diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index 98b929e9f3..c0ccb01cad 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -14,6 +14,8 @@
 /* ----------------------------------------------------------------------
    Contributing author: Hasan Metin Aktulga, Purdue University
    (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
+
+     Hybrid and sub-group capabilities: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
 #include "math.h"
@@ -30,6 +32,7 @@
 #include "neigh_request.h"
 #include "update.h"
 #include "force.h"
+#include "group.h"
 #include "pair.h"
 #include "respa.h"
 #include "memory.h"
@@ -68,8 +71,6 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
   if (narg != 8) error->all(FLERR,"Illegal fix qeq/reax command");
 
   nevery = force->inumeric(FLERR,arg[3]);
-  if (nevery <= 0) error->all(FLERR,"Illegal fix qeq/reax command");
-
   swa = force->numeric(FLERR,arg[4]);
   swb = force->numeric(FLERR,arg[5]);
   tolerance = force->numeric(FLERR,arg[6]);
@@ -103,15 +104,6 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
   H.jlist = NULL;
   H.val = NULL;
 
-  // GMRES
-  //g = NULL;
-  //y = NULL;
-  //hstr = NULL;
-  //v = NULL;
-  //h = NULL;
-  //hc = NULL;
-  //hs = NULL;
-
   // perform initial allocation of atom-based arrays
   // register with Atom class
 
@@ -124,6 +116,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
 
   reaxc = NULL;
   reaxc = (PairReaxC *) force->pair_match("reax/c",1);
+
 }
 
 /* ---------------------------------------------------------------------- */
@@ -262,7 +255,8 @@ void FixQEqReax::reallocate_storage()
 
 void FixQEqReax::allocate_matrix()
 {
-  int i,ii;
+  int i,ii,inum,m;
+  int *ilist, *numneigh;
 
   int mincap;
   double safezone;
@@ -280,10 +274,20 @@ void FixQEqReax::allocate_matrix()
 
   // determine the total space for the H matrix
 
-  int m = 0;
-  for( ii = 0; ii < list->inum; ii++ ) {
-    i = list->ilist[ii];
-    m += list->numneigh[i];
+  if (reaxc) {
+    inum = reaxc->list->inum;
+    ilist = reaxc->list->ilist;
+    numneigh = reaxc->list->numneigh;
+  } else {
+    inum = list->inum;
+    ilist = list->ilist;
+    numneigh = list->numneigh;
+  }
+
+  m = 0;
+  for( ii = 0; ii < inum; ii++ ) {
+    i = ilist[ii];
+    m += numneigh[i];
   }
   m_cap = MAX( (int)(m * safezone), mincap * MIN_NBRS );
 
@@ -322,15 +326,24 @@ void FixQEqReax::init()
   if (!force->pair_match("reax/c",1))
     error->all(FLERR,"Must use pair_style reax/c with fix qeq/reax");
 
+  ngroup = group->count(igroup);
+  if (ngroup == 0) error->all(FLERR,"Fix qeq/reax group has no atoms");
+
+  /*
+  if (reaxc)
+    if (ngroup != reaxc->ngroup)
+      error->all(FLERR,"Fix qeq/reax group and pair reax/c have "
+		       "different numbers of atoms");
+  */
+
   // need a half neighbor list w/ Newton off and ghost neighbors
-  // make it occasional if QeQ not performed every timestep
+  // built whenever re-neighboring occurs
 
   int irequest = neighbor->request(this);
   neighbor->requests[irequest]->pair = 0;
   neighbor->requests[irequest]->fix = 1;
   neighbor->requests[irequest]->newton = 2;
   neighbor->requests[irequest]->ghost = 1;
-  if (nevery > 1) neighbor->requests[irequest]->occasional = 1;
 
   init_shielding();
   init_taper();
@@ -427,8 +440,14 @@ void FixQEqReax::min_setup_pre_force(int vflag)
 
 void FixQEqReax::init_storage()
 {
-  N = atom->nlocal + atom->nghost;
-  for( int i = 0; i < N; i++ ) {
+  int NN;
+
+  if (reaxc) 
+    NN = reaxc->list->inum + reaxc->list->gnum;
+  else
+    NN = list->inum + list->gnum;
+
+  for( int i = 0; i < NN; i++ ) {
     Hdia_inv[i] = 1. / eta[atom->type[i]];
     b_s[i] = -chi[atom->type[i]];
     b_t[i] = -1.0;
@@ -449,15 +468,17 @@ void FixQEqReax::pre_force(int vflag)
 
   n = atom->nlocal;
   N = atom->nlocal + atom->nghost;
+
   // grow arrays if necessary
   // need to be atom->nmax in length
+
   if( atom->nmax > nmax ) reallocate_storage();
   if( n > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE )
     reallocate_matrix();
 
   init_matvec();
-  matvecs = CG(b_s, s);        // CG on s - parallel
-  matvecs += CG(b_t, t); // CG on t - parallel
+  matvecs = CG(b_s, s);    	// CG on s - parallel
+  matvecs += CG(b_t, t); 	// CG on t - parallel
   calculate_Q();
 
   if( comm->me == 0 ) {
@@ -487,23 +508,38 @@ void FixQEqReax::init_matvec()
   /* fill-in H matrix */
   compute_H();
 
-  for( int i = 0; i < n; ++i ) {
-    /* init pre-conditioner for H and init solution vectors */
-    Hdia_inv[i] = 1. / eta[ atom->type[i] ];
-    b_s[i]      = -chi[ atom->type[i] ];
-    b_t[i]      = -1.0;
+  int nn, ii, i;
+  int *ilist;
 
-    /* linear extrapolation for s & t from previous solutions */
-    //s[i] = 2 * s_hist[i][0] - s_hist[i][1];
-    //t[i] = 2 * t_hist[i][0] - t_hist[i][1];
+  if (reaxc) {
+    nn = reaxc->list->inum;
+    ilist = reaxc->list->ilist;
+  } else {
+    nn = list->inum;
+    ilist = list->ilist;
+  }
 
-    /* quadratic extrapolation for s & t from previous solutions */
-    //s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] );
-    t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] );
+  for( ii = 0; ii < nn; ++ii ) {
+    i = ilist[ii];
+    if (atom->mask[i] & groupbit) {
+    
+      /* init pre-conditioner for H and init solution vectors */
+      Hdia_inv[i] = 1. / eta[ atom->type[i] ];
+      b_s[i]      = -chi[ atom->type[i] ];
+      b_t[i]      = -1.0;
 
-    /* cubic extrapolation for s & t from previous solutions */
-    s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]);
-    //t[i] = 4*(t_hist[i][0]+t_hist[i][2])-(6*t_hist[i][1]+t_hist[i][3]);
+      /* linear extrapolation for s & t from previous solutions */
+      //s[i] = 2 * s_hist[i][0] - s_hist[i][1];
+      //t[i] = 2 * t_hist[i][0] - t_hist[i][1];
+
+      /* quadratic extrapolation for s & t from previous solutions */
+      //s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] );
+      t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] );
+
+      /* cubic extrapolation for s & t from previous solutions */
+      s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]);
+      //t[i] = 4*(t_hist[i][0]+t_hist[i][2])-(6*t_hist[i][1]+t_hist[i][3]);
+    }
   }
 
   pack_flag = 2;
@@ -517,60 +553,67 @@ void FixQEqReax::init_matvec()
 void FixQEqReax::compute_H()
 {
   int inum, jnum, *ilist, *jlist, *numneigh, **firstneigh;
-  int i, j, ii, jj, flag;
+  int i, j, ii, jj, temp, newnbr, flag;
   double **x, SMALL = 0.0001;
   double dx, dy, dz, r_sqr;
 
   int *type = atom->type;
   tagint *tag = atom->tag;
   x = atom->x;
+  int *mask = atom->mask;
 
-  if (nevery > 1) neighbor->build_one(list->index);
-  inum = list->inum;
-  ilist = list->ilist;
-  numneigh = list->numneigh;
-  firstneigh = list->firstneigh;
-
+  if (reaxc) {
+    inum = reaxc->list->inum;
+    ilist = reaxc->list->ilist;
+    numneigh = reaxc->list->numneigh;
+    firstneigh = reaxc->list->firstneigh;
+  } else {
+    inum = list->inum;
+    ilist = list->ilist;
+    numneigh = list->numneigh;
+    firstneigh = list->firstneigh;
+  }
+  
   // fill in the H matrix
-
   m_fill = 0;
   r_sqr = 0;
   for( ii = 0; ii < inum; ii++ ) {
     i = ilist[ii];
-    jlist = firstneigh[i];
-    jnum = numneigh[i];
-    H.firstnbr[i] = m_fill;
+    if (mask[i] & groupbit) {
+      jlist = firstneigh[i];
+      jnum = numneigh[i];
+      H.firstnbr[i] = m_fill;
 
-    for( jj = 0; jj < jnum; jj++ ) {
-      j = jlist[jj];
+      for( jj = 0; jj < jnum; jj++ ) {
+        j = jlist[jj];
 
-      dx = x[j][0] - x[i][0];
-      dy = x[j][1] - x[i][1];
-      dz = x[j][2] - x[i][2];
-      r_sqr = SQR(dx) + SQR(dy) + SQR(dz);
+        dx = x[j][0] - x[i][0];
+        dy = x[j][1] - x[i][1];
+        dz = x[j][2] - x[i][2];
+        r_sqr = SQR(dx) + SQR(dy) + SQR(dz);
 
-      flag = 0;
-      if (r_sqr <= SQR(swb)) {
-        if (j < n) flag = 1;
-        else if (tag[i] < tag[j]) flag = 1;
-        else if (tag[i] == tag[j]) {
-          if (dz > SMALL) flag = 1;
-          else if (fabs(dz) < SMALL) {
-            if (dy > SMALL) flag = 1;
-            else if (fabs(dy) < SMALL && dx > SMALL)
-              flag = 1;
-          }
+        flag = 0;
+        if (r_sqr <= SQR(swb)) {
+          if (j < n) flag = 1;
+          else if (tag[i] < tag[j]) flag = 1;
+          else if (tag[i] == tag[j]) {
+            if (dz > SMALL) flag = 1;
+            else if (fabs(dz) < SMALL) {
+              if (dy > SMALL) flag = 1;
+              else if (fabs(dy) < SMALL && dx > SMALL)
+                flag = 1;
+	    }
+	  }
+	}
+
+        if( flag ) {
+          H.jlist[m_fill] = j;
+          H.val[m_fill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] );
+          m_fill++;
         }
       }
-
-      if( flag ) {
-        H.jlist[m_fill] = j;
-        H.val[m_fill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] );
-        m_fill++;
-      }
+      H.numnbrs[i] = m_fill - H.firstnbr[i];
     }
-
-    H.numnbrs[i] = m_fill - H.firstnbr[i];
   }
 
   if (m_fill >= H.m) {
@@ -608,7 +651,17 @@ int FixQEqReax::CG( double *b, double *x )
 {
   int  i, j, imax;
   double tmp, alpha, beta, b_norm;
-  double sig_old, sig_new;
+  double sig_old, sig_new, sig0;
+
+  int nn, jj;
+  int *ilist;
+  if (reaxc) {
+    nn = reaxc->list->inum;
+    ilist = reaxc->list->ilist;
+  } else {
+    nn = list->inum;
+    ilist = list->ilist;
+  }
 
   imax = 200;
 
@@ -616,35 +669,44 @@ int FixQEqReax::CG( double *b, double *x )
   sparse_matvec( &H, x, q );
   comm->reverse_comm_fix( this ); //Coll_Vector( q );
 
-  vector_sum( r , 1.,  b, -1., q, n );
-  for( j = 0; j < n; ++j )
-    d[j] = r[j] * Hdia_inv[j]; //pre-condition
+  vector_sum( r , 1.,  b, -1., q, nn );
 
-  b_norm = parallel_norm( b, n );
-  sig_new = parallel_dot( r, d, n );
+  for( jj = 0; jj < nn; ++jj ) {
+    j = ilist[jj];
+    if (atom->mask[j] & groupbit)
+      d[j] = r[j] * Hdia_inv[j]; //pre-condition
+  }
+
+  int ttype = 1;
+  b_norm = parallel_norm( b, nn );
+  sig_new = parallel_dot( r, d, nn);
+  sig0 = sig_new;
 
   for( i = 1; i < imax && sqrt(sig_new) / b_norm > tolerance; ++i ) {
     comm->forward_comm_fix(this); //Dist_vector( d );
     sparse_matvec( &H, d, q );
     comm->reverse_comm_fix(this); //Coll_vector( q );
 
-    tmp = parallel_dot( d, q, n );
+    ttype = 2;
+    tmp = parallel_dot( d, q, nn);
     alpha = sig_new / tmp;
-    //  comm->me, i, parallel_norm( d, n ), parallel_norm( q, n ), tmp );
 
-    vector_add( x, alpha, d, n );
-    vector_add( r, -alpha, q, n );
+    vector_add( x, alpha, d, nn );
+    vector_add( r, -alpha, q, nn );
 
     // pre-conditioning
-    for( j = 0; j < n; ++j )
-      p[j] = r[j] * Hdia_inv[j];
+    for( jj = 0; jj < nn; ++jj ) {
+      j = ilist[jj];
+      if (atom->mask[j] & groupbit)
+        p[j] = r[j] * Hdia_inv[j];
+    }
 
     sig_old = sig_new;
-    sig_new = parallel_dot( r, p, n );
-
+    sig_new = parallel_dot( r, p, nn);
 
     beta = sig_new / sig_old;
-    vector_sum( d, 1., p, beta, d, n );
+    vector_sum( d, 1., p, beta, d, nn );
+
   }
 
   if (i >= imax && comm->me == 0) {
@@ -663,19 +725,42 @@ int FixQEqReax::CG( double *b, double *x )
 void FixQEqReax::sparse_matvec( sparse_matrix *A, double *x, double *b )
 {
   int i, j, itr_j;
+  int nn, NN, ii;
+  int *ilist;
 
-  for( i = 0; i < n; ++i )
-    b[i] = eta[ atom->type[i] ] * x[i];
-  for( i = n; i < N; ++i )
-    b[i] = 0;
+  if (reaxc) {
+    nn = reaxc->list->inum;
+    NN = reaxc->list->inum + reaxc->list->gnum;
+    ilist = reaxc->list->ilist;
+  } else {
+    nn = list->inum;
+    NN = list->inum + list->gnum;
+    ilist = list->ilist;
+  }
 
-  for( i = 0; i < n; ++i ) {
-    for( itr_j=A->firstnbr[i]; itr_j<A->firstnbr[i]+A->numnbrs[i]; itr_j++) {
-      j = A->jlist[itr_j];
-      b[i] += A->val[itr_j] * x[j];
-      b[j] += A->val[itr_j] * x[i];
+  for( ii = 0; ii < nn; ++ii ) {
+    i = ilist[ii];
+    if (atom->mask[i] & groupbit)
+      b[i] = eta[ atom->type[i] ] * x[i];
+  }
+
+  for( ii = nn; ii < NN; ++ii ) {
+    i = ilist[ii];
+    if (atom->mask[i] & groupbit)
+      b[i] = 0;
+  }
+
+  for( ii = 0; ii < nn; ++ii ) {
+    i = ilist[ii];
+    if (atom->mask[i] & groupbit) {
+      for( itr_j=A->firstnbr[i]; itr_j<A->firstnbr[i]+A->numnbrs[i]; itr_j++) {
+        j = A->jlist[itr_j];
+        b[i] += A->val[itr_j] * x[j];
+        b[j] += A->val[itr_j] * x[i];
+      }
     }
   }
+
 }
 
 /* ---------------------------------------------------------------------- */
@@ -686,20 +771,34 @@ void FixQEqReax::calculate_Q()
   double u, s_sum, t_sum;
   double *q = atom->q;
 
-  s_sum = parallel_vector_acc( s, n );
-  t_sum = parallel_vector_acc( t, n);
+  int nn, ii;
+  int *ilist;
+
+  if (reaxc) {
+    nn = reaxc->list->inum;
+    ilist = reaxc->list->ilist;
+  } else {
+    nn = list->inum;
+    ilist = list->ilist;
+  }
+
+  s_sum = parallel_vector_acc( s, nn );
+  t_sum = parallel_vector_acc( t, nn);
   u = s_sum / t_sum;
 
-  for( i = 0; i < n; ++i ) {
-    q[i] = s[i] - u * t[i];
+  for( ii = 0; ii < nn; ++ii ) {
+    i = ilist[ii];
+    if (atom->mask[i] & groupbit) {
+      q[i] = s[i] - u * t[i];
 
-    /* backup s & t */
-    for( k = 4; k > 0; --k ) {
-      s_hist[i][k] = s_hist[i][k-1];
-      t_hist[i][k] = t_hist[i][k-1];
+      /* backup s & t */
+      for( k = 4; k > 0; --k ) {
+        s_hist[i][k] = s_hist[i][k-1];
+        t_hist[i][k] = t_hist[i][k-1];
+      }
+      s_hist[i][0] = s[i];
+      t_hist[i][0] = t[i];
     }
-    s_hist[i][0] = s[i];
-    t_hist[i][0] = t[i];
   }
 
   pack_flag = 4;
@@ -825,9 +924,21 @@ double FixQEqReax::parallel_norm( double *v, int n )
   int  i;
   double my_sum, norm_sqr;
 
-  my_sum = 0;
-  for( i = 0; i < n; ++i )
-    my_sum += SQR( v[i] );
+  int ii;
+  int *ilist;
+
+  if (reaxc)
+    ilist = reaxc->list->ilist;
+  else
+    ilist = list->ilist;
+
+  my_sum = 0.0;
+  norm_sqr = 0.0;
+  for( ii = 0; ii < n; ++ii ) {
+    i = ilist[ii];
+    if (atom->mask[i] & groupbit)
+      my_sum += SQR( v[i] );
+  }
 
   MPI_Allreduce( &my_sum, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
 
@@ -836,16 +947,27 @@ double FixQEqReax::parallel_norm( double *v, int n )
 
 /* ---------------------------------------------------------------------- */
 
-double FixQEqReax::parallel_dot( double *v1, double *v2, int n )
+double FixQEqReax::parallel_dot( double *v1, double *v2, int n)
 {
   int  i;
   double my_dot, res;
 
-  my_dot = 0;
-  res = 0;
-  for( i = 0; i < n; ++i )
-    my_dot += v1[i] * v2[i];
+  int ii;
+  int *ilist;
 
+  if (reaxc)
+    ilist = reaxc->list->ilist;
+  else
+    ilist = list->ilist;
+
+  my_dot = 0.0;
+  res = 0.0;
+  for( ii = 0; ii < n; ++ii ) {
+    i = ilist[ii];
+    if (atom->mask[i] & groupbit)
+      my_dot += v1[i] * v2[i];
+  }
+  
   MPI_Allreduce( &my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world );
 
   return res;
@@ -858,9 +980,21 @@ double FixQEqReax::parallel_vector_acc( double *v, int n )
   int  i;
   double my_acc, res;
 
-  my_acc = 0;
-  for( i = 0; i < n; ++i )
-    my_acc += v[i];
+  int ii;
+  int *ilist;
+
+  if (reaxc)
+    ilist = reaxc->list->ilist;
+  else
+    ilist = list->ilist;
+
+  my_acc = 0.0;
+  res = 0.0;
+  for( ii = 0; ii < n; ++ii ) {
+    i = ilist[ii];
+    if (atom->mask[i] & groupbit)
+      my_acc += v[i];
+  }
 
   MPI_Allreduce( &my_acc, &res, 1, MPI_DOUBLE, MPI_SUM, world );
 
@@ -869,49 +1003,40 @@ double FixQEqReax::parallel_vector_acc( double *v, int n )
 
 /* ---------------------------------------------------------------------- */
 
-double FixQEqReax::norm( double* v1, int k )
-{
-  double ret = 0;
-
-  for( --k; k>=0; --k )
-    ret +=  ( v1[k] * v1[k] );
-
-  return sqrt( ret );
-}
-
-/* ---------------------------------------------------------------------- */
-
 void FixQEqReax::vector_sum( double* dest, double c, double* v,
                                 double d, double* y, int k )
 {
-  for( --k; k>=0; --k )
-    dest[k] = c * v[k] + d * y[k];
-}
+  int kk;
+  int *ilist;
 
-/* ---------------------------------------------------------------------- */
+  if (reaxc)
+    ilist = reaxc->list->ilist;
+  else
+    ilist = list->ilist;
 
-void FixQEqReax::vector_scale( double* dest, double c, double* v, int k )
-{
-  for( --k; k>=0; --k )
-    dest[k] = c * v[k];
-}
-
-/* ---------------------------------------------------------------------- */
-
-double FixQEqReax::dot( double* v1, double* v2, int k )
-{
-  double ret = 0;
-
-  for( --k; k>=0; --k )
-    ret +=  v1[k] * v2[k];
-
-  return ret;
+  for( --k; k>=0; --k ) {
+    kk = ilist[k];
+    if (atom->mask[kk] & groupbit)
+      dest[kk] = c * v[kk] + d * y[kk];
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixQEqReax::vector_add( double* dest, double c, double* v, int k )
 {
-  for( --k; k>=0; --k )
-    dest[k] += c * v[k];
+  int kk;
+  int *ilist;
+
+  if (reaxc)
+    ilist = reaxc->list->ilist;
+  else
+    ilist = list->ilist;
+
+  for( --k; k>=0; --k ) {
+    kk = ilist[k];
+    if (atom->mask[kk] & groupbit)
+      dest[kk] += c * v[kk];
+  }
+
 }
diff --git a/src/USER-REAXC/fix_qeq_reax.h b/src/USER-REAXC/fix_qeq_reax.h
index bab202c178..8aeecd7bb4 100644
--- a/src/USER-REAXC/fix_qeq_reax.h
+++ b/src/USER-REAXC/fix_qeq_reax.h
@@ -70,6 +70,8 @@ class FixQEqReax : public Fix {
   double *chi,*eta,*gamma;  // qeq parameters
   double **shld;
 
+  bigint ngroup;
+
   // fictitious charges
 
   double *s, *t;
@@ -132,10 +134,7 @@ class FixQEqReax : public Fix {
   double parallel_dot( double*, double*, int );
   double parallel_vector_acc( double*, int );
 
-  double norm(double*,int);
   void vector_sum(double*,double,double*,double,double*,int);
-  void vector_scale(double*,double,double*,int);
-  double dot(double*,double*,int);
   void vector_add(double*, double, double*,int);
 };
 
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index d488289411..f68d92ae69 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -53,6 +53,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
 
   vector_flag = 1;
   size_vector = 2;
+  extvector = 0;
 
   peratom_flag = 1;
   size_peratom_cols = 0;
diff --git a/src/USER-REAXC/pair_reax_c.cpp b/src/USER-REAXC/pair_reax_c.cpp
index c6f98c7f77..47c9ea24a6 100644
--- a/src/USER-REAXC/pair_reax_c.cpp
+++ b/src/USER-REAXC/pair_reax_c.cpp
@@ -17,6 +17,7 @@
    Per-atom energy/virial added by Ray Shan (Sandia)
    Fix reax/c/bonds and fix reax/c/species for pair_style reax/c added by 
    	Ray Shan (Sandia)
+   Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
 #include "pair_reax_c.h"
@@ -283,11 +284,12 @@ void PairReaxC::coeff( int nargs, char **args )
   // read args that map atom types to elements in potential file
   // map[i] = which element the Ith atom type is, -1 if NULL
 
-  int itmp;
+  int itmp = 0;
   int nreax_types = system->reax_param.num_atom_types;
   for (int i = 3; i < nargs; i++) {
     if (strcmp(args[i],"NULL") == 0) {
       map[i-2] = -1;
+      itmp ++;
       continue;
     }
   }
@@ -295,7 +297,6 @@ void PairReaxC::coeff( int nargs, char **args )
   int n = atom->ntypes;
 
   // pair_coeff element map
-  itmp = 0;
   for (int i = 3; i < nargs; i++)
     for (int j = 0; j < nreax_types; j++)
       if (strcasecmp(args[i],system->reax_param.sbp[j].name) == 0) {
@@ -307,14 +308,22 @@ void PairReaxC::coeff( int nargs, char **args )
   if (itmp != n) 
     error->all(FLERR,"Non-existent ReaxFF type");
 
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  // set setflag i,j for type pairs where both are mapped to elements
+
   int count = 0;
   for (int i = 1; i <= n; i++)
-    for (int j = i; j <= n; j++) {
-      setflag[i][j] = 1;
-      count++;
-    }
+    for (int j = i; j <= n; j++)
+      if (map[i] >= 0 && map[j] >= 0) {
+        setflag[i][j] = 1;
+        count++;
+      }
 
   if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+
 }
 
 /* ---------------------------------------------------------------------- */
@@ -367,6 +376,7 @@ void PairReaxC::init_style( )
     delete [] fixarg;
     fix_reax = (FixReaxC *) modify->fix[modify->nfix-1];
   }
+
 }
 
 /* ---------------------------------------------------------------------- */
@@ -429,12 +439,23 @@ void PairReaxC::setup( )
 
     ReAllocate( system, control, data, workspace, &lists, mpi_data );
   }
+
+  ngroup = 0;
+  int ngroup_sum = 0;
+  for (int i = 0; i < list->inum; i++) {
+    ngroup ++;
+  }
+  MPI_Allreduce( &ngroup, &ngroup_sum, 1, MPI_INT, MPI_SUM, world );
+  ngroup = ngroup_sum;
+
 }
 
 /* ---------------------------------------------------------------------- */
 
 double PairReaxC::init_one(int i, int j)
 {
+  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
   cutghost[i][j] = cutghost[j][i] = cutmax;
   return cutmax;
 }
@@ -485,7 +506,7 @@ void PairReaxC::compute(int eflag, int vflag)
   // forces
 
   Compute_Forces(system,control,data,workspace,&lists,out_control,mpi_data);
-  read_reax_forces();
+  read_reax_forces(vflag);
 
   for(int k = 0; k < system->N; ++k) {
     num_bonds[k] = system->my_atoms[k].num_bonds;
@@ -609,12 +630,12 @@ void PairReaxC::set_far_nbr( far_neighbor_data *fdest,
 
 int PairReaxC::estimate_reax_lists()
 {
-  int itr_i, itr_j, i, j;
+  int itr_i, itr_j, itr_g, i, j, g;
   int nlocal, nghost, num_nbrs, num_marked;
   int *ilist, *jlist, *numneigh, **firstneigh, *marked;
-  double d_sqr;
-  rvec dvec;
-  double *dist, **x;
+  double d_sqr, g_d_sqr;
+  rvec dvec, g_dvec;
+  double **x;
   reax_list *far_nbrs;
   far_neighbor_data *far_list;
 
@@ -634,11 +655,12 @@ int PairReaxC::estimate_reax_lists()
   num_nbrs = 0;
   num_marked = 0;
   marked = (int*) calloc( system->N, sizeof(int) );
-  dist = (double*) calloc( system->N, sizeof(double) );
 
-  int numall = list->inum + list->gnum;
+  int inum = list->inum;
+  int gnum = list->gnum;
+  int numall = inum + gnum;
 
-  for( itr_i = 0; itr_i < numall; ++itr_i ){
+  for( itr_i = 0; itr_i < inum+gnum; ++itr_i ){
     i = ilist[itr_i];
     marked[i] = 1;
     ++num_marked;
@@ -655,7 +677,6 @@ int PairReaxC::estimate_reax_lists()
   }
 
   free( marked );
-  free( dist );
 
   return static_cast<int> (MAX( num_nbrs*safezone, mincap*MIN_NBRS ));
 }
@@ -664,12 +685,12 @@ int PairReaxC::estimate_reax_lists()
 
 int PairReaxC::write_reax_lists()
 {
-  int itr_i, itr_j, i, j;
+  int itr_i, itr_j, itr_g, i, j, g, flag;
   int nlocal, nghost, num_nbrs;
-  int *ilist, *jlist, *numneigh, **firstneigh, *marked;
-  double d_sqr;
-  rvec dvec;
-  double *dist, **x;
+  int *ilist, *jlist, *numneigh, **firstneigh;
+  double d_sqr, g_d, g_d_sqr;
+  rvec dvec, g_dvec;
+  double *dist, **x, SMALL = 0.0001;
   reax_list *far_nbrs;
   far_neighbor_data *far_list;
 
@@ -684,14 +705,14 @@ int PairReaxC::write_reax_lists()
   far_list = far_nbrs->select.far_nbr_list;
 
   num_nbrs = 0;
-  marked = (int*) calloc( system->N, sizeof(int) );
   dist = (double*) calloc( system->N, sizeof(double) );
 
-  int numall = list->inum + list->gnum;
+  int inum = list->inum;
+  int gnum = list->gnum;
+  int numall = inum + gnum;
 
-  for( itr_i = 0; itr_i < numall; ++itr_i ){
+  for( itr_i = 0; itr_i < inum+gnum; ++itr_i ){
     i = ilist[itr_i];
-    marked[i] = 1;
     jlist = firstneigh[i];
     Set_Start_Index( i, num_nbrs, far_nbrs );
 
@@ -709,7 +730,6 @@ int PairReaxC::write_reax_lists()
     Set_End_Index( i, num_nbrs, far_nbrs );
   }
 
-  free( marked );
   free( dist );
 
   return num_nbrs;
@@ -717,17 +737,18 @@ int PairReaxC::write_reax_lists()
 
 /* ---------------------------------------------------------------------- */
 
-void PairReaxC::read_reax_forces()
+void PairReaxC::read_reax_forces(int vflag)
 {
   for( int i = 0; i < system->N; ++i ) {
     system->my_atoms[i].f[0] = workspace->f[i][0];
     system->my_atoms[i].f[1] = workspace->f[i][1];
     system->my_atoms[i].f[2] = workspace->f[i][2];
 
-    atom->f[i][0] = -workspace->f[i][0];
-    atom->f[i][1] = -workspace->f[i][1];
-    atom->f[i][2] = -workspace->f[i][2];
+    atom->f[i][0] += -workspace->f[i][0];
+    atom->f[i][1] += -workspace->f[i][1];
+    atom->f[i][2] += -workspace->f[i][2];
   }
+
 }
 
 /* ---------------------------------------------------------------------- */
@@ -771,6 +792,8 @@ double PairReaxC::memory_usage()
   bytes += 19.0 * system->total_cap * sizeof(real);
   bytes += 3.0 * system->total_cap * sizeof(int);
 
+  double mem1 = bytes;
+
   // From reaxc_lists
   bytes += 2.0 * lists->n * sizeof(int);
   bytes += lists->num_intrs * sizeof(three_body_interaction_data);
@@ -790,8 +813,8 @@ double PairReaxC::memory_usage()
 
 void PairReaxC::FindBond()
 {
-  int i, j, pj, nj;
-  double bo_tmp, bo_cut, r_tmp;
+  int i, ii, j, pj, nj, jtmp, jj;
+  double bo_tmp, bo_cut, rij, rsq, r_tmp;
 
   bond_data *bo_ij;
   bo_cut = 0.10;
@@ -815,5 +838,3 @@ void PairReaxC::FindBond()
     }
   }
 }
-
-/* ---------------------------------------------------------------------- */
diff --git a/src/USER-REAXC/pair_reax_c.h b/src/USER-REAXC/pair_reax_c.h
index 5f89a95d87..968158f1ae 100644
--- a/src/USER-REAXC/pair_reax_c.h
+++ b/src/USER-REAXC/pair_reax_c.h
@@ -57,8 +57,12 @@ class PairReaxC : public Pair {
   reax_list *lists;
   mpi_datatypes *mpi_data;
 
+  bigint ngroup;
+
  private:
   double cutmax;
+  int nelements;                // # of unique elements
+  char **elements;              // names of unique elements
   int *map;
   class FixReaxC *fix_reax;
 
@@ -68,17 +72,20 @@ class PairReaxC : public Pair {
   int firstwarn;
 
   void allocate();
+  void setup();
+  void create_compute();
+  void create_fix();
   void write_reax_atoms();
   void get_distance(rvec, rvec, double *, rvec *);
   void set_far_nbr(far_neighbor_data *, int, double, rvec);
   int estimate_reax_lists();
   int write_reax_lists();
-  void read_reax_forces();
-  void setup();
+  void read_reax_forces(int);
 
   int nmax;
   void FindBond();
   double memory_usage();
+
 };
 
 }
diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp
index 7df5241a93..1bf3d85750 100644
--- a/src/USER-REAXC/reaxc_allocate.cpp
+++ b/src/USER-REAXC/reaxc_allocate.cpp
@@ -25,20 +25,11 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "allocate.h"
-#include "list.h"
-#include "reset_tools.h"
-#include "tool_box.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_allocate.h"
 #include "reaxc_list.h"
 #include "reaxc_reset_tools.h"
 #include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
-#endif
-
 
 /* allocate space for my_atoms
    important: we cannot know the exact number of atoms that will fall into a
@@ -55,28 +46,9 @@ int PreAllocate_Space( reax_system *system, control_params *control,
   system->local_cap = MAX( (int)(system->n * safezone), mincap );
   system->total_cap = MAX( (int)(system->N * safezone), mincap );
 
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: local_cap=%d total_cap=%d\n",
-           system->my_rank, system->local_cap, system->total_cap );
-#endif
-
   system->my_atoms = (reax_atom*)
     scalloc( system->total_cap, sizeof(reax_atom), "my_atoms", comm );
 
-  /* space for keeping restriction info, if any */
-  // not yet implemented in the parallel version!!!
-  // if( control->restrict_bonds ) {
-  //   workspace->restricted  = (int*)
-  //     scalloc( system->local_cap, sizeof(int), "restricted_atoms", comm );
-
-  //   workspace->restricted_list = (int**)
-  //     scalloc( system->local_cap, sizeof(int*), "restricted_list", comm );
-
-  //   for( i = 0; i < system->local_cap; ++i )
-  //     workspace->restricted_list[i] = (int*)
-  //         scalloc( MAX_RESTRICT, sizeof(int), "restricted_list[i]", comm );
-  // }
-
   return SUCCESS;
 }
 
@@ -228,57 +200,12 @@ void DeAllocate_Workspace( control_params *control, storage *workspace )
   sfree( workspace->p2, "p2" );
 
   /* integrator */
-  // sfree( workspace->f_old );
   sfree( workspace->v_const, "v_const" );
 
-  /*workspace->realloc.num_far = -1;
-    workspace->realloc.Htop = -1;
-    workspace->realloc.hbonds = -1;
-    workspace->realloc.bonds = -1;
-    workspace->realloc.num_3body = -1;
-    workspace->realloc.gcell_atoms = -1;*/
-
-  /* storage for analysis */
-  // if( control->molecular_analysis || control->diffusion_coef ) {
-  //   sfree( workspace->mark, "mark" );
-  //   sfree( workspace->old_mark, "old_mark" );
-  // }
-
-  // if( control->diffusion_coef )
-  //   sfree( workspace->x_old, "x_old" );
-
   /* force related storage */
   sfree( workspace->f, "f" );
   sfree( workspace->CdDelta, "CdDelta" );
-#ifdef TEST_FORCES
-  sfree(workspace->dDelta, "dDelta" );
-  sfree( workspace->f_ele, "f_ele" );
-  sfree( workspace->f_vdw, "f_vdw" );
-  sfree( workspace->f_bo, "f_bo" );
-  sfree( workspace->f_be, "f_be" );
-  sfree( workspace->f_lp, "f_lp" );
-  sfree( workspace->f_ov, "f_ov" );
-  sfree( workspace->f_un, "f_un" );
-  sfree( workspace->f_ang, "f_ang" );
-  sfree( workspace->f_coa, "f_coa" );
-  sfree( workspace->f_pen, "f_pen" );
-  sfree( workspace->f_hb, "f_hb" );
-  sfree( workspace->f_tor, "f_tor" );
-  sfree( workspace->f_con, "f_con" );
-  sfree( workspace->f_tot, "f_tot" );
 
-  sfree( workspace->rcounts, "rcounts" );
-  sfree( workspace->displs, "displs" );
-  sfree( workspace->id_all, "id_all" );
-  sfree( workspace->f_all, "f_all" );
-#endif
-
-  /* hbond storage */
-  //sfree( workspace->Hindex, "Hindex" );
-  //sfree( workspace->num_bonds );
-  //sfree( workspace->num_hbonds );
-  //sfree( workspace->hash, "hash" );
-  //sfree( workspace->rev_hash, "rev_hash" );
 }
 
 
@@ -328,7 +255,6 @@ int Allocate_Workspace( reax_system *system, control_params *control,
     scalloc( total_cap, sizeof(int), "bond_mark", comm );
   workspace->done_after = (int*)
     scalloc( total_cap, sizeof(int), "done_after", comm );
-  // fprintf( stderr, "p%d: bond order storage\n", system->my_rank );
 
   /* QEq storage */
   workspace->Hdia_inv = (real*)
@@ -371,61 +297,11 @@ int Allocate_Workspace( reax_system *system, control_params *control,
   /* integrator storage */
   workspace->v_const = (rvec*) smalloc( local_rvec, "v_const", comm );
 
-  /* storage for analysis */
-  // not yet implemented in the parallel version!!!
-  // if( control->molecular_analysis || control->diffusion_coef ) {
-  //   workspace->mark = (int*) scalloc( local_cap, sizeof(int), "mark", comm );
-  //   workspace->old_mark = (int*)
-  //     scalloc( local_cap, sizeof(int), "old_mark", comm );
-  // }
-  // else
-  //   workspace->mark = workspace->old_mark = NULL;
-
-  // if( control->diffusion_coef )
-  //   workspace->x_old = (rvec*)
-  //     scalloc( local_cap, sizeof(rvec), "x_old", comm );
-  // else workspace->x_old = NULL;
-
   // /* force related storage */
   workspace->f = (rvec*) scalloc( total_cap, sizeof(rvec), "f", comm );
   workspace->CdDelta = (real*)
     scalloc( total_cap, sizeof(real), "CdDelta", comm );
 
