumeric(FLERR,arg[1]);
     return 2;
   }
   if (strcmp(arg[0],"bptype") == 0) {
-    bptype = atoi(arg[1]);
+    bptype = force->inumeric(FLERR,arg[1]);
     return 2;
   }
   return 0;

src/USER-MISC/fix_ti_spring.cpp

@@ -18,9 +18,9 @@
              Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_ti_spring.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "domain.h"

src/USER-MISC/fix_ttm_mod.cpp

@@ -17,17 +17,14 @@
    Vasily Pisarev (Joint Institute for High Temperatures of RAS)
 ------------------------------------------------------------------------- */
 
-#include "lmptype.h"
+#include "fix_ttm_mod.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_ttm_mod.h"
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
 #include "random_mars.h"

src/USER-MISC/fix_wall_ees.cpp

@@ -15,21 +15,13 @@
    Contributing author:  Abdoreza Ershadinia, a.ershadinia at gmail.com
 ------------------------------------------------------------------------- */
 
+#include "fix_wall_ees.h"
 #include <cmath>
 #include "math_extra.h"
-#include "fix_wall_ees.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
-#include "domain.h"
-#include "region.h"
-#include "force.h"
-#include "lattice.h"
-#include "update.h"
-#include "output.h"
-#include "respa.h"
 #include "error.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-MISC/fix_wall_region_ees.cpp

@@ -15,19 +15,16 @@
    Contributing author:  Abdoreza Ershadinia, a.ershadinia at gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_region_ees.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
 #include "domain.h"
 #include "region.h"
 #include "force.h"
-#include "lattice.h"
 #include "update.h"
-#include "output.h"
 #include "respa.h"
 #include "error.h"
 #include "math_extra.h"