-#ifdef TEST_FORCES
-  workspace->dDelta=(rvec*) smalloc( total_rvec, "dDelta", comm );
-  workspace->f_ele =(rvec*) smalloc( total_rvec, "f_ele", comm );
-  workspace->f_vdw =(rvec*) smalloc( total_rvec, "f_vdw", comm );
-  workspace->f_bo =(rvec*) smalloc( total_rvec, "f_bo", comm );
-  workspace->f_be =(rvec*) smalloc( total_rvec, "f_be", comm );
-  workspace->f_lp =(rvec*) smalloc( total_rvec, "f_lp", comm );
-  workspace->f_ov =(rvec*) smalloc( total_rvec, "f_ov", comm );
-  workspace->f_un =(rvec*) smalloc( total_rvec, "f_un", comm );
-  workspace->f_ang =(rvec*) smalloc( total_rvec, "f_ang", comm );
-  workspace->f_coa =(rvec*) smalloc( total_rvec, "f_coa", comm );
-  workspace->f_pen =(rvec*) smalloc( total_rvec, "f_pen", comm );
-  workspace->f_hb =(rvec*) smalloc( total_rvec, "f_hb", comm );
-  workspace->f_tor =(rvec*) smalloc( total_rvec, "f_tor", comm );
-  workspace->f_con =(rvec*) smalloc( total_rvec, "f_con", comm );
-  workspace->f_tot =(rvec*) smalloc( total_rvec, "f_tot", comm );
-
-  if( system->my_rank == MASTER_NODE ) {
-    workspace->rcounts = (int*)
-      smalloc( system->wsize*sizeof(int), "rcount", comm );
-    workspace->displs = (int*)
-      smalloc( system->wsize*sizeof(int), "displs", comm );
-    workspace->id_all = (int*)
-      smalloc( system->bigN*sizeof(int), "id_all", comm );
-    workspace->f_all = (rvec*)
-      smalloc( system->bigN*sizeof(rvec), "f_all", comm );
-  }
-  else{
-    workspace->rcounts = NULL;
-    workspace->displs = NULL;
-    workspace->id_all = NULL;
-    workspace->f_all = NULL;
-  }
-#endif
-
   return SUCCESS;
 }
 
@@ -477,11 +353,6 @@ int Reallocate_Matrix( sparse_matrix **H, int n, int m, char *name,
     MPI_Abort( comm, INSUFFICIENT_MEMORY );
   }
 
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "reallocating %s matrix, n = %d, m = %d\n", name, n, m );
-  fprintf( stderr, "memory allocated: %s = %dMB\n",
-           name, (int)(m * sizeof(sparse_matrix_entry) / (1024*1024)) );
-#endif
   return SUCCESS;
 }
 
@@ -497,9 +368,6 @@ int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds,
   total_hbonds = 0;
   for( i = 0; i < system->n; ++i )
     if( (id = system->my_atoms[i].Hindex) >= 0 ) {
-      // commented out - already updated in validate_lists in forces.c
-      // system->my_atoms[i].num_hbonds = MAX(Num_Entries(id,hbonds)*SAFER_ZONE,
-      //                                   MIN_HBONDS);
       total_hbonds += system->my_atoms[i].num_hbonds;
     }
   total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS ));
@@ -526,8 +394,6 @@ int Reallocate_Bonds_List( reax_system *system, reax_list *bonds,
   *est_3body = 0;
   for( i = 0; i < system->N; ++i ){
     *est_3body += SQR(system->my_atoms[i].num_bonds);
-    // commented out - already updated in validate_lists in forces.c
-    // system->my_atoms[i].num_bonds = MAX( Num_Entries(i,bonds)*2, MIN_BONDS );
     *total_bonds += system->my_atoms[i].num_bonds;
   }
   *total_bonds = (int)(MAX( *total_bonds * safezone, mincap*MIN_BONDS ));
@@ -567,13 +433,6 @@ int Estimate_GCell_Population( reax_system* system, MPI_Comm comm )
       else if( c[d] < g->native_str[d] )
         c[d] = g->native_str[d];
     }
-#if defined(DEBUG)
-    fprintf( stderr, "p%d bin_my_atoms: l:%d - atom%d @ %.5f %.5f %.5f"        \
-             "--> cell: %d %d %d\n",
-             system->my_rank, l, atoms[l].orig_id,
-             atoms[l].x[0], atoms[l].x[1], atoms[l].x[2],
-             c[0], c[1], c[2] );
-#endif
     gc = &( g->cells[c[0]][c[1]][c[2]] );
     gc->top++;
   }
@@ -585,18 +444,10 @@ int Estimate_GCell_Population( reax_system* system, MPI_Comm comm )
         gc = &(g->cells[i][j][k]);
         if( max_atoms < gc->top )
           max_atoms = gc->top;
-#if defined(DEBUG)
-        fprintf( stderr, "p%d gc[%d,%d,%d]->top=%d\n",
-                 system->my_rank, i, j, k, gc->top );
-#endif
       }
 
   my_max = (int)(MAX(max_atoms*SAFE_ZONE, MIN_GCELL_POPL));
   MPI_Allreduce( &my_max, &all_max, 1, MPI_INT, MPI_MAX, comm );
-#if defined(DEBUG)
-  fprintf( stderr, "p%d max_atoms=%d, my_max=%d, all_max=%d\n",
-           system->my_rank, max_atoms, my_max, all_max );
-#endif
 
   return all_max;
 }
@@ -650,18 +501,6 @@ void Allocate_Grid( reax_system *system, MPI_Comm comm )
       for( k = g->native_str[2]; k < g->native_end[2]; ++k )
         g->cells[i][j][k].atoms = (int*) scalloc( g->max_atoms, sizeof(int),
                                                   "g:atoms", comm );
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d-allocated %dx%dx%d grid: nbrs=%d atoms=%d space=%dMB\n",
-           system->my_rank, g->ncells[0], g->ncells[1], g->ncells[2],
-           g->max_nbrs, g->max_atoms,
-           (int)
-           ((g->total*sizeof(grid_cell)+g->total*g->max_nbrs*sizeof(int*) +
-             g->total*g->max_nbrs*sizeof(rvec) +
-             (g->native_end[0]-g->native_str[0])*
-             (g->native_end[1]-g->native_str[1])*
-             (g->native_end[2]-g->native_str[2])*g->max_atoms*sizeof(int))/
-            (1024*1024)) );
-#endif
 }
 
 
@@ -691,15 +530,6 @@ void Deallocate_Grid( grid *g )
 }
 
 
-/************ mpi buffers ********************/
- /* make the allocations based on the largest need by the three comms:
-    1- transfer an atom who has moved into other proc's domain (mpi_atom)
-    2- exchange boundary atoms (boundary_atom)
-    3- update position info for boundary atoms (mpi_rvec)
-
-    the largest space by far is required for the 2nd comm operation above.
-    buffers are void*, type cast to the correct pointer type to access
-    the allocated buffers */
 int  Allocate_MPI_Buffers( mpi_datatypes *mpi_data, int est_recv,
                            neighbor_proc *my_nbrs, char *msg )
 {
@@ -766,26 +596,6 @@ void ReAllocate( reax_system *system, control_params *control,
   g = &(system->my_grid);
   comm = mpi_data->world;
 
-#if defined(DEBUG)
-  fprintf( stderr, "p%d@reallocate: n: %d, N: %d, numH: %d\n",
-           system->my_rank, system->n, system->N, system->numH );
-  fprintf( stderr, "p%d@reallocate: local_cap: %d, total_cap: %d, Hcap: %d\n",
-           system->my_rank, system->local_cap, system->total_cap,
-           system->Hcap);
-  fprintf( stderr, "p%d: realloc.num_far: %d\n",
-           system->my_rank, realloc->num_far );
-  fprintf( stderr, "p%d: realloc.H: %d, realloc.Htop: %d\n",
-           system->my_rank, realloc->H, realloc->Htop );
-  fprintf( stderr, "p%d: realloc.Hbonds: %d, realloc.num_hbonds: %d\n",
-           system->my_rank, realloc->hbonds, realloc->num_hbonds );
-  fprintf( stderr, "p%d: realloc.bonds: %d, num_bonds: %d\n",
-           system->my_rank, realloc->bonds, realloc->num_bonds );
-  fprintf( stderr, "p%d: realloc.num_3body: %d\n",
-           system->my_rank, realloc->num_3body );
-#endif
-
-  // IMPORTANT: LOOSE ZONES CHECKS ARE DISABLED FOR NOW BY &&'ing with 0!!!
-
   int nflag = 0;
   if( system->n >= DANGER_ZONE * system->local_cap ||
       (0 && system->n <= LOOSE_ZONE * system->local_cap) ) {
@@ -802,12 +612,6 @@ void ReAllocate( reax_system *system, control_params *control,
 
   if( Nflag ) {
     /* system */
-#if defined(DEBUG_FOCUS)
-    fprintf( stderr, "p%d: reallocating system and workspace -"\
-             "n=%d  N=%d  local_cap=%d  total_cap=%d\n",
-             system->my_rank, system->n, system->N,
-             system->local_cap, system->total_cap );
-#endif
     ret = Allocate_System( system, system->local_cap, system->total_cap, msg );
     if( ret != SUCCESS ) {
       fprintf( stderr, "not enough space for atom_list: total_cap=%d",
@@ -843,46 +647,12 @@ void ReAllocate( reax_system *system, control_params *control,
 
       newsize = static_cast<int>
         (MAX( realloc->num_far*safezone, mincap*MIN_NBRS ));
-#if defined(DEBUG_FOCUS)
-      fprintf( stderr, "p%d: reallocating far_nbrs: num_fars=%d, space=%dMB\n",
-               system->my_rank, (int)(realloc->num_far*SAFE_ZONE),
-               (newsize*sizeof(far_neighbor_data)/(1024*1024)) );
-#endif
 
       Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize, comm );
       realloc->num_far = 0;
     }
   }
 
-#if defined(PURE_REAX)
-  /* qeq coef matrix */
-  H = workspace->H;
-  if( nflag || realloc->Htop >= H->m * DANGER_ZONE ) {
-    if( realloc->Htop > H->m ) {
-      fprintf( stderr,
-               "step%d - ran out of space on H matrix: Htop=%d, max = %d",
-               data->step, realloc->Htop, H->m );
-      MPI_Abort( comm, INSUFFICIENT_MEMORY );
-    }
-#if defined(DEBUG_FOCUS)
-    fprintf( stderr, "p%d: reallocating H matrix: Htop=%d, space=%dMB\n",
-             system->my_rank, (int)(realloc->Htop*SAFE_ZONE),
-             (int)(realloc->Htop * SAFE_ZONE * sizeof(sparse_matrix_entry) /
-                   (1024*1024)) );
-#endif
-
-    newsize = static_cast<int>
-        (MAX( realloc->Htop*safezone, mincap*MIN_NBRS ));
-    Reallocate_Matrix( &(workspace->H), system->local_cap,
-                       newsize, "H", comm );
-    //Deallocate_Matrix( workspace->L );
-    //Deallocate_Matrix( workspace->U );
-    workspace->L = NULL;
-    workspace->U = NULL;
-    realloc->Htop = 0;
-  }
-#endif /*PURE_REAX*/
-
   /* hydrogen bonds list */
   if( control->hbond_cut > 0 ) {
     Hflag = 0;
@@ -895,10 +665,6 @@ void ReAllocate( reax_system *system, control_params *control,
     if( Hflag || realloc->hbonds ) {
       ret = Reallocate_HBonds_List( system, (*lists)+HBONDS, comm );
       realloc->hbonds = 0;
-#if defined(DEBUG_FOCUS)
-      fprintf(stderr, "p%d: reallocating hbonds: total_hbonds=%d space=%dMB\n",
-              system->my_rank, ret, (int)(ret*sizeof(hbond_data)/(1024*1024)));
-#endif
     }
   }
 
@@ -909,21 +675,10 @@ void ReAllocate( reax_system *system, control_params *control,
                            &est_3body, comm );
     realloc->bonds = 0;
     realloc->num_3body = MAX( realloc->num_3body, est_3body );
-#if defined(DEBUG_FOCUS)
-    fprintf( stderr, "p%d: reallocating bonds: total_bonds=%d, space=%dMB\n",
-             system->my_rank, num_bonds,
-             (int)(num_bonds*sizeof(bond_data)/(1024*1024)) );
-#endif
   }
 
   /* 3-body list */
   if( realloc->num_3body > 0 ) {
-#if defined(DEBUG_FOCUS)
-    fprintf( stderr, "p%d: reallocating 3body list: num_3body=%d, space=%dMB\n",
-             system->my_rank, realloc->num_3body,
-             (int)(realloc->num_3body * sizeof(three_body_interaction_data) /
-                   (1024*1024)) );
-#endif
     Delete_List( (*lists)+THREE_BODIES, comm );
 
     if( num_bonds == -1 )
@@ -939,88 +694,4 @@ void ReAllocate( reax_system *system, control_params *control,
     realloc->num_3body = -1;
   }
 
-#if defined(PURE_REAX)
-  /* grid */
-  if( renbr && realloc->gcell_atoms > -1 ) {
-#if defined(DEBUG_FOCUS)
-    fprintf(stderr, "reallocating gcell: g->max_atoms: %d\n", g->max_atoms);
-#endif
-    for( i = g->native_str[0]; i < g->native_end[0]; i++ )
-      for( j = g->native_str[1]; j < g->native_end[1]; j++ )
-        for( k = g->native_str[2]; k < g->native_end[2]; k++ ) {
-          // reallocate g->atoms
-          sfree( g->cells[i][j][k].atoms, "g:atoms" );
-          g->cells[i][j][k].atoms = (int*)
-            scalloc( realloc->gcell_atoms, sizeof(int), "g:atoms", comm);
-        }
-    realloc->gcell_atoms = -1;
-  }
-
-  /* mpi buffers */
-  // we have to be at a renbring step -
-  // to ensure correct values at mpi_buffers for update_boundary_positions
-  if( !renbr )
-    mpi_flag = 0;
-  // check whether in_buffer capacity is enough
-  else if( system->max_recved >= system->est_recv * 0.90 )
-    mpi_flag = 1;
-  else {
-    // otherwise check individual outgoing buffers
-    mpi_flag = 0;
-    for( p = 0; p < MAX_NBRS; ++p ) {
-      nbr_pr   = &( system->my_nbrs[p] );
-      nbr_data = &( mpi_data->out_buffers[p] );
-      if( nbr_data->cnt >= nbr_pr->est_send * 0.90 ) {
-        mpi_flag = 1;
-        break;
-      }
-    }
-  }
-
-  if( mpi_flag ) {
-#if defined(DEBUG_FOCUS)
-    fprintf( stderr, "p%d: reallocating mpi_buf: old_recv=%d\n",
-             system->my_rank, system->est_recv );
-    for( p = 0; p < MAX_NBRS; ++p )
-      fprintf( stderr, "p%d: nbr%d old_send=%d\n",
-               system->my_rank, p, system->my_nbrs[p].est_send );
-#endif
-    /* update mpi buffer estimates based on last comm */
-    system->est_recv = MAX( system->max_recved*SAFER_ZONE, MIN_SEND );
-    system->est_trans =
-      (system->est_recv * sizeof(boundary_atom)) / sizeof(mpi_atom);
-    total_send = 0;
-    for( p = 0; p < MAX_NBRS; ++p ) {
-      nbr_pr   = &( system->my_nbrs[p] );
-      nbr_data = &( mpi_data->out_buffers[p] );
-      nbr_pr->est_send = MAX( nbr_data->cnt*SAFER_ZONE, MIN_SEND );
-      total_send += nbr_pr->est_send;
-    }
-#if defined(DEBUG_FOCUS)
-    fprintf( stderr, "p%d: reallocating mpi_buf: recv=%d send=%d total=%dMB\n",
-             system->my_rank, system->est_recv, total_send,
-             (int)((system->est_recv+total_send)*sizeof(boundary_atom)/
-                   (1024*1024)));
-    for( p = 0; p < MAX_NBRS; ++p )
-      fprintf( stderr, "p%d: nbr%d new_send=%d\n",
-               system->my_rank, p, system->my_nbrs[p].est_send );
-#endif
-
-    /* reallocate mpi buffers */
-    Deallocate_MPI_Buffers( mpi_data );
-    ret = Allocate_MPI_Buffers( mpi_data, system->est_recv,
-                                system->my_nbrs, msg );
-    if( ret != SUCCESS ) {
-      fprintf( stderr, "%s", msg );
-      fprintf( stderr, "terminating...\n" );
-      MPI_Abort( comm, INSUFFICIENT_MEMORY );
-    }
-  }
-#endif /*PURE_REAX*/
-
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d @ step%d: reallocate done\n",
-           system->my_rank, data->step );
-  MPI_Barrier( comm );
-#endif
 }
diff --git a/src/USER-REAXC/reaxc_basic_comm.cpp b/src/USER-REAXC/reaxc_basic_comm.cpp
index 70d9d070d9..b63d08dec0 100644
--- a/src/USER-REAXC/reaxc_basic_comm.cpp
+++ b/src/USER-REAXC/reaxc_basic_comm.cpp
@@ -25,204 +25,9 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "basic_comm.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_basic_comm.h"
 #include "reaxc_vector.h"
-#endif
 
-#if defined(PURE_REAX)
-void real_packer( void *dummy, mpi_out_data *out_buf )
-{
-  int i;
-  real *buf = (real*) dummy;
-  real *out = (real*) out_buf->out_atoms;
-
-  for( i = 0; i < out_buf->cnt; ++i )
-    out[i] = buf[ out_buf->index[i] ];
-}
-
-
-void rvec_packer( void *dummy, mpi_out_data *out_buf )
-{
-  int i;
-  rvec *buf = (rvec*) dummy;
-  rvec *out = (rvec*)out_buf->out_atoms;
-
-  for( i = 0; i < out_buf->cnt; ++i )
-    memcpy( out[i], buf[ out_buf->index[i] ], sizeof(rvec) );
-}
-
-
-void rvec2_packer( void *dummy, mpi_out_data *out_buf )
-{
-  int i;
-  rvec2 *buf = (rvec2*) dummy;
-  rvec2 *out = (rvec2*) out_buf->out_atoms;
-
-  for( i = 0; i < out_buf->cnt; ++i )
-    memcpy( out[i], buf[ out_buf->index[i] ], sizeof(rvec2) );
-}
-
-
-void Dist( reax_system* system, mpi_datatypes *mpi_data,
-           void *buf, MPI_Datatype type, int scale, dist_packer pack )
-{
-  int d;
-  mpi_out_data *out_bufs;
-  MPI_Comm comm;
-  MPI_Request req1, req2;
-  MPI_Status stat1, stat2;
-  neighbor_proc *nbr1, *nbr2;
-
-#if defined(DEBUG)
-  fprintf( stderr, "p%d dist: entered\n", system->my_rank );
-#endif
-  comm = mpi_data->comm_mesh3D;
-  out_bufs = mpi_data->out_buffers;
-
-  for( d = 0; d < 3; ++d ) {
-    /* initiate recvs */
-    nbr1 = &(system->my_nbrs[2*d]);
-    if( nbr1->atoms_cnt )
-      MPI_Irecv( buf + nbr1->atoms_str*scale, nbr1->atoms_cnt, type,
-                 nbr1->rank, 2*d+1,comm, &req1 );
-
-    nbr2 = &(system->my_nbrs[2*d+1]);
-    if( nbr2->atoms_cnt )
-      MPI_Irecv( buf + nbr2->atoms_str*scale, nbr2->atoms_cnt, type,
-                 nbr2->rank, 2*d, comm, &req2 );
-
-    /* send both messages in dimension d */
-    if( out_bufs[2*d].cnt ) {
-      pack( buf, out_bufs + (2*d) );
-      MPI_Send( out_bufs[2*d].out_atoms, out_bufs[2*d].cnt, type,
-                nbr1->rank, 2*d, comm );
-    }
-
-    if( out_bufs[2*d+1].cnt ) {
-      pack( buf, out_bufs + (2*d+1) );
-      MPI_Send( out_bufs[2*d+1].out_atoms, out_bufs[2*d+1].cnt, type,
-                nbr2->rank, 2*d+1, comm );
-    }
-
-    if( nbr1->atoms_cnt ) MPI_Wait( &req1, &stat1 );
-    if( nbr2->atoms_cnt ) MPI_Wait( &req2, &stat2 );
-  }
-
-#if defined(DEBUG)
-  fprintf( stderr, "p%d dist: done\n", system->my_rank );
-#endif
-}
-
-
-void real_unpacker( void *dummy_in, void *dummy_buf, mpi_out_data *out_buf )
-{
-  int i;
-  real *in = (real*) dummy_in;
-  real *buf = (real*) dummy_buf;
-
-  for( i = 0; i < out_buf->cnt; ++i )
-    buf[ out_buf->index[i] ] += in[i];
-}
-
-
-void rvec_unpacker( void *dummy_in, void *dummy_buf, mpi_out_data *out_buf )
-{
-  int i;
-  rvec *in = (rvec*) dummy_in;
-  rvec *buf = (rvec*) dummy_buf;
-
-  for( i = 0; i < out_buf->cnt; ++i ) {
-    rvec_Add( buf[ out_buf->index[i] ], in[i] );
-#if defined(DEBUG)
-    fprintf( stderr, "rvec_unpacker: cnt=%d  i =%d  index[i]=%d\n",
-             out_buf->cnt, i, out_buf->index[i] );
-#endif
-  }
-}
-
-
-void rvec2_unpacker( void *dummy_in, void *dummy_buf, mpi_out_data *out_buf )
-{
-  int i;
-  rvec2 *in = (rvec2*) dummy_in;
-  rvec2 *buf = (rvec2*) dummy_buf;
-
-  for( i = 0; i < out_buf->cnt; ++i ) {
-    buf[ out_buf->index[i] ][0] += in[i][0];
-    buf[ out_buf->index[i] ][1] += in[i][1];
-  }
-}
-
-
-void Coll( reax_system* system, mpi_datatypes *mpi_data,
-           void *buf, MPI_Datatype type, int scale, coll_unpacker unpack )
-{
-  int d;
-  void *in1, *in2;
-  mpi_out_data *out_bufs;
-  MPI_Comm comm;
-  MPI_Request req1, req2;
-  MPI_Status stat1, stat2;
-  neighbor_proc *nbr1, *nbr2;
-
-#if defined(DEBUG)
-  fprintf( stderr, "p%d coll: entered\n", system->my_rank );
-#endif
-  comm = mpi_data->comm_mesh3D;
-  in1 = mpi_data->in1_buffer;
-  in2 = mpi_data->in2_buffer;
-  out_bufs = mpi_data->out_buffers;
-
-  for( d = 2; d >= 0; --d ) {
-    /* initiate recvs */
-    nbr1 = &(system->my_nbrs[2*d]);
-    if( out_bufs[2*d].cnt )
-      MPI_Irecv(in1, out_bufs[2*d].cnt, type, nbr1->rank, 2*d+1, comm, &req1);
-
-    nbr2 = &(system->my_nbrs[2*d+1]);
-    if( out_bufs[2*d+1].cnt )
-      MPI_Irecv(in2, out_bufs[2*d+1].cnt, type, nbr2->rank, 2*d, comm, &req2);
-
-    /* send both messages in dimension d */
-    if( nbr1->atoms_cnt )
-      MPI_Send( buf + nbr1->atoms_str*scale, nbr1->atoms_cnt, type,
-                nbr1->rank, 2*d, comm );
-
-    if( nbr2->atoms_cnt )
-      MPI_Send( buf + nbr2->atoms_str*scale, nbr2->atoms_cnt, type,
-                nbr2->rank, 2*d+1, comm );
-
-#if defined(DEBUG)
-    fprintf( stderr, "p%d coll[%d] nbr1: str=%d cnt=%d recv=%d\n",
-             system->my_rank, d, nbr1->atoms_str, nbr1->atoms_cnt,
-             out_bufs[2*d].cnt );
-    fprintf( stderr, "p%d coll[%d] nbr2: str=%d cnt=%d recv=%d\n",
-             system->my_rank, d, nbr2->atoms_str, nbr2->atoms_cnt,
-             out_bufs[2*d+1].cnt );
-#endif
-
-    if( out_bufs[2*d].cnt ) {
-      MPI_Wait( &req1, &stat1 );
-      unpack( in1, buf, out_bufs + (2*d) );
-    }
-
-    if( out_bufs[2*d+1].cnt ) {
-      MPI_Wait( &req2, &stat2 );
-      unpack( in2, buf, out_bufs + (2*d+1) );
-    }
-  }
-
-#if defined(DEBUG)
-  fprintf( stderr, "p%d coll: done\n", system->my_rank );
-#endif
-}
-#endif /*PURE_REAX*/
-
-/*****************************************************************************/
 real Parallel_Norm( real *v, int n, MPI_Comm comm )
 {
   int  i;
@@ -237,8 +42,6 @@ real Parallel_Norm( real *v, int n, MPI_Comm comm )
   return sqrt( norm_sqr );
 }
 
-
-
 real Parallel_Dot( real *v1, real *v2, int n, MPI_Comm comm )
 {
   int  i;
@@ -253,8 +56,6 @@ real Parallel_Dot( real *v1, real *v2, int n, MPI_Comm comm )
   return res;
 }
 
-
-
 real Parallel_Vector_Acc( real *v, int n, MPI_Comm comm )
 {
   int  i;
@@ -268,50 +69,3 @@ real Parallel_Vector_Acc( real *v, int n, MPI_Comm comm )
 
   return res;
 }
-
-
-/*****************************************************************************/
-#if defined(TEST_FORCES)
-void Coll_ids_at_Master( reax_system *system, storage *workspace,
-                         mpi_datatypes *mpi_data )
-{
-  int i;
-  rc_tagint *id_list;
-
-  MPI_Gather( &system->n, 1, MPI_INT, workspace->rcounts, 1, MPI_INT,
-              MASTER_NODE, mpi_data->world );
-
-  if( system->my_rank == MASTER_NODE ){
-    workspace->displs[0] = 0;
-    for( i = 1; i < system->wsize; ++i )
-      workspace->displs[i] = workspace->displs[i-1] + workspace->rcounts[i-1];
-  }
-
-  id_list = (int*) malloc( system->n * sizeof(int) );
-  for( i = 0; i < system->n; ++i )
-    id_list[i] = system->my_atoms[i].orig_id;
-
-  MPI_Gatherv( id_list, system->n, MPI_INT,
-               workspace->id_all, workspace->rcounts, workspace->displs,
-               MPI_INT, MASTER_NODE, mpi_data->world );
-
-  free( id_list );
-
-#if defined(DEBUG)
-  if( system->my_rank == MASTER_NODE ) {
-    for( i = 0 ; i < system->bigN; ++i )
-      fprintf( stderr, "id_all[%d]: %d\n", i, workspace->id_all[i] );
-  }
-#endif
-}
-
-
-void Coll_rvecs_at_Master( reax_system *system, storage *workspace,
-                           mpi_datatypes *mpi_data, rvec* v )
-{
-  MPI_Gatherv( v, system->n, mpi_data->mpi_rvec,
-               workspace->f_all, workspace->rcounts, workspace->displs,
-               mpi_data->mpi_rvec, MASTER_NODE, mpi_data->world );
-}
-
-#endif
diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp
index 6f37d91c9c..11f862f64b 100644
--- a/src/USER-REAXC/reaxc_bond_orders.cpp
+++ b/src/USER-REAXC/reaxc_bond_orders.cpp
@@ -26,370 +26,9 @@
 
 #include "pair_reax_c.h"
 #include "reaxc_types.h"
-#if defined(PURE_REAX)
-#include "bond_orders.h"
-#include "list.h"
-#include "vector.h"
-#include "io_tools.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
-#endif
-
-#ifdef TEST_FORCES
-void Get_dBO( reax_system *system, reax_list **lists,
-              int i, int pj, real C, rvec *v )
-{
-  reax_list *bonds = (*lists) + BONDS;
-  reax_list *dBOs = (*lists) + DBOS;
-  int start_pj, end_pj, k;
-
-  pj = bonds->select.bond_list[pj].dbond_index;
-  start_pj = Start_Index(pj, dBOs);
-  end_pj = End_Index(pj, dBOs);
-
-  for( k = start_pj; k < end_pj; ++k )
-    rvec_Scale( v[dBOs->select.dbo_list[k].wrt],
-                C, dBOs->select.dbo_list[k].dBO );
-}
-
-
-void Get_dBOpinpi2( reax_system *system, reax_list **lists,
-                    int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
-{
-  reax_list *bonds = (*lists) + BONDS;
-  reax_list *dBOs = (*lists) + DBOS;
-  dbond_data *dbo_k;
-  int start_pj, end_pj, k;
-
-  pj = bonds->select.bond_list[pj].dbond_index;
-  start_pj = Start_Index(pj, dBOs);
-  end_pj = End_Index(pj, dBOs);
-
-  for( k = start_pj; k < end_pj; ++k )
-    {
-      dbo_k = &(dBOs->select.dbo_list[k]);
-      rvec_Scale( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
-      rvec_Scale( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
-    }
-}
-
-
-void Add_dBO( reax_system *system, reax_list **lists,
-              int i, int pj, real C, rvec *v )
-{
-  reax_list *bonds = (*lists) + BONDS;
-  reax_list *dBOs = (*lists) + DBOS;
-  int start_pj, end_pj, k;
-
-  pj = bonds->select.bond_list[pj].dbond_index;
-  start_pj = Start_Index(pj, dBOs);
-  end_pj = End_Index(pj, dBOs);
-  //fprintf( stderr, "i=%d j=%d start=%d end=%d\n", i, pj, start_pj, end_pj );
-
-  for( k = start_pj; k < end_pj; ++k )
-    rvec_ScaledAdd( v[dBOs->select.dbo_list[k].wrt],
-                    C, dBOs->select.dbo_list[k].dBO );
-
-}
-
-
-void Add_dBOpinpi2( reax_system *system, reax_list **lists,
-                    int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
-{
-  reax_list *bonds = (*lists) + BONDS;
-  reax_list *dBOs = (*lists) + DBOS;
-  dbond_data *dbo_k;
-  int start_pj, end_pj, k;
-
-  pj = bonds->select.bond_list[pj].dbond_index;
-  start_pj = Start_Index(pj, dBOs);
-  end_pj = End_Index(pj, dBOs);
-
-  for( k = start_pj; k < end_pj; ++k )
-    {
-      dbo_k = &(dBOs->select.dbo_list[k]);
-      rvec_ScaledAdd( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
-      rvec_ScaledAdd( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
-    }
-}
-
-
-void Add_dBO_to_Forces( reax_system *system, reax_list **lists,
-                        int i, int pj, real C )
-{
-  reax_list *bonds = (*lists) + BONDS;
-  reax_list *dBOs = (*lists) + DBOS;
-  int start_pj, end_pj, k;
-
-  pj = bonds->select.bond_list[pj].dbond_index;
-  start_pj = Start_Index(pj, dBOs);
-  end_pj = End_Index(pj, dBOs);
-
-  for( k = start_pj; k < end_pj; ++k )
-    rvec_ScaledAdd( system->my_atoms[dBOs->select.dbo_list[k].wrt].f,
-                    C, dBOs->select.dbo_list[k].dBO );
-}
-
-
-void Add_dBOpinpi2_to_Forces( reax_system *system, reax_list **lists,
-                              int i, int pj, real Cpi, real Cpi2 )
-{
-  reax_list *bonds = (*lists) + BONDS;
-  reax_list *dBOs = (*lists) + DBOS;
-  dbond_data *dbo_k;
-  int start_pj, end_pj, k;
-
-  pj = bonds->select.bond_list[pj].dbond_index;
-  start_pj = Start_Index(pj, dBOs);
-  end_pj = End_Index(pj, dBOs);
-
-  for( k = start_pj; k < end_pj; ++k )
-    {
-      dbo_k = &(dBOs->select.dbo_list[k]);
-      rvec_ScaledAdd( system->my_atoms[dbo_k->wrt].f, Cpi, dbo_k->dBOpi );
-      rvec_ScaledAdd( system->my_atoms[dbo_k->wrt].f, Cpi2, dbo_k->dBOpi2 );
-    }
-}
-
-
-void Add_dDelta( reax_system *system, reax_list **lists, int i, real C, rvec *v )
-{
-  reax_list *dDeltas = &((*lists)[DDELTAS]);
-  int start = Start_Index(i, dDeltas);
-  int end = End_Index(i, dDeltas);
-  int k;
-
-  for( k = start; k < end; ++k )
-    rvec_ScaledAdd( v[dDeltas->select.dDelta_list[k].wrt],
-                    C, dDeltas->select.dDelta_list[k].dVal );
-}
-
-
-void Add_dDelta_to_Forces( reax_system *system, reax_list **lists,
-                           int i, real C )
-{
-  reax_list *dDeltas = &((*lists)[DDELTAS]);
-  int start = Start_Index(i, dDeltas);
-  int end = End_Index(i, dDeltas);
-  int k;
-
-  for( k = start; k < end; ++k )
-    rvec_ScaledAdd( system->my_atoms[dDeltas->select.dDelta_list[k].wrt].f,
-                    C, dDeltas->select.dDelta_list[k].dVal );
-}
-
-
-
-void Calculate_dBO( int i, int pj,
-                    storage *workspace, reax_list **lists, int *top )
-{
-  /* Initializations */
-  reax_list *bonds, *dBOs;
-  int j, k, l, start_i, end_i, end_j;
-  bond_data *nbr_l, *nbr_k;
-  bond_order_data *bo_ij;
-  dbond_data *top_dbo;
-
-  //  rvec due_j[1000], due_i[1000];
-  //  rvec due_j_pi[1000], due_i_pi[1000];
-
-  //  memset(due_j, 0, sizeof(rvec)*1000 );
-  //  memset(due_i, 0, sizeof(rvec)*1000 );
-  //  memset(due_j_pi, 0, sizeof(rvec)*1000 );
-  //  memset(due_i_pi, 0, sizeof(rvec)*1000 );
-
-  bonds = *lists + BONDS;
-  dBOs  = *lists + DBOS;
-
-  start_i = Start_Index(i, bonds);
-  end_i = End_Index(i, bonds);
-
-  j = bonds->select.bond_list[pj].nbr;
-  l = Start_Index(j, bonds);
-  end_j = End_Index(j, bonds);
-
-  bo_ij = &(bonds->select.bond_list[pj].bo_data);
-  top_dbo = &(dBOs->select.dbo_list[ (*top) ]);
-
-  for( k = start_i; k < end_i; ++k ) {
-    nbr_k = &(bonds->select.bond_list[k]);
-
-    for( ; l < end_j && bonds->select.bond_list[l].nbr < nbr_k->nbr; ++l ) {
-      /* These are the neighbors of j which are not in the nbr_list of i
-         Note that they might also include i! */
-      nbr_l = &(bonds->select.bond_list[l]);
-      top_dbo->wrt = nbr_l->nbr;
-
-      //rvec_ScaledAdd( due_j[top_dbo->wrt],
-      //                -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
-
-      /*3rd, dBO*/
-      rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
-      /*4th, dBOpi*/
-      rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, nbr_l->bo_data.dBOp );
-      /*4th, dBOpp*/
-      rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, nbr_l->bo_data.dBOp );
-
-      if( nbr_l->nbr == i ) {
-        /* do the adjustments on i */
-        //rvec_ScaledAdd( due_i[i], bo_ij->A0_ij+bo_ij->BO*bo_ij->A1_ij,
-        //                bo_ij->dBOp );  /*1st, dBO*/
-        //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
-        //                workspace->dDeltap_self[i] ); /*2nd, dBO*/
-
-        /*1st, dBO*/
-        rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
-        /*2nd, dBO*/
-        rvec_ScaledAdd( top_dbo->dBO,
-                        bo_ij->C2dbo, workspace->dDeltap_self[i] );
-
-        /*1st, dBOpi*/
-        rvec_ScaledAdd(top_dbo->dBOpi,bo_ij->C1dbopi,bo_ij->dln_BOp_pi );
-        /*2nd, dBOpi*/
-        rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp );
-        /*3rd, dBOpi*/
-        rvec_ScaledAdd( top_dbo->dBOpi,
-                        bo_ij->C3dbopi, workspace->dDeltap_self[i] );
-
-        /*1st, dBO_p*/
-        rvec_ScaledAdd( top_dbo->dBOpi2,
-                        bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2 );
-        /*2nd, dBO_p*/
-        rvec_ScaledAdd( top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp );
-        /*3rd, dBO_p*/
-        rvec_ScaledAdd( top_dbo->dBOpi2,
-                        bo_ij->C3dbopi2, workspace->dDeltap_self[i] );
-      }
-
-      //rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
-      ++(*top), ++top_dbo;
-    }
-
-    /* Now we are processing neighbor k of i. */
-    top_dbo->wrt = nbr_k->nbr;
-
-    //2nd, dBO
-    //rvec_ScaledAdd( due_i[top_dbo->wrt],
-    //                -bo_ij->BO * bo_ij->A2_ij, nbr_k->bo_data.dBOp );
-
-    /*2nd, dBO*/
-    rvec_Scale( top_dbo->dBO, -bo_ij->C2dbo, nbr_k->bo_data.dBOp );
-    /*3rd, dBOpi*/
-    rvec_Scale( top_dbo->dBOpi, -bo_ij->C3dbopi, nbr_k->bo_data.dBOp );
-    /*3rd, dBOpp*/
-    rvec_Scale( top_dbo->dBOpi2, -bo_ij->C3dbopi2, nbr_k->bo_data.dBOp );
-
-    if( l < end_j && bonds->select.bond_list[l].nbr == nbr_k->nbr ) {
-      /* This is a common neighbor of i and j. */
-      nbr_l = &(bonds->select.bond_list[l]);
-
-      /*3rd, dBO*/
-      //rvec_ScaledAdd( due_j[top_dbo->wrt],
-      //                -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
-
-      /*3rd, dBO*/
-      rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
-      /*4th, dBOpi*/
-      rvec_ScaledAdd(top_dbo->dBOpi, -bo_ij->C4dbopi, nbr_l->bo_data.dBOp);
-      /*4th, dBOpp*/
-      rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C4dbopi2,nbr_l->bo_data.dBOp);
-      ++l;
-    }
-    else if( k == pj ) {
-      /* This negihbor is j. */
-      //rvec_ScaledAdd( due_j[j], -(bo_ij->A0_ij+bo_ij->BO*bo_ij->A1_ij),
-      //                bo_ij->dBOp );  /*1st, dBO*/
-      //rvec_ScaledAdd( due_j[j], bo_ij->BO * bo_ij->A2_ji,
-      //                workspace->dDeltap_self[j] );  /*3rd, dBO*/
-
-      /*1st, dBO*/
-      rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C1dbo, bo_ij->dBOp );
-      /*3rd, dBO*/
-      rvec_ScaledAdd(top_dbo->dBO,bo_ij->C3dbo,workspace->dDeltap_self[j]);
-
-      /*1st, dBOpi*/
-      rvec_ScaledAdd( top_dbo->dBOpi, -bo_ij->C1dbopi, bo_ij->dln_BOp_pi );
-      /*2nd, dBOpi*/
-      rvec_ScaledAdd( top_dbo->dBOpi, -bo_ij->C2dbopi, bo_ij->dBOp );
-      /*4th, dBOpi*/
-      rvec_ScaledAdd( top_dbo->dBOpi,
-                      bo_ij->C4dbopi, workspace->dDeltap_self[j] );
-
-      /*1st, dBOpi2*/
-      rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C1dbopi2,bo_ij->dln_BOp_pi2);
-      /*2nd, dBOpi2*/
-      rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C2dbopi2,bo_ij->dBOp );
-      /*4th, dBOpi2*/
-      rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C4dbopi2,
-                     workspace->dDeltap_self[j] );
-    }
-
-    // rvec_Add( workspace->dDelta[nbr_k->nbr], top_dbo->dBO );
-    ++(*top), ++top_dbo;
-  }
-
-  for( ; l < end_j; ++l ) {
-    /* These are the remaining neighbors of j which are not in the
-       neighbor_list of i. Note that they might also include i!*/
-    nbr_l = &(bonds->select.bond_list[l]);
-    top_dbo->wrt = nbr_l->nbr;
-
-    // fprintf( stdout, "\tl: %d nbr:%d\n", l, nbr_l->nbr+1 );
-
-    // rvec_ScaledAdd( due_j[top_dbo->wrt],
-    //                 -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
-
-    /*3rd, dBO*/
-    rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
-    /*4th, dBOpi*/
-    rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, nbr_l->bo_data.dBOp );
-    /*4th, dBOpp*/
-    rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, nbr_l->bo_data.dBOp );
-
-    if( nbr_l->nbr == i )
-      {
-        /* do the adjustments on i */
-        //rvec_ScaledAdd( due_i[i], bo_ij->A0_ij + bo_ij->BO * bo_ij->A1_ij,
-        //                bo_ij->dBOp );  /*1st, dBO*/
-        //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
-        //                workspace->dDeltap_self[i] ); /*2nd, dBO*/
-
-        /*1st, dBO*/
-        rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
-        /*2nd, dBO*/
-        rvec_ScaledAdd(top_dbo->dBO,bo_ij->C2dbo,workspace->dDeltap_self[i]);
-
-        /*1st, dBO_p*/
-        rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C1dbopi, bo_ij->dln_BOp_pi );
-        /*2nd, dBOpi*/
-        rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp );
-        /*3rd,dBOpi*/
-        rvec_ScaledAdd( top_dbo->dBOpi,
-                        bo_ij->C3dbopi, workspace->dDeltap_self[i] );
-
-        /*1st, dBO_p*/
-        rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2);
-        /*2nd, dBO_p*/
-        rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp);
-        /*3rd,dBO_p*/
-        rvec_ScaledAdd(top_dbo->dBOpi2,
-                       bo_ij->C3dbopi2, workspace->dDeltap_self[i]);
-      }
-
-    // rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
-    ++(*top), ++top_dbo;
-  }
-
-  //  for( k = 0; k < 21; ++k ){
-  //  fprintf( stderr, "%d %d %d, due_i:[%g %g %g]\n",
-  //           i+1, j+1, k+1, due_i[k][0], due_i[k][1], due_i[k][2] );
-  //  fprintf( stderr, "%d %d %d, due_j:[%g %g %g]\n",
-  //           i+1, j+1, k+1, due_j[k][0], due_j[k][1], due_j[k][2] );
-}
-#endif
-
 
 void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
                               storage *workspace, reax_list **lists )
@@ -426,11 +65,6 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
   coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
   coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
 
-
-  /************************************
-   * forces related to atom i          *
-   * first neighbors of atom i         *
-   ************************************/
   for( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk ) {
     nbr_k = &(bonds->select.bond_list[pk]);
     k = nbr_k->nbr;
@@ -446,16 +80,6 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
     rvec_iMultiply( ext_press, nbr_k->rel_box, temp );
     rvec_Add( data->my_ext_press, ext_press );
 
-    /* if( !ivec_isZero( nbr_k->rel_box ) )
-       fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
-       "ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
-       i+1, system->my_atoms[i].x[0],
-       system->my_atoms[i].x[1], system->my_atoms[i].x[2],
-       j+1, k+1, system->my_atoms[k].x[0],
-       system->my_atoms[k].x[1], system->my_atoms[k].x[2],
-       nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
-       nbr_k->rel_box[0], nbr_k->rel_box[1], nbr_k->rel_box[2],
-       temp[0], temp[1], temp[2] ); */
   }
 
   /* then atom i itself  */
@@ -473,13 +97,7 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
 
   /* force */
   rvec_Add( workspace->f[i], temp );
-  /* ext pressure due to i is dropped, counting force on j will be enough */
 
-
-  /******************************************************
-   * forces and pressure related to atom j               *
-   * first neighbors of atom j                           *
-   ******************************************************/
   for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) {
     nbr_k = &(bonds->select.bond_list[pk]);
     k = nbr_k->nbr;
@@ -497,16 +115,6 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
       rvec_iMultiply( ext_press, rel_box, temp );
       rvec_Add( data->my_ext_press, ext_press );
 
-      /* if( !ivec_isZero( rel_box ) )
-         fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
-         "ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
-         i+1, j+1, system->my_atoms[j].x[0],
-         system->my_atoms[j].x[1], system->my_atoms[j].x[2],
-         k+1, system->my_atoms[k].x[0],
-         system->my_atoms[k].x[1], system->my_atoms[k].x[2],
-         nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
-         rel_box[0], rel_box[1], rel_box[2],
-         temp[0], temp[1], temp[2] ); */
     }
   }
 
@@ -530,20 +138,8 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
   rvec_iMultiply( ext_press, nbr_j->rel_box, temp );
   rvec_Add( data->my_ext_press, ext_press );
 
-  /* if( !ivec_isZero( nbr_j->rel_box ) )
-     fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
-     "ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
-     i+1, system->my_atoms[i].x[0], system->my_atoms[i].x[1],
-     system->my_atoms[i].x[2],
-     j+1,system->my_atoms[j].x[0], system->my_atoms[j].x[1],
-     system->my_atoms[j].x[2],
-     j+1, nbr_j->dvec[0], nbr_j->dvec[1], nbr_j->dvec[2],
-     nbr_j->rel_box[0], nbr_j->rel_box[1], nbr_j->rel_box[2],
-     temp[0], temp[1], temp[2] ); */
 }
 
-
-
 void Add_dBond_to_Forces( reax_system *system, int i, int pj,
                           storage *workspace, reax_list **lists )
 {
@@ -554,6 +150,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
   int pk, k, j;
 
   /* Virial Tallying variables */
+  real f_scaler;
   rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp;
 
   /* Initializations */
@@ -738,8 +335,6 @@ int BOp( storage *workspace, reax_list *bonds, real bo_cut,
     rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi );
     rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 );
 
-    /* Only dBOp wrt. dr_i is stored here, note that
-       dBOp/dr_i = -dBOp/dr_j and all others are 0 */
     rvec_Scale( bo_ij->dBOp,
                 -(bo_ij->BO_s * Cln_BOp_s +
                   bo_ij->BO_pi * Cln_BOp_pi +
@@ -758,35 +353,6 @@ int BOp( storage *workspace, reax_list *bonds, real bo_cut,
     bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
     bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
 
-    /*fprintf( stderr, "%d %d %g %g %g\n",
-      i+1, j+1, bo_ij->BO, bo_ij->BO_pi, bo_ij->BO_pi2 );*/
-
-    /*fprintf( stderr, "Cln_BOp_s: %f, pbo2: %f, C12:%f\n",
-      Cln_BOp_s, twbp->p_bo2, C12 );
-      fprintf( stderr, "Cln_BOp_pi: %f, pbo4: %f, C34:%f\n",
-      Cln_BOp_pi, twbp->p_bo4, C34 );
-      fprintf( stderr, "Cln_BOp_pi2: %f, pbo6: %f, C56:%f\n",
-      Cln_BOp_pi2, twbp->p_bo6, C56 );*/
-    /*fprintf(stderr, "pbo1: %f, pbo2:%f\n", twbp->p_bo1, twbp->p_bo2);
-      fprintf(stderr, "pbo3: %f, pbo4:%f\n", twbp->p_bo3, twbp->p_bo4);
-      fprintf(stderr, "pbo5: %f, pbo6:%f\n", twbp->p_bo5, twbp->p_bo6);
-      fprintf( stderr, "r_s: %f, r_p: %f, r_pp: %f\n",
-      twbp->r_s, twbp->r_p, twbp->r_pp );
-      fprintf( stderr, "C12: %g, C34:%g, C56:%g\n", C12, C34, C56 );*/
-
-    /*fprintf( stderr, "\tfactors: %g %g %g\n",
-      -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi +
-      bo_ij->BO_pi2 * Cln_BOp_pp),
-      -bo_ij->BO_pi * Cln_BOp_pi, -bo_ij->BO_pi2 * Cln_BOp_pi2 );*/
-    /*fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
-      bo_ij->dBOp[0], bo_ij->dBOp[1], bo_ij->dBOp[2] );
-      fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
-      bo_ij->dln_BOp_pi[0], bo_ij->dln_BOp_pi[1],
-      bo_ij->dln_BOp_pi[2] );
-      fprintf( stderr, "dBOpi2:\t[%g, %g, %g]\n\n",
-      bo_ij->dln_BOp_pi2[0], bo_ij->dln_BOp_pi2[1],
-      bo_ij->dln_BOp_pi2[2] );*/
-
     return 1;
   }
 
@@ -804,7 +370,7 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
          storage *workspace, reax_list **lists, output_controls *out_control )
 {
   int i, j, pj, type_i, type_j;
-  int start_i, end_i, sym_index;
+  int start_i, end_i, sym_index, num_bonds;
   real val_i, Deltap_i, Deltap_boc_i;
   real val_j, Deltap_j, Deltap_boc_j;
   real f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5;
@@ -817,71 +383,45 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
   two_body_parameters *twbp;
   bond_order_data *bo_ij, *bo_ji;
   reax_list *bonds = (*lists) + BONDS;
-#ifdef TEST_FORCES
-  int  k, pk, start_j, end_j;
-  int  top_dbo, top_dDelta;
-  dbond_data *pdbo;
-  dDelta_data *ptop_dDelta;
-  reax_list *dDeltas, *dBOs;
-  top_dbo=0;
-  top_dDelta=0;
-  dDeltas = (*lists) + DDELTAS;
-  dBOs = (*lists) + DBOS;
-
-  //for( i = 0; i < system->N; ++i )
-  //  qsort( &(bonds->select.bond_list[Start_Index(i, bonds)]),
-  //   Num_Entries(i, bonds), sizeof(bond_data), compare_bonds );
-#endif
 
+  num_bonds = 0;
   p_boc1 = system->reax_param.gp.l[0];
   p_boc2 = system->reax_param.gp.l[1];
 
  /* Calculate Deltaprime, Deltaprime_boc values */
   for( i = 0; i < system->N; ++i ) {
     type_i = system->my_atoms[i].type;
+    if (type_i < 0) continue;
     sbp_i = &(system->reax_param.sbp[type_i]);
     workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency;
     workspace->Deltap_boc[i] =
       workspace->total_bond_order[i] - sbp_i->valency_val;
 
-    //fprintf( stdout, "%d(%d) %24.15f\n",
-    //     i, workspace->bond_mark[i], workspace->total_bond_order[i] );
     workspace->total_bond_order[i] = 0;
   }
-  // fprintf( stderr, "done with uncorrected bond orders\n" );
 
   /* Corrected Bond Order calculations */
   for( i = 0; i < system->N; ++i ) {
     type_i = system->my_atoms[i].type;
+    if (type_i < 0) continue;
     sbp_i = &(system->reax_param.sbp[type_i]);
     val_i = sbp_i->valency;
     Deltap_i = workspace->Deltap[i];
     Deltap_boc_i = workspace->Deltap_boc[i];
     start_i = Start_Index(i, bonds);
     end_i = End_Index(i, bonds);
-    // fprintf( stderr, "i:%d Dp:%g Dbocp:%g s:%d e:%d\n",
-    //       i+1, Deltap_i, Deltap_boc_i, start_i, end_i );
 
     for( pj = start_i; pj < end_i; ++pj ) {
       j = bonds->select.bond_list[pj].nbr;
       type_j = system->my_atoms[j].type;
+      if (type_j < 0) continue;
       bo_ij = &( bonds->select.bond_list[pj].bo_data );
       // fprintf( stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO );
 
       if( i < j || workspace->bond_mark[j] > 3 ) {
         twbp = &( system->reax_param.tbp[type_i][type_j] );
-#ifdef TEST_FORCES
-        Set_Start_Index( pj, top_dbo, dBOs );
-        /* fprintf( stderr, "%6d%6d%12.6f%12.6f%12.6f\n",
-           workspace->reverse_map[i], workspace->reverse_map[j],
-           twbp->ovc, twbp->v13cor, bo_ij->BO ); */
-#endif
 
         if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) {
-          /* There is no correction to bond orders nor to derivatives
-             of bond order prime! So we leave bond orders unchanged and
-             set derivative of bond order coefficients such that
-             dBO = dBOp & dBOxx = dBOxxp in Add_dBO_to_Forces */
           bo_ij->C1dbo = 1.000000;
           bo_ij->C2dbo = 0.000000;
           bo_ij->C3dbo = 0.000000;
@@ -896,24 +436,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
           bo_ij->C3dbopi2 = 0.000000;
           bo_ij->C4dbopi2 = 0.000000;
 
-#ifdef TEST_FORCES
-          pdbo = &(dBOs->select.dbo_list[ top_dbo ]);
-
-          // compute dBO_ij/dr_i
-          pdbo->wrt = i;
-          rvec_Copy( pdbo->dBO, bo_ij->dBOp );
-          rvec_Scale( pdbo->dBOpi, bo_ij->BO_pi, bo_ij->dln_BOp_pi );
-          rvec_Scale( pdbo->dBOpi2, bo_ij->BO_pi2, bo_ij->dln_BOp_pi2);
-
-          // compute dBO_ij/dr_j
-          pdbo++;
-          pdbo->wrt = j;
-          rvec_Scale( pdbo->dBO, -1.0, bo_ij->dBOp );
-          rvec_Scale( pdbo->dBOpi, -bo_ij->BO_pi, bo_ij->dln_BOp_pi );
-          rvec_Scale(pdbo->dBOpi2, -bo_ij->BO_pi2, bo_ij->dln_BOp_pi2);
-
-          top_dbo += 2;
-#endif
         }
         else {
           val_j = system->reax_param.sbp[type_j].valency;
@@ -933,14 +455,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
             f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) +
                          ( val_j + f2 )/( val_j + f2 + f3 ) );
 
-            /*fprintf( stderr,"%d %d\t%g %g   j:%g %g  p_boc:%g %g\n"
-              "\tf:%g  %g  %g, exp:%g %g %g %g\n",
-              i+1, j+1,
-              val_i, Deltap_i, val_j, Deltap_j, p_boc1, p_boc2,
-              f1, f2, f3, exp_p1i, exp_p2i, exp_p1j, exp_p2j );*/
-
-            /* Now come the derivates */
-            /* Bond Order pages 5-7, derivative of f1 */
             temp = f2 + f3;
             u1_ij = val_i + temp;
             u1_ji = val_j + temp;
@@ -949,8 +463,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
             Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
                               ( u1_ji - f3 ) / SQR( u1_ji ));
 
-            //Cf1_ij = -Cf1A_ij * p_boc1 * exp_p1i +
-            //          Cf1B_ij * exp_p2i / ( exp_p2i + exp_p2j );
             Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
                               ((val_i+f2) / SQR(u1_ij)) *
                               ( -p_boc1 * exp_p1i +
@@ -964,7 +476,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
             Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
               Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
 
-            //fprintf( stderr, "\tCf1:%g  %g\n", Cf1_ij, Cf1_ji );
           }
           else {
             /* No overcoordination correction! */
@@ -984,12 +495,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
             f4f5 = f4 * f5;
 
             /* Bond Order pages 8-9, derivative of f4 and f5 */
-            /*temp = twbp->p_boc5 -
-              twbp->p_boc3 * twbp->p_boc4 * SQR( bo_ij->BO );
-              u_ij = temp + twbp->p_boc3 * Deltap_boc_i;
-              u_ji = temp + twbp->p_boc3 * Deltap_boc_j;
-              Cf45_ij = Cf45( u_ij, u_ji ) / f4f5;
-              Cf45_ji = Cf45( u_ji, u_ij ) / f4f5;*/
             Cf45_ij = -f4 * exp_f4;
             Cf45_ji = -f5 * exp_f5;
           }
@@ -1007,12 +512,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
           A3_ij = A2_ij + Cf1_ij / f1;
           A3_ji = A2_ji + Cf1_ji / f1;
 
-          /*fprintf( stderr, "\tBO: %f, A0: %f, A1: %f"
-            "A2_ij: %f A2_ji: %f, A3_ij: %f, A3_ji: %f\n",
-            bo_ij->BO,
-            A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji );*/
-
-
           /* find corrected bond orders and their derivative coef */
           bo_ij->BO    = bo_ij->BO    * A0_ij;
           bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1;
@@ -1033,9 +532,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
           bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
           bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
 
-#ifdef TEST_FORCES
-          Calculate_dBO( i, pj, workspace, lists, &top_dbo );
-#endif
         }
 
         /* neglect bonds that are < 1e-10 */
@@ -1050,27 +546,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
 
         workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO
 
-
-        /* fprintf( stderr, "%d %d\t%g %g %g %g\n"
-           "Cdbo:\t%g %g %g\n"
-           "Cdbopi:\t%g %g %g %g\n"
-           "Cdbopi2:%g %g %g %g\n\n",
-           i+1, j+1,
-           bonds->select.bond_list[ pj ].d,
-           bo_ij->BO,bo_ij->BO_pi, bo_ij->BO_pi2,
-           bo_ij->C1dbo, bo_ij->C2dbo, bo_ij->C3dbo,
-           bo_ij->C1dbopi, bo_ij->C2dbopi,
-           bo_ij->C3dbopi, bo_ij->C4dbopi,
-           bo_ij->C1dbopi2,bo_ij->C2dbopi2,
-           bo_ij->C3dbopi2, bo_ij->C4dbopi2 ); */
-
-        /* fprintf( stderr, "%d %d  BO:%f BO_s:%f BO_pi:%f BO_pi2:%f\n",
-           i+1,j+1,bo_ij->BO,bo_ij->BO_s,bo_ij->BO_pi,bo_ij->BO_pi2 );*/
-
-#ifdef TEST_FORCES
-        Set_End_Index( pj, top_dbo, dBOs );
-        Add_dBO( system, lists, i, pj, 1.0, workspace->dDelta );
-#endif
       }
       else {
         /* We only need to update bond orders from bo_ji
@@ -1083,63 +558,15 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
         bo_ij->BO_pi2 = bo_ji->BO_pi2;
 
         workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
-#ifdef TEST_FORCES
-        Add_dBO( system, lists, j, sym_index, 1.0, workspace->dDelta );
-#endif
       }
     }
 
-#ifdef TEST_FORCES
-    // fprintf( stderr, "dDelta computations\nj:" );
-    Set_Start_Index( i, top_dDelta, dDeltas );
-    ptop_dDelta = &( dDeltas->select.dDelta_list[top_dDelta] );
-
-    for( pj = start_i; pj < end_i; ++pj ) {
-      j = bonds->select.bond_list[pj].nbr;
-      // fprintf( stderr, "%d  ", j );
-
-      if( !rvec_isZero( workspace->dDelta[j] ) ) {
-        ptop_dDelta->wrt = j;
-        rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[j] );
-        rvec_MakeZero( workspace->dDelta[j] );
-        ++top_dDelta, ++ptop_dDelta;
-      }
-
-      start_j = Start_Index(j, bonds);
-      end_j = End_Index(j, bonds);
-      for( pk = start_j; pk < end_j; ++pk ) {
-        k = bonds->select.bond_list[pk].nbr;
-        if( !rvec_isZero( workspace->dDelta[k] ) ) {
-          ptop_dDelta->wrt = k;
-          rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[k] );
-          rvec_MakeZero( workspace->dDelta[k] );
-          ++top_dDelta, ++ptop_dDelta;
-        }
-      }
-    }
-
-    Set_End_Index( i, top_dDelta, dDeltas );
-
-    /*for(pj = Start_Index(i,dDeltas); pj < End_Index(i,dDeltas); ++pj)
-      fprintf( stdout, "dDel: %d %d [%g %g %g]\n",
-      i+1, dDeltas->select.dDelta_list[pj].wrt+1,
-      dDeltas->select.dDelta_list[pj].dVal[0],
-      dDeltas->select.dDelta_list[pj].dVal[1],
-      dDeltas->select.dDelta_list[pj].dVal[2] );*/
-#endif
   }
 
-  /* fprintf( stderr, "\tCalculated actual bond orders ...\n" );
-     fprintf( stderr, "j\tDelta\tDelta_e\tDelta_boc\tnlp"
-     "\tDelta_lp\tClp\tdDelta_lp\n" );
-     fprintf( stderr, "Atom\tDelta\t\tDelta_e\t\tDelta_boc\tnlp"
-     "\t\tnlp_opt\t\tDelta_lp\tClp\t\tdDelta_lp\n" );*/
-
   p_lp1 = system->reax_param.gp.l[15];
-  /* Calculate some helper variables that are  used at many places
-     throughout force calculations */
   for( j = 0; j < system->N; ++j ){
     type_j = system->my_atoms[j].type;
+    if (type_j < 0) continue;
     sbp_j = &(system->reax_param.sbp[ type_j ]);
 
     workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency;
@@ -1155,11 +582,7 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
     workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0);
     workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j];
     workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]);
-    /* Adri uses different dDelta_lp values than the ones in notes... */
     workspace->dDelta_lp[j] = workspace->Clp[j];
-    //workspace->dDelta_lp[j] = workspace->Clp[j] + (0.5-workspace->Clp[j]) *
-    //((fabs(workspace->Delta_e[j]/2.0 -
-    //       (int)(workspace->Delta_e[j]/2.0)) < 0.1) ? 1 : 0 );
 
     if( sbp_j->mass > 21.0 ) {
       workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency);
@@ -1171,49 +594,7 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
       workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
       workspace->dDelta_lp_temp[j] = workspace->Clp[j];
     }
+
   }
 
-#if defined(TEST_ENERGIES) || defined(TEST_FORCES)
-  Print_Bond_List( system, control, data, lists, out_control);
-#endif
 }
-
-
-#if defined(DEPRECATED)
-/* Locate j on i's list.
-   This function assumes that j is there for sure!
-   And this is the case given our method of neighbor generation*/
-int Locate_Symmetric_Bond( reax_list *bonds, int i, int j )
-{
-  int start = Start_Index(i, bonds);
-  int end = End_Index(i, bonds);
-  int mid = (start + end) / 2;
-  int mid_nbr;
-
-  while( (mid_nbr = bonds->select.bond_list[mid].nbr) != j ) {
-    /*fprintf( stderr, "\tstart: %d   end: %d   mid: %d\n",
-      start, end, mid );*/
-    if( mid_nbr < j )
-      start = mid+1;
-    else end = mid - 1;
-
-    mid = (start + end) / 2;
-  }
-
-  return mid;
-}
-
-
-inline void Copy_Bond_Order_Data( bond_order_data *dest, bond_order_data *src )
-{
-  dest->BO = src->BO;
-  dest->BO_s = src->BO_s;
-  dest->BO_pi = src->BO_pi;
-  dest->BO_pi2 = src->BO_pi2;
-
-  rvec_Scale( dest->dBOp, -1.0, src->dBOp );
-  rvec_Scale( dest->dln_BOp_s, -1.0, src->dln_BOp_s );
-  rvec_Scale( dest->dln_BOp_pi, -1.0, src->dln_BOp_pi );
-  rvec_Scale( dest->dln_BOp_pi2, -1.0, src->dln_BOp_pi2 );
-}
-#endif
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index 45b493237f..c6fb8b372e 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -25,20 +25,11 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "bonds.h"
-#include "bond_orders.h"
-#include "list.h"
-#include "tool_box.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_bonds.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"
 #include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
-#endif
-
 
 void Bonds( reax_system *system, control_params *control,
             simulation_data *data, storage *workspace, reax_list **lists,
@@ -101,19 +92,6 @@ void Bonds( reax_system *system, control_params *control,
         bo_ij->Cdbopi -= (CEbo + twbp->De_p);
         bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
 
-#ifdef TEST_ENERGY
-        //fprintf( out_control->ebond, "%6d%6d%24.15e%24.15e%24.15e\n",
-        fprintf( out_control->ebond, "%6d%6d%12.4f%12.4f%12.4f\n",
-                 system->my_atoms[i].orig_id,
-                 system->my_atoms[j].orig_id,
-                 bo_ij->BO, ebond, data->my_en.e_bond );
-#endif
-#ifdef TEST_FORCES
-        Add_dBO( system, lists, i, pj, CEbo, workspace->f_be );
-        Add_dBOpinpi2( system, lists, i, pj,
-                       -(CEbo + twbp->De_p), -(CEbo + twbp->De_pp),
-                       workspace->f_be, workspace->f_be );
-#endif
         /* Stabilisation terminal triple bond */
         if( bo_ij->BO >= 1.00 ) {
           if( gp37 == 2 ||
@@ -142,17 +120,6 @@ void Bonds( reax_system *system, control_params *control,
             bo_ij->Cdbo += decobdbo;
             workspace->CdDelta[i] += decobdboua;
             workspace->CdDelta[j] += decobdboub;
-#ifdef TEST_ENERGY
-            //fprintf( out_control->ebond,
-            //  "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
-            //  system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-            //  estriph, decobdbo, decobdboua, decobdboub );
-#endif
-#ifdef TEST_FORCES
-            Add_dBO( system, lists, i, pj, decobdbo, workspace->f_be );
-            Add_dDelta( system, lists, i, decobdboua, workspace->f_be );
-            Add_dDelta( system, lists, j, decobdboub, workspace->f_be );
-#endif
           }
         }
       }
diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp
index 2902d51617..eadce53a0c 100644
--- a/src/USER-REAXC/reaxc_control.cpp
+++ b/src/USER-REAXC/reaxc_control.cpp
@@ -25,14 +25,8 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "control.h"
-#include "tool_box.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_control.h"
 #include "reaxc_tool_box.h"
-#endif
-
 
 char Read_Control_File( char *control_file, control_params* control,
                         output_controls *out_control )
@@ -122,7 +116,6 @@ char Read_Control_File( char *control_file, control_params* control,
   while (!feof(fp)) {
     fgets( s, MAX_LINE, fp );
     c = Tokenize( s, &tmp );
-    //fprintf( stderr, "%s\n", s );
 
     if( strcmp(tmp[0], "simulation_name") == 0 ) {
       strcpy( control->sim_name, tmp[1] );
@@ -152,13 +145,6 @@ char Read_Control_File( char *control_file, control_params* control,
       control->nprocs = control->procs_by_dim[0]*control->procs_by_dim[1]*
         control->procs_by_dim[2];
     }
-    //else if( strcmp(tmp[0], "restart") == 0 ) {
-    //  ival = atoi(tmp[1]);
-    //  control->restart = ival;
-    //}
-    //else if( strcmp(tmp[0], "restart_from") == 0 ) {
-    //  strcpy( control->restart_from, tmp[1] );
-    //}
     else if( strcmp(tmp[0], "random_vel") == 0 ) {
       ival = atoi(tmp[1]);
       control->random_vel = ival;
@@ -395,13 +381,5 @@ char Read_Control_File( char *control_file, control_params* control,
 
   fclose(fp);
 
-  // fprintf( stderr,"%d %d %10.5f %d %10.5f %10.5f\n",
-  //   control->ensemble, control->nsteps, control->dt,
-  //   control->tabulate, control->T, control->P );
-
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "control file read\n" );
-#endif
-
   return SUCCESS;
 }
diff --git a/src/USER-REAXC/reaxc_defs.h b/src/USER-REAXC/reaxc_defs.h
index 6a1406387c..d0a75d431b 100644
--- a/src/USER-REAXC/reaxc_defs.h
+++ b/src/USER-REAXC/reaxc_defs.h
@@ -117,7 +117,7 @@
 #define MAX_BOND 20
 
 #define MAXREAXBOND 24 /* used in fix_reaxc_bonds.cpp and pair_reax_c.cpp */
-#define MAXSPECBOND 24 /* used in fix_species.cpp and pair_reax_c.cpp */
+#define MAXSPECBOND 24 /* used in fix_reaxc_species.cpp and pair_reax_c.cpp */
 
 /******************* ENUMERATIONS *************************/
 enum geo_formats { CUSTOM, PDB, ASCII_RESTART, BINARY_RESTART, GF_N };
diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp
index a0a23777e5..bd75498a42 100644
--- a/src/USER-REAXC/reaxc_ffield.cpp
+++ b/src/USER-REAXC/reaxc_ffield.cpp
@@ -26,14 +26,8 @@
 
 #include "pair_reax_c.h"
 #include "error.h"
-#if defined(PURE_REAX)
-#include "ffield.h"
-#include "tool_box.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_ffield.h"
 #include "reaxc_tool_box.h"
-#endif
-
 
 char Read_Force_Field( char *ffield_file, reax_interaction *reax,
                        control_params *control )
@@ -158,15 +152,8 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
     }
   }
 
-  // vdWaals type: 1: Shielded Morse, no inner-wall
-  //               2: inner wall, no shielding
-  //               3: inner wall+shielding
   reax->gp.vdw_type = 0;
 
-  /* reading single atom parameters */
-  /* there are 4 or 5 lines of each single atom parameters in ff files,
-     depending on using lgvdw or not. These parameters later determine
-     some of the pair and triplet parameters using combination rules. */
 
   for( i = 0; i < reax->num_atom_types; i++ ) {
     /* line one */
@@ -261,10 +248,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
         }
         else{
           reax->gp.vdw_type = 3;
-#if defined(DEBUG)
-          fprintf( stderr, "vdWaals type for element %s: Shielding+inner-wall",
-                   reax->sbp[i].name );
-#endif
         }
       }
       else {  // No shielding vdWaals parameters present
@@ -278,10 +261,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
                    reax->sbp[i].name );
         else{
           reax->gp.vdw_type = 2;
-#if defined(DEBUG)
-          fprintf( stderr,"vdWaals type for element%s: No Shielding,inner-wall",
-                   reax->sbp[i].name );
-#endif
         }
       }
     }
@@ -297,10 +276,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
                    reax->sbp[i].name );
         else{
           reax->gp.vdw_type = 1;
-#if defined(DEBUG)
-          fprintf( stderr,"vdWaals type for element%s: Shielding,no inner-wall",
-                   reax->sbp[i].name );
-#endif
         }
       }
       else{
@@ -312,10 +287,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
     }
   }
 
-#if defined(DEBUG)
-  fprintf( stderr, "vdWaals type: %d\n", reax->gp.vdw_type );
-#endif
-
   /* Equate vval3 to valf for first-row elements (25/10/2004) */
   for( i = 0; i < reax->num_atom_types; i++ )
     if( reax->sbp[i].mass < 21 &&
@@ -325,7 +296,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
       reax->sbp[i].valency_val = reax->sbp[i].valency_boc;
     }
 
-
   /* next line is number of two body combination and some comments */
   fgets(s,MAX_LINE,fp);
   c=Tokenize(s,&tmp);
@@ -385,8 +355,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
     }
   }
 
-  /* calculating combination rules and filling up remaining fields. */
-
   for (i=0; i < reax->num_atom_types; i++)
     for (j=i; j < reax->num_atom_types; j++) {
       reax->tbp[i][j].r_s = 0.5 *
@@ -486,10 +454,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
 
     }
 
-
-  /* next line is number of two body offdiagonal combinations and comments */
-  /* these are two body offdiagonal terms that are different from the
-     combination rules defined above */
   fgets(s,MAX_LINE,fp);
   c=Tokenize(s,&tmp);
   l = atoi(tmp[0]);
@@ -546,16 +510,11 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
     }
   }
 
-
-  /* 3-body parameters -
-     supports multi-well potentials (upto MAX_3BODY_PARAM in mytypes.h) */
-  /* clear entries first */
   for( i = 0; i < reax->num_atom_types; ++i )
     for( j = 0; j < reax->num_atom_types; ++j )
       for( k = 0; k < reax->num_atom_types; ++k )
         reax->thbp[i][j][k].cnt = 0;
 
-  /* next line is number of 3-body params and some comments */
   fgets( s, MAX_LINE, fp );
   c = Tokenize( s, &tmp );
   l = atoi( tmp[0] );
@@ -604,15 +563,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
     }
   }
 
-
-  /* 4-body parameters are entered in compact form. i.e. 0-X-Y-0
-     correspond to any type of pair of atoms in 1 and 4
-     position. However, explicit X-Y-Z-W takes precedence over the
-     default description.
-     supports multi-well potentials (upto MAX_4BODY_PARAM in mytypes.h)
-     IMPORTANT: for now, directions on how to read multi-entries from ffield
-     is not clear */
-
   /* clear all entries first */
   for( i = 0; i < reax->num_atom_types; ++i )
     for( j = 0; j < reax->num_atom_types; ++j )
@@ -639,16 +589,11 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
     if (j >= 0 && n >= 0) { // this means the entry is not in compact form
       if (j < reax->num_atom_types && k < reax->num_atom_types &&
           m < reax->num_atom_types && n < reax->num_atom_types) {
-        /* these flags ensure that this entry take precedence
-           over the compact form entries */
         tor_flag[j][k][m][n] = 1;
         tor_flag[n][m][k][j] = 1;
 
         reax->fbp[j][k][m][n].cnt = 1;
         reax->fbp[n][m][k][j].cnt = 1;
-        /* cnt = reax->fbp[j][k][m][n].cnt;
-           reax->fbp[j][k][m][n].cnt++;
-           reax->fbp[n][m][k][j].cnt++; */
 
         val = atof(tmp[4]);
         reax->fbp[j][k][m][n].prm[0].V1 = val;
@@ -677,9 +622,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
           for( o = 0; o < reax->num_atom_types; o++ ) {
             reax->fbp[p][k][m][o].cnt = 1;
             reax->fbp[o][m][k][p].cnt = 1;
-            /* cnt = reax->fbp[p][k][m][o].cnt;
-               reax->fbp[p][k][m][o].cnt++;
-               reax->fbp[o][m][k][p].cnt++; */
 
             if (tor_flag[p][k][m][o] == 0) {
               reax->fbp[p][k][m][o].prm[0].V1 = atof(tmp[4]);
@@ -731,7 +673,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
     }
   }
 
-
   /* deallocate helper storage */
   for( i = 0; i < MAX_TOKENS; i++ )
     free( tmp[i] );
@@ -755,9 +696,5 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
 
   fclose(fp);
 
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "force field read\n" );
-#endif
-
   return SUCCESS;
 }
diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp
index d10b2e8e2f..d581cbebbd 100644
--- a/src/USER-REAXC/reaxc_forces.cpp
+++ b/src/USER-REAXC/reaxc_forces.cpp
@@ -25,23 +25,6 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "forces.h"
-#include "bond_orders.h"
-#include "bonds.h"
-#include "basic_comm.h"
-#include "hydrogen_bonds.h"
-#include "io_tools.h"
-#include "list.h"
-#include "lookup.h"
-#include "multi_body.h"
-#include "nonbonded.h"
-#include "qEq.h"
-#include "tool_box.h"
-#include "torsion_angles.h"
-#include "valence_angles.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_forces.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_bonds.h"
@@ -56,7 +39,6 @@
 #include "reaxc_torsion_angles.h"
 #include "reaxc_valence_angles.h"
 #include "reaxc_vector.h"
-#endif
 
 interaction_function Interaction_Functions[NUM_INTRS];
 
@@ -91,23 +73,10 @@ void Compute_Bonded_Forces( reax_system *system, control_params *control,
 {
   int i;
 
-  /* Mark beginning of a new timestep in bonded energy files */
-#if defined(TEST_ENERGY)
-  Debug_Marker_Bonded( out_control, data->step );
-#endif
-
   /* Implement all force calls as function pointers */
   for( i = 0; i < NUM_INTRS; i++ ) {
-#if defined(DEBUG)
-    fprintf( stderr, "p%d: starting f%d\n", system->my_rank, i );
-    MPI_Barrier( comm );
-#endif
     (Interaction_Functions[i])( system, control, data, workspace,
                                 lists, out_control );
-#if defined(DEBUG)
-    fprintf( stderr, "p%d: f%d done\n", system->my_rank, i );
-    MPI_Barrier( comm );
-#endif
   }
 }
 
@@ -117,10 +86,6 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
                                reax_list **lists, output_controls *out_control,
                                MPI_Comm comm )
 {
-  /* Mark beginning of a new timestep in nonbonded energy files */
-#if defined(TEST_ENERGY)
-  Debug_Marker_Nonbonded( out_control, data->step );
-#endif
 
   /* van der Waals and Coulomb interactions */
   if( control->tabulate == 0 )
@@ -129,18 +94,9 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
   else
     Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
                                   lists, out_control );
-
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: nonbonded forces done\n", system->my_rank );
-  MPI_Barrier( comm );
-#endif
 }
 
 
-
-/* this version of Compute_Total_Force computes forces from
-   coefficients accumulated by all interaction functions.
-   Saves enormous time & space! */
 void Compute_Total_Force( reax_system *system, control_params *control,
                           simulation_data *data, storage *workspace,
                           reax_list **lists, mpi_datatypes *mpi_data )
@@ -157,33 +113,6 @@ void Compute_Total_Force( reax_system *system, control_params *control,
           Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists );
       }
 
-  //Print_Total_Force( system, data, workspace );
-#if defined(PURE_REAX)
-  /* now all forces are computed to their partially-final values
-     based on the neighbors information each processor has had.
-     final values of force on each atom needs to be computed by adding up
-     all partially-final pieces */
-  Coll( system, mpi_data, workspace->f, mpi_data->mpi_rvec,
-        sizeof(rvec)/sizeof(void), rvec_unpacker );
-  for( i = 0; i < system->n; ++i )
-    rvec_Copy( system->my_atoms[i].f, workspace->f[i] );
-
-#if defined(TEST_FORCES)
-  Coll( system, mpi_data, workspace->f_ele, mpi_data->mpi_rvec, rvec_unpacker);
-  Coll( system, mpi_data, workspace->f_vdw, mpi_data->mpi_rvec, rvec_unpacker);
-  Coll( system, mpi_data, workspace->f_be, mpi_data->mpi_rvec, rvec_unpacker );
-  Coll( system, mpi_data, workspace->f_lp, mpi_data->mpi_rvec, rvec_unpacker );
-  Coll( system, mpi_data, workspace->f_ov, mpi_data->mpi_rvec, rvec_unpacker );
-  Coll( system, mpi_data, workspace->f_un, mpi_data->mpi_rvec, rvec_unpacker );
-  Coll( system, mpi_data, workspace->f_ang, mpi_data->mpi_rvec, rvec_unpacker);
-  Coll( system, mpi_data, workspace->f_coa, mpi_data->mpi_rvec, rvec_unpacker);
-  Coll( system, mpi_data, workspace->f_pen, mpi_data->mpi_rvec, rvec_unpacker);
-  Coll( system, mpi_data, workspace->f_hb, mpi_data->mpi_rvec, rvec_unpacker );
-  Coll( system, mpi_data, workspace->f_tor, mpi_data->mpi_rvec, rvec_unpacker);
-  Coll( system, mpi_data, workspace->f_con, mpi_data->mpi_rvec, rvec_unpacker);
-#endif
-
-#endif
 }
 
 void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
@@ -201,12 +130,8 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
     bonds = *lists + BONDS;
 
     for( i = 0; i < N; ++i ) {
-      // if( i < n ) - we need to update ghost estimates for delayed nbrings
       system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS);
 
-      //if( End_Index(i, bonds) >= Start_Index(i+1, bonds)-2 )
-      //workspace->realloc.bonds = 1;
-
       if( i < N-1 )
         comp = Start_Index(i+1, bonds);
       else comp = bonds->num_intrs;
@@ -315,7 +240,6 @@ void Init_Forces( reax_system *system, control_params *control,
     workspace->bond_mark[i] = 0;
   for( i = system->n; i < system->N; ++i ) {
     workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
-    //workspace->done_after[i] = Start_Index( i, far_nbrs );
   }
 
   H = workspace->H;
@@ -329,6 +253,7 @@ void Init_Forces( reax_system *system, control_params *control,
   for( i = 0; i < system->N; ++i ) {
     atom_i = &(system->my_atoms[i]);
     type_i  = atom_i->type;
+    if (type_i < 0) continue;
     start_i = Start_Index(i, far_nbrs);
     end_i   = End_Index(i, far_nbrs);
     btop_i = End_Index( i, bonds );
@@ -364,11 +289,6 @@ void Init_Forces( reax_system *system, control_params *control,
       nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
       j = nbr_pj->nbr;
       atom_j = &(system->my_atoms[j]);
-      //fprintf( stderr, "%d%d i=%d x_i: %f %f %f,j=%d x_j: %f %f %f, d=%f\n",
-      //         MIN(atom_i->orig_id, atom_j->orig_id),
-      //         MAX(atom_i->orig_id, atom_j->orig_id),
-      //         i, atom_i->x[0], atom_i->x[1], atom_i->x[2],
-      //         j, atom_j->x[0], atom_j->x[1], atom_j->x[2], nbr_pj->d );
       if( renbr ) {
         if(nbr_pj->d <= cutoff)
           flag = 1;
@@ -390,6 +310,7 @@ void Init_Forces( reax_system *system, control_params *control,
 
       if( flag ){
         type_j = atom_j->type;
+	if (type_j < 0) continue;
         r_ij = nbr_pj->d;
         sbp_j = &(system->reax_param.sbp[type_j]);
         twbp = &(system->reax_param.tbp[type_i][type_j]);
@@ -398,11 +319,6 @@ void Init_Forces( reax_system *system, control_params *control,
           /* H matrix entry */
           if( j < system->n || atom_i->orig_id < atom_j->orig_id ) {//tryQEq||1
             H->entries[Htop].j = j;
-            //fprintf( stdout, "%d%d %d %d\n",
-            //     MIN(atom_i->orig_id, atom_j->orig_id),
-            //     MAX(atom_i->orig_id, atom_j->orig_id),
-            //     MIN(atom_i->orig_id, atom_j->orig_id),
-            //     MAX(atom_i->orig_id, atom_j->orig_id) );
             if( control->tabulate == 0 )
               H->entries[Htop].val = Compute_H(r_ij,twbp->gamma,workspace->Tap);
             else H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
@@ -412,7 +328,6 @@ void Init_Forces( reax_system *system, control_params *control,
           /* hydrogen bond lists */
           if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
               nbr_pj->d <= control->hbond_cut ) {
-            // fprintf( stderr, "%d %d\n", atom1, atom2 );
             jhb = sbp_j->p_hbond;
             if( ihb == 1 && jhb == 2 ) {
               hbonds->select.hbond_list[ihb_top].nbr = j;
@@ -444,11 +359,7 @@ void Init_Forces( reax_system *system, control_params *control,
             workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
           else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
             workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
-            //if( workspace->bond_mark[i] == 1000 )
-            //  workspace->done_after[i] = pj;
           }
-          //fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
-          //   i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
         }
       }
     }
@@ -461,77 +372,10 @@ void Init_Forces( reax_system *system, control_params *control,
     }
   }
 
-  //fprintf( stderr, "after the first init loop\n" );
-  /*for( i = system->n; i < system->N; ++i )
-    if( workspace->bond_mark[i] > 3 ) {
-      start_i = Start_Index(i, bonds);
-      end_i = End_Index(i, bonds);
-      num_bonds -= (end_i - start_i);
-      Set_End_Index(i, start_i, bonds );
-      }*/
-
-  /*for( i = system->n; i < system->N; ++i ) {
-    start_i = Start_Index(i, far_nbrs);
-    end_i = workspace->done_after[i];
-
-    if( workspace->bond_mark[i] >= 2 && start_i < end_i ) {
-      atom_i = &(system->my_atoms[i]);
-      type_i = atom_i->type;
-      btop_i = End_Index( i, bonds );
-      sbp_i = &(system->reax_param.sbp[type_i]);
-
-      for( pj = start_i; pj < end_i; ++pj ) {
-        nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
-        j = nbr_pj->nbr;
-
-        if( workspace->bond_mark[j] >= 2 && nbr_pj->d <= control->bond_cut ) {
-          atom_j = &(system->my_atoms[j]);
-          type_j = atom_j->type;
-          sbp_j = &(system->reax_param.sbp[type_j]);
-          twbp = &(system->reax_param.tbp[type_i][type_j]);
-
-          if( BOp( workspace, bonds, control->bo_cut,
-                   i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
-            num_bonds += 2;
-            ++btop_i;
-
-            if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
-              workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
-            else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
-              workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
-
-            //fprintf( stdout, "%d%d - %d(%d) %d(%d) new\n",
-            // i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
-          }
-        }
-      }
-      Set_End_Index( i, btop_i, bonds );
-    }
-    }*/
-
   workspace->realloc.Htop = Htop;
   workspace->realloc.num_bonds = num_bonds;
   workspace->realloc.num_hbonds = num_hbonds;
 
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
-           system->my_rank, data->step, Htop, num_bonds, num_hbonds );
-  MPI_Barrier( comm );
-#endif
-#if defined( DEBUG )
-  Print_Bonds( system, bonds, "debugbonds.out" );
-  Print_Bond_List2( system, bonds, "pbonds.out" );
-  Print_Sparse_Matrix( system, H );
-  for( i = 0; i < H->n; ++i )
-    for( j = H->start[i]; j < H->end[i]; ++j )
-      fprintf( stderr, "%d %d %.15e\n",
-               MIN(system->my_atoms[i].orig_id,
-                   system->my_atoms[H->entries[j].j].orig_id),
-               MAX(system->my_atoms[i].orig_id,
-                   system->my_atoms[H->entries[j].j].orig_id),
-               H->entries[j].val );
-#endif
-
   Validate_Lists( system, workspace, lists, data->step,
                   system->n, system->N, system->numH, comm );
 }
@@ -562,7 +406,6 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
     workspace->bond_mark[i] = 0;
   for( i = system->n; i < system->N; ++i ) {
     workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
-    //workspace->done_after[i] = Start_Index( i, far_nbrs );
   }
 
   num_bonds = 0;
@@ -573,6 +416,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
   for( i = 0; i < system->N; ++i ) {
     atom_i = &(system->my_atoms[i]);
     type_i  = atom_i->type;
+    if (type_i < 0) continue;
     start_i = Start_Index(i, far_nbrs);
     end_i   = End_Index(i, far_nbrs);
     btop_i = End_Index( i, bonds );
@@ -623,6 +467,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
 
       if( flag ) {
         type_j = atom_j->type;
+	if (type_j < 0) continue;
         r_ij = nbr_pj->d;
         sbp_j = &(system->reax_param.sbp[type_j]);
         twbp = &(system->reax_param.tbp[type_i][type_j]);
@@ -651,8 +496,6 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
           }
         }
 
-
-        /* uncorrected bond orders */
         if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
             nbr_pj->d <= control->bond_cut &&
             BOp( workspace, bonds, control->bo_cut,
@@ -664,11 +507,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
             workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
           else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
             workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
-            //if( workspace->bond_mark[i] == 1000 )
-            //  workspace->done_after[i] = pj;
           }
-          //fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
-          //   i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
         }
       }
     }
@@ -678,27 +517,10 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
       Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
   }
 
-  /*for( i = system->n; i < system->N; ++i )
-    if( workspace->bond_mark[i] > 3 ) {
-      start_i = Start_Index(i, bonds);
-      end_i = End_Index(i, bonds);
-      num_bonds -= (end_i - start_i);
-      Set_End_Index(i, start_i, bonds );
-      }*/
 
   workspace->realloc.num_bonds = num_bonds;
   workspace->realloc.num_hbonds = num_hbonds;
 
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d @ step%d: num_bonds = %d num_hbonds = %d\n",
-           system->my_rank, data->step, num_bonds, num_hbonds );
-  MPI_Barrier( comm );
-#endif
-#if defined( DEBUG )
-  Print_Bonds( system, bonds, "debugbonds.out" );
-  Print_Bond_List2( system, bonds, "pbonds.out" );
-#endif
-
   Validate_Lists( system, workspace, lists, data->step,
                   system->n, system->N, system->numH, comm );
 }
@@ -736,6 +558,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
   for( i = 0; i < system->N; ++i ) {
     atom_i = &(system->my_atoms[i]);
     type_i  = atom_i->type;
+    if (type_i < 0) continue;
     start_i = Start_Index(i, far_nbrs);
     end_i   = End_Index(i, far_nbrs);
     sbp_i = &(system->reax_param.sbp[type_i]);
@@ -759,6 +582,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
 
       if(nbr_pj->d <= cutoff) {
         type_j = system->my_atoms[j].type;
+        if (type_j < 0) continue;
         r_ij = nbr_pj->d;
         sbp_j = &(system->reax_param.sbp[type_j]);
         twbp = &(system->reax_param.tbp[type_i][type_j]);
@@ -818,16 +642,9 @@ void Estimate_Storages( reax_system *system, control_params *control,
 
   for( i = 0; i < system->N; ++i ) {
     *num_3body += SQR(bond_top[i]);
-    //if( i < system->n )
     bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
-      //else bond_top[i] = MAX_BONDS;
   }
 
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d @ estimate storages: Htop = %d, num_3body = %d\n",
-           system->my_rank, *Htop, *num_3body );
-  MPI_Barrier( comm );
-#endif
 }
 
 
@@ -838,23 +655,9 @@ void Compute_Forces( reax_system *system, control_params *control,
 {
   MPI_Comm comm;
   int qeq_flag;
-#if defined(LOG_PERFORMANCE)
-  real t_start = 0;
-
-  //MPI_Barrier( mpi_data->world );
-  if( system->my_rank == MASTER_NODE )
-    t_start = Get_Time( );
-#endif
 
   comm = mpi_data->world;
-  /********* init forces ************/
-#if defined(PURE_REAX)
-  if( control->qeq_freq && (data->step-data->prev_steps)%control->qeq_freq==0 )
-    qeq_flag = 1;
-  else qeq_flag = 0;
-#elif defined(LAMMPS_REAX)
   qeq_flag = 0;
-#endif
 
   if( qeq_flag )
     Init_Forces( system, control, data, workspace, lists, out_control, comm );
@@ -862,79 +665,16 @@ void Compute_Forces( reax_system *system, control_params *control,
     Init_Forces_noQEq( system, control, data, workspace,
                        lists, out_control, comm );
 
-#if defined(LOG_PERFORMANCE)
-  //MPI_Barrier( mpi_data->world );
-  if( system->my_rank == MASTER_NODE )
-    Update_Timing_Info( &t_start, &(data->timing.init_forces) );
-#endif
-
 
   /********* bonded interactions ************/
   Compute_Bonded_Forces( system, control, data, workspace,
                          lists, out_control, mpi_data->world );
 
-#if defined(LOG_PERFORMANCE)
-  //MPI_Barrier( mpi_data->world );
-  if( system->my_rank == MASTER_NODE )
-    Update_Timing_Info( &t_start, &(data->timing.bonded) );
-#endif
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d @ step%d: completed bonded\n",
-           system->my_rank, data->step );
-  MPI_Barrier( mpi_data->world );
-#endif
-
-
-  /**************** qeq ************************/
-#if defined(PURE_REAX)
-  if( qeq_flag )
-    QEq( system, control, data, workspace, out_control, mpi_data );
-
-#if defined(LOG_PERFORMANCE)
-  //MPI_Barrier( mpi_data->world );
-  if( system->my_rank == MASTER_NODE )
-    Update_Timing_Info( &t_start, &(data->timing.qEq) );
-#endif
-#if defined(DEBUG_FOCUS)
-  fprintf(stderr, "p%d @ step%d: qeq completed\n", system->my_rank, data->step);
-  MPI_Barrier( mpi_data->world );
-#endif
-#endif //PURE_REAX
-
-
   /********* nonbonded interactions ************/
   Compute_NonBonded_Forces( system, control, data, workspace,
                             lists, out_control, mpi_data->world );
 
-#if defined(LOG_PERFORMANCE)
-  //MPI_Barrier( mpi_data->world );
-  if( system->my_rank == MASTER_NODE )
-    Update_Timing_Info( &t_start, &(data->timing.nonb) );
-#endif
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d @ step%d: nonbonded forces completed\n",
-           system->my_rank, data->step );
-  MPI_Barrier( mpi_data->world );
-#endif
-
-
   /*********** total force ***************/
   Compute_Total_Force( system, control, data, workspace, lists, mpi_data );
 
-#if defined(LOG_PERFORMANCE)
-  //MPI_Barrier( mpi_data->world );
-  if( system->my_rank == MASTER_NODE )
-    Update_Timing_Info( &t_start, &(data->timing.bonded) );
-#endif
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d @ step%d: total forces computed\n",
-           system->my_rank, data->step );
-  //Print_Total_Force( system, data, workspace );
-  MPI_Barrier( mpi_data->world );
-#endif
-
-#if defined(TEST_FORCES)
-  Print_Force_Files( system, control, data, workspace,
-                     lists, out_control, mpi_data );
-#endif
 }
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
index 12a929d3b8..b366872b7a 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
@@ -25,20 +25,11 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "hydrogen_bonds.h"
-#include "bond_orders.h"
-#include "list.h"
-#include "valence_angles.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_hydrogen_bonds.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"
 #include "reaxc_valence_angles.h"
 #include "reaxc_vector.h"
-#endif
-
 
 void Hydrogen_Bonds( reax_system *system, control_params *control,
                      simulation_data *data, storage *workspace,
@@ -55,7 +46,6 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
   real e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3;
   rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk;
   rvec dvec_jk, force, ext_press;
-  // rtensor temp_rtensor, total_rtensor;
   hbond_parameters *hbp;
   bond_order_data *bo_ij;
   bond_data *pbond_ij;
@@ -72,15 +62,9 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
   hbonds = (*lists) + HBONDS;
   hbond_list = hbonds->select.hbond_list;
 
-  /* loops below discover the Hydrogen bonds between i-j-k triplets.
-     here j is H atom and there has to be some bond between i and j.
-     Hydrogen bond is between j and k.
-     so in this function i->X, j->H, k->Z when we map
-     variables onto the ones in the handout.*/
   for( j = 0; j < system->n; ++j )
-    /* j has to be of type H */
+    if (system->my_atoms[j].type < 0) continue;
     if( system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1 ) {
-      /*set j's variables */
       type_j     = system->my_atoms[j].type;
       start_j    = Start_Index(j, bonds);
       end_j      = End_Index(j, bonds);
@@ -91,21 +75,20 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
       for( pi = start_j; pi < end_j; ++pi )  {
         pbond_ij = &( bond_list[pi] );
         i = pbond_ij->nbr;
-        bo_ij = &(pbond_ij->bo_data);
         type_i = system->my_atoms[i].type;
+	if (type_i < 0) continue;
+        bo_ij = &(pbond_ij->bo_data);
 
         if( system->reax_param.sbp[type_i].p_hbond == 2 &&
             bo_ij->BO >= HB_THRESHOLD )
           hblist[top++] = pi;
       }
 
-      // fprintf( stderr, "j: %d, top: %d, hb_start_j: %d, hb_end_j:%d\n",
-      //          j, top, hb_start_j, hb_end_j );
-
       for( pk = hb_start_j; pk < hb_end_j; ++pk ) {
         /* set k's varibles */
         k = hbond_list[pk].nbr;
         type_k = system->my_atoms[k].type;
+	if (type_k < 0) continue;
         nbr_jk = hbond_list[pk].ptr;
         r_jk = nbr_jk->d;
         rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
@@ -118,6 +101,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
           if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
             bo_ij = &(pbond_ij->bo_data);
             type_i = system->my_atoms[i].type;
+	    if (type_i < 0) continue;
             r_ij = pbond_ij->d;
             hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
             ++num_hb_intrs;
@@ -146,12 +130,6 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
             CEhb3 = -hbp->p_hb3 *
               (-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb;
 
-            /*fprintf( stdout,
-              "%6d%6d%6d%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f\n",
-              system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-              system->my_atoms[k].orig_id,
-              r_jk, theta, hbp->p_hb1, exp_hb2, hbp->p_hb3, hbp->r0_hb,
-              exp_hb3, sin_xhz4, e_hb ); */
 
             /* hydrogen bond forces */
             bo_ij->Cdbo += CEhb1; // dbo term
@@ -166,8 +144,6 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
               rvec_ScaledAdd( workspace->f[k], +CEhb3/r_jk, dvec_jk );
             }
             else {
-              /* for pressure coupling, terms that are not related to bond order
-                 derivatives are added directly into pressure vector/tensor */
               rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
               rvec_Add( workspace->f[i], force );
               rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
@@ -202,41 +178,8 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
 
               system->pair_ptr->ev_tally3(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj);
             }
-
-#ifdef TEST_ENERGY
-            /* fprintf( out_control->ehb,
-               "%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n",
-               dcos_theta_di[0], dcos_theta_di[1], dcos_theta_di[2],
-               dcos_theta_dj[0], dcos_theta_dj[1], dcos_theta_dj[2],
-               dcos_theta_dk[0], dcos_theta_dk[1], dcos_theta_dk[2]);
-               fprintf( out_control->ehb, "%24.15e%24.15e%24.15e\n",
-               CEhb1, CEhb2, CEhb3 ); */
-            fprintf( out_control->ehb,
-                     //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-                     "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
-                     system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-                     system->my_atoms[k].orig_id,
-                     r_jk, theta, bo_ij->BO, e_hb, data->my_en.e_hb );
-#endif
-#ifdef TEST_FORCES
-            Add_dBO( system, lists, j, pi, +CEhb1, workspace->f_hb ); //dbo term
-            // dcos terms
-            rvec_ScaledAdd( workspace->f_hb[i], +CEhb2, dcos_theta_di );
-            rvec_ScaledAdd( workspace->f_hb[j], +CEhb2, dcos_theta_dj );
-            rvec_ScaledAdd( workspace->f_hb[k], +CEhb2, dcos_theta_dk );
-            // dr terms
-            rvec_ScaledAdd( workspace->f_hb[j], -CEhb3/r_jk, dvec_jk );
-            rvec_ScaledAdd( workspace->f_hb[k], +CEhb3/r_jk, dvec_jk );
-#endif
           }
         }
       }
     }
-
-#if defined(DEBUG)
-  fprintf( stderr, "Number of hydrogen bonds: %d\n", num_hb_intrs );
-  fprintf( stderr, "Hydrogen Bond Energy: %g\n", data->my_en.e_hb );
-  fprintf( stderr, "hydbonds: ext_press (%24.15e %24.15e %24.15e)\n",
-           data->ext_press[0], data->ext_press[1], data->ext_press[2] );
-#endif
 }
diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp
index 0b21bdcab1..df1a857028 100644
--- a/src/USER-REAXC/reaxc_init_md.cpp
+++ b/src/USER-REAXC/reaxc_init_md.cpp
@@ -25,24 +25,6 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "init_md.h"
-#include "allocate.h"
-#include "box.h"
-#include "comm_tools.h"
-#include "forces.h"
-#include "grid.h"
-#include "integrate.h"
-#include "io_tools.h"
-#include "list.h"
-#include "lookup.h"
-#include "neighbors.h"
-#include "random.h"
-#include "reset_tools.h"
-#include "system_props.h"
-#include "tool_box.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_init_md.h"
 #include "reaxc_allocate.h"
 #include "reaxc_forces.h"
@@ -53,228 +35,7 @@
 #include "reaxc_system_props.h"
 #include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
-#endif
 
-
-#if defined(PURE_REAX)
-/************************ initialize system ************************/
-int Reposition_Atoms( reax_system *system, control_params *control,
-                      simulation_data *data, mpi_datatypes *mpi_data,
-                      char *msg )
-{
-  int   i;
-  rvec  dx;
-
-  /* reposition atoms */
-  if( control->reposition_atoms == 0 ) { //fit atoms to periodic box
-    rvec_MakeZero( dx );
-  }
-  else if( control->reposition_atoms == 1 ) { //put center of mass to center
-    rvec_Scale( dx, 0.5, system->big_box.box_norms );
-    rvec_ScaledAdd( dx, -1., data->xcm );
-  }
-  else if( control->reposition_atoms == 2 ) { //put center of mass to origin
-    rvec_Scale( dx, -1., data->xcm );
-  }
-  else {
-    strcpy( msg, "reposition_atoms: invalid option" );
-    return FAILURE;
-  }
-
-  for( i = 0; i < system->n; ++i )
-    // Inc_on_T3_Gen( system->my_atoms[i].x, dx, &(system->big_box) );
-    rvec_Add( system->my_atoms[i].x, dx );
-
-  return SUCCESS;
-}
-
-
-
-void Generate_Initial_Velocities( reax_system *system, real T )
-{
-  int i;
-  real m, scale, norm;
-
-
-  if( T <= 0.1 ) {
-    for( i = 0; i < system->n; i++ )
-      rvec_MakeZero( system->my_atoms[i].v );
-  }
-  else {
-    Randomize();
-
-    for( i = 0; i < system->n; i++ ) {
-      rvec_Random( system->my_atoms[i].v );
-
-      norm = rvec_Norm_Sqr( system->my_atoms[i].v );
-      m = system->reax_param.sbp[ system->my_atoms[i].type ].mass;
-      scale = sqrt( m * norm / (3.0 * K_B * T) );
-
-      rvec_Scale( system->my_atoms[i].v, 1./scale, system->my_atoms[i].v );
-
-      // fprintf( stderr, "v = %f %f %f\n",
-      // system->my_atoms[i].v[0],
-      // system->my_atoms[i].v[1],
-      // system->my_atoms[i].v[2] );
-
-      // fprintf( stderr, "scale = %f\n", scale );
-      // fprintf( stderr, "v = %f %f %f\n",
-      // system->my_atoms[i].v[0],
-      // system->my_atoms[i].v[1],
-      // system->my_atoms[i].v[2] );
-    }
-  }
-}
-
-
-int Init_System( reax_system *system, control_params *control,
-                 simulation_data *data, storage *workspace,
-                 mpi_datatypes *mpi_data, char *msg )
-{
-  int i;
-  reax_atom *atom;
-  int nrecv[MAX_NBRS];
-
-  Setup_New_Grid( system, control, mpi_data->world );
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d GRID:\n", system->my_rank );
-  Print_Grid( &(system->my_grid), stderr );
-#endif
-  Bin_My_Atoms( system, &(workspace->realloc) );
-  Reorder_My_Atoms( system, workspace );
-
-  /* estimate N and total capacity */
-  for( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = 0;
-  system->max_recved = 0;
-  system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
-                        Estimate_Boundary_Atoms, Unpack_Estimate_Message, 1 );
-  system->total_cap = MAX( (int)(system->N * SAFE_ZONE), MIN_CAP );
-  Bin_Boundary_Atoms( system );
-
-  /* estimate numH and Hcap */
-  system->numH = 0;
-  if( control->hbond_cut > 0 )
-    for( i = 0; i < system->n; ++i ) {
-      atom = &(system->my_atoms[i]);
-      if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
-        atom->Hindex = system->numH++;
-      else atom->Hindex = -1;
-    }
-  system->Hcap = MAX( system->numH * SAFER_ZONE, MIN_CAP );
-
-  //Allocate_System( system, system->local_cap, system->total_cap, msg );
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: n=%d local_cap=%d\n",
-           system->my_rank, system->n, system->local_cap );
-  fprintf( stderr, "p%d: N=%d total_cap=%d\n",
-           system->my_rank, system->N, system->total_cap );
-  fprintf( stderr, "p%d: numH=%d H_cap=%d\n",
-           system->my_rank, system->numH, system->Hcap );
-#endif
-
-  // if( Reposition_Atoms( system, control, data, mpi_data, msg ) == FAILURE )
-  //   return FAILURE;
-
-  /* initialize velocities so that desired init T can be attained */
-  if( !control->restart || (control->restart && control->random_vel) )
-    Generate_Initial_Velocities( system, control->T_init );
-
-  return SUCCESS;
-}
-
-
-/************************ initialize simulation data ************************/
-int Init_Simulation_Data( reax_system *system, control_params *control,
-                          simulation_data *data, mpi_datatypes *mpi_data,
-                          char *msg )
-{
-  Reset_Simulation_Data( data, control->virial );
-
-  if( !control->restart )
-    data->step = data->prev_steps = 0;
-
-  Compute_Total_Mass( system, data, mpi_data->comm_mesh3D );
-  Compute_Center_of_Mass( system, data, mpi_data, mpi_data->comm_mesh3D );
-  Compute_Kinetic_Energy( system, data, mpi_data->comm_mesh3D );
-
-  switch( control->ensemble ){
-  case NVE:
-    data->N_f = 3 * system->bigN;
-    Evolve = Velocity_Verlet_NVE;
-    break;
-
-  case bNVT:
-    data->N_f = 3 * system->bigN + 1;
-    Evolve = Velocity_Verlet_Berendsen_NVT;
-    break;
-
-  case nhNVT:
-    fprintf( stderr, "WARNING: Nose-Hoover NVT is still under testing.\n" );
-    //return FAILURE;
-    data->N_f = 3 * system->bigN + 1;
-    Evolve = Velocity_Verlet_Nose_Hoover_NVT_Klein;
-    if( !control->restart || (control->restart && control->random_vel) ) {
-      data->therm.G_xi = control->Tau_T *
-        (2.0 * data->sys_en.e_kin - data->N_f * K_B * control->T );
-      data->therm.v_xi = data->therm.G_xi * control->dt;
-      data->therm.v_xi_old = 0;
-      data->therm.xi = 0;
-    }
-    break;
-
-  case sNPT: /* Semi-Isotropic NPT */
-    data->N_f = 3 * system->bigN + 4;
-    Evolve = Velocity_Verlet_Berendsen_NPT;
-    if( !control->restart )
-      Reset_Pressures( data );
-    break;
-
-  case iNPT: /* Isotropic NPT */
-    data->N_f = 3 * system->bigN + 2;
-    Evolve = Velocity_Verlet_Berendsen_NPT;
-    if( !control->restart )
-      Reset_Pressures( data );
-    break;
-
-  case NPT: /* Anisotropic NPT */
-    strcpy( msg, "init_simulation_data: option not yet implemented" );
-    return FAILURE;
-
-    data->N_f = 3 * system->bigN + 9;
-    Evolve = Velocity_Verlet_Berendsen_NPT;
-    /*if( !control->restart ) {
-      data->therm.G_xi = control->Tau_T *
-      (2.0 * data->my_en.e_Kin - data->N_f * K_B * control->T );
-      data->therm.v_xi = data->therm.G_xi * control->dt;
-      data->iso_bar.eps = 0.33333 * log(system->box.volume);
-      data->inv_W = 1.0 /
-      ( data->N_f * K_B * control->T * SQR(control->Tau_P) );
-      Compute_Pressure( system, control, data, out_control );
-      }*/
-    break;
-
-  default:
-    strcpy( msg, "init_simulation_data: ensemble not recognized" );
-    return FAILURE;
-  }
-
-  /* initialize the timer(s) */
-  MPI_Barrier( mpi_data->world );  // wait for everyone to come here
-  if( system->my_rank == MASTER_NODE ) {
-    data->timing.start = Get_Time( );
-#if defined(LOG_PERFORMANCE)
-    Reset_Timing( &data->timing );
-#endif
-  }
-
-
-#if defined(DEBUG)
-      fprintf( stderr, "data->N_f: %8.3f\n", data->N_f );
-#endif
-  return SUCCESS;
-}
-
-#elif defined(LAMMPS_REAX)
 int Init_System( reax_system *system, control_params *control, char *msg )
 {
   int i;
@@ -294,21 +55,13 @@ int Init_System( reax_system *system, control_params *control, char *msg )
   if( control->hbond_cut > 0 )
     for( i = 0; i < system->n; ++i ) {
       atom = &(system->my_atoms[i]);
+      if (atom->type < 0) continue;
       if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
         atom->Hindex = system->numH++;
       else atom->Hindex = -1;
     }
   system->Hcap = (int)(MAX( system->numH * saferzone, mincap ));
 
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: n=%d local_cap=%d\n",
-           system->my_rank, system->n, system->local_cap );
-  fprintf( stderr, "p%d: N=%d total_cap=%d\n",
-           system->my_rank, system->N, system->total_cap );
-  fprintf( stderr, "p%d: numH=%d H_cap=%d\n",
-           system->my_rank, system->numH, system->Hcap );
-#endif
-
   return SUCCESS;
 }
 
@@ -321,22 +74,13 @@ int Init_Simulation_Data( reax_system *system, control_params *control,
   /* initialize the timer(s) */
   if( system->my_rank == MASTER_NODE ) {
     data->timing.start = Get_Time( );
-#if defined(LOG_PERFORMANCE)
-    Reset_Timing( &data->timing );
-#endif
   }
 
-  //if( !control->restart )
   data->step = data->prev_steps = 0;
 
   return SUCCESS;
 }
-#endif
 
-
-
-/************************ initialize workspace ************************/
-/* Initialize Taper params */
 void Init_Taper( control_params *control,  storage *workspace, MPI_Comm comm )
 {
   real d1, d7;
@@ -399,241 +143,14 @@ int Init_Workspace( reax_system *system, control_params *control,
 int Init_MPI_Datatypes( reax_system *system, storage *workspace,
                         mpi_datatypes *mpi_data, MPI_Comm comm, char *msg )
 {
-#if defined(PURE_REAX)
-  int           i, block[11];
-  MPI_Aint      base, disp[11];
-  MPI_Datatype  type[11];
-  mpi_atom      sample;
-  boundary_atom b_sample;
-  restart_atom  r_sample;
-  rvec          rvec_sample;
-  rvec2         rvec2_sample;
-#endif
 
   /* setup the world */
   mpi_data->world = comm;
   MPI_Comm_size( comm, &(system->wsize) );
 
-#if defined(PURE_REAX)
-  /* init mpi buffers  */
-  mpi_data->in1_buffer = NULL;
-  mpi_data->in2_buffer = NULL;
-
-  /* mpi_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, name,
-                 x, v, f_old, s, t] */
-  block[0] = block[1] = block[2] = block[3] = block[4] = 1;
-  block[5] = 8;
-  block[6] = block[7] = block[8] = 3;
-  block[9] = block[10] = 4;
-
-  MPI_Address( &(sample.orig_id),    disp + 0 );
-  MPI_Address( &(sample.imprt_id),   disp + 1 );
-  MPI_Address( &(sample.type),       disp + 2 );
-  MPI_Address( &(sample.num_bonds),  disp + 3 );
-  MPI_Address( &(sample.num_hbonds), disp + 4 );
-  MPI_Address( &(sample.name),       disp + 5 );
-  MPI_Address( &(sample.x[0]),       disp + 6 );
-  MPI_Address( &(sample.v[0]),       disp + 7 );
-  MPI_Address( &(sample.f_old[0]),   disp + 8 );
-  MPI_Address( &(sample.s[0]),       disp + 9 );
-  MPI_Address( &(sample.t[0]),       disp + 10 );
-
-  base = (MPI_Aint)(&(sample));
-  for( i = 0; i < 11; ++i ) disp[i] -= base;
-
-  type[0] = type[1] = type[2] = type[3] = type[4] = MPI_INT;
-  type[5] = MPI_CHAR;
-  type[6] = type[7] = type[8] = type[9] = type[10] = MPI_DOUBLE;
-
-  MPI_Type_struct( 11, block, disp, type, &(mpi_data->mpi_atom_type) );
-  MPI_Type_commit( &(mpi_data->mpi_atom_type) );
-
-  /* boundary_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, x] */
-  block[0] = block[1] = block[2] = block[3] = block[4] = 1;
-  block[5] = 3;
-
-  MPI_Address( &(b_sample.orig_id),    disp + 0 );
-  MPI_Address( &(b_sample.imprt_id),   disp + 1 );
-  MPI_Address( &(b_sample.type),       disp + 2 );
-  MPI_Address( &(b_sample.num_bonds),  disp + 3 );
-  MPI_Address( &(b_sample.num_hbonds), disp + 4 );
-  MPI_Address( &(b_sample.x[0]),       disp + 5 );
-
-  base = (MPI_Aint)(&(b_sample));
-  for( i = 0; i < 6; ++i ) disp[i] -= base;
-
-  type[0] = type[1] = type[2] = type[3] = type[4] = MPI_INT;
-  type[5] = MPI_DOUBLE;
-
-  MPI_Type_struct( 6, block, disp, type, &(mpi_data->boundary_atom_type) );
-  MPI_Type_commit( &(mpi_data->boundary_atom_type) );
-
-  /* mpi_rvec */
-  block[0] = 3;
-  MPI_Address( &(rvec_sample[0]), disp + 0 );
-  base = disp[0];
-  for( i = 0; i < 1; ++i ) disp[i] -= base;
-  type[0] = MPI_DOUBLE;
-  MPI_Type_struct( 1, block, disp, type, &(mpi_data->mpi_rvec) );
-  MPI_Type_commit( &(mpi_data->mpi_rvec) );
-
-  /* mpi_rvec2 */
-  block[0] = 2;
-  MPI_Address( &(rvec2_sample[0]), disp + 0 );
-  base = disp[0];
-  for( i = 0; i < 1; ++i ) disp[i] -= base;
-  type[0] = MPI_DOUBLE;
-  MPI_Type_struct( 1, block, disp, type, &(mpi_data->mpi_rvec2) );
-  MPI_Type_commit( &(mpi_data->mpi_rvec2) );
-
-  /* restart_atom - [orig_id, type, name[8], x, v] */
-  block[0] = block[1] = 1 ;
-  block[2] = 8;
-  block[3] = block[4] = 3;
-
-  MPI_Address( &(r_sample.orig_id),    disp + 0 );
-  MPI_Address( &(r_sample.type),       disp + 1 );
-  MPI_Address( &(r_sample.name),       disp + 2 );
-  MPI_Address( &(r_sample.x[0]),       disp + 3 );
-  MPI_Address( &(r_sample.v[0]),       disp + 4 );
-
-  base = (MPI_Aint)(&(r_sample));
-  for( i = 0; i < 5; ++i ) disp[i] -= base;
-
-  type[0] = type[1] = MPI_INT;
-  type[2] = MPI_CHAR;
-  type[3] = type[4] = MPI_DOUBLE;
-
-  MPI_Type_struct( 5, block, disp, type, &(mpi_data->restart_atom_type) );
-  MPI_Type_commit( &(mpi_data->restart_atom_type) );
-#endif
-
   return SUCCESS;
 }
 
-
-/********************** allocate lists *************************/
-#if defined(PURE_REAX)
-int  Init_Lists( reax_system *system, control_params *control,
-                 simulation_data *data, storage *workspace, reax_list **lists,
-                 mpi_datatypes *mpi_data, char *msg )
-{
-  int i, num_nbrs;
-  int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
-  int *hb_top, *bond_top;
-  MPI_Comm comm;
-
-  comm = mpi_data->world;
-  //for( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = system->my_nbrs[i].est_recv;
-  //system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
-  //                Sort_Boundary_Atoms, Unpack_Exchange_Message, 1 );
-  num_nbrs = Estimate_NumNeighbors( system, lists );
-  if(!Make_List( system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
-                 *lists+FAR_NBRS, comm )){
-    fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
-    MPI_Abort( comm, INSUFFICIENT_MEMORY );
-  }
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: allocated far_nbrs: num_far=%d, space=%dMB\n",
-           system->my_rank, num_nbrs,
-           (int)(num_nbrs*sizeof(far_neighbor_data)/(1024*1024)) );
-#endif
-
-  Generate_Neighbor_Lists( system, data, workspace, lists );
-  bond_top = (int*) calloc( system->total_cap, sizeof(int) );
-  hb_top = (int*) calloc( system->local_cap, sizeof(int) );
-  Estimate_Storages( system, control, lists,
-                     &Htop, hb_top, bond_top, &num_3body, comm );
-
-  Allocate_Matrix( &(workspace->H), system->local_cap, Htop, comm );
-  workspace->L = NULL;
-  workspace->U = NULL;
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: allocated H matrix: Htop=%d, space=%dMB\n",
-           system->my_rank, Htop,
-           (int)(Htop * sizeof(sparse_matrix_entry) / (1024*1024)) );
-#endif
-
-  if( control->hbond_cut > 0 ) {
-    /* init H indexes */
-    total_hbonds = 0;
-    for( i = 0; i < system->n; ++i ) {
-      system->my_atoms[i].num_hbonds = hb_top[i];
-      total_hbonds += hb_top[i];
-    }
-    total_hbonds = MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS );
-
-    if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
-                    *lists+HBONDS, comm ) ) {
-      fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
-      MPI_Abort( comm, INSUFFICIENT_MEMORY );
-    }
-#if defined(DEBUG_FOCUS)
-    fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
-             system->my_rank, total_hbonds,
-             (int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
-#endif
-  }
-
-  /* bonds list */
-  //Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
-  //num_bonds = bond_top[system->N-1];
-  total_bonds = 0;
-  for( i = 0; i < system->N; ++i ) {
-    system->my_atoms[i].num_bonds = bond_top[i];
-    total_bonds += bond_top[i];
-  }
-  bond_cap = MAX( total_bonds*SAFE_ZONE, MIN_CAP*MIN_BONDS );
-
-  if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
-                  *lists+BONDS, comm ) ) {
-    fprintf( stderr, "not enough space for bonds list. terminating!\n" );
-    MPI_Abort( comm, INSUFFICIENT_MEMORY );
-  }
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
-           system->my_rank, bond_cap,
-           (int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
-#endif
-
-  /* 3bodies list */
-  cap_3body = MAX( num_3body*SAFE_ZONE, MIN_3BODIES );
-  if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
-                  *lists+THREE_BODIES, comm ) ){
-    fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
-    MPI_Abort( comm, INSUFFICIENT_MEMORY );
-  }
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
-           system->my_rank, cap_3body,
-           (int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
-#endif
-
-#if defined(TEST_FORCES)
-  if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
-                  *lists+DDELTAS, comm ) ) {
-    fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
-    MPI_Abort( comm, INSUFFICIENT_MEMORY );
-  }
-  fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
-           system->my_rank, bond_cap*30,
-           bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
-
-  if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, *lists+DBOS, comm ) ) {
-    fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
-    MPI_Abort( comm, INSUFFICIENT_MEMORY );
-  }
-  fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
-           system->my_rank, bond_cap*MAX_BONDS*3,
-           bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
-#endif
-
-  free( hb_top );
-  free( bond_top );
-
-  return SUCCESS;
-}
-#elif defined(LAMMPS_REAX)
 int  Init_Lists( reax_system *system, control_params *control,
                  simulation_data *data, storage *workspace, reax_list **lists,
                  mpi_datatypes *mpi_data, char *msg )
@@ -668,16 +185,8 @@ int  Init_Lists( reax_system *system, control_params *control,
       fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
       MPI_Abort( comm, INSUFFICIENT_MEMORY );
     }
-#if defined(DEBUG_FOCUS)
-    fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
-             system->my_rank, total_hbonds,
-             (int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
-#endif
   }
 
-  /* bonds list */
-  //Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
-  //num_bonds = bond_top[system->N-1];
   total_bonds = 0;
   for( i = 0; i < system->N; ++i ) {
     system->my_atoms[i].num_bonds = bond_top[i];
@@ -690,11 +199,6 @@ int  Init_Lists( reax_system *system, control_params *control,
     fprintf( stderr, "not enough space for bonds list. terminating!\n" );
     MPI_Abort( comm, INSUFFICIENT_MEMORY );
   }
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
-           system->my_rank, bond_cap,
-           (int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
-#endif
 
   /* 3bodies list */
   cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES ));
@@ -703,136 +207,13 @@ int  Init_Lists( reax_system *system, control_params *control,
     fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
     MPI_Abort( comm, INSUFFICIENT_MEMORY );
   }
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
-           system->my_rank, cap_3body,
-           (int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
-#endif
-
-#if defined(TEST_FORCES)
-  if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
-                  *lists+DDELTAS, comm ) ) {
-    fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
-    MPI_Abort( comm, INSUFFICIENT_MEMORY );
-  }
-  fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
-           system->my_rank, bond_cap*30,
-           bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
-
-  if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, (*lists)+DBOS, comm ) ) {
-    fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
-    MPI_Abort( comm, INSUFFICIENT_MEMORY );
-  }
-  fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
-           system->my_rank, bond_cap*MAX_BONDS*3,
-           bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
-#endif
 
   free( hb_top );
   free( bond_top );
 
   return SUCCESS;
 }
-#endif
 
-
-
-#if defined(PURE_REAX)
-void Initialize( reax_system *system, control_params *control,
-                 simulation_data *data, storage *workspace,
-                 reax_list **lists, output_controls *out_control,
-                 mpi_datatypes *mpi_data )
-{
-  char msg[MAX_STR];
-
-  if( Init_MPI_Datatypes( system, workspace, mpi_data, MPI_COMM_WORLD, msg ) ==
-      FAILURE ) {
-    fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
-             system->my_rank );
-    fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
-             system->my_rank );
-    MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
-  }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
-#endif
-
-  if( Init_System(system, control, data, workspace, mpi_data, msg) == FAILURE ){
-    fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
-    fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
-             system->my_rank );
-    MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
-  }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: system initialized\n", system->my_rank );
-#endif
-
-  if( Init_Simulation_Data(system, control, data, mpi_data, msg) == FAILURE ) {
-    fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
-    fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n",
-             system->my_rank );
-    MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
-  }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
-#endif
-
-  if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
-      FAILURE ) {
-    fprintf( stderr, "p%d:init_workspace: not enough memory\n",
-             system->my_rank );
-    fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n",
-             system->my_rank );
-    MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
-  }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
-#endif
-
-  if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
-      FAILURE ) {
-      fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
-      fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
-               system->my_rank );
-      MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
-    }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized lists\n", system->my_rank );
-#endif
-
-  if(Init_Output_Files(system,control,out_control,mpi_data,msg) == FAILURE) {
-    fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
-    fprintf( stderr, "p%d: could not open output files! terminating...\n",
-             system->my_rank );
-    MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
-  }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: output files opened\n", system->my_rank );
-#endif
-
-  if( control->tabulate ) {
-    if( Init_Lookup_Tables(system,control,workspace,mpi_data,msg) == FAILURE ) {
-      fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
-      fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
-               system->my_rank );
-      MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
-    }
-#if defined(DEBUG)
-    fprintf( stderr, "p%d: initialized lookup tables\n", system->my_rank );
-#endif
-  }
-
-  Init_Force_Functions( control );
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized force functions\n", system->my_rank );
-#endif
-  /*#ifdef TEST_FORCES
-    Init_Force_Test_Functions();
-    fprintf(stderr,"p%d: initialized force test functions\n",system->my_rank);
-    #endif */
-}
-
-#elif defined(LAMMPS_REAX)
 void Initialize( reax_system *system, control_params *control,
                  simulation_data *data, storage *workspace,
                  reax_list **lists, output_controls *out_control,
@@ -848,9 +229,6 @@ void Initialize( reax_system *system, control_params *control,
              system->my_rank );
     MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
   }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
-#endif
 
   if( Init_System(system, control, msg) == FAILURE ){
     fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
@@ -858,9 +236,6 @@ void Initialize( reax_system *system, control_params *control,
              system->my_rank );
     MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
   }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: system initialized\n", system->my_rank );
-#endif
 
   if( Init_Simulation_Data( system, control, data, msg ) == FAILURE ) {
     fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
@@ -868,9 +243,6 @@ void Initialize( reax_system *system, control_params *control,
              system->my_rank );
     MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
   }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
-#endif
 
   if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
       FAILURE ) {
@@ -880,9 +252,6 @@ void Initialize( reax_system *system, control_params *control,
              system->my_rank );
     MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
   }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
-#endif
 
   if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
       FAILURE ) {
@@ -891,9 +260,6 @@ void Initialize( reax_system *system, control_params *control,
                system->my_rank );
       MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
     }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized lists\n", system->my_rank );
-#endif
 
   if( Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) {
     fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
@@ -901,9 +267,6 @@ void Initialize( reax_system *system, control_params *control,
              system->my_rank );
     MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
   }
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: output files opened\n", system->my_rank );
-#endif
 
   if( control->tabulate ) {
     if( Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE ) {
@@ -912,19 +275,8 @@ void Initialize( reax_system *system, control_params *control,
                system->my_rank );
       MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
     }
-#if defined(DEBUG)
-    fprintf( stderr, "p%d: initialized lookup tables\n", system->my_rank );
-#endif
   }
 
 
   Init_Force_Functions( control );
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: initialized force functions\n", system->my_rank );
-#endif
-  /*#if defined(TEST_FORCES)
-    Init_Force_Test_Functions();
-    fprintf(stderr,"p%d: initialized force test functions\n",system->my_rank);
-  #endif*/
 }
-#endif
diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h
index ddaf587a4f..25333c744f 100644
--- a/src/USER-REAXC/reaxc_init_md.h
+++ b/src/USER-REAXC/reaxc_init_md.h
@@ -29,12 +29,6 @@
 
 #include "reaxc_types.h"
 
-#if defined(PURE_REAX)
-void Initialize( reax_system*, control_params*, simulation_data*,
-                 storage*, reax_list**, output_controls*, mpi_datatypes* );
-#elif defined(LAMMPS_REAX)
 void Initialize( reax_system*, control_params*, simulation_data*, storage*,
                  reax_list**, output_controls*, mpi_datatypes*, MPI_Comm );
 #endif
-
-#endif
diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp
index 841a779254..9645234bd4 100644
--- a/src/USER-REAXC/reaxc_io_tools.cpp
+++ b/src/USER-REAXC/reaxc_io_tools.cpp
@@ -26,16 +26,6 @@
 
 #include "pair_reax_c.h"
 #include "update.h"
-#if defined(PURE_REAX)
-#include "io_tools.h"
-#include "basic_comm.h"
-#include "list.h"
-#include "reset_tools.h"
-#include "system_props.h"
-#include "tool_box.h"
-#include "traj.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_io_tools.h"
 #include "reaxc_basic_comm.h"
 #include "reaxc_list.h"
@@ -44,11 +34,9 @@
 #include "reaxc_tool_box.h"
 #include "reaxc_traj.h"
 #include "reaxc_vector.h"
-#endif
 
 print_interaction Print_Interactions[NUM_INTRS];
 
-/************************ initialize output controls ************************/
 int Init_Output_Files( reax_system *system, control_params *control,
                        output_controls *out_control, mpi_datatypes *mpi_data,
                        char *msg )
@@ -65,43 +53,10 @@ int Init_Output_Files( reax_system *system, control_params *control,
   if( system->my_rank == MASTER_NODE ) {
     /* These files are written only by the master node */
     if( out_control->energy_update_freq > 0 ) {
-#if defined(PURE_REAX)
-      /* init out file */
-      sprintf( temp, "%s.out", control->sim_name );
-      if( (out_control->out = fopen( temp, "w" )) != NULL ) {
-#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
-        fprintf( out_control->out, "%-6s%14s%14s%14s%11s%13s%13s\n",
-                 "step", "total energy", "potential", "kinetic",
-                 "T(K)", "V(A^3)", "P(Gpa)" );
-#else
-        fprintf( out_control->out, "%-6s%24s%24s%24s%13s%16s%13s\n",
-                 "step", "total energy", "potential", "kinetic",
-                 "T(K)", "V(A^3)", "P(GPa)" );
-#endif
-        fflush( out_control->out );
-      }
-      else {
-        strcpy( msg, "init_out_controls: .out file could not be opened\n" );
-        return FAILURE;
-      }
-#endif
 
       /* init potentials file */
       sprintf( temp, "%s.pot", control->sim_name );
       if( (out_control->pot = fopen( temp, "w" )) != NULL ) {
-#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
-        fprintf( out_control->pot,
-                 "%-6s%14s%14s%14s%14s%14s%14s%14s%14s%14s%14s%14s\n",
-                 "step", "ebond", "eatom", "elp",
-                 "eang", "ecoa", "ehb", "etor", "econj",
-                 "evdw","ecoul", "epol" );
-#else
-        fprintf( out_control->pot,
-                 "%-6s%24s%24s%24s%24s%24s%24s%24s%24s%24s%24s%24s\n",
-                 "step", "ebond", "eatom", "elp",
-                 "eang", "ecoa", "ehb", "etor", "econj",
-                 "evdw","ecoul", "epol" );
-#endif
         fflush( out_control->pot );
       }
       else {
@@ -110,19 +65,6 @@ int Init_Output_Files( reax_system *system, control_params *control,
       }
 
       /* init log file */
-#if defined(LOG_PERFORMANCE)
-      sprintf( temp, "%s.log", control->sim_name );
-      if( (out_control->log = fopen( temp, "w" )) != NULL ) {
-        fprintf( out_control->log, "%6s%8s%8s%8s%8s%8s%8s%8s%8s\n",
-                 "step", "total", "comm", "nbrs", "init", "bonded", "nonb",
-                 "qeq", "matvecs" );
-        fflush( out_control->log );
-      }
-      else {
-        strcpy( msg, "init_out_controls: .log file could not be opened\n" );
-        return FAILURE;
-      }
-#endif
     }
 
     /* init pressure file */
@@ -141,285 +83,8 @@ int Init_Output_Files( reax_system *system, control_params *control,
         return FAILURE;
       }
     }
-
-    /* init electric dipole moment analysis file */
-    // not yet implemented in the parallel version!!!
-    // if( control->dipole_anal ) {
-    //   sprintf( temp, "%s.dpl", control->sim_name );
-    //   if( (out_control->dpl = fopen( temp, "w" )) != NULL ) {
-    //         fprintf( out_control->dpl, "%6s%20s%30s",
-    //                  "step", "molecule count", "avg dipole moment norm" );
-    //         fflush( out_control->dpl );
-    //   }
-    //   else {
-    //         strcpy(msg, "init_out_controls: .dpl file couldn't be opened\n");
-    //         return FAILURE;
-    //   }
-    // }
-
-    /* init diffusion coef analysis file */
-    // not yet implemented in the parallel version!!!
-    // if( control->diffusion_coef ) {
-    //   sprintf( temp, "%s.drft", control->sim_name );
-    //   if( (out_control->drft = fopen( temp, "w" )) != NULL ) {
-    //         fprintf( out_control->drft, "%7s%20s%20s\n",
-    //                  "step", "type count", "avg disp^2" );
-    //         fflush( out_control->drft );
-    //   }
-    //   else {
-    //         strcpy(msg,"init_out_controls: .drft file couldn't be opened\n");
-    //         return FAILURE;
-    //   }
-    // }
   }
 
-
-  /* init molecular analysis file */
-  /* proc0 opens this file and shares it with everyone.
-     then all processors write into it in a round-robin
-     fashion controlled by their rank */
-  /*if( control->molecular_analysis ) {
-    if( system->my_rank == MASTER_NODE ) {
-      sprintf( temp, "%s.mol", control->sim_name );
-      if( (out_control->mol = fopen( temp, "w" )) == NULL ) {
-        strcpy(msg,"init_out_controls: .mol file could not be opened\n");
-        return FAILURE;
-      }
-    }
-
-    MPI_Bcast( &(out_control->mol), 1, MPI_LONG, 0, MPI_COMM_WORLD );
-    }*/
-
-
-#ifdef TEST_ENERGY
-  /* open bond energy file */
-  sprintf( temp, "%s.ebond.%d", control->sim_name, system->my_rank );
-  if( (out_control->ebond = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .ebond file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open lone-pair energy file */
-  sprintf( temp, "%s.elp.%d", control->sim_name, system->my_rank );
-  if( (out_control->elp = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .elp file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open overcoordination energy file */
-  sprintf( temp, "%s.eov.%d", control->sim_name, system->my_rank );
-  if( (out_control->eov = fopen( temp, "w" )) == NULL )        {
-    strcpy(msg,"Init_Out_Files: .eov file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open undercoordination energy file */
-  sprintf( temp, "%s.eun.%d", control->sim_name, system->my_rank );
-  if( (out_control->eun = fopen( temp, "w" )) == NULL )        {
-    strcpy(msg,"Init_Out_Files: .eun file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open angle energy file */
-  sprintf( temp, "%s.eval.%d", control->sim_name, system->my_rank );
-  if( (out_control->eval = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .eval file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open coalition energy file */
-  sprintf( temp, "%s.ecoa.%d", control->sim_name, system->my_rank );
-  if( (out_control->ecoa = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .ecoa file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open penalty energy file */
-  sprintf( temp, "%s.epen.%d", control->sim_name, system->my_rank );
-  if( (out_control->epen = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .epen file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open torsion energy file */
-  sprintf( temp, "%s.etor.%d", control->sim_name, system->my_rank );
-  if( (out_control->etor = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .etor file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open conjugation energy file */
-  sprintf( temp, "%s.econ.%d", control->sim_name, system->my_rank );
-  if( (out_control->econ = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .econ file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open hydrogen bond energy file */
-  sprintf( temp, "%s.ehb.%d", control->sim_name, system->my_rank );
-  if( (out_control->ehb = fopen( temp, "w" )) == NULL )        {
-    strcpy(msg,"Init_Out_Files: .ehb file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open vdWaals energy file */
-  sprintf( temp, "%s.evdw.%d", control->sim_name, system->my_rank );
-  if( (out_control->evdw = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .evdw file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open coulomb energy file */
-  sprintf( temp, "%s.ecou.%d", control->sim_name, system->my_rank );
-  if( (out_control->ecou = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .ecou file couldn't be opened\n");
-    return FAILURE;
-  }
-#endif
-
-
-#ifdef TEST_FORCES
-  /* open bond orders file */
-  sprintf( temp, "%s.fbo.%d", control->sim_name, system->my_rank );
-  if( (out_control->fbo = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .fbo file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open bond orders derivatives file */
-  sprintf( temp, "%s.fdbo.%d", control->sim_name, system->my_rank );
-  if( (out_control->fdbo = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .fdbo file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* produce a single force file - to be written by p0 */
-  if( system->my_rank == MASTER_NODE ) {
-    /* open bond forces file */
-    sprintf( temp, "%s.fbond", control->sim_name );
-    if( (out_control->fbond = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fbond file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open lone-pair forces file */
-    sprintf( temp, "%s.flp", control->sim_name );
-    if( (out_control->flp = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .flp file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open overcoordination forces file */
-    sprintf( temp, "%s.fov", control->sim_name );
-    if( (out_control->fov = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fov file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open undercoordination forces file */
-    sprintf( temp, "%s.fun", control->sim_name );
-    if( (out_control->fun = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fun file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open angle forces file */
-    sprintf( temp, "%s.fang", control->sim_name );
-    if( (out_control->fang = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fang file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open coalition forces file */
-    sprintf( temp, "%s.fcoa", control->sim_name );
-    if( (out_control->fcoa = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fcoa file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open penalty forces file */
-    sprintf( temp, "%s.fpen", control->sim_name );
-    if( (out_control->fpen = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fpen file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open torsion forces file */
-    sprintf( temp, "%s.ftor", control->sim_name );
-    if( (out_control->ftor = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .ftor file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open conjugation forces file */
-    sprintf( temp, "%s.fcon", control->sim_name );
-    if( (out_control->fcon = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fcon file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open hydrogen bond forces file */
-    sprintf( temp, "%s.fhb", control->sim_name );
-    if( (out_control->fhb = fopen( temp, "w" )) == NULL )        {
-      strcpy(msg,"Init_Out_Files: .fhb file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open vdw forces file */
-    sprintf( temp, "%s.fvdw", control->sim_name );
-    if( (out_control->fvdw = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fvdw file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open nonbonded forces file */
-    sprintf( temp, "%s.fele", control->sim_name );
-    if( (out_control->fele = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fele file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open total force file */
-    sprintf( temp, "%s.ftot", control->sim_name );
-    if( (out_control->ftot = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .ftot file couldn't be opened\n");
-      return FAILURE;
-    }
-
-    /* open force comprison file */
-    sprintf( temp, "%s.fcomp", control->sim_name );
-    if( (out_control->fcomp = fopen( temp, "w" )) == NULL ) {
-      strcpy(msg,"Init_Out_Files: .fcomp file couldn't be opened\n");
-      return FAILURE;
-    }
-  }
-#endif
-
-#if defined(PURE_REAX)
-#if defined(TEST_FORCES) || defined(TEST_ENERGY)
-    /* open far neighbor list file */
-  sprintf( temp, "%s.far_nbrs_list.%d", control->sim_name, system->my_rank );
-  if( (out_control->flist = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .far_nbrs_list file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open bond list file */
-  sprintf( temp, "%s.bond_list.%d", control->sim_name, system->my_rank );
-  if( (out_control->blist = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .bond_list file couldn't be opened\n");
-    return FAILURE;
-  }
-
-  /* open near neighbor list file */
-  sprintf( temp, "%s.near_nbrs_list.%d", control->sim_name, system->my_rank );
-  if( (out_control->nlist = fopen( temp, "w" )) == NULL ) {
-    strcpy(msg,"Init_Out_Files: .near_nbrs_list file couldn't be opened\n");
-    return FAILURE;
-  }
-#endif
-#endif
-
   return SUCCESS;
 }
 
@@ -433,70 +98,14 @@ int Close_Output_Files( reax_system *system, control_params *control,
 
   if( system->my_rank == MASTER_NODE ) {
     if( out_control->energy_update_freq > 0 ) {
-#if defined(PURE_REAX)
-      fclose( out_control->out );
-#endif
       fclose( out_control->pot );
-#if defined(LOG_PERFORMANCE)
-      fclose( out_control->log );
-#endif
     }
 
     if( control->ensemble == NPT || control->ensemble == iNPT ||
         control->ensemble == sNPT )
       fclose( out_control->prs );
-
-    // not yet implemented in the parallel version
-    //if( control->dipole_anal ) fclose( out_control->dpl );
-    //if( control->diffusion_coef ) fclose( out_control->drft );
-    //if( control->molecular_analysis ) fclose( out_control->mol );
   }
 
-#ifdef TEST_ENERGY
-  fclose( out_control->ebond );
-  fclose( out_control->elp );
-  fclose( out_control->eov );
-  fclose( out_control->eun );
-  fclose( out_control->eval );
-  fclose( out_control->epen );
-  fclose( out_control->ecoa );
-  fclose( out_control->ehb );
-  fclose( out_control->etor );
-  fclose( out_control->econ );
-  fclose( out_control->evdw );
-  fclose( out_control->ecou );
-#endif
-
-#ifdef TEST_FORCES
-  fclose( out_control->fbo );
-  fclose( out_control->fdbo );
-
-  if( system->my_rank == MASTER_NODE ) {
-    fclose( out_control->fbond );
-    fclose( out_control->flp );
-    fclose( out_control->fov );
-    fclose( out_control->fun );
-    fclose( out_control->fang );
-    fclose( out_control->fcoa );
-    fclose( out_control->fpen );
-    fclose( out_control->ftor );
-    fclose( out_control->fcon );
-    fclose( out_control->fhb );
-    fclose( out_control->fvdw );
-    fclose( out_control->fele );
-    fclose( out_control->ftot );
-    fclose( out_control->fcomp );
-  }
-#endif
-
-#if defined(PURE_REAX)
-#if defined(TEST_FORCES) || defined(TEST_ENERGY)
-  fclose( out_control->flist );
-  fclose( out_control->blist );
-  fclose( out_control->nlist );
-#endif
-#endif
-
   return SUCCESS;
 }
 
@@ -514,35 +123,6 @@ void Print_Box( simulation_box* box, char *name, FILE *out )
   fprintf( out, "\tdims[%8.3f%8.3f%8.3f]\n",
            box->box_norms[0], box->box_norms[1], box->box_norms[2] );
 
-  // fprintf( out, "box: {" );
-  // for( i = 0; i < 3; ++i )
-  //   {
-  //     fprintf( out, "{" );
-  //     for( j = 0; j < 3; ++j )
-  //       fprintf( out, "%8.3f ", box->box[i][j] );
-  //     fprintf( out, "}" );
-  //   }
-  // fprintf( out, "}\n" );
-
-  // fprintf( out, "box_trans: {" );
-  // for( i = 0; i < 3; ++i )
-  //   {
-  //     fprintf( out, "{" );
-  //     for( j = 0; j < 3; ++j )
-  //         fprintf( out, "%8.3f ", box->trans[i][j] );
-  //     fprintf( out, "}" );
-  //   }
-  // fprintf( out, "}\n" );
-
-  // fprintf( out, "box_trinv: {" );
-  // for( i = 0; i < 3; ++i )
-  //   {
-  //     fprintf( out, "{" );
-  //     for( j = 0; j < 3; ++j )
-  //         fprintf( out, "%8.3f ", box->trans_inv[i][j] );
-  //     fprintf( out, "}" );
-  //   }
-  // fprintf( out, "}\n" );
 }
 
 
@@ -584,8 +164,6 @@ void Print_Grid( grid* g, FILE *out )
           g->ghost_hbond_span[0],g->ghost_hbond_span[1],g->ghost_hbond_span[2]);
   fprintf( out, "\tbonded ghost gcell span: %d %d %d\n",
            g->ghost_bond_span[0],g->ghost_bond_span[1],g->ghost_bond_span[2]);
-  //fprintf(out, "\t---------------------------------\n" );
-  //fprintf(out, "\tmax number of gcells at the boundary: %d\n", g->gcell_cap);
   fprintf( out, "\t---------------------------------\n" );
 
   fprintf( stderr, "GCELL MARKS:\n" );
@@ -612,51 +190,6 @@ void Print_Grid( grid* g, FILE *out )
   fprintf( out, "-------------------------------------\n" );
 }
 
-
-#if 0
-void Print_GCell_Exchange_Bounds( int my_rank, neighbor_proc *my_nbrs )
-{
-  ivec r;
-  int nbr;
-  neighbor_proc *nbr_pr;
-  char fname[100];
-  FILE *f;
-  char exch[3][10] = { "NONE", "NEAR_EXCH", "FULL_EXCH" };
-
-  sprintf( fname, "gcell_exchange_bounds%d", my_rank );
-  f = fopen( fname, "w" );
-
-  /* loop over neighbor processes */
-  for( r[0] = -1; r[0] <= 1; ++r[0])
-    for( r[1] = -1; r[1] <= 1; ++r[1] )
-      for( r[2] = -1; r[2] <= 1; ++r[2] )
-        if( r[0]!=0 || r[1]!=0 || r[2]!=0 ) {
-          nbr_pr = &(my_nbrs[nbr]);
-
-          fprintf( f, "p%-2d GCELL BOUNDARIES with r(%2d %2d %2d):\n",
-                   my_rank, r[0], r[1], r[2] );
-
-          fprintf( f, "\tsend_type %s: send(%d %d %d) to (%d %d %d)\n",
-                   exch[nbr_pr->send_type],
-                   nbr_pr->str_send[0], nbr_pr->str_send[1],
-                   nbr_pr->str_send[2],
-                   nbr_pr->end_send[0], nbr_pr->end_send[1],
-                   nbr_pr->end_send[2] );
-
-          fprintf( f, "\trecv_type %s: recv(%d %d %d) to (%d %d %d)\n",
-                   exch[nbr_pr->recv_type],
-                   nbr_pr->str_recv[0], nbr_pr->str_recv[1],
-                   nbr_pr->str_recv[2],
-                   nbr_pr->end_recv[0], nbr_pr->end_recv[1],
-                   nbr_pr->end_recv[2] );
-        }
-
-  fclose(f);
-}
-#endif
-
-
-
 void Print_Native_GCells( reax_system *system )
 {
   int        i, j, k, l;
@@ -744,9 +277,6 @@ void Print_My_Atoms( reax_system *system )
       MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND );
     }
 
-  // fprintf( stderr, "p%d had %d atoms\n",
-  //   system->my_rank, system->n );
-
   for( i = 0; i < system->n; ++i )
     fprintf( fh, "p%-2d %-5d %2d %24.15e%24.15e%24.15e\n",
              system->my_rank,
@@ -772,9 +302,6 @@ void Print_My_Ext_Atoms( reax_system *system )
       MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND );
     }
 
-  // fprintf( stderr, "p%d had %d atoms\n",
-  //   system->my_rank, system->n );
-
   for( i = 0; i < system->N; ++i )
     fprintf( fh, "p%-2d %-5d imprt%-5d %2d %24.15e%24.15e%24.15e\n",
              system->my_rank, system->my_atoms[i].orig_id,
@@ -901,27 +428,6 @@ void Print_Linear_System( reax_system *system, control_params *control,
   sprintf( fname, "%s.p%dH%d", control->sim_name, system->my_rank, step );
   Print_Symmetric_Sparse( system, workspace->H, fname );
 
-  // print the incomplete H matrix
-  /*sprintf( fname, "%s.p%dHinc%d", control->sim_name, system->my_rank, step );
-  out = fopen( fname, "w" );
-  H = workspace->H;
-  for( i = 0; i < H->n; ++i ) {
-    ai = &(system->my_atoms[i]);
-    for( j = H->start[i]; j < H->end[i]; ++j )
-      if( H->entries[j].j < system->n ) {
-        aj = &(system->my_atoms[H->entries[j].j]);
-        fprintf( out, "%d %d %.15e\n",
-                 ai->orig_id, aj->orig_id, H->entries[j].val );
-        if( ai->orig_id != aj->orig_id )
-          fprintf( out, "%d %d %.15e\n",
-                   aj->orig_id, ai->orig_id, H->entries[j].val );
-      }
-  }
-  fclose( out );*/
-
-  // print the L from incomplete cholesky decomposition
-  /*sprintf( fname, "%s.p%dL%d", control->sim_name, system->my_rank, step );
-    Print_Sparse_Matrix2( system, workspace->L, fname );*/
 }
 
 
@@ -974,9 +480,6 @@ void Print_Bonds( reax_system *system, reax_list *bonds, char *fname )
       pbond = &(bonds->select.bond_list[pj]);
       bo_ij = &(pbond->bo_data);
       j = pbond->nbr;
-      //fprintf( f, "%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
-      //       system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-      //       pbond->d, bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
       fprintf( f, "%8d%8d %24.15f %24.15f\n",
                i, j,//system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
                pbond->d, bo_ij->BO );
@@ -1037,9 +540,6 @@ void Output_Results( reax_system *system, control_params *control,
                      simulation_data *data, reax_list **lists,
                      output_controls *out_control, mpi_datatypes *mpi_data )
 {
-#if defined(LOG_PERFORMANCE)
-  real t_elapsed, denom;
-#endif
 
   if((out_control->energy_update_freq > 0 &&
       data->step%out_control->energy_update_freq == 0) ||
@@ -1052,68 +552,6 @@ void Output_Results( reax_system *system, control_params *control,
     if( system->my_rank == MASTER_NODE &&
         out_control->energy_update_freq > 0 &&
         data->step % out_control->energy_update_freq == 0 ) {
-#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
-#if defined(PURE_REAX)
-      fprintf( out_control->out,
-               "%-6d%14.2f%14.2f%14.2f%11.2f%13.2f%13.5f\n",
-               data->step, data->sys_en.e_tot, data->sys_en.e_pot,
-               E_CONV * data->sys_en.e_kin, data->therm.T,
-               system->big_box.V, data->iso_bar.P );
-      fflush( out_control->out );
-#endif
-
-      fprintf( out_control->pot,
-               "%-6d%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f\n",
-               data->step,
-               data->sys_en.e_bond,
-               data->sys_en.e_ov + data->sys_en.e_un,  data->sys_en.e_lp,
-               data->sys_en.e_ang + data->sys_en.e_pen, data->sys_en.e_coa,
-               data->sys_en.e_hb,
-               data->sys_en.e_tor, data->sys_en.e_con,
-               data->sys_en.e_vdW, data->sys_en.e_ele, data->sys_en.e_pol);
-      fflush( out_control->pot );
-#else
-#if defined(PURE_REAX)
-      fprintf( out_control->out,
-               "%-6d%24.15e%24.15e%24.15e%13.5f%16.5f%13.5f\n",
-               data->step, data->sys_en.e_tot, data->sys_en.e_pot,
-               E_CONV * data->sys_en.e_kin, data->therm.T,
-               system->big_box.V, data->iso_bar.P );
-      fflush( out_control->out );
-#endif
-
-      fprintf( out_control->pot,
-               "%-6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-               data->step,
-               data->sys_en.e_bond,
-               data->sys_en.e_ov + data->sys_en.e_un,  data->sys_en.e_lp,
-               data->sys_en.e_ang + data->sys_en.e_pen, data->sys_en.e_coa,
-               data->sys_en.e_hb,
-               data->sys_en.e_tor, data->sys_en.e_con,
-               data->sys_en.e_vdW, data->sys_en.e_ele, data->sys_en.e_pol);
-      fflush( out_control->pot );
-#endif //DEBUG
-
-#if defined(LOG_PERFORMANCE)
-      t_elapsed = Get_Timing_Info( data->timing.total );
-      if( data->step - data->prev_steps > 0 )
-        denom = 1.0 / out_control->energy_update_freq;
-      else denom = 1;
-
-      fprintf( out_control->log, "%6d%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f%6d\n",
-               data->step,
-               t_elapsed * denom,
-               data->timing.comm * denom,
-               data->timing.nbrs * denom,
-               data->timing.init_forces * denom,
-               data->timing.bonded * denom,
-               data->timing.nonb * denom,
-               data->timing.qEq * denom,
-               (int)((data->timing.s_matvecs+data->timing.t_matvecs)*denom) );
-
-      Reset_Timing( &(data->timing) );
-      fflush( out_control->log );
-#endif //LOG_PERFORMANCE
 
       if( control->virial ){
         fprintf( out_control->prs,
@@ -1141,582 +579,4 @@ void Output_Results( reax_system *system, control_params *control,
     }
   }
 
-#if defined(DEBUG)
-  fprintf( stderr, "output_results... done\n" );
-#endif
 }
-
-
-#ifdef TEST_ENERGY
-void Debug_Marker_Bonded( output_controls *out_control, int step )
-{
-  fprintf( out_control->ebond, "step: %d\n%6s%6s%12s%12s%12s\n",
-           step, "atom1", "atom2", "bo", "ebond", "total" );
-  fprintf( out_control->elp, "step: %d\n%6s%12s%12s%12s\n",
-           step, "atom", "nlp", "elp", "total" );
-  fprintf( out_control->eov, "step: %d\n%6s%12s%12s\n",
-           step, "atom", "eov", "total" );
-  fprintf( out_control->eun, "step: %d\n%6s%12s%12s\n",
-           step, "atom", "eun", "total" );
-  fprintf( out_control->eval, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
-           step, "atom1", "atom2", "atom3", "angle", "theta0",
-           "bo(12)", "bo(23)", "eval", "total" );
-  fprintf( out_control->epen, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
-           step, "atom1", "atom2", "atom3", "angle", "bo(12)", "bo(23)",
-           "epen", "total" );
-  fprintf( out_control->ecoa, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
-           step, "atom1", "atom2", "atom3", "angle", "bo(12)", "bo(23)",
-           "ecoa", "total" );
-  fprintf( out_control->ehb,  "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
-           step, "atom1", "atom2", "atom3", "r(23)", "angle", "bo(12)",
-           "ehb", "total" );
-  fprintf( out_control->etor, "step: %d\n%6s%6s%6s%6s%12s%12s%12s%12s\n",
-           step, "atom1", "atom2", "atom3", "atom4", "phi", "bo(23)",
-           "etor", "total" );
-  fprintf( out_control->econ,"step:%d\n%6s%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
-           step, "atom1", "atom2", "atom3", "atom4",
-           "phi", "bo(12)", "bo(23)", "bo(34)", "econ", "total" );
-}
-
-void Debug_Marker_Nonbonded( output_controls *out_control, int step )
-{
-  fprintf( out_control->evdw, "step: %d\n%6s%6s%12s%12s%12s\n",
-           step, "atom1", "atom2", "r12", "evdw", "total" );
-  fprintf( out_control->ecou, "step: %d\n%6s%6s%12s%12s%12s%12s%12s\n",
-           step, "atom1", "atom2", "r12", "q1", "q2", "ecou", "total" );
-}
-
-#endif
-
-
-#ifdef TEST_FORCES
-void Dummy_Printer( reax_system *system, control_params *control,
-                    simulation_data *data, storage *workspace,
-                    reax_list **lists, output_controls *out_control )
-{
-}
-
-
-
-void Print_Bond_Orders( reax_system *system, control_params *control,
-                        simulation_data *data, storage *workspace,
-                        reax_list **lists, output_controls *out_control )
-{
-  int i, pj, pk;
-  bond_order_data *bo_ij;
-  dbond_data *dbo_k;
-  reax_list *bonds = (*lists) + BONDS;
-  reax_list *dBOs  = (*lists) + DBOS;
-
-  /* bond orders */
-  fprintf( out_control->fbo, "step: %d\n", data->step );
-  fprintf( out_control->fbo, "%6s%6s%12s%12s%12s%12s%12s\n",
-           "atom1", "atom2", "r_ij", "total_bo", "bo_s", "bo_p", "bo_pp" );
-
-  for( i = 0; i < system->N; ++i )
-    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
-        bo_ij = &(bonds->select.bond_list[pj].bo_data);
-        fprintf( out_control->fbo,
-                 "%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-                 system->my_atoms[i].orig_id,
-                 system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
-                 bonds->select.bond_list[pj].d,
-                 bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
-    }
-
-
-  /* derivatives of bond orders */
-  fprintf( out_control->fdbo, "step: %d\n", data->step );
-  fprintf( out_control->fdbo, "%6s%6s%6s%24s%24s%24s\n",
-           "atom1", "atom2", "atom2", "dBO", "dBOpi", "dBOpi2" );
-  for( i = 0; i < system->N; ++i )
-    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
-      /* fprintf( out_control->fdbo, "%6d %6d\tstart: %6d\tend: %6d\n",
-         system->my_atoms[i].orig_id,
-         system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
-         Start_Index( pj, dBOs ), End_Index( pj, dBOs ) ); */
-      for( pk = Start_Index(pj, dBOs); pk < End_Index(pj, dBOs); ++pk ) {
-        dbo_k = &(dBOs->select.dbo_list[pk]);
-        fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
-                 system->my_atoms[i].orig_id,
-                 system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
-                 system->my_atoms[dbo_k->wrt].orig_id,
-                 dbo_k->dBO[0], dbo_k->dBO[1], dbo_k->dBO[2] );
-
-        fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
-                 system->my_atoms[i].orig_id,
-                 system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
-                 system->my_atoms[dbo_k->wrt].orig_id,
-                 dbo_k->dBOpi[0], dbo_k->dBOpi[1], dbo_k->dBOpi[2] );
-
-        fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
-                 system->my_atoms[i].orig_id,
-                 system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
-                 system->my_atoms[dbo_k->wrt].orig_id,
-                 dbo_k->dBOpi2[0], dbo_k->dBOpi2[1], dbo_k->dBOpi2[2] );
-      }
-    }
-}
-
-
-void Print_Forces( FILE *f, storage *workspace, int N, int step )
-{
-  int i;
-
-  fprintf( f, "step: %d\n", step );
-  for( i = 0; i < N; ++i )
-    //fprintf( f, "%6d %23.15e %23.15e %23.15e\n",
-    //fprintf( f, "%6d%12.6f%12.6f%12.6f\n",
-    fprintf( f, "%6d %19.9e %19.9e %19.9e\n",
-             workspace->id_all[i], workspace->f_all[i][0],
-             workspace->f_all[i][1], workspace->f_all[i][2] );
-}
-
-
-void Print_Force_Files( reax_system *system, control_params *control,
-                        simulation_data *data, storage *workspace,
-                        reax_list **lists, output_controls *out_control,
-                        mpi_datatypes *mpi_data )
-{
-  int i, d;
-
-  Coll_ids_at_Master( system, workspace, mpi_data );
-
-  Print_Bond_Orders( system, control, data, workspace, lists, out_control );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_be );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fbond, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_lp );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->flp, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_ov );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fov, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_un );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fun, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_ang );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fang, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_coa );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fcoa, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_pen );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fpen, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_tor );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->ftor, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_con );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fcon, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_hb );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fhb, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_vdw );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fvdw, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_ele );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fele, workspace, system->bigN, data->step );
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->ftot, workspace, system->bigN, data->step );
-
-  for( i = 0; i < system->n; ++i ) {
-    for( d = 0; d < 3; ++d )
-      workspace->f_tot[i][d] = workspace->f_be[i][d] +
-        workspace->f_lp[i][d]+workspace->f_ov[i][d]+workspace->f_un[i][d] +
-        workspace->f_ang[i][d]+workspace->f_pen[i][d]+workspace->f_coa[i][d] +
-        workspace->f_tor[i][d]+workspace->f_con[i][d] +
-        workspace->f_vdw[i][d]+workspace->f_ele[i][d] +
-        workspace->f_hb[i][d];
-  }
-
-  Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_tot );
-  if( system->my_rank == MASTER_NODE )
-    Print_Forces( out_control->fcomp, workspace, system->bigN, data->step );
-}
-#endif
-
-
-#if defined(TEST_FORCES) || defined(TEST_ENERGY)
-
-void Print_Far_Neighbors_List( reax_system *system, reax_list **lists,
-                               control_params *control, simulation_data *data,
-                               output_controls *out_control )
-{
-  int   i, j, nbr, natoms;
-  rc_tagint id_i, id_j;
-  int num=0;
-  int temp[500];
-  reax_list *far_nbrs;
-
-  far_nbrs = (*lists) + FAR_NBRS;
-  fprintf( out_control->flist, "step: %d\n", data->step );
-  fprintf( out_control->flist, "%6s\t%-38s\n", "atom", "Far_nbrs_list");
-
-
-  natoms = system->n;
-  for( i = 0; i < natoms; ++i ) {
-    id_i = system->my_atoms[i].orig_id;
-    fprintf( out_control->flist, "%6d:",id_i);
-    num=0;
-
-    for( j = Start_Index(i,far_nbrs); j < End_Index(i,far_nbrs); ++j ) {
-      nbr = far_nbrs->select.far_nbr_list[j].nbr;
-      id_j = system->my_atoms[nbr].orig_id;
-      temp[num++] = id_j;
-    }
-
-    qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
-    for(j=0; j < num; j++)
-      fprintf(out_control->flist, "%6d",temp[j]);
-    fprintf( out_control->flist, "\n");
-  }
-}
-
-void Print_Bond_List( reax_system *system, control_params *control,
-                      simulation_data *data, reax_list **lists,
-                      output_controls *out_control)
-{
-  int i,j, nbr, pj;
-  rc_tagint id_i, id_j;
-  reax_list *bonds = (*lists) + BONDS;
-
-  int temp[500];
-  int num=0;
-
-  fprintf( out_control->blist, "step: %d\n", data->step );
-  fprintf( out_control->blist, "%6s\t%-38s\n", "atom", "Bond_list");
-
-  /* bond list */
-  for( i = 0; i < system->n; ++i ) {
-    num=0;
-    id_i = system->my_atoms[i].orig_id;
-    fprintf( out_control->blist, "%6d:", id_i);
-    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
-      nbr = bonds->select.bond_list[pj].nbr;
-      id_j = system->my_atoms[nbr].orig_id;
-      if( id_i < id_j )
-        temp[num++] = id_j;
-    }
-
-    qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
-    for(j=0; j < num; j++)
-      fprintf(out_control->blist, "%6d",temp[j]);
-    fprintf(out_control->blist, "\n");
-  }
-}
-
-
-#endif
-
-
-#ifdef OLD_VERSION
-void Print_Init_Atoms( reax_system *system, storage *workspace )
-{
-  int i;
-
-  fprintf( stderr, "p%d had %d atoms\n",
-           system->my_rank, workspace->init_cnt );
-
-  for( i = 0; i < workspace->init_cnt; ++i )
-    fprintf( stderr, "p%d, atom%d: %d  %s  %8.3f %8.3f %8.3f\n",
-             system->my_rank, i,
-             workspace->init_atoms[i].type, workspace->init_atoms[i].name,
-             workspace->init_atoms[i].x[0],
-             workspace->init_atoms[i].x[1],
-             workspace->init_atoms[i].x[2] );
-}
-#endif //OLD_VERSION
-
-
-/*void Print_Bond_Forces( reax_system *system, control_params *control,
-                        simulation_data *data, storage *workspace,
-                        reax_list **lists, output_controls *out_control )
-{
-  int i;
-
-  fprintf( out_control->fbond, "step: %d\n", data->step );
-  fprintf( out_control->fbond, "%6s%24s%24s%24s\n",
-           "atom", "f_be[0]", "f_be[1]", "f_be[2]" );
-
-  for( i = 0; i < system->bigN; ++i )
-    fprintf(out_control->fbond, "%6d%24.15e%24.15e%24.15e\n",
-            system->my_atoms[i].orig_id,
-            workspace->f_all[i][0], workspace->f_all[i][1],
-            workspace->f_all[i][2]);
-}
-
-void Print_LonePair_Forces( reax_system *system, control_params *control,
-                            simulation_data *data, storage *workspace,
-                            reax_list **lists, output_controls *out_control )
-{
-  int i;
-
-  fprintf( out_control->flp, "step: %d\n", data->step );
-  fprintf( out_control->flp, "%6s%24s\n", "atom", "f_lonepair" );
-
-  for( i = 0; i < system->bigN; ++i )
-    fprintf(out_control->flp, "%6d%24.15e%24.15e%24.15e\n",
-            system->my_atoms[i].orig_id,
-            workspace->f_all[i][0], workspace->f_all[i][1],
-            workspace->f_all[i][2]);
-}
-
-
-void Print_OverCoor_Forces( reax_system *system, control_params *control,
-                            simulation_data *data, storage *workspace,
-                            reax_list **lists, output_controls *out_control )
-{
-  int i;
-
-  fprintf( out_control->fov, "step: %d\n", data->step );
-  fprintf( out_control->fov, "%6s%-38s%-38s%-38s\n",
-           "atom","f_over[0]", "f_over[1]", "f_over[2]" );
-
-  for( i = 0; i < system->bigN; ++i )
-    fprintf( out_control->fov,
-             "%6d %24.15e%24.15e%24.15e 0 0 0\n",
-             system->my_atoms[i].orig_id,
-             workspace->f_all[i][0], workspace->f_all[i][1],
-             workspace->f_all[i][2] );
-}
-
-
-void Print_UnderCoor_Forces( reax_system *system, control_params *control,
-                             simulation_data *data, storage *workspace,
-                             reax_list **lists, output_controls *out_control )
-{
-  int i;
-
-  fprintf( out_control->fun, "step: %d\n", data->step );
-  fprintf( out_control->fun, "%6s%-38s%-38s%-38s\n",
-           "atom","f_under[0]", "f_under[1]", "f_under[2]" );
-
-  for( i = 0; i < system->bigN; ++i )
-    fprintf( out_control->fun,
-             "%6d %24.15e%24.15e%24.15e 0 0 0\n",
-             system->my_atoms[i].orig_id,
-             workspace->f_all[i][0], workspace->f_all[i][1],
-             workspace->f_all[i][2] );
-}
-
-
-void Print_ValAngle_Forces( reax_system *system, control_params *control,
-                            simulation_data *data, storage *workspace,
-                            reax_list **lists, output_controls *out_control )
-{
-  int j;
-
-  fprintf( out_control->f3body, "step: %d\n", data->step );
-  fprintf( out_control->f3body, "%6s%-37s%-37s%-37s%-38s\n",
-           "atom", "3-body total", "f_ang", "f_pen", "f_coa" );
-
-  for( j = 0; j < system->N; ++j ){
-    if( rvec_isZero(workspace->f_pen[j]) && rvec_isZero(workspace->f_coa[j]) )
-      fprintf( out_control->f3body,
-               "%6d %24.15e%24.15e%24.15e  0 0 0  0 0 0\n",
-               system->my_atoms[j].orig_id,
-               workspace->f_ang[j][0], workspace->f_ang[j][1],
-               workspace->f_ang[j][2] );
-    else if( rvec_isZero(workspace->f_coa[j]) )
-      fprintf( out_control->f3body,
-               "%6d %24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "        \
-               "%24.15e%24.15e%24.15e\n",
-               system->my_atoms[j].orig_id,
-               workspace->f_ang[j][0] + workspace->f_pen[j][0],
-               workspace->f_ang[j][1] + workspace->f_pen[j][1],
-               workspace->f_ang[j][2] + workspace->f_pen[j][2],
-               workspace->f_ang[j][0], workspace->f_ang[j][1],
-               workspace->f_ang[j][2],
-               workspace->f_pen[j][0], workspace->f_pen[j][1],
-               workspace->f_pen[j][2] );
-    else{
-      fprintf( out_control->f3body, "%6d %24.15e%24.15e%24.15e ",
-             system->my_atoms[j].orig_id,
-               workspace->f_ang[j][0] + workspace->f_pen[j][0] +
-               workspace->f_coa[j][0],
-               workspace->f_ang[j][1] + workspace->f_pen[j][1] +
-               workspace->f_coa[j][1],
-               workspace->f_ang[j][2] + workspace->f_pen[j][2] +
-               workspace->f_coa[j][2] );
-
-      fprintf( out_control->f3body,
-               "%24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "\
-               "%24.15e%24.15e%24.15e\n",
-               workspace->f_ang[j][0], workspace->f_ang[j][1],
-               workspace->f_ang[j][2],
-               workspace->f_pen[j][0], workspace->f_pen[j][1],
-               workspace->f_pen[j][2],
-               workspace->f_coa[j][0], workspace->f_coa[j][1],
-               workspace->f_coa[j][2] );
-        }
-  }
-}
-
-
-void Print_Hydrogen_Bond_Forces( reax_system *system, control_params *control,
-                                 simulation_data *data, storage *workspace,
-                                 reax_list **lists, output_controls *out_control)
-{
-  int j;
-
-  fprintf( out_control->fhb, "step: %d\n", data->step );
-  fprintf( out_control->fhb, "%6s\t%-38s\n", "atom", "f_hb[0,1,2]" );
-
-  for( j = 0; j < system->N; ++j )
-    fprintf(out_control->fhb, "%6d%24.15e%24.15e%24.15e\n",
-             system->my_atoms[j].orig_id,
-             workspace->f_hb[j][0],
-             workspace->f_hb[j][1],
-             workspace->f_hb[j][2] );
-}
-
-
-void Print_Four_Body_Forces( reax_system *system, control_params *control,
-                             simulation_data *data, storage *workspace,
-                             reax_list **lists, output_controls *out_control )
-{
-  int j;
-
-  fprintf( out_control->f4body, "step: %d\n", data->step );
-  fprintf( out_control->f4body, "%6s\t%-38s%-38s%-38s\n",
-           "atom", "4-body total", "f_tor", "f_con" );
-
-  for( j = 0; j < system->N; ++j ){
-    if( !rvec_isZero( workspace->f_con[j] ) )
-      fprintf( out_control->f4body,
-               "%6d %24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "\
-               "%24.15e%24.15e%24.15e\n",
-             system->my_atoms[j].orig_id,
-               workspace->f_tor[j][0] + workspace->f_con[j][0],
-               workspace->f_tor[j][1] + workspace->f_con[j][1],
-               workspace->f_tor[j][2] + workspace->f_con[j][2],
-               workspace->f_tor[j][0], workspace->f_tor[j][1],
-               workspace->f_tor[j][2],
-               workspace->f_con[j][0], workspace->f_con[j][1],
-               workspace->f_con[j][2] );
-    else
-      fprintf( out_control->f4body,
-               "%6d %24.15e%24.15e%24.15e  0 0 0\n",
-               system->my_atoms[j].orig_id, workspace->f_tor[j][0],
-               workspace->f_tor[j][1], workspace->f_tor[j][2] );
-  }
-
-}
-
-
-void Print_vdW_Coulomb_Forces( reax_system *system, control_params *control,
-                               simulation_data *data, storage *workspace,
-                               reax_list **lists, output_controls *out_control )
-{
-  int  i;
-
-  return;
-
-  fprintf( out_control->fnonb, "step: %d\n", data->step );
-  fprintf( out_control->fnonb, "%6s\t%-38s%-38s%-38s\n",
-           "atom", "nonbonded_total[0,1,2]", "f_vdw[0,1,2]", "f_ele[0,1,2]" );
-
-  for( i = 0; i < system->N; ++i )
-    fprintf( out_control->fnonb,
-             "%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-             system->my_atoms[i].orig_id,
-             workspace->f_vdw[i][0] + workspace->f_ele[i][0],
-             workspace->f_vdw[i][1] + workspace->f_ele[i][1],
-             workspace->f_vdw[i][2] + workspace->f_ele[i][2],
-             workspace->f_vdw[i][0],
-             workspace->f_vdw[i][1],
-             workspace->f_vdw[i][2],
-             workspace->f_ele[i][0],
-             workspace->f_ele[i][1],
-             workspace->f_ele[i][2] );
-}
-
-
-void Print_Total_Force( reax_system *system, control_params *control,
-                        simulation_data *data, storage *workspace,
-                        reax_list **lists, output_controls *out_control )
-{
-  int    i;
-
-  return;
-
-  fprintf( out_control->ftot, "step: %d\n", data->step );
-  fprintf( out_control->ftot, "%6s\t%-38s\n", "atom", "atom.f[0,1,2]");
-
-  for( i = 0; i < system->n; ++i )
-    fprintf( out_control->ftot, "%6d%24.15e%24.15e%24.15e\n",
-             system->my_atoms[i].orig_id,
-             system->my_atoms[i].f[0],
-             system->my_atoms[i].f[1],
-             system->my_atoms[i].f[2] );
-}
-
-
-void Compare_Total_Forces( reax_system *system, control_params *control,
-                           simulation_data *data, storage *workspace,
-                           reax_list **lists, output_controls *out_control )
-{
-  int i;
-
-  return;
-
-  fprintf( out_control->ftot2, "step: %d\n", data->step );
-  fprintf( out_control->ftot2, "%6s\t%-38s%-38s\n",
-           "atom", "f_total[0,1,2]", "test_force_total[0,1,2]" );
-
-  for( i = 0; i < system->N; ++i )
-    fprintf( out_control->ftot2, "%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-             system->my_atoms[i].orig_id,
-             system->my_atoms[i].f[0],
-             system->my_atoms[i].f[1],
-             system->my_atoms[i].f[2],
-             workspace->f_be[i][0] + workspace->f_lp[i][0] +
-             workspace->f_ov[i][0] + workspace->f_un[i][0] +
-             workspace->f_ang[i][0]+ workspace->f_pen[i][0]+
-             workspace->f_coa[i][0]+ + workspace->f_hb[i][0] +
-             workspace->f_tor[i][0] + workspace->f_con[i][0] +
-             workspace->f_vdw[i][0] + workspace->f_ele[i][0],
-             workspace->f_be[i][1] + workspace->f_lp[i][1] +
-             workspace->f_ov[i][1] + workspace->f_un[i][1] +
-             workspace->f_ang[i][1]+ workspace->f_pen[i][1]+
-             workspace->f_coa[i][1]+ + workspace->f_hb[i][1] +
-             workspace->f_tor[i][1] + workspace->f_con[i][1] +
-             workspace->f_vdw[i][1] + workspace->f_ele[i][1],
-             workspace->f_be[i][2] + workspace->f_lp[i][2] +
-             workspace->f_ov[i][2] + workspace->f_un[i][2] +
-             workspace->f_ang[i][2]+ workspace->f_pen[i][2] +
-             workspace->f_coa[i][2]+ + workspace->f_hb[i][2] +
-             workspace->f_tor[i][2] + workspace->f_con[i][2] +
-             workspace->f_vdw[i][2] + workspace->f_ele[i][2] );
-}*/
-
-/*void Init_Force_Test_Functions( )
-{
-  Print_Interactions[0] = Print_Bond_Orders;
-  Print_Interactions[1] = Print_Bond_Forces;
-  Print_Interactions[2] = Print_LonePair_Forces;
-  Print_Interactions[3] = Print_OverUnderCoor_Forces;
-  Print_Interactions[4] = Print_Three_Body_Forces;
-  Print_Interactions[5] = Print_Four_Body_Forces;
-  Print_Interactions[6] = Print_Hydrogen_Bond_Forces;
-  Print_Interactions[7] = Print_vdW_Coulomb_Forces;
-  Print_Interactions[8] = Print_Total_Force;
-  Print_Interactions[9] = Compare_Total_Forces;
-  }*/
diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp
index 9a6ee51b1f..d22ac4ca7f 100644
--- a/src/USER-REAXC/reaxc_list.cpp
+++ b/src/USER-REAXC/reaxc_list.cpp
@@ -25,14 +25,8 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "list.h"
-#include "tool_box.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_list.h"
 #include "reaxc_tool_box.h"
-#endif
-
 
 /************* allocate list space ******************/
 int Make_List(int n, int num_intrs, int type, reax_list *l, MPI_Comm comm)
@@ -46,9 +40,6 @@ int Make_List(int n, int num_intrs, int type, reax_list *l, MPI_Comm comm)
   l->end_index = (int*) smalloc( n * sizeof(int), "list:end_index", comm );
 
   l->type = type;
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "list: n=%d num_intrs=%d type=%d\n", n, num_intrs, type );
-#endif
 
   switch(l->type) {
   case TYP_VOID:
@@ -133,30 +124,3 @@ void Delete_List( reax_list *l, MPI_Comm comm )
   }
 }
 
-
-#if defined(PURE_REAX)
-inline int Num_Entries( int i, reax_list *l )
-{
-  return l->end_index[i] - l->index[i];
-}
-
-inline int Start_Index( int i, reax_list *l )
-{
-  return l->index[i];
-}
-
-inline int End_Index( int i, reax_list *l )
-{
-  return l->end_index[i];
-}
-
-inline void Set_Start_Index( int i, int val, reax_list *l )
-{
-  l->index[i] = val;
-}
-
-inline void Set_End_Index( int i, int val, reax_list *l )
-{
-  l->end_index[i] = val;
-}
-#endif
diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp
index 48a6c19aa5..fe01d4bb46 100644
--- a/src/USER-REAXC/reaxc_lookup.cpp
+++ b/src/USER-REAXC/reaxc_lookup.cpp
@@ -25,25 +25,17 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "lookup.h"
-#include "nonbonded.h"
-#include "tool_box.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_lookup.h"
 #include "reaxc_nonbonded.h"
 #include "reaxc_tool_box.h"
-#endif
 
 LR_lookup_table **LR;
 
-/* Fills solution into x. Warning: will modify c and d! */
 void Tridiagonal_Solve( const real *a, const real *b,
                         real *c, real *d, real *x, unsigned int n){
   int i;
   real id;
 
-  /* Modify the coefficients. */
   c[0] /= b[0];        /* Division by zero risk. */
   d[0] /= b[0];        /* Division by zero would imply a singular matrix. */
   for(i = 1; i < n; i++){
@@ -52,7 +44,6 @@ void Tridiagonal_Solve( const real *a, const real *b,
     d[i] = (d[i] - d[i-1] * a[i])/id;
   }
 
-  /* Now back substitute. */
   x[n - 1] = d[n - 1];
   for(i = n - 2; i >= 0; i--)
     x[i] = d[i] - c[i] * x[i + 1];
@@ -216,17 +207,12 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
   fCEclmb = (real*)
     smalloc( (control->tabulate+2) * sizeof(real), "lookup:fCEclmb", comm );
 
-  /* allocate Long-Range LookUp Table space based on
-     number of atom types in the ffield file */
   LR = (LR_lookup_table**)
     scalloc( num_atom_types, sizeof(LR_lookup_table*), "lookup:LR", comm );
   for( i = 0; i < num_atom_types; ++i )
     LR[i] = (LR_lookup_table*)
       scalloc( num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]", comm );
 
-  /* most atom types in ffield file will not exist in the current
-     simulation. to avoid unnecessary lookup table space, determine
-     the atom types that exist in the current simulation */
   for( i = 0; i < MAX_ATOM_TYPES; ++i )
     existing_types[i] = 0;
   for( i = 0; i < system->n; ++i )
@@ -235,11 +221,8 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
   MPI_Allreduce( existing_types, aggregated, MAX_ATOM_TYPES,
                  MPI_INT, MPI_SUM, mpi_data->world );
 
-  /* fill in the lookup table entries for existing atom types.
-     only lower half should be enough. */
   for( i = 0; i < num_atom_types; ++i ) {
     if( aggregated[i] ) {
-      //for( j = 0; j < num_atom_types; ++j )
       for( j = i; j < num_atom_types; ++j ) {
         if( aggregated[j] ) {
           LR[i][j].xmin = 0;
diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp
index 4744aba38c..220fcb072c 100644
--- a/src/USER-REAXC/reaxc_multi_body.cpp
+++ b/src/USER-REAXC/reaxc_multi_body.cpp
@@ -25,18 +25,10 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "multi_body.h"
-#include "bond_orders.h"
-#include "list.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_multi_body.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
-#endif
-
 
 void Atom_Energy( reax_system *system, control_params *control,
                   simulation_data *data, storage *workspace, reax_list **lists,
@@ -51,17 +43,19 @@ void Atom_Energy( reax_system *system, control_params *control,
   real exp_ovun2n, exp_ovun6, exp_ovun8;
   real inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
   real e_un, CEunder1, CEunder2, CEunder3, CEunder4;
-  real p_lp2, p_lp3;
+  real p_lp1, p_lp2, p_lp3;
   real p_ovun2, p_ovun3, p_ovun4, p_ovun5, p_ovun6, p_ovun7, p_ovun8;
-  real eng_tmp;
+  real eng_tmp, f_tmp;
+  int numbonds;
 
-  single_body_parameters *sbp_i;
+  single_body_parameters *sbp_i, *sbp_j;
   two_body_parameters *twbp;
   bond_data *pbond;
   bond_order_data *bo_ij;
   reax_list *bonds = (*lists) + BONDS;
 
   /* Initialize parameters */
+  p_lp1 = system->reax_param.gp.l[15];
   p_lp3 = system->reax_param.gp.l[5];
   p_ovun3 = system->reax_param.gp.l[32];
   p_ovun4 = system->reax_param.gp.l[31];
@@ -72,6 +66,7 @@ void Atom_Energy( reax_system *system, control_params *control,
   for( i = 0; i < system->n; ++i ) {
     /* set the parameter pointer */
     type_i = system->my_atoms[i].type;
+    if (type_i < 0) continue;
     sbp_i = &(system->reax_param.sbp[ type_i ]);
 
     /* lone-pair Energy */
@@ -79,37 +74,32 @@ void Atom_Energy( reax_system *system, control_params *control,
     expvd2 = exp( -75 * workspace->Delta_lp[i] );
     inv_expvd2 = 1. / (1. + expvd2 );
 
+    numbonds = 0;
+    e_lp = 0.0;
+    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+      numbonds ++;
+
     /* calculate the energy */
-    data->my_en.e_lp += e_lp =
-      p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
+    if (numbonds > 0)
+      data->my_en.e_lp += e_lp =
+        p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
 
     dElp = p_lp2 * inv_expvd2 +
       75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
     CElp = dElp * workspace->dDelta_lp[i];
 
-    workspace->CdDelta[i] += CElp;  // lp - 1st term
+    if (numbonds > 0) workspace->CdDelta[i] += CElp;  // lp - 1st term
 
     /* tally into per-atom energy */
     if( system->pair_ptr->evflag)
       system->pair_ptr->ev_tally(i,i,system->n,1,e_lp,0.0,0.0,0.0,0.0,0.0);
 
-#ifdef TEST_ENERGY
-//  fprintf( out_control->elp, "%24.15e%24.15e%24.15e%24.15e\n",
-//             p_lp2, workspace->Delta_lp_temp[i], expvd2, dElp );
-//  fprintf( out_control->elp, "%6d%24.15e%24.15e%24.15e\n",
-    fprintf( out_control->elp, "%6d%12.4f%12.4f%12.4f\n",
-             system->my_atoms[i].orig_id, workspace->nlp[i],
-             e_lp, data->my_en.e_lp );
-#endif
-#ifdef TEST_FORCES
-    Add_dDelta( system, lists, i, CElp, workspace->f_lp );  // lp - 1st term
-#endif
-
     /* correction for C2 */
     if( p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C") )
       for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
         j = bonds->select.bond_list[pj].nbr;
         type_j = system->my_atoms[j].type;
+	if (type_j < 0) continue;
 
         if( !strcmp( system->reax_param.sbp[type_j].name, "C" ) ) {
           twbp = &( system->reax_param.tbp[type_i][type_j]);
@@ -130,15 +120,6 @@ void Atom_Energy( reax_system *system, control_params *control,
             if( system->pair_ptr->evflag)
               system->pair_ptr->ev_tally(i,j,system->n,1,e_lph,0.0,0.0,0.0,0.0,0.0);
 
-#ifdef TEST_ENERGY
-            fprintf(out_control->elp,"C2cor%6d%6d%12.6f%12.6f%12.6f\n",
-                    system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-                    e_lph, deahu2dbo, deahu2dsbo );
-#endif
-#ifdef TEST_FORCES
-            Add_dBO(system, lists, i, pj, deahu2dbo, workspace->f_lp);
-            Add_dDelta(system, lists, i, deahu2dsbo, workspace->f_lp);
-#endif
           }
         }
       }
@@ -147,6 +128,7 @@ void Atom_Energy( reax_system *system, control_params *control,
 
   for( i = 0; i < system->n; ++i ) {
     type_i = system->my_atoms[i].type;
+    if (type_i < 0) continue;
     sbp_i = &(system->reax_param.sbp[ type_i ]);
 
     /* over-coordination energy */
@@ -159,18 +141,15 @@ void Atom_Energy( reax_system *system, control_params *control,
     for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
         j = bonds->select.bond_list[pj].nbr;
         type_j = system->my_atoms[j].type;
+	if (type_j < 0) continue;
         bo_ij = &(bonds->select.bond_list[pj].bo_data);
+        sbp_j = &(system->reax_param.sbp[ type_j ]);
         twbp = &(system->reax_param.tbp[ type_i ][ type_j ]);
 
         sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
         sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])*
           ( bo_ij->BO_pi + bo_ij->BO_pi2 );
 
-        /*fprintf( stdout, "%4d%4d%12.6f%12.6f%12.6f\n",
-            i+1, j+1,
-            dfvl * workspace->Delta_lp_temp[j],
-            sbp_j->nlp_opt,
-            workspace->nlp_temp[j] );*/
       }
 
     exp_ovun1 = p_ovun3 * exp( p_ovun4 * sum_ovun2 );
@@ -205,8 +184,14 @@ void Atom_Energy( reax_system *system, control_params *control,
     inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n);
     inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);
 
-    data->my_en.e_un += e_un =
-      -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
+    numbonds = 0;
+    e_un = 0.0;
+    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+      numbonds ++;
+
+    if (numbonds > 0)
+      data->my_en.e_un += e_un =
+        -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
 
     CEunder1 = inv_exp_ovun2n *
       ( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 +
@@ -218,18 +203,15 @@ void Atom_Energy( reax_system *system, control_params *control,
 
     /* tally into per-atom energy */
     if( system->pair_ptr->evflag) {
-      eng_tmp = e_ov + e_un;
+      eng_tmp = e_ov;
+      if (numbonds > 0) eng_tmp += e_un;
+      f_tmp = CEover3 + CEunder3;
       system->pair_ptr->ev_tally(i,i,system->n,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
     }
 
     /* forces */
     workspace->CdDelta[i] += CEover3;   // OvCoor - 2nd term
-    workspace->CdDelta[i] += CEunder3;  // UnCoor - 1st term
-
-#ifdef TEST_FORCES
-    Add_dDelta( system, lists, i, CEover3, workspace->f_ov ); // OvCoor 2nd
-    Add_dDelta( system, lists, i, CEunder3, workspace->f_un ); // UnCoor 1st
-#endif
+    if (numbonds > 0) workspace->CdDelta[i] += CEunder3;  // UnCoor - 1st term
 
     for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
       pbond = &(bonds->select.bond_list[pj]);
@@ -255,72 +237,7 @@ void Atom_Energy( reax_system *system, control_params *control,
       bo_ij->Cdbopi2 += CEunder4 *
         (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);  // UnCoor-2b
 
-
-#ifdef TEST_ENERGY
-/*          fprintf( out_control->eov, "%6d%12.6f\n",
-                   workspace->reverse_map[j],
-                   // CEover1 * twbp->p_ovun1 * twbp->De_s, CEover3,
-                   CEover4 * (1.0 - workspace->dDelta_lp[j]) *
-                   (bo_ij->BO_pi + bo_ij->BO_pi2)
-*///                   /*CEover4 * (workspace->Delta[j]-workspace->Delta_lp[j])*/);
-//          fprintf( out_control->eov, "%6d%12.6f\n",
-//          fprintf( out_control->eov, "%6d%24.15e\n",
-//                   system->my_atoms[j].orig_id,
-                   // CEover1 * twbp->p_ovun1 * twbp->De_s, CEover3,
-//                   CEover4 * (1.0 - workspace->dDelta_lp[j]) *
-//                   (bo_ij->BO_pi + bo_ij->BO_pi2)
-//                   /*CEover4 * (workspace->Delta[j]-workspace->Delta_lp[j])*/);
-
-          // CEunder4 * (1.0 - workspace->dDelta_lp[j]) *
-          // (bo_ij->BO_pi + bo_ij->BO_pi2),
-          // CEunder4 * (workspace->Delta[j] - workspace->Delta_lp[j]) );
-#endif
-
-#ifdef TEST_FORCES
-      Add_dBO( system, lists, i, pj, CEover1 * twbp->p_ovun1 * twbp->De_s,
-               workspace->f_ov ); // OvCoor - 1st term
-
-      Add_dDelta( system, lists, j,
-                  CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
-                  (bo_ij->BO_pi + bo_ij->BO_pi2),
-                  workspace->f_ov );   // OvCoor - 3a
-
-      Add_dBOpinpi2( system, lists, i, pj,
-                     CEover4 * (workspace->Delta[j] -
-                                dfvl * workspace->Delta_lp_temp[j]),
-                     CEover4 * (workspace->Delta[j] -
-                                dfvl * workspace->Delta_lp_temp[j]),
-                     workspace->f_ov, workspace->f_ov ); // OvCoor - 3b
-
-      Add_dDelta( system, lists, j,
-                  CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
-                  (bo_ij->BO_pi + bo_ij->BO_pi2),
-                  workspace->f_un ); // UnCoor - 2a
-
-      Add_dBOpinpi2( system, lists, i, pj,
-                     CEunder4 * (workspace->Delta[j] -
-                                 dfvl * workspace->Delta_lp_temp[j]),
-                     CEunder4 * (workspace->Delta[j] -
-                                 dfvl * workspace->Delta_lp_temp[j]),
-                     workspace->f_un, workspace->f_un ); // UnCoor - 2b
-#endif
     }
 
-#ifdef TEST_ENERGY
-    //fprintf( out_control->elp, "%6d%24.15e%24.15e%24.15e\n",
-    //fprintf( out_control->elp, "%6d%12.4f%12.4f%12.4f\n",
-    //     system->my_atoms[i].orig_id, workspace->nlp[i],
-    //     e_lp, data->my_en.e_lp );
-
-    //fprintf( out_control->eov, "%6d%24.15e%24.15e\n",
-    fprintf( out_control->eov, "%6d%12.4f%12.4f\n",
-             system->my_atoms[i].orig_id,
-             e_ov, data->my_en.e_ov + data->my_en.e_un );
-
-    //fprintf( out_control->eun, "%6d%24.15e%24.15e\n",
-    fprintf( out_control->eun, "%6d%12.4f%12.4f\n",
-             system->my_atoms[i].orig_id,
-             e_un, data->my_en.e_ov + data->my_en.e_un );
-#endif
   }
 }
diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp
index e38c4e2247..5cb9c9ee43 100644
--- a/src/USER-REAXC/reaxc_nonbonded.cpp
+++ b/src/USER-REAXC/reaxc_nonbonded.cpp
@@ -26,17 +26,10 @@
 
 #include "pair_reax_c.h"
 #include "reaxc_types.h"
-#if defined(PURE_REAX)
-#include "nonbonded.h"
-#include "bond_orders.h"
-#include "list.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_nonbonded.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
-#endif
 
 void vdW_Coulomb_Energy( reax_system *system, control_params *control,
                          simulation_data *data, storage *workspace,
@@ -56,7 +49,6 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
   two_body_parameters *twbp;
   far_neighbor_data *nbr_pj;
   reax_list *far_nbrs;
-  // rtensor temp_rtensor, total_rtensor;
 
   // Tallying variables:
   real pe_vdw, f_tmp, delij[3];
@@ -70,19 +62,17 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
   e_lg = de_lg = 0.0;
 
   for( i = 0; i < natoms; ++i ) {
+    if (system->my_atoms[i].type < 0) continue;
     start_i = Start_Index(i, far_nbrs);
     end_i   = End_Index(i, far_nbrs);
     orig_i  = system->my_atoms[i].orig_id;
-    //fprintf( stderr, "i:%d, start_i: %d, end_i: %d\n", i, start_i, end_i );
 
     for( pj = start_i; pj < end_i; ++pj ) {
       nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
       j = nbr_pj->nbr;
+      if (system->my_atoms[j].type < 0) continue;
       orig_j  = system->my_atoms[j].orig_id;
 
-#if defined(PURE_REAX)
-      if( nbr_pj->d <= control->nonb_cut && (j < natoms || orig_i < orig_j) ) {
-#elif defined(LAMMPS_REAX)
       flag = 0;
       if(nbr_pj->d <= control->nonb_cut) {
         if (j < natoms) flag = 1;
@@ -98,14 +88,11 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
       }
 
       if (flag) {
-#endif
 
       r_ij = nbr_pj->d;
       twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
                                        [ system->my_atoms[j].type ]);
 
-      /* Calculate Taper and its derivative */
-      // Tap = nbr_pj->Tap;   -- precomputed during compte_H
       Tap = workspace->Tap[7] * r_ij + workspace->Tap[6];
       Tap = Tap * r_ij + workspace->Tap[5];
       Tap = Tap * r_ij + workspace->Tap[4];
@@ -194,18 +181,11 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
                         f_tmp,delij[0],delij[1],delij[2]);
       }
 
-      /* fprintf(stderr, "%5d %5d %10.6f %10.6f\n",
-        MIN( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ),
-        MAX( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ),
-        CEvd, CEclmb );                 */
-
       if( control->virial == 0 ) {
         rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
         rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
       }
       else { /* NPT, iNPT or sNPT */
-        /* for pressure coupling, terms not related to bond order
-           derivatives are added directly into pressure vector/tensor */
         rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
 
         rvec_ScaledAdd( workspace->f[i], -1., temp );
@@ -213,46 +193,11 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
 
         rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
         rvec_Add( data->my_ext_press, ext_press );
-
-        /* fprintf( stderr, "nonbonded(%d,%d): rel_box (%f %f %f)
-          force(%f %f %f) ext_press (%12.6f %12.6f %12.6f)\n",
-          i, j, nbr_pj->rel_box[0], nbr_pj->rel_box[1], nbr_pj->rel_box[2],
-          temp[0], temp[1], temp[2],
-          data->ext_press[0], data->ext_press[1], data->ext_press[2] );          */
       }
-
-#ifdef TEST_ENERGY
-      // fprintf( out_control->evdw,
-      // "%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f\n",
-      // workspace->Tap[7],workspace->Tap[6],workspace->Tap[5],
-      // workspace->Tap[4],workspace->Tap[3],workspace->Tap[2],
-      // workspace->Tap[1], Tap );
-      //fprintf( out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n",
-      fprintf( out_control->evdw, "%6d%6d%12.4f%12.4f%12.4f\n",
-               system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-               r_ij, e_vdW, data->my_en.e_vdW );
-      //fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-      fprintf( out_control->ecou, "%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
-               system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-               r_ij, system->my_atoms[i].q, system->my_atoms[j].q,
-               e_ele, data->my_en.e_ele );
-#endif
-#ifdef TEST_FORCES
-      rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
-      rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec );
-      rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec );
-      rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec );
-#endif
       }
     }
   }
 
-#if defined(DEBUG)
-  fprintf( stderr, "nonbonded: ext_press (%12.6f %12.6f %12.6f)\n",
-           data->ext_press[0], data->ext_press[1], data->ext_press[2] );
-  MPI_Barrier( MPI_COMM_WORLD );
-#endif
-
   Compute_Polarization_Energy( system, data );
 }
 
@@ -284,6 +229,7 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
 
   for( i = 0; i < natoms; ++i ) {
     type_i  = system->my_atoms[i].type;
+    if (type_i < 0) continue;
     start_i = Start_Index(i,far_nbrs);
     end_i   = End_Index(i,far_nbrs);
     orig_i  = system->my_atoms[i].orig_id;
@@ -291,11 +237,10 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
     for( pj = start_i; pj < end_i; ++pj ) {
       nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
       j = nbr_pj->nbr;
+      type_j = system->my_atoms[j].type;
+      if (type_j < 0) continue;
       orig_j  = system->my_atoms[j].orig_id;
 
-#if defined(PURE_REAX)
-      if( nbr_pj->d <= control->nonb_cut && (j < natoms || orig_i < orig_j) ) {
-#elif defined(LAMMPS_REAX)
       flag = 0;
       if(nbr_pj->d <= control->nonb_cut) {
         if (j < natoms) flag = 1;
@@ -311,22 +256,17 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
       }
 
       if (flag) {
-#endif
-      j = nbr_pj->nbr;
-      type_j = system->my_atoms[j].type;
 
       r_ij   = nbr_pj->d;
       tmin  = MIN( type_i, type_j );
       tmax  = MAX( type_i, type_j );
       t = &( LR[tmin][tmax] );
-      //t = &( LR[type_i][type_j] );
 
       /* Cubic Spline Interpolation */
       r = (int)(r_ij * t->inv_dx);
       if( r == 0 )  ++r;
       base = (real)(r+1) * t->dx;
       dif = r_ij - base;
-      //fprintf(stderr, "r: %f, i: %d, base: %f, dif: %f\n", r, i, base, dif);
 
       e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
         t->vdW[r].a;
@@ -345,7 +285,6 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
         t->CEclmb[r].a;
       CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q;
 
-
       /* tally into per-atom energy */
       if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
         rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
@@ -360,8 +299,6 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
         rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
       }
       else { // NPT, iNPT or sNPT
-        /* for pressure coupling, terms not related to bond order derivatives
-           are added directly into pressure vector/tensor */
         rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
 
         rvec_ScaledAdd( workspace->f[i], -1., temp );
@@ -370,24 +307,6 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
         rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
         rvec_Add( data->my_ext_press, ext_press );
       }
-
-#ifdef TEST_ENERGY
-      //fprintf( out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n",
-      fprintf( out_control->evdw, "%6d%6d%12.4f%12.4f%12.4f\n",
-               system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-               r_ij, e_vdW, data->my_en.e_vdW );
-      //fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-      fprintf( out_control->ecou, "%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
-               system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
-               r_ij, system->my_atoms[i].q, system->my_atoms[j].q,
-               e_ele, data->my_en.e_ele );
-#endif
-#ifdef TEST_FORCES
-      rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
-      rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec );
-      rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec );
-      rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec );
-#endif
       }
     }
   }
@@ -404,8 +323,9 @@ void Compute_Polarization_Energy( reax_system *system, simulation_data *data )
 
   data->my_en.e_pol = 0.0;
   for( i = 0; i < system->n; i++ ) {
-    q = system->my_atoms[i].q;
     type_i = system->my_atoms[i].type;
+    if (type_i < 0) continue;
+    q = system->my_atoms[i].q;
 
     en_tmp = KCALpMOL_to_EV * (system->reax_param.sbp[type_i].chi * q +
                 (system->reax_param.sbp[type_i].eta / 2.) * SQR(q));
@@ -507,17 +427,6 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
   tmp = Tap / dr3gamij_3;
   lr->H = EV_to_KCALpMOL * tmp;
   lr->e_ele = C_ele * tmp;
-  // fprintf( stderr,
-  //    "i:%d(%d), j:%d(%d), gamma:%f, Tap:%f, dr3gamij_3:%f, qi: %f, qj: %f\n",
-  //    i, system->my_atoms[i].type, j, system->my_atoms[j].type,
-  //    twbp->gamma, Tap, dr3gamij_3,
-  //    system->my_atoms[i].q, system->my_atoms[j].q );
 
   lr->CEclmb = C_ele * ( dTap -  Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
-  // fprintf( stdout, "%d %d\t%g\t%g  %g\t%g  %g\t%g  %g\n",
-  //    i+1, j+1, r_ij, e_vdW, CEvd * r_ij,
-  //    system->my_atoms[i].q, system->my_atoms[j].q, e_ele, CEclmb * r_ij );
-
-  // fprintf(stderr,"LR_Lookup: %3d %3d %5.3f-%8.5f %8.5f %8.5f %8.5f %8.5f\n",
-  //   i, j, r_ij, lr->H, lr->e_vdW, lr->CEvd, lr->e_ele, lr->CEclmb ); */
 }
diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp
index d57296a1c1..7c3ba779ab 100644
--- a/src/USER-REAXC/reaxc_reset_tools.cpp
+++ b/src/USER-REAXC/reaxc_reset_tools.cpp
@@ -25,18 +25,10 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "reset_tools.h"
-#include "list.h"
-#include "tool_box.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_reset_tools.h"
 #include "reaxc_list.h"
 #include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
-#endif
-
 
 void Reset_Atoms( reax_system* system, control_params *control )
 {
@@ -47,6 +39,7 @@ void Reset_Atoms( reax_system* system, control_params *control )
   if( control->hbond_cut > 0 )
     for( i = 0; i < system->n; ++i ) {
       atom = &(system->my_atoms[i]);
+      if (atom->type < 0) continue;
       if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
         atom->Hindex = system->numH++;
       else atom->Hindex = -1;
@@ -99,7 +92,6 @@ void Reset_Simulation_Data( simulation_data* data, int virial )
   Reset_Energies( &data->my_en );
   Reset_Energies( &data->sys_en );
   Reset_Temperatures( data );
-  //if( virial )
   Reset_Pressures( data );
 }
 
@@ -117,26 +109,6 @@ void Reset_Timing( reax_timing *rt )
   rt->t_matvecs = 0;
 }
 
-#ifdef TEST_FORCES
-void Reset_Test_Forces( reax_system *system, storage *workspace )
-{
-  memset( workspace->f_ele, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_vdw, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_bo, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_be, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_lp, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_ov, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_un, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_ang, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_coa, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_pen, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_hb, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_tor, 0, system->total_cap * sizeof(rvec) );
-  memset( workspace->f_con, 0, system->total_cap * sizeof(rvec) );
-}
-#endif
-
-
 void Reset_Workspace( reax_system *system, storage *workspace )
 {
   memset( workspace->total_bond_order, 0, system->total_cap * sizeof( real ) );
@@ -144,10 +116,6 @@ void Reset_Workspace( reax_system *system, storage *workspace )
   memset( workspace->CdDelta, 0, system->total_cap * sizeof( real ) );
   memset( workspace->f, 0, system->total_cap * sizeof( rvec ) );
 
-#ifdef TEST_FORCES
-  memset( workspace->dDelta, 0, sizeof(rvec) * system->total_cap );
-  Reset_Test_Forces( system, workspace );
-#endif
 }
 
 
@@ -205,10 +173,6 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
     }
   }
 
-  // fprintf( stderr, "p%d: n:%d num_intrs:%d  num_H:%d\n",
-  //   system->my_rank, hbonds->n, hbonds->num_intrs, workspace->num_H );
-  // MPI_Barrier( comm );
-  /* hbonds list */
   if( control->hbond_cut > 0 && system->numH > 0 ) {
     hbonds = (*lists) + HBONDS;
     total_hbonds = 0;
@@ -234,8 +198,6 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
       }
     }
   }
-  // fprintf( stderr, "p%d: cleared hbonds\n", system->my_rank );
-  // MPI_Barrier( comm );
 }
 
 
@@ -250,9 +212,4 @@ void Reset( reax_system *system, control_params *control, simulation_data *data,
 
   Reset_Neighbor_Lists( system, control, workspace, lists, comm );
 
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d @ step%d: reset done\n", system->my_rank, data->step );
-  MPI_Barrier( comm );
-#endif
-
 }
diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp
index 0410b625a9..f9abcc770a 100644
--- a/src/USER-REAXC/reaxc_system_props.cpp
+++ b/src/USER-REAXC/reaxc_system_props.cpp
@@ -25,16 +25,9 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "system_props.h"
-#include "tool_box.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_system_props.h"
 #include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
-#endif
-
 
 void Temperature_Control( control_params *control, simulation_data *data )
 {
@@ -255,36 +248,8 @@ void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
   /* Compute the rotational energy */
   data->erot_cm = 0.5 * E_CONV * rvec_Dot( data->avcm, data->amcm );
 
-#if defined(DEBUG)
-  fprintf( stderr, "xcm:  %24.15e %24.15e %24.15e\n",
-           data->xcm[0], data->xcm[1], data->xcm[2] );
-  fprintf( stderr, "vcm:  %24.15e %24.15e %24.15e\n",
-           data->vcm[0], data->vcm[1], data->vcm[2] );
-  fprintf( stderr, "amcm: %24.15e %24.15e %24.15e\n",
-           data->amcm[0], data->amcm[1], data->amcm[2] );
-  /* fprintf( stderr, "mat:  %f %f %f\n     %f %f %f\n     %f %f %f\n",
-     mat[0][0], mat[0][1], mat[0][2],
-     mat[1][0], mat[1][1], mat[1][2],
-     mat[2][0], mat[2][1], mat[2][2] );
-     fprintf( stderr, "inv:  %g %g %g\n     %g %g %g\n     %g %g %g\n",
-     inv[0][0], inv[0][1], inv[0][2],
-     inv[1][0], inv[1][1], inv[1][2],
-     inv[2][0], inv[2][1], inv[2][2] ); */
-  fprintf( stderr, "avcm: %24.15e %24.15e %24.15e\n",
-           data->avcm[0], data->avcm[1], data->avcm[2] );
-#endif
 }
 
-
-
-/* IMPORTANT: This function assumes that current kinetic energy
- * the system is already computed
- *
- * IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
- *  to be added when there are long-range interactions or long-range
- *  corrections to short-range interactions present.
- *  We may want to add that for more accuracy.
- */
 void Compute_Pressure(reax_system* system, control_params *control,
                       simulation_data* data, mpi_datatypes *mpi_data)
 {
@@ -308,35 +273,14 @@ void Compute_Pressure(reax_system* system, control_params *control,
       rvec_Multiply( tmp, p_atom->f, tx );
       rvec_Add( int_press, tmp );
 
-#if defined(DEBUG)
-      fprintf( stderr, "%8d%8.2f%8.2f%8.2f",
-               i+1, p_atom->x[0], p_atom->x[1], p_atom->x[2] );
-      fprintf( stderr, "%8.2f%8.2f%8.2f",
-               p_atom->f[0], p_atom->f[1], p_atom->f[2] );
-      fprintf( stderr, "%8.2f%8.2f%8.2f\n",
-               int_press[0], int_press[1], int_press[2] );
-#endif
     }
   }
 
   /* sum up internal and external pressure */
-#if defined(DEBUG)
-  fprintf(stderr,"p%d:p_int(%10.5f %10.5f %10.5f)p_ext(%10.5f %10.5f %10.5f)\n",
-          system->my_rank, int_press[0], int_press[1], int_press[2],
-          data->my_ext_press[0], data->my_ext_press[1], data->my_ext_press[2] );
-#endif
   MPI_Allreduce( int_press, data->int_press,
                  3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
   MPI_Allreduce( data->my_ext_press, data->ext_press,
                  3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
-#if defined(DEBUG)
-  fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n",
-           system->my_rank,
-           data->int_press[0], data->int_press[1], data->int_press[2] );
-  fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n",
-           system->my_rank,
-           data->ext_press[0], data->ext_press[1], data->ext_press[2] );
-#endif
 
   /* kinetic contribution */
   data->kin_press = 2.*(E_CONV*data->sys_en.e_kin) / (3.*big_box->V*P_CONV);
@@ -354,63 +298,6 @@ void Compute_Pressure(reax_system* system, control_params *control,
     (( data->int_press[2] + data->ext_press[2] ) /
      ( big_box->box_norms[0] * big_box->box_norms[1] * P_CONV ));
 
-  /* Average pressure for the whole box */
   data->iso_bar.P =
     ( data->tot_press[0] + data->tot_press[1] + data->tot_press[2] ) / 3.;
 }
-
-
-
-/*
-void Compute_Pressure_Isotropic_Klein( reax_system* system,
-                                       simulation_data* data )
-{
-  int i;
-  reax_atom *p_atom;
-  rvec dx;
-
-  // IMPORTANT: This function assumes that current kinetic energy and
-  // the center of mass of the system is already computed before.
-  data->iso_bar.P = 2.0 * data->my_en.e_kin;
-
-  for( i = 0; i < system->N; ++i ) {
-    p_atom = &( system->my_atoms[i] );
-    rvec_ScaledSum(dx,1.0,p_atom->x,-1.0,data->xcm);
-    data->iso_bar.P += ( -F_CONV * rvec_Dot(p_atom->f, dx) );
-  }
-
-  data->iso_bar.P /= (3.0 * system->my_box.V);
-
-  // IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
-  // to be added when there are long-range interactions or long-range
-  // corrections to short-range interactions present.
-  // We may want to add that for more accuracy.
-}
-
-
-void Compute_Pressure( reax_system* system, simulation_data* data )
-{
-  int i;
-  reax_atom *p_atom;
-  rtensor temp;
-
-  rtensor_MakeZero( data->flex_bar.P );
-
-  for( i = 0; i < system->N; ++i ) {
-    p_atom = &( system->my_atoms[i] );
-
-    // Distance_on_T3_Gen( data->rcm, p_atom->x, &(system->my_box), &dx );
-
-    rvec_OuterProduct( temp, p_atom->v, p_atom->v );
-    rtensor_ScaledAdd( data->flex_bar.P,
-                       system->reax_param.sbp[ p_atom->type ].mass, temp );
-
-    // rvec_OuterProduct(temp,workspace->virial_forces[i],p_atom->x); //dx);
-    rtensor_ScaledAdd( data->flex_bar.P, -F_CONV, temp );
-  }
-
-  rtensor_Scale( data->flex_bar.P, 1.0 / system->my_box.V, data->flex_bar.P );
-
-  data->iso_bar.P = rtensor_Trace( data->flex_bar.P ) / 3.0;
-}
-*/
diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp
index 5f18a9800c..55feac209f 100644
--- a/src/USER-REAXC/reaxc_tool_box.cpp
+++ b/src/USER-REAXC/reaxc_tool_box.cpp
@@ -25,67 +25,13 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "tool_box.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_tool_box.h"
-#endif
 
-
-#if defined(PURE_REAX)
-/************** taken from comm_tools.c **************/
-int SumScan( int n, int me, int root, MPI_Comm comm )
-{
-  int  i, my_order, wsize;;
-  int *nbuf = NULL;
-
-  if( me == root ) {
-    MPI_Comm_size( comm, &wsize );
-    nbuf = (int *) calloc( wsize, sizeof(int) );
-
-    MPI_Gather( &n, 1, MPI_INT, nbuf, 1, MPI_INT, root, comm );
-
-    for( i = 0; i < wsize-1; ++i ) {
-      nbuf[i+1] += nbuf[i];
-    }
-
-    MPI_Scatter( nbuf, 1, MPI_INT, &my_order, 1, MPI_INT, root, comm );
-
-    free( nbuf );
-  }
-  else {
-    MPI_Gather( &n, 1, MPI_INT, nbuf, 1, MPI_INT, root, comm );
-    MPI_Scatter( nbuf, 1, MPI_INT, &my_order, 1, MPI_INT, root, comm );
-  }
-
-  return my_order;
-}
-
-
-void SumScanB( int n, int me, int wsize, int root, MPI_Comm comm, int *nbuf )
-{
-  int  i;
-
-  MPI_Gather( &n, 1, MPI_INT, nbuf, 1, MPI_INT, root, comm );
-
-  if( me == root ) {
-    for( i = 0; i < wsize-1; ++i )
-      nbuf[i+1] += nbuf[i];
-  }
-
-  MPI_Bcast( nbuf, wsize, MPI_INT, root, comm );
-}
-#endif
-
-
-/************** taken from box.c **************/
 void Transform( rvec x1, simulation_box *box, char flag, rvec x2 )
 {
   int i, j;
   real tmp;
 
-  //  printf(">x1: (%lf, %lf, %lf)\n",x1[0],x1[1],x1[2]);
-
   if (flag > 0) {
     for (i=0; i < 3; i++) {
       tmp = 0.0;
@@ -102,7 +48,6 @@ void Transform( rvec x1, simulation_box *box, char flag, rvec x2 )
       x2[i] = tmp;
     }
   }
-  //  printf(">x2: (%lf, %lf, %lf)\n", x2[0], x2[1], x2[2]);
 }
 
 
@@ -115,8 +60,6 @@ void Transform_to_UnitBox( rvec x1, simulation_box *box, char flag, rvec x2 )
   x2[2] /= box->box_norms[2];
 }
 
-
-/* determine whether point p is inside the box */
 void Fit_to_Periodic_Box( simulation_box *box, rvec *p )
 {
   int i;
@@ -135,126 +78,6 @@ void Fit_to_Periodic_Box( simulation_box *box, rvec *p )
   }
 }
 
-#if defined(PURE_REAX)
-/* determine the touch point, tp, of a box to
-   its neighbor denoted by the relative coordinate rl */
-inline void Box_Touch_Point( simulation_box *box, ivec rl, rvec tp )
-{
-  int d;
-
-  for( d = 0; d < 3; ++d )
-    if( rl[d] == -1 )
-      tp[d] = box->min[d];
-    else if( rl[d] == 0 )
-      tp[d] = NEG_INF - 1.;
-    else
-      tp[d] = box->max[d];
-}
-
-
-/* determine whether point p is inside the box */
-/* assumes orthogonal box */
-inline int is_Inside_Box( simulation_box *box, rvec p )
-{
-  if( p[0] < box->min[0] || p[0] >= box->max[0] ||
-      p[1] < box->min[1] || p[1] >= box->max[1] ||
-      p[2] < box->min[2] || p[2] >= box->max[2] )
-     return 0;
-
-  return 1;
-}
-
-
-inline int iown_midpoint( simulation_box *box, rvec p1, rvec p2 )
-{
-  rvec midp;
-
-  midp[0] = (p1[0] + p2[0]) / 2;
-  midp[1] = (p1[1] + p2[1]) / 2;
-  midp[2] = (p1[2] + p2[2]) / 2;
-
-  if( midp[0] < box->min[0] || midp[0] >= box->max[0] ||
-      midp[1] < box->min[1] || midp[1] >= box->max[1] ||
-      midp[2] < box->min[2] || midp[2] >= box->max[2] )
-     return 0;
-
-  return 1;
-}
-
-
-
-/**************** from grid.c ****************/
-/* finds the closest point of grid cell cj to ci.
-   no need to consider periodic boundary conditions as in the serial case
-   because the box of a process is not periodic in itself */
-inline void GridCell_Closest_Point( grid_cell *gci, grid_cell *gcj,
-                                    ivec ci, ivec cj, rvec cp )
-{
-  int  d;
-
-  for( d = 0; d < 3; d++ )
-    if( cj[d] > ci[d] )
-      cp[d] = gcj->min[d];
-    else if ( cj[d] == ci[d] )
-      cp[d] = NEG_INF - 1.;
-    else
-      cp[d] = gcj->max[d];
-}
-
-
-
-inline void GridCell_to_Box_Points( grid_cell *gc, ivec rl, rvec cp, rvec fp )
-{
-  int d;
-
-  for( d = 0; d < 3; ++d )
-    if( rl[d] == -1 ) {
-      cp[d] = gc->min[d];
-      fp[d] = gc->max[d];
-    }
-    else if( rl[d] == 0 ) {
-      cp[d] = fp[d] = NEG_INF - 1.;
-    }
-    else{
-      cp[d] = gc->max[d];
-      fp[d] = gc->min[d];
-    }
-}
-
-
-inline real DistSqr_between_Special_Points( rvec sp1, rvec sp2 )
-{
-  int  i;
-  real d_sqr = 0;
-
-  for( i = 0; i < 3; ++i )
-    if( sp1[i] > NEG_INF && sp2[i] > NEG_INF )
-      d_sqr += SQR( sp1[i] - sp2[i] );
-
-  return d_sqr;
-}
-
-
-inline real DistSqr_to_Special_Point( rvec cp, rvec x )
-{
-  int  i;
-  real d_sqr = 0;
-
-  for( i = 0; i < 3; ++i )
-    if( cp[i] > NEG_INF )
-      d_sqr += SQR( cp[i] - x[i] );
-
-  return d_sqr;
-}
-
-
-inline int Relative_Coord_Encoding( ivec c )
-{
-  return 9 * (c[0] + 1) + 3 * (c[1] + 1) + (c[2] + 1);
-}
-#endif
-
-
 /************** from geo_tools.c *****************/
 void Make_Point( real x, real y, real z, rvec* p )
 {
@@ -267,14 +90,6 @@ void Make_Point( real x, real y, real z, rvec* p )
 
 int is_Valid_Serial( storage *workspace, int serial )
 {
-  // if( workspace->map_serials[ serial ] < 0 )
-  // {
-  // fprintf( stderr, "CONECT line includes invalid pdb serial number %d.\n",
-  // serial );
-  // fprintf( stderr, "Please correct the input file.Terminating...\n" );
-  //  MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
-  // }
-
   return SUCCESS;
 }
 
@@ -303,8 +118,6 @@ void Trim_Spaces( char *element )
   element[j-i] = 0; // finalize the string
 }
 
-
-/************ from system_props.c *************/
 struct timeval tim;
 real t_end;
 
@@ -331,8 +144,6 @@ void Update_Timing_Info( real *t_start, real *timing )
   *t_start = t_end;
 }
 
-
-/*********** from io_tools.c **************/
 int Get_Atom_Type( reax_interaction *reax_param, char *s, MPI_Comm comm )
 {
   int i;
@@ -402,8 +213,6 @@ int Tokenize( char* s, char*** tok )
   return count;
 }
 
-
-/***************** taken from lammps ************************/
 /* safe malloc */
 void *smalloc( long n, const char *name, MPI_Comm comm )
 {
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index b19598d97c..16f6a4539f 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -25,19 +25,11 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "torsion_angles.h"
-#include "bond_orders.h"
-#include "list.h"
-#include "tool_box.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_torsion_angles.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"
 #include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
-#endif
 
 #define MIN_SINE 1e-10
 
@@ -71,12 +63,6 @@ real Calculate_Omega( rvec dvec_ij, real r_ij,
 
   omega = atan2( unnorm_sin_omega, unnorm_cos_omega );
 
-
-  /* derivatives */
-  /* coef for adjusments to cos_theta's */
-  /* rla = r_ij, rlb = r_jk, rlc = r_kl, r4 = r_li;
-     coshd = cos_ijk, coshe = cos_jkl;
-     sinhd = sin_ijk, sinhe = sin_jkl; */
   htra = r_ij + cos_ijk * ( r_kl * cos_jkl - r_jk );
   htrb = r_jk - r_ij * cos_ijk - r_kl * cos_jkl;
   htrc = r_kl + cos_jkl * ( r_ij * cos_ijk - r_jk );
@@ -87,7 +73,6 @@ real Calculate_Omega( rvec dvec_ij, real r_ij,
   hnhd = r_ij * r_kl * cos_ijk * sin_jkl;
   hnhe = r_ij * r_kl * sin_ijk * cos_jkl;
 
-
   poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl;
   if( poem < 1e-20 ) poem = 1e-20;
 
@@ -99,27 +84,6 @@ real Calculate_Omega( rvec dvec_ij, real r_ij,
   if( arg >  1.0 ) arg =  1.0;
   if( arg < -1.0 ) arg = -1.0;
 
-
-  /* fprintf( out_control->etor,
-     "%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f\n",
-     htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe );
-     fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
-     dvec_ij[0]/r_ij, dvec_ij[1]/r_ij, dvec_ij[2]/r_ij );
-     fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
-     -dvec_jk[0]/r_jk, -dvec_jk[1]/r_jk, -dvec_jk[2]/r_jk );
-     fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
-     -dvec_kl[0]/r_kl, -dvec_kl[1]/r_kl, -dvec_kl[2]/r_kl );
-     fprintf( out_control->etor, "%12.6f%12.6f%12.6f%12.6f\n",
-     r_li, dvec_li[0], dvec_li[1], dvec_li[2] );
-     fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
-     poem, tel, arg ); */
-  /* fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
-     -p_ijk->dcos_dk[0]/sin_ijk, -p_ijk->dcos_dk[1]/sin_ijk,
-     -p_ijk->dcos_dk[2]/sin_ijk );
-     fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
-     -p_jkl->dcos_dk[0]/sin_jkl, -p_jkl->dcos_dk[1]/sin_jkl,
-     -p_jkl->dcos_dk[2]/sin_jkl );*/
-
   if( sin_ijk >= 0 && sin_ijk <= MIN_SINE ) sin_ijk = MIN_SINE;
   else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE ) sin_ijk = -MIN_SINE;
   if( sin_jkl >= 0 && sin_jkl <= MIN_SINE ) sin_jkl = MIN_SINE;
@@ -160,7 +124,7 @@ void Torsion_Angles( reax_system *system, control_params *control,
 {
   int i, j, k, l, pi, pj, pk, pl, pij, plk, natoms;
   int type_i, type_j, type_k, type_l;
-  int start_j, end_j;
+  int start_j, end_j, start_k, end_k;
   int start_pj, end_pj, start_pk, end_pk;
   int num_frb_intrs = 0;
 
@@ -198,15 +162,10 @@ void Torsion_Angles( reax_system *system, control_params *control,
   real p_cot2 = system->reax_param.gp.l[27];
   reax_list *bonds = (*lists) + BONDS;
   reax_list *thb_intrs = (*lists) + THREE_BODIES;
-  // char  fname[100];
-  // FILE *ftor;
 
   // Virial tallying variables
   real delil[3], deljl[3], delkl[3];
-  real eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3];
-
-  // sprintf( fname, "tor%d.out", system->my_rank );
-  // ftor = fopen( fname, "w" );
+  real eng_tmp, f_scaler, fi_tmp[3], fj_tmp[3], fk_tmp[3];
 
   natoms = system->n;
 
@@ -222,16 +181,12 @@ void Torsion_Angles( reax_system *system, control_params *control,
       bo_jk = &( pbond_jk->bo_data );
       BOA_jk = bo_jk->BO - control->thb_cut;
 
-      /* see if there are any 3-body interactions involving j&k
-         where j is the central atom. Otherwise there is no point in
-         trying to form a 4-body interaction out of this neighborhood */
       if( system->my_atoms[j].orig_id < system->my_atoms[k].orig_id &&
           bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs) ) {
+        start_k = Start_Index(k, bonds);
+        end_k = End_Index(k, bonds);
         pj = pbond_jk->sym_index; // pj points to j on k's list
 
-        /* do the same check as above:
-           are there any 3-body interactions involving k&j
-           where k is the central atom */
         if( Num_Entries(pj, thb_intrs) ) {
           type_k = system->my_atoms[k].type;
           Delta_k = workspace->Delta_boc[k];
@@ -249,15 +204,12 @@ void Torsion_Angles( reax_system *system, control_params *control,
           exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
           f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
 
-
-          /* pick i up from j-k interaction where j is the central atom */
           for( pi = start_pk; pi < end_pk; ++pi ) {
             p_ijk = &( thb_intrs->select.three_body_list[pi] );
             pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
             pbond_ij = &( bonds->select.bond_list[pij] );
             bo_ij = &( pbond_ij->bo_data );
 
-
             if( bo_ij->BO > control->thb_cut/*0*/ ) {
               i = p_ijk->thb;
               type_i = system->my_atoms[i].type;
@@ -277,8 +229,6 @@ void Torsion_Angles( reax_system *system, control_params *control,
               exp_tor2_ij = exp( -p_tor2 * BOA_ij );
               exp_cot2_ij = exp( -p_cot2 * SQR(BOA_ij -1.5) );
 
-
-              /* pick l up from j-k interaction where k is the central atom */
               for( pl = start_pj; pl < end_pj; ++pl ) {
                 p_jkl = &( thb_intrs->select.three_body_list[pl] );
                 l = p_jkl->thb;
@@ -291,7 +241,6 @@ void Torsion_Angles( reax_system *system, control_params *control,
                 fbp = &(system->reax_param.fbp[type_i][type_j]
                         [type_k][type_l].prm[0]);
 
-
                 if( i != l && fbh->cnt &&
                     bo_kl->BO > control->thb_cut/*0*/ &&
                     bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/ ){
@@ -371,7 +320,6 @@ void Torsion_Angles( reax_system *system, control_params *control,
                      1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega)));
                   /* end  of torsion energy */
 
-
                   /* 4-body conjugation energy */
                   fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
                   data->my_en.e_con += e_con =
@@ -512,104 +460,6 @@ void Torsion_Angles( reax_system *system, control_params *control,
                     if( system->pair_ptr->vflag_atom)
                             system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl);
                   }
-
-
-#ifdef TEST_ENERGY
-                  /* fprintf( out_control->etor,
-                     "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
-                     r_ij, r_jk, r_kl, cos_ijk, cos_jkl, sin_ijk, sin_jkl );
-                     fprintf( out_control->etor, "%12.8f\n", dfn11 ); */
-                  /* fprintf( out_control->etor,
-                     "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
-                     CEtors2, CEtors3, CEtors4, CEtors5, CEtors6,
-                     CEtors7, CEtors8, CEtors9 ); */
-                  /* fprintf( out_control->etor,
-                     "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
-                     htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe ); */
-                  /* fprintf( out_control->etor,
-                     "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
-                     CEconj1, CEconj2, CEconj3, CEconj4, CEconj5, CEconj6 ); */
-
-                  /* fprintf( out_control->etor, "%12.6f%12.6f%12.6f%12.6f\n",
-                     fbp->V1, fbp->V2, fbp->V3, fbp->p_tor1 );*/
-
-                  fprintf(out_control->etor,
-                          //"%6d%6d%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
-                          "%6d%6d%6d%6d%12.4f%12.4f%12.4f%12.4f\n",
-                          system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
-                          system->my_atoms[k].orig_id,system->my_atoms[l].orig_id,
-                           RAD2DEG(omega), BOA_jk, e_tor, data->my_en.e_tor );
-
-                  fprintf(out_control->econ,
-                          //"%6d%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-                          "%6d%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n",
-                          system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
-                          system->my_atoms[k].orig_id,system->my_atoms[l].orig_id,
-                          RAD2DEG(omega), BOA_ij, BOA_jk, BOA_kl,
-                          e_con, data->my_en.e_con );
-#endif
-
-#ifdef TEST_FORCES
-                  /* Torsion Forces */
-                  Add_dBOpinpi2( system, lists, j, pk, CEtors2, 0.0,
-                                 workspace->f_tor, workspace->f_tor );
-                  Add_dDelta( system, lists, j, CEtors3, workspace->f_tor );
-                  Add_dDelta( system, lists, k, CEtors3, workspace->f_tor );
-                  Add_dBO( system, lists, j, pij, CEtors4, workspace->f_tor );
-                  Add_dBO( system, lists, j, pk, CEtors5, workspace->f_tor );
-                  Add_dBO( system, lists, k, plk, CEtors6, workspace->f_tor );
-
-                  rvec_ScaledAdd( workspace->f_tor[i],
-                                  CEtors7, p_ijk->dcos_dk );
-                  rvec_ScaledAdd( workspace->f_tor[j],
-                                  CEtors7, p_ijk->dcos_dj );
-                  rvec_ScaledAdd( workspace->f_tor[k],
-                                  CEtors7, p_ijk->dcos_di );
-
-                  rvec_ScaledAdd( workspace->f_tor[j],
-                                  CEtors8, p_jkl->dcos_di );
-                  rvec_ScaledAdd( workspace->f_tor[k],
-                                  CEtors8, p_jkl->dcos_dj );
-                  rvec_ScaledAdd( workspace->f_tor[l],
-                                  CEtors8, p_jkl->dcos_dk );
-
-                  rvec_ScaledAdd( workspace->f_tor[i],
-                                  CEtors9, dcos_omega_di );
-                  rvec_ScaledAdd( workspace->f_tor[j],
-                                  CEtors9, dcos_omega_dj );
-                  rvec_ScaledAdd( workspace->f_tor[k],
-                                  CEtors9, dcos_omega_dk );
-                  rvec_ScaledAdd( workspace->f_tor[l],
-                                  CEtors9, dcos_omega_dl );
-
-                  /* Conjugation Forces */
-                  Add_dBO( system, lists, j, pij, CEconj1, workspace->f_con );
-                  Add_dBO( system, lists, j, pk, CEconj2, workspace->f_con );
-                  Add_dBO( system, lists, k, plk, CEconj3, workspace->f_con );
-
-                  rvec_ScaledAdd( workspace->f_con[i],
-                                  CEconj4, p_ijk->dcos_dk );
-                  rvec_ScaledAdd( workspace->f_con[j],
-                                  CEconj4, p_ijk->dcos_dj );
-                  rvec_ScaledAdd( workspace->f_con[k],
-                                  CEconj4, p_ijk->dcos_di );
-
-                  rvec_ScaledAdd( workspace->f_con[j],
-                                  CEconj5, p_jkl->dcos_di );
-                  rvec_ScaledAdd( workspace->f_con[k],
-                                  CEconj5, p_jkl->dcos_dj );
-                  rvec_ScaledAdd( workspace->f_con[l],
-                                  CEconj5, p_jkl->dcos_dk );
-
-                  rvec_ScaledAdd( workspace->f_con[i],
-                                  CEconj6, dcos_omega_di );
-                  rvec_ScaledAdd( workspace->f_con[j],
-                                  CEconj6, dcos_omega_dj );
-                  rvec_ScaledAdd( workspace->f_con[k],
-                                  CEconj6, dcos_omega_dk );
-                  rvec_ScaledAdd( workspace->f_con[l],
-                                  CEconj6, dcos_omega_dl );
-#endif
                 } // pl check ends
               } // pl loop ends
             } // pi check ends
@@ -618,13 +468,4 @@ void Torsion_Angles( reax_system *system, control_params *control,
       } // j<k && j-k neighbor check ends
     } // pk loop ends
   } // j loop
-
-#if defined(DEBUG)
-  fprintf( stderr, "Number of torsion angles: %d\n", num_frb_intrs );
-  fprintf( stderr, "Torsion Energy: %g\t Conjugation Energy: %g\n",
-           data->my_en.e_tor, data->my_en.e_con );
-
-  fprintf( stderr, "4body: ext_press (%12.6f %12.6f %12.6f)\n",
-           data->ext_press[0], data->ext_press[1], data->ext_press[2] );
-#endif
 }
diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp
index e74cb4ef52..3a94ed45ef 100644
--- a/src/USER-REAXC/reaxc_traj.cpp
+++ b/src/USER-REAXC/reaxc_traj.cpp
@@ -25,56 +25,9 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "traj.h"
-#include "list.h"
-#include "tool_box.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_traj.h"
 #include "reaxc_list.h"
 #include "reaxc_tool_box.h"
-#endif
-
-
-#if defined(PURE_REAX)
-int Set_My_Trajectory_View( MPI_File trj, int offset, MPI_Datatype etype,
-                            MPI_Comm comm, int my_rank, int my_n, int big_n )
-{
-  int my_disp;
-  int length[3];
-  MPI_Aint line_len;
-  MPI_Aint disp[3];
-  MPI_Datatype type[3];
-  MPI_Datatype view;
-
-  /* line length inferred from etype */
-  MPI_Type_extent( etype, &line_len );
-  line_len /= sizeof(char);
-
-  /* determine where to start writing into the mpi file */
-  my_disp = SumScan( my_n, my_rank, MASTER_NODE, comm );
-  my_disp -= my_n;
-
-  /* create atom_info_view */
-  length[0] = 1;
-  length[1] = my_n;
-  length[2] = 1;
-  disp[0] = 0;
-  disp[1] = line_len * my_disp;
-  disp[2] = line_len * big_n;
-  type[0] = MPI_LB;
-  type[1] = etype;
-  type[2] = MPI_UB;
-
-  MPI_Type_struct( 3, length, disp, type, &view );
-  MPI_Type_commit( &view );
-
-  MPI_File_set_view( trj, offset, etype, view, "native", MPI_INFO_NULL );
-
-  return my_disp;
-}
-#endif
-
 
 int Reallocate_Output_Buffer( output_controls *out_control, int req_space,
                               MPI_Comm comm )
@@ -98,31 +51,9 @@ int Reallocate_Output_Buffer( output_controls *out_control, int req_space,
 void Write_Skip_Line( output_controls *out_control, mpi_datatypes *mpi_data,
                       int my_rank, int skip, int num_section )
 {
-#if defined(PURE_REAX)
-  MPI_Status status;
-
-  if( out_control->traj_method == MPI_TRAJ ) {
-    MPI_File_set_view( out_control->trj, out_control->trj_offset,
-                       mpi_data->header_line, mpi_data->header_line,
-                       "native", MPI_INFO_NULL );
-    if( my_rank == MASTER_NODE ) {
-      sprintf( out_control->line, INT2_LINE, "chars_to_skip_section:",
-               skip, num_section );
-      MPI_File_write( out_control->trj, out_control->line, 1,
-                      mpi_data->header_line, &status );
-    }
-    out_control->trj_offset += HEADER_LINE_LEN;
-  }
-  else {
-    if( my_rank == MASTER_NODE )
-      fprintf( out_control->strj, INT2_LINE,
-               "chars_to_skip_section:", skip, num_section );
-  }
-#elif defined(LAMMPS_REAX)
   if( my_rank == MASTER_NODE )
     fprintf( out_control->strj, INT2_LINE,
              "chars_to_skip_section:", skip, num_section );
-#endif
 
 }
 
@@ -191,14 +122,6 @@ int Write_Header( reax_system *system, control_params *control,
              (control->restart ? "yes" : "no") );
     strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
 
-    //sprintf( out_control->line, STR_LINE, "restarted_from_file:",
-    //     (control->restart ? control->restart_from : "NA") );
-    //strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
-    //sprintf( out_control->line, STR_LINE, "kept_restart_velocities?:",
-    //     (control->restart ? (control->random_vel ? "no":"yes"):"NA") );
-    //strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
     sprintf( out_control->line, STR_LINE, "write_restart_files?:",
              ((out_control->restart_freq > 0) ? "yes" : "no") );
     strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
@@ -330,25 +253,8 @@ int Write_Header( reax_system *system, control_params *control,
   }
 
   /* dump out the buffer */
-#if defined(PURE_REAX)
-  if( out_control->traj_method == MPI_TRAJ ) {
-    out_control->trj_offset = 0;
-    Set_My_Trajectory_View( out_control->trj,
-                            out_control->trj_offset, mpi_data->header_line,
-                            mpi_data->world, system->my_rank,
-                            my_hdr_lines, num_hdr_lines );
-    MPI_File_write_all( out_control->trj, out_control->buffer,
-                        num_hdr_lines, mpi_data->header_line, MPI_STATUS_IGNORE );
-    out_control->trj_offset = (num_hdr_lines) * HEADER_LINE_LEN;
-  }
-  else {
-    if( system->my_rank == MASTER_NODE )
-      fprintf( out_control->strj, "%s", out_control->buffer );
-  }
-#elif defined(LAMMPS_REAX)
   if( system->my_rank == MASTER_NODE )
     fprintf( out_control->strj, "%s", out_control->buffer );
-#endif
 
   return SUCCESS;
 }
@@ -387,33 +293,6 @@ int Write_Init_Desc( reax_system *system, control_params *control,
              out_control->line, INIT_DESC_LEN+1 );
   }
 
-#if defined(PURE_REAX)
-  if( out_control->traj_method == MPI_TRAJ ) {
-    Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
-                            mpi_data->init_desc_line, mpi_data->world,
-                            me, system->n, system->bigN );
-    MPI_File_write( out_control->trj, out_control->buffer, system->n,
-                    mpi_data->init_desc_line, &status );
-    out_control->trj_offset += system->bigN * INIT_DESC_LEN;
-  }
-  else{
-    if( me != MASTER_NODE )
-      MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
-                np * INIT_DESCS + me, mpi_data->world );
-    else{
-      buffer_len = system->n * INIT_DESC_LEN;
-      for( i = 0; i < np; ++i )
-        if( i != MASTER_NODE ) {
-          MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
-                    MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status );
-          MPI_Get_count( &status, MPI_CHAR, &cnt );
-          buffer_len += cnt;
-        }
-      out_control->buffer[buffer_len] = 0;
-      fprintf( out_control->strj, "%s", out_control->buffer );
-    }
-  }
-#elif defined(LAMMPS_REAX)
   if( me != MASTER_NODE )
     MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
               np * INIT_DESCS + me, mpi_data->world );
@@ -429,7 +308,6 @@ int Write_Init_Desc( reax_system *system, control_params *control,
     out_control->buffer[buffer_len] = 0;
     fprintf( out_control->strj, "%s", out_control->buffer );
   }
-#endif
 
   return SUCCESS;
 }
@@ -464,58 +342,7 @@ int Init_Traj( reax_system *system, control_params *control,
   out_control->buffer_len = 0;
   out_control->buffer = NULL;
 
-  /* fprintf( stderr, "p%d: init_traj: atom_line_len = %d "                \
-     "bond_line_len = %d, angle_line_len = %d\n"                        \
-     "max_line = %d, max_buffer_size = %d\n",
-     system->my_rank, out_control->atom_line_len,
-     out_control->bond_line_len, out_control->angle_line_len,
-     MAX_TRJ_LINE_LEN, MAX_TRJ_BUFFER_SIZE ); */
-
   /* write trajectory header and atom info, if applicable */
-#if defined(PURE_REAX)
-  if( out_control->traj_method == MPI_TRAJ ) {
-    /* attemp to delete the file to get rid of remnants of previous runs */
-    if( system->my_rank == MASTER_NODE ) {
-      MPI_File_delete( fname, MPI_INFO_NULL );
-    }
-
-    /* open a fresh trajectory file */
-    if( MPI_File_open( mpi_data->world, fname,
-                       MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL,
-                       &(out_control->trj) ) ) {
-      strcpy( msg, "init_traj: unable to open trajectory file" );
-      return FAILURE;
-    }
-
-    /* build the mpi structs for trajectory */
-    /* header_line */
-    MPI_Type_contiguous( HEADER_LINE_LEN, MPI_CHAR, &(mpi_data->header_line) );
-    MPI_Type_commit( &(mpi_data->header_line) );
-    /* init_desc_line */
-    MPI_Type_contiguous( INIT_DESC_LEN, MPI_CHAR, &(mpi_data->init_desc_line) );
-    MPI_Type_commit( &(mpi_data->init_desc_line) );
-    /* atom */
-    MPI_Type_contiguous( out_control->atom_line_len, MPI_CHAR,
-                         &(mpi_data->atom_line) );
-    MPI_Type_commit( &(mpi_data->atom_line) );
-    /* bonds */
-    MPI_Type_contiguous( out_control->bond_line_len, MPI_CHAR,
-                         &(mpi_data->bond_line) );
-    MPI_Type_commit( &(mpi_data->bond_line) );
-    /* angles */
-    MPI_Type_contiguous( out_control->angle_line_len, MPI_CHAR,
-                         &(mpi_data->angle_line) );
-    MPI_Type_commit( &(mpi_data->angle_line) );
-  }
-  else if( out_control->traj_method == REG_TRAJ) {
-    if( system->my_rank == MASTER_NODE )
-      out_control->strj = fopen( fname, "w" );
-  }
-  else {
-    strcpy( msg, "init_traj: unknown trajectory option" );
-    return FAILURE;
-  }
-#elif defined(LAMMPS_REAX)
   if( out_control->traj_method == REG_TRAJ) {
     if( system->my_rank == MASTER_NODE )
       out_control->strj = fopen( fname, "w" );
@@ -524,20 +351,8 @@ int Init_Traj( reax_system *system, control_params *control,
     strcpy( msg, "init_traj: unknown trajectory option" );
     return FAILURE;
   }
-#endif
-
-
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: initiated trajectory\n", system->my_rank );
-#endif
   Write_Header( system, control, out_control, mpi_data );
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: header written\n", system->my_rank );
-#endif
   Write_Init_Desc( system, control, out_control, mpi_data );
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: atom descriptions written\n", system->my_rank );
-#endif
 
   return SUCCESS;
 }
@@ -661,24 +476,8 @@ int Write_Frame_Header( reax_system *system, control_params *control,
   }
 
   /* dump out the buffer */
-#if defined(PURE_REAX)
-  if( out_control->traj_method == MPI_TRAJ ) {
-    Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
-                            mpi_data->header_line, mpi_data->world,
-                            me, my_frm_hdr_lines, num_frm_hdr_lines );
-
-    MPI_File_write_all(out_control->trj, out_control->buffer, my_frm_hdr_lines,
-                       mpi_data->header_line, MPI_STATUS_IGNORE);
-    out_control->trj_offset += (num_frm_hdr_lines) * HEADER_LINE_LEN;
-  }
-  else {
-    if( system->my_rank == MASTER_NODE )
-      fprintf( out_control->strj, "%s", out_control->buffer );
-  }
-#elif defined(LAMMPS_REAX)
   if( system->my_rank == MASTER_NODE )
     fprintf( out_control->strj, "%s", out_control->buffer );
-#endif
 
   return SUCCESS;
 }
@@ -743,33 +542,6 @@ int Write_Atoms( reax_system *system, control_params *control,
     strncpy( out_control->buffer + i*line_len, out_control->line, line_len+1 );
   }
 
-#if defined(PURE_REAX)
-  if( out_control->traj_method == MPI_TRAJ ) {
-    Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
-                            mpi_data->atom_line, mpi_data->world,
-                            me, system->n, system->bigN );
-    MPI_File_write( out_control->trj, out_control->buffer, system->n,
-                    mpi_data->atom_line, &status );
-    out_control->trj_offset += (system->bigN) * out_control->atom_line_len;
-  }
-  else{
-    if( me != MASTER_NODE )
-      MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
-                np*ATOM_LINES+me, mpi_data->world );
-    else{
-      buffer_len = system->n * line_len;
-      for( i = 0; i < np; ++i )
-        if( i != MASTER_NODE ) {
-          MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
-                    MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status );
-          MPI_Get_count( &status, MPI_CHAR, &cnt );
-          buffer_len += cnt;
-        }
-      out_control->buffer[buffer_len] = 0;
-      fprintf( out_control->strj, "%s", out_control->buffer );
-    }
-  }
-#elif defined(LAMMPS_REAX)
   if( me != MASTER_NODE )
     MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
               np*ATOM_LINES+me, mpi_data->world );
@@ -785,7 +557,6 @@ int Write_Atoms( reax_system *system, control_params *control,
     out_control->buffer[buffer_len] = 0;
     fprintf( out_control->strj, "%s", out_control->buffer );
   }
-#endif
 
   return SUCCESS;
 }
@@ -861,34 +632,6 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
     }
   }
 
-
-#if defined(PURE_REAX)
-  if( out_control->traj_method == MPI_TRAJ ) {
-    Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
-                            mpi_data->bond_line, mpi_data->world,
-                            me, my_bonds, num_bonds );
-    MPI_File_write( out_control->trj, out_control->buffer, my_bonds,
-                    mpi_data->bond_line, &status );
-    out_control->trj_offset += num_bonds * line_len;
-  }
-  else{
-    if( me != MASTER_NODE )
-      MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
-                np*BOND_LINES+me, mpi_data->world );
-    else{
-      buffer_len = my_bonds * line_len;
-      for( i = 0; i < np; ++i )
-        if( i != MASTER_NODE ) {
-          MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
-                    MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status );
-          MPI_Get_count( &status, MPI_CHAR, &cnt );
-          buffer_len += cnt;
-        }
-      out_control->buffer[buffer_len] = 0;
-      fprintf( out_control->strj, "%s", out_control->buffer );
-    }
-  }
-#elif defined(LAMMPS_REAX)
   if( me != MASTER_NODE )
     MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
               np*BOND_LINES+me, mpi_data->world );
@@ -904,7 +647,6 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
     out_control->buffer[buffer_len] = 0;
     fprintf( out_control->strj, "%s", out_control->buffer );
   }
-#endif
 
   return SUCCESS;
 }
@@ -985,33 +727,6 @@ int Write_Angles( reax_system *system, control_params *control,
         }
     }
 
-#if defined(PURE_REAX)
-  if( out_control->traj_method == MPI_TRAJ ){
-    Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
-                            mpi_data->angle_line, mpi_data->world,
-                            me, my_angles, num_angles );
-    MPI_File_write( out_control->trj, out_control->buffer, my_angles,
-                    mpi_data->angle_line, &status );
-    out_control->trj_offset += num_angles * line_len;
-  }
-  else{
-    if( me != MASTER_NODE )
-      MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
-                np*ANGLE_LINES+me, mpi_data->world );
-    else{
-      buffer_len = my_angles * line_len;
-      for( i = 0; i < np; ++i )
-        if( i != MASTER_NODE ) {
-          MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
-                    MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status );
-          MPI_Get_count( &status, MPI_CHAR, &cnt );
-          buffer_len += cnt;
-        }
-      out_control->buffer[buffer_len] = 0;
-      fprintf( out_control->strj, "%s", out_control->buffer );
-    }
-  }
-#elif defined(LAMMPS_REAX)
   if( me != MASTER_NODE )
     MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
               np*ANGLE_LINES+me, mpi_data->world );
@@ -1027,7 +742,6 @@ int Write_Angles( reax_system *system, control_params *control,
     out_control->buffer[buffer_len] = 0;
     fprintf( out_control->strj, "%s", out_control->buffer );
   }
-#endif
 
   return SUCCESS;
 }
@@ -1037,9 +751,6 @@ int Append_Frame( reax_system *system, control_params *control,
                   simulation_data *data, reax_list **lists,
                   output_controls *out_control, mpi_datatypes *mpi_data )
 {
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: appending frame %d\n", system->my_rank, data->step );
-#endif
   Write_Frame_Header( system, control, data, out_control, mpi_data );
 
   if( out_control->write_atoms )
@@ -1051,9 +762,6 @@ int Append_Frame( reax_system *system, control_params *control,
   if( out_control->write_angles )
     Write_Angles( system, control, (*lists + BONDS), (*lists + THREE_BODIES),
                   out_control, mpi_data );
-#if defined(DEBUG_FOCUS)
-  fprintf( stderr, "p%d: appended frame %d\n", system->my_rank, data->step );
-#endif
 
   return SUCCESS;
 }
@@ -1061,15 +769,8 @@ int Append_Frame( reax_system *system, control_params *control,
 
 int End_Traj( int my_rank, output_controls *out_control )
 {
-#if defined(PURE_REAX)
-  if( out_control->traj_method == MPI_TRAJ )
-    MPI_File_close( &(out_control->trj) );
-  else if( my_rank == MASTER_NODE )
-    fclose( out_control->strj );
-#elif defined(LAMMPS_REAX)
   if( my_rank == MASTER_NODE )
     fclose( out_control->strj );
-#endif
 
   free( out_control->buffer );
   free( out_control->line );
diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h
index 8b9eb2ba4c..816906ff3e 100644
--- a/src/USER-REAXC/reaxc_types.h
+++ b/src/USER-REAXC/reaxc_types.h
@@ -40,7 +40,6 @@
 
 /************* SOME DEFS - crucial for reax_types.h *********/
 
-//#define PURE_REAX
 #define LAMMPS_REAX
 
 //#define DEBUG
@@ -48,8 +47,8 @@
 //#define TEST_ENERGY
 //#define TEST_FORCES
 //#define CG_PERFORMANCE
-#define LOG_PERFORMANCE
-#define STANDARD_BOUNDARIES
+//#define LOG_PERFORMANCE
+//#define STANDARD_BOUNDARIES
 //#define OLD_BOUNDARIES
 //#define MIDPOINT_BOUNDARIES
 
@@ -69,8 +68,6 @@ typedef real rtensor[3][3];
 typedef real rvec2[2];
 typedef real rvec4[4];
 
-// import LAMMPS' definition of tagint
-
 typedef LAMMPS_NS::tagint rc_tagint;
 
 typedef struct {
@@ -92,7 +89,6 @@ typedef struct
   int  type;
   int  num_bonds;
   int  num_hbonds;
-  //int  pad;  // pad to 8-byte address boundary
   char name[8];
   rvec x;     // position
   rvec v;     // velocity
@@ -107,20 +103,14 @@ typedef struct
   int  type;
   int  num_bonds;
   int  num_hbonds;
-  //int  pad;
   rvec x;     // position
 } boundary_atom;
 
 
 typedef struct
 {
-  //int  ncells;
-  //int *cnt_by_gcell;
-
   int  cnt;
-  //int *block;
   int *index;
-  //MPI_Datatype out_dtype;
   void *out_atoms;
 } mpi_out_data;
 
@@ -147,62 +137,12 @@ typedef struct
   MPI_Datatype angle_line;
   MPI_Datatype angle_view;
 
-  //MPI_Request  send_req1[REAX_MAX_NBRS];
-  //MPI_Request  send_req2[REAX_MAX_NBRS];
-  //MPI_Status   send_stat1[REAX_MAX_NBRS];
-  //MPI_Status   send_stat2[REAX_MAX_NBRS];
-  //MPI_Status   recv_stat1[REAX_MAX_NBRS];
-  //MPI_Status   recv_stat2[REAX_MAX_NBRS];
-
   mpi_out_data out_buffers[REAX_MAX_NBRS];
   void *in1_buffer;
   void *in2_buffer;
 } mpi_datatypes;
 
 
-/* Global params mapping */
-/*
-l[0]  = p_boc1
-l[1]  = p_boc2
-l[2]  = p_coa2
-l[3]  = N/A
-l[4]  = N/A
-l[5]  = N/A
-l[6]  = p_ovun6
-l[7]  = N/A
-l[8]  = p_ovun7
-l[9]  = p_ovun8
-l[10] = N/A
-l[11] = swa
-l[12] = swb
-l[13] = N/A
-l[14] = p_val6
-l[15] = p_lp1
-l[16] = p_val9
-l[17] = p_val10
-l[18] = N/A
-l[19] = p_pen2
-l[20] = p_pen3
-l[21] = p_pen4
-l[22] = N/A
-l[23] = p_tor2
-l[24] = p_tor3
-l[25] = p_tor4
-l[26] = N/A
-l[27] = p_cot2
-l[28] = p_vdW1
-l[29] = v_par30
-l[30] = p_coa4
-l[31] = p_ovun4
-l[32] = p_ovun3
-l[33] = p_val8
-l[34] = N/A
-l[35] = N/A
-l[36] = N/A
-l[37] = version number
-l[38] = p_coa3
-*/
-
 typedef struct
 {
   int n_global;
@@ -815,37 +755,8 @@ typedef struct
   /* force calculations */
   real *CdDelta;  // coefficient of dDelta
   rvec *f;
-#ifdef TEST_FORCES
-  rvec *f_ele;
-  rvec *f_vdw;
-  rvec *f_bo;
-  rvec *f_be;
-  rvec *f_lp;
-  rvec *f_ov;
-  rvec *f_un;
-  rvec *f_ang;
-  rvec *f_coa;
-  rvec *f_pen;
-  rvec *f_hb;
-  rvec *f_tor;
-  rvec *f_con;
-  rvec *f_tot;
-  rvec *dDelta;   // calculated on the fly in bond_orders.c together with bo'
-
-  int  *rcounts;
-  int  *displs;
-  int  *id_all;
-  rvec *f_all;
-#endif
 
   reallocate_data realloc;
-  //int *num_bonds;
-  /* hydrogen bonds */
-  //int   num_H, Hcap;
-  //int  *Hindex;
-  //int *num_hbonds;
-  //int *hash;
-  //int *rev_hash;
 } storage;
 
 
@@ -879,9 +790,6 @@ typedef _reax_list  reax_list;
 
 typedef struct
 {
-#if defined(PURE_REAX)
-  MPI_File trj;
-#endif
   FILE *strj;
   int   trj_offset;
   int   atom_line_len;
@@ -916,31 +824,6 @@ typedef struct
   int   debug_level;
   int   energy_update_freq;
 
-#ifdef TEST_ENERGY
-  FILE *ebond;
-  FILE *elp, *eov, *eun;
-  FILE *eval, *epen, *ecoa;
-  FILE *ehb;
-  FILE *etor, *econ;
-  FILE *evdw, *ecou;
-#endif
-
-#ifdef TEST_FORCES
-  FILE *fbo, *fdbo;
-  FILE *fbond;
-  FILE *flp, *fov, *fun;
-  FILE *fang, *fcoa, *fpen;
-  FILE *fhb;
-  FILE *ftor, *fcon;
-  FILE *fvdw, *fele;
-  FILE *ftot, *fcomp;
-#endif
-
-#if defined(TEST_ENERGY) || defined(TEST_FORCES)
-  FILE *flist; // far neighbor list
-  FILE *blist; // bond list
-  FILE *nlist; // near neighbor list
-#endif
 } output_controls;
 
 
@@ -987,9 +870,6 @@ extern LR_lookup_table **LR;
 typedef void (*evolve_function)(reax_system*, control_params*,
                                 simulation_data*, storage*, reax_list**,
                                 output_controls*, mpi_datatypes* );
-#if defined(PURE_REAX)
-evolve_function  Evolve;
-#endif
 
 typedef void (*interaction_function) (reax_system*, control_params*,
                                       simulation_data*, storage*,
diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp
index 5049fb769f..532d9a6a7e 100644
--- a/src/USER-REAXC/reaxc_valence_angles.cpp
+++ b/src/USER-REAXC/reaxc_valence_angles.cpp
@@ -25,20 +25,11 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "valence_angles.h"
-#include "bond_orders.h"
-#include "list.h"
-#include "vector.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_valence_angles.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
-#endif
 
-
-/* calculates the theta angle between i-j-k */
 void Calculate_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
                       real *theta, real *cos_theta )
 {
@@ -49,8 +40,6 @@ void Calculate_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
   (*theta) = acos( *cos_theta );
 }
 
-
-/* calculates the derivative of the cosine of the angle between i-j-k */
 void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
                            rvec* dcos_theta_di,
                            rvec* dcos_theta_dj,
@@ -75,8 +64,6 @@ void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
 }
 
 
-/* this is a 3-body interaction in which the main role is
-   played by j which sits in the middle of the other two. */
 void Valence_Angles( reax_system *system, control_params *control,
                      simulation_data *data, storage *workspace,
                      reax_list **lists, output_controls *out_control )
@@ -104,7 +91,6 @@ void Valence_Angles( reax_system *system, control_params *control,
   real r_ij, r_jk;
   real BOA_ij, BOA_jk;
   rvec force, ext_press;
-  // rtensor temp_rtensor, total_rtensor;
 
   // Tallying variables
   real eng_tmp, f_scaler, fi_tmp[3], fj_tmp[3], fk_tmp[3];
@@ -127,8 +113,8 @@ void Valence_Angles( reax_system *system, control_params *control,
 
 
   for( j = 0; j < system->N; ++j ) {         // Ray: the first one with system->N
-    // fprintf( out_control->eval, "j: %d\n", j );
     type_j = system->my_atoms[j].type;
+    if (type_j < 0) continue;
     start_j = Start_Index(j, bonds);
     end_j = End_Index(j, bonds);
 
@@ -145,7 +131,6 @@ void Valence_Angles( reax_system *system, control_params *control,
       prod_SBO *= exp( -temp );
     }
 
-    /* modifications to match Adri's code - 09/01/09 */
     if( workspace->vlpex[j] >= 0 ){
       vlpadj = 0;
       dSBO2 = prod_SBO - 1;
@@ -185,14 +170,8 @@ void Valence_Angles( reax_system *system, control_params *control,
         i = pbond_ij->nbr;
         r_ij = pbond_ij->d;
         type_i = system->my_atoms[i].type;
-        // fprintf( out_control->eval, "i: %d\n", i );
 
-
-        /* first copy 3-body intrs from previously computed ones where i>k.
-           in the second for-loop below,
-           we compute only new 3-body intrs where i < k */
         for( pk = start_j; pk < pi; ++pk ) {
-          // fprintf( out_control->eval, "pk: %d\n", pk );
           start_pk = Start_Index( pk, thb_intrs );
           end_pk = End_Index( pk, thb_intrs );
 
@@ -213,8 +192,6 @@ void Valence_Angles( reax_system *system, control_params *control,
             }
         }
 
-
-        /* and this is the second for loop mentioned above */
         for( pk = pi+1; pk < end_j; ++pk ) {
           pbond_jk = &(bonds->select.bond_list[pk]);
           bo_jk    = &(pbond_jk->bo_data);
@@ -249,23 +226,7 @@ void Valence_Angles( reax_system *system, control_params *control,
             r_jk = pbond_jk->d;
             thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] );
 
-            /* if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id )
-               fprintf( fval, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
-               system->my_atoms[i].orig_id,
-               system->my_atoms[j].orig_id,
-               system->my_atoms[k].orig_id,
-               bo_ij->BO, bo_jk->BO, p_ijk->theta );
-               else
-               fprintf( fval, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
-               system->my_atoms[k].orig_id,
-               system->my_atoms[j].orig_id,
-               system->my_atoms[i].orig_id,
-               bo_jk->BO, bo_ij->BO, p_ijk->theta ); */
-
             for( cnt = 0; cnt < thbh->cnt; ++cnt ) {
-              // fprintf( out_control->eval, "%6d%6d%6d -- exists in thbp\n",
-              //          i+1, j+1, k+1 );
-
               if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) {
                 thbp = &( thbh->prm[cnt] );
 
@@ -319,7 +280,6 @@ void Valence_Angles( reax_system *system, control_params *control,
                   f7_ij * f7_jk * f8_Dj * expval12theta;
                 /* END ANGLE ENERGY*/
 
-
                 /* PENALTY ENERGY */
                 p_pen1 = thbp->p_pen1;
                 p_pen2 = system->reax_param.gp.l[19];
@@ -346,7 +306,6 @@ void Valence_Angles( reax_system *system, control_params *control,
                 CEpen3 = temp * (BOA_jk - 2.0);
                 /* END PENALTY ENERGY */
 
-
                 /* COALITION ENERGY */
                 p_coa1 = thbp->p_coa1;
                 p_coa2 = system->reax_param.gp.l[2];
@@ -370,7 +329,6 @@ void Valence_Angles( reax_system *system, control_params *control,
                   (workspace->total_bond_order[k]-BOA_jk) * e_coa;
                 /* END COALITION ENERGY */
 
-
                 /* FORCES */
                 bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
                 bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
@@ -385,10 +343,6 @@ void Valence_Angles( reax_system *system, control_params *control,
                     temp = CUBE( temp_bo_jt );
                     pBOjt7 = temp * temp * temp_bo_jt;
 
-                    // fprintf( out_control->eval, "%6d%12.8f\n",
-                    // workspace->reverse_map[bonds->select.bond_list[t].nbr],
-                    // (CEval6 * pBOjt7) );
-
                     bo_jt->Cdbo += (CEval6 * pBOjt7);
                     bo_jt->Cdbopi += CEval5;
                     bo_jt->Cdbopi2 += CEval5;
@@ -400,8 +354,6 @@ void Valence_Angles( reax_system *system, control_params *control,
                   rvec_ScaledAdd( workspace->f[k], CEval8, p_ijk->dcos_dk );
                 }
                 else {
-                  /* terms not related to bond order derivatives are
-                     added directly into forces and pressure vector/tensor */
                   rvec_Scale( force, CEval8, p_ijk->dcos_di );
                   rvec_Add( workspace->f[i], force );
                   rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
@@ -435,104 +387,6 @@ void Valence_Angles( reax_system *system, control_params *control,
                   if( system->pair_ptr->vflag_atom)
                           system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj);
                 }
-
-#ifdef TEST_ENERGY
-                /*fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n",
-                  p_val3, p_val4, BOA_ij, BOA_jk );
-                fprintf(out_control->eval, "%13.8f%13.8f%13.8f%13.8f%13.8f\n",
-                        workspace->Delta_e[j], workspace->vlpex[j],
-                        dSBO1, dSBO2, vlpadj );
-                fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n",
-                         f7_ij, f7_jk, f8_Dj, expval12theta );
-                fprintf( out_control->eval,
-                         "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
-                         CEval1, CEval2, CEval3, CEval4,
-                         CEval5, CEval6, CEval7, CEval8 );
-
-                fprintf( out_control->eval,
-                "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
-                   p_ijk->dcos_di[0]/sin_theta, p_ijk->dcos_di[1]/sin_theta,
-                   p_ijk->dcos_di[2]/sin_theta,
-                   p_ijk->dcos_dj[0]/sin_theta, p_ijk->dcos_dj[1]/sin_theta,
-                   p_ijk->dcos_dj[2]/sin_theta,
-                   p_ijk->dcos_dk[0]/sin_theta, p_ijk->dcos_dk[1]/sin_theta,
-                   p_ijk->dcos_dk[2]/sin_theta);
-
-                fprintf( out_control->eval,
-                         "%6d%6d%6d%15.8f%15.8f\n",
-                         system->my_atoms[i].orig_id,
-                         system->my_atoms[j].orig_id,
-                         system->my_atoms[k].orig_id,
-                         RAD2DEG(theta), e_ang );*/
-
-                fprintf( out_control->eval,
-                //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-                         "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n",
-                         system->my_atoms[i].orig_id,
-                         system->my_atoms[j].orig_id,
-                         system->my_atoms[k].orig_id,
-                         RAD2DEG(theta), theta_0, BOA_ij, BOA_jk,
-                         e_ang, data->my_en.e_ang );
-
-                fprintf( out_control->epen,
-                         //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-                         "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
-                         system->my_atoms[i].orig_id,
-                         system->my_atoms[j].orig_id,
-                         system->my_atoms[k].orig_id,
-                         RAD2DEG(theta), BOA_ij, BOA_jk, e_pen,
-                         data->my_en.e_pen );
-
-                fprintf( out_control->ecoa,
-                         //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
-                         "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
-                         system->my_atoms[i].orig_id,
-                         system->my_atoms[j].orig_id,
-                         system->my_atoms[k].orig_id,
-                         RAD2DEG(theta), BOA_ij, BOA_jk,
-                         e_coa, data->my_en.e_coa );
-#endif
-
-#ifdef TEST_FORCES            /* angle forces */
-                Add_dBO( system, lists, j, pi, CEval1, workspace->f_ang );
-                Add_dBO( system, lists, j, pk, CEval2, workspace->f_ang );
-                Add_dDelta( system, lists, j,
-                            CEval3 + CEval7, workspace->f_ang );
-
-                for( t = start_j; t < end_j; ++t ) {
-                  pbond_jt = &( bonds->select.bond_list[t] );
-                  bo_jt = &(pbond_jt->bo_data);
-                  temp_bo_jt = bo_jt->BO;
-                  temp = CUBE( temp_bo_jt );
-                  pBOjt7 = temp * temp * temp_bo_jt;
-
-                  Add_dBO( system, lists, j, t, pBOjt7 * CEval6,
-                           workspace->f_ang );
-                  Add_dBOpinpi2( system, lists, j, t, CEval5, CEval5,
-                                 workspace->f_ang, workspace->f_ang );
-                }
-
-                rvec_ScaledAdd( workspace->f_ang[i], CEval8, p_ijk->dcos_di );
-                rvec_ScaledAdd( workspace->f_ang[j], CEval8, p_ijk->dcos_dj );
-                rvec_ScaledAdd( workspace->f_ang[k], CEval8, p_ijk->dcos_dk );
-                /* end angle forces */
-
-                /* penalty forces */
-                Add_dDelta( system, lists, j, CEpen1, workspace->f_pen );
-                Add_dBO( system, lists, j, pi, CEpen2, workspace->f_pen );
-                Add_dBO( system, lists, j, pk, CEpen3, workspace->f_pen );
-                /* end penalty forces */
-
-                /* coalition forces */
-                Add_dBO( system, lists, j, pi, CEcoa1 - CEcoa4,
-                         workspace->f_coa );
-                Add_dBO( system, lists, j, pk, CEcoa2 - CEcoa5,
-                         workspace->f_coa );
-                Add_dDelta( system, lists, j, CEcoa3, workspace->f_coa );
-                Add_dDelta( system, lists, i, CEcoa4, workspace->f_coa );
-                Add_dDelta( system, lists, k, CEcoa5, workspace->f_coa );
-                /* end coalition forces */
-#endif
               }
             }
           }
@@ -551,16 +405,5 @@ void Valence_Angles( reax_system *system, control_params *control,
       MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
     }
   }
-  //fprintf( stderr,"%d: Number of angle interactions: %d\n",
-  // data->step, num_thb_intrs );
 
-#if defined(DEBUG)
-  fprintf( stderr, "Number of angle interactions: %d\n", num_thb_intrs );
-  fprintf( stderr,
-           "Angle Energy: %g\t Penalty Energy: %g\t Coalition Energy: %g\t\n",
-           data->my_en.e_ang, data->my_en.e_pen, data->my_en.e_coa );
-
-  fprintf( stderr, "3body: ext_press (%12.6f %12.6f %12.6f)\n",
-           data->ext_press[0], data->ext_press[1], data->ext_press[2] );
-#endif
 }
diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp
index 1008eabe34..4d56442172 100644
--- a/src/USER-REAXC/reaxc_vector.cpp
+++ b/src/USER-REAXC/reaxc_vector.cpp
@@ -25,12 +25,7 @@
   ----------------------------------------------------------------------*/
 
 #include "pair_reax_c.h"
-#if defined(PURE_REAX)
-#include "vector.h"
-#include "random.h"
-#elif defined(LAMMPS_REAX)
 #include "reaxc_vector.h"
-#endif
 
 int Vector_isZero( real* v, int k )
 {
@@ -243,29 +238,14 @@ int rvec_isZero( rvec v )
 
 void rvec_MakeZero( rvec v )
 {
-//  v[0] = v[1] = v[2] = 0.0000000000000;
   v[0] = v[1] = v[2] = 0.000000000000000e+00;
 }
 
-
-#if defined(PURE_REAX)
-void rvec_Random( rvec v )
-{
-  v[0] = Random(2.0)-1.0;
-  v[1] = Random(2.0)-1.0;
-  v[2] = Random(2.0)-1.0;
-}
-#endif
-
-
 void rtensor_Multiply( rtensor ret, rtensor m1, rtensor m2 )
 {
   int i, j, k;
   rtensor temp;
 
-  // check if the result matrix is the same as one of m1, m2.
-  // if so, we cannot modify the contents of m1 or m2, so
-  // we have to use a temp matrix.
   if( ret == m1 || ret == m2 )
     {
       for( i = 0; i < 3; ++i )
@@ -298,8 +278,6 @@ void rtensor_MatVec( rvec ret, rtensor m, rvec v )
   int i;
   rvec temp;
 
-  // if ret is the same vector as v, we cannot modify the
-  // contents of v until all computation is finished.
   if( ret == v )
     {
       for( i = 0; i < 3; ++i